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TYPES OF MECHANISM FOR ENZYMIC CATALYSIS

The definitions given so far have been operational, i.e. they provide a way of describing what may be observed independently of any interpretation that may been placed on it. Little has been said about mechanisms, i.e., the detailed descriptions of the chemical events that make up the catalytic process. Nonetheless, the ultimate objective of most investigations in enzyme kinetics is to propose a mechanism. It is to be emphasized at the outset that a kinetic investigation can disprove a proposed mechanism but can never establish a mechanism beyond doubt. A mechanism may be consistent with all of the known facts, yet it is always possible to propose other mechanisms that are also consistent with the facts.

The procedure that is adopted, and the only one that allows progress to be made, is to accept the simplest mechanism that is consistent with all the known facts. This is the principle of Occam's razor. A steady-state study of the effect of substrate concentrations on the rate, leading to an empirical rate equation, can often lead to a proposed mechanism. Such a mechanism can be tested by additional investigations, such as of the pre-steady-state kinetics, and of the effects of inhibitors, pH, temperature and solvent composition.

It is not a practical proposition to institute a consistent system for naming mechanisms, although attempts to do this have been made, because except in the most trivial cases it is always simpler and clearer to specify a mechanism by reference to a scheme. Nonetheless, certain terms occur frequently in the descriptions of mechanisms of enzymic catalysts and will be defined here.

The form of an enzyme that exists in solution in the absence of any substrate or other small molecule that can bind to it is called the free enzyme. An intermediate derived from the free enzyme by binding of a substrate molecule is called an enzyme-substrate complex, and terms such as enzyme-product complex, enzyme-inhibitor complex, EA complex may also be used by an obvious extension of this definition. A complex derived from the free enzyme and one other molecule is called a binary complex; one derived from the free enzyme and two other molecules is called a ternary complex; one derived from the free enzyme and three other molecules is called a quaternary complex. If the catalytic process proceeds through a second form of free enzyme that differs from the first by the presence of a covalently bound group that is transferred in the reaction this second form of free enzyme is called a substituted enzyme.

Complexes that do not undergo further reactions that are part of the catalytic pathway are called dead-end complexes, and the reactions producing them are called dead-end reactions. Enzyme-substrate complexes that do not lead to reaction, which are often but not necessarily dead-end complexes, are called abortive or non-productive complexes.

When a reaction proceeds through a series of steps that must occur in a specified order, e.g. the substrates must bind in a particular order and the products are released in a particular order, it is said to obey a compulsory-order mechanism. (The alternative term linear mechanism is sometimes used, but it is discouraged because it can invite confusion with other uses of the term linear in enzyme kinetics.) When this is not the case the reaction is said to follow a random-order mechanism or a branched mechanism. These terms may also be applied to parts of mechanisms: for example, it may happen that substrates bind in random order but products are released in a compulsory order. The distinction between compulsory-order and random-order mechanisms is rarely absolute in practice. The term preferred-order mechanism may be used to emphasize that although more than one pathway exists most of the flux is through one of them. The term random-order mechanism does not, however, exclude this intermediate case unless explicitly stated to do so.

Elementary steps in which the enzyme forms complexes with small molecules are called binding steps and the reverse steps are called release steps, usually with a qualifier to indicate the type of species bound or released: e.g. substrate binding step or product-release step, etc. Elementary steps in which no binding or release occurs may be called isomerizations.

An allosteric effector is one that acts by binding to the enzyme at a site different from the active site. There is no necessary connection between allosteric effects and co-operative effects, though they often occur together in real systems.

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