CONFORMATION GATING AS A MECHANISM FOR ENZYME SPECIFICITY

Acetylcholinesterase, with an active site located at the bottom of a n arrow and deep gorge, provides a striking example of enzymes with buri ed active sites. Recent molecular dynamics simulations showed that reo rientation of five aromatic rings leads to rapid opening and closing o f the gate to the active site. Hn the present study the molecular dyna mics trajectory is used to quantitatively analyze the effect of the ga te on the substrate binding rate constant. For a 2.4-Angstrom probe mo deling acetylcholine, the gate is open only 2.4% of the time, but the quantitative analysis reveals that the substrate binding rate is slowe d by merely a factor of 2, We rationalize this result by noting that t he substrate, by virtue of Brownian motion, will make repeated attempt s to enter the gate each time it is near the gate. Hf the gate is rapi dly switching between the open and closed states, one of these attempt s will coincide with an open state, and then the substrate succeeds in entering the gate. However, there is a limit on the extent to which r apid gating dynamics can compensate for the small equilibrium probabil ity of the open state. Thus the crate is effective in reducing the bin ding rate for a ligand 0.4 Angstrom bulkier by three orders of magnitu de. This relationship suggests a mechanism for achieving enzyme specif icity without sacrificing efficiency.