The Prediction of B Cell Epitopes for VP73 Protein of African Fever Virus

[Objective] The B cell epitopes for VP73 protein of African swine fever virus was predicted. [ Method] Based on the analysis of the amino acid sequence and the flexible regions of VP73 protein, the B cell epitopes for VP73 protein of African swine fever virus were predicted by method of Kyte-Doolittie, Emini and Jameson-Wolf. [Result] The B cell epitopes were located at or adjacent to the N-terminal No. 11 - 18,26 -48,73 -82,136 - 150,159 - 174,181 - 189,191 - 210,247 - 276,279 - 295,313 - 323 and 382 - 392. [Conclusion] The multi-parameters analytic method was adopted to predict the B cell epitopes for VP73 protein of African swine fever virus, which laid solid foundation for further characterizing the protein of VP73 and researching epitope vaccine.

Bioinformatics Analysis on B cell Epitopes of Rice Allergen RAG1

[Objective] To predict the secondary structure and B cell epitopes of the rice major allergen RAG1. [Method] The amino acid sequence of rice allergen RAG1 was acquired from Expasy protein database. The secondary structure of RAG1 was predicted by DNAStar Protean software with Gamier-Robson program, Chou-Fasman program and Karplus-Schulz program; the B cell epitopes of RAG1 was predicted with the Kyte Doolittle hydrophilic program, Emini surface accessibility program and Jameson-Wolf antigenic index program. [Result] The predictions on secondary structure and B cell epitopes showed that the regions of 33-44, 119-129, 155-163 were the dominant B cell epitopes. [Conclusion] This study predicted the potential dominant B cell epitopes in rice allergen RAG1 by comprehensive use of multi-methods and multi-parameters, and provided a theoretical basis for further researches on identification, antigen modification and epitope vaccine design of RAG1 B cell epitopes.

Prediction of T cell and B cell epitopes of the 22-, 47-, 56-, and 58-kDa proteins of Orientia tsutsugamushi

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.

Bioinformatics analysis of the structure and linear B-cell epitopes of aquaporin-3 from Schistosoma japonicum

Objective:To analyze the structure of aquaporins-3(AQP-3) from Schistosoma japonicum(SJAQP-3) using bioinformalical methods,and to provid of references for vaccine targets research.Methods:Protparam,BepiPred,TMHMM Server,MLRC,Geno3d,DNA star software packages were used to predict the physical and chemical properties,hydrophilicity plot, flexibility regions,antigenic index,surface probability plot,secondary structure,and tertiary structure of amino acid sequence of SJAQP-3.Results:SJAQP-3 had six transmembrane regions and two half-spanning helices that form a central channel.The half-spanning helices fold into the centre of the channel.Either of the half-spanning helix had a conserved motif of NPA common to all aquaporins.Predicted linear B-Cell epitopes were most likely at the N-terminal amino acid residues of Saa-7aa,59aa- 62aa,225aa-230aa,282aa -288aa,294aa -29Saa and 305aa -307aa area.59aa- 62aa,22Saa-230aa located outside the membrane,the others located inside the cell.Conclusions:SJAQP-3 is a integral membrane protein in Schistosoma japonicum tegument.There are six potential epitopes in SJ AQP-3.It might be a potential molecular target for the development of vaccines.

