草莓轻型黄边病毒外壳蛋白抗原表位预测

doi:10.7668/hbnxb.2016.S1.019

华北农学报 ›› 2016, Vol. 31 ›› Issue (S1): 106-111. doi: 10.7668/hbnxb.2016.S1.019

所属专题： 草莓；

• 作物遗传育种·种质资源·生物技术 • 上一篇下一篇

草莓轻型黄边病毒外壳蛋白抗原表位预测

邓子兵¹, 马建忠¹, 王永刚¹, 杨菊梅¹, 魏艳¹, 潘博², 李印武²

1. 兰州理工大学生命科学与工程学院, 甘肃兰州 730050;
2. 甘肃启明星节能科技有限公司, 甘肃兰州 730913

收稿日期:2016-08-13 出版日期:2016-12-28
通讯作者: 马建忠(1963-),男,甘肃兰州人,研究员,博士,主要从事植物分子生物学研究。
作者简介:邓子兵(1989-),男,甘肃民乐人,在读硕士,主要从事植物基因工程研究。
基金资助:
甘肃省科技计划项目（1504WKCA020）；甘肃启明星节能科技有限公司；国家大学生创新创业训练项目（DC2015085）

Prediction of Antigens of the Coat Protein of the Strawberry mild yellow edge virus

DENG Zibing¹, MA Jianzhong¹, WANG Yonggang¹, YANG Jumei¹, WEI Yan¹, PAN Bo², LI Yinwu²

1. School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou 730050, China;
2. Gansu Venus Energy Saving Company Co., Ltd., Lanzhou 730913, China

Received:2016-08-13 Published:2016-12-28

摘要/Abstract

摘要： 抗原表位是抗体识别并结合抗原的部位。抗原表位的预测有助于重组抗原的设计、快速筛选和高活性抗原的快速制备。通过DNAStar、ExPASy、TMHMM Sever2.0和IEDB等软件对草莓轻型黄边病毒的外壳蛋白的二级结构、理化及生物学性质进行了分析。分析结果显示，草莓轻型黄边病毒的外壳蛋白中不存在跨膜区域；平均亲水性为-0.252，属于可溶性蛋白；潜在的抗原表位有5个，平均抗原指数为0.026 5~0.077 3。预测的上述5个抗原表位是否有抗原活性及其活性强弱仍有待于相应的试验论证。

关键词: 草莓轻型黄边病毒, 外壳蛋白, 抗原表位, 结构预测

Abstract: An epitope of antigen is a key part recognized and combined by antibodies. Epitope prediction is helpful to recombinant antigen design and rapid screening,and to preparation of high activity antigen. In this paper,the coat protein of the Strawberry mild yellow edge virus was analyzed and predicted for its secondary structure and physicochemical and biological properties by programs including DNAStar,ExPASy,TMHMM Sever2.0,and IEDB. The results showed that there was no transmembrane regions in the SMYEV coat protein. The average hydrophility of the coat protein was -0.252,which belonged to a soluble protein. There were 5 potential antigen epitopes,of which values of the average antigen index range from 0.026 5 to 0.077 3. Antigen activities of the above predicted epitopes,however,are still to be verified by experiments.

Key words: Strawberry mild yellow edge virus, Coat protein, Epitope, Prediction

中图分类号:

Q78
S668.03

邓子兵, 马建忠, 王永刚, 杨菊梅, 魏艳, 潘博, 李印武. 草莓轻型黄边病毒外壳蛋白抗原表位预测[J]. 华北农学报, 2016, 31(S1): 106-111. doi: 10.7668/hbnxb.2016.S1.019.

DENG Zibing, MA Jianzhong, WANG Yonggang, YANG Jumei, WEI Yan, PAN Bo, LI Yinwu. Prediction of Antigens of the Coat Protein of the Strawberry mild yellow edge virus[J]. ACTA AGRICULTURAE BOREALI-SINICA, 2016, 31(S1): 106-111. doi: 10.7668/hbnxb.2016.S1.019.

