Chemical enzyme reaction mechanism studies

Thermodynamic concepts are useful to apply to the study of enzyme-mediated enzyme kinetics. Through a variety of reaction mechanisms, specific enzymes catalyze specific biochemical reactions to turn over faster than they would without the enzyme present. Making use of the fact that enzymes are not able to alter the overall thermodynamics (free energy, etc.) of a chemical reaction, we can develop sets of mathematical constraints that apply to the kinetic constants of enzyme reaction mechanism. 

A variety of techniques have been applied to investigate enzyme reaction mechanisms. Kinetic and X-ray crystallographic studies have made major contributions to the elucidation of enzyme mechanisms. Valuable information has been gained from chanical, spectroscopic and biochemical studies of the transition-state structures and intermediates of enzyme catalysis. Computational studies provide necessary refinement toward our understanding of enzyme mechanisms. The ability of an enzyme to accelerate the rate of a chemical reaction derives from the complementarity of the enzyme s active site structure to the activated complex. The transition state by definition has a very short lifetime ( 10 s). Stabilization of the transition state alone is necessary but not sufficient to give catalysis, which requires differential binding of substrate and transition state. Thus a detailed enzyme reaction mechanism can be proposed only when kinetic, chemical and structural components have been studied. The online enzyme catalytic mechanism database is accessible at EzCatDB (http //mbs.cbrc.jp/EzCatDB/). 

Kinetics is the branch of science concerned with the rates of chemical reactions. The study of enzyme kinetics addresses the biological roles of enzymatic catalysts and how they accomplish their remarkable feats. In enzyme kinetics, we seek to determine the maximum reaction velocity that the enzyme can attain and its binding affinities for substrates and inhibitors. Coupled with studies on the structure and chemistry of the enzyme, analysis of the enzymatic rate under different reaction conditions yields insights regarding the enzyme s mechanism of catalytic action. Such information is essential to an overall understanding of metabolism. 

In this chapter we have seen that enzymatic catalysis is initiated by the reversible interactions of a substrate molecule with the active site of the enzyme to form a non-covalent binary complex. The chemical transformation of the substrate to the product molecule occurs within the context of the enzyme active site subsequent to initial complex formation. We saw that the enormous rate enhancements for enzyme-catalyzed reactions are the result of specific mechanisms that enzymes use to achieve large reductions in the energy of activation associated with attainment of the reaction transition state structure. Stabilization of the reaction transition state in the context of the enzymatic reaction is the key contributor to both enzymatic rate enhancement and substrate specificity. We described several chemical strategies by which enzymes achieve this transition state stabilization. We also saw in this chapter that enzyme reactions are most commonly studied by following the kinetics of these reactions under steady state conditions. We defined three kinetic constants—kai KM, and kcJKM—that can be used to define the efficiency of enzymatic catalysis, and each reports on different portions of the enzymatic reaction pathway. Perturbations... 

Chorismate mutase catalyzes the Claisen rearrangement of chorismate to prephenate at a rate 106 times greater than that in solution (Fig. 5.5). This enzyme reaction has attracted the attention of computational (bio)chemists, because it is a rare example of an enzyme-catalyzed pericyclic reaction. Several research groups have studied the mechanism of this enzyme by use of QM/MM methods [76-78], It has also been studied with the effective fragment potential (EFP) method [79, 80]. In this method the chemically active part of an enzyme is treated by use of the ab initio QM method and the rest of the system (protein environment) by effective fragment potentials. These potentials account... 

The partitioning of the system in a QM/MM calculation is simpler if it is possible to avoid separating covalently bonded atoms at the border between the QM and the MM regions. An example is the enzyme chorismate mutase [39] for which the QM region could include only the substrate, because the enzyme does not chemically catalyze this pericyclic reaction. In studies of enzyme mechanisms, however, this situation is exceptional, and usually it will be essential, or desirable, to include parts of the protein (for example catalytic residues) in the QM region of a QM/MM calculation, i.e. the boundary between the QM and MM regions will separate covalently bonded atoms (Fig. 6.1). 

MD simulations can aid in the understanding of enzymic reactions by providing new insights into the structures and intermolecular interactions fundamental to the chemical catalysis. By studying the structures from the simulation of the lysozyme-(GlcNAc)g complex, we have proposed an alternative to the accepted mechanism which accounts for the available experimental observations. The proposal of this lysozyme mechanism illustrates one way in which simulations can serve to generate new ideas which can be explored by experiment and computation. 

The study of cellulases has progressed considerably in the present decade. Recombinant DNA techniques have been applied and protein-chemical and structural studies have provided new insights. Crystallization of the first cellulases has succeeded recently and detailed structural information may be expected soon. It is hoped that this will give a further incentive to studying the intricate reaction mechanism of these enzymes and their substrate interactions (adsorptions). The important synergy phenomena certainly need a more systematic approach and new techniques should be applied in this area. 

We continue our study of chemical kinetics with a presentation of reaction mechanisms. As time permits, we complete this section of the course with a presentation of one or more of the topics Lindemann theory, free radical chain mechanism, enzyme kinetics, or surface chemistry. The study of chemical kinetics is unlike both thermodynamics and quantum mechanics in that the overarching goal is not to produce a formal mathematical structure. Instead, techniques are developed to help design, analyze, and interpret experiments and then to connect experimental results to the proposed mechanism. We devote the balance of the semester to a traditional treatment of classical thermodynamics. In Appendix 2 the reader will find a general outline of the course in place of further detailed descriptions. 

Although the metaphosphate mechanism for hydrolysis is well documented, such a pathway remains to be demonstrated in a biological system. Our present knowledge of many enzymic reactions allows, at best, the formulation of a preliminary mechanism, i.e. the chemical identity of substrates and enzymic intermediates and the minimal kinetic scheme. For example, much recent attention has been focused on the remarkable stability of the covalent phos-phoryl-enzyme (an O-phosphoryl serine) derived from E. coii alkaline phosphatase28 and inorganic phosphate, and on a systematic kinetic study of the enzyme s substrate specificity (O-, N- and S-monoesters) -9. Dephosphorylation of the enzyme, however, does not appear to be via a metaphosphate mechanism30. 

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