AVS 51st International Symposium
    Biomaterial Interfaces Monday Sessions
       Session BI-MoP

Paper BI-MoP21
Empirical Force Field Evaluation for the Molecular Simulation of Protein Adsorption

Monday, November 15, 2004, 5:00 pm, Room Exhibit Hall B

Session: Poster Session
Presenter: V. Raut, Clemson University
Authors: V. Raut, Clemson University
S.J. Stuart, Clemson University
R.A. Latour, Clemson University
Correspondent: Click to Email
Molecular simulation provides a direct method to theoretically investigate the molecular mechanisms governing the adsorption behavior of proteins to biomaterials surfaces. Because of their size, empirical force field based methods must be used for these types of simulations. Force fields (ffs), however, must be parameterized for specific molecular systems. While ffs have been designed to accurately represent the behavior of proteins in solution, none have considered peptide-surface adsorption behavior in their parameterization. Therefore, there is currently no basis to support the accuracy of simulation results. The objective of this research was to develop computational methods to complement our previous experimental studies that measured the adsorption free energy (G*) for a host-guest peptide on Au-alkanethiol self assembled monolayer surfaces (SAMs), and to use these methods for ff evaluation. Host-guest peptides were modeled in the form of SGSG-X-GSGS, where G=glycine, S=serine, and X=any selected peptide type. Molecular dynamics simulations were conducted using the GROMACS ff to calculate G* for these peptides over functionalized SAMs (CH3, OH, NH2, COOH, PEG) in a 40@Ao@ x 40@Ao@ x 60@Ao@ simulation cell with explicit solvation (water with Na+ and Cl- ions) contained within periodic boundary conditions. While simulation results for certain peptide-SAM systems are generally in agreement with experiments, others show substantial deviations from expected adsorption behavior. Parameter modifications of this ff are thus required for this application. Further work is planned for the eventual development of a validated ff for protein adsorption simulations.