ConA激活小鼠胸腺T淋巴细胞增殖过程中c-myc与核骨架蛋白的结合

采用DNA-蛋白质体外吸附的方法研究伴刀豆球蛋白激活小鼠胸腺T淋巴细胞增殖过程中c-myc与核骨架蛋白的结合.实验结果显示,c-myc与核骨架蛋白的结合具有特异性,在淋巴细胞激活过程中c-myc与P₃₄/P₃₆核骨架蛋白及核纤层蛋白结合,并发生动态变化.     

一种蛋白质B细胞表位展示系统的构建及验证

目的:建立一种能够有效展示蛋白质B细胞表位的载体系统,以用于表位特异性抗体的制备和表位疫苗的设计。方法:选用抗体的可变区作为蛋白质B细胞表位展示的骨架蛋白,B细胞表位的展示部位为CDR3区。全基因合成骨架蛋白基因,通过重叠PCR将B细胞表位编码序列插入到骨架蛋白基因中,原核表达目的蛋白,利用Sephacryl S-100层析柱进行蛋白纯化,用纯化的蛋白按常规方法免疫小鼠,采用ELISA法检测免疫血清的滴度及特异性,通过Western blot和间接免疫荧光技术进一步验证免疫血清对目的蛋白的识别。结果:成功构建了3种表位展示蛋白,均表现出了很好的抗原性,表位展示蛋白免疫血清具有较好的特异性,能够特异识别所展示的B细胞表位。结论:抗体可变区作为骨架蛋白能够很好地展示B细胞表位,免疫小鼠后获得的免疫血清表现出了较好的特异性。     

蛋白骨架在随机肽库构建及靶分子筛选中的应用*

自然界有着丰富的蛋白骨架来源。选择适宜的蛋白骨架和展示、筛选方法,可构建基于合理蛋白骨架结构的优化限制性随机肽库。与非限制性随机肽库相比,可望获得针对靶分子具有新功能的蛋白结构或更高亲和力的配体分子。目前,骨架蛋白限制的随机肽库已在高效靶分子筛选、基础研究、临床诊断和医学治疗等方面显示出巨大的潜在应用价值。以S-S限制性骨架、抗体分子、锌指蛋白、Z结构域、FN3结构域等为主要代表,综合介绍了蛋白骨架的结构基础、分类、基于蛋白骨架的限制性随机肽库构建及近年来在靶分子筛选等方面的应用最新进展。     

丙型肝炎病毒复合高变区1模拟表位蛋白的免疫原性分析

将丙型肝炎病毒高变区1(HVR1)模拟表位融合基因插入原核表达载体pGEX-4T-1,在大肠杆菌BL21(DE3)中进行表达,经亲和层析和凝胶过滤层析获得HCVHVR1模拟表位融合蛋白。用Westernblot和ELISA检测融合蛋白与HCV抗体阳性血清的结合情况。皮下注射免疫BALB/c小鼠,用ELISA检测小鼠血清中的抗HCV抗体水平及其与天然HCV高变区1合成肽的交叉反应。结果表明融合蛋白能与HCV抗体阳性血清特异结合,融合蛋白与HCV抗体阳性血清的结合频率为71.6%(25/35)。融合蛋白免疫小鼠后能有效诱导免疫应答,其诱生的特异性抗体最高滴度达104(免疫后第8周),且该抗体能同2条天然HCVHVR1合成肽发生交叉反应。本研究提示,HCV复合HVR1模拟表位融合蛋白在丙型肝炎疫苗的研发中可能具有潜在应用价值。     

