蛋白质组学技术及其在生物医学上的应用

蛋白质组学部分承用了创立于二十多年前的二维电泳技术。基于其高分辩能力 ,二维电泳主要用于分离和检测复杂混合物中的蛋白质。虽然没有获得更多的改进 ,但是二维电泳结合了通过质谱测定蛋白质的最新进展而成为蛋白质组学中的一项重要技术。随着人类基因组计划项目的完成及由此而产生的大量基因数据库和使用这些数据的生物信息技术 ,科学家们的下一个目标是解析生物体的完整蛋白质组 ,把蛋白质组学数据与基因组学数据关联起来并有机地结合而成为一项有力的工具以阐明病理学中的蛋白质功能、衰老的过程及发现新药目标蛋白质和疾病标识物等。文章综述了蛋白质组学技术的最新知识及其在生物医学研究中的潜在应用     

乳腺癌蛋白质组学研究

乳腺癌是妇女中最常见的一种癌症,鉴定出与乳腺癌癌变相关的蛋白质以及病情发展过程中蛋白质的变化对揭示乳腺癌变机理及早期诊断是非常重要的。早在蛋白质组学这一概念提出以前,人们已应用2－维凝胶电泳技术（2DE）研究乳腺癌的癌变机理,且随着人类基因序列测序的完成,质谱的应用,以及生物信息学的引入,蛋白质组的研究获得了飞速发展,高通量的蛋白质组研究以及新的技术如激光捕获显微切割（LCM）,表面加强激光解吸／电离飞行时间质谱（SELDI－TOF）,蛋白质阵列,组织阵列等蛋白质组学技术已被用于乳腺癌研究并获得了很快速的发展。乳腺癌蛋白质组学研究已经鉴定了一些具有诊断潜能的生物分子靶标和信号传导因子。介绍了乳腺癌蛋白质组学研究中所使用的最新研究方法和研究进展。     

Pten^＋/＋MEFs与Pten^-/-MEFs细胞系的差异表达蛋白质组分析

目的：研究PTEN缺失细胞的蛋白表达规律。方法：用双向电泳技术比较Pten^＋/＋MEFs与Pten^-/-EFs细胞的蛋白表达差异;用基质辅助激光解吸／电离飞行时间质谱（MALDI-TOF-MS）对差异蛋白进行质谱分析;用肽质量指纹图谱检索数据库对差异蛋白进行鉴定;用Northern印迹和Western印迹验证蛋白的差异表达。结果：与Pten^＋/＋MEFs细胞相比。Pten^-/-MEFs细胞有明显的差异性蛋白表达谱,Pten^-/-MEFs细胞中表达下降的蛋白有铜锌超氧化物歧化酶、过氧化物氧化还原酶5和6等,表达增加的蛋白有低分子量蛋白酪氨酸磷酸酶和丝切蛋白（cofflin）1。结论：PTEN的缺失引起细胞内多种蛋白表达改变,这些表达改变的蛋白可能与PTEN缺失后细胞癌变相关。     

大鼠海马的表达蛋白质组学实验研究

目的：用蛋白质组学方法初步分析大鼠海马蛋白质的表达。方法：提取大鼠海马蛋白质样品后,用双向凝胶电泳对其分离,经考马斯亮蓝染色后,产生大鼠海马蛋白质双向凝胶电泳图谱。从凝胶上切割分离的蛋白质,经胰蛋白酶胶内酶解,通过基质辅助激光解吸／电离飞行时间质谱（MALDI-TOF-MS）对酶解后的肽段进行分析。根据肽段质谱数据,经数据库（NCBI）检索,对蛋白质进行鉴定。结果：鉴定了37种具有明确功能的蛋白质,它们分别属于代谢酶、细胞骨架蛋白、热休克蛋白、抗氧化蛋白、信号传导蛋白、蛋白酶体相关蛋白、神经元特异蛋白及神经胶质蛋白。另外,鉴定了3种未知功能蛋白。结论：为建立大鼠海马蛋白质组数据库提供必要的资料,为在大鼠模型上研究神经疾病发病机理奠定基础。     

小麦质核互作型雄性不育系及其保持系花药差异蛋白质组学分析

为了能从蛋白质水平揭示小麦细胞质雄性不育的分子遗传机制,采用IEF/SDS-PAGE双向凝胶电泳技术,对小麦质核互作型雄性不育系(S)-1376A及其保持系(A)-1376B在花药发育的单核期、二核期蛋白质进行了差异蛋白质组学研究,经考马斯亮蓝染色,得到了重复性较好的双向电泳图谱．PDQuest 软件在分子质量9.0～100.0 ku、等电点4～7 线性范围内,可识别约610个蛋白质点,对28个差异表达的蛋白质点采用基质辅助激光解吸分离飞行时间质谱进行肽指纹图谱分析,并利用Mascot 软件在NCBInr数据库搜索,鉴定出12个差异表达蛋白,其中5个差异表达蛋白可能与雄性不育有关,分别是泛素结合酶E2、甘氨酸富集蛋白、抗坏血酸过氧化物酶、假定半胱氨酸蛋白酶抑制剂及1, 5-二磷酸核酮糖羧化酶/加氧酶小链克隆512,它们参与了物质能量代谢、细胞程序化死亡及花发育调控等过程,推测不育系(S)-1376A 雄性不育性可能与这些生理生化代谢有关．研究结果为揭示雄性不育机理提供了理论依据．     

