ArticleProceedings of the National Academy of Sciences of the United States of America2007
Specificity in protein interactions and its relationship with sequence diversity and coevolution.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 61 papers.
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61 citing papers in PubMed.
- Polymers for Disrupting Protein-Protein Interactions: Where Are We and Where Should We Be?Biomacromolecules · 2024Review
- Special Issue: "Molecular Dynamics Simulations and Structural Analysis of Protein Domains".International journal of molecular sciences · 2024Article
- Comparative Genomic Analysis of the Pattern of Evolution of Male and Female Reproductive Proteins in Seed Beetles.Genome biology and evolution · 2024Article
- Article
- An Update on Protein Kinases as Therapeutic Targets-Part II: Peptides as Allosteric Protein Kinase C Modulators Targeting Protein-Protein Interactions.International journal of molecular sciences · 2023Review
- Distinct chromosomal "niches" in the genome ofNAR genomics and bioinformatics · 2022Article
- Correlations from structure and phylogeny combine constructively in the inference of protein partners from sequences.PLoS computational biology · 2022Article
- Classification and prediction of protein-protein interaction interface using machine learning algorithm.Scientific reports · 2021Article
- Distribution, expression and methylation analysis of positively selected genes provides insights into the evolution in Brassica rapa.PloS one · 2021Article
- Combinations of Legume Protein Hydrolysates Synergistically Inhibit Biological Markers Associated with Adipogenesis.Foods (Basel, Switzerland) · 2020Article
- Review
- The membrane receptors that appeared before their ligand: The different proposed scenarios.PloS one · 2020Article
- Molecular evolution of the meiotic recombination pathway in mammals.Evolution; international journal of organic evolution · 2019Article
- Phylogenetic correlations can suffice to infer protein partners from sequences.PLoS computational biology · 2019Article
- Genomic Signatures of Sexual Conflict.The Journal of heredity · 2017Article
- A coevolution analysis for identifying protein-protein interactions by Fourier transform.PloS one · 2017Article
- Binding interface change and cryptic variation in the evolution of protein-protein interactions.BMC evolutionary biology · 2016Article
- Adaptive selection and coevolution at the proteins of the Polycomb repressive complexes in Drosophila.Heredity · 2016Article
- Coupling high-throughput genetics with phylogenetic information reveals an epistatic interaction on the influenza A virus M segment.BMC genomics · 2016Article
- A new ensemble coevolution system for detecting HIV-1 protein coevolution.Biology direct · 2015Article
1 more citing papers are in PubMed but not listed here.
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4 authors.
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Abstract
Studies of interacting proteins have found correlated evolution of the sequences of binding partners, apparently as a result of compensating mutations to maintain specificity (i.e., molecular coevolution). Here, we analyze the coevolution of interacting proteins in yeast and demonstrate correlated evolution of binding partners in eukaryotes. Detailed investigation of this apparent coevolution, focusing on the proteins' surface and binding interface, surprisingly leads to no improvement in the correlation. We conclude that true coevolution, as characterized by compensatory mutations between binding partners, is unlikely to be chiefly responsible for the apparent correlated evolution. We postulate that the correlation between sequence alignments is simply due to interacting proteins being subject to similar constraints on their evolutionary rate. Because gene expression has a strong influence on evolutionary rate, and interacting proteins will tend to have similar levels of expression, we investigated this particular constraint. We found that the absolute expression level outperformed correlated evolution for predicting interacting protein partners. A correlation between sequence alignments could also be identified not only between pairs of proteins that physically interact but also between those that are merely functionally related (i.e., within the same protein complex). This indicates that the observed correlated evolution of interacting proteins is due to similar constraints on evolutionary rate and not coevolution.
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