Epitope Mapping with Mimotopes Figure 3. Three-dimensional modeling of putative epitopes. Three-dimensional model of rat HER-2 is presented in two orientations. A. clusters found for HER-2FLserum, B. clusters found for HER-2ECD-serum, C. clusters found for HER-2TUBO –serum. Serum- specific clusters of amino acid pairs are numbered. Amino acid are coloured according to RasMol amino acid colour code: red = Glu and Asp, blue = Arg and Lys, brown = Pro, orange = Ser and Thr, Cyan = Asn and Gln, violet = Trp and Phe, purple = His. doi:10.1371/journal.pone.0005309.g003 Measurement of HER-2 specific antibody by FACS 106 TUBO cells, which express high levels of rat HER-2, were incubated with serial dilutions of mouse sera. The TUBO cells were then washed to remove free mouse antibodies and incubated with goat anti-mouse IgG conjugated with phycoerethrin (PE) ((Jackson Immunoresearch Laboratories Inc. West Grove, Penn- sylvania, USA). Fluorescence intensity was measured using an LSRII flow cytometer (BD Biosciences). MFI was calculated on a minimum of 10000 events. Phage display library screening We employed a phage display library presenting random peptides with the structure XC(X)10CX inserted into N-terminus of pVIII, a major coat protein of filamentous bacteriophage, PLoS ONE | www.plosone.org 8 April 2009 | Volume 4 | Issue 4 | e5309