Introduction to Molecular Biology: From Cells to Atoms - Anthony Rees, Michael Sternberg 2002

Proteins
Principles of Enzyme Action

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Fig. 12.1.

An enzyme is a protein that increases The rate of a biochemical reaction (i.e., acts as a catalyst). The reaction rate can increase by up to 10¹⁰ times compared to the rate of the same reaction in the absence of the enzyme.

A substrate is a molecule (designated as S) that is converted into a product (P) after interacting with an enzyme (E).

The Active Site of an enzyme is a region of the protein molecule where a substrate (or substrates) can bind to form an enzyme-substrate (E—S) complex. The active site is almost always formed by just a few amino acid residues. Although these residues are spatially close, they are often far apart in the linear protein chain. As a rule, The formation of the E—S complex occurs without the creation of covalent bonds; instead, it relies on weaker yet more specific types of interactions, such as Hydrogen Bonds, salt bridges, hydrophobic forces, and tight atomic packing. However, exceptions are known where a covalent bond forms between the enzyme and the substrate, for example, during the formation of an intermediate product in the functioning of Enzymes belonging to the Serine protease family.

Enzyme Specificity refers to its ability to distinguish its true substrate from other related molecules. This selectivity is driven by the high specificity of enzyme-substrate interactions. The early model of this interaction, known as the "lock-and-key" model, was later supplemented by METABOLISM/2.html">THE CONCEPT OF "induced fit" (see below). Recognition specificity varies significantly among different enzymes—some enzymes can catalyze a reaction involving only a single substrate, whereas others can act on several chemically related substances. For instance, formamidase hydrolyizes only formamide, whereas amidase hydrolyzes any aliphatic amide.

A similar "lock-and-key" concept to explain enzyme specificity was proposed in the 1890s by Fischer: only its matching substrate (the key) fits the enzyme (the lock).

The "induced fit" hypothesis to explain enzyme specificity was put forward by Koshland in 1959. According to this now widely accepted hypothesis, the binding of the correct substrate to an enzyme induces minor Conformational Changes in the protein. As a result of these changes, the catalytic groups of the enzyme are oriented in such a way that The conversion of the substrate into product becomes possible. Further Development of the induced fit model involves taking into account that the conformation of the substrate may also undergo slight alterations upon binding to the enzyme. In this case, one speaks of strain within the substrate molecule. The hypothesis of conformational changes in both the enzyme and the substrate upon binding explains why molecules very similar in shape to the true substrate can bind to the enzyme yet fail to be converted into product—i.e., they act as inhibitors. Thus, the correct substrate is much more than just a "key" for a corresponding "lock."

The equilibrium position of a reaction is independent of the presence or absence of the enzyme in the reaction mixture. Let us consider The change in Free energy for a reversible reaction S ↔ P (the corresponding graph is shown on the previous page). The Free energy of the reaction, ∆С⁰, is equal to the difference between the free energies of S and P and determines the reaction equilibrium position. In the presence of any catalyst, including an enzyme, the free energy of the starting reactants (S) and reaction products (P) remains unchanged, and consequently, ∆С⁰ does not change.

The Transition State, or activated complex (designated as X), is a high-energy intermediate Structure that forms during a reaction. The difference between the free energies of the starting reactants (i.e., substrates) and the transition state is called the free energy of activation and is denoted as ∆С^‡. The reaction rate depends on the magnitude of ∆С^‡: the smaller it is, the higher the reaction rate, and vice versa.

The enzyme increases the reaction rate in the following ways:

1. By lowering the free energy of the transition state through the stabilization of the activated complex.

2. By increasing the energy of the substrate when it binds to the enzyme to form the enzyme-substrate (E—S) complex. As a result, the difference in free energy between the E—S complex and the transition state is reduced.

3. By maintaining the microenvironment of the active site in a state different from that of an aqueous medium. Often, the side chains of amino acid residues located in the active site region exhibit altered abilities to acquire an electrical charge compared to when these chains are fully immersed in an aqueous environment. Consequently, these side chains may display "enhanced reactivity."

4. By positioning the reacting atoms in the correct orientation and at the necessary distance from one another to ensure optimal reaction progress. Atomic collisions in the absence of an enzyme rarely lead to a chemical reaction because atoms are very infrequently found in the correct orientation under such conditions.

Inhibitors are molecules that bind to an enzyme and block some stage of the enzymatic reaction. Inhibitors can be reversible or irreversible. Reversible inhibition is subdivided into competitive, non-competitive, and uncompetitive.

A competitive inhibitor is a molecule so structurally similar to the substrate molecule that the enzyme cannot distinguish between them. As a result of the Competitive inhibitor binding to the active site of the enzyme, the concentration of E—S complexes drops, and consequently, the reaction rate decreases. The inhibitor is usually not converted into a product.

A non-competitive inhibitor is a molecule that binds not to the active site, but to some other region of the enzyme. Since binding with a non-competitive inhibitor does not prevent the enzyme from forming the E—S complex, this inhibitor does not lower the concentration of such complexes, but instead affects the efficiency of converting S into P.

An uncompetitive inhibitor is a molecule that binds exclusively to the enzyme-substrate complex and cannot bind to the free enzyme. In single-substrate enzyme systems, this type of inhibition is quite rare. An irreversible inhibitor continuously modifies enzyme molecules, causing them to partially or completely lose their activity.