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

作者：Wang Qiang; Wang Jian Wu; Cai Zheng Ting^*; Xu Wei Ren

来源：Chinese Chemical Letters, 2008, 19(4): 497-500.

DOI：10.1016/j.cclet.2008.01.027

• peptide deformylase
• Leptospira interrogan
• molecular dynamics simulation

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.

• 出版日期2008-4
• 单位山东大学; 天津药物研究院有限公司