ArticlePloS one2012
Protein fragments: functional and structural roles of their coevolution networks.
Article in PloS one, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed, 35 citations in OpenAlex.
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- Evolution and co-evolution: insights into the divergence of plant heat shock factor genes.Physiology and molecular biology of plants : an international journal of functional plant biology · 2022Article
- Iron Acquisition Systems of Gram-negative Bacterial Pathogens Define TonB-Dependent Pathways to Novel Antibiotics.Chemical reviews · 2021Review
- COVTree: Coevolution in OVerlapped sequences by Tree analysis server.Nucleic acids research · 2020Article
- Disease-relevant mutations alter amino acid co-evolution networks in the second nucleotide binding domain of CFTR.PloS one · 2020Article
- Coevolution analysis of amino-acids reveals diversified drug-resistance solutions in viral sequences: a case study of hepatitis B virus.Virus evolution · 2020Article
- CoevDB: a database of intramolecular coevolution among protein-coding genes of the bony vertebrates.Nucleic acids research · 2019Article
- Polymorphic sites preferentially avoid co-evolving residues in MHC class I proteins.PLoS computational biology · 2018Article
- A protein coevolution method uncovers critical features of the Hepatitis C Virus fusion mechanism.PLoS pathogens · 2018Article
- BIS2Analyzer: a server for co-evolution analysis of conserved protein families.Nucleic acids research · 2017Article
- Coevolution analysis of Hepatitis C virus genome to identify the structural and functional dependency network of viral proteins.Scientific reports · 2016Article
- Coevolutionary Analysis Identifies Protein-Protein Interaction Sites between HIV-1 Reverse Transcriptase and Integrase.Virus evolution · 2016Article
- Design of Heteronuclear Metalloenzymes.Methods in enzymology · 2016Article
- Coev-web: a web platform designed to simulate and evaluate coevolving positions along a phylogenetic tree.BMC bioinformatics · 2015Article
Corrections and comments
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Authors and funding
2 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Small protein fragments, and not just residues, can be used as basic building blocks to reconstruct networks of coevolved amino acids in proteins. Fragments often enter in physical contact one with the other and play a major biological role in the protein. The nature of these interactions might be multiple and spans beyond binding specificity, allosteric regulation and folding constraints. Indeed, coevolving fragments are indicators of important information explaining folding intermediates, peptide assembly, key mutations with known roles in genetic diseases, distinguished subfamily-dependent motifs and differentiated evolutionary pressures on protein regions. Coevolution analysis detects networks of fragments interaction and highlights a high order organization of fragments demonstrating the importance of studying at a deeper level this structure. We demonstrate that it can be applied to protein families that are highly conserved or represented by few sequences, enlarging in this manner, the class of proteins where coevolution analysis can be performed and making large-scale coevolution studies a feasible goal.
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