Table Of ContentEnzyme Physics
Enzyme Physics
Mikhail V. Vol'kenshtein
Institute of Molecular Biology
Academy of Seiences of the USSR, Moscow
Translated lrom the Russian
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Springer Science+Business Media, LLC 1969
Library of Congress Catalog Card Number 69-12546
The original Russian textwas published by Nauka Press in
Moscow in 1967 as part of a series entitled Fizika Zhiznennykh
protsessov (Physics of Life Processes)
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FIZIKA FERMENTOV
ENZYME PHYSICS
ISBN 978-1-4899-2836-8 ISBN 978-1-4899-2834-4 (eBook)
DOI 10.1007/978-1-4899-2834-4
© 1969 Springer Science+Business Media New York
Originally published by Plenum Press,New York in 1969.
All rights reserved
No part of this publication may be reproduced in any form
without written permission from the publisher.
FOREWORD
This book treats a new, far-from-fully-developed area of
molecular biophysics-enzyme physics. An attempt is made to
survey this field, but primary consideration is given tothreeprob
lems under investigation in the Polymer Structure Labaratory of
the Institue of High-Molecular Compounds, Academy of Seiences
ofthe USSR.
The first problern is the genetic coding of the biologically
fun.ctional structure of proteins. Its solution is based on physical
theories of hydrophobic interactions.
The second problern is the conformational properties of pro
teins as the factor governing enzyme activity. The most direct
methods for experimental investigation of questions in this area
are optical, principally those involving natural and magnetic rota
tion of the plane of polarization. A substantial portion of the book
concerns optical activity; the Faraday effect is discussed in an
appendix.
The third problern is the manifestation of the cooperative
properties of enzymes in the kinetics of enzymatic reactions and
the solution of complex kinetic problems. This problern is espe
cially pressing in connection with research on allosteric enzymes,
which are responsible for feedback in metabolic processes. An
appendix describes a new method for solving kinetic problems,
based on the theory of graphs.
This volume extends and details certain of the ideas ex
pressed in my previous book, Molecules and Life: An Introduction
to Molecular Biophysics, which was published in this series in
1965.
V
vi FOREWORD
The writing of this book was directly connected with my par
ticipation in two winter schools on molecular biology in Dubna,
both as a lecturer and as an auditor.
I wish to thank my colleagues and graduate students I. A.
Bolotina, B. N. Goi 'dshtein,D. S. Markovich, and Yu. A. Sharonov
for their assistance in the preparation of this work. Special thanks
is due to Academician A. E. Braunshtein for the valuable criti
cisms he offered after reading the manuscript.
M. Vol'kenshtein
Leningrad, May 1966
CONTENTS
CHAPTER 1
Introduction 1
CHAPTER 2
Protein Structure . . . . . . . . . . . . . . . . . . . . . . . 5
CHAPTER 3
Hydrophobie Interactions and Protein Structure. • • 18
CHAPTER 4
Genetic Coding of Protein Structure. • • • • • • • • • • 30
CHAPTER 5
Macromolecular Properties of Enzymes. • • • • • • • 40
CHAPTER 6
Induced Structural Correspondence of Enzyme
and Substrate. . . . . . . . . . . . . . . . . . . . . . . . . . 47
CHAPTER 7
Optical Acti vity ••••••••••••••••••••• 59
0 • o
CHAPTER 8
Optical Activity of Polypeptide Chains ••••••• 71
0 •
CHAPTER 9
Optical Activity and Conformational Properties
of Enzymes. . . . . . . . . . . . . . . . . . . . . . . . . . . 84
CHAPTER 10
Conformational Properties of Enzymes and
Ionization . . . . . . . . . . . . . . . . . . . . . . . . . . . . 94
vii
viii CONTENTS
CHAPTER 11
Cooperative Properlies of Enzymes and
Reaction Kinetics. • • • • • • • • • • • • • • • • • • • • • • 110
CHAPTER 12
Allosterle Enzymes • • • • • • • • • • • • • • • • • • • • • 120
CHAPTER 13
Hemoglobin . . . . . . . . . . . . . . . . . . . . . . . . . . . 133
CHAPTER 14
Enzymes and Mechanochemistry. • • • • • • • • • • • • 143
APPENDIX I
Kinetics of Enzymatic Reactions and Graph Theory 149
APPENDIX II
Anomalaus Dispersion of Magnetic Rotation • • • • • 164
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 182
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 193
Chapter 1
INTRODUCTION
Enzymes are proteins that serve as catalysts in biochemical
processes. The catalytic function of proteins is of the greatest im
portance for life. In crude terms, the molecular plan for cellular
and organismic structure laid down in the genome consists princi
pally in a program for synthesis of definite enzymes at gi ven stages
of development. A single gene corresponds to a single protein
chain. The existence of this program is also the basis of heredity.
