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题名: Determination of the Structure Form, of the Fourth Ligand of Zinc in Acutolysin A Using Combined Quantum Mechanical and Molecular Mechanical Simulation
作者: Wu, Emilia L.1;  Wong, Kin-Yiu2, 3;  Zhang, Xin1;  Han, Keli1;  Gao, Jiali2, 3
刊名: JOURNAL OF PHYSICAL CHEMISTRY B
发表日期: 2009-02-26
DOI: 10.1021/jp808182y
卷: 113, 期:8, 页:2477-2485
收录类别: SCI
文章类型: Article
WOS标题词: Science & Technology ;  Physical Sciences
类目[WOS]: Chemistry, Physical
研究领域[WOS]: Chemistry
英文摘要: Acutolysin A, which is isolated from the snake venom of Agkistrodon acutus, is a member of the SVMPs subfamily of the metzincin family, and it is a snake venom zinc metalloproteinase possessing only one catalytic domain. The catalytic zinc ion, in the active site, is coordinated in a tetrahedral manner with three imidazole nitrogen atoms of histidine and one oxygen atom. It is uncertain whether this oxygen atom is a water molecule or a hydroxide ion just from the three-dimensional X-ray crystal structure. The identity of the fourth ligand of zinc is theoretically determined for the first time by performing both combined quantum mechanical and molecular mechanical (QM/MM) simulation and high-level quantum mechanical calculations. All of the results obtained indicate that the fourth ligand in the active site of the reported X-ray crystal structure is a water molecule rather than a hydroxide anion. On the basis of these theoretical results, we note that the experimental observed pH dependence of the proteolytic and hemorrhagic activity of Acutolysin A can be attributed to the deprotonation of the zinc-bound water to yield a better nucleophile, the hydroxide ion. Structural analyses revealed structural details useful for the understanding of acutolysin catalytic mechanism.
关键词[WOS]: SNAKE-VENOM METALLOPROTEINASES ;  DYNAMICS SIMULATIONS ;  AGKISTRODON-ACUTUS ;  ENZYME-KINETICS ;  ACTIVE-SITE ;  HALOALKANE DEHALOGENASE ;  SUBSTITUTION-REACTION ;  CHEMICAL CALCULATION ;  SYNTHETIC ANALOGS ;  COMBINED QM/MM
语种: 英语
WOS记录号: WOS:000263529500033
Citation statistics: 
内容类型: 期刊论文
URI标识: http://cas-ir.dicp.ac.cn/handle/321008/141335
Appears in Collections:中国科学院大连化学物理研究所_期刊论文

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作者单位: 1.Chinese Acad Sci, Dalian Inst Chem Phys, Dalian 116023, Peoples R China
2.Univ Minnesota, Dept Chem, Digital Technol Ctr, Minneapolis, MN 55455 USA
3.Univ Minnesota, Minnesota Supercomp Inst, Minneapolis, MN 55455 USA

Recommended Citation:
Wu, Emilia L.,Wong, Kin-Yiu,Zhang, Xin,et al. Determination of the Structure Form, of the Fourth Ligand of Zinc in Acutolysin A Using Combined Quantum Mechanical and Molecular Mechanical Simulation[J]. JOURNAL OF PHYSICAL CHEMISTRY B,2009,113(8):2477-2485.
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