Secondary structure bias in generalized Born solvent models: comparison of conformational ensembles and free energy of solvent polarization from explicit and implicit solvation.

ABSTRACT: The effects of the use of three generalized Born (GB) implicit solvent models on the thermodynamics of a simple polyalanine peptide are studied via comparing several hundred nanoseconds of well-converged replica exchange molecular dynamics (REMD) simulations using explicit TIP3P solvent to REMD simulations with the GB solvent models. It is found that when compared to REMD simulations using TIP3P the GB REMD simulations contain significant differences in secondary structure populations, most notably an overabundance of alpha-helical secondary structure. This discrepancy is explored via comparison of the differences in the electrostatic component of the free energy of solvation (DeltaDeltaG(pol)) between TIP3P (via thermodynamic Integration calculations), the GB models, and an implicit solve

SUBMITTER: Roe DR 

PROVIDER: S-EPMC4810457 | biostudies-literature | 2007 Feb

REPOSITORIES: biostudies-literature