ASFV pp62 Protein Has 9 Dominant B-T Cell Combined Epitopes

[Objective]The paper was to study the basic characteristics of the pp62 protein of the African swine fever virus strain Pig/HLJ/2018,and to provide more basic data for the study of the virus.[Method]We used the ProtParam program to analyze the physical and chemical properties of the pp62 protein.TMHMM-2.0 and SignalP-5.0 were used to analyze protein transmembrane region and signal peptide,and Lasergene 7.0 Protean program was used to study protein antigen index,hydrophilicity,surface accessibility and titration curve.Protein N-glycosylation site and O-glycosylation site came out with NetNGlyc-1.0 and NetOGlyc-4.0 online servers.Then,PSIPRED-4.0,NetSurfP-2.0,and PSRSM were used to analyze protein secondary structure,BepiPred1.0 and IEDB tools were used to analyze protein B-cell epitopes,and NetMHC 4.0 and NetMHCpan tools were used to analyze protein T-cell epitopes.And we used Swiss-Model to analyze the high-level structure of the protein,the EzMol tool to visually analyze B-T cell combined epitopes,and finally,MEGA 7.0 to analyze the genetic evolutionary relationship of the protein.[Result]The pp62 protein of African swine fever viral strain Pig/HLJ/2018 had a molecular weight of 60.5 kDa.It was a hydrophilic acid labile protein,and had no transmembrane region and signal peptide.There were 5 N-glycosylation sites and 4 O-glycosylation sites.Analysis of the secondary structure of the protein showed that the proportions of helix,coil and strands were 45.5%,41.7%and 12.8%,respectively.The study of dominant epitopes revealed that there were 14 dominant B-cell epitopes and 16 dominant T-cell epitopes.And 9 dominant B-T cell combined epitopes located on the surface of the protein molecule were found.The phylogenetic tree constructed with the pp62 protein showed that the evolutionary relationship of Pig/HLJ/2018 strain was the closest to Georgia/2007/1,which belonged to genotype II.[Conclusion]The results will provide basic information for pp62 research.

Prediction of promiscuous T cell epitopes in RNA dependent RNA polymerase of Chikungunya virus

Objective: To explore RNA dependent RNA polymerase of Chikungunya virus(CHIKV) and develop T cell based epitopes with high antigenicity and good binding affinity for the human leukocyte antigen(HLA) classes as targets for epitopes based CHIKV vaccine. Methods: In this study we downloaded 371 non-structural protein 4 protein sequences of CHIKV belonging to different regions of the world from the US National Institute of Allergy and Infectious Diseases(NIAID) virus pathogen resource database. All the sequences were aligned by using CLUSTALW software and a consensus sequence was developed by using Uni Pro U Gene Software version 1.2.1. PropredⅠand Propred software were used to predict HLAⅠ and HLAⅡ binding promiscuous epitopes from the consensus sequence of non-structural protein 4 protein. The predicted epitopes were analyzed to determine their antigenicity through Vaxijen server version 2.0. All the HLAⅠ binding epitopes were scanned to determine their immunogenic potential through the Immune Epitope Database(IEDB). All the predicted epitopes of our study were fed to IEDB database to determine whether they had been tested earlier. Results: Twenty two HLA class Ⅱ epitopes and eight HLA classⅠepitopes were predicted. The promiscuous epitopes WMNMEVKII at position 486–494 and VRRLNAVLL at 331–339 were found to bind with 37 and 36 of the 51 HLA class Ⅱ alleles respectively. Epitope MANRSRYQS at position 58–66 and epitopes YQSRKVENM at positions 64–72 were predicted to bind with 12 and 9 HLAⅠI alleles with antigenicity scores of 0.754 9 and 1.013 0 respectively. Epitope YSPPINVRL was predicted to bind 18 HLAⅠ alleles and its antigenicity score was 1.425 9 and immunogenicity score was 0.173 83. This epitope is very useful in the preparation of a universal vaccine against CHIKV infection. Conclusions: Epitopes reported in this study showed promiscuity, antigenicity as well as good binding affinity for the HLA classes. These epitopes will provide the baseline for development of efficacious vaccine for CHIKV.

Prediction of promiscuous T-cell epitopes in the Zika virus polyprotein:An in silico approach

