Computational Study of the Catalytic Mechanism of the Cruzain Cysteine Protease

Cysteine proteases of the papain family are involved in many diseases, making them attractive targets for developing drugs. In this paper, different catalytic mechanisms of cruzain cysteine protease have been studied on the basis of molecular dynamics simulations within hybrid quantum mechanics/molecular mechanics potentials. The obtained free energy surfaces have allowed characterizing every single step along the mechanisms. The results confirm that the full process can be divided into an acylation and a deacylation stage, but important differences with respect to previous studies can be deduced from our calculations. Thus, our calculations suggest that the acylation stage takes place in a stepwise mechanism where a proton from a conserved His159 is transferred first to the N1 atom of the peptide and, after a transient intermediate is located, the Cys25 attacks the carbonyl carbon atom. The stabilization of the activated Cys25 is achieved by an effect of the local environment through interactions with re...