利用抗原结合多肽嫁接抗体技术制备抗hCG单域抗体

本研究旨在人绒毛膜促性腺激素(hCG)的结合多肽的基础上应用嫁接抗体技术制备抗hCG单域抗体,简化单域抗体制备过程,提高多肽生化稳定性。利用单域抗体通用骨架(cAbBCII10),以hCG结合多肽取代互补决定区CDR1或CDR3,合成cAb BCII10嫁接抗体全基因序列并与sfGFP基因序列融合后,插入到带有His标签的原核表达载体pET30a(+)中,成功构建了pET30a-(His6)-cAbBCII10-CDR1/hCGBP1-sfGFP与pET30a-(His6)-cAbBCII10-CDR3/hCGBP3-sfGFP融合蛋白表达质粒。将重组质粒转化大肠杆菌BL21(DE3),用IPTG诱导表达融合蛋白,得到高表达量的可溶性融合蛋白。利用Ni-NTA亲和柱纯化得到纯蛋白,应用SDS-PAGE鉴定纯化的蛋白为正确表达的目标蛋白。通过抗原抗体结合实验,发现hCG结合多肽嫁接到单域抗体通用骨架的互补决定区CDR1或CDR3后都有抗原结合活性,具有相似的抗体滴度,且嫁接到CDR3后的抗原结合活性比CDR1要高(2–3倍)。嫁接抗体基本保留了所用单域抗体框架较为稳定的生化特性,具有一定的热稳定性和较好的碱耐受性,同时,所接入的hCG结合片段对hCG具有较特异的结合活性,为进一步优化抗原结合多肽嫁接抗体技术制备抗hCG单域抗体提供了可靠的实验基础     

早期脓毒血症患者Gelsolin 与HS-1 蛋白检测及其意义

要目的：探讨脓毒血症患者血小板骨架蛋白Gelsolin和造血系细胞特异性蛋白(HS-1)及其和凝血功能的关系。方法：纳入脓毒 血症患者30 例和对照组健康人群30 例,用双抗体夹心法测定血浆中血小板骨架蛋白,用酶联免疫法测定血清中HS-1 蛋白含 量,采用免疫荧光观察血小板Gelsolin 蛋白的表达,分析Gelsolin、HS-1、血小板计数和凝血功能(PT、APTT)之间的关系。结果：对 照组Gelsolin 主要位于血小板胞浆内,观察组包浆内外及间质内均可见。观察组血小板骨架蛋白Gelsolin、HS-1 水平明显高于对 照组,差异均存在统计学意义(P<0.05)。观察组血小板计数、PT、APTT 水平均低于对照组,差异存在统计学意义(P <0.05)。Galsolin 和血小板计数呈负相关关系,相关系数r = -0.76 (P <0.05),HS-1和血小板计数间呈负相关关系相关系数r = - 0.69 (P<0.05)。结论： 早期脓毒血症患者血小板骨架蛋白Gelsolin 和HS-1表达水平明显升高,与脓毒血症患者血小板大量破坏有关。     

应用RAD多肽展示体系制备抗hCG类抗体分子

应用基于激烈火球菌Pyrococcus furiosus重组酶RadA的ATP酶结构域(RAD骨架)的多肽展示体系,通过嫁接人绒毛膜促性腺激素(hCG)结合多肽,制备抗hCG类抗体分子。通过合成hCG结合多肽插入RAD多肽展示位点的类抗体基因,成功构建了pET30a-RAD/hCGBP-sfGFP原核表达载体,在大肠杆菌中诱导蛋白表达,分离、纯化获得类抗体蛋白,通过亲和吸附-GFP荧光检测方法测定类抗体对hCG的结合活性,并与应用单域抗体通用骨架制备的嫁接抗体比较活性差异。结果显示,RAD类抗体分子对hCG分子具有较高的亲和性和特异性,显著优于单域嫁接抗体,并与商业单克隆抗体的活性相当;同时,利用RAD多肽展示骨架制备的抗hCG类抗体,具有较高的生化稳定性,是一种具有应用潜力的抗体替代分子。     

丙型肝炎病毒复合高变区1模拟表位蛋白的免疫原性分析

将丙型肝炎病毒高变区1(HVR1)模拟表位融合基因插入原核表达载体pGEX-4T-1,在大肠杆菌BL21(DE3)中进行表达,经亲和层析和凝胶过滤层析获得HCV HVR1模拟表位融合蛋白.用Western blot和ELISA检测融合蛋白与HCV抗体阳性血清的结合情况.皮下注射免疫BALB/c小鼠,用ELISA检测小鼠血清中的抗HCV抗体水平及其与天然HCV高变区1合成肽的交叉反应.结果表明融合蛋白能与HCV抗体阳性血清特异结合,融合蛋白与HCV抗体阳性血清的结合频率为71.6%(25/35).融合蛋白免疫小鼠后能有效诱导免疫应答,其诱生的特异性抗体最高滴度达104(免疫后第8周),且该抗体能同2条天然HCV HVR1合成肽发生交叉反应.本研究提示,HCV复合HVR1模拟表位融合蛋白在丙型肝炎疫苗的研发中可能具有潜在应用价值.     

