Chemical Genomics: Reviews and Protocols

279 Pages·2005·3.915 MB·English

by  Paul R. Caron (auth.), Edward D. Zanders PhD (eds.)

Chemical Genomics
M E T H O D S I N M O L E C U L A R B I O L O G Y™
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M E T H O D S I N M O L E C U L A R B I O L O G Y™
Chemical Genomics
Reviews and Protocols
Edited by
Edward D. Zanders,
PhD
CamBP Ltd., Cambridge, UK
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Library of Congress Cataloging in Publication Data
Chemical genomics : reviews and protocols / edited by Edward D. Zanders.
p. ; cm. -- (Methods in molecular biology ; v. 310)
Includes bibliographical references and index.
ISBN 1-58829-399-8 (alk. paper)
1. Genomics. 2. Proteomics. 3. Pharmacogenetics. 4. Biochemical genetics. 5. DNA microarrays.
6. Combinatorial chemistry.
[DNLM: 1. Molecular Probes--chemical synthesis--Laboratory Manuals. 2. Protein Array Analysis--
methods--Laboratory Manuals. 3. Combinatorial Chemistry Techniques--Laboratory Manuals.
4. Genomics--methods--Laboratory Manuals. QU 25 C517 2005] I. Zanders, Edward D. II. Series.
QH431.C45197 2005
572.8'6--dc22
2005013118
Preface
Chemical genomics is an exciting new field that aims to transform biologi-
cal chemistry into a high-throughput industrialized process, much in the same
way that molecular biology has been transformed by genomics. The interac-
tion of small organic molecules with biological systems (mostly proteins)
underpins drug discovery in the pharmaceutical and biotechnology industries,
and therefore a volume of laboratory protocols that covers the key aspects of
chemical genomics would be of use to biologists and chemists in these organi-
zations. Academic scientists have been exploring the functions of proteins
using small molecules as probes for many years and therefore would also ben-
efit from sharing ideas and laboratory procedures. Whatever the organizational
backgrounds of the scientists involved, the challenges of extracting the maxi-
mum human benefit from genome sequencing projects remains considerable,
and one where it is increasingly recognized that chemical genomics will play
an important part.
Chemical Genomics: Reviews and Protocols is divided into two sections,
the first being a series of reviews to describe what chemical genomics is about
and to set the scene for the protocol chapters. The subject is introduced by Paul
Caron, who explains the various “flavors” of chemical genomics. This is fol-
lowed by Lutz Weber and Philip Dean who cover the interaction between
organic molecules and protein targets from the different perspectives of labo-
ratory experimentation and in silico design. The protocols begin with the meth-
ods developed in Christopher Lowes’ laboratory (Roque et al.) for what could
be described as a classical example of chemical genomics, namely the design
of small molecules as affinity ligands for specific protein families. The theme
is continued with detailed protocols for in silico docking by Jongejan et al. that
highlights the importance of computational approaches to protein–small mol-
ecule interactions. The remaining protocols are directed towards the aim of
producing highly diverse collections of proteins, carbohydrates, and small mol-
ecules for use in arrays containing large numbers of molecules. This high-
throughput approach to screening for interaction between small and large
biological molecules is the essence of chemical genomics. The chapters by
Ryu, Doyle, Murphy, Sawasaki, Endo, Kohno, and Hoyt cover methods for the
production of proteins and carbohydrates using different expression systems.
Webster and Oxley give a protocol for analyzing the proteins using mass spec-
trometry. The techniques for arraying these proteins and carbohydrates on solid
supports are detailed in the chapters by Blackburn, Marik, and Wang. Finally
v
vi Preface
an in vivo method for identifying small molecule–protein interactions is
described by Khazak et al. using the yeast two-hybrid system.
Although we recognize that no single book on chemical genomics can be
totally comprehensive in its coverage, we hope that the protocols here, in cov-
ering the key elements of the subject, will be of genuine use to the wide variety
of scientists in this rapidly expanding field.
