Spectral Techniques In Proteomics 1st Edition

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SPECTRAL
TECHNIQUES
IN
PROTEOMICS
Edited by

DANIEL S. SEM

Boca Raton London New York

CRC Press is an imprint of the

Taylor & Francis Group, an informa business
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CRC Press
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© 2007 by Taylor & Francis Group, LLC
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Library of Congress Cataloging-in-Publication Data

Spectral techniques in proteomics / editor, Daniel S. Sem.

p. ; cm.
“A CRC title.”
Includes bibliographical references and index.
ISBN-13: 978-1-57444-580-0 (alk. paper)
ISBN-10: 1-57444-580-4 (alk. paper)
1. Proteins--Spectra. 2. Proteomics--Methodology. 3. Mass spectrometry. I.
Sem, Daniel S.
[DNLM: 1. Proteomics--methods. 2. Mass Spectrometry--methods. 3.
Spectrum Analysis--methods. QU 58.5 S741 2007]

QP551.S675 2007
572’.633--dc22 2006103310

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Dedication
In loving thanks to my wife, Teresa, and children, Lucas, Camille, and Isaac,
for being a constant source of inspiration and support and for tolerating
the countless hours I had to spend immersed in my laptop.
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Table of Contents
Preface....................................................................................................................... xi
Editor ......................................................................................................................xiii
Contributors ............................................................................................................. xv
Abbreviations .......................................................................................................... xix

PART I The Scope of Proteomic and

Chemical Proteomic Studies

Chapter 1 The Systems-Based Approach to Proteomics and

Chemical Proteomics ........................................................................... 3
Daniel S. Sem

Chapter 2 Similarities in Protein Binding Sites ................................................. 13

Hugo O. Villar, Mark R. Hansen, and Richard Kho

Chapter 3 Survey of Spectral Techniques Used to Study Proteins.................... 25

Daniel S. Sem

PART II Mass Spectral Studies of Proteome and

Subproteome Mixtures

Chapter 4 Capillary Electrophoresis—Mass Spectrometry for

Characterization of Peptides and Proteins......................................... 47
Christian Neusüß and Matthias Pelzing

Chapter 5 Protein and Peptide Analysis by Matrix-Assisted Laser

Desorption/Ionization Tandem Mass Spectrometry
(MALDI MS/MS) .............................................................................. 67
Emmanuelle Sachon and Ole Nørregaard Jensen

Chapter 6 Characterization of Glycosylated Proteins by Mass Spectrometry

Using Microcolumns and Enzymatic Digestion................................ 81
Per Hägglund and Martin R. Larsen
vii
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viii Table of Contents

Chapter 7 Surface-Enhanced Laser Desorption/Ionization Protein Biochip

Technology for Proteomics Research and Assay Development ..... 101
Scot R. Weinberger, Lee Lomas, Eric Fung, and
Cynthia Enderwick

Chapter 8 An Approach to the Reproducibility of SELDI Profiling............... 133

Walter S. Liggett, Peter E. Barker, Lisa H. Cazares, and
O. John Semmes

PART III Protein–Protein (or Peptide) Interactions:

Studies in Parallel and with Mixtures

Chapter 9 Mass Spectrometric Applications in Immunoproteomics ............... 157

Anthony W. Purcell, Nicholas A. Williamson, Andrew I. Webb, and
Kim Lau

Chapter 10 Near-Infrared Fluorescence Detection of Antigen–Antibody

Interactions on Microarrays ............................................................. 185
Vehary Sakanyan and Garabet Yeretssian

Chapter 11 Application of Shotgun Proteomics to Transcriptional

Regulatory Pathways........................................................................ 207
Amber L. Mosley and Michael P. Washburn

Chapter 12 Electrophoretic NMR of Protein Mixtures and

Its Proteomic Applications............................................................... 223
Qiuhong He, Sunitha B. Thakur, and Jeremy Spater

PART IV Chemical Proteomics: Studies of

Protein–Ligand Interactions in
Pools and Pathways

Chapter 13 Characterizing Proteins and Proteomes Using Isotope-Coded

Mass Spectrometry........................................................................... 255
Uma Kota and Michael B. Goshe
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Table of Contents ix

Chapter 14 Surface Plasmon Resonance Biosensors’ Contributions to

Proteome Mapping........................................................................... 287
Rebecca L. Rich and David G. Myszka

