title: Connecting free energy surfaces in implicit and explicit solvent: an efficient method to compute conformational and solvation free energies.
abstract: The ability to accurately model solvent effects on free energy surfaces is important for understanding many biophysical processes including protein folding and misfolding, allosteric transitions, and protein–ligand binding. Although all-atom simulations in explicit solvent can provide an accurate model for biomolecules in solution, explicit solvent simulations are hampered by the slow equilibration on rugged landscapes containing multiple basins separated by barriers. In many cases, implicit solvent models can be used to significantly speed up the conformational sampling; however, implicit solvent simulations do not fully capture the effects of a molecular solvent, and this can lead to loss of accuracy in the estimated free energies. Here we introduce a new approach to compute free energy changes in which the molecular details of explicit solvent simulations are retained while also taking advantage of the speed of the implicit solvent simulations. In this approach, the slow equilibration in explicit solvent, due to the long waiting times before barrier crossing, is avoided by using a thermodynamic cycle which connects the free energy basins in implicit solvent and explicit solvent using a localized decoupling scheme. We test this method by computing conformational free energy differences and solvation free energies of the model system alanine dipeptide in water. The free energy changes between basins in explicit solvent calculated using fully explicit solvent paths agree with the corresponding free energy differences obtained using the implicit/explicit thermodynamic cycle to within 0.3 kcal/mol out of ∼3 kcal/mol at only ∼8% of the computational cost. We note that WHAM methods can be used to further improve the efficiency and accuracy of the implicit/explicit thermodynamic cycle.
authors.affiliation: Center for Biophysics & Computational Biology and Institute for Computational Molecular Sciences Temple University, Philadelphia, Pennsylvania 19122, United States
authors.forename: Nanjie
authors.initials: N
authors.lastname: Deng
authors.forename: Bin W
authors.initials: BW
authors.lastname: Zhang
authors.forename: Ronald M
authors.initials: RM
authors.lastname: Levy
mesh_terms: D056004:Molecular Dynamics Simulation; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D012995:Solubility; D012997:Solvents / Q000737:chemistry*; D013499:Surface Properties; D013816:Thermodynamics
chemical_list: D011506:Proteins; D012997:Solvents