ArticlePloS one2009
Identification of coevolving residues and coevolution potentials emphasizing structure, bond formation and catalytic coordination in protein evolution.
Article in PloS one, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- Modeling transcriptional regulation of the cell cycle using a novel cybernetic-inspired approach.Biophysical journal · 2024Article
- Enhanced thermal stability enables human mismatch-specific thymine-DNA glycosylase to catalyse futile DNA repair.PloS one · 2024Article
- Integrating structure-based machine learning and co-evolution to investigate specificity in plant sesquiterpene synthases.PLoS computational biology · 2021Article
- Structural Insights into Carboxylic Polyester-Degrading Enzymes and Their Functional Depolymerizing Neighbors.International journal of molecular sciences · 2021Article
- Information Theory in Computational Biology: Where We Stand Today.Entropy (Basel, Switzerland) · 2020Article
- IMPContact: An Interhelical Residue Contact Prediction Method.BioMed research international · 2020Article
- Ensemble stacking mitigates biases in inference of synaptic connectivity.Network neuroscience (Cambridge, Mass.) · 2018Article
- Protein sites with more coevolutionary connections tend to evolve slower, while more variable protein families acquire higher coevolutionary connections.F1000Research · 2017Article
- Article
- A new ensemble coevolution system for detecting HIV-1 protein coevolution.Biology direct · 2015Article
- Control of catalytic efficiency by a coevolving network of catalytic and noncatalytic residues.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- Multidimensional mutual information methods for the analysis of covariation in multiple sequence alignments.BMC bioinformatics · 2014Article
- Coevolution analyses illuminate the dependencies between amino acid sites in the chaperonin system GroES-L.BMC evolutionary biology · 2013Article
- Bi-factor analysis based on noise-reduction (BIFANR): a new algorithm for detecting coevolving amino acid sites in proteins.PloS one · 2013Article
- Improving the thermostability of alpha-amylase by combinatorial coevolving-site saturation mutagenesis.BMC bioinformatics · 2012Article
- Mutual information and variants for protein domain-domain contact prediction.BMC research notes · 2012Article
- Accurate simulation and detection of coevolution signals in multiple sequence alignments.PloS one · 2012Article
- Protein sequence alignment analysis by local covariation: coevolution statistics detect benchmark alignment errors.PloS one · 2012Article
- A coevolutionary residue network at the site of a functionally important conformational change in a phosphohexomutase enzyme family.PloS one · 2012Article
- Integrated analysis of residue coevolution and protein structure in ABC transporters.PloS one · 2012Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
The structure and function of a protein is dependent on coordinated interactions between its residues. The selective pressures associated with a mutation at one site should therefore depend on the amino acid identity of interacting sites. Mutual information has previously been applied to multiple sequence alignments as a means of detecting coevolutionary interactions. Here, we introduce a refinement of the mutual information method that: 1) removes a significant, non-coevolutionary bias and 2) accounts for heteroscedasticity. Using a large, non-overlapping database of protein alignments, we demonstrate that predicted coevolving residue-pairs tend to lie in close physical proximity. We introduce coevolution potentials as a novel measure of the propensity for the 20 amino acids to pair amongst predicted coevolutionary interactions. Ionic, hydrogen, and disulfide bond-forming pairs exhibited the highest potentials. Finally, we demonstrate that pairs of catalytic residues have a significantly increased likelihood to be identified as coevolving. These correlations to distinct protein features verify the accuracy of our algorithm and are consistent with a model of coevolution in which selective pressures towards preserving residue interactions act to shape the mutational landscape of a protein by restricting the set of admissible neutral mutations.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.