多肽噬菌体展示

噬菌体展示技术已被广泛地应用于生物学研究的各个方面.利用它可融合表达多肽、蛋白质结构域和蛋白质.尤其是多肽噬菌体展示,已被作为一种便利的研究工具去发现和研究那些与受体、酶、凝集素、抗体、核酸以及其他生物分子亲和的多肽配基和酶的底物专一性,该技术在药物的发现,疫苗的设计等医学领域也有着潜在的应用价值.     

从噬菌体随机肽库中筛选流感病毒神经氨酸酶的抑制多肽

目的:从噬菌体呈现12肽库中筛选与流感病毒神经氨酸酶特异性结合的肽。方法:以甲三型流感病毒裂解疫苗原液为靶分子,经过3轮生物淘选,从噬菌体随机肽库中筛选与之结合的噬菌体。用ELISA方法鉴定噬菌体克隆与靶分子的结合力,用荧光方法测定噬菌体克隆对流感病毒A/Sydney/5/97(H3N2)神经氨酸酶的抑制活性。对筛选到的阳性克隆进行DNA序列测定并推导出相应的氨基酸序列。结果:经过3轮筛选后,42个噬菌体克隆与靶分子有高度亲和力,23个噬菌体克隆对流感病毒A/Sydney/5/97(H3N2)神经氨酸酶有抑制活性。对27个噬菌体克隆的测序结果表明,分别有10个和2个克隆的序列是一致的,其氨基酸序列分别为KSLSRHDHIHHH和WPRHHHSASVQT。结论:通过噬菌体肽库筛选到抑制流感病毒神经氨酸酶的12肽,为进一步研究对流感病毒神经氨酸酶有抑制活性的分子药物奠定了基础。     

核受体PPARγ结合小肽的筛选及其功能

为筛选与核受体过氧化物酶体增殖物激活受体γ(PPARγ)结合的功能短肽,在大肠杆菌BL21(DE3)中表达PPARγ配体结合域(LBD)的融合蛋白,并利用Ni2+-NTA离子交换树脂对表达蛋白进行纯化.以此纯化蛋白为靶,采用固体包被法对噬菌体展示随机十二肽库及环七肽库进行亲和筛选.经ELISA法鉴定特异结合的高亲和力阳性噬菌体单克隆并测序.同时利用PPARγ的配体rosiglitazone与噬菌体小肽进行竞争性结合抑制实验.最终获得与PPARγ-LBD高亲和力的十二肽3个,环七肽5个,分别含LXXLL和DXXRW(其中X为非特异氨基酸残基)保守序列.Rosiglitazone不影响噬菌体小肽与靶蛋白的结合,说明获得与配体rosiglitazone结合位点不同的目的肽.     

Generation and characterization of C305, a murine neutralizing scFv antibody that can inhibit BLyS binding to its receptor BCMA

B-lymphocyte stimulator (BLyS) is a member of the tumor necrosis factor (TNF) family and a key regulator of B cell response. Neutralizing single-chain fragment variable (scFv) antibody against BLyS binding to its receptor BCMA has the potential to play a prominent role in autoimmune disease therapy. A phage display scFv library constructed on pill protein of MI 3 filamentous phage was screened using BLyS.After five rounds of panning, their binding activity was characterized by phage-ELISA. Nucleotide sequencing revealed that at least two different scFv gene fragments (C305 and D416) were obtained. The two different scFv gene fragments were expressed to obtain the soluble scFv antibodies, then the soluble scFv antibodies were characterized by means of competitive ELISA and in vitro neutralization assay. The results indicated that C305 is the neutralizing scFv antibody that can inhibit BLyS binding to its receptor BCMA.     

Selection of Burkholderia pseudomallei protease-binding peptides by phage display

Burkholderia pseudomallei is a causative agent of melioidosis, a fatal community acquired septicemia in Southeast Asia and Northern Australia. A protease has been proposed to be one of the major pathogenic factors to play a significant role in melioidosis. We have used phage display technology to identify peptides binding to B. pseudomallei protease. By screening a constrained cyclic heptapeptide library, five independent clones with affinity to this protease were isolated and the amino acid sequences were determined. The cyclic heptapeptides from two of the phage clones (Cys-Phe-Phe-Met-Pro-His-Thr-Phe-Cys) were identical and showed the strongest phage-protease interaction as detected by ELISA. Four of the five selected phages at the amount of 10¹³ phages could inhibit B. pseudomallei protease activity by approximately 50%.     

