中蜂囊状幼虫病毒LN-QY株VP3蛋白空间结构及其B细胞抗原表位的预测

目的预测中蜂囊状幼虫病毒(Chinese sacbrood virus,CSBV)LN-QY株VP3蛋白的空间结构及其B细胞抗原表位。方法采用RT-PCR法从感染CSBV的蜜蜂幼虫总RNA中扩增结构蛋白VP3基因,与pMD18-T载体连接后,转化感受态大肠杆菌DH5α,提取质粒,双酶切鉴定并测序,通过与SBV-KOR、CSBV-UK株VP3基因序列的比对,获得LN-QY株VP3基因的核苷酸序列及推导的氨基酸序列,建立VP3蛋白的3D结构。在此基础上,应用DNAStar软件中的Protean模块综合分析结构蛋白的柔性区域、亲水性、表面可能性以及抗原指数等参数。结果 VP3结构蛋白的空间构象较规则,其可能的B细胞抗原表位区域位于4个区域:25-50,101-109,112-120,250-268氨基酸区段,其中,可能出现抗原表位的2个区域在100-150和250-300氨基酸区段,应作为抗原表位研究的重点区域。结论预测了CSBV LN-QY株VP3蛋白的空间结构及其B细胞抗原表位,为CSBVVP3蛋白单克隆抗体的制备以及表位疫苗的设计奠定了理论基础。     

埃博拉病毒包膜糖蛋白二级结构及B细胞表位的预测

目的预测并分析从2014年西非埃博拉出血热暴发地区感染患者分离的扎伊尔型病毒株包膜糖蛋白(glycoprotein,GP)的二级结构及B细胞表位。方法通过Gen Bank搜索近期公布的分离自西非地区的扎伊尔型埃博拉病毒株基因组,获得GP1、GP2和s GP 3种包膜糖蛋白的基因及氨基酸序列,采用互联网服务器在线预测其二级结构及B细胞表位,并分析蛋白的各种氨基酸组成比例及可能的蛋白结合位点,通过亲/疏水性等参数判断氨基酸序列中可能暴露在蛋白结构表面或隐藏在内部的区段。结果在编码GP1、GP2和s GP的氨基酸中,占组成比例最多的均为苏氨酸。GP1和s GP可能的蛋白结合位点较多,且整个蛋白暴露于表面的区域和隐藏区域呈均匀相间分布;GP2结构较前二者特殊,存在一个暴露在蛋白结构表面的大片段的无序结构区域。GP1 N-末端第20~37和166~186区段,GP2 N-末端第361~379区段,s GP N-末端第20~37和166~185区段,可能为跨膜螺旋结构。s GP可能存在4个含有二硫键的区域。B细胞表位分析结果显示,GP1和GP2中疏水区域主要集中在N-末端第1~325位氨基酸之间;亲水区域主要集中在N-末端第326~676位氨基酸之间;亲水与疏水区域分界明显,几乎无交叉;可能存在2个线性表位,分别位于N-末端第324~450、461~676区段;预测共存在25个可能形成构象表位的氨基酸位点或序列,其中可能性在90%以上的位点或序列有6个。结论通过对此次流行于西非的埃博拉病毒包膜糖蛋白的二级结构及可能性B细胞表位的预测,为实验确定埃博拉病毒包膜糖蛋白的结构与功能、B细胞表位免疫识别以及埃博拉病毒预防、治疗和诊断制品的研发提供了参考。     

