Enzyme catalysis specificity

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 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. 

The effects of the feed ratio in the lipase CA-catalyzed polymerization of adipic acid and 1,6-hexanediol were examined by using NMR and MALDI-TOF mass spectroscopies. NMR analysis showed that the hydroxyl terminated product was preferentially formed at the early stage of the polymerization in the stoichiometric substrates. As the reaction proceeded, the carboxyl-terminated product was mainly formed. Even in the use of an excess of the dicarboxylic acid monomer, the hydroxy-terminated polymer was predominantly formed at the early reaction stage, which is a specific polymerization behavior due to the unique enzyme catalysis. 

The function of enzymes is to accelerate the rates of reaction for specific chemical species. Enzyme catalysis can be understood by viewing the reaction pathway, or catalytic cycle, in terms of a sequential series of specific enzyme-ligand complexes (as illustrated in Figure 1.6), with formation of the enzyme-substrate transition state complex being of paramount importance for both the speed and reactant fidelity that typifies enzyme catalysis. 

Owing to their reliance on enzyme catalysis to generate the inhibitory species, mechanism-based inactivators can be very specific for the target enzyme, or at the very least, highly selective for a family of enzymes that catalyze a common reac-... 

First-order rate constants are used to describe reactions of the type A — B. In the simple mechanism for enzyme catalysis, the reactions leading away from ES in both directions are of this type. The velocity of ES disappearance by any single pathway (such as the ones labeled k2 and k3) depends on the fraction of ES molecules that have sufficient energy to get across the specific activation barrier (hump) and decompose along a specific route. ES gets this energy from collision with solvent and from thermal motions in ES itself. The velocity of a first-order reaction depends linearly on the amount of ES left at any time. Since velocity has units of molar per minute (M/min) and ES has units of molar (M), the little k (first-order rate constant) must have units of reciprocal minutes (1/min, or min ). Since only one molecule of ES is involved in the reaction, this case is called first-order kinetics. The velocity depends on the substrate concentration raised to the first power (v = /c[A]). 

Enzyme catalysis. Enzymes are proteins, polymers of amino acids, which catalyze reactions in living organisms-biochemical and biological reactions. The systems involved may be colloidal-that is, between homogeneous and heterogeneous. Some enzymes are very specific in catalyzing a particular reaction (e.g., the enzyme sucrase catalyzes the inversion of sucrose). Enzyme catalysis is usually molecular catalysis. Since enzyme catalysis is involved in many biochemical reactions, we treat it separately in Chapter 10. 

As already stated, Fischer was deeply intrigued by the phenomenon of enzyme activity. He realized that the substances were proteins and this undoubtedly was why he next undertook the study of amino acids and peptides. He fully appreciated that the specificity of enzyme catalysis depended on the occurrence of a complementarity for interacting dissymmetric surfaces. In this regard, he wrote (3) ... 

As already mentioned, the glucoamylase project was chosen to illustrate Emil Fischer s lock and key concept for enzyme specificity. It is seen that his vision has become unequivocally established. Many other developments could have been chosen, as can be appreciated from recent reviews by Hehre (54) and by Svensson (55). Comforth (56) provided a fine overview of asymmetry and enzyme action in his Nobel prize lecture. Noteworthy is the conclusion that stereospecificity is something not just incidental, but essential to enzyme catalysis. In other words, the key must fit the lock. 

Many attempts have been made during the past 30 years to imitate enzymes. Studies in the preparation of artificial enzymes (6) and model enzymes abound. While it is undoubtedly true that most enzymes can achieve the transformation of an achiral substrate to a chiral one more rapidly and with higher specificity than can be achieved using nonenzymic catalysts, the many limitations to which enzymic catalysis is subject should be properly evaluated. These are as follows ... 

Because both the passive fluctuations and the modulating vibrations can require thermal excitation, this model is capable of accounting for temperature-dependent isotope effects, including those traditionally described by the BeU model. Theoretical studies, which will be the topic of the second and third parts of this three-part series of articles, have not yet produced a consensus on the contribution of specific protein motions to enzyme catalysis. 

As with chemical synthesis, the first step when prospecting for a particular biotransformation is to perform a literature search to check whether a suitable precedent has been described. Extensive technical literature resources in the public domain provide both examples of specific enzyme-catalysed reactions and descriptions of transformations where enzyme activity is inferred if not explicitly described. Currently, searches of online databases such as PubMed reveal over 2000 new publications per annum in the subject of enzyme catalysis (excluding reviews). 

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