Local fluctuation control of papain by changing a highly fluctuating residue

Abstract

To control the local fluctuation of the amino acid residues of papain, ARG59, a highly fluctuating residue in papain, has been changed to GLY. We investigated the binding properties of 2-10GLY (peptides with between 2 and 10 glycine residues) to the modified papain structure via molecular dynamics and docking simulations. The change of the ARG59 residue to GLY alters the binding sites for some peptides, and changed its substrate specificity. Furthermore, the modification alters the binding stability of some peptides. Thus, control of the local fluctuations of residues in proteins has the potential to alter the protein’s function.