中蜂囊状幼虫病毒LN-QY株VP1蛋白的空间结构与B细胞抗原表位预测

目的预测中蜂囊状幼虫病毒(Chinese sacbrood virus,CSBV)LN-QY株VP1蛋白的空间结构及其B细胞抗原表位。方法以CSBV LN-QY株RNA为模板,RT-PCR扩增结构蛋白VP1基因,与pMD18-T载体连接后,转化感受态大肠杆菌DH5α,对经EcoRⅠ和HindⅢ双酶切鉴定为阳性的重组质粒进行测序,通过序列比对,获得LN-QY株VP1的核苷酸序列和推导的氨基酸序列,建立VP1结构蛋白的3D模型,在此基础上,应用DNAStar软件中的Protean模块综合分析结构蛋白的柔性区域,亲水性,表面可能性以及抗原指数等参数。结果 VP1结构蛋白的空间构象比较规则,其可能的B细胞抗原表位区域位于47-53,139-145,273-284氨基酸区段。结论本研究为CSBV LN-QY株VP1蛋白表位疫苗的设计以及血清诊断试剂盒的研制奠定了理论基础。     

四价重组A群链球菌多肽疫苗基因序列的合成及克隆

目的设计针对可引起风湿热的A群链球菌M1、3、6、18四个血清型的重组多肽疫苗,合成并克隆该重组多肽疫苗的核苷酸序列。方法从美国疾病预防和控制中心(CDC)数据库获得A群链球菌1、3、6、18四个血清型M蛋白型特异性序列,根据文献报道并结合生物信息学的方法,筛选每一个血清型的特异性序列中与人体组织蛋白无同源性的区段,将其按1-3-6-18型的顺序串连,在串联序列的C-端加上一个四个血清型所共有的与人体组织蛋白无交叉表位、且具有一定免疫原性的保守序列J14。对设计的多肽疫苗的氨基酸序列进行与人体组织蛋白的BlastP比对、亲水性分析、二级结构分析、空间结构分析以及B细胞表位预测。采用DNAWORK2.0在线软件设计一组寡核苷酸引物,OverlapPCR方法合成该多肽疫苗的核苷酸序列,并在5′端和3′端分别引入BamHⅠ和HindⅢ的酶切位点,将该序列双酶切后克隆至pUC18载体上,并测序。结果软件分析显示,设计的多肽疫苗与人体组织蛋白无同源性,有较好的亲水性,二级结构与空间结构均与天然M蛋白相似,在每一个血清型的区段都可能存在B细胞表位。成功扩增出了该多肽疫苗的DNA序列,并获得了一个与设计序列完全一致的重组克隆载体。结论已成功设计了一种四价重组A群链球菌多肽疫苗,为其重组表达和免疫原性的研究奠定了基础。     

狂犬病病毒4aG株G蛋白基因的克隆及其生物信息学分析

目的克隆狂犬病病毒(Rabies virus,RV)4aG株G蛋白基因,并与其他疫苗毒株G蛋白基因序列进行比较,为我国狂犬病疫苗的研制提供理论依据。方法从RV 4aG株中扩增G蛋白基因,并进行序列测定,利用生物信息学软件绘制系统进化树,预测G蛋白功能位点、二级结构和B细胞抗原表位,并与其他疫苗毒株进行比较。结果克隆的4aG株G蛋白基因序列与GenBank中登录的序列一致。进化树分析显示,4aG株与CVS株的进化关系较远;4aG、4aGV18、CVS、PV及RC-HL毒株跨膜区域在第460～479氨基酸之间,其他毒株在459～478氨基酸之间;PV株有5个糖基化位点,RV-97株有3个糖基化位点,其他毒株均有4个糖基化位点;G蛋白抗原表位位于氨基酸100～300及480～520之间;不同毒株G蛋白抗原位点区域有所不同,与CVS株比较,PV株抗原表位与其最为接近,4aG、4aGV18、CTN-1-31及Flury-HEP株与其抗原表位较为接近。结论4aG株G蛋白功能位点和抗原表位与CVS株相差较大,但其在Vero细胞上传代稳定,可用于制备Vero细胞纯化疫苗。     

