表位九肽库的构建及人Ⅳ型胶原酶特异结合肽的筛选

将人工合成的编码九肽的随机序列DNA片段克隆进丝状噬菌体表达载体FUSE5,经多次电击转化和表达,获得肽段与噬菌体pⅢ蛋白融合并展示在噬菌体表面的随机序列九肽表位肽库。库容量达10 10个克隆。以Ⅳ型胶原酶为靶蛋白,采用亲和纯化筛选模式,从中筛选出Ⅳ型胶原酶结合肽。进一步ELISA检测筛选出与Ⅳ型胶原酶特异结合的20个阳性克隆。序列分析发现一组肽含有WDXXD的共同序列,一组含有WVGXXR的共同序列。其中WDXXD的序列与Ⅳ型胶原酶单链抗体可变区序列同源。结果表明,多肽库是筛选蛋白特异结合肽的有力工具,表位九肽库的构建和筛选方法的建立为进一步应用筛选具有高亲和力的特异结合肽奠定了基础。     

脑膜炎大肠杆菌IbeA蛋白结合肽序列的亲和筛选

应用噬菌体展示肽库技术,以重组的脑膜炎大肠杆菌致病蛋白IbeA作为靶分子,经过吸附-洗脱-扩增-再吸附的亲和筛选,随机挑选亲和力强的噬菌体克隆,进行ELISA、竞争抑制实验和序列测定。结果显示,经3轮淘选后,间接ELISA鉴定得到高亲和性结合IbeA蛋白的15个阳性克隆。竞争抑制实验结果表明,游离IbeA蛋白能竞争抑制噬菌体结合肽克隆与固相包被的IbeA蛋白的结合,其抑制作用随游离IbeA蛋白浓度的降低而减弱。测序结果得到5种阳性噬菌体克隆展示肽序列。上述结果提示以脑膜炎大肠杆菌IbeA蛋白为靶筛选所获得的噬菌体12肽克隆,具有特异性,其结合肽序列呈现相对保守性。建立的从噬菌体随机肽库筛选IbeA蛋白结合肽的方法具有方便、灵活和高效可行的特点。     

噬菌体展示肽文库及其应用

肽库是研究与特定靶分子高亲和结合配体的有力工具,肽文库可被分为合成文库和噬菌体肽文库两类,作者综述了噬菌体肽文库及其蛋白质结构域分析定位,疫苗研制及抗原表位分析和药物设计等方面的应用。     

噬菌体显示技术在短肽库中的应用现状

噬菌体显示技术是近年来出现的一种新技术、它是将外源蛋白通过与丝状噬菌体外壳蛋白融合而将外源蛋白表达于噬菌体颗粒的表达。该技术已经被广泛地应用于噬菌体短肽库的构建。由于该表达的短肽可以与其相应的结合分子相识别而发挥其生物活性,因而,噬菌体短肽库技术在分子间识别机理的研究,蛋白工程的改造以及药物的筛选、疫苗的研制等方面具有广泛应用前景。本综述了近年来噬菌体显示技术在短肽库中的应用进展。     

具有GCSF活性的噬菌体展示肽

从NFS 6 0细胞中克隆了小鼠粒细胞集落刺激因子 (granulocytecolony stimulatingfactor,G CSF)受体的细胞因子受体同源区 (cytokinereceptorhomologous ,CRH)结构域 ,采用GST融合表达策略 ,实现了CRH结构域的表达 .以纯化的GST CRH融合蛋白为靶 ,从噬菌体随机环七肽库中筛选CRH结构域的结合肽 ,找到两组具有核心序列的噬菌体展示肽 .其中C2和C13噬菌体展示肽能刺激NFS 6 0细胞增殖 ,说明C2和C13噬菌体展示肽具有G CSF活性     

