Peptide Antibodies: Methods and Protocols

369 Pages·2015·12.52 MB·English

by  Gunnar Houen (eds.)

Methods in
Molecular Biology 1348
Gunnar Houen Editor
Peptide
Antibodies
Methods and Protocols
M M B
ETHODS IN OLECULAR IOLOGY
Series Editor
John M. Walker
School of Life and Medical Sciences
University of Hertfordshire
Hat fi eld, Hertfordshire, AL10 9AB, UK
For further volumes:
http://www.springer.com/series/7651

Peptide Antibodies
Methods and Protocols
Edited by
Gunnar Houen
Statens Serum Institut, Copenhagen, Denmark
Editor
Gunnar H ouen
Statens Serum Institut
Copenhagen, Denmark
ISSN 1064-3745 ISSN 1940-6029 (electronic)
Methods in Molecular Biology
ISBN 978-1-4939-2998-6 ISBN 978-1-4939-2999-3 (eBook)
DOI 10.1007/978-1-4939-2999-3
Library of Congress Control Number: 2015948252
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Prefa ce
The ability to design and produce peptide antibodies has had a large impact on molecular
cell biology and immunology, including all the different techniques involved (immunoas-
says, immunoprecipitation, immunoblotting, immunohistochemistry, etc).
This large impact is a result of several technical and scientifi c advances: solid phase pep-
tide synthesis, peptide carrier conjugation and immunization, genomics, transcriptomics,
proteomics and elucidation of the molecular basis of antigen presentation and recognition
by dendritic cells, macrophages, B cells, and T cells.
Moreover, although peptide antibodies have been available for many years, they con-
tinue to be a fi eld of active research and method development. For example, peptide anti-
bodies which are dependent on specifi c posttranslational modifi cations are of great interest
(phosphorylation, citrullination, etc.) and different forms of recombinant peptide antibod-
ies are gaining interest (nanobodies, single chain antibodies, TCR-like antibodies, etc.).
This volume covers basic and advanced aspects of peptide antibody production, charac-
terization, and uses.
I thank all contributors and editorial staff for their work, especially the series editor,
John Walker. Also, I want to thank all my collaborators and students throughout the years.
Copenhagen, Denmark G unnar H ouen
v

