The epitope space of the human proteome
2008 (English)In: Protein Science, ISSN 0961-8368, Vol. 17, no 4, 606-613 p.Article in journal (Refereed) Published
In the post-genome era, there is a great need for protein-specific affinity reagents to explore the human proteome. Antibodies are suitable as reagents, but generation of antibodies with low cross-reactivity to other human proteins requires careful selection of antigens. Here we show the results from a proteomewide effort to map linear epitopes based on uniqueness relative to the entire human proteome. The analysis was based on a sliding window sequence similarity search using short windows (8, 10, and 12 amino acid residues). A comparison of exact string matching (Hamming distance) and a heuristic method (BLAST) was performed, showing that the heuristic method combined with a grid strategy allows for whole proteome analysis with high accuracy and feasible run times. The analysis shows that it is possible to find unique antigens for a majority of the human proteins, with relatively strict rules involving low sequence identity of the possible linear epitopes. The implications for human antibody-based proteomics efforts are discussed.
Place, publisher, year, edition, pages
2008. Vol. 17, no 4, 606-613 p.
proteomics; antigen; epitope; sequence similarity; antibody; grid; B-CELL EPITOPES; ANTIGENIC DETERMINANTS; DATA-BANK; PREDICTION; ANTIBODIES; MYOGLOBIN; PEPTIDES; SEQUENCE; LIBRARIES; PROTEINS
IdentifiersURN: urn:nbn:se:kth:diva-8255DOI: 10.1110/ps.073347208ISI: 000254197800002ScopusID: 2-s2.0-41649104373OAI: oai:DiVA.org:kth-8255DiVA: diva2:13529
QC 201007052008-04-222008-04-222010-07-05Bibliographically approved