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Title: Novel QM/MM Investigations of Enzyme Catalysis
Author: Williamson, Mark J.
Awarding Body: Imperial College London
Current Institution: Imperial College London
Date of Award: 2008
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Enzymes facilitate specific chemical reactions by lowering the Gibbs free energy of activation (AG++), thus increasing the rate of catalysis. It would be advantageous to understand exactly what within the enzyme leads to this lowering ofthe activation energy. This work describes the development ofa protocol for calculating the free energy barrier between two states of an enzyme, or other condensed phase system using computer simulation. The natute of the calculation enables it to be decomposed to reveal which vibrational modes observed in a molecular dynamics simulation are contributing to the catalytic effects. The energy gap fluctuations between the two states can be used to calculate a free energy function for the reaction coordinate between two states. A probability distribution function can be generated using , these values and, given sufficient equilibrium sampling, the Central Limit Theorem may be invoked so that the distribution can be represented by a Gaussian function. Using this distribution to represent the equilibrium constant within Transition State Theory, the free energy difference is quadratic with respect to the energy gap value. Assuming a linear response ofthe solvent bath (Marcus theory), the free energy difference function is extrapolated to a zero energy gap value, thus giving the, experimentally comparable, free energy of activation between those two states. The thesis presents the progress made in developing this novel approach for obtaining the energy gap between two states, and its initial application to the rate limiting hydride transfer step catalysed by the extensively studied horse liver alcohol dehydrogenase (LADH) enzyme. Two, independent, equilibrium trajectories ofthe states either side ofthis rate limiting step are propagated classically using the AMBER force field. Time ordered snapshots ofthe simulation's coordinates are postprocessed using a QMlMM method to obtain the ground state energy ofthe system; the active site is treated quantum mechanically, with the polarising effects ofthe surrounding protein and water bath incorporated as point charges in its one electron Hamiltonian. Development ofthe approach was facilitated using the smaller test system ofMalachite Green. This protocol offers a computationally cheaper alternative to the normal Empirical Valence Bond (EVB) I Free Energy Perturbation (PEP) approach, since only two equilibrium trajectories of both states are required instead of an ovedapping set of trajectories in the range between the states. The additional complexity of a switching Hamiltonian is also avoided. The subtracted spectrum of oscillators gives insight into which vibrational modes within the system are contributing to the catalytic effect. ' 1, I
Supervisor: Not available Sponsor: Not available
Qualification Name: Imperial College London, 2008 Qualification Level: Doctoral
EThOS ID:  DOI: Not available