Substrate-induced fit

Li de La Sierra, I.M. Gallay, J. Vincent, M. Bertrand, T. Briozzo, P. Barzu, O. Gilles, A.M. Substrate-induced fit of the ATP binding site of cytidine monophosphate kinase from Escherichia coli time-resolved fluorescence of 3 -anthraniloyl-2 -deoxy-ADP and molecular modeling. Biochemistry, 39, 15870-15878 (2000)... 

Loo TW, Bartlett MC, Clarke DM. Substrate-induced conformational changes in the transmembrane segments of human P-glycoprotein. Direct evidence for the substrate-induced fit mechanism for drug binding. J Biol Chem 2003 278 13603-13606. 

Fig. 2. Principle mechanisms of formation of a receptor—substrate complex (a) Fischer s rigid "lock-and-key" model (b) "induced fit" model showing...

Living cells contain thousands of different kinds of catalysts, each of which is necessary to life. Many of these catalysts are proteins called enzymes, large molecules with a slotlike active site, where reaction takes place (Fig. 13.39). The substrate, the molecule on which the enzyme acts, fits into the slot as a key fits into a lock (Fig. 13.40). However, unlike an ordinary lock, a protein molecule distorts slightly as the substrate molecule approaches, and its ability to undergo the correct distortion also determines whether the key will fit. This refinement of the original lock-and-key model is known as the induced-fit mechanism of enzyme action. 

Figure 7-5. Two-dimensional representation of Koshland s induced fit model of the active site of a lyase. Binding of the substrate A—B induces conformational changes In the enzyme that aligns catalytic residues which participate in catalysis and strains the bond between A and B, facilitating its cleavage.

Later on12, Koshland proposed the induced fit model of the active site action that considers that during the formation of the enzyme-substrate complex, the enzyme can change its conformation so as to wrap the substrate like it happens when a hand (substrate) fits in a globe (enzyme). This flexing puts the active site and bonds in the substrate under strain, which weakens the bonds and helps to lower the activation energy for the catalyzed reaction. 

What the induced-fit model is good at explaining is why bad substrates are bad, but like the lock and key model, it too fails to tell us exactly why good substrates are good. What is it about the proper arrangement that makes the chemistry fast ... 

The INDUCED-FIT model for enzyme specificity says that good substrates must be able to cause the enzyme to change shape (conformation) so that catalytic and functional groups on the enzyme are brought into just the right place to catalyze the reaction. Bad substrates are bad because they aren t able to make the specific interactions that cause the conformation change, and the enzyme stays in its inactive conformation. 

The use of the symbol E in 5.1 for the environment had a double objective. It stands there for general environments, and it also stands for the enzyme considered as a very specific environment to the chemical interconversion step [102, 172], In the theory discussed above catalysis is produced if the energy levels of the quantum precursor and successor states are shifted below the energy value corresponding to the same species in a reference surrounding medium. Both the catalytic environment E and the substrates S are molded into complementary surface states to form the complex between the active precursor complex Si and the enzyme structure adapted to it E-Si. In enzyme catalyzed reactions the special productive binding has been confussed with the possible mechanisms to attain it lock-key represents a static view while the induced fit concept... 

Wester, M.R., Johnson, E.F., Marques-Soares, C., Dijols, S., Dansette, P.M., Mansuy, D. and Stout, C.D. (2003) Structure of mammalian cytochrome P450 2C5 complexed with diclofenac at 2.1 A resolution evidence for an induced fit model of substrate binding. Biochemistry, 42, 9335-9345. 

Figure 6. Enzymes act as recycling catalysts in biochemical reactions. A substrate molecule binds (reversible) to the active site of an enzyme, forming an enzyme substrate complex. Upon binding, a series of conformational changes is induced that strengthens the binding (corresponding to the induced fit model of Koshland [148]) and leads to the formation of an enzyme product complex. To complete the cycle, the product is released, allowing the enzyme to bind further substrate molecules. (Adapted from Ref. 1). See color insert.

Two models currently exist to explain how an enzyme and its substrate interact. One model, called the lock and key model, suggests that an enzyme is like a lock, and its substrate is like a key. The shape of the active site on the enzyme exactly fits the shape of the substrate. A second model, called the induced fit model, suggests that the active site of an enzyme changes its shape to fit its substrate. Figure 6.21 shows both models. 

One of the important consequences of studying catalysis by mutant enzymes in comparison with wild-type enzymes is the possibility of identifying residues involved in catalysis that are not apparent from crystal structure determinations. This has been usefully applied (Fersht et al., 1988) to the tyrosine activation step in tyrosine tRNA synthetase (47) and (49). The residues Lys-82, Arg-86, Lys-230 and Lys-233 were replaced by alanine. Each mutation was studied in turn, and comparison with the wild-type enzyme revealed that each mutant was substantially less effective in catalysing formation of tyrosyl adenylate. Kinetic studies showed that these residues interact with the transition state for formation of tyrosyl adenylate and pyrophosphate from tyrosine and ATP and have relatively minor effects on the binding of tyrosine and tyrosyl adenylate. However, the crystal structures of the tyrosine-enzyme complex (Brick and Blow, 1987) and tyrosyl adenylate complex (Rubin and Blow, 1981) show that the residues Lys-82 and Arg-86 are on one side of the substrate-binding site and Lys-230 and Lys-233 are on the opposite side. It would be concluded from the crystal structures that not all four residues could be simultaneously involved in the catalytic process. Movement of one pair of residues close to the substrate moves the other pair of residues away. It is therefore concluded from the kinetic effects observed for the mutants that, in the wild-type enzyme, formation of the transition state for the reaction involves a conformational change to a structure which differs from the enzyme structure in the complex with tyrosine or tyrosine adenylate. The induced fit to the transition-state structure must allow interaction with all four residues simultaneously. 

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