ArticleProteins2009
Coevolution in defining the functional specificity.
Article in Proteins, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
40 citing papers in PubMed.
- Co-Var, a Measure to Determine Intra-protein, Inter-protein, Protein-DNA, or Protein-RNA Coevolution.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Designing modular genetic sensors with TtgR/AcrR family transcriptional regulators by using a statistical and data-driven approach.Nucleic acids research · 2025Article
- Co-evolution-based prediction of metal-binding sites in proteomes by machine learning.Nature chemical biology · 2023Article
- Computational Docking Reveals Co-Evolution of C4 Carbon Delivery Enzymes in Diverse Plants.International journal of molecular sciences · 2022Article
- Molecular dynamics study on the strengthening behavior of Delta and Omicron SARS-CoV-2 spike RBD improved receptor-binding affinity.PloS one · 2022Article
- Modulating Glycoside Hydrolase Activity between Hydrolysis and Transfer Reactions Using an Evolutionary Approach.Molecules (Basel, Switzerland) · 2021Article
- Co-evolutionary landscape at the interface and non-interface regions of protein-protein interaction complexes.Computational and structural biotechnology journal · 2021Article
- Predicting the Specificity- Determining Positions of Receptor Tyrosine Kinase Axl.Frontiers in molecular biosciences · 2021Article
- Coevolution, Dynamics and Allostery Conspire in Shaping Cooperative Binding and Signal Transmission of the SARS-CoV-2 Spike Protein with Human Angiotensin-Converting Enzyme 2.International journal of molecular sciences · 2020Article
- Host-membrane interacting interface of the SARS coronavirus envelope protein: Immense functional potential of C-terminal domain.Biophysical chemistry · 2020Review
- Integrated Computational Approaches and Tools forAllosteric Drug Discovery.International journal of molecular sciences · 2020Review
- Allosteric Regulation at the Crossroads of New Technologies: Multiscale Modeling, Networks, and Machine Learning.Frontiers in molecular biosciences · 2020Review
- Evolutionary coupling analysis identifies the impact of disease-associated variants at less-conserved sites.Nucleic acids research · 2019Article
- Engineering repressors with coevolutionary cues facilitates toggle switches with a master reset.Nucleic acids research · 2019Article
- Recognition of sites of functional specialisation in all known eukaryotic protein kinase families.PLoS computational biology · 2018Article
- Correlated positions in protein evolution and engineering.Journal of industrial microbiology & biotechnology · 2017Review
- Protein sites with more coevolutionary connections tend to evolve slower, while more variable protein families acquire higher coevolutionary connections.F1000Research · 2017Article
- Computational Analysis of Residue Interaction Networks and Coevolutionary Relationships in the Hsp70 Chaperones: A Community-Hopping Model of Allosteric Regulation and Communication.PLoS computational biology · 2017Article
- Surface energetics and protein-protein interactions: analysis and mechanistic implications.Scientific reports · 2016Article
- Intramolecular allosteric communication in dopamine D2 receptor revealed by evolutionary amino acid covariation.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
Covariation between sites can arise due to a common evolutionary history. At the same time, structure and function of proteins play significant role in evolvability of different sites that are not directly connected with the common ancestry. The nature of forces which cause residues to coevolve is still not thoroughly understood, it is especially not clear how coevolutionary processes are related to functional diversification within protein families. We analyzed both functional and structural factors that might cause covariation of specificity determinants and showed that they more often participate in coevolutionary relationships with each other and other sites compared with functional sites and those sites that are not under strong functional constraints. We also found that protein sites with higher number of coevolutionary connections with other sites have a tendency to evolve slower. Our results indicate that in some cases coevolutionary connections exist between specificity sites that are located far away in space but are under similar functional constraints. Such correlated changes and compensations can be realized through the stepwise coevolutionary processes which in turn can shed light on the mechanisms of functional diversification.
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Registered trials
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