Edward D. Zanders
Contents
Preface ..............................................................................................................v
Contributors .....................................................................................................ix
PART I REVIEWS
1 Introduction to Chemical Genomics
Paul R. Caron........................................................................................3
2 Chemistry for Chemical Genomics
Lutz Weber.........................................................................................11
3 Computer-Aided Design of Small Molecules
for Chemical Genomics
Philip M. Dean....................................................................................25
PART II PROTOCOLS
4 Design, Synthesis, and Screening of Biomimetic Ligands
for Affinity Chromatography
Ana Cecília A. Roque, Geeta Gupta, and Christopher R. Lowe.........43
5 The Role and Application of In Silico Docking
in Chemical Genomics Research
Aldo Jongejan, Chris de Graaf, Nico P. E. Vermeulen,
Rob Leurs, and Iwan J. P. de Esch..................................................63
6 Synthesis of Complex Carbohydrates and Glyconjugates:
Enzymatic Synthesis of Globotetraose Using (cid:71)-1,3-N-
Acetylgalactosaminyltransferase LgtD From
Haemophilus infuenzae Strain Rd
Kang Ryu, Steven Lin, Jun Shao, Jing Song, Min Chen,
Wei Wang, Hanfen Li, Wen Yi, and Peng George Wang...............93
7 High-Throughput Cloning for Proteomics Research
Sharon A. Doyle................................................................................107
8 Screening for the Expression of Soluble Recombinant Protein
inEscherichia coli
Sharon A. Doyle................................................................................115
9 High-Throughput Purification of Hexahistidine-Tagged Proteins
Expressed in E. coli
Michael B. Murphy and Sharon A. Doyle.........................................123
vii
viii Contents
10 The Wheat Germ Cell-Free Expression System:
Methods for High-Throughput Materialization
of Genetic Information
Tatsuya Sawasaki, Mudeppa D. Gouda, Takayasu Kawasaki,
Takafumi Tsuboi, Yuzuru Tozawa, Kazuyuki Takai,
and Yaeta Endo.............................................................................131
11 Advances in Genome-Wide Protein Expression
Using the Wheat Germ Cell-Free System
Yaeta Endo and Tatsuya Sawasaki....................................................145
12 Production of Proteins for NMR Studies
Using the Wheat Germ Cell-Free System
Toshiyuki Kohno...............................................................................169
13 Adenoviral Expression of Reporter Proteins
for High-Throughput Cell-Based Screening
Jon Hoyt and Randall W. King..........................................................187
14 Fabrication of Protein Function Microarrays
for Systems-Oriented Proteomic Analysis
Jonathan M. Blackburn and Darren J. Hart......................................197
15 Peptide and Small-Molecule Microarrays
Jan Marik and Kit S. Lam..................................................................217
16 Peptide Mass Fingerprinting: Protein Identification
Using MALDI-TOF Mass Spectrometry
Judith Webster and David Oxley......................................................227
17 A Practical Protocol for Carbohydrate Microarrays
Ruobing Wang, Shaoyi Liu, Dhaval Shah, and Denong Wang.........241
18 Development of a Yeast Two-Hybrid Screen for Selection
of Human Ras–Raf Protein Interaction Inhibitors
Vladimir Khazak, Erica A. Golemis, and Lutz Weber.......................253
Index ............................................................................................................ 273
Contributors
JONATHAN M. BLACKBURN • Department of Biotechnology, University of the
