Low-resolution structural modeling of protein interactome

Protein-protein alternative binding modes do not overlap

Proteins often bind other proteins in more than one way. Thus alternative binding modes is an essential feature of protein interactions. Such binding modes may be detected by X-ray crystallography and thus reflected in Protein Data Bank. The alternative binding is often observed not for the protein itself but for its structural homolog. The results of this study based on the analysis of a comprehensive set of co-crystallized protein-protein complexes show that the alternative binding modes generally do not overlap, but are spatially separated. This effect is based on molecular recognition characteristics of the protein structures. The results are also in excellent agreement with the intermolecular energy funnel size estimates obtained previously by an independent methodology. The results provide an important insight into the principles of protein association, as well as potential guidelines for modeling of protein complexes and the design of protein interfaces.

InterEvScore: a novel coarse-grained interface scoring function using a multi-body statistical potential coupled to evolution

MOTIVATION

Structural prediction of protein interactions currently remains a challenging but fundamental goal. In particular, progress in scoring functions is critical for the efficient discrimination of near-native interfaces among large sets of decoys. Many functions have been developed using knowledge-based potentials, but few make use of multi-body interactions or evolutionary information, although multi-residue interactions are crucial for protein-protein binding and protein interfaces undergo significant selection pressure to maintain their interactions.

RESULTS

This article presents InterEvScore, a novel scoring function using a coarse-grained statistical potential including two- and three-body interactions, which provides each residue with the opportunity to contribute in its most favorable local structural environment. Combination of this potential with evolutionary information considerably improves scoring results on the 54 test cases from the widely used protein docking benchmark for which evolutionary information can be collected. We analyze how our way to include evolutionary information gradually increases the discriminative power of InterEvScore. Comparison with several previously published scoring functions (ZDOCK, ZRANK and SPIDER) shows the significant progress brought by InterEvScore.

AVAILABILITY

http://biodev.cea.fr/interevol/interevscore

CONTACT

guerois@cea.fr

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.