Reaction mechanism of metalloenzymes studied by theoretical methods

Abstract: Metalloenzymes catalyse a wide variety of reactions in nature. In the thesis, I have studied the reaction mechanism of three metalloenzymes, viz. [NiFe] hydrogenase (H2ase), dimethyl sulfoxide reductase (DMSOR) and formate dehydrogenase (FDH), by theoretical methods, namely quantum mechanics (QM), combined quantum mechanical and molecular mechanics (QM/MM), as well as QM/MM thermodynamic cycle perturbation (QTCP). For H2ase, we have studied the protonation states of the four cysteine residues in the active site at four intermediate states, the H2 binding site and the full reaction mechanism. Our results demonstrate that the Cys546 residue is most easily protonated by 14−51 kJ/mol, H2 binding to Ni ion in singlet state is most favourable by at least 47 kJ/mol, and the Ni-L state is not involved in the reaction mechanism. For the H2 binding, we have calibrated density-functional methods with advanced QM methods, like CCSD(T), DMRG-CASPT2 and CAS-srDFT.For DMSOR, we have studied the effect of the protein ligand in reaction mechanism. Our results indicate that enzymes with ligand with a single negative charge (serine, cysteine, selenocysteine, SH– and OH–) are predicted to have two-step reaction mechanisms, giving an activation energy of 69−85 kJ/mol. However, the O2– and S2– ligands gave much higher activation energies of 212 and 168 kJ/mol. For FDH, we have studied the reaction mechanism. Our results indicate that the substrate formate does not coordinate directly to Mo ion when it enters the oxidised active site of FDH, but instead resides in the second coordination sphere. The sulfido ligand abstracts a hydride from substrate, giving a Mo(IV)−SH state. Finally, the CO2 will be released when the active site is oxidised by two electrons.