Peptides epitope identification

Yao, Z.-J., Kao, M. C. C., and Chung, M. C. M. (1995). Epitope identification by polyclonal antibody from phage-displayed random peptide library. J. Protein Chem. 14, 161-166. 

The source of the peptides in these complexes can be either "self", i.e., derived from endogenous protons, or fordgn, from pathogenic sources. In inbred mice there are at least 22 allelic forms of heavy chain, each of which is thought to bind peptides with a specific structural motif, e.g., peptide length and position of specific amino acid side chains. The P2-microglobulin chain is invariant. Analysis of natural MHC molecules has led to identification of specific peptide epitopes for several of these alleles. The pq>tide motifs of two of the most well-characterized murine alleles, H-2K and H-2D , have been identified, and the 3- dimensional structures of their ternary complexes have been solved (2,3). 

D Suckau, J Kohl, G Karwath, K Schneider, M Casaretto, D Bitter-Sauermann, M Przybylski. Molecular epitope identification by limited proteolysis of a immobilized antigen-anitbody complex and mass spectrometric peptide mapping. Proc Natl Acad Sci USA 87 9848 9852, 1990. 

An innovative immunochemo-proteomics method was developed that allowed the identification of an inhibitor of the heme-binding protein (83). This method is based on the coupling of a small molecule, bis-indolylmaleimide-III, a known inhibitor of protein kinase C-a, to the FLAG peptidic epitope. This leads to the isolation of binding proteins from a cell lysate via the reaction of the FLAG epitope with anti-FLAG antibody beads. 

To verify the immunogenic potential of the peptides identified via MAPPs, candidate epitopes are routinely screened in a T cell activation assay which involves human blood-derived APCs and autologous T cells from the same blood donor. In comparison to in silico tools described above, MAPPs has several advantages in T cell epitope identification (i) it narrows down the number of potentially relevant epitopes, as predictable by in silico tools, to a few immunodominant epitopes so that the potency of the drug can be retained more easily (ii) it takes into account post-translational modifications of biologies that may change the pattern of relevant epitopes and (iii) it can be done with fully formulated biologies—a feature not covered by any of the other approaches described above. 

There are two general methods for identifying antibody epitopes (1) evaluate peptides whose composition is based on the sequence of the native protein, or (2) evaluate peptides that are selected from a random combinatorial peptide library. The former is only effective if the epitope is composed of a linear sequence of amino acids in the native protein sequence. If it is, then analysis of overlapping peptides from the native protein is a simple method for identifying antibody epitopes. Each peptide is tested for immunoreactivity to the antibody. Those peptides that are immunoreactive contain the epitope. The other method of epitope identihcation, selection from a random combinatorial library, will identify peptides that represent both linear and conformationally dependent epitopes. The drawback of this method is that biopanning from a random combinatorial peptide library is more time consuming. Phage-displayed peptide libraries have previously been used for epitope identification in this context. ... 

Savoie, G.J., Kamikawaji, N., Sasazuki, T., Kuhara, S. Use of BONSAI decision trees for the identification of potential MHG class I peptide epitope motifs. In Pacific Symposium on Biocomputing, 1999, pp. 182-9. 

Suckau, D., Kohl, J., Karwath, G., et al. (1990) Molecular Epitope Identification by Limited Proteolysis of an Immobilized Antigen-Antibody Complex and Mass Spectrometric Peptide Mapping. Proceedings of the National Academy of Sciences of the United States of America, 87 (24), 9848-9852. 

Development of a peptide vaccine is derived from the identification of the immunodominant epitope of an antigen (141). A polypeptide based on the amino acid sequence of the epitope can then be synthesized. Preparation of a peptide vaccine has the advantage of allowing for large-scale production of a vaccine at relatively low cost. It also allows for selecting the appropriate T- or B-ceU epitopes to be included in the vaccine, which may be advantageous in some cases. Several vaccines based on peptide approaches, such as SPf66 (95) for malaria and an HIV-1 peptide (142) have been in clinical trials. No peptide vaccines are Hcensed as yet. 

A. Saul and H. Geysen, iu G. Woodrow and M. Leviue, eds.. Identification of Epitopes through Peptide Technology in New Generation Vaccines, Marcel Dekker, New York, 1990. 

The most frequent application of SPOT-synthesis has been in the preparation of peptide arrays for the identification of linear B-cell epitopes. If the protein antigen is known, a set of overlapping peptides that encompass the entire sequence can be readily synthesized and assayed for binding of antibody (Reineke et al., 1999). The individual residues critical for binding can then be determined by SPOT-synthesis of peptides containing amino acid substitutions. 

Precise definition of the host-protection epitope(s) of the Taenia and Echinococcus vaccine antigens would be valuable if it were to lead to the development of a synthetic vaccine or provide reagents to assist with quality control of vaccine production. Identification of a limited number of host-protective fragments may allow the recombinant antigen to be replaced by synthetic peptides. This would have significant advantages in the production... 

The use of peptide libraries to study T cell specificity was first demonstrated by Gundlach et al.45 Since then studies have focused on T cell specificity with emphasis on the identification of immunodominant epitopes in infectious diseases and autoimmune disorders, and on the determination of tumor antigens. The PS-SCL approach, as described above, was successfully used to study T cell recognition and to identify and optimize peptides having a range of activities in stimulating proliferative responses, cytokine production, and/or lysis by CD4+ and CD8+ murine and human T cell clones and T cell lines of known and unknown specificity.46-53... 

Reineke, U Ivascu, C Schlief, M., et al. (2002) Identification of distinct antibody epitopes and mimotopes from a peptide array of 5520 randomly generated sequences../. Immunol. Methods 267, 37-51. 

Identification of relevant epitopes using overlapping peptides spotted onto membranes... 

This approach offers a number of significant advantages. Since whole cells are used as the affinity support, the receptors are likely to be in their native conformation, allowing the isolation of peptide ligands directed against conformationally structured epitopes [70, 71]. Moreover, the technique leads to the identification of cell surface markers which distinguish otherwise similar cell types such as antigens, epitopes, or receptors, without the need to either identify or purify a particular receptor in advance [38, 42, 43, 72]. 

Ploug M, Ostergaard S, Gardsvoll H, Kovalski K, Holst-Hansen C, Holm A, et al. Peptide-derived antagonists of the urokinase receptor. Affinity maturation by combinatorial chemistry, identification of functional epitopes, and inhibitory effect on cancer cell intravasation. Biochemistry 2001 40(40) 12157-12168. 

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