Computational Studies of Metalloenzymes

Sammanfattning: Enzymes are involved in most reactions in nature. They are important both for the understanding of biological life and for reactions of industrial interest, e.g. in the production of artificial fertilizers, the production of biomass or biofuels. Enzymes with one or several metal ions are called metalloenzymes. In this thesis we study three different metalloenzymes, nitrogenase, lytic polysaccharide monooxygenase (LPMO) and particulate methane monooxygenase (pMMO) with computer simulations. We use mainly combined quantum mechanical and molecular mechanical (QM/MM) calculations with the density functional theory (DFT) method.Nitrogenase is the only enzyme that can break the triple bond in nitrogen molecules, making nitrogen available for plant metabolism. Previous studies have shown that different DFT methods give widely different results for the relative energies of different structures of putative intermediates in the reaction mechanism of nitrogenase. Therefore, we have tried to calibrate DFT calculations in two different ways. First, we use experimental data of structures and reactions related to nitrogenase to see what DFT functionals give the most accurate results.Our results indicate that BLYP, B97D and MN15 give the best results.Second, we have developed a small and simple model system of the active site of nitrogenase, [Fe(SH)4H]−.This model still shows a large variation in DFT estimate of the energy difference between structures protonated on Fe or on S, 25–163 kJ/mol. We then use a series of advanced and accurate QM methods, including coupled-cluster, selected configuration-interaction and multicon gurational perturbation theory methods to calibrate the DFT methods. With this model, M06 and B3LYP give the most accurate results.The second studied enzyme is LPMO, which is a copper dependent enzyme used for the degradation of polysaccharides, such as cellulose and chitin. The mechanism of this enzyme is quite well known but it has an unusual methyl modi cation of one of the ligands. Our calculations suggest that this group may protect the enzyme from self-oxidation. The third studied enzyme is pMMO. This enzyme can hydroxylate methane. This enzyme is hard to study experimentally and the nature and location of the active site is still controversial. We have studied the reactivity of three putative active sites, involving mononuclear copper sites, and have shown that theycan support similar reactions. The CuC site gives the most favourable energetics.