Using quantum mechanics (QM) and mixed quantum mechanics/molecular mechanics (QM/MM) methods to study reaction mechanisms in enzymes

Quantum mechanics (QM) and mixed quantum mechanics/molecular mechanics (QM/MM) methods are applied to the study of enzyme reaction mechanisms. The QM computations use ab initio quantum chemical methods based upon density functional theory. QM/MM calculations combine QM methods with an all-atom force field to represent the remainder of the protein, enabling the active site chemistry to be modeled with quantum accuracy while explicitly including the protein environment in the calculations. The work has as its foundation experimental data (e.g. crystallographic structures, spectroscopic and kinetic data), and seeks to discover reaction mechanisms consistent with those data, from which physical and electronic insights concerning the catalytic chemistry are ascertained.; The first system studied is the metalloprotein methane monooxygenase (MMO). The process of dioxygen activation in this enzyme involves sequential formation of superoxo and peroxo intermediates, followed by decay of the latter to yield intermediate Q, the catalytically competent species which reacts with the substrate methane. Key features of the dioxygen activation pathway include a carboxylate shift in the ligands coordinated to the MMO diiron core and homolytic cleavage of the peroxo bond in the final step of Q formation.; Next, methane hydroxylation by species Q is investigated. The reaction rate-determining step, methanol is formed via either of two reaction channels—a bound-radical recoil/rebound mechanism or a nonsynchronous concerted pathway in which radical recoil is suppressed. Hydroxylation of substituted methanes is subsequently investigated in order to explain the wide range of kinetic isotope effects observed experimentally for these seemingly very similar substrates.; The other subject of computations is the deacylation reaction in class C β-lactamases and penicillin binding proteins (PBPs). The much more rapid rate of reaction in the former is one of the principal factors leading to bacterial resistance to β-lactam antibiotics. The difference in rates is attributable mainly to the creation of a more favorable electrostatic environment around the general base in the β-lactamase. This work will lead to the selection of mutations capable of converting a PBP into a β-lactamase and vice versa.