Antibody Engineering Protocols

444 Pages·1995·8.43 MB·English

by  George Johnson

Antibody Engineering Protocols
Methods in Molecular Biology^'^ Series
John M. WalkeVy SERIES EDITOR
35. Plant Cell Electroporation and Eledrofusion Protocols, 28. Protocols for Nucleic Acid Analysis by Nonradioactive
edited by Jac A. Nkkoloff. 1995 Probes, edited by Peter G. Isaac, 1994
54. YAC Protocols, edited by David Markie, 1995 27. Biomembrane Protocols: //. Architecture and Function,
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52. Capillary Electrophoresis: Principles. Inslrumenlalion, Analytical Techniques, edited by Sudhir Agrawal, 1994
and Applications, edited by Kevin D. Altria, 1995 25. Computer Analysis of Sequence Data: Part II, edited by
51. Antibody Engineering Protocols, edited by SudhirPaul, Annette M. Griffin and Hugh G. Griffin, 1994
1995 24. Computer Analysis of Sequence Data: Part 1, edited by
50. Species Diagnostics Protocols: PCR and Other Nucleic Annette M. Griffin and Hugh G. Griffin, 1994
Acid Methods, edited by Justin P. Clapp, 1995 23. DNA Sequencing Protocols, edited by Hugh G. Griffin and
49. Plant Gene Transfer and Expression Protocols, Annette M. Griffin, 199S
edited by Heddwyn Jones, 1995 22, Microscopy, Optical Spectroscopy, and Macroscopic
48. Animal Cell Electroporation and Electrofusion Proto Techniques, edited by Christopher Jones, Barbara Mulloy,
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Jac A. Nickoloff, 1995 Hyde, 1993
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Hoviard and David M. Whitcombe, 1995 Properties, edited by Sudhir Agraval, 1993
45. Monoclonal Antibody Protocols, edited by William C. 19. Biomembrane Protocols: /. Isolation and Analysis,
Davis, 1995 edited by John M. Graham and Joan A. Higgins, 1993
44. Agrobacterium Protocols, edited by Kevan U. A. Gartland 18. Transgenesis Techniques: Principles and Protocols,
and Michael R. Davey, 1995 edited by David Murphy and David A. Carter, 1993
43. In Vitro Toxicity Testing Protocols, edited by Sheila 17. Spectroscopic Methods and Analyses: NMR, Mass Spec
O'Hare and Chris K. Atterwill, 1995 trometry, and Metalloprotein Techniques, edited by Chris
42. ELISA: Theory and Practice, by John R. Crowther, 1995 topher Jones, Barbara Mulloy, and Adrian H. Thomas. 1993
41. Signal Transduction Protocols, edited by OaviW.4. ATcniia// 16. Enzymes of Molecular Biology, edited by Michael M.
and Stephen J Hill, 1995 Burrell. 1993
40. Protein Stability and Folding: Theory and Practice, 15. PCR Protocols: Current Methods and Applications, edited
edited by Bret A. Shirley, 1995 by Bruce A. White, 1993
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D. Richardson, 1995 beth F. Hounsell, 1993
38. Cryopreservation and Freeze-Drying Protocols, 13. Protocols in Molecular Neurobiology, edited by Alan
edited by John G. Day and Mark R. McLellan, 1995 Longstaff and Patricia Revest, 1992
37. In Vitro Transcription and Translation Protocols, 12. Pulsed-Field Gel Electrophoresis: Protocols, Methods, and
edited by Martin J. Tymms, 1995 Theories, edited by Margit Burmeister and Levy Ulanovsky,
36. Peptide Analysis Protocols, edited by Ben M. Dunn and 1992
Michael W. Pennington, 1994 II. Practical Protein Chromatography, edited by Andrew
35. Peptide Synthesis Protocols, edited by Michael W. Kenney and Susan Fov/ell, 1992
Pennington and Ben M. Dunn, 1994 10. Immunochemical Protocols, edited by Margaret M.
34. Immunocytochemicai Methods and Protocols, edited by Manson, 1992
lorette C. Javois, 1994 9. Protocols in Human Molecular Genetics, edited by Chris
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Choo, 1994 8. Practical Molecular Virology: Viral Vectors for Gene
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Walker, 1994 7. Gene Transfer and Expression Protocols, edited by
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1994 6. Plant Cell and Tissue Culture, edited by Jeffrey W.
