Volume 62, Supplement FEBS LETTERS 4 February 1976

ROLE OF FLEXIBILITY IN THE SPECIFICITY, CONTROL AND EVOLUTION OF ENZYMES

D. E. KOSHLAND, Jr.

Department of Biochemistry, University of California, Berkeley, California 92740 USA

Introduction

In 100 years of enzyme research the importance of

specificity has not changed at all but its explanation

in terms of enzyme structure has changed enormously.

Enzyme specificity is essential to function, not only

to maintain the faithful reproduction of metabolic

pathways but also to prevent unwanted side reactions

at a particular active site. Specificity must involve a

fit between enzyme and substrate but this fit turns

out to be a dynamic one. A particular conformation

of substrate is selected in most cases from among a

number of conformational isomers and the substrate

induces a change in.the conformation of the protein.

Simple binding provides specificity but binding plus

a conformational change gives added specificity and

with it new features of regulatory control.

To explore the new assessment of specificity it

may be valuable to examine three aspects of this pro-

cess: (a) the advantages of flexibility in enzyme func-

tion (b) the role of flexibility in co-o'perativity and

(c) the evolution of enzyme function.

Advantages of flexibility in enzyme

function

To begin such a section, one must first define what

is meant by flexible and what is meant by rigid. Cer-

tainly no one expects protein structure to be totally

rigid. There are vibrations within chemical bonds in

the simplest compounds and rotation about single

bonds of groups such as lysines on the surface of a

protein which might be considered classical 'template'

structures. What might be a good modern definition

of rigid is one in which there is no significant change

in the average position of residues on binding of

ligand. The protein may breath, or surface groups may

rotate, but the protein in the presence of bound ligand

is essentially congruent with the protein alone. On the

other hand, a flexible protein is one in which signifi-

cant conformation changes are induced by binding

ligand, changes which may be sufficient to turn a pro-

tein from 'off" to 'on' in regard to its catalytic action.

Some advantages of such a flexible enzyme as com-

pared to a rigid one are given below.

Kinetic specificity

A flexible protein can readily explain the exclu-

sion of molecules which are similar in structure to the

substrate, but which lack structural features needed

to induce catalysis [ 1 ]. This can explain many features

of specificity, e.g. deoxyglucose versus glucose or

propionate versus butyrate, but its greatest impor-

tance probably lies in the ability to exclude water in

an active site designed for a hydroxylic molecule. The

specificity in these cases is kinetic since it is failure

to react after binding not steric exclusion which con-

trois the reaction.

Ordered binding

An ordered binding of substrates indicates that one

substrate makes it easier for a subsequent one to bind

[2]. Sequential binding can be rationalized on a rigid

enzyme if it is postulated that there is steric blocking

of active sites or if the first substrate itself provides

structural features that attract the second substrate.

These mechanisms can be excluded in most cases and

evidence for conformational changes is extensive where

ordered binding is observed. An obligatory order of

binding is particularly important if a highly reactive

intermediate is formed. If the highly reactive com-

pound binds only after a conformation change induced

by the acceptor, the reactive compound need only

exist transiently on the enzyme surface. Hence waste-

ful side reactions are avoided.

North-Holland Publishing Company - Amsterdam

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