ArticleProceedings of the National Academy of Sciences of the United States of America2017
Patterns of coevolving amino acids unveil structural and dynamical domains.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers, 1 of them a synthesis that pooled it.
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Who cites it
21 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Evolutionary Comparative Analyses of DNA-Editing Enzymes of the Immune System: From 5-Dimensional Description of Protein Structures to Immunological Insights and Applications to Protein Engineering.Frontiers in immunology · 2021Pooled it
- SGCRNA: spectral clustering-guided co-expression network analysis without scale-free constraints for multi-omic data.Briefings in bioinformatics · 2026Article
- Article
- Genetic diversity and molecular evolution of 3-carboxymuconate cyclase (Gp60-70), the major antigen in pathogenicMycology · 2025Article
- Reused Protein Segments Linked to Functional Dynamics.Molecular biology and evolution · 2024Article
- Decrypting Allostery in Membrane-Bound K-Ras4B Using ComplementaryJournal of the American Chemical Society · 2024Article
- Functional Protein Dynamics Directly from Sequences.The journal of physical chemistry. B · 2023Article
- Protein dynamics: The future is bright and complicated!Structural dynamics (Melville, N.Y.) · 2023Article
- Origin of acetylcholine antagonism in ELIC, a bacterial pentameric ligand-gated ion channel.Communications biology · 2022Article
- Protein Design: From the Aspect of Water Solubility and Stability.Chemical reviews · 2022Review
- Conserved conformational dynamics determine enzyme activity.Science advances · 2022Article
- OBI: A computational tool for the analysis and systematization of the positive selection in proteins.MethodsX · 2022Article
- Synergistic stabilization of a double mutant in chymotrypsin inhibitor 2 from a library screen in E. coli.Communications biology · 2021Article
- Evolution of frustrated and stabilising contacts in reconstructed ancient proteins.European biophysics journal : EBJ · 2021Article
- Episodic evolution of coadapted sets of amino acid sites in mitochondrial proteins.PLoS genetics · 2021Article
- Unravelling the effect of the E545K mutation on PI3Kα kinase.Chemical science · 2020Article
- Evolutionarily Conserved Interactions within the Pore Domain of Acid-Sensing Ion Channels.Biophysical journal · 2020Article
- Protein ensembles link genotype to phenotype.PLoS computational biology · 2019Review
- Revealing evolutionary constraints on proteins through sequence analysis.PLoS computational biology · 2019Article
- Statistical investigations of protein residue direct couplings.PLoS computational biology · 2018Article
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Authors and funding
4 authors.
Funding
Abstract
Patterns of interacting amino acids are so preserved within protein families that the sole analysis of evolutionary comutations can identify pairs of contacting residues. It is also known that evolution conserves functional dynamics, i.e., the concerted motion or displacement of large protein regions or domains. Is it, therefore, possible to use a pure sequence-based analysis to identify these dynamical domains? To address this question, we introduce here a general coevolutionary coupling analysis strategy and apply it to a curated sequence database of hundreds of protein families. For most families, the sequence-based method partitions amino acids into a few clusters. When viewed in the context of the native structure, these clusters have the signature characteristics of viable protein domains: They are spatially separated but individually compact. They have a direct functional bearing too, as shown for various reference cases. We conclude that even large-scale structural and functionally related properties can be recovered from inference methods applied to evolutionary-related sequences. The method introduced here is available as a software package and web server (spectrus.sissa.it/spectrus-evo_webserver).
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