Pollard and John M. Walker, 1990
30. DNA-ProteIn Interactions, edited by G. Geoff Kneale, 1994
5. Animal Cell Culture, edited by ye/f^re)' W. Pollard and John
29. Chromosome Analysis Protocols, edited by John R.
M. Walker. 1990
Gosden, 1994
Methods in Molecular Biology™ • S I
Antibody
E n g i n e e r i n g
Protocols
Edited by
Sudhir Paul
University of Nebraska Medical Center, Omaha, NE
Humana Press ^fe Totowa, New Jersey
© 1995 Humana Press Inc.
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Library of Congress Cataloging in Publication Data
Main entry under title:
Methods in molecular biology'".
Antibody engineering protocols / edited by Sudhir Paul,
p. cm. ~ (Methods in molecular biology'" ; 51)
Includes index.
ISBN 0-89603-275-2 (alk. paper)
1. Immunoglobulins-Biotechnology. 2. Protein engineering.
I. Paul, Sudhir. II. Series: Methods in molecular biology'" (Totowa,
NJ); 51.
TP248.65.149A585 1995
616.07'93-dc20 95-423
CIP
Preface
Antibodies are the instraments of immune defense and attack.
They can bind small atomic arrays as well as large epitopes with high
affinity. Antibody Engineering Protocols presents advanced protocols
in the field of antibody engineering, reviews of basic principles and
methodology, and a historical perspective on the development of cur
rently held beliefs about antibody structure-function relationships. The
topics cover analysis of antibody sequences, three-dimensional structure,
delineation of antibody characteristics in polyclonal mixtures, phage
display of natural and synthetic antibodies, and antibody catalysis.
Ligand recognition by antibodies occurs primarily at a subset of
amino acid residues located in the complementarity determining
regions (CDRs) found in the light (L) and heavy (H) chain subunits.
Specific antibodies are developed by immunization with molecules
identical to or related in structure to the target ligand. The immune
repertoire from nonimmunized individuals also contains pre-existing
specificities that can be selected by screening libraries composed of
hybridoma cells or phage particles displaying F domains or indi
vidual variable domains of the light (VJ and heavy (V^^) chains. Ran
dom or site-directed mutagenesis in vitro can be used to refine the
pre-existing specificities or produce new specificities de novo. Another
level at which new specificities may be generated in vitro is V^ and
V^ domain-swapping and CDR-swapping. The former procedure
embodies a variation of natural mechanisms of generating antibody
diversity. The latter procedure produces new intramolecular CDR
combinations not found in nature. Application of anti-idiotypic
imagery can also be utilized to replicate and modify the active site of
antibodies and enzymes.
In the biological sciences, many conceptual advances have been
driven by new methodology. In the case of antibody research, recent
vi Preface
methodological developments make possible mechanistic study of
the role of antibodies in immune defense and autoimmune disease,
and encourage the belief that antibody fragments will find important
uses in industry and medicine. In particular, the discovery of cataly
sis by natural antibodies offers simple means to derive new catalysts
from the immune response. Inmiunization with transition-state and
charged-substrate analogs has previously been observed to generate
esterolytic and amidolytic antibodies. Combined with the natural pro
pensity of the immune system to produce catalytic antibodies, the
"nudge" toward catalysis by substrate and transition state analog
immunizations may permit development of efficient catalysts.
I thank each of the authors for painstaking descriptions of the
nuts and bolts of their techniques. Donna Dutch and Angela Plendl
typed many of the manuscripts, scanned them into the computer, and
generally helped in generating a comprehensible text, for which I am
in their debt. I thank John Walker for editorial guidance and Humana
Press for producing this volume.
