噬菌体展示重组人淋巴毒素突变体库及受体亲和筛选

淋巴毒素 (lymphotoxin , LT) 通过 TNFR1 受体传递凋亡信号,从而发挥抗肿瘤活性 . 对 LT 的受体结合区域进行多点随机突变,利用噬菌体展示重组人淋巴毒素 (rhLT) R46 , S106 , L130 三点随机突变组合文库和 S106 ～ F110 区域随机突变体库 . 噬菌体库与固相化 TNFR1 受体进行亲和筛选,富集了能与 TNFR1 受体结合的 rhLT 突变体 . 随机挑选 20 个单克隆噬菌体进行 ELISA 受体结合鉴定,其中 80 ％的克隆与 TNFR1 受体特异性结合,有 4 个克隆与 TNFR1 受体的结合能力高于野生型序列的 rhLT. 将这 4 个结合力高的突变体克隆于 pET32a(+) 载体,经过大肠杆菌表达和纯化操作后,检测这些突变体蛋白与 TNFR1 受体的结合活性和对 L929 细胞的杀伤活性,发现 3 个克隆的受体结合性质与其展示于噬菌体上时基本吻合,其中 C199 克隆与 TNFR1 的结合活性比野生型序列的 rhLT 提高了近 30 ％,且其对 L929 细胞的杀伤活性提高了近 90%. 应用噬菌体展示技术对淋巴毒素进行体外进化研究的尝试,为下一步的蛋白质结构和功能研究提供了思路,可成为大分子药物开发的有效工具 .     

枯草杆菌蛋白酶E基因多位点定点突变库的构建及其筛选

利用化学合成的15个寡聚核苷酸片段作为诱变引物,同时对枯草杆菌蛋白酶E(Subtilisin E或Apr E)基因进行体外突变,获得了合全部突变位点各种随机组合突变的突变库,通过点杂交法和DNA序列分析肯定了该突变库的可靠性.从突变库中选择一单点突变(Met222Ala)和3点突变(Asn76Asp/Asn109Ser/Ile205Cys)的基因进行克隆、表达和产物的酶学性质研究,发现其抗氧化性和热稳定性分别比野生型的有显著提高,与文献报道的一致.表明了该突变库在枯草杆菌蛋白酶工程研究中的应用价值.     

噬菌体展示HIV-1 Tat38-61碱性区51和55位随机突变体文库的构建

为了构建噬菌体展示Tat38-61(51N/55N) 碱性区突变体文库,进一步研究HIV-1 Tat38-61表位的分子进化筛选,采用含随机核苷酸序列的引物,通过Overlap PCR的方法获得51和55位氨基酸随机突变的全长Tat编码序列,再以此为模板PCR扩增出两端含有Xba I识别序列的Tat38-61突变体片段HIV-1 Tat38-61(51N/55N),克隆至噬菌体展示载体pCANTAB5S上,转化大肠杆菌TG1,经M13K07辅助噬菌体拯救,构建噬菌体展示Tat38-61(51N/55N) 碱性区突变体文库。结果显示文库的库容量为5.0×106,滴度为2.65×1012 TU/mL,阳性克隆率为56.50％;序列分析显示文库中51、55位核苷酸与氨基酸均呈随机性分布,达到了对文库进行分子进化筛选的要求,为获得可用作疫苗候选物的新型Tat突变体奠定基础。     

基于多重计算设计策略提高枯草芽孢杆菌脂肪酶的热稳定性

提高酶的热稳定性是生物催化领域的热点和难点,计算机辅助的理性设计相比于传统的定向进化更加高效,在酶工程领域中的应用越来越广泛和深入。文中以枯草芽孢杆菌脂肪酶A为模式蛋白,首先,利用Rosetta-VIP计算设计对酶的结构空腔进行分析,选择了16个有利于结构空腔填充(ΔΔE0)的单点突变,并以突变位点的溶剂可及表面积和进化保守性为二次筛选依据,测定了其热稳定性与酶活性。有6个单点突变体(F17A、V74I、L114P、I135V、M137A、I157L)的热稳定性得到了提高,其中Tm值最大提高3.18℃。结果表明,单点突变体满足ΔΔE越低、蛋白溶剂可及表面积减少且符合序列保守性,则得到保留原有酶活力的正向突变的可能性越大。此外,将热稳定性提高的6个单点突变进行迭代组合突变,两点组合突变体的Tm最大提高4.04℃,三点组合突变体的Tm最大提高5.13℃,四点组合突变体的Tm提高了7.30℃,六点组合突变体的Tm提高了7.43℃。因此,基于酶的分子结构的空腔分析、溶剂可及表面积及氨基酸序列保守性计算的多重虚拟筛选方法,可有效提高酶的热稳定性。     

