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Determination of the Structure Form, of the Fourth Ligand of Zinc in Acutolysin A Using Combined Quantum Mechanical and Molecular Mechanical Simulation
Wu, Emilia L.1; Wong, Kin-Yiu2,3; Zhang, Xin1; Han, Keli1; Gao, Jiali2,3
刊名JOURNAL OF PHYSICAL CHEMISTRY B
2009-02-26
DOI10.1021/jp808182y
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
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
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.
语种英语
WOS记录号WOS:000263529500033
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被引频次:26[WOS]   [WOS记录]     [WOS相关记录]
文献类型期刊论文
条目标识符http://cas-ir.dicp.ac.cn/handle/321008/141335
专题中国科学院大连化学物理研究所
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
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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.
APA Wu, Emilia L.,Wong, Kin-Yiu,Zhang, Xin,Han, Keli,&Gao, Jiali.(2009).Determination of the Structure Form, of the Fourth Ligand of Zinc in Acutolysin A Using Combined Quantum Mechanical and Molecular Mechanical Simulation.JOURNAL OF PHYSICAL CHEMISTRY B,113(8),2477-2485.
MLA Wu, Emilia L.,et al."Determination of the Structure Form, of the Fourth Ligand of Zinc in Acutolysin A Using Combined Quantum Mechanical and Molecular Mechanical Simulation".JOURNAL OF PHYSICAL CHEMISTRY B 113.8(2009):2477-2485.
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