Stabilization of enzyme reactions transition states

The fundamental concept of the transition state stabilization was introduced to Linus Pauling in 1948 who said I think that enzymes are molecules that are complementary in structure to the activated complex of the reactions that they catalyze, that is, the molecular configuration that is intermediate between the reacting substances and the product of the reaction . This concept was widely accepted and used for the interpretation of experimental structural and kinetics data on enzyme catalysis, for the design of new substrates and inhibitors and for chemical mimicking of enzyme reactions. Decisive contributions in this area have been made by structural physical methods, X-ray analysis, in particular, and site-directed mutagenesis. 

In low dielectric organic solvents and enzyme active sites a number of hydrogen bonds between groups with similar pKa exhibit highly deshielded 1H NMR peaks ( 16 ppm), low isotopic fraction factors and relatively short H-bonds (data on neutron and x-ray diffraction analysis (Gerlt and Gassman, 1992 Zundel, 2000 Cleland and Northrop, 1999). 

One of the most important factors providing acceleration of enzymatic reactions as compared to chemical reactions is drastic changes of chemical reactivity catalytic groups inside and outside the enzyme protein globule. Drawing the charges of metal ions, carboxylate and protonated residues into the protein interior is accompanied by essential alternation of its acid-base and redox properties. This effect can be illustrated by the reaction of cleavage and formation of an a-C-H bond in enzymatic reactions of racemization, transamination, and isomerization (Ha et al., 2000 and references therein). 

In these reactions a proton is abstracted from a carbon adjacent to carbonyl, carboxylic acid, or the carboxylate anion group by active cite residues. In water the pKa of a-protones of most aldehydes, ketons, thioesters, and carboxylate anions lies between 16-32, whereas pKa of most carboxylate bases is usually 7. Thus, the thermodynamic barrier for the 

In serine proteases the hydrogen bonds between Asp and the His of the catalytic triad is normally weak. At the substrate presence the histidine becomes unusually protonated and a LBHB forms between Asp and His. The LBHB formation is proven by the low field 

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