Proximity and Orientation

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. 

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... 

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. 

Enzymes are able to bind the reactants (their substrates) specifically at the active center. In the process, the substrates are oriented in relation to each other in such a way that they take on the optimal orientation for the formation of the transition state (1-3). The proximity and orientation of the substrates therefore strongly increase the likelihood... 

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... 

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)... 

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. 

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. 

White KJ, Kiser PD, Nichols DE, Barker EL (2006) Engineered zinc-binding sites confirm proximity and orientation of transmembrane helices I and III in the human serotonin transporter. Protein Sci 15 2411-2422... 

The peptide bond that is cleaved is the bond between Leu-189 and Asp-190. There are two peptide bonds in close proximity to the iron chelate on Cys-212. The other peptide bond is between He-144 and Gly-145. The Cys-212 sulfur is 5.1 A from the carbonyl carbon of Gly-145, and 5.3 A from the carbonyl carbon of Leu-189. However, the main difference is that the peptide bond of Leu-189-Asp-190 is oriented parallel to Cys-212, while the peptide bond of lie-144-Gly-145 is oriented away for Cys-212. As was seen with cobalt(lll) hydrolysis of peptide bonds, the proximity and orientation of the carbonyl carbon is important for hydrolysis. This approach has been extended to the cleavage of multisubunit proteins. Palladium(n) and platinum(ll) complexes as synthetic peptidases have been reviewed elsewhere. ... 

Solubilization of a drug by incorporation into micelles may affect its stability.i In the micelle, the molecular environment of the drug molecules changes their proximity and orientation with respect to each other, which may affect activity. In a micelle, the drug molecules may be protected from attacking species such as hydronium or hydroxide ions and the stability of the drug may be increased. The difference in environment between the micellar and bulk aqueous phases may be such that reaction rates may be radically changed by the transfer of solute to micelles. Micellar systems may be used to deliberately alter the rates and directions of chemical reactions. ... 

There are five main areas of body language gaze or eye contact, facial expression, proximity and orientation, posture, and touch. 

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. 

Proximity and Orientation of Dipoles (Including NH S Hydrogen Bonds)... 

The catalytic strategies employed by chymotrypsin to increase the reaction rate are common to many enzymes. One of these catalytic strategies, proximity and orientation, is an intrinsic feature of substrate binding and part of the catalytic mechanism of all enzymes. All enzymes also stabilize the transition state by electrostatic interactions, but not all enzymes form covalent intermediates. 

Coenzymes have very little activity in the absence of the enzyme and very little specificity. The enzyme provides specificity, proximity, and orientation in the substrate recognition site, as well as other functional groups for stabilization of the transition state, acid-base catalysis, etc. For example, thiamine is made into a better nucleophilic attacking group by a basic amino acid residue in the enzyme that removes the dissociable proton (EnzB in Fig. 8.11), thereby generating a negatively charged thiamine carbon anion. Later in the reaction, the enzyme returns the proton. 

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