Comparison of implicit solvent models for the simulation of protein-surface interactions.
Empirical force field-based molecular simulations can provide valuable atomistic-level insights into protein-surface interactions in aqueous solution. While the implicit treatment of solvation effects is desired as a means of improving simulation efficiency, existing implicit solvent models were primarily developed for the simulation of peptide or protein behavior in solution alone, and thus may not be appropriate for protein interactions with synthetic material surfaces. The objective of this research was to calculate the change in free energy as a function of surface-separation distance for peptide-surface interactions using different empirical force field-based implicit solvation models (ACE, ASP, EEF1, and RDIE with the CHARMM 19 force field), and to compare these results with the same calculations conducted using density functional theory (DFT) combined with the self-consistent reaction field (SCRF) implicit solvation model. These comparisons show that distinctly different types of behavior are predicted with each implicit solvation method, with ACE providing the best overall agreement with DFT/SCRF calculations. These results also identify areas where ACE is in need of improvement for this application and provide a basis for subsequent parameter refinement.
Sun
Yu
Y
Department of Bioengineering, Clemson University, Clemson, South Carolina 29634, USA.
Latour
Robert A
RA
D003198:Computer Simulation; D008956:Models, Chemical; D008958:Models, Molecular; D011506:Proteins / Q000737:chemistry*; D012996:Solutions / Q000737:chemistry; D012997:Solvents / Q000737:chemistry; D013499:Surface Properties; D014867:Water / Q000737:chemistry
D011506:Proteins; D012996:Solutions; D012997:Solvents; D014867:Water