Protein Purification Protocols

473 Pages·2004·3.36 MB·English

by  Shawn Doonan, Paul Cutler (auth.), Paul Cutler (eds.)

Protein Purification Protocols
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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 ™
Protein Purification
Protocols
Second Edition
Edited by
Paul Cutler
Genomic and Proteomic Sciences, Medicines Research Center,
GlaxoSmithKline Pharmaceuticals, Stevenage, UK
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Protein Purification Protocols.--2nd ed. / edited by Paul Cutler.
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Includes bibliographical references and index.
ISBN 1-58829-067-0 (alk. paper) e-ISBN 1-59259-655-X
ISSN 1064-3745
1. Proteins--Purification--Laboratory manuals.
[DNLM: 1. Proteins--isolation & purification--Laboratory Manuals. QU
25 P967 2004] I. Cutler, Paul, 1962- II. Methods in molecular biology
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Preface
The first edition of Protein Purification Protocols (1996), edited by Professor Shawn
Doonan, rapidly became very successful. Professor Doonan achieved his aims of pro-
ducing a list of protocols that were invaluable to newcomers in protein purification and
of significant benefit to established practitioners. Each chapter was written by an expe-
rienced expert in the field. In the intervening time, a number of advances have war-
ranted a second edition. However, in attempting to encompass the recent developments
in several areas, the intention has been to expand on the original format, retaining the
concepts that made the initial edition so successful. This is reflected in the structure of
this second edition. I am indebted to Professor Doonan for his involvement in this new
edition and the continuity that this brings.
Each chapter that appeared in the original volume has been reviewed and updated to
reflect advances and bring the topic into the 21st century. In many cases, this reflects
new applications or new matrices available from vendors. Many of these have increased
the performance and/or scope of the given method. Several new chapters have been
introduced, including chapters on all the currently used protein fractionation and chro-
matographic techniques. They introduce the theory and background for each method,
providing lists of the equipment and reagents required for their successful execution,
as well as a detailed description of how each is performed. The Notes section consti-
tutes a reference guide on the issues and pitfalls that may be encountered and provides
the means for circumventing or overcoming them effectively.
Around the time of the first edition, the concept of proteomics was being forged and
has subsequently led to a rapid growth in a new and exciting area of protein isolation
and analysis. Techniques such as two-dimensional gel electrophoresis have now entered
the mainstream, not only in analysis, but also as a preparative technique for protein
characterization. Even newer techniques combine with analytical chromatography as
multidimensional separations of proteins and peptides. In combination with mass spec-
trometric techniques, these are now the most powerful methods for isolating proteins.
Protein Purification Protocols reflects these developments, with chapters encompass-
ing all the current thinking. In addition, since the advance of technology means that
simple spectrometric detection is no longer the only option for separating proteins, the
various methods for detecting proteins are covered.
Each chapter is designed to allow a particular step of a purification to be performed
in isolation; however, it is understood that a number of steps may need to be run in
sequence from initial sample fractionation (e.g., tissue homogenization) to chromatog-
raphy and final polishing steps (e.g., buffer exchange). Our book’s format allows for
this, and the initial chapter addresses strategies that should place the various method-
ologies in context. At the end of the book it was also felt timely to include brief
descriptions of how to scale-up purification methods and evaluate the purification of
proteins for therapeutic use. These do not rigidly follow the regular pattern for the main
body of protocols, but should give an insight into the strategies needed for different
final applications.
