Enzymes use combinations of four general mechanistic strategies to achieve dramatic enhancements of the rates of chemical reactions.
Catalysis by Proximity
In order to chemically interact, substrate molecules must come within bond-forming distance of one another. The higher their concentration, the more frequently they will encounter one another, and the greater will be the rate at which reaction products appear. When an enzyme binds substrate molecules at its active site, it creates a region of high local substrate con centration, one in which they are oriented in an ideal position to chemically interact. In and of itself, this proximity results in rate enhancements of at least a 1000-fold over that observed in the absence of an enzyme.
Acid–Base Catalysis
In addition to contributing to the ability of the active site to bind substrates, the ionizable functional groups of aminoacyl side chains and, where present, of prosthetic groups, can con tribute to catalysis by acting as acids or bases. We distinguish two types of acid–base catalysis. Specific acid or base catalysis refers to reactions for which the only participating acids or bases are protons or hydroxide ions. The rate of reaction thus is sensitive to changes in the concentration of protons or hydroxide ions, but is independent of the concentrations of other acids (proton donors) or bases (proton acceptors) present in the solution or at the active site. Reactions whose rates are responsive to all the acids or bases present are said to be subject to general acid catalysis or general base catalysis.
Catalysis by Strain
For catalysis of lytic reactions, which involve breaking a covalent bond, enzymes typically bind their substrates in a conformation that weakens the bond targeted for cleavage through physical distortion and electronic polarization. This strained conformation mimics that of the transition state intermediate, a transient species that represents the midway point in the transformation of substrates to products. Nobel Laureate Linus Pauling was the first to suggest a role for transition state stabilization as a general mechanism by which enzymes accelerate the rates of chemical reactions. Knowledge of the transition state of an enzyme-catalyzed reaction is frequently exploited by chemists to design and synthesize more effective enzyme inhibitors, called transition state analogs, as potential pharmacophores.
Covalent Catalysis
The process of covalent catalysis involves the formation of a covalent bond between the enzyme and one or more substrates. The modified enzyme thus becomes a reactant. Covalent catalysis provides a new reaction pathway whose activation energy is lower—and rate of reaction therefore faster—than the pathways available in homogeneous solution. The chemically modified state of the enzyme is, however, transient. Completion of the reaction returns the enzyme to its original, unmodified state. Its role thus remains catalytic. Covalent catalysis is particularly common among enzymes that catalyze group transfer reactions. Residues on the enzyme that participate in covalent catalysis generally are cysteine or serine, and occasionally histidine. Covalent catalysis often follows a “ping-pong” mechanism—one in which the first substrate is bound and its product released prior to the binding of the second substrate (Figure1).
“Ping-pong” mechanism for transamination.E—CHO and E—CH2 NH2 represent the enzyme-pyridoxal phosphate and enzyme-pyridoxamine complexes, respectively. (Ala, alanine; Glu, glutamate; KG, α-ketoglutarate; Pyr, pyruvate.)
