Molecular Modeling Reveals the Mechanism of Ran-RanGAP-Catalyzed Guanosine Triphosphate Hydrolysis without an Arginine Fingerстатья
Статья опубликована в высокорейтинговом журнале
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Дата последнего поиска статьи во внешних источниках: 23 сентября 2021 г.
Аннотация:We report results of a computational study of thereaction mechanism of guanosine triphosphate (GTP) hydrolysiscatalyzed by the GTP-binding (GTPase) enzyme rat sarcomarelated nuclear (Ran) in complex with its activating proteinRanGAP. According to structural investigations, Ran-RanGAPoperates without the so-called arginine finger, an arginine residuefrom a distinct promoter (GTPase-accelerating protein (GAP))that completes the active site in many GTPases. In this work, weconstruct model systems for Ran with and without GAP by motifsof the crystal structure of Ran-RanGAP with the GTP analogueand simulate the GTP hydrolysis reaction in these systems.Enzyme−substrate and enzyme−product complexes and reactionintermediates are obtained in quantum mechanics/molecularmechanics (QM/MM) simulations. Calculations of the free-energy reaction profiles are performed at the molecular dynamicslevel with the ab initio-type QM(DFT(PBE0-D3)/6-31G**)/MM potentials. We show that the computed activation barriers on thepathways for Ran catalysis with and without GAP are in line with the experimentally estimated rate constants. We demonstrate thatmapping the Laplacian of the electron density provides easily visible images of substrate activation, which help distinguish betweenthe reactive and nonreactive enzyme−substrate complexes and explain qualitative features of the enzyme-catalyzed GTP hydrolysisreactions consistent with the computed free-energy profiles. A comparison of reactions in Ran and Ran-RanGAP allows us tocharacterize the role of GAP operating without an arginine finger