Molecular dynamics study of macromolecular motions and polypeptide helical stabilities in solution

Abstract

Molecular dynamics simulations have been performed to investigate the relative importance of solvent effect and intramolecular conformational potentials on the properties of polymers in dilute solition. Bead-spring, free-rotating and polyethylene model chains, each composed of 30 beads, have been simulated in 738 solvent molecules. Results indicate that chain statistics are equally sensitive to solvent effect and intramolecular constraints, whereas local chain dynamics are predominantly described by intramolecular potentials. Translational diffusivities of all chains exhibit a linear decrease with increasing polymer-solvent interactions. A power law relation of the form t na is observed betveen the orientational correlation times t and the size n of chains segments for n = 8. a values increase with solvent quality. Stability of short helical polypeptides have been studied by molecular dynamics simulations. 13-residue polypeptides, composed of alanine, valine, serine or glycine, have been simulated in water and in vacuum. Water destabilizes the helical structure of alanine and valine, whereas glycine and serine exhibit intrinsic helix-breaking propensities in vacuum. Local solvation patterns around alanine Cb, valine Cg and serine Og atom are similar in helical state. Backbone hydrogen bonds are well protected by valine side chains, compared to alanine and serine.