P-糖蛋白的表达及其结合肽的筛选

为获得P 糖蛋白胞外段 ,构建了高效表达载体pGEX Pgp ,转化大肠杆菌DH5α ,进行表达、鉴定及纯化 ,以获得的融合蛋白为靶蛋白 ,筛选噬菌体随机 12肽库 ,免疫细胞化学方法进行鉴定 .SDS PAGE分析 ,表达出约 30kD大小的蛋白 ;从噬菌体随机肽库中筛选获得了与P 糖蛋白特异性结合的噬菌体阳性克隆 ,测序获得了其特异性结合肽序列 :NDGLLFTWQPSP .免疫细胞化学结果显示 :筛选得到的噬菌体阳性克隆可与耐药细胞BIU 87 ADM结合 ,而与敏感细胞BIU 87不结合 .结果表明 ,筛选获得的结合肽可与耐药的肿瘤细胞结合 ,表现出一定的肿瘤特异性 .P 糖蛋白结合肽的筛选 ,为进行人膀胱癌多药耐药的靶向治疗等工作奠定了基础 .     

脑膜炎大肠杆菌IbeA蛋白结合肽序列的亲和筛选*

应用噬菌体展示肽库技术,以重组的脑膜炎大肠杆菌致病蛋白IbeA作为靶分子,经过吸附-洗脱-扩增-再吸附的亲和筛选,随机挑选亲和力强的噬菌体克隆,进行ELISA、竞争抑制实验和序列测定。结果显示,经3轮淘选后,间接ELISA鉴定得到高亲和性结合IbeA蛋白的15个阳性克隆。竞争抑制实验结果表明,游离IbeA蛋白能竞争抑制噬菌体结合肽克隆与固相包被的IbeA蛋白的结合,其抑制作用随游离IbeA蛋白浓度的降低而减弱。测序结果得到5种阳性噬菌体克隆展示肽序列。上述结果提示以脑膜炎大肠杆菌IbeA蛋白为靶筛选所获得     

噬菌体展示文库及其应用

近十几年来,噬菌体展示技术得到了迅速的发展。通过展示随机肽库可用来筛选与特殊靶分子相结合的配基;模拟非蛋白的配基;也可用作确定抗体表位的工具。展示蛋白;或其功能结构的文库为我们提供了分析结构与功能关系的体系,并能产生具有改变结合位点或新的催化活性的蛋白。展示短的抗原决定簇的融合噬菌体为开发新的疫苗提供了基础,而表达抗体片段的文库则提供了一种产生单克隆抗体的方法。     

噬菌体肽库技术的应用

噬菌体肽库是由大量带有不同肽段的单个噬菌体组成的重组噬菌体库,通过分析筛选到的多肽的结构和序列,可以了解蛋白质分子之间的相互作用。随着生物技术的发展,噬菌体肽库技术在基因治疗、抗原表位定位、确定核酸结合蛋白、基因疫苗研究和药物筛选等方面得到广泛应用并取得了很大进展。     

从七肽噬菌体展示库中筛选内毒素结合蛋白质配基

目的:研究从噬茵体展示库中筛选内毒素结合蛋白质配基,为其在内毒素致病作用机理及在内毒素血症防治研究中的应用奠定基础.方法:以内毒素为靶分子从随机七肽噬菌体展示库中筛选内毒素的高亲和力噬菌体配体,通过ELISA鉴定,DNA测序及相关软件分析.结果:所筛选的亲和力最高的噬菌体的ELISA检测值A405nm可达1.965通过比较亲和性噬菌体外源插入肽的DNA序列,认为FHENWPS肽段中包含有与内毒素分子发生亲和结合的一个共有序列.该序列展示肽的等电点为5.36,具有双嗜性,这有利于肽与LPS分子表面的位点相互作用从而产生亲和吸附.结论:运用亲和筛选方法从肽库中筛选内毒素结合蛋白质配基是可行的.     

