8885dc06_190-2371/27/047:13 AM Page197mac76mac76:385 6.2 How Enzymes Work 197 of the earliest considerations of enzyme mechanisms be- Consider an imaginary reaction, the breaking of a gan with this idea. Studies on enzyme specificity car- magnetized metal stick. The uncatalyzed reaction is ried out by Emil Fischer led him to propose, in 1894, shown in Figure 6-5a. Let's examine two imaginary that enzymes were structurally complementary to their enzymes--two"stickases-that could catalyze this re- substrates, so that they fit together like a lock and key action, both of which employ magnetic forces as a par (Fig. 6-4). This elegant idea, that a specific(exclusive) adigm for the binding energy used by real enzymes. We interaction between two biological molecules is medi- first design an enzyme perfectly complementary to the ated by molecular surfaces with complementary shapes, substrate (Fig. 6-5b). The active site of this stickase is has greatly influenced the development of biochemistry, a pocket lined with magnets. To react(break), the stick and such interactions lie at the heart of many bio- must reach the transition state of the reaction, but the chemical processes. However, the " lock and key" hy- stick fits so tightly in the active site that it cannot bend pothesis can be misleading when applied to enzymatic because bending would eliminate some of the magnetic atalysis. An enzyme completely complementary to its interactions between stick and enzyme. Such an enzyme substrate would be a very poor enzyme, as we can impedes the reaction, stabilizing the substrate instead emonstrate In a reaction coordinate diagram(fig. 6-5b, this kind of Es complex would correspond to an energy trough from which the substrate would have difficulty escap- ing. Such an enzyme would be useless The modern notion of enzymatic catalysis, first pro posed by Michael Polanyi(1921) and Haldane(1930) was elaborated by Linus Pauling in 1946: in order to cat- alyze reactions, an enzyme must be complementary to the reaction transition state. This means that optimal interactions between substrate and enzyme occur only in the transition state. Figure 6-5c demonstrates how such an enzyme can work. The metal stick binds to the stickase, but only a subset of the possible magnetic in- teractions are used rming the Es complex. The bound substrate must still undergo the increase in free energy needed to reach the transition state. Now, how- ever, the increase in free energy required to draw the stick into a bent and partially broken conformation is offset, or"paid for, by the magnetic interactions(bind- ing energy) that form between the enzyme and sub- strate in the transition state. Many of these interactions involve parts of the stick that are distant from the point of breakage; thus interactions between the stickase and nonreacting parts of the stick provide some of the en ergy needed to catalyze stick breakage. This"energy payment" translates into a lower net activation energy and a faster reaction rate Real enzymes work on an analogous principle. Some weak interactions are formed in the ES complex, but the full complement of such interactions between substrate and enzyme is formed only when the substrate reaches FIGURE 6-4 Complementary shapes of a substrate and its binding the transition state. The free energy(binding energy) site on an enzyme The enzyme dihydrofolate reductase with its sub- released by the formation of these interactions partially rate NADP+(red), unbound (top) and bound (bottom). Another bound offsets the energy required to reach the top of the en- bstrate te ahydrofolate(yellow), is also visible (PDB ID 1RA2) The ergy hill. The summation of the unfavorable (positive) NADP+binds to a pocket that is complementary to it in shape and activation energy AG and the favorable(negative)bind- onic properties. In reality, the complementarity between protein and ing energy AGB results in a lower net activation energy ligand (in this case substrate) is rarely perfect, as we saw in Chapter (Fig. 6-6). Even on the enzyme, the transition state 5. The interaction of a protein with a ligand often involves changes in is not a stable species but a brief point in time that the conformation of one or both molecules, a process called induced the substrate spends atop an energy hill. The enzyme- fit. This lack of perfect complementarity between enzyme and sub- catalyzed reaction is much faster than the uncatalyzed strate(not evident in this figure)is important to enzymatic catalysis. process, however, because the hill is much smaller. Theof the earliest