SIMULATION OF THE DIFFUSIONAL ASSOCIATION OF BARNASE AND BARSTAR

The rate of protein association places an upper limit on the response time due to protein interactions, which, under certain circumstances, can be diffusion-controlled. Simulations of model proteins show that d iffusion-limited association rates are similar to 10(6)-10(7) M-1 s(-1 ) in the absence of long-range forces (Northrup, S. H., and H. P. Eric kson. 1992. Kinetics of protein-protein association explained by Brown ian dynamics computer simulations. Proc. Natl. Acad. Sci. U.S.A. 89:33 38-3342), The measured association rates of barnase and barstar are 10 (8)-10(9) M-1 s(-1) at 50 mM ionic strength, and depend on ionic stren gth (Schreiber, G., and A. R. Fersht. 1996. Rapid, electrostatically a ssisted association of proteins. Nat. Struct Biol. 3:427-431), implyin g that their association is electrostatically facilitated. We report B rownian dynamics simulations of the diffusional association of barnase and barstar to compute association rates and their dependence on ioni c strength and protein mutation. Crucial to the ability to reproduce e xperimental rates is the definition of encounter complex formation at the endpoint of diffusional motion. Simple definitions, such as a requ ired root mean square (RMS) distance to the fully bound position, fail to explain the large influence of some mutations on association rates . Good agreement with experiments could be obtained if satisfaction of two intermolecular residue contacts was required for encounter comple x formation. In the encounter complexes, barstar tends to be shifted f rom its position in the bound complex toward the guanine-binding loop on barnase.