Molecular dynamics simulations to study the solvent influence on protein structure

Molecular simulations were carried out to study the influence of different water models in two protein systems. Most of the solvents used in protein simulations, e.g., SPC/E or TIP3P, fail to reproduce the bulk water static dielectric constant. Recently a new water model, TIP4P/epsilon, which reproduces the experimental dielectric constant was reported. Therefore, simulations for two different proteins, Lysozyme and Ubiquitin with SPC/E, TIP3P and TIP4P/epsilon solvents were carried out. Dielectric constants and structural properties were calculated and comparisons were conducted. The structural properties between the three models are very similar, however, the dielectric constants are different in each case. (C) 2016 Elsevier B.V. All rights reserved.