细粒棘球绦虫AgB1抗原表位的生物信息学预测

 以细粒棘球绦虫AgB1基因序列为基础,采用PredictProtein软件预测其编码蛋白的二级结构;应用在线预测软件Bcepred、Abcpred、IEDB及SYFPEITHI等对细粒棘球绦虫AgB1的B细胞表位和T细胞表位进行预测。结果提示,AgB1抗原蛋白存在可以构成抗原表位的区域,经软件分析,分值高的B细胞表位区域:2~9、15~20、22~35和41~52氨基酸序列;T细胞表位区域:3~12、26~33、34~44和52~61氨基酸序列。研究运用生物信息学确定AgB1抗原的4个B细胞优势表位和4个T细胞优势表位,对进一步研究AgB1的抗原性和研发更有价值的免疫诊断方法具有重要意义。     

旋毛虫21 KDa排泄分泌抗原二级结构及T细胞和B细胞表位预测

应用SYFPEITHI和Propred程序和多种预测方案对旋毛虫21 KDa排泄分泌抗原的T细胞表位、二级结构、疏水性、柔韧性、表面可能性、两性区以及B细胞表位进行预测.旋毛虫21 KDa排泄分泌抗原存在2个较强的T细胞表位区,分别为第9~23位和第135~150位氨基酸位点;潜在的B细胞表位存在于从第28个氨基酸残基开始的广大区域内.预测结果为旋毛虫病诊断和新型疫苗研制提供候选抗原.     

加权贝叶斯线性B细胞表位特征提取方法

特征提取方法对线性B细胞表位预测起到非常重要的作用,但贝叶斯特征提取方法忽略了氨基酸之间的相互关系.为了更准确地描述表位序列的关系,提出一种基于氨基酸对量表加权的贝叶斯特征提取方法,该方法对单个氨基酸在序列分布的基础上充分考虑了氨基酸之间的关系,并使用支持向量机作为分类器进行分类.在El-Manzalawy,Saha数据集上的测试表明改进的贝叶斯特征提取方法.相比传统的贝叶斯特征提取方法,提取精度有一定的提升.     

HPV-58型E7蛋白抗原模拟表位的筛选及分析

利用该实验室成熟的噬菌体随机十二肽库筛选平台,对HPV-58型E7蛋白单克隆抗体株4C4a、6C7a进行3轮亲和筛选,得到2组、各8个阳性噬菌体克隆.阳性噬菌体氨基酸序列用以模拟单抗(靶蛋白)特异性识别的HPV-58型E7蛋白的抗原表位.将测得的阳性噬菌体多肽序列及HPV-58型E7蛋白氨基酸序列进行生物信息学分析后,进行线性序列比对及构象性表位预测及分析.构象性表位的预测借力于EpiSearch Server和Pepitope Server,对构象性表位匹配及簇的寻找提供有力支持,也为早期诊断及研制多肽疫苗提供参考.     

马铃薯钙调素表位的微机多参数预测

据文献报道［１－３］,分析蛋白氨基酸序列的某些参数,如 Ｈｏｐｐ　＆ Ｗｏｏｄｓ　亲水性和Ｗｅｌｌｉｎｇ抗原性,可达到预测蛋白抗原分子表位的目的。本研究借助微机,对马铃薯钙调素分子表位进行了预测和分析,结果表明,该种钙调素分子存在７个表位,其中至少有３个表位可能严生相应抗体。鉴于钙调素分子一级结构具有高度保守性,以上预测结果对研制各种植物钙调素单克隆抗体均有较大的参考价值。     

人凝血因子Ⅸ的线性B细胞表位预测及鉴定

为预测并鉴定人凝血因子IX(FIX)的线性B细胞表位.通过IEDB数据库及Discovery Studio软件预测FIX的B表位和白喉毒素T结构域(DTT)的B表位,用所预测的FIX的B表位替换某预测的DTT的B表位形成DTT-表位融合蛋白.通过基因工程技术制备各重组蛋白,并免疫小鼠,通过ELISA和Western-blot检测抗血清效价和特异性,通过等温量热滴定技术(ITC)测定抗体的亲和力.预测到4个FIX的B表位.用重组蛋白FIX-2-DTT免疫的小鼠产生了识别完整FIX的抗体,该抗体具有良好的特异性,其结合常数KD为106 M-1.表明FIX-2(306 NAAINKY312)是FIX的B表位,用重组蛋白FIX-2-DTT免疫小鼠能够产生特异性识别FIX且亲和力温和的抗体.     

