Molecular dynamics simulation study of peptide isomerization at aqueous interfaces

Abstract

Aqueous interfaces are one of the important systems in which biomolecules such as peptides and proteins play a major role in chemistry and biology. In this study, molecular dynamics (MD) simulation was performed to calculate the conformational free energy surface and isomerization rate constant for the structure of peptides at the air/water interface and graphene/water interface, which are typical examples of hydrophilic-hydrophobic interfaces. Through meta-dynamics simulation, we analyzed how the β, α, and αL structures of peptides were stabilized near aqueous interfaces by calculating the Ramachandran plot. In addition, the value of αL to β isomerization rate constant decreased by three times at the air/water interface compared to the bulk state, while the value of α to β isomerization rate constant increased by three times. In the case of the graphene/water interface, there was a negligible change in the conformational equilibria of peptides when the surface polarization was accounted for. But when the external voltage is applied, however, the value of αL to β isomerization rate constant was enhanced when the surface polarization effect was accounted for.