High affinity peptides for the recognition of the heart disease biomarker troponin I identified using phage display

Troponin I is a specific and sensitive clinical biomarker for myocardial injury. In this study we have used polyvalent phage display to isolate unique linear peptide motifs which recognize both the human and rat homologs of troponin I. The peptide specific for human troponin I has a sequence of FYSHSFHENWPS and the peptide specific for the rat troponin I has a sequence of FHSSWPVNGSTI. Enzyme‐linked immunosorbent assays (ELISAs) were used to evaluate the binding interactions, and the two phage‐displayed peptides exhibited some cross‐reactivity, but they were both more specific for the troponin I homolog they were selected against. The binding affinities of the phage‐displayed peptides were decreased by the presence of complex tissue culture media (MEM), and the addition of 10% calf serum further interfered with the binding of the target proteins. Kinetic indirect phage ELISAs revealed that both troponin I binding peptides were found to have nanomolar affinities for the troponin proteins while attached to the phage particles. To our knowledge, this is the first example of isolation and characterization of troponin I binders using phage display technology. These new peptides may have potential utility in the development of new clinical assays for cardiac injury as well as in monitoring of cardiac cells grown in culture. Biotechnol. Bioeng. 2010. 105: 678–686. © 2009 Wiley Periodicals, Inc.     

高致病性禽流感病毒血凝素蛋白广谱中和表位模拟肽的筛选与鉴定

以H5N1型禽流感病毒HA蛋白广谱中和单抗8H5为基础,利用噬菌体展示肽库技术及类病毒颗粒融合表达技术研究HA模拟表位。ELISA检测结果显示:筛选获得模拟HA表位的模拟肽123,进行类病毒颗粒融合蛋白表达后,仍具有与8H5单抗特异结合的能力。免疫荧光检测结果说明,类病毒颗粒免疫小鼠后产生了能与HA交叉反应的抗体。禽流感病毒HA模拟表位的研究与性质的分析及类病毒颗粒融合蛋白的表达与活性分析、免疫原性分析,都为研制禽流感通用表位疫苗奠定了基础。     

Phage display screening for peptidic chitinase inhibitors

A phage display library with disulfide-cyclized peptides was screened for peptides binding to chitinases from Serratia marcescens. One of those peptides was found to efficiently inhibit chitinase A and two others were inhibitors of chitinase B. Complete substitutional analysis of all three peptides using cellulose-bound peptide spot synthesis revealed key interaction positions and allowed optimization of the chitinase B inhibitory peptides towards higher affinity, with inhibitory constants in the lower nanomolar range. Inhibition by all peptides proved to be competitive and highly specific for the chitinase used to select them, as shown with a series of chitinases from different organisms.     

Efficient identification of tubby‐binding proteins by an improved system of T7 phage display

Mutation in the tubby gene causes adult‐onset obesity, progressive retinal, and cochlear degeneration with unknown mechanism. In contrast, mutations in tubby‐like protein 1 (Tulp1), whose C‐terminus is highly homologous to tubby, only lead to retinal degeneration. We speculate that their diverse N‐terminus may define their distinct disease profile. To elucidate the binding partners of tubby, we used tubby N‐terminus (tubby‐N) as bait to identify unknown binding proteins with open‐reading‐frame (ORF) phage display. T7 phage display was engineered with three improvements: high‐quality ORF phage display cDNA library, specific phage elution by protease cleavage, and dual phage display for sensitive high throughput screening. The new system is capable of identifying unknown bait‐binding proteins in as fast as ～4–7 days. While phage display with conventional cDNA libraries identifies high percentage of out‐of‐frame unnatural short peptides, all 28 tubby‐N‐binding clones identified by ORF phage display were ORFs. They encode 16 proteins, including 8 nuclear proteins. Fourteen proteins were analyzed by yeast two‐hybrid assay and protein pull‐down assay with ten of them independently verified. Comparative binding analyses revealed several proteins binding to both tubby and Tulp1 as well as one tubby‐specific binding protein. These data suggest that tubby‐N is capable of interacting with multiple nuclear and cytoplasmic protein binding partners. These results demonstrated that the newly‐engineered ORF phage display is a powerful technology to identify unknown protein–protein interactions. Copyright © 2009 John Wiley & Sons, Ltd.     

