Enzyme substrate binding forces

Recent opinion, for example calculations by Levitt (1974), does not generally support this idea. Proteins are not rigid structures, and from estimates of the maximum force an enzyme can be expected to exert on a substrate he concludes that small distortions of substrate. .. that cause large increases in strain energy cannot be caused by binding to an enzyme . There is little doubt that this conclusion is correct, and that enzyme-substrate binding cannot cause substantial strain of the sort described in this section (Fersht and Kirby, 1980). 

Hydrophobicity and charge Hydrophobic to polyionic Alteration of substrate selectivity, shift of pH/rate optimum, enzyme stabilization, binding force and capacity... 

In order to account for the inability of many enzymes to bind the protonated form of the basic inhibitors or permanently cationic ones better than uncharged analogs (for example, yS-o-galactosidase from E. coli, and P-v>-glucosidase from almonds), it was proposed that the enzyme could proton-ate the inhibitor at the active site by a cationic acid (for example, protonated histidine). If proton transfer cannot occur, the attractive forces due to the carboxylate would be canceled by the repulsion from the cationic acid. Experimental evidence for this proposal is, however, still lacking. In fi-D-gn-lactosidase from E. coli, a tyrosine is presumed to be responsible for the protonation of substrates. ... 

Schultz and coworkers (Jackson et a ., 1988) have generated an antibody which exhibits behaviour similar to the enzyme chorismate mutase. The enzyme catalyses the conversion of chorismate [49] to prephenate [50] as part of the shikimate pathway for the biosynthesis of aromatic amino acids in plants and micro-organisms (Haslam, 1974 Dixon and Webb, 1979). It is unusual for an enzyme in that it does not seem to employ acid-base chemistry, nucleophilic or electrophilic catalysis, metal ions, or redox chemistry. Rather, it binds the substrate and forces it into the appropriate conformation for reaction and stabilizes the transition state, without using distinct catalytic groups. 

Another hypothesis suggests that the binding of a substrate to an enzyme causes a strain or deformation of some of the bonds in the substrate molecule, which are subsequently broken. The effectiveness of this mechanism depends upon the strength of the binding force and does not necessarily involve any movement of the protein but suggests the idea of a flexible enzyme. 

Natural enzymes use the hydrophobic effect as a binding force in forming the enzyme-substrate complex. Artificial enzymes can be used to bind substrates and enhance reactivities in water (Breslow, 1995). Cyclodextrins, which are cyclic compounds composed of glucose units, can be used as the artificial enzymes (Bender and... 

FIGURE 2-8 Release of ordered water favors formation of an enzyme-substrate complex. While separate, both enzyme and substrate force neighboring water molecules into an ordered shell. Binding of substrate to enzyme releases some of the ordered water, and the resulting increase in entropy provides a thermodynamic push toward formation of the enzyme-substrate complex. 

Dissociation rate constants are much lower than the diffusion-controlled limit, since the forces responsible for the binding must be overcome in the dissociation step. In some cases, enzyme-substrate dissociation is slower than the subsequent chemical steps, and this gives rise to Briggs-Haldane kinetics. 

As noted earlier, protein structure is stabilised by a series of weak forces which often give rise to the properties which are functionally important (models of active sites and substrate binding are discussed above). On the other hand, because active sites involve a set of subtle molecular interactions involving weak forces, they are vulnerable and can be transformed into less active configurations by small perturbations in environmental conditions. It is therefore not surprising that a multitude of physical and chemical parameters may cause perturbations in native protein-geometry and structure. Thus, enzyme deactivation rates are usually multi-factorial, e.g. enzyme sensitivity to temperature varies with pH and/or ionic strength of the medium. 

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