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

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.