Enzymes elementary steps

Let us consider the basic enzyme catalysis mechanism described by the Michaelis-Menten equation (Eq. 2). It includes three elementary steps, namely, the reversible formation and breakdown of the ES complex (which does not mean that it is at equilibrium) and the decomposition of the ES complex into the product and the regenerated enzyme ... 

Enzyme-catalyzed reactions can be described at least at two distinct levels. At the basic level, the interconversion of substrates by enzymes is governed by a set of elementary steps, including enzyme substrate binding, isomerization and dissociation steps, see Fig. 6 for a schematic depiction. Assuming the intracellular medium is an ideal solution, each elementary step is governed by mass-action kinetics, that is, the reaction rates are proportional to the probability of collision of the reactants. For a reaction of the type... 

Using mass-action kinetics for the elementary steps, the rates of change for the substrate and enzyme substrate complex concentrations are... 

The application of very low temperatures to detect, to thermally trap, and to characterize intermediates in enzyme-catalyzed reactions. This is made possible by the fact that each individual, elementary step in a reaction pathway has its own activation energy. Lowering the temperature reduces the fraction of molecules that can react in certain steps, thereby permitting otherwise reactive species to accumulate. 

The control of enzyme activity by the environment of a polyatomic framework is a vast topic, which I shall not attempt to cover fully in this report. Instead I will concentrate on some selected interactions between and within polypeptide chains that influence enzymatic activity. First, elementary steps involved in ligand-protein, intraprotein, and interprotein interactions are considered. Then enzymes consisting of a single polypeptide chain are discussed, followed by enzymes consisting of multiple polypeptide chains. The concluding sections are concerned with multienzyme complexes and enzymes associated with membranes. 

The Michaelis-Menten equation, especially if derived with the steady-state concept as above, is a rigorous rate law which not only fits almost all one-substrate enzyme kinetics, except in the case of inhibition (see Section 5.3), but also allows identification of the kinetic constants with the elementary steps in Eq. (5.1). 

The postulation of a model of the mechanism of an enzyme reaction encompasses consideration of the elementary steps. In an enzyme reaction, there are always several steps which make up a mechanism, including at least one binding step and a catalytic one. The Michaelis-Menten equation [Eq. (9.1)] discussed in Chapters 2 and 5 is the kinetic manifestation of a simple mechanism encompassing binding and reaction ... 

Once the substrate is bound, other residues at the active site carry out the catalytic reaction. The elementary steps involved are similar to those we covered in Chapters 3 and 4. Broadly speaking, enzyme catalysis is divided into two common mechanisms Bronsted acid/base catalysis and nucleophilic catalysis [26]. 

These properties are likely to have an important influence on the behavior of intact biochemical systems, e.g., within the living cell, enzymes do not function in dilute homogeneous conditions isolated from one another. The postulates of the Michaelis-Menten formalism are violated in these processes and other formalisms must be considered for the analysis of kinetics in situ. The intracellular environment is very heterogeneous indeed. Many enzymes are now known to be localized within 2-dimensional membranes or quasi 1-dimensional channels, and studies of enzyme organization in situ [26] have shown that essentially all enzymes are found in highly organized states. The mechanisms are more complex, but they are still composed of elementary steps governed by fractal kinetics. 

The anomalies pointed out above, including compensation effects, may be accounted for in general bases of the assumption that the chemical elementary steps on the enzyme are accompanied by the arrangement of the conformational structure of protein globules and surrounding water molecules. The kinetic and thermodynamic parameters of such structural rearrangements make a contribution to the experimentally measured and whose reflect cooperative properties of the water-protein matrix. 

A heterogeneous catalytic reaction involves adsorption of reactants from a fluid phase onto a solid surface, surface reaction of adsorbed species, and desorption of products into the fluid phase. Clearly, the presence of a catalyst provides an alternative sequence of elementary steps to accomplish the desired chemical reaction from that in its absence. If the energy barriers of the catalytic path are much lower than the barrier(s) of the noncatalytic path, significant enhancements in the reaction rate can be realized by use of a catalyst. This concept has already been introduced in the previous chapter with regard to the Cl catalyzed decomposition of ozone (Figure 4.1.2) and enzyme-catalyzed conversion of substrate (Figure 4.2.4). A similar reaction profile can be constructed with a heterogeneous catalytic reaction. 

In all of these systems, chemical reactions have a hierarchical structure. What we normally think of as one reaction is actually composed from several elementary steps, which are often called, collectively, the mechanism of the reaction. For processes with a solid catalyst, these steps describe the interaction of the catalyst s active sites with the fluid-phase reactants. For biochemical reactions, there are association and dissociation steps that involve complexes of the enzyme and the substrates. In all cases, unstable, short-lived intermediates may be formed and destroyed in a rapid succession of steps the overall reaction we observe might not... 

Cryoenzymology utilizes the following features of enzyme catalysis the existence on the catalytic reaction pathway of several enzyme-substrate (or product) intermediate species, typically separated by energy barriers with enthalpies of activation of 7 to 20 kcal mol"1 and the fact that the energies (enthalpies) of activation for the individual steps in the overall catalytic pathway are usually significantly different. For such elementary steps temperatures of —100 °C will result in rate reductions on the order of 105 to 1011 compared to those at 25 or 37°C (5). The theoretical basis of cryoenzymology has been presented in detail elsewhere (5, 7, 9, 10). If the reaction is initiated by mixing enzyme and substrate at a suitably low temperature, only the initial noncovalent ES... 

The mathematical treatment of enzyme kinetics is quite complex, even when we know the basic steps involved in the reaction. A simplified scheme is given by the following elementary steps ... 

Structure Correlation to Describe Elementary Steps in Enzyme Reactions and Differences in Ligand Binding Geometry... 

In the remainder of this section, three different types of chemical reaction will be considered in more detail nucleophilic addition, nucleophilic substitution and an electron transfer reaction via change of coordination state. Structural evidence from protein structure determinations is complemented by results of structure correlations, derived from small molecule crystal data, to get a more detailed picture of the elementary steps during enzyme reaction and to sketch possible modes of inhibition. 

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