多房棘球蚴四跨膜蛋白的生物信息学分析
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摘要
目的采用生物信息学方法分析多房棘球蚴四跨膜蛋白(EmTspan)的结构与抗原表位。方法从NCBI数据库中下载EmTspan蛋白的氨基酸序列,运用ProtParam、ProtScale、SOSUI、DNASTAR、SignalP、Cell-PLoc、SOMPA、NetPhos、Motif Scan、Phyre 2、TMHMM等生物信息学软件分析蛋白质的理化性质、亚细胞定位、跨膜区域、磷酸化和翻译后修饰位点及二、三级结构,利用ABCpred、IEDB、SYFPEITHI软件分析并预测B细胞、T细胞的抗原表位,通过MEGA-X软件构建Tspan的分子进化树。结果 EmTspan蛋白是由236个氨基酸序列组成,分子式为C_(1163)H_(1853)N_(291)O_(315)S_(21),不稳定指数为32.77,为稳定蛋白;有4个跨膜区,定位于细胞膜;二级结构中,α螺旋占46.19%,β折叠占20.34%,β转角占8.05%,无规则卷曲占25.42%;EmTspan蛋白含有的B细胞、TCL细胞及Th细胞的抗原表位分别为7、15、8个;分子进化分析多房棘球蚴的Tspan和小口膜壳绦虫的Tspan亲缘关系较近。结论生物信息学预测EmTspan蛋白存在多个潜在的B细胞及T细胞表位,抗原性好,可为多房棘球蚴疫苗的研制、免疫诊断等提供理论依据。
Objective To use bioinformatic software to predict and analyze the structure and epitopes of tetraspanin proteins from Echinococcus multilocularis(EmTspan). Methods Amino acid sequences of EmTspan proteins were downloaded from the NCBI database. ProtParam, ProtScale, SOSUI, DNASTAR, SignalP, Cell-PLoc, SOMPA, NetPhos, Motif Scan, Phyre 2, TMHMM, and other bioinformatic software were used to predict and analyze the physicochemical properties, subcellular localization, transmembrane regions, phosphorylation and post-translational modification sites, and secondary and tertiary structures of the protein. B-and T-cell epitopes were analyzed and predicted using the software ABCpred, IEDB, and SYFPEITHI. A molecular evolutionary tree was constructed for Tspan using MEGA-X. Results EmTspan protein consisted of 236 amino acids, its molecular formula was C_(1163)H_(1853)N_(291)O_(315)S_(21), and its instability index was 32.77, so it is a stable protein. The protein has four transmembrane regions located in the cell membrane. α-helices account for 46.19% of the protein's secondary structure, β-sheets account for 20.34%, β-turns account for 8.05%, and random coils account for 25.42%. EmTspan protein contains many phosphorylation and post-translational modification sites. The protein has 7 B-cell epitopes, 15 CTL-cell epitopes, and 8 Th-cell epitopes. The Tspan of E. multilocularis is closely related to the Tspan of Hymenolepis microstoma. Conclusion According to bioinformatics, EmTspan protein is predicted to have several B-and T-cell epitopes and good antigenicity. These findings can provide a theoretical basis for immunodiagnosis of echinococcosis and the development of vaccine against E. multilocularis.
Objective To use bioinformatic software to predict and analyze the structure and epitopes of tetraspanin proteins from Echinococcus multilocularis(EmTspan). Methods Amino acid sequences of EmTspan proteins were downloaded from the NCBI database. ProtParam, ProtScale, SOSUI, DNASTAR, SignalP, Cell-PLoc, SOMPA, NetPhos, Motif Scan, Phyre 2, TMHMM, and other bioinformatic software were used to predict and analyze the physicochemical properties, subcellular localization, transmembrane regions, phosphorylation and post-translational modification sites, and secondary and tertiary structures of the protein. B-and T-cell epitopes were analyzed and predicted using the software ABCpred, IEDB, and SYFPEITHI. A molecular evolutionary tree was constructed for Tspan using MEGA-X. Results EmTspan protein consisted of 236 amino acids, its molecular formula was C_(1163)H_(1853)N_(291)O_(315)S_(21), and its instability index was 32.77, so it is a stable protein. The protein has four transmembrane regions located in the cell membrane. α-helices account for 46.19% of the protein's secondary structure, β-sheets account for 20.34%, β-turns account for 8.05%, and random coils account for 25.42%. EmTspan protein contains many phosphorylation and post-translational modification sites. The protein has 7 B-cell epitopes, 15 CTL-cell epitopes, and 8 Th-cell epitopes. The Tspan of E. multilocularis is closely related to the Tspan of Hymenolepis microstoma. Conclusion According to bioinformatics, EmTspan protein is predicted to have several B-and T-cell epitopes and good antigenicity. These findings can provide a theoretical basis for immunodiagnosis of echinococcosis and the development of vaccine against E. multilocularis.