Chapter 15 Application of In-Cell NMR Spectroscopy to

Investigation of Protein Behavior and Ligand–Protein Interaction
inside Living Cells ........................................................................... 305
Volker Dötsch

Chapter 16 An Overview of Metabonomics Techniques and Applications....... 321

John C. Lindon, Elaine Holmes, and Jeremy K. Nicholson

PART V Structural Proteomics:

Parallel Studies of Proteins

Chapter 17 NMR-Based Structural Proteomics ................................................. 349

John L. Markley

Chapter 18 Leveraging X-Ray Structural Information in Gene

Family-Based Drug Discovery: Application to Protein Kinases .... 373
Marc Jacobs, Harmon Zuccola, Brian Hare, Alex Aronov,
Al Pierce, and Guy Bemis

Chapter 19 EPR Spectroscopy in Genome-Wide Expression Studies............... 391

Richard Cammack

PART VI Summary

Chapter 20 Summary of Chapters and Future Prospects for

Spectral Techniques in Proteomics.................................................. 409
Daniel S. Sem

Index ...................................................................................................................... 421

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Preface
A significant challenge in presenting an overview of Spectral Techniques in Proteomics
is in defining the scope of the topic. Proteomics means different things to different
people; for years, the dominant technique employed was 2D gel electrophoresis,
followed by mass spectrometry (MS). While many exciting MS applications are
presented (e.g., matrix-assisted laser desorption/ionization [MALDI], electrospray
ionization [ESI], tandem MS, liquid chromatography [LC]-MS, surface-enhanced
laser desorption/ionization [SELDI], isotope-coded affinity tag [ICAT]), a comprehen-
sive survey of MS methods and applications in proteomics is certainly beyond the
scope of this book. Since Spectral Techniques in Proteomics is intended for a broad
audience of protein biochemists and biophysicists, topics such as structural proteomics
and chemical proteomics will also be covered, along with fluorescence/array-based
screening, SPR (surface plasmon resonance), and other “lab-on-a-chip” technologies.
Furthermore, a disproportionate amount of time will be spent on some less
established spectroscopic methods in proteomics, with forward-looking speculation
on future applications. The intention of this book is therefore to facilitate the inno-
vation, development, and application of new spectroscopic methods in proteomics
while giving a modest overview of existing and proven techniques. To this end, a
broader view of proteomics is taken in order to include studies that go beyond the
usual scope of 2D gels and MS, attempting to address function and mechanism at
the level of protein–ligand interactions. After all, this is the realm in which protein
spectroscopists have always excelled and felt most at home.
Proteomics is defined broadly as the “systems-based” study of proteins in the
organelles, cells, tissues, or organs of an organism. It is the study of the protein
complement of the genome in time and space. In practice, this definition sometimes
limits proteomics to the study of proteins in 2D gels, since this is one of the few
contexts in which so many proteins can be studied at once. It is also possible to simplify
a proteome into a more manageable subset (a subproteome) by focusing on a smaller
number of proteins related in a systems-based manner. Such systems of interrelated
proteins can include: (1) regulatory cascades connected via protein–protein inter-
actions; (2) metabolic pathways; (3) proteins with related modifications (acylation,
phosphorylation, glycosylation, methylation, etc.); and (4) any collection of proteins
associated with a biological effect, such as uncontrolled cell growth (cancer), an
immune response, or drug metabolism. This approach to simplifying a proteome
into systems-related subproteomes is described in chapter 1.
Thus, for purposes of this book, proteomic studies are extended to include the
parallel study of subsets of related proteins, some of which were described previously.
Such subsets might also include proteins that comprise a unique basis set of protein
folds in an organism’s proteome, as currently defines the scope of most structural
proteomic initiatives. Another systems-related subset could comprise proteins with
xi
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xii Preface

