A molecular dynamics simulation study of peptide deformylase from Leptospira interrogans complex:Exploring the closing mechanism of the substrate pocket  

作　　者：Qiang Wang Jian Wu Wang Zheng Ting Cai Wei Ren Xu 

机构地区：[1]Institute of Theoretical Chemistry,Shandong University,Jinan 250100,China [2]Institute of Organic Chemistry,Shandong University,Jinan 250100,China [3]Tianjin Institute of the Pharmaceutical Research,Tianjin 300193,China

出　　处：《Chinese Chemical Letters》2008年第4期497-500,共4页中国化学快报（英文版）

基　　金：supports of the National Key Basic Research Priorities Program(No.2003CCA027);the National Natural Science Foundation of China(No.20573064).

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.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.

关 键 词：Peptide deformylase Leptospira interrogan Molecular dynamics simulation 

分 类 号：O623.73[理学—有机化学]