PhD_thesis.bib

@article{Alberts1998,
  title = {Analysis of Zinc Binding Sites in Protein Crystal Structures},
  author = {Alberts, Ian L. and Nadassy, Katalin and Wodak, Shoshana J.},
  year = {1998},
  month = aug,
  journal = {Protein Science},
  volume = {7},
  number = {8},
  pages = {1700--1716},
  issn = {09618368},
  doi = {10.1002/pro.5560070805},
  abstract = {The geometrical properties of zinc binding sites in a dataset of high quality protein crystal structures deposited in the Protein Data Bank have been examined to identify important differences between zinc sites that are directly involved in catalysis and those that play a structural role. Coordination angles in the zinc primary coordination sphere are compared with ideal values for each coordination geometry, and zinc coordination distances are compared with those in small zinc complexes from the Cambridge Structural Database as a guide of expected trends. We find that distances and angles in the primary coordination sphere are in general close to the expected (or ideal) values. Deviations occur primarily for oxygen coordinating atoms and are found to be mainly due to H-bonding of the oxygen coordinating ligand to protein residues, bidentate binding arrangements, and multi-zinc sites. We find that H-bonding of oxygen containing residues (or water) to zinc bound histidines is almost universal in our dataset and defines the elec-His-Zn motif. Analysis of the stereochemistry shows that carboxyl elec-His-Zn motifs are geometrically rigid, while water elec-His-Zn motifs show the most geometrical variation. As catalytic motifs have a higher proportion of carboxyl elec atoms than structural motifs, they provide a more rigid framework for zinc binding. This is understood biologically, as a small distortion in the zinc position in an enzyme can have serious consequences on the enzymatic reaction. We also analyze the sequence pattern of the zinc ligands and residues that provide elecs, and identify conserved hydrophobic residues in the endopeptidases that also appear to contribute to stabilizing the catalytic zinc site. A zinc binding template in protein crystal structures is derived from these observations.},
  pmid = {10082367},
  keywords = {Bidentate,Catalytic,Coordination,Ligand,Sequence pattern,Structural,Template,Zinc},
  file = {C\:\\Users\\makro\\Zotero\\storage\\VLEUGJP3\\Alberts, Nadassy, Wodak - 1998 - Analysis of zinc binding sites in protein crystal structures.pdf}
}

@article{AlexanderWesley2009,
  title = {History of the {{Medical Use}} of {{Silver}}},
  author = {Alexander, J. Wesley},
  year = {2009},
  month = jun,
  journal = {Surgical Infections},
  volume = {10},
  number = {3},
  pages = {289--292},
  issn = {1096-2964},
  doi = {10.1089/sur.2008.9941},
  file = {C\:\\Users\\makro\\Zotero\\storage\\KT6LLHID\\Alexander - 2009 - History of the Medical Use of Silver.pdf}
}

@article{Andreini2006,
  title = {Zinc through the {{Three Domains}} of {{Life}} Research Articles},
  author = {Andreini, Claudia and Banci, Lucia and Bertini, Ivano and Rosato, Antonio},
  year = {2006},
  journal = {Journal of Proteom Research},
  volume = {5},
  pages = {3173--3178},
  abstract = {Zinc is one of the metal ions essential for life, as it is required for the proper functioning of a large number of proteins. Despite its importance, the annotation of zinc-binding proteins in gene banks or protein domain databases still has significant room for improvement. In the present work, we compiled a list of known zinc-binding protein domains and of known zinc-binding sequence motifs (zinc-binding patterns), and then used them jointly to analyze the proteome of 57 different organisms to obtain an overview of zinc usage by archaeal, bacterial, and eukaryotic organisms. Zinc-binding proteins are an abundant fraction of these proteomes, ranging between 4\% and 10\%. The number of zinc-binding proteins correlates linearly with the total number of proteins encoded by the genome of an organism, but the proportionality constant of Eukaryota (8.8\%) is significantly higher than that observed in Bacteria and Archaea (from 5\% to 6\%). Most of this enrichment is due to the larger portfolio of regulatory proteins in Eukaryota. Keywords:},
  keywords = {gene expression,metalloproteins,zinc,zinc fingers},
  file = {C\:\\Users\\makro\\Zotero\\storage\\A77EIX8B\\Andreini et al. - 2006 - Zinc through the Three Domains of Life research articles.pdf}
}

@article{Andreini2006a,
  title = {Counting the Zinc-Proteins Encoded in the Human Genome},
  author = {Andreini, Claudia and Banci, Lucia and Bertini, Ivano and Rosato, Antonio},
  year = {2006},
  journal = {Journal of Proteome Research},
  volume = {5},
  number = {1},
  pages = {196--201},
  issn = {15353893},
  doi = {10.1021/pr050361j},
  abstract = {Metalloproteins are proteins capable of binding one or more metal ions, which may be required for their biological function, or for regulation of their activities or for structural purposes. Genome sequencing projects have provided a huge number of protein primary sequences, but, even though several different elaborate analyses and annotations have been enabled by a rich and ever-increasing portfolio of bioinformatic tools, metal-binding properties remain difficult to predict as well as to investigate experimentally. Consequently, the present knowledge about metalloproteins is only partial. The present bioinformatic research proposes a strategy to answer the question of how many and which proteins encoded in the human genome may require zinc for their physiological function. This is achieved by a combination of approaches, which include: (i) searching in the proteome for the zinc-binding patterns that, on their turn, are obtained from all available X-ray data; (ii) using libraries of metal-binding protein domains based on multiple sequence alignments of known metalloproteins obtained from the Pfam database; and (iii) mining the annotations of human gene sequences, which are based on any type of information available. It is found that 1684 proteins in the human proteome are independently identified by all three approaches as zinc-proteins, 746 are identified by two, and 777 are identified by only one method. By assuming that all proteins identified by at least two approaches are truly zinc-binding and inspecting the proteins identified by a single method, it can be proposed that ca. 2800 human proteins are potentially zinc-binding in vivo, corresponding to 10\% of the human proteome, with an uncertainty of 400 sequences. Available functional information suggests that the large majority of human zinc-binding proteins are involved in the regulation of gene expression. The most abundant class of zinc-binding proteins in humans is that of zinc-fingers, with Cys 4 and Cys2His2 being the most common types of coordination environment. \textcopyright{} 2006 American Chemical Society.},
  pmid = {16396512},
  keywords = {Metalloprotease,Metalloproteins,Zinc,Zinc finger},
  file = {C\:\\Users\\makro\\Zotero\\storage\\GJPUX23A\\Andreini et al. - 2006 - Counting the zinc-proteins encoded in the human genome.pdf}
}

@article{Andreini2008,
  title = {Metal Ions in Biological Catalysis: {{From}} Enzyme Databases to General Principles},
  author = {Andreini, Claudia and Bertini, Ivano and Cavallaro, Gabriele and Holliday, Gemma L. and Thornton, Janet M.},
  year = {2008},
  journal = {Journal of Biological Inorganic Chemistry},
  volume = {13},
  number = {8},
  pages = {1205--1218},
  issn = {09498257},
  doi = {10.1007/s00775-008-0404-5},
  abstract = {We analysed the roles and distribution of metal ions in enzymatic catalysis using available public databases and our new resource Metal-MACiE ( http://www.ebi.ac.uk/thornton-srv/databases/Metal\_MACiE/home.html ). In Metal-MACiE, a database of metal-based reaction mechanisms, 116 entries covering 21\% of the metal-dependent enzymes and 70\% of the types of enzyme-catalysed chemical transformations are annotated according to metal function. We used Metal-MACiE to assess the functions performed by metals in biological catalysis and the relative frequencies of different metals in different roles, which can be related to their individual chemical properties and availability in the environment. The overall picture emerging from the overview of Metal-MACiE is that redox-inert metal ions are used in enzymes to stabilize negative charges and to activate substrates by virtue of their Lewis acid properties, whereas redox-active metal ions can be used both as Lewis acids and as redox centres. Magnesium and zinc are by far the most common ions of the first type, while calcium is relatively less used. Magnesium, however, is most often bound to phosphate groups of substrates and interacts with the enzyme only transiently, whereas the other metals are stably bound to the enzyme. The most common metal of the second type is iron, which is prevalent in the catalysis of redox reactions, followed by manganese, cobalt, molybdenum, copper and nickel. The control of the reactivity of redox-active metal ions may involve their association with organic cofactors to form stable units. This occurs sometimes for iron and nickel, and quite often for cobalt and molybdenum. \textcopyright{} 2008 SBIC.},
  pmid = {18604568},
  keywords = {Catalysis,Database,Enzyme,Metal,Metalloenzyme},
  file = {C\:\\Users\\makro\\Zotero\\storage\\N3YHJ3FW\\Andreini et al. - 2008 - Metal ions in biological catalysis From enzyme databases to general principles.pdf}
}

@article{Andreini2009,
  title = {Metalloproteomes: {{A Bioinformatic Approach}}},
  author = {Andreini, Claudia and Bertini, Ivano and Rosato, Antonio},
  year = {2009},
  month = oct,
  journal = {Accounts of Chemical Research},
  volume = {42},
  number = {10},
  pages = {1471--1479},
  issn = {0001-4842},
  doi = {10.1021/ar900015x},
  abstract = {Genome-wide studies are providing researchers with a potentially complete list of the molecular components present In living systems. It is now evident that several metal ions are essential to life and that metalloproteins, that is, proteins that require a metal ion to perform their physiological function, are widespread in all organisms. However, there is currently a lack of well-established experimental methods aimed at analyzing the complete set of metalloproteins encoded by an organism (the metalloproteome). This information is essential for a comprehensive understanding of the whole of the processes occurring in living systems. Predictive tools must thus be applied to define metalloproteomes. In this Account, we discuss the current progress in the development of bioinformatics methods for the prediction, based solely on protein sequences, of metalloproteins. With these methods, it is possible to scan entire proteomes for metalloproteins, such as zinc proteins or copper proteins, which are identified by the presence of specific metal-binding sites, metal-binding domains, or both. The predicted metalloproteins can be then analyzed to obtain information on their function and evolution. For example, the comparative analysis of the content and usage of different metalloproteins across living organisms can be used to obtain hints on the evolution of metalloproteomes. As case studies, we predicted the content of zinc, nonheme iron, and copper-proteins in a representative set of organisms taken from the three domains of life. The zinc proteome represents about 9\% of the entire proteome in eukaryotes, but it ranges from 5\% to 6\% in prokaryotes, therefore indicating a substantial increase of the number of zinc proteins in higher organisms. In contrast, the number of nonheme iron proteins is relatively constant in eukaryotes and prokaryotes, and therefore their relative share diminishes in passing from archaea (about 7\%), to bacteria (about 4\%), to eukaryotes (about 1\%). Copper proteins represent less than 1\% of the proteomes in all the organisms studied. We also discuss the limits of these methods, the approaches used to overcome some of these limits to improve our predictions, and possible future developments in the field of bioinformatics-based investigation of metalloproteins. As a longstanding goal of the biological sciences, the understanding of life at the systems level, or systems biology, is experiencing a rekindling of interest; ready access to complete information on metalloproteomes is crucial to correctly represent the role of metal ions in living organisms. \textcopyright{} 2009 American Chemical Society.},
  pmid = {19697929},
  file = {C\:\\Users\\makro\\Zotero\\storage\\SU3VUCBI\\Andreini, Bertini, Rosato - 2009 - Metalloproteomes A bioinformatic approach.pdf}
}

@article{Andreini2011,
  title = {Minimal Functional Sites Allow a Classification of Zinc Sites in Proteins},
  author = {Andreini, Claudia and Bertini, Ivano and Cavallaro, Gabriele},
  year = {2011},
  journal = {PLoS ONE},
  volume = {6},
  number = {10},
  issn = {19326203},
  doi = {10.1371/journal.pone.0026325},
  abstract = {Zinc is indispensable to all forms of life as it is an essential component of many different proteins involved in a wide range of biological processes. Not differently from other metals, zinc in proteins can play different roles that depend on the features of the metal-binding site. In this work, we describe zinc sites in proteins with known structure by means of three-dimensional templates that can be automatically extracted from PDB files and consist of the protein structure around the metal, including the zinc ligands and the residues in close spatial proximity to the ligands. This definition is devised to intrinsically capture the features of the local protein environment that can affect metal function, and corresponds to what we call a minimal functional site (MFS). We used MFSs to classify all zinc sites whose structures are available in the PDB and combined this classification with functional annotation as available in the literature. We classified 77\% of zinc sites into ten clusters, each grouping zinc sites with structures that are highly similar, and an additional 16\% into seven pseudo-clusters, each grouping zinc sites with structures that are only broadly similar. Sites where zinc plays a structural role are predominant in eight clusters and in two pseudo-clusters, while sites where zinc plays a catalytic role are predominant in two clusters and in five pseudo-clusters. We also analyzed the amino acid composition of the coordination sphere of zinc as a function of its role in the protein, highlighting trends and exceptions. In a period when the number of known zinc proteins is expected to grow further with the increasing awareness of the cellular mechanisms of zinc homeostasis, this classification represents a valuable basis for structure-function studies of zinc proteins, with broad applications in biochemistry, molecular pharmacology and de novo protein design. \textcopyright{} 2011 Andreini et al.},
  pmid = {22043316},
  file = {C\:\\Users\\makro\\Zotero\\storage\\J2KFAMQG\\Andreini, Bertini, Cavallaro - 2011 - Minimal functional sites allow a classification of zinc sites in proteins.pdf}
}

@article{Andreini2013,
  title = {{{MetalPDB}}: {{A}} Database of Metal Sites in Biological Macromolecular Structures},
  author = {Andreini, Claudia and Cavallaro, Gabriele and Lorenzini, Serena and Rosato, Antonio},
  year = {2013},
  journal = {Nucleic Acids Research},
  volume = {41},
  number = {D1},
  pages = {312--319},
  issn = {03051048},
  doi = {10.1093/nar/gks1063},
  abstract = {We present here MetalPDB (freely accessible at http://metalweb.cerm.unifi. it), a novel resource aimed at conveying the information available on the three-dimensional (3D) structures of metal-binding biological macromolecules in a consistent and effective manner. This is achieved through the systematic and automated representation of metal-binding sites in proteins and nucleic acids by way of Minimal Functional Sites (MFSs). MFSs are 3D templates that describe the local environment around the metal(s) independently of the larger context of the macromolecular structure embedding the site(s), and are the central objects of MetalPDB design. MFSs are grouped into equistructural (broadly defined as sites found in corresponding positions in similar structures) and equivalent sites (equistructural sites that contain the same metals), allowing users to easily analyse similarities and variations in metal-macromolecule interactions, and to link them to functional information. The web interface of MetalPDB allows access to a comprehensive overview of metal-containing biological structures, providing a basis to investigate the basic principles governing the properties of these systems. MetalPDB is updated monthly in an automated manner. \textcopyright{} The Author(s) 2012.},
  pmid = {23155064},
  file = {C\:\\Users\\makro\\Zotero\\storage\\8HM4GCSG\\Andreini et al. - 2013 - MetalPDB A database of metal sites in biological macromolecular structures.pdf}
}

@book{asimov1951,
  title = {Foundation},
  author = {Asimov, Isaac},
  year = {1951}
}

@article{Auld2001,
  title = {Zinc Coordination Sphere in Biochemical Zinc Sites},
  author = {Auld, David S.},
  year = {2001},
  journal = {BioMetals},
  volume = {14},
  number = {3-4},
  pages = {271--313},
  issn = {09660844},
  doi = {10.1023/A:1012976615056},
  abstract = {Zinc is known to be indispensable to growth and development and transmission of the genetic message. It does this through a remarkable mosaic of zinc binding motifs that orchestrate all aspects of metabolism. There are now nearly 200 three dimensional structures for zinc proteins, representing all six classes of enzymes and covering a wide range of phyla and species. These structures provide standards of reference for the identity and nature of zinc ligands in other proteins for which only the primary structure is known. Three primary types of zinc sites are apparent from examination of these structures: structural, catalytic and cocatalytic. The most common amino acids that supply ligands to these sites are His, Glu, Asp and Cys. In catalytic sites zinc generally forms complexes with water and any three nitrogen, oxygen and sulfur donors with His being the predominant amino acid chosen. Water is always a ligand to such sites. Structural zinc sites have four protein ligands and no bound water molecule. Cys is the preferred ligand in such sites. Cocatalytic sites contain two or three metals in close proximity with two of the metals bridged by a side chain moiety of a single amino acid residue, such as Asp, Glu or His and sometimes a water molecule. Asp and His are the preferred amino acids for these sites. No Cys ligands are found in such sites. The scaffolding of the zinc sites is also important to the function and reactivity of the bound metal. The influence of zinc on quaternary protein structure has led to the identification of a fourth type of zinc binding site, protein interface. In this case zinc sites are formed from ligands supplied from amino acid residues residing in the binding surface of two proteins. The resulting zinc site usually has the coordination properties of a catalytic or structural zinc binding site.},
  pmid = {11831461},
  keywords = {Crystal structure,Metalloenzyme,NMR,Protein sequence,X-ray crystallography,XAFS or X-ray absorption fine structure},
  file = {C\:\\Users\\makro\\Zotero\\storage\\M2X882WX\\Auld - 2001 - Zinc coordination sphere in biochemical zinc sites.pdf}
}

@article{Babor2007,
  title = {Prediction of Transition Metal-Binding Sites from Apo Protein Structures},
  author = {Babor, Mariana and Gerzon, Sergey and Raveh, Barak and Sobolev, Vladimir and Edelman, Marvin},
  year = {2007},
  month = jul,
  journal = {Proteins: Structure, Function, and Bioinformatics},
  volume = {70},
  number = {1},
  pages = {208--217},
  issn = {08873585},
  doi = {10.1002/prot.21587},
  isbn = {9789876301596},
  file = {C\:\\Users\\makro\\Zotero\\storage\\4ATDNX97\\Babor et al. - 2007 - Prediction of transition metal-binding sites from apo protein structures.pdf}
}

@article{Bafaro2017,
  title = {The Emerging Role of Zinc Transporters in Cellular Homeostasis and Cancer},
  author = {Bafaro, Elizabeth and Liu, Yuting and Xu, Yan and Dempski, Robert E.},
  year = {2017},
  month = jul,
  journal = {Signal Transduction and Targeted Therapy},
  volume = {2},
  number = {1},
  pages = {17029},
  publisher = {{The Author(s)}},
  issn = {2059-3635},
  doi = {10.1038/sigtrans.2017.29},
  abstract = {Zinc is an essential micronutrient that plays a role in the structural or enzymatic functions of many cellular proteins. Cellular zinc homeostasis involves the opposing action of two families of metal transporters: the ZnT (SLC30) family that functions to reduce cytoplasmic zinc concentrations and the ZIP (SLC39) family that functions to increase cytoplasmic zinc concentrations. Fluctuations in intracellular zinc levels mediated by these transporter families affect signaling pathways involved in normal cell development, growth, differentiation and death. Consequently, changes in zinc transporter localization and function resulting in zinc dyshomeostasis have pathophysiological effects. Zinc dyshomeostasis has been implicated in the progression of cancer. Here we review recent progress toward understanding the structural basis for zinc transport by ZnT and ZIP family proteins, as well as highlight the roles of zinc as a signaling molecule in physiological conditions and in various cancers. As zinc is emerging as an important signaling molecule in the development and progression of cancer, the ZnT and ZIP transporters that regulate cellular zinc homeostasis are promising candidates for targeted cancer therapy.},
  pmid = {29218234},
  file = {C\:\\Users\\makro\\Zotero\\storage\\KCQJHU5Z\\Bafaro et al. - 2017 - The emerging role of zinc transporters in cellular homeostasis and cancer.pdf}
}

@article{Bateman2022,
  title = {{{UniProt}}: The {{Universal Protein Knowledgebase}} in 2023},
  author = {Bateman, Alex and Martin, Maria-Jesus and Orchard, Sandra and Magrane, Michele and Ahmad, Shadab and Alpi, Emanuele and {Bowler-Barnett}, Emily H and Britto, Ramona and {Bye-A-Jee}, Hema and Cukura, Austra and Denny, Paul and Dogan, Tunca and Ebenezer, ThankGod and Fan, Jun and Garmiri, Penelope and {da Costa Gonzales}, Leonardo Jose and {Hatton-Ellis}, Emma and Hussein, Abdulrahman and Ignatchenko, Alexandr and Insana, Giuseppe and Ishtiaq, Rizwan and Joshi, Vishal and Jyothi, Dushyanth and Kandasaamy, Swaathi and Lock, Antonia and Luciani, Aurelien and Lugaric, Marija and Luo, Jie and Lussi, Yvonne and MacDougall, Alistair and Madeira, Fabio and Mahmoudy, Mahdi and Mishra, Alok and Moulang, Katie and Nightingale, Andrew and Pundir, Sangya and Qi, Guoying and Raj, Shriya and Raposo, Pedro and Rice, Daniel L and Saidi, Rabie and Santos, Rafael and Speretta, Elena and Stephenson, James and Totoo, Prabhat and Turner, Edward and Tyagi, Nidhi and Vasudev, Preethi and Warner, Kate and Watkins, Xavier and Zaru, Rossana and Zellner, Hermann and Bridge, Alan J and Aimo, Lucila and {Argoud-Puy}, Ghislaine and Auchincloss, Andrea H and Axelsen, Kristian B and Bansal, Parit and Baratin, Delphine and Batista Neto, Teresa M and Blatter, Marie-Claude and Bolleman, Jerven T and Boutet, Emmanuel and Breuza, Lionel and Gil, Blanca Cabrera and {Casals-Casas}, Cristina and Echioukh, Kamal Chikh and Coudert, Elisabeth and Cuche, Beatrice and {de Castro}, Edouard and Estreicher, Anne and Famiglietti, Maria L and Feuermann, Marc and Gasteiger, Elisabeth and Gaudet, Pascale and Gehant, Sebastien and Gerritsen, Vivienne and Gos, Arnaud and Gruaz, Nadine and Hulo, Chantal and {Hyka-Nouspikel}, Nevila and Jungo, Florence and Kerhornou, Arnaud and Le Mercier, Philippe and Lieberherr, Damien and Masson, Patrick and Morgat, Anne and Muthukrishnan, Venkatesh and Paesano, Salvo and Pedruzzi, Ivo and Pilbout, Sandrine and Pourcel, Lucille and Poux, Sylvain and Pozzato, Monica and Pruess, Manuela and Redaschi, Nicole and Rivoire, Catherine and Sigrist, Christian J A and Sonesson, Karin and Sundaram, Shyamala and Wu, Cathy H and Arighi, Cecilia N and Arminski, Leslie and Chen, Chuming and Chen, Yongxing and Huang, Hongzhan and Laiho, Kati and McGarvey, Peter and Natale, Darren A and Ross, Karen and Vinayaka, C R and Wang, Qinghua and Wang, Yuqi and Zhang, Jian},
  year = {2022},
  month = nov,
  journal = {Nucleic Acids Research},
  pages = {1--9},
  issn = {0305-1048},
  doi = {10.1093/nar/gkac1052},
  abstract = {The aim of the UniProt Knowledgebase is to provide users with a comprehensive, high-quality and freely accessible set of protein sequences annotated with functional information. In this publication we describe enhancements made to our data processing pipeline and to our website to adapt to an ever-increasing information content. The number of sequences in UniProtKB has risen to over 227 million and we are working towards including a reference proteome for each taxonomic group. We continue to extract detailed annotations from the literature to update or create reviewed entries, while unreviewed entries are supplemented with annotations provided by automated systems using a variety of machine-learning techniques. In addition, the scientific community continues their contributions of publications and annotations to UniProt entries of their interest. Finally, we describe our new website (https://www.uniprot.org/), designed to enhance our users' experience and make our data easily accessible to the research community. This interface includes access to AlphaFold structures for more than 85\% of all entries as well as improved visualisations for subcellular localisation of proteins.},
  file = {C\:\\Users\\makro\\Zotero\\storage\\QKEB4AVN\\Bateman et al. - 2022 - UniProt the Universal Protein Knowledgebase in 2023.pdf}
}

@article{Beck2011,
  title = {The Quantitative Proteome of a Human Cell Line},
  author = {Beck, Martin and Schmidt, Alexander and Malmstroem, Johan and Claassen, Manfred and Ori, Alessandro and Szymborska, Anna and Herzog, Franz and Rinner, Oliver and Ellenberg, Jan and Aebersold, Ruedi},
  year = {2011},
  journal = {Molecular Systems Biology},
  volume = {7},
  number = {549},
  pages = {1--8},
  publisher = {{Nature Publishing Group}},
  issn = {17444292},
  doi = {10.1038/msb.2011.82},
  abstract = {The generation of mathematical models of biological processes, the simulation of these processes under different conditions, and the comparison and integration of multiple data sets are explicit goals of systems biology that require the knowledge of the absolute quantity of the system's components. To date, systematic estimates of cellular protein concentrations have been exceptionally scarce. Here, we provide a quantitative description of the proteome of a commonly used human cell line in two functional states, interphase and mitosis. We show that these human cultured cells express at least g\^\^1/410 000 proteins and that the quantified proteins span a concentration range of seven orders of magnitude up to 20 000 000 copies per cell. We discuss how protein abundance is linked to function and evolution. \textcopyright{} 2011 EMBO and Macmillan Publishers Limited All rights reserved.},
  pmid = {22068332},
  keywords = {mass spectrometry,protein abundance,proteomics},
  file = {C\:\\Users\\makro\\Zotero\\storage\\HFA52TV6\\Beck et al. - 2011 - The quantitative proteome of a human cell line.pdf}
}

@book{Berg2007,
  title = {Biochemistry},
  author = {Berg, Jeremy M and Tymoczko, John L and Stryer, Lubert},
  year = {2007},
  publisher = {{W. H. Freeman}},
  isbn = {978-0-7167-8724-2}
}

@article{Berman,
  title = {The {{Protein Data Bank}}},
  author = {Berman, H. M. and Westbrook, John and Feng, Zukang},
  year = {2000},
  month = jan,
  journal = {Nucleic Acids Research},
  volume = {28},
  number = {1},
  pages = {235--242},
  issn = {13624962},
  doi = {10.1093/nar/28.1.235},
  abstract = {The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), the US data center for the global PDB archive and a founding member of the Worldwide Protein Data Bank partnership, serves tens of thousands of data depositors in the Americas and Oceania and makes 3D macromolecular structure data available at no charge and without restrictions to millions of RCSB.org users around the world, including \>660 000 educators, students and members of the curious public using PDB101.RCSB.org. PDB data depositors include structural biologists using macromolecular crystallography, nuclear magnetic resonance spectroscopy, 3D electron microscopy and micro-electron diffraction. PDB data consumers accessing our web portals include researchers, educators and students studying fundamental biology, biomedicine, biotechnology, bioengineering and energy sciences. During the past 2 years, the research-focused RCSB PDB web portal (RCSB.org) has undergone a complete redesign, enabling improved searching with full Boolean operator logic and more facile access to PDB data integrated with \>40 external biodata resources. New features and resources are described in detail using examples that showcase recently released structures of SARS-CoV-2 proteins and host cell proteins relevant to understanding and addressing the COVID-19 global pandemic.},
  pmid = {33293618},
  file = {C\:\\Users\\makro\\Zotero\\storage\\K9I92GG7\\Berman - 2000 - The Protein Data Bank.pdf}
}

@article{Bernhoft2012,
  title = {Mercury {{Toxicity}} and {{Treatment}}: {{A Review}} of the {{Literature}}},
  author = {Bernhoft, Robin A},
  year = {2012},
  journal = {Journal of Environmental and Public Health},
  volume = {2012},
  pages = {1--10},
  issn = {1687-9805},
  doi = {10.1155/2012/460508},
  abstract = {Mercury is a toxic heavy metal which is widely dispersed in nature. Most human exposure results from fish consumption or dental amalgam. Mercury occurs in several chemical forms, with complex pharmacokinetics. Mercury is capable of inducing a wide range of clinical presentations. Diagnosis of mercury toxicity can be challenging but can be obtained with reasonable reliability. Effective therapies for clinical toxicity have been described.},
  pmid = {22235210},
  file = {C\:\\Users\\makro\\Zotero\\storage\\4ZDSCRIL\\Bernhoft - 2012 - Mercury Toxicity and Treatment A Review of the Literature.pdf}
}

@article{Bertini2010,
  title = {The Annotation of Full Zinc Proteomes},
  author = {Bertini, Ivano and Decaria, Leonardo and Rosato, Antonio},
  year = {2010},
  month = sep,
  journal = {JBIC Journal of Biological Inorganic Chemistry},
  volume = {15},
  number = {7},
  pages = {1071--1078},
  issn = {0949-8257},
  doi = {10.1007/s00775-010-0666-6},
  abstract = {We obtained an extended functional annotation of zinc proteins using a combination of bioinformatic methods. This work was performed using a number of available predicted zinc proteomes of various representative organisms, leading to the almost complete annotation of, among others, the predicted human zinc proteome. The computational tools exploited included sequence-based and, when possible, structure-based functional predictions. We assigned a hypothetical function to 74\% of the 1,472 sequences analyzed that lacked annotation in the starting dataset. We also added new functional categories, not described in the reference dataset, such as ubiquitin binding and DNA replication. As a general conclusion, we can state that the quality of each functional prediction parallels the amount of information for the sequence analyzed: the larger the amount of information, the more detailed and reliable is the proposed functional prediction. Among the findings, we have propose a zinc binding site for archaeal zinc-importing proteins. Furthermore, we propose two groups of transcriptional regulators that are involved in fatty acid metabolism. \textcopyright{} 2010 SBIC.},
  pmid = {20443034},
  keywords = {Metalloproteome,Metalloproteomics,Zinc,Zinc finger},
  file = {C\:\\Users\\makro\\Zotero\\storage\\GTSVPWNR\\Bertini, Decaria, Rosato - 2010 - The annotation of full zinc proteomes.pdf}
}

@article{Betts2021,
  title = {The Biochemical Fate of {{Ag}}{\textsuperscript{+}} Ions in {{{\emph{Staphylococcus}}}}{\emph{ Aureus}}, {{{\emph{Escherichia}}}}{\emph{ Coli}}, and Biological Media},
  author = {Betts, Harley D. and Neville, Stephanie L. and McDevitt, Christopher A. and Sumby, Christopher J. and Harris, Hugh H.},
  year = {2021},
  journal = {Journal of Inorganic Biochemistry},
  volume = {225},
  number = {August},
  pages = {111598},
  publisher = {{Elsevier Inc.}},
  issn = {18733344},
  doi = {10.1016/j.jinorgbio.2021.111598},
  abstract = {Silver is commonly included in a range of household and medical items to provide bactericidal action. Despite this, the chemical fate of the metal in both mammalian and bacterial systems remains poorly understood. Here, we applied a metallomics approach using X-ray absorption spectroscopy (XAS) and size-exclusion chromatography hyphenated with inductively coupled plasma mass spectrometry (SEC-ICP-MS) to advance our understanding of the biochemical fate of silver ions in bacterial culture and cells, and the chemistry associated with these interactions. When silver ions were added to lysogeny broth, silver was exclusively associated with moderately-sized species (\textasciitilde 30 kDa) and bound by thiolate ligands. In two representative bacterial pathogens cultured in lysogeny broth including sub-lethal concentrations of ionic silver, silver was found in cells to be predominantly coordinated by thiolate species. The silver biomacromolecule-binding profile in Staphylococcus aureus and Escherichia coli was complex, with silver bound by a range of species spanning from 20 kDa to {$>$}1220 kDa. In bacterial cells, silver was nonuniformly colocalised with copper-bound proteins, suggesting that cellular copper processing may, in part, confuse silver for nutrient copper. Notably, in the treated cells, silver was not detected bound to low molecular weight compounds such as glutathione or bacillithiol.},
  pmid = {34517168},
  keywords = {Biomacromolecular binding profile,Silver,Size-exclusion chromatography,Sublethal bacterial processing,X-ray absorption spectroscopy},
  file = {C\:\\Users\\makro\\Zotero\\storage\\5TKLNXYB\\Betts et al. - 2021 - The biochemical fate of Ag ions in Staphylococcus aureus, Escherichia coli, and biological media.pdf}
}

@article{Boder1997,
  title = {Yeast Surface Display for Screening Combinatorial Polypeptide Libraries},
  author = {Boder, Eric T and Wittrup, K Dane},
  year = {1997},
  month = jun,
  journal = {Nature Biotechnology},
  volume = {15},
  number = {6},
  pages = {553--557},
  issn = {1087-0156},
  doi = {10.1038/nbt0697-553},
  abstract = {Display on the yeast cell wall is well suited for engineering mammalian cell-surface and secreted proteins (e.g., antibodies, receptors, cytokines) that require endoplasmic reticulum-specific post-translational processing for efficient folding and activity. C-terminal fusion to the Aga2p mating adhesion niceptor of Saccharomyces cerevis/ae has been used for the selection of scfv antibody fragments with threefold decreased antigen dissoci-ation rate from a randomly mutated library. A eukaryotic host should alleviate expression biases present in bacterially propagated combinatorial libraries. Quantitative flow cytometric analysis enables fine discrimination of kinetic parameters for protein binding to soluble ligands.},
  keywords = {affinity maturation,antibody engineering,combinatorial library,have,in rapidly altering protein,in the absence of,limited potential for success,molecular,quantitative computational structure-function,rational approaches to mutagenesis,relationships for proteins,scfv,surface display},
  file = {C\:\\Users\\makro\\Zotero\\storage\\SR5QHC2A\\Boder, Wittrup - 1997 - Yeast surface display for screening combinatorial polypeptide libraries.pdf}
}

@incollection{Boone2016,
  title = {Top-{{Down Proteomics}}},
  booktitle = {Proteomic {{Profiling}} and {{Analytical Chemistry}}},
  author = {Boone, C. and Adamec, J.},
  year = {2016},
  pages = {175--191},
  publisher = {{Elsevier}},
  issn = {0003-2700},
  doi = {10.1016/B978-0-444-63688-1.00010-0},
  abstract = {Top-Down approach refers to the ionization of intact proteins and MS or MS/MS analysis of intact species or fragment ions generated in mass spectrometer by induced dissociation. This tehnique can eliminate most of the problems associated with the Bottom-Up approach and allow for high specificity protein identification and characterization of different proteoforms: information that would otherwise be lost with protein digestion and unattainable with other large scale, whole proteome approaches. Major obstacle problem in Top-Down proteomics represent sample complexity - biological samples are inherently complex with a multitude of different proteins and their proteoforms; thus, effective implementation of the Top-Down approach requires extensive separation and/or enrichment step preceding mass analysis. In this chapter, we will first describe methods of used for fractionation of intact proteins. Following that, we will discuss ionization techniques and instrumentation used in Top-Down proteomics.},
  isbn = {978-0-444-63688-1},
  pmid = {15190879},
  keywords = {Biological sample,Data analysis,Ionization techniques,Mass spectrometry,Protein separation,Proteoforms,Sample complexity,Top-down proteomics},
  file = {C\:\\Users\\makro\\Zotero\\storage\\3NMLZH4I\\Boone, Adamec - 2016 - Top-Down Proteomics.pdf}
}

@article{Bucio1998,
  title = {Uptake, Cellular Distribution and {{DNA}} Damage Produced by Mercuric Chloride in a Human Fetal Hepatic Cell Line},
  author = {Bucio, Leticia and Garc{\'{\i}}a, Cecilia and Souza, Ver{\'o}nica and Hern{\'a}ndez, Elizabeth and Gonz{\'a}lez, Cristina and Betancourt, Miguel and {Guti{\'e}rrez-Ruiz}, Ma.Concepci{\'o}n},
  year = {1999},
  month = jan,
  journal = {Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis},
  volume = {423},
  number = {1-2},
  pages = {65--72},
  issn = {00275107},
  doi = {10.1016/S0027-5107(98)00226-7},
  abstract = {Cadmium (Cd) is one of the most important heavy metal environmental toxicants. It alters a wide variety of cellular and biochemical processes. The objective of this work was to study DNA damage and recovery after acute and chronic CdCl2 treatment in a human fetal hepatic cell line (WRL-68 cells). Using the alkaline microgel electrophoresis assay that detects DNA single-strand breaks and/or alkali-labile sites in individual cells, we evaluated for levels of DNA damage. The mean migration length in control cells was 35.37 {$\pm$} 1.43 {$\mu$}m (8\% damaged cells), whereas the mean migration in cells treated with 0.005 {$\mu$}M CdCl2 for 3 h (acute low dose) was 65.87 {$\pm$} 2.07 {$\mu$}m (88\% damaged cells). Treatment with 0.01 {$\mu$}M CdCl2 for the same time (acute high dose) increased the mean migration length to 125.79 {$\pm$} 2.91 {$\mu$}m(92\% damaged cells). However, a 0.005 {$\mu$}M CdCl2 treatment for 7 days (chronic treatment) only increased 65\% DNA migration to 58.38 {$\pm$} 2.59 {$\mu$}m (88\% damaged nucleus). Lipoperoxidative damage expressed as malondialdehyde (MDA) production per milligram of protein was 15.7 {$\pm$} 2.6 for control cells, whereas in Cd-treated cells the values were 20.2 {$\pm$} 2.4 (acute low dose), 22.9 {$\pm$} 2.2 (acute high dose), and 22.6 {$\pm$} 2.1 (chronic treatment). To study the repair of DNA damage, cells were washed with 0.01 {$\mu$}M meso-2,3-dimercaptosuccinic acid (DMSA), and fresh Dulbecco's modified essential medium (DMEM) added. The percentage of damaged cells diminished after 90 min, with DNA migration returning to control values by 120 min. Cd treatment produced DNA single-strand breaks and the damage was greater in acute high dose treated cells, Lipid peroxidation values did not correlate with DNA single-strand breaks.},
  isbn = {5257236451},
  pmid = {10023089},
  keywords = {Cd,DNA damage,WRL-68 cell},
  file = {C\:\\Users\\makro\\Zotero\\storage\\A99PBKER\\Bucio et al. - 1999 - Uptake, cellular distribution and DNA damage produced by mercuric chloride in a human fetal hepatic cell line.pdf}
}