引文
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[7] 杨梅, 李文桂. 多房棘球绦虫重组Bb-EmⅡ/3-Em14-3-3疫苗诱导小鼠细胞因子变化的研究[J]. 细胞与分子免疫学杂志, 2008, 24(8): 781-4.
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[9] Jiang X, Zhang J, Huang Y. Tetraspanins in cell migration[J]. Cell Adhes Migr, 2015, 9(5): 406-15.
[10] Chen L, Yuan D, Zhao R, et al. Suppression of TSPAN1 by RNA interference inhibits proliferation and invasion of colon cancer cells in vitro[J]. Tumori J, 2010, 96(5): 744-50.
[11] Holters S, Anacker J, Jansen L, et al. Tetraspanin 1 promotes invasiveness of cervical cancer cells[J]. Int J Oncol, 2013, 43(2): 503-12.
[12] Chen Y, Peng W, Lu Y, et al. MiR-200a enhances the migrations of A549 and SK-MES-1 cells by regulating the expression of TSPAN1[J]. J Biosci, 2013, 38(3): 523-32.
[13] Chen L, Zhu Y, Li H, et al. Knockdown of TSPAN1 by RNA silencing and antisense technique inhibits proliferation and infiltration of human skin squamous carcinoma cells[J]. Tumori J, 2010, 96(2): 289-95.
[14] Yanez-Mo M, Mittelbrunn M, Sanchez-Madrid F. Tetraspanins and intercellular interactions[J]. Microcirculation, 2001, 8(3): 153-68.
[15] Levy S, Shoham T. Protein-protein interactions in the tetraspanin web[J]. Physiology, 2005, 20(4): 218-24.
[16] 孙琪, 张辉, 马语曼, 等. 蛋白质翻译后修饰及其生物学功能研究进展[J]. 中华老年心脑血管病杂志, 2014, 16(9): 989-91.
[17] 龚非力. 医学免疫学[M]. 科学出版社, 2016: 1-464.
[18] Hopp TP, Woods KR. Prediction of protein antigenic determinants from amino acid sequences[J]. PNAS, 1981, 78(6): 3824-8.
[19] Wang F, Ye B. In silico cloning and B/T cell epitope prediction of triosephosphate isomerase from Echinococcus granulosus[J]. Parasitol Res, 2016, 115(10): 3991-8.
[20] Testa JS, Vivekananda S, Julie H, et al. MHC class I-presented T cell epitopes identified by immunoproteomics analysis are targets for a cross reactive influenza-specific T cell response[J]. Plos One, 2012, 7(11): e48484.
[21] Taneja V, Giphart MJ, Verduijn W, et al. Polymorphism of HLA-DRB,-DQA1, and-DQB1 in rheumatoid arthritis in Asian Indians: association with DRB1*0405 and DRB1*1001[J]. Human Immunol, 1996, 46(1): 35-41.
[22] Weyand CM, Xie C, Goronzy JJ. Homozygosity for the HLA-DRB1 allele selects for extraarticular manifestations in rheumatoid arthritis[J]. J Clin Invest, 1992, 89(6): 2033-39.
[23] 张耀刚, 曹得萍, 李超群, 等. 细粒棘球绦虫转酮醇酶生物信息学分析[J]. 中国病原生物学杂志, 2017, 12(3): 233-7.
[2] Torgerson P R, Macpherson CNL. The socioeconomic burden of parasitic zoonoses: global trends[J]. Vet Parasit, 2011, 182(1): 79-95.