Paul Cutler
v
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Contents
Preface ...........................................................................................................................v
Contributors ..................................................................................................................xi
1 General Strategies
Shawn Doonan and Paul Cutler............................................................................1
2 Preparation of Extracts From Animal Tissues
J. Mark Skehel.....................................................................................................15
3 Protein Extraction From Plant Tissues
Roger J. Fido, E. N. Clare Mills, Neil M. Rigby, and Peter R. Shewry................21
4 Extraction of Recombinant Protein From Bacteria
Anne F. McGettrick and D. Margaret Worrall...................................................29
5 Protein Extraction From Fungi
Paul D. Bridge, Tetsuo Kokubun, and Monique S. J. Simmonds.........................37
6 Subcellular Fractionation of Animal Tissues
Norma M. Ryan...................................................................................................47
7 Subcellular Fractionation of Plant Tissues: Isolation
of Plastids and Mitochondria
Alyson K. Tobin and Caroline G. Bowsher.........................................................53
8 The Extraction of Enzymes From Plant Tissues Rich in Phenolic Compounds
William S. Pierpoint............................................................................................65
9 Avoidance of Proteolysis in Extracts
Robert J. Beynon and Simon Oliver (Revised by Paul Cutler)............................75
10 Concentration of Extracts
Shawn Doonan....................................................................................................85
11 Making and Changing Buffers
Shawn Doonan....................................................................................................91
12 Purification and Concentration by Ultrafiltration
Paul Schratter (Revised by Paul Cutler)............................................................101
13 Bulk Purification by Fractional Precipitation
Shawn Doonan..................................................................................................117
14 Ion-Exchange Chromatography
Chris Selkirk......................................................................................................125
15 Hydrophobic Interaction Chromatography
Paul A. O’Farrell...............................................................................................133
16 Affinity Chromatography
Paul Cutler........................................................................................................139
17 Dye-Ligand Affinity Chromatography
Anne F. McGettrick and D. Margaret Worrall.................................................151
vii
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viii Contents
18 Lectin Affinity Chromatography
Iris West and Owen Goldring (Revised by Paul Cutler)...................................159
19 Immunoaffinity Chromatography
Paul Cutler........................................................................................................167
20 Immobilized Metal-Ion Affinity Chromatography
Tai-Tung Yip and T. William Hutchens (Revised by Paul Cutler).....................179
21 Chromatography on Hydroxyapatite
Shawn Doonan..................................................................................................191
22 Thiophilic Affinity Chromatography and Related Methods
Paul Matejtschuk...............................................................................................195
23 Affinity Precipitation Methods
Jane A. Irwin and Keith F. Tipton.....................................................................205
24 Isoelectric Focusing
Reiner Westermeier..........................................................................................225
25 Chromatofocusing
Timothy J. Mantle and Patricia Noone.............................................................233
26 Size-Exclusion Chromatography
Paul Cutler........................................................................................................239
27 Fast Protein Liquid Chromatography
David Sheehan and Siobhan O’Sullivan...........................................................253
28 Reversed-Phase Chromatography of Proteins
William A. Neville.............................................................................................259
29 Extraction of Membrane Proteins
Kay Ohlendieck.................................................................................................283
30 Removal of Detergent From Protein Fractions
Kay Ohlendieck.................................................................................................295
31 Purification of Membrane Proteins
Kay Ohlendieck.................................................................................................301
32 Lyophilization of Proteins
Ciarán Ó’Fágáin................................................................................................309
33 Storage of Pure Proteins
Ciarán Ó’Fágáin................................................................................................323
34 Electroelution of Proteins From Polyacrylamide Gels
Michael J. Dunn................................................................................................339
35 Electroblotting of Proteins From Polyacrylamide Gels
Michael J. Dunn................................................................................................345
36 Two-Dimensional Polyacrylamide Gel Electrophoresis
for Proteome Analyses
Neil A. Jones......................................................................................................353
37 Microscale Solution Isoelectrofocusing: A Sample Prefractionation
Method for Comprehensive Proteome Analysis
Xun Zuo and David W. Speicher......................................................................361
