细菌运载蛋白及在表面展示技术中的应用进展

细菌细胞表面展示技术是一项新的蛋白质应用技术,其体系由运载蛋白、靶蛋白和宿主菌三者构成,一般可将其分为革兰阴性菌展示体系和革兰阳性菌展示体系两大类。目前已证实多种具有锚定活性的运载蛋白,并用于不同靶蛋白的细胞表面展示体系。该技术现已被应用于活体重组疫苗的开发、蛋白质文库构建与筛选、生物传感器、全细胞生物催化剂、全细胞生物吸附与降解等多个研发领域。     

冰晶核蛋白及其在细菌表面展示技术中的应用

冰晶核蛋白(ice nucleation protein,INP)是一种分泌型外膜蛋白,广泛分布于丁香假单胞菌,荧光假单胞菌和其他革兰氏阴性菌中。由于其在相对高温下(-2~-4℃)形成冰核的特性,INP最早应用于生物制冷领域。在细菌表面展示技术中,冰晶核蛋白作为运载蛋白得到广泛的应用。与其他的表面技术载体蛋白相比较,冰晶核蛋白具有稳定表达外源蛋白及展示分子量较大的外源蛋白的优点。INP细胞表面展示技术已被应用于全细胞生物催化剂、全细胞吸附剂和环境污染物降解剂等的开发,本文将简述INP表面展示技术的研究进展。     

酿酒酵母表面展示表达系统及应用

酵母细胞表面展示表达系统是一种固定化表达异源蛋白质的真核展示系统,即把异源靶蛋白基因序列与特定的载体基因序列融合后导入酵母细胞,利用酿酒酵母细胞内蛋白转运到膜表面的机制（GPI锚定）使靶蛋白定位于酵母细胞表面并进行表达。它利用细胞表面展示技术使外源蛋白固定化于细胞表面,从而生产微生物细胞表面蛋白,可应用于生物催化剂、细胞吸附剂、活疫苗、环境治理、蛋白质文库筛选、高亲和抗体、生物传感器、抗原／抗体库构建、免疫检测及亲和纯化、癌症诊断等领域。国内对这一方面研究较少,本文主要介绍了该技术的基本原理、研究现状、应用及其发展前景。     

pH敏感型荧光蛋白及其在植物细胞生物学中的应用

pH敏感型荧光蛋白, 即pHluorin, 是荧光强度及光谱特征随环境pH值的变化而改变的一类荧光蛋白。人们通过对密码子使用偏好和特定剪切位点的修饰, 已使pHluorin及其衍生物成功地在动物、植物和真菌细胞中正常表达, 为测量细胞内微环境pH值的变化, 并研究活细胞内依赖或导致pH变化的生理过程提供了有力工具。该文总结了目前已报道的pH敏感型荧光蛋白的种类及特性, 并对其在细胞生物学, 特别是植物细胞生物学中的应用进行了详细介绍。随着报告基因技术及检测方法的不断改进, pHluorin将在植物科学领域发挥更大的作用。     

拟核结合蛋白与细菌基因的表达调控

拟核结合蛋白是细菌遗传物质组织和基因表达调控的关键. 细菌基因组压缩为致密的拟核必需有拟核结合蛋白的支撑. 拟核结合蛋白、DNA超螺旋和大分子簇在拟核的结构形成中起到重要作用,其中拟核结合蛋白最重要.拟核结合蛋白还影响细菌DNA的复制、重组、转录和修复等多个重要生理过程.作为全局调控因子,拟核结合蛋白是调控细菌适应环境变化所需基因表达的关键. 本文总结拟核结合蛋白的结构、功能和调控,特别是其在致病与非致病分枝杆菌中的差别,为寻找新药物靶标提供线索.     

细菌表面展示技术研究新进展

细菌表面展示是将靶标蛋白质表达于细菌表面以更好地实现其功能的一种技术,它在重组细菌疫苗、生物燃料电池、全细胞催化剂和生物修复等多个领域均有广泛的应用.随着相关技术的发展,表面展示系统的各种性能被不断地改良,同时新的表面展示系统也陆续被开发和应用,使该技术得到持续的丰富和发展.本文重点关注近年研究得较多的细菌表面展示系统,主要对各类细菌表面展示系统的开发、改造和修饰,以及该技术在生物修复和生物传感器方面的应用作一综述.     

