title: Comparison of volume and surface area nonpolar solvation free energy terms for implicit solvent simulations.
abstract: Implicit solvent models for molecular dynamics simulations are often composed of polar and nonpolar terms. Typically, the nonpolar solvation free energy is approximated by the solvent-accessible-surface area times a constant factor. More sophisticated approaches incorporate an estimate of the attractive dispersion forces of the solvent and∕or a solvent-accessible volume cavitation term. In this work, we confirm that a single volume-based nonpolar term most closely fits the dispersion and cavitation forces obtained from benchmark explicit solvent simulations of fixed protein conformations. Next, we incorporated the volume term into molecular dynamics simulations and find the term is not universally suitable for folding up small proteins. We surmise that while mean-field cavitation terms such as volume and SASA often tilt the energy landscape towards native-like folds, they also may sporadically introduce bottlenecks into the folding pathway that hinder the progression towards the native state.
authors.affiliation: Computational Sciences Division, U.S. Army Research Laboratory, Aberdeen, Maryland 21005, USA. michael.s.lee131.civ@mail.mil
authors.forename: Michael S
authors.initials: MS
authors.lastname: Lee
authors.forename: Mark A
authors.initials: MA
authors.lastname: Olson
mesh_terms: D003198:Computer Simulation; D056004:Molecular Dynamics Simulation; D009842:Oligopeptides / Q000737:chemistry; D010316:Particle Size; D017510:Protein Folding; D012997:Solvents / Q000737:chemistry*; D013499:Surface Properties; D013816:Thermodynamics
chemical_list: D009842:Oligopeptides; D012997:Solvents; C506175:chignolin