Calcium Independent Substrate and Product Diffusion Process of Secretary Phospholipase A2 from Taiwan Cobra

Abstract

Understanding how membrane lipids can be delivered to the active site distant from the interfacial binding surface of the enzyme and how the products got released from the active site are important to depict the interfacial enzyme reaction mechanism. Based on the crystal structure of the trimeric complex structure of the cobra phospholipase A2 (PLA2) from Naja atra with the enyzymatic substrate of diacylheptanoyl phosphatidylcholine (PC) and products of lyso PC and fatty acids (minic by SDS), we suggest that promiscuous bindings of phospholipids to the interfacial enzyme may boost the lipid desorption process via a cooperative hydrophobic interaction among the hydrocarbon chains of phospholipids and that with the interfacial surface of the enzyme. We also show that phospholipids in membranes surface with high curvature can promote the diffusion of the lipid into the substrate binding hydrophobic channel of cobra PLA2 in a calcium independent manner. The PC substrate binding site within the channel without calcium is distinct from that in the presence of calcium as one compares its binding position with that of transition binding intermediates. Interestingly, calcium appears to destabilize the binding of both substrate and product binding at the hydrophobic channel even though it is required for the enzymatic catalysis. Our results suggest that the calcium independent lipid diffusion process play an important role in the interfacial binding activation of secretary PLA2 and shed new light for the future depiction of the energy landscape.