Objective:To predict B cell and T cell epitopes of 22-kDa,47-kDa,56-kDa and 58-kDa proteins.Methods:The sequences of 22-kDa,47-kDa,56-kDa and 58-kDa proteins which were derived from Orientia tsutsugamushi were analyze...Objective:To predict B cell and T cell epitopes of 22-kDa,47-kDa,56-kDa and 58-kDa proteins.Methods:The sequences of 22-kDa,47-kDa,56-kDa and 58-kDa proteins which were derived from Orientia tsutsugamushi were analyzed by SOPMA,DNAstar,Bcepred,ABCpred,NetMHC,NetMHCⅡand IEDB.The 58-kDa tertiary structure model was built by MODELLER9.17.Results:The 22-kDa B-cell epitopes were located at positions 194-200,20-26 and 143-154,whereas the T-cell epitopes were located at positions 154-174,95-107,17-25 and 57-65.The 47-kD a protein B-cell epitopes were at positions 413-434,150-161 and 283-322,whereas the T-cell epitopes were located at positions 129-147,259-267,412-420 and 80-88.The 56-kDa protein B-cell epitopes were at positions 167-173,410-419 and 101-108,whereas the T-cell epitopes were located at positions 88-104,429-439,232-240 and 194-202.The 58-kDa protein B-cell epitopes were at positions 312-317,540-548 and 35-55,whereas the T-cell epitopes were located at positions 415-434,66-84 and 214-230.Conclusions:We identified candidate epitopes of 22-kDa,47-kDa,56-kDa and 58-kDa proteins from Orientia tsutsugamushi.In the case of 58-kDa,the dominant antigen is displayed on tertiary structure by homology modeling.Our findings will help target additional recombinant antigens with strong specificity,high sensitivity,and stable expression and will aid in their isolation and purification.展开更多
In order to identify continuous B-cell epitopes effectively and to increase the success rate of experimental identification, the modified Back Propagation artificial neural network (BP neural network) was used to pred...In order to identify continuous B-cell epitopes effectively and to increase the success rate of experimental identification, the modified Back Propagation artificial neural network (BP neural network) was used to predict the continuous B-cell epitopes, and finally the predictive model for the B-cells epitopes was established. Comparing with the other predictive models, the prediction performance of this model is more excellent (AUC = 0.723). For the purpose of verifying the performance of the model, the prediction to the SWISS PROT NUMBER: P08677 was carried on, and the satisfying results were obtained.展开更多
旨在通过免疫信息学方法预测非洲猪瘟病毒(ASFV)结构蛋白的T、B细胞表位,为非洲猪瘟(ASF)表位疫苗的设计研制提供参考。从NCBI和RCSB数据库获取ASFV蛋白质序列和三维结构,利用IEDB、DTU Health Tech等数据库的生物信息学工具对ASFV的5...旨在通过免疫信息学方法预测非洲猪瘟病毒(ASFV)结构蛋白的T、B细胞表位,为非洲猪瘟(ASF)表位疫苗的设计研制提供参考。从NCBI和RCSB数据库获取ASFV蛋白质序列和三维结构,利用IEDB、DTU Health Tech等数据库的生物信息学工具对ASFV的5种结构蛋白p72、p17、p49、M1249L和H240R的细胞毒性T细胞表位、线性B细胞和构象B细胞表位进行鉴定。结果显示:5种蛋白质均为亲水性,二级结构以无规则卷曲为主,仅M1249L例外;预测到抗原性良好、无毒、无致敏的细胞毒性T细胞优势表位27个,线性B细胞优势表位35个;预测到仅针对p72的构象B细胞优势表位2个。结论:ASFV的5种蛋白质可能具有多个潜在T、B细胞表位,其中B细胞表位相对占优,5种蛋白质中p72和M1249L最具疫苗研发前景,可结合蛋白质相关参数信息为构建ASF表位疫苗提供参考。展开更多
AIM To identify hepatitis C virus (HCV) core protein epitopes recognized by HLA-A2 restricted cytotoxic T lymphocyte (CTL).METHODS Utilizing the method of computer prediction followed by a 4 h 51 Cr-release assay conf...AIM To identify hepatitis C virus (HCV) core protein epitopes recognized by HLA-A2 restricted cytotoxic T lymphocyte (CTL).METHODS Utilizing the method of computer prediction followed by a 4 h 51 Cr-release assay confirmation.RESULTS The results showed that peripheral blood mononuclear cells (PBMC) obtained from two HLA-A2 positive donors who were infected with HCV could lyse autologous target cells labeled with peptide 'ALAHGVFAL (core TS0-158)'.The rates of specific lysis of the cells from the two donors were 37.5% and 15.8%,respectively. Blocking of the CTL response with anti-CD4 mAb caused no significant decrease of the specific lysis.But blocking of CTL response with anti-CD8 mAb could abolish the Iysis.CONCLUSION The peptide (core 150 - 158 ) is the candidate epitope recognized by HLA-A2 restricted CTL.展开更多