青海高原春小麦PEG胁迫与复水后叶片差异蛋白质组学研究

春小麦是青海省的主要粮食作物,青海高原干旱频繁且严重,尤以春旱为首,对小麦生长发育造成严重影响．为了从蛋白质组学水平分析小麦对干旱胁迫的应答特征,探讨小麦可能的抗旱机制,本研究对青海主栽春小麦品种青春38幼苗进行聚乙二醇 (polyethylene glycol,PEG) 6000胁迫和复水处理,采用IEF/SDS PAGE双向凝胶电泳技术,对PEG胁迫和复水处理的小麦叶片总蛋白质分别与正常浇水的对照进行差异蛋白质组学研究,经考马斯亮蓝G 250染色获得清晰度和重复性较好的双向电泳图谱．PD Quest软件处理分析各对照和处理图谱,在等电点4.0～7.0线性范围内,均可识别650个以上清晰蛋白质点,获得比较明显的差异表达蛋白点43个,其中8个蛋白点重复.从35个差异蛋白点中选取24个差异点进行MALDI-TOF-TOF-MS肽质量指纹图谱分析,应用Mascot软件在NCBInr数据库中搜索鉴定蛋白质,得到22个阳性结果．对鉴定得到的差异表达蛋白进行功能分析,它们分别参与了光合作用、蛋白质合成、能量代谢途径、细胞防御、氧化还原、运输、信号转导等过程,而且根据差异表达蛋白功能分类所占比例,发现干旱胁迫与光合作用关系最为紧密.     

慢性阻塞性肺疾病与非慢性阻塞性肺疾病吸烟者肺组织蛋白质组学比较分析

吸烟是导致慢性阻塞性肺疾病（COPD）发生发展的主要原因之一.但吸烟者是否发生COPD存在个体差异,其机制尚未完全阐明.蛋白质组学研究能够高效率发现疾病相关蛋白并为深入研究疾病的发病机制提供线索.本研究运用二维凝胶电泳（2-DE）和基质辅助激光解吸电离飞行时间质谱(MALDI-TOF-MS)蛋白质组学研究方法结合生物信息学数据,对吸烟COPD患者和非COPD吸烟者肺组织表达的差异蛋白进行筛选和鉴定,共鉴定出24种差异蛋白,涉及基本代谢酶类、氧化应激相关酶类、凝血/纤溶相关蛋白、蛋白降解相关酶以及细胞生长分化相关蛋白等.本研究结果为进一步探索COPD的发病机制提供了新的线索.     

基质辅助激光解吸电离飞行时间质谱在微生物鉴定中的研究进展

与传统的微生物鉴定技术相比,基质辅助激光解吸电离飞行时间质谱(matrix-assisted laser desorption ionization time-of-flight mass spectrometry, MALDI-TOF MS)是一种准确、可靠和快速的鉴定和分型的技术。本文通过检索近年来国内外相关研究论文,总结最新的研究进展,发现MALDI-TOF MS在临床病原微生物、食源性微生物以及环境微生物等鉴定中有较大的优势,加快了微生物鉴定的进程,同时探索该技术在新领域的最新进展和面临的挑战,以期为我国基质辅助激光解吸电离飞行时间质谱技术的发展提供参考。     

MALDI-TOF MS技术在临床病原真菌鉴定中的应用进展

基质辅助激光解吸电离飞行时间质谱技术（MALDI-TOF-MS）目前是一种快速而可靠的微生物鉴定方法.随着可鉴定真菌谱的完善,MALDI-TOF MS技术已逐步应用于临床常见致病酵母菌、酵母样真菌和丝状菌的鉴定中,本文将就此做一综述.     

