Continuous epitope

Actually antibodies are either directed against a continuous aminoacid sequence, the continuous epitopes, or a domain which is located on various sites in the aminoacid chain, discontinuous epitopes, or conformational epitopes. Continuous epitopes have served as affinity ligands for antibody... 

FIG. 4.1. Schematic representation of two antibodies reacting with a continuous and a discontinuous epitope of a protein antigen interacting residues are indicated in black. If the individual loops of a discontinuous epitope are able to bind to the antibody paratope on their own, they may be given the status of continuous epitope. The inset shows the three loops of an antibody VH chain which form part of the paratope... 

Whereas molecular design is a strategy applicable to the chemical level of epitope-paratope interactions, it cannot be used for optimizing the many cellular interactions required for achieving an immune response that leads to infectivity neutralization of a pathogen. As a result, the future development of vaccines will continue to rely more on the empirical testing of the protection afforded by candidate vaccine preparations than on the rational design of biomolecules defined in a reductionist manner by their chemical structure. 

For the cycloscan, conformational libraries are synthesized by cyclization of continuous or noncontinuous bioactive epitopes and not by their insertion into a scaffold. Originally, the concept of cycloscan was introduced for the generation of backbone-cyclized peptide libraries 467 however, cycloscan can also be applied to other modes of cyclization. In this approach all components of each sublibrary bear the identical sequence, and differ from each other in distinct parameters that affect their conformation, but do not alter their connectivity, and hence their potential bioactivity. This is achieved by gradually introducing discrete conformational perturbations, which allow an efficient screening of the conformational space of the parent peptide. The majority of the components of such libraries should be inactive, because they do not overlap the bioactive conformation. However, the peptide that does fit the bioactive conformation should be very potent and have all the pharmacological advantages of cyclic peptides. 

Canine parvovirus Tobacco chloroplasts Epitope 2L21 Molina et ah, 2005 —continued... 

Continuing from step 11, the resin is treated with 1% TFA in DCM 5 x 12 min to remove the Mtt group from the side chain of the lysine residue situated between the two epitopes. 

In 2008 Ponomarenko et al. (36) developed the ElliPro Web server with approximation of the protein shape as ellipsoid. They implemented Thornton s method (15), which was originally developed for continuous epitopes and, together with protrusion index and neighboring residue clustering, allows the prediction of antibody epitopes in a given protein sequence or structure. 

Odorico M, Pellequer J (2003) BEPITOPE predicting the location of continuous epitopes and patterns in proteins. J Mol Recognit 16 20-22... 

Saha S, Raghava G (2004) BcePred prediction of continuous B-cell epitopes in antigenic sequences using physico-chemical properties. In Proceedings of the 3rd international conference on artificial immune systems (ICARUS), 13-16 Sep 2004, Catania, Italy. LNCS 3239 197-204... 

Sweredoski M, Baldi P (2009) COBEpro a novel system for predicting continuous B-cell epitopes. Protein Eng Des Sel 22 113-120... 

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