Principles of Protein X-ray Crystallography

354 Pages·1999·12.211 MB·English

by  Jan Drenth (auth.)

Springer Advanced Texts in Chemistry
Springer Science+Business Media, LLC
Springer Advanced Texts in Chemistry
Series Editor: Charles R. Cantor
Principles of Protein Structure
G.E. Schulz and R.H. Schirmer
Bioorganic Chemistry: A Chemical Approach to Enzyme Action
(Third Edition)
H. Dugas
Protein Purification: Principles and Practice (Third Edition)
R.K. Scopes
Principles of Nucleic Acid Structure
W. Saenger
Biomembranes: Molecular Structure and Function
R.B. Gennis
Basic Principles and Techniques of Molecular Quantum Mechanics
R.E. Christoffersen
Energy Transduction in Biological Membranes:
A Textbook of Bioenergetics
w.A.
Cramer and D.B. Knaff
Principles of Protein X-Ray Crystallography (Second Edition)
J. Drenth
Essentials of Carbohydrate Chemistry
J.F. Robyt
Jan Drenth
Principles of
Protein X-Ray
Crystallography
Second Edition
With 154 Illustrations
, Springer
Jan Drenth
Laboratory of Biophysical Chemistry
Nijenborgh 4
9747 AG Groningen
The Netherlands
Series Editor:
Charles R. Cantor
Boston University
Center for Advanced Biotechnology
Boston, MA 02215
USA
Cover illustration: Courtesy of Adrian R. Ferre-D'Amare and Stephen K. Burley, The
Rockefeller University. The four-a.-helix bundle moiety of transcription factor Max.
Reproduced with permission from Nature 363:38-45 (1993).
Library of Congress Cataloging-in-Publication Data
Drenth, Jan.
Principles of protein x-ray crystallography/Jan Drenth.-[2nd
ed.]
p. cm.-(Springer advanced texts in chemistry)
Includes bibliographical references and index.
ISBN 978-1-4757-3094-4 ISBN 978-1-4757-3092-0 (eBook)
DOI 10.1007/978-1-4757-3092-0
1. Proteins-Analysis. 2. X-ray crystallography. 1. Title.
II. Series.
QD431.D84 1999
547'.75046-dc21 98-26970
Printed on acid-free paper.
© 1999, 1994 Springer Science+Business Media New York
Originally published by Springer-Verlag New York, Inc in 1999.
Softcover reprint of the hardcover 2nd edition 1999
All rights reserved. This work may not be translated in whole or in part without the written
permission of the publisher Springer Science+Business Media, LLC,
except for brief excerpts in connection with reviews or scholarly analysis.
Use in connection with any form of information storage and retrieval, electronic adaptation,
computer software, or by similar or dissimilar methodology now known or hereafter devel
oped is forbidden.
The use of general descriptive names, trade names, trademarks, etc., in this publication, even
if the former are not especially identified, is not to be taken as a sign that such names, as
understood by the Trade Marks and Merchandise Marks Act, may accordingly be used freely
by anyone.
Production coordinated by Chernow Editorial Services, Inc., and managed by Francine
McNeill; manufacturing supervised by Nancy Wu.
Typeset by Best-set Typesetter Ltd., Hong Kong.
9 R 7 6 5 432 1
SPIN 10685242
Series Preface
New textbooks at all levels of chemistry appear with great regularity.
Some fields such as basic biochemistry, organic reaction mechanisms, and
chemical thermodynamics are well represented by many excellent texts,
and new or revised editions are published sufficiently often to keep up
with progress in research. However, some areas of chemistry, especially
many of those taught at the graduate level, suffer from a real lack of up
to-date textbooks. The most serious needs occur in fields that are rapidly
changing. Textbooks in these subjects usually have to be written by
scientists actually involved in the research that is advancing the field. It
is not often easy to persuade such individuals to set time aside to help
spread the knowledge they have accumulated. Our goal, in this series, is
to pinpoint areas of chemistry where recent progress has outpaced what is
covered in any available textbooks, and then seek out and persuade
experts in these fields to produce relatively concise but instructive intro
ductions to their fields. These should serve the needs of one-semester or
one-quarter graduate courses in chemistry and biochemistry. In some cases,
the availability of texts in active research areas should help stimulate the
creation of new courses.
Charles R. Cantor
v
Preface to the Second Edition
Since the publication of the previous edition in 1994, X-ray crystallography
of proteins has advanced by improvements in existing techniques and by
addition of new techniques. Examples are, for instance, MAD, which
has developed into an important method for phase determination. Least
squares as a technique for refinement is gradually being replaced by the
formalism of maximum likelihood. With several new sections, the book has
been updated, and I hope it will be as well received as the previous edition.
In the preparation of this second edition, I was greatly assisted by experts
who commented on relevant subjects. I acknowledge the contributions of
Jan Pieter Abrahams, Eleanor Dodson, Elspeth Garman, Eric de La
Fortelle, Keith Moffat, Garib Murshudov, Jorge Navaza, Randy Read,
Willem Schaafsma, George Sheldrick, Johan Turkenburg, Gert Vriend,
Charles Weeks, and my colleagues in the Groningen Laboratory.
I am especially grateful to Bauke Dijkstra for the generous hospitality in
his laboratory.
Jan Drenth
vii
