Conformation of the Ras-binding domain of Raf studied by molecular dynamics and free energy simulations

Recognition of Ras by its downstream target Raf is mediated by a Ras-recognition region in the Ras-binding domain (RBD) of Raf. Residues 78-89 in this region occupy two different conformations in the ensemble of NMR solution structures of the RBD: a fully alpha-helical one, and one where 87-90 form a type IV beta-turn. Molecular dynamics simulations of the RBD in solution were performed to explore the stability of these and other possible conformations of both the wild-type RBD and the R89K mutant, which does not bind Ras. The simulations sample a fully helical conformation for residues 78-89 similar to the NMR helical structures, a conformation where 85-89 form a 3(10)-helical turn, and a conformation where 87-90 form a type I beta-turn, whose free energies are all within 0.3 kcal/mol of each other. NOE patterns and H(alpha) chemical shifts from the simulations are in reasonable agreement with experiment. The NMR turn structure is calculated to be 3 kcal/mol higher than the three above conformations. In a simulation with the same implicit solvent model used in the NMR structure generation, the turn conformation relaxes into the fully helical conformation, illustrating possible structural artifacts introduced by the implicit solvent model. With the Raf R89K mutant, simulations sample a fully helical and a turn conformation, the turn being 0.9 kcal/mol more stable. Thus, the mutation affects the population of RBD conformations, and this is expected to affect Ras binding. For example, if the fully helical conformation of residues 78-89 is required for binding, its free energy increase in R89K will increase the binding free energy by about 0.6 kcal/mol.