Objective:To predict immunogenic promiscuous T-cell epitopes from the polyprotein of the Zika virus using a range of bioinformatics tools.To date,no epitope data are available for the Zika virus in the IEDB database.Methods:We retrieved nearly 54 full length polyprotein sequences of the Zika virus from the NCBI database belonging to different outbreaks.A consensus sequence was then used to predict the promiscuous T cell epitopes that bind MHC 1 and MHC II alleles using Propred1 and Propred immunoinformatic algorithms respectively.The antigencity predicted score was also calculated for each predicted epitope using the Vaxi Jen 2.0 tool.Results:By using Pro Pred1,23 antigenic epitopes for HLA class I and 48 antigenic epitopes for HLA class II were predicted from the consensus polyprotein sequence of Zika virus.The greatest number of MHC class I binding epitopes were projected within the NS5(21%),followed by Envelope(17%).For MHC class II,greatest number of predicted epitopes were in NS5(19%) followed by the Envelope,NS1 and NS2(17% each).A variety of epitopes with good binding affinity,promiscuity and antigenicity were predicted for both the HLA classes.Conclusion:The predicted conserved promiscuous T-cell epitopes examined in this study were reported for the first time and will contribute to the imminent design of Zika virus vaccine candidates,which will be able to induce a broad range of immune responses in a heterogeneous HLA population.However,our results can be verified and employed in future efficacious vaccine formulations only after successful experimental studies.

Exact Location of Linear B-cell Epitopes of VP3 Protein of Goose Parvovirus

Four monoclonal antibodies (MAbs) against Goose Parvovirus (GPV) VP3 protein already available were used to precisely locate linear B-cell epitopes in VP3 of GPV. The epitopes, recognized by four MAbs, had already been identified at low levels of resolution. Complementary oligonucleotides encoding ten amino acid fragments, with five amino acid overlaps were designed with suitable sticky ends for recombination with pET-32a and subsequent expression as small-fragment fusion proteins. Antigenicity of specific oligopeptides was determined by Western blotting with the MAbs. Using the same methods, amino acids were deleted one by one from the peptides of interest, enabling the two epitopes to be precisely located at amino acids 430-435 (-DRIMNP-) and 643-647 (-VFIKN-).

Conservation of T cell epitopes between seasonal influenza viruses and the novel influenza A H7N9 virus

A novel avian influenza A(H7N9) virus recently emerged in the Yangtze River delta and caused diseases, often severe, in over 130 people. This H7N9 virus appeared to infect humans with greater ease than previous avian influenza virus subtypes such as H5N1 and H9N2. While there are other potential explanations for this large number of human infections with an avian influenza virus, we investigated whether a lack of conserved T-cell epitopes between endemic H1N1 and H3N2 influenza viruses and the novel H7N9 virus contributes to this observation. Here we demonstrate that a number of T cell epitopes are conserved between endemic H1N1 and H3N2 viruses and H7N9 virus. Most of these conserved epitopes are from viral internal proteins. The extent of conservation between endemic human seasonal influenza and avian influenza H7N9 was comparable to that with the highly pathogenic avian influenza H5N1. Thus, the ease of inter-species transmission of H7N9 viruses(compared with avian H5N1 viruses) cannot be attributed to the lack of conservation of such T cell epitopes. On the contrary, our findings predict significant T-cell based cross-reactions in the human population to the novel H7N9 virus. Our findings also have implications for H7N9 virus vaccine design.

Theoretical Study of Continuous B-Cell Epitopes with Developed BP Neural Network

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.

Prediction of Secondary Structure and B Cell Epitope of GH Protein from Acipenser sinensis

[ Objective] The aim was to predict the secondary structure and B cell epitope of growth hormone （GH） protein from Acipenser sinensis. [Method] With the amino acid sequence of GH protein from A. sinensis as the base, the secondary structure of GH protein from A. sinensis was predicted by the method of Gamier-Robson, Chou-Fasman and Karpius-Schulz, and its cell epitope was predicted by the method of Kyte- Doolittle, Emini and Jameson-Wolf. [Result] The sections of 18 -23, 55 -55, 67 -73, 83 -86,112 -114,151 -157 and 209 -211 in the N terminal of GH protein molecule had softer structure and these sections could sway or fold to produce more complex tertiary structure. The sections of 19 -23, 51 -71,84 -95, 128 -139, 164 -176 and 189 -195 in the N terminal of GH protein could be the epitope of B cell and there were flexible regions in these sections or near these sections of GH protein molecule. So the dominant regions could be in these sections or near these sections. [ Conclusion] The research provided the basis for the preparation of monoctonal antibody of GH protein from A. sinensis and provided the reference for the discussion for the molecular regulation mechanism of A. sinensis.