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Contents ix
38 Practical Column Chromatography
Shawn Doonan..................................................................................................377
39 Detection Methods
Jacek Mozdzanowski and Sudhir Burman........................................................389
40 Peptide Proteomics
Dean E. McNulty and J. Randall Slemmon.......................................................411
41 Multidimensional Liquid Chromatography of Proteins
Rod Watson and Tim Nadler.............................................................................425
42 Mass Spectrometry
David J. Bell......................................................................................................447
43 Purification of Therapeutic Proteins
Julian Bonnerjea................................................................................................455
44 Purification Process Scale-Up
Karl Prince and Martin Smith...........................................................................463
Index .........................................................................................................................481
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Contributors
DAVID J. BELL • Genomic and Proteomic Sciences, Medicines Research Center,
GlaxoSmithKline Pharmaceuticals, Stevenage, UK
ROBERT J. BEYNON • Protein Function Group, Faculty of Veterinary Science,
University of Liverpool, Liverpool, UK
JULIAN BONNERJEA • Lonza Biologics, Slough, UK
CAROLINE G. BOWSHER • School of Biological Sciences, University of Manchester,
Manchester, UK
PAUL D. BRIDGE • School of Biological and Chemical Sciences, University of London,
London, UK and Mycology Section, Royal Botanic Gardens, Kew, Richmond, UK
SUDHIR BURMAN • Biopharmaceutical Analytical Development, GlaxoSmithKline
Pharmaceuticals, King of Prussia, PA
PAUL CUTLER • Genomic and Proteomic Sciences, Medicines Research Center,
GlaxoSmithKline Pharmaceuticals, Stevenage, UK
SHAWN DOONAN • School of Biosciences, University of East London, UK
MICHAEL J. DUNN • Department of Neuroscience, Institute of Psychiatry, King’s
College London, London, UK
ROGER J. FIDO • Long Ashton Research Station, Department of Agricultural Sciences,
University of Bristol, Bristol, UK
OWEN GOLDRING • North East Surrey College of Technology, Ewell, Surrey, IK
T. WILLIAM HUTCHENS • LumiCyte Inc., Fremont, CA
JANE A. IRWIN • Department of Veterinary Physiology and Biochemistry, University
College Dublin, Dublin, Ireland
NEIL A. JONES • Genomic and Proteomic Sciences, Medicines Research Center,
GlaxoSmithKline Pharmaceuticals, Stevenage, UK
TETSUO KOKUBUN • Biological Interactions Section, Royal Botanic Gardens, Kew,
Richmond, UK
TIMOTHY J. MANTLE • Department of Biochemistry, Trinity College, Dublin, Ireland
ANNE F. MCGETTRICK • Department of Biochemistry Trinity College, Dublin, Ireland
DEAN E. MCNULTY • Department of Computational, Analytical, and Structural
Sciences, GlaxoSmithKline Pharmaceuticals, King of Prussia, PA
PAUL MATEJTSCHUK • National Institute for Biological Standards and Control, South
Mimms, Potters Bar, UK
E. N. CLARE MILLS • Institute of Food Research, Norwich Laboratory, Norwich, UK
JACEK MOZDZANOWSKI • Biopharmaceutical Analytical Development, GlaxoSmithKline
Pharmaceuticals, King of Prussia, PA
TIM NADLER • Applied Biosystems, Framingham, MA
WILLIAM A. NEVILLE • Safety Assessment, GlaxoSmithKline Pharmaceuticals, Ware, UK
PATRICIA NOONE • Department of Biochemistry, Trinity College, Dublin, Ireland
CIARÁN Ó’FÁGÁIN • School of Biotechnology, Dublin City University, Dublin, Ireland
PAUL A. O’FARRELL • W. M. Keck Structural Biology Laboratory, Cold Spring
Harbor Laboratory, Cold Spring Harbor, NY
xi
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xii Contributors
SIMON OLIVER • Department of Biochemistry and Applied Microbiology, UMIST,
Manchester, UK
SIOBHAN O’SULLIVAN • Department of Biochemistry and Analytical and Biological
Chemistry Research Facility, University College Cork, Mardyke, Cork, Ireland
KAY OHLENDIECK • Department of Biology, National University of Ireland, Maynooth,
Ireland
WILLIAM S. PIERPOINT • Rothamsted Research, Harpenden, UK
KARL PRINCE • Lonza Biologics, Portsmouth, NH
NEIL M. RIGBY • Institute of Food Research, Norwich Laboratory, Norwich, UK
NORMA M. RYAN • Department of Biochemistry, University College, Cork, Ireland
PAUL SCHRATTER • Millipore Corporation, Bedford, MA
CHRIS SELKIRK • Biotherapeutics Development Unit, Cancer Research UK, South
Mimms, UK
DAVID SHEEHAN • Department of Biochemistry and Analytical and Biological
Chemistry Research Facility, University College Cork, Mardyke, Cork, Ireland
PETER R. SHEWRY • Long Ashton Research Station, Department of Agricultural
Sciences, University of Bristol, Bristol, UK
J. MARK SKEHEL • Genomic and Proteomic Sciences, Medicines Research Center,
GlaxoSmithKline Pharmaceuticals, Stevenage, UK
MONIQUE S. J. SIMMONDS • Biological Interactions Section, Royal Botanic Gardens,
Kew, Richmond, UK
J. RANDALL SLEMMON • Department of Genomics and Biotechnology, Pharmacia
Corporation, Skokie, IL
MARTIN SMITH • Lonza Biologics, Slough, UK
DAVID W. SPEICHER • The Wistar Institute, Philadelphia, PA
KEITH F. TIPTON • Department of Biochemistry, Trinity College, Dublin, Ireland
ALYSON K. TOBIN • Plant Science Laboratory, School of Biology, Sir Harold
Mitechell Building, University of St Andrews, St. Andrews, Scotland, UK
ROD WATSON • Applied Biosystems, Warrington, UK
IRIS WEST • North East Surrey College of technology, Ewell, Surrey, UK
REINER WESTERMEIER • Amersham Biosciences Europe GmbH, Freiburg, Germany
D. MARGARET WORRALL • Department of Biochemistry and Conway Institute
for Biomolecular and Biomedical Research, University College Dublin,
Dublin, Ireland
TAI-TUNG YIP • Ciphergen Biosystems Inc., Fremont, CA
XUN ZUO • The Wistar Institute, Philadelphia, PA
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