文献类型：期刊文献

英文题名：Investigation of the Catalytic Mechanism of Sir2 Enzyme with QM/MM Approach: SN1 vs SN2?

作者：Liang, Zhongjie[1];Shi, Ting[1];Ouyang, Sisheng[1];Li, Honglin[2];Yu, Kunqian[1];Zhu, Weiliang[1,2];Luo, Cheng[1,3];Jiang, Hualiang[1,2]

机构：[1]Chinese Acad Sci, Shanghai Inst Mat Med, State Key Lab Drug Res, Drug Discovery & Design Ctr, Shanghai 201203, Peoples R China;[2]E China Univ Sci & Technol, Sch Pharm, Shanghai 200237, Peoples R China;[3]Soochow Univ, Ctr Syst Biol, Suzhou 215006, Peoples R China

年份：2010

卷号：114

期号：36

起止页码：11927

外文期刊名：JOURNAL OF PHYSICAL CHEMISTRY B

收录：;EI(收录号：20103713235974);WOS:【SCI-EXPANDED(收录号:WOS:000281404500027)】；

基金：We gratefully thank Dr. Marmorstein for his helpful comments. We also gratefully acknowledge financial support from the National Natural Science Foundation of China (20720102040, 20803022, and 20972174), the Hi-Tech Research and Development Program of China (2006AA01A124), the State Key Program of Basic Research of China Grant (2009CB918502 and 2009CB940901), Shanghai Committee of Science and Technology Grant (10410703900), and National S&T Major Project (2009ZX09501-001), Information Construction Project of the Chinese Academy of Sciences (no. INFO-115-B01), State Key Laboratory Grant (SIMM1004KF-15) and Guangdong Science and Technology Department (2010A030100006).

语种：英文

外文关键词：Amino acids - Cell death - Molecular modeling - Quantum theory - Computational chemistry - Quantum chemistry - Potential energy - Enzyme inhibition - Substrates - Surface reactions - Reaction kinetics - Catalysis - Acetylation - Amides

摘要：Sir2, the histone deacetylase III family, has been subjected to a wide range of studies because of their crucial roles in DNA repair, longevity, transcriptional silencing, genome stability, apoptosis, and fat mobilization. The enzyme binds NAD(+) and acetyllysine as substrates and generates lysine, 2 '-O-acetyl-ADP-ribose, and nicotinamide as products. However, the mechanism of the first step in Sir2 deacetylation reaction from various studies is controversial. To characterize this catalytic mechanism of acetyllysine deacetylation by Sir2, we employed a combined computational approach to carry out molecular modeling, molecular dynamics (MD) simulations, quantum mechanics/molecular mechanics (QM/MM) calculations on catalysis by both yeast Hst2 (homologue of SIR two 2) and bacterial Sir2TM (Sir2 homologue from Thermatoga maritima). Our three-dimensional (3D) model of the complex is composed of Sir2 protein, NAD(+), and acetyllysine (ALY) substrate. A 15-ns MD simulation of the complex revealed that Gln115 and His135 play a determining role in deacetylation. These two residues can act as bases to facilitate the deprotonation of 2 '-OH from N-ribose. The result is in great agreement with previous mutagenesis analysis data. QM/MM calculations were further performed to study the mechanism of the first step in deacetylation in the two systems. The predicted potential energy barriers for yHst2 and Sir2TM are 12.0 and 15.7 kcal/mol, respectively. The characteristics of the potential energy surface indicated this reaction belongs to a SN2-like mechanism. These results provide insights into the Sir2 mechanism of nicotinamide inhibition and have important implications for the discovery of effectors against Sir2 enzymes.