Barnase-Barstar: from first encounter to final complex.
Formation of transient protein complexes is an important process in cells. Details of the association process as well as the energy landscapes of association are not well understood. In particular, the nature, height and position of the energy barriers during complexation are debated. Computational studies are well suited for atomistically investigating protein association processes. The Barnase-Barstar complex constitutes a well-studied target for computational studies as a small system with fast association rates. Here, we performed constraint biased Molecular Dynamics simulations along the reaction coordinate reaching from the diffusion regime to the bound complex. We simulated the wild-type and different mutants at different salt concentrations. A structural analysis of our simulation trajectories revealed not a single, but two distinct association patterns dominated by an interplay between two charged contact points near the binding site. Electrostatics and/or mutations influence the relative population of these patterns. Further, we computed the energy landscape of association as PMF (Potential of Mean Force) profiles within a reasonable agreement to experiment. We find a single energy barrier at a distance of ~0.3 nm, which corresponds to the final desolvation transition. Electrostatics has a profound influence on the height of this energy barrier, but not on its position.
Hoefling
Martin
M
Biophysics and Molecular Materials & CeNS, Ludwig-Maximilians University, Amalienstr. 54, 80799 Munich, Germany.
Gottschalk
Kay E
KE
D001426:Bacterial Proteins / Q000737:chemistry* / Q000235:genetics; D001665:Binding Sites; D007700:Kinetics; D056004:Molecular Dynamics Simulation; D009154:Mutation; D011487:Protein Conformation; D012260:Ribonucleases / Q000737:chemistry* / Q000235:genetics; D055672:Static Electricity
D001426:Bacterial Proteins; C057438:barstar protein, Bacillus amyloliquefaciens; D012260:Ribonucleases; C019760:Bacillus amyloliquefaciens ribonuclease