ArticleBioMed research international2014
Local packing density is the main structural determinant of the rate of protein sequence evolution at site level.
Article in BioMed research international, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- Estimating the Influence of Physicochemical and Biochemical Property Indexes on Selection for Amino Acids Usage in Eukaryotic Cells.Journal of molecular evolution · 2021Article
- Quantifying evolutionary importance of protein sites: A Tale of two measures.PLoS genetics · 2021Article
- Abundance Imparts Evolutionary Constraints of Similar Magnitude on the Buried, Surface, and Disordered Regions of Proteins.Frontiers in molecular biosciences · 2021Article
- Article
- Beyond Thermodynamic Constraints: Evolutionary Sampling Generates Realistic Protein Sequence Variation.Genetics · 2018Article
- Experimental Determination and Prediction of the Fitness Effects of Random Point Mutations in the Biosynthetic Enzyme HisA.Molecular biology and evolution · 2018Article
- Evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family.Journal of the Royal Society, Interface · 2017Article
- Computational prediction of the tolerance to amino-acid deletion in green-fluorescent protein.PloS one · 2017Article
- Calculating site-specific evolutionary rates at the amino-acid or codon level yields similar rate estimates.PeerJ · 2017Article
- Measuring evolutionary rates of proteins in a structural context.F1000Research · 2017Article
- Intermediate divergence levels maximize the strength of structure-sequence correlations in enzymes and viral proteins.Protein science : a publication of the Protein Society · 2016Article
- Dissecting the roles of local packing density and longer-range effects in protein sequence evolution.Proteins · 2016Article
- Causes of evolutionary rate variation among protein sites.Nature reviews. Genetics · 2016Review
- Structure-Encoded Global Motions and Their Role in Mediating Protein-Substrate Interactions.Biophysical journal · 2015Review
- (PS)2: protein structure prediction server version 3.0.Nucleic acids research · 2015Article
- Relationship between protein thermodynamic constraints and variation of evolutionary rates among sites.Physical biology · 2015Article
- Synthetic biology for the directed evolution of protein biocatalysts: navigating sequence space intelligently.Chemical Society reviews · 2015Review
- Sequence Conservation, Radial Distance and Packing Density in Spherical Viral Capsids.PloS one · 2015Article
- Too packed to change: side-chain packing and site-specific substitution rates in protein evolution.PeerJ · 2015Article
- Predicting evolutionary site variability from structure in viral proteins: buriedness, packing, flexibility, and design.Journal of molecular evolution · 2014Article
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7 authors.
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Abstract
Functional and biophysical constraints result in site-dependent patterns of protein sequence variability. It is commonly assumed that the key structural determinant of site-specific rates of evolution is the Relative Solvent Accessibility (RSA). However, a recent study found that amino acid substitution rates correlate better with two Local Packing Density (LPD) measures, the Weighted Contact Number (WCN) and the Contact Number (CN), than with RSA. This work aims at a more thorough assessment. To this end, in addition to substitution rates, we considered four other sequence variability scores, four measures of solvent accessibility (SA), and other CN measures. We compared all properties for each protein of a structurally and functionally diverse representative dataset of monomeric enzymes. We show that the best sequence variability measures take into account phylogenetic tree topology. More importantly, we show that both LPD measures (WCN and CN) correlate better than all of the SA measures, regardless of the sequence variability score used. Moreover, the independent contribution of the best LPD measure is approximately four times larger than that of the best SA measure. This study strongly supports the conclusion that a site's packing density rather than its solvent accessibility is the main structural determinant of its rate of evolution.
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