一种特异识别SV40启动子的人工转录因子的构建

转录因子是真核表达调控中非常重要的一类反式作用因子,通常由DNA结合域与效应域两部分组成,而锌指结构是DNA结合域的常见组成单元。人工转录因子就是基于转录因子的这种结构特点,人为地选择针对特定序列的DNA结合域与具有特定作用的效应域组合而成。利用噬菌体展示技术,筛选到与SV40启动子上9bp序列特异结合的锌指结构,再连接KOX1的KRAB域构建了一种人工转录因子。转染实验表明它对SV40下游的报告基因的表达有很显著的抑制作用。     

Radiolabeling and biodistribution of a nasopharyngeal carcinoma-targeting peptide identified by in vivo phage display

A dodecapeptide EDIKPKTSLAFR ligand targeting CEN- 1 human nasopharyngeal carcinoma （NPC） was identified by in vivo phage display. Two tridecapeptides and their derivatives, named YR13 （YEDIKPKTSLAFR）, EY 1 3 （EDIKPKTSLAFRY）, EY 1 3-NH2 （EDIKPKTSLAFRY-NH2） and Fmoc-YR 1 3 （Fmoc-YEDIKPKTSLAFR）, were synthesized and radiolabeled with ^[3]I. The stability in vitro, biodistribution and tissue distribution of selected phage particles in mice bearing NPC tumor were determined, and plasma metabolites analysis of radiolabeled peptides was carried out. Although Fmoc and NH2 groups could protect the peptide from deiodination, only Fmoc group inhibited the binding of Fmoc-YR13 to NPC tumors. The compound EY13-NH2, the C-terminal amide of peptide EY13, had the greatest serum stability, the least deiodination, and showed favorable tumor/blood ratios. The selected phage particles （phage 3 or phage 5） were more concentrated in NPC tumors than the control phage （initial phage display peptide library）. EY13 could also inhibit the binding of selected phage particles to tumors. The results indicated that EDIKPKTSLAFR was a good candidate in diagnostic and therapeutic NPC.     

Preferential selection of Cys‐constrained peptides from a random phage‐displayed library by anti‐glucitollysine antibodies

Phage‐displayed peptides recognized by two monoclonal antibodies against glucitollysine were selected. The most prominent feature of the peptide panel was the presence of paired Cys in most of them (21/24 peptides). The availability of a wide variety of peptides having differently spaced paired Cys, as well as truly linear Cys‐free peptides, gave the opportunity to explore the role of disulfide bridges in phage selection. Some Cys‐containing peptides came from a Cys‐flanked cyclic 9‐mer library, but most of them (18/21) were derived from a totally random 12‐mer library, and hence the presence of Cys was dictated by the selector antibodies. Motifs shared by several peptides (potentially involved in binding) often contained or were flanked by Cys residues. Binding of all Cys‐containing phage‐displayed peptides was abolished/decreased after a reducing treatment. Screening a random peptide library (without invariant Cys residues) is powerful enough to clearly reveal the need, preferences, and diversity of Cys‐mediated structural constraints for recognition. Copyright © 2008 European Peptide Society and John Wiley & Sons, Ltd.     

