Applications Of Combined Quantum Mechanics And Molecular Mechanics Methods In The Study Of Enzyme Catalysis

Combined quantum mechanics and molecular mechanics (QM/MM)methods have become the method of choice for the studies on the mechanism ofenzyme catalysis. On one hand, the size and conformational complexity ofenzymes require highly efficient methods capable of treating up to tens ofthousands of atoms and allowing for extensive simulations on the nanosecondtime scale. On the other hand, the description of chemical reactions and otherprocesses that involve changes in the electronic structure require quantummechanics methods. And the QM/MM methods enable the modeling of reactivebiomolecular systems at reasonable computational cost while providing thenecessary accuracy. In this thesis, we employed the QM/MM methods,combined with geometry optimization, molecular dynamics, and free-energysimulation techniques to investigate the catalytic mechanisms of thiopurineS-methyltransferase, aliphatic aldoxime dehydratase, and α-galactosidase, andexplored the applications of the different approaches in the study of enzymecatalysis.1. QM(PDDG-PM3)/MM molecular dynamics simulations with theumbrella sampling technique were performed to investigate themethylation of6-mercaptopurine catalyzed by thiopurineS-methyltransferase. Several setups with different tautomeric formsand orientations of the substrate were considered. It is found that, theorientation of the substrate in chain A of the X-ray structure favors themethylation reaction which may take place after the deprotonation ofthe substrate by the conserved residue Asp23through a water chain.The potential of mean force of the methyl-transfer step for the mostfavorable pathway is in good agreement with the availableexperimental rate constant data.2. QM(B3LYP)/MM structure and reaction path optimizations are performed to elucidate the catalytic mechanism of the enzyme on thebasis of the X-ray crystal structure of the Michaelis complex. Theelimination of the hydroxyl group of aldoxime is facilitated by His320acting as a general acid. The formed intermediate has a ferric hemeiron and an unpaired electron coupled to a singlet state. The secondstep is the deprotonation of the β-hydrogen of the substrate by His320after the substrate rotates about the Fe N bond for～180°to yield theneutral product. In the meantime, the heme iron recovers the ferrousstate and His320goes back to the protonated state to proceed with thefollowing reaction.3. The glycosylation step catalyzed by human α-galactosidase wascomputationally simulated with QM(PM6-D)/MM metadynamics. Oursimulations show that the overall catalytic mechanism follows asubstrate retaining and DN*AN-like mechanism, and the transition statehas a oxocarbenium ion like character with a partially formed doublebond between the ring oxygen and C5’ carbon atoms. In addition, thegalactosyl ring of the substrate follows a conformational itinerary ofalong the reaction coordinate.