ArticlePhysical biology2015
Relationship between protein thermodynamic constraints and variation of evolutionary rates among sites.
Article in Physical biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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30 citing papers in PubMed.
- Site-Specific Structure and Stability Constrained Substitution Models Improve Phylogenetic Inference.Systematic biology · 2026Article
- Accurate prediction of substitution rates at protein sites with a mutation-selection model.Scientific reports · 2025Article
- Repeatability of protein structural evolution following convergent gene fusions.Nature communications · 2025Article
- Improved prediction of site-rates from structure with averaging across homologs.Protein science : a publication of the Protein Society · 2024Article
- A mutational atlas for Parkin proteostasis.Nature communications · 2024Article
- Atomistic simulation of protein evolution reveals sequence covariation and time-dependent fluctuations of site-specific substitution rates.PLoS computational biology · 2023Article
- Secretory quality control constrains functional selection-associated protein structure innovation.Communications biology · 2022Article
- Evolution of Amino Acid Propensities under Stability-Mediated Epistasis.Molecular biology and evolution · 2022Article
- Evolutionary coupling range varies widely among enzymes depending on selection pressure.Biophysical journal · 2021Article
- Prediction and Evolution of the Molecular Fitness of SARS-CoV-2 Variants: Introducing SpikePro.Viruses · 2021Article
- Abundance Imparts Evolutionary Constraints of Similar Magnitude on the Buried, Surface, and Disordered Regions of Proteins.Frontiers in molecular biosciences · 2021Article
- Site-Specific Amino Acid Distributions Follow a Universal Shape.Journal of molecular evolution · 2020Article
- Large-scale in silico mutagenesis experiments reveal optimization of genetic code and codon usage for protein mutational robustness.BMC biology · 2020Article
- Computer-Assisted Recombination (CompassR) Teaches us How to Recombine Beneficial Substitutions from Directed Evolution Campaigns.Chemistry (Weinheim an der Bergstrasse, Germany) · 2020Article
- The variation among sites of protein structure divergence is shaped by mutation and scaled by selection.Current research in structural biology · 2020Article
- Sequence-structure-function relationships in class I MHC: A local frustration perspective.PloS one · 2020Article
- The Site-Specific Amino Acid Preferences of Homologous Proteins Depend on Sequence Divergence.Genome biology and evolution · 2019Article
- Article
- Biophysical Models of Protein Evolution: Understanding the Patterns of Evolutionary Sequence Divergence.Annual review of biophysics · 2017Review
- Identification of positive selection in genes is greatly improved by using experimentally informed site-specific models.Biology direct · 2017Article
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3 authors.
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Abstract
Evolutionary-rate variation among sites within proteins depends on functional and biophysical properties that constrain protein evolution. It is generally accepted that proteins must be able to fold stably in order to function. However, the relationship between stability constraints and among-sites rate variation is not well understood. Here, we present a biophysical model that links the thermodynamic stability changes due to mutations at sites in proteins ([Formula: see text]) to the rate at which mutations accumulate at those sites over evolutionary time. We find that such a 'stability model' generally performs well, displaying correlations between predicted and empirically observed rates of up to 0.75 for some proteins. We further find that our model has comparable predictive power as does an alternative, recently proposed 'stress model' that explains evolutionary-rate variation among sites in terms of the excess energy needed for mutants to adopt the correct active structure ([Formula: see text]). The two models make distinct predictions, though, and for some proteins the stability model outperforms the stress model and vice versa. We conclude that both stability and stress constrain site-specific sequence evolution in proteins.
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