similar binding sites (chapter 2), as currently defines the scope of chemical proteomic
studies. In this case, the subset of proteins can be considered to be part of a
biologically relevant network in the sense that they represent all of the protein–ligand
interactions that would occur when an organism is exposed to a given chemical
perturbant (drug, pollutant, chemical genetic probe, etc.). One prominent example
of such systems-related proteins is those that use the same cofactor or prosthetic
group, such as kinases, which all bind ATP (chapter 18).
This broader definition of proteomics and systems-based studies is not only a
convenience for framing proteome-wide questions, but also has biological relevance.
This book aims to provide a broad overview of the spectroscopic toolbox that can
be applied in such systems-based studies of proteins, whether they are studied in
the context of proteome or subproteome mixtures (traditional proteomics) or as
individual/purified proteins studied in parallel (the broader, systems-based view of
proteomics), as in structural proteomics.
This book begins in part I by defining the scope of the field in order to give
coherence to the chapters from the various expert contributors. Proteomics is defined
in a way that is relevant to a spectroscopist (chapters 1 and 2) and then a very brief
overview of commonly used spectroscopic methods is given (chapter 3). In part II,
commonly used MS methods are presented, including separation techniques that
typically precede ESI studies, as well as MALDI MS/MS-based protein identifica-
tion. SELDI is presented as a tool that combines separation with MS analysis on
the same chip. Part III focuses on studies of protein–protein interactions using a
variety of techniques, including near-infrared (NIR) fluorescence, nuclear magnetic
resonance (NMR), and MS. Part IV covers protein–ligand interactions with tech-
niques ranging from MS to SPR to NMR. Recent developments in ICAT labeling
strategies are covered, and the section ends with a discussion of metabonomics, since
metabolites represent an important functional output of the proteome. Part V covers
advances in structural proteomics using NMR, x-ray crystallography, and electron
paramagnetic resonance (EPR). The book ends with chapter 20, a summary of current
technology and future prospects extracted from the various contributors, again to
give added coherence to the topic.
Spectral Techniques in Proteomics will be useful for graduate students and other
scientists wanting to develop and apply spectroscopic methods in proteomics. It will
also be of value to more experienced researchers thinking of moving into this field
or those in proteomics looking to broaden the scope of their studies. In short, it is
intended for anyone wanting to take a systems-based approach to studying proteins,
their function, and their mechanisms using various spectroscopic tools.

Daniel Sem
DK3714_C000.fm Page xiii Friday, February 16, 2007 3:37 PM

Editor
Daniel Sem is an assistant professor in the chemistry department at Marquette
University in Milwaukee, Wisconsin. He also serves as director of the Chemical
Proteomics Facility at Marquette (CPFM) and is a member of the Marine and
Freshwater Biomedical Sciences Center at the University of Wisconsin–Milwaukee
in the endocrine disruptor core group. His current research is focused on the devel-
opment and application of chemical proteomic probes for the study of protein–ligand
interactions. Emphasis is on fluorescence and NMR-based assays, as well as on
proteins that are drug targets and proteins that are antitargets, leading to the adverse
and toxic side effects of drugs and pollutants.
Prior to joining Marquette, Dr. Sem cofounded Triad Therapeutics in San Diego,
California, where he served as vice-president for biophysics. In that capacity, he was
involved in NMR-based characterization of large protein–ligand complexes, chem-
informatic characterization of combinatorial libraries, bioinformatic analysis of gene
families, high-throughput screening, and enzymology/assay development. Triad was
the first company founded around NMR-driven, structure-based drug design. It had
a technology based on a systems-based approach to drug design, targeting gene
families of proteins like kinases and dehydrogenases with focused combinatorial
chemistry libraries.
Dr. Sem graduated from the University of Wisconsin–Milwaukee with a B.S. in
chemistry (summa cum laude) and from University of Wisconsin–Madison with a
Ph.D. in biochemistry, specializing in mechanistic enzymology. He then pursued
postdoctoral studies at McArdle Laboratory for Cancer Research (Madison,
Wisconsin), followed by the Scripps Research Institute (La Jolla, California), where
he did NMR-based structural biology. He has 20 years of experience using spectral
techniques to study protein–ligand interactions in basic and applied research settings.

xiii
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Contributors
Alex Aronov Eric Fung
Vertex Pharmaceuticals Incorporated Ciphergen Biosystems Inc.
Cambridge, Massachusetts Fremont, California

Peter E. Barker Michael B. Goshe

Biotechnology Division Department of Molecular and
National Institute of Standards and Structural Biochemistry
Technology North Carolina State University
Gaithersburg, Maryland Raleigh, North Carolina

