蛋白质微阵列技术及其在医学领域中的应用

蛋白质微阵列是生物芯片的一种,其主要优势在于应用平面上的有序排列的许多管、腔(孔)或各自独立的点来进行样本检测,使大量样本的平行分析成为可能。应用此技术可同时分析诸多蛋白质的生物化学活性、蛋白质与蛋白质间、蛋白质与DNA间、蛋白质与RNA间,以及蛋白质与配体间的相互作用,从而在临床诊断、药物研究、环境监测、食品卫生等方面显示出其广阔的应用前景。     

蛋白质芯片在蛋白质组学研究中的作用

蛋白质芯片是以高度并行性、高通量、微型化和自动化为特点的蛋白质组检测技术。本文综述了蛋白质芯片在蛋白质组学研究中的多种作用,包括普通蛋白质芯片在微量蛋白质分离、蛋白质与蛋白质之间以及蛋白质与其他小分子间相互作用和蛋白质定量检测方面的作用,普通蛋白质芯片通过与质谱技术、生物传感器技术的结合而拓展其应用范围,以及蛋白质组芯片、活性的蛋白质芯片在蛋白质组学研究中应用的进展。     

生物传感芯片质谱及其在蛋白质组研究中的应用

目前蛋白质组研究技术在已有的研究基础上取得了长足进展 ,包括固相 ｐＨ梯度双向凝胶电泳、生物质谱技术、蛋白质双向电泳图谱的数字化和各种分析技术、蛋白质间相互作用分析的方法如酵母双杂交系统、噬菌体展示、表面等离子共振等。但均各有其利弊。目前质谱是进行蛋白质组成分鉴定的支撑技术 ,但是它在蛋白质间相互作用分析及结构与功能的关系分析方面显得无能为力 ,而生物分子相互作用分析技术 (Ｂｉｏｍｏｌｅｃｕｌａｒｉｎｔｅｒａｃｔｉｏｎａｎａｌｙｓｉｓ ,ＢＩＡ)是进行蛋白质相互作用分析的较好技术 ,将两者结合起来在蛋白质组…     

双杂交和质谱技术在蛋白质-蛋白质相互作用研究中的应用

基因的功能是由蛋白质来执行的,而蛋白质要通过与其他生物分子相互作用来完成其各种生物功能。因此,如果能够快速做出蛋白质在不同时间、空间和不同环境中的相互作用图谱,就会帮助我们了解这些蛋白质的功能,进而了解许多生命活动的机制。目前,用于大规模研究蛋白质间相互作用的方法主要有酵母双杂交系统及其衍生系统、亲和纯化与质谱分析联用技术,前者用于研究蛋白分子间的两两相互作用,后者用于研究蛋白质复合物间的相互作用。本文主要阐述了酵母双杂交、细菌双杂交、哺乳动物细胞双杂交、亲和纯化与质谱联用技术在大规模蛋白质相互作用研究中的应用。     

蛋白质芯片技术进展

人类基因组测序工作的完成 ,引起人们对蛋白质组研究的热忱。蛋白质作为生命活动的执行者 ,种类繁多 ,结构复杂 ,并且其活性与空间结构密切相关 ,需要更为先进的技术去研究和探索。近来出现的蛋白质芯片以并行、高通量检测、分析和处理蛋白质样品 ,发展迅速 ,应用前景广泛。介绍蛋白质芯片的种类、蛋白质固定的表面化学以及不同的检测方法 ,简述蛋白质芯片在不同领域的应用 ,并讨论蛋白质芯片目前存在的问题。     

差异蛋白质组学的研究进展

差异蛋白质组是蛋白质组学研究的一个主要内容,其核心在于寻找某种特定臣寸素引起样本之间蛋白质组的差异,揭示并验证蛋白质组在生理或病理过程中的变化。进一步对蛋白质组差异信息分析后,理论上可以推断造成这种变化的原因。因此,对于临床上肿瘤预诊、药物靶标寻找、细胞调控分子的鉴别等有着极大的实际意义。差异蛋白质组研究要求可靠性和可重复性。因此,对于样本处理要求较高,激光微切割技术和高丰度蛋白去除技术的应用优化了样本处理方法。目前差异蛋白质组的主要研究方法仍是2-DE分离和MS鉴定联合应用,基于2-DE的2-DDIGE方法弥补了2-DE的弱点,更适用于差异蛋白质组研究。除2-DE技术外的其他几种技术手段,如多维液相色谱分离技术、ICAT技术、蛋白芯片技术等差异蛋白质组学研究技术可以作为2-DE技术的补充,甚至或替代技术。     

