ArticleScientific reports2015
Hidden relationships between metalloproteins unveiled by structural comparison of their metal sites.
Article in Scientific reports, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- Structural Bioinformatics and Deep Learning of Metalloproteins: Recent Advances and Applications.International journal of molecular sciences · 2022Review
- A New Paradigm of Multiheme Cytochrome Evolution by Grafting and Pruning Protein Modules.Molecular biology and evolution · 2022Article
- Identifying metal binding amino acids based on backbone geometries as a tool for metalloprotein engineering.Protein science : a publication of the Protein Society · 2021Article
- Electric field stimulates production of highly conductive microbial OmcZ nanowires.Nature chemical biology · 2020Article
- MetalPDB in 2018: a database of metal sites in biological macromolecular structures.Nucleic acids research · 2018Article
- Heavy Metal Removal by Bioaccumulation Using Genetically Engineered Microorganisms.Frontiers in bioengineering and biotechnology · 2018Review
- Minimal Functional Sites in Metalloproteins and Their Usage in Structural Bioinformatics.International journal of molecular sciences · 2016Review
- Structural principles for computational and de novo design of 4Fe-4S metalloproteins.Biochimica et biophysica acta · 2016Review
Corrections and comments
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Authors and funding
3 authors.
Funding
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Abstract
Metalloproteins account for a substantial fraction of all proteins. They incorporate metal atoms, which are required for their structure and/or function. Here we describe a new computational protocol to systematically compare and classify metal-binding sites on the basis of their structural similarity. These sites are extracted from the MetalPDB database of minimal functional sites (MFSs) in metal-binding biological macromolecules. Structural similarity is measured by the scoring function of the available MetalS2 program. Hierarchical clustering was used to organize MFSs into clusters, for each of which a representative MFS was identified. The comparison of all representative MFSs provided a thorough structure-based classification of the sites analyzed. As examples, the application of the proposed computational protocol to all heme-binding proteins and zinc-binding proteins of known structure highlighted the existence of structural subtypes, validated known evolutionary links and shed new light on the occurrence of similar sites in systems at different evolutionary distances. The present approach thus makes available an innovative viewpoint on metalloproteins, where the functionally crucial metal sites effectively lead the discovery of structural and functional relationships in a largely protein-independent manner.
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