Modeling the Interaction between Integrin-Binding Peptide (RGD) and Rutile Surface: The Effect of Na⁺ on Peptide Adsorption

The dynamics of a single tripeptide Arg-Gly-Asp (RGD) adsorbing onto negatively charged hydroxylated rutile (110) surface in aqueous solution was studied using molecular dynamics (MD) simulations. The results indicate that the adsorbed Na⁺ ions play an important role in determining the binding geometry of RGD. With an initial "horseshoe" configuration, the charged side groups (COO^- and NH₂) of the peptide are able to interact with the surface through direct hydrogen bonds (H bonds) in the very early stage of adsorption. The Na⁺ ions approach the positively charged Arg side chain, competing with the Arg side chain for adsorption to the negatively charged hydroxyl oxygen. In coordination with the structural adjustment of the peptide, the Arg residue is driven to detach from the rutile surface. In contrast, the Na⁺ ions in close proximity to the negatively charged Asp side chain contribute to the binding of the COO ^- group on the surface, helping the carboxyl oxygen not involved in COO^--surface H bonds to orientate toward the hydroxyl hydrogens. Once both carboxyl oxygens form enough H bonds with the hydroxyl hydrogens, the redundant ions move toward a more favorable adsorption site.