Structural organization of a chain molecule with specific charge distribution: A molecular dynamics study

Abstract

We report the results of molecular dynamics simulations of a charged bead-monomer chain molecule with charge distribution adopted from immunoglobulin-binding domain B1 of protein-g. The beads of the model are connected by invariable bonds and interact with each other via the Coulomb potential. To study the low-temperature conformational space of the designed model we use standard canonical, microcanonical and multicanonical molecular dynamics simulations. We find that at low temperature T ¼ T c the chain undergoes a continuous freezing transition into one of many low-energy conformations. Below T c the molecule is a compact globule composed of an inner core, containing mostly charged monomers, and an outer corona, consisting of all the rest neutral units. All frozen conformations have almost equal potential energy but differ in structure. The potential energy surface of the model does not posses a pronounced ground-state minimum-an essential feature of proteinlike heteropolymers.

A Multicanonical Molecular Dynamics Study on a Simple Bead-Spring Model for Protein Folding

“…Therefore, we employ the following interactions between monomers:(i) the excluded volume interaction (soft-core model), (ii) the covalent bond interaction (spring model), (iii) Coulomb interaction, and (iv) hydrophobic interaction. Recently, molecular dynamics simulations for the model with (i)-(iii) interactions have been performed by Baumketner et al 7) In the present study, the hydrophobic interaction, which originates from solvent effects, is also involved. Thus, in this paper we will in particular discuss the competition between effects of the Coulomb interaction and those of the hydrophobic interaction.…”