Stepwise prediction of conformational discontinuous B‐cell epitopes using the Mapitope algorithm
Identifieur interne : 001655 ( Main/Exploration ); précédent : 001654; suivant : 001656Stepwise prediction of conformational discontinuous B‐cell epitopes using the Mapitope algorithm
Auteurs : Erez M. Bublil [Israël] ; Natalia Tarnovitski Freund [Israël] ; Itay Mayrose [Israël] ; Osnat Penn [Israël] ; Anna Roitburd-Berman [Israël] ; Nimrod D. Rubinstein [Israël] ; Tal Pupko [Israël] ; Jonathan M. Gershoni [Israël]Source :
- Proteins: Structure, Function, and Bioinformatics [ 0887-3585 ] ; 2007-07.
Abstract
Mapping the epitope of an antibody is of great interest, since it contributes much to our understanding of the mechanisms of molecular recognition and provides the basis for rational vaccine design. Here we present Mapitope, a computer algorithm for epitope mapping. The algorithm input is a set of affinity isolated peptides obtained by screening phage display peptide‐libraries with the antibody of interest. The output is usually 1–3 epitope candidates on the surface of the atomic structure of the antigen. We have systematically tested the performance of Mapitope by assessing the effect of the algorithm parameters on the final prediction. Thus, we have examined the effect of the statistical threshold (ST) parameter, relating to the frequency distribution and enrichment of amino acid pairs from the isolated peptides and the D (distance) and E (exposure) parameters which relate to the physical parameters of the antigen. Two model systems were analyzed in which the antibody of interest had previously been co‐crystallized with the antigen and thus the epitope is a given. The Mapitope algorithm successfully predicted the epitopes in both models. Accordingly, we formulated a stepwise paradigm for the prediction of discontinuous conformational epitopes using peptides obtained from screening phage display libraries. We applied this paradigm to successfully predict the epitope of the Trastuzumab antibody on the surface of the Her‐2/neu receptor in a third model system. Proteins 2007. © 2007 Wiley‐Liss, Inc.
Url:
DOI: 10.1002/prot.21387
Affiliations:
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Accordingly, we formulated a stepwise paradigm for the prediction of discontinuous conformational epitopes using peptides obtained from screening phage display libraries. We applied this paradigm to successfully predict the epitope of the Trastuzumab antibody on the surface of the Her‐2/neu receptor in a third model system. Proteins 2007. © 2007 Wiley‐Liss, Inc.</div></front></TEI><affiliations><list><country><li>Israël</li></country></list><tree><country name="Israël"><noRegion><name sortKey="Bublil, Erez M" sort="Bublil, Erez M" uniqKey="Bublil E" first="Erez M." last="Bublil">Erez M. Bublil</name></noRegion><name sortKey="Freund, Natalia Tarnovitski" sort="Freund, Natalia Tarnovitski" uniqKey="Freund N" first="Natalia Tarnovitski" last="Freund">Natalia Tarnovitski Freund</name><name sortKey="Gershoni, Jonathan M" sort="Gershoni, Jonathan M" uniqKey="Gershoni J" first="Jonathan M." last="Gershoni">Jonathan M. Gershoni</name><name sortKey="Gershoni, Jonathan M" sort="Gershoni, Jonathan M" uniqKey="Gershoni J" first="Jonathan M." last="Gershoni">Jonathan M. Gershoni</name><name sortKey="Gershoni, Jonathan M" sort="Gershoni, Jonathan M" uniqKey="Gershoni J" first="Jonathan M." last="Gershoni">Jonathan M. Gershoni</name><name sortKey="Mayrose, Itay" sort="Mayrose, Itay" uniqKey="Mayrose I" first="Itay" last="Mayrose">Itay Mayrose</name><name sortKey="Penn, Osnat" sort="Penn, Osnat" uniqKey="Penn O" first="Osnat" last="Penn">Osnat Penn</name><name sortKey="Pupko, Tal" sort="Pupko, Tal" uniqKey="Pupko T" first="Tal" last="Pupko">Tal Pupko</name><name sortKey="Roitburd Erman, Anna" sort="Roitburd Erman, Anna" uniqKey="Roitburd Erman A" first="Anna" last="Roitburd-Berman">Anna Roitburd-Berman</name><name sortKey="Rubinstein, Nimrod D" sort="Rubinstein, Nimrod D" uniqKey="Rubinstein N" first="Nimrod D." last="Rubinstein">Nimrod D. 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