Enzyme catalysis, reactions

Keywords Ab initio QM/MM method, Pseudobond approach, Enzyme catalysis, Reaction... 

Note Esterification of the hydroxy functionalised imidazole was achieved by an enzyme catalysis reaction (C. antarctica) [173-175],... 

Lodola, A., Mor, M., Zurek, J., Tarzia, G., PiomeUi, D., Harvey, J.N., MulhoUand, A.J. Conformational effects in enzyme catalysis Reaction via a high energy conformation in fatty acid amide hydrolase. Biophys. J. 2007, 92(2), L20-2. 

Enzymatic resolution (Section 7 13) Resolution of a mixture of enantiomers based on the selective reaction of one of them under conditions of enzyme catalysis... 

The chemical reaction catalyzed by triosephosphate isomerase (TIM) was the first application of the QM-MM method in CHARMM to the smdy of enzyme catalysis [26]. The study calculated an energy pathway for the reaction in the enzyme and decomposed the energetics into specific contributions from each of the residues of the enzyme. TIM catalyzes the interconversion of dihydroxyacetone phosphate (DHAP) and D-glyceraldehyde 3-phosphate (GAP) as part of the glycolytic pathway. Extensive experimental studies have been performed on TIM, and it has been proposed that Glu-165 acts as a base for deprotonation of DHAP and that His-95 acts as an acid to protonate the carbonyl oxygen of DHAP, forming an enediolate (see Fig. 3) [58]. 

The QM-MM study of TIM was the first illustration of the potential of these methods for studying enzyme catalysis and has served as a reference for the protocol needed for subsequent studies of enzyme reactions. 

This idea also helps to explain some of the mystery surrounding the enormous catalytic power of enzymes In enzyme catalysis, precise orientation of catalytic residues comprising the active site is necessary for the reaction to occur substrate binding induces this precise orientation by the changes it causes in the protein s conformation. 

Enzyme catalysis requires that Kj- < Kg. According to transition-state theory (see references at end of chapter), the rate constants for the enzyme-catalyzed k ) and uncatalyzed k reactions can be related to Kg and K by ... 

If the enzyme-catalyzed reaction is to be faster than the uncatalyzed case, the acceptor group on the enzyme must be a better attacking group than Y and a better leaving group than X. Note that most enzymes that carry out covalent catalysis have ping-pong kinetic mechanisms. 

Keller, H. J., and Soos,-Z. G. Solid Charge-Transfer Complexes of Phenazines. 127, 169-216 (1985). Kellogg, R. M. Bioorganic Modelling — Stereoselective Reactions with Chiral Neutral Ligand Complexes as Model Systems for Enzyme Catalysis. 101, 111-145 (1982). 

Bioorganic modelling. Stereoselective reactions with chiral neutral ligand complexes as model systems for enzyme catalysis. R. M. Kellogg, Top. Curr. Chem., 1982,101,111-145 (93). 

Enthalpy of activation, 10, 156-160 Entropy of activation, 10, 156-160 compared with AV, 169 concentration units and, 168 precision of, 168 Enzyme catalysis, 90-94 Equilibria, complexation, 145-148 Exchange reactions, kinetics of,... 

The previous chapters taught us how to ask questions about specific enzymatic reactions. In this chapter we will attempt to look for general trends in enzyme catalysis. In doing so we will examine various working hypotheses that attribute the catalytic power of enzymes to different factors. We will try to demonstrate that computer simulation approaches are extremely useful in such examinations, as they offer a way to dissect the total catalytic effect into its individual contributions. 

It has been frequently suggested that dynamical factors are important in enzyme catalysis (Ref. 9), implying that enzymes might accelerate reactions by utilizing special fluctuations which are not available for the corresponding reaction in solutions. This hypothesis, however, looks less appealing when one examines its feasibility by molecular simulations. That is, as demonstrated in Chapter 2, it is possible to express the rate constant as... 

The entropic hypothesis seems at first sight to gain strong support from experiments with model compounds of the type listed in Table 9.1. These compounds show a huge rate acceleration when the number of degrees of freedom (i.e., rotation around different bonds) is restricted. Such model compounds have been used repeatedly in attempts to estimate entropic effects in enzyme catalysis. Unfortunately, the information from the available model compounds is not directly transferable to the relevant enzymatic reaction since the observed changes in rate constant reflect interrelated factors (e.g., strain and entropy), which cannot be separated in a unique way by simple experiments. Apparently, model compounds do provide very useful means for verification and calibration of reaction-potential surfaces... 

In view of the arguments presented in this chapter, as well as in previous chapters, it seems that electrostatic effects are the most important factors in enzyme catalysis. Entropic factors might also be important in some cases but cannot contribute to the increase of kcJKM. Furthermore, as much as the correlation between structure and catalysis is concerned, it seems that the complimentarity between the electrostatic potential of the enzyme and the change in charges during the reaction will remain the best correlator. Finally, even in cases where the source of the catalytic activity of a given enzyme is hard to elucidate, it is expected that the methods presented in this book will provide the crucial ability to examine different hypothesis in a reliable way. 

Hypothermia slows down enzyme catalysis of enzymes in plasma membranes or organelle membranes, as well as enzymes floating around in the cytosol. The primary reason enzyme activity is decreased is related to the decrease in molecular motion by lowering the temperature as expressed in the Arrhenius relationship (k = where k is the rate constant of the reaction, Ea the activation energy,... 

The interest and success of the enzyme-catalyzed reactions in this kind of media is due to several advantages such as (i) solubilization of hydrophobic substrates (ii) ease of recovery of some products (iii) catalysis of reactions that are unfavorable in water (e.g. reversal of hydrolysis reactions in favor of synthesis) (iv) ease of recovery of insoluble biocatalysts (v) increased biocatalyst thermostability (vi) suppression of water-induced side reactions. Furthermore, as already said, enzyme selectivity can be markedly influenced, and even reversed, by the solvent. 

The form of Equation (10.12) is widely used for multiphase reactions. The same model, with slightly diflerent physical interpretations, is used for enzyme catalysis and cell growth. See Chapter 12. 

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