Sudhir Paul
Contents
Preface v
Contributors ix
Ch. 1. SEQHUNT: A Program to Screen Aligned Nucleotide
and Amino Acid Sequences,
George Johnson, Tai Te Wu, and Elvin A. Rabat /
Ch. 2. Molecular Modeling of Antibody-Combining Sites,
David M. Webster and Anthony R. Rees 17
Ch. 3. Structure and Properties of Human Immunoglobulin Light-Chain Dimers,
Fred J. Stevens and Marianne Schiffer 51
Ch. 4. Crystallographic and Chromatographic Methods for Study
of Antibody Light Chains and Other Proteins,
Marianne Schiffer and Fred J. Stevens 83
Ch. 5. Detection of Human Variable Gene Family Expression
at the Single-Cell Level,
MoncefZouali 99
Ch. 6. Purification of Reduced and Alkylated Antibody Subunits,
Mei Sun and Sudhir Paul ///
Ch. 7. Murine Monoclonal Antibody Development,
Donald R. Johnson 123
Ch. 8. ComparativePropertiesof Polyclonal and Monoclonal Antibodies,
L. Scott Rodkey 139
Ch. 9. Evaluation of Antibody Clonality,
L. Scott Rodkey 151
Ch. 10. Affinity Immunoblotting,
Keith A. KnisleyandL. Scott Rodkey 165
Ch. 11. Epitope and Idiotope Mapping Using Monoclonal Antibodies,
Srinivas Kaveri 171
Ch. 12. Anti-Idiotypic Antibodies That Mimic Opioids,
Jay A. Glasel and Dianne Agarwal 183
Ch. 13. CaX&Xyiic Aniiho&its: Structure and Possible Applications,
Howard Amital, Ilan Tur-Kaspa, Zeev Tashma,
Israel Hendler, and Yehuda Shoenfeld 203
Ch. 14. Preparation and Assay of Acetylcholinesterase Antibody,
Alain Friboulet and Ladan Iz/adyar-Demichele 211
vii
via Contents
Ch. 15. DNA Hydrolysis by Antibodies,
Alexander G. Gabibov and Oxana Makarevitch 223
Ch. 16. Screening Strategies for Catalytic Antitransition-State Analog Antibodies,
Alfonso Tramontano 237
Ch. 17. Expression of Chimeric Immunoglobulin Genes in Mammalian Cells,
Sergey M. Deyev and Oleg L. Polanovsky 251
Ch. 18. Single-Chain Anti-DNA F^,
Michael Polymenis and B. David Stollar 265
Ch. 19. Molecular Cloning of Antiground-State Proteolytic Antibody Fragments,
Qing-Sheng Gao and Sudhir Paul 281
Ch. 20. Cloning and Bacterial Expression of an Esterolytic sF^,
Rodger G. Smith, Mark T. Martin, Rosa Sanchez,
and John H. Kenten 297
Ch. 21. Site-Directed Mutagenesis of Antibody-Variable Regions,
Qing-Sheng Gao and Sudhir Paul 319
Ch. 22. Synthetic Antibody Gene Libraries for In Vitro Affinity Maturation,
Su-jun Deng, C. Roger MacKenzie, and SaranA. Narang 329
Ch. 23. Chaperonins in Phage Display of Antibody Fragments,
Eskil Soderlind, Marta Duenas, and Carl A. K. Borrebaeck... 343
Ch. 24. Phage-Display Libraries of Murine and Human Antibody Fab Fragments,
Jan Engberg, Peter Sejer Andersen, Leif Kofoed Nielsen,
Morten Dziegiel, Lene K. Johansen,
and Bjarne Albrechtsen 355
Ch. 25. Selection of Human Immunoglobulin Light Chains
from a Phage-Display Library,
Sonia Tyutyulkova, Qing-Sheng Gao, and Sudhir Paul 377
Ch. 26. Purification of Antibody Light Chains by Metal Affinity
and Protein L Chromatography,
Sonia Tyutyulkova and Sudhir Paul 395
Ch. 27 Rapid Purification of Recombinant Antibody Fragments
for Catalysis Screening,
Han Huang, Brian Fichter, Robert Dannenbring,
and Sudhir Paul 403
Ch. 28. Assay of Radiolabeled VIP Binding and Hydrolysis by Antibodies,
Han Huang and Sudhir Paul 409
Ch. 29 Methods of Measuring Thyroglobulin and Peptide-
Methylcoumarinamide Hydrolysis by Autoantibodies,
Lan Li, Ravishankar Kalaga, Srinivas Kaveri,
and Sudhir Paul 417
Ch. 30. Radiolabeling of Antibodies for Therapy and Diagnosis,