Novel p16 binding peptide development for p16‐overexpressing cancer cell detection using phage display

Protein p^16INK4a (p16) is a well‐known biomarker for diagnosis of human papillomavirus (HPV) related cancers. In this work, we identify novel p16 binding peptides by using phage display selection method. A random heptamer phage display library was screened on purified recombinant p16 protein‐coated plates to elute only the bound phages from p16 surfaces. Binding affinity of the bound phages was compared with each other by enzyme‐linked immunosorbent assay (ELISA), fluorescence imaging technique, and bioinformatic computations. Binding specificity and binding selectivity of the best candidate phage‐displayed p16 binding peptide were evaluated by peptide blocking experiment in competition with p16 monoclonal antibody and fluorescence imaging technique, respectively. Five candidate phage‐displayed peptides were isolated from the phage display selection method. All candidate p16 binding phages show better binding affinity than wild‐type phage in ELISA test, but only three of them can discriminate p16‐overexpressing cancer cell, CaSki, from normal uterine fibroblast cell, HUF, with relative fluorescence intensities from 2.6 to 4.2‐fold greater than those of wild‐type phage. Bioinformatic results indicate that peptide ‘Ser‐His‐Ser‐Leu‐Leu‐Ser‐Ser’ binds to p16 molecule with the best binding score and does not interfere with the common protein functions of p16. Peptide blocking experiment shows that the phage‐displayed peptide ‘Ser‐His‐Ser‐Leu‐Leu‐Ser‐Ser’ can conceal p16 from monoclonal antibody interaction. This phage clone also selectively interacts with the p16 positive cell lines, and thus, it can be applied for p16‐overexpressing cell detection. Copyright © 2015 European Peptide Society and John Wiley & Sons, Ltd.     

Motifier: An IgOme Profiler Based on Peptide Motifs Using Machine Learning

Antibodies provide a comprehensive record of the encounters with threats and insults to the immune system. The ability to examine the repertoire of antibodies in serum and discover those that best represent “discriminating features” characteristic of various clinical situations, is potentially very useful. Recently, phage display technologies combined with Next-Generation Sequencing (NGS) produced a powerful experimental methodology, coined “Deep-Panning”, in which the spectrum of serum antibodies is probed. In order to extract meaningful biological insights from the tens of millions of affinity-selected peptides generated by Deep-Panning, advanced bioinformatics algorithms are a must. In this study, we describe Motifier, a computational pipeline comprised of a set of algorithms that systematically generates discriminatory peptide motifs based on the affinity-selected peptides identified by Deep-Panning. These motifs are shown to effectively characterize antibody binding activities and through the implementation of machine-learning protocols are shown to accurately classify complex antibody mixtures representing various biological conditions.     

抗乙型肝炎病毒表面抗原T7噬菌体抗体库的构建

构建T7噬菌体单链抗体(scFv)库筛选抗乙型肝炎病毒表面抗原抗体.从抗-HBs阳性患者外周血淋巴细胞中提取总RNA,反转录合成cDNA第1条链,PCR分别扩增抗体重链可变区基因(VH)和轻链可变区基因(VL),经重叠延伸拼接(SOE)PCR组成scFv基因,并将其与T7噬菌体载体的2个臂相连接.体外包装后,在宿主菌BLT5403中,扩增重组噬菌体抗体库.以乙型肝炎病毒表面抗原进行4轮“吸附-洗脱-扩增”的筛选,酶免疫实验检测抗体活性.所建抗体库库容为1.53×107,扩增后初级库滴度为2.42×1010pfu/mL.以乙型肝炎病毒表面抗原筛选后抗体出现特异性富集,经酶免疫实验鉴定,得到2株与HBsAg抗原特异结合的噬菌体抗体,成功构建了抗HBsAg蛋白T7噬菌体抗体库.     

