Molecular dynamics simulations of the adsorption of proteins on clay mineral surfaces

Abstract Some initial results of molecular dynamics simulations of the adsorption of proteins on clay mineral surfaces are being reported. Specifically, the interactions of pyrophyllite surfaces with crambin, rubredoxin, and several oligopeptides were investigated. It is found that clay mineral surfaces can have a denaturing effect on adsorbed proteins for two reasons: (1) they are dehydrating agents, because they perturb the random environment of water molecules that globular proteins need to maintain their native structure; and (2) clay surfaces can establish non-bonded interactions with proteins which compete effectively with the interactions inside a peptide chain. The changes in secondary and tertiary protein structure induced by adsorption to pristine surfaces, or surfaces coated with water, lead to backbone torsions away from the most populated regions of φ,ψ-space, to regions which are not frequently populated in unperturbed proteins. β- and α R -conformations, specifically, are not stable on pyrophyllite but undergo transitions, with some preference, to an area close to C 7 eq . Because of the size of the adsorbed systems, unit cells with adsorbed peptides may be distorted, bulging at the site of adsorption, and displaying a continuously varying interlayer space between the empty parts and those that are occupied by an adsorbate. As a result, warped, or S-shaped basal planes are found.