ArticleJournal of chemical theory and computation2025
Molecular Mechanism of ATP Hydrolysis Catalyzed by p97: A QM/MM Study.
Article in Journal of chemical theory and computation, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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Abstract
A computational study of p97/VCP ATPase using hybrid quantum mechanics/molecular mechanics (QM/MM) simulations is presented that explores the conformational landscape of the active site and hydrolysis-competent states of the crystallographic water molecules. Our investigation focuses on the reaction mechanism, particularly the events of the rate-determining first reaction step, which we study using extensive sampling with the path well-tempered metadynamics extended-system adaptive biasing force (WTM-eABF) enhanced sampling method. We identify the highly conserved glutamate (Glu305) from the Walker B motif as a catalytic base that activates the lytic water molecule for nucleophilic attack on the γ-phosphate in the first reaction step, while the final product is formed in a second step that involves proton transfer and rearrangements in the Mg
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