从大容量噬菌体抗体库中筛选抗DNA-PKcs单链抗体

目的：从单链大容量噬菌体抗体库中筛选特异性的抗DNA-PKcs的人源抗体,用于肿瘤治疗或诊断目的。方法：经抗原性分析及BLAST比对,选定人DNA-PKcs蛋白中抗原性高且与其他蛋白没有同源性的片段,进行原核表达及纯化后将其固定在抗原管上,通过4轮“吸附－洗脱－扩增”过程从大容量抗体库中筛选特异性抗体,转化HB2151菌,制备抗DNA-PKcs的可溶性单链抗体;ELISA检测抗原-抗体结合活性。结果：经生物信息学分析,确定抗原性高且与其他蛋白没有同源性的DNA-PKcs片段DPK3（250个AA）、DPK4（257个AA）。经过4轮筛选,获得26个特异性结合DPK3及31个特异结合DPK4的克隆,指纹分析分别有5种和21种不同的可变区片段;成功制备了可溶性抗体。并做了抗原结合活性鉴定。结论：利用单链大容量抗体库获得抗DNA-PKcs的噬菌体抗体基因并且成功制备成可溶性抗体,为今后的研究和应用奠定了基础。     

植物油体在生物技术中的应用研究进展

油体是植物种子尤其是油料植物种子的重要贮脂细胞器,具有较强的物化稳定性,而且易于通过离心法分离提取。研究表明,油体是由外层的磷脂和油体结合蛋白以及包裹在内部的液态基质（主要为三酰甘油）形成的弹性球体或椭球体。目前,在植物中共发现三类油体结合蛋白,它们主要存在于油体表面。鉴于油体和油体结合蛋白的结构特殊性,二者在生物技术领域得到了广泛应用。本文重点综述了油体在表达纯化外源蛋白方面的优势、策略以及在生产药用蛋白、制备固定化酶、捕捉抗体和药用酶、生产营养素和提高植物抗性等多个领域的研究进展,并介绍了人工油体和油体乳化剂方面的开发应用情况。     

DARPins and other repeat protein scaffolds: advances in engineering and applications

Antibodies have long been regarded as the only class of binding proteins. With the emergence of protein engineering techniques, new binding proteins based on alternative scaffolds have been designed. Additionally, modern technologies for selection and evolution from libraries are independent of the antibody scaffold and could thus be readily used for obtaining specific binding proteins. One important group of alternative scaffolds is based on repeat proteins. Nature is widely using these proteins to modulate protein-protein interactions, and even in the adaptive immune system of jawless vertebrates; the step to their application as an alternative to antibodies seems therefore logical. In this review, progress on DARPins and other repeat protein scaffolds will be discussed. Advances in their design as well as novel applications will be highlighted.     

Computational design of protein antigens that interact with the CDR H3 loop of HIV broadly neutralizing antibody 2F5

