Antibody molecules interact with antigen proteins through the epitope area,where the epitope residues are found to be discontinuous or spatial or conformational rather than linear on the protein surface.There are various computational algorithms to predict the spatial epitopes,and each of them have an outstanding performance based on their individual testing dataset.In this work,an independent dataset was created through collection of the epitope residual sites which have been confirmed by experiments. Based on this dataset,6 popular web-servers developed for B-cell structural epitope prediction,including SEPPA,CEP,DiscoTope,ElliPro,PEPOP and BEpro,were evaluated and compared according to sensitivity,the positive predictive value,the successful pick-up rate and the area under the curve of the receiver operator characteristic(AUC).The results showed that the general performance of spatial epitope prediction tools did obtain substantial advancement,and SEPPA gave the best performance among the 6 tools.However,the current prediction accuracy was still far from satisfaction.Moreover,our comparison elucidated that the performance of the web-servers was significantly affected by their training datasets and the algorithms adopted.In this sense,the results of our research may improve the design of B-cell epitope prediction tools and provide additional clues when the users utilize these tools in their related research.
Interleukin-2 （IL）-2 signaling plays a pivotal role in the activation of immune responses, and drugs that block this pathway have been shown to be effective for the immunosuppression in patients with organ transplantation to alleviate/eliminate allograft rejection. The first humanized monoclonal antibody （mAb） daclizumab falls into this category and shows high specificity and affinity against a key component of the IL-2 receptor complex, namely IL-2Ra. To reveal the molecular mechanism of the inhibition of the IL-2 signaling pathway by dacllzumab, we determined the crystal structures of the daclizumab Fab in free form and in complex with the IL-2Ra ectodomain at 2.6 and 2.8 A resolution, respectively. The daclizumab Fab adopts a similar conformation in the presence or absence of the IL- 2Ra ectodomain. The antigen-binding site of daclizumab is mainly composed of live complementarity determining regions （CDRs） that form a large positively charged surface depression and two flanking patches that are generally hydrophobic. The conformational epitope consists of several discontinuous segments of the IL-2Ru ectodomain, a large portion of which overlaps with the regions that interact with IL-2, suggesting that the binding of daclizumab to IL-2Ra would prevent the IL-2 binding to IL-2Ra and the subsequent formation of the IL-2fIL-2Ra[~/c complex, and therefore block the IL-2 signaling pathway. These results also have implications for the design and development of improved mAb drugs targeting IL-2Ra.