适体家族新成员－肽适体

肽适体是一种从随机氨基酸的肽文库中筛选出来,可以高亲合力地与靶物质特异性结 合的短肽序列．它的主要结构包括恒定的展示支架蛋白及通过两端限制性插入的高变肽环． 酵母双杂交技术常用于筛选针对细胞内特异性靶蛋白的肽适体过程,筛选出的肽适体通过特 异性结合识别靶标发挥类似“干扰基因”的作用从而影响蛋白的生物学活性．     

Novel high-affinity binders of human interferon gamma derived from albumin-binding domain of protein G

Recombinant ligands derived from small protein scaffolds show promise as robust research and diagnostic reagents and next generation protein therapeutics. Here, we derived high-affinity binders of human interferon gamma (hIFNγ) from the three helix bundle scaffold of the albumin-binding domain (ABD) of protein G from Streptococcus G148. Computational interaction energy mapping, solvent accessibility assessment, and in silico alanine scanning identified 11 residues from the albumin-binding surface of ABD as suitable for randomization. A corresponding combinatorial ABD scaffold library was synthesized and screened for hIFNγ binders using in vitro ribosome display selection, to yield recombinant ligands that exhibited K(d) values for hIFNγ from 0.2 to 10 nM. Molecular modeling, computational docking onto hIFNγ, and in vitro competition for hIFNγ binding revealed that four of the best ABD-derived ligands shared a common binding surface on hIFNγ, which differed from the site of human IFNγ receptor 1 binding. Thus, these hIFNγ ligands provide a proof of concept for design of novel recombinant binding proteins derived from the ABD scaffold.     

A conformation-constrained peptide library based on insect defensin A

Here, we reported a conformation-constrained peptide library, that was constructed based on the scaffold of a 29 amino acids peptide derived from insect defensin A. The peptide scaffold was designed utilizing the InsightII molecular modeling software and then displayed on M13 filamentous bacteriophage by fusion with coat protein III. The library was constructed by randomization of seven positions located within the two loops of the peptide scaffold generating approximately 8.3 x 10(8) transformants. Sequences from 14 randomly selected phage clones indicated that the distribution of nucleotides and amino acids paralleled with the expected frequency. Screening against the target proteins: tumor necrosis factor alpha, TNF receptor 1, TNF receptor 2 and monoclonal antibody against BMP-2 showed significant enrichment in all cases. The results presented here show that the reconstructed insect defensin A domain will be a promising non-antibody protein scaffold for the presentation of a phage-displayed constrained peptide library.     

Repetitive Arg-Gly-Asp peptide as a cell-stimulating agent on electrospun poly(ϵ-caprolactone) scaffold for tissue engineering

Electrospun scaffolds derived from poly(ϵ-caprolactone) (PCL), a well known biodegradable material, have an architecture that is suitable for hosting cells. However, their biomedical applications are restricted because these scaffolds lack the bioactivity necessary to stimulate cell responses. In this work, a repetitive Arg-Gly-Asp (rRGD) peptide was produced as a cell-stimulating agent to provide the PCL scaffold with bioactivity. DNA encoding rRGD was amplified by polymerase chain reaction using overlap primers without a DNA template, and cloned into a protein expression vector to produce a His-tag fusion peptide. In an in vitro cell adhesion assay, the purified rRGD peptide, comprising 30 RGD repeats, promoted a 1.5-fold greater cell adhesion than the commercial tripeptide RGD. The rRGD peptide was immobilized onto an electrospun PCL scaffold that had been pretreated with argon plasma and graft-polymerized with acrylic acid. Fourier transform infrared (FTIR) analysis indicated that covalently linked rRGD peptide was present on the scaffold. The PCL scaffold with immobilized rRGD showed significantly changed hydrophilic properties and an enhanced adhesion and proliferation of mouse fibroblast cells by 2.3- and 2.9-fold, respectively, compared to the PCL scaffold alone. Through its ability to promote cell adhesion and proliferation, the rRGD peptide has great potential as a stimulant for improving the suboptimal cell-matrix interaction of polymeric scaffolds for tissue engineering applications.     

