title: Hydrolysis of Guanosine Triphosphate (GTP) by the Ras·GAP Protein Complex: Reaction Mechanism and Kinetic Scheme.
abstract: Molecular mechanisms of the hydrolysis of guanosine triphosphate (GTP) to guanosine diphosphate (GDP) and inorganic phosphate (Pi) by the Ras·GAP protein complex are fully investigated by using modern modeling tools. The previously hypothesized stages of the cleavage of the phosphorus-oxygen bond in GTP and the formation of the imide form of catalytic Gln61 from Ras upon creation of Pi are confirmed by using the higher-level quantum-based calculations. The steps of the enzyme regeneration are modeled for the first time, providing a comprehensive description of the catalytic cycle. It is found that for the reaction Ras·GAP·GTP·H2O → Ras·GAP·GDP·Pi, the highest barriers correspond to the process of regeneration of the active site but not to the process of substrate cleavage. The specific shape of the energy profile is responsible for an interesting kinetic mechanism of the GTP hydrolysis. The analysis of the process using the first-passage approach and consideration of kinetic equations suggest that the overall reaction rate is a result of the balance between relatively fast transitions and low probability of states from which these transitions are taking place. Our theoretical predictions are in excellent agreement with available experimental observations on GTP hydrolysis rates.
authors.affiliation: Chemistry Department, M.V. Lomonosov Moscow State University , Leninskie Gory 1/3, Moscow 119991, Russian Federation.
authors.forename: Maria G
authors.initials: MG
authors.lastname: Khrenova
authors.affiliation: Chemistry Department, M.V. Lomonosov Moscow State University , Leninskie Gory 1/3, Moscow 119991, Russian Federation.|N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences , Kosygina 4, Moscow 119334, Russian Federation.
authors.forename: Bella L
authors.initials: BL
authors.lastname: Grigorenko
authors.affiliation: Department of Chemistry and Center for Theoretical Biological Physics, Rice University , Houston, Texas 77005, United States.
authors.forename: Anatoly B
authors.initials: AB
authors.lastname: Kolomeisky
authors.affiliation: Chemistry Department, M.V. Lomonosov Moscow State University , Leninskie Gory 1/3, Moscow 119991, Russian Federation.|N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences , Kosygina 4, Moscow 119334, Russian Federation.
authors.forename: Alexander V
authors.initials: AV
authors.lastname: Nemukhin
mesh_terms: D006160:Guanosine Triphosphate / Q000378:metabolism*; D006868:Hydrolysis; D007700:Kinetics; D008958:Models, Molecular; D011789:Quantum Theory; D020703:ras GTPase-Activating Proteins / Q000378:metabolism*
chemical_list: D020703:ras GTPase-Activating Proteins; D006160:Guanosine Triphosphate