Peptide Arrays on Membrane Supports: Synthesis and Applications

177 Pages·2002·3.35 MB·English

by  Ronald Frank

SPRINGER
LAB MANUALS
Springer-Verlag Berlin Heidelberg GmbH
JOACHIM KOCH MICHAEL MAHLER (EDS.)
Peptide Arrays
on Membrane Supports
Synthesis and Applications
With 31 Figures
i
Springer
JOACHIM KOCH MrCHAEL MAHLER
Forschungsstelle Hantaviren Institut fUr Molekulare Genetik
Heidelberger Akademie Universităt Heidelberg
der Wissenschaften
Current address: Current address:
Institut fUr Biochemie Pharmacia Deutschland GmbH
Biozentrum N210120 Munzinger StraGe 7
Marie-Curie-StraGe 9 79111 Freiburg
60439 Frankfurt am Main Germany
Germany
e-mail: e-mail:
j [e-mail] [e-mail]
Library of Congress Cataloging-in-Publication Data
Peptide arrays on membane supports : synthesis and applications / Joachim Koch,
Michael Mahler (eds.).
p. cm. - (Springer lab manual)
Includes bibliographieal referenees and index.
1. Protein microarray. 1: Koch, Joachim, 1972-II. Mahler, Michael, 1974-III. Series.
QP551 .P394 2002
572'.65-dc21 2001049848
ISBN 978-3-642-07639-8 ISBN 978-3-662-09229-3 (eBook)
DOI 10.1007/978-3-662-09229-3
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Preface
Since protein interactions are of immense interest not only for
basic research but also for applied science purposes, many studies
aim to shed more light on the character of the cross-talk of
proteins, including antibody-antigen, protein-protein and pro
tein-nucleic acid interactions. For this approach, a variety of dif
ferent biochemical and immunological methods, such as Western
blotting or ELISA, have been traditionally used. More recently,
truncation studies and mutational analysis, as well as yeast two
hybrid, phage display and surface plasmon resonance techniques
have been developed and applied to interaction studies in many
disciplines including biochemistry, immunology, cell biology,
developmental and molecular biology. Since all these methods
have their individual limitations, a universal method is not
available at present. In this book, we present a collection of
straightforward methods based on the synthesis of oligopeptides
on activated cellulose membranes that allow the investigation of
protein interactions on a molecular level. This SPOT technology
represents a powerful proteomics technique for a variety of
applications, such as epitope mapping and the analysis of pro
tein-protein and protein-nucleic acid interactions.
Epitope mapping has proven to be important for both basic
research and diagnostic and therapeutic applications. Peptides
comprising the epitope sequence(s) recognized by the majority
of sera from patients with certain infectious or autoimmune
diseases can serve as target antigens for new sensitive and spe
cific diagnostic systems. For therapeutic approaches, knowledge
of the exact binding site of antibodies on their antigen can
further the development of new vaccination strategies against
pathogens. Furthermore, such insights may also be used for the
development of new therapeutic strategies in autoimmune
diseases. Since signal transduction processes are highly complex
VI Preface
and involve a large number of different interacting proteins, it is
obvious that the determination of interaction sites could en
lighten the character of such signal transduction cascades.
Additionally, detailed knowledge of the precise interaction
site(s) may lead to the creation of artificial ligands with thera
peutic relevance in cancer and a variety of other dysfunctions.
The flood of data derived from the deciphering of the human
genome sequence requires technologies to evaluate the bio
logical functions of the discovered open reading frames (ORF)
and to make this knowledge available for basic research and the
development of therapeutic and diagnostic products. During the
last few years, sophisticated micro-array systems for the in
vestigation of protein-protein and protein-DNA interactions
have been under development. The SPOT system, in combination
with these high-throughput systems, may well represent a key
technology to cope with the demand for information on the
cross-talk of proteins.
