Chen Nanhao, Zhao Yuan, Lu Jianing, Wu Ruibo, Cao Zexing
School of Pharmaceutical Sciences, Sun Yat-sen University , Guangzhou, 510006, People's Republic of China.
State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University , Xiamen, 360015, People's Republic of China.
J Chem Theory Comput. 2015 Jul 14;11(7):3180-8. doi: 10.1021/acs.jctc.5b00045. Epub 2015 Jun 22.
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 Ca(2+) 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.
肌苷 - 腺苷 - 鸟苷特异性核苷水解酶（IAG - NH）中的完整酶催化循环被认为由四个步骤组成：底物结合、化学反应、碱基释放和核糖释放。然而，尽管核糖释放可能是最困难的阶段，但整个酶促反应限速步骤的机制细节仍然未知。基于最先进的量子力学和分子力学（QM/MM）分子动力学（MD）模拟，核糖释放过程可分为两个步骤：“核糖解离”和“核糖释放”。“核糖解离”包括“裂解”和“交换”阶段，其中在脱辅基IAG - NH中观察到的亚稳态六重中间体将恢复为Ca(2+)的八重配位壳。已采用广泛的随机加速分子动力学和MD模拟来验证合理的释放通道，并且整个反应限速步骤的估计势垒为13.0千卡/摩尔，这与16.7千卡/摩尔的实验值相当。此外，已发现由环1和环2以及活性口袋周围的关键残基产生的门控机制在控制核糖释放中起重要作用。