Guy Bemis Per Hägglund

Vertex Pharmaceuticals Incorporated Biochemistry and Nutrition Group
Cambridge, Massachusetts Technical University of Denmark
Lyngby, Denmark
Richard Cammack
Mark R. Hansen
Department of Life Sciences
Altoris, Inc.
Pharmaceutical Sciences
San Diego, California
Research Division
King’s College
Brian Hare
London, United Kingdom
Vertex Pharmaceuticals Incorporated
Cambridge, Massachusetts
Lisa H. Cazares
The Center for Biomedical Proteomics Qiuhong He
Eastern Virginia Medical School Departments of Radiology and
Norfolk, Virginia Bioengineering
University of Pittsburgh Cancer Institute
Volker Dötsch MR Research Center,
Institute for Biophysical Chemistry University of Pittsburgh
Center for Biomolecular Magnetic Pittsburgh, Pennsylvania
Resonance
University of Frankfurt Elaine Holmes
Frankfurt, Germany Department of Biomolecular Medicine
Faculty of Medicine
Cynthia Enderwick Imperial College London
Ciphergen Biosystems Inc. South Kensington, London,
Fremont, California United Kingdom

xv
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xvi Contributors

Marc Jacobs John C. Lindon

Vertex Pharmaceuticals Incorporated Department of Biomolecular Medicine
Cambridge, Massachusetts Faculty of Medicine
Imperial College London
Ole Nørregaard Jensen South Kensington, London,
Protein Research Group United Kingdom
Department of Biochemistry and
Molecular Biology Lee Lomas
University of Southern Denmark Ciphergen Biosystems Inc.
Odense, Denmark Fremont, California

Richard Kho John L. Markley

Altoris, Inc. Center for Eukaryotic Structural
San Diego, California Genomics
National Magnetic Resonance Facility
Uma Kota at Madison
Department of Molecular and Biochemistry Department
Structural Biochemistry University of Wisconsin–Madison
North Carolina State University Madison, Wisconsin
Raleigh, North Carolina
Amber L. Mosley
Stowers Institute for Medical Research
Martin R. Larsen
Kansas City, Missouri
Department of Biochemistry and
Molecular Biology David G. Myszka
University of Southern Denmark Center for Biomolecular Interaction
Odense, Denmark Analysis
School of Medicine
Kim Lau University of Utah
Department of Biochemistry and Salt Lake City, Utah
Molecular Biology
Bio21 Molecular Science and Christian Neusüß
Biotechnology Institute Bruker Daltonik GmbH
University of Melbourne Leipzig, Germany
Victoria, Australia
Jeremy K. Nicholson
Walter S. Liggett Department of Biomolecular Medicine
Statistical Engineering Division Faculty of Medicine
National Institute of Standards and Imperial College London
Technology South Kensington, London,
Gaithersburg, Maryland United Kingdom
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Contributors xvii

Matthias Pelzing Jeremy Spater

Bruker Daltonik GmbH Departments of Radiology and
Leipzig, Germany Bioengineering
University of Pittsburgh Cancer Institute
Al Pierce MR Research Center
Vertex Pharmaceuticals Incorporated University of Pittsburgh
Cambridge, Massachusetts Pittsburgh, Pennsylvania

Anthony W. Purcell Sunitha B. Thakur

Department of Biochemistry and Departments of Radiology and
Molecular Biology Bioengineering
Bio21 Molecular Science and University of Pittsburgh Cancer Institute
Biotechnology Institute MR Research Center
University of Melbourne University of Pittsburgh
Victoria, Australia Pittsburgh, Pennsylvania

Rebecca L. Rich Sakanyan Vehary

Center for Biomolecular Interaction ProtNeteomix
Analysis Université de Nantes
School of Medicine Nantes, France
University of Utah
Salt Lake City, Utah
Hugo O. Villar
Altoris, Inc.
Emmanuelle Sachon
San Diego, California
Protein Research Group
Department of Biochemistry and
Molecular Biology Michael P. Washburn
University of Southern Denmark Stowers Institute for Medical Research
Odense, Denmark Kansas City, Missouri

Daniel S. Sem Andrew I. Webb

Chemical Proteomics Facility at Department of Biochemistry and
Marquette Molecular Biology
Department of Chemistry Bio21 Molecular Science and
Marquette University Biotechnology Institute
Milwaukee, Wisconsin University of Melbourne
Victoria, Australia
O. John Semmes
The Center for Biomedical Proteomics Scot R. Weinberger
Eastern Virginia Medical School GenNext Technologies™
Norfolk, Virginia Montara, California