Keywords

Molecular simulations, Molecular dynamics, Free energy, Hydrophobic effect, Amino acid, Coarse-grain model, Peptides, Lysozyme, Proteins, Cytochrome

Abstract

The interaction of proteins with surfaces is important in numerous applications in many fields—such as biotechnology, proteomics, sensors, and medicine—but fundamental understanding of how protein stability and structure are affected by surfaces remains incomplete. Over the last several years, molecular simulation using coarse grain models has yielded significant insights, but the formalisms used to represent the surface interactions have been rudimentary. We present a new model for protein surface interactions that incorporates the chemical specificity of both the surface and the residues comprising the protein in the context of a one-bead-per-residue, coarse grain approach that maintains computational efficiency. The model is parameterized against experimental adsorption energies for multiple model peptides on different types of surfaces. The validity of the model is established by its ability to quantitatively and qualitatively predict the free energy of adsorption and structural changes for multiple biologically-relevant proteins on different surfaces. The validation, done with proteins not used in parameterization, shows that the model produces remarkable agreement between simulation and experiment.

Original Publication Citation

S. Wei and T. A. Knotts IV, A Coarse Grain Model for Protein-Surface Interactions, J. Chem. Phys., 139, 095102 (2013).