融合标签技术及其应用

融合标签最初是作为一种有效的工具用于纯化重组蛋白质,近几年的研究表明,融合标签的作用并不局限于此。本文综述了融合标签技术的发展及在生命科学研究中的各种应用,包括重组蛋白质的纯化;目的蛋白质的检测、定向固定;体内生物事件的可视化;提高重组蛋白质的产量;增强重组蛋白质的可溶性及稳定性。     

噬菌体展示技术及其在肿瘤研究中的应用

噬菌体表面展示技术是一项特异性多肽或蛋白的筛选技术,它将随机序列的多肽或蛋白片段与噬菌体衣壳蛋白融合表达而呈现于病毒表面,被展示的多肽能保持相对独立的空间结构,使其能够与配体作用而达到模仿性筛选特异性分子表位,从而提供了高通量高效率的筛选系统。近年来噬菌体展示技术已广泛应用于肿瘤抗原抗体库的建立、单克隆抗体制备、多肽筛选、疫苗研制、肿瘤相关抗原筛选和抗原表位研究、药物设计、癌症检测和诊断、基因治疗及细胞信号转导研究等。就近年来噬菌体展示技术在肿瘤相关研究中的运用作以综述。     

条形码微流控芯片在分泌蛋白检测方面的应用

微流控芯片具有液体流动可控、消耗试样少、分析速度快等特点,它可以在几分钟甚至更短的时间内进行上百个样品的同时分析,并且可以实现在线样品的预处理及分析全过程。一种条形码微流控芯片能够以高密度的单链DNA为模板,从而克服了传统蛋白质微流控芯片固定在固体表面容易变性的缺点,既解决了稳定性的要求,又满足芯片平行处理大量数据的要求,可以用来大量的、快速的定量检测细胞的分泌蛋白。条形码微流控芯片因其对样品要求简单、低耗高效、高通量等特点正在成为分泌蛋白检测的最具吸引力的分析工具,在样品分析与检测以及临床检测研究等领域得到了广泛的应用。     

Autotransporter-Based Antigen Display in Bacterial Ghosts

Bacterial ghosts are empty cell envelopes of Gram-negative bacteria that can be used as vehicles for antigen delivery. Ghosts are generated by releasing the bacterial cytoplasmic contents through a channel in the cell envelope that is created by the controlled production of the bacteriophage ϕX174 lysis protein E. While ghosts possess all the immunostimulatory surface properties of the original host strain, they do not pose any of the infectious threats associated with live vaccines. Recently, we have engineered the Escherichia coli autotransporter hemoglobin protease (Hbp) into a platform for the efficient surface display of heterologous proteins in Gram-negative bacteria, HbpD. Using the Mycobacterium tuberculosis vaccine target ESAT6 (early secreted antigenic target of 6 kDa), we have explored the application of HbpD to decorate E. coli and Salmonella ghosts with antigens. The use of different promoter systems enabled the concerted production of HbpD-ESAT6 and lysis protein E. Ghost formation was monitored by determining lysis efficiency based on CFU, the localization of a set of cellular markers, fluorescence microscopy, flow cytometry, and electron microscopy. Hbp-mediated surface display of ESAT6 was monitored using a combination of a protease accessibility assay, fluorescence microscopy, flow cytometry and (immuno-)electron microscopy. Here, we show that the concerted production of HbpD and lysis protein E in E. coli and Salmonella can be used to produce ghosts that efficiently display antigens on their surface. This system holds promise for the development of safe and cost-effective vaccines with optimal intrinsic adjuvant activity and exposure of heterologous antigens to the immune system.     

融合标签技术在膜蛋白结构研究中的应用

膜蛋白高级结构的研究包括不同的层次,即膜蛋白拓扑学结构的研究、利用核磁共振技术和蛋白质晶体衍射技术对三维结构的研究,以及膜蛋白复合体的研究。在研究过程中,如果能够基于膜蛋白的拓扑学结构预测,选择合适的蛋白质或多肽融合标签,利用基因融合技术在基因水平上对膜蛋白进行改造,可以产生含有融合标签的重组膜蛋自,不仅具有原有膜蛋白的功能活性,还具有融合标签所特有的生理生化特性,将会极大地促进膜蛋白结构和功能的研究。我们就目前膜蛋白结构研究中所涉及的融合标签技术及其应用策略和所取得的进展做一简述。     

生长素输出载体PIN家族研究进展

生长素极性运输调控植物的生长发育。生长素极性运输主要依赖3类转运蛋白: AUX/LAX、PIN和ABCB蛋白家族。生长素在细胞间流动的方向与PIN蛋白在细胞上的极性定位密切相关。PIN蛋白由1个中心亲水环和2个由中心亲水环隔开的疏水区组成。中心亲水环上含多个磷酸化位点,其为一些蛋白激酶的靶点。PIN蛋白受多方面调控,包...     