@article{Burley2021,
  title = {{{RCSB Protein Data Bank}}: Powerful New Tools for Exploring {{3D}} Structures of Biological Macromolecules for Basic and Applied Research and Education in Fundamental Biology, Biomedicine, Biotechnology, Bioengineering and Energy Sciences},
  author = {Burley, Stephen K. and Bhikadiya, Charmi and Bi, Chunxiao and Bittrich, Sebastian and Chen, Li and Crichlow, Gregg V. and Christie, Cole H. and Dalenberg, Kenneth and Di Costanzo, Luigi and Duarte, Jose M. and Dutta, Shuchismita and Feng, Zukang and Ganesan, Sai and Goodsell, David S. and Ghosh, Sutapa and Green, Rachel Kramer and Guranovi{\'c}, Vladimir and Guzenko, Dmytro and Hudson, Brian P. and Lawson, Catherine L and Liang, Yuhe and Lowe, Robert and Namkoong, Harry and Peisach, Ezra and Persikova, Irina and Randle, Chris and Rose, Alexander and Rose, Yana and Sali, Andrej and Segura, Joan and Sekharan, Monica and Shao, Chenghua and Tao, Yi-Ping and Voigt, Maria and Westbrook, John D and Young, Jasmine Y. and Zardecki, Christine and Zhuravleva, Marina},
  year = {2021},
  month = jan,
  journal = {Nucleic Acids Research},
  volume = {49},
  number = {D1},
  pages = {D437-D451},
  issn = {0305-1048},
  doi = {10.1093/nar/gkaa1038},
  abstract = {The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), the US data center for the global PDB archive and a founding member of the Worldwide Protein Data Bank partnership, serves tens of thousands of data depositors in the Americas and Oceania and makes 3D macromolecular structure data available at no charge and without restrictions to millions of RCSB.org users around the world, including \>660 000 educators, students and members of the curious public using PDB101.RCSB.org. PDB data depositors include structural biologists using macromolecular crystallography, nuclear magnetic resonance spectroscopy, 3D electron microscopy and micro-electron diffraction. PDB data consumers accessing our web portals include researchers, educators and students studying fundamental biology, biomedicine, biotechnology, bioengineering and energy sciences. During the past 2 years, the research-focused RCSB PDB web portal (RCSB.org) has undergone a complete redesign, enabling improved searching with full Boolean operator logic and more facile access to PDB data integrated with \>40 external biodata resources. New features and resources are described in detail using examples that showcase recently released structures of SARS-CoV-2 proteins and host cell proteins relevant to understanding and addressing the COVID-19 global pandemic.},
  pmid = {33211854},
  file = {C\:\\Users\\makro\\Zotero\\storage\\U4UADW6X\\Burley et al. - 2021 - RCSB Protein Data Bank Powerful new tools for exploring 3D structures of biological macromolecules for basic and.pdf}
}

@article{Burnouf2012,
  title = {{{kinITC}}: {{A}} New Method for Obtaining Joint Thermodynamic and Kinetic Data by Isothermal Titration Calorimetry},
  author = {Burnouf, Dominique and Ennifar, Eric and Guedich, Sondes and Puffer, Barbara and Hoffmann, Guillaume and Bec, Guillaume and Disdier, Fran{\c c}ois and Baltzinger, Mireille and Dumas, Philippe},
  year = {2012},
  journal = {Journal of the American Chemical Society},
  volume = {134},
  number = {1},
  pages = {559--565},
  issn = {00027863},
  doi = {10.1021/ja209057d},
  abstract = {Isothermal titration calorimetry (ITC) is the method of choice for obtaining thermodynamic data on a great variety of systems. Here we show that modern ITC apparatus and new processing methods allow researchers to obtain a complete kinetic description of systems more diverse than previously thought, ranging from simple ligand binding to complex RNA folding. We illustrate these new features with a simple case (HIV-1 reverse transcriptase/inhibitor interaction) and with the more complex case of the folding of a riboswitch triggered by the binding of its ligand. The originality of the new kinITC method lies in its ability to dissect, both thermodynamically and kinetically, the two components: primary ligand binding and subsequent RNA folding. We are not aware of another single method that can yield, in a simple way, such deep insight into a composite process. Our study also rationalizes common observations from daily ITC use. \textcopyright{} 2011 American Chemical Society.},
  pmid = {22126339},
  file = {C\:\\Users\\makro\\Zotero\\storage\\EZYZEV3L\\Burnouf et al. - 2012 - KinITC A new method for obtaining joint thermodynamic and kinetic data by isothermal titration calorimetry.pdf}
}

@article{Bushmarina2006,
  title = {Cofactor Effects on the Protein Folding Reaction: {{Acceleration}} of {$\alpha$}-Lactalbumin Refolding by Metal Ions},
  shorttitle = {Cofactor Effects on the Protein Folding Reaction},
  author = {Bushmarina, Natalia A. and Blanchet, Cl{\'e}ment E. and Vernier, Gr{\'e}gory and Forge, Vincent},
  year = {2006},
  journal = {Protein Science},
  volume = {15},
  number = {4},
  pages = {659--671},
  issn = {1469-896X},
  doi = {10.1110/ps.051904206},
  urldate = {2023-03-16},
  abstract = {About 30\% of proteins require cofactors for their proper folding. The effects of cofactors on the folding reaction have been investigated with {$\alpha$}-lactalbumin as a model protein and metal ions as cofactors. Metal ions accelerate the refolding of {$\alpha$}-lactalbumin by lessening the energy barrier between the molten globule state and the transition state, mainly by decreasing the difference of entropy between the two states. These effects are linked to metal ion binding to the protein in the native state. Hence, relationships between the metal affinities for the intermediate states and those for the native state are observed. Some residual specificity for the calcium ion is still observed in the molten globule state, this specificity getting closer in the transition state to that of the native state. The comparison between kinetic and steady-state data in association with the {$\Phi$} value method indicates the binding of the metal ions on the unfolded state of {$\alpha$}-lactalbumin. Altogether, these results provide insight into cofactor effects on protein folding. They also suggest new possibilities to investigate the presence of residual native structures in the unfolded state of protein and the effects of such structures on the protein folding reaction and on protein stability.},
  langid = {english},
  keywords = {a -lactalbumin,and,and calcium are among,cofactors,cofactors are often required,copper,f value,for the proper folding,metal ions such as,protein folding,proteins,the biological function of,the most common,zinc,α-lactalbumin,Φ value},
  file = {C\:\\Users\\makro\\Zotero\\storage\\56WGUVQR\\Bushmarina et al. - 2006 - Cofactor effects on the protein folding reaction .pdf;C\:\\Users\\makro\\Zotero\\storage\\RUYKAT7X\\ps.html}
}

@article{Butler2004,
  title = {The Role of Vanadium Bromoperoxidase in the Biosynthesis of Halogenated Marine Natural Products},
  author = {Butler, Alison and {Carter-Franklin}, Jayme N.},
  year = {2004},
  journal = {Natural Product Reports},
  volume = {21},
  number = {1},
  pages = {180},
  issn = {0265-0568},
  doi = {10.1039/b302337k},
  abstract = {Halogenated natural products are frequently reported metabolites in marine seaweeds. These compounds span a range from halogenated indoles, terpenes, acetogenins, phenols, etc., to volatile halogenated hydrocarbons that are produced on a very large scale. In many cases these halogenated marine metabolites possess biological activities of pharmacological interest. Given the abundance of halogenated marine natural products found in marine organisms and their potentially important biological activities, the biogenesis of these compounds has intrigued marine natural product chemists for decades. Over a quarter of a century ago, a possible role for haloperoxidase enzymes was first suggested in the biogenesis of certain halogenated marine natural products, although this was long before haloperoxidases were discovered in marine organisms. Since that time, FeHeme- and Vanadium-haloperoxidases (V-HPO) have been discovered in many marine organisms. The structure and catalytic activity of vanadium haloperoxidases is reviewed herein, including the importance of V-HPO-catalyzed bromination and cyclization of terpene substrates.},
  pmid = {15039842},
  file = {C\:\\Users\\makro\\Zotero\\storage\\R76DZIGA\\Butler, Carter-Franklin - 2004 - The role of vanadium bromoperoxidase in the biosynthesis of halogenated marine natural products.pdf}
}

@article{Cafarelli2017,
  title = {Mapping, Modeling, and Characterization of Protein\textendash Protein Interactions on a Proteomic Scale},
  author = {Cafarelli, {\relax TM} and Desbuleux, A. and Wang, Y. and Choi, {\relax SG} and De Ridder, D. and Vidal, M.},
  year = {2017},
  month = jun,
  journal = {Current Opinion in Structural Biology},
  volume = {44},
  pages = {201--210},
  publisher = {{Elsevier Ltd}},
  issn = {0959440X},
  doi = {10.1016/j.sbi.2017.05.003},
  abstract = {Proteins effect a number of biological functions, from cellular signaling, organization, mobility, and transport to catalyzing biochemical reactions and coordinating an immune response. These varied functions are often dependent upon macromolecular interactions, particularly with other proteins. Small-scale studies in the scientific literature report protein\textendash protein interactions (PPIs), but slowly and with bias towards well-studied proteins. In an era where genomic sequence is readily available, deducing genotype\textendash phenotype relationships requires an understanding of protein connectivity at proteome-scale. A proteome-scale map of the protein\textendash protein interaction network provides a global view of cellular organization and function. Here, we discuss a summary of methods for building proteome-scale interactome maps and the current status and implications of mapping achievements. Not only do interactome maps serve as a reference, detailing global cellular function and organization patterns, but they can also reveal the mechanisms altered by disease alleles, highlight the patterns of interaction rewiring across evolution, and help pinpoint biologically and therapeutically relevant proteins. Despite the considerable strides made in proteome-wide mapping, several technical challenges persist. Therefore, future considerations that impact current mapping efforts are also discussed.},
  pmid = {28575754},
  file = {C\:\\Users\\makro\\Zotero\\storage\\7QDY5AM5\\Cafarelli et al. - 2017 - Mapping, modeling, and characterization of protein–protein interactions on a proteomic scale.pdf}
}

@article{Camacho2009,
  title = {{{BLAST}}+: Architecture and Applications},
  author = {Camacho, Christiam and Coulouris, George and Avagyan, Vahram and Ma, Ning and Papadopoulos, Jason and Bealer, Kevin and Madden, Thomas L.},
  year = {2009},
  month = dec,
  journal = {BMC Bioinformatics},
  volume = {10},
  number = {1},
  pages = {421},
  issn = {1471-2105},
  doi = {10.1186/1471-2105-10-421},
  abstract = {Background: Sequence similarity searching is a very important bioinformatics task. While Basic Local Alignment Search Tool (BLAST) outperforms exact methods through its use of heuristics, the speed of the current BLAST software is suboptimal for very long queries or database sequences. There are also some shortcomings in the user-interface of the current command-line applications.Results: We describe features and improvements of rewritten BLAST software and introduce new command-line applications. Long query sequences are broken into chunks for processing, in some cases leading to dramatically shorter run times. For long database sequences, it is possible to retrieve only the relevant parts of the sequence, reducing CPU time and memory usage for searches of short queries against databases of contigs or chromosomes. The program can now retrieve masking information for database sequences from the BLAST databases. A new modular software library can now access subject sequence data from arbitrary data sources. We introduce several new features, including strategy files that allow a user to save and reuse their favorite set of options. The strategy files can be uploaded to and downloaded from the NCBI BLAST web site.Conclusion: The new BLAST command-line applications, compared to the current BLAST tools, demonstrate substantial speed improvements for long queries as well as chromosome length database sequences. We have also improved the user interface of the command-line applications. \textcopyright{} 2009 Camacho et al; licensee BioMed Central Ltd.},
  isbn = {1471210510},
  pmid = {20003500},
  file = {C\:\\Users\\makro\\Zotero\\storage\\56YTCL7N\\Camacho et al. - 2009 - BLAST architecture and applications.pdf}
}

@article{Canny2022,
  title = {{{LRET-derived HADDOCK}} Structural Models Describe the Conformational Heterogeneity Required for {{DNA}} Cleavage by the {{Mre11-Rad50 DNA}} Damage Repair Complex},
  author = {Canny, Marella D. and Latham, Michael P.},
  year = {2022},
  journal = {eLife},
  volume = {11},
  pages = {1--22},
  issn = {2050084X},
  doi = {10.7554/eLife.69579},
  abstract = {The Mre11-Rad50-Nbs1 protein complex is one of the first responders to DNA double strand breaks. Studies have shown that the catalytic activities of the evolutionarily conserved Mre11-Rad50 (MR) core complex depend on an ATP-dependent global conformational change that takes the macromolecule from an open, extended structure in the absence of ATP to a closed, globular structure when ATP is bound. We have previously identified an additional `partially open' conformation using Luminescence Resonance Energy Transfer (LRET) experiments. Here, a combination of LRET and the molecular docking program HADDOCK was used to further investigate this partially open state and identify three conformations of MR in solution: closed, partially open, and open, which are in addition to the extended, apo conformation. Mutants disrupting specific Mre11-Rad50 interactions within each conformation were used in nuclease activity assays on a variety of DNA substrates to help put the three states into a functional perspective. LRET data collected on MR bound to DNA demonstrate that the three conformations also exist when nuclease substrates are bound. These models were further supported with SAXS data which corroborate the presence of multiple states in solution. Together, the data suggest a mechanism for the nuclease activity of the MR complex along the DNA.},
  pmid = {35084331},
  file = {C\:\\Users\\makro\\Zotero\\storage\\WKQVTHV4\\Canny, Latham - 2022 - LRET-derived HADDOCK structural models describe the conformational heterogeneity required for DNA cleavage by the.pdf}
}

@article{Cao2011,
  title = {Dynamics of {{Protein Folding}} and {{Cofactor Binding Monitored}} by {{Single-Molecule Force Spectroscopy}}},
  author = {Cao, Yi and Li, Hongbin},
  year = {2011},
  month = oct,
  journal = {Biophysical Journal},
  volume = {101},
  number = {8},
  pages = {2009--2017},
  publisher = {{Biophysical Society}},
  issn = {00063495},
  doi = {10.1016/j.bpj.2011.08.051},
  abstract = {Many proteins in living cells require cofactors to carry out their biological functions. To reach their functional states, these proteins need to fold into their unique three-dimensional structures in the presence of their cofactors. Two processes, folding of the protein and binding of cofactors, intermingle with each other, making the direct elucidation of the folding mechanism of proteins in the presence of cofactors challenging. Here we use single-molecule atomic force microscopy to directly monitor the folding and cofactor binding dynamics of an engineered metal-binding protein G6-53 at the single-molecule level. Using the mechanical stability of different conformers of G6-53 as sensitive probes, we directly identified different G6-53 conformers (unfolded, apo- and Ni 2+-bound) populated along the folding pathway of G6-53 in the presence of its cofactor Ni 2+. By carrying out single-molecule atomic force microscopy refolding experiments, we monitored kinetic evolution processes of these different conformers. Our results suggested that the majority of G6-53 folds through a binding-after-folding mechanism, whereas a small fraction follows a binding-before-folding pathway. Our study opens an avenue to utilizing force spectroscopy techniques to probe the folding dynamics of proteins in the presence of cofactors at the single-molecule level, and we anticipated that this method can be used to study a wide variety of proteins requiring cofactors for their function. \textcopyright{} 2011 Biophysical Society.},
  pmid = {22004755},
  file = {C\:\\Users\\makro\\Zotero\\storage\\92FI4EYG\\Cao, Li - 2011 - Dynamics of Protein Folding and Cofactor Binding Monitored by Single-Molecule Force Spectroscopy.pdf}
}

@article{Chakraborty2010,
  title = {Structural {{Comparisons}} of {{Apo-}} and {{Metalated Three-Stranded Coiled Coils Clarify Metal Binding Determinants}} in {{Thiolate Containing Designed Peptides}}},
  author = {Chakraborty, Saumen and Touw, Debra S. and Peacock, Anna F. A. and Stuckey, Jeanne and Pecoraro, Vincent L.},
  year = {2010},
  month = sep,
  journal = {Journal of the American Chemical Society},
  volume = {132},
  number = {38},
  pages = {13240--13250},
  issn = {0002-7863},
  doi = {10.1021/ja101812c},
  abstract = {Over the past two decades, designed metallopeptides have held the promise for understanding a variety of fundamental questions in metallobiochemistry; however, these dreams have not yet been realized because of a lack of structural data to elaborate the protein scaffolds before metal complexation and the resultant metalated structures which ultimately exist. This is because there are few reports of structural characterization of such systems either in their metalated or nonmetalated forms and no examples where an apo structure and the corresponding metalated peptide assembly have both been defined by X-ray crystallography. Herein we present X-ray structures of two de novo designed parallel three-stranded coiled coils (designed using the heptad repeat (a \textrightarrow{} g)) CSL9C (CS = Coil Ser) and CSL19C in their nonmetalated forms, determined to 1.36 and 2.15 \AA{} resolutions, respectively. Leucines from either position 9 (a site) or 19 (d site) are replaced by cysteine to generate the constructs CSL9C and CSL19C, respectively, yielding thiol-rich pockets at the hydrophobic interior of these peptides, suitable to bind heavy metals such as As(III), Hg(II), Cd(II), and Pb(II). We use these structures to understand the inherent structural differences between a and d sites to clarify the basis of the observed differential spectroscopic behavior of metal binding in these types of peptides. Cys side chains of (CSL9C)3 show alternate conformations and are partially preorganized for metal binding, whereas cysteines in (CSL19C)3 are present as a single conformer. Zn(II) ions, which do not coordinate or influence Cys residues at the designed metal sites but are essential for forming X-ray quality crystals, are bound to His and Glu residues at the crystal packing interfaces of both structures. These "apo" structures are used to clarify the changes in metal site organization between metalated As(CSL9C)3 and to speculate on the differential basis of Hg(II) binding in a versus d peptides. Thus, for the first time, one can establish general rules for heavy metal binding to Cys-rich sites in designed proteins which may provide insight for understanding how heavy metals bind to metallochaperones or metalloregulatory proteins. \textcopyright{} 2010 American Chemical Society.},
  pmid = {20825181},
  file = {C\:\\Users\\makro\\Zotero\\storage\\KPN8X4HF\\Chakraborty et al. - 2010 - Structural Comparisons of Apo- and Metalated Three-Stranded Coiled Coils Clarify Metal Binding Determinants.pdf}
}

@article{Cherepanov2002,
  title = {Kinetic Mechanism of the {{Mg}}{\textsuperscript{2+}}-Dependent Nucleotidyl Transfer Catalyzed by {{T4 DNA}} and {{RNA}} Ligases},
  author = {Cherepanov, Alexei V. and {de Vries}, Simon},
  year = {2002},
  journal = {Journal of Biological Chemistry},
  volume = {277},
  number = {3},
  pages = {1695--1704},
  issn = {00219258},
  doi = {10.1074/jbc.M109616200},
  abstract = {The Mg2+-dependent adenylylation of the T4 DNA and RNA ligases was studied in the absence of a DNA substrate using transient optical absorbance and fluorescence spectroscopy. The concentrations of Mg2+, ATP, and pyrophosphate were systematically varied, and the results led to the conclusion that the nucleotidyl transfer proceeds according to a two-metal ion mechanism. According to this mechanism, only the di-magnesium-coordinated form Mg2ATP0 reacts with the enzyme forming the covalent complex E-AMP. The reverse reaction (ATP synthesis) occurs between the mono-magnesium-coordinated pyrophosphate form MgP2O72- and the enzyme-MgAMP complex. The nucleotide binding rate decreases in the sequence ATP4- {$>$} MgATP2- {$>$} Mg2ATP0, indicating that the formation of the non-covalent enzyme-nucleotide complex is driven by electrostatic interactions. T4 DNA ligase shows notably higher rates of ATP binding and of subsequent adenylylation compared with RNA ligase, in part because it decreases the Kd of Mg2+ for the enzyme-bound Mg2ATP0 more than 10-fold. To elucidate the role of Mg2+ in the nucleotidyl transfer catalyzed by T4 DNA and RNA ligases, we propose a transition state configuration, in which the catalytic Mg2+ ion coordinates to both reacting nucleophiles: the lysyl moiety of the enzyme that forms the phosphoramidate bond and the {$\alpha$}-{$\beta$}-bridging oxygen of ATP.},
  pmid = {11687591},
  file = {C\:\\Users\\makro\\Zotero\\storage\\BY5UXK4J\\Cherepanov, De Vries - 2002 - Kinetic mechanism of the Mg2-dependent nucleotidyl transfer catalyzed by T4 DNA and RNA ligases.pdf}
}

@article{Christakis2021,
  title = {Expanded {{Diversity}} and {{Phylogeny}} of Mer {{Genes Broadens Mercury Resistance Paradigms}} and {{Reveals}} an {{Origin}} for {{MerA Among Thermophilic Archaea}}},
  author = {Christakis, Christos A. and Barkay, Tamar and Boyd, Eric S.},
  year = {2021},
  journal = {Frontiers in Microbiology},
  volume = {12},
  number = {June},
  pages = {1--20},
  issn = {1664302X},
  doi = {10.3389/fmicb.2021.682605},
  abstract = {Mercury (Hg) is a highly toxic element due to its high affinity for protein sulfhydryl groups, which upon binding, can destabilize protein structure and decrease enzyme activity. Prokaryotes have evolved enzymatic mechanisms to detoxify inorganic Hg and organic Hg (e.g., MeHg) through the activities of mercuric reductase (MerA) and organomercury lyase (MerB), respectively. Here, the taxonomic distribution and evolution of MerAB was examined in 84,032 archaeal and bacterial genomes, metagenome assembled genomes, and single-cell genomes. Homologs of MerA and MerB were identified in 7.8 and 2.1\% percent of genomes, respectively. MerA was identified in the genomes of 10 archaeal and 28 bacterial phyla previously unknown to code for this functionality. Likewise, MerB was identified in 2 archaeal and 11 bacterial phyla previously unknown to encode this functionality. Surprisingly, homologs of MerB were identified in a number of genomes ({$\sim$}50\% of all MerB-encoding genomes) that did not encode MerA, suggesting alternative mechanisms to detoxify Hg(II) once it is generated in the cytoplasm. Phylogenetic reconstruction of MerA place its origin in thermophilic Thermoprotei (Crenarchaeota), consistent with high levels of Hg(II) in geothermal environments, the natural habitat of this archaeal class. MerB appears to have been recruited to the mer operon relatively recently and likely among a mesophilic ancestor of Euryarchaeota and Thaumarchaeota. This is consistent with the functional dependence of MerB on MerA and the widespread distribution of mesophilic microorganisms that methylate Hg(II) at lower temperature. Collectively, these results expand the taxonomic and ecological distribution of mer-encoded functionalities, and suggest that selection for Hg(II) and MeHg detoxification is dependent not only on the availability and type of mercury compounds in the environment but also the physiological potential of the microbes who inhabit these environments. The expanded diversity and environmental distribution of MerAB identify new targets to prioritize for future research.},
  pmid = {34248899},
  keywords = {Hg(II),merA,MerB,mercuric reductase,mercury,methylmercury,organomercury lyase,Thermoprotei},
  file = {C\:\\Users\\makro\\Zotero\\storage\\R9H37FGW\\Christakis, Barkay, Boyd - 2021 - Expanded Diversity and Phylogeny of mer Genes Broadens Mercury Resistance Paradigms and Reveals an Ori.pdf}
}

@article{Christensen1988,
  title = {Toxicity and Ultrastructural Localization of Mercuric Chloride in Cultured Murine Macrophages},
  author = {Christensen, Margot and Mogensen, Soren C. and Rungby, Jorgen},
  year = {1988},
  journal = {Archives of Toxicology},
  volume = {62},
  number = {6},
  pages = {440--446},
  issn = {0340-5761},
  doi = {10.1007/BF00288347},
  abstract = {The effects of mercuric chloride on cell survival, phagocytosis and cell migration were examined in cultured mouse peritoneal macrophages, and the accumulation of mercuric chloride in the cells was visualized by autometallography and evaluated by light and electron microscopy. Macrophages exposed to mercury concentrations from 1.25 {$\mu$}M to 10 {$\mu$}M mercuric chloride showed a concentration- and time-dependent increase in mercuric chloride accumulation, while cells exposed to 20 {$\mu$}M and 40 {$\mu$}M mercury showed an inverse relationship between mercury concentration and the accumulation of mercury. Mercury concentrations above these levels caused cell necrosis. Electron microscopy revealed that mercury was located primarily within lysosomes but also in the nucleus and cytoplasm. Mercury increased the death rate of macrophages in a concentration-dependent manner when cells were treated with mercury concentrations not causing cell necrosis. Further, we found that mercury clearly impaired macrophage random migration and possibly the capability for phagocytosis. \textcopyright{} 1988 Springer-Verlag.},
  pmid = {3250374},
  keywords = {Autometallography,Macrophages,Mercuric chloride,Migration,Phagocytosis,Toxicity},
  file = {C\:\\Users\\makro\\Zotero\\storage\\KUX2YRDY\\Christensen, Mogensen, Rungby - 1988 - Toxicity and ultrastructural localization of mercuric chloride in cultured murine macrophages.pdf}
}

@misc{chromium_nih,
  title = {Chromium\textemdash{{Fact Sheet}} for {{Health Professionals}}},
  year = {2022},
  howpublished = {https://ods.od.nih.gov/factsheets/Chromium-HealthProfessional/\#h2}
}

@book{Citation2001,
  title = {Dietary {{Reference Intakes}} for {{Vitamin A}}, {{Vitamin K}}, {{Arsenic}}, {{Boron}}, {{Chromium}}, {{Copper}}, {{Iodine}}, {{Iron}}, {{Manganese}}, {{Molybdenum}}, {{Nickel}}, {{Silicon}}, {{Vanadium}}, and {{Zinc}}},
  author = {{Institute of Medicine}},
  year = {2001},
  month = jun,
  journal = {Dietary Reference Intakes for Vitamin A, Vitamin K, Arsenic, Boron, Chromium, Copper, Iodine, Iron, Manganese, Molybdenum, Nickel, Silicon, Vanadium, and Zinc},
  publisher = {{National Academies Press}},
  address = {{Washington, D.C.}},
  doi = {10.17226/10026},
  abstract = {Mycotoxins are small (MW approximately 700), toxic chemical products formed as secondary metabolites by a few fungal species that readily colonise crops and contaminate them with toxins in the field or after harvest. Ochratoxins and Aflatoxins are mycotoxins of major significance and hence there has been significant research on broad range of analytical and detection techniques that could be useful and practical. Due to the variety of structures of these toxins, it is impossible to use one standard technique for analysis and/or detection. Practical requirements for high-sensitivity analysis and the need for a specialist laboratory setting create challenges for routine analysis. Several existing analytical techniques, which offer flexible and broad-based methods of analysis and in some cases detection, have been discussed in this manuscript. There are a number of methods used, of which many are lab-based, but to our knowledge there seems to be no single technique that stands out above the rest, although analytical liquid chromatography, commonly linked with mass spectroscopy is likely to be popular. This review manuscript discusses (a) sample pre-treatment methods such as liquid-liquid extraction (LLE), supercritical fluid extraction (SFE), solid phase extraction (SPE), (b) separation methods such as (TLC), high performance liquid chromatography (HPLC), gas chromatography (GC), and capillary electrophoresis (CE) and (c) others such as ELISA. Further currents trends, advantages and disadvantages and future prospects of these methods have been discussed.},
  isbn = {978-0-309-07279-3},
  file = {C\:\\Users\\makro\\Zotero\\storage\\4BNE36GQ\\Institute of Medicine - 2001 - Dietary Reference Intakes for Vitamin A, Vitamin K, Arsenic, Boron, Chromium, Copper, Iodine, Iron, Manga.pdf}
}

@article{Cock2009,
  title = {Biopython: {{Freely}} Available {{Python}} Tools for Computational Molecular Biology and Bioinformatics},
  author = {Cock, Peter J.A. and Antao, Tiago and Chang, Jeffrey T. and Chapman, Brad A. and Cox, Cymon J. and Dalke, Andrew and Friedberg, Iddo and Hamelryck, Thomas and Kauff, Frank and Wilczynski, Bartek and De Hoon, Michiel J.L.},
  year = {2009},
  journal = {Bioinformatics},
  volume = {25},
  number = {11},
  pages = {1422--1423},
  issn = {13674803},
  doi = {10.1093/bioinformatics/btp163},
  abstract = {Summary: The Biopython project is a mature open source international collaboration of volunteer developers, providing Python libraries for a wide range of bioinformatics problems. Biopython includes modules for reading and writing different sequence file formats and multiple sequence alignments, dealing with 3D macro molecular structures, interacting with common tools such as BLAST, ClustalW and EMBOSS, accessing key online databases, as well as providing numerical methods for statistical learning. \textcopyright{} The Author 2009. Published by Oxford University Press. All rights reserved.},
  pmid = {19304878},
  file = {C\:\\Users\\makro\\Zotero\\storage\\V4IAJQG9\\Cock et al. - 2009 - Biopython Freely available Python tools for computational molecular biology and bioinformatics.pdf}
}

@article{Connelly1996,
  title = {The {{sbcC}} and {{sbcD}} Genes of {{Escherichia}} Coli Encode a Nuclease Involved in Palindrome Inviability and Genetic Recombination},
  author = {Connelly, John C. and Leach, David R. F.},
  year = {1996},
  month = mar,
  journal = {Genes to Cells},
  volume = {1},
  number = {3},
  pages = {285--291},
  issn = {13569597},
  doi = {10.1046/j.1365-2443.1996.23024.x},
  abstract = {Background: Long DNA palindromes have the potential to adopt hairpin or cruciform secondary structures that inhibit DNA replication. In Escherichia coli, this palindrome-mediated inviability results from the activity of the sbcC and sbcD genes, and genetic observations have suggested that they may encode a nuclease. Mutations in these genes also restore the defect in genetic recombination associated with recBC sbcB mutants. Results: We have purified the E. coli SbcCD protein from an overexpressing strain and have shown that it has an ATP-dependent DNA double-strand exonuclease activity. Co-purification of nuclease with protein, antibody inhibition and the absence of activity in extracts lacking the sbcCD genes confirm that the activity is intrinsic to SbcCD. The purified protein also has an ATP-independent single-strand DNA endonuclease activity. Conclusions: We have shown that sbcCD encodes a nuclease. The purified protein has double-strand DNA exonuclease and single-strand DNA endonuclease activities. We propose that SbcCD cleaves secondary structures formed at replication forks and that the broken forks can be repaired by homologous recombination.},
  pmid = {9133662},
  file = {C\:\\Users\\makro\\Zotero\\storage\\BAGZV2C7\\Connelly, Leach - 1996 - The sbcC and sbcD genes of Escherichia coli encode a nuclease involved in palindrome inviability and genetic re.pdf}
}

@article{Connelly1997,
  title = {Overexpression, Purification, and Characterization of the {{SbcCD}} Protein from {{{\emph{Escherichia}}}}{\emph{ Coli}}},
  author = {Connelly, John C. and De Leau, Erica S. and Okely, Ewa A. and Leach, David R.F.},
  year = {1997},
  journal = {Journal of Biological Chemistry},
  volume = {272},
  number = {32},
  pages = {19819--19826},
  publisher = {{\^A\textcopyright{} 1997 ASBMB. Currently published by Elsevier Inc; originally published by American Society for Biochemistry and Molecular Biology.}},
  issn = {00219258},
  doi = {10.1074/jbc.272.32.19819},
  abstract = {The sbcC and sbcD genes mediate palindrome inviability in Escherichia coli. The sbcCD operon has been cloned into the plasmid pTrc99A under the control of the strong trc promoter and introduced into a strain carrying a chromosomal deletion of sbcCD. The SbcC and SbcD polypeptides were overexpressed to 6\% of total cell protein, and both polypeptides copurified in a four-step purification procedure. Purified SbcCD is a processive double- strand exonuclease that has an absolute requirement for Mn2+ and uses ATP as a preferred energy source. Gel filtration chromatography and sedimentation equilibrium analyses were used to show that the SbcC and SbcD polypeptides dissociate at some stage after purification and that this dissociation is reversed by the addition of Mn2+. We demonstrate that SbcD has the potential to form a secondary structural motif found in a number of protein phosphatases and suggest that it is a metalloprotein that contains the catalytic center of the SbcCD exonuclease.},
  pmid = {9242643},
  file = {C\:\\Users\\makro\\Zotero\\storage\\5QW9NFNM\\Connelly et al. - 1997 - Overexpression, purification, and characterization of the SbcCD protein from Escherichia coli.pdf}
}

@article{Connelly2003,
  title = {Nucleolytic Processing of a Protein-Bound {{DNA}} End by the {{{\emph{E}}}}{\emph{. Coli}} {{SbcCD}} ({{MR}}) Complex},
  author = {Connelly, John C. and {de Leau}, Erica S. and Leach, David R.F.},
  year = {2003},
  month = jul,
  journal = {DNA Repair},
  volume = {2},
  number = {7},
  pages = {795--807},
  issn = {15687864},
  doi = {10.1016/S1568-7864(03)00063-6},
  abstract = {SbcCD and other Mre11/Rad50 (MR) complexes are implicated in the metabolism of DNA ends. They cleave ends sealed by hairpin structures and have been postulated to play roles in removing protein bound to DNA termini. Here we provide direct evidence that the Escherichia coli MR complex (SbcCD) removes protein from a protein-bound DNA end by inserting a double-strand break (DSB). These observations indicate a more complex biochemical action than has been assumed previously and argue that this class of protein has the potential to play a direct role in deprotecting protein-bound DNA ends in vivo. \textcopyright{} 2003 Elsevier Science B.V. All rights reserved.},
  pmid = {12826280},
  keywords = {ABC-ATPase,DNA end/terminus,Double-strand break,Mre11/Rad50,SbcCD,Topoisomerase},
  file = {C\:\\Users\\makro\\Zotero\\storage\\QMKU25W6\\Connelly, de Leau, Leach - 2003 - Nucleolytic processing of a protein-bound DNA end by the E. coli SbcCD (MR) complex.pdf}
}

@article{Costello2016,
  title = {Chromium Supplements for Glycemic Control in Type 2 Diabetes: Limited Evidence of Effectiveness},
  author = {Costello, Rebecca B. and Dwyer, Johanna T. and Bailey, Regan L.},
  year = {2016},
  month = jul,
  journal = {Nutrition Reviews},
  volume = {74},
  number = {7},
  pages = {455--468},
  issn = {0029-6643},
  doi = {10.1093/nutrit/nuw011},
  abstract = {Some adults with type 2 diabetes mellitus (T2DM) believe that chromium-containing supplements will help control their disease, but the evidence is mixed. This narrative review examines the efficacy of chromium supplements for improving glycemic control as measured by decreases in fasting plasma glucose (FPG) or hemoglobin A1c (HbA1c). Using systematic search criteria, 20 randomized controlled trials of chromium supplementation in T2DM patients were identified. Clinically meaningful treatment goals were defined as an FPG of {$\geq$}7.2mmol/dL, a decline in HbA1c to {$\leq$}7\%, or a decrease of {$\geq$}0.5\% in HbA1c. In only a few randomized controlled trials did FPG (5 of 20), HbA1c (3 of 14), or both (1 of 14) reach the treatment goals with chromium supplementation. HbA1c declined by {$\geq$}0.5\% in 5 of 14 studies. On the basis of the low strength of existing evidence, chromium supplements have limited effectiveness, and there is little rationale to recommend their use for glycemic control in patients with existing T2DM. Future meta-analyses should include only high-quality studies with similar forms of chromium and comparable inclusion/exclusion criteria to provide scientifically sound recommendations for clinicians.},
  pmid = {27261273},
  keywords = {Chromium,Fasting plasma glucose,Hemoglobin A1c,Type 2 diabetes mellitus},
  file = {C\:\\Users\\makro\\Zotero\\storage\\N4KWYASH\\Costello, Dwyer, Bailey - 2016 - Chromium supplements for glycemic control in type 2 diabetes limited evidence of effectiveness.pdf}
}

@article{Coudray2013,
  title = {Inward-Facing Conformation of the Zinc Transporter {{YiiP}} Revealed by Cryoelectron Microscopy},
  author = {Coudray, Nicolas and Valvo, Salvatore and Hu, Minghui and Lasala, Ralph and Kim, Changki and Vink, Martin and Zhou, Ming and Provasi, Davide and Filizola, Marta and Tao, Juoehi and Fang, Jia and Penczek, Pawel A. and {Ubarretxena-Belandia}, Iban and Stokes, David L.},
  year = {2013},
  journal = {Proceedings of the National Academy of Sciences of the United States of America},
  volume = {110},
  number = {6},
  pages = {2140--2145},
  issn = {00278424},
  doi = {10.1073/pnas.1215455110},
  abstract = {YiiP is a dimeric Zn2+/H+ antiporter from Escherichia coli belonging to the cation diffusion facilitator family. We used cryoelectron microscopy to determine a 13-\AA{} resolution structure of a YiiP homolog from Shewanella oneidensis within a lipid bilayer in the absence of Zn 2+. Starting from the X-ray structure in the presence of Zn 2+, we used molecular dynamics flexible fitting to build a model consistent with our map. Comparison of the structures suggests a conformational change that involves pivoting of a transmembrane, fourhelix bundle (M1, M2, M4, and M5) relative to the M3-M6 helix pair. Although accessibility of transport sites in the X-ray model indicates that it represents an outward-facing state, our model is consistent with an inward-facing state, suggesting that the conformational change is relevant to the alternating access mechanism for transport. Molecular dynamics simulation of YiiP in a lipid environment was used to address the feasibility of this conformational change. Association of the C-terminal domains is the same in both states, and we speculate that this association is responsible for stabilizing the dimer that, in turn, may coordinate the rearrangement of the transmembrane helices.},
  pmid = {23341604},
  keywords = {FieF,Membrane protein,Secondary transporter,Zinc antiporter},
  file = {C\:\\Users\\makro\\Zotero\\storage\\7FMT5VUS\\Coudray et al. - 2013 - Inward-facing conformation of the zinc transporter YiiP revealed by cryoelectron microscopy.pdf}
}

@article{Dahiyat1997,
  title = {{\emph{De Novo}} Protein Design: Towards Fully Automated Sequence Selection},
  author = {Dahiyat, Bassil I. and Sarisky, Catherine A. and Mayo, Stephen L.},
  year = {1997},
  month = nov,
  journal = {Journal of Molecular Biology},
  volume = {273},
  number = {4},
  pages = {789--796},
  issn = {00222836},
  doi = {10.1006/jmbi.1997.1341},
  abstract = {Several groups have applied and experimentally tested systematic, quantitative methods to protein design with the goal of developing general design algorithms. We have sought to expand the range of computational protein design by developing quantitative design methods for residues of all parts of a protein: the buried core, the solvent exposed surface, and the boundary between core and surface. Our goal is an objective, quantitative design algorithm that is based on the physical properties that determine protein structure and stability and which is not limited to specific folds or motifs. We chose the {$\beta\beta\alpha$} motif typified by the zinc finger DNA binding module to test our design methodology. Using previously published sequence scoring functions developed with a combined experimental and computational approach and the Dead-End Elimination theorem to search for the optimal sequence, we designed 20 out of 28 positions in the test motif. The resulting sequence has less than 40\% homology to any known sequence and does not contain any metal binding sites or cysteine residues. The resulting peptide, pda8d, is highly soluble and monomeric and circular dichroism measurements showed it to be folded with a weakly cooperative thermal unfolding transition. The NMR solution structure of pda8d was solved and shows that it is well-defined with a backbone ensemble rms deviation of 0.55 \AA. Pda8d folds into the desired {$\beta\beta\alpha$} motif with well-defined elements of secondary structure and tertiary organization. Superposition of the pda8d backbone to the design target is excellent, with an atomic rms deviation of 1.04 \AA.},
  pmid = {9367772},
  keywords = {Dead-End Elimination,Force field,NMR,Protein design,Sequence optimization},
  file = {C\:\\Users\\makro\\Zotero\\storage\\K6UF9LH6\\Dahiyat, Sarisky, Mayo - 1997 - De Novo protein design towards fully automated sequence selection.pdf}
}