Prediction of B Cell Epitope of DMRT Protein in Oreochromis niloticus

[Objective] The research aimed to predict the B cell epitope of DMRT protein in Oreochromis niloticus. [Method] The secondary structure of amino acid sequence of DMRT protein was revealed by Garnier-Robson, Chou-Fasman and Karplus-Schulz methods. The hydrophilicity plot, surface probability and antigenic index were obtained by Kyte-Doolittle, Emini and Jameson-Wolf methods, respectively. Based on the above results, the B cell epitopes for DMRT were predicted. [Result] Both the prediction results from Garnier-Robson, Chou-Fasman methods indicated that the α-helix centers of DMRT protein in O. niloticus were in the N terminal No. 31-56, 68-75, 110-116, 209-211 and 239-243; the β-sheet centers of DMRT protein in O. niloticus were in the N terminal No. 95-99, 177-183, 225-234 and 251-254. With the assistant of Kyte-Doolittle, Emini and Jameson-Wolf methods, the B cell epitopes for DMRT were located in or nearby the N terminal No. 13-16, 35-38, 47-54,84-93, 101-109, 127-156, 166-177 and 198-201. [Conclusion] These results are helpful for preparing the antibody of DMRT protein and revealing the sex determination mechanism of O. niloticus.

Hepatocellular carcinoma-specific immunotherapy with synthesized α1,3-galactosyl epitope-ulsed dendritic cells and cytokine-induced killer cells

AIM： To evaluate the safety and clinical efficacy of a new immunotherapy using both α-Gal epitope-pulsed dendritic cells （DCs） and cytokine-induced killer cells. METHODS： Freshly collected hepatocellular carcinoma （HCC） tumor tissues were incubated with a mixture of neuraminidase and recombinant αl,3-galactosyltrans- ferase （αI,3GT） to synthesize α-Gal epitopes on car- bohydrate chains of the glycoproteins of tumor mem- branes. The subsequent incubation of the processed membranes in the presence of human natural anti-Gal IgG resulted in the effective phagocytosis to the tumor membrane by DCs. Eighteen patients aged 38-78 years with stage 111 primary HCC were randomly chosen for the study; 9 patients served as controls, and 9 patients were enrolled in the study group.RESULTS： The evaluation demonstrated that the pro- cedure was safe; no serious side effects or autoimmune diseases were observed. The therapy significantly pro- longed the survival of treated patients as compared with the controls （17.1 ± 2.01 mo vs 10.1 ±4.5 mo, P = 0.00121）. After treatment, all patients in the study group had positive delayed hypersensitivity and robust systemic cytotoxicity in response to tumor lysate as measured by interferon-y-expression in peripheral blood mononuclear cells using enzyme-linked immunosorbent spot assay. They also displayed increased numbers of CD8-, CD45RO- and CD56-positive cells in the peripheral blood and decreased α-fetoprotein level in the se- rum. CONCLUSION： This new tumor-specific immunotherapy is safe, effective and has a great potential for the treat- ment of tumors.

Identification of an HLA-A~* 0201-restricted CD8^+ T-cell epitope SSp-1 of SARS-CoV spike protein

A novel coronavirus, severe acute respiratory syndrome (SA RS)-associated coronavirus (SARS-CoV), has been identified as the causal agent of SARS. Spike (S) protein is a major structural glycoprotein of the SARS virus and a potential target for SARS-specific cell-mediated immune responses. A pa nel of S protein-derived peptides was tested for their binding affinity to HLA -A *0201 molecules. Peptides with high affinity for HLA-A *0201 were then as se ssed for their capacity to elicit specific immune responses mediated by cytotoxi c T lymphocytes (CTLs) both in vivo, in HLA-A2.1/K b transgenic mice, a nd in vitro, from peripheral blood lymphocytes (PBLs) harvested from healthy HLA-A 2.1 + donors. SARS-CoV protein-derived peptide-1 (SSp-1 RLNEVAKNL), induced pepti de-specific CTLs both in vivo (transgenic mice) and in vitro (human PBL s), which specifically released interferon-gamma (IFN-gamma) upon stimulation with SSp-1-pulsed autologous dendritic cells (DCs) or T2 cells. SSp-1-specif ic CTLs also lysed major histocompatibility complex (MHC)-matched tumor cell lines engineered to express S proteins. HLA-A *0201-SSp-1 tetramer staining re vealed the presence of significant populations of SSp-1-specific CTLs in SSp- 1-induced CD8 + T cells. We propose that the newly identified epitope SSp-1 w ill help in the characterization of virus control mechanisms and immunopathology in SARS-CoV infection, and may be relevant to the development of immunotherape utic approaches for SARS.

