Direct-coupling analysis of residue coevolution captures native contacts across many protein families Faruck Morcos, Andrea Pagnani, Bryan Lunt, Arianna Bertolino, Debora S. Marks, Chris Sander, Riccardo Zecchina, José N. Onuchic, Terence Hwa, and Martin Weigt PNAS December 6, 2011 108 (49) E1293-E1301; https://doi.org/10.1073/pnas.1111471108 Direct-coupling analysis of residue coevolution captures native contacts across many protein families. The similarity in the three-dimensional structures of homologous proteins imposes strong constraints on their sequence variability. Can three-dimensional contacts in protein structures be predicted by analysis of correlated mutations? Direct coupling analysis for protein contact prediction. Furthermore, our analysis captures clear signals beyond intradomain residue contacts, arising, e.g., from alternative protein conformations, ligand-mediated residue couplings, and interdomain interactions in protein oligomers. Statistical Investigations of Protein Residue Direct Couplings, Direct coevolutionary couplings reflect biophysical residue interactions in proteins. Supplementary text: Direct-coupling analysis of residue co-evolution captures native contacts across many protein families F. Morcos, A. Pagnani, B. Lunt, A. Bertolino, D. Marks, C. Sander, R. Zecchina, J.N. It has long been suggested that the resulting correlations among amino acid compositions at different sequence positions can be exploited to infer spatial contacts within the … Inference of direct residue contacts in two-component signaling. Quantitative Biology - Quantitative Methods; Condensed Matter - Statistical Mechanics. Disentangling Direct from Indirect Co-Evolution of Residues in Protein Alignments, On the accuracy of inferring energetic coupling between distant sites in protein families from evolutionary imprints: Illustrations using lattice model, Determination of network of residues that regulate allostery in protein families using sequence analysis, Identification of direct residue contacts in protein–protein interaction by message passing, Correlated mutations and residue contacts in proteins. Faruck Morcos Center for Theoretical Biological Physics, University of California at San Diego, La Jolla, CA 92093-0374, USA. Some features of the site may not work correctly. Onuchic, T. Hwa, and M. Weigt I. INPUT DATA Data are given as a multiple sequence alignment It has long been suggested that the resulting correlations among amino acid compositions at different sequence positions can be exploited to infer spatial contacts within the tertiary protein structure. The similarity in the three-dimensional structures of homologous proteins imposes strong constraints on their sequence variability. The similarity in the three-dimensional structures of homologous proteins imposes strong constraints on their sequence variability. How Pairwise Coevolutionary Models Capture the Collective Residue Variability in Proteins? Direct coevolutionary couplings reflect biophysical residue interactions in proteins. Large-scale identification of coevolution signals across homo-oligomeric protein interfaces by direct coupling analysis, Statistical investigations of protein residue direct couplings, Evolutionary couplings detect side-chain interactions, From residue coevolution to protein conformational ensembles and functional dynamics, Patterns of coevolving amino acids unveil structural and dynamical domains. The basic hypothesis connecting correlated substitution pat- terns and residue–residue contacts is very simple: If two residues of a protein or a pair of interacting proteins form a contact, a destabilizing amino acid substitution at one position is expected tobecompensatedbyasubstitutionoftheotherpositionoverthe evolutionary timescale, in order for the residue pair to maintain attractive interaction. It has long been suggested that the resulting correlations among amino acid compositions at different sequence positions can be exploited to infer spatial contacts within the tertiary protein structure. Astrophysical Observatory. The ADS is operated by the Smithsonian Astrophysical Observatory under NASA Cooperative

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