Evaluation of Salt Bridge Structure and Energetics in Peptides Using Explicit, Implicit, and Hybrid Solvation Models.

Abstract

Replica exchange or parallel tempering molecular dynamics (REMD) is widely used to enhance the exploration of free energy landscapes for complex molecular systems. However its application to large systems is hampered by the scaling of the number of required replicas with an increasing system size. We recently proposed an improved REMD method where the exchange probabilities were calculated using a hybrid explicit/implicit solvent model. We previously tested this hybrid solvent REMD approach on alanine polypeptides of 1, 3, and 10 residues and obtained very good agreement with fully solvated REMD simulations while significantly reducing the number of replicas required. In this study we continue evaluating the applicability of the hybrid solvent REMD method through comparing the free energy of formation of ion pairs using model peptides. In accord with other studies, pure GB simulations resulted in overstabilized salt bridges, whereas the hybrid models produced free energy profiles in close agreement with fully solvated simulations, including solvent separated minima. Furthermore, the structure of the salt bridge in explicit solvent is reproduced by the hybrid solvent REMD method, while the GB simulations favor a different geometry.