The catalytic activity of enzymes is responsible for the synthesis
of all biologically functional compounds in the cell, for the storage
of chemical energy (mainly in molecules of adenosine triphosphate,
ATP), for the expenditure of this energy in biosynthetic processes,
mechanochemical processes, and the active transport of molecules
and ions, etc. As has recently been established, special enzymes,
referred to as allosteric enzymes, regulate multistage biochemical
processes through feedback. The cybernetic processes in the cell
(information storage and transfer, regulation, and control) have a
chemical character and are effected at the molecular level. This
distinguishes the living cell or organism from any modern machine,
in which such processes are carried out through mechanical, elec
trical, or magnetic phenomena. Since all chemical reactions in the
cell involve the direct participation of enzymes, their significance
in biology cannot be overemphasized. Enzymes carry out their
function either in the form of free molecules in a homogeneaus me
dium (an aqueous solution of inorganic ions and complex organic
compounds) or as components of condensed supermolecular struc
tures, which are also in contact with the aqueous medium. Examples
of dissolved enzymes include the proteolytic enzymes in the diges
tive system, while examples of enzymes in condensed structures in
clude the cytochromes in the mitochondria and myosin in muscle
1
2 CHAPTERl
fibers. There is at present no reason to suppose that enzymatic
activity differs in these two cases, but we cannot exclude the pos
sibility that such differences will be discovered during further
studies of supermolecular structures. In any event, the mechano
chemical properties of the supermolecular structures forming
cell and organoid membranes and contractile systenis (muscle,
etc.) are inseparably associated with the functions of the enzymes
they contain. Enzymes differ from all other catalysts known to
chemistry in their exceptionally efficient Operation under mild
conditions (in an aqueous medium at normal pressure and a low,
physiological temperature). At the same time, most enzymes are
very specific, acting selectively on definite compounds (substrates)
or groups of compounds. Research on the structure and proper
ties of enzymes is naturally an important and extensive branch of
modern science and is called enzymology. This field is a com
ponent area of biochemistry and a great deal has been achieved in
it. General theories have been devised to account for the mech
anism and kinetics of enzymatic catalysis and advanced methods
have been developed for studying this process. The detailed chem
ical reaction mechanisms of specific enzymes have been investi
gated in a number of cases. The molecular structure of many
enzyme~ has been studied and the primary structure of ribonucle
ase, cytochrome c, chymotrypsin, and lysozyme has been complete
ly deciphered. The three-dimensional structure of lysozyme and
ribonuclease has been determined. Physicochemical hypotheses
have been advanced to more or less successfully account for the
special properties of enzymes as biological catalysts and regu
lators.
The development of biology since mid-century has led to a
close and fruitful cooperation with both chemistry and physics in
the solution of a number of extremely important problems. Ap
plication of the ideas and methods of modern physics to biology
has proved to be very useful. We can now speak of enzyme phys
ics as an important branch of molecular biophysics, inseparably
associated with biochemistry and enzymology.
The problems of enzyme physics coincide with certain bio
chemical problems, but various aspects of research in these areas
differ.