@article{Davis2009,
  title = {Homodimerization and {{Heterodimerization}} of {{Minimal Zinc}}({{II}})-{{Binding-Domain Peptides}} of {{T-Cell Proteins CD4}}, {{CD8$\alpha$}}, and {{Lck}}},
  author = {Davis, Alisa M. and Berg, Jeremy M.},
  year = {2009},
  month = aug,
  journal = {Journal of the American Chemical Society},
  volume = {131},
  number = {32},
  pages = {11492--11497},
  issn = {0002-7863},
  doi = {10.1021/ja9028928},
  abstract = {Metal-mediated protein oligomerization is an emerging mode of protein-protein interaction. The C-terminal cytosolic domains of T-cell coreceptors CD4 and CD8{$\alpha$} form zinc-bridged heterodimers with the N-terminal region of the kinase Lck, with each protein contributing two cysteinate ligands to the complex. Using size exclusion chromatography, 1H NMR, and UV/visible absorption spectroscopy with cobalt(II) as a spectroscopic probe, we demonstrate that small peptides derived from these regions form metal-bridged heterodimers but also homodimers, in contrast to previous reports. The Lck-CD4 and Lck-CD8{$\alpha$} cobalt(II)-bridged heterodimer complexes are more stable than the corresponding (Lck)2cobalt(II) complex by factors of 11 {$\pm$} 4 and 22 {$\pm$} 9, respectively. These studies were aided by the discovery that cobalt(II) complexes with a cobalt(II)(-Cys-X-X-Cys-)(-Cys-X-Cys-) chromophore show unusual optical spectra with one component of the visible d-d (4A2-to- 4T1(P)) transition red-shifted and well separated from the other components. These results provide insights into the basis of specificity of metal-bridged complex formation and on the potential biological significance of metal-bridged homodimers in T-cells.},
  pmid = {19624124},
  file = {C\:\\Users\\makro\\Zotero\\storage\\ZWDFA47U\\Davis, Berg - 2009 - Homodimerization and Heterodimerization of Minimal Zinc(II)-Binding-Domain Peptides of T-Cell Proteins CD4, CD8α, a.pdf}
}

@article{Deshpande2016,
  title = {Nbs1 {{Converts}} the {{Human Mre11}}/{{Rad50 Nuclease Complex}} into an {{Endo}}/{{Exonuclease Machine Specific}} for {{Protein-DNA Adducts}}},
  author = {Deshpande, Rajashree A and Lee, Ji Hoon and Arora, Sucheta and Paull, Tanya T},
  year = {2016},
  journal = {Molecular Cell},
  volume = {64},
  number = {3},
  pages = {593--606},
  publisher = {{Elsevier Inc.}},
  issn = {10974164},
  doi = {10.1016/j.molcel.2016.10.010},
  abstract = {The human Mre11/Rad50/Nbs1 (hMRN) complex is critical for the sensing, processing, and signaling of DNA double-strand breaks. The nuclease activity of Mre11 is essential for mammalian development and cell viability, although the regulation and substrate specificity of Mre11 have been difficult to define. Here we show that hMRN catalyzes sequential endonucleolytic and exonucleolytic activities on both 5{${'}$} and 3{${'}$} strands of DNA ends containing protein adducts, and that Nbs1, ATP, and adducts are essential for this function. In contrast, Nbs1 inhibits Mre11/Rad50-catalyzed 3{${'}$}-to-5{${'}$} exonucleolytic degradation of clean DNA ends. The hMRN endonucleolytic cleavage events are further stimulated by the phosphorylated form of the human C-terminal binding protein-interacting protein (CtIP) DNA repair enzyme, establishing a role for CtIP in regulating hMRN activity. These results illuminate the important role of Nbs1 and CtIP in determining the substrates and consequences of human Mre11/Rad50 nuclease activities on protein-DNA lesions.},
  pmid = {27814491},
  file = {C\:\\Users\\makro\\Zotero\\storage\\22UZYGUC\\Deshpande et al. - 2016 - Nbs1 Converts the Human Mre11Rad50 Nuclease Complex into an EndoExonuclease Machine Specific for Protein-DNA A.pdf}
}

@article{Deshpande2017,
  title = {Rad50 {{ATPase}} Activity Is Regulated by {{DNA}} Ends and Requires Coordination of Both Active Sites},
  author = {Deshpande, Rajashree A. and Lee, Ji Hoon and Paull, Tanya T.},
  year = {2017},
  journal = {Nucleic Acids Research},
  volume = {45},
  number = {9},
  pages = {5255--5268},
  issn = {13624962},
  doi = {10.1093/nar/gkx173},
  abstract = {The Mre11-Rad50-Nbs1(Xrs2) (MRN/X) complex is critical for the repair and signaling of DNA double strand breaks. The catalytic core of MRN/X comprised of the Mre11 nuclease and Rad50 adenosine triphosphatase (ATPase) active sites dimerizes through association between the Rad50 ATPase catalytic domains and undergoes extensive conformational changes upon ATP binding. This ATP-bound 'closed' state promotes binding to DNA, tethering DNA ends and ATM activation, but prevents nucleolytic processing of DNA ends, while ATP hydrolysis is essential for Mre11 endonuclease activity at blocked DNA ends. Here we investigate the regulation of ATP hydrolysis as well as the interdependence of the two functional active sites.We find that doublestranded DNA stimulates ATP hydrolysis by hMRN over {$\sim$}20-fold in an end-dependent manner. Using catalytic site mutants to create Rad50 dimers with only one functional ATPase site, we find that both ATPase sites are required for the stimulation by DNA. MRN-mediated endonucleolytic cleavage of DNA at sites of protein adducts requires ATP hydrolysis at both sites, as does the stimulation of ATM kinase activity. These observations suggest that symmetrical engagement of the Rad50 catalytic head domains with ATP bound at both sites is important for MRN functions in eukaryotic cells.},
  pmid = {28369545},
  file = {C\:\\Users\\makro\\Zotero\\storage\\ZR9ZZ8HX\\Deshpande, Lee, Paull - 2017 - Rad50 ATPase activity is regulated by DNA ends and requires coordination of both active sites.pdf}
}

@article{Dokmanic2008,
  title = {Metals in Proteins: {{Correlation}} between the Metal-Ion Type, Coordination Number and the Amino-Acid Residues Involved in the Coordination},
  author = {Dokmani{\'c}, Ivan and {\v S}iki{\'c}, Mile and Tomi{\'c}, Sanja},
  year = {2008},
  journal = {Acta Crystallographica Section D: Biological Crystallography},
  volume = {64},
  number = {3},
  pages = {257--263},
  issn = {09074449},
  doi = {10.1107/S090744490706595X},
  abstract = {Metal ions are constituents of many metalloproteins, in which they have either catalytic (metalloenzymes) or structural functions. In this work, the characteristics of various metals were studied (Cu, Zn, Mg, Mn, Fe, Co, Ni, Cd and Ca in proteins with known crystal structure) as well as the specificity of their environments. The analysis was performed on two data sets: the set of protein structures in the Protein Data Bank (PDB) determined with resolution {$<$}1.5 \AA{} and the set of nonredundant protein structures from the PDB. The former was used to determine the distances between each metal ion and its electron donors and the latter was used to assess the preferred coordination numbers and common combinations of amino-acid residues in the neighbourhood of each metal. Although the metal ions considered predominantly had a valence of two, their preferred coordination number and the type of amino-acid residues that participate in the coordination differed significantly from one metal ion to the next. This study concentrates on finding the specificities of a metal-ion environment, namely the distribution of coordination numbers and the amino-acid residue types that frequently take part in coordination. Furthermore, the correlation between the coordination number and the occurrence of certain amino-acid residues (quartets and triplets) in a metal-ion coordination sphere was analysed. The results obtained are of particular value for the identification and modelling of metal-binding sites in protein structures derived by homology modelling. Knowledge of the geometry and characteristics of the metal-binding sites in metalloproteins of known function can help to more closely determine the biological activity of proteins of unknown function and to aid in design of proteins with specific affinity for certain metals. \textcopyright{} International Union of Crystallography 2008.},
  pmid = {18323620},
  keywords = {Metal coordination number,Metal coordination sphere,Metal ions},
  file = {C\:\\Users\\makro\\Zotero\\storage\\DAB8DJ89\\Dokmanić, Šikić, Tomić - 2008 - Metals in proteins Correlation between the metal-ion type, coordination number and the amino-acid residu.pdf}
}

@article{Driscoll2013,
  title = {Mercury as a {{Global Pollutant}}: {{Sources}}, {{Pathways}}, and {{Effects}}},
  author = {Driscoll, Charles T and Mason, Robert P and Chan, Hing Man and Jacob, Daniel J and Pirrone, Nicola},
  year = {2013},
  month = may,
  journal = {Environmental Science \& Technology},
  volume = {47},
  number = {10},
  pages = {4967--4983},
  issn = {0013-936X},
  doi = {10.1021/es305071v},
  file = {C\:\\Users\\makro\\Zotero\\storage\\I4B3RIR2\\Driscoll et al. - 2013 - Mercury as a Global Pollutant Sources, Pathways, and Effects.pdf}
}

@article{Faller2000,
  title = {Optical and {{TDPAC}} Spectroscopy of {{Hg}}({{II}})-Rubredoxin: Model for a Mononuclear Tetrahedral [{{Hg}}({{CysS}}){\textsubscript{4}}]{\textsuperscript{2-}} Center},
  author = {Faller, Peter and Ctortecka, Bernd and Tr{\"o}ger, Wolfgang and Butz, Tilman and Va{\v s}{\'a}k, Milan},
  year = {2000},
  month = jun,
  journal = {JBIC Journal of Biological Inorganic Chemistry},
  volume = {5},
  number = {3},
  pages = {393--401},
  issn = {0949-8257},
  doi = {10.1007/PL00010668},
  abstract = {Rubredoxins possess a well-defined mononuclear tetrahedral tetrathiolate metal binding site, a feature exploited by several investigations to study the spectroscopic characteristics and the coordination chemistry of different metal ions at this binding site. In the present work, Hg(II)-substituted rubredoxin (Rd) from Desulfovibrio gigas has been studied by electronic absorption, circular dichroism (CD), magnetic circular dichroism (MCD), and time differential perturbed angular correlation of {$\gamma$}-rays (TDPAC) spectroscopies. The TDPAC spectrum of 199mHg-Rd at pH 8 exhibits a prevailing nuclear quadrupole interaction (NQI) with a precession frequency of {$\omega$}1 = 0.09 Grad/s and an asymmetry parameter {$\eta$} = 0, features characteristic of a slightly distorted tetrahedral tetrathiolate metal coordination, i.e, a HgCysS4 center. In addition, three minor populated NQIs have also been detected. They may represent a trigonal HgS3 ({$\omega$}1 = 1.13 Grad/s, {$\eta$} = 0.21), a digonal HgS2 ({$\omega$}1 = 1.34 Grad/s, {$\eta$} = 0.20), and a digonal Hg(II) coordination ({$\omega$}1 = 1.58 Grad/s, {$\eta$} = 0.18) with unidentified ligands. Since similar studies at pH 2.5 revealed a time-dependent increase of the HgCysS4 population, the low populated sites may represent intermediate Hg(II) complexes formed prior to the generation of the thermodynamically stable structure. The metal-induced absorption envelope of Hg-Rd reveals three distinct transitions with Gaussian-resolved maxima located at 230, 257, and 284 nm, which are paralleled by dichroic features in the corresponding difference CD spectrum of Hg(II)-Rd versus apo-Rd. Based on the optical electronegativity theory of Jorgensen, the lowest energy transition has been attributed to a CysS-Hg(II) charge-transfer excitation. The T(d) type of metal coordination in Hg-Rd is supported by the presence of an unresolved A-term with a negative lobe at 295 nm in the difference MCD spectrum. These results point to the usefulness of optical and TDPAC spectroscopies for studying Hg(II) sites in other proteins.},
  pmid = {10907750},
  keywords = {Cysteine ligation,Electronic spectroscopy,Mercury-substituted rubredoxin,Mercury-thiolate charge-transfer bands,Perturbed angular correlation of γ-rays spectrosco},
  file = {C\:\\Users\\makro\\Zotero\\storage\\9LH9ME9T\\Faller et al. - 2000 - Optical and TDPAC spectroscopy of Hg(II)-rubredoxin model for a mononuclear tetrahedral Hg(CysS)42− center.pdf}
}

@article{Fields1989,
  title = {A Novel Genetic System to Detect Protein\textendash Protein Interactions},
  author = {Fields, Stanley and Song, Ok-kyu},
  year = {1989},
  month = jul,
  journal = {Nature},
  volume = {340},
  number = {6230},
  pages = {245--246},
  issn = {0028-0836},
  doi = {10.1038/340245a0},
  abstract = {PROTEIN-protein interactions between two proteins have generally been studied using biochemical techniques such as crosslinking, co-immunoprecipitation and co-fractionation by chromatography. We have generated a novel genetic system to study these interactions by taking advantage of the properties of the GAL4 protein of the yeast Saccharomyces cerevisiae. This protein is a transcriptional activator required for the expression of genes encoding enzymes of galactose utilization. It consists of two separable and functionally essential domains: an N-terminal domain which binds to specific DNA sequences (UASG); and a C-terminal domain containing acidic regions, which is necessary to activate transcription. We have generated a system of two hybrid proteins containing parts of GAL4: the GAL4 DNA-binding domain fused to a protein 'X' and a GAL4 activating region fused to a protein 'Y'. If X and Y can form a protein-protein complex and reconstitute proximity of the GAL4 domains, tran-scription of a gene regulated by UASG occurs. We have tested this system using two yeast proteins that are known to interact-SNF1 and SNF4. High transcriptional activity is obtained only when both hybrids are present in a cell. This system may be applicable as a general method to identify proteins that interact with a known protein by the use of a simple galactose selection. \textcopyright{} 1989 Nature Publishing Group.},
  pmid = {2547163},
  file = {C\:\\Users\\makro\\Zotero\\storage\\K3MTA4WA\\Fields, Song - 1989 - A novel genetic system to detect protein–protein interactions.pdf}
}

@incollection{Freisinger2013,
  title = {Cadmium in {{Metallothioneins}}},
  booktitle = {Metal {{Ions}} in {{Life Sciences}}},
  author = {Freisinger, Eva and Va{\v s}{\'a}k, Milan},
  year = {2013},
  volume = {11},
  pages = {339--371},
  issn = {20419821},
  doi = {10.1007/978-94-007-5179-8_11},
  isbn = {978-94-007-5178-1},
  file = {C\:\\Users\\makro\\Zotero\\storage\\XBYX458H\\Freisinger, Vašák - 2013 - Cadmium in Metallothioneins.pdf}
}

@misc{frontiersin,
  title = {The {{Role}} of {{Cofactors}} in {{Protein Stability}} and {{Homeostasis}}: {{Focus}} on {{Human Metabolism}}},
  howpublished = {https://www.frontiersin.org/research-topics/35664/the-role-of-cofactors-in-protein-stability-and-homeostasis-focus-on-human-metabolism\#:\textasciitilde :text=to structural roles.-,It is known that more than 30\%25 of proteins require,to perform their biological functions}
}

@article{Fu2012,
  title = {{{CD-HIT}}: Accelerated for Clustering the next-Generation Sequencing Data},
  author = {Fu, Limin and Niu, Beifang and Zhu, Zhengwei and Wu, Sitao and Li, Weizhong},
  year = {2012},
  month = dec,
  journal = {Bioinformatics},
  volume = {28},
  number = {23},
  pages = {3150--3152},
  issn = {1367-4803},
  doi = {10.1093/bioinformatics/bts565},
  abstract = {CD-HIT is a widely used program for clustering biological sequences to reduce sequence redundancy and improve the performance of other sequence analyses. In response to the rapid increase in the amount of sequencing data produced by the next-generation sequencing technologies, we have developed a new CD-HIT program accelerated with a novel parallelization strategy and some other techniques to allow efficient clustering of such datasets. Our tests demonstrated very good speedup derived from the parallelization for up to {$\sim$}24 cores and a quasi-linear speedup for up to {$\sim$}8 cores. The enhanced CD-HIT is capable of handling very large datasets in much shorter time than previous versions. \textcopyright{} The Author 2012. Published by Oxford University Press. All rights reserved.},
  pmid = {23060610},
  file = {C\:\\Users\\makro\\Zotero\\storage\\FRZJSEU6\\Fu et al. - 2012 - CD-HIT accelerated for clustering the next-generation sequencing data.pdf}
}

@article{Garcia2011,
  title = {Bidirectional Resection of {{DNA}} Double-Strand Breaks by {{Mre11}} and {{Exo1}}},
  author = {Garcia, Valerie and Phelps, Sarah E.L. and Gray, Stephen and Neale, Matthew J.},
  year = {2011},
  journal = {Nature},
  volume = {479},
  number = {7372},
  pages = {241--244},
  publisher = {{Nature Publishing Group}},
  issn = {00280836},
  doi = {10.1038/nature10515},
  abstract = {Repair of DNA double-strand breaks (DSBs) by homologous recombination requires resection of 5{${'}$}-termini to generate 3{${'}$}-single-strand DNA tails. Key components of this reaction are exonuclease 1 and the bifunctional endo/exonuclease, Mre11 (refs 2-4). Mre11 endonuclease activity is critical when DSB termini are blocked by bound protein-such as by the DNA end-joining complex, topoisomerases or the meiotic transesterase Spo11 (refs 7-13)-but a specific function for the Mre11 3{${'}$}-5{${'}$} exonuclease activity has remained elusive. Here we use Saccharomyces cerevisiae to reveal a role for the Mre11 exonuclease during the resection of Spo11-linked 5{${'}$}-DNA termini in vivo. We show that the residual resection observed in Exo1-mutant cells is dependent on Mre11, and that both exonuclease activities are required for efficient DSB repair. Previous work has indicated that resection traverses unidirectionally. Using a combination of physical assays for 5{${'}$}-end processing, our results indicate an alternative mechanism involving bidirectional resection. First, Mre11 nicks the strand to be resected up to 300 nucleotides from the 5{${'}$}-terminus of the DSB-much further away than previously assumed. Second, this nick enables resection in a bidirectional manner, using Exo1 in the 5{${'}$}-3{${'}$} direction away from the DSB, and Mre11 in the 3{${'}$}-5{${'}$} direction towards the DSB end. Mre11 exonuclease activity also confers resistance to DNA damage in cycling cells, suggesting that Mre11-catalysed resection may be a general feature of various DNA repair pathways. \textcopyright{} 2011 Macmillan Publishers Limited. All rights reserved.},
  pmid = {22002605},
  file = {C\:\\Users\\makro\\Zotero\\storage\\4IQFN7GJ\\Garcia et al. - 2011 - Bidirectional resection of DNA double-strand breaks by Mre11 and Exo1.pdf}
}

@article{Greenfield2007,
  title = {Using Circular Dichroism Spectra to Estimate Protein Secondary Structure},
  author = {Greenfield, Norma J.},
  year = {2007},
  journal = {Nature Protocols},
  volume = {1},
  number = {6},
  pages = {2876--2890},
  issn = {17542189},
  doi = {10.1038/nprot.2006.202},
  abstract = {Circular dichroism (CD) is an excellent tool for rapid determination of the secondary structure and folding properties of proteins that have been obtained using recombinant techniques or purified from tissues. The most widely used applications of protein CD are to determine whether an expressed, purified protein is folded, or if a mutation affects its conformation or stability. In addition, it can be used to study protein interactions. This protocol details the basic steps of obtaining and interpreting CD data, and methods for analyzing spectra to estimate the secondary structural composition of proteins. CD has the advantage that measurements may be made on multiple samples containing {$\leq$}20 {$\mu$}g of proteins in physiological buffers in a few hours. However, it does not give the residue-specific information that can be obtained by x-ray crystallography or NMR.},
  pmid = {17406547},
  file = {C\:\\Users\\makro\\Zotero\\storage\\6ZJDCXC8\\Greenfield - 2007 - Using circular dichroism spectra to estimate protein secondary structure.pdf}
}

@article{Harding2014,
  title = {Mespeus-{{A}} Database of Metal Interactions with Proteins},
  author = {Harding, Marjorie M. and Hsin, Kun-Yi},
  year = {2014},
  journal = {Methods in Molecular Biology},
  volume = {1091},
  pages = {333--342},
  issn = {10643745},
  doi = {10.1007/978-1-62703-691-7_23},
  abstract = {Modeling and analogy are commonly used to identify the part that a metal may play in the structure or function of a new protein which has been recognized by structural genomics. Mespeus (http://mespeus.bch.ed.ac.uk/MESPEUS-10/) lists metal protein interactions whose geometry has been experimentally determined and allows them to be visualized. This can contribute to the modeling process. The use of Mespeus is described with a series of examples. \textcopyright{} 2014 Springer Science+Business Media, LLC.},
  isbn = {9781627036900},
  pmid = {24203343},
  keywords = {Database,Metal,Metal coordination group,Metal site,Metal site geometry,Metalloprotein,Metalloprotein structure},
  file = {C\:\\Users\\makro\\Zotero\\storage\\FB2Y5Q3C\\Harding, Hsin - 2014 - Mespeus-A database of metal interactions with proteins.pdf}
}

@article{He2012,
  title = {Rad50 {{Zinc Hook Is Important}} for the {{Mre11 Complex}} to {{Bind Chromosomal DNA Double-stranded Breaks}} and {{Initiate Various DNA Damage Responses}}},
  author = {He, Jing and Shi, Linda Z. and Truong, Lan N. and Lu, Chi-Sheng and Razavian, Niema and Li, Yongjiang and Negrete, Alejandro and Shiloach, Joseph and Berns, Michael W. and Wu, Xiaohua},
  year = {2012},
  month = sep,
  journal = {Journal of Biological Chemistry},
  volume = {287},
  number = {38},
  pages = {31747--31756},
  issn = {00219258},
  doi = {10.1074/jbc.M112.384750},
  abstract = {The Mre11-Rad50-Nbs1 (MRN) complex plays critical roles in checkpoint activation and double-stranded break (DSB) repair. The Rad50 zinc hook domain mediates zinc-dependent intercomplex associations of MRN, which is important for DNA tethering. Studies in yeast suggest that the Rad50 zinc hook domain is essential for MRN functions, but its role in mammalian cells is not clear. We demonstrated that the human Rad50 hook mutants are severely defective in various DNA damage responses including ATM (Ataxia telangiectasia mutated) activation, homologous recombination, sensitivity to IR, and activation of the ATR pathway. By using live cell imaging, we observed that the Rad50 hook mutants fail to be recruited to chromosomal DSBs, suggesting a novel mechanism underlying the severe defects observed for the Rad50 hook mutants. In vitro analysis showed that Zn2+ promotes wild type but not the hook mutant of MR to bind double-stranded DNA. In vivo, the Rad50 hook mutants are defective in being recruited to chromosomal DSBs in both H2AX-proficient and -deficient cells, suggesting that the Rad50 hook mutants are impaired in direct binding to chromosomal DSB ends. We propose that the Rad50 zinc hook domain is important for the initial binding of MRN to DSBs, leading to ATM activation to phosphorylate H2AX, which recruits more MRN to the DSB-flanking chromosomal regions. Our studies reveal a critical role for the Rad50 zinc hook domain in establishing and maintaining MRN recruitment to chromosomal DSBs and suggest an important mechanism of how the Rad50 zinc hook domain contributes to DNA repair and checkpoint activation.},
  isbn = {8587847910},
  pmid = {22833675},
  file = {C\:\\Users\\makro\\Zotero\\storage\\HYRQFN3P\\He et al. - 2012 - Rad50 Zinc Hook Is Important for the Mre11 Complex to Bind Chromosomal DNA Double-stranded Breaks and Initiate Variou.pdf}
}

@article{Herdendorf2011,
  title = {Biochemical Characterization of Bacteriophage {{T4 Mre11-Rad50}} Complex},
  author = {Herdendorf, Timothy J. and Albrecht, Dustin W. and Benkovic, Stephen J. and Nelson, Scott W.},
  year = {2011},
  journal = {Journal of Biological Chemistry},
  volume = {286},
  number = {4},
  pages = {2382--2392},
  publisher = {{\^A\textcopyright{} 2011 ASBMB. Currently published by Elsevier Inc; originally published by American Society for Biochemistry and Molecular Biology.}},
  issn = {00219258},
  doi = {10.1074/jbc.M110.178871},
  abstract = {The Mre11-Rad50 complex (MR) from bacteriophage T4 (gp46/47) is involved in the processing of DNA double-strand breaks. Here, we describe the activities of the T4 MR complex and its modulation by proteins involved in homologous recombination. T4 Mre11 is a Rad50- and Mn2+-dependent dsDNA exonuclease and ssDNA endonuclease. ATP hydrolysis is required for the removal of multiple nucleotides via dsDNA exonuclease activity but not for the removal of the first nucleotide or for ssDNA endonuclease activity, indicating ATP hydrolysis is only required for repetitive nucleotide removal. By itself, Rad50 is a relatively inefficient ATPase, but the presence of Mre11 and dsDNA increases ATP hydrolysis by 20-fold. The ATP hydrolysis reaction exhibits positive cooperativity with Hill coefficients ranging from 1.4 for Rad50 alone to 2.4 for the Rad50-Mre11-DNA complex. Kinetic assays suggest that approximately four nucleotides are removed per ATP hydrolyzed. Directionality assays indicate that the prevailing activity is a 3{${'}$} to 5{${'}$} dsDNA exonuclease, which is incompatible with the proposed role of MR in the production of 3{${'}$} ssDNA ends. Interestingly, we found that in the presence of a recombination mediator protein (UvsY) and ssDNA-binding protein (gp32), Mre11 is capable of using Mg2+ as a cofactor for its nuclease activity. Additionally, the Mg2+-dependent nuclease activity, activated by UvsY and gp32, results in the formation of endonuclease reaction products. These results suggest that gp32 and UvsY may alter divalent cation preference and facilitate the formation of a 3{${'}$} ssDNA overhang, which is a necessary intermediate for recombination-mediated double-strand break repair. \textcopyright{} 2011 by The American Society for Biochemistry and Molecular Biology, Inc.},
  pmid = {21081488},
  keywords = {DNA Damage,DNA Enzymes,DNA Exonuclease,DNA Recombination,DNA Repair,DNA-binding Protein,Gene Product 46; gp46,Gene Product 47; gp47},
  file = {C\:\\Users\\makro\\Zotero\\storage\\8HJMTDJN\\Herdendorf et al. - 2011 - Biochemical characterization of bacteriophage T4 Mre11-Rad50 complex.pdf}
}

@book{Hill1939,
  title = {Argyria: {{The Pharmacology}} of {{Silver}}},
  author = {Hill, William Robinson and Pillsbury, Donald Marion},
  year = {1939},
  publisher = {{Williams \& Wilkins}}
}

@article{Hohl2010,
  title = {The {{Rad50}} Coiled-Coil Domain Is Indispensable for {{Mre11}} Complex Functions},
  author = {Hohl, Marcel and Kwon, Youngho and Galv{\'a}n, Sandra Mu{\~n}oz and Xue, Xiaoyu and Tous, Cristina and Aguilera, Andr{\'e}s and Sung, Patrick and Petrini, John H.J.},
  year = {2010},
  journal = {Nature Structural and Molecular Biology},
  volume = {18},
  number = {10},
  pages = {1124--1131},
  publisher = {{Nature Publishing Group}},
  issn = {15459993},
  doi = {10.1038/nsmb.2116},
  abstract = {The Mre11 complex (Mre11, Rad50 and Xrs2 in Saccharomyces cerevisiae) influences diverse functions in the DNA damage response. The complex comprises the globular DNA-binding domain and the Rad50 hook domain, which are linked by a long and extended Rad50 coiled-coil domain. In this study, we constructed rad50 alleles encoding truncations of the coiled-coil domain to determine which Mre11 complex functions required the full length of the coils. These mutations abolished telomere maintenance and meiotic double-strand break (DSB) formation, and severely impaired homologous recombination, indicating a requirement for long-range action. Nonhomologous end joining, which is probably mediated by the globular domain of the Mre11 complex, was also severely impaired by alteration of the coiled-coil and hook domains, providing the first evidence of their influence on this process. These data show that functions of Mre11 complex are integrated by the coiled coils of Rad50. \textcopyright{} 2011 Nature America, Inc. All rights reserved.},
  pmid = {21892167},
  file = {C\:\\Users\\makro\\Zotero\\storage\\PMDXNL2H\\Hohl et al. - 2010 - The Rad50 coiled-coil domain is indispensable for Mre11 complex functions.pdf}
}

@article{Hopfner2000,
  title = {Mre11 and {{Rad50}} from {{Pyrococcus}} Furiosus: {{Cloning}} and Biochemical Characterization Reveal an Evolutionarily Conserved Multiprotein Machine},
  author = {Hopfner, K P and Karcher, A and Shin, D and Agostoni, C and Tainer, J A and Carney, J P},
  year = {2000},
  journal = {Journal of Bacteriology},
  volume = {182},
  number = {21},
  pages = {6036--6041},
  issn = {00219193},
  doi = {10.1128/JB.182.21.6036-6041.2000},
  abstract = {The processing of DNA double-strand breaks is a critical event in nucleic acid metabolism. This is evidenced by the severity of phenotypes associated with deficiencies in this process in multiple organisms. The core component involved in double-strand break repair in eukaryotic cells is the Mre11-Rad50 protein complex, which includes a third protein, p95, in humans and Xrs2 in yeasts. Homologues of Mre11 and Rad50 have been identified in all kingdoms of life, while the Nbs1 protein family is found only in eukaryotes. In eukaryotes the Mre11-Rad50 complex has nuclease activity that is modulated by the addition of ATP. We have isolated the Mre11 and Rad50 homologues from the thermophilic archaeon Pyrococcus furiosus and demonstrate that the two proteins exist in a large, heat-stable complex that possesses single-strand endonuclease activity and ATP-dependent double-strand-specific exonuclease activity. These findings verify the identification of the P. furiosus Rad50 and Mre11 homologues and demonstrate that functional homologues with similar biochemical properties exist in all kingdoms of life.},
  pmid = {11029422},
  file = {C\:\\Users\\makro\\Zotero\\storage\\PU4B2V5Z\\Hopfner et al. - 2000 - Mre11 and Rad50 from Pyrococcus furiosus Cloning and biochemical characterization reveal an evolutionarily conse.pdf}
}

@article{Hopfner2000a,
  title = {Structural Biology of {{Rad50 ATPase}}: {{ATP-driven}} Conformational Control in {{DNA}} Double-Strand Break Repair and the {{ABC-ATPase}} Superfamily},
  author = {Hopfner, Karl Peter and Karcher, Annette and Shin, David S. and Craig, Lisa and Arthur, L. Matthew and Carney, James P. and Tainer, John A.},
  year = {2000},
  journal = {Cell},
  volume = {101},
  number = {7},
  pages = {789--800},
  issn = {00928674},
  doi = {10.1016/S0092-8674(00)80890-9},
  abstract = {To clarify the key role of Rad50 in DNA double-strand break repair (DSBR), we biochemically and structurally characterized ATP-bound and ATP-free Rad50 catalytic domain (Rad50cd) from Pyrococcus furiosus. Rad50cd displays ATPase activity plus ATP-controlled dimerization and DNA binding activities. Rad50cd crystal structures identify probable protein and DNA interfaces and reveal an ABC-ATPase fold, linking Rad50 molecular mechanisms to ABC transporters, including P glycoprotein and cystic fibrosis transmembrane conductance regulator. Binding of ATP {$\gamma$}-phosphates to conserved signature motifs in two opposing Rad50cd molecules promotes dimerization that likely couples ATP hydrolysis to dimer dissociation and DNA release. These results, validated by mutations, suggest unified molecular mechanisms for ATP-driven cooperativity and allosteric control of ABC-ATPases in DSBR, membrane transport, and chromosome condensation by SMC proteins.},
  pmid = {10892749},
  file = {C\:\\Users\\makro\\Zotero\\storage\\IVNWLI7P\\Hopfner et al. - 2000 - Structural biology of Rad50 ATPase ATP-driven conformational control in DNA double-strand break repair and the A.pdf}
}

@article{Hopfner2001,
  title = {Structural Biochemistry and Interaction Architecture of the {{DNA}} Double-Strand Break Repair {{Mre11}} Nuclease and {{Rad50-ATPase}}},
  author = {Hopfner, Karl Peter and Karcher, Annette and Craig, Lisa and Woo, Tammy T. and Carney, James P. and Tainer, John A.},
  year = {2001},
  journal = {Cell},
  volume = {105},
  number = {4},
  pages = {473--485},
  issn = {00928674},
  doi = {10.1016/S0092-8674(01)00335-X},
  abstract = {To clarify functions of the Mre11/Rad50 (MR) complex in DNA double-strand break repair, we report Pyrococcus furiosus Mre11 crystal structures, revealing a protein phosphatase-like, dimanganese binding domain capped by a unique domain controlling active site access. These structures unify Mre11's multiple nuclease activities in a single endo/exonuclease mechanism and reveal eukaryotic macromolecular interaction sites by mapping human and yeast Mre11 mutations. Furthermore, the structure of the P. furiosus Rad50 ABC-ATPase with its adjacent coiled-coil defines a compact Mre11/Rad50-ATPase complex and suggests that Rad50-ATP-driven conformational switching directly controls the Mre11 exonuclease. Electron microscopy, small angle X-ray scattering, and ultracentrifugation data of human and P. furiosus MR reveal a dual functional complex consisting of a (Mre11)2/(Rad50)2 heterotetrameric DNA processing head and a double coiled-coil linker.},
  pmid = {11371344},
  file = {C\:\\Users\\makro\\Zotero\\storage\\MWQKQP88\\Hopfner et al. - 2001 - Structural biochemistry and interaction architecture of the DNA double-strand break repair Mre11 nuclease and Ra.pdf}
}

@article{Hopfner2002,
  title = {The {{Rad50}} Zinc-Hook Is a Structure Joining {{Mre11}} Complexes in {{DNA}} Recombination and Repair},
  author = {Hopfner, Karl-Peter and Craig, Lisa and Moncalian, Gabriel and Zinkel, Robert A. and Usui, Takehiko and Owen, Barbara A. L. and Karcher, Annette and Henderson, Brendan and Bodmer, Jean-Luc and McMurray, Cynthia T. and Carney, James P. and Petrini, John H. J. and Tainer, John A.},
  year = {2002},
  month = aug,
  journal = {Nature},
  volume = {418},
  number = {6897},
  pages = {562--566},
  issn = {0028-0836},
  doi = {10.1038/nature00922},
  abstract = {The Mre11 complex (Mre11-Rad50-Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. These functions all imply that the linked binding of two DNA substrates occurs, although the molecular basis for this process remains unknown. Here we present a 2.2 \AA{} crystal structure of the Rad50 coiled-coil region that reveals an unexpected dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn2+ ion. Biochemical, X-ray and electron microscopy data indicate that these hooks can join oppositely protruding Rad50 coiled-coil domains to form a flexible bridge of up to 1, 200 \AA. This suggests a function for the long insertion in the Rad50 ABC-ATPase domain. The Rad50 hook is functional, because mutations in this motif confer radiation sensitivity in yeast and disrupt binding at the distant Mre11 nuclease interface. These data support an architectural role for the Rad50 coiled coils in forming metal-mediated bridging complexes between two DNA-binding heads. The resulting assemblies have appropriate lengths and conformational properties to link sister chromatids in homologous recombination and DNA ends in non-homologous end-joining.},
  pmid = {12152085},
  file = {C\:\\Users\\makro\\Zotero\\storage\\WSEXDGV2\\Hopfner et al. - 2002 - The Rad50 zinc-hook is a structure joining Mre11 complexes in DNA recombination and repair.pdf}
}

@article{Hsiao2015,
  title = {Trojan-{{Horse Mechanism}} in the {{Cellular Uptake}} of {{Silver Nanoparticles Verified}} by {{Direct Intra-}} and {{Extracellular Silver Speciation Analysis}}},
  author = {Hsiao, I-Lun and Hsieh, Yi-Kong and Wang, Chu-Fang and Chen, I-Chieh and Huang, Yuh-Jeen},
  year = {2015},
  month = mar,
  journal = {Environmental Science \& Technology},
  volume = {49},
  number = {6},
  pages = {3813--3821},
  issn = {0013-936X},
  doi = {10.1021/es504705p},
  abstract = {The so-called "Trojan-horse" mechanism, in which nanoparticles are internalized within cells and then release high levels of toxic ions, has been proposed as a behavior in the cellular uptake of Ag nanoparticles (AgNPs). While several reports claim to have proved this mechanism by measuring AgNPs and Ag ions (I) in cells, it cannot be fully proven without examining those two components in both intra- and extracellular media. In our study, we found that even though cells take up AgNPs similarly to (microglia (BV-2)) or more rapidly than (astrocyte (ALT)) Ag (I), the ratio of AgNPs to total Ag (AgNPs+Ag (I)) in both cells was lower than that in outside media. It could be explained that H2O2, a major intracellular reactive oxygen species (ROS), reacts with AgNPs to form more Ag (I). Moreover, the major speciation of Ag (I) in cells was Ag(cysteine) and Ag(cysteine)2, indicating the possible binding of monomer cysteine or vital thiol proteins/peptides to Ag ions. Evidence we found indicates that the Trojan-horse mechanism really exists.},
  pmid = {25692749},
  file = {C\:\\Users\\makro\\Zotero\\storage\\QQHUJ7JX\\Hsiao et al. - 2015 - Trojan-Horse Mechanism in the Cellular Uptake of Silver Nanoparticles Verified by Direct Intra- and Extracellular.pdf}
}

