title: Computational characterization of the chemical step in the GTP hydrolysis by Ras-GAP for the wild-type and G13V mutated Ras.
abstract: The free energy profiles for the chemical reaction of the guanosine triphosphate hydrolysis GTP + H2O → GDP + Pi by Ras-GAP for the wild-type and G13V mutated Ras were computed by using molecular dynamics protocols with the QM(ab initio)/MM potentials. The results are consistent with the recent measurements of reaction kinetics in Ras-GAP showing about two-order reduction of the rate constant upon G13V mutation in Ras: the computed activation barrier on the free energy profile is increased by 3 kcal/mol upon the G13V replacement. The major reason for a higher energy barrier is a shift of the "arginine finger" (R789 from GAP) from the favorable position in the active site. The results of simulations provide support for the mechanism of the reference reaction according to which the Q61 side chain directly participates in chemical transformations at the proton transfer stage.
authors.affiliation: Chemistry Department, M.V, Lomonosov Moscow State University, Moscow, 119991, Russia.
authors.forename: Vladimir A
authors.initials: VA
authors.lastname: Mironov
authors.affiliation: Chemistry Department, M.V, Lomonosov Moscow State University, Moscow, 119991, Russia.
authors.forename: Maria G
authors.initials: MG
authors.lastname: Khrenova
authors.affiliation: Chemistry Department, M.V, Lomonosov Moscow State University, Moscow, 119991, Russia.
authors.forename: Leonora A
authors.initials: LA
authors.lastname: Lychko
authors.affiliation: Chemistry Department, M.V, Lomonosov Moscow State University, Moscow, 119991, Russia.|N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, 119334, Russia.
authors.forename: Alexander V
authors.initials: AV
authors.lastname: Nemukhin
mesh_terms: D019295:Computational Biology; D006160:Guanosine Triphosphate / Q000737:chemistry / Q000378:metabolism*; D006868:Hydrolysis; D008958:Models, Molecular; D009154:Mutation / Q000235:genetics / Q000502:physiology; D011487:Protein Conformation; D013816:Thermodynamics; D020703:ras GTPase-Activating Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D018631:ras Proteins / Q000737:chemistry / Q000378:metabolism*
chemical_list: D020703:ras GTPase-Activating Proteins; D006160:Guanosine Triphosphate; D018631:ras Proteins
keywords: Ras mutants; Ras-GAP catalysis; free energy profiles; guanosine triphosphate; hydrolysis reaction