Epitope mapping : a practical approach /

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Bibliographic Details
Imprint:Oxford ; New York : Oxford University Press, 2001.
Description:xviii, 284 p. : ill. ; 25 cm.
Language:English
Series:The practical approach series
Practical approach series.
Subject:
Format: Print Book
URL for this record:http://pi.lib.uchicago.edu/1001/cat/bib/4653351
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Other authors / contributors:Westwood, Olwyn M. R.
Hay, Frank C.
ISBN:0199636532 (hbk. : alk. paper)
0199636524 (pbk.)
Notes:Includes bibliographical references and index.
Table of Contents:
  • List of protocols
  • Abbreviations
  • 1. An introduction to epitope mapping
  • 1. Environmental conditions can influence protein structure
  • Locating the epitope of the molecule
  • 2. Lessons from an historical perspective
  • Enzymatic cleavage for epitope mapping
  • Protein sequence analysis
  • Chemical characteristics of sequences
  • 3. Synthetic peptide technologies for epitope mapping
  • 4. Chemical modification of antigens
  • 5. Site-directed mutagenesis as a tool for epitope mapping
  • 6. Hybridoma technology and epitope analysis
  • Protein footprinting in epitope analysis
  • 7. Generating monoclonal antibody
  • 8. Phage display libraries
  • 9. Carbohydrates and their significance when epitope mapping
  • 10. Approaches to epitope mapping
  • Polyclonal or monoclonal antibody?
  • Whole antigen available?
  • Amino acid sequence known?
  • Nucleotide sequence available?
  • References
  • 2. Multiple Pin Peptide Scanning ("Pepscan")
  • 1. Introduction
  • Brief outline of Pepscan
  • 2. Solid phase peptide synthesis
  • Attachment
  • Deprotection and coupling
  • Elongation of peptide chain
  • Cleavage
  • 3. Multiple peptide synthesis on pins
  • Pins
  • Choice of peptide length
  • 4. Testing of antibody epitopes
  • Pin-bound non-cleavable peptides
  • Biotinylated peptides
  • 5. Results and data analysis
  • 6. Further analysis
  • Window net analysis
  • Replacement net analysis
  • 7. Applications of Pepscan
  • 8. Other systems for epitope analysis
  • Simple precision original test system (SPOTs)
  • Tea-bag synthesis
  • Peptide epitope libraries
  • Acknowledgements
  • References
  • 3. Methodological tips for human T cell epitope mapping when using pin technology peptide arrays
  • 1. Introduction
  • 2. Historic foundations to large scale T cell epitope mapping
  • 3. Fundamental considerations
  • Lessons from B cell epitope mapping
  • The nature of the peptide antigen
  • Protein sequence databases and sequence analysis
  • 4. Peptide synthesis considerations
  • Types of peptides
  • Features of T cell epitopes
  • 5. Use of pin peptides in human PBMC proliferation and cell culture assays
  • Buffers systems
  • Cleavage of peptide and peptide concentration
  • Using human cells
  • Cell culture conditions
  • Pulse radiolabelling
  • 6. Data analysis using the ALLOC algorithm
  • 7. Example of assay conditions for large scale mapping of T cell epitopes
  • Individual steps in the T cell epitope mapping protocol
  • Example of results obtained
  • References
  • Published methods to detect cellular antigenic stimulation
  • 4. Combined B cell and T cell epitopes
  • 1. Introduction
  • 2. Molecular mapping of antigenic and immunogenic epitopes
  • Identification of antigenic epitopes in vitro
  • Identification of T cell epitopes in vitro
  • 3. In vivo analysis of immunogenicity and antigenicity
  • Investigation of the core sequence of B cell and T cell epitopes
  • Inhibition ELISA for the measurement of antibody affinity as a method to determine the B cell epitope
  • Determination of precise helper T cell epitopes by proliferative and cytokine responses
  • 4. General summary
  • References
  • 5. CTL epitopes
  • 1. Introduction
  • TcR recognizes a complex between MHC and antigenic peptide
  • Antigen processing
  • Immunodominance
  • 2. Indirect methods of CTL epitope identification using synthetic peptides
  • Peptide binding to class I MHC molecules
  • Correspondence between motifs and binding efficacy
  • Correspondence between peptide binding and immunogenicity/immunodominance
  • 3. Direct identification of CTL epitopes
  • Direct identification of CTL epitopes by immuno-isolation and sequencing
  • Direct identification of CTL epitopes by expression cloning
  • References
  • Appendix 1. Class I MHC peptide motifs
  • Appendix 2. Class I MHC alleles expressed by TAP-deficient cell lines
  • Appendix 3. Monoclonal antibodies specific for class I MHC molecules
  • Appendix 4. Index peptides suitable for modification
  • 6. The design, synthesis, and characterization of molecular mimetics
  • 1. Introduction
  • 2. Design, synthesis, and characterization of peptoid oligomers
  • Design of peptoid oligomers
  • The synthesis of peptoid oligomers
  • Characterization of peptoids
  • 3. Further oligomeric peptide mimetics
  • [beta]-Peptides, [beta]-peptoids, retro-peptoids, and amide surrogates
  • 4. Non-oligomeric peptide mimetics
  • Natural templates
  • Non-natural templates
  • References
  • 7. Generating monoclonal antibody probes and techniques for characterizing and localizing reactivity to antigenic determinants
  • 1. Introduction
  • 2. Immunization strategies
  • 3. Hybridization and culture of hybridomas
  • 4. Monoclonal purification
  • 5. Monoclonal conjugation
  • 6. Techniques for screening and characterizing mAb reactivity to antigenic determinants
  • Enzyme-linked immunosorbent assay (ELISA)
  • Haemagglutination
  • Slot-blotting
  • Immunocytochemistry
  • 7. Physicochemical and chemical modification, pepsin digestion
  • 8. Sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and Western blotting
  • 9. Protein determination
  • UV absorption
  • Fluorescence
  • Acknowledgements
  • References
  • 8. Epitope mapping of carbohydrate binding proteins using synthetic carbohydrates
  • 1. Introduction
  • 2. Synthetic carbohydrate analogues
  • Oligosaccharide fragments
  • Deoxy analogues
  • Deoxyfluoro analogues
  • O- and C-methyl analogues
  • Amino and carboxy analogues
  • Conformationally restricted or altered analogues
  • Combinatorial synthesis of carbohydrate libraries
  • 3. Measuring carbohydrate-protein interactions
  • Haemagglutination inhibition
  • Competitive ELISA
  • Techniques for direct measurement of carbohydrate-protein interaction
  • Enzyme assays
  • Qualitative in situ assays
  • 4. Data interpretation
  • Conformational analysis
  • Fragments of oligosaccharides
  • Deoxy and deoxyfluoro analogues
  • Amino and carboxy analogues
  • Conformationally altered analogues
  • References
  • 9. Phage display libraries
  • 1. Introduction
  • General
  • Overview of phage display libraries
  • Applications of phage display libraries
  • 2. Case study: identification of dominant epitopes
  • Project strategy
  • Procedure for the identification of peptide epitopes by phage display
  • Deriving peptide binding antibody fragments
  • 3. Conclusions
  • Acknowledgements
  • References
  • 10. Site-directed mutagenesis in epitope mapping
  • 1. Introduction
  • 2. General approaches to mutagenesis in epitope mapping: techniques in site-directed mutagenesis
  • Traditional approach
  • PCR approach
  • 3. Conclusions
  • References
  • A1. List of suppliers
  • Index