Local deformations of polymers with nonplanar rigid main-chain internal coordinates

Abstract

A procedure for local deformation of a polymer by concerted rotation of several main-chain dihedral angles has been adapted recently to be an elementary move in Monte Carlo simulations. We expand the applicability of the move by generalizing the formalism to allow fixed dihedral angles that sequentially interrupt the rotatable bonds to be nonplanar. The method is applied to the simulation of a small protein in which the dihedral angles of the peptide bonds are allowed to deviate from their ideal values and to the simulation of an RNA hairpin loop in which the main chain (C3′C4′) bonds that are constrained by the sugar rings are rigid but nonplanar. The move is found to increase the rate at which the systems explore their accessible configuration spaces. The relation of the results to previous studies and possible enhancements of the method are discussed. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 1132–1144, 2000