Langevin Dynamics Simulations to Predict Sidechain Dihedral Angle Distributions

Abstract

Despite recent improvements in computational methods for protein design, we still lack a predictive understanding of protein structure and interactions. We perform Langevin dynamics simulations of protein models that include only hard-sphere and geometric constraints to investigate the distribution of sidechain dihedral angles. We first study dipeptides of nonpolar amino acids as a function of the backbone dihedral angles and cooling rate, and compare the sidechain dihedral angle distributions to those from protein crystal structures in the protein data bank. In addition, we predict the sidechain dihedral angle propensities in the core region of the protein ROP and several mutants. The studies serve as a first step in developing the ability to quantitatively rank the energies of designed protein constructs.