Rational design of proteins with novel binding specificities and increased affinity is one of the major goals of computational protein design. Epitope‐scaffolds are a new class of antigens engineered by transplanting viral epitopes of predefined structure to protein scaffolds, or by building protein scaffolds around such epitopes. Epitope‐scaffolds are of interest as vaccine components to attempt to elicit neutralizing antibodies targeting the specified epitope. In this study we developed a new computational protocol, MultiGraft Interface, that transplants epitopes but also designs additional scaffold features outside the epitope to enhance antibody‐binding specificity and potentially influence the specificity of elicited antibodies. We employed MultiGraft Interface to engineer novel epitope‐scaffolds that display the known epitope of human immunodeficiency virus 1 (HIV‐1) neutralizing antibody 2F5 and that also interact with the functionally important CDR H3 antibody loop. MultiGraft Interface generated an epitope‐scaffold that bound 2F5 with subnanomolar affinity (K_D = 400 pM) and that interacted with the antibody CDR H3 loop through computationally designed contacts. Substantial structural modifications were necessary to engineer this antigen, with the 2F5 epitope replacing a helix in the native scaffold and with 15% of the native scaffold sequence being modified in the design stage. This epitope‐scaffold represents a successful example of rational protein backbone engineering and protein–protein interface design and could prove useful in the field of HIV vaccine design. MultiGraft Interface can be generally applied to engineer novel binding partners with altered specificity and optimized affinity. Proteins 2014; 82:2770–2782. © 2014 Wiley Periodicals, Inc.     

Redesign of a protein–peptide interaction: Characterization and applications

The design of protein–peptide interactions has a wide array of practical applications and also reveals insight into the basis for molecular recognition. Here, we present the redesign of a tetratricopeptide repeat (TPR) protein scaffold, along with its corresponding peptide ligand. We show that the binding properties of these protein–peptide pairs can be understood, quantitatively, using straightforward chemical considerations. The recognition pairs we have developed are also practically useful for the specific identification of tagged proteins. We demonstrate the facile replacement of these proteins, which we have termed T‐Mods (TPR‐based recognition module), for antibodies in both detection and purification applications. The new protein–peptide pair has a dissociation constant that is weaker than typical antibody–antigen interactions, yet the recognition pair is highly specific and we have shown that this affinity is sufficient for both Western blotting and affinity purification. Moreover, we demonstrate that this more moderate affinity is actually advantageous for purification applications, because extremely harsh conditions are not required to dissociate the T‐Mod‐peptide interaction. The results we present are important, not only because they represent a successful application of protein design but also because they help define the properties that should be sought in other scaffolds that are being developed as antibody replacements.     

Alternative scaffold proteins

Review is devoted to the challenging direction in modem molecular biology and bioengineering - the properties of alternative scaffold proteins (ASP) and methods for obtaining ASP binding molecules. ASP molecules incorporate conservative protein core and hypervariable regions, providing for the binding function. Structural classification of ASP includes several types which differ also in their molecular targets and potential applications. Construction of artificial binding proteins on the ASP basis implies a combinatorial library design with subsequent selection of specific binders with the use of phage display or the modem cell-free systems. Alternative binding proteins on non-immunoglobulin scaffolds find broad applications in different fields ofbiotechnology and molecular medicine.     

Extremophilic 50S Ribosomal RNA-Binding Protein L35Ae as a Basis for Engineering of an Alternative Protein Scaffold

Due to their remarkably high structural stability, proteins from extremophiles are particularly useful in numerous biological applications. Their utility as alternative protein scaffolds could be especially valuable in small antibody mimetic engineering. These artificial binding proteins occupy a specific niche between antibodies and low molecular weight substances, paving the way for development of innovative approaches in therapeutics, diagnostics, and reagent use. Here, the 50S ribosomal RNA-binding protein L35Ae from the extremophilic archaea Pyrococcus horikoshii has been probed for its potential to serve as a backbone in alternative scaffold engineering. The recombinant wild type L35Ae has a native-like secondary structure, extreme thermal stability (mid-transition temperature of 90°C) and a moderate resistance to the denaturation by guanidine hydrochloride (half-transition at 2.6 M). Chemical crosslinking and dynamic light scattering data revealed that the wild type L35Ae protein has a propensity for multimerization and aggregation correlating with its non-specific binding to a model cell surface of HEK293 cells, as evidenced by flow cytometry. To suppress these negative features, a 10-amino acid mutant (called L35Ae 10X) was designed, which lacks the interaction with HEK293 cells, is less susceptible to aggregation, and maintains native-like secondary structure and thermal stability. However, L35Ae 10X also shows lowered resistance to guanidine hydrochloride (half-transition at 2.0M) and is more prone to oligomerization. This investigation of an extremophile protein’s scaffolding potential demonstrates that lowered resistance to charged chemical denaturants and increased propensity to multimerization may limit the utility of extremophile proteins as alternative scaffolds.     

