To obtain the HLA-A2.1-restricted CTL epitopes of EWS-FLI1 fusion protein of Ewing s sarcoma, EWS-FLI1 protein was synthetically predicted by BIMAS, SYFPEITHI, Predep and IEDB methods. Eight epitopes predicted by above methods were further screened by the polynomial method and the quantitative motif method as well. Four screened peptides were stimulated to dock with HLA-A2.1 by molecular dynamics simulation. All peptides were synthesized with standard Fmoc strategy, then detected beyond 98% in purity by reverse phase high performance liquid chromatography (RP-HPLC) and measured the values of molecular weight of them by mass spectrometry (MS). Infinity experiment validated the infinity of peptide QIQLWQFLL_{(EWS-FLI1 304)} with HLA-A2.1 molecule, which could afford the foundation of immunological characteristics study of this screened peptide. This research provides a rational and high efficient method to screen epitope.

Key words: Ewing s sarcoma, EWS-FLI1 fusion protein, CTL epitope, molecular dynamics simulation