ArticleMolecular biology and evolution2019
Modeling Structural Constraints on Protein Evolution via Side-Chain Conformational States.
Article in Molecular biology and evolution, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed, 22 citations in OpenAlex.
- Advances and opportunities for computational interrogation of plant proteins.The Plant journal : for cell and molecular biology · 2026Review
- Protein Structural Phylogenetics.Genome biology and evolution · 2025Review
- Detecting Interspecific Positive Selection Using Convolutional Neural Networks.Molecular biology and evolution · 2025Article
- Amino Acid Properties, Substitution Rates, and the Nearly Neutral Theory.Genome biology and evolution · 2025Article
- 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
- A sequence-based evolutionary distance method for Phylogenetic analysis of highly divergent proteins.Scientific reports · 2023Article
- An excavate root for the eukaryote tree of life.Science advances · 2023Article
- Characterization of active peptides derived from three leeches and comparison of their anti-thrombotic mechanisms using the tail vein thrombosis model in mice and metabonomics.Frontiers in pharmacology · 2023Article
- Ambiguity Coding Allows Accurate Inference of Evolutionary Parameters from Alignments in an Aggregated State-Space.Systematic biology · 2021Article
- Integrated structural and evolutionary analysis reveals common mechanisms underlying adaptive evolution in mammals.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- The search of sequence variants using a constrained protein evolution simulation approach.Computational and structural biotechnology journal · 2020Article
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Authors and funding
5 authors at 2 institutions in 2 countries.
Funding
Abstract
Few models of sequence evolution incorporate parameters describing protein structure, despite its high conservation, essential functional role and increasing availability. We present a structurally aware empirical substitution model for amino acid sequence evolution in which proteins are expressed using an expanded alphabet that relays both amino acid identity and structural information. Each character specifies an amino acid as well as information about the rotamer configuration of its side-chain: the discrete geometric pattern of permitted side-chain atomic positions, as defined by the dihedral angles between covalently linked atoms. By assigning rotamer states in 251,194 protein structures and identifying 4,508,390 substitutions between closely related sequences, we generate a 55-state "Dayhoff-like" model that shows that the evolutionary properties of amino acids depend strongly upon side-chain geometry. The model performs as well as or better than traditional 20-state models for divergence time estimation, tree inference, and ancestral state reconstruction. We conclude that not only is rotamer configuration a valuable source of information for phylogenetic studies, but that modeling the concomitant evolution of sequence and structure may have important implications for understanding protein folding and function.
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