The B-cell epitopes of virus are associated with the antiviral drug and the vaccine screening. As the nucleotide sequences of neuraminidase (NA) of stain GD-01-06 were sequenced, we predicted the α-helix and β-fold ...The B-cell epitopes of virus are associated with the antiviral drug and the vaccine screening. As the nucleotide sequences of neuraminidase (NA) of stain GD-01-06 were sequenced, we predicted the α-helix and β-fold structure and the indexes of the flexible regions of secondary structure of NA with methods of the Hydrophilicity plot by Kyte-Doolittle, the Surface probability plot by Emini and the Antigenic index by Jameson-Wolf, and then screened statistically the parameters to predict B-cell epitopes by the Hierarchical cluster and the Bivariate correlation and the quartiles with SPSS 13.0. The impact of variation of amino acids in NA on its epitopes was analyzed. The predictive results were evaluated by Wu’s Antigenic Index and SWISS-MODEL. We found that the most possible epitopes on NA were located within or nearby its N-terminal Nos. 120―137, 81―84, 408―415, 273―282, 429―432, 356―368, 46―55, 146―155, 341―350 and 198―209, which were the dominant regions of NA epitopes. Peptide 120―137 including the glycoprotein domain (NGT126―128) was first chosen as the B-cell epitopes on NA. NA in H5N1 strain isolated after 2003 lacked in No. 53 amino acid (I), resulting in an increase in the surface flexible region of NA in GD-01-06 and an enlargement to their epitope regions (VEP46―48→ VEPISNTNFL46―55). Conclusively, prediction of the B-cell epitopes on the NA based on multiple parameters is useful for researches on the molecular immunology and drug screening and immuno-prophylaxis. A deletion of No. 53 amino acid (I) in NA in strain GD-01-06 might increase its antigenicity.展开更多
目的通过免疫信息学方法预测针对中东呼吸综合征冠状病毒(MERS-CoV)的T/B细胞抗原表位。方法从NCBI获取S蛋白序列后,运用MEGA11进行多序列比对及系统发育树构建,Expasy Protparam分析其理化性质,SOPMA预测其二级结构。随后对S蛋白建模...目的通过免疫信息学方法预测针对中东呼吸综合征冠状病毒(MERS-CoV)的T/B细胞抗原表位。方法从NCBI获取S蛋白序列后,运用MEGA11进行多序列比对及系统发育树构建,Expasy Protparam分析其理化性质,SOPMA预测其二级结构。随后对S蛋白建模并进行模型验证。再通过NetCTL-1.2、NetMHC pan EL 4.1和IEDB预测杀伤性T细胞(CTL)表位,NetMHCⅡpan-4.0、IFNepitope和IL-4pred预测辅助性T细胞表位(HTL),ABCpred和BepiPred-2.0预测线性B细胞表位(LBL),ElliPro工具预测构象B细胞表位(CBL)。最后对上述预测得到的线性表位进行抗原性、致敏性和毒性预测。结果S蛋白序列保守性较高,且来自不同国家的100个MERS-CoV S蛋白可以装进同一系统进化枝。理化性质分析结果显示,S蛋白亲水性总平均值为-0.078,在哺乳动物网织红细胞中半衰期约为30 h。模型验证结果显示构建的S蛋白模型是合理的。从S蛋白中预测得到具有抗原性、无致敏性和无毒性的CTL表位2个、HTL表位2个,LBL表位15个。ElliPro工具预测得到的CBL表位5个。结论MERS-CoV的S蛋白是亲水性的稳定蛋白;综合多种生物信息学方法可以预测得到T/B细胞抗原表位,对开发针对MERS-CoV的多肽疫苗具有重要借鉴意义。展开更多
基金supported by the Finance Science and Technology Project of Hainan Province(ZDYF2018106,ZDXM2014069)the National Natural Science Foundation of China(81860373,51762012,81760376,81460306 and 31160030)+4 种基金the Education Department of Hainan Province(Hnky2019ZD-27)the National Innovation and Entrepreneurship Training Program for College Students(201511810007,201811810024)the Innovation and Entrepreneurship Training Program for College Students of Hainan Province(S201911810034)Innovation and Entrepreneurship Training Program for College Students of Hainan Medical University(HYCX2014013,HYCX2018024)Research Unit of Island Emergency Medicine of Chinese Academy of Medical Sciences(2019RU013).
