Why does mutation of <scp>G</scp>ln61 in Ras by the nitro analog <scp>NG</scp>ln maintain activity of <scp>R</scp>as‐<scp>GAP</scp> in hydrolysis of guanosine triphosphate?

Khrenova, Maria G.; Grigorenko, Bella L.; Mironov, Vladimir; Nemukhin, Alexander V.

doi:10.1002/prot.24927

Cited by 10 publications

(8 citation statements)

References 41 publications

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“…The computed structures and the energy profiles for the complete pathway from the enzyme-substrate to enzyme-product complexes for the wild-type and mutated Ras suggest that the reaction mechanism is not affected by this mutation. 45 Finally, we comment on the kinetic scheme consistent with the energy profile depicted in Fig.4.…”

Section: New Piecesmentioning

confidence: 92%

Hydrolysis of Guanosine Triphosphate (GTP) by the Ras·GAP Protein Complex: Reaction Mechanism and Kinetic Scheme

et al. 2015

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Molecular mechanisms of 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·H 2 O → 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 reactions 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.3

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Section: New Piecesmentioning

confidence: 92%

Hydrolysis of Guanosine Triphosphate (GTP) by the Ras·GAP Protein Complex: Reaction Mechanism and Kinetic Scheme

et al. 2015

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“…Moreover, the diverse conformations of Ras are expected to have a major impact on the GTP hydrolysis process in the active site. Previous studies − have postulated several possible mechanisms for GTP hydrolysis, including the Gln61-mediated general base mechanism and the substrate-assisted mechanism. A recent theoretical analysis by Calixto et al proposed a solvent-assisted mechanism, in which Gln61 was not explicitly involved in the hydrolysis reaction.…”

Section: Introductionmentioning

confidence: 99%

Conformational Features of Ras: Key Hydrogen-Bonding Interactions of Gln61 in the Intermediate State during GTP Hydrolysis

et al. 2021

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The Ras protein is one of the most important drug targets for battling cancers. To effectively design novel drugs of Ras, we characterize here its conformational ensembles for the hydrolysis intermediate state RasGDP•Pi and the product state RasGDP by extensive replica-exchange molecular dynamics simulations. Several substates for RasGDP•Pi have been identified, while structural analyses have revealed an unrecognized hydrogen-bonding network that stabilizes the hydrolysis intermediate state. More interestingly, Gln61, which is involved in numerous oncogenic mutations, was found to be engaged in this hydrogen-bonding network, adopting a specific conformation that always points to Pi in contrast to that in the RasGTP state. The simulations also reveal that RasGDP has more than one substate, suggesting a conformational selection mechanism for the interaction between Ras and the guanine nucleotide exchange factors (GEFs). These findings offer new opportunities for the drug design of Ras by stabilizing the hydrolysis intermediate or disrupting its interaction with the GEFs.

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“…Several studies have suggested that Ras functional diversity might involve variations in the population of conformational states spanning a spectrum of inactive, intermediate, and active states. [38][39][40] In addition to the bound nucleotide 38,41 and mutations 40,42-44 (see also more recent elegant calculations on the impact of mutations on GTP hydrolysis [45][46][47] the population of these states may be affected by oligomerization and interaction with membrane or other partners. [11][12][13][48][49][50][51][52] Interaction with partner proteins can induce relatively large conformational changes especially at the switch loops.…”

Section: Introductionmentioning

confidence: 99%

Distinct dynamics and interaction patterns in H- and K-Ras oncogenic P-loop mutants

2017

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Despite years of study the structural or dynamical basis for the differential reactivity and oncogenicity of Ras isoforms and mutants remains unclear. In this study, we investigated the effects of amino acid variations on the structure and dynamics of wild type and oncogenic mutants G12D, G12V and G13D of H- and K-Ras proteins. Based on data from μs-scale molecular dynamics simulations, we show that the overall structure of the proteins remains similar but there are crucial differences in dynamics and interaction networks. We identified differences in residue interaction patterns around the canonical switch and distal loop regions, and persistent sodium ion binding near the GTP particularly in the G13D mutants. Our results also suggest that different Ras variants have distinct local structural features and interactions with the GTP, variations that have the potential to affect GTP release and hydrolysis. Furthermore, we found that H-Ras proteins and particularly the G12V and G13D variants are significantly more flexible than their K-Ras counterparts. Finally, while most of the simulated proteins sampled the effector-interacting state 2 conformational state, G12V and G13D H-Ras adopted an open switch state 1 conformation that is defective in effector interaction. These differences have implications for Ras GTPase activity, effector or exchange factor binding, dimerization and membrane interaction.

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Why does mutation of Gln61 in Ras by the nitro analog NGln maintain activity of Ras‐GAP in hydrolysis of guanosine triphosphate?

Cited by 10 publications

References 41 publications

Hydrolysis of Guanosine Triphosphate (GTP) by the Ras·GAP Protein Complex: Reaction Mechanism and Kinetic Scheme

Hydrolysis of Guanosine Triphosphate (GTP) by the Ras·GAP Protein Complex: Reaction Mechanism and Kinetic Scheme

Conformational Features of Ras: Key Hydrogen-Bonding Interactions of Gln61 in the Intermediate State during GTP Hydrolysis

Distinct dynamics and interaction patterns in H- and K-Ras oncogenic P-loop mutants

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