ArticleMethods in enzymology2005
Context dependence and coevolution among amino acid residues in proteins.
Article in Methods in enzymology, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 32 citations in OpenAlex.
- WheatRPred: deep learning framework for predicting disease resistance protein in wheat and its wild relatives.Journal, genetic engineering & biotechnology · 2026Article
- Allostery and Epistasis: Emergent Properties of Anisotropic Networks.Entropy (Basel, Switzerland) · 2020Article
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- Comparing Residue Clusters from Thermophilic and Mesophilic Enzymes Reveals Adaptive Mechanisms.PloS one · 2016Article
- Amino acid coevolution induces an evolutionary Stokes shift.Proceedings of the National Academy of Sciences of the United States of America · 2012Article
- Exploiting models of molecular evolution to efficiently direct protein engineering.Journal of molecular evolution · 2011Article
- The coevolution of phycobilisomes: molecular structure adapting to functional evolution.Comparative and functional genomics · 2011Article
- Compensatory mutations are repeatable and clustered within proteins.Proceedings. Biological sciences · 2009Article
- Detecting coevolution without phylogenetic trees? Tree-ignorant metrics of coevolution perform as well as tree-aware metrics.BMC evolutionary biology · 2008Article
- Article
- Reducing the false positive rate in the non-parametric analysis of molecular coevolution.BMC evolutionary biology · 2008Article
- Detecting coevolution in and among protein domains.PLoS computational biology · 2007Article
- Coevolutionary patterns in cytochrome c oxidase subunit I depend on structural and functional context.Journal of molecular evolution · 2007Article
- EGenBio: a data management system for evolutionary genomics and biodiversity.BMC bioinformatics · 2006Article
- Divergence, recombination and retention of functionality during protein evolution.Human genomics · 2005Article
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Authors and funding
2 authors at 1 institution in 1 country.
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Abstract
As complete genomes accumulate and the generation of genomic biodiversity proceeds at an accelerating pace, the need to understand the interaction between sequence evolution and protein structure and function rises in prominence. The pattern and pace of substitutions in proteins can provide important clues to functional importance, functional divergence, and adaptive response. Coevolution between amino acid residues and the context dependence of the evolutionary process are often ignored, however, because of their complexity, but they are critical for the accurate interpretation of reconstructed evolutionary events. Because residues interact with one another, and because the effect of substitutions can depend on the structural and physiological environment in which they occur, an accurate science of evolutionary functional genomics and a complete understanding of selection in proteins require a better understanding of how context dependence affects protein evolution. Here, we present new evidence from vertebrate cytochrome oxidase sequences that pairwise coevolutionary interactions between protein residues are highly dependent on tertiary and secondary structure. We also discuss theoretical predictions that impinge on our expectations of how protein residues may interact over long distances because of their shared need to maintain protein stability.
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