从抗TNF抗体的CDR肽库中获得拮抗TNF的短肽

为设计来自抗体的短肽 ,以抗肿瘤坏死因子 (TNF)嵌合抗体 (cA2 )CDRs为模板 ,在其两侧各加 3个随机氨基酸残基 ( X3 CDR X3 ) ,构建了 6个以CDR为基础的肽库 .经过 3轮亲和选择 ,挑取单克隆 ,进一步经ELISA检测TNF阳性噬菌体克隆 ,分离得到 7个ELISA阳性较好的噬菌体肽克隆 ,分别命名为CDR2L1、CDR2L2、CDR2L3、CDR1L1、CDR2H1、CDR3H1、CDR3H 2 .应用MTT方法 ,检测 7个克隆对TNF生物学活性的拮抗作用 .结果显示 :来自CDR2L ,CDR3H肽库中的CDR2L2、CDR2L3,CDR3H2噬菌体肽具有明显的拮抗TNF诱导L92 9细胞的细胞毒作用 ,其中以CDR2L2噬菌体肽的拮抗活性最强 .而来源于CDR1L ,CDR2H肽库的CDR1L1和CDR2H1噬菌体肽和来自CDR2L ,CDR3H肽库中的CDR2L1和CDR3H1噬菌体肽没有明显的拮抗TNF作用 .研究结果初步表明 :从cA2抗体CDR肽库中筛选得到的噬菌体CDR模拟肽具有亲本抗体相似的结合活性和生物学效应 ,从而为开发已知抗体 (特别是治疗用抗体 )CDR为基础的肽药物创建一个技术平台奠定基础     

Selection and mass spectrometry characterization of peptides targeting semiconductor surfaces

We report on elaboration of 12‐mer peptides that reveal specific recognition for the following semiconductor (SC) surfaces: GaAs(100), InAs(100), GaN(0001), ZnSe(100), ZnTe(100), GaAs(111)A, GaSb(100), CdSe(100). A M13 bacteriophage library was used to screen 10⁹ different 12‐mer peptides against these substrates to finally isolate, in maximum six amplification cycles, peptides that bind to the target surfaces. The specific peptides for the InAs and ZnSe surfaces were obtained. Contrary, for the other SC surfaces several peptides with high affinities have been isolated. Aiming for a better specificity, when the phage display has been conducted through six cycles, the screening procedure got dominated by a phage present in the M13 bacteriophage library and the SVSVGMKPSPRP peptide has been selected for different SCs. The high amplification potential of this phage has been observed previously with different targets. Thus, precaution should be undertaken in defining adhesion peptides with the phage display technique and real affinity of the obtained biolinkers should be studied with other methods. We employed mass spectrometry (MALDI‐TOF/TOF) to demonstrate the preferential attachment (or not) of the SVSVGMKPSPRP peptide to the different SC surfaces. This allows us to define a realistic selection of the expressed peptides presenting affinity for the studied eight SC surfaces. We demonstrate that with increasing the dielectric constants of the employed solvents, adhesion of the SVSVGMKPSPRP peptide onto GaN(0001) is hindered. Biotechnol. Bioeng. 2009; 104: 1121–1131. © 2009 Wiley Periodicals, Inc.     

Discovery of targeting peptides for selective therapy of medullary thyroid carcinoma

BACKGROUND: Adenovirus efficiently infects a broad range of target cells, thereby preventing selective gene transfer. Moreover, several cell types and tissues including primary tumors are refractory to adenoviral infection, mainly because of low expression levels of coxsackie-adenovirus receptor (CAR). Thus, identification of cancer-selective ligands which yield gene transfer to neoplastic cells by minimizing transduction of normal cells is a key issue for successful cancer therapy. METHODS: We initially analyzed adenoviral receptor expression in human medullary thyroid carcinoma (MTC) cells. MTC cell-specific peptides were isolated by biopanning a phage display peptide library on cultured cancer cells and on tumors in vivo and further characterized. RESULTS: We found significant differences in CAR and alphav-integrin protein levels between MTC-derived TT cells in vitro and established xenograft tumors in mice, indicating a lack of alphav-integrin expression on growing tumors. MTC-specific candidates were identified by performing three rounds of subtraction. Selected phages showed up to 22-fold higher binding efficiency for TT cells when compared with wild-type M13 phage or other human cell lines and tumor tissue in vivo. Homing to TT cells of the best binding phage was clearly blocked in the presence of specific peptide, whereas no phage competition was observed with an unspecific peptide. The best binding peptide mediated efficient internalization of the phage. Importantly, specific binding and internalization was also mediated by the identified peptide within the adenoviral context. CONCLUSIONS: Our results indicate that the identified ligand should be suitable to improve selectivity of adenoviral gene transfer to medullary thyroid tumors in vivo.