The possible mechanism by which the insulin-degrading enzyme (IDE) zinc-binding protease carries out its catalytic function toward two peptides of different length, simulating a portion of B chain of insulin, was investigated on an enzymatic model consisting of 130 /159 atoms, using the density functional theory method and the hybrid exchange-correlation functional B3LYP in gas phase and in the protein environment. Based on the geometry and relative stabilities of minima and transition states on the potential energy profiles, we determined that proteolysis reaction is exothermic and proceeds quickly as the barrier in the rate-limiting step falls widely within the range of values expected for an enzymatic catalysis, both in vacuum and in protein medium.

The carbonic anhydrase is the enzyme that catalyzes the reversible hydration of carbon dioxide and represents one of the most ancient proteins to which a plethora of works was devoted. The three main classes rely on zinc ion for activity. Most recently a new class of CA was discovered in marine diatoms to use naturally a cadmium ion as catalytic metal. In the present investigation we focused our attention on a carbonic anhydrase cambialistic enzyme (CDCA1) belonging to this new class. The study was inspired by the discovery that the replacement of zinc ion with cadmium does not entail significant differences in the catalytic performance of the enzyme. Our aim was to give further insight of the enzymatic work mechanism. Different possible reaction paths were considered for both metallic forms of the enzyme and comparison with previous studies concerning other carbonic anhydrases was made. The effects of the solvent on the energetics of the catalytic process, was also taken into account by means of a polarizable continuum model. The results obtained from density functional calculations, using a well consolidated mixing of exchange-correlation potential and basis set, and performed with a model of the active site designed on the basis of the X-ray crystal structure, proposed for both metal ions similar reaction pathways consisting in the nucleophilic attack by the metal bound hydroxide to the carbon dioxide with bicarbonate formation, in a next internal rotation of this last fragment, and then in the formation of a species ready for the product removal. Similar activation barriers were found in the rate determining steps that confirm the experimental indication concerning the comparable efficiency of the enzyme in the presence of a zinc or cadmium metal ion.

The reaction mechanism of the Mitochondrial Processing Peptidase enzyme (MPP) was investigated by using hybrid density functional theory. This enzyme removes the NH(2)-terminal targeting signals of nuclear-encoded mitochondrial protein precursors in the mitochondrial matrix. The catalytic process was studied using a model for the active site consisting of 161 atoms locating all the stationary points on the potential energy curve and determining the main energetic, structural, and electronic features that drive the catalysis. Despite the differences between the B3LYP and MPWB1K descriptions, it is possible hypothesize that the rate-limiting step of the reaction is most likely the nucleophilic attack of zinc-bound hydroxide to a carbonyl carbon of the substrate. The results allowed assignment of the proper roles to some active site residues in this mechanism.