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• W2419371841 startingPage "3180" @default.
• W2419371841 abstract "A full enzymatic catalysis cycle in the inosine–adenosine–guanosine specific nucleoside hydrolase (IAG-NH) was assumed to be comprised of four steps: substrate binding, chemical reaction, base release, and ribose release. Nevertheless, the mechanistic details for the rate-limiting step of the entire enzymatic reaction are still unknown, even though the ribose release was likely to be the most difficult stage. Based on state-of-the-art quantum mechanics and molecular mechanics (QM/MM) molecular dynamics (MD) simulations, the ribose release process can be divided into two steps: “ribose dissociation” and “ribose release”. The “ribose dissociation” includes “cleavage” and “exchange” stages, in which a metastable 6-fold intermediate will recover to an 8-fold coordination shell of Ca2+ as observed in apo- IAG-NH. Extensive random acceleration molecular dynamics and MD simulations have been employed to verify plausible release channels, and the estimated barrier for the rate-determining step of the entire reaction is 13.0 kcal/mol, which is comparable to the experimental value of 16.7 kcal/mol. Moreover, the gating mechanism arising from loop1 and loop2, as well as key residues around the active pocket, has been found to play an important role in manipulating the ribose release." @default.
• W2419371841 created "2016-06-24" @default.
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• W2419371841 date "2015-06-22" @default.
• W2419371841 modified "2023-09-24" @default.
• W2419371841 title "Mechanistic Insights into the Rate-Limiting Step in Purine-Specific Nucleoside Hydrolase" @default.
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• W2419371841 doi "https://doi.org/10.1021/acs.jctc.5b00045" @default.
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• W2419371841 hasPublicationYear "2015" @default.
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