Article

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

Center for Theoretical Biological Physics, University of California at San Diego, La Jolla, CA 92093-0374, USA.
Proceedings of the National Academy of Sciences (Impact Factor: 9.67). 11/2011; 108(49):E1293-301. DOI: 10.1073/pnas.1111471108
Source: PubMed

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 alternative protein conformations, protein complex formation, and even the de novo prediction of protein domain structures, contingent on the existence of a large number of homologous sequences which are being rapidly made available due to advances in genome sequencing.

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    • "SP Round X ( Moult et al . 2014 ) , a new category of " contact - assisted " pre - diction was proposed . Experimental data such as NMR , chemical shift , cross - linking , and surface labeling have been proved to be instrumental . Previously , contacts inferred from evolutionary information also achieved success in pro - tein structure modeling ( Morcos et al . 2011 ) but , at the time of writing , they still have not had an impact in blind structure prediction tests ( Moult et al . 2014 ) . Nevertheless , these explorations have revealed a trend in structure modeling : With the help of simple experimental constraints , structure modeling could achieve the application level in providing structural "
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