面向蛋白质功能位点识别的机器学习平台构建

有关蛋白质功能的研究是解析生命奥秘的基础,机器学习技术在该领域已有广泛应用。利用支持向量机(support vectormachine,SVM)方法,构建一个预测蛋白质功能位点的通用平台。该平台先提取非同源蛋白质序列,再对这些序列进行特征编码(包括序列的基本信息、物化特征、结构信息及序列保守性特征等),以编码好的样本作为训练数据,利用SVM进行训练,得到敏感性、特异性、Matthew相关系数、准确率及ROC曲线等评价指标,反复测试,得到评价指标最优的SVM模型后,便可以用来预测蛋白质序列上的功能位点。该平台除了应用在预测蛋白质功能位点之外,还可以应用于疾病相关单核苷酸多态性(SNP)预测分析、预测蛋白质结构域分析、生物分子间的相互作用等。     

无细胞体系非天然蛋白质合成研究进展

无细胞非天然蛋白质合成作为蛋白质研究的新兴手段,已成功用于表征蛋白质分子间、蛋白质与核酸分子间相互作用等基础科学研究及医药蛋白、蛋白质材料等工业生产领域。无细胞非天然蛋白质合成系统不需维持细胞的生长,无细胞膜阻碍,可依据研究目的添加基因元件或化学物质从而增强工程设计和过程调控的自由性;也可赋予蛋白质新的特性、结构及功能,如可实现蛋白翻译后修饰、反应手柄引入、生物物理探针及多聚蛋白质合成等。文中系统地综述了目前应用于无细胞蛋白质合成系统中的非天然氨基酸嵌入方法,包括全局抑制及基于正交翻译体系的终止密码子抑制、移码抑制、有义密码子再分配和非天然碱基等方法的研究进展,及非天然氨基酸在蛋白质修饰、生物物理探针、酶工程、蛋白质材料以及医药蛋白质生产等领域的应用进展,并分析了该体系的发展前景及广泛工业化应用的机遇与挑战。     

酵母蛋白质相互作用与基因表达谱和亚细胞定位的相关性

研究酵母（yeast）蛋白质相互作用与基因表达谱和蛋白质亚细胞定位的关系.首先,构建了蛋白质相互作用正样本集、负样本集、随机组对负样本集和混合样本集.然后,对于4个数据集中的所有蛋白质对,通过比较它们的基于距离的基因共表达的分布以及它们中具有已知亚细胞定位的蛋白质对的共定位出现率,实现了这些高通量数据的交叉量化分析.结果揭示,与非相互作用蛋白质对相比,相互作用蛋白质对的基因表达谱具有较高的相似性;相互作用蛋白质对更倾向于具有相同的亚细胞定位.结果还揭示出这些蛋白质特征相关的总体趋势.     

蛋白质芯片技术

以前对蛋白质的研究集中在一次研究一种蛋白质 ,通常费时费力 ;而蛋白质芯片技术是研究蛋白质组的新技术 ,是高通量、微型化和自动化的蛋白质分析技术。它可以用来研究蛋白质的亚细胞定位和蛋白质与蛋白质之间的相互作用 ,以及对蛋白质的功能进行生物化学分析 ,将对蛋白质组研究及医学生物学的发展有很大的推动作用。较系统地介绍了蛋白质芯片的概念、制作及检测方法 ;同时也讨论了蛋白质芯片的两种功能形式、存在问题和应用前景。     

蛋白质与抗体微阵列及其在生物医学研究中的应用

随着人类基因组测序的顺利完成及其他相关领域如机械制造、微电子加工技术及生物信息学方面所取得的进展,以蛋白质为研究对象的蛋白质组学愈显重要,高通量的蛋白质与抗体阵列芯片分析技术正日益为人们关注.对蛋白质分析策略及以阵列为基础的蛋白质芯片分析原理、相关的制备方法与检测技术及其在生物学研究、医学与实验诊断应用方面进行了阐述,并对现阶段该技术存在的不足与发展前景进行了讨论.     

Diagnostic and analytical applications of protein microarrays

DNA microarrays have changed the field of biomedical sciences over the past 10 years. For several reasons, antibody and other protein microarrays have not developed at the same rate. However, protein and antibody arrays have emerged as a powerful tool to complement DNA microarrays during the past 5 years. A genome-scale protein microarray has been demonstrated for identifying protein–protein interactions as well as for rapid identification of protein binding to a particular drug. Furthermore, protein microarrays have been shown as an efficient tool in cancer profiling, detection of bacteria and toxins, identification of allergen reactivity and autoantibodies. They have also demonstrated the ability to measure the absolute concentration of small molecules. Besides their capacity for parallel diagnostics, microarrays can be more sensitive than traditional methods such as enzyme-linked immunosorbent assay, mass spectrometry or high-performance liquid chromatography-based assays. However, for protein and antibody arrays to be successfully introduced into diagnostics, the biochemistry of immunomicroarrays must be better characterized and simplified, they must be validated in a clinical setting and be amenable to automation or integrated into easy-to-use systems, such as micrototal analysis systems or point-of-care devices.     

