How Enzymes Work:- Weak Interactions between Enzyme and Substrate Are Optimized in the Transition State

How does an enzyme use binding energy to lower the activation energy for a reaction? Formation of the ES complex is not the explanation in itself, although some of the earliest considerations of enzyme mechanisms began with this idea. Studies on enzyme specificity carried 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 mediated 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” hypothesis 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.

FIGURE 6–4 Complementary shapes of a substrate and its binding site on an enzyme. The enzyme dihydrofolate reductase with its substrate 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 substrate (not evident in this figure) is important to enzymatic catalysis.

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 paradigm 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 escaping. 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, however, 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 (binding energy) that form between the enzyme and substrate 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 energy 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 energy hill. The summation of the unfavorable (positive) activation energy G‡ and the favorable (negative) binding 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 important principle is that weak binding interactions between the enzyme and the substrate provide a sub stantial driving force for enzymatic catalysis. The groups on the substrate that are involved in these weak interactions can be at some distance from the bonds that are broken or changed. The weak interactions formed only in the transition state are those that make the primary contribution to catalysis. The requirement for multiple weak interactions to drive catalysis is one reason why enzymes (and some coenzymes) are so large. An enzyme must provide functional groups for ionic, hydrogen-bond, and other inter actions, and also must precisely position these groups so that binding energy is optimized in the transition state. Adequate binding is accomplished most readily by positioning a substrate in a cavity (the active site) where it is effectively removed from water. The size of proteins reflects the need for superstructure to keep interacting groups properly positioned and to keep the cavity from collapsing.

FIGURE 6–5 An imaginary enzyme (stickase) designed to catalyze breakage of a metal stick. (a) Before the stick is broken, it must first be bent (the transition state). In both stickase examples, magnetic in teractions take the place of weak bonding interactions between enzyme and substrate. (b) A stickase with a magnet-lined pocket com plementary in structure to the stick (the substrate) stabilizes the substrate. Bending is impeded by the magnetic attraction between stick and stickase. (c) An enzyme with a pocket complementary to the re action transition state helps to destabilize the stick, contributing to catalysis of the reaction. The binding energy of the magnetic interactions compensates for the increase in free energy required to bend the stick. Reaction coordinate diagrams (right) show the energy consequences of complementarity to substrate versus complementarity to transition state (EP complexes are omitted). GM, the difference between the transition-state energies of the uncatalyzed and catalyzed reactions, is contributed by the magnetic interactions between the stick and stickase. When the enzyme is complementary to the substrate (b), the ES complex is more stable and has less free energy in the ground state than substrate alone. The result is an increase in the activation energy.

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مواضيع ذات صلة

Enzyme Kinetics as an Approach to Understanding Mechanism: -Kinetic Parameters Are Used to Compare Enzyme Activities

Enzyme Kinetics as an Approach to Understanding Mechanism: -The Relationship between Substrate Concentration and Reaction Rate Can Be Expressed Quantitatively

Enzyme Kinetics as an Approach to Understanding Mechanism: -Substrate Concentration Affects the Rate of Enzyme-Catalyzed Reactions

How Enzymes Work:- Specific Catalytic Groups Contribute to Catalysis

How Enzymes Work:- Binding Energy Contributes to Reaction Specificity and Catalysis

Protein Interactions Modulated by Chemical Energy: Actin, Myosin, and Molecular Motors: -Additional Proteins Organize the Thin and Thick Filaments into Ordered Structures

Protein Interactions Modulated by Chemical Energy: Actin, Myosin, and Molecular Motors: - The Major Proteins of Muscle Are Myosin and Actin

Reversible Binding of a Protein to a Ligand: Oxygen-Binding Proteins: -The Antibody-Antigen Interaction Is the Basis for a Variety of Important Analytical Procedures

Reversible Binding of a Protein to a Ligand: Oxygen-Binding Proteins: -Antibodies Bind Tightly and Specifically to Antigen

Complementary Interactions between Proteins and Ligands: The Immune System and Immunoglobulins: -Antibodies Have Two Identical Antigen-Binding Sites

Complementary Interactions between Proteins and Ligands: The Immune System and Immunoglobulins: -Self Is Distinguished from Nonself by the Display of Peptides on Cell Surfaces

Complementary Interactions between Proteins and Ligands: The Immune System and Immunoglobulins: -The Immune Response Features a Specialized Array of Cells and Proteins