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Enzymatic Transition State Theory and Transition State Analogue Design * Published, JBC Papers in Press, August 9, 2007, DOI 10.1074/jbc.R700018200 Vern L. Schramm 1 From the Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461 Transition State Theory and Tight Binding The incredible catalytic rate enhancements caused by enzymes led Linus Pauling (1) to suggest that enzymes bind tightly to substrates distorted toward the transition state, thereby concentrating them and enforcing catalysis. Wolfenden (2) explained that chemically stable analogues that resemble the transition state would be expected to bind more tightly than substrate by factors resembling the rate enhance- ment imposed by enzymes. The theory for tight binding of tran- sition state analogues was supported by natural product chem- istry and synthetic approaches to mimics of proposed enzymatic transition states (3–5). The well documented tight binding of transition state analogues confirms the thermody- namic aspects of tight binding by mimics of enzymatic transi- tion states. Recently, protein dynamic motion has been proposed to account for catalysis without the necessity of tight binding at the transition state, where the transition state is formed by the instantaneous and optimal alignment of functional groups at the catalytic site (6). Single molecule kinetics of enzymes sup- ports the dynamic search mode of catalysis, with individual cat- alytic events showing a wide range of time intervals that average to the observed collective property of the enzyme (7). In the dynamic theory of catalysis, tight binding of a chemi- cally stable transition state analogue arises from a conforma- tional collapse of the protein around the inhibitor (8). The pres- ence of a stable, attractive analogue causes a conformational convergence to the transition state geometry. Without catalysis the analogue forms a tightly bound complex. The dynamics of transition state formation is converted into static binding energy. Experimental Determination of Enzymatic Transition States Transition state analysis of enzymatic reactions and the use of transition state (TS) 2 information to design transition state analogues requires: 1) a target enzyme with chemistry suited for kinetic isotope effect (KIE) analysis; 2) substrates with isotopic substitutions at the reaction center; 3) intrinsic KIEs (isotope effects from the chemical step); 4) a computed transition state matching the intrinsic KIEs; 5) a molecular electrostatic poten- tial (MESP) map of the TS; 6) a stable compound to match the MESP map; and 7) testing of the TS analogue against the target enzyme. This procedure has been developed gradually in parallel with the advances in KIE enzymology, computational chemistry, and synthetic organic chemistry with numerous laboratories mak- ing important contributions (9–15). Some examples of this newly developing field are provided here.
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