Exploring Strong Interactions in Proteins with Quantum Chemistry and Examples of Their Applications in Drug Design

Objectives

Three strong interactions between amino acid side chains (salt bridge, cation-π, and amide bridge) are studied that are stronger than (or comparable to) the common hydrogen bond interactions, and play important roles in protein-protein interactions.

Methods

Quantum chemical methods MP2 and CCSD(T) are used in calculations of interaction energies and structural optimizations.

Results

The energies of three types of amino acid side chain interactions in gaseous phase and in aqueous solutions are calculated using high level quantum chemical methods and basis sets. Typical examples of amino acid salt bridge, cation-π, and amide bridge interactions are analyzed, including the inhibitor design targeting neuraminidase (NA) enzyme of influenza A virus, and the ligand binding interactions in the HCV p7 ion channel. The inhibition mechanism of the M2 proton channel in the influenza A virus is analyzed based on strong amino acid interactions.

Conclusion

(1) The salt bridge interactions between acidic amino acids (Glu^- and Asp^-) and alkaline amino acids (Arg⁺, Lys⁺ and His⁺) are the strongest residue-residue interactions. However, this type of interaction may be weakened by solvation effects and broken by lower pH conditions. (2) The cation- interactions between protonated amino acids (Arg⁺, Lys⁺ and His⁺) and aromatic amino acids (Phe, Tyr, Trp and His) are 2.5 to 5-fold stronger than common hydrogen bond interactions and are less affected by the solvation environment. (3) The amide bridge interactions between the two amide-containing amino acids (Asn and Gln) are three times stronger than hydrogen bond interactions, which are less influenced by the pH of the solution. (4) Ten of the twenty natural amino acids are involved in salt bridge, or cation-, or amide bridge interactions that often play important roles in protein-protein, protein-peptide, protein-ligand, and protein-DNA interactions.     

Efficient and Stable Display of Functional Proteins on Bacterial Magnetic Particles Using Mms13 as a Novel Anchor Molecule

Magnetic particles are increasingly used for various biomedical applications because they are easy to handle and separate from biological samples. In this work, a novel anchor molecule was used for targeted protein display onto magnetic nanoparticles. The magnetic bacterium Magnetospirillum magneticum AMB-1 synthesizes intracellular bacterial magnetic particles (BMPs) covered with a lipid bilayer membrane. In our recent research, an integral BMP membrane protein, Mms13, was isolated and used as an anchor molecule to display functional proteins onto BMPs. The anchoring properties of Mms13 were confirmed by luciferase fusion studies. The C terminus of Mms13 was shown to be expressed on the surface of BMPs, and Mms13 was bound to magnetite directly and tightly permitting stable localization of a large protein, luciferase (61 kDa), on BMPs. Consequently, luminescence intensity obtained from BMPs using Mms13 as an anchor molecule was >400 or 1,000 times higher than Mms16 or MagA, which previously were used as anchor molecules. Furthermore, the immunoglobulin G-binding domain of protein A (ZZ) was displayed uniformly on BMPs using Mms13, and antigen was detected by transmission electron microscopy using antibody-labeled gold nanoparticles on a single BMP displaying the ZZ-antibody complex. The results of this study demonstrated the utility of Mms13 as a molecular anchor, which will facilitate the assembly of other functional proteins onto BMPs in the near feature.     

Construction of Artificial TNF-Binding Proteins Based on the 10th Human Fibronectin Type III Domain Using Bacterial Display

Construction of antibody mimetics on the base of alternative scaffold proteins is a promising strategy for obtaining new products for medicine and biotechnology. The aim of our work was to optimize the cell display system for the 10th human fibronectin type III domain (¹⁰Fn3) scaffold protein based on the AT877 autotransporter from Psychrobacter cryohalolentis K5^T and to construct new artificial TNF-binding proteins. We obtained a ¹⁰Fn3 gene combinatorial library and screened it using the bacterial display method. After expression of the selected ¹⁰Fn3 variants in Escherichia coli cells and analysis of their TNF-binding activity, we identified proteins that display high affinity for TNF and characterized their properties.     

