Comparison of solvation-effect methods for the simulation of peptide interactions with a hydrophobic surface

✍ Scribed by Yu Sun; Brian N. Dominy; Robert A. Latour

• Publisher: John Wiley and Sons
• Year: 2007
• Tongue: English
• Weight: 759 KB
• Volume: 28
• Category: Article
• ISSN: 0192-8651
• DOI: 10.1002/jcc.20716

✦ Synopsis

Abstract

In this study we investigated the interaction behavior between thirteen different small peptides and a hydrophobic surface using three progressively more complex methods of representing solvation effects: a united‐atom implicit solvation method [CHARMM 19 force field (C19) with Analytical Continuum Electrostatics (ACE)], an all‐atom implicit solvation method (C22 with GBMV), and an all‐atom explicit solvation method (C22 with TIP3P). The adsorption behavior of each peptide was characterized by the calculation of the potential of mean force as a function of peptide‐surface separation distance. The results from the C22/TIP3P model suggest that hydrophobic peptides exhibit relatively strong adsorption behavior, polar and positively‐charged peptides exhibit negligible to relatively weak favorable interactions with the surface, and negatively‐charged peptides strongly resist adsorption. Compared to the TIP3P model, the ACE and GBMV implicit solvent models predict much stronger attractions for the hydrophobic peptides as well as stronger repulsions for the negatively‐charged peptides on the CH~3~‐SAM surface. These comparisons provide a basis from which each of these implicit solvation methods may be reparameterized to provide closer agreement with explicitly represented solvation in simulations of peptide and protein adsorption to functionalized surfaces. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007