Effects of local repositioning of charged surface residues on the kinetics of protein dimerization probed by Brownian dynamics simulations

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The correct and efficient recognition of proteins by each other is a fundamental biomolecular process of crucial importance to a vast number of biological transformations, but is only beginning to be understood. An area within this greater question which receives a great deal of attention currently is the role played by charged amino acid residues on the surfaces of the interacting proteins. The work presented here addresses that problem by examining the sensitivity of the association rate coefficient for dimerization of a hemoglobin monomer to local changes in the positions of individual charged amino acid residues on the surface of the monomer. The changes in position are accomplished without affecting the fold of the protein by double mutation, exchanging each charged residue's identity, one at a time, with that of a nearby residue, such that the residue of interest adopts the neighbor's charge, and the neighbor adopts the subject residue's. The amino acid residues most sensitive to this local exchange of charge position are those lying along the edges of the binding and rear (opposite) faces of the monomer, with the greatest effect observed for Arg104, which is a positively charged residue located near the negatively charged propionate groups of the heme moiety, and is isolated from other charged residues. Residues near the binding face showed significantly more frequent sensitivity to charge–position exchange than did those near the rear face, and a conical protrusion at the edge of each subunit, marked by Gln59 at its apex, bears no residues exhibiting significant sensitivity. There was little correlation between the sensitivity of a residue to movement and to deletion of its charge, and residues at the edge of the binding face showed a broad range of sensitivities to local repositioning, both of which observations suggest that the two monomers associate following a specific set of trajectories, consisting of both broad and narrow avenues of interaction as they rotate past one another to attain the bound configuration.