SELDI蛋白质芯片检测技术

从基因组学到蛋白质组学,到当前有关小RNA对蛋白质合成调控的研究无一例外地说明蛋白质是直接发挥对生命活动调控的物质。同基因研究相比较,由于蛋白质分子种类繁多,有复杂的修饰成份和空间结构,使得蛋白质研究比较困难。新近发展起来的蛋白质芯片技术为蛋白质的检测和研究提供了新的技术平台,比如荧光标记技术,蛋白质指纹图谱．飞行时间．质谱联用技术（SELDI蛋白质芯片）,表面等离子基元共振生物传感器技术（SPR芯片）以及初步应用的光学蛋白质芯片技术,其中,后三种是新兴的无需标记进行蛋白质检测的技术。就SELDI蛋白质芯片及其新近研究作一综述。     

蛋白质检测新技术——邻位连接技术及初步应用

邻位连接技术（proximity ligation assay,PLA）,是新研发的一项高灵敏度的蛋白质体外分析技术。该方法利用一对邻位探针（proximity probes）对靶分子进行双识别,通过连接反应产生可扩增的检测信号,以实时 PCR进行放大和检测,将对蛋白质的检测转变成为对DNA的检测,实现痕量蛋白的分析,具有极高的检测灵敏度和特异性。综述了邻位连接技术的原理、研究进展以及该技术在蛋白质分析及疾病诊断领域的初步应用。     

蛋白质芯片技术的发展与应用

蛋白质芯片（proteinchip）,狭义上可以称为蛋白质微阵列（proteinarray）,是继基因芯片后发展起来的生物检测技术,是蛋白质组学研究中除了酵母双杂交、双向电泳技术、质谱技术等之外的一种重要的工具。蛋白质芯片是一种高通量的蛋白质功能分析技术,具有平行、快速、自动化的优点,     

血管生成素相互作用蛋白质的筛选与鉴定

血管生成素（angiogenin, ANG）在肿瘤、神经退行性疾病和先天免疫过程中均发挥作用,但对其具体生理病理功能和作用机制的了解并不深入全面.蛋白质 蛋白质相互作用调控着细胞内的各个生物学过程,可以为目标蛋白质功能和机制的探索提供信息.本文利用酵母双杂交技术,分别从人心肌和肝cDNA文库中筛选了ANG的可能相互作用蛋白质.对筛选获得的20个候选蛋白质进行生物信息学分析,显示10个蛋白质含有EGF结构域;有5个蛋白质在KEGG 数据库已有记录,主要参与细胞黏附、通讯和迁移等过程.在以往的研究中,我们已经验证α 辅肌动蛋白2（α-actinin 2）、卵泡抑素（follistatin）、磷脂混杂酶1（phospholipid scramblase 1）和腓骨蛋白1（fibulin1）与ANG作用的真实性.本文的蛋白质沉降实验显示,ANG与腓骨蛋白2、3、4之间也存在相互作用.     

双分子荧光互补技术

双分子荧光互补（bimolecular fluorescence complementation, BiFC）是近年发展起来的用于体内或体外检测蛋白质相互作用的一项新技术.该技术是将荧光蛋白在合适的位点切开形成不发荧光的2个片段,这2个片段借助融合于其上的目标蛋白的相互作用,彼此靠近,重新形成能具有活性的荧光蛋白.BiFC方法简单直观,既可以检测蛋白之间的相互作用,也可以定位相互作用蛋白质的位点.多色BiFC系统共用或与荧光共振能量转移（FRET）技术联用,还可以检测细胞内多个蛋白质的相互作用.     

