Chemical Relaxation in Molecular Biology

434 Pages·1977·17.95 MB·English

by  G. Ilgenfritz (auth.)

Molecular Biology
Biochemistry and Biophysics
24
Editors:
A. Kleinzeller, Philadelphia· G. F. Springer, Evanston
H. G. Wittmann, Berlin
Advisory Editors:
C. R. Cantor, New York· F. Cramer, Gottingen . F. Egami, Tokyo
M. Eigen, Gottingen . F. Gros, Paris· H. Gutfreund, Bristol
B. Hess, Dortmund· H. Jahrmiirker, Munich· R. W Jeanloz, Boston
E. Katzir, Rehovot . B. Keil, Gif-sur-Yvette· M. Klingenberg, Munich
I. M. Klotz, Evanston· F. Lynen, Martinsried/Munich
W T. J. Morgan, London· K. Muhlethaler, Zurich· S. Ochoa, New York
G. Palmer, Houston· I. Pecht, Rehovot . R. R. Porter, Oxford
W Reichardt, Tiibingen . H. Tuppy, Vienna
J. Waldenstrom, Malmo
Chemical Relaxation in
Molecular Biology
Edited by
I. Pecht and R. Rigler
With Contributions by
M. Ehrenberg· E. Grell· D. N. Hague
G. Ilgenfritz. T. M. Jovin . D. Lancet· D. Magde
I. Oberbaumer .1. Pecht· F. M. Pohl . D. Porschke
R. Rigler· P. Schuster· G. Striker· D. Thusius
K. Tortschanoff· W. Wintermeyer . P. Wolschann
With 141 Figures
Springer-Verlag Berlin· Heidelberg· New York 1977
Dr. ISRAEL PECHT
The Weizmann Institute of Science
Department of Chemical Immunology
Rehovot/Israel
Dr. RUDOLF RIGLER
Department of Medical Biophysics
. Karolinska Institutet
S-10401 Stockholm 60
ISBN-13:978-3-642-81119-7 e-ISBN-13:978-3-642-81117-3
DOl: 10.1007/978-3-642-81117-3
Library of Congress Cataloging in Publication Data. Main entry under title: Chemical relaxation in molecular biology.
(Molecular biology. biochemistry, and biophysics; 24) Includes bibliographical references. 1. Chemical reaction, Rate
of-Addresses, essays, lectures. 2. Molecular biology-Addresses, essays, lectures. I. Pecht, I., 1937- . II. Rigler,
Rudolf. III. Series. QD502.C47. 574.lf8. 77-7167
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© by Springer-Verlag Berlin· Heidelberg 1977.
Softcover reprint of the hardcover 1st edition 1977
The use of registered names, trademarks, etc. in this publication does not imply, even in the absence of a specific statement, that
such names are exempt from the relevant protective laws and regnlations and therefore free for general use.
2131/3130-543210
Dedicated to Manfred Eigen
Preface
The development of an area of scientific research is a dynamic
process with its own kinetic equations and its own physical mech
anism. The study of fast chemical interactions and transformations
is such an area, and while it is tempting to draw analogies or
to speculate about the simplest model system, the lack of ade
quately averaged observables is an annoying obstacle to such an
undertaking. Sciences suffering from such conditions usually avoid
quantitative models, be they primitive or complex. Instead, they
prove their point by "case histories".
Chemical relaxation kinetics started as an offspring of research
in acoustics. In some aqueous ionic solutions anomalous acoustic
absorption had been observed. A systematic study traced the cause
of this absorption, showing that the covered frequency range and
the intensity of the absorption were related in a predictable
manner to the rate at which ions can interact and form structures
differing in volume from the non interacting species.
The step from this experimental observation and its correct, non
trivial explanation to the discovery that all fast chemical pro
cesses must reveal themselves quantitatively in the relaxation
rate of a perturbed equilibrium state, and that perturbation para
meters other than sound waves can be used for its exploitation,
was made by MANFRED EIGEN in 1954. The foresightedness of K.F.
BONHOEFFER in securing the early beginnings of a purposefully de
lineated research program to this end was but one example of his
admirable faith in the abilities of the young scientists he gath
ered around him.
Early progress was fast and rewarding, despite the unconventional
and sometimes rather difficult experimental arrangements used.