Engineered proteins as specific binding reagents

Over the past 30 years, monoclonal antibodies have become the standard binding proteins and currently find applications in research, diagnostics and therapy. Yet, monoclonal antibodies now face strong competition from synthetic antibody libraries in combination with powerful library selection technologies. More recently, an increased understanding of other natural binding proteins together with advances in protein engineering, selection and evolution technologies has also triggered the exploration of numerous other protein architectures for the generation of designed binding molecules. Valuable protein-binding scaffolds have been obtained and represent promising alternatives to antibodies for biotechnological and, potentially, clinical applications.     

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.     

AutoMatch: target-binding protein design and enzyme design by automatic pinpointing potential active sites in available protein scaffolds

Proteins perform their functions mainly via active sites, whereas other parts of the proteins comprise the scaffolds, which support the active sites. One strategy for protein functional design is transplanting active sites, such as catalytic sites for enzyme or binding hot spots for protein-protein interactions, onto a new scaffold. AutoMatch is a new program designed for efficiently elucidating suitable scaffolds and potential sites on the scaffolds. Backrub motions are used to treat backbone flexibility during the design process. A step-by-step checking strategy and cluster-representation examination strategy were developed to solve the large combinatorial problem for the matching of active-site conformations. In addition, a grid-based binding energy scoring method was used to filter the solutions. An enzyme design benchmark and a protein-protein interaction design benchmark were built to test the algorithm. AutoMatch could identify the hot spots in the nonbinding protein and rank them within the top five results for 8 of 10 target-binding protein design cases. In addition, among the 15 enzymes tested, AutoMatch can identify the catalytic active sites in the apoprotein and rank them within the top five results for 13 cases. AutoMatch was also tested for screening scaffold library in designing binding proteins targeting influenza hemagglutinin, HIV gp120, and epidermal growth factor receptor kinase, respectively. AutoMatch, and the two test sets, ActApo and ActFree, are available for noncommercial applications at http://mdl.ipc.pku.edu.cn/cgi-bin/down.cgi.     

Parameters and determinants of responses to selection in antibody libraries

The sequences of antibodies from a given repertoire are highly diverse at few sites located on the surface of a genome-encoded larger scaffold. The scaffold is often considered to play a lesser role than highly diverse, non-genome-encoded sites in controlling binding affinity and specificity. To gauge the impact of the scaffold, we carried out quantitative phage display experiments where we compare the response to selection for binding to four different targets of three different antibody libraries based on distinct scaffolds but harboring the same diversity at randomized sites. We first show that the response to selection of an antibody library may be captured by two measurable parameters. Second, we provide evidence that one of these parameters is determined by the degree of affinity maturation of the scaffold, affinity maturation being the process by which antibodies accumulate somatic mutations to evolve towards higher affinities during the natural immune response. In all cases, we find that libraries of antibodies built around maturated scaffolds have a lower response to selection to other arbitrary targets than libraries built around germline-based scaffolds. We thus propose that germline-encoded scaffolds have a higher selective potential than maturated ones as a consequence of a selection for this potential over the long-term evolution of germline antibody genes. Our results are a first step towards quantifying the evolutionary potential of biomolecules.     

Comparison of antibody functionality using different immobilization methods

This study investigates the influence of antibody immobilization methods on antigen capture. Adsorption and two surface chemistries, an aminosilane chemistry and a common heterobifunctional crosslinker (N-gamma-maleimidobutyryloxy-succinimide ester, GMBS), were compared and evaluated for their ability to immobilize antibodies and capture antigen. The role of protein A as an orienting protein scaffold component in each of these techniques was also evaluated. Through experimentation it was determined that the GMBS technique immobilized the highest amount of antibody and minimized nonspecific binding. For all techniques, the most functional antibodies were found to be those immobilized with protein A. Interestingly, the aminosilane technique demonstrated the highest antigen capture with antibody alone but also exhibited the highest level of nonspecific binding.