B细胞表位预测研究进展

B细胞表位的鉴定是研制疫苗、疾病诊断的关键步骤,表位预测是研究蛋白质表位一种筛选技术,能降低传统方法的大量投入,大幅降低研制时间、研发经费投入、研究人员精力花费等。表位预测的计算工具和方法不断推出,但预测性能却难言理想。回顾B细胞表位预测的最新进展,梳理B细胞的研究趋势及有希望的方向。     

鸡新城疫病毒HN蛋白多表位抗原的表达与免疫原性研究

有效抗原及表位的预测和筛选是疫苗研究的基础,在对鸡新城疫病毒HN蛋白抗原表位预测的基础上,对多表位抗原进行表达与免疫原性测定。根据生物信息学表位预测方法获得的家禽新城疫病毒抗原表位,利用PCR技术合成基因,构建pBVIL1-HN重组载体,转化大肠杆菌HB101,进行基因工程表达;经纯化蛋白后免疫小鼠,抗体滴度用酶联免疫吸附方法测定,确定抗原的免疫原活性。结果表明,多表位抗原基因经测序结果正确,融合基因在大肠杆菌得到高效表达,电泳纯融合多表位抗原经三次免疫得到抗血清,抗体滴度为1：8000。鸡新城疫病毒HN蛋白多表位抗原得到高效表达,且具有良好的免疫原性。     

HLA-A*0201限制性CTL表位肽的分子力场分析

运用比较分子力场(CoMFA)和比较相似性指数分析(CoMSIA)方法研究了50个HLA-A* 0201限制性CTL表位九肽结构与亲和性间的关系,另外15个表位九肽作为预测集用于检验模型的预测能力。结果表明,采用CoMSIA得到的构效关系模型(q2 =0.608,r2 =0.987,F=440.4,SD=0. 111)要明显优于采用CoMFA得到的构效关系模型。在CoMSIA计算中,当引入疏水场时,三维构效关系模型得到明显改善,通过该三维构效关系模型,可较精确地估算预测集中15个CTL表位肽与HLA-A* 0201间的亲和力(r2pred=0. 703,SD=0. 368)。通过分析分子场等势面图在空间的分布,可以观察到表位肽分子周围的立体及疏水特征对表位肽与HLA-A* 0201间结合亲和力的影响,从而为进一步对CTL表位肽进行结构改造并基于此进行治疗性疫苗分子设计提供理论基础。     

HLA-A2限制性CTL表位肽定量构效关系研究

基于SCORE打分函数，运用定量构效关系的理论和方法研究了HLA—A2限制性CTL表位九肽结构与亲和性间的定量关系，并建立了SCORE得分与亲和性的定量关系模型，并用外部样本（5个HLA—A2限制性CTL表位九肽）作为预测集用于检验模型的预测能力．基于SCORE打分函数建立的定量模型具有较好的相关性（r=0，9165，RMS=0．38）和对外部样本的预测能力（rpred=0．9847，RMS=0．135）．基于SCORE打分函数，运用定量构效关系研究的理论和方法建立了HLA—A2限制性CTL表位亲和性的定量预测方法，为实验鉴定高亲和性HLA—A2限制性CTL表位提供了理论依据．     

Evaluation of spatial epitope computational tools based on experimentally-confirmed dataset for protein antigens