@article{Hsin2008,
  title = {{{MESPEUS}}: {{A}} Database of the Geometry of Metal Sites in Proteins},
  author = {Hsin, K. and Sheng, Y. and Harding, M. M. and Taylor, P. and Walkinshaw, M. D.},
  year = {2008},
  journal = {Journal of Applied Crystallography},
  volume = {41},
  number = {5},
  pages = {963--968},
  issn = {00218898},
  doi = {10.1107/S002188980802476X},
  abstract = {A database with details of the geometry of metal sites in proteins has been set up. The data are derived from metalloprotein structures that are in the Protein Data Bank [PDB; Berman, Henrick, Nakamura \& Markley (2006). Nucleic Acids Res. 35, D301-D303] and have been determined at 2.5 \AA{} resolution or better. The database contains all contacts within the crystal asymmetric unit considered to be chemical bonds to any of the metals Na, Mg, K, Ca, Mn, Fe, Co, Ni, Cu or Zn. The stored information includes PDB code, crystal data, resolution of structure determination, refinement program and R factor, protein class (from PDB header), contact distances, atom names of metal and interacting atoms as they appear in the PDB, site occupancies, B values, coordination numbers, information on coordination shapes, and metal-metal distances. This may be accessed by SQL queries, or by a user-friendly web interface which searches for contacts between specified types of atoms [for example Ca and carboxylate O of aspartate, Co and imidazole N{$\delta$} of histidine] or which delivers details of all the metal sites in a specified protein. The web interface allows graphical display of the metal site, on its own or within the whole protein molecule, and may be accessed at http://eduliss.bch.ed.ac.uk/MESPEUS/. Some applications are briefly described, including a study of the characteristics of Mg sites that bind adenosine triphosphate, the derivation of an average Mg-O phosphate distance and some problems that arise when average bond distances with high precision are required. \textcopyright{} 2008 International Union of Crystallography.},
  keywords = {Metal coordination,Metal-protein bonds,Metal-protein interaction distances,Metal-site geometry,Metalloproteins},
  file = {C\:\\Users\\makro\\Zotero\\storage\\MFIJ6J9Q\\Hsin et al. - 2008 - MESPEUS A database of the geometry of metal sites in proteins.pdf}
}

@article{Ireland2019,
  title = {{{ZincBind}} - {{The}} Database of Zinc Binding Sites},
  author = {Ireland, Sam M. and Martin, Andrew C.R.},
  year = {2019},
  journal = {Database},
  volume = {2019},
  pages = {1--8},
  issn = {17580463},
  doi = {10.1093/database/baz006},
  abstract = {Zinc is one of the most important biologically active metals. Ten per cent of the human genome is thought to encode a zinc binding protein and its uses encompass catalysis, structural stability, gene expression and immunity. At present, there is no specific resource devoted to identifying and presenting all currently known zinc binding sites. Here we present ZincBind, a database of zinc binding sites and its web front-end. Using the structural data in the Protein Data Bank, ZincBind identifies every instance of zinc binding to a protein, identifies its binding site and clusters sites based on 90\% sequence identity. There are currently 24 992 binding sites, clustered into 7489 unique sites. The data are available over the web where they can be browsed and downloaded, and via a REST API. ZincBind is regularly updated and will continue to be updated with new data and features.},
  pmid = {30722040},
  file = {C\:\\Users\\makro\\Zotero\\storage\\6EGSL4ZX\\Ireland, Martin - 2019 - ZincBind - The database of zinc binding sites.pdf}
}

@article{Ireland2020,
  title = {Atomium-a {{Python}} Structure Parser},
  author = {Ireland, Sam M. and Martin, Andrew C.R.},
  year = {2020},
  journal = {Bioinformatics},
  volume = {36},
  number = {9},
  pages = {2750--2754},
  issn = {14602059},
  doi = {10.1093/bioinformatics/btaa072},
  abstract = {Structural biology relies on specific file formats to convey information about macromolecular structures. Traditionally this has been the PDB format, but increasingly newer formats, such as PDBML, mmCIF and MMTF are being used. Here we present atomium, a modern, lightweight, Python library for parsing, manipulating and saving PDB, mmCIF and MMTF file formats. In addition, we provide a web service, pdb2json, which uses atomium to give a consistent JSON representation to the entire Protein Data Bank.},
  pmid = {32044951},
  file = {C\:\\Users\\makro\\Zotero\\storage\\ZXWWQ3MR\\Ireland, Martin - 2020 - Atomium-a Python structure parser.pdf}
}

@article{Jayakanthan2009,
  title = {{{ZifBASE}}: A Database of Zinc Finger Proteins and Associated Resources},
  author = {Jayakanthan, Mannu and Muthukumaran, Jayaraman and Chandrasekar, Sanniyasi and Chawla, Konika and Punetha, Ankita and Sundar, Durai},
  year = {2009},
  month = dec,
  journal = {BMC Genomics},
  volume = {10},
  number = {1},
  pages = {421},
  issn = {1471-2164},
  doi = {10.1186/1471-2164-10-421},
  abstract = {Background: Information on the occurrence of zinc finger protein motifs in genomes is crucial to the developing field of molecular genome engineering. The knowledge of their target DNA-binding sequences is vital to develop chimeric proteins for targeted genome engineering and site-specific gene correction. There is a need to develop a computational resource of zinc finger proteins (ZFP) to identify the potential binding sites and its location, which reduce the time of in vivo task, and overcome the difficulties in selecting the specific type of zinc finger protein and the target site in the DNA sequence. Description: ZifBASE provides an extensive collection of various natural and engineered ZFP. It uses standard names and a genetic and structural classification scheme to present data retrieved from UniProtKB, GenBank, Protein Data Bank, ModBase, Protein Model Portal and the literature. It also incorporates specialized features of ZFP including finger sequences and positions, number of fingers, physiochemical properties, classes, framework, PubMed citations with links to experimental structures (PDB, if available) and modeled structures of natural zinc finger proteins. ZifBASE provides information on zinc finger proteins (both natural and engineered ones), the number of finger units in each of the zinc finger proteins (with multiple fingers), the synergy between the adjacent fingers and their positions. Additionally, it gives the individual finger sequence and their target DNA site to which it binds for better and clear understanding on the interactions of adjacent fingers. The current version of ZifBASE contains 139 entries of which 89 are engineered ZFPs, containing 3-7F totaling to 296 fingers. There are 50 natural zinc finger protein entries ranging from 2-13F, totaling to 307 fingers. It has sequences and structures from literature, Protein Data Bank, ModBase and Protein Model Portal. The interface is cross linked to other public databases like UniprotKB, PDB, ModBase and Protein Model Portal and PubMed for making it more informative. Conclusion: A database is established to maintain the information of the sequence features, including the class, framework, number of fingers, residues, position, recognition site and physio-chemical properties (molecular weight, isoelectric point) of both natural and engineered zinc finger proteins and dissociation constant of few. ZifBASE can provide more effective and efficient way of accessing the zinc finger protein sequences and their target binding sites with the links to their three-dimensional structures. All the data and functions are available at the advanced web-based search interface http://web.iitd.ac.in/\textasciitilde sundar/zifbase. \textcopyright{} 2009 Jayakanthan et al; licensee BioMed Central Ltd.},
  pmid = {19737425},
  file = {C\:\\Users\\makro\\Zotero\\storage\\E298J592\\Jayakanthan et al. - 2009 - ZifBASE a database of zinc finger proteins and associated resources.pdf}
}

@book{johnson2010molecular,
  title = {Molecular {{Probes Handbook}}: {{A Guide}} to {{Fluorescent Probes}} and {{Labeling Technologies}}},
  author = {Johnson, Iain D},
  year = {2010},
  publisher = {{Life Technologies Corporation}},
  isbn = {978-0-9829279-1-5}
}

@article{Johnson2021,
  title = {Concerted Cutting by {{Spo11}} Illuminates Meiotic {{DNA}} Break Mechanics},
  author = {Johnson, Dominic and Crawford, Margaret and Cooper, Tim and Claeys Bouuaert, Corentin and Keeney, Scott and Llorente, Bertrand and Garcia, Valerie and Neale, Matthew J.},
  year = {2021},
  month = jun,
  journal = {Nature},
  volume = {594},
  number = {7864},
  pages = {572--576},
  publisher = {{Springer US}},
  issn = {0028-0836},
  doi = {10.1038/s41586-021-03389-3},
  abstract = {Genetic recombination arises during meiosis through the repair of DNA double-strand breaks (DSBs) that are created by Spo11, a topoisomerase-like protein1,2. Spo11 DSBs form preferentially in nucleosome-depleted regions termed hotspots3,4, yet how Spo11 engages with its DNA substrate to catalyse DNA cleavage is poorly understood. Although most recombination events are initiated by a single Spo11 cut, here we show in Saccharomyces cerevisiae that hyperlocalized, concerted Spo11 DSBs separated by 33 to more than 100 base pairs also form, which we term `double cuts'. Notably, the lengths of double cuts vary with a periodicity of 10.5 base pairs, which is conserved in yeast and mice. This finding suggests a model in which the orientation of adjacent Spo11 molecules is fixed relative to the DNA helix\textemdash a proposal supported by the in vitro DNA-binding properties of the Spo11 core complex. Deep sequencing of meiotic progeny identifies recombination scars that are consistent with repair initiated from gaps generated by adjacent Spo11 DSBs. Collectively, these results revise our present understanding of the mechanics of Spo11-DSB formation and expand on the original concepts of gap repair during meiosis to include DNA gaps that are generated by Spo11 itself.},
  pmid = {34108687},
  file = {C\:\\Users\\makro\\Zotero\\storage\\3ZECNJ9T\\Johnson et al. - 2021 - Concerted cutting by Spo11 illuminates meiotic DNA break mechanics.pdf}
}

@article{Kashammer2019,
  title = {Mechanism of {{DNA End Sensing}} and {{Processing}} by the {{Mre11-Rad50 Complex}}},
  author = {K{\"a}shammer, Lisa and Saathoff, Jan Hinnerk and Lammens, Katja and Gut, Fabian and Bartho, Joseph and Alt, Aaron and Kessler, Brigitte and Hopfner, Karl Peter},
  year = {2019},
  journal = {Molecular Cell},
  volume = {76},
  number = {3},
  pages = {382-394.e6},
  issn = {10974164},
  doi = {10.1016/j.molcel.2019.07.035},
  abstract = {DNA double-strand breaks (DSBs) threaten genome stability throughout life and are linked to tumorigenesis in humans. To initiate DSB repair by end joining or homologous recombination, the Mre11-nuclease Rad50-ATPase complex detects and processes diverse and obstructed DNA ends, but a structural mechanism is still lacking. Here we report cryo-EM structures of the E. coli Mre11-Rad50 homolog SbcCD in resting and DNA-bound cutting states. In the resting state, Mre11's nuclease is blocked by ATP-Rad50, and the Rad50 coiled coils appear flexible. Upon DNA binding, the two coiled coils zip up into a rod and, together with the Rad50 nucleotide-binding domains, form a clamp around dsDNA. Mre11 moves to the side of Rad50, binds the DNA end, and assembles a DNA cutting channel for the nuclease reactions. The structures reveal how Mre11-Rad50 can detect and process diverse DNA ends and uncover a clamping and gating function for the coiled coils.},
  pmid = {31492634},
  keywords = {ABC ATPase,coiled-coil,cryoelectron microscopy,DNA double-strand breaks,DNA repair,homologous recombination,Mre11-Rad50 complex,nuclease,SbcC-SbcD complex,SMC-like proteins},
  file = {C\:\\Users\\makro\\Zotero\\storage\\CBR2AH8H\\Käshammer et al. - 2019 - Mechanism of DNA End Sensing and Processing by the Mre11-Rad50 Complex.pdf}
}

@article{Kluska2018,
  title = {Metal Binding Properties, Stability and Reactivity of Zinc Fingers},
  author = {Kluska, Katarzyna and Adamczyk, Justyna and Kr{\k{e}}{\.z}el, Artur},
  year = {2018},
  journal = {Coordination Chemistry Reviews},
  volume = {367},
  pages = {18--64},
  issn = {00108545},
  doi = {10.1016/j.ccr.2018.04.009},
  abstract = {Zinc fingers (ZFs) are among the most structurally diverse protein domains. They interact with nucleic acids, other proteins and lipids to facilitate a multitude of biological processes. Currently, there are more than 10 known classes of ZFs, with various architectures, metal binding modes, functions and reactivity. The versatility, selectivity and stability of these short amino acid sequences is achieved mainly by (i) residues participating in Zn(II) coordination (mostly Cys and His), (ii) hydrophobic core and ZF structure formation, and (iii) variable residues responsible for inter- and intramolecular interactions. Since their discovery, ZFs have been extensively studied in terms of their structure, stability and recognition targets by the application of various methodologies. Studies based on interactions with other metal ions and their complexes have contributed to the understanding of their chemical properties and the discovery of new types of ZF complexes, such as gold fingers or lead fingers. Moreover, due to the presence of nucleophilic thiolates, ZFs are targets for reactive oxygen and nitrogen species as well as alkylating agents. Interactions with many reactive molecules lead to disturb the native Zn(II) coordination site which further result in structural and functional damage of the ZFs. The post-translational modifications including phosphorylation, acetylation, methylation or nitrosylation frequently affect ZFs function via changes in the protein structure and dynamics. Even though the literature is replete with structural and stability data regarding classical ({$\beta\beta\alpha$}) ZFs, there is still a huge gap in the knowledge on physicochemical properties and reactivity of other ZF types. In this review, metal binding properties of ZFs and stability factors that modulate their functions are reviewed. These include interactions of ZFs with biogenic and toxic metal ions as well as damage occurring upon reaction with reactive oxygen and nitrogen species, the methodology used for ZFs characterization, and aspects related to coordination chemistry.},
  keywords = {DNA-recognition,Metalloprotein,Oxidation,Stability constants,Transcription factor,Zinc finger,Zinc finger damage},
  file = {C\:\\Users\\makro\\Zotero\\storage\\9N95E6IT\\Kluska, Adamczyk, Krężel - 2018 - Metal binding properties, stability and reactivity of zinc fingers.pdf}
}

@article{Kochanczyk2015a,
  title = {Relationship between the Architecture of Zinc Coordination and Zinc Binding Affinity in Proteins \textendash{} Insights into Zinc Regulation},
  author = {Kocha{\'n}czyk, Tomasz and Drozd, Agnieszka and Kr{\k{e}}{\.z}el, Artur},
  year = {2015},
  journal = {Metallomics},
  volume = {7},
  number = {2},
  pages = {244--257},
  issn = {1756-5901},
  doi = {10.1039/C4MT00094C},
  abstract = {Relationship between the architecture and stability of zinc proteins.},
  pmid = {25255078},
  file = {C\:\\Users\\makro\\Zotero\\storage\\N8R77GBI\\Kochańczyk, Drozd, Krężel - 2015 - Relationship between the architecture of zinc coordination and zinc binding affinity in proteins –(2).pdf;C\:\\Users\\makro\\Zotero\\storage\\T7DIBRH4\\Kochańczyk, Drozd, Krężel - 2015 - Relationship between the architecture of zinc coordination and zinc binding affinity in proteins – in.pdf}
}

@phdthesis{Kochanczyk2016,
  title = {Charakterystyka Biofizyczna i Funkcjonalna Domeny Haczyka Cynkowego Bia\l ka {{Rad50}} i Jego Homolog\'ow},
  author = {Kocha{\'n}czyk, Tomasz},
  year = {2016},
  journal = {PhD thesis},
  school = {University of Wroc\l aw},
  file = {C\:\\Users\\makro\\Zotero\\storage\\SI26IL7Q\\Kochańczyk - 2016 - Charakterystyka biofizyczna i funkcjonalna domeny haczyka cynkowego białka Rad50 i jego homologów.pdf}
}

@article{Kochanczyk2016a,
  title = {Metal-Coupled Folding as the Driving Force for the Extreme Stability of {{Rad50}} Zinc Hook Dimer Assembly},
  author = {Kocha{\'n}czyk, Tomasz and Nowakowski, Micha{\l} and Wojewska, Dominika and Kocy{\l}a, Anna and Ejchart, Andrzej and Ko{\'z}mi{\'n}ski, Wiktor and Kr{\k{e}}{\.z}el, Artur},
  year = {2016},
  month = nov,
  journal = {Scientific Reports},
  volume = {6},
  number = {1},
  pages = {36346},
  publisher = {{Nature Publishing Group}},
  issn = {2045-2322},
  doi = {10.1038/srep36346},
  abstract = {The binding of metal ions at the interface of protein complexes presents a unique and poorly understood mechanism of molecular assembly. A remarkable example is the Rad50 zinc hook domain, which is highly conserved and facilitates the Zn 2+ -mediated homodimerization of Rad50 proteins. Here, we present a detailed analysis of the structural and thermodynamic effects governing the formation and stability (log K 12 = 20.74) of this evolutionarily conserved protein assembly. We have dissected the determinants of the stability contributed by the small {$\beta$}-hairpin of the domain surrounding the zinc binding motif and the coiled-coiled regions using peptides of various lengths from 4 to 45 amino acid residues, alanine substitutions and peptide bond-to-ester perturbations. In the studied series of peptides, an {$>$}650 000-fold increase of the formation constant of the dimeric complex arises from favorable enthalpy because of the increased acidity of the cysteine thiols in metal-free form and the structural properties of the dimer. The dependence of the enthalpy on the domain fragment length is partially compensated by the entropic penalty of domain folding, indicating enthalpy-entropy compensation. This study facilitates understanding of the metal-mediated protein-protein interactions in which the metal ion is critical for the tight association of protein subunits.},
  pmid = {27808280},
  file = {C\:\\Users\\makro\\Zotero\\storage\\WX5ZI6MX\\Kochańczyk et al. - 2016 - Metal-coupled folding as the driving force for the extreme stability of Rad50 zinc hook dimer assembly.pdf}
}

@article{Kocya2015,
  title = {Molar Absorption Coefficients and Stability Constants of Metal Complexes of 4-(2-Pyridylazo)Resorcinol ({{PAR}}): {{Revisiting}} Common Chelating Probe for the Study of Metalloproteins},
  author = {Kocy{\l}a, Anna and Pomorski, Adam and Kr{\k{e}}{\.z}el, Artur},
  year = {2015},
  month = nov,
  journal = {Journal of Inorganic Biochemistry},
  volume = {152},
  pages = {82--92},
  issn = {01620134},
  doi = {10.1016/j.jinorgbio.2015.08.024},
  abstract = {4-(2-Pyridylazo)resorcinol (PAR) is one of the most popular chromogenic chelator used in the determination of the concentrations of various metal ions from the d, p and f blocks and their affinities for metal ion-binding biomolecules. The most important characteristics of such a sensor are the molar absorption coefficient and the metal-ligand complex dissociation constant. However, it must be remembered that these values are dependent on the specific experimental conditions (e.g. pH, solvent components, and reactant ratios). If one uses these values to process data obtained in different conditions, the final result can be under- or overestimated. We aimed to establish the spectral properties and the stability of PAR and its complexes accurately with Zn2 +, Cd2 +, Hg2 +, Co2 +, Ni2 +, Cu2 +, Mn2 + and Pb2 + at a multiple pH values. The obtained results account for the presence of different species of metal-PAR complexes in the physiological pH range of 5 to 8 and have been frequently neglected in previous studies. The effective molar absorption coefficient at 492 nm for the ZnHx(PAR)2 complex at pH 7.4 in buffered water solution is 71,500 M- 1 cm- 1, and the dissociation constant of the complex in these conditions is 7.08 \texttimes{} 10- 13 M2. To confirm these values and estimate the range of the dissociation constants of zinc-binding biomolecules that can be measured using PAR, we performed several titrations of zinc finger peptides and zinc chelators. Taken together, our results provide the updated parameters that are applicable to any experiment conducted using inexpensive and commercially available PAR.},
  pmid = {26364130},
  keywords = {4-(2-Pyridylazo)resorcinol (PAR),Dissociation constant,Molar absorption coefficient,Stability constant,Zinc protein},
  file = {C\:\\Users\\makro\\Zotero\\storage\\UCXBLNIB\\Kocyła, Pomorski, Krężel - 2015 - Molar absorption coefficients and stability constants of metal complexes of 4-(2-pyridylazo)resorcinol.pdf}
}

@article{Kocya2018,
  title = {Interdependence of Free Zinc Changes and Protein Complex Assembly \textendash{} Insights into Zinc Signal Regulation},
  author = {Kocy{\l}a, Anna and Adamczyk, Justyna and Kr{\k{e}}{\.z}el, Artur},
  year = {2018},
  journal = {Metallomics},
  volume = {10},
  number = {1},
  pages = {120--131},
  issn = {1756-5901},
  doi = {10.1039/C7MT00301C},
  abstract = {Small and local changes in cellular free zinc concentration affect protein assembly.},
  pmid = {29240217},
  file = {C\:\\Users\\makro\\Zotero\\storage\\5R9X3S4H\\Kocyła, Adamczyk, Krężel - 2018 - Interdependence of free zinc changes and protein complex assembly – insights into zinc signal regulati.pdf}
}

@article{Kocya2018a,
  title = {Zinc Clasp-Based Reversible Toolset for Selective Metal-Mediated Protein Heterodimerization},
  author = {Kocy{\l}a, Anna and Kr{\k{e}}{\.z}el, Artur},
  year = {2018},
  journal = {Chemical Communications},
  volume = {54},
  number = {96},
  pages = {13539--13542},
  issn = {1359-7345},
  doi = {10.1039/C8CC06301J},
  abstract = {Zinc clasp motif derived from natural Zn( ii )-mediated interaction of CD4 co-receptor and Lck protein tyrosine kinase was used for specific and efficient protein heterodimerization. Optimized set of peptide tags forms highly stable complex in the selective heterodimer framework. Utility of obtained toolset demonstrates high specificity, Zn( ii )-dependent reversibility and remarkable kinetic properties.},
  pmid = {30443653},
  file = {C\:\\Users\\makro\\Zotero\\storage\\7K99K2ZC\\Kocyła, Krężel - 2018 - Zinc clasp-based reversible toolset for selective metal-mediated protein heterodimerization(2).pdf;C\:\\Users\\makro\\Zotero\\storage\\AU5R9ZQE\\Kocyła, Krężel - 2018 - Zinc clasp-based reversible toolset for selective metal-mediated protein heterodimerization.pdf}
}

@article{Kocyla2021,
  title = {Galvanization of {{Protein}}\textendash{{Protein Interactions}} in a {{Dynamic Zinc Interactome}}},
  author = {Kocy{\l}a, Anna and Tran, J{\'o}zef Ba and Kr{\k{e}}{\.z}el, Artur},
  year = {2021},
  month = jan,
  journal = {Trends in Biochemical Sciences},
  volume = {46},
  number = {1},
  pages = {64--79},
  issn = {09680004},
  doi = {10.1016/j.tibs.2020.08.011},
  abstract = {The presence of Zn2+ at protein\textendash protein interfaces modulates complex function, stability, and introduces structural flexibility/complexity, chemical selectivity, and reversibility driven in a Zn2+-dependent manner. Recent studies have demonstrated that dynamically changing Zn2+ affects numerous cellular processes, including protein\textendash protein communication and protein complex assembly. How Zn2+-involved protein\textendash protein interactions (ZPPIs) are formed and dissociate and how their stability and reactivity are driven in a zinc interactome remain poorly understood, mostly due to experimental obstacles. Here, we review recent research advances on the role of Zn2+ in the formation of interprotein sites, their architecture, function, and stability. Moreover, we underline the importance of zinc networks in intersystemic communication and highlight bioinformatic and experimental challenges required for the identification and investigation of ZPPIs.},
  pmid = {32958327},
  keywords = {interprotein metal binding site,metal affinity,metalloprotein,zinc buffering,zinc fluctuations},
  file = {C\:\\Users\\makro\\Zotero\\storage\\ILU4PL5A\\1-s2.0-S0968000420302085-main.pdf}
}

@article{Konigsberg2001,
  title = {Uncoupling Effect of Mercuric Chloride on Mitochondria Isolated from an Hepatic Cell Line},
  author = {K{\"o}nigsberg, Mina and {L{\'o}pez-D{\'i}azguerrero}, Norma Edith and Bucio, Leticia and {Guti{\'e}rrez-Ruiz}, Mar{\'i}a Concepci{\'o}n},
  year = {2001},
  month = jul,
  journal = {Journal of Applied Toxicology},
  volume = {21},
  number = {4},
  pages = {323--329},
  issn = {0260437X},
  doi = {10.1002/jat.763},
  abstract = {A human fetal hepatic cell line (WRL-68) was used as a model to study the damage produced by mercury. The Hg(II) uptake by WRL-68 cells was found to be in a biphasic manner with a rapid initial uptake phase lasting about 5 min, followed by a sustained phase of slower accumulation. Distribution of mercury was studied and mitochondria were found to be the major target for mercury in this cell line (48\%), followed by nuclei (38\%), cytosol (8\%) and microsomes (7\%). Mitochondrial morphological damage after mercury treatment was observed by transmission electron microscopy. To determine if the toxic effect of mercury on mitochondrial bioenergetics was direct or indirect, mitochondria were isolated from WRL-68 cells after 1 h of pre-incubation with 0.5 {$\mu$}M HgCl2. Oxygen consumption was quantified in two sets of experiments: in the presence of classical mitochondrial respiratory inhibitors; and in the presence of oligomycin. No significant difference was found in respiration with classical inhibitors, indicating that mercury does not affect directly the mitochondrial respiratory chain. However, mitochondria of Hg-treated cells were not inhibited when oligomycin was added, probably due to an uncoupling effect. This effect was prevented with dithiothreitol (DTT) treatment. A possible explanation for mercury's effect on mitochondria and its relation with oxidative stress is presented. \textcopyright{} 2001 John Wiley \& Sons, Ltd.},
  pmid = {11481667},
  keywords = {Mercuric chloride,Mercury toxicity,Mitochondria,Respiration,Respiratory chain,WRL-68},
  file = {C\:\\Users\\makro\\Zotero\\storage\\9XKE8VHM\\Königsberg et al. - 2001 - Uncoupling effect of mercuric chloride on mitochondria isolated from an hepatic cell line.pdf}
}

@article{Krezel2007,
  title = {Dual {{Nanomolar}} and {{Picomolar Zn}}({{II}}) {{Binding Properties}} of {{Metallothionein}}},
  author = {Kr{\k{e}}{\.z}el, Artur and Maret, Wolfgang},
  year = {2007},
  month = sep,
  journal = {Journal of the American Chemical Society},
  volume = {129},
  number = {35},
  pages = {10911--10921},
  issn = {0002-7863},
  doi = {10.1021/ja071979s},
  abstract = {Each of the seven Zn(II) ions in the Zn3S9 and Zn4S11 clusters of human metallothionein is in a tetrathiolate coordination environment. Yet analysis of Zn(II) association with thionein, the apoprotein, and analysis of Zn(II) dissociation from metallothionein using the fluorescent chelating agents FluoZin-3 and RhodZin-3 reveal at least three classes of sites with affinities that differ by 4 orders of magnitude. Four Zn(II) ions are bound with an apparent average log K of 11.8, and with the methods employed, their binding is indistinguishable. This binding property makes thionein a strong chelating agent. One Zn(II) ion is relatively weakly bound, with a log K of 7.7, making metallothionein a zinc donor in the absence of thionein. The binding data demonstrate that Zn(II) binds with at least four species: Zn4T, Zn5T, Zn6T, and Zn7T. Zn5T and Zn6T bind Zn(II) with a log Kof {$\sim$}10 and are the predominant species at micromolar concentrations of metallothionein in cells. Central to the function of the protein is the reactivity of its cysteine side chains in the absence and presence of Zn(II). Chelating agents, such as physiological ligands with moderate affinities for Zn(II), cause dissociation of Zn(II) ions from metallothionein at pH 7.4 (Zn7T \textrightarrow{$\leftarrow$} Zn7-nT + nZn2+), thereby affecting the reactivity of its thiols. Thus, the rate of thiol oxidation increases in the presence of Zn(II) acceptors but decreases if more free Zn(II) becomes available. Thionein is such an acceptor. It regulates the reactivity and availability of free Zn(II) from metallothionein. At thionein/metallothionein ratios {$>$} 0.75, free Zn(II) ions are below a pZn (-log[Zn2+] tree) of 11.8, and at ratios {$<$} 0.75, relatively large fluctuations of free Zn(II) ions are possible (pZn between 7 and 11). These chemical characteristics match cellular requirements for Zn(II) and suggest how the molecular structures and redox chemistries of metallothionein and thionein determine Zn(II) availability for biological processes. \textcopyright{} 2007 American Chemical Society.},
  pmid = {17696343},
  file = {C\:\\Users\\makro\\Zotero\\storage\\8V44YZQZ\\Krȩżel, Maret - 2007 - Dual Nanomolar and Picomolar Zn(II) Binding Properties of Metallothionein.pdf}
}

@article{Krezel2016,
  title = {The Biological Inorganic Chemistry of Zinc Ions},
  author = {Kr{\k{e}}{\.z}el, Artur and Maret, Wolfgang},
  year = {2016},
  month = dec,
  journal = {Archives of Biochemistry and Biophysics},
  volume = {611},
  pages = {3--19},
  issn = {00039861},
  doi = {10.1016/j.abb.2016.04.010},
  abstract = {The solution and complexation chemistry of zinc ions is the basis for zinc biology. In living organisms, zinc is redox-inert and has only one valence state: Zn(II). Its coordination environment in proteins is limited by oxygen, nitrogen, and sulfur donors from the side chains of a few amino acids. In an estimated 10\% of all human proteins, zinc has a catalytic or structural function and remains bound during the lifetime of the protein. However, in other proteins zinc ions bind reversibly with dissociation and association rates commensurate with the requirements in regulation, transport, transfer, sensing, signalling, and storage. In contrast to the extensive knowledge about zinc proteins, the coordination chemistry of the ``mobile'' zinc ions in these processes, i.e. when not bound to proteins, is virtually unexplored and the mechanisms of ligand exchange are poorly understood. Knowledge of the biological inorganic chemistry of zinc ions is essential for understanding its cellular biology and for designing complexes that deliver zinc to proteins and chelating agents that remove zinc from proteins, for detecting zinc ion species by qualitative and quantitative analysis, and for proper planning and execution of experiments involving zinc ions and nanoparticles such as zinc oxide (ZnO). In most investigations, reference is made to zinc or Zn2+ without full appreciation of how biological zinc ions are buffered and how the d-block cation Zn2+ differs from s-block cations such as Ca2+ with regard to significantly higher affinity for ligands, preference for the donor atoms of ligands, and coordination dynamics. Zinc needs to be tightly controlled. The interaction with low molecular weight ligands such as water and inorganic and organic anions is highly relevant to its biology but in contrast to its coordination in proteins has not been discussed in the biochemical literature. From the discussion in this article, it is becoming evident that zinc ion speciation is important in zinc biochemistry and for biological recognition as a variety of low molecular weight zinc complexes have already been implicated in biological processes, e.g. with ATP, glutathione, citrate, ethylenediaminedisuccinic acid, nicotianamine, or bacillithiol.},
  pmid = {27117234},
  keywords = {zinc,zinc biochemistry,zinc biophysics,zinc ions,zinc speciation},
  file = {C\:\\Users\\makro\\Zotero\\storage\\A6WNY359\\Krężel, Maret - 2016 - The biological inorganic chemistry of zinc ions.pdf}
}

@article{Krishnamurthy2008,
  title = {Carbonic {{Anhydrase}} as a {{Model}} for {{Biophysical}} and {{Physical-Organic Studies}} of {{Proteins}} and {{Protein}}-{{Ligand Binding}}},
  author = {Krishnamurthy, Vijay M. and Kaufman, George K. and Urbach, Adam R. and Gitlin, Irina and Gudiksen, Katherine L. and Weibel, Douglas B. and Whitesides, George M.},
  year = {2008},
  month = mar,
  journal = {Chemical Reviews},
  volume = {108},
  number = {3},
  pages = {946--1051},
  issn = {0009-2665},
  doi = {10.1021/cr050262p},
  pmid = {18335973},
  file = {C\:\\Users\\makro\\Zotero\\storage\\BLFE7PRR\\Krishnamurthy et al. - 2008 - Carbonic Anhydrase as a Model for Biophysical and Physical-Organic Studies of Proteins and Protein−Ligand.pdf}
}

@article{Kuppuraj2009,
  title = {Factors {{Governing Metal}}-{{Ligand Distances}} and {{Coordination Geometries}} of {{Metal Complexes}}},
  author = {Kuppuraj, Gopi and Dudev, Minko and Lim, Carmay},
  year = {2009},
  month = mar,
  journal = {The Journal of Physical Chemistry B},
  volume = {113},
  number = {9},
  pages = {2952--2960},
  issn = {1520-6106},
  doi = {10.1021/jp807972e},
  abstract = {The metal-ligand (M-L) distances play a central role in determining the structure and reactivity of the metal complex and in metal discrimination in proteins. They reflect properties of the metal ion and the ligand during their coordination as well as the environment. However, the variation of the M-L distances as a function of the properties of the metal cation and its donor atoms had not been systematically analyzed, and no public website listing the M-L distances from metal complexes was available. Herein, the distances around 63 different types of metal ions in{\~ }200 000 high-resolution crystal structures in the Cambridge Structural Database as well as their preferred coordination geometries have been determined. The dependence of these distances on (i) the donor atom's charge and charge-donating ability, (ii) the donor atom's size, (iii) the metal ion's oxidation state and charge-accepting ability, and (iv) the metal ion's size has also been determined. The concept of ligand coordination number (CN) was introduced to take into account the effect of the number of constituent ligand atoms on the M-L distances in addition to the number of metal-bound ligands. We propose grouping the M-L distances according to both the metal CN and the ligand CN. The mean M-L distance corresponding to a given metal CN and ligand CN was found to be linearly correlated with the metal's ionic radius in going down a main group or in going across the first three rows of the periodic table. The M-L distances as a function of the metal and ligand coordination numbers are available via http://bioit.ibms.sinica. edu.tw/CSD.htm. \textcopyright{} 2009 American Chemical Society.},
  file = {C\:\\Users\\makro\\Zotero\\storage\\CT59CZYD\\Kuppuraj, Dudev, Lim - 2009 - Factors Governing Metal−Ligand Distances and Coordination Geometries of Metal Complexes.pdf}
}

@article{Lachenmann2004,
  title = {Why {{Zinc Fingers Prefer Zinc}}: {{Ligand-Field Symmetry}} and the {{Hidden Thermodynamics}} of {{Metal Ion Selectivity}} ,},
  author = {Lachenmann, Marcel J. and Ladbury, John E. and Dong, Jian and Huang, Kun and Carey, Paul and Weiss, Michael A.},
  year = {2004},
  month = nov,
  journal = {Biochemistry},
  volume = {43},
  number = {44},
  pages = {13910--13925},
  issn = {0006-2960},
  doi = {10.1021/bi0491999},
  abstract = {The zinc finger, a motif of protein-nucleic acid recognition broadly conserved among eukaryotes, is a globular minidomain containing a tetrahedral metal-binding site. Preferential coordination of Zn2+ (relative to Co2+) is proposed to reflect differences in ligand-field stabilization energies (LFSEs) due to complete or incomplete occupancy of d orbitals. LFSE predicts that the preference for Zn2+ should be purely enthalpic in accord with calorimetric studies of a high-affinity consensus peptide (CP-1; Blasie, C. A., and Berg, J. (2002) Biochemistry 41, 15068-73). Despite its elegance, the general predominance of LFSE is unclear as (i) the magnitude by which CP-1 prefers Zn2+ is greater than that expected and (ii) the analogous metal ion selectivity of a zinc metalloenzyme (carbonic anhydrase) is driven by changes in entropy rather than enthalpy. Because CP-1 was designed to optimize zinc binding, we have investigated the NMR structure and metal ion selectivity of a natural finger of lower stability derived from human tumor-suppressor protein WT1. Raman spectroscopy suggests that the structure of the WT1 domain is unaffected by interchange of Zn2+ and Co2+. As in CP-1, preferential binding of Zn2+ (relative to Co2+) is driven predominantly by differences in enthalpy, but in this case the enthalpic advantage is less than that predicted by LFSE. A theoretical framework is presented to define the relationship between LFSE and other thermodynamic factors, such as metal ion electroaffinities, enthalpies of hydration, and the topography of the underlying folding landscape. The contribution of environmental coupling to entropy-enthalpy compensation is delineated in a formal thermodynamic cycle. Together, these considerations indicate that LFSE provides an important but incomplete description of the stringency and thermodynamic origin of metal-ion selectivity.},
  pmid = {15518539},
  file = {C\:\\Users\\makro\\Zotero\\storage\\DVEF39R9\\Lachenmann et al. - 2004 - Why Zinc Fingers Prefer Zinc Ligand-Field Symmetry and the Hidden Thermodynamics of Metal Ion Selectivity ,.pdf}
}

@article{Lafrance-Vanasse2015,
  title = {Envisioning the Dynamics and Flexibility of {{Mre11-Rad50-Nbs1}} Complex to Decipher Its Roles in {{DNA}} Replication and Repair},
  author = {{Lafrance-Vanasse}, Julien and Williams, Gareth J. and Tainer, John A.},
  year = {2015},
  month = mar,
  journal = {Progress in Biophysics and Molecular Biology},
  volume = {117},
  number = {2-3},
  pages = {182--193},
  publisher = {{Elsevier Ltd}},
  issn = {00796107},
  doi = {10.1016/j.pbiomolbio.2014.12.004},
  abstract = {The Mre11-Rad50-Nbs1 (MRN) complex is a dynamic macromolecular machine that acts in the first steps of DNA double strand break repair, and each of its components has intrinsic dynamics and flexibility properties that are directly linked with their functions. As a result, deciphering the functional structural biology of the MRN complex is driving novel and integrated technologies to define the dynamic structural biology of protein machinery interacting with DNA. Rad50 promotes dramatic long-range allostery through its coiled-coil and zinc-hook domains. Its ATPase activity drives dynamic transitions between monomeric and dimeric forms that can be modulated with mutants modifying the ATPase rate to control end joining versus resection activities. The biological functions of Mre11's dual endo- and exonuclease activities in repair pathway choice were enigmatic until recently, when they were unveiled by the development of specific nuclease inhibitors. Mre11 dimer flexibility, which may be regulated in cells to control MRN function, suggests new inhibitor design strategies for cancer intervention. Nbs1 has FHA and BRCT domains to bind multiple interaction partners that further regulate MRN. One of them, CtIP, modulates the Mre11 excision activity for homologous recombination repair. Overall, these combined properties suggest novel therapeutic strategies. Furthermore, they collectively help to explain how MRN regulates DNA repair pathway choice with implications for improving the design and analysis of cancer clinical trials that employ DNA damaging agents or target the DNA damage response.},
  pmid = {25576492},
  keywords = {Allostery,Conformational change,CtIP,Double strand break repair,Dynamics,Mre11-Rad50-Nbs1},
  file = {C\:\\Users\\makro\\Zotero\\storage\\M4R2656I\\Lafrance-Vanasse, Williams, Tainer - 2015 - Envisioning the dynamics and flexibility of Mre11-Rad50-Nbs1 complex to decipher its roles i.pdf}
}