Using Protein Dimers to Maximize the Protein Hybridization Efficiency with Multisite DNA Origami Scaffolds

DNA origami provides a versatile platform for conducting ‘architecture-function’ analysis to determine how the nanoscale organization of multiple copies of a protein component within a multi-protein machine affects its overall function. Such analysis requires that the copy number of protein molecules bound to the origami scaffold exactly matches the desired number, and that it is uniform over an entire scaffold population. This requirement is challenging to satisfy for origami scaffolds with many protein hybridization sites, because it requires the successful completion of multiple, independent hybridization reactions. Here, we show that a cleavable dimerization domain on the hybridizing protein can be used to multiplex hybridization reactions on an origami scaffold. This strategy yields nearly 100% hybridization efficiency on a 6-site scaffold even when using low protein concentration and short incubation time. It can also be developed further to enable reliable patterning of a large number of molecules on DNA origami for architecture-function analysis.     

A novel unstructured scaffold based on 4EBP1 enables the functional display of a wide range of bioactive peptides

Target validation using protein aptamers enables the characterization of a specific function of a target protein in an environment that resembles native conditions as closely as possible. A major obstacle to the use of this technology has been the generation of bioactive aptamers, which is dependent on the choice of scaffold. Constraining binding peptides within a particular scaffold does not necessarily result in binding aptamers, as suboptimal presentation of peptides can occur. It is therefore understandable that different peptides might require different scaffolds for optimal presentation. In this article, we describe a novel scaffold protein that bypasses the conventional requirement for scaffolds to have known rigid structures and yet successfully presents several peptides that need to adopt a wide range of conformations for binding to their target protein. Using an unstructured protein, 4EBP1, as scaffold, we successfully construct binding aptamers to three different target proteins: Mdm2, proliferating cell nuclear antigen, and cyclin A. The Mdm2-binding aptamer constructed using 4EBP1 as scaffold demonstrates better stability and bioactivity compared to that constructed using thioredoxin as scaffold. This new scaffold protein, which makes it relatively easy to create bioactive aptamers based on known interaction sequences, will greatly facilitate the aptamer approach to target validation.     

Cystine‐knot peptides targeting cancer‐relevant human cytotoxic T lymphocyte‐associated antigen 4 (CTLA‐4)

Cystine‐knot peptides sharing a common fold but displaying a notably large diversity within the primary structure of flanking loops have shown great potential as scaffolds for the development of therapeutic and diagnostic agents. In this study, we demonstrated that the cystine‐knot peptide MCoTI‐II, a trypsin inhibitor from Momordica cochinchinensis, can be engineered to bind to cytotoxic T lymphocyte‐associated antigen 4 (CTLA‐4), an inhibitory receptor expressed by T lymphocytes, that has emerged as a target for the treatment of metastatic melanoma. Directed evolution was used to convert a cystine‐knot trypsin inhibitor into a CTLA‐4 binder by screening a library of variants using yeast surface display. A set of cystine‐knot peptides possessing dissociation constants in the micromolar range was obtained; the most potent variant was synthesized chemically. Successive conjugation with neutravidin, fusion to antibody Fc domain or the oligomerization domain of C4b binding protein resulted in oligovalent variants that possessed enhanced (up to 400‐fold) dissociation constants in the nanomolar range. Our data indicate that display of multiple knottin peptides on an oligomeric scaffold protein is a valid strategy to improve their functional affinity with ramifications for applications in diagnostics and therapy. Copyright © 2015 European Peptide Society and John Wiley & Sons, Ltd.     