But the attack was systematic. Simple exc~ange reactions involving
protons and coordination ligands yielded ~ time scale with the
diffusion-controlled encounter time as a yardstick. Chemical equi
libria were perturbed by electric fi·elds and sudden temperature
and pressure changes. Sensitive devices for the observation of
fast transient changes in almost any optical or electrical system
parameter were designed. Many exotic instruments with special com
binations were dreamed up and never made. Consistent and general
ized theoretical treatments were worked out, dealing with an ar
bitrary reaction mechanism. An increasing number of scientists
became aware of the field. A highly nonlinear, cooperative growth
period was the consequence.
VIII
The mechanism of the catalytic activity of enzymes was the first
challenge where the new method had to cope with chemical proper
ties and interactions between particles with a different degree
of molecular organization. The potential applications in biology
at the molecular level were attractive to biochemists1 at the
same time they created new situations and solutions for the ex
perimental approach.
The development of chemical relaxation as an approach to the dy
namics of systems with a high degree of complexity may not seem
to proceed with the same rapid advances as the study of simpler
reactions ten or more years ago, although the experimental tech
niques are greatly improved. This reflects the complexity of the
subject, rather than a deficiency in the method. As in chemical
reactions, the coupling of fast elementary processes is not pos
sible without introducing slower, mixed reaction coordinates.
In molecular biology, progress in understanding dynamics and ki
netic behavior cannot be uncoupled from progress in analytical
and preparative procedures and from progress in obtaining infor
mation on molecular structure and organization.
Gottingen, April 1977 L. DE MAEYER
Introduction
Two decades elapsed since the introduction of the concept of chem
ical relaxation for the study of chemical kinetics by EIGEN and
DE MAEYER (1, 2). From the very beginning, aspects of molecular
biology were in the foreground of the problems investigated by
this novel approach. A wide range of reactions was characterized
in terms of their detailed mechanisms and specific rates; this
ranged from proton transfer processes to the allosteric control
of protein function.
The purpose of this monograph is to give a representative cross
section of the current research activities dedicated to the anal
ysis of elementary steps in biological reactions. This covers the
range of the following topics: hydrogen-bond formation, nucleotide
base pairing, protein folding, isomerisation of protein and nucle
ic acid conformations, interactions between protein and proteins,
nucleic acid,and proteins, enzymes and substrates, antibody and
haptens or ionic transport through membranes. A common denominator
in these studies is the search for an understanding of the laws
that govern the dynamic behavior of living systems.
To make this volume useful also for the nonexpert, a comprehensive
introduction to the theory of chemical relaxation is given. The
instrumentation used in most of the studies presented here has
been reviewed in detail previously (2, 3, 4). New developments
and perspectives in the methodology have been treated by the in
dividual authors.
We hope that this book reflecting the current state of art in the
analysis of chemical kinetics of complex of biological systems
will serve as an incentive for future studies of the large number
of important biological reactions for which an understanding of
the mechanisms of action at the molecular level is still lacking.
1. EIGEN, M.: Discussion Faraday Soc. II, ~94 (1954).
2. EIGEN, M., DE MAEYER, L.: Techniques of Organic Chemistry (ed.
A. WEISSBERGER), Vol. III, part 2, p. 835. New York: Wiley 1963.
3. KUSTIN, K.: Fast reactions. In: Methods of Enzymology (eds.
S.P. COLOWICK, N.O. KAPLAN), Vol. XVI. New York: Academic Press
1969.
4. YAPEL, A.F., Jr., LUMRY, R.: Methods in Biochemical Analysis,
Vol. XX, pp. 169-350. New York: Wiley 1971.