http://www.hbnxb.net/CN/Y2016/V31/IS1/106

参考文献

[1] 王国平.我国草莓病毒种类鉴定研究初报[J].中国果树,1988(2):32-34.
[2] Chen J,Zhang H P,Feng M F,et al. Transcriptome analysis of woodland strawberry(Fragaria vesca)response to the infection by Strawberry vein banding virus(SVBV)[J]. Virology Journal,2016,13(1):1-7.
[3] Torrico A K,Celli M G,Cafrune E E,et al. Genetic variability and recombination analysis of the coat protein gene of Strawberry mild yellow edge virus[J]. Australasian Plant Pathology,2016,45(4):401-409.
[4] Thompson J R1,Jelkmann W. Strain diversity and conserved genome elements in Strawberry mild yellow edge virus[J]. Arch Virol,2004(10):1897-1909
[5] Jelkmann W,Maiss E W,Martin R R.The nucleotide sequence and genome organization of Strawberry mild yellow edge-associated potexvirus[J].Journal of General Virology,1992,73(2):475-479.
[6] Bhagwat B,Dickison V,Su L,et al. Molecular characterization of divergent Strawberry mild yellow edge virus isolates from eastern Canada[J]. Journal of Phytopathology,2015,596(10):1681-1684.
[7] 杨洪一,张志宏,李丽丽,等.利用多重RT-PCR技术检测草莓病毒的研究[J].植物病理学报,2007,37(5):549-552.
[8] Bhagwat B,Dickison V,Ding X L,et al. Genome sequence analysis of five Canadian isolates of Strawberry mottle virus reveals extensive intra-species diversity and a longer RNA2 with increased coding capacity compared to a previously characterized European isolate[J]. Archives of Virology,2016,161(6):1657-1663.
[9] 徐东生.我国草莓脱毒研究进展[J].湖北农业科学,2002(3):43-46.
[10] 蒋明杉,林霞,王升,等.草莓病毒检测技术[J].北方果树,2001(2):13-14.
[11] 蔡斌华,张计育,黄海,等.结合内标的RT-PCR技术检测草莓轻型黄边病毒(SMYEV)[J].江苏农业学报,2009,25(6):1432-1434.
[12] 王正华,邵永春,尹涛.草莓病毒的检测方法及症状识别[J].山东农业科学,1999(1):31-33.
[13] Cui M U,Zhang Z H,Liu Y X,et al. Cloning,sequence analysis and prokaryotic expression of coat protein gene of Strawberry mild yellow edge virus[J]. Acta Agriculturae Boreali-sinica,2012,27(1):30-34.
[14] Li L I. RNA secondary structure and sequence variability of the 3'end of Strawberry mild yellow edge virus genome[C]//International Conference on Bioinformatics and Biomedical Engineering,2009:1-4.
[15] Sompuram S R,Bastas G,Vani K,et al. Accurate identification of paraprotein antigen targets by epitope Reconstruction[J]. Blood,2008,111(1):302-308.
[16] Lafarga T. O'connor P,hayes M.identification of novel dipeptidyl peptidase-Ⅳ and angiotensin-Ⅰ-converting enzyme inhibitory peptides from meat proteins using in silico,analysis[J]. Peptides,2014,59(9):53-62.
[17] Mishra P K,Pandey R,Chaudhry U,et al. Identification of putative secretory and membranous proteins of Chlamydia trachomatis using bioinformatics tools[J]. BMC Infectious Diseases,2014,14(S3):1-1.
[18] Vita R,Overton J A,Greenbaum J A,et al. Query enhancement through the practical application of ontology:the IEDB and OBI[J]. Journal of Biomedical Semantics,2013,4(S1):1-10.
[19] 吴玉章,朱锡华.蛋白质抗原表位的研究[J].科学:中文版,1994(1):93-94.
[20] Wu Y Z,Zhu X H. A new approach for B-cell epitope prediction in viral proteins[J]. Chinese Science Bulletin,1995,40(9):761-763.
[21] Florea L,Halldorsson B,Kohlbacher O,et al. Epitope predictional gorithms for peptide-based vaccine design[J]. Proceedings of Computer Society Bioinformatics Conference,2003(2):17-26.
[22] 万涛,孙涛,吴家金.蛋白顺序性抗原决定簇的多参数综合预测[J].中国免疫学杂志,1997,13(6):329-333.
[23] 吴玉章,朱锡华.Pre-S2蛋白抗原表位及二级结构的预测与比较[J].免疫学杂志,2006,25(6):593-595.
[24] 王文敬,李明,董文其.鼠疫耶尔森菌LcrV抗原B细胞表位的预测[J].中国地方病学杂志,2006,25(6):593-595.
[25] Hassan K A,Badr A,Hegazy A F. On predicting conformational b-cell epitopes:a comparative study and a new model[J]. American Journal of Bioinformatics Research,2011,1(1):6-17.