Janina Baranowska-Kortylewicz, Glenn V. Dalrymple,
Syed M. Quadri, and Katherine A. Harrison 423
Index 441
Contributors
DiANNE AGARWAL • Department of Biochemistry, University
of Connecticut Health Center, Farmington, CT
BJARNE ALBRECHTSEN • Department of Biology, Danmarks
Farmaceutiske H0jskole, Copenhagen, Denmark
HOWARD AMITAL • Department of Medicine 'B' and Research Unit
of Autoimmune Diseases, Sheba Medical Center,
Tel-Hashomer, Sackler Faculty of Medicine, Tel-Aviv University
PETER SEJER ANDERSEN • Department of Biology, Royal Danish
School of Pharmacy, Copenhagen, Denmark
JANINA BARANOWSKA-KORTYLEWICZ • Department of Radiology,
University of Nebraska Medical Center, Omaha, NE
CARL A. K. BORREBAECK • Department of Immunotechnology,
Lund University, Lund, Sweden
GLENN V. DALRYMPLE • Department of Radiology, University
of Nebraska Medical Center, Omaha, NE
ROBERT DANNENBRING • Department of Anesthesiology, University
of Nebraska Medical Center, Omaha, NE
SU-JUN DENG • Institute for Biological Sciences, National Research
Council of Canada, Ottawa, Ontario, Canada
SERGEY M. DEYEV • Engelhardt Institute of Molecular Biology,
Russian Academy of Sciences, Moscow, Russia
MARTA DUENAS • Department of Immunotechnology, Lund University,
Lund, Sweden
MORTEN DZIEGIEL • Department of Biology, Royal Danish School
of Pharmacy, Copenhagen, Denmark
JAN ENGBERG • Department of Biology, Royal Danish School
of Pharmacy, Copenhagen, Denmark
BRIAN FIGHTER • Department of Anesthesiology, University
of Nebraska Medical Center, Omaha, NE
ix
jc Contributors
ALAIN FRIBOULET • Laboratoire de Technologie Enzymatique,
Universite de Technologie de Compiegne, France
ALEXANDER G. GABIBOV • Engelhardt Institute of Molecular
Biology, Russian Academy of Sciences, Moscow, Russia
QING-SHENG GAO • Department of Anesthesiology, University
of Nebraska Medical Center, Omaha, NE
JAY A. GLASEL • Department of Biochemistry, University
of Connecticut Health Center, Farmington, CT
KATHERINE A. HARRISON • Department of Radiology, University
of Nebraska Medical Center, Omaha, NE
ISRAEL HENDLER • Israeli Defense Forces-Medical Corps, Tel-Aviv, Israel
HAN HUANG • Department of Anesthesiology, University
of Nebraska Medical Center, Omaha, NE
LADAN IZADYAR-DEMICH6LE • Laboratoire de Technologie
Enzymatique, Universite de Technologie de Compiegne,
France
LENE K. JOHANSEN • Department of Biology, Royal Danish School
of Pharmacy, Copenhagen, Denmark
DONALD R. JOHNSON • Department of Pathology and Microbiology,
University of Nebraska Medical Center, Omaha, NE
GEORGE JOHNSON • Department of Biochemistry and Molecular Cell
Biology, Northwestern University, Evanston, IL
ELVIN A. KABAT • Department of Microbiology, Columbia
University, New York, NY
RAVISHANKAR KALAGA • Department of Anesthesiology, University
of Nebraska Medical Center, Omaha, NE
SRINIVAS KAVERI • INSERM U28, Hopital Broussais, Paris, France
JOHN H. KENTEN • Proneuron, Inc., Rockville, MD
KEITH A. KNISLEY • Department of Cell Biology and Biochemistry,
Texas Tech University Health Science Center, Lubbock, TX
LAN LI • Department of Anesthesiology, University of Nebraska
Medical Center, Omaha, NE
C. ROGER MACKENZIE • Institute for Biological Sciences, National
Research Council of Canada, Ottawa, Ontario, Canada
OxANA MAKAREVITCH • Engelhardt Institute of Molecular Biology,
Russian Academy of Sciences, Moscow, Russia