J. PECHT
R. RIGLER
Contents
Theory and Simulation of Chemical Relaxation Spectra
G. ILGENFRITZ ...........•.................................
I. Introduction •.............•••....................... 1
A. The Relaxation Kinetic Progress Curve ............ 2
B. Optical Detection Signals ........................ 4
C. Theoretical Description of Relaxation Kinetics ... 7
D. Single Reaction Steps............................ 16
E. Approximations for Complex Reaction Systems ...... 19
F. Average Relaxation Times .•....................... 24
G. Computer Program for Simulation of Relaxation
Spectra (FORTRAN IV).............................. 26
1. Numbering of Reacting Species ...•............. 27
2. Numbering of Individual Reaction Steps ........ 28
References •............................•............... 31
Concentration Correlation Analysis and Chemical Kinetics
D. MAGDE ..•...•...........•.............•..•.•............ 43
I. Introduction ......•...........•..................... 43
II. Properties of Thermodynamic Fluctuations .....•...... 44
A. Magnitude of Occupation Number Fluctuations ...... 44
B. Dissipation of Number Fluctuations ............... 49
III. Measurement of Number Fluctuations ...•...........•.. 52
A. Fluorescence Correlation Analysis (FCA) .......... 54
1. Design of the FCA Experiment .................. 55
2. Correlation Computers ................•........ 60
3. Experimental Results •...•..................... 64
B. Resistance Correlation Analysis (RCA) ............ 68
C. Absorbance Correlation Analysis (ACA) ........•... 74
D. Quasi-Elastic Light Scattering (QELS) and
Turbidity Correlation Analysis (TCA) ............. 76
E. Orientation Correlation Analysis (OCA) .....•..... 78
IV. Summary and Conclusions •......•.•................... 80
References ...••....•........................•........... 82
Dynamics of Substitution at Metal Ions
D • N. HAGUE •.....•..•..•.....................•............. 84
I. Introduction 84
II. Formation of 1:1 Complexes with Small Ligands ...•... 86
III. Formation of 1:1 Complexes with Large Ligands ...... . 91
IV. The Effect of Bound Ligands ......•.................. 97
XI
A. Non-Ring Systems •.•••••••.••••.•••••••.••••••••• 97
1. Outer-Sphere Complex Formation •••••.••.•••••• 98
2. Labilisation of Remaining Water Molecules •.•• 99
3. Steric and Electronic Interaction Between
Ligands •••••••••••.••••.•.•.••..••••••••••.•• 103
4. Coordination Number Change at the Metal •••••• 103
B. Ring Systems-•••••.•••••••.••.•.••••••••••••••••• 103
V. S urnrnary •••••.•••.••••.•••..•••••.••..••••••••.•.••. 1 04
References •••••••.••.•.••••••••••.••.•.••.•.••.•..•.•• 105
Dynamics of Proton Transfer in Solution
P. SCHUSTER, P. WOLSCHANN, and K. TORTSCHANOFF .•••••••••• 107
I. Introduction •..•••..••.•.•••.•••••••.•.••.••..••••• 107
II. Theoretical Background of Proton Transfer •.••.••••• 108
A. Proton Affinities ••.•••••••••••••..•••••.•..•.•• 108
B. Stability of Hydrogen Bonded Molecular Complexes. 109
C. Potential Curves for Proton Transfer ••••••••..•• 114
D. Dynamics of Proton Transfer in the Vapor Phase •• 115
E. Gas Phase Solvation •••••••••••.••••..••..••..••. 116
F. Theoretical Concepts and Mechanisms of Proton
Transfer in Solution ••...••••..•.••.•.••••••••.. 119
III. Proton Transfer in Aqueous Solution •...•..••.••.•.• 121
A. Intermolecular Proton Transfer •••.••.•••.•..•.•• 122
B. Intramolecular Proton Transfer .••.••••••..•••••• 129
IV. Proton Transfer in Non-Aqueous Solvents .•.•••••.••. 139
A. Protic, Non-Aqueous Solvents ••••••••••.••••...•. 139
B. Aprotic Solvents................................ 142
V. Biochemical Model Studies ....••.•..•.••.•••••••.•.• 147
A. Amino Acids .••.•••••...•••••..••••.••.••••••.••• 148
B. Purines and Pyrimidines ••.••••..••.••••••...•..• 150
1. Formation of Hydrogen Bonded Complexes .•••••. 151
2. Proton Transfer Reactions on Purines, Pyrimi-
dines and Some Related Heterocyclic Compounds. 155
