Specific bindings of glycine peptides of distinctly different chain length on dynamic papain surfaces

We investigated the specific bindings of peptides of 1–10 glycine residues (1–10GLY) on dynamic papain surfaces via molecular dynamics and docking simulations. Although the binding specificities of 1–5GLY on papain fluctuated little with time, the binding specificities of 6–10GLY on papain considerably fluctuated with time. Some residues had a significant impact on bindings of 6–10GLY to sites near active center of papain, and some of their residues were specific for each 6GLY, 8GLY, and 10GLY. Modification of these specific residues should allow for control of binding specificity of 6GLY, 8GLY, and 10GLY to the active center.