Table Of ContentR. M. KAMP D. KYRIAKIDIS TH. CHOLI-PAPADOPOULOU (Eds.)
Proteome and Protein Analysis
Springer
Berlin
Heidelberg
New York
Barcelona
Hong Kong
London
Milan
Paris
Singapore
Tokyo
R. M. Kamp D. Kyriakidis
Th. Choli-Papadopoulou (Eds.)
Proteome and
Protein Analysis
With 147 Figures
Springer
Prof. Dr. ROZA MARIA KAMP
Technische Fachhochschule Berlin, FBV (Biotechnologie)
SeestraBe 65
D-13347 Berlin
Germany
E-mail: [email protected]
Prof. Dr. DIMITRIS KYRIAKIDIS
Aristotelian University Thessaloniki
School of Chemistry, Laboratory of Biochemistry
Thessaloniki, 54006
Greece
E-mail: [email protected]
Ass. Prof. Dr. THEODORA CHOLI-PAPADOPOULOU
Aristotelian University Thessaloniki
School of Chemistry, Laboratory of Biochemistry
Thessaloniki, 54006
Greece
E-mail: [email protected]
Selected papers presented at Xiith International Conference on Methods in Pro
tein Structure Analysis (MPSA) September 1998, Halkidiki, Greece
Library of Congress Cataloging-in-Publication Data
Proteome and protein analysis I R.M. Kamp, D. Kyriakidis, Th. Choli - Papadopoulou
(eds.). p.cm. Includes bibliographical references and index.
ISBN-13: 978-3-642-64060-5 e-ISBN-13: 978-3-642-59631-5
001: 10.1007/978-3-642-59631-5
l. Proteins-Analysis. I. Kamp, R. M. (Roza Maria), 1951- . II. Kyriakidis,
D. (Dimitris), 1948- . III. Choli-Papadopoulou, Th. (Theodora), 1956-
QP55l.P7553 1999 572'.633-dc21
This work is subject to copyright. All rights are reserved, whether the whole or part
of the material is concerned, specifically the rights of translation, reprinting, reuse of
illustrations, recitation, broadcasting, reproduction on microfilm or in any other way,
and storage in data banks. Duplication of this publication or parts thereof is permit
ted only under the provisions of the German Copyright Law of September 9, 1965, in
its current version, and permissions for use must always be obtained from Springer
Verlag. Violations are liable for prosecution under the German Copyright Law.
© Springer-Verlag Berlin Heidelberg 2000
Softcover reprint of the hardcover 1st edition 200
The use of general descriptive names, registered names, trademarks, etc. in this pub
lication does not imply, even in the absence of a specific statement, that such names
are exempt from the relevant protective laws and regulations and therefore free for
general use.
Product liability: The publisher cannot guarantee the accuracy of any information
about dosage and application thereof contained in this book. In every individual case
the user must check such information by consulting the relevant literature.
Cover design: d & P, D-69121 Heidelberg
Typesetting: Mitterweger & Partner Kommunikationsgesellschaft mbH
Production: PRO EDIT GmbH, D-69126 Heidelberg
SPIN 10689115 3113136 5 4 3 2 1 0 - Printed on acid free paper
To Don Sheer Memory
Dr. Donald Sheer and his wife, Diane, were aboard Swissair
Fllight 111 when it crashed off the coast of Nova Scotia on Sep
tember 2, 1998. There were no survivors. The news of their
untimely deaths came as a shock to all of those who knew the cou
pIe.
Don was Consulting Scientist in the Analytical Division of Mil
lip ore Corp. where he was active in the development of new sepa
ration products and applications for the research, biotech and
pharmaceutical industries. Don had worked in the Millipore/
Amicon organizations for over 5 years and had contributed
greatly to setting the product development targets for innovative
products. Don worked closely with scientists in many fields of
technology and his ability to establish collaborative projects was
legendary.