C. Coenzymes and Other Model Compounds ••••.•.•.••.• 157
D. Macromolecules ••.•••..••••.•..•..••..••..•.•..•• 160
VI. Polypeptides and Proteins •.•.•.•••.•....••••••••.•• 163
A. Oligopeptides ...•••••..•.•••••..••••.••••.•....• 163
B. High Molecular Weight Polypeptides and Proteins. 164
VII. Experimental Techniques ••..•••••••••••••••....•.... 169
VIII. Conclusion......................................... 171
IX. Other Review Articles and Books on Proton Transfer. 173
References ••.••••.•....••..•......•..•.•••••••••••••••• 174
Elementary Steps of Base Recognition and Helix-Coil Tran
sitions in Nucleic Acids
D. P(:)RSCHKE .••••••.•••..•.•••••••.••.•.••.••••..••••..•.• 191
I. Introduction ••.•.•.•.•..•..••...•.••.•••..•..•••••• 191
II. Elementary Steps of Bases Stacking ••.•.•.•••.•••..• 192
A. Stacking of Monomer Bases and Hydrophobic Inter-
actions ••..•••••..••...••.••.••••••.•.•••••...•. 192
B. Conformation Change of Single-Stranded poly-
nucleotides .•••.•......•.•••••••••••••.••••••••. 194
III. Ion Condensation to Polynucleotides •••••..•••.••.•• 196
XII
IV. Recognition of Monomer Bases on a polymer Template. 197
V. Helix-Coil Transition of Oligo (A) ·Oligo(U) ••••••••• 198
A. Equilibrium Parameters According to the Coopera-
ti ve Reaction Model •••.•••••••••••••...•.••...•• 198
B. Relaxation Data and Their Interpretation Accord-
ing to an "Allor None" Model •.••••.•.•.••...•.• 200
C. Unzippering at Helix Ends •...••.••.•.•.•••...•.. 206
D. Chain Sliding .•.•••••..••••.••••••••.•••••••.•.. 209
VI. The Influence of GC Base Pairs •.•.•.••••••.•••••••. 210
VII. Specific Effects in Helix Loops .••..•.•••...•.••..• 210
VIII. Dynamics of Polymer Helix-Coil Transitions ••••..... 212
IX. Rate and Specificity of Genetic Information Transfer 213
X. Summary............................................ 213
References .•...••.•.••.••••.•..••••..•.•.•••...•••.•.• 216
Structural Dynamics of tRNA. A Fluorescence Relaxation
Study of tRNA~~~st
R. RIGLER, M.EHRENBERG, and W. WINTERMEYER .•..••.....•.•• 219
I • Introduction .•••.••..•.••••••••.•.••••.•••..••••••. 219
II. Fluorescent Probes for the Structure of tRNA •••••.• 219
III. Pulsed Fluorescence Measurements ..•••••.•.•••.•.••• 221
A. The Lifetime of Excited States of the Fluorescent
Probe and the Distribution of Conformational
States .•••.•••.••••••.••••..•.•.•••••.••••.•.••• 221
B. Rotational Brownian Motion and Time-Dependent
Fluorescence Anisotropy ••••••••••.•••••••.•••.•. 221
C. Instrumentation •••••••••..••••••••.•••..••.••..• 222
D. Results .•.•.•••••••••.•.•.•.••.••••••••.•••••••• 223
IV. Measurements Under Stationary Excitation •....•••••. 227
V. Measurements of Chemical Rates ••••.•.•••..•..••...• 228
A. Instrumentation and Data Evaluation ••••••.•.••.. 228
B. Results •.•••••••••••••.••••..•••.•••.•.....••.•. 231
VI. A Model for Allosteric Conformations of tRNA •..•••• 233
A. Evaluation of the Parameters •••..•.••••••.•.••.. 235
VII. Conformational States of tRNA with Regard to the
Biological Role of tRNA ••••••..••••••••••..•..••.•• 237
References •.•....•••••••.••••••••••..•.•.••.•.•..•••.•.. 240
Chemical Relaxation Kinetic Studies of E. aoLi RNA Poly
merase Binding to poly[d(A-T)] Using Ethidium Bromide as
a Fluorescence Probe
T.M. JOVIN and G. STRIKER................................ 245
I. Introduction •.•••••••••.••..•• ~..................... 245
II. Experimental Procedures and Data Analysis .•..••.••• 249
A. Materials ••••••••••••••...•.••••••.••••••.••.••• 249
B. Fluorescence Temperature-Jump Measurements.
Instrumentation and Conditions ••••••.•.•••.••••• 249
C. On-Line Computer Acquisition of Relaxation Data. 250
D. Analysis of Relaxation Curves by the Method of
Modulating Functions .•••.••••••.•.••••.••••••.•• 251
III. Excluded Site Binding of Ethidium Bromide to
Poly[d(A-T)] •.••••••••.•.••••••.•••••••.••.••••••.• 253
A. Theory for the Equilibrium State •.••••.•.•.•.••• 253