[3] Jenkins DJ. WHO/OIE manual on Echinococcosis, in humans and animals: a public health problem of global concern [J]. Int J Parasit, 2001, 31(14): 1717-8.
[4] 邵英梅, 蒋铁民, 吐尔干艾力·阿吉, 等. 根治性及准根治性手术治疗终末期肝泡型包虫病[J]. 中华消化外科杂志, 2011, 10(4): 296-8.
[5] Kouguchi H, Matsumoto J, Katoh Y, et al. The vaccination potential of EMY162 antigen against Echinococcus multilocularis infection[J]. Biocheml Biophys Res Commun, 2007, 363(4): 915-20.
[6] 李文桂, 陈雅棠. 多房棘球绦虫Em18研究进展[J]. 中国人兽共患病学报, 2009, 25(1): 67-9.
[7] 杨梅, 李文桂. 多房棘球绦虫重组Bb-EmⅡ/3-Em14-3-3疫苗诱导小鼠细胞因子变化的研究[J]. 细胞与分子免疫学杂志, 2008, 24(8): 781-4.
[8] Qin C, Sun Y, Dong Y. A New Method for Identifying essential proteins based on network topology properties and protein complexes[J]. Plos One, 2016, 11(8): e0161042.
[9] Jiang X, Zhang J, Huang Y. Tetraspanins in cell migration[J]. Cell Adhes Migr, 2015, 9(5): 406-15.
[10] Chen L, Yuan D, Zhao R, et al. Suppression of TSPAN1 by RNA interference inhibits proliferation and invasion of colon cancer cells in vitro[J]. Tumori J, 2010, 96(5): 744-50.
[11] Holters S, Anacker J, Jansen L, et al. Tetraspanin 1 promotes invasiveness of cervical cancer cells[J]. Int J Oncol, 2013, 43(2): 503-12.
[12] Chen Y, Peng W, Lu Y, et al. MiR-200a enhances the migrations of A549 and SK-MES-1 cells by regulating the expression of TSPAN1[J]. J Biosci, 2013, 38(3): 523-32.
[13] Chen L, Zhu Y, Li H, et al. Knockdown of TSPAN1 by RNA silencing and antisense technique inhibits proliferation and infiltration of human skin squamous carcinoma cells[J]. Tumori J, 2010, 96(2): 289-95.
[14] Yanez-Mo M, Mittelbrunn M, Sanchez-Madrid F. Tetraspanins and intercellular interactions[J]. Microcirculation, 2001, 8(3): 153-68.
[15] Levy S, Shoham T. Protein-protein interactions in the tetraspanin web[J]. Physiology, 2005, 20(4): 218-24.
[16] 孙琪, 张辉, 马语曼, 等. 蛋白质翻译后修饰及其生物学功能研究进展[J]. 中华老年心脑血管病杂志, 2014, 16(9): 989-91.
[17] 龚非力. 医学免疫学[M]. 科学出版社, 2016: 1-464.
[18] Hopp TP, Woods KR. Prediction of protein antigenic determinants from amino acid sequences[J]. PNAS, 1981, 78(6): 3824-8.
[19] Wang F, Ye B. In silico cloning and B/T cell epitope prediction of triosephosphate isomerase from Echinococcus granulosus[J]. Parasitol Res, 2016, 115(10): 3991-8.
[20] Testa JS, Vivekananda S, Julie H, et al. MHC class I-presented T cell epitopes identified by immunoproteomics analysis are targets for a cross reactive influenza-specific T cell response[J]. Plos One, 2012, 7(11): e48484.
[21] Taneja V, Giphart MJ, Verduijn W, et al. Polymorphism of HLA-DRB,-DQA1, and-DQB1 in rheumatoid arthritis in Asian Indians: association with DRB1*0405 and DRB1*1001[J]. Human Immunol, 1996, 46(1): 35-41.
[22] Weyand CM, Xie C, Goronzy JJ. Homozygosity for the HLA-DRB1 allele selects for extraarticular manifestations in rheumatoid arthritis[J]. J Clin Invest, 1992, 89(6): 2033-39.
[23] 张耀刚, 曹得萍, 李超群, 等. 细粒棘球绦虫转酮醇酶生物信息学分析[J]. 中国病原生物学杂志, 2017, 12(3): 233-7.
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