Docking and molecular dynamics studies on the mechanism of phospholipase D-mediated transphosphatidylation to construct the reaction kinetic model: Application in phosphatidylserine production

Abstract

Abstract The mechanism of phospholipase D (PLD)-mediated transphosphatidylation was systematically studied through docking and molecular dynamics (MD) studies. Special attention has been given to the binding process of transphosphatidylation and the binding order of substrates. Next, the byproduct (choline) inhibition mechanism was theoretically investigated to guide the reuse of free PLD solution and improve the reaction kinetic model of transphosphatidylation. All computational results were employed to elucidate the reaction profile of transphosphatidylation involving the binding process, reaction pathway and byproduct choline inhibition. The molecular simulations helped us understand the biocatalytic mechanism deeply. A reaction kinetic model based on the docking and MD results was firstly introduced to accurately anticipate the extent of reaction, calculate the optimal reaction time, the amount of substrate required and numbers of recycling of the free enzyme solution in the production of phosphatidylserine (PS).