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A less-biased analysis of metalloproteins reveals novel zinc coordination geometries
2015
Proteins: Structure, Function, and Bioinformatics
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Thus, we developed a less-biased method that directly handles potential exceptions without pre-assuming any CG model. ...
Local structure around the zinc ion, especially the coordination geometry (CG), is dictated by the protein sequence and is often directly related to the function of the protein. ...
The contents of this work are solely the responsibility of the authors and do not represent the official views of the NIH or the National Institute for General Medical Sciences (NIGMS). ...
doi:10.1002/prot.24834
pmid:26009987
pmcid:PMC4539273
fatcat:ndmuhjpz65gyhhz7g7g4r26qeu
A less-biased analysis of metalloproteins reveals novel zinc coordination geometries
2015
Proteins: Structure, Function, and Bioinformatics
unpublished
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Thus, we developed a less-biased method that directly handles potential exceptions without pre-assuming any CG model. ...
Local structure around the zinc ion, especially the coordination geometry (CG), is dictated by the protein sequence and is often directly related to the function of the protein. ...
The contents of this work are solely the responsibility of the authors and do not represent the official views of the NIH or the National Institute for General Medical Sciences (NIGMS). ...
fatcat:aena7qyxj5gl5m2p6ewgyhviwi
Perspectives and Expectations in Structural Bioinformatics of Metalloproteins
2017
Figshare
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Pre-acceptance version of the manuscript.Published manuscript is available at: https://dx.doi.org/10.1002/prot.25263 ...
A critical look at a recently published classification of "novel" Zn binding sites" (1), a "critique" of our previously published paper "A less-biased analysis of metalloproteins reveals novel zinc coordination ...
on discrediting the existence of "novel" zinc coordination geometries. ...
doi:10.6084/m9.figshare.4754263
fatcat:jyckjdoghvdstnra55k3vxqrxq
Perspectives and expectations in structural bioinformatics of metalloproteins
2017
Proteins: Structure, Function, and Bioinformatics
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Recent papers highlight the presence of large numbers of compressed angles in metal ion coordination geometries for metalloprotein entries in the worldwide Protein Data Bank, due mainly to multidentate ...
Some of these papers have undergone severe criticism, apparently due to views held that only canonical coordination geometries exist in significant numbers. ...
Acknowledgments The authors have no conflict of interest with this work. This work was supported in part by National Science ...
doi:10.1002/prot.25263
pmid:28168746
pmcid:PMC5389925
fatcat:z2ydvi7bjvgkbp7e6nnyk5sw6a
GM-DockZn: A Geometry Matching based Docking Algorithm for Zinc Proteins
2020
Bioinformatics
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The proposed geometry-based sampling technique will be useful for ligand docking to other metalloproteins. ...
This is true not only for a nonredundant dataset of zinc proteins but also for a homolog set of different ligand and zinc-coordination systems for the same zinc proteins. ...
The day of resubmission is also the 6 th birthday of my (Ruibo Wu) son (Zhengyu Joey Wu), who gave me many inspirations on science, herein I want to wish him a happy childhood. ...
doi:10.1093/bioinformatics/btaa292
pmid:32369579
fatcat:k6oel6g6zjaxhezrfzpdibd7vi
Analysis of the structural consensus of the zinc coordination centers of metalloprotein structures
2007
Biochimica et Biophysica Acta - Proteins and Proteomics
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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. ...
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 ...
Acknowledgements This work was supported by grant from Board of Research in Nuclear Sciences, India (BRNS) and Council of Scientific and Industrial Research (CSIR), Government of India. ...
doi:10.1016/j.bbapap.2007.07.010
pmid:17855175
fatcat:jdmeggg2nfebrprwwjoinssgey
Aberrant coordination geometries discovered in the most abundant metalloproteins
2017
Proteins: Structure, Function, and Bioinformatics
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Metalloproteins bind and utilize metal ions for a variety of biological purposes. ...
number of unexpected compressed angles and subsequent aberrant metal ion coordination geometries (CGs) within structurally known metalloproteins. ...
The contents of this work are solely the responsibility of the authors and do not represent the official views of the NIH or the National Institute for General Medical Sciences (NIGMS). ...
doi:10.1002/prot.25257
pmid:28142195
pmcid:PMC5389913
fatcat:33z4l5ommngtbcykmilxh4g5ia
Transition metal binding selectivity in proteins and its correlation with the phylogenomic classification of the cation diffusion facilitator protein family
2017
Scientific Reports
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To better understand such processes, we scanned the RCSB Protein Data Bank, performed a de novo structuralbased comprehensive analysis of seven DDMCs and found their amino acid binding and coordination ...
geometry propensities. ...