HBcAg-VEGF抗原表位融合蛋白的原核表达、纯化及其免疫原性

目的原核表达、纯化HBcAg-VEGF抗原表位融合蛋白,并分析其免疫原性。方法生物信息学方法预测鼠血管内皮生长因子(vascular endothelial growth factor,VEGF)的B细胞抗原表位,采用重叠延伸PCR(splicing by overlap extension PCR,SOE-PCR)法将VEGF抗原表位基因插入到HBcAg基因的免疫优势区内,合成HBcAg-VEGF基因序列,克隆至原核表达载体pET-32a中,构建重组表达质粒pET-32a-HBcAg-VEGF,转化大肠埃希菌BL21(DE3),IPTG诱导表达。表达产物经羟基磷灰石CHT层析、Sephacryl S-400 HR凝胶过滤层析纯化后,与A(lOH)3佐剂混合,分别于第0、7、14、21天经肌肉免疫BALB/c小鼠1次,第28天采血,ELISA法检测血清中抗VEGF抗原表位抗体,VEGF受体结合抑制试验筛选具有良好免疫原性的VEGF优势抗原表位。对筛选出的优势抗原表位融合蛋白进行表达及纯化条件的优化。结果生物信息学软件预测了6个VEGF的B细胞抗原表位;6个重组表达质粒经菌落PCR及测序证实构建正确;表达的HBcAg-VEGF抗原表位融合蛋白相对分子质量为14 400²0 100,纯度均在85%以上,除HBcAg-VEGF3以单体形式存在、不形成颗粒外,其他融合蛋白均能形成VLP;各组HBcAg-VEGF融合蛋白免疫小鼠后,均刺激机体产生了针对VEGF抗原表位肽的特异性抗体,其中HBcAg-VEGF1组抗体水平最高,且抑制VEGF与VEGFR结合的能力最强;采用优化的条件表达、纯化的HBcAg-VEGF1抗原表位融合蛋白纯度达95%以上。结论筛选得到的HBcAg-VEGF1抗原表位融合蛋白显示出较好的免疫原性,为进一步研究其抗肿瘤效应奠定了基础。     

旋毛虫两个发育时期丝氨酸蛋白酶的结构及功能的比较与分析

目的比较并分析旋毛虫成虫期及新生幼虫期丝氨酸蛋白酶基因和蛋白的结构及功能。方法应用NCBI、EMBL、MEGA、ExPasy、TMHMM、SignalP、PROSITE、Coils、SYFPEITHI等多种在线生物信息学网站和软件,对旋毛虫成虫期和新生幼虫期丝氨酸蛋白酶基因(Zh68和T668)的同源性、系统发育进化状况进行分析,并预测相应蛋白(SP1和SP2)的基本理化性质、跨膜区、motif、结构域、亚细胞定位、二级及三级结构、细胞抗原表位等。结果 Zh68和T668为旋毛虫特有基因,但核苷酸同源性仅为48%,SP1和SP2的氨基酸同源性为27.5%。SP1和SP2均为不稳定的亲水性蛋白,N-末端均有一个信号肽的分泌蛋白;二级及三级结构类似,并预测出两者最佳B及T细胞抗原表位,但SP2有一个跨膜螺旋结构,为膜蛋白。结论旋毛虫成虫期的SP1是非跨膜蛋白,可能参与虫体在肠道寄生及发育、繁殖;新生幼虫期的SP2是跨膜蛋白,可能参与虫体的入侵及迁移。     

HCV多表位抗原的选择及结构分析

目的：设计HCV复合多表位抗原,分析其空间结构,探讨其用于疫苗研究和HCV-Ag检测的潜在可行性。方法：选择HCV多表位抗原并将其串联成HCV复合多表位抗原基因B2,利用软件和网站分析其空间结构。结果：该HCV复合多表位抗原具备涵盖多种天然表位的抗原特性,且二级结构提示具有形成T细胞位点的倾向,易于诱导T细胞介导的细胞免疫应答,三级结构有良好的亲水性,可能激发良好的体液免疫应答。结论：该HCV复合多表位抗原选择合理,空间结构分析能激发良好的免疫反应,有望用于疫苗研究和HCV-Ag检测。     