Contents
Preface. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . v
Contributors. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . x i
1 Peptide Antibodies: Past, Present, and Future . . . . . . . . . . . . . . . . . . . . . . . . . 1
Gunnar H ouen
2 T he Structure of Natural and Recombinant Antibodies. . . . . . . . . . . . . . . . . . 7
Hui M a and Richard O ’Kennedy
3 P rediction of Antigenic B and T Cell Epitopes via Energy Decomposition
Analysis: Description of the Web-Based Prediction Tool BEPPE . . . . . . . . . . . 13
Claudio Peri , Oscar C. S olé , Dario Corrada , A lessandro Gori ,
Xavier D aura , and Giorgio Colombo
4 P rediction of Antibody Epitopes. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
Morten Nielsen and P aolo M arcatili
5 F moc Solid-Phase Peptide Synthesis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 3
Paul R . H ansen and Alberto O ddo
6 P eptide-Carrier Conjugation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
Paul R. Hansen
7 Solid-Phase Peptide-Carrier Conjugation . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5 9
Gunnar H ouen and Dorthe T. O lsen
8 A nalysis of Peptides and Conjugates by Amino Acid Analysis. . . . . . . . . . . . . . 6 5
Peter H øjrup
9 C haracterization of Synthetic Peptides by Mass Spectrometry . . . . . . . . . . . . . 7 7
Bala K. Prabhala , O sman Mirza , P eter H øjrup ,
and Paul R . H ansen
10 Interpretation of Tandem Mass Spectrometry (MSMS) Spectra
for Peptide Analysis. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83
Karin H jernø and Peter Højrup
11 P olyclonal Peptide Antisera. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 103
Tina H. P ihl , Kristin E . I lligen , and Gunnar Houen
12 Production and Screening of Monoclonal Peptide Antibodies . . . . . . . . . . . . . 1 09
Nicole H artwig T rier , A nne Mortensen , A nnette Schiolborg ,
and Tina Friis
13 Production of Epitope-Specific Antibodies by Immunization
with Synthetic Epitope Peptide Formulated with CpG-DNA- Liposome
Complex Without Carriers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 27
Dongbum Kim , Y ounghee Lee , and Hyung-Joo Kwon
vii
viii Contents
14 Thioredoxin-Displayed Multipeptide Immunogens . . . . . . . . . . . . . . . . . . . . . 1 37
Angelo Bolchi , Elena Canali , A ndrea S antoni , Gloria Spagnoli ,
Daniele Viarisio , R osita A ccardi , M assimo T ommasino ,
Martin Müller , and Simone O ttonello
15 T he Purification of Natural and Recombinant Peptide Antibodies
by Affinity Chromatographic Strategies. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 153
Hui Ma and Richard O ’Kennedy
16 Isolation of Camelid Single-Domain Antibodies Against Native Proteins
Using Recombinant Multivalent Peptide Ligands . . . . . . . . . . . . . . . . . . . . . . 1 67
Norah A. Alturki , K evin A. H enry , C. R oger MacKenzie ,
and Mehdi Arbabi-Ghahroudi
17 G eneration of TCR-Like Antibodies Using Phage Display. . . . . . . . . . . . . . . . 1 91
B rian H. Santich , Hong L iu , Cheng L iu , and Nai-Kong V . C heung
18 S tructural Characterization of Peptide Antibodies . . . . . . . . . . . . . . . . . . . . . . 2 05
Anna Chailyan and Paolo M arcatili
19 A utomated High-Throughput Mapping of Linear B-Cell Epitopes
Using a Statistical Analysis of High-Density Peptide Microarray Data . . . . . . . 215
Thomas Østerbye and Søren B uus
20 Characterization of Peptide Antibodies by Epitope Mapping
Using Resin-Bound and Soluble Peptides . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 29
Nicole Hartwig T rier
21 S creening and Characterization of Linear B-Cell Epitopes
by Biotinylated Peptide Libraries. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 241
Ida R osenkrands and Anja O lsen
22 Bead-Based Peptide Arrays for Profiling the Specificity
of Modification State-Specific Antibodies . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 51
Angela F ilomena , Yvonne B eiter , Markus F. T emplin ,
Thomas O. Joos , Nicole Schneiderhan-Marra , and Oliver P oetz
23 Surface Plasmon Resonance Method to Evaluate Anti-c itrullinated
Protein/Peptide Antibody Affinity to Citrullinated Peptides . . . . . . . . . . . . . . 2 67
Feliciana R eal-Fernández , G iada Rossi , F ilomena P anza ,
Federico Pratesi , Paola M igliorini , and Paolo R overo
24 S pecificity Analysis of Histone Modification-Specific Antibodies
or Reading Domains on Histone Peptide Arrays . . . . . . . . . . . . . . . . . . . . . . . 275
Goran K ungulovski , Ina K ycia , R ebekka Mauser , and Albert Jeltsch
25 Prion-Specific Antibodies Produced in Wild-Type Mice. . . . . . . . . . . . . . . . . . 2 85
Peter M. H. H eegaard , Ann-Louise B ergström , H eidi Gertz Andersen ,
and H enriette C ordes
26 I mmunoblotting with Peptide Antibodies: Differential Immunoreactivities
Caused by Certain Amino Acid Substitutions in a Short Peptide
and Possible Effects of Differential Refolding of the Peptide
on a Nitrocellulose or PVDF Membrane. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 303
Takenori Yamamoto , Taisuke Matsuo , Atsushi Yamamoto ,
Ryohei Yamagoshi , Kazuto O hkura , Masatoshi Kataoka ,
and Yasuo Shinohara
Contents ix
27 Immunocytochemical and Immunohistochemical Staining
with Peptide Antibodies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 11
Tina F riis , K laus B oberg P edersen , D avid Hougaard ,
and Gunnar H ouen
28 D esigning B-Cell Epitopes for Immunotherapy and Subunit Vaccines . . . . . . . 3 27
Harinder Singh , S udheer Gupta , Ankur G autam ,
and G ajendra P. S . R aghava
29 E nterovirus-Specific Anti-peptide Antibodies. . . . . . . . . . . . . . . . . . . . . . . . . . 3 41
Chit Laa Poh , K atherine K irk , Hui N a C hua , and Lara G rollo
30 T herapeutic HIV Peptide Vaccine. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 351
Anders F omsgaard
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 59