News in Brief

Protein microarrays are versatile tools for parallel, miniaturized screening of binding events involving large numbers of immobilized proteins in a time- and cost-effective manner. They are increasingly applied for high-throughput protein analyses in many research areas, such as protein interactions, expression profiling and target discovery. While conventionally made by the spotting of purified proteins, recent advances in technology have made it possible to produce protein microarrays through in situ cell-free synthesis directly from corresponding DNA arrays. This article reviews recent developments in the generation of protein microarrays and their applications in proteomics and diagnostics.     

Protein microarrays and their applications

In recent years, the importance of proteomic works, such as protein expression, detection and identification, has grown in the fields of proteomic and diagnostic research. This is because complete genome sequences of humans, and other organisms, progress as cellular processing and controlling are performed by proteins as well as DNA or RNA. However, conventional protein analyses are time-consuming; therefore, high throughput protein analysis methods, which allow fast, direct and quantitative detection, are needed. These are so-called protein microarrays or protein chips, which have been developed to fulfill the need for high-throughput protein analyses. Although protein arrays are still in their infancy, technical development in immobilizing proteins in their native conformation on arrays, and the development of more sensitive detection methods, will facilitate the rapid deployment of protein arrays as high-throughput protein assay tools in proteomics and diagnostics. This review summarizes the basic technologies that are needed in the fabrication of protein arrays and their recent applications.     

Diagnostic and analytical applications of protein microarrays

DNA microarrays have changed the field of biomedical sciences over the past 10 years. For several reasons, antibody and other protein microarrays have not developed at the same rate. However, protein and antibody arrays have emerged as a powerful tool to complement DNA microarrays during the past 5 years. A genome-scale protein microarray has been demonstrated for identifying protein-protein interactions as well as for rapid identification of protein binding to a particular drug. Furthermore, protein microarrays have been shown as an efficient tool in cancer profiling, detection of bacteria and toxins, identification of allergen reactivity and autoantibodies. They have also demonstrated the ability to measure the absolute concentration of small molecules. Besides their capacity for parallel diagnostics, microarrays can be more sensitive than traditional methods such as enzyme-linked immunosorbent assay, mass spectrometry or high-performance liquid chromatography-based assays. However, for protein and antibody arrays to be successfully introduced into diagnostics, the biochemistry of immunomicroarrays must be better characterized and simplified, they must be validated in a clinical setting and be amenable to automation or integrated into easy-to-use systems, such as micrototal analysis systems or point-of-care devices.     

Measuring and analyzing tissue specificity of human genes and protein complexes

Proteins and their interactions are essential for the survival of each human cell. Knowledge of their tissue occurrence is important for understanding biological processes. Therefore, we analyzed microarray and high-throughput RNA-sequencing data to identify tissue-specific and universally expressed genes. Gene expression data were used to investigate the presence of proteins, protein interactions and protein complexes in different tissues. Our comparison shows that the detection of tissue-specific genes and proteins strongly depends on the applied measurement technique. We found that microarrays are less sensitive for low expressed genes than high-throughput sequencing. Functional analyses based on microarray data are thus biased towards high expressed genes. This also means that previous biological findings based on microarrays might have to be re-examined using high-throughput sequencing results.     

Biomarker discovery using protein microarray technology platforms: antibody-antigen complex profiling

Protein microarrays represent an important new tool in proteomic systems biology. This review focuses on the contributions of protein microarrays to the discovery of novel disease biomarkers through antibody-based assays. Of particular interest is the use of protein microarrays for immune response profiling, through which a disease-specific antibody repertoire may be defined. The antigens and antibodies revealed by these studies are useful for clinical assay development, with enormous potential to aid in diagnosis, prognosis, disease staging and treatment selection. The discovery and characterization of novel biomarkers specifically tailored to disease type and stage are expected to enable personalized medicine by facilitating preventative medicine, predictive diagnostics and individualized curative therapies.     

Antibody microarrays: an evaluation of production parameters

Antibody microarrays could have an enormous impact on the functional analysis of cellular activity and regulation, especially at the level of protein expression and protein-protein interaction, and might become an invaluable tool in disease diagnostics. The array surface is bound to have a tremendous influence on the findings from such studies. Apart from the basic issue of how to attach antibodies optimally without affecting their function, it is also important that the cognate antigens, applied within a complex protein mixture, all bind to the arrayed antibodies irrespective of their enormous variety in structure. In this study, various factors in the production of antibody microarrays on glass support were analysed: the modification of the glass surface; kind and length of cross-linkers; composition and pH of the spotting buffer; blocking reagents; antibody concentration and storage procedures, in order to evaluate their effect on array performance. Altogether, data from more than 700 individual array experiments were taken into account. In addition to home-made slides, commercially available systems were also included in the analysis.     

糖芯片的制备和检测应用研究进展

近数十年来,糖芯片逐渐成为分析糖介导的识别和结合作用的强有力工具,具有样品检测用量少、特异性强和高通量等优点,可以大大提高糖生物学研究的效率。主要介绍了通过糖库的构建、共价结合和非共价吸附法等方法制备糖芯片的过程,糖芯片的检测方法及其在生物学研究和生物医学领域的应用,以期为糖芯片相关研究提供参考。