蛋白质体外定向进化策略研究进展

定向进化已广泛应用于蛋白质的分子改造,是改善蛋白质特性的最有效策略之一。为了获得更高的突变效率,构建含有更多突变体的文库,不断地发明创新各种高效的蛋白质体外定向进化方法。对近年来出现的几种定向进化方法三核苷酸突变(TriNex)、序列饱和突变(SeSaM)、随机链交换突变法(RAISE)、重叠延伸蛋白域文库法(PDLGO)和迭代饱和突变法(ISM)的原理、特点及应用进行综述。     

SELEX技术筛选纤维蛋白适配子的研究

目的:用纤维蛋白作为靶物质对ss DNA随机序列文库进行筛选,旨在获得高亲和力的纤维蛋白适配子。方法:在体外人工合成长度为99个核苷酸的ss DNA随机序列文库,文库中间区域为63个核苷酸的随机序列,两端为18个核苷酸的固定的引物序列;然后以羧基磁珠为介质包被纤维蛋白,利用指数级富集的配体系统进化技术(SELEX)对ss DNA随机序列文库进行反复筛选,当结合率不再提高时对筛选出的适配子进行连接、转化及测序分析。结果:羧基磁珠成功地包被了纤维蛋白,包被效率为87.65%,经15轮逐步递增压力的筛选,获得了纤维蛋白适配子群,经测序分析比对发现适配子有很好的多样性。结论:应用SELEX技术初步筛选出了亲和力较高的纤维蛋白适配子群,为下一步的鉴定及功能研究奠定了良好基础。     

丙型肝炎病毒E2糖蛋白糖基化作用的研究

本研究构建丙型肝炎病毒(HCV)糖蛋白E2的N-糖基化位点定点突变体。采用高保真性的Pfx DNA聚合酶,设计两对引物,分别引入两个突变位点,通过PCR体外定点突变,使E2第535、583位核苷酸由A突变为T,从而使AAC编码的天冬酰氨突变为TAC编码的酪氨酸,使得N-糖苷化位点NNT、NST突变为YNT、YST.结果得到两个单位点以及一个双位点突变体,并将突变型E2连接到真核表达载体peDNA3．1(-)／Myc—HisB上。成功获得的3个HCVE2糖蛋白糖基化位点定点突变体,为进一步进行HCVE2糖蛋白糖基化位点与分子伴侣之间的相互关系以及突变体对机体的免疫功能的影响的研究奠定了基础。     

判断基因中点突变使用的寡聚核苷酸探针

本文简明扼要地介绍了人工合成寡聚核苷酸探针的设计原则,以及用 ³²P标记等方法。同时还从理论上阐述了19聚体探针在生物实验使用中的合理性,并强调在检测基因的点突变时,设计人工合成的寡聚核苷酸探针应将点突变位点置于探针序列的中间为宜。在选择序列时,要注意避免发生G-T错配,这样有利于鉴别基因的点突变。     

人尿激酶原突变体的构建及其特性的研究

由于人尿激酶原（pro-UK）存在凝血酶和纤溶酶原激活剂抑制剂（PAI-1）的作用位点,在生产和治疗过程中容易失去活性。采用PCR介导的定点突变技术对pro-UK基因进行了突变,构建了3种人pro-UK突变体, 分别将蛋白序列中的凝血酶作用位点Arg¹⁵⁶突变成His¹⁵⁶,构建成pro-UKM1;将PAI-1的作用位点Arg¹⁷⁸、Arg¹⁷⁹、Arg¹⁸¹突变为Lys¹⁷⁸、Lys¹⁷⁹、His¹⁸¹构建成pro-UKM2;同时将凝血酶和PAI-1的作用位点突变构建成pro-UKM3。分别在CHO细胞中获得稳定表达。并对3种突变体进行了SDS-PAGE纤维蛋白自显影和Western blot分析,证明3种细胞表达的pro-UKM与天然尿激酶原带型一致,绝大多数为单链。体外溶栓试验表明,pro-UKM1对凝血酶有抵抗性,pro-UKM2对PAI有抵抗性,pro-Ukm3能有效抵抗凝血酶和PAI的活性抑制。特别是pro-UKM3具有开发成新型溶血栓药物的潜力     