considerations of enzyme mechanisms be￾gan with this idea. Studies on enzyme specificity car￾ried out by Emil Fischer led him to propose, in 1894, that enzymes were structurally complementary to their substrates, so that they fit together like a lock and key (Fig. 6–4). This elegant idea, that a specific (exclusive) interaction between two biological molecules is medi￾ated by molecular surfaces with complementary shapes, has greatly influenced the development of biochemistry, and such interactions lie at the heart of many bio￾chemical processes. However, the “lock and key” hy￾pothesis can be misleading when applied to enzymatic catalysis. An enzyme completely complementary to its substrate would be a very poor enzyme, as we can demonstrate. Consider an imaginary reaction, the breaking of a magnetized metal stick. The uncatalyzed reaction is shown in Figure 6–5a. Let’s examine two imaginary enzymes—two “stickases”—that could catalyze this re￾action, both of which employ magnetic forces as a par￾adigm for the binding energy used by real enzymes. We first design an enzyme perfectly complementary to the substrate (Fig. 6–5b). The active site of this stickase is a pocket lined with magnets. To react (break), the stick must reach the transition state of the reaction, but the stick fits so tightly in the active site that it cannot bend, because bending would eliminate some of the magnetic interactions between stick and enzyme. Such an enzyme impedes the reaction, stabilizing the substrate instead. In a reaction coordinate diagram (Fig. 6–5b), this kind of ES complex would correspond to an energy trough from which the substrate would have difficulty escap￾ing. Such an enzyme would be useless. The modern notion of enzymatic catalysis, first pro￾posed by Michael Polanyi (1921) and Haldane (1930), was elaborated by Linus Pauling in 1946: in order to cat￾alyze reactions, an enzyme must be complementary to the reaction transition state. This means that optimal interactions between substrate and enzyme occur only in the transition state. Figure 6–5c demonstrates how such an enzyme can work. The metal stick binds to the stickase, but only a subset of the possible magnetic in￾teractions are used in forming the ES complex. The bound substrate must still undergo the increase in free energy needed to reach the transition state. Now, how￾ever, the increase in free energy required to draw the stick into a bent and partially broken conformation is offset, or “paid for,” by the magnetic interactions (bind￾ing energy) that form between the enzyme and sub￾strate in the transition state. Many of these interactions involve parts of the stick that are distant from the point of breakage; thus interactions between the stickase and nonreacting parts of the stick provide some of the en￾ergy needed to catalyze stick breakage. This “energy payment” translates into a lower net activation energy and a faster reaction rate. Real enzymes work on an analogous principle. Some weak interactions are formed in the ES complex, but the full complement of such interactions between substrate and enzyme is formed only when the substrate reaches the transition state. The free energy (binding energy) released by the formation of these interactions partially offsets the energy required to reach the top of the en￾ergy hill. The summation of the unfavorable (positive) activation energy G‡ and the favorable (negative) bind￾ing energy GB results in a lower net activation energy (Fig. 6–6). Even on the enzyme, the transition state is not a stable species but a brief point in time that the substrate spends atop an energy hill. The enzyme￾catalyzed reaction is much faster than the uncatalyzed process, however, because the hill is much smaller. The 6.2 How Enzymes Work 197 FIGURE 6–4 Complementary shapes of a substrate and its binding site on an enzyme. The enzyme dihydrofolate reductase with its sub￾strate NADP
(red), unbound (top) and bound (bottom). Another bound substrate, tetrahydrofolate (yellow), is also visible (PDB ID 1RA2). The NADP
binds to a pocket that is complementary to it in shape and ionic properties. In reality, the complementarity between protein and ligand (in this case substrate) is rarely perfect, as we saw in Chapter 5. The interaction of a protein with a ligand often involves changes in the conformation of one or both molecules, a process called induced fit. This lack of perfect complementarity between enzyme and sub￾strate (not evident in this figure) is important to enzymatic catalysis. 8885d_c06_190-237 1/27/04 7:13 AM Page 197 mac76 mac76:385_reb: