ROTAS: a rotamer-dependent, atomic statistical potential for assessment and prediction of protein structures.

Jungkap Park,Kazuhiro Saitou

doi:10.1186/1471-2105-15-307

Abstract

BackgroundMultibody potentials accounting for cooperative effects of molecular interactions have shown better accuracy than typical pairwise potentials. The main challenge in the development of such potentials is to find relevant structural features that characterize the tightly folded proteins. Also, the side-chains of residues adopt several specific, staggered conformations, known as rotamers within protein structures. Different molecular conformations result in different dipole moments and induce charge reorientations. However, until now modeling of the rotameric state of residues had not been incorporated into the development of multibody potentials for modeling non-bonded interactions in protein structures.ResultsIn this study, we develop a new multibody statistical potential which can account for the influence of rotameric states on the specificity of atomic interactions. In this potential, named “rotamer-dependent atomic statistical potential” (ROTAS), the interaction between two atoms is specified by not only the distance and relative orientation but also by two state parameters concerning the rotameric state of the residues to which the interacting atoms belong. It was clearly found that the rotameric state is correlated to the specificity of atomic interactions. Such rotamer-dependencies are not limited to specific type or certain range of interactions. The performance of ROTAS was tested using 13 sets of decoys and was compared to those of existing atomic-level statistical potentials which incorporate orientation-dependent energy terms. The results show that ROTAS performs better than other competing potentials not only in native structure recognition, but also in best model selection and correlation coefficients between energy and model quality.ConclusionsA new multibody statistical potential, ROTAS accounting for the influence of rotameric states on the specificity of atomic interactions was developed and tested on decoy sets. The results show that ROTAS has improved ability to recognize native structure from decoy models compared to other potentials. The effectiveness of ROTAS may provide insightful information for the development of many applications which require accurate side-chain modeling such as protein design, mutation analysis, and docking simulation.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2105-15-307) contains supplementary material, which is available to authorized users.

Highlights

Multibody potentials accounting for cooperative effects of molecular interactions have shown better accuracy than typical pairwise potentials
While GOAP only reflects in some average sense the preferred orientation between interacting atoms, rotamer-dependent atomic statistical potential” (ROTAS) adjusts the preferred orientation accurately depending on the rotameric state
Classification of near-native and non-native model In order to compare the performance of ROTAS and other potentials in a more robust way, we evaluated the performance of statistical potentials using receiver operating characteristic (ROC) technique [69]

Summary

Introduction

Multibody potentials accounting for cooperative effects of molecular interactions have shown better accuracy than typical pairwise potentials. The introduction of orientation dependencies of interactions into typical distance-dependent pairwise potentials has achieved substantial improvements in both residue-level [33,34,35,36] and atomic-level potentials [37,38,39,40]. These multibody potentials are able to describe the 3-D interactions more completely and able to account for cooperative effects of molecular interactions more accurately than typical pairwise potentials

Methods

Results

Conclusion