@article{Laitaoja2013,
  title = {Zinc {{Coordination Spheres}} in {{Protein Structures}}},
  author = {Laitaoja, Mikko and Valjakka, Jarkko and J{\"a}nis, Janne},
  year = {2013},
  month = oct,
  journal = {Inorganic Chemistry},
  volume = {52},
  number = {19},
  pages = {10983--10991},
  issn = {0020-1669},
  doi = {10.1021/ic401072d},
  abstract = {Zinc metalloproteins are one of the most abundant and structurally diverse proteins in nature. In these proteins, the Zn(II) ion possesses a multifunctional role as it stabilizes the fold of small zinc fingers, catalyzes essential reactions in enzymes of all six classes, or assists in the formation of biological oligomers. Previously, a number of database surveys have been conducted on zinc proteins to gain broader insights into their rich coordination chemistry. However, many of these surveys suffer from severe flaws and misinterpretations or are otherwise limited. To provide a more comprehensive, up-to-date picture on zinc coordination environments in proteins, zinc containing protein structures deposited in the Protein Data Bank (PDB) were analyzed in detail. A statistical analysis in terms of zinc coordinating amino acids, metal-to-ligand bond lengths, coordination number, and structural classification was performed, revealing coordination spheres from classical tetrahedral cysteine/histidine binding sites to more complex binuclear sites with carboxylated lysine residues. According to the results, coordination spheres of hundreds of crystal structures in the PDB could be misinterpreted due to symmetry-related molecules or missing electron densities for ligands. The analysis also revealed increasing average metal-to-ligand bond length as a function of crystallographic resolution, which should be taken into account when interrogating metal ion binding sites. Moreover, one-third of the zinc ions present in crystal structures are artifacts, merely aiding crystal formation and packing with no biological significance. Our analysis provides solid evidence that a minimal stable zinc coordination sphere is made up by four ligands and adopts a tetrahedral coordination geometry. \textcopyright{} 2013 American Chemical Society.},
  pmid = {24059258},
  file = {C\:\\Users\\makro\\Zotero\\storage\\MRW7B53M\\Laitaoja, Valjakka, Jänis - 2013 - Zinc coordination spheres in protein structures.pdf}
}

@article{Lammens2011,
  title = {The {{Mre11}}:{{Rad50}} Structure Shows an {{ATP-dependent}} Molecular Clamp in {{DNA}} Double-Strand Break Repair},
  author = {Lammens, Katja and Bemeleit, Derk J. and M{\"o}ckel, Carolin and Clausing, Emanuel and Schele, Alexandra and Hartung, Sophia and Schiller, Christian B. and Lucas, Maria and Angerm{\"u}ller, Christof and S{\"o}ding, Johannes and Str{\"a}{\ss}er, Katja and Hopfner, Karl Peter},
  year = {2011},
  journal = {Cell},
  volume = {145},
  number = {1},
  pages = {54--66},
  issn = {00928674},
  doi = {10.1016/j.cell.2011.02.038},
  abstract = {The MR (Mre11 nuclease and Rad50 ABC ATPase) complex is an evolutionarily conserved sensor for DNA double-strand breaks, highly genotoxic lesions linked to cancer development. MR can recognize and process DNA ends even if they are blocked and misfolded. To reveal its mechanism, we determined the crystal structure of the catalytic head of Thermotoga maritima MR and analyzed ATP-dependent conformational changes. MR adopts an open form with a central Mre11 nuclease dimer and two peripheral Rad50 molecules, a form suited for sensing obstructed breaks. The Mre11 C-terminal helix-loop-helix domain binds Rad50 and attaches flexibly to the nuclease domain, enabling large conformational changes. ATP binding to the two Rad50 subunits induces a rotation of the Mre11 helix-loop-helix and Rad50 coiled-coil domains, creating a clamp conformation with increased DNA-binding activity. The results suggest that MR is an ATP-controlled transient molecular clamp at DNA double-strand breaks. PaperFlick: \textcopyright{} 2011 Elsevier Inc.},
  pmid = {21458667},
  file = {C\:\\Users\\makro\\Zotero\\storage\\9QD6UYRQ\\Lammens et al. - 2011 - The Mre11Rad50 structure shows an ATP-dependent molecular clamp in DNA double-strand break repair.pdf}
}

@article{Langard1975,
  title = {A Cohort Study of Bronchial Carcinomas in Workers Producing Chromate Pigments.},
  author = {L{\aa}ngard, S and Norseth, T},
  year = {1975},
  month = feb,
  journal = {Occupational and Environmental Medicine},
  volume = {32},
  number = {1},
  pages = {62--65},
  issn = {1351-0711},
  doi = {10.1136/oem.32.1.62},
  file = {C\:\\Users\\makro\\Zotero\\storage\\E3J76L7E\\Langard, Norseth - 1975 - A cohort study of bronchial carcinomas in workers producing chromate pigments.pdf}
}

@article{Ledwidge2010,
  title = {{{NmerA}} of {{Tn}}{\emph{501}} Mercuric Ion Reductase: {{Structural}} Modulation of the p{{{\emph{K}}}}{\textsubscript{a}} Values of the Metal Binding Cysteine Thiols},
  author = {Ledwidge, Richard and Hong, Baoyu and D{\"o}tsch, Volker and Miller, Susan M.},
  year = {2010},
  journal = {Biochemistry},
  volume = {49},
  number = {41},
  pages = {8988--8998},
  issn = {00062960},
  doi = {10.1021/bi100537f},
  abstract = {To avoid nonspecific and/or undesirable binding and reactivity of metal ions with cellular components, organisms have evolved metal-specific systems for trafficking proteins. Although systems differ, those handling soft metal ions such as Hg2+, Cu+, Zn2+, etc., all utilize heavy metal-associated (HMA) proteins and domains of {$\sim$}70 amino acids with a conserved GMXCXXC motif in a {$\beta\alpha\beta\beta\alpha\beta$} structural fold. While the conserved cysteines define a common metal binding site in these proteins, other structural features must be utilized to create metal ion, protein partner, and contextual specificities. This paper presents initial structure-function studies of the N-terminal HMA domain (NmerA) of Tn501 mercuric ion reductase (MerA) aimed at identifying structural features critical to its role in facilitating efficient transfer of Hg2+ to the MerA catalytic core for reductive detoxification. First, NMR solution structures of reduced and Hg2+-bound forms of NmerA are presented that allow definition and comparison of the structure of the metal binding loop in the two states. Structural differences between the two forms are compared with differences observed in three HMA domains with different metal ion and functional contexts. Second, analyses of the UV absorbance properties of wild-type, Cys11Ala, and Cys14Ala forms of NmerA are presented that provide assignments of the pKa values for the two cysteine thiols of the metal binding motif. Third, results from 13C NMR studies with wild-type and Y62F NmerA labeled with [{$\beta$}-13C]cysteine are presented that define a role for Tyr62 in modulating the pKa values of the cysteine thiols. \textcopyright{} 2010 American Chemical Society.},
  pmid = {20828160},
  file = {C\:\\Users\\makro\\Zotero\\storage\\R3PVB4JK\\Ledwidge et al. - 2010 - NmerA of Tn 501 mercuric ion reductase Structural modulation of the p K a values of the metal binding cysteine.pdf}
}

@article{Lee2008,
  title = {Physical {{Basis}} of {{Structural}} and {{Catalytic Zn-Binding Sites}} in {{Proteins}}},
  author = {Lee, Yu-ming and Lim, Carmay},
  year = {2008},
  month = jun,
  journal = {Journal of Molecular Biology},
  volume = {379},
  number = {3},
  pages = {545--553},
  issn = {00222836},
  doi = {10.1016/j.jmb.2008.04.004},
  abstract = {Zn2+, an element that is essential to all life forms, can play a catalytic or a solely structural role. Previous works have shown that Zn2+ binds preferentially to water molecules and His in catalytic sites, but to Cys- instructural sites, but the molecular basis for the observed ligand preference is unclear. Here, we show that the different Zn2+ roles are also reflected in the different bond distances to Zn2+ in structural and catalytic sites. We reveal the physical basis for the observed differences between structural and catalytic Zn sites: In most catalytic sites, water is found bound to Zn2+ as it transfers the least charge to Zn2+ and is less bulky compared to the protein ligands, enabling Zn2+ to serve as a Lewis acid in catalysis. In most structural sites, however, {$\geq$} 2 Cys- are found bound to Zn2+, as Cys- transfers the most charge to Zn2+ and reduces the Zn charge to such an extent that Zn2+ can no longer act as a Lewis acid; furthermore, steric repulsion among the bulky Cys(S-) prevents Zn2+ from accommodating another ligand. Based on the observed ligand preference and Zn-ligand distance differences between structural and catalytic Zn sites, we present a simple method for distinguishing the two types of sites and for verifying the catalytic role of Zn2+. Finally, we discuss how the physical bases revealed aid in designing potential drug molecules that target Zn proteins. \textcopyright{} 2008 Elsevier Ltd. All rights reserved.},
  pmid = {18462757},
  keywords = {bond-valence sum,catalytic sites,structural sites,zinc,Zn proteins},
  file = {C\:\\Users\\makro\\Zotero\\storage\\ZGLIWWT5\\Lee, Lim - 2008 - Physical Basis of Structural and Catalytic Zn-Binding Sites in Proteins.pdf}
}

@article{Li2006,
  title = {Cd-Hit: A Fast Program for Clustering and Comparing Large Sets of Protein or Nucleotide Sequences},
  author = {Li, Weizhong and Godzik, Adam},
  year = {2006},
  month = jul,
  journal = {Bioinformatics},
  volume = {22},
  number = {13},
  pages = {1658--1659},
  issn = {1367-4811},
  doi = {10.1093/bioinformatics/btl158},
  abstract = {Motivation: In 2001 and 2002, we published two papers (Bioinformatics, 17, 282\textendash 283, Bioinformatics, 18, 77\textendash 82) describing an ultrafast protein sequence clustering program called cd-hit. This program can efficiently cluster a huge protein database with millions of sequences. However, the applications of the underlying algorithm are not limited to only protein sequences clustering, here we present several new programs using the same algorithm including cd-hit-2d, cd-hit-est and cd-hit-est-2d. Cd-hit-2d compares two protein datasets and reports similar matches between them; cd-hit-est clusters a DNA/RNA sequence database and cd-hit-est-2d compares two nucleotide datasets. All these programs can handle huge datasets with millions of sequences and can be hundreds of times faster than methods based on the popular sequence comparison and database search tools, such as BLAST.},
  pmid = {16731699},
  file = {C\:\\Users\\makro\\Zotero\\storage\\9HP32GHU\\Li, Godzik - 2006 - Cd-hit a fast program for clustering and comparing large sets of protein or nucleotide sequences.pdf}
}

@article{Lim2011,
  title = {Crystal Structure of the {{Mre11}}\textendash{{Rad50}}\textendash{{ATP$\gamma$S}} Complex: {{Understanding}} the Interplay between {{Mre11}} and {{Rad50}}},
  author = {Lim, Hye Seong and Kim, Jin Seok and Park, Young Bong and Gwon, Gwang Hyeon and Cho, Yunje},
  year = {2011},
  journal = {Genes and Development},
  volume = {25},
  number = {10},
  pages = {1091--1104},
  issn = {08909369},
  doi = {10.1101/gad.2037811},
  abstract = {Communication between Mre11 and Rad50 in the MR complex is critical for the sensing, damage signaling, and repair of DNA double-strand breaks. To understand the basis for interregulation between Mre11 and Rad50, we determined the crystal structure of the Mre11-Rad50-ATPgS complex. Mre11 brings the two Rad50 molecules into close proximity and promotes ATPase activity by (1) holding the coiled-coil arm of Rad50 through its C-terminal domain, (2) stabilizing the signature motif and P loop of Rad50 via its capping domain, and (3) forming a dimer through the nuclease domain. ATP-bound Rad50 negatively regulates the nuclease activity of Mre11 by blocking the active site of Mre11. Hydrolysis of ATP disengages Rad50 molecules, and, concomitantly, the flexible linker that connects the C-terminal domain and the capping domain of Mre11 undergoes substantial conformational change to relocate Rad50 and unmask the active site of Mre11. Our structural and biochemical data provide insights into understanding the interplay between Mre11 and Rad50 to facilitate efficient DNA damage repair.},
  pmid = {21511873},
  keywords = {DNA damage signaling,DNA repair,Genomic stability,Mre11-Rad50,Structural biology},
  file = {C\:\\Users\\makro\\Zotero\\storage\\MIDH7I2C\\Lim et al. - 2011 - Crystal structure of the Mre11-Rad50-ATPγS complex Understanding the interplay between Mre11 and Rad50.pdf}
}

@article{Liu2007,
  title = {Label Transfer Chemistry for the Characterization of Protein-Protein Interactions},
  author = {Liu, Bo and Archer, Chase T. and Burdine, Lyle and Gillette, Thomas G. and Kodadek, Thomas},
  year = {2007},
  journal = {Journal of the American Chemical Society},
  volume = {129},
  number = {41},
  pages = {12348--12349},
  issn = {00027863},
  doi = {10.1021/ja072904r},
  abstract = {A new label transfer method is presented that overcomes most of the limitations of current systems. A protein of interest is tagged with a tetracysteine sequence (FlAsH receptor peptide (FRP)) that binds tightly and specifically to a chimeric molecule 3,4-dihydroxyphenylalanine-biotin-4{${'}$},5{${'}$}-bis(1,3,2-dithioarsolan-2-yl)fluorescein (DOPA-biotin-FlAsH). Upon brief periodate oxidation, the DOPA moiety is cross-linked to nearby surface-exposed nucleophiles. Boiling the products in excess dithiol dissolves the FlAsH-FRP interaction, resulting in transfer of the biotin tag to the partner proteins, allowingthem to be identified by standard methods. Copyright \textcopyright{} 2007 American Chemical Society.},
  pmid = {17894490},
  file = {C\:\\Users\\makro\\Zotero\\storage\\ECEMY5FU\\Liu et al. - 2007 - Label transfer chemistry for the characterization of protein-protein interactions.pdf}
}

@article{Liu2016,
  title = {{{ATP}}-dependent {{DNA}} Binding, Unwinding, and Resection by the {{Mre11}}/{{Rad50}} Complex},
  author = {Liu, Yaqi and Sung, Sihyun and Kim, Youngran and Li, Fuyang and Gwon, Gwanghyun and Jo, Aera and Kim, Ae-Kyoung and Kim, Taeyoon and Song, Ok-kyu and Lee, Sang Eun and Cho, Yunje},
  year = {2016},
  journal = {The EMBO Journal},
  volume = {35},
  number = {7},
  pages = {743--758},
  issn = {0261-4189},
  doi = {10.15252/embj.201592462},
  abstract = {ATP-dependent DNA end recognition and nucleolytic processing are central functions of the Mre11/Rad50 (MR) complex in DNA double-strand break repair. However, it is still unclear how ATP binding and hydrolysis primes the MR function and regulates repair pathway choice in cells. Here, Methanococcus jannaschii MR- ATPcS-DNA structure reveals that the partly deformed DNA runs symmetrically across central groove between two ATPcS-bound Rad50 nucleotide-binding domains. Duplex DNA cannot access the Mre11 active site in the ATP-free full-length MR complex. ATP hydrolysis drives rotation of the nucleotide-binding domain and induces the DNA melting so that the substrate DNA can access Mre11. Our findings suggest that the ATP hydrolysis-driven confor- mational changes in both DNA and the MR complex coordinate the melting and endonuclease activity.},
  pmid = {26717941},
  keywords = {central groove,dna binding,dna melting,mre 11,nuclease,rad 50,recombination,repair,structural,subject categories dna replication},
  file = {C\:\\Users\\makro\\Zotero\\storage\\5AQUN93B\\Liu et al. - 2016 - ATP ‐dependent DNA binding, unwinding, and resection by the Mre11Rad50 complex.pdf}
}

@article{Llorente2004,
  title = {The {{Mre11 Nuclease Is Not Required}} for 5{${'}$} to 3{${'}$} {{Resection}} at {{Multiple HO-Induced Double-Strand Breaks}}},
  author = {Llorente, Bertrand and Symington, Lorraine S.},
  year = {2004},
  journal = {Molecular and Cellular Biology},
  volume = {24},
  number = {21},
  pages = {9682--9694},
  issn = {0270-7306},
  doi = {10.1128/mcb.24.21.9682-9694.2004},
  abstract = {Current hypotheses suggest the Mre11 nuclease activity could be directly involved in double-strand break (DSB) resection in the presence of a large number of DSBs or limited to processing abnormal DNA ends. To distinguish between these possibilities, we used two methods to create large numbers of DSBs in Saccharomyces cerevisiae chromosomes, without introducing other substrates for the Mre11 nuclease. Multiple DSBs were created either by expressing the HO endonuclease in strains containing several HO cut sites embedded within randomly dispersed Ty1 elements or by phleomycin treatment. Analysis of resection by single-strand DNA formation in these systems showed no difference between strains containing MRE11 or the mre11-D56N nuclease defective allele, suggesting that the Mre11 nuclease is not involved in the extensive 5{${'}$} to 3{${'}$} resection of DSBs. We postulate that the ionizing radiation (IR) sensitivity of mre11 nuclease-defective mutants results from the accumulation of IR-induced DNA damage that is normally processed by the Mre11 nuclease. We also report that the processivity of 5{${'}$} to 3{${'}$} DSB resection and the yield of repaired products are affected by the number of DSBs in a dose-dependent manner. Finally, we show that the exonuclease Exo1 is involved in the processivity of 5{${'}$} to 3{${'}$} resection of an HO-induced DSB at the MAT locus.},
  pmid = {15485933},
  file = {C\:\\Users\\makro\\Zotero\\storage\\2Z2ZFHUB\\Llorente, Symington - 2004 - The Mre11 Nuclease Is Not Required for 5′ to 3′ Resection at Multiple HO-Induced Double-Strand Breaks.pdf}
}

@article{Lok2007,
  title = {Silver Nanoparticles: Partial Oxidation and Antibacterial Activities},
  author = {Lok, Chun-Nam and Ho, Chi-Ming and Chen, Rong and He, Qing-Yu and Yu, Wing-Yiu and Sun, Hongzhe and Tam, Paul Kwong-Hang and Chiu, Jen-Fu and Che, Chi-Ming},
  year = {2007},
  month = may,
  journal = {JBIC Journal of Biological Inorganic Chemistry},
  volume = {12},
  number = {4},
  pages = {527--534},
  issn = {0949-8257},
  doi = {10.1007/s00775-007-0208-z},
  abstract = {The physical and chemical properties of silver nanoparticles that are responsible for their antimicrobial activities have been studied with spherical silver nanoparticles (average diameter approximately 9 nm) synthesized by the borohydride reduction of Ag+ ions, in relation to their sensitivity to oxidation, activities towards silver-resistant bacteria, size-dependent activities, and dispersal in electrolytic solutions. Partially (surface) oxidized silver nanoparticles have antibacterial activities, but zero-valent nanoparticles do not. The levels of chemisorbed Ag+ that form on the particle's surface, as revealed by changes in the surface plasmon resonance absorption during oxidation and reduction, correlate well with the observed antibacterial activities. Silver nanoparticles, like Ag+ in the form of AgNO3 solution, are tolerated by the bacteria strains resistant to Ag+. The antibacterial activities of silver nanoparticles are related to their size, with the smaller particles having higher activities on the basis of equivalent silver mass content. The silver nanoparticles aggregate in media with a high electrolyte content, resulting in a loss of antibacterial activities. However, complexation with albumin can stabilize the silver nanoparticles against aggregation, leading to a retention of the antibacterial activities. Taken together, the results show that the antibacterial activities of silver nanoparticles are dependent on chemisorbed Ag+, which is readily formed owing to extreme sensitivity to oxygen. The antibacterial activities of silver nanoparticles are dependent on optimally displayed oxidized surfaces, which are present in well-dispersed suspensions. \textcopyright{} 2007 SBIC.},
  pmid = {17353996},
  keywords = {Antibacterial agents,Oxidation,Silver ions,Silver nanoparticles,Surface plasmon resonance absorption},
  file = {C\:\\Users\\makro\\Zotero\\storage\\6JAHPJKP\\Lok et al. - 2007 - Silver nanoparticles partial oxidation and antibacterial activities.pdf}
}

@article{Luczkowski2022,
  title = {An {{Extremely Stable Interprotein Tetrahedral Hg}}({{Cys}}) {\textsubscript{4}} {{Core Forms}} in the {{Zinc Hook Domain}} of {{Rad50 Protein}} at {{Physiological pH}}},
  author = {{\L}uczkowski, Marek and Padjasek, Micha{\l} and Tran, J{\'o}zef Ba and Hemmingsen, Lars and Kerber, Olga and Habjani{\v c}, Jelena and Freisinger, Eva and Kr{\k{e}}{\.z}el, Artur},
  year = {2022},
  month = nov,
  journal = {Chemistry \textendash{} A European Journal},
  volume = {28},
  number = {66},
  issn = {0947-6539},
  doi = {10.1002/chem.202202738},
  file = {C\:\\Users\\makro\\Zotero\\storage\\MZ34NWH5\\Chemistry A European J - 2022 - uczkowski - An Extremely Stable Interprotein Tetrahedral Hg Cys 4 Core Forms in the Zinc.pdf}
}

@article{Majka2012,
  title = {{{ATP}} Hydrolysis by {{RAD50}} Protein Switches {{MRE11}} Enzyme from Endonuclease to Exonuclease},
  author = {Majka, Jerzy and Alford, Brian and Ausio, Juan and Finn, Ron M. and McMurray, Cynthia T.},
  year = {2012},
  journal = {Journal of Biological Chemistry},
  volume = {287},
  number = {4},
  pages = {2328--2341},
  issn = {00219258},
  doi = {10.1074/jbc.M111.307041},
  abstract = {MRE11-RAD50 is a key early response protein for processing DNA ends of broken chromosomes for repair, yet how RAD50 nucleotide dynamics regulate MRE11 nuclease activity is poorly understood. We report here that ATP binding and ATP hydrolysis cause a striking butterfly-like opening and closing of the RAD50 subunits, and each structural state has a dramatic functional effect on MRE11. RAD50-MRE11 has an extended conformation in solution when MRE11 is an active nuclease. However, ATP binding to RAD50 induces a closed conformation, and in this state MRE11 is an endonuclease. ATP hydrolysis opens the RAD50-MRE11 complex, and MRE11 maintains exonuclease activity. Thus, ATP hydrolysis is a molecular switch that converts MRE11 from an endonuclease to an exonuclease. We propose a testable model in which the open-closed transitions are used by RAD50-MRE11 to discriminate among DNA ends and drive the choice of recombination pathways.},
  pmid = {22102415},
  file = {C\:\\Users\\makro\\Zotero\\storage\\BD7CC3ZF\\Majka et al. - 2012 - ATP hydrolysis by RAD50 protein switches MRE11 enzyme from endonuclease to exonuclease.pdf}
}

@article{Marchioni2018,
  title = {Silver Nanoparticle Fate in Mammals: {{Bridging}} {\emph{in Vitro}} and {\emph{in Vivo }}Studies},
  author = {Marchioni, Marianne and Jouneau, Pierre-Henri and Chevallet, Mireille and {Michaud-Soret}, Isabelle and Deniaud, Aur{\'e}lien},
  year = {2018},
  month = jun,
  journal = {Coordination Chemistry Reviews},
  volume = {364},
  pages = {118--136},
  publisher = {{Elsevier B.V.}},
  issn = {00108545},
  doi = {10.1016/j.ccr.2018.03.008},
  abstract = {Silver nanoparticles (AgNPs) are exponentially used in various consumer products including medical devices. This production leads to an increasing human exposure to silver in different forms. Indeed, AgNPs are subject to various transformations in aqueous aerobic conditions that trigger the production of Ag(I) species. The main environmental transformation produces the non-toxic species silver sulfide. Transformations occurring in mammals are more diverse and mainly depend on the interaction of AgNPs with thiol, chloride and proteins. Any of these species have a different impact on AgNPs and induces AgNP dissolution into Ag(I) species, aggregation and/or stabilization. The transformations occurring also depend on the exposure route. The main one is dietary but medical exposure is also growing with the massive use of nanosilver as biocide in medical devices. For the former, AgNP modifications and Ag distribution has been extensively studied using in vitro and in vivo models, while data related to medical use of nanosilver are scarce. However, most of the in vitro and in vivo data often remain inconsistent. In this review, we describe both in vitro, in cellulo and in vivo data about AgNP transformations, silver speciation and biodistribution. We try to reconcile all these data and describe the latest methods for the future studies of AgNP fate in mammals.},
  keywords = {Cellular imaging,Chloride,Electron microscopy,Silver nanoparticles,Silver speciation,Sulfur},
  file = {C\:\\Users\\makro\\Zotero\\storage\\VDDIYGVN\\Marchioni et al. - 2018 - Silver nanoparticle fate in mammals Bridging in vitro and in vivo studies.pdf}
}

@article{Maret2017,
  title = {Zinc in {{Cellular Regulation}}: {{The Nature}} and {{Significance}} of ``{{Zinc Signals}}''},
  author = {Maret, Wolfgang},
  year = {2017},
  month = oct,
  journal = {International Journal of Molecular Sciences},
  volume = {18},
  number = {11},
  pages = {2285},
  issn = {1422-0067},
  doi = {10.3390/ijms18112285},
  abstract = {In the last decade, we witnessed discoveries that established Zn2+ as a second major signalling metal ion in the transmission of information within cells and in communication between cells. Together with Ca2+ and Mg2+, Zn2+ covers biological regulation with redox-inert metal ions over many orders of magnitude in concentrations. The regulatory functions of zinc ions, together with their functions as a cofactor in about three thousand zinc metalloproteins, impact virtually all aspects of cell biology. This article attempts to define the regulatory functions of zinc ions, and focuses on the nature of zinc signals and zinc signalling in pathways where zinc ions are either extracellular stimuli or intracellular messengers. These pathways interact with Ca2+, redox, and phosphorylation signalling. The regulatory functions of zinc require a complex system of precise homeostatic control for transients, subcellular distribution and traffic, organellar homeostasis, and vesicular storage and exocytosis of zinc ions.},
  pmid = {29088067},
  keywords = {Homeostasis,Regulation,Signalling,Zinc},
  file = {C\:\\Users\\makro\\Zotero\\storage\\PK99FQPJ\\Maret - 2017 - Zinc in Cellular Regulation The Nature and Significance of “Zinc Signals”.pdf}
}

@article{Mari2006,
  title = {Dynamic Assembly of End-Joining Complexes Requires Interaction between {{Ku70}}/80 and {{XRCC4}}},
  author = {Mari, Pierre Olivier and Florea, Bogdan I. and Persengiev, Stephan P. and Verkaik, Nicole S. and Br{\"u}ggenwirth, Hennie T. and Modesti, Mauro and {Giglia-Mari}, Giuseppina and Bezstarosti, Karel and Demmers, Jeroen A.A. and Luider, Theo M. and Houtsmuller, Adriaan B. and Van Gent, Dik C.},
  year = {2006},
  journal = {Proceedings of the National Academy of Sciences of the United States of America},
  volume = {103},
  number = {49},
  pages = {18597--18602},
  issn = {00278424},
  doi = {10.1073/pnas.0609061103},
  abstract = {DNA double-strand break (DSB) repair by nonhomologous end joining (NHEJ) requires the assembly of several proteins on DNA ends. Although biochemical studies have elucidated several aspects of the NHEJ reaction mechanism, much less is known about NHEJ in living cells, mainly because of the inability to visualize NHEJ repair proteins at DNA damage. Here we provide evidence that a pulsed near IR laser can produce DSBs without any visible alterations in the nucleus, and we show that NHEJ proteins accumulate in the irradiated areas. The levels of DSBs and Ku accumulation diminished in time, showing that this approach allows us to study DNA repair kinetics in vivo. Remarkably, the Ku heterodimers on DNA ends were in dynamic equilibrium with Ku70/80 in solution, showing that NHEJ complex assembly is reversible. Accumulation of XRCC4/ligase IV on DSBs depended on the presence of Ku70/80, but not DNA-PKcs. We detected a direct interaction between Ku70 and XRCC4 that could explain these requirements. Our results suggest that this assembly constitutes the core of the NHEJ reaction and that XRCC4 may serve as a flexible tether between Ku70/80 and ligase IV. \textcopyright{} 2006 by The National Academy of Sciences of the USA.},
  pmid = {17124166},
  keywords = {DNA repair,DNA-dependent protein kinase,Double-strand break repair,Fluorescence recovery after photobleaching,Live cell imaging},
  file = {C\:\\Users\\makro\\Zotero\\storage\\YNVKE22M\\Mari et al. - 2006 - Dynamic assembly of end-joining complexes requires interaction between Ku7080 and XRCC4.pdf}
}

@book{McGrayne2001,
  title = {Nobel {{Prize Women}} in {{Science}}: {{Their Lives}}, {{Struggles}}, and {{Momentous Discoveries}}: {{Second Edition}}},
  author = {McGrayne, Sharon B},
  year = {2001},
  publisher = {{National Academies Press}},
  isbn = {978-0-309-07270-0}
}

@article{Merickel2002,
  title = {Subunit Exchange and the Role of Dimer Flexibility in {{DNA}} Binding by the {{Fis}} Protein},
  author = {Merickel, Stacy K. and Sanders, Erin R. and {V{\'a}zquez-Ibar}, Jos{\'e} Luis and Johnson, Reid C.},
  year = {2002},
  journal = {Biochemistry},
  volume = {41},
  number = {18},
  pages = {5788--5798},
  issn = {00062960},
  doi = {10.1021/bi020019+},
  abstract = {Fis is an abundant bacterial DNA binding protein that functions in many different reactions. We show here that Fis subunits rapidly exchange between dimers in solution by disulfide cross-linking mixtures of Fis mutants with different electrophoretic mobilities and by monitoring energy transfer between fluorescently labeled Fis subunits upon heterodimer formation. The effects of detergents and salt concentrations on subunit exchange imply that the dimer is predominantly stabilized by hydrophobic forces, consistent with the X-ray crystal structures. Specific and nonspecific DNA strongly inhibit Fis subunit exchange. In all crystal forms of Fis, the separation between the DNA recognition helices within the Fis dimer is too short to insert into adjacent major grooves on canonical B-DNA, implying that conformational changes within the Fis dimer and/or the DNA must occur upon binding. We therefore investigated the functional importance of dimer interface flexibility for Fis-DNA binding by studying the DNA binding properties of Fis mutants that were cross-linked at different positions in the dimer. Flexibility within the core dimer interface does not appear to be required for efficient DNA binding, Fis-DNA complex dissociation, or Fis-induced DNA bending. Moreover, FRET-based experiments provided no evidence for a change in the spatial relationship between the two helix-turn-helix motifs in the Fis dimer upon DNA binding. These results support a model in which the unusually short distance between DNA recognition helices on Fis is accommodated primarily through bending of the DNA.},
  pmid = {11980482},
  file = {C\:\\Users\\makro\\Zotero\\storage\\5PY6VLLW\\Merickel et al. - 2002 - Subunit exchange and the role of dimer flexibility in DNA binding by the Fis protein.pdf}
}

@book{Miessler2013,
  title = {Inorganic {{Chemistry}}},
  author = {Miessler, Gary L. and Fischer, Paul J. and Tarr, Donald A.},
  year = {2013},
  month = apr,
  journal = {Pearson Education},
  edition = {Fifth edition},
  publisher = {{Pearson}},
  isbn = {0-321-81105-4},
  file = {C\:\\Users\\makro\\Zotero\\storage\\VZGKG6RA\\Miessler, Fischer, Tarr - 2013 - Inorganic Chemistry.pdf}
}

@article{Mimitou2008,
  title = {Sae2, {{Exo1}} and {{Sgs1}} Collaborate in {{DNA}} Double-Strand Break Processing},
  author = {Mimitou, Eleni P. and Symington, Lorraine S.},
  year = {2008},
  month = oct,
  journal = {Nature},
  volume = {455},
  number = {7214},
  pages = {770--774},
  issn = {0028-0836},
  doi = {10.1038/nature07312},
  abstract = {DNA ends exposed after introduction of double-strand breaks (DSBs) undergo 5{${'}$}-3{${'}$} nucleolytic degradation to generate single-stranded DNA, the substrate for binding by the Rad51 protein to initiate homologous recombination. This process is poorly understood in eukaryotes, but several factors have been implicated, including the Mre11 complex (Mre11-Rad50-Xrs2/NBS1), Sae2/CtIP/Ctp1 and Exo1. Here we demonstrate that yeast Exo1 nuclease and Sgs1 helicase function in alternative pathways for DSB processing. Novel, partially resected intermediates accumulate in a double mutant lacking Exo1 and Sgs1, which are poor substrates for homologous recombination. The early processing step that generates partly resected intermediates is dependent on Sae2. When Sae2 is absent, in addition to Exo1 and Sgs1, unprocessed DSBs accumulate and homology-dependent repair fails. These results suggest a two-step mechanism for DSB processing during homologous recombination. First, the Mre11 complex and Sae2 remove a small oligonucleotide(s) from the DNA ends to form an early intermediate. Second, Exo1 and/or Sgs1 rapidly process this intermediate to generate extensive tracts of single-stranded DNA that serve as substrate for Rad51. \textcopyright 2008 Macmillan Publishers Limited. All rights reserved.},
  pmid = {18806779},
  file = {C\:\\Users\\makro\\Zotero\\storage\\4SRUUFRI\\Mimitou, Symington - 2008 - Sae2, Exo1 and Sgs1 collaborate in DNA double-strand break processing.pdf}
}

@article{Minton2016,
  title = {Recent Applications of Light Scattering Measurement in the Biological and Biopharmaceutical Sciences},
  author = {Minton, Allen P.},
  year = {2016},
  month = may,
  journal = {Analytical Biochemistry},
  volume = {501},
  pages = {4--22},
  publisher = {{Elsevier Inc}},
  issn = {00032697},
  doi = {10.1016/j.ab.2016.02.007},
  pmid = {26896682},
  file = {C\:\\Users\\makro\\Zotero\\storage\\6ETTK46F\\Minton - 2016 - Recent applications of light scattering measurement in the biological and biopharmaceutical sciences.pdf}
}

@article{Mirdita2019,
  title = {{{MMseqs2}} Desktop and Local Web Server App for Fast, Interactive Sequence Searches},
  author = {Mirdita, Milot and Steinegger, Martin and S{\"o}ding, Johannes},
  year = {2019},
  journal = {Bioinformatics},
  volume = {35},
  number = {16},
  pages = {2856--2858},
  issn = {14602059},
  doi = {10.1093/bioinformatics/bty1057},
  abstract = {Summary: The MMseqs2 desktop and web server app facilitates interactive sequence searches through custom protein sequence and profile databases on personal workstations. By eliminating MMseqs2's runtime overhead, we reduced response times to a few seconds at sensitivities close to BLAST.},
  pmid = {30615063},
  file = {C\:\\Users\\makro\\Zotero\\storage\\CYVR6A5P\\Mirdita, Steinegger, Söding - 2019 - MMseqs2 desktop and local web server app for fast, interactive sequence searches.pdf}
}

@article{Mirdita2021,
  title = {Fast and Sensitive Taxonomic Assignment to Metagenomic Contigs},
  author = {Mirdita, M. and Steinegger, M. and Breitwieser, F. and S{\"o}ding, J. and Levy Karin, E.},
  editor = {Kelso, Janet},
  year = {2021},
  month = sep,
  journal = {Bioinformatics},
  volume = {37},
  number = {18},
  pages = {3029--3031},
  issn = {1367-4803},
  doi = {10.1093/bioinformatics/btab184},
  abstract = {MMseqs2 taxonomy is a new tool to assign taxonomic labels to metagenomic contigs. It extracts all possible protein fragments from each contig, quickly retains those that can contribute to taxonomic annotation, assigns them with robust labels and determines the contig's taxonomic identity by weighted voting. Its fragment extraction step is suitable for the analysis of all domains of life. MMseqs2 taxonomy is 2-18\texttimes{} faster than state-of-the-art tools and also contains new modules for creating and manipulating taxonomic reference databases as well as reporting and visualizing taxonomic assignments.},
  file = {C\:\\Users\\makro\\Zotero\\storage\\APHHBTDP\\Mirdita et al. - 2021 - Fast and sensitive taxonomic assignment to metagenomic contigs.pdf}
}

@article{Mockel2012,
  title = {{{ATP}} Driven Structural Changes of the Bacterial {{Mre11}}:{{Rad50}} Catalytic Head Complex},
  author = {M{\"o}ckel, Carolin and Lammens, Katja and Schele, Alexandra and Hopfner, Karl Peter},
  year = {2012},
  journal = {Nucleic Acids Research},
  volume = {40},
  number = {2},
  pages = {914--927},
  issn = {03051048},
  doi = {10.1093/nar/gkr749},
  abstract = {DNA double-strand breaks (DSBs) threaten genome stability in all kingdoms of life and are linked to cancerogenic chromosome aberrations in humans. The Mre11:Rad50 (MR) complex is an evolutionarily conserved complex of two Rad50 ATPases and a dimer of the Mre11 nuclease that senses and processes DSBs and tethers DNA for repair. ATP binding and hydrolysis by Rad50 is functionally coupled to DNA-binding and tethering, but also regulates Mre11's nuclease in processing DNA ends. To understand how ATP controls the interaction between Mre11 and Rad50, we determined the crystal structure of Thermotoga maritima (Tm) MR trapped in an ATP/ADP state. ATP binding to Rad50 induces a large structural change from an open form with accessible Mre11 nuclease sites into a closed form. Remarkably, the NBD dimer binds in the Mre11 DNA-binding cleft blocking Mre11's dsDNA-binding sites. An accompanying large swivel of the Rad50 coiled coil domains appears to prepare the coiled coils for DNA tethering. DNA-binding studies show that within the complex, Rad50 likely forms a dsDNA-binding site in response to ATP, while the Mre11 nuclease module retains a ssDNA-binding site. Our results suggest a possible mechanism for ATP-dependent DNA tethering and DSB processing by MR. \textcopyright{} The Author(s) 2011. Published by Oxford University Press.},
  pmid = {21937514},
  file = {C\:\\Users\\makro\\Zotero\\storage\\GQ9FSKDI\\Möckel et al. - 2012 - ATP driven structural changes of the bacterial Mre11Rad50 catalytic head complex.pdf}
}