Antibody molecules interact with antigen proteins through the epitope area, where the epitope residues are found to be discontinuous or spatial or conformational rather than linear on the protein surface. There are various computational algorithms to predict the spatial epitopes, and each of them have an outstanding performance based on their individual testing dataset. In this work, an independent dataset was created through collection of the epitope residual sites which have been confirmed by experiments. Based on this dataset, 6 popular web-servers developed for B-cell structural epitope prediction, including SEPPA, CEP, DiscoTope, ElliPro, PEPOP and BEpro, were evaluated and compared according to sensitivity, the positive predictive value, the successful pick-up rate and the area under the curve of the receiver operator characteristic (AUC). The results showed that the general performance of spatial epitope prediction tools did obtain substantial advancement, and SEPPA gave the best performance among the 6 tools. However, the current prediction accuracy was still far from satisfaction. Moreover, our comparison elucidated that the performance of the web-servers was significantly affected by their training datasets and the algorithms adopted. In this sense, the results of our research may improve the design of B-cell epitope prediction tools and provide additional clues when the users utilize these tools in their related research.     

Repeated epitope in the recombinant epitope-peptide could enhance ELDKWA-epitope-specific antibody response

Based on the hypothesis suggested by us that epitope-vaccine may be a new strategy against HIV mutation, we have studied several neutralizing epitopes on HIV envelope proteins. However we do not know whether a repeated epitope in a recombinant epitope-peptide can enhance epitope-specific antibody response or not. ELDKWA-epitope (aa669-674) on the C-domain of HIV-1 gp41 is a neutralizing epitope defined by the monoclonal antibody (mAb) 2F5 with broad neutralizing activity. In this study, we designed and prepared a series of the recombinant epitope-peptides bearing 1, 4 and 8 copies of ELDKWA-epitope respectively. In the comparison of the antisera induced by the three recombinant antigens, an obviously increased titre of ELDKWA-epitope-specific antibody was observed in the case of four and eight repeated epitopes. In flow cytometry analysis, the epitope-specific antibodies in both antisera showed stronger activity to bind the transfected CHO-WT cells that stably express HIV-1 envelope glycoprotein on the cell surfaces. These experimental results indicated that repeated epitope in the recombinant epitope-peptide could enhance ELDKWA-epitope-specific antibody response, which could contribute to designing an effective recombinant epitope-vaccine.     

T细胞功能学与结构免疫学结合方法鉴定HLA-A2限制性的细胞毒性T淋巴细胞表位富集区

 T细胞表位在抗病毒的T细胞免疫中发挥核心作用,目前已在多种病原微生物的蛋白序列上发现存在T细胞表位的聚集现象。本文建立了一套功能学与结构学结合的策略鉴定病原体上细胞毒性T细胞(Cytotoxic T Lymphocyte,CTL)表位富集区的方法,并以严重急性呼吸道综合征(SARS)相关冠状病毒(SARS-CoV)的M蛋白为例,成功地鉴定了一个HLA-A2限制性的表位富集区。首先通过生物信息学的方法预测并合成M蛋白跨膜区的HLA-A2潜在结合多肽,通过体外复性实验和T2细胞结合实验验证多肽与HLA-A2的结合力;然后在HLA-A2.1/Kb转基因小鼠中检测这些多肽的免疫原性;最后通过X射线衍射技术,成功解析了其中一条多肽与HLA-A^*0201的复合物结构,其结构显示该多肽具有典型的HLA-A^*0201表位的结构特点,但却呈现出与以往鉴定多肽不同的构象和锚定残基。本文对于理解机体对SARS-CoV等病原体产生的T细胞免疫反应,以及为更广泛的人群设计T细胞疫苗具有重要意义。     

