Transition state affinity

Wolfenden, R., and Frick, L., 1987. Transition state affinity and die design of enzyme inhibitors. Chapter 7 in Enzyme Mechanisms, edited by M. I. Page and A. Williams. London, England Royal Society of London. 

A. Radzicka, R. Wolfenden, Rates of Uncatalyzed Peptide Bond Hydrolysis in Neutral Solution and the Transition State Affinities of Proteases , J. Am. Chem. Soc. 1996, 118, 6105 - 6109. 

Mandelate racemase, another pertinent example, catalyzes the kinetically and thermodynamically unfavorable a-carbon proton abstraction. Bearne and Wolfenden measured deuterium incorporation rates into the a-posi-tion of mandelate and the rate of (i )-mandelate racemi-zation upon incubation at elevated temperatures. From an Arrhenius plot, they obtained a for racemization and deuterium exchange rate was estimated to be around 35 kcal/mol at 25°C under neutral conditions. The magnitude of the latter indicated mandelate racemase achieves the remarkable rate enhancement of 1.7 X 10, and a level of transition state affinity (K x = 2 X 10 M). These investigators also estimated the effective concentrations of the catalytic side chains in the native protein for Lys-166, the effective concentration was 622 M for His-297, they obtained a value 3 X 10 M and for Glu-317, the value was 3 X 10 M. The authors state that their observations are consistent with the idea that general acid-general base catalysis is efficient mode of catalysis when enzyme s structure is optimally complementary with their substrates in the transition-state. See Reference Reaction Catalytic Enhancement... 

Radzicka, A. and Wolfenden, R. (1996). Rates of uncatalyzed peptide bond hydrolysis in neutral solution and the transition state affinities of proteases. J. Am. Chem. Soc.,... 

Contribution of Enzyme-Ribofuranosyl Contacts to Ground State and Transition State Affinity... 

R. Wolfenden Transition-State Affinity as a Basis for the Design of Enzyme Inhibitors (Trahsition States of Biochemical Processes, Eds. R. D. Gandour and R. L. Schowen) pp. 555-578 (1978). 

The principle of transition state affinity requires the development during enzyme catalysis of very powerful forces of attraction between the enzyme and the altered form of the substrate that is present in the transition state. > This principle has served as a basis for the synthesis of some very strong reversible enzyme inhibitors/" and may also in principle be useful in the design of affinity labeling reagents. The latter possibility remains to be explored, but seems already to be partly substantiated by a few serendipitous examples of inhibitors of glycosidases and proteases. 

Snider MJ, Gaunitz S, Ridgway C, Short SA, Wolfenden R (2000) Temperature effects on the catalytic efficiency, rate enhancement, and transition state affinity of cytidine deaminase, and the thermodynamic consequences for catalysis of removing a substrate Anchor . Biochemistry 38 9746-9753... 

Wolfeden, R., 1974, Enzyme catalysis, conflicting requirements of substrate access and transition state affinity, Molec. Cell. Biochem. 3 207. 

Herbicidal Inhibition of Enzymes. The Hst of known en2yme inhibitors contains five principal categories group-specific reagents substrate or ground-state analogues, ie, rapidly reversible inhibitors affinity and photo-affinity labels suicide substrate, or inhibitors and transition-state, or reaction-intermediate, analogues, ie, slowly reversible inhibitors (106). 

The a carbon of mandelic acid is sp hybridized. The corresponding carbons of both a-phenylglycidic acid, 49, and the carbanion intermediate 48 are neither sp hybridized nor sp hybridized, but presumably between these two extremes. It is therefore possible that the a-phenylglycidic acid is restricted to a conformation which resembles a transition state in the racemization process, a transition state which would have much of the character of the intermediate 48, and for which the enzyme would presumably have a high affinity (1). 

We have just discussed several common strategies that enzymes can use to stabilize the transition state of chemical reactions. These strategies are most often used in concert with one another to lead to optimal stabilization of the binary enzyme-transition state complex. What is most critical to our discussion is the fact that the structures of enzyme active sites have evolved to best stabilize the reaction transition state over other structural forms of the reactant and product molecules. That is, the active-site structure (in terms of shape and electronics) is most complementary to the structure of the substrate in its transition state, as opposed to its ground state structure. One would thus expect that enzyme active sites would bind substrate transition state species with much greater affinity than the ground state substrate molecule. This expectation is consistent with transition state theory as applied to enzymatic catalysis. 

Miller and Wolfenden, 2002). This latter ratio is the inverse of the rate enhancement achieved by the enzyme. In other words, the enzyme active site will have greater affinity for the transition state structure than for the ground state substrate structure, by an amount equivalent to the fold rate enhancement of the enzyme (rearranging, we can calculate KJX = Ksik Jk, )). Table 2.2 provides some examples of enzymatic rate enhancements and the calculated values of the dissociation constant for the /A binary complex (Wolfenden, 1999). 

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