ИСТИНА

We focus our simulations of GTP hydrolysis by GTPases on chemical transformations in the enzyme active sites using quantum-based approaches. According to previous modeling results [1-3], the molecular events of these chemical steps include: (i) cleavage of the phosphorus (Pγ) -oxygen bond in GTP upon approach of the properly aligned catalytic water molecule, producing GDP; (ii) formation of a new chemical bond between phosphorus and oxygen of water; (iii) redistribution of protons between reacting species leading to inorganic phosphate Pi. More recent experimental and theoretical papers describing details of enzymatic GTP hydrolysis, as well a request to study molecular polymorphism in Ras encouraged us to reconsider the chemical reactions in the enzyme active site by using modern molecular modeling tools. Firstly, we markedly improved the quantum mechanical – molecular mechanical (QM/MM) model for the Ras-GAP protein complex including a substrate and a fairly large fraction of the active site residues to the QM-part and using more advanced quantum chemistry approaches than applied before. Secondly, we carried out molecular dynamics simulations with the QM/MM potentials aiming to construct free energy reaction profiles for comparison to the minimum energy profile. The newly obtained results are qualitatively consistent with the proposed reaction mechanism and form a basis for better understanding GTP hydrolysis in GTPases. Supported by the Russian Foundation for Basic Research (project #13-03-00210). References [1] Grigorenko, B.L.; Nemukhin, A.V.; Topol, I.A.; Cachau, R.E.; Burt S.K., QM/MM modeling the Ras–GAP catalyzed hydrolysis of guanosine triphosphate, Proteins: Struct. Funct. Bioinf., 2005, 60, 495-503. [2] Grigorenko, B.L.; Nemukhin, A.V.; Shadrina, M.S.; Topol, I.A.; Burt S.K., Mechanisms of guanosine triphosphate hydrolysis by Ras and Ras-GAP proteins as rationalized by ab initio QM/MM simulations, Proteins: Struct., Funct. Bioinf., 2007, 66, 456-466. [3] Grigorenko, B.L.; Shadrina M.S.; Topol, I.A.; Collins J.R.; Nemukhin A.V., Mechanism of the Chemical Step for the Guanosine Triphosphate (GTP) Hydrolysis Catalyzed by Elongation Factor Tu, Biochim. Biophys. Acta: Proteins and Proteomics, 2008, 1784, 1908-1917.