All authors analyzed the results and approved the final version of the manuscript. not peer-reviewed) is the author/funder. All rights reserved. No reuse allowed without permission. ...
doi:10.1038/s41598-017-16777-5
pmid:29180655
pmcid:PMC5703985
fatcat:4mphwg7wwvd3vftvbe4gew2dxa
Transition metal binding selectivity in proteins and its correlation with the phylogenomic classification of the cation diffusion facilitator protein family
[article]
2017
bioRxiv
pre-print
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To better understand such processes, we scanned the RCSB Protein Data Bank, performed a de novo structural-based comprehensive analysis of seven DDMCs and found their amino acid binding and coordination ...
geometry propensities. ...
The authors of this work are supported by the Israel Ministry of Science, Technology and Space, the Israel Science Foundation (grant no. 167/16), the European Molecular Biology Organization and CMST COST ...
doi:10.1101/164509
fatcat:ee7vaoxfjnh6dgckumbufy6lga
Machine Learning Approaches for Metalloproteins
2022
Molecules
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Metalloproteins are a family of proteins characterized by metal ion binding, whereby the presence of these ions confers key catalytic and ligand-binding properties. ...
Ultimately, having a comprehensive understanding of metalloproteins will lead to tangible applications, such as designing potent inhibitors in drug discovery. ...
Gray, who sparked his interest in metalloproteins.
Conflicts of Interest: The authors have no conflicts of interest to declare. ...
doi:10.3390/molecules27041277
pmid:35209064
pmcid:PMC8878495
fatcat:htlft2i7ifcwjbfzrza4ubqela
Hidden relationships between metalloproteins unveiled by structural comparison of their metal sites
2015
Scientific Reports
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Metalloproteins account for a substantial fraction of all proteins. They incorporate metal atoms, which are required for their structure and/or function. ...
The comparison of all representative MFSs provided a thorough structure-based classification of the sites analyzed. ...
MetalPDB shows that the iron coordination geometry in heme-containing MFSs is quite constant, being either square pyramidal or octahedral in the vast majority of cases, with four donor atoms out of a maximum ...
doi:10.1038/srep09486
pmid:25820752
pmcid:PMC4377587
fatcat:xsh64hb4qjd4zdkevckscee4we
Machine learning differentiates enzymatic and non-enzymatic metals in proteins
2021
Nature Communications
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In this work, we develop the largest structural dataset of enzymatic and non-enzymatic metalloprotein sites to date. ...
We then use a decision-tree ensemble machine learning model to classify metals bound to proteins as enzymatic or non-enzymatic with 92.2% precision and 90.1% recall. ...
We appreciate Patrick Mahomes for inspiring the name of our most valuable predictor (MVP). ...
doi:10.1038/s41467-021-24070-3
pmid:34140507
pmcid:PMC8211803
fatcat:oy2vjdj7xfblzgseg73jvmg3ba
Machine Learning Differentiates Enzymatic and Non-Enzymatic Metals in Proteins
[article]
2021
bioRxiv
pre-print
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In this work, we develop the largest structural dataset of enzymatic and non-enzymatic metalloprotein sites to date. ...
We then use a decision-tree ensemble machine learning model to distinguish metal ions bound to a protein as enzymatic or non-enzymatic with 92.2% precision and 90.1% recall. ...
for the name of our most valuable predictor (MVP). ...
doi:10.1101/2021.02.01.429261
fatcat:f6jfwkitejei3nnw5yamb3ncxa
Metal-Directed Protein Self-Assembly
2010
Accounts of Chemical Research
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At its core, MDPSA is inspired by supramolecular coordination chemistry which exploits metal coordination for the self-assembly of small molecules into discrete, more-or-less predictable higherorder structures ...
This approach of metal templating followed by the redesign of protein interfaces (Metal-Templated Interface Redesign, MeTIR) not only provides a route to engineer de novo PPIs and novel metal coordination ...
.), a Beckman Young Investigator Award (F.A.T.) and NSF (CHE-0908115). ...
doi:10.1021/ar900273t
pmid:20192262
pmcid:PMC2873059
fatcat:mxi2xjy2f5cqldoui3lgqh7wgu
De Novo Design of Tetranuclear Transition Metal Clusters Stabilized by Hydrogen-Bonded Networks in Helical Bundles
2018
Journal of the American Chemical Society
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De novo design provides an attractive approach to test the mechanism by which metalloproteins define the geometry and reactivity of their metal ion cofactors. ...
Here, we describe the design of tetranuclear clusters, consisting of four Zn 2+ and four carboxylate oxygens situated at the vertices of a distorted cube-like structure. ...
number B25B0900000000 for a postdoctoral fellowship to M. ...
doi:10.1021/jacs.7b08261
pmid:29249157
pmcid:PMC5860638
fatcat:m6uossaafvd6znzllsbg2dz37i
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