2 Структура и функция белка (1160071), страница 30
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The energy derivedfrom enzyme-substrate interaction is called binding energy. Its significance extends beyond a simple stabilization of the enzymesubstrate interaction. Binding energy is the major source of free energyused by enzymes to lower the activation energies of reactions.Two fundamental and interrelated principles provide a generalexplanation for how enzymes work. First, the catalytic power of enzymes is ultimately derived from the free energy released in formingthe multiple weak bonds and interactions that occur between an enzyme and its substrate.
This binding energy provides specificity as wellas catalysis. Second, weak interactions are optimized in the reactiontransition state; enzyme active sites are complementary not to the substrates per se, but to the transition states of the reactions they catalyze. These themes are critical to an understanding of enzymes, andthey now become the primary focus of the chapter.Weak Interactions between Enzyme and SubstrateAre Optimized in the Transition StateHow does an enzyme use binding energy to lower the activation energyfor reaction? Formation of the ES complex is not the explanation initself, although some of the earliest considerations of enzyme mechanisms began with this idea. Studies on enzyme specificity carried outby Emil Fischer led him to propose, in 1894, that enzymes were structurally complementary to their substrates, so that they fit together likea "lock and key" (Fig.
8-5).This elegant idea, that a specific (exclusive) interaction betweentwo biological molecules is mediated by molecular surfaces with complementary shapes, has greatly influenced the development of biochemistry, and lies at the heart of many biochemical processes. However, the "lock and key" hypothesis can be misleading when applied tothe question of enzymatic catalysis. An enzyme completely complementary to its substrate would be a very poor enzyme.
Consider animaginary reaction, the breaking of a metal stick. The uncatalyzedreaction is shown in Figure 8-6a. We will examine two imaginary enzymes to catalyze this reaction, both of which employ magnetic forcesas a paradigm for the binding energy used by real enzymes. We firstFigure 8-5 Complementary shapes of a substrateand its binding site on an enzyme. The enzyme dihydrofolate reductase is shown with its substrate,NADP+ (red), unbound (top) and bound (bottom).Part of a tetrahydrofolate molecule (yellow), alsobound to the enzyme, is visible. The NADP+ bindsto a pocket that is complementary to it in shapeand ionic properties.
Emil Fischer proposed thatenzymes and their substrates have shapes thatclosely complement each other, like a lock and key.This idea can readily be extended to the interactions of other types of proteins with ligands orother proteins. In reality, the complementarity israrely perfect, and the interaction of a protein witha ligand often involves changes in the conformationof one or both molecules. This lack of perfect complementarity between an enzyme and its substrate(not evident in this figure) is important to enzymatic catalysis.Part II Structure and CatalysisNo enzymeo- i/% -) —Substrate(metal stick)Transition state(bent stick)Products(broken stick)Fre e energy, C206(a)Enzyme complementary to substrate,; y*'*/A/MagnetsAGs 1/ v_l[(b)ESpLat|A GMEnzyme complementary to transition stateESReaction coordinateFigure 8—6 An imaginary enzyme (stickase) designed to catalyze the breaking of a metal stick,(a) To break, the stick must first be bent (the transition state).
In the stickase, magnetic interactionstake the place of weak-bonding interactions between enzyme and substrate, (b) An enzyme witha magnet-lined pocket complementary in structureto the stick (the substrate) will stabilize this substrate.
Bending will be impeded by the magneticattraction between stick and stickase. (c) An enzyme complementary to the reaction transitionstate will help to destabilize the stick, resulting incatalysis of the reaction. The magnetic interactionsprovide energy that compensates for the increasein free energy required to bend the stick. Reactioncoordinate diagrams show the energetic consequences of complementarity to substrate versuscomplementarity to transition state. The term AGMrepresents the energy contributed by the magneticinteractions between the stick and stickase. Whenthe enzyme is complementary to the substrate, asin (b), the ES complex is more stable and has lessfree energy in the ground state than substratealone.
The result is an increase in the activationenergy. For simplicity, the EP complexes are notshown.(c)design an enzyme perfectly complementary to the substrate (Fig. 86b). The active site of this "stickase" enzyme is a pocket lined withmagnets. To react (break), the stick must reach the transition state ofthe reaction. The stick fits so tightly in the active site that it cannotbend, because bending of the stick would eliminate some of the magnetic interactions between stick and enzyme. Such an enzyme impedesthe reaction, stabilizing the substrate instead.
In a reaction coordinatediagram (Fig. 8-6b), this kind of ES complex would correspond to anenergy well from which it would be difficult for the substrate to escape.Such an enzyme would be useless.The modern notion of enzymatic catalysis was first proposed byHaldane in 1930, and elaborated by Linus Pauling in 1946. In order tocatalyze reactions, an enzyme must be complementary to the reactiontransition state. This means that the optimal interactions (throughweak bonding) between substrate and enzyme can occur only in thetransition state.
Figure 8-6c demonstrates how such an enzyme canwork. The metal stick binds, but only a few magnetic interactions areused 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 stickinto a bent and partially broken conformation is offset or "paid for" bythe magnetic interactions that form between the enzyme and substratein the transition state. Many of these interactions involve parts of thestick that are distant from the point of breakage; thus interactions207Chapter 8 Enzymesbetween the stickase and nonreacting parts of the stick provide some ofthe 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 possibleweak interactions between substrate and enzyme are formed onlywhen the substrate reaches the transition state. The free energy (binding energy) released by the formation of these interactions partiallyoffsets the energy required to get to the top of the energy hill. Thesummation of the unfavorable (positive) AG^ and the favorable (negative) binding energy (AGB) results in a lower net activation energy (Fig.8-7).
Even on the enzyme, the transition state represents a brief pointin time that the substrate spends atop an energy hill. The enzymecatalyzed reaction is much faster than the uncatalyzed process, however, because the hill is much smaller. The important principle is thatweak-bonding interactions between the enzyme and the substrate provide the major driving force for enzymatic catalysis.
The groups on thesubstrate that are involved in these weak interactions can be at somedistance from the bonds that are broken or changed. The weak interactions that are formed only in the transition state are those that makethe primary contribution to catalysis.The requirement for multiple weak interactions to drive catalysisis one reason why enzymes (and some coenzymes) are so large.
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