AVS 52nd International Symposium
    Biomaterial Interfaces Wednesday Sessions
       Session BI1-WeM

Paper BI1-WeM6
The Development of Molecular Simulation Capabilities as a Tool to Understand Protein Adsorption Behavior at the Molecular Level

Wednesday, November 2, 2005, 10:00 am, Room 311

Session: Protein-Surface Interactions
Presenter: R.A. Latour, Clemson University
Authors: F. Wang, Clemson University
Y. Sun, Clemson University
S.J. Stuart, Clemson University
R.A. Latour, Clemson University
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Although important, the molecular mechanisms involved in protein adsorption processes are still not well understood. Empirical force field-based molecular simulation methods have been successfully developed to enable molecular mechanisms to be studied for other applications, such as protein folding and ligand-receptor binding; these methods have similar potential to help elucidate the molecular mechanisms for protein adsorption. Two of the most important problems that must be addressed before methods can be developed for this application are the force field problem and the sampling problem. The force field problem relates to the design of the energy function and its parameters that control how atoms interact with one another during a simulation. The sampling problem relates to the need to sample molecular events over timeframes that extend far beyond those that are capable of being reached using standard molecular dynamics methods. The objective of our research is to develop computational methods to address both of these issues, with an initial focus on the development of methods to calculate the free energy of peptide adsorption. In conventional simulations, peptides become stuck in low-energy conformations and this prevents adsorption free energy from being accurately calculated. We are therefore developing biased-sampling methods to enable adequate conformational space to be sampled in peptide-surface simulations so that adsorption free energy can be properly calculated. With this capability, the accuracy of a protein adsorption force field can be evaluated, modified, and validated by comparison between calculated adsorption free energy and experimentally measured values.