Modeling Structural Constraints on Protein Evolution via Side-Chain Conformational States

Umberto Perron, Alexey M. Kozlov, Alexandros Stamatakis, Nick Goldman*, Iain H. Moal, Tal Pupko (Editor)

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review


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.

Original languageEnglish
Pages (from-to)2086-2103
Number of pages18
JournalMolecular Biology and Evolution
Issue number9
StatePublished - 1 Sep 2019


FundersFunder number
European Molecular Biology Laboratory
Biotechnology and Biological Sciences Research CouncilBB/N011600/1
Klaus Tschira Stiftung


    • molecular evolution
    • phylogenetic estimation
    • phylogenetics
    • protein evolution
    • protein structure
    • rotamer
    • substitution model


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