Jump to main content
Jump to site search


The Effects of Implicit Modeling of Nonpolar Solvation on Protein Folding Simulation

Abstract

Implicit solvent models, in which the polar and nonpolar solvation free-energies of solute molecule are treated separately, have been widely adopted for molecular dynamics simulation of protein folding. While the development of implicit models is mainly focused on the methodological improvement and key parameter optimization for the polar solvation, the nonpolar solvation has been either ignored or described by simplistic surface area (SA) model. In this work, we performed the folding simulations of multiple β-hairpin and α-helical proteins with varied surface tension coefficients embedded in SA model to clearly demonstrate the effects of nonpolar solvation treated by popular SA model on protein folding. The results indicate that the change in surface tension coefficient does not alter the ability of implicit solvent simulation to reproduce protein native structure but indeed controls the components of the equilibrium conformational ensemble and modifies the energetic characterization of the folding transition pathway. The suitably set surface tension coefficient can yield explicit solvent simulation and/or experimentally suggested folding mechanism of protein. In addition, the implicit treatment of both polar and nonpolar components of solvation free-energy contributes to the overestimate of secondary structure in implicit solvent simulation.

Back to tab navigation

Supplementary files

Publication details

The article was accepted on 14 Jun 2018 and first published on 14 Jun 2018


Article type: Paper
DOI: 10.1039/C8CP03156H
Citation: Phys. Chem. Chem. Phys., 2018, Accepted Manuscript
  •   Request permissions

    The Effects of Implicit Modeling of Nonpolar Solvation on Protein Folding Simulation

    Q. Shao and W. Zhu, Phys. Chem. Chem. Phys., 2018, Accepted Manuscript , DOI: 10.1039/C8CP03156H

Search articles by author

Spotlight

Advertisements