选择文件类型/文献管理软件名称

选择包含的内容

草莓轻型黄边病毒外壳蛋白抗原表位预测

Prediction of Antigens of the Coat Protein of the Strawberry mild yellow edge virus

PDF

可视化

被引次数

摘要/Abstract

引用本文

使用本文

参考文献

相关文章 13

编辑推荐

Metrics

本文评价

[1]	李林杰, 常秋燕, 马鹏, 王悦萦, 马晓霞, 柏家林. PPRV Nigeria75/1 H蛋白原核表达及抗原表位预测[J]. 华北农学报, 2018, 33(5): 111-116.
[2]	韩磊, 迟胜起, 张剑峰. 番茄褪绿病毒CP基因克隆、序列分析及原核表达[J]. 华北农学报, 2016, 31(4): 57-62.
[3]	陈瑾, 黄春娟, 于晓明, 侯立婷, 乔绪稳, 郑其升, 侯继波. PEDV亚单位疫苗免疫增强剂的筛选[J]. 华北农学报, 2016, 31(2): 205-210.
[4]	金凤媚, 薛俊, 宋建, 于海涛, 段红英. 天津地区番茄褪绿病毒的分子检测与基因组部分序列分析[J]. 华北农学报, 2016, 31(2): 23-27.
[5]	于翠梅, 张志宏, 刘月学, 马跃, 李贺, 代红艳. 草莓轻型黄边病毒CP基因的克隆、序列分析及原核表达[J]. 华北农学报, 2012, 27(1): 30-34.
[6]	肖治军, 张改平, 杨汉春, 杨艳艳, 赵东, 李学伍, 邓瑞广, 柴书军, 邢广旭, 杨继飞. 传染性法氏囊病病毒VP2蛋白B细胞抗原表位免疫小鼠试验[J]. 华北农学报, 2010, 25(2): 233-235.
[7]	谢昆, 朱志雄, 杨军. 鸡集落刺激因子(CSF)基因的克隆、序列分析及蛋白结构预测[J]. 华北农学报, 2009, 24(2): 36-41.
[8]	贾海丽, 韩立强, 杨国宇, 钟凯, 郭豫杰, 台玉磊, 刘涛, 李平, 王艳玲. CD147基因在家兔肠道的克隆与结构预测河南郑州 450002[J]. 华北农学报, 2009, 24(1): 93-96.
[9]	周建华, 丛国正, 高闪电, 常惠芸. 口蹄疫OA/58病毒株VP2蛋白结构模拟与B细胞抗原表位的分析[J]. 华北农学报, 2008, 23(3): 1-4.
[10]	周建华, 丛国正, 高闪电, 常惠芸. FMDV OA/58病毒株VP1蛋白结构构建与B细胞抗原表位的预测[J]. 华北农学报, 2007, 22(4): 176-179.
[11]	田兆丰, 裘季燕, 丁翠珍, 刘伟成, 魏蕾, 刘德文. 黄瓜花叶病毒番茄蕨叶分离物外壳蛋白基因的克隆和序列分析[J]. 华北农学报, 2007, 22(4): 203-206.
[12]	周巧梅, 谢晓亮, 温春秀, 马恢, 尹江, 吴志明. 河北省马铃薯S病毒株系的分子鉴定研究[J]. 华北农学报, 2007, 22(3): 39-42.
[13]	周钟信, 粟密兰, 陈德芬, 宋兰英, 杨静惠. 辣椒诱导再生及黄瓜花叶病毒外壳蛋白基因转化研究初报[J]. 华北农学报, 1991, 6(4): 69-72.

模态框（Modal）标题

选择文件类型/文献管理软件名称

选择包含的内容

草莓轻型黄边病毒外壳蛋白抗原表位预测

Prediction of Antigens of the Coat Protein of the Strawberry mild yellow edge virus

PDF

可视化

被引次数

摘要/Abstract

引用本文

使用本文

参考文献

相关文章 13

编辑推荐

Metrics

本文评价