Don's most recent effort was developing applications for a new
Millipore product named ZipTipsTM, which are novel sample
preparation devices containing absorptive resins that allow the
VI To Don Sheer Memory
cleanup and concentration of microliter volumes of solution. Don
was traveling to Halkidiki, Greece to present a paper at the XIIth
International Conference on Methods in Protein Structure Analy
sis on this new technology.
Before Millipore, Don worked as Associate Director of Protein
Chemistry at Ares Technology (Serono Labs) and as a Senior Sci
entist at Genesis Pharmaceuticals in the Boston area. Prior to that
he worked in the Protein Applications Group at Applied Biosys
terns Inc. in Foster City, CA. He also spent five years as a Biotech
nology Training Fellow at the National Cancer Institute in
Bethesda, MD.
Don received his doctorate degree in Biochemistry from the
University of Arizona (1983) and an undergraduate degree in
Chemistry from Ohio State (1976).
Don was an unique character dedicated to his work and was
known to many researchers around the world. He will be missed
by all.
May 1999 RICK GARRETSON
MILLIPORE CORPORATION
Preface
This book includes selected papers presented at the XlIth Interna
tional Conference on Methods in Protein Structure Analysis
(MPSA), which took place in Halkidiki, Greece, in September
1998, under a scientific atmosphere, good weather and the spirit
of the greek philosopher Aristotle, who was born in that area of
Greece. To insure the highest quality and the most rapid publica
tion, the MPSA Book Advisory subcommittee has chosen for the
book the most interesting and useful presentations from the
meeting. This book includes papers covering new, sensitive and
rapid methodologies, as well as various aspects of the Protein
Chemistry field, reflecting the multidisciplinary nature of the
problems concerning the analysis of the total cell proteins, namely
proteome, a term which was first used in 1994 at the Siena 2D
Electrophoresis meeting. So, we finally decided on the title of
"Proteome and Protein Analysis", which indeed corresponds to
our thoughts and to the wishes of most scientists, as we believe, in
the protein area.
Several methodologies from different fields, like Edman degra
dation, DNA sequencing, mass spectrometry have to be combined
for an elaborate study of proteins' function in biological pro
cesses. For example the combination of mass spectrometry tech
niques with proteome analysis answers a large number of scien
tific questions.
Different mass spectrometry methods such as MALDI, ESI - or
Nano Electrospray are described and discussed for their use in
proteome and protein analysis. The importance of the mass spec
trometry in proteome and protein analysis was acknowledged with
the presentation of the Edman Award 1998 to three mass spec
trometry experts: Matthias Mann, Matthias Wilm and John Yates.
We believe that this book contains new and interesting contri
butions to bioscience, describing new methodologies, new devel
opments on structural studies, functional implication of proteins,
NMR analysis, database searches of multi-alignments and mass
spectrometry analysis of proteins.
The chapters have been written by scientists with extensive
experience in these fields. The contributors of this volume are all
VIII Preface
active researchers in various aspects of protein study and they
have attempted to guide the reader by introducing briefly their
subject and giving details for experimental work, which in their
own experience give good results.
We express our great sorrow at the loss of both Dr. Don Sheer,
coworker of Millipore, and his wife, whose tragic death, after an
airplane crash on the way from USA to Greece, was announced
before the opening ceremony of the XIIth International MPSA.
We would like to acknowledge all contributors of this volume,
the participants of the XIIth MPSA for their active contribution as
well as Springer-Verlag for their kind offer to publish this work.
We are grateful to the conference Book Advisory subcommittee
Drs C.W. Anderson, E. Appella and B. Wittmann-Liebold for all
their efforts to select the most important topics.
We hope that this volume will stimulate further research in the
field of Protein Chemistry and be beneficial because of the new
and interesting ideas it introduces.