Generation of bivalent and bispecific kringle single domains by loop grafting as potent agonists against death receptors 4 and 5

Bivalent or bispecific binding activity of proteins has been mainly achieved by assembling two or more domains in a single molecule. Here we report bivalent/bispecific single-domain proteins based on the kringle domain (KD), which has a cystine knot structural motif and is highly tolerant of sequence modifications. KD has seven loops protruding from the core fold into two largely opposite directions, dubbed loop cluster regions (LCRs) 1 and 2. Mutational analysis of previously isolated agonistic KD variants against human death receptors (DRs) 4 and 5 revealed that they can simultaneously recognize two target molecules of DR4 and/or DR5 via the two independent binding sites of LCR1 and LCR2. Binding loop mapping of yeast-surface-displayed KD mutants identified high-affinity target binding loops in LCR2, which were then grafted into conformationally compatible loops located on the opposite side of LCR1 within the same or different KD variants to generate bivalent/bispecific KD variants against DR4 and/or DR5 with improved affinity. The loop-grafted bivalent/bispecific KD variants showed enhanced cell-death-inducing activity of tumor cells compared with their monovalent/monospecific and bivalent/monospecific counterparts, demonstrating an advantage of bispecific targeting to both DR4 and DR5 over the targeting of only one of the two pro-apoptotic receptors. Our results suggest that the KD with the two independent binding surfaces for target recognition is an appropriate scaffold for the development of bivalency and/or bispecificity by loop grafting on the single domain, which offers a distinct advantage over other protein scaffolds with a single binding surface.     

Highly efficient selection of epitope specific antibody through competitive yeast display library sorting

Combinatory antibody library display technologies have been invented and successfully implemented for the selection and engineering of therapeutic antibodies. Precise targeting of important epitopes on the protein of interest is essential for such isolated antibodies to serve as effective modulators of molecular interactions. We developed a strategy to efficiently isolate antibodies against a specific epitope on a target protein from a yeast display antibody library using dengue virus envelope protein domain III as a model target. A domain III mutant protein with a key mutation inside a cross-reactive neutralizing epitope was designed, expressed, and used in the competitive panning of a yeast display naïve antibody library. All the yeast display antibodies that bound to the wild type domain III but not to the mutant were selectively sorted and characterized. Two unique clones were identified and showed cross-reactive binding to envelope protein domain IIIs from different serotypes. Epitope mapping of one of the antibodies confirmed that its epitope overlapped with the intended neutralizing epitope. This novel approach has implications for many areas of research where the isolation of epitope-specific antibodies is desired, such as selecting antibodies against conserved epitope(s) of viral envelope proteins from a library containing high titer, high affinity non-neutralizing antibodies, and targeting unique epitopes on cancer-related proteins.     

Computational protein design using flexible backbone remodeling and resurfacing: case studies in structure-based antigen design

Computational protein design has promise for vaccine design and other applications. We previously transplanted the HIV 4E10 epitope onto non-HIV protein scaffolds for structural stabilization and immune presentation. Here, we developed two methods to optimize the structure of an antigen, flexible backbone remodeling and resurfacing, and we applied these methods to a 4E10 scaffold. In flexible-backbone remodeling, an existing backbone segment is replaced by a de novo designed segment of prespecified length and secondary structure. With remodeling, we replaced a potentially immunodominant domain on the scaffold with a helix-loop segment that made intimate contact to the protein core. All three domain trim designs tested experimentally had improved thermal stability and similar binding affinity for the 4E10 antibody compared to the parent scaffold. A crystal structure of one design had a 0.8 Å backbone RMSD to the computational model in the rebuilt region. Comparison of parent and trimmed scaffold reactivity to anti-parent sera confirmed the deletion of an immunodominant domain. In resurfacing, the surface of an antigen outside a target epitope is redesigned to obtain variants that maintain only the target epitope. Resurfaced variants of two scaffolds were designed in which 50 positions amounting to 40% of the protein sequences were mutated. Surface-patch analyses indicated that most potential antibody footprints outside the 4E10 epitope were altered. The resurfaced variants maintained thermal stability and binding affinity. These results indicate that flexible-backbone remodeling and resurfacing are useful tools for antigen optimization and protein engineering generally.