Evaluation of Staphylococcal Cell Surface Display and Flow Cytometry for Postselectional Characterization of Affinity Proteins in Combinatorial Protein Engineering Applications

For efficient generation of high-affinity protein-based binding molecules, fast and reliable downstream characterization platforms are needed. In this work, we have explored the use of staphylococcal cell surface display together with flow cytometry for affinity characterization of candidate affibody molecules directly on the cell surface. A model system comprising three closely related affibody molecules with different affinities for immunoglobulin G and an albumin binding domain with affinity for human serum albumin was used to investigate advantages and differences compared to biosensor technology in a side-by-side manner. Equilibrium dissociation constant (K_D) determinations as well as dissociation rate analysis were performed using both methods, and the results show that the on-cell determinations give both K_D and dissociation rate values in a very fast and reproducible manner and that the relative affinities are very similar to the biosensor results. Interestingly, the results also show that there are differences between the absolute affinities determined with the two different technologies, and possible explanations for this are discussed. This work demonstrates the advantages of cell surface display for directed evolution of affinity proteins in terms of fast postselectional, on-cell characterization of candidate clones without the need for subcloning and subsequent protein expression and purification but also demonstrates that it is important to be aware that absolute affinities determined using different methods often vary substantially and that such comparisons therefore could be difficult.     

两种主流载体蛋白在大肠杆菌表面展示抗体应用中的系统分析

抗体表面展示技术对于新抗体的筛选和抗体亲和力的成熟是非常重要的工具．目前,较为广泛应用的表面展示技术是噬菌体的表面展示和酵母的表面展示．大肠杆菌,以其培养简单和基因改造便捷,有望成为非常好的一种表面展示的宿主．但是,目前为止,大肠杆菌还没有被广泛地应用于抗体的表面展示技术中．主要的原因之一是在大肠杆菌外膜展示抗体的效率还不够高．作为外膜展示的载体,许多蛋白都被研究过,其中自转运蛋白(autotransporter,AT)和冰核蛋白(ice nucleation protein,INP)是人们研究最多的两种载体蛋白．还有一个原因是大肠杆菌作为宿主,在表达异源基因和展示异源蛋白过程中的存活率问题．在本研究中,系统地研究了Ag43β(一种自转运蛋白Antigen43的β结构域)和INPNC(去掉中间冗余序列的冰核蛋白的N端和C端)两种载体蛋白在强弱不同的三种启动子(T7、araBAD和lac)诱导表达的情况下,表达量、展示率、抗原亲和力以及宿主菌存活率的差异．我们发现,Ag43β展示的抗体在抗原亲和力上优于INPNC展示的抗体．在存活率方面,T7启动子诱导表达的存活率很低：用INPNC作为载体蛋白时只有0.0033%,用Ag43β作为载体蛋白时只有0.02%存活率．lac启动子诱导表达的存活率：用INPNC作为载体蛋白时为2.04%,用Ag43β作为载体蛋白时为13.27%．araBAD启动子诱导表达的存活率很高：用INPNC作为载体蛋白时为37.80%,用Ag43β作为载体蛋白时高达90.23%．但是araBAD诱导表达量和展示率都很低,所以其表现出的宿主高存活率意义有限．综合看来,由lac启动子驱动的、以Ag43?茁为载体蛋白的抗体表面展示系统是最好的选择．     

Evolution of Structural Shape in Bacterial Globin-Related Proteins

The globin family of proteins has a characteristic structural pattern of helix interactions that nonetheless exhibits some variation. A simplified model for globin structural evolution was developed in which protein shape evolved by random change of contacts between helices. A conserved globin domain of 15 bacterial proteins representing four structural families was studied. Using a parsimony approach ancestral structural states could be reconstructed. The distribution of number of contact changes per site for a fixed topology tree fit a gamma distribution. Homoplasy was high, with multiple changes per site and no support for an invariant class of residue-residue contacts. Contacts changed more slowly than sequence. A phylogenetic reconstruction using a distance measure based on the proportion of shared contacts was generally consistent with a sequence-based phylogeny but not highly resolved. Contact pattern convergence between members of different globin family proteins could not be detected. Simulation studies indicated the convergence test was sensitive enough to have detected convergence involving only 10% of the contacts, suggesting a limit on the extent of selection for a specific contact pattern. Contact site methods may provide additional approaches to study the relationship between protein structure and sequence evolution. [Reviewing Editior: Dr. Lauren Ancel Meyers]