人ZP3B-细胞表位嵌合肽DNA的设计和合成

目的：设计和合成适合在昆虫细胞中表达的一个人ＺＰ３ Ｂ细胞表位的ＤＮＡ序列。方法：根据国外的研究基础，设计由人ＺＰ３的Ｂ细胞表位肽段和外源Ｔｈ细胞表位肽段串联而成的４５肽嵌合肽序列，并根据昆虫细胞对密码子的偏爱性设计出该嵌合肽的ＤＮＡ序列。然后人工合成该嵌合肽的ＤＮＡ链，并克隆到ＰＵＣ１８载体上。结果：通过酶切分析和测序证明，合成的ＤＮＡ与所设计的嵌合肽ＤＮＡ序列一致。结论：按设计合成了人ＺＰ３的     

亲环素A抗原表位在三维结构中的初步定位

以抗人亲环素A单克隆抗体D4作捕获抗体，用噬菌体展示库鉴定出亲环素A模拟抗原表位的氨基酸序列为WSLQSFL，在亲环素A的一级结构中没有相同的序列，提示亲环素A抗原表位为构象型的，亲环素A的三维空间结构已测定，利用RasMol等蛋白质三维结构观察软件，可以初步确定亲环素A的抗原表位的时间位置，此抗原表位与环孢素的结合位点有重叠。     

利用搭桥PCR法实现轮状病毒VP7表位片段的重组

选择了RV VP7的3个高度保守可诱发高水平体液免疫反应的中和性抗原表位,人工合成了这3个表位片段。采用了一种不需要限制性内切酶和连接酶的重组DNA方法-搭桥PCR法,方便快速地构建了轮状病毒VF7蛋白的重组表位基因,将其T／A克隆入PBS-T载体,经过测序与报道序列同源性达100％。结果表明：搭桥法PCR简单易行,快速准确,尤其是在构建2个或多个小基因片段的融合时,比酶切、连接方法更具优越性。     

Structure modeling and spatial epitope analysis for HA protein of the novel H1N1 influenza virus

In recent months, a novel influenza virus H1N1 broke out around the world. With bioinformatics technology, the 3D structure of HA protein was obtained, and the epitope residues were predicted with the method developed in our group for this novel flu virus. 58 amino acids were identified as potential epitope residues, the majority of which clustered at the surface of the globular head of HA protein. Although it is located at the similar position, the epitope of HA protein for the novel H1N1 flu virus has obvious differences in the electrostatic potential compared to that of HA proteins from previous flu viruses.     

Three Candidate Epitope—Vaccines in Combination Inducing High Levels of Multiantibodies Against HIV—1

HIV-1 mutation results in immune evasion, which presents a serious challenge for conventional strategies for developing effective vaccines. So far, much experimental evidence indicates that HIV-1 particles in the blood of patients can be cleaned principally by neutralizing antibodies. Based on these facts, we prepared triple combination of epitope-vaccines with the objective of inducing antibodies with predefined multi-epitope-specificity against HW-1. According to the sequences of three neutralizing epitopes (RILAVERYLKD, ELDKWA and GPGRAFY, designated El, E2, and E3, respectively) on HIV-1 envelope proteins, three epitope-peptides ((E1)2: C-(RILAVERYLKDG)2; (E2)4: C-(ELDKWAG)4; and (E3)2:C-(GPGRAFY)2) were synthesized and then conjugated with carrier protein keyhole limpet hemocyanin (KLH) or bovine serum albumin (BSA), and used for immunizing rabbits. After the vaccine course, the triple combination of epitope-vaccines induced high levels of predefined multi-epitope-specific antibodies. An immunoblotting-analysis demonstrated that the antibodies could recognize the native epitopes on both gp41 protein and V3 loop peptide. Furthermore, we compared the immune responses of three doses of epitope-peptides in the candidate epitope-vaccine. Strong antibody responses to three epitopes were observed in a dose dependent manner, with increasing dose raising the immune response. This result indicated that immunotolerance did not occur using an epitope vaccine dose of 80 ~tg. Thus, our results demonstrate that epitope-vaccines in combination can synchronously induce high levels of antibodies with predefined multi-epitope-specificity against HIV-1, and may be used to develop effective vaccines against HIV as a new strategy.