A Coarse Grained Approach for the Simulation of Proteins

Authors: İvet BAHAR

Abstract: Data related to mean field potentials between residue pairs have been collected from 150 protein structures. The radial distributions of specific pairs are used to estimate potentials of mean force. The effective contact potentials between residue pairs obtained from the integration of radial distributions over the distance interval r\leq r_c = 6.4 \AA are in excellent agreement with those obtained by Miyazawa and Jernigan (1985, 1995). The hydrophobic interactions are verified to be dominantly strong in this range. Comparison of these with a new set of effective interresidue potentials for closer interresidue separations (r\leq 4.0\AA) demonstrates drastic changes in the most favorable interactions. In the closer approach case, highly specific interactions between charged and polar side chains predominate. These closer approach values could be utilized to select relative directions of residue side chains in protein simulations. The homogeneous contribution to side chain - side chain interactions appears to be significantly stronger than the specific terms. Local interactions have been considered from the viewpoint of the distributions of angles and torsions of virtual bonds connecting C^{\alpha} atoms. Bimodal distributions of torsional angles and bond angles are observed: a sharp peak associated with the gauche rotations in \alpha-helices and a second more diffuse peak attributed to the more extended backbone conformation in \beta-strands. \alpha--helical and \beta--strand propensities dependent on residue type, derived from the distributions, correlate well with a large variety of experiments.