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STUDY ON THE INTERACTIONS OF Smac MIMETICS WITH XIAP-BIR3 DOMAIN BY DOCKING AND MOLECULAR DYNAMICS SIMULATIONS
Ling, Baoping1; Zhang, Rui2; Wang, Zhiguo2; Liu, Yongjun1,2; Liu, Chengbu1
2010-08-01
发表期刊JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY
ISSN0219-6336
卷号9期号:4页码:797-812
文章类型Article
摘要Upon receiving an apoptotic stimulus, the mature mitochondrial protein second mitochondria-derived activator of caspases (Smac)direct IAP-binding protein with low PI (DIABLO), which could be released from mitochondria into the cytosol together with cytochrome C, specifically binds to inhibitor of apoptosis proteins (IAPs) and relieves the inhibitory effect of caspase, thus promotes cell death. Some artificial small molecules (called Smac mimetics) can mimic the N-terminal four residues Ala1-Val2-Pro3-Ile4 (AVPI) sequence of mitochondrial protein Smac, and competitively bind to X-linked inhibitor of apoptosis protein baculoviral IAP repeats (XIAP-BIR3) domain with caspase-9, which leads to the removal of the inhibition of caspase-9 by XIAP and induce apoptosis. To gain an insight into the nature of XIAP-BIR3 domain recognizing Smac mimetics, we used docking and molecular dynamics simulations methods to study four representative Smac mimetics. The docking results show that the orientations of these backbones of ligands are identical with that of AVPI in the binding pocket. Each ligand corresponds to two competitive conformations, which are called extended and bended conformations. The results of molecular dynamics simulations show that the extended conformation is more stable, and the calculations of energy decomposition reveal that the residue Thr308 makes the strongest interaction with XIAP-BIR3. In addition, Asp309, Glu314, and Trp323 are indispensable for XIAP-BIR3 recognizing and binding Smac mimetics.; Upon receiving an apoptotic stimulus, the mature mitochondrial protein second mitochondria-derived activator of caspases (Smac)direct IAP-binding protein with low PI (DIABLO), which could be released from mitochondria into the cytosol together with cytochrome C, specifically binds to inhibitor of apoptosis proteins (IAPs) and relieves the inhibitory effect of caspase, thus promotes cell death. Some artificial small molecules (called Smac mimetics) can mimic the N-terminal four residues Ala1-Val2-Pro3-Ile4 (AVPI) sequence of mitochondrial protein Smac, and competitively bind to X-linked inhibitor of apoptosis protein baculoviral IAP repeats (XIAP-BIR3) domain with caspase-9, which leads to the removal of the inhibition of caspase-9 by XIAP and induce apoptosis. To gain an insight into the nature of XIAP-BIR3 domain recognizing Smac mimetics, we used docking and molecular dynamics simulations methods to study four representative Smac mimetics. The docking results show that the orientations of these backbones of ligands are identical with that of AVPI in the binding pocket. Each ligand corresponds to two competitive conformations, which are called extended and bended conformations. The results of molecular dynamics simulations show that the extended conformation is more stable, and the calculations of energy decomposition reveal that the residue Thr308 makes the strongest interaction with XIAP-BIR3. In addition, Asp309, Glu314, and Trp323 are indispensable for XIAP-BIR3 recognizing and binding Smac mimetics.
关键词Inhibitor Of Apoptosis Protein (Iap) Smac Mimetics Molecular Docking Molecular Dynamics Simulations Binding Free Energy
WOS标题词Science & Technology ; Physical Sciences
关键词[WOS]X-LINKED INHIBITOR ; MITOCHONDRIA-DERIVED ACTIVATOR ; STRUCTURE-BASED DESIGN ; APOPTOSIS PROTEIN XIAP ; PROGRAMMED CELL-DEATH ; BINDING FREE-ENERGY ; STRUCTURAL BASIS ; CASPASE ACTIVATION ; AUTOMATED DOCKING ; BIR3 DOMAIN
收录类别SCI
语种英语
WOS研究方向Chemistry
WOS类目Chemistry, Multidisciplinary
WOS记录号WOS:000282444600008
引用统计
被引频次:7[WOS]   [WOS记录]     [WOS相关记录]
文献类型期刊论文
条目标识符http://210.75.249.4/handle/363003/1658
专题中国科学院西北高原生物研究所
作者单位1.Shandong Univ, Sch Chem & Chem Engn, Jinan 250100, Shandong, Peoples R China
2.Chinese Acad Sci, NW Inst Plateau Biol, Xining 810001, Qinghai, Peoples R China
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GB/T 7714
Ling, Baoping,Zhang, Rui,Wang, Zhiguo,et al. STUDY ON THE INTERACTIONS OF Smac MIMETICS WITH XIAP-BIR3 DOMAIN BY DOCKING AND MOLECULAR DYNAMICS SIMULATIONS[J]. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY,2010,9(4):797-812.
APA Ling, Baoping,Zhang, Rui,Wang, Zhiguo,Liu, Yongjun,&Liu, Chengbu.(2010).STUDY ON THE INTERACTIONS OF Smac MIMETICS WITH XIAP-BIR3 DOMAIN BY DOCKING AND MOLECULAR DYNAMICS SIMULATIONS.JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY,9(4),797-812.
MLA Ling, Baoping,et al."STUDY ON THE INTERACTIONS OF Smac MIMETICS WITH XIAP-BIR3 DOMAIN BY DOCKING AND MOLECULAR DYNAMICS SIMULATIONS".JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 9.4(2010):797-812.
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