Favored Reaction Mechanism of Calcium-Dependent Phospholipase A2. Insights from Density Functional Exploration

The sn-2 acyl hydrolysis of phospholipids catalyzed by phospholipase A(2) (PLA(2)) was investigated at the density functional B3LYP level. The PLA(2) active site is represented by quantum-chemical models that are based on available X-ray crystal structures. The two still controversial catalytic triad and calcium-coordinated oxyanion reaction mechanisms were considered. Tetrahedral intermediate formation in the first mechanism and the cleavage of the C-O bond in the second one are the rate-determining steps. Both mechanisms, in the gas phase and in the protein-like environment, yielded potential energy profiles with low energy barriers and consequently the comparison did not indicate a clear preference for one or the other path. An alternative mechanism, based on some corrections to the previously suggested ones, provides for an optional pathway for the enzyme activity.