EGFRvⅢ蛋白的生物信息学分析及其在HEK293T细胞中的表达

目的对表皮生长因子受体Ⅲ(epithelial growth factor receptor variantⅢ,EGFRvⅢ)突变蛋白进行生物信息学分析,并构建表达该突变蛋白的HEK293T细胞系。方法根据NCBI公布的EGFR外显子序列,拼接成EGFRvⅢ编码基因,运用Protparam、ProtScale、SignalP 4. 1 Server、TMHMM Server v. 2. 0、SOPMA、SWISS-MODEL和SMART软件对其编码的氨基酸序列进行生物信息学分析。设计融合PCR引物,克隆EGFRvⅢ基因,并连接到真核表达载体pEGFP-N1上,转染HEK293T细胞,Western blot法检测EGFRvⅢ-EGFP的表达。结果 EGFRvⅢ蛋白含943个氨基酸,预测相对分子质量约为104 335;理论等电点为6. 22;平均亲水性系数为-0. 306,亲水性氨基酸占63. 6%,疏水性氨基酸占36. 4%。EGFRvⅢ蛋白N-端1～24个氨基酸序列为信号肽序列,是一个细胞质膜定位的单次跨膜蛋白。二级结构预测显示,EGFRvⅢ蛋白主要由α螺旋和无规则卷曲组成,三级结构预测与二级结构预测结果一致。结构域预测显示,胞内酪氨酸激酶结构域完整,胞外受体结构域受损。融合PCR克隆出EGFRvⅢ编码基因,并在HEK293T细胞中表达出目的蛋白EGFRvⅢ-EGFP。结论成功获得表达EGFRvⅢ蛋白的HEK293T细胞系,为开展肿瘤浸润淋巴细胞免疫治疗或T细胞受体的研究奠定了基础。     

信号肽对SARS-CoV-2 S1、RBD、RBD二聚体蛋白在Expisf9昆虫细胞中分泌表达的影响

目的 比较不同信号肽对SARS-CoV-2 S1、受体结合域(receptor binding domain,RBD)、RBD二聚体蛋白在Expisf9昆虫细胞中分泌表达的影响。方法 选取SARS-CoV-2 S1(M1-E661)、RBD(R319-P545)、RBD二聚体(R319-K537串联)3种蛋白的基因序列,按照N-端信号肽序列不同[内源(Endo)、蜂素honeybee melittin(HBM)、GP64、GP67、几丁质酶chitinase(Chi)、HIV-ENV]和C-端标签序列的不同,分为25组。通过Bac-to-Bac系统构建25种重组杆状病毒,建立25组三级毒种库。将B2和C4病毒分别接种至对数生长前期细胞(2.8×10⁶个/mL)和对数生长中期细胞(1.2×10⁷个/mL)。将各组病毒培养至100 mL(500 mL摇瓶),进行蛋白表达,并取样进行SDS-PAGE、Western blot和ELISA检测。S1、RBD、RBD二聚体蛋白各选择表达量较高的2组,进行重复验证。结果 B2、C4病毒接种至高密度细胞,分...     

A Single Amino Acid Substitution Changes Antigenicity of ORF2-Encoded Proteins of Hepatitis E Virus