Western Cape, Cape Town, South Africa; Procognia Ltd, Maidenhead, UK
PAUL R. CARON • Head of Informatics, Vertex Pharmaceuticals,
Cambridge MA
MIN CHEN • The State Key of Microbial Technology, School of Life Science,
Shandong University, Jinan, Shandong, People’s Republic of China
PHILIP M. DEAN • Chief Scientific Officer, De Novo Pharmaceuticals Ltd,
Cambridge, UK
SHARON A. DOYLE • Proteomics Group, DOE Joint Genome Institute, Walnut
Creek, CA
YAETA ENDO • Cell-Free Science and Technology Research Center, Ehime
University, Matsuyama, Japan
IWAN J. P. DE ESCH• Division of Medicinal Chemistry, Leiden/Amsterdam
Center for Drug Research (LACDR), Faculty of Sciences, Vrije
Universiteit, Amsterdam, The Netherlands
ERICA A. GOLEMIS • Division of Basic Sciences, Fox Chase Cancer Center,
Philadelphia, PA
MUDEPPA D. GOUDA • Cell-Free Science and Technology Research Center,
Ehime University, Matsuyama, Japan
CHRIS DE GRAAF • Division of Molecular Toxicology, Leiden/Amsterdam
Center for Drug Research (LACDR), Faculty of Sciences, Vrije
Universiteit, Amsterdam, The Netherlands
GEETA GUPTA • Institute of Biotechnology, University of Cambridge,
Cambridge, UK
DARREN J. HART • High Throughput Group, Grenoble Outstation, European
Molecular Biology Laboratory, Grenoble, France
JON HOYT • Department of Cell Biology, Institute of Chemistry and Cell
Biology, Boston, MA
ALDO JONGEJAN • Division of Medicinal Chemistry, Leiden/Amsterdam
Center for Drug Research (LACDR), Faculty of Sciences, Vrije
Universiteit, Amsterdam, The Netherlands
TAKAYASU KAWASAKI • Cell-Free Science and Technology Research Center,
Ehime University, Matsuyama, Japan
VLADIMIR KHAZAK • Director of Biology, NexusPharma, Langhorne, PA
RANDALL W. KING • Department of Cell Biology, Institute of Chemistry and
Cell Biology, Boston, MA
ix
x Contributors
TOSHIYUKI KOHNO • Laboratory of Structural Biology, Mitsubishi Kagaku
Institute of Life Sciences (MITILS), Tokyo, Japan
KIT S. LAM • Division of Hematology & Oncology, Department of Internal
Medicine, UC Davis Cancer Center, University of California, Davis, CA
ROB LEURS • Division of Medicinal Chemistry, Leiden/Amsterdam Center for
Drug Research (LACDR), Faculty of Sciences, Vrije Universiteit,
Amsterdam, The Netherlands
HANFEN LI • Department of Biochemistry, The Ohio State University,
Columbus, OH
STEVEN LIN • Department of Biochemistry, The Ohio State University,
Columbus, OH
SHAOYI LIU • Columbia Genome Center, Columbia University College of
Physicians & Surgeons, New York, NY
CHRISTOPHER R. LOWE • Institute of Biotechnology, University of Cambridge,
Cambridge, UK
JAN MARIK • Division of Hematology & Oncology, Department of Internal
Medicine, UC Davis Cancer Center, University of California, Davis, CA
MICHAEL B. MURPHY • Proteomics Group, DOE Joint Genome Institute,
Walnut Creek, CA
DAVID OXLEY • Proteomics Research Group, Babraham Institute,
Cambridge, UK
ANA CECÍLIA A. ROQUE • Institute of Biotechnology, University of
Cambridge, Cambridge, UK
KANG RYU • Department of Biochemistry, The Ohio State University,
Columbus, OH
TATSUYA SAWASAKI • Cell-Free Science and Technology Research Center,
Ehime University, Matsuyama, Japan
DHAVAL SHAH • Columbia Genome Center, Columbia University College of
Physicians & Surgeons, New York, NY
JUN SHAO • Department of Biochemistry, The Ohio State University,
Columbus, OH
JING SONG • The State Key of Microbial Technology, School of Life Science,
Shandong University, Jinan, Shandong, People’s Republic of China
KAZUYUKI TAKAI • Cell-Free Science and Technology Research Center,
Ehime University, Matsuyama, Japan
YUZURU TOZAWA • Cell-Free Science and Technology Research Center,
Ehime University, Matsuyama, Japan
TAKAFUMI TSUBOI • Cell-Free Science and Technology Research Center,
Ehime University, Matsuyama, Japan