通过DNA改组技术获得高活性β-葡萄糖苷酸酶

β 葡萄糖苷酸酶是在植物转基因中广泛应用的报告基因 .以质粒pBI12 1中的GUS基因为基础 ,利用DNA改组方法 ,经DNaseⅠ降解 ,PrimerlessPCR ,PrimerPCR对GUS基因进行了突变和改组 ,然后将改组的GUS基因连接到原核表达载体pG2 5 1中 ,构建了库容为 10 8的突变体库 .经过活性的筛选 ,得到活性提高的克隆 ,再以此为基础 ,经过新的改组、筛选得到活性大幅度提高的克隆GUS2 4 .基因测序显示 ,GUS2 4与GUS基因之间的同源性为 99 7% ,共有 6个核苷酸位点发生了改变 ,分别是 :379位的A突变为G ,396位的T突变为C ,711位的G突变为A ,95 8位T突变为C ,990位的T突变为C ,1649位的A突变为G .核苷酸序列推导的氨基酸序列显示 ,3个氨基酸发生了突变 ,12 7位的Ser突变为Gly ,32 0位的Trp突变为Arg ,5 5 0位的Asn突变为Ser.X gluc染色检测和荧光测活结果显示GUS2 4基因表达的 β 葡萄糖苷酸酶基较GUS基因表达产物活性提高 3倍     

结合单酶切位点的融合PCR技术对SCN1A基因的定点诱变

目的:利用结合单酶切位点的融合PCR技术对癫痫相关基因SCN1A进行定点突变。方法:首先设计两对引物PF1/PR1和PF2/PR2,PF1和PR2均位于突变位点最近的单酶切位点处,而突变位点设计在第一对反向引物(PR1)和第二对正向引物上(PF2)。通过重叠延伸法两次PCR扩增:第一次用PF1/PR1和PF2/PR2分开扩增,以扩增产物作模板,PF1/PR2作引物进行融合PCR,得到的扩增产物即含有所需要的突变位点,最后将扩增片段克隆入pMD18-T载体,经测序筛选阳性克隆。结果:DNA测序表明SCN1A基因所编码的第946位密码子由精氨酸(Arg)突变为组氨酸(His),再通过酶切和连接反应将重组质粒上的突变片段替换SCN1A表达质粒上的对应片段,成功构建了SCN1A突变载体。结论:与现在常用的长距离PCR定点诱导突变相比较,结合单酶切位点的融合PCR定点突变技术具备扩增距离短的优点,大大降低了自发突变的概率,适合于大肠杆菌中易自发突变的较大载体的定点诱变。     

毛霉△6-脂肪酸脱氢酶随机突变文库的构建与分析

毛霉Mucor sp.EIM-10△6-脂肪酸脱氢酶是γ-亚麻酸合成途径的关键酶。为提高脂肪酸脱氢酶的活性以及研究该酶一级结构对酶活性的影响,利用易错PCR对毛霉△6-脂肪酸脱氢酶基因(mcd6)进行随机突变,将PCR产物与大肠杆菌-酿酒酵母穿梭表达载体PYMD6PMCD6连接,获得随机突变质粒PYTBMCD6,转化酿酒酵母Saccharomyces cerevisiae,构建了原始库容为4.6×104 CFU的△6-脂肪酸脱氢酶的随机突变表达文库。随机突变表达文库的构建与分析为定点突变等酶蛋白的理性设计奠定基础。     

Site-directed mutagenesis by overlap extension using the polymerase chain reaction

Overlap extension represents a new approach to genetic engineering. Complementary oligodeoxyribonucleotide (oligo) primers and the polymerase chain reaction are used to generate two DNA fragments having overlapping ends. These fragments are combined in a subsequent 'fusion' reaction in which the overlapping ends anneal, allowing the 3' overlap of each strand to serve as a primer for the 3' extension of the complementary strand. The resulting fusion product is amplified further by PCR. Specific alterations in the nucleotide (nt) sequence can be introduced by incorporating nucleotide changes into the overlapping oligo primers. Using this technique of site-directed mutagenesis, three variants of a mouse major histocompatibility complex class-I gene have been generated, cloned and analyzed. Screening of mutant clones revealed at least a 98% efficiency of mutagenesis. All clones sequenced contained the desired mutations, and a low frequency of random substitution estimated to occur at approx. 1 in 4000 nt was detected. This method represents a significant improvement over standard methods of site-directed mutagenesis because it is much faster, simpler and approaches 100% efficiency in the generation of mutant product.     

