Mechanistic Insights into the Rate-Limiting Step in Purine-Specific Nucleoside Hydrolase
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- 作者：Nanhao Chen ; Yuan Zhao ; Jianing Lu ; Ruibo Wu ; Zexing Cao
- 刊名：Journal of Chemical Theory and Computation
- 出版年：2015
- 出版时间：July 14, 2015
- 年：2015
- 卷：11
- 期：7
- 页码：3180-3188
- 全文大小：661K
- ISSN：1549-9626
文摘
A full enzymatic catalysis cycle in the inosine鈥揳denosine鈥揼uanosine 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: 鈥渞ibose dissociation鈥?and 鈥渞ibose release鈥? The 鈥渞ibose dissociation鈥?includes 鈥渃leavage鈥?and 鈥渆xchange鈥?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.