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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. It results show that the CD-loop, a 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 actinon-bound LiPDF complex approaches to the crystal structure. These are consistent with experiment very well.