| 牛病毒性腹泻病毒NS3蛋白的生物信息学分析及多表位筛选 |
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| 引用本文： | 何金科,杨亚军,邓肖玉,何延华,张超,马忠臣,王勇,陈创夫.牛病毒性腹泻病毒NS3蛋白的生物信息学分析及多表位筛选[J].中国畜牧兽医,2019,46(12):3475-3485. |
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| 作者姓名： | 何金科 杨亚军 邓肖玉 何延华 张超 马忠臣 王勇 陈创夫 |
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| 作者单位： | 1. 石河子大学生命科学学院, 石河子 832000;2. 石河子大学动物科技学院, 石河子 832000 |
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| 基金项目： | 国家自然科学基金项目（U1803236）；兵团重大科技项目（2017AA003） |
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| 摘 要： | 本研究旨在对牛病毒性腹泻病毒（BVDV）NS3蛋白进行生物信息学分析及T细胞和B细胞表位的筛选。从GenBank数据库中找到NS3蛋白的氨基酸序列，用Expasy ProtParam在线服务器分析所得序列理化性质。使用TMHMM Server分析跨膜结构域，使用DNAStar软件预测NS3蛋白的二级结构，为了更准确地预测蛋白质的二级结构，使用SOPMA分析软件进行了二次预测。使用Phyre2在线服务器预测NS3蛋白的三级结构，并用Raswin软件标出各个元素所处的位置。使用4种预测软件（BCPREDS、ABCpred、BepiPred和SVMTriP）分析NS3蛋白的线性B细胞表位，使用NetMHCⅡpan预测CD4+ T细胞表位，使用NetBoLApan和IEDB预测CD8+ T细胞表位，将所得到的结果进行T细胞和B细胞表位筛选。结果表明，NS3蛋白质由683个氨基酸组成，分子质量为75 ku，理论等电点（pI）为8.31，化学式为C3347H5346N916O1009S28，不稳定系数为35.93，平均亲水性（GRAVY）值为-0.267，表明NS3为稳定性亲水蛋白质。TMHMM结果显示，NS3蛋白不具有跨膜结构域。SOPMA结果表明，在NS3蛋白的二级结构中，α-螺旋、β-折叠、β-转角和无规则卷曲分别约占30.75%、22.55%、8.35%和38.35%，用DNAStar软件分别标出了α-螺旋、β-折叠、β-转角和无规则卷曲所处的位置。运用4种不同的B细胞预测软件筛选出8个线性表位：12-16、289-298、349-360、394-407、421-432、489-498、515-525和665-679位氨基酸。用NetMHCⅡpan筛选出4个T细胞表位：248-262、315-320、400-414和482-496位氨基酸。本研究为BVDV NS3蛋白优势抗原的筛选提供了理论依据。
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| 关 键 词： | 牛病毒性腹泻病毒(BVDV) NS3蛋白 生物信息学分析 B细胞 T细胞 表位筛选 |
| 收稿时间： | 2019-07-22 |
Bioinformatics Analysis and Multi-epitope Screening of NS3 Protein of Bovine Viral Diarrhea Virus |
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| HE Jinke,YANG Yajun,DENG Xiaoyu,HE Yanhua,ZHANG Chao,MA Zhongchen,WANG Yong,CHEN Chuangfu.Bioinformatics Analysis and Multi-epitope Screening of NS3 Protein of Bovine Viral Diarrhea Virus[J].China Animal Husbandry & Veterinary Medicine,2019,46(12):3475-3485. |
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| Authors: | HE Jinke YANG Yajun DENG Xiaoyu HE Yanhua ZHANG Chao MA Zhongchen WANG Yong CHEN Chuangfu |
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| Institution: | 1. College of Life Sciences, Shihezi University, Shihezi 832000, China;2. College of Animal Science and Technology, Shihezi University, Shihezi 832000, China |
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| Abstract: | This study was aimed to perform bioinformatics analysis and screening of T cell and B cell epitopes for bovine viral diarrhea virus (BVDV) NS3 protein.First,the amino acid sequence of the NS3 protein was found in GenBank database.The resulting sequence was analyzed for physicochemical properties using an Expasy ProtParam online server.Then TMHMM Server was used to analyze the transmembrane domain.The DNAStar software was used to predict the secondary structure of the NS3 protein.To more accurately predict the secondary structure of a protein,the SOPMA analysis software performed a second prediction.The Phyre2 online server was used to predict the tertiary structure of the NS3 protein,and Raswin software was used to identify the location of each element.Linear B cell epitopes of NS3 protein were analyzed by four predictive software (BCPREDS,ABCpred,BepiPred and SVMTriP),CD4+ T cell epitopes were predicted by NetMHCⅡpan,NetBoLApan and IEDB were used to predict CD8+ T cell epitopes.Finally,the results obtained were screened for T cell and B cell epitopes.The results showed that the NS3 protein consisted of 683 amino acids,the molecular weight was 75 ku,the theoretical pI value was 8.31,chemical formula was C3347H5346N916O1009S28,the instability coefficient was 35.93,the average value of hydrophilicity (GRAVY) was -0.267,it was indicated that NS3 was a stable and hydrophilic protein.The TMHMM results showed that the NS3 protein did not have a transmembrane domain.SOPMA results showed that in the secondary structure of NS3 protein,α-helix β-fold,β-turn and random coil accounted for about 30.75%,22.55%,8.35% and 38.35%,respectively.DNAStar software marked their respective position.Eight linear epitopes were screened using four different B cell prediction software:12-16,289-298,349-360,394-407,421-432,489-498,515-525 and 665-679 amino acids.Four T cell epitopes were screened using NetMHCⅡpan:248-262,315-320,400-414 and 482-496 amino acids.This study provided a theoretical basis for the screening of the dominant antigen of NS3 protein in BVDV. |
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| Keywords: | bovine viral diarrhea virus (BVDV) NS3 protein bioinformatics analysis B cells T cells epitope screening |
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