文摘Objective:To predict B cell and T cell epitopes of 22-kDa,47-kDa,56-kDa and 58-kDa proteins.Methods:The sequences of 22-kDa,47-kDa,56-kDa and 58-kDa proteins which were derived from Orientia tsutsugamushi were analyzed by SOPMA,DNAstar,Bcepred,ABCpred,NetMHC,NetMHCⅡand IEDB.The 58-kDa tertiary structure model was built by MODELLER9.17.Results:The 22-kDa B-cell epitopes were located at positions 194-200,20-26 and 143-154,whereas the T-cell epitopes were located at positions 154-174,95-107,17-25 and 57-65.The 47-kD a protein B-cell epitopes were at positions 413-434,150-161 and 283-322,whereas the T-cell epitopes were located at positions 129-147,259-267,412-420 and 80-88.The 56-kDa protein B-cell epitopes were at positions 167-173,410-419 and 101-108,whereas the T-cell epitopes were located at positions 88-104,429-439,232-240 and 194-202.The 58-kDa protein B-cell epitopes were at positions 312-317,540-548 and 35-55,whereas the T-cell epitopes were located at positions 415-434,66-84 and 214-230.Conclusions:We identified candidate epitopes of 22-kDa,47-kDa,56-kDa and 58-kDa proteins from Orientia tsutsugamushi.In the case of 58-kDa,the dominant antigen is displayed on tertiary structure by homology modeling.Our findings will help target additional recombinant antigens with strong specificity,high sensitivity,and stable expression and will aid in their isolation and purification.
文摘In order to identify continuous B-cell epitopes effectively and to increase the success rate of experimental identification, the modified Back Propagation artificial neural network (BP neural network) was used to predict the continuous B-cell epitopes, and finally the predictive model for the B-cells epitopes was established. Comparing with the other predictive models, the prediction performance of this model is more excellent (AUC = 0.723). For the purpose of verifying the performance of the model, the prediction to the SWISS PROT NUMBER: P08677 was carried on, and the satisfying results were obtained.
文摘旨在通过免疫信息学方法预测非洲猪瘟病毒(ASFV)结构蛋白的T、B细胞表位,为非洲猪瘟(ASF)表位疫苗的设计研制提供参考。从NCBI和RCSB数据库获取ASFV蛋白质序列和三维结构,利用IEDB、DTU Health Tech等数据库的生物信息学工具对ASFV的5种结构蛋白p72、p17、p49、M1249L和H240R的细胞毒性T细胞表位、线性B细胞和构象B细胞表位进行鉴定。结果显示:5种蛋白质均为亲水性,二级结构以无规则卷曲为主,仅M1249L例外;预测到抗原性良好、无毒、无致敏的细胞毒性T细胞优势表位27个,线性B细胞优势表位35个;预测到仅针对p72的构象B细胞优势表位2个。结论:ASFV的5种蛋白质可能具有多个潜在T、B细胞表位,其中B细胞表位相对占优,5种蛋白质中p72和M1249L最具疫苗研发前景,可结合蛋白质相关参数信息为构建ASF表位疫苗提供参考。
基金the National Nature Science Foundation of China,No.39800121
文摘AIM To identify hepatitis C virus (HCV) core protein epitopes recognized by HLA-A2 restricted cytotoxic T lymphocyte (CTL).METHODS Utilizing the method of computer prediction followed by a 4 h 51 Cr-release assay confirmation.RESULTS The results showed that peripheral blood mononuclear cells (PBMC) obtained from two HLA-A2 positive donors who were infected with HCV could lyse autologous target cells labeled with peptide 'ALAHGVFAL (core TS0-158)'.The rates of specific lysis of the cells from the two donors were 37.5% and 15.8%,respectively. Blocking of the CTL response with anti-CD4 mAb caused no significant decrease of the specific lysis.But blocking of CTL response with anti-CD8 mAb could abolish the Iysis.CONCLUSION The peptide (core 150 - 158 ) is the candidate epitope recognized by HLA-A2 restricted CTL.
