Molecular dynamics simulations of the Ras : Raf and Rap : Raf complexes

The protein Raf is an immediate downstream target of Ras in the MAP kinase signalling pathway. The complex of Ras with the Ras-binding domain (RBD) of Raf has been modelled by homology to the (E30D,K31E)-Rap1A:RBD complex, an d both have been subjected to multiple molecular dynamics simulations in so lution. While both complexes are stable, several rearrangements occur in th e Ras:RBD simulations: the RBD loop 100-109 moves closer to Ras, Arg73 in t he RBD moves towards Ras to form a salt bridge with Ras-Asp33, and Loop 4 o f the Ras switch II region shifts upwards toward the RBD. The Ras:RBD inter actions (including the RBD-Arg73 interaction) are consistent with available MMR and mutagenesis data on the Ras: RBD complex in solution. The Ras swit ch II region does not interact directly with the RBD, although indirect int eractions exist through the effector domain and bridging water molecules. N o large-scale RBD motion is seen in the Ras:RBD complex, compared to the Ra p:RBD complex, to suggest an allosteric activation of Raf by Ras. This may be because the Raf kinase domain (whose structure is unknown) is not includ ed in the model. Proteins 1999;35:89-100. (C) 1999 Wiley-Liss, Inc.