May 1999 The Editors
Contents
Part I Proteomics and Mass Spectrometry
Chapter 1 Strategies and Methods for Proteome Analysis ............ 3
D. R. GOODLETT, A. TIM PERMAN, S. P. GYGI, J. WATTS,
G. CORTHALS, D. FIGEYS and R. AEBERSOLD
Chapter 2 Protein Sequencing or Genome Sequencing.
Where Does
Mass Spectrometry Fit into the Picture? .................. 15
P. ROEPSTORFF
Chapter 3 Reversible Negative Staining of Protein on Electrophoresis
Gels by Imidazole-Zinc Salts: Micropreparative Applications
to Proteome Analysis by Mass Spectrometry .............. 29
1. R. CASTELLANOS-SERRA, E. HARDY, W. PROENZA,
V. HUERTA, 1. J. GONZALEZ, J. P. LE CAER, R. 1. MORITZ
and R. J. SIMPSON
Chapter 4 Direct Analysis of Protein Complexes .................... 53
J. R. YATES, A. J. LINK, D. SCHIELTZ, J. K. ENG
Chapter 5 De novo Sequencing of Proteins With Mass Spectrometry
...............
Using the Differential Scanning Technique 65
M. WILM, G. NEUBAUER, 1. TAYLOR, A. SHEVCHENKO,
A. BACH!
Chapter 6 Characterization Of Gel Separated Proteins ............... 81
A.-CH. BERGMAN, M. OPPERMANN, U. OPPERMANN,
H. J(IRNVALL and T. BERGMAN
Part II Structure Analysis
Chapter 7 Protein Structure and Dynamics by NMR in Solution ...... 91
B. BERSCH, M. BLACKLEDGE, B. BRUTSCHER, F. CORDIER,
J.-CH. Hus and D. MARION
x Contents
Chapter 8 Elucidation of Functionally Significant Structural
Modifications by Matrix-Assisted Laser Deorption/Ionization
Time-of-Flight Mass Spectrometry
with Post-Source Decay Analysis ........................ 117
J. J. GORMAN, B. 1. FERGUSON, S. LOPATICKI, J. J. PITT,
A. W. PURCELL and CH. J. MORROW
Chapter 9 Detection of Specific Zinc Finger Peptide Complexes
with Matrix-Assisted Laser Desorption/Ionization Mass
Spectrometry ........................................ 139
E. LEHMANN and R. ZENOBI
Chapter 10 Epitode Mapping for the Monoclonal Antibody that Inhibits
Intramolecular Flavin to Heme Electron Transfer
in Flavocytochrome B2 from Baker's Yeast
(L-Lactate Dehydrogenase) ............................. 149
K. H. DIEP LE, M. MAYER and F. LEDERER
Chapter 11 A MALDI-TOF Mass Spectrometry Approach to Investigate
the Defense Reactions in Drosophila Melanogaster,
an Insect Model for the Study of Innate Immunity ........ 157
P. BULET and S. UTTENWEILER-JOSEPH
Chapter 12 A New Method for the Isolation of the C-Terminal Peptide
of Proteins by the Combination of Selective Blocking
of Proteolytic Peptides and Cation Exchange
Chromatography. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 175
1. J. GONZALEZ, E. TORRES, Y. GARciA, 1. H. BETANCOURT,
G. MOYA, V. HUERTA, V. BESADA and G. PADRON
Chapter 13 The Folding Pathway of Disulfide Containing Proteins ..... 189
J.-Y. CHANG
Chapter 14 Cavity Supported HPLC of cis/trans Isomers of Proline
Containing Peptides Using Cyclodextrins and Calixarenes .. 199
S. MENGE, S. GEBAUER and G.-J. KRAUSS
Chapter 15 The Perception of Hydrophobic Clusters in the Native
and Partially Unfolded States of a Protein ................ 211
G. VANDERHEEREN and I. HANSSENS
Chapter 16 Structure, Dynamics and Function
of the Proton Pump Bacteriorhodopsin .................. 225
G. BULDT, J. HEBERLE, R. SCHLESINGER and H.-J. SASS