In this book we provide a detailed overview of the technology,
including insights into basic chemistry and established ap
plications. All protocols have been written by experienced
researchers in SPOT technology and have therefore been
optimized for practical use. We would like to thank all of the
authors for their contribution and we hope that their efforts will
inspire the reader to find new implementations of this technique.
This may, in turn, encourage more scientists to take advantage of
the powerful tool of peptide arrays prepared with the SPOT
method.
Heidelberg, Autumn 2001 JoACHIM KocH
MICHAEL MAHLER
Naturally Occuring Amino Acids
Amino add Three-letter code One-letter code
Alanine Ala A
Arginine Arg R
Asparagine Asn N
Aspartic acid Asp D
c
Cysteine Cys
Glutamine Gln Q
Glutamic acid Glu E
Glycine Gly G
Histidine His H
Isoleucine Ile I
Leucine Leu L
Lysine Lys K
Methionine Met M
Phylalanine Phe F
Proline Pro p
s
Serine Ser
Threonine Thr T
Tryptophane Trp w
Tyrosine Tyr y
v
Valine Val
Contents
Chapter 1
SPOT Synthesis - Scope of Applications
RONALD FRANK and JENS SCHNEIDER-MERGENER . 1
Chapter 2
Chemistry of Fmoc Peptide Synthesis on Membranes
NORBERT ZANDER and HEINRICH GAUSEPOHL 23
Chapter 3
Manual Peptide Synthesis
GABRIELE PETERSEN 41
Chapter4
Automated Synthesis of Solid-Phase Bound Peptides
HEINRICH GAUSEPOHL and CHRISTIAN BEHN 55
Chapter 5
Epitope Mapping of Antibodies with Solid-Phase
0 ligopeptides
JoACHIM KocH, MICHAEL MAHLER,
and MARTIN BLiiTHNER . . . . . . . . . . . . . . . . . . . 69
Chapter 6
Protein-Protein Interactions
MATTHEW R. GROVES and IRMGARD SINNING 83
Chapter 7
Analysis of Protein-DNA Interactions
MoNIKA REUTER and ELISABETH MoNCKE-BUCHNER 97
Chapter 8
Affinity Purification and Competition Assays
Using Solid-Phase Oligopeptides
MICHAEL MAHLER, MARTIN BLijTHNER,
and JOACHIM KOCH . . . . . . . . . . . . . . . . . . . . . . 107
X Contents
Chapter 9
Mutational Analysis and Structure Predictions
MARTIN BLUTHNER, JoACHIM KocH,
and MICHAEL MAHLER . . . . . . . . . . . . . . . . . . . . 123
Chapter 10
Modification of Immobilized Peptides
JoCHEN BODEM and MARTIN BLUTHNER . . . . . . . . . . 141
Chapter 11
Immobilized Peptides to Study Protein-Protein
Interactions - Potential and Pitfalls
RUDIGER BRAUNING, MICHAEL MAHLER,
BARBARA HUGLE-DORR,MARTIN BLUTHNER,
JoACHIM KocH, and GABRIELE PETERSEN 153
Abbreviations 165
Subject Index 167
Chapter 1 OVERVIEW
SPOT Synthesis - Scope of Applications
RONALD FRANK and JENS SCHNEIDER-MERGENER
Introduction
The currently very successful paradigm in scientific research of
applying a systematic empirical search rather than an iterative
rational design to solve complex scientific questions heavily
relies on technologies that allow for a rapid and comprehensive
screening of diverse types of molecular probes. Combinatorial
chemical or biological synthesis applied to molecular biology,
immunology and drug discovery was the technology that paved
the way (Gallop et al. 1994). Massive miniaturization and auto
mation are central and relevant topics in the further develop
ment of these technologies. A steady increase in the number of
probes and samples that can be screened together with further
reductions in the assay dimensions and costs readily allows for
many new applications.
In 1988, Southern reported the synthesis of oligonucleotides
and their arrangement in a micro-scale chessboard pattern on a
planar glass surface, providing a tool in the identification of
individual nucleic acid sequences in the context of the entire
genome (Southern 1988) and initiating another technological
breakthrough: micro-array technology. The impact of this
R. Frank (C'-j) (e-mail: [e-mail], Tel.: [phone], Fax: +49-531-
6181795); AG Molecular Recognition, GBF (German Research Centre for
Biotechnology), Mascheroder Weg 1, 38124 Braunschweig, Germany
J. Schneider-Mergener
Institut fUr Medizinische Immunologie, Medizinische Fakultat,
Humboldt-Universitat zu Berlin, Berlin, Germany
Current address: J. Schneider-Mergener, Jerini AG, Rudower Chaussee 4,
12489 Berlin, Germany
Springer Lab Manual
J. Koch, M. Mahler (Eds.) Peptide Arrays
on Membrane Supports
©Springer-Verlag Berlin Heidelberg 2002