Active site structure and general reaction

Active Site Structure and General Reaction Catalyzed... 

By virtue of their complex macromolecular structure, including a highly defined active site, enzymatic transformations generally proceed with a high degree of chemical selectivity and stereospecificity. Reactions are typically conducted under mild conditions of temperature, pressure, and pH, thus minimizing losses caused by unwanted side reactions or partial racemization. The use of extremo-philes or cross-linked enzymes such as CLECs... 

This chapter summarizes (i) the intellectual problem associated with understanding the rates of these reactions, i.e., the required reduction in the kinetic barrier for proton transfer from carbon to an active site general base so that kcat will not be limited by the rate of this overall reaction (ii) the active site structural features that allow the necessary reduction in kinetic barrier and (iii) specific enzymatic examples of how these strategies are employed. 

Since both alcoholic oxidation and O2 reduction are two-electron processes, the catalytic reaction is conceptually equivalent to a transfer of the elements of dihydrogen between the two substrates. Biological hydrogen transfer generally involves specialized organic redox factors (e.g., flavins, nicotinamide, quinones), with well-characterized reaction mechanisms. Galactose oxidase does not contain any of these conventional redox factors and instead utilizes a very different type of active site, a free radical-coupled copper complex, to perform this chemistry. The new type of active site structure implies that the reaction follows a novel biochemical redox mechanisms based on free radicals and the two-electron reactivity of the metalloradical complex. 

For Class B (substitution labile) metal complexes, reequilibration to more thermodynamically favorable coordination modes will be very rapid relative to immobilization. Such behavior is typical of first-row TM complexes. In addition, these ions are usually very oxophilic, so the metal complexes are typically subject to ICC interactions with oxide materials. Since these metal ions are generally immobilized under conditions of thermodynamic control, all pertinent speciation equilibria, including ICC reactions (Section III.B), must be considered in order to understand or predict the outcome of immobilization reactions. It is essential to understand the relevant equilibria if direct imprinting of active site structures is to be successful. The studies of Klonkowski et al. (210-213), for example, underscore this point Sol-gel immobilization of copper complexes bearing silylated amine and ethylenediamine ligands were shown by EPR to result in multiple copper environments, suggesting competition between immobilization and ICC reactions. 

Enzymes are highly stereospecific in binding chiral substrates and in catalyzing reactions. This stereospecificity arises because enzymes are made of L-amino acids and form asymmetric active sites. Similar to homogeneous and heterogeneous catalysis, chemical reactions proceed on active sites of enzymes, which represent a small part of the total protein. Due to the complex enzyme structure, the active site components are generally far apart in the linear amino acid sequence. 

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