Paper Citing NAMD - Abstract
Verde, Ana Vila; Acres, Jacqueline M.; Maranas, Janna K.
Investigating the Specificity of Peptide Adsorption on Gold Using Molecular Dynamics Simulations
BIOMACROMOLECULES, 10:2118-2128, AUG 2009
We report all-atom molecular dynamics simulations following adsorption of gold-binding and non-gold-binding peptides on gold Surfaces modeled with dispersive interactions. We examine the dependence of adsorption on both identity of the amino acids and mobility of the peptides. Within the limitations of the approach, results indicate that when the peptides are solvated, adsorption requires both configurational changes and local flexibility of individual amino acids. This is achieved when peptides consist mostly of random coils or when their secondary structural motifs (helices, sheets) are short and connected by flexible hinges. In the absence of solvent, only affinity for the surface is required: mobility is not important. In combination, these results suggest the barrier to adsorption presented by displacement of water molecules requires conformational sampling enabled through mobility.