Identification of the epitopes on HCV core protein recognized by HLA-A2 restricted cytotoxic T lymphocytes

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 4h(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 "ALAHGVRAL (core 150-158)". 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 lysis. CONCLUSION: The peptide (core 150-158) is the candidate epitope recognized by HLAA2 restricted CTL.

Adenovirus-mediated expression of pig α(1,3) galactosyltransferase reconstructs Gal α(1,3) Gal epitope on the surface of human tumor cells

Gal alpha(1, 3) Gal (gal epitope) is a carbohydrate epitope and synthesized in large amount by alpha(1, 3) galactosyltransferase [alpha(1, 3) GT] enzyme on the cells of lower mammalian animals such as pigs and mice. Human has no gal epitope due to the inactivation of alpha(1, 3) GT gene but produces a large amount of antibodies (anti-Gal) which recognize Gal alpha(1, 3) Gal structures specifically. In this study, a replication-deficient recombinant adenoviral vector Ad5sGT containing pig alpha(1, 3) GT cDNA was constructed and characterized. Adenoviral vector-mediated transfer of pig alpha(1, 3) GT gene into human tumor cells such as malignant melanoma A375, stomach cancer SGC-7901, and lung cancer SPC-A-1 was reported for the first time. Results showed that Gal epitope did not increase the sensitivity of human tumor cells to human complement-mediated lysis, although human complement activation and the binding of human IgG and IgM natural antibodies to human tumor cells were enhanced significantly after Ad5sGT transduction. Appearance of gal epitope on the human tumor cells changed the expression of cell surface carbohydrates reacting with Ulex europaeus I (UEA I) lectins, Vicia villosa agglutinin (VVA), Arachis hypogaea agglutinin (PNA), and Glycine max agglutinin (SBA) to different degrees. In addition, no effect of gal epitope on the growth in vitro of human tumor cells was observed in MTT assay.

Identification of an HLA-A*0201-restricted CD8^+ T-cell epitope SSp-1 of SARS-CoV spike protein

A novel coronavirus, severe acute respiratory syndrome (SARS)-associated coronavirus (SARS-CoV), has been identified as the causal agent of SARS. Spike (S) protein is a major structural glycoprotein of the SARS virus and a potential target for SARS-specific cell-mediated immune responses. A panel of S protein-derived peptides was tested for their binding affinity to HLA-A*0201 molecules. Peptides with high affinity for HLA-A*0201 were then assessed for their capacity to elicit specific immune responses mediated by cytotoxic T lymphocytes (CTLs) both in vivo, in HLA-A2.1/K b transgenic mice, and in vitro, from peripheral blood lymphocytes (PBLs) harvested from healthy HLA-A2.1(+) donors. SARS-CoV protein-derived peptide-1 (SSp-1 RLNEVAKNL), induced peptide-specific CTLs both in vivo (transgenic mice) and in vitro (human PBLs), which specifically released interferon-gamma (IFN-γ) upon stimulation with SSp-1-pulsed autologous dendritic cells (DCs) or T2 cells. SSp-1-specific CTLs also lysed major histocompatibility complex (MHC)-matched tumor cell lines engineered to express S proteins. HLA-A*0201-SSp-1 tetramer staining revealed the presence of significant populations of SSp-1-specific CTLs in SSp-1-induced CD8+ T cells. We propose that the newly identified epitope SSp-1 will help in the characterization of virus control mechanisms and immunopathology in SARS-CoV infection, and may be relevant to the development of immunotherapeutic approaches for SARS.

