Lecture 12 Summary

We develop further the idea of an enzyme-substrate (ES) complex as at the heart of any understanding of enzyme specificity and catalytic ability. The best evidence for the existence of an ES complex is the determination of the structure of an enzyme with its substrate or a substrate analog. (An analog is typically used because in most cases the substrate is acted on by the enzyme and thus disappears rapidly.) Two contrasting models for ES complex formation are the "lock and key" model, and "induced fit". The latter idea, that the conformation of the enzyme and its active site that is catalytically competent is only formed (or "induced") when the substrate is present. The idea that the enzyme may change its conformation to suit the substrate leads to consideration of the complementary idea that the substrate's conformation could also change upon binding to the enzyme active site. In fact, in many cases we see that the interaction between enzyme and substrate leads to a distortion of the substrate's structure so that it more resembles a high energy intermediate or transition state-like form. The balance of an enzyme's interactions with the substrate are quite favorable and this makes the free energy of the ES complex lower, relative to free enzyme and free substrate, but the enzyme can use some of this binding energy to distort the substrate. The result is a selective stabilization of the transition state, which lowers its energy, and as we saw earlier, a lower ΔG‡ leads to the rate enhancement that is the raison d’être of enzymes. As an illustration of this principle, we take a look at the interaction of lysozyme with its polysaccharide substrate, in which one of the pyranose rings is distorted from its normal chair conformation to a half-chair conformation.

From here, we move on to the nuts and bolts of simple models for catalytic mechanisms and the hyperbolic initial rate vs. substrate concentration curve characteristic of the great majority of enzyme-catalyzed reactions. It can be shown that the form of this curve can be modeled by the Michaelis-Menten equation, and equation with two parameters that we can determine experimentally, K_M and V_max.

We will in due course, examine the meaning of the kinetic parameters k_cat and K_M.

Learning objectives

• Describe binding energy, and how it contributes to (i) substrate specificity, and (ii) catalysis.
• Diagram a simple mechanism for an enzyme-catalyzed reaction, including formation of an enzyme-substrate complex and rate constants.
• Describe the steady-state assumption and show how it leads to hyperbolic (Michaelis-Menten) kinetics.

Page updated 10-11-09

References

1. Fersht A. Structure and Mechanism in Protein Science (1999, WH Freeman and Co.)
2. Jencks WP. Catalysis in Chemistry and Enzymology (1987, Dover)