Citation: 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 shu

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

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

Received Date: 5 November 2007

Fund Project: The authors acknowledge the supports of the National Key Basic Research Priorities Program (No. 2003CCA027) and the National Natural Science Foundation of China (No. 20573064).

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.
- Peptide deformylase,
- Leptospira interrogan,
- Molecular dynamics simulation
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