@article{Moncalian2004,
  title = {The {{Rad50 Signature Motif}}: {{Essential}} to {{ATP Binding}} and {{Biological Function}}},
  author = {Moncalian, Gabriel and Lengsfeld, Bettina and Bhaskara, Venugopal and Hopfner, Karl Peter and Karcher, Annette and Alden, Erinn and Tainer, John A. and Paull, Tanya T.},
  year = {2004},
  journal = {Journal of Molecular Biology},
  volume = {335},
  number = {4},
  pages = {937--951},
  issn = {00222836},
  doi = {10.1016/j.jmb.2003.11.026},
  abstract = {The repair of double-strand breaks in DNA is an essential process in all organisms, and requires the coordinated activities of evolutionarily conserved protein assemblies. One of the most critical of these is the Mre11/Rad50 (M/R) complex, which is present in all three biological kingdoms, but is not well-understood at the biochemical level. Previous structural analysis of a Rad50 homolog from archaebacteria illuminated the catalytic core of the enzyme, an ATP-binding domain related to the ABC transporter family of ATPases. Here, we present the crystallographic structure of the Rad50 mutant S793R. This missense signature motif mutation changes the key serine residue in the signature motif that is conserved among Rad50 homologs and ABC ATPases. The S793R mutation is analogous to the mutation S549R in the cystic fibrosis transmembrane conductance regulator (CFTR) that results in cystic fibrosis. We show here that the serine to arginine change in the Rad50 protein prevents ATP binding and disrupts the communication among the other ATP-binding loops. This structural change, in turn, alters the communication between Rad50 monomers and thus prevents Rad50 dimerization. The equivalent mutation was made in the human Rad50 gene, and the resulting mutant protein did form a complex with Mre11 and Nbs1, but was specifically deficient in all ATP-dependent enzymatic activities. This signature motif structure-function homology extends to yeast, because the same mutation introduced into the Saccharomyces cerevisiae RAD50 gene generated an allele that failed to complement a rad50 deletion strain in DNA repair assays in vivo. These structural and biochemical results extend our understanding of the Rad50 catalytic domain and validate the use of the signature motif mutant to test the role of Rad50 ATP binding in diverse organisms. \textcopyright{} 2003 Elsevier Ltd. All rights reserved.},
  pmid = {14698290},
  keywords = {ATPase,DNA repair,Mre11,Rad50,Signature motif},
  file = {C\:\\Users\\makro\\Zotero\\storage\\PMMBJ66E\\Moncalian et al. - 2004 - The Rad50 Signature Motif Essential to ATP Binding and Biological Function.pdf}
}

@article{Morimoto2019,
  title = {Type {{II DNA}} Topoisomerases Cause Spontaneous Double-Strand Breaks in Genomic {{DNA}}},
  author = {Morimoto, Suguru and Tsuda, Masataka and Bunch, Heeyoun and Sasanuma, Hiroyuki and Austin, Caroline and Takeda, Shunichi},
  year = {2019},
  journal = {Genes},
  volume = {10},
  number = {11},
  pages = {1--18},
  issn = {20734425},
  doi = {10.3390/genes10110868},
  abstract = {Type II DNA topoisomerase enzymes (TOP2) catalyze topological changes by strand passage reactions. They involve passing one intact double stranded DNA duplex through a transient enzyme-bridged break in another (gated helix) followed by ligation of the break by TOP2. A TOP2 poison, etoposide blocks TOP2 catalysis at the ligation step of the enzyme-bridged break, increasing the number of stable TOP2 cleavage complexes (TOP2ccs). Remarkably, such pathological TOP2ccs are formed during the normal cell cycle as well as in postmitotic cells. Thus, this `abortive catalysis' can be a major source of spontaneously arising DNA double-strand breaks (DSBs). TOP2-mediated DSBs are also formed upon stimulation with physiological concentrations of androgens and estrogens. The frequent occurrence of TOP2-mediated DSBs was previously not appreciated because they are efficiently repaired. This repair is performed in collaboration with BRCA1, BRCA2, MRE11 nuclease, and tyrosyl-DNA phosphodiesterase 2 (TDP2) with nonhomologous end joining (NHEJ) factors. This review first discusses spontaneously arising DSBs caused by the abortive catalysis of TOP2 and then summarizes proteins involved in repairing stalled TOP2ccs and discusses the genotoxicity of the sex hormones.},
  pmid = {31671674},
  keywords = {BRCA1,BRCA2,Breast cancer,Cell cycle,Estrogen,Genotoxicity,Topoisomerase II,Transcription},
  file = {C\:\\Users\\makro\\Zotero\\storage\\3MVV8BGY\\Morimoto et al. - 2019 - Type II DNA topoisomerases cause spontaneous double-strand breaks in genomic DNA.pdf}
}

@article{Morris2022,
  title = {Uncovering Protein Function: {{From}} Classification to Complexes},
  author = {Morris, Rhiannon and Black, Katrina A. and Stollar, Elliott J.},
  year = {2022},
  journal = {Essays in Biochemistry},
  volume = {66},
  number = {2},
  pages = {255--285},
  issn = {00711365},
  doi = {10.1042/EBC20200108},
  abstract = {Almost all interactions and reactions that occur in living organisms involve proteins. The various biological roles of proteins include, but are not limited to, signal transduction, gene transcription, cell death, immune function, structural support, and catalysis of all the chemical reactions that enable organisms to survive. The varied roles of proteins have led to them being dubbed `the workhorses of all living organisms'. This article discusses the functions of proteins and how protein function is studied in a laboratory setting. In this article, we begin by examining the functions of protein domains, followed by a discussion of some of the major classes of proteins based on their function. We consider protein binding in detail, which is central to protein function. We then examine how protein function can be altered through various mechanisms including post-translational modification, and changes to environment, oligomerisation and mutations. Finally, we consider a handful of the techniques employed in the laboratory to understand and measure the function of proteins.},
  pmid = {35946411},
  file = {C\:\\Users\\makro\\Zotero\\storage\\4I4L3SY3\\Morris, Black, Stollar - 2022 - Uncovering protein function From classification to complexes.pdf}
}

@article{Mukhopadhyay2019,
  title = {Finding Enzyme Cofactors in {{Protein Data Bank}}},
  author = {Mukhopadhyay, Abhik and Borkakoti, Neera and Pravda, Luk{\'a}{\v s} and Tyzack, Jonathan D. and Thornton, Janet M. and Velankar, Sameer},
  editor = {Wren, Jonathan},
  year = {2019},
  month = sep,
  journal = {Bioinformatics},
  volume = {35},
  number = {18},
  pages = {3510--3511},
  issn = {1367-4803},
  doi = {10.1093/bioinformatics/btz115},
  abstract = {Cofactors are essential for many enzyme reactions. The Protein Data Bank (PDB) contains {$>$}67 000 entries containing enzyme structures, many with bound cofactor or cofactor-like molecules. This work aims to identify and categorize these small molecules in the PDB and make it easier to find them. Results: The Protein Data Bank in Europe (PDBe; pdbe.org) has implemented a pipeline to identify enzyme cofactor and cofactor-like molecules, which are now part of the PDBe weekly release process. Availability and implementation: Information is made available on the individual PDBe entry pages at pdbe.org and programmatically through the PDBe REST API (pdbe.org/api). Supplementary information: Supplementary data are available at Bioinformatics online.},
  pmid = {30759194},
  file = {C\:\\Users\\makro\\Zotero\\storage\\UI22UZXP\\Mukhopadhyay et al. - 2019 - Finding enzyme cofactors in Protein Data Bank.pdf}
}

@article{Myler2017,
  title = {Single-{{Molecule Imaging Reveals How Mre11-Rad50-Nbs1 Initiates DNA Break Repair}}},
  author = {Myler, Logan R. and Gallardo, Ignacio F. and Soniat, Michael M. and Deshpande, Rajashree A. and Gonzalez, Xenia B. and Kim, Yoori and Paull, Tanya T. and Finkelstein, Ilya J.},
  year = {2017},
  journal = {Molecular Cell},
  volume = {67},
  number = {5},
  pages = {891-898.e4},
  publisher = {{Elsevier Inc.}},
  issn = {10974164},
  doi = {10.1016/j.molcel.2017.08.002},
  abstract = {DNA double-strand break (DSB) repair is essential for maintaining our genomes. Mre11-Rad50-Nbs1 (MRN) and Ku70-Ku80 (Ku) direct distinct DSB repair pathways, but the interplay between these complexes at a DSB remains unclear. Here, we use high-throughput single-molecule microscopy to show that MRN searches for free DNA ends by one-dimensional facilitated diffusion, even on nucleosome-coated DNA. Rad50 binds homoduplex DNA and promotes facilitated diffusion, whereas Mre11 is required for DNA end recognition and nuclease activities. MRN gains access to occluded DNA ends by removing Ku or other DNA adducts via an Mre11-dependent nucleolytic reaction. Next, MRN loads exonuclease 1 (Exo1) onto the free DNA ends to initiate DNA resection. In the presence of replication protein A (RPA), MRN acts as a processivity factor for Exo1, retaining the exonuclease on DNA for long-range resection. Our results provide a mechanism for how MRN promotes homologous recombination on nucleosome-coated DNA.},
  pmid = {28867292},
  keywords = {DNA repair,double-strand break,Ku,MRN,resection,resectosome,single-molecule},
  file = {C\:\\Users\\makro\\Zotero\\storage\\BQAVTUM9\\Myler et al. - 2017 - Single-Molecule Imaging Reveals How Mre11-Rad50-Nbs1 Initiates DNA Break Repair.pdf}
}

@article{Na2021,
  title = {{{SPRTN}} Protease-Cleaved {{MRE11}} Decreases {{DNA}} Repair and Radiosensitises Cancer Cells},
  author = {Na, Juri and Newman, Joseph A. and Then, Chee Kin and Syed, Junetha and Vendrell, Iolanda and Torrecilla, Ignacio and Ellermann, Sophie and Ramadan, Kristijan and Fischer, Roman and Kiltie, Anne E.},
  year = {2021},
  month = feb,
  journal = {Cell Death \& Disease},
  volume = {12},
  number = {2},
  pages = {165},
  publisher = {{Springer US}},
  issn = {2041-4889},
  doi = {10.1038/s41419-021-03437-w},
  abstract = {The human MRE11/RAD50/NBS1 (MRN) complex plays a crucial role in sensing and repairing DNA DSB. MRE11 possesses dual 3{${'}-$}5{${'}$} exonuclease and endonuclease activity and forms the core of the multifunctional MRN complex. We previously identified a C-terminally truncated form of MRE11 (TR-MRE11) associated with post-translational MRE11 degradation. Here we identified SPRTN as the essential protease for the formation of TR-MRE11 and characterised the role of this MRE11 form in its DNA damage response (DDR). Using tandem mass spectrometry and site-directed mutagenesis, the SPRTN-dependent cleavage site for MRE11 was identified between 559 and 580 amino acids. Despite the intact interaction of TR-MRE11 with its constitutive core complex proteins RAD50 and NBS1, both nuclease activities of truncated MRE11 were dramatically reduced due to its deficient binding to DNA. Furthermore, lack of the MRE11 C-terminal decreased HR repair efficiency, very likely due to abolished recruitment of TR-MRE11 to the sites of DNA damage, which consequently led to increased cellular radiosensitivity. The presence of this DNA repair-defective TR-MRE11 could explain our previous finding that the high MRE11 protein expression by immunohistochemistry correlates with improved survival following radical radiotherapy in bladder cancer patients.},
  pmid = {33558481},
  file = {C\:\\Users\\makro\\Zotero\\storage\\QJPZVGMJ\\Na et al. - 2021 - SPRTN protease-cleaved MRE11 decreases DNA repair and radiosensitises cancer cells.pdf}
}

@article{Owczarzy2004,
  title = {Effects of {{Sodium Ions}} on {{DNA Duplex Oligomers}}: {{Improved Predictions}} of {{Melting Temperatures}}},
  author = {Owczarzy, Richard and You, Yong and Moreira, Bernardo G. and Manthey, Jeffrey A. and Huang, Lingyan and Behlke, Mark A. and Walder, Joseph A.},
  year = {2004},
  journal = {Biochemistry},
  volume = {43},
  number = {12},
  pages = {3537--3554},
  issn = {00062960},
  doi = {10.1021/bi034621r},
  abstract = {Melting temperatures, Tm, were systematically studied for a set of 92 DNA duplex oligomers in a variety of sodium ion concentrations ranging from 69 mM to 1.02 M. The relationship between Tm and 1n [Na +] was nonlinear over this range of sodium ion concentrations, and the observed melting temperatures were poorly predicted by existing algorithms. A new empirical relationship was derived from UV melting data that employs a quadratic function, which better models the melting temperatures of DNA duplex oligomers as sodium ion concentration is varied. Statistical analysis shows that this improved salt correction is significantly more accurate than previously suggested algorithms and predicts salt-corrected melting temperatures with an average error of only 1.6 \textdegree C when tested against an independent validation set of Tm measurements obtained from the literature. Differential scanning calorimetry studies demonstrate that this Tm salt correction is insensitive to DNA concentration. The Tm salt correction function was found to be sequence-dependent and varied with the fraction of G{$\cdot$}C base pairs, in agreement with previous studies of genomic and polymeric DNAs. The salt correction function is independent of oligomer length, suggesting that end-fraying and other end effects have little influence on the amount of sodium counterions released during duplex melting. The results are discussed in the context of counterion condensation theory.},
  pmid = {15035624},
  file = {C\:\\Users\\makro\\Zotero\\storage\\PC82HF33\\Owczarzy et al. - 2004 - Effects of Sodium Ions on DNA Duplex Oligomers Improved Predictions of Melting Temperatures.pdf}
}

@article{Padjasek2020,
  title = {Structural Zinc Binding Sites Shaped for Greater Works: {{Structure-function}} Relations in Classical Zinc Finger, Hook and Clasp Domains},
  author = {Padjasek, Micha{\l} and Kocy{\l}a, Anna and Kluska, Katarzyna and Kerber, Olga and Tran, J{\'o}zef Ba and Kr{\k{e}}{\.z}el, Artur},
  year = {2020},
  month = mar,
  journal = {Journal of Inorganic Biochemistry},
  volume = {204},
  number = {December 2019},
  pages = {110955},
  publisher = {{Elsevier}},
  issn = {01620134},
  doi = {10.1016/j.jinorgbio.2019.110955},
  abstract = {Metal ions are essential elements present in biological systems able to facilitate many cellular processes including proliferation, signaling, DNA synthesis and repair. Zinc ion (Zn(II)) is an important cofactor for numerous biochemical reactions. Commonly, structural zinc sites demonstrate high Zn(II) affinity and compact architecture required for sequence-specific macromolecule binding. However, how Zn(II)-dependent proteins fold, how their dissociation occurs, and which factors modulate zinc protein affinity as well as stability remains not fully understood. The molecular rules governing precise regulation of zinc proteins function are hidden in the relationship between sequence and structure, and hence require deep understanding of their folding mechanism under metal load, reactivity and metal-to-protein affinity. Even though, this sequence-structure relationship has an impact on zinc proteins function, it has been shown that other biological factors including cellular localization and Zn(II) availability influence overall protein behavior. Taking into account all of the mentioned factors, in this review, we aim to describe the relationship between structure-function-stability of zinc structural sites, found in a zinc finger, zinc hook and zinc clasps, and reach far beyond a structural point of view in order to appreciate the balance between chemistry and biology that govern the protein world.},
  pmid = {31841759},
  file = {C\:\\Users\\makro\\Zotero\\storage\\6Y5J78WK\\1-s2.0-S0162013419305549-main.pdf}
}

@article{Padjasek2020a,
  title = {Metal {{Exchange}} in the {{Interprotein Zn}}{{{\textsuperscript{II}}}}-{{Binding Site}} of the {{Rad50 Hook Domain}}: {{Structural Insights}} into {{Cd}}{{{\textsuperscript{II}}}}-{{Induced DNA-Repair Inhibition}}},
  author = {Padjasek, Micha{\l} and Maciejczyk, Maciej and Nowakowski, Micha{\l} and Kerber, Olga and Pyrka, Maciej and Ko{\'z}mi{\'n}ski, Wiktor and Kr{\k{e}}{\.z}el, Artur},
  year = {2020},
  journal = {Chemistry - A European Journal},
  volume = {26},
  number = {15},
  pages = {3297--3313},
  issn = {15213765},
  doi = {10.1002/chem.201904942},
  abstract = {CdII is a major genotoxic agent that readily displaces ZnII in a multitude of zinc proteins, abrogates redox homeostasis, and deregulates cellular metalloproteome. To date, this displacement has been described mostly for cysteine(Cys)-rich intraprotein binding sites in certain zinc finger domains and metallothioneins. To visualize how a ZnII-to-CdII swap can affect the target protein's status and thus understand the molecular basis of CdII-induced genotoxicity an intermolecular ZnII-binding site from the crucial DNA repair protein Rad50 and its zinc hook domain were examined. By using a length-varied peptide base, ZnII-to-CdII displacement in Rad50's hook domain is demonstrated to alter it in a bimodal fashion: 1) CdII induces around a two-orders-of-magnitude stabilization effect (log (Formula presented.) =20.8 vs. log (Formula presented.) =22.7), which defines an extremely high affinity of a peptide towards a metal ion, and 2) the displacement disrupts the overall assembly of the domain, as shown by NMR spectroscopic and anisotropy decay data. Based on the results, a new model explaining the molecular mechanism of CdII genotoxicity that underlines CdII's impact on Rad50's dimer stability and quaternary structure that could potentially result in abrogation of the major DNA damage response pathway is proposed.},
  pmid = {31846102},
  keywords = {cadmium,DNA damage,Rad50,zinc,zinc hook},
  file = {C\:\\Users\\makro\\Zotero\\storage\\5PRWLKCG\\Padjasek et al. - 2020 - Metal Exchange in the Interprotein ZnII-Binding Site of the Rad50 Hook Domain Structural Insights into CdII-Ind.pdf}
}

@phdthesis{Padjasek2022,
  title = {Wp\l yw Dynamiki Koordynacyjnej {{Zn}}({{II}}) Na Struktur\k{e} Domeny Haczykowej Bia\l ka {{Rad50}}.},
  author = {Padjasek, Micha{\l}},
  year = {2022},
  school = {University of Wroc\l aw}
}

@incollection{Pal2020,
  title = {Recombination},
  booktitle = {Fundamentals of {{Molecular Structural Biology}}},
  author = {Pal, Subrata},
  year = {2020},
  number = {c},
  pages = {377--404},
  publisher = {{Elsevier}},
  doi = {10.1016/B978-0-12-814855-6.00013-4},
  isbn = {978-0-12-814855-6},
  file = {C\:\\Users\\makro\\Zotero\\storage\\AF6QJE8H\\Pal - 2020 - Recombination.pdf}
}

@article{Panel2014,
  title = {Scientific {{Opinion}} on {{Dietary Reference Values}} for Chromium},
  author = {Agostoni, Carlo and Canani, Roberto Berni and {Fairweather-Tait}, Susan and Heinonen, Marina and Korhonen, Hannu and Vieille, S{\'e}bastien La and Marchelli, Rosangela and Martin, Ambroise and Naska, Androniki and {Neuh{\"a}user-Berthold}, Monika and Nowicka, Gra{\.z}yna and Sanz, Yolanda and Siani, Alfonso and Sj{\"o}, Anders and Tom{\'e}, Daniel and Turck, Dominique and Verhagen, Hans},
  year = {2014},
  month = oct,
  journal = {EFSA Journal},
  volume = {12},
  number = {10},
  pages = {3845},
  issn = {18314732},
  doi = {10.2903/j.efsa.2014.3845},
  abstract = {Following a request from the European Commission, the Panel on Dietetic Products, Nutrition and Allergies (NDA) considered the evidence for setting Dietary Reference Values for chromium. Trivalent chromium (Cr(III)) has been postulated to be necessary for the efficacy of insulin in regulating the metabolism of carbohydrates, lipids and proteins. However, the mechanism(s) for these roles and the essential function of Cr(III) in metabolism have not been substantiated. The criteria for the essentiality of a trace element were considered. It was noted that attempts to create chromium deficiency in animal models have not produced consistent results, and that there is no evidence of essentiality of Cr(III) in animal nutrition. Evaluating the possibility of Cr(III) as an essential element for humans, the evidence from reported improvements associated with chromium supplementation in patients on total parenteral nutrition was considered to be the most convincing, but overall data do not provide sufficient information on the reversibility of the possible deficiencies and the nature of any dose-response curve in order to identify a dietary requirement for humans. The Panel concludes that no Average Requirement and no Population Reference Intake for chromium can be defined. Several studies assessed the effect of chromium supplementation on glucose and/or lipid metabolism. In the only study for which information on total chromium intake was available, there was no difference in parameters of glucose metabolism of normoglycaemic subjects between the placebo and chromium-supplemented periods. The Panel considered that there is no evidence of beneficial effects associated with chromium intake in healthy subjects. The Panel concluded that the setting of an Adequate Intake for chromium is also not appropriate.},
  keywords = {chromium,Dietary Reference Value,essentiality},
  file = {C\:\\Users\\makro\\Zotero\\storage\\MIH9Y9CB\\Agostoni et al. - 2014 - Scientific Opinion on Dietary Reference Values for chromium.pdf}
}

@article{Park2011,
  title = {Crystal {{Structure}} of {{Human Mre11}}: {{Understanding Tumorigenic Mutations}}},
  author = {Park, Young Bong and Chae, Jina and Kim, Young Chang and Cho, Yunje},
  year = {2011},
  month = nov,
  journal = {Structure},
  volume = {19},
  number = {11},
  pages = {1591--1602},
  publisher = {{Elsevier Ltd}},
  issn = {09692126},
  doi = {10.1016/j.str.2011.09.010},
  abstract = {Mre11 plays an important role in repairing damaged DNA by cleaving broken ends and by providing a platform for other DNA repair proteins. Various Mre11 mutations have been identified in several types of cancer. We have determined the crystal structure of the human Mre11 core (hMre11), which contains the nuclease and capping domains. hMre11 dimerizes through the interfaces between loop {$\beta$}3-{$\alpha$}3 from one Mre11 and loop {$\beta$}4-{$\beta$}5 from another Mre11, and between loop {$\alpha$}2-{$\beta$}3 from one Mre11 and helices {$\alpha$}2 and {$\alpha$}3 from another Mre11, and assembles into a completely different dimeric architecture compared with bacterial or archaeal Mre11 homologs. Nbs1 binds to the region containing loop {$\alpha$}2-{$\beta$}3 which participates in dimerization. The hMre11 structure in conjunction with biochemical analyses reveals that many tumorigenic mutations are primarily associated with Nbs1 binding and partly with nuclease activities, providing a framework for understanding how mutations inactivate Mre11. \textcopyright{} 2011 Elsevier Ltd. All rights reserved.},
  pmid = {22078559},
  file = {C\:\\Users\\makro\\Zotero\\storage\\3EAN4RT2\\Park et al. - 2011 - Crystal Structure of Human Mre11 Understanding Tumorigenic Mutations.pdf}
}

@article{Park2017,
  title = {Eukaryotic {{Rad50}} Functions as a Rod-Shaped Dimer},
  author = {Park, Young Bong and Hohl, Marcel and Padjasek, Micha{\l} and Jeong, Eunyoung and Jin, Kyeong Sik and Kr{\k{e}}{\.z}el, Artur and Petrini, John H J and Cho, Yunje},
  year = {2017},
  month = mar,
  journal = {Nature Structural \& Molecular Biology},
  volume = {24},
  number = {3},
  pages = {248--257},
  issn = {1545-9993},
  doi = {10.1038/nsmb.3369},
  abstract = {The Rad50 hook interface is crucial for assembly and various functions of the Mre11 complex. Previous analyses suggested that Rad50 molecules interact within (intracomplex) or between (intercomplex) dimeric complexes. In this study, we determined the structure of the human Rad50 hook and coiled-coil domains. The data suggest that the predominant structure is the intracomplex, in which the two parallel coiled coils proximal to the hook form a rod shape, and that a novel interface within the coiled-coil domains of Rad50 stabilizes the interaction of Rad50 protomers in the dimeric assembly. In yeast, removal of the coiled-coil interface compromised Tel1 activation without affecting DNA repair, while simultaneous disruption of that interface and the hook phenocopied a null mutation. The results demonstrate that the hook and coiled-coil interfaces coordinately promote intracomplex assembly and define the intracomplex as the functional form of the Mre11 complex.},
  pmid = {28134932},
  file = {C\:\\Users\\makro\\Zotero\\storage\\KDPJ73TN\\Park et al. - 2017 - Eukaryotic Rad50 functions as a rod-shaped dimer.pdf}
}

@article{Patel2007,
  title = {Analysis of the Structural Consensus of the Zinc Coordination Centers of Metalloprotein Structures},
  author = {Patel, Kirti and Kumar, Anil and Durani, Susheel},
  year = {2007},
  journal = {Biochimica et Biophysica Acta - Proteins and Proteomics},
  volume = {1774},
  number = {10},
  pages = {1247--1253},
  issn = {15709639},
  doi = {10.1016/j.bbapap.2007.07.010},
  abstract = {In a recent sequence-analysis study it was concluded that up to 10\% of the human proteome could be comprised of zinc proteins, quite varied in the functional spread. The native structures of only few of the proteins are actually established. The elucidation of rest of the sequences of not just human but even other actively investigated genomes may benefit from knowledge of the structural consensus of the zinc-binding centers of the currently known zinc proteins. Nearly four hundred X-ray and NMR structures in the database of zinc-protein structures available as of April 2007 were investigated for geometry and conformation in the zinc-binding centers; separately for the structural and catalytic proteins and individually in the zinc centers coordinated to three and four amino-acid ligands. Enhanced cysteine involvement in agreement with the observation in human proteome has been detected in contrast with previous reports. Deviations from ideal coordination geometries are detected, possible underlying reasons are investigated, and correlations of geometry and conformation in zinc-coordination centers with protein function are established, providing possible benchmarks for putative zinc-binding patterns of the burgeoning genome data. \textcopyright{} 2007 Elsevier B.V. All rights reserved.},
  pmid = {17855175},
  keywords = {Catalytic zinc-center,Metalloprotein,Structural zinc-center,Zinc binding pattern,Zinc coordination,Zinc-protein},
  file = {C\:\\Users\\makro\\Zotero\\storage\\6IUHG52P\\Patel, Kumar, Durani - 2007 - Analysis of the structural consensus of the zinc coordination centers of metalloprotein structures.pdf}
}

@incollection{Patil2018,
  title = {Protein\textendash{{Protein Interaction Databases}}},
  booktitle = {Encyclopedia of {{Bioinformatics}} and {{Computational Biology}}},
  author = {Patil, Ashwini},
  year = {2019},
  volume = {1--3},
  pages = {849--855},
  publisher = {{Elsevier}},
  doi = {10.1016/B978-0-12-809633-8.20660-2},
  abstract = {Protein-protein interactions are central to understanding the functional relationships between proteins. Over the past three decades, the number of protein-protein interactions identified has increased significantly. As a result, a large number of databases have been created to catalog and annotate these interactions. This article gives an overview of the existing protein-protein interaction databases. It introduces the common terminology used in the interaction databases and describes their features, the strategies they use to curate and assess interactions, and highlights their differences. Some of the community standards defined to deal with data compatibility across databases are also described.},
  isbn = {978-0-12-811432-2},
  keywords = {Annotation,Biological databases,Curation,Interaction reliability,Interaction scoring,Protein networks,Protein-protein interaction databases,Protein-protein interactions},
  file = {C\:\\Users\\makro\\Zotero\\storage\\W8UAE7UL\\Patil - 2019 - Protein–Protein Interaction Databases.pdf}
}

@article{Paull1998,
  title = {The 3{${'}$} to 5{${'}$} Exonuclease Activity of {{Mre11}} Facilitates Repair of {{DNA}} Double-Strand Breaks},
  author = {Paull, Tanya T. and Gellert, Martin},
  year = {1998},
  journal = {Molecular Cell},
  volume = {1},
  number = {7},
  pages = {969--979},
  issn = {10972765},
  doi = {10.1016/S1097-2765(00)80097-0},
  abstract = {MRE11 and RAD50 are known to be required for non-homologous joining of DNA ends in vivo. We have investigated the enzymatic activities of the purified proteins and found that Mre11 by itself has 3{${'}$} to 5{${'}$} exonuclease activity that is increased when Mre11 is in a complex with Rad50. Mre11 also exhibits endonuclease activity, as shown by the asymmetric opening of DNA hairpin loops. In conjunction with a DNA ligase, Mre11 promotes the joining of noncomplementary ends in vitro by utilizing short homologies near the ends of the DNA fragments. Sequence identities of 1-5 base pairs are present at all of these junctions, and their diversity is consistent with the products of non-homologous end-joining observed in vivo.},
  pmid = {9651580},
  file = {C\:\\Users\\makro\\Zotero\\storage\\B857I4CU\\Paull, Gellert - 1998 - The 3′ to 5′ exonuclease activity of Mre11 facilitates repair of DNA double-strand breaks.pdf}
}

@article{Paull1999,
  title = {Nbs1 Potentiates {{ATP-driven DNA}} Unwinding and Endonuclease Cleavage by the {{Mre11}}/{{Rad50}} Complex},
  author = {Paull, Tanya T and Gellert, Martin},
  year = {1999},
  journal = {Genes and Development},
  volume = {13},
  number = {10},
  pages = {1276--1288},
  issn = {08909369},
  doi = {10.1101/gad.13.10.1276},
  abstract = {The Nijmegen breakage syndrome gene product (Nbs1) was shown recently to associate in vivo with the Mre11 and Rad50 proteins, which play pivotal roles in eukaryotic DNA double-strand break repair, meiotic recombination, and telomere maintenance. We show in this work that the triple complex of recombinant Nbs1, Mre11, and Rad50 proteins binds cooperatively to DNA and forms a distinct protein-DNA species. The Mre11/Rad50/Nbs1 complex displays several enzymatic activities that are not seen without Nbs1, including partial unwinding of a DNA duplex and efficient cleavage of fully paired hairpins. Unwinding and hairpin cleavage are both increased by the presence of ATP. On nonhairpin DNA ends, ATP controls a switch in endonuclease specificity that allows Mre11/Rad50/Nbs1 to cleave a 3'-protruding strand at a double-/single-strand transition. Mutational analysis demonstrates that Rad50 is responsible for ATP binding by the complex, but the ATP-dependent activities are expressed only with Nbs1 present.},
  pmid = {10346816},
  keywords = {ATP binding,DNA unwinding,Mre11/Rad50 protein,Nijmegen breakage syndrome},
  file = {C\:\\Users\\makro\\Zotero\\storage\\YW2LD6JR\\Paull, Gellert - 1999 - Nbs1 potentiates ATP-driven DNA unwinding and endonuclease cleavage by the Mre11Rad50 complex.pdf}
}

@article{Pearson1963,
  title = {Hard and {{Soft Acids}} and {{Bases}}},
  author = {Pearson, Ralph G.},
  year = {1963},
  month = nov,
  journal = {Journal of the American Chemical Society},
  volume = {85},
  number = {22},
  pages = {3533--3539},
  issn = {0002-7863},
  doi = {10.1021/ja00905a001},
  abstract = {A number of Lewis acids of diverse types are classified as (a) or (b) following the criterion of Ahrland, Chatt, and Davies. Other, auxiliary criteria are proposed. Class (a) acids prefer to bind to ``hard'' or nonpolarizable bases. Class (b) acids prefer to bind to ``soft'' or polarizable bases. Since class (a) acids are themselves ``hard'' and since class (b) acids are ``soft'' a simple, useful rule is proposed: hard acids bind strongly to hard bases and soft acids bind strongly to soft bases. The explanations for such behavior include: (1) various degrees of ionic and covalent {$\sigma$}-binding; (2) {$\pi$}-bonding; (3) electron correlation phenomena; (4) solvation effects. \textcopyright{} 1963, American Chemical Society. All rights reserved.},
  file = {C\:\\Users\\makro\\Zotero\\storage\\V375Z7F6\\Pearson - 1963 - Hard and Soft Acids and Bases.pdf}
}

@article{Penner-Hahn2005,
  title = {Characterization of ``Spectroscopically Quiet'' Metals in Biology},
  author = {{Penner-Hahn}, James E.},
  year = {2005},
  month = jan,
  journal = {Coordination Chemistry Reviews},
  volume = {249},
  number = {1-2},
  pages = {161--177},
  issn = {00108545},
  doi = {10.1016/j.ccr.2004.03.011},
  abstract = {The use of X-ray absorption spectroscopy (XAS) to characterize the local environment of "spectroscopically quiet" metals in metalloproteins is reviewed, with an emphasis on studies of Cu(I) and Zn(II). Both the advantages and the weaknesses of X-ray absorption are discussed, with examples taken from the recent literature. \textcopyright{} 2004 Elsevier B.V. All rights reserved.},
  isbn = {1734764732},
  keywords = {Cu(I),EXAFS,Spectroscopically quiet,X-ray absorption,XANES,XAS,Zn (II)},
  file = {C\:\\Users\\makro\\Zotero\\storage\\72Y2LTAJ\\Penner-Hahn - 2005 - Characterization of “spectroscopically quiet” metals in biology.pdf}
}

@article{Petrotchenko2022,
  title = {Protein {{Chemistry Combined}} with {{Mass Spectrometry}} for {{Protein Structure Determination}}},
  author = {Petrotchenko, Evgeniy V. and Borchers, Christoph H.},
  year = {2022},
  month = apr,
  journal = {Chemical Reviews},
  volume = {122},
  number = {8},
  pages = {7488--7499},
  issn = {0009-2665},
  doi = {10.1021/acs.chemrev.1c00302},
  abstract = {The advent of soft-ionization mass spectrometry for biomolecules has opened up new possibilities for the structural analysis of proteins. Combining protein chemistry methods with modern mass spectrometry has led to the emergence of the distinct field of structural proteomics. Multiple protein chemistry approaches, such as surface modification, limited proteolysis, hydrogen-deuterium exchange, and cross-linking, provide diverse and often orthogonal structural information on the protein systems studied. Combining experimental data from these various structural proteomics techniques provides a more comprehensive examination of the protein structure and increases confidence in the ultimate findings. Here, we review various types of experimental data from structural proteomics approaches with an emphasis on the use of multiple complementary mass spectrometric approaches to provide experimental constraints for the solving of protein structures.},
  pmid = {34968047},
  file = {C\:\\Users\\makro\\Zotero\\storage\\MHLKAEDV\\Petrotchenko, Borchers - 2022 - Protein Chemistry Combined with Mass Spectrometry for Protein Structure Determination.pdf}
}

@misc{ProteinDataBank,
  title = {Protein {{Data Bank}} | {{Nucleic Acids Research}} | {{Oxford Academic}}},
  urldate = {2023-03-16},
  howpublished = {https://academic.oup.com/nar/article/28/1/235/2384399?login=false},
  file = {C\:\\Users\\makro\\Zotero\\storage\\ANMLWT9I\\2384399.html}
}

@article{Putignano2018,
  title = {{{MetalPDB}} in 2018: A Database of Metal Sites in Biological Macromolecular Structures},
  author = {Putignano, Valeria and Rosato, Antonio and Banci, Lucia and Andreini, Claudia},
  year = {2018},
  month = jan,
  journal = {Nucleic Acids Research},
  volume = {46},
  number = {D1},
  pages = {D459-D464},
  publisher = {{Oxford University Press}},
  issn = {0305-1048},
  doi = {10.1093/nar/gkx989},
  abstract = {MetalPDB (http://metalweb.cerm.unifi.it/) is a database providing information on metal-binding sites detected in the three-dimensional (3D) structures of biological macromolecules. MetalPDB represents such sites as 3D templates, called Minimal Functional Sites (MFSs), which describe the local environment around the metal(s) independently of the larger context of the macromolecular structure. The 2018 update of MetalPDB includes new contents and tools. A major extension is the inclusion of proteins whose structures do not contain metal ions although their sequences potentially contain a known MFS. In addition, MetalPDB now provides extensive statistical analyses addressing several aspects of general metal usage within the PDB, across protein families and in catalysis. Users can also query MetalPDB to extract statistical information on structural aspects associated with individual metals, such as preferred coordination geometries or aminoacidic environment. A further major improvement is the functional annotation of MFSs; the annotation is manually performed via a password-protected annotator interface. At present, {$\sim$}50\% of all MFSs have such a functional annotation. Other noteworthy improvements are bulk query functionality, through the upload of a list of PDB identifiers, and ftp access to MetalPDB contents, allowing users to carry out in-depth analyses on their own computational infrastructure.},
  pmid = {29077942},
  file = {C\:\\Users\\makro\\Zotero\\storage\\U6AFHWIH\\Putignano et al. - 2018 - MetalPDB in 2018 a database of metal sites in biological macromolecular structures.pdf}
}

@article{Qiao2006,
  title = {Zinc Binding to a Regulatory Zinc-Sensing Domain Monitored in Vivo by Using {{FRET}}},
  author = {Qiao, Wei and Mooney, Michelle and Bird, Amanda J. and Winge, Dennis R. and Eide, David J.},
  year = {2006},
  month = jun,
  journal = {Proceedings of the National Academy of Sciences},
  volume = {103},
  number = {23},
  pages = {8674--8679},
  issn = {0027-8424},
  doi = {10.1073/pnas.0600928103},
  abstract = {We have generated probes of metal binding to zinc fingers (ZFs) that provide tools to study zinc trafficking in vivo . In this study, we used these probes to examine zinc binding by the Zap1 transcription factor of Saccharomyces cerevisiae . Zap1 contains two zinc-regulated activation domains (ADs), AD1 and AD2. AD2 is located within two C 2 H 2 ZFs, ZF1 and ZF2. Studies have indicated that apoAD2 activates transcription and zinc binding to ZF1 and that ZF2 forms an interacting-finger-pair structure that is necessary to inhibit AD function. A related structural finger pair, ZF3 and ZF4, is found in the Zap1 DNA binding domain. In vitro studies indicated that, although the ZF1/2 and ZF3/4 finger pairs bind zinc with similar affinities, zinc that was bound to ZF1/2 was much more labile. We examined the properties of Zap1 ZFs in vivo by FRET. ZF pairs were flanked by enhanced yellow fluorescent protein and enhanced cyan fluorescent protein, allowing detection of zinc-induced conformation changes by FRET. By using these reporters, we found that ZF1/2 and ZF3/4 showed similar responses to zinc under steady-state conditions in vivo . In contrast, ZF1/2 zinc binding was significantly more labile than was ZF3/4. Also, ZF1/2 accumulated in an apo form that could rapidly bind zinc, whereas the ZF3/4 pair did not. Last, we show that these properties are evolutionarily conserved indicating their importance to Zap1 function. These results indicate that the kinetic lability of ZF1/2 in vivo is a key component of Zap1 zinc responsiveness.},
  pmid = {16720702},
  keywords = {Regulation,Transcription,Zinc finger},
  file = {C\:\\Users\\makro\\Zotero\\storage\\PPTEMVC6\\Qiao et al. - 2006 - Zinc binding to a regulatory zinc-sensing domain monitored in vivo by using FRET.pdf}
}

