my_publications.bib

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@article{Kerber2023,
abstract = {The widespread application of silver nanoparticles in medicinal and daily life products increases the exposure to Ag(I) of thiol-rich biological environments, which help control the cellular metallome. A displacement of native metal cofactors from their cognate protein sites is a known phenomenon for carcinogenic and otherwise toxic metal ions. Here, we examined the interaction of Ag(I) with the peptide model of the interprotein zinc hook (Hk) domain of Rad50 protein from Pyrococcus furiosus, a key player in DNA double-strand break (DSB) repair. The binding of Ag(I) to 14 and 45 amino acid long peptide models of apo- and Zn(Hk)2 was experimentally investigated by UV-vis spectroscopy, circular dichroism, isothermal titration calorimetry, and mass spectrometry. The Ag(I) binding to the Hk domain was found to disrupt its structure via the replacement of the structural Zn(II) ion by multinuclear Agx(Cys)y complexes. The ITC analysis indicated that the formed Ag(I)-Hk species are at least 5 orders of magnitude stronger than the otherwise extremely stable native Zn(Hk)2 domain. These results show that Ag(I) ions may easily disrupt the interprotein zinc binding sites as an element of silver toxicity at the cellular level.},
author = {Kerber, Olga and Tran, J{\'{o}}zef and Misiaszek, Alicja and Chor{\k{a}}{\.{z}}ewska, Aleksandra and Bal, Wojciech and Kr{\k{e}}{\.{z}}el, Artur},
doi = {10.1021/acs.inorgchem.2c03767},
file = {:C$\backslash$:/Users/makro/Documents/Mendeley Desktop/Kerber et al. - 2023 - Zn(II) to Ag(I) Swap in Rad50 Zinc Hook Domain Leads to Interprotein Complex Disruption through the Formation (2).pdf:pdf},
issn = {0020-1669},
journal = {Inorganic Chemistry},
month = {mar},
number = {10},
pages = {4076--4087},
title = {{Zn(II) to Ag(I) Swap in Rad50 Zinc Hook Domain Leads to Interprotein Complex Disruption through the Formation of Highly Stable Ag x (Cys) y Cores}},
url = {https://pubs.acs.org/doi/10.1021/acs.inorgchem.2c03767},
volume = {62},
year = {2023}
}
@article{Tran2021,
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.},
author = {Tran, J{\'{o}}zef Ba and Kr{\k{e}}{\.{z}}el, Artur},
doi = {10.1021/acs.jproteome.0c00906},
file = {:C$\backslash$:/Users/makro/Documents/Mendeley Desktop/Tran, Kr{\k{e}}{\.{z}}el - 2021 - InterMetalDB A Database and Browser of Intermolecular Metal Binding Sites in Macromolecules with Structural Inform.pdf:pdf},
issn = {1535-3893},
journal = {Journal of Proteome Research},
keywords = {interfacial metal,interprotein site,metalloprotein,protein assembly,protein-protein interaction},
month = {apr},
number = {4},
pages = {1889--1901},
pmid = {33502860},
title = {{InterMetalDB: A Database and Browser of Intermolecular Metal Binding Sites in Macromolecules with Structural Information}},
url = {https://pubs.acs.org/doi/10.1021/acs.jproteome.0c00906},
volume = {20},
year = {2021}
}
@article{Kocyla2021,
abstract = {The presence of Zn2+ at protein--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--protein communication and protein complex assembly. How Zn2+-involved protein--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.},
author = {Kocy{\l}a, Anna and Tran, J{\'{o}}zef Ba and Kr{\k{e}}{\.{z}}el, Artur},
doi = {10.1016/j.tibs.2020.08.011},
file = {:C$\backslash$:/Users/makro/Documents/Mendeley Desktop/Kocy{\l}a, Tran, Kr{\k{e}}{\.{z}}el - 2021 - Galvanization of Protein--Protein Interactions in a Dynamic Zinc Interactome.pdf:pdf},
issn = {09680004},
journal = {Trends in Biochemical Sciences},
keywords = {interprotein metal binding site,metal affinity,metalloprotein,zinc buffering,zinc fluctuations},
month = {jan},
number = {1},
pages = {64--79},
pmid = {32958327},
title = {{Galvanization of Protein--Protein Interactions in a Dynamic Zinc Interactome}},
url = {https://linkinghub.elsevier.com/retrieve/pii/S0968000420302085},
volume = {46},
year = {2021}
}
@article{Luczkowski2022,
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},
doi = {10.1002/chem.202202738},
file = {:C$\backslash$:/Users/makro/Documents/Mendeley Desktop/{\L}uczkowski et al. - 2022 - An Extremely Stable Interprotein Tetrahedral Hg(Cys) 4 Core Forms in the Zinc Hook Domain of Rad50 Protein at.pdf:pdf},
issn = {0947-6539},
journal = {Chemistry -- A European Journal},
month = {nov},
number = {66},
title = {{An Extremely Stable Interprotein Tetrahedral Hg(Cys) 4 Core Forms in the Zinc Hook Domain of Rad50 Protein at Physiological pH}},
url = {https://onlinelibrary.wiley.com/doi/10.1002/chem.202202738},
volume = {28},
year = {2022}
}
@article{Tran2022,
abstract = {The metal binding at protein--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--structure--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--protein interactions and illuminates their molecular basis.},
author = {Tran, J{\'{o}}zef Ba and Padjasek, Micha{\l} and Kr{\k{e}}{\.{z}}el, Artur},
doi = {10.3390/ijms231911140},
file = {:C$\backslash$:/Users/makro/Documents/Mendeley Desktop/Tran, Padjasek, Kr{\k{e}}{\.{z}}el - 2022 - Relations between Structure and Zn(II) Binding Affinity Shed Light on the Mechanisms of Rad50 Hook Domai.pdf:pdf},
issn = {1422-0067},
journal = {International Journal of Molecular Sciences},
keywords = {DNA damage,Mre11-Rad50-Nbs1 (MRN),Rad50,zinc,zinc hook},
month = {sep},
number = {19},
pages = {11140},
title = {{Relations between Structure and Zn(II) Binding Affinity Shed Light on the Mechanisms of Rad50 Hook Domain Functioning and Its Phosphorylation}},
url = {https://www.mdpi.com/1422-0067/23/19/11140},
volume = {23},
year = {2022}
}
@article{Padjasek2020,
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.},
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},
doi = {10.1016/j.jinorgbio.2019.110955},
file = {:C$\backslash$:/Users/makro/Documents/Mendeley Desktop/Padjasek et al. - 2020 - Structural zinc binding sites shaped for greater works Structure-function relations in classical zinc finger, h.pdf:pdf},
issn = {01620134},
journal = {Journal of Inorganic Biochemistry},
month = {mar},
number = {December 2019},
pages = {110955},
pmid = {31841759},
publisher = {Elsevier},
title = {{Structural zinc binding sites shaped for greater works: Structure-function relations in classical zinc finger, hook and clasp domains}},
url = {https://doi.org/10.1016/j.jinorgbio.2019.110955 https://linkinghub.elsevier.com/retrieve/pii/S0162013419305549},
volume = {204},
year = {2020}
}