Protective antitumor immunity induced by tumor cell lysates conjugated with diphtheria toxin and adjuvant epitope in mouse breast tumor models

Cancer cell vaccine-based immunotherapy has received increasing interest in many clinical trials involving patients with breast cancer. Combining with appropriate adjuvants can enhance the weak immunogenic properties of tumor cell lysates (TCL). In this study, diphtheria toxin (DT) and two tandem repeats of mycobacterial heat shock protein 70 (mHSP70) fragment 407-426 (M2) were conjugated to TCL with glutaraldehyde, and the constructed cancer cell vaccine was named DT-TCL-M2. Subcutaneous injection of DT-TCL-M2in mice effectively elicited tumor-specific polyclonal immune responses, including humoral and cellular immune responses. High levels of antibodies against TCL were detected in the serum of immunized mice with ELISA and verified with Western blot analyses. The splenocytes from immunized mice showed potent cytotoxicity on Ehrlich ascites carcinoma cells. Moreover, the protective antitumor immunity induced by DT-TCL-M2 inhibited tumor growth in a mouse breast tumor model. DT-TCL-M2 also attenuated tumor-induced angiogenesis and slowed tumor growth in a mouse intradermal tumor model. These findings demonstrate that TCL conjugated with appropriate adjuvants induced effective antitumor immunity in vivo. Improvements in potency could further make cancer cell vaccines a useful and safe method for preventing cancer recurrence after resection.

CD36蛋白B细胞抗原表位的生信预测及其多抗原肽的制备

目的分析CD36蛋白的结构,寻找可能的B细胞抗原表位,制备含有B细胞表位的多抗原肽(multiple antigenic peptide,MAP),为基于B细胞表位的MAP用于CD36抗体的制备提供前期实验基础。方法通过生物信息学方法分析CD36蛋白的理化性质、二级结构、潜在磷酸化及糖基化位点等,预测可能的B细胞表位。以多聚赖氨酸为核心基质,采用Fmoc方法合成含有CD36 B细胞表位的八分枝MAP,并利用反向高效液相色谱(RP-HPLC)分析MAP的纯度、质谱分析法测定MAP的分子量,对合成的CD36-MAP进行鉴定。结果CD36是1种稳定的、亲水性的碱性蛋白,二级结构以无规则卷曲为主,具有多个磷酸化、糖基化位点,抗原性较强。综合分析获得可能的优势B细胞表位4个,制备了4个含有优势B细胞表位的MAP,RP-HPLC分析表明合成的MAP的纯度均在85%以上,其中3个MAP的分子量与理论预期值相符。结论CD36具有较强的抗原性,利用预测得到的4个可能的B细胞表位合成MAP,为CD36抗体的制备和相关研究提供实验基础。

虾源肌球蛋白抗原表位的计算机辅助计算

利用在线软件和线下软件对来源于刀额新对虾(Metapenaeus ensis)的过敏原Met e1的B细胞抗原表位和T细胞抗原表位进行预测、筛选以及辅助计算.首先,通过uniprot蛋白数据库获取Met e1蛋白质氨基酸序列;其次,用ExPASY ProtParam, SignalP-5.0 Server和TMHMM Server v.2.0在线工具对Met e1的理化性质、信号肽与跨膜区域进行分析,用PSIPRED在线工具、 SOPMA在线工具和DNAstar软件联合预测计算Met e1二级结构,用Swiss model在线软件预测计算Met e1三级结构;再次,用DNAStar线下软件和IEDB在线软件综合预测计算线性B细胞表位,用IEDB在线软件预测计算CD4+T细胞表位和CD8+T细胞表位;最后将所得结果进行B细胞表位和T细胞表的筛选.结果表明:Met e1蛋白的B细胞表位为15~28, 45~49, 92~95, 125~130, 150~153, 255~258位氨基酸;T细胞表位为78~84, 223~232位氨基酸.