Preface to the First Edition
Macromolecules are the principal nonaqueous components of living cells.
Among the macromolecules (proteins, nucleic acids, and carbohydrates),
proteins are the largest group. Enzymes are the most diverse class of
proteins because nearly every chemical reaction in a cell requires a
specific enzyme. To understand cellular processes, knowledge of the
three-dimensional structure of enzymes and other macromolecules is
vital. Two techniques are widely used for the structural determination
of macromolecules at atomic resolution: X-ray diffraction of crystals
and nuclear magnetic resonance (NMR). While NMR does not require
crystals and provides more detailed information on the dynamics of
the molecule in question, it can be used only for biopolymers with
a molecular weight of less than 30,000. X-ray crystallography can be ap
plied to compounds with molecular weight up to at least 106• For many
proteins, the difference is decisive in favor of X-ray diffraction.
The pioneering work by Perutz and Kendrew on the structure of
hemoglobin and myoglobin in the 1950s led to a slow but steady increase
in the number of proteins whose structure was determined using X-ray
diffraction. The introduction of sophisticated computer hardware and
software dramatically reduced the time required to determine a structure
while increasing the accuracy of the results. In recent years, recombinant
DNA technology has further stimulated interest in protein structure
determination. A protein that was difficult to isolate in sufficient quantities
from its natural source can often be produced in arbitrarily large amounts
using expression of its cloned gene in a microorganism. Also, a protein
modified by site-directed mutagenesis of its gene can be created for
scientific investigation and industrial application. Here, X-ray diffraction
plays a crucial role in guiding the molecular biologist to the best amino
ix
x Preface to the First Edition
acid positions for modification. Moreover, it is often important to learn
what effect a change in a protein's sequence will have on its three
dimensional structure. Chemical and pharmaceutical companies have
become very active in the field of protein structure determination because
of their interest in protein and drug design ..
This book presents the principles of the X-ray diffraction method.
Although I will discuss protein X-ray crystallography exclusively, the
same techniques can in principle be applied to other types of macro
molecules and macromolecular complexes. The book is intended to serve
both as a textbook for the student learning crystallography, and as a
reference for the practicing scientist. It presupposes a familiarity with
mathematics at the level of upper level undergraduates in chemistry and
biology, and is designed for the researcher in cell and molecular biology,
biochemistry, or biophysics who has a need to understand the basis for
crystallographic determination of a protein structure.
I would like to thank the many colleagues who have read the
manuscript and have given valuable comments, especially Aafje Vos,
Shekhar and Sharmila Mande, Boris Strokopytov, and Risto Lapatto.
Jan Drenth
Contents
Series Preface v
Preface to the Second Edition vii
Preface to the First Edition ix
Chapter 1
Crystallizing a Protein
1.1 Introduction 1
1.2 Principles of Protein Crystallization 1
1.3 Crystallization Techniques 4
1.4 Crystallization of Lysozyme 8
1.5 A Preliminary Note on Crystals 11
1.6 Preparation for an X-ray Diffraction Experiment 12
1.7 Cryocooling 16
1.8 Notes 18
Summary 21
Chapter 2
X-ray Sources and Detectors 22
2.1 Introduction 22
2.2 X-ray Sources 22
2.3 Monochromators 32
2.4 Introduction to Cameras and Detectors 34
2.5 Detectors 35
2.6 The Rotation (Oscillation) Instrument 41
2.7 Electronic Area Detectors 47
Summary 49
xi
xii Contents
Chapter 3
Crystals 50
3.1 Introduction 50
3.2 Symmetry 55
3.3 Possible Symmetry for Protein Crystals 58
3.4 Coordinate Triplets: General and Special Positions 62
3.5 Asymmetric Unit 63
3.6 Point Groups 64
3.7 Crystal Systems 64
3.8 Radiation Damage 66
3.9 Characterization of the Crystals 67
Summary 69
Chapter 4
The Theory of X-ray Diffraction by a Crystal 70
4.1 Introduction 70
4.2 Waves and Their Addition 71
4.3 A System of Two Electrons 74
4.4 Scattering by an Atom 78
4.5 Scattering by a Unit Cell 80
4.6 Scattering by a Crystal 81
4.7 Diffraction Conditions 82
4.8 Reciprocal Lattice and Ewald Construction 84
4.9 The Temperature Factor 89
4.10 Calculation of the Electron Density p (x y z) 92
4.11 Comparison of F(h k l) and F(Ji ld) 98
4.12 Symmetry in the Diffraction Pattern 99
4.13 Integral Reflection Conditions for Centered Lattices 103
4.14 The Intensity Diffracted by a Crystal 103
4.15 Scattering by a Plane of Atoms 111
4.16 Choice of Wavelength, Size of Unit Cell, and
Correction of the Diffracted Intensity 113
Summary 115
Chapter 5
Average Reflection Intensity and Distribution of Structure
Factor Data 117
5.1 Introduction 117
5.2 Average Intensity; Wilson Plots 120
5.3 The Distribution of Structure Factors F and
Structure Factor Amplitudes IFI 122
Summary 124
Chapter 6
Special Forms of the Structure Factor 125
6.1 Introduction 125
6.2 The Unitary Structure Factor 125
6.3 The Normalized Structure Factor 126
Summary 128