PT  - JOURNAL ARTICLE
AU  - Thomas A. Hopf
AU  - Charlotta P. I. Schärfe
AU  - João P. G. L. M. Rodrigues
AU  - Anna G. Green
AU  - Chris Sander
AU  - Alexandre M. J. J. Bonvin
AU  - Debora S. Marks
TI  - Sequence co-evolution gives 3D contacts and structures of protein complexes
AID  - 10.1101/004762
DP  - 2014 Jan 01
TA  - bioRxiv
PG  - 004762
4099  - http://biorxiv.org/content/early/2014/09/15/004762.short
4100  - http://biorxiv.org/content/early/2014/09/15/004762.full
AB  - Protein-protein interactions are fundamental to many biological processes. Experimental screens have identified tens of thousands of interactions and structural biology has provided detailed functional insight for select 3D protein complexes. An alternative rich source of information about protein interactions is the evolutionary sequence record. Building on earlier work, we show that analysis of correlated evolutionary sequence changes across proteins identifies residues that are close in space with sufficient accuracy to determine the three-dimensional structure of the protein complexes. We evaluate prediction performance in blinded tests on 76 complexes of known 3D structure, predict protein-protein contacts in 32 complexes of unknown structure, and demonstrate how evolutionary couplings can be used to distinguish between interacting and non-interacting protein pairs in a large complex. With the current growth of sequence databases, we expect that the method can be generalized to genome-wide elucidation of protein-protein interaction networks and used for interaction predictions at residue resolution.