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Article Dans Une Revue Journal of Chemical Physics Année : 2016

Direct coevolutionary couplings reflect biophysical residue interactions in proteins

Résumé

Coevolution of residues in contact imposes strong statistical constraints on the sequence variability between homologous proteins. Direct-Coupling Analysis (DCA), a global statistical inference method, successfully models this variability across homologous protein families to infer structural information about proteins. For each residue pair, DCA infers 21 x 21 matrices describing the coevolutionary coupling for each pair of amino acids (or gaps). To achieve the residue-residue contact prediction, these matrices are mapped onto simple scalar parameters; the full information they contain gets lost. Here, we perform a detailed spectral analysis of the coupling matrices resulting from 70 protein families, to show that they contain quantitative information about the physico-chemical properties of amino-acid interactions. Results for protein families are corroborated by the analysis of synthetic data from lattice-protein models, which emphasizes the critical effect of sampling quality and regularization on the biochemical features of the statistical coupling matrices. Published by AIP Publishing.
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Dates et versions

hal-01528504 , version 1 (15-01-2024)

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Alice Coucke, Guido Uguzzoni, Francesco Oteri, Simona Cocco, Rémi Monasson, et al.. Direct coevolutionary couplings reflect biophysical residue interactions in proteins. Journal of Chemical Physics, 2016, 145 (17), pp.174102. ⟨10.1063/1.4966156⟩. ⟨hal-01528504⟩
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