Mechanism of action of cyclophilin A explored by metadynamics simulations

Peptidyl prolyl isomerases (PPiases) are ubiquitous enzymes that catalyze the interconversion of the cis and trans isomers of the peptidyl prolyl bond. Their action is crucial in several biological processes as, for instance, in cellular signalling and in the onset of several diseases. In the HIV-1 capside protein (CA), such process takes place in the uncoating and recruitment of the virion and is catalyzed by cyclophilin A (CypA). Previous studies identified several residues that play an important role in the trans/cis interconversion process. However, the role of some active site residues remains still obscure, since their catalytic importance depend crucially on the stabilization of both ground and transition states. Here, we report the results of classical AMBER99 calculations on a substrate fragment of the capside protein (the /HAGPIA/ peptide) in aqueous solution and in complex with CypA. By applying replica exchange metadynamics, we calculate the free energy profile of the isomerization process in both cases as a function of several reaction coordinates. We find that CypA catalyzes only one isomerization pathway in the trans-to-cis direction and enhances the stability of a particular cis conformer. Based on our computational results, we propose a novel hypothesis for the working mechanism of cyclophilin A that explains, for the first time, all the available data and awaits further experimental tests.