Rauta Pradipta Ranjan, Ashe Sarbani, Nayak Debasis, Nayak Bismita
Immunology and Molecular Medicine Laboratory, Department of Life Science, National Institute of Technology, Rourkela, Odisha, 769008 India.
Immunology and Molecular Medicine Laboratory, Department of Life Science, National Institute of Technology, Rourkela, Odisha, 769008 India.
Comput Biol Chem. 2016 Dec;65:61-68. doi: 10.1016/j.compbiolchem.2016.10.004. Epub 2016 Oct 12.
Virulence-related outer membrane proteins (Omps) are expressed in bacteria (Gram-negative) such as V. cholerae and are vital to bacterial invasion in to eukaryotic cell and survival within macrophages that could be best candidate for development of vaccine against V. cholerae. Applying in silico approaches, the 3-D model of the Omp was developed using Swiss model server and validated byProSA and Procheck web server. The continuous stretch of amino acid sequences 26mer: RTRSNSGLLTWGDKQTITLEYGDPAL and 31mer: FFAGGDNNLRGYGYKSISPQDASGALTGAKY having B-cell binding sites were selected from sequence alignment after B cell epitopes prediction by BCPred and AAP prediction modules of BCPreds. Further, the selected antigenic sequences (having B-cell epitopes) were analyzed for T-cell epitopes (MHC I and MHC II alleles binding sequence) by using ProPred 1 and ProPred respectively. The epitope (9mer: YKSISPQDA) that binds to both the MHC classes (MHC I and MHC II) and covers maximum MHC alleles were identified. The identified epitopes can be useful in designing comprehensive peptide vaccine development against V. cholerae by inducing optimal immune response.
与毒力相关的外膜蛋白（Omps）在诸如霍乱弧菌等细菌（革兰氏阴性菌）中表达，对于细菌侵入真核细胞以及在巨噬细胞内存活至关重要，这可能是开发霍乱弧菌疫苗的最佳候选对象。应用计算机模拟方法，使用瑞士模型服务器构建了Omp的三维模型，并通过ProSA和Procheck网络服务器进行了验证。通过BCPred的BCell表位预测和AAP预测模块进行B细胞表位预测后，从序列比对中选择了具有B细胞结合位点的连续氨基酸序列26聚体：RTRSNSGLLTWGDKQTITLEYGDPAL和31聚体：FFAGGDNNLRGYGYKSISPQDASGALTGAKY。此外，分别使用ProPred 1和ProPred对所选的抗原序列（具有B细胞表位）进行T细胞表位（MHC I和MHC II等位基因结合序列）分析。鉴定出了与两种MHC类别（MHC I和MHC II）结合且覆盖最大数量MHC等位基因的表位（9聚体：YKSISPQDA）。所鉴定的表位可通过诱导最佳免疫反应，在设计针对霍乱弧菌的综合肽疫苗开发中发挥作用。