Extensive genomic diversity has been observed among hepatitis E virus (HEV) strains. However, the implication of the genetic heterogeneity on HEV antigenic properties is uncertain. In this study, monoclonal antibodies (Mabs) against truncated ORF2-encoded proteins (aa452-617, designated p166 proteins) derived from HEV strains of Burma (genotype 1a, p166Bur), Pakistan (1b, p166Pak) and Morocco (1c, p166Mor) were raised and used for identification of HEV antigenic diversity. Six Mabs reacted to these 3 p166 proteins as well as p166 proteins constructed from strains derived from Mexico (genotype 2), US (genotype 3) and China (genotype 4), indicating the existence of pan-genotypic epitopes. Two Mabs, 1B5 and 6C7, reacted with p166Bur and p166Mor, but not p166Pak or p166s derived from genotypes 2, 3, and 4, indicating that these 2 Mabs recognized strain-specific HEV epitopes. Both the common and specific epitopes could not be mapped by 23 synthetic peptides spanning the p166Bur sequence, suggesting that they are confirmation-dependent. Comparative sequence analysis showed that p166Bur and p166Mor shared an identical aa sequence along their entire lengths, whereas for p166Pak the aas occupying positions 606 and 614 are different from aas at corresponding positions of p166Bur and p166Mor. Reactivity between 1B5 and p166Bur was abrogated with mutation of p166Bur/A606V, whereas p166Pak acquired the reactivity to 1B5 with mutation of p166Pak/V606A. However, mutations of p166Bur/L614M and P166Pak/M614L did not affect the immunoreactivity. Therefore, the aa occupying position 606 plays a critical role in maintaining the antigenicity of the HEV p166 proteins.     

赤子爱胜蚓Calreticulin的cDNA和氨基酸序列分析

目的分析赤子爱胜蚓Calreticulin的cDNA和氨基酸序列。方法从本院构建的赤子爱胜蚓cDNA文库中经测序获得其Calreticulin cDNA序列。采用生物信息学分析工具DNAMAN、NCBI ORF finder、ExPASy Protparam、ExPASY Protscale、NCBI Conserved Domains、SignalP 4.1 Server、TMHMM Server v.2.0、SOSUI、NetPhos 3.1 Server、PSORT、SOPMA、ExPASy COILS、SWISS-MODEL分别对Calreticulin的cDNA序列、氨基酸序列、一级结构基本理化性质、亲/疏水性、保守结构域、信号肽、跨膜区、可溶性、磷酸化修饰、亚细胞定位、二级结构、卷曲螺旋域以及三级结构进行预测及分析。结果赤子爱胜蚓Calreticulin cDNA序列长476 bp,其中包含354 bp的开放阅读框,编码118个氨基酸残基;Calreticulin由19种氨基酸组成,呈酸性,为稳定的可溶性亲水蛋白;具有1段Calreticulin超家族保守结构域;不存在信号肽和跨膜结构;具有12个潜在的磷酸化位点;主要存在于细胞核中;二级结构元件主要由α-螺旋(29.66%)和无规则卷曲(50.85%)组成,具有卷曲螺旋;三级结构预测结果与二级结构一致。结论掌握了赤子爱胜蚓Calreticulin的理化性质,预测了其潜在的特征,并分析了其结构,为后续深入开展其功能及分子作用机制的研究提供了理论依据。     

Fimbriae of Bacteroides nodosus: protein engineering of the structural subunit for the production of an exogenous peptide

The pattern of sequence variation between Bacteroides nodosusfimbrial subuits of different serotypes suggests a degree offlexibility, which might be exploited for protein engineeringapproaches for the expression of other peptides. We have testedthis using the well-characterized peptide epitope from VP1 offoot-and-mouth disease virus (FMDV), residues 144–159:LRGDLQVLAQKVARTL (strain 01-BFS). Using bacterial codon usage,several oligonucleotides were designed for the substitutionof this sequence internally at hypervariable regions of thefimbrial subunit (aligned for maximum homology), and for itsaddition at the carboxy-terminus with a diglycine spacer asa flexible hinge. Following site-directed mutagenesis in phageM13, the modified genes were placed under P_L promoter controland placed in a broad host range vector. Analysis of the variantproteins expressed in E.coli showed that these substitutionsaffected, to varying extents, recognition by both anti-fimbrialand anti-FMDV antibodies, indicating that hypervariable region2 is a major antigenic determinant of the fimbrial subunit andthat local stereochemical effects can influence antibody bindingto the FMDV peptide antigenic determinant. In Pseudomonas aeruginosa,viable transformants could only be obtained with the mutantgene encoding the carboxy-terminal graft. These cells providedfimbrial preparations comprised of the modified subunit. Thisthen constitutes the prototype for the development of a generalexpression system for the production of vaccine epitopes andother bioactive peptides. Furthermore, there is considerablescope for further modification of the system, for example byengineering specific chemical or protease cleavage sites forrelease of the grafted peptide. Alternatively, the fimbriaethemselves may serve as a useful supramoleuclar carrier or adjuvantfor immune provocation.     