低浓度多聚甲醛固定对蛋白免疫印迹技术的改良

蛋白质免疫印迹（protein immunoblot,或Western blot）是一种广泛应用于检测细胞或组织蛋白质表达及蛋白质翻译后修饰的方法．前期的研究发现,使用低浓度（0.4%）多聚甲醛在蛋白质免疫印迹封闭环节前做膜固定,有助于提高蛋白质的检测效果．本文通过设置多聚甲醛的不同浓度和固定时间,进一步探索其在蛋白质免疫印迹技术中的应用．结果发现,低浓度（≤0.4%）多聚甲醛处理30 min,能明显提升蛋白质的检测效率．通过检测不同大小蛋白质的固定效果发现,大分子量的蛋白质使用多聚甲醛固定效果不明显,中等分子量和小分子量的蛋白质的固定效果较佳．综上研究表明,在中等或小分子量的蛋白质免疫印迹检测中,封闭环节前加入低浓度多聚甲醛固定,可以提高蛋白质的检测效果．     

B族G蛋白偶联受体PAC1的N端基序HSDCIF对其二聚化和上膜运输的影响

B族G蛋白偶联受体（G protein-coupled receptors, GPCRs）PAC1是垂体腺苷酸环化酶激活多肽（pituitary adenylate cyclase activating polypeptide, PACAP）的特异受体,介导PACAP神经保护等功能,是神经系统疾病药物开发的重要靶点之一. HSDCIF（His-Ser-Asp-Cys-Ile-Phe）为位于PAC1的N端胞外1区（extracellar domain 1, EC1）的一段短肽序列,与特定负责激活PAC1受体的激动域PACAP（1-6）具有极高的同源性.利用基因敲除技术构建出缺陷HSDCIF基序的PAC1突变体（简称D PAC1）|利用基因工程原理和技术构建系列真核表达重组载体,包括融合了增强型黄色荧光蛋白（enhanced yellow fluorescent protein, EYFP）的表达载体D-PAC1-EYFP|用于生物发光能量转移（bioluminescence resonance energy transfer, BRET）检测的D-PAC1-Rluc|以及用于双分子荧光互补（bimolecular fluorescence complementation, BiFC）实验的D-PAC1-EYFP/N和D-PAC1-EYFP/C.免疫荧光检测（immunofluorescence assay）测定D PAC1的表达|荧光共聚焦显微观察D-PAC1的细胞运输,然后通过 Western印迹、BRET与BiFC方法来检测D PAC1的二聚化情况,综合评价HSDCIF基序对PAC1二聚化和在细胞中定位的影响.检测结果显示,缺陷HSDCIF基序的突变体D PAC1不能发生二聚化,也不能正常的进行上膜运输,而是滞留在内质网中,同时外源化学合成的寡肽HSDCIF可以竞争性地抑制正常PAC1的二聚化.     

异源生物中筛选高剪接活性Intein系统的建立

原始物种体内蛋白质内含子（intein）介导的自催化蛋白剪接反应以100%效率进行.当这些蛋白质内含子被克隆入异源物种时,其剪接效率往往大大降低,绝大多数甚至完全失去剪接能力.本研究根据蛋白质内含子剪接活性与蛋白质外显子（extein）C端第1个保守氨基酸直接相关的特点,设计含有所有这些保守氨基酸的多个短的蛋白质外显子序列,通过PCR引入到卡那霉素抗性蛋白（KanR）的不同位点中,在此外显子中克隆入相应的蛋白质内含子,构建在大肠杆菌中依赖卡那霉素抗性来筛选高剪接活性蛋白质内含子的系统.结果显示,卡那霉素平板上菌落生长的结果与Western印迹检测的结果基本一致.说明建立的筛选高剪接活性蛋白质内含子系统成功.这种含有可选择蛋白质外显子的筛选系统,将蛋白质剪接与卡那霉素抗性相结合,直接从平板上观测剪接结果,成为快速、稳定筛选在异源物种中具有剪接活性蛋白内含子的新手段.     

质谱技术解析磷酸化蛋白质组

蛋白质磷酸化是生物体内存在的一种普遍的调节方式,在细胞信号传递中占有极重要的地位.质谱已逐渐被人们认为是挑战这一领域的有利工具.综述了目前利用质谱技术分析磷酸化蛋白质的方法,包括利用固定化的金属亲和层析柱、抗体和化学标签技术富集目的分子,肽片段质量图和前体离子扫描（precusor ion scans）等技术检测磷酸化肽段,串联质谱对磷酸化肽段测序鉴定磷酸化位点,以及引入质量标签对蛋白质的磷酸化水平进行定量等.虽然现在已经有很多可行的方法用于分析磷酸化蛋白质,但要达到从少量生物样品中解析其全部磷酸化蛋白质仍需要有很多技术上的突破.     