HIV-1 protease catalytic efficiency effects caused by random single amino acid substitutions

Protein evolution has occurred by successive fixation of individual mutations. The probability of fixation depends on the fitness of the mutation, and the arising variant can be deleterious, neutral, or beneficial. Despite its relevance, only few studies have estimated the distribution of fitness effects caused by random single mutations on protein function. The human immunodeficiency virus type 1 (HIV-1) protease was chosen as a model protein to quantify protein's tolerability to random single mutations. After determining the enzymatic activity of 107 single random mutants, we found that 86% of single mutations were deleterious for the enzyme catalytic efficiency and 54% lethal. Only 2% of the mutations significantly increased the catalytic efficiency of the enzyme. These data demonstrate the vulnerability of HIV-1 protease to single random mutations. When a second random mutagenesis library was constructed from an HIV-1 protease carrying a highly deleterious single mutation (D30N), a higher proportion of mutations with neutral or beneficial effect were found, 26% and 9%, respectively. Importantly, antagonist epistasis was observed between deleterious mutations. In particular, the mutation N88D, lethal for the wild-type protease, restored the wild-type catalytic efficiency when combined with the highly deleterious mutation D30N. The low tolerability to single random substitutions shown here for the wild-type HIV-1 protease contrasts with its in vivo ability to generate an adaptive variation. Thus, the antagonist epistasis between deleterious or lethal mutations may be responsible for increasing the protein mutational robustness and evolvability.     

QuikChange shuffling: a convenient and robust method for site-directed mutagenesis and random recombination of homologous genes

Here we describe a robust method, termed QuikChange shuffling, for efficient site-directed mutagenesis and random recombination of homologous genes. The homologous genes are fragmented, and the random fragments are reassembled in a self-priming polymerase reaction to obtain chimeric genes. The product is then mixed with linearized vector and two pairs of complementary mutagenic primers, followed by assembly of the chimeric genes and linearized vector through QuikChange-like amplification to introduce recombinant plasmids with a site-directed mutation. The method, which can yield 100% chimeric genes after library construction, is more convenient and efficient than current DNA shuffling methods.     

部分扩增结合双片段连接法克隆系列截短基因突变体

体外合成DNA伴随的随机突变是制约基因定点突变效率的重要因素。以克隆周期蛋白E（cyclin E）及其截短基因的激酶活性缺失突变体为例,对传统重叠延伸PCR（overlap extension PCR,OE-PCR）作适当改进,提出一种系列相关基因定点突变的优化方案。前期研究中已克隆了cyclin E基因及其2个截短基因T1、T2,并通过EcoRⅠ/SalⅠ双酶切插入pEGFP_C2载体。限制性酶切分析发现cyclin E基因序列中含有1个AgeⅠ位点将其分为F1、F2两段,目标突变位点KD位于F2段。对于cyclin E及其截短基因,F2段是完全一致的。因此,通过重叠延伸PCR扩增含突变位点的共有片段F2,从C2-cyclin E、C2-cyclin E_T1和C2-cyclin E_T2这3个原始质粒中切取相应的F1片段,再将F1与酶切的F2一起连接插入载体以重构完整突变体。对比检测发现OE-PCR扩增较短DNA片段更易成功。C2-cyclin E、C2-cyclin E_T1和C2-cyclin E_T2这3组均能筛选出一定数量克隆,经检测和序列鉴定,每组各得到1个序列完全准确的目标突变体。研究表明,采用部分扩增可以缩短DNA合成长度,避免了目标基因反复扩增等不利因素,从而减少随机突变;双片段连接避免了双AgeⅠ位点对常规酶切-连接的限制。两者相结合,可作为其他系列相关基因定点突变的优化方案。     

Directed evolution for increased chitinase activity

Directed evolution through DNA shuffling and screening was used to enhance the catalytic ability of a fungal, Beauveria bassiana, chitinase, Bbchit1. The Bbchit gene was first linked to various prokaryotic signal sequences and expressed in Escherichia coli. The signal peptide, PelB, from Erwinia carotovora resulted in greatest chitinase secretion into broth. The nucleotide sequence expressing PelB signal peptide was then incorporated into an E. coli vector to express Bbchit1 variants generated by three rounds of DNA shuffling. A Bbchit1 library with 150,000 variants was constructed with a nucleotide point mutation frequency of 0.6% and screened for chitinolytic activity. Two Bbchit1 variants (SHU-1 and SHU-2) were selected that showed increased chitinolytic activity compared to the wild type. Sequence analysis of these variants revealed mutations in amino acid residues that would not normally be considered for rational design of improved chitinase activity. The amino acid substitutions occurred outside of the two putative substrate-binding sites and the catalytic region.