Enzymatic transition state theory and transition state analogue design.

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 enhancement imposed by enzymes. The theory for tight binding of transition state analogues was supported by natural product chemistry and synthetic approaches to mimics of proposed enzymatic transition states (3–5). The well documented tight binding of transition state analogues confirms the thermodynamic aspects of tight binding by mimics of enzymatic transition 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 supports the dynamic searchmode of catalysis, with individual catalytic events showing awide 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 chemically stable transition state analogue arises from a conformational collapse of the protein around the inhibitor (8). The presence 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.