Date of Award

8-3-2017

Degree Type

Thesis

Degree Name

M.Sc.

Department

Chemistry and Biochemistry

First Advisor

Gauld, James

Keywords

beta lactamase, enzyme catalysis, enzyme inhibition, glucosamine 6 phosphate synthase, molecular dynamics, qm/mm

Abstract

Using a range of computational chemistry methods including Molecular Dynamics (MD) simulations, quantum mechanical (QM)-­‐chemical cluster, and quantum mechanics/molecular mechanics (QM/M) methods, we have investigated the catalytic mechanism and inhibition of two physiologically important enzymes; glucosamine-­‐6-­‐phosphate synthase and CTX-­‐M β-­‐lactamase, respectively. More specifically, for the inhibition of CTX-­‐M β-­‐lactamase it was observed that an active site serinyl (Ser130) residue initially assists in stabilizing the reactive complex. The side-­‐chain hydroxyl (β-­‐OH) of Ser130 is deprotonated by the nearby side-­‐chain amine of Lys73. This enables the resulting now oxyanionic β-­‐oxygen to nucleophilically attack the substrate's key ring carbonyl carbon centre. This reaction step occurs with a barrier of 74.5 kJ mol-­‐1 and results in the formation of a covalently cross-­‐linked enzyme-­‐ligand intermediate. Interestingly, whether Lys73 is initially in its protonated or neutral state in the reactive complex, due to the nearby presence of a glutamate residue, it is able to readily act as a base to deprotonate the side-­‐chain hydroxyl of Ser130. For glucosamine-­‐6-­‐phosphate synthase, the protonation state of His504 and its catalytic role were elucidated. The mechanism for opening of the substrate's sugar ring in which His504 initially acts as an acid but later as a base, occurs with a barrier of 107.2 kJ mol-­‐1. An alternative pathway was considered in which Glu488 is able to act as a base and His504 as an acid. This mechanism was found to occur with a lower reaction barrier of 91.5 kJ mol-­‐1. The results of MD simulations also supported the suggesting of His504 being protonated as it results in a more consistent active site-­‐bound reactive complex. The work in this thesis highlight the significance of approaching enzymatic systems through both molecular dynamic and quantum mechanical/molecular mechanical techniques.

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