Binding energy substrate reactivity

This principle has been utilized to assess intrinsic subsite binding energies for enzymes that have substrate binding subsites and exosites topologically distant from the reactive site (e.g., polysaccharide depolymerases and pro-teinases). 

CoA, the coenzyme A derivative of acetoacetate, reduces its reactivity as a substrate for /3-ketoacyl-CoA transferase (an enzyme of lipid metabolism) by a factor of 106. Although this requirement for adenosine has not been investigated in detail, it must involve the binding energy between enzyme and substrate (or cofactor) that is used both in catalysis and in stabilizing the initial enzyme-substrate complex (Chapter 6). In the case of /3-ketoacyl-CoA transferase, the nucleotide moiety of coenzyme A appears to be a binding handle that helps to pull the substrate (acetoacetyl-CoA) into the active site. Similar roles may be found for the nucleoside portion of other nucleotide cofactors. 

Although the overall catalytic activity of an enzyme catalyzed reaction can be accounted for both by the affinity of the substrate to the enzyme (K,n or more accurately l/K ) and the substrate reactivity (kcat), the latter value seems to be more important in reflecting the extra binding energy in the ES complex. This binding energy, as mentioned before, will decrease the energy of activation for the reactivity process (kcat). 

ELECTROSTATIC EFFECTS Recall that the strength of electrostatic interactions is related to the capacity of surrounding solvent molecules to reduce the attractive forces between chemical groups (Chapter 3). Because water is largely excluded from the active site as the substrate binds, the local dielectric constant is often low. The charge distribution in the relatively anhydrous active site may influence the chemical reactivity of the substrate. In addition, weak electrostatic interactions, such as those between permanent and induced dipoles in both the active site and the substrate, are believed to contribute to catalysis. A more efficient binding of substrate lowers the free energy of the transition state, which accelerates the reaction. 

Enzymes bind their substrates by multiple non-covalent interactions on a specific surface. This way, a micro-heterogenization occurs and the local concentration of substrates is increased relative to the bulk solution. In addition, the chemical potential of specific groups may be drastically changed temporarily compared to aqueous solutions by the exclusion of water in the reactive site upon binding of substrate. Both aspects contribute to the observed phenomenon of high acceleration in reaction rate some examples are presented in Table 1-2. Enzymes often bind the substrate in the transition state better than in the ground state, which lowers the activation energy. 

In Eqn. 43 one of the reactants, B, is covalently bonded to the enzyme and a comparison of this reaction with that of Eqn. 42 illustrates the advantage of binding the substrate to the enzyme even if the chemical reactivity of B in the enzyme may be similar to that of B in intermolecular reaction (Eqn. 42). Any free-energy advantage of the enzymic reaction is then given by Eqn. 44 which may be simplified to Eqn. 45 if it is assumed that the entropy of activation TAS is equal to the entropy change of binding the substrate A to the enzyme, TAS. ... 

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