Archiviertes Physik-Kolloquium:

08. Dec. 2011, 16:15 Uhr, Gebäude NW1, Raum H3

The Synergistic Combination of Molecular Simulation and Experimental Methods to Understand and Control Protein-Surface Interactions

Prof. Dr. Robert A. Latour, Clemson University, USA

Molecular simulation methods have the potential to provide the ability to visualize and predict protein-surface interactions at the atomic level, thus potentially providing a valuable tool for surface design to control the behavior of proteins at interfaces. However, this potential can only be realized if methods are properly developed and validated to accurately represent these types of complex interactions. Advancements in both simulation and experimental methods are required to achieve this goal. Developments in simulation methods are needed to enable large molecular systems to be adequately represented, equilibrated, and sampled so that simulation results can be properly compared with experiment. Likewise, experimental methods are needed to provide the kinds of data that can be used to assess, tune, and validate molecular simulations. To address these needs, we are working to develop a broad set of synergistic experimental and simulation methods to characterize adsorption behavior using a set of unstructured host-guest peptides, peptides designed to have secondary structure, and small bioactive proteins on alkanethiol self-assembled monolayers (SAMs) and other material surfaces. Experimental methods being developed include surface plasmon resonance spectroscopy (SPR), atomic force microscopy (AFM), circular dichroism spectropolarimetry (CD), and amino acid side-chain modification/mass spectrometry to quantitatively probe the binding affinity, orientation, conformation, and bioactivity of adsorbed proteins. Simulations using existing protein force fields (CHARMM, AMBER, OPLS) have been conducted using similar model peptide/protein-surface systems for comparison with experimental results to assess their ability to accurately represent protein adsorption behavior. Results with structured α-helix and β-sheet forming peptides on SAM surfaces reveal that the CHARMM force field provides the closest agreement to experimental results while results using AMBER or OPLS-AA deviate substantially. Further investigations using unstructured host-guest peptides show that simulations using the CHARMM force field, however, substantially under predict the adsorption free energy obtained by SPR experiments. To correct these problems, modifications in the CHARMM program have been made to enable the use of an interfacial force field that enables peptide adsorption behavior to be tuned while still using CHARMM to represent protein conformational behavior in solution. Once properly developed, these methods have great potential for use for surface design at the atomic level to control protein-surface interactions for a broad range of applications in biotechnology.