ArticleBioinformatics (Oxford, England)2013
Protein evolution along phylogenetic histories under structurally constrained substitution models.
Article in Bioinformatics (Oxford, England), 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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33 citing papers in PubMed.
- Integrating evolutionary signals and predicted protein structure reveals localized molecular divergence in Cereus lineages.Genetica · 2026Article
- Article
- nT4X and nT4M: Novel Time Non-reversible Mixture Amino Acid Substitution Models.Journal of molecular evolution · 2025Article
- Empirical substitution models of protein evolution: database, relationships, and modeling considerations.Database : the journal of biological databases and curation · 2025Article
- Genome-wide identification of the key kinesin genes during fiber and boll development in upland cotton (Gossypium hirsutum L.).Molecular genetics and genomics : MGG · 2024Article
- Selection among site-dependent structurally constrained substitution models of protein evolution by approximate Bayesian computation.Bioinformatics (Oxford, England) · 2024Article
- Substitution Models of Protein Evolution with Selection on Enzymatic Activity.Molecular biology and evolution · 2024Article
- Genome-wide identification of the key Kinesin genes during fiber and boll development in upland cotton (Gossypium hirsutum L).Molecular genetics and genomics : MGG · 2024Article
- Consequences of Genetic Recombination on Protein Folding Stability.Journal of molecular evolution · 2023Article
- Proteome-Wide Structural Computations Provide Insights into Empirical Amino Acid Substitution Matrices.International journal of molecular sciences · 2023Article
- Immunoescape of HIV-1 in Env-EL9 CD8 + T cell response restricted by HLA-B*14:02 in a Non progressor who lost twenty-seven years of HIV-1 control.Retrovirology · 2022Article
- From structure to function - Ligand recognition by myeloid C-type lectin receptors.Computational and structural biotechnology journal · 2022Review
- Methodologies for Microbial Ancestral Sequence Reconstruction.Methods in molecular biology (Clifton, N.J.) · 2022Review
- Article
- ProteinEvolverABC: coestimation of recombination and substitution rates in protein sequences by approximate Bayesian computation.Bioinformatics (Oxford, England) · 2021Article
- Felsenstein Phylogenetic Likelihood.Journal of molecular evolution · 2021Article
- A common root for coevolution and substitution rate variability in protein sequence evolution.Scientific reports · 2019Article
- ASPEN, a methodology for reconstructing protein evolution with improved accuracy using ensemble models.eLife · 2019Article
- Evaluating Statistical Multiple Sequence Alignment in Comparison to Other Alignment Methods on Protein Data Sets.Systematic biology · 2019Article
- The intrinsic dimension of protein sequence evolution.PLoS computational biology · 2019Article
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4 authors.
Funding
Abstract
motivationModels of molecular evolution aim at describing the evolutionary processes at the molecular level. However, current models rarely incorporate information from protein structure. Conversely, structure-based models of protein evolution have not been commonly applied to simulate sequence evolution in a phylogenetic framework, and they often ignore relevant evolutionary processes such as recombination. A simulation evolutionary framework that integrates substitution models that account for protein structure stability should be able to generate more realistic in silico evolved proteins for a variety of purposes.
resultsWe developed a method to simulate protein evolution that combines models of protein folding stability, such that the fitness depends on the stability of the native state both with respect to unfolding and misfolding, with phylogenetic histories that can be either specified by the user or simulated with the coalescent under complex evolutionary scenarios, including recombination, demographics and migration. We have implemented this framework in a computer program called ProteinEvolver. Remarkably, comparing these models with empirical amino acid replacement models, we found that the former produce amino acid distributions closer to distributions observed in real protein families, and proteins that are predicted to be more stable. Therefore, we conclude that evolutionary models that consider protein stability and realistic evolutionary histories constitute a better approximation of the real evolutionary process.
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