蛋白质双向电泳图像分析

随着人类基因组计划的接近完成,蛋白质组（proteome）研究成为新的热点.其中高分辨率的双向电泳（two-dimensional gel electrophoresis,2-DE）技术使对组织或细胞的整个蛋白质组的综合分析成为可能.近年来这一技术有了很大的改进和提高,特别是图像分析系统,算法更为先进,功能日益强大,操作也更简便,为大规模研究提供了良好的工具.使用新一代的2D图像分析系统,对离体培养的雪旺氏细胞的蛋白质样品双向电泳结果进行了初步分析,探讨了在图像扫描、点检测、背景消除、匹配、结果报告和数据分析各步中的技术问题,并报告了进行2D图像分析的体会.     

Comparison of enhanced bioluminescence energy transfer donors for protease biosensors

Bioluminescence energy transfer (BRET) is a powerful tool for the study of protein-protein interactions and conformational changes within proteins. We directly compared two recently developed variants of Renilla luciferase (RLuc), RLuc2 and RLuc8, as BRET donors using an in vitro thrombin assay. The comparison was carried out by placing a thrombin-specific cleavage sequence between the donor luciferase and a green fluorescent protein (GFP(2)) acceptor. Substitution of native RLuc with the RLuc mutants, RLuc2 and 8, in a BRET(2) fusion protein increased the light output by a factor of ~10. Substitution of native RLuc with either of the RLuc mutants resulted in a decrease in BRET(2) ratio by a factor of ~2 when BRET(2) components were separated by the thrombin cleavage sequence. BRET(2) ratios changed by factors of 18.8±1.2 and 18.2±0.4 for GFP(2)-RG-RLuc2 and GFP(2)-RG-RLuc8 fusion proteins, respectively, on thrombin cleavage compared to 28.8±0.20 for GFP(2)-RG-RLuc. The detection limits for thrombin were 0.23 and 0.26 nM for RLuc2 and RLuc8 BRET(2) systems, respectively, and 15 pM for GFP(2)-RG-RLuc. However, overall, the mutant BRET systems remain more sensitive than FRET and brighter than standard BRET(2).     

Multiplexing of multicolor bioluminescence resonance energy transfer

Bioluminescence resonance energy transfer (BRET) is increasingly being used to monitor protein-protein interactions and cellular events in cells. However, the ability to monitor multiple events simultaneously is limited by the spectral properties of the existing BRET partners. Taking advantage of newly developed Renilla luciferases and blue-shifted fluorescent proteins (FPs), we explored the possibility of creating novel BRET configurations using a single luciferase substrate and distinct FPs. Three new (to our knowledge) BRET assays leading to distinct color bioluminescence emission were generated and validated. The spectral properties of two of the FPs used (enhanced blue (EB) FP2 and mAmetrine) and the selection of appropriate detection filters permitted the concomitant detection of two independent BRET signals, without cross-interference, in the same cells after addition of a unique substrate for Renilla luciferase-II, coelentrazine-400a. Using individual BRET-based biosensors to monitor the interaction between G-protein-coupled receptors and G-protein subunits or activation of different G-proteins along with the production of a second messenger, we established the proof of principle that two new BRET configurations can be multiplexed to simultaneously monitor two dependent or independent cellular events. The development of this new multiplexed BRET configuration opens the way for concomitant monitoring of various independent biological processes in living cells.     

