X-ray crystal analysis
molecular dynamics simulation
Biochemistry and Biotechnology
Wiley InterScience Backfile Collection 1832-2000
The crystal structure of n-dodecylphosphorylcholine (n-C12PC)-bovine pancreas phospholipase A2 (PLA2) complex provided the following structural.characteristics: (1) the dodecyl chain of n-C12PC was located at the PLA2 N -terminal helical region by hydrophobic interactions, which corresponds to the binding pocket of 2-acyl fatty acid chain (β-chain) of the substrate phospholipid, (2) the region from Lys-53 to Lys-56 creates a cholinereceiving pocket of n-C12PC and (3) the N-termillal group of Ala-1 shifts significantly toward the Tyr-52 OH group by the binding of the n-C12PC inhibitor. Since the accuracy of the X-ray analysis (R = 0.275 at 2.3 Å resolution) was insufficient to establish these important X-ray insights, the complex structure was further investigated through the molecular dynamics (M D) simulation, assuming a system in aqueous solution at 310K. The M D simulation covering 176 ps showed that the structural characteristics observed by X-ray analysis are intrinsic and also stable in the dynamic state. Furthermore, the M D simulation made clear that the PLA2 binding pocket is large enough to permit the conformational fluctuation of the n-C12PC hydrocarbon chain. © 1994 Wiley-Liss, Inc. © 1994 Wiley-Liss, Inc.
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