Enzyme orientation effect

More accurate due to inclusion of some transport processes and enzyme orientation effects... 

Clearly, proximity and orientation play a role in enzyme catalysis, but there is a problem with each of the above comparisons. In both cases, it is impossible to separate true proximity and orientation effects from the effects of entropy loss when molecules are brought together (described the Section 16.4). The actual rate accelerations afforded by proximity and orientation effects in Figures 16.14 and 16.15, respectively, are much smaller than the values given in these figures. Simple theories based on probability and nearest-neighbor models, for example, predict that proximity effects may actually provide rate increases of only 5- to 10-fold. For any real case of enzymatic catalysis, it is nonetheless important to remember that proximity and orientation effects are significant. 

Enzymes are often considered to function by general acid-base catalysis or by covalent catalysis, but these considerations alone cannot account for the high efficiency of enzymes. Proximity and orientation effects may be partially responsible for the discrepancy, but even the inclusion of these effects does not resolve the disparity between observed and theoretically predicted rates. These and other aspects of the theories of enzyme catalysis are treated in the monographs by Jencks (33) and Bender (34). 

The source of the enormous rate enhancements in enzymatic catalysis has been discussed from physical organic points of view (Jencks, 1969 Bruice, 1970). The kinetic behavior is attributed to factors such as an orientation effect, a microenvironmental effect and multifunctional catalysis. The active sites of enzymes are generally located in a hydrophobic hole or cleft. Therefore, the microenvironmental effect is mainly concerned with the behavior of enzyme catalytic groups in this hydrophobic microenvironment and the specific... 

In the intramolecular reactions studied by Bruice and Koshland and their co-workers, proximity effects (reduction in kinetic order and elimination of unfavourable ground state conformations) and orientation effects might give rate accelerations of 10 -10 . Hence, these effects can by themselves account for the enhancements seen in most intramolecular reactions. However, a factor of 10 -10 is less than the rate acceleration calculated for many enzyme reactions and certain intramolecular reactions, for example, hydrolysis of benzalde-hyde disalicyl acetal (3 X 10 ) (Anderson and Fife, 1973) and the lactonization reaction of[l] (10 ) where a trimethyl lock has been built into the system. If hydrolysis of tetramethylsuccinanilic acid (Higuchi et al., 1966) represents a steric compression effect (10 rate acceleration), then proximity, orientation, and steric compression... 

Of what magnitude are orientation effects due to binding of substrate to enzyme Certainly no more than a factor of 10 need be ascribed to such effects. 

In terms of enzyme catalysis, the following factors are likely to influence the magnitude of the rate enhancement in enzymatic processes (a) proximity and orientation effects (b) electrostatic complementarity of the enzyme s active site with respect to the reactant s stabilized transition state configuration (c) enzyme-bound metal ions that serve as template, that alter pK s of catalytic groups, that facilitate nucleophilic attack, and that have... 

In enzymic reactions the central ES<= EP transformation is very fast, and the value of kcat is very high. In addition to correctly oriented binding of the substrate at the active center of the enzyme, an effective decrease in activation energy of this reaction step might also be provided by stabilization of the transition state of the substrate molecule in the ES complex. 

It is a major challenge to elucidate the mechanisms responsible for the efficiencies of enzymes. Jencks (1) offered the following classification of the mechanisms by which enzymes achieve transition state stabilization and the resulting acceleration of the reactions proximity and orientation effects of reactants, covalent catalysis, general acid-base catalysis, conformational distortion of the reactants, and preorganization of the active sites for transition state complementarity. 

Approaching and orientating effects between enzyme and substrate have the following roles for catalytic reactions ... 

A rigorous reciprocal orientation of reagents, cofactors, and the active center (orientation effect). The induced character of correspondence between enzyme and substrate has been examined in Reference (8). Within the framework of this theory a more active and diversified role is attributed to the substrate. If the substrate fails to induce a proper arrangement at the active center, its settling on the protein does not lead to a reaction. 

Schiff base enzymes, reflects essentially the sensitivity of carbonyl functions toward acid or base catalysis. Whereas the protein side chains provide adequate nucleophiles and bases for catalytic activity, the superiority of metal ions as acidic catalysts in comparison with protons is amply demonstrated by metallo-enzymes. A further reason for the occurrence of numerous metalloenzymes might be sought in the multidentate nature of metal complexes. The precise stereochemical positioning of several reaction components in the same complex provides an easy optimization of proximity and orientation effects. 

Proximity and orientation effects substrates may interact with the enzyme and be positioned close to each other, close to the catalytic group and accurately oriented to minimize the activation energy requirement for entry into the transition state. 

Destabilization of the ES complex can involve structural strain, desolvation, or electrostatic effects. Destabilization by strain or distortion is usually just a consequence of the fact (noted previously) that the enzyme is designed to bind the transition state more strongly than the substrate. When the substrate binds, the imperfect nature of the fit results in distortion or strain in the substrate, the enzyme, or both. This means that the amino acid residues that make up the active site are oriented to coordinate the transition-state structure precisely, but will interact with the substrate or product less effectively. 

In some cases one finds that steric effects lead to clear changes in activity. The most obvious examples are the cases where the enzyme or the substrate are modified so that the reacting part of the substrate cannot assume the proper orientation in the active site. For example, introducing a bulky... 

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