A rigorous experimental framework for detecting protein oligomerization using bioluminescence resonance energy transfer

Bioluminescence resonance energy transfer (BRET), which relies on nonradiative energy transfer between luciferase-coupled donors and GFP-coupled acceptors, is emerging as a useful tool for analyzing the quaternary structures of cell-surface molecules. Conventional BRET analyses are generally done at maximal expression levels and single acceptor/donor ratios. We show that under these conditions substantial energy transfer arises from random interactions within the membrane. The dependence of BRET efficiency on acceptor/donor ratio at fixed surface density, or expression level at a defined acceptor/donor ratio, can nevertheless be used to correctly distinguish between well-characterized monomeric and oligomeric proteins, including a very weak dimer. The pitfalls associated with the nonrigorous treatment of BRET data are illustrated for the case of G protein-coupled receptors (GPCRs) proposed to form homophilic and/or mixed oligomers on the basis of previous, conventional BRET experiments.     

Mapping human protease-activated receptor 4 (PAR4) homodimer interface to transmembrane helix 4

Thrombin activates platelets by binding and cleaving protease-activated receptors 1 and 4 (PAR1 and PAR4). Because of the importance of PAR4 activation on platelets in humans and mice and emerging roles for PAR4 in other tissues, experiments were done to characterize the interaction between PAR4 homodimers. Bimolecular fluorescence complementation and bioluminescence resonance energy transfer (BRET) were used to examine the PAR4 homodimer interface. In bimolecular fluorescence complementation experiments, PAR4 formed homodimers that were disrupted by unlabeled PAR4 in a concentration-dependent manner, but not by rhodopsin. In BRET experiments, the PAR4 homodimers showed a specific interaction as indicated by a hyperbolic BRET signal in response to increasing PAR4-GFP expression. PAR4 did not interact with rhodopsin in BRET assays. The threshold maximum BRET signal was disrupted in a concentration-dependent manner by unlabeled PAR4. In contrast, rhodopsin was unable to disrupt the BRET signal, indicating that the disruption of the PAR4 homodimer is not due to nonspecific interactions. A panel of rho-PAR4 chimeras and PAR4 point mutants has mapped the dimer interface to hydrophobic residues in transmembrane helix 4. Finally, mutations that disrupted dimer formation had reduced calcium mobilization in response to the PAR4 agonist peptide. These results link the loss of dimer formation to a loss of PAR4 signaling.     

Fusion of Aequorea victoria GFP and aequorin provides their Ca(2+)-induced interaction that results in red shift of GFP absorption and efficient bioluminescence energy transfer

The bioluminescence emitted by Aequorea victoria jellyfish is greenish while its single bioluminescent photoprotein aequorin emits blue light. This phenomenon may be explained by a bioluminescence resonance energy transfer (BRET) from aequorin chromophore to green fluorescent protein (GFP) co-localized with it. However, a slight overlapping of the aequorin bioluminescence spectrum with the GFP absorption spectrum and the absence of marked interaction between these proteins in vitro pose a question on the mechanism providing the efficient BRET in A. victoria. Here we report the in vitro study of BRET between homologous Ca(2+)-activated photoproteins, aequorin or obelin (Obelia longissima), as bioluminescence energy donors, and GFP, as an acceptor. The fusions containing donor and acceptor proteins linked by a 19 aa peptide were purified after expressing their genes in Escherichia coli cells. It was shown that the GFP-aequorin fusion has a significantly greater BRET efficiency, compared to the GFP-obelin fusion. Two main factors responsible for the difference in BRET efficiency of these fusions were revealed. First, it is the presence of Ca(2+)-induced interaction between the donor and acceptor in the aequorin-containing fusion and the absence of the interaction in the obelin-containing fusion. Second, it is a red shift of GFP absorption toward better overlapping with aequorin bioluminescence induced by the interaction of aequorin with GFP. Since the connection of the two proteins in vitro mimics their proximity in vivo, Ca(2+)-induced interaction between aequorin and GFP may occur in A. victoria jellyfish providing efficient BRET in this organism.     