猪流感复合多表位核酸疫苗的构建及其表达研究

目的构建猪流感病毒复合多表位核酸疫苗,并研究其表达产物的抗原性。方法以H3、H9亚型流感的HA抗原表位及流感病毒的其它主要抗原(NP、NA、M)表位基因为基础,再附以Kozak序列和适当的酶切位点,设计并合成一段长765bp的复合多表位基因(Epi),其中各表位基本独立,将其克隆入真核表达载体pIRES1neo,构建重组质粒pIRE-Epi。将多表位抗原基因Epi插入到融合表达基因H57中,构建重组质粒pIRE-H57-Epi。将构建的重组质粒在Hela细胞中表达,并用免疫荧光方法初步检测所表达蛋白的抗原性。结果所构建的融合表达载体pIRE-Epi和pIRE-H57-Epi,在Hela细胞中表达出流感病毒多表位抗原蛋白,并具有抗原性。结论已成功构建猪流感病毒多表位基因,有可能成为较理想的猪流感候选疫苗。     

Cross-Recognition of SARS-CoV-2 B-Cell Epitopes with Other Betacoronavirus Nucleoproteins

The B and T lymphocytes of the adaptive immune system are important for the control of most viral infections, including COVID-19. Identification of epitopes recognized by these cells is fundamental for understanding how the immune system detects and removes pathogens, and for antiviral vaccine design. Intriguingly, several cross-reactive T lymphocyte epitopes from SARS-CoV-2 with other betacoronaviruses responsible for the common cold have been identified. In addition, antibodies that cross-recognize the spike protein, but not the nucleoprotein (N protein), from different betacoronavirus have also been reported. Using a consensus of eight bioinformatic methods for predicting B-cell epitopes and the collection of experimentally detected epitopes for SARS-CoV and SARS-CoV-2, we identified four surface-exposed, conserved, and hypothetical antigenic regions that are exclusive of the N protein. These regions were analyzed using ELISA assays with two cohorts: SARS-CoV-2 infected patients and pre-COVID-19 samples. Here we describe four epitopes from SARS-CoV-2 N protein that are recognized by the humoral response from multiple individuals infected with COVID-19, and are conserved in other human coronaviruses. Three of these linear surface-exposed sequences and their peptide homologs in SARS-CoV-2 and HCoV-OC43 were also recognized by antibodies from pre-COVID-19 serum samples, indicating cross-reactivity of antibodies against coronavirus N proteins. Different conserved human coronaviruses (HCoVs) cross-reactive B epitopes against SARS-CoV-2 N protein are detected in a significant fraction of individuals not exposed to this pandemic virus. These results have potential clinical implications.     

Modelling the structure of the fusion protein from human respiratory syncytial virus

The fusion protein of respiratory syncytial virus (RSV-F) isresponsible for fusion of virion with host cells and infectionof neighbouring cells through the formation of syncytia. A three-dimensionalmodel structure of RSV-F was derived by homology modelling fromthe structure of the equivalent protein in Newcastle diseasevirus (NDV). Despite very low sequence homology between thetwo structures, most features of the model appear to have highcredibility, although a few small regions in RSV-F whose secondarystructure is predicted to be different to that in NDV are likelyto be poorly modelled. The organization of individual residuesidentified in escape mutants against monoclonal antibodies correlateswell with known antigenic sites. The location of residues involvedin point mutations in several drug-resistant variants is alsoexamined.