| A molecular dynamics simulation study of peptide deformylase from Leptospira interrogans complex：Exploring the closing mechanism of the substrate pocket |
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| 引用本文： | Qiang Wang~a Jian Wu Wang~b Zheng Ting Cai~(a,*)Wei Ren Xu~c ~aInstitute of Theoretical Chemistry,Shandong University,Jinan 250100,China ~bInstitute of Organic Chemistry,Shandong University,Jinan 250100,China ~cTianjin Institute of the Pharmaceutical Research,Tianjin 300193,China. A molecular dynamics simulation study of peptide deformylase from Leptospira interrogans complex：Exploring the closing mechanism of the substrate pocket[J]. 中国化学快报, 2008, 19(4): 497-500. DOI: 10.1016/j.cclet.2008.01.027 |
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| 作者姓名： | Qiang Wang~a Jian Wu Wang~b Zheng Ting Cai~(a *)Wei Ren Xu~c ~aInstitute of Theoretical Chemistry Shandong University Jinan 250100 China ~bInstitute of Organic Chemistry Shandong University Jinan 250100 China ~cTianjin Institute of the Pharmaceutical Research Tianjin 300193 China |
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| 作者单位： | a Institute of Theoretical Chemistry, Shandong University, Jinan 250100, China;b Institute of Organic Chemistry, Shandong University, Jinan 250100, China;c Tianjin Institute of the Pharmaceutical Research, Tianjin 300193, China |
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| 基金项目： | 国家重点基础研究发展计划(973计划)，国家自然科学基金 |
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| 摘 要： | To explore the closing mechanism of the substrate pocket,we perform a 16,000 ps molecular dynamics simulation separately on the ligand-free and actinonin-bound peptide deformylase from Leptospira interrogans.Our results show that the CD-loop, hydrophilic inhibitor and hydrophobic cluster are necessary for the formation of semi-open conformation,and Tyr71 plays an important role in mediating the movements of CD-loop.The average MD structure of the actinonin-bound LiPDF complex approaches to the crystal structure.These are consistent with experiment very well.
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| 关 键 词： | 缩氨酸去甲酰化 螺旋体 分子动态模拟 晶体结构分析 |
A molecular dynamics simulation study of peptide deformylase from Leptospira interrogans complex:Exploring the closing mechanism of the substrate pocket |
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| Qiang Wang,Jian Wu Wang,Zheng Ting Cai,Wei Ren Xu. A molecular dynamics simulation study of peptide deformylase from Leptospira interrogans complex:Exploring the closing mechanism of the substrate pocket[J]. Chinese Chemical Letters, 2008, 19(4): 497-500. DOI: 10.1016/j.cclet.2008.01.027 |
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| Authors: | Qiang Wang Jian Wu Wang Zheng Ting Cai Wei Ren Xu |
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| Affiliation: | a Institute of Theoretical Chemistry, Shandong University, Jinan 250100, China;b Institute of Organic Chemistry, Shandong University, Jinan 250100, China;c Tianjin Institute of the Pharmaceutical Research, Tianjin 300193, China |
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| Abstract: | To explore the closing mechanism of the substrate pocket,we perform a 16,000 ps molecular dynamics simulation separately on the ligand-free and actinonin-bound peptide deformylase from Leptospira interrogans.Our results show that the CD-loop,hydrophilic inhibitor and hydrophobic cluster are necessary for the formation of semi-open conformation,and Tyr71 plays an important role in mediating the movements of CD-loop.The average MD structure of the actinonin-bound LiPDF complex approaches to the crystal structure.These are consistent with experiment very well. |
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| Keywords: | Peptide deformylase Leptospira interrogan Molecular dynamics simulation |
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