Short-range and long-range interactions in Monte Carlo free energy calculations on polypeptide chains

Abstract

Monte Carlo simulations based on a partition of the conformational energy into short-range and long-range interactions are performed in order to estimate the free energy and entropy of short polypeptide chains. Values of these quantities are obtained by using an ‘‘umbrella-sampling’’method particularly adapted to the partition of energy. Reference systems are completely determined by considering short-range interactions alone. In this case, the chain model allows us to calculate the average energy, the free energy and entropy. Moreover, the configuration of minimum energy is determined by an algorithm proposed for chain models with only nearest neighbor interacting units. When long-range interactions are also considered, the relative effects of the two types of interactions on the chain configuration can be appreciated by estimates of entropy variations. Such variations are related to the folding of the chain which can be modulated by using different dielectric constants in order to take into account solvent effects. The different methods of calculation are applied on models of the polypeptide hormones enkephalin and β-casomorphin.