Epitope mapping : a practical approach /
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| 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 |
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
