Direct-coupling analysis of residue coevolution captures native contacts across many protein families

Proceedings of the National Academy of Sciences of the United States of America
Faruck MorcosMartin Weigt

Abstract

The similarity in the three-dimensional structures of homologous proteins imposes strong constraints on their sequence variability. 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. Crucial to this inference is the ability to disentangle direct and indirect correlations, as accomplished by the recently introduced direct-coupling analysis (DCA). Here we develop a computationally efficient implementation of DCA, which allows us to evaluate the accuracy of contact prediction by DCA for a large number of protein domains, based purely on sequence information. DCA is shown to yield a large number of correctly predicted contacts, recapitulating the global structure of the contact map for the majority of the protein domains examined. 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. Our findings suggest that contacts predicted by DCA can be used as a reliable guide to facilitate computational predictions of alte...Continue Reading

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Related Concepts

Gene Products, Protein
Plasma Protein Binding Capacity
Protein Complex Location Assembly
Protein Interaction Mapping
Protein Multimerization
Protein Conformation
Protein Domain
Ligands Activity
Genome Sequencing
Amino Acid [EPC]

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