Two dimensional umbrella sampling techniques for the computer simulation study of helical peptides at thermal equilibrium: The 3K(I) peptide in vacuo and solution

Abstract

New computational techniques are developed to study conformational equilibrium in helical peptides at finite temperature. Two dimensional umbrella sampling methods involving coordinate systems which incorporate the α-helical hydrogen bonding distances along the peptide backbone as collective variables are presented. The umbrella sampling techniques are combined with new extended system multiple time step molecular dynamics simulation methods to allow peptide equilibria to be examined on a realistic potential energy surface. In particular, this combination of methods is employed to study a sixteen residue alanine-based peptide, Ac−(AAAAK)3A−NH2, at T=300 K in vacuo and solution, under the all-atom CHARMM22 force field. The efficiency of the multiple time step integration methodology permitted a minimum total run length of 30 ns to be employed in each umbrella sampling calculation reported.