Protein-protein binding pathways and calculations of rate constants using fully continuous explicit solvent simulations

A grand challenge in the field of biophysics has been the complete characterization of protein-protein binding processes at atomic resolution. This characterization requires the direct simulation of binding pathways starting from the initial unbound state and proceeding through states that are too transient to be captured by experiment. Here we applied the weighted ensemble path sampling strategy to enable atomistic simulation of protein-protein binding pathways. Our simulation generated 203 fully continuous binding pathways for the bacterial proteins, barnase and barstar, yielding a computed kon that is within error of experiment. Results reveal that the formation of the \"encounter complex\" intermediate is rate limiting with ~11% of all diffusional collisions being productive. Consistent with experiment, our simulations identify R59 as the most kinetically important barnase residue for the binding process. Furthermore, protein desolvation occurs late in the binding process during the rearrangement of the encounter complex to the native complex. Notably, the positions of interfacial crystallographic water molecules that bridge hydrogen bonds between barnase and barstar are occupied upon formation of the native complex in our simulations. Our simulations were completed within a month using 1600 CPU cores at a time, demonstrating that it is now practical to carry out atomistic simulations of protein-protein binding processes, particularly using the latest GPU-accelerated computing.