@article{Ramirez-Bello2022,
  title = {Zinc and {{Copper Ions Induce Aggregation}} of {{Human}} {$\beta$}-{{Crystallins}}},
  author = {{Ramirez-Bello}, Vanesa and {Martinez-Seoane}, Javier and {Fern{\'a}ndez-Silva}, Arline and Amero, Carlos},
  year = {2022},
  month = may,
  journal = {Molecules},
  volume = {27},
  number = {9},
  pages = {2970},
  issn = {1420-3049},
  doi = {10.3390/molecules27092970},
  abstract = {Cataracts are defined as the clouding of the lens due to the formation of insoluble protein aggregates. Metal ions exposure has been recognized as a risk factor in the cataract formation process. The {$\gamma$} and {$\beta$} crystallins are members of a larger family and share several structural features. Several studies have shown that copper and zinc ions induce the formation of {$\gamma$}-crystallins aggregates. However, the interaction of metal ions with {$\beta$}-crystallins, some of the most abundant crystallins in the lens, has not been explored until now. Here, we evaluate the effect of Cu(II) and Zn(II) ions on the aggregation of H{$\beta$}A1, as a representative of the acidic form, and H{$\beta$}B2, as a representative of the basic {$\beta$}-crystallins. We used several biophysical techniques and computational methods to show that Cu(II) and Zn(II) induce aggregation following different pathways. Both metal ions destabilize the proteins and impact protein folding. Copper induced a small conformational change in H{$\beta$}A1, leading to high-molecular-weight light-scattering aggregates, while zinc is more aggressive towards H{$\beta$}B2 and induces a larger conformational change. Our work provides information on the mechanisms of metal-induced aggregation of {$\beta$}-crystallins.},
  pmid = {35566320},
  keywords = {cataracts,copper,crystallins,human beta crystallins,zinc},
  file = {C\:\\Users\\makro\\Zotero\\storage\\5R82UZFJ\\Ramirez-Bello et al. - 2022 - Zinc and Copper Ions Induce Aggregation of Human β-Crystallins.pdf}
}

@article{Ranjha2018,
  title = {Main Steps in {{DNA}} Double-Strand Break Repair: An Introduction to Homologous Recombination and Related Processes},
  author = {Ranjha, Lepakshi and Howard, Sean M. and Cejka, Petr},
  year = {2018},
  journal = {Chromosoma},
  volume = {127},
  number = {2},
  pages = {187--214},
  publisher = {{Chromosoma}},
  issn = {14320886},
  doi = {10.1007/s00412-017-0658-1},
  abstract = {DNA double-strand breaks arise accidentally upon exposure of DNA to radiation and chemicals or result from faulty DNA metabolic processes. DNA breaks can also be introduced in a programmed manner, such as during the maturation of the immune system, meiosis, or cancer chemo- or radiotherapy. Cells have developed a variety of repair pathways, which are fine-tuned to the specific needs of a cell. Accordingly, vegetative cells employ mechanisms that restore the integrity of broken DNA with the highest efficiency at the lowest cost of mutagenesis. In contrast, meiotic cells or developing lymphocytes exploit DNA breakage to generate diversity. Here, we review the main pathways of eukaryotic DNA double-strand break repair with the focus on homologous recombination and its various subpathways. We highlight the differences between homologous recombination and end-joining mechanisms including non-homologous end-joining and microhomology-mediated end-joining and offer insights into how these pathways are regulated. Finally, we introduce noncanonical functions of the recombination proteins, in particular during DNA replication stress.},
  pmid = {29327130},
  keywords = {DNA double-strand break repair,DNA end resection,DNA strand exchange,End-joining,Homologous recombination,Meiosis,Replication stress},
  file = {C\:\\Users\\makro\\Zotero\\storage\\DFJTIT8Z\\Ranjha, Howard, Cejka - 2018 - Main steps in DNA double-strand break repair an introduction to homologous recombination and related proc.pdf}
}

@article{Rodgers2001,
  title = {Mercuric Ion Inhibition of Eukaryotic Transcription Factor Binding to {{DNA}}},
  author = {Rodgers, Justin S. and Hocker, James R. and Hanas, Rushie J. and Nwosu, Evelyn C. and Hanas, Jay S.},
  year = {2001},
  journal = {Biochemical Pharmacology},
  volume = {61},
  number = {12},
  pages = {1543--1550},
  issn = {00062952},
  doi = {10.1016/S0006-2952(01)00629-3},
  abstract = {Mercury has harmful effects in both rodents and humans. In rodent tissue culture cells exposed to HgCl2, the metal ions were observed to concentrate in cell nuclei and to associate with chromatin. Thus, transcription factors and other proteins associated with chromatin are possible targets of mercuric ion toxicity. In this study, mercuric ions were found to inhibit the DNA binding activity of the Cys2His2 zinc finger proteins transcription factor IIIA (TFIIIA) and Sp1. These factors are prototypes of the largest eukaryotic protein superfamily. Neither the presence of excess zinc ions nor {$\beta$}-mercaptoethanol prevented inhibition by mercuric ions. Mercuric ions also inhibited DNA binding by the non-zinc finger protein AP2. Zinc finger-DNA binding was inhibited when both TFIIIA/5S RNA complex and TFIIIA alone were preincubated with concentrations as low as 15 {$\mu$}M mercuric ion. Inhibition occurred in less than 1 min and was not readily reversible. Mercuric ions also inhibited the digestion of DNA by the restriction enzymes BamHI or EcoRI. Inhibition of transcription factors as well as potentially other DNA binding proteins by micromolar concentrations of mercuric ion suggests additional biochemical mechanisms for mercury toxicity in promoting disease via alterations in gene transcription patterns. \textcopyright{} 2001 Elsevier Science Inc.},
  isbn = {1405271299},
  pmid = {11377384},
  keywords = {Cys2His2 protein motifs,DNA-protein interactions,DNase I footprinting,Mercury toxicity,Restriction enzymes,Xenobiotics,Zinc fingers},
  file = {C\:\\Users\\makro\\Zotero\\storage\\3U26M9MV\\Rodgers et al. - 2001 - Mercuric ion inhibition of eukaryotic transcription factor binding to DNA.pdf}
}

@article{Rosenzweig2002,
  title = {Metallochaperones: {{Bind}} and {{Deliver}}},
  shorttitle = {Metallochaperones},
  author = {Rosenzweig, Amy C.},
  year = {2002},
  month = jun,
  journal = {Chemistry \& Biology},
  volume = {9},
  number = {6},
  pages = {673--677},
  publisher = {{Elsevier}},
  issn = {1074-5521},
  doi = {10.1016/S1074-5521(02)00156-4},
  urldate = {2023-03-16},
  langid = {english},
  pmid = {12079778},
  file = {C\:\\Users\\makro\\Zotero\\storage\\TWMZE3FL\\Rosenzweig - 2002 - Metallochaperones Bind and Deliver.pdf}
}

@article{Rotheneder2023,
  title = {Cryo-{{EM}} Structure of the {{Mre11-Rad50-Nbs1}} Complex Reveals the Molecular Mechanism of Scaffolding Functions},
  author = {Rotheneder, Matthias and Stakyte, Kristina and {van de Logt}, Erik and Bartho, Joseph D. and Lammens, Katja and Fan, Yilan and Alt, Aaron and Kessler, Brigitte and Jung, Christophe and Roos, Wynand P. and Steigenberger, Barbara and Hopfner, Karl Peter},
  year = {2023},
  journal = {Molecular Cell},
  volume = {83},
  number = {2},
  pages = {167-185.e9},
  publisher = {{Elsevier Inc.}},
  issn = {10974164},
  doi = {10.1016/j.molcel.2022.12.003},
  abstract = {The DNA double-strand break repair complex Mre11-Rad50-Nbs1 (MRN) detects and nucleolytically processes DNA ends, activates the ATM kinase, and tethers DNA at break sites. How MRN can act both as nuclease and scaffold protein is not well understood. The cryo-EM structure of MRN from Chaetomium thermophilum reveals a 2:2:1 complex with a single Nbs1 wrapping around the autoinhibited Mre11 nuclease dimer. MRN has two DNA-binding modes, one ATP-dependent mode for loading onto DNA ends and one ATP-independent mode through Mre11's C terminus, suggesting how it may interact with DSBs and intact DNA. MRNs two 60-nm-long coiled-coil domains form a linear rod structure, the apex of which is assembled by the two joined zinc-hook motifs. Apices from two MRN complexes can further dimerize, forming 120-nm spanning MRN-MRN structures. Our results illustrate the architecture of MRN and suggest how it mechanistically integrates catalytic and tethering functions.},
  pmid = {36577401},
  keywords = {coiled-coil domain,cryo-EM,DNA damage signaling,DNA double-strand breaks,DNA protein interactions,DNA repair,X-ray crystallography,zinc-hook},
  file = {C\:\\Users\\makro\\Zotero\\storage\\AK256IK3\\Rotheneder et al. - 2023 - Cryo-EM structure of the Mre11-Rad50-Nbs1 complex reveals the molecular mechanism of scaffolding functions.pdf}
}

@article{Sakurai2002,
  title = {Antidiabetic Vanadium({{IV}}) and Zinc({{II}}) Complexes},
  author = {Sakurai, Hiromu and Kojima, Yoshitane and Yoshikawa, Yutaka and Kawabe, Kenji and Yasui, Hiroyuki},
  year = {2002},
  month = mar,
  journal = {Coordination Chemistry Reviews},
  volume = {226},
  number = {1-2},
  pages = {187--198},
  issn = {00108545},
  doi = {10.1016/S0010-8545(01)00447-7},
  abstract = {Diabetes mellitus (DM), which develops many secondary complications such as atherosclerosis, microangiopathy, renal dysfunction and failure, cardiac abnormality, diabetes retinopathy and ocular disorders, is classified as either insulin-dependent type 1 or non-insulin-dependent type 2, according to the definition of WHO. Although several types of insulin preparations for type I DM and those of synthetic drugs for type 2 DM have been developed and clinically used, they have several problems such as physical and mental pain due to daily insulin injections and defects involving side effects, respectively. In the 21st century, a new class of pharmaceuticals should be introduced. For this reason, metallopharmaceutical compounds containing vanadium and zinc ions are expected to treat both types of DM, by making effective use of unique characteristics of the metals. In this article, the current state of development of insulin-mimetic vanadium and zinc complexes with different coordination modes are reviewed, focusing on the preparations and coordination structures of the complexes and in vitro and in vivo evaluations as well as the possible mechanism. \textcopyright{} 2002 Elsevier Science B.V. All rights reserved.},
  keywords = {Adipocytes,Diabetes mellitus,Insulin-mimetic activity,Vanadium(IV) complexes,Zinc(II) complexesStructure-activity relationship},
  file = {C\:\\Users\\makro\\Zotero\\storage\\FBK5MSSW\\Sakurai et al. - 2002 - Antidiabetic vanadium(IV) and zinc(II) complexes.pdf}
}

@article{Sartori2007,
  title = {Human {{CtIP}} Promotes {{DNA}} End Resection},
  author = {Sartori, Alessandro A. and Lukas, Claudia and Coates, Julia and Mistrik, Martin and Fu, Shuang and Bartek, Jiri and Baer, Richard and Lukas, Jiri and Jackson, Stephen P.},
  year = {2007},
  journal = {Nature},
  volume = {450},
  number = {7169},
  pages = {509--514},
  issn = {14764687},
  doi = {10.1038/nature06337},
  abstract = {In the S and G2 phases of the cell cycle, DNA double-strand breaks (DSBs) are processed into single-stranded DNA, triggering ATR-dependent checkpoint signalling and DSB repair by homologous recombination. Previous work has implicated the MRE11 complex in such DSB-processing events. Here, we show that the human CtIP (RBBP8) protein confers resistance to DSB-inducing agents and is recruited to DSBs exclusively in the S and G2 cell-cycle phases. Moreover, we reveal that CtIP is required for DSB resection, and thereby for recruitment of replication protein A (RPA) and the protein kinase ATR to DSBs, and for the ensuing ATR activation. Furthermore, we establish that CtIP physically and functionally interacts with the MRE11 complex, and that both CtIP and MRE11 are required for efficient homologous recombination. Finally, we reveal that CtIP has sequence homology with Sae2, which is involved in MRE11-dependent DSB processing in yeast. These findings establish evolutionarily conserved roles for CtIP-like proteins in controlling DSB resection, checkpoint signalling and homologous recombination. \textcopyright 2007 Nature Publishing Group.},
  pmid = {17965729},
  file = {C\:\\Users\\makro\\Zotero\\storage\\3SKVGL5M\\Sartori et al. - 2007 - Human CtIP promotes DNA end resection.pdf}
}

@article{Sathyaseelan2023,
  title = {Sequence Patterns and {{HMM}} Profiles to Predict Proteome Wide Zinc Finger Motifs},
  author = {Sathyaseelan, Chakkarai and Patro, L. Ponoop Prasad and Rathinavelan, Thenmalarchelvi},
  year = {2023},
  month = mar,
  journal = {Pattern Recognition},
  volume = {135},
  pages = {109134},
  issn = {00313203},
  doi = {10.1016/j.patcog.2022.109134},
  abstract = {Zinc finger (ZnF) is an important class of nucleic acid and protein recognition domain, wherein, zinc ion is the inorganic co-factor that forms a tetrahedral geometry with the cysteine and/or histidine residues. ZnF domains take up diverse architectures with different ZnF motifs and have a wide range of biological functions. Nonetheless, predicting the ZnF motif(s) from the sequence is quite challenging. To this end, 74 unique ZnF sequence patterns are collected from the literature and classified into 32 different classes. Since the shorter length of ZnF sequence patterns leads to inaccurate predictions, ZnF domain Pfam HMM profiles defined under 6 ZnF Pfam clans (215 HMM profiles) and a few undefined Pfam clans (74 HMM profiles) are used for the prediction. A web server, namely, ZnF-Prot (https://project.iith.ac.in/znprot/) is developed which can predict the presence of 31 ZnF domains in a protein/proteome sequence of any organism. The use of ZnF sequence patterns and Pfam HMM profiles resulted in an accurate prediction of 610 test cases (taken randomly from 249 organisms) considered here. Additionally, the application of ZnF-Prot is demonstrated by considering Arabidopsis thaliana, Homo sapiens, Saccharomyces cerevisiae, Caenorhabditis elegans and Ciona intestinalis proteomes as test cases, wherein, 87\textendash 96\% of the predicted ZnF motifs are cross-validated.},
  keywords = {Pfam HMM profile,Zinc finger classification,Zinc finger motif,Zinc finger prediction,Zinc finger proteome},
  file = {C\:\\Users\\makro\\Zotero\\storage\\428NTF9F\\Sathyaseelan, Patro, Rathinavelan - 2023 - Sequence patterns and HMM profiles to predict proteome wide zinc finger motifs.pdf}
}

@article{Sayers2022,
  title = {Database Resources of the National Center for Biotechnology Information},
  author = {Sayers, Eric W. and Bolton, Evan E. and Brister, J. Rodney and Canese, Kathi and Chan, Jessica and Comeau, Donald C and Connor, Ryan and Funk, Kathryn and Kelly, Chris and Kim, Sunghwan and Madej, Tom and {Marchler-Bauer}, Aron and Lanczycki, Christopher and Lathrop, Stacy and Lu, Zhiyong and {Thibaud-Nissen}, Francoise and Murphy, Terence and Phan, Lon and Skripchenko, Yuri and Tse, Tony and Wang, Jiyao and Williams, Rebecca and Trawick, Barton W and Pruitt, Kim D and Sherry, Stephen T},
  year = {2022},
  month = jan,
  journal = {Nucleic Acids Research},
  volume = {50},
  number = {D1},
  pages = {D20-D26},
  publisher = {{Oxford University Press}},
  issn = {0305-1048},
  doi = {10.1093/nar/gkab1112},
  abstract = {The National Center for Biotechnology Information (NCBI) produces a variety of online information resources for biology, including the GenBank\textregistered{} nucleic acid sequence database and the PubMed\textregistered{} database of citations and abstracts published in life science journals. NCBI provides search and retrieval operations for most of these data from 35 distinct databases. The E-utilities serve as the programming interface for the most of these databases. Resources receiving significant updates in the past year include PubMed, PMC, Bookshelf, RefSeq, SRA, Virus, dbSNP, dbVar, ClinicalTrials.gov, MMDB, iCn3D and PubChem. These resources can be accessed through the NCBI home page at https://www.ncbi.nlm.nih.gov.},
  pmid = {34850941},
  file = {C\:\\Users\\makro\\Zotero\\storage\\RE27XXSS\\Sayers et al. - 2022 - Database resources of the national center for biotechnology information.pdf}
}

@article{Schmalen2014,
  title = {Interaction of {{Circadian Clock Proteins CRY1}} and {{PER2 Is Modulated}} by {{Zinc Binding}} and {{Disulfide Bond Formation}}},
  author = {Schmalen, Ira and Reischl, Silke and Wallach, Thomas and Klemz, Roman and Grudziecki, Astrid and Prabu, J. Rajan and Benda, Christian and Kramer, Achim and Wolf, Eva},
  year = {2014},
  month = may,
  journal = {Cell},
  volume = {157},
  number = {5},
  pages = {1203--1215},
  publisher = {{Elsevier}},
  issn = {00928674},
  doi = {10.1016/j.cell.2014.03.057},
  abstract = {Period (PER) proteins are essential components of the mammalian circadian clock. They form complexes with cryptochromes (CRY), which negatively regulate CLOCK/BMAL1-dependent transactivation of clock and clock-controlled genes. To define the roles of mammalian CRY/PER complexes in the circadian clock, we have determined the crystal structure of a complex comprising the photolyase homology region of mouse CRY1 (mCRY1) and a C-terminal mouse PER2 (mPER2) fragment. mPER2 winds around the helical mCRY1 domain covering the binding sites of FBXL3 and CLOCK/BMAL1, but not the FAD binding pocket. Our structure revealed an unexpected zinc ion in one interface, which stabilizes mCRY1-mPER2 interactions in vivo. We provide evidence that mCRY1/mPER2 complex formation is modulated by an interplay of zinc binding and mCRY1 disulfide bond formation, which may be influenced by the redox state of the cell. Our studies may allow for the development of circadian and metabolic modulators. \textcopyright{} 2014 Elsevier Inc.},
  pmid = {24855952},
  file = {C\:\\Users\\makro\\Zotero\\storage\\MTBVLE2I\\Schmalen et al. - 2014 - Interaction of circadian clock proteins CRY1 and PER2 is modulated by zinc binding and disulfide bond formation.pdf}
}

@article{Schwartz2014,
  title = {Formation of {{Ternary Complexes}} with {{MgATP}}: {{Effects}} on the {{Detection}} of {{Mg}}{\textsuperscript{2+}} in {{Biological Samples}} by {{Bidentate Fluorescent Sensors}}},
  author = {Schwartz, Sarina C. and {Pinto-Pacheco}, Brismar and Pitteloud, Jean-Philippe and Buccella, Daniela},
  year = {2014},
  month = mar,
  journal = {Inorganic Chemistry},
  volume = {53},
  number = {6},
  pages = {3204--3209},
  issn = {0020-1669},
  doi = {10.1021/ic5000606},
  abstract = {Fluorescent indicators based on {$\beta$}-keto-acid bidentate coordination motifs display superior metal selectivity profiles compared to current o-aminophenol-N,N,O-triacetic acid (APTRA) based chelators for the study of biological magnesium. These low denticity chelators, however, may allow for the formation of ternary complexes with Mg2+ and common ligands present in the cellular milieu. In this work, absorption, fluorescence, and NMR spectroscopy were employed to study the interaction of turn-on and ratiometric fluorescent indicators based on 4-oxo-4H-quinolizine-3-carboxylic acid with Mg2+ and ATP, the most abundant chelator of biological magnesium, thus revealing the formation of ternary complexes under conditions relevant to fluorescence imaging. The formation of ternary species elicits comparable or greater optical changes than those attributed to the formation of binary complexes alone. Dissociation of the fluorescent indicators from both ternary and binary species have apparent equilibrium constants in the low millimolar range at pH 7 and 25 C. These results suggest that these bidentate sensors are incapable of distinguishing between free Mg2+ and MgATP based on ratio or intensity-based steady-state fluorescence measurements, thus posing challenges in the interpretation of results from fluorescence imaging of magnesium in nucleotide-rich biological samples. \textcopyright{} 2014 American Chemical Society.},
  pmid = {24593871},
  file = {C\:\\Users\\makro\\Zotero\\storage\\UQIUPZS7\\Schwartz et al. - 2014 - Formation of Ternary Complexes with MgATP Effects on the Detection of Mg 2 in Biological Samples by Bidentate F.pdf}
}

@article{Scully2019,
  title = {{{DNA}} Double-Strand Break Repair-Pathway Choice in Somatic Mammalian Cells},
  author = {Scully, Ralph and Panday, Arvind and Elango, Rajula and Willis, Nicholas A.},
  year = {2019},
  month = nov,
  journal = {Nature Reviews Molecular Cell Biology},
  volume = {20},
  number = {11},
  pages = {698--714},
  publisher = {{Springer US}},
  issn = {1471-0072},
  doi = {10.1038/s41580-019-0152-0},
  abstract = {The major pathways of DNA double-strand break (DSB) repair are crucial for maintaining genomic stability. However, if deployed in an inappropriate cellular context, these same repair functions can mediate chromosome rearrangements that underlie various human diseases, ranging from developmental disorders to cancer. The two major mechanisms of DSB repair in mammalian cells are non-homologous end joining (NHEJ) and homologous recombination. In this Review, we consider DSB repair-pathway choice in somatic mammalian cells as a series of `decision trees', and explore how defective pathway choice can lead to genomic instability. Stalled, collapsed or broken DNA replication forks present a distinctive challenge to the DSB repair system. Emerging evidence suggests that the `rules' governing repair-pathway choice at stalled replication forks differ from those at replication-independent DSBs.},
  pmid = {31263220},
  file = {C\:\\Users\\makro\\Zotero\\storage\\WRK75CT6\\Scully et al. - 2019 - DNA double-strand break repair-pathway choice in somatic mammalian cells.pdf}
}

@article{Seifert2016,
  title = {Structural Mechanism of {{ATP}} -dependent {{DNA}} Binding and {{DNA}} End Bridging by Eukaryotic {{Rad50}}},
  author = {Seifert, Florian Ulrich and Lammens, Katja and Stoehr, Gabriele and Kessler, Brigitte and Hopfner, Karl-Peter},
  year = {2016},
  journal = {The EMBO Journal},
  volume = {35},
  number = {7},
  pages = {759--772},
  issn = {0261-4189},
  doi = {10.15252/embj.201592934},
  abstract = {\textcopyright{} 2016 The Authors. The Mre11-Rad50-Nbs1 (MRN) complex is a central factor in the repair of DNA double-strand breaks (DSBs). The ATP-dependent mechanisms of how MRN detects and endonucleolytically processes DNA ends for the repair by microhomology-mediated end-joining or further resection in homologous recombination are still unclear. Here, we report the crystal structures of the ATP{$\gamma$}S-bound dimer of the Rad50NBD (nucleotide-binding domain) from the thermophilic eukaryote Chaetomium thermophilum (Ct) in complex with either DNA or CtMre11RBD (Rad50-binding domain) along with small-angle X-ray scattering and cross-linking studies. The structure and DNA binding motifs were validated by DNA binding experiments in vitro and mutational analyses in Saccharomyces cerevisiae in vivo. Our analyses provide a structural framework for the architecture of the eukaryotic Mre11-Rad50 complex. They show that a Rad50 dimer binds approximately 18 base pairs of DNA along the dimer interface in an ATP-dependent fashion or bridges two DNA ends with a preference for 3{${'}$} overhangs. Finally, our results may provide a general framework for the interaction of ABC ATPase domains of the Rad50/SMC/RecN protein family with DNA.},
  pmid = {26896444},
  keywords = {dna repair,end joining,homologous recombination,microhomology-mediated,protein dna complex,recombination,repair,structural,subject categories dna replication,x-ray crystallography},
  file = {C\:\\Users\\makro\\Zotero\\storage\\3J3IUMF6\\Seifert et al. - 2016 - Structural mechanism of ATP ‐dependent DNA binding and DNA end bridging by eukaryotic Rad50.pdf}
}

@article{Soh2021,
  title = {A Rod Conformation of the {{Pyrococcus}} Furiosus {{Rad50}} Coiled Coil},
  author = {Soh, Young-Min and Basquin, Jerome and Gruber, Stephan},
  year = {2021},
  month = feb,
  journal = {Proteins: Structure, Function, and Bioinformatics},
  volume = {89},
  number = {2},
  pages = {251--255},
  issn = {0887-3585},
  doi = {10.1002/prot.26005},
  abstract = {The Rad50-Mre11 nuclease complex plays a vital role in DNA repair in all domains of life. It recognizes and processes DNA double-strand breaks. Rad50 proteins fold into an extended structure with a 20 to 60 nm long coiled coil connecting a globular ABC ATPase domain with a zinc hook dimerization domain. A published structure of an archaeal Rad50 zinc hook shows coiled coils pointing away from each other. Here we present the crystal structure of an alternate conformation displaying co-aligned coiled coils. Archaeal Rad50 may thus switch between rod-shaped and ring-like conformations as recently proposed for a bacterial homolog.},
  pmid = {32875643},
  keywords = {coiled coil,DNA repair,Mre11,Rad50,rod,SMC,SMC-like,zinc hook},
  file = {C\:\\Users\\makro\\Zotero\\storage\\97U9LDZ4\\Soh, Basquin, Gruber - 2021 - A rod conformation of the Pyrococcus furiosus Rad50 coiled coil.pdf}
}

@article{Song2014,
  title = {Metals in {{Protein}}\textendash{{Protein Interfaces}}},
  author = {Song, Woon Ju and Sontz, Pamela A. and Ambroggio, Xavier I. and Tezcan, F. Akif},
  year = {2014},
  month = may,
  journal = {Annual Review of Biophysics},
  volume = {43},
  number = {1},
  pages = {409--431},
  issn = {1936-122X},
  doi = {10.1146/annurev-biophys-051013-023038},
  abstract = {From the catalytic reactions that sustain the global oxygen, nitrogen, and carbon cycles to the stabilization of DNA processing proteins, transition metal ions and metallocofactors play key roles in biology. Although the exquisite interplay between metal ions and protein scaffolds has been studied extensively, the fact that the biological roles of the metals often stem from their placement in the interfaces between proteins and protein subunits is not always recognized. Interfacial metal ions stabilize permanent or transient protein-protein interactions, enable protein complexes involved in cellular signaling to adopt distinct conformations in response to environmental stimuli, and catalyze challenging chemical reactions that are uniquely performed by multisubunit protein complexes. This review provides a structural survey of transition metal ions and metallocofactors found in protein-protein interfaces, along with a series of selected examples that illustrate their diverse biological utility and significance. Copyright \textcopyright{} 2014 by Annual Reviews. All rights reserved.},
  pmid = {24773016},
  keywords = {Interfacial metal clusters,Metal-mediated oligomerization,Metal/metallocofactors,Protein self-assembly,Protein-protein interactions},
  file = {C\:\\Users\\makro\\Zotero\\storage\\YSXKN6M6\\Song et al. - 2014 - Metals in Protein–Protein Interfaces.pdf}
}

@article{Sousa2009,
  title = {The {{Zinc}} Proteome: {{A}} Tale of Stability and Functionality},
  author = {Sousa, S{\'e}rgio Filipe and Lopes, Ana Branca and Fernandes, Pedro Alexandrino and Ramos, Maria Jo{\~a}o},
  year = {2009},
  journal = {Dalton Transactions},
  number = {38},
  pages = {7946--7956},
  issn = {14779226},
  doi = {10.1039/b904404c},
  abstract = {Zinc proteins constitute a very important portion of the large number of Metalloproteins currently known. However, contrary to what happens with biological systems containing Fe(II), Fe(III), Cu(II), Mn(II), Mn(III), Ni(II), Co(III) or other commonly found biologically relevant metal cofactors, the particular chemical properties of the Zn(II) ion mean that only a very small number of experimental techniques can be directly applied in the study of the metal coordination spheres present in Zinc proteins. The information obtainable from publicly available structural databases such as the Protein Data Bank can therefore be of particularly high significance to a better understanding of these proteins. In this study, we draw a detailed statistical portrait of the Zinc proteome by analysing the metal coordination spheres of the large number of X-ray crystallographic structures of Zinc proteins currently available on the Protein Data Bank. This data is further complemented with quantum mechanical calculations on the most common Zinc coordination spheres to evaluate the intrinsic thermodynamic stability of the several combinations of ligands on a generic and non-specific enzymatic environment, and with molecular electrostatic potential maps. These results provide useful insights into this difficult to characterize but very important Zn-containing subset of the proteome. \textcopyright{} 2009 The Royal Society of Chemistry.},
  pmid = {19771357},
  file = {C\:\\Users\\makro\\Zotero\\storage\\JJG8NN5E\\Sousa et al. - 2009 - The Zinc proteome A tale of stability and functionality.pdf}
}

@article{Stehle2016,
  title = {Parenteral Trace Element Provision: {{Recent}} Clinical Research and Practical Conclusions},
  author = {Stehle, P. and {Stoffel-Wagner}, B. and Kuhn, K. S.},
  year = {2016},
  journal = {European Journal of Clinical Nutrition},
  volume = {70},
  number = {8},
  pages = {886--893},
  publisher = {{Nature Publishing Group}},
  issn = {14765640},
  doi = {10.1038/ejcn.2016.53},
  abstract = {The aim of this systematic review (PubMed, www.ncbi.nlm.nih.gov/pubmed and Cochrane, www.cochrane.org; last entry 31 December 2014) was to present data from recent clinical studies investigating parenteral trace element provision in adult patients and to draw conclusions for clinical practice. Important physiological functions in human metabolism are known for nine trace elements: selenium, zinc, copper, manganese, chromium, iron, molybdenum, iodine and fluoride. Lack of, or an insufficient supply of, these trace elements in nutrition therapy over a prolonged period is associated with trace element deprivation, which may lead to a deterioration of existing clinical symptoms and/or the development of characteristic malnutrition syndromes. Therefore, all parenteral nutrition prescriptions should include a daily dose of trace elements. To avoid trace element deprivation or imbalances, physiological doses are recommended.},
  pmid = {27049031},
  file = {C\:\\Users\\makro\\Zotero\\storage\\9PWTLC6H\\Stehle, Stoffel-Wagner, Kuhn - 2016 - Parenteral trace element provision Recent clinical research and practical conclusions.pdf}
}

@book{Stephanos2014,
  title = {Chemistry of {{Metalloproteins}}: {{Problems}} and {{Solutions}} in {{Bioinorganic Chemistry}}},
  author = {Joseph J. Stephanos, Anthony W. Addison},
  year = {2014},
  volume = {4},
  isbn = {978-1-118-47044-2},
  file = {C\:\\Users\\makro\\Zotero\\storage\\TBVH3MJC\\Joseph J. Stephanos - 2014 - Chemistry of Metalloproteins Problems and Solutions in Bioinorganic Chemistry.pdf}
}

@article{Suda1992,
  title = {Degradation of Methyl and Ethyl Mercury into Inorganic Mercury by Other Reactive Oxygen Species besides Hydroxyl Radical},
  author = {Suda, Ikuo and Takahashi, Hitoshi},
  year = {1992},
  month = jan,
  journal = {Archives of Toxicology},
  volume = {66},
  number = {1},
  pages = {34--39},
  issn = {0340-5761},
  doi = {10.1007/BF02307267},
  keywords = {formation - reactive oxygen,mercury - biotrans-,methyl mercury - ethyl},
  file = {C\:\\Users\\makro\\Zotero\\storage\\HBEVGEPH\\Suda, Takahashi - 1992 - Degradation of methyl and ethyl mercury into inorganic mercury by other reactive oxygen species besides hydroxy.pdf}
}

@article{Sundell2014,
  title = {Interaction {{Analysis}} through {{Proteomic Phage Display}}},
  author = {Sundell, Gustav N. and Ivarsson, Ylva},
  year = {2014},
  journal = {BioMed Research International},
  volume = {2014},
  pages = {1--9},
  issn = {2314-6133},
  doi = {10.1155/2014/176172},
  abstract = {Phage display is a powerful technique for profiling specificities of peptide binding domains. The method is suited for the identification of high-affinity ligands with inhibitor potential when using highly diverse combinatorial peptide phage libraries. Such experiments further provide consensus motifs for genome-wide scanning of ligands of potential biological relevance. A complementary but considerably less explored approach is to display expression products of genomic DNA, cDNA, open reading frames (ORFs), or oligonucleotide libraries designed to encode defined regions of a target proteome on phage particles. One of the main applications of such proteomic libraries has been the elucidation of antibody epitopes. This review is focused on the use of proteomic phage display to uncover protein-protein interactions of potential relevance for cellular function. The method is particularly suited for the discovery of interactions between peptide binding domains and their targets. We discuss the largely unexplored potential of this method in the discovery of domain-motif interactions of potential biological relevance.},
  pmid = {25295249},
  file = {C\:\\Users\\makro\\Zotero\\storage\\54EMLKFF\\Sundell, Ivarsson - 2014 - Interaction Analysis through Proteomic Phage Display.pdf}
}

@article{Tainer1992,
  title = {Protein Metal-Binding Sites},
  author = {Tainer, John A. and Roberts, Victoria A. and Getzoff, Elizabeth D.},
  year = {1992},
  month = aug,
  journal = {Current Opinion in Biotechnology},
  volume = {3},
  number = {4},
  pages = {378--387},
  issn = {09581669},
  doi = {10.1016/0958-1669(92)90166-G},
  abstract = {Metal ions have a role in a variety of important functions in proteins including protein folding, assembly, stability, conformational change, and catalysis. The presence or absence of a given metal ion is crucial to the conformation or activity of over one third of all proteins. Recent developments have been made in the understanding and design of metal-binding sites in proteins, an important and rapidly advancing area of protein engineering. \textcopyright{} 1992.},
  pmid = {1368439},
  file = {C\:\\Users\\makro\\Zotero\\storage\\MVCK5KT8\\Tainer, Roberts, Getzoff - 1992 - Protein metal-binding sites.pdf}
}

@article{Takeda2003,
  title = {Manganese Action in Brain Function},
  author = {Takeda, Atsushi},
  year = {2003},
  journal = {Brain Research Reviews},
  volume = {41},
  number = {1},
  pages = {79--87},
  issn = {01650173},
  doi = {10.1016/S0165-0173(02)00234-5},
  abstract = {Manganese, an essential trace metal, is supplied to the brain via both the blood-brain and the blood-cerebrospinal fluid barriers. There are some mechanisms in this process and transferrin may be involved in manganese transport into the brain. A large portion of manganese is bound to manganese metalloproteins, especially glutamine synthetase in astrocytes. A portion of manganese probably exists in the synaptic vesicles in glutamatergic neurons and the manganese is dynamically coupled to the electrophysiological activity of the neurons. Manganese released into the synaptic cleft may influence synaptic neurotransmission. Dietary manganese deficiency, which may enhance susceptibility to epileptic functions, appears to affect manganese homeostasis in the brain, probably followed by alteration of neural activity. On the other hand, manganese also acts as a toxicant to the brain because this metal has prooxidant activity. Abnormal concentrations of manganese in the brain, especially in the basal ganglia, are associated with neurological disorders similar to Parkinson's disease. Understanding the movement and action of manganese in synapses may be important to clarify the function and toxicity of manganese in the brain. \textcopyright{} 2002 Elsevier Science B.V. All rights reserved.},
  pmid = {12505649},
  keywords = {Brain function,Manganese,Neurological disease,Synapse,Transition metal},
  file = {C\:\\Users\\makro\\Zotero\\storage\\ABMKPCV5\\Takeda - 2003 - Manganese action in brain function.pdf}
}

@article{Tatebe2020,
  title = {Rad50 Zinc Hook Functions as a Constitutive Dimerization Module Interchangeable with {{SMC}} Hinge},
  author = {Tatebe, Hisashi and Lim, Chew Theng and Konno, Hiroki and Shiozaki, Kazuhiro and Shinohara, Akira and Uchihashi, Takayuki and Furukohri, Asako},
  year = {2020},
  month = jan,
  journal = {Nature Communications},
  volume = {11},
  number = {1},
  pages = {370},
  publisher = {{Springer US}},
  issn = {2041-1723},
  doi = {10.1038/s41467-019-14025-0},
  abstract = {The human Mre11/Rad50 complex is one of the key factors in genome maintenance pathways. Previous nanoscale imaging by atomic force microscopy (AFM) showed that the ring-like structure of the human Mre11/Rad50 complex transiently opens at the zinc hook of Rad50. However, imaging of the human Mre11/Rad50 complex by high-speed AFM shows that the Rad50 coiled-coil arms are consistently bridged by the dimerized hooks while the Mre11/Rad50 ring opens by disconnecting the head domains; resembling other SMC proteins such as cohesin or condensin. These architectural features are conserved in the yeast and bacterial Mre11/Rad50 complexes. Yeast strains harboring the chimeric Mre11/Rad50 complex containing the SMC hinge of bacterial condensin MukB instead of the RAD50 hook properly functions in DNA repair. We propose that the basic role of the Rad50 hook is similar to that of the SMC hinge, which serves as rather stable dimerization interface.},
  pmid = {31953386},
  file = {C\:\\Users\\makro\\Zotero\\storage\\Q5G5KXLV\\Tatebe et al. - 2020 - Rad50 zinc hook functions as a constitutive dimerization module interchangeable with SMC hinge.pdf}
}

