Proximity and 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). 

As shown in the preceding paragraph, theoretical approaches to rates and equilibria of cyclisation reactions of short- to moderate-length chain molecules explicitly taking into account proximity and orientation effects are faced with discouraging conceptual and mathematical difficulties. 

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... 

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. 

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. 

Approximation refers to the bringing together of the substrate molecules and reactive functionalities of the enzyme active site into the required proximity and orientation for rapid reaction. Consider the reaction of two molecules, A and B, to form a covalent product A-B. For this reaction to occur in solution, the two molecules would need to encounter each other through diffusion-controlled collisions. The rate of collision is dependent on the temperature of the solution and molar concentrations of reactants. The physiological conditions that support human life, however, do not allow for significant variations in temperature or molarity of substrates. For a collision to lead to bond formation, the two molecules would need to encounter one another in a precise orientation to effect the molecular orbitial distortions necessary for transition state attainment. The chemical reaction would also require... 

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... 

These and other observations (51-55) suggest that the tendency towards hydroxylation in these kinds of chemical systems is very sensitive to electronic effects, as well as copper chelation and peroxide proximity and orientation toward xylyl substrate. This view is supported by observations involving an unsymmetrical system, [Cu2(UN)]2+ (56), an analogue of [Cu2(XYL)]2+ (6)... 

The key element of the strategy described in this section is the provision of a binding site for the substrate close to a catalytic center. Of the mechanistic effects described by Jencks (I), the following contribute proximity and orientation of reactants and covalent catalysis. 

The key element of the strategy described in the following section is the simultaneous complexation of two reactants to facilitate a bimolecular reaction. Mechanistic effects include proximity, matchmakers (orientation effects of reactants), and self-replication. 

It is believed that proximity and orientation are critical to the way enzymes accelerate reactions. The key is to increase the number of effective collisions between reactive partners. Not only are the reactive partners undergoing a huge number of collisions within the active site of the enzyme, but the active site is also orienting them correctly. The slow step for some enzymes is just getting the reactants into the active site, the diffusion-controlled limit. 

After the substrate is bound and the transition state is subsequently formed, catalysis can occur. This means that bonds must be rearranged. In the transition state, the substrate is bound close to atoms with which it is to react. Furthermore, the substrate is placed in the correct orientation with respect to those atoms. Both effects, proximity and orientation, speed up the reaction. As bonds are broken and new bonds are formed, the substrate is transformed into product. The product is released from the enzyme, which can then catalyze the reaction of more substrate to form more product (Figure 6.5). Each enzyme... 

Besides proximity effect and orientation effect, steric compression effect could be a third factor to consider. Nonetheless there can still be an enhancement of 10 to 10" in rate constants not accounted for by these factors. Among the likely candidates, electrostatic stabilization of the transition state and release of ground state strain should be mentioned. The notion of freezing of substrate specificity by Bender is also a factor for consideration. An example is the aromatic hole in a-chymotrypsin (see below) which allows a favorable steric situation for the amino add side chain of the substrate. 

A third class of sequence elements can either increase or decrease the rate of transcription initiation of eukaryotic genes. These elements are called either enhancers or repressors (or silencers), depending on which effect they have. They have been found in a variety of locations both upstream and downstream of the transcription start site and even within the transcribed portions of some genes. In contrast to proximal and upstream promoter elements, enhancers and silencers can exert their effects when located hundreds or even thousands of bases away from transcription units located on the same chromosome. Surprisingly, enhancers and silencers can function in an orientation-independent fashion. Literally hundreds of these elements have been described. In some cases, the sequence requirements for binding are rigidly constrained in others, considerable sequence variation is... 

The reason for this phase effect is the apparent necessity for the proximity and proper orientation of two monomer molecules before dimer formation can take place (the mechanistic significance of this will be discussed later). Thus dinucleotides such as TpT form dimers even in solution, and the yield of dimers in polynucleotides and nucleic acids is even higher. 

The orientational effect of a lone-pair on a proximate C-H bond was discussed some years ago from both experimental383 385 and theoretical386... 

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