Abstract
Molecular Dynamics (MD) simulation was carried out to study the conformation changes of the active zone of a Peptide Deformylase. Both the simulation with and without ligand were initialed from the crystal structure (1bs8). The tripeptide, Met-Ala-Ser (MAS), was used as the ligand in simulation. After thermal equilibrium, trajectories of one nanosecond MD run was collected and analyzed. The simulation result was compared with the NMR and crystal observed structures. The simulation shows that within one nanosecond time domain, only local deformation of protein occurred. The active zone was defined by the associated active atomic sites and torsion angles. It is indicated that the active zone from the simulation without ligand is similar to that determined from NMR experiment in solution. The active zone is altered at some residues by comparison with the data from the simulation with or without ligand, which is different from the results obtained from crystal structures. It is suggested that the active zone of PDF in solution could be influenced by the ligand locally.
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