Demonstration of improvements to the bioluminescence resonance energy transfer (BRET) technology for the monitoring of G protein-coupled receptors in live cells

The bioluminescence resonance energy transfer (BRET) technique has become extremely popular for studying protein-protein interactions in living cells and real time. Of particular interest is the ability to monitor interactions between G protein-coupled receptors, such as the thyrotropin-releasing hormone receptor (TRHR), and proteins critical for regulating their function, such as beta-arrestin. Using TRHR/beta-arrestin interactions, we have demonstrated improvements to all 3 generations of BRET (BRET(1), BRET(2), and eBRET) by using the novel forms of luciferase, Rluc2 and Rluc8, developed by the Gambhir laboratory. Furthermore, for the 1st time it was possible to use the BRET2 system to detect ligand-induced G protein-coupled receptor/beta-arrestin interactions over prolonged periods (on the scale of hours rather than seconds) with a very stable signal. As demonstrated by our Z'-factor data, these luciferases increase the sensitivity of BRET to such an extent that they substantially increase the potential applicability of this technology for effective drug discovery high-throughput screening.     

Bioluminescence resonance energy transfer (BRET) for the real-time detection of protein-protein interactions

A substantial range of protein-protein interactions can be readily monitored in real time using bioluminescence resonance energy transfer (BRET). The procedure involves heterologous coexpression of fusion proteins, which link proteins of interest to a bioluminescent donor enzyme or acceptor fluorophore. Energy transfer between these proteins is then detected. This protocol encompasses BRET1, BRET2 and the recently described eBRET, including selection of the donor, acceptor and substrate combination, fusion construct generation and validation, cell culture, fluorescence and luminescence detection, BRET detection and data analysis. The protocol is particularly suited to studying protein-protein interactions in live cells (adherent or in suspension), but cell extracts and purified proteins can also be used. Furthermore, although the procedure is illustrated with references to mammalian cell culture conditions, this protocol can be readily used for bacterial or plant studies. Once fusion proteins are generated and validated, the procedure typically takes 48-72 h depending on cell culture requirements.     

Homogeneous assay for biotin based on Aequorea victoria bioluminescence resonance energy transfer system

Here we describe a homogeneous assay for biotin based on bioluminescence resonance energy transfer (BRET) between aequorin and enhanced green fluorescent protein (EGFP). The fusions of aequorin with streptavidin (SAV) and EGFP with biotin carboxyl carrier protein (BCCP) were purified after expression of the corresponding genes in Escherichia coli cells. Association of SAV-aequorin and BCCP-EGFP fusions was followed by BRET between aequorin (donor) and EGFP (acceptor), resulting in significantly increasing 510 nm and decreasing 470 nm bioluminescence intensity. It was shown that free biotin inhibited BRET due to its competition with BCCP-EGFP for binding to SAV-aequorin. These properties were exploited to demonstrate competitive homogeneous BRET assay for biotin.     

Monitoring for dynamic biological processing by intramolecular bioluminescence resonance energy transfer system using secreted luciferase

Proteolytic processing plays crucial roles in physiological and pathophysiological cellular functions such as peptide generation, cell cycle, and apoptosis. We developed a novel biophysical bioluminescence resonance energy transfer (BRET) system between a secreted Vargula luciferase (Vluc) and an enhanced yellow fluorescent protein (EYFP) for visualization of cell biological processes. The bioluminescence spectrum of the fusion protein (Vluc-EYFP) is bimodal (lambdamax = 460 nm (Vluc) and 525nm (EYFP)), indicating that the excited-state energy of Vluc transfers to EYFP (in short, BRET). The BRET signal can be measured in the culture medium and pursue quantitative production of two neuropeptides, nocistatin (NST) and nociceptin/orphanin FQ (N/OFQ) in living cells. NST and N/OFQ are located in tandem on the same precursor, but NST exhibits antagonistic action against N/OFQ-induced central functions. Insertion of a portion of the NST-N/OFQ precursor (Glu-Gln-Lys-Gln-Leu-Gln-Lys-Arg-Phe-Gly-Gly-Phe-Tyr-Gly) in Vluc-EYFP makes the fusion protein cleavable at Lys-Arg in NG108-15 cells, and proprotein convertase 1 enhances this digestion. The change in BRET signals quantifies the processing of the fusion protein. Our novel intramolecular BRET system using a secreted luciferase is useful for investigating peptide processing in living cells.