• molecular dynamics;
  • essential dynamics;
  • nonlinear Poisson-Boltzmann signal transduction;
  • molecular switches;
  • catalytic mechanism


The hydrolysis of GTP in p21ras triggers conformational changes that regulate the ras/ERK signaling pathway. An important active site residue is Gln61, which has been found to be mutated in 30% of human tumors. The dynamics of the active site conformation is studied by using molecular dynamics simulation of two independent structures of the GTP-bound uncomplexed enzyme. Two distinct conformations of the enzyme are observed, in which the side-chain residue Gln61 is in different orientations. Essential dynamics analysis is used to describe the essential motions in the transition between the two conformations. Results are compared with earlier simulations of p21ras and its complex with GTPase activating protein p21-GAP. Proteins 2001;45:297–312. © 2001 Wiley-Liss, Inc.