ArticleJournal of molecular evolution2008
Contact density affects protein evolutionary rate from bacteria to animals.
Article in Journal of molecular evolution, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
29 citing papers in PubMed, 59 citations in OpenAlex.
- Linking Protein Stability to Pathogenicity: Predicting Clinical Significance of Single-Missense Mutations in Ocular Proteins Using Machine Learning.International journal of molecular sciences · 2024Article
- Functional Optimization in Distinct Tissues and Conditions Constrains the Rate of Protein Evolution.Molecular biology and evolution · 2024Article
- Analysis of the Contribution of Intrinsic Disorder in Shaping Potyvirus Genetic Diversity.Viruses · 2022Article
- Evaluation of residue-residue contact prediction methods: From retrospective to prospective.PLoS computational biology · 2021Article
- ProteomeVis: a web app for exploration of protein properties from structure to sequence evolution across organisms' proteomes.Bioinformatics (Oxford, England) · 2018Article
- The Role of Evolutionary Selection in the Dynamics of Protein Structure Evolution.Biophysical journal · 2017Article
- Measuring evolutionary rates of proteins in a structural context.F1000Research · 2017Article
- Calculating site-specific evolutionary rates at the amino-acid or codon level yields similar rate estimates.PeerJ · 2017Article
- Alpha Helices Are More Robust to Mutations than Beta Strands.PLoS computational biology · 2016Article
- Complex Patterns of Association between Pleiotropy and Transcription Factor Evolution.Genome biology and evolution · 2016Article
- Causes of evolutionary rate variation among protein sites.Nature reviews. Genetics · 2016Review
- The organization of domains in proteins obeys Menzerath-Altmann's law of language.BMC systems biology · 2015Article
- Universal distribution of mutational effects on protein stability, uncoupling of protein robustness from sequence evolution and distinct evolutionary modes of prokaryotic and eukaryotic proteins.Physical biology · 2015Article
- Impacts of pretranscriptional DNA methylation, transcriptional transcription factor, and posttranscriptional microRNA regulations on protein evolutionary rate.Genome biology and evolution · 2014Article
- The impact of trans-regulation on the evolutionary rates of metazoan proteins.Nucleic acids research · 2013Article
- Three independent determinants of protein evolutionary rate.Journal of molecular evolution · 2013Review
- Modeling coding-sequence evolution within the context of residue solvent accessibility.BMC evolutionary biology · 2012Article
- Structure and age jointly influence rates of protein evolution.PLoS computational biology · 2012Article
- Independent effects of protein core size and expression on residue-level structure-evolution relationships.PloS one · 2012Article
- The relationship between relative solvent accessibility and evolutionary rate in protein evolution.Genetics · 2011Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
Abstract
The density of contacts or the fraction of buried sites in a protein structure is thought to be related to a protein's designability, and genes encoding more designable proteins should evolve faster than other genes. Several recent studies have tested this hypothesis but have found conflicting results. Here, we investigate how a gene's evolutionary rate is affected by its protein's contact density, considering the four species Escherichia coli, Saccharomyces cerevisiae, Drosophila melanogaster, and Homo sapiens. We find for all four species that contact density correlates positively with evolutionary rate, and that these correlations do not seem to be confounded by gene expression level. The strength of this signal, however, varies widely among species. We also study the effect of contact density on domain evolution in multidomain proteins and find that a domain's contact density influences the domain's evolutionary rate. Within the same protein, a domain with higher contact density tends to evolve faster than a domain with lower contact density. Our study provides evidence that contact density can increase evolutionary rates, and that it acts similarly on the level of entire proteins and of individual protein domains.
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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.