基金the Scientific and Technological Project of Guangdong Province (Grant No. 2004A2090102).
文摘The B-cell epitopes of virus are associated with the antiviral drug and the vaccine screening. As the nucleotide sequences of neuraminidase (NA) of stain GD-01-06 were sequenced, we predicted the α-helix and β-fold structure and the indexes of the flexible regions of secondary structure of NA with methods of the Hydrophilicity plot by Kyte-Doolittle, the Surface probability plot by Emini and the Antigenic index by Jameson-Wolf, and then screened statistically the parameters to predict B-cell epitopes by the Hierarchical cluster and the Bivariate correlation and the quartiles with SPSS 13.0. The impact of variation of amino acids in NA on its epitopes was analyzed. The predictive results were evaluated by Wu’s Antigenic Index and SWISS-MODEL. We found that the most possible epitopes on NA were located within or nearby its N-terminal Nos. 120―137, 81―84, 408―415, 273―282, 429―432, 356―368, 46―55, 146―155, 341―350 and 198―209, which were the dominant regions of NA epitopes. Peptide 120―137 including the glycoprotein domain (NGT126―128) was first chosen as the B-cell epitopes on NA. NA in H5N1 strain isolated after 2003 lacked in No. 53 amino acid (I), resulting in an increase in the surface flexible region of NA in GD-01-06 and an enlargement to their epitope regions (VEP46―48→ VEPISNTNFL46―55). Conclusively, prediction of the B-cell epitopes on the NA based on multiple parameters is useful for researches on the molecular immunology and drug screening and immuno-prophylaxis. A deletion of No. 53 amino acid (I) in NA in strain GD-01-06 might increase its antigenicity.
文摘目的通过免疫信息学方法预测针对中东呼吸综合征冠状病毒(MERS-CoV)的T/B细胞抗原表位。方法从NCBI获取S蛋白序列后,运用MEGA11进行多序列比对及系统发育树构建,Expasy Protparam分析其理化性质,SOPMA预测其二级结构。随后对S蛋白建模并进行模型验证。再通过NetCTL-1.2、NetMHC pan EL 4.1和IEDB预测杀伤性T细胞(CTL)表位,NetMHCⅡpan-4.0、IFNepitope和IL-4pred预测辅助性T细胞表位(HTL),ABCpred和BepiPred-2.0预测线性B细胞表位(LBL),ElliPro工具预测构象B细胞表位(CBL)。最后对上述预测得到的线性表位进行抗原性、致敏性和毒性预测。结果S蛋白序列保守性较高,且来自不同国家的100个MERS-CoV S蛋白可以装进同一系统进化枝。理化性质分析结果显示,S蛋白亲水性总平均值为-0.078,在哺乳动物网织红细胞中半衰期约为30 h。模型验证结果显示构建的S蛋白模型是合理的。从S蛋白中预测得到具有抗原性、无致敏性和无毒性的CTL表位2个、HTL表位2个,LBL表位15个。ElliPro工具预测得到的CBL表位5个。结论MERS-CoV的S蛋白是亲水性的稳定蛋白;综合多种生物信息学方法可以预测得到T/B细胞抗原表位,对开发针对MERS-CoV的多肽疫苗具有重要借鉴意义。