@article{Thangaraj2019,
  title = {Thermokinetic {{Analysis}} of {{Protein Subunit Exchange}} by {{Variable-Temperature Native Mass Spectrometry}}},
  author = {Thangaraj, Senthil K. and James, Salman and Rouvinen, Juha and J{\"a}nis, Janne},
  year = {2019},
  month = dec,
  journal = {Biochemistry},
  volume = {58},
  number = {50},
  pages = {5025--5029},
  issn = {0006-2960},
  doi = {10.1021/acs.biochem.9b00911},
  abstract = {Many protein complexes are assembled from a varying number of subunits, which are continuously exchanging with diverse time scales. This structural dynamics is considered to be important for many regulatory and sensory adaptation processes that occur in vivo. We have developed an accurate method for monitoring protein subunit exchange by using native electrospray ionization mass spectrometry (ESI-MS), exemplified here for an extremely stable Rad50 zinc hook (Hk) dimer assembly, Zn(Hk)2. The method has two steps: appropriate protein/peptide mutation and native ESI-MS analysis using a variable-temperature sample inlet. In this work, two Hk mutants were produced, mixed with wild-type Hk, and measured at three different temperatures. A thermokinetic analysis of heterodimer formation allowed us to determine the enthalpy, entropy, and Gibbs free energy of activation for subunit exchange, showing that the reaction is slow and associated with a high enthalpic barrier, consistent with the exceptionally high stability of the Zn(Hk)2 assembly.},
  pmid = {31790206},
  file = {C\:\\Users\\makro\\Zotero\\storage\\38HV4G97\\Thangaraj et al. - 2019 - Thermokinetic Analysis of Protein Subunit Exchange by Variable-Temperature Native Mass Spectrometry.pdf}
}

@article{Tran2021,
  title = {{{InterMetalDB}}: {{A Database}} and {{Browser}} of {{Intermolecular Metal Binding Sites}} in {{Macromolecules}} with {{Structural Information}}},
  author = {Tran, J{\'o}zef Ba and Kr{\k{e}}{\.z}el, Artur},
  year = {2021},
  month = apr,
  journal = {Journal of Proteome Research},
  volume = {20},
  number = {4},
  pages = {1889--1901},
  issn = {1535-3893},
  doi = {10.1021/acs.jproteome.0c00906},
  abstract = {InterMetalDB is a free-of-charge database and browser of intermolecular metal binding sites that are present on the interfaces of macromolecules forming larger assemblies based on structural information deposited in Protein Data Bank (PDB). It can be found and freely used at https://intermetaldb.biotech.uni.wroc.pl/. InterMetalDB collects the interfacial binding sites with involvement of metal ions and clusters them on the basis of 50\% sequence similarity and the nearest metal environment (5 \AA{} radius). The data are available through the web interface where they can be queried, viewed, and downloaded. Complexity of the query depends on the user, because the questions in the query are connected with each other by a logical AND. InterMetalDB offers several useful options for filtering records including searching for structures by particular parameters such as structure resolution, structure description, and date of deposition. Records can be filtered by coordinated metal ion, number of bound amino acid residues, coordination sphere, and other features. InterMetalDB is regularly updated and will continue to be regularly updated with new content in the future. InterMetalDB is a useful tool for all researchers interested in metalloproteins, protein engineering, and metal-driven oligomerization.},
  pmid = {33502860},
  keywords = {interfacial metal,interprotein site,metalloprotein,protein assembly,protein-protein interaction},
  file = {C\:\\Users\\makro\\Zotero\\storage\\MNTU57CH\\acs.jproteome.0c00906.pdf}
}

@article{Tran2022,
  title = {Relations between {{Structure}} and {{Zn}}({{II}}) {{Binding Affinity Shed Light}} on the {{Mechanisms}} of {{Rad50 Hook Domain Functioning}} and {{Its Phosphorylation}}},
  author = {Tran, J{\'o}zef Ba and Padjasek, Micha{\l} and Kr{\k{e}}{\.z}el, Artur},
  year = {2022},
  month = sep,
  journal = {International Journal of Molecular Sciences},
  volume = {23},
  number = {19},
  pages = {11140},
  issn = {1422-0067},
  doi = {10.3390/ijms231911140},
  abstract = {The metal binding at protein\textendash protein interfaces is still uncharted territory in intermolecular interactions. To date, only a few protein complexes binding Zn(II) in an intermolecular manner have been deeply investigated. The most notable example of such interfaces is located in the highly conserved Rad50 protein, part of the Mre11-Rad50-Nbs1 (MRN) complex, where Zn(II) is required for homodimerization (Zn(Rad50)2). The high stability of Zn(Rad50)2 is conserved not only for the protein derived from the thermophilic archaeon Pyrococcus furiosus (logK12 = 20.95 for 130-amino-acid-long fragment), which was the first one studied, but also for the human paralog studied here (logK12 = 19.52 for a 183-amino-acid-long fragment). As we reported previously, the extremely high stability results from the metal-coupled folding process where particular Rad50 protein fragments play a critical role. The sequence\textendash structure\textendash stability analysis based on human Rad50 presented here separates the individual structural components that increase the stability of the complex, pointing to amino acid residues far away from the Zn(II) binding site as being largely responsible for the complex stabilization. The influence of the individual components is very well reflected by the previously published crystal structure of the human Rad50 zinc hook (PDB: 5GOX). In addition, we hereby report the effect of phosphorylation of the zinc hook domain, which exerts a destabilizing effect on the domain. This study identifies factors governing the stability of metal-mediated protein\textendash protein interactions and illuminates their molecular basis.},
  keywords = {DNA damage,Mre11-Rad50-Nbs1 (MRN),Rad50,zinc,zinc hook},
  file = {C\:\\Users\\makro\\Zotero\\storage\\WPQFLYY7\\ijms-23-11140.pdf}
}

@article{Trujillo1998,
  title = {Nuclease {{Activities}} in a {{Complex}} of {{Human Recombination}} and {{DNA Repair Factors Rad50}}, {{Mre11}}, and P95},
  author = {Trujillo, Kelly M. and Yuan, Shyng-Shiou F. and Lee, Eva Y.-H. P. and Sung, Patrick},
  year = {1998},
  month = aug,
  journal = {Journal of Biological Chemistry},
  volume = {273},
  number = {34},
  pages = {21447--21450},
  issn = {00219258},
  doi = {10.1074/jbc.273.34.21447},
  abstract = {Genetic studies in yeast have indicated a role of the RAD50 and MRE11 genes in homologous recombination, telomere length maintenance, and DNA repair processes. Here, we purify from nuclear extract of Raji cells a complex consisting of human Rad50, Mre11, and another protein factor with a size of about 95 kDa (p95), which is likely to be Nibrin, the protein encoded by the gene mutated in Nijmegen breakage syndrome. We show that the Rad50- Mre11-p95 complex possesses manganese-dependent single-stranded DNA endonuclease and 3' to 5' exonuclease activities. These nuclease activities are likely to be important for recombination, repair, and genomic stability.},
  pmid = {9705271},
  file = {C\:\\Users\\makro\\Zotero\\storage\\6G8ZUN5A\\Trujillo et al. - 1998 - Nuclease Activities in a Complex of Human Recombination and DNA Repair Factors Rad50, Mre11, and p95.pdf}
}

@article{Trujillo2001,
  title = {{{DNA Structure-specific Nuclease Activities}} in the {{{\emph{Saccharomyces}}}}{\emph{ Cerevisiae }} {{Rad50}}{$\cdot$}{{Mre11 Complex}}},
  author = {Trujillo, Kelly M. and Sung, Patrick},
  year = {2001},
  journal = {Journal of Biological Chemistry},
  volume = {276},
  number = {38},
  pages = {35458--35464},
  publisher = {{\^A\textcopyright{} 2001 ASBMB. Currently published by Elsevier Inc; originally published by American Society for Biochemistry and Molecular Biology.}},
  issn = {00219258},
  doi = {10.1074/jbc.M105482200},
  abstract = {Saccharomyces cerevisiae RAD50 and MRE11 genes are required for the nucleolytic processing of DNA double-strand breaks. We have overexpressed Rad50 and Mre11 in yeast cells and purified them to near homogeneity. Consistent with the genetic data, we show that the purified Rad50 and Mre11 proteins form a stable complex. In the Rad50-Mre11 complex, the protein components exist in equimolar amounts. Mre11 has a 3{${'}$} to 5{${'}$} exonuclease activity that results in the release of mononucleotides. The addition of Rad50 does not significantly alter the exonucleolytic function of Mre11. Using homopolymeric oligonucleotide-based substrates, we show that the exonuclease activity of Mre11 and Rad50-Mre11 is enhanced for substrates with duplex DNA ends. We have examined the endonucleolytic function of Mre11 on defined, radio-labeled hairpin structures that also contain 3{${'}$} and 5{${'}$} single-stranded DNA overhangs. Mre11 is capable of cleaving hairpins and the 3{${'}$} single-stranded DNA tail. These endonuclease activities of Mre11 are enhanced markedly by Rad50 but only in the presence of ATP. Based on these results, we speculate that the Mre11 nuclease complex may mediate the nucleolytic digestion of the 5{${'}$} strand at secondary structures formed upon DNA strand separation.},
  pmid = {11454871},
  file = {C\:\\Users\\makro\\Zotero\\storage\\XLT7FQ7X\\Trujillo, Sung - 2001 - DNA Structure-specific Nuclease Activities in the Saccharomyces cerevisiae Rad50-Mre11 Complex.pdf}
}

@article{Tubbs2017,
  title = {Endogenous {{DNA Damage}} as a {{Source}} of {{Genomic Instability}} in {{Cancer}}},
  author = {Tubbs, Anthony and Nussenzweig, Andr{\'e}},
  year = {2017},
  journal = {Cell},
  volume = {168},
  number = {4},
  pages = {644--656},
  issn = {10974172},
  doi = {10.1016/j.cell.2017.01.002},
  abstract = {Genome instability, defined as higher than normal rates of mutation, is a double-edged sword. As a source of genetic diversity and natural selection, mutations are beneficial for evolution. On the other hand, genomic instability can have catastrophic consequences for age-related diseases such as cancer. Mutations arise either from inactivation of DNA repair pathways or in a repair-competent background due to genotoxic stress from celluar processes such as transcription and replication that overwhelm high-fidelity DNA repair. Here, we review recent studies that shed light on endogenous sources of mutation and epigenomic features that promote genomic instability during cancer evolution.},
  pmid = {28187286},
  keywords = {cancer,DNA damage,DNA repair,DNA replication,Genome instability,mutagenesis,transcription},
  file = {C\:\\Users\\makro\\Zotero\\storage\\ZH5888NQ\\Tubbs, Nussenzweig - 2017 - Endogenous DNA Damage as a Source of Genomic Instability in Cancer.pdf}
}

@article{uczkowski2013,
  title = {Probing the {{Coordination Environment}} of the {{Human Copper Chaperone HAH1}}: {{Characterization}} of {{Hg}}{{{\textsuperscript{II}}}} -{{Bridged Homodimeric Species}} in {{Solution}}},
  author = {{\L}uczkowski, Marek and Zeider, Brian A. and Hinz, Alia V. H. and Stachura, Monika and Chakraborty, Saumen and Hemmingsen, Lars and Huffman, David L. and Pecoraro, Vincent L.},
  year = {2013},
  month = jul,
  journal = {Chemistry - A European Journal},
  volume = {19},
  number = {27},
  pages = {9042--9049},
  issn = {09476539},
  doi = {10.1002/chem.201204184},
  abstract = {Although metal ion homeostasis in cells is often mediated through metallochaperones, there are opportunities for toxic metals to be sequestered through the existing transport apparatus. Proper trafficking of CuI in human cells is partially achieved through complexation by HAH1, the human metallochaperone responsible for copper delivery to the Wilson and Menkes ATPase located in the trans-Golgi apparatus. In addition to binding copper, HAH1 strongly complexes HgII, with the X-ray structure of this complex previously described. It is important to clarify the solution behavior of these systems and, therefore, the binding of HgII to HAH1 was probed over the pH range 7.5 to 9.4 using 199Hg NMR, 199mHg PAC and UV-visible spectroscopies. The metal-dependent protein association over this pH range was examined using analytical gel-filtration. It can be concluded that at pH 7.5, HgII is bound to a monomeric HAH1 as a two coordinate, linear complex (HgS2), like the HgII-Atx1 X-ray structure (PDB ID: 1CC8). At pH 9.4, HgII promotes HAH1 association, leading to formation of HgS3 and HgS4 complexes, which are in exchange on the {$\mu$}s-ns time scale. Thus, structures that may represent central intermediates in the process of metal ion transfer, as well as their exchange kinetics have been characterized. HAH1, the HgII carrier? Trafficking of CuI in human cells is achieved through complexation by the metallochaperone, HAH1. In addition, HAH1 strongly binds HgII; the solution behavior of HgII-HAH1 complexation (see figure) has remained obscure, but is elucidated in this work. Structures are reported that may represent central intermediates in the processing of HgII ions. Copyright \textcopyright{} 2013 WILEY-VCH Verlag GmbH \& Co. KGaA, Weinheim.},
  pmid = {23677531},
  keywords = {199mHg PAC,copper,mercury,metallochaperones,NMR spectroscopy},
  file = {C\:\\Users\\makro\\Zotero\\storage\\H9HK7QWE\\Łuczkowski et al. - 2013 - Probing the Coordination Environment of the Human Copper Chaperone HAH1 Characterization of Hg II -Bridged Ho.pdf}
}

@article{Ueki2003,
  title = {Vanadium-Binding Proteins (Vanabins) from a Vanadium-Rich Ascidian {{Ascidia}} Sydneiensis Samea},
  author = {Ueki, Tatsuya and Adachi, Takahiro and Kawano, Sonoko and Aoshima, Masato and Yamaguchi, Nobuo and Kanamori, Kan and Michibata, Hitoshi},
  year = {2003},
  month = apr,
  journal = {Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression},
  volume = {1626},
  number = {1-3},
  pages = {43--50},
  issn = {01674781},
  doi = {10.1016/S0167-4781(03)00036-8},
  abstract = {Since the beginning of the last century, it has been known that ascidians accumulate high levels of a transition metal, vanadium, in their blood cells, although the mechanism for this curious biological function remains unknown. Recently, we identified three vanadium-binding proteins (vanabins), previously denoted as vanadium-associated proteins (VAPs) [Zool. Sci. 14 (1997) 37], from the cytoplasm fraction of vanadium-containing blood cells (vanadocytes) of the vanadium-rich ascidian Ascidia sydneiensis samea. Here, we describe the cloning, expression, and analysis of the metal-binding ability of vanabins. Recombinant proteins of two independent but related vanabins, vanabin1 and vanabin2, bound to 10 and 20 vanadium(IV) ions with dissociation constants of 2.1\texttimes 10-5 and 2.3\texttimes 10-5 M, respectively. The binding of vanadium(IV) to these vanabins was inhibited by the addition of copper(II) ions, but not by magnesium(II) or molybdate(VI) ions. Vanabins are the first proteins reported to show specific binding to vanadium ions; this should provide a clue to resolving the problem regarding the selective accumulation of vanadium in ascidians. \textcopyright{} 2003 Elsevier Science B.V. All rights reserved.},
  pmid = {12697328},
  keywords = {Ascidian,Metal accumulation,Vanadium},
  file = {C\:\\Users\\makro\\Zotero\\storage\\C5RP7GG5\\Ueki et al. - 2003 - Vanadium-binding proteins (vanabins) from a vanadium-rich ascidian Ascidia sydneiensis samea.pdf}
}

@article{Usui1998,
  title = {Complex {{Formation}} and {{Functional Versatility}} of {{Mre11}} of {{Budding Yeast}} in {{Recombination}}},
  author = {Usui, Takehiko and Ohta, Tsutomu and Oshiumi, Hiroyuki and Tomizawa, Jun-ichi and Ogawa, Hideyuki and Ogawa, Tomoko},
  year = {1998},
  month = nov,
  journal = {Cell},
  volume = {95},
  number = {5},
  pages = {705--716},
  issn = {00928674},
  doi = {10.1016/S0092-8674(00)81640-2},
  abstract = {Meiotic recombination of S. cerevisiae contains two temporally coupled processes, formation and processing of double-strand breaks (DSBs). Mre11 forms a complex with Rad50 and Xrs2, acting as the binding core, and participates in DSB processing. Although these proteins are also involved in DSB formation, Mre11 is not necessarily holding them. The C-terminal region of Mre11 is required only for DSB formation and binds to some meiotic proteins. The N-terminal half specifies nuclease activities that are collectively required for DSB processing. Mre11 has a DNA-binding site for DSB formation and another site for DSB processing. It has two regions to bind to Rad50. Mre11 repairs methyl methanesulfonate-induced DSBs by reactions that require the nuclease activities and those that do not.},
  pmid = {9845372},
  file = {C\:\\Users\\makro\\Zotero\\storage\\2EUJIWSK\\Usui et al. - 1998 - Complex Formation and Functional Versatility of Mre11 of Budding Yeast in Recombination.pdf}
}

@article{Vallee1990,
  title = {Zinc Coordination, Function, and Structure of Zinc Enzymes and Other Proteins},
  author = {Vallee, Bert L. and Auld, David S.},
  year = {1990},
  month = jun,
  journal = {Biochemistry},
  volume = {29},
  number = {24},
  pages = {5647--5659},
  issn = {0006-2960},
  doi = {10.1021/bi00476a001},
  pmid = {2200508},
  file = {C\:\\Users\\makro\\Zotero\\storage\\6FF8SHTP\\Vallee, Auld - 1990 - Zinc coordination, function, and structure of zinc enzymes and other proteins.pdf}
}

@article{Varnai2004,
  title = {{{DNA}} and Its Counterions: A Molecular Dynamics Study},
  author = {Varnai, P. and Zakrzewska, Krystyna},
  year = {2004},
  month = aug,
  journal = {Nucleic Acids Research},
  volume = {32},
  number = {14},
  pages = {4269--4280},
  issn = {1362-4962},
  doi = {10.1093/nar/gkh765},
  abstract = {The behaviour of mobile counterions, Na+ and K+, was analysed around a B-DNA double helix with the sequence CCATGCGCTGAC in aqueous solution during two 50 ns long molecular dynamics trajectories. The movement of both monovalent ions remains diffusive in the presence of DNA. Ions sample the complete space available during the simulation time, although individual ions sample only about one-third of the simulation box. Ions preferentially sample electronegative sites around DNA, but direct binding to DNA bases remains a rather rare event, with highest site occupancy values of {$<$}13\%. The location of direct binding sites depends greatly on the nature of the counterion. While Na+ binding in both grooves is strongly sequence-dependent with the preferred binding site in the minor groove, K+ mainly visits the major groove and binds close to the centre of the oligomer. The electrostatic potential of an average DNA structure therefore cannot account for the ability of a site to bind a given cation; other factors must also play a role. An extensive analysis of the influence of counterions on DNA conformation showed no evidence of minor groove narrowing upon ion binding. A significant difference between the conformations of the double helix in the different simulations can be attributed to extensive {$\alpha$}/{$\gamma$} transitions in the phosphate backbone during the simulation with Na+. These transitions, with lifetimes over tens of nano-seconds, however, appear to be correlated with ion binding to phosphates. The ion-specific conformational properties of DNA, hitherto largely overlooked, may play an important role in DNA recognition and binding. \textcopyright{} Oxford University Press 2004; all rights reserved.},
  pmid = {15304564},
  file = {C\:\\Users\\makro\\Zotero\\storage\\ARW3XQA7\\Varnai - 2004 - DNA and its counterions a molecular dynamics study.pdf}
}

@article{Vasak1981,
  title = {Zinc({{II}}), Cadmium({{II}}), and Mercury({{II}}) Thiolate Transitions in Metallothionein},
  author = {Vasak, Milan and Kaegi, Jeremias H. R. and Hill, H. Allen O.},
  year = {1981},
  month = may,
  journal = {Biochemistry},
  volume = {20},
  number = {10},
  pages = {2852--2856},
  issn = {0006-2960},
  doi = {10.1021/bi00513a022},
  abstract = {The metal-specific absorption envelopes of zinc-, cadmium-, and mercury-metallothioneins and of complexes of these metal ions with 2-mercaptoethanol have been analyzed in terms of Jorgensen's electronegativity theory for chargetransfer excitations by using the spectra of zinc(II), cadmium(II), and mercury(II) tetrahalides as references. By Gaussian analysis the difference absorption spectra of the various forms of metallothionein vs. thionein and of the corresponding 2-mercaptoethanol complexes vs. 2-mercaptoethanol were resolved into three components. For each metal derivative the location of the lowest energy band is in good agreement with the position of the first ligand-metal charge-transfer (LMCT) transition (type t2 \textrightarrow{} a1) predicted from the optical electronegativity difference of the thiolate ligands and of the central metal ion by assuming tetrahedral coordination. There is also a correspondence between the effects of the metal ion on the position of the first LMCT band and the binding energy of the 2p electrons of the sulfur ligands as found by X-ray photoelectron spectroscopic measurements [Sokolowski, G., Pilz, W., \& Weser, U. (1974) FEBS Lett. 48, 222], Due to the lack of exact structural information, the assignment of the two other resolved metal-dependent bands remains conjectural, but it is likely that they include a second LMCT transition (type t2 \textrightarrow{} a1) analogous to that occurring in tetrahalide complexes of group-2B metal ions. The simplicity of the resolved thiolate spectra and their correspondence to those of tetrahedral models support the view that the various metal-binding sites of metallothionein are chemically similar and that the coordination environment of the metal ion has a symmetry related to that of a tetrahedron [Vasak, M. (1980) J. Am. Chem. Soc. 102, 3953]. \textcopyright{} 1981, American Chemical Society. All rights reserved.},
  pmid = {7248252},
  file = {C\:\\Users\\makro\\Zotero\\storage\\D77IX4LE\\Vasak, Kaegi, Hill - 1981 - Zinc(II), cadmium(II), and mercury(II) thiolate transitions in metallothionein.pdf}
}

@article{Waldron2009,
  title = {Metalloproteins and Metal Sensing},
  author = {Waldron, Kevin J. and Rutherford, Julian C. and Ford, Dianne and Robinson, Nigel J.},
  year = {2009},
  journal = {Nature},
  volume = {460},
  number = {7257},
  pages = {823--830},
  issn = {00280836},
  doi = {10.1038/nature08300},
  abstract = {Almost half of all enzymes must associate with a particular metal to function. An ambition is to understand why each metal-protein partnership arose and how it is maintained. Metal availability provides part of the explanation, and has changed over geological time and varies between habitats but is held within vital limits in cells. Such homeostasis needs metal sensors, and there is an ongoing search to discover the metal-sensing mechanisms. For metalloproteins to acquire the right metals, metal sensors must correctly distinguish between the inorganic elements. \textcopyright 2009 Macmillan Publishers Limited. All rights reserved.},
  pmid = {19675642},
  file = {C\:\\Users\\makro\\Zotero\\storage\\N89KW3CR\\Waldron et al. - 2009 - Metalloproteins and metal sensing.pdf}
}

@article{Westbrook2019,
  title = {How {{Structural Biologists}} and the {{Protein Data Bank Contributed}} to {{Recent FDA New Drug Approvals}}},
  author = {Westbrook, John D. and Burley, Stephen K.},
  year = {2019},
  month = feb,
  journal = {Structure},
  volume = {27},
  number = {2},
  pages = {211--217},
  publisher = {{Elsevier Ltd.}},
  issn = {09692126},
  doi = {10.1016/j.str.2018.11.007},
  abstract = {Discovery/development of 210 new molecular entities (NMEs; new drugs) approved by the US Food and Drug Administration 2010\textendash 2016 was facilitated by open access to 3D structures stored in the PDB. Nearly 6,000 relevant PDB structures contributed to approval of 88\% of these NMEs across all therapeutic areas.},
  pmid = {30595456},
  keywords = {biopharmaceutical industry,data deposition,drugs,FAIR principles,macromolecular crystallography,new molecular entities,open access,PDB,RCSB PDB,Research Collaboratory for Structural Bioinformati,Worldwide PDB,wwPDB},
  file = {C\:\\Users\\makro\\Zotero\\storage\\JP6CB98W\\Westbrook, Burley - 2019 - How Structural Biologists and the Protein Data Bank Contributed to Recent FDA New Drug Approvals.pdf}
}

@article{Williams2008,
  title = {Mre11 {{Dimers Coordinate DNA End Bridging}} and {{Nuclease Processing}} in {{Double-Strand-Break Repair}}},
  author = {Williams, R Scott and Moncalian, Gabriel and Williams, Jessica S and Yamada, Yoshiki and Limbo, Oliver and Shin, David S and Groocock, Lynda M and Cahill, Dana and Hitomi, Chiharu and Guenther, Grant and Moiani, Davide and Carney, James P and Russell, Paul and Tainer, John A},
  year = {2008},
  journal = {Cell},
  volume = {135},
  number = {1},
  pages = {97--109},
  issn = {00928674},
  doi = {10.1016/j.cell.2008.08.017},
  abstract = {Mre11 forms the core of the multifunctional Mre11-Rad50-Nbs1 (MRN) complex that detects DNA double-strand breaks (DSBs), activates the ATM checkpoint kinase, and initiates homologous recombination (HR) repair of DSBs. To define the roles of Mre11 in both DNA bridging and nucleolytic processing during initiation of DSB repair, we combined small-angle X-ray scattering (SAXS) and crystal structures of Pyrococcus furiosus Mre11 dimers bound to DNA with mutational analyses of fission yeast Mre11. The Mre11 dimer adopts a four-lobed U-shaped structure that is critical for proper MRN complex assembly and for binding and aligning DNA ends. Further, mutations blocking Mre11 endonuclease activity impair cell survival after DSB induction without compromising MRN complex assembly or Mre11-dependant recruitment of Ctp1, an HR factor, to DSBs. These results show how Mre11 dimerization and nuclease activities initiate repair of DSBs and collapsed replication forks, as well as provide a molecular foundation for understanding cancer-causing Mre11 mutations in ataxia telangiectasia-like disorder (ATLD). \textcopyright{} 2008 Elsevier Inc. All rights reserved.},
  pmid = {18854158},
  keywords = {DNA},
  file = {C\:\\Users\\makro\\Zotero\\storage\\ZESYUES7\\Williams et al. - 2008 - Mre11 Dimers Coordinate DNA End Bridging and Nuclease Processing in Double-Strand-Break Repair.pdf}
}

@article{Williams2011,
  title = {{{ABC ATPase}} Signature Helices in {{Rad50}} Link Nucleotide State to {{Mre11}} Interface for {{DNA}} Repair},
  author = {Williams, Gareth J and Williams, R Scott and Williams, Jessica S and Moncalian, Gabriel and Arvai, Andrew S and Limbo, Oliver and Guenther, Grant and SilDas, Soumita and Hammel, Michal and Russell, Paul and Tainer, John A},
  year = {2011},
  journal = {Nature Structural \& Molecular Biology},
  volume = {18},
  number = {4},
  pages = {423--431},
  issn = {1545-9985},
  doi = {10.1038/nsmb.2038},
  abstract = {Rad50 is an ABC-type ATPase that forms a complex with the nuclease Mre11 and plays an essential role in the signaling and repair of DNA damage. Now crystal structures and SAXS analyses, along with functional assays, reveal how Rad50 transmits information between the ATPase and Mre11-binding sites, and the mechanism uncovered may be general to other ABC ATPases.}
}

@article{Ye2022,
  title = {A {{Comprehensive Review}} of {{Computation-Based Metal-Binding Prediction Approaches}} at the {{Residue Level}}},
  author = {Ye, Nan and Zhou, Feng and Liang, Xingchen and Chai, Haiting and Fan, Jianwei and Li, Bo and Zhang, Jian},
  editor = {Wang, Bing},
  year = {2022},
  month = mar,
  journal = {BioMed Research International},
  volume = {2022},
  pages = {1--19},
  issn = {2314-6141},
  doi = {10.1155/2022/8965712},
  abstract = {Clear evidence has shown that metal ions strongly connect and delicately tune the dynamic homeostasis in living bodies. They have been proved to be associated with protein structure, stability, regulation, and function. Even small changes in the concentration of metal ions can shift their effects from natural beneficial functions to harmful. This leads to degenerative diseases, malignant tumors, and cancers. Accurate characterizations and predictions of metalloproteins at the residue level promise informative clues to the investigation of intrinsic mechanisms of protein-metal ion interactions. Compared to biophysical or biochemical wet-lab technologies, computational methods provide open web interfaces of high-resolution databases and high-throughput predictors for efficient investigation of metal-binding residues. This review surveys and details 18 public databases of metal-protein binding. We collect a comprehensive set of 44 computation-based methods and classify them into four categories, namely, learning-, docking-, template-, and meta-based methods. We analyze the benchmark datasets, assessment criteria, feature construction, and algorithms. We also compare several methods on two benchmark testing datasets and include a discussion about currently publicly available predictive tools. Finally, we summarize the challenges and underlying limitations of the current studies and propose several prospective directions concerning the future development of the related databases and methods.},
  pmid = {35402609},
  file = {C\:\\Users\\makro\\Zotero\\storage\\RGDJ4IQN\\Ye et al. - 2022 - A Comprehensive Review of Computation-Based Metal-Binding Prediction Approaches at the Residue Level.pdf}
}

@article{Yoneyama1985,
  title = {Cellular Uptake and Subcellular Distribution of Mercury in Chick Embryonic Retinal Cell Aggregates},
  author = {Yoneyama, M. and Sharma, R.P. and Kleinschuster, S.J.},
  year = {1985},
  month = aug,
  journal = {Ecotoxicology and Environmental Safety},
  volume = {10},
  number = {1},
  pages = {112--119},
  issn = {01476513},
  doi = {10.1016/0147-6513(85)90012-0},
  abstract = {Cellular uptake and subcellular distribution of mercury (203HgCl2) were determined in the chick embryonic retinal cell aggregation system. The accumulation of mercury was dependent upon its concentration in the medium. The uptake was rapid; a maximum deposition of mercury at 5 {$\mu$}M occurred within the first 30 min followed by a decline. Accumulation of mercury at 1 {$\mu$}M was constant between 15 min and 24 hr. The subcellular distribution of mercury was observed in the following order: nuclei and cell debris {$>$} mitochondria-lysosomes {$>$} 105,000g supernatant {$>$} microsomes. The activity of acid phosphatase markedly decreased in the aggregates treated with mercury at 50 to 100 {$\mu$}M for 24 hr. Low concentrations of mercury at 0.5 to 5 {$\mu$}M showed an inhibition of this enzyme activity in a cell-free system. The results indicate a relationship between the amount of mercury in the cells and the toxicity it produced on the retinal cell aggregation system. \textcopyright{} 1985.},
  pmid = {4029057},
  file = {C\:\\Users\\makro\\Zotero\\storage\\TZ4CK4AU\\Yoneyama, Sharma, Kleinschuster - 1985 - Cellular uptake and subcellular distribution of mercury in chick embryonic retinal cell aggrega.pdf}
}

@incollection{Zambelli2013,
  title = {Nickel and {{Human Health}}},
  booktitle = {Metal Ions in Life Sciences},
  author = {Zambelli, Barbara and Ciurli, Stefano},
  editor = {Sigel, Astrid and Sigel, Helmut and Sigel, Roland K O},
  year = {2013},
  volume = {13},
  pages = {321--357},
  publisher = {{Springer Netherlands}},
  address = {{Dordrecht}},
  doi = {10.1007/978-94-007-7500-8_10},
  isbn = {978-94-007-7499-5},
  file = {C\:\\Users\\makro\\Zotero\\storage\\XGAM5W3B\\Zambelli, Ciurli - 2013 - Nickel and Human Health.pdf}
}

@article{Zhang2022,
  title = {The Role of Chromatin Loop Extrusion in Antibody Diversification},
  author = {Zhang, Yu and Zhang, Xuefei and Dai, Hai-Qiang and Hu, Hongli and Alt, Frederick W},
  year = {2022},
  month = sep,
  journal = {Nature Reviews Immunology},
  volume = {22},
  number = {9},
  pages = {550--566},
  issn = {1474-1733},
  doi = {10.1038/s41577-022-00679-3},
  abstract = {Cohesin mediates chromatin loop formation across the genome by extruding chromatin between convergently oriented CTCF-binding elements. Recent studies indicate that cohesin-mediated loop extrusion in developing B cells presents immunoglobulin heavy chain (Igh) variable (V), diversity (D) and joining (J) gene segments to RAG endonuclease through a process referred to as RAG chromatin scanning. RAG initiates V(D)J recombinational joining of these gene segments to generate the large number of different Igh variable region exons that are required for immune responses to diverse pathogens. Antigen-activated mature B cells also use chromatin loop extrusion to mediate the synapsis, breakage and end joining of switch regions flanking Igh constant region exons during class-switch recombination, which allows for the expression of different antibody constant region isotypes that optimize the functions of antigen-specific antibodies to eliminate pathogens. Here, we review recent advances in our understanding of chromatin loop extrusion during V(D)J recombination and class-switch recombination at the Igh locus.}
}

@article{Zheng2008,
  title = {Data Mining of Metal Ion Environments Present in Protein Structures},
  author = {Zheng, Heping and Chruszcz, Maksymilian and Lasota, Piotr and Lebioda, Lukasz and Minor, Wladek},
  year = {2008},
  journal = {Journal of Inorganic Biochemistry},
  volume = {102},
  number = {9},
  pages = {1765--1776},
  issn = {01620134},
  doi = {10.1016/j.jinorgbio.2008.05.006},
  abstract = {Analysis of metal-protein interaction distances, coordination numbers, B-factors (displacement parameters), and occupancies of metal-binding sites in protein structures determined by X-ray crystallography and deposited in the PDB shows many unusual values and unexpected correlations. By measuring the frequency of each amino acid in metal ion-binding sites, the positive or negative preferences of each residue for each type of cation were identified. Our approach may be used for fast identification of metal-binding structural motifs that cannot be identified on the basis of sequence similarity alone. The analysis compares data derived separately from high and medium-resolution structures from the PDB with those from very high-resolution small-molecule structures in the Cambridge Structural Database (CSD). For high-resolution protein structures, the distribution of metal-protein or metal-water interaction distances agrees quite well with data from CSD, but the distribution is unrealistically wide for medium (2.0-2.5 \AA ) resolution data. Our analysis of cation B-factors versus average B-factors of atoms in the cation environment reveals substantial numbers of structures contain either an incorrect metal ion assignment or an unusual coordination pattern. Correlation between data resolution and completeness of the metal coordination spheres is also found. \textcopyright{} 2008 Elsevier Inc. All rights reserved.},
  pmid = {18614239},
  keywords = {Metal binding,Metalloprotein,Protein structure},
  file = {C\:\\Users\\makro\\Zotero\\storage\\XHTUYWW2\\Zheng et al. - 2008 - Data mining of metal ion environments present in protein structures.pdf}
}

@article{Zheng2015,
  title = {Magnesium-Binding Architectures in {{RNA}} Crystal Structures: Validation, Binding Preferences, Classification and Motif Detection},
  author = {Zheng, Heping and Shabalin, Ivan G. and Handing, Katarzyna B. and Bujnicki, Janusz M. and Minor, Wladek},
  year = {2015},
  month = apr,
  journal = {Nucleic Acids Research},
  volume = {43},
  number = {7},
  pages = {3789--3801},
  issn = {1362-4962},
  doi = {10.1093/nar/gkv225},
  abstract = {The ubiquitous presence of magnesium ions in RNA has long been recognized as a key factor governing RNA folding, and is crucial for many diverse functions of RNA molecules. In this work, Mg2+-binding architectures in RNA were systematically studied using a database of RNA crystal structures from the Protein Data Bank (PDB). Due to the abundance of poorly modeled or incorrectly identified Mg2+ ions, the set of all sites was comprehensively validated and filtered to identify a benchmark dataset of 15 334 'reliable' RNA-bound Mg2+ sites. The normalized frequencies by which specific RNA atoms coordinate Mg2+ were derived for both the inner and outer coordination spheres. A hierarchical classification system of Mg2+ sites in RNA structures was designed and applied to the benchmark dataset, yielding a set of 41 types of inner-sphere and 95 types of outer-sphere coordinating patterns. This classification system has also been applied to describe six previously reported Mg2+-binding motifs and detect them in new RNA structures. Investigation of the most populous site types resulted in the identification of seven novel Mg2+-binding motifs, and all RNA structures in the PDB were screened for the presence of these motifs.},
  pmid = {25800744},
  file = {C\:\\Users\\makro\\Zotero\\storage\\NCNI9C5D\\Zheng et al. - 2015 - Magnesium-binding architectures in RNA crystal structures validation, binding preferences, classification and moti.pdf}
}

@article{Zhu2008,
  title = {Sgs1 {{Helicase}} and {{Two Nucleases Dna2}} and {{Exo1 Resect DNA Double-Strand Break Ends}}},
  author = {Zhu, Zhu and Chung, Woo-Hyun and Shim, Eun Yong and Lee, Sang Eun and Ira, Grzegorz},
  year = {2008},
  month = sep,
  journal = {Cell},
  volume = {134},
  number = {6},
  pages = {981--994},
  issn = {00928674},
  doi = {10.1016/j.cell.2008.08.037},
  abstract = {Formation of single-strand DNA (ssDNA) tails at a double-strand break (DSB) is a key step in homologous recombination and DNA-damage signaling. The enzyme(s) producing ssDNA at DSBs in eukaryotes remain unknown. We monitored 5{${'}$}-strand resection at inducible DSB ends in yeast and identified proteins required for two stages of resection: initiation and long-range 5{${'}$}-strand resection. We show that the Mre11-Rad50-Xrs2 complex (MRX) initiates 5{${'}$} degradation, whereas Sgs1 and Dna2 degrade 5{${'}$} strands exposing long 3{${'}$} strands. Deletion of SGS1 or DNA2 reduces resection and DSB repair by single-strand annealing between distant repeats while the remaining long-range resection activity depends on the exonuclease Exo1. In exo1{$\Delta$} sgs1{$\Delta$} double mutants, the MRX complex together with Sae2 nuclease generate, in a stepwise manner, only few hundred nucleotides of ssDNA at the break, resulting in inefficient gene conversion and G2/M damage checkpoint arrest. These results provide important insights into the early steps of DSB repair in eukaryotes. \textcopyright{} 2008 Elsevier Inc. All rights reserved.},
  pmid = {18805091},
  keywords = {DNA},
  file = {C\:\\Users\\makro\\Zotero\\storage\\5NAGCAFX\\Zhu et al. - 2008 - Sgs1 Helicase and Two Nucleases Dna2 and Exo1 Resect DNA Double-Strand Break Ends.pdf}
}