后基因组时代的植物蛋白质组学

蛋白质组学是后基因组时代功能基因组学研究的新兴学科和热点领域。简要介绍了蛋白质组学产生的科学背景、研究内容和研究方法。重点综述了植物个体水平、组织、器官和亚细胞水平蛋白组研究 ,植物蛋白质组学在植物遗传多样性、遗传突变体、植物的逆境生理等方面的研究进展。最后展望了今后的发展前景。     

Proteomics analysis of cerebral cortex in Wistar rats

To analyze the protein expression pattern of the cerebral cortex in Wistar rats using the proteomics approach, proteins were separated by two-dimensional gel electrophoresis, stained with Coomassie brilliant blue and digested with trypsin. Then, we analyzed the peptide section using a matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF-MS) and identified the protein by indexing special database (SwissProt) according to the finger printing of the peptide quality. Eighty-four protein spots were identified, including metabolic enzymes, skeleton proteins, heat shock proteins, antioxidant proteins, signaling proteins, proteasome related proteins, neuron and glial specific proteins and serum associated proteins. The result of this study enriches the database of the proteome in the cerebral cortex of rats and lays a foundation for further research of neurological disorders in rat models. __________ Translated from Acta Biophysica Sinica, 2007, 23 (1): 151–156 [译自: 生物物理学报]     

Proteomics analysis of cerebral cortex in Wistar rats

To analyze the protein expression pattern of the cerebral cortex in Wistar rats using the proteomics approach, proteins were separated by two-dimensional gel electrophoresis, stained with Coomassie brilliant blue and digested with trypsin. Then, we analyzed the peptide section using a matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF-MS) and identified the protein by indexing special database (SwissProt) according to the finger printing of the peptide quality. Eighty-four protein spots were identified, includ-ing metabolic enzymes, skeleton proteins, heat shock pro-teins, antioxidant proteins, signaling proteins, proteasome related proteins, neuron and glial specific proteins and serum associated proteins. The result of this study enriches the database of the proteome in the cerebral cortex of rats and lays a foundation for further research of neurological disorders in rat models.     

正常与脑缺血大鼠的脑皮质蛋白质差异分析鉴定

Wistar大鼠随机分为正常组和模型组,采用改进的线栓法制备模型,在规定的时间点快速断头取脑,分离脑皮质组织,提取蛋白质后双向电泳展示,以ImageMaster 2D Elite v301软件对2_DE图谱进行差异表达分析,目标蛋白点用基质辅助激光解析电离质谱测定肽质量指纹图进行鉴定。线粒体应激70蛋白前体、血小板活化因子乙酰基水解酶Ibβ亚单位、ADP核糖基化因子蛋白3、电压依赖性阴离子选择通道蛋白1、泛素C末端水解酶同工酶L1、突触结合蛋白等11个蛋白在模型6h组表达上调,谷胱甘肽S-转移酶omega 1、 谷胱甘肽S-转移酶P、Cu-Zn超氧化物歧化酶、 ATP合酶D链、G蛋白β亚单位1、微管蛋白β链15、苹果酸脱氢酶等15个蛋白在模型6h组表达上调。胆绿素还原酶B、细胞因子A4前体为模型组新出现点,腺苷酸激酶同工酶1在模型组消失,Thiore doxin peroxidase 1在模型组分为2个点。以双向电泳技术得到分辨率较好的电泳图谱,并初步鉴定脑缺血后差异表达蛋白,为深入研究缺血性脑损伤病理机制奠定了基础。     

正常与重金属铅注射的兔脑蛋白质双向电泳图谱比较与鉴定

重金属污染对人类健康的威胁日益受到关注,为了了解大量重金属摄入对脑蛋白质的影响,对比研究了正常兔脑组织蛋白质与重金属铅腹腔注射2周后的兔脑组织在蛋白质双向电泳图谱中的差异,分析重金属注射对脑蛋白质表达的可能影响.通过对脑组织蛋白质的提取,分离出水溶性的蛋白质组分,经双向电泳图谱比较正常与注射重金属铅的兔子在脑蛋白质表达上的差异,其中3个蛋白质斑点经提取,反相高效液相色谱(RP-HPLC)分离,基质辅助激光解析电离质谱(MALDI-TOF MS)确定了分子质量,并利用肽质量指纹图谱检索数据库确定蛋白质的归属.实验结果表明正常兔脑与金属铅注射的兔脑在水溶性蛋白质的表达上具有显著性差异.     

Proteomic analysis of nuclear proteins from proliferative and differentiated human colonic intestinal epithelial cells

Self-renewing tissues such as the intestine contain progenitor proliferating cells which subsequently differentiate. Cell proliferation and differentiation involve gene regulation processes which take place in the nucleus. A human intestinal epithelial cell line model (Caco2/TC7) which reproduces these dynamic processes has been used to perform proteomic studies on nuclear proteins. Nuclei from Caco2/TC7 cells at proliferative and differentiated stages were purified by subcellular fractionation. After two-dimensional gel electrophoresis separation and ruthenium staining, 400 protein spots were detected by image analysis. Eighty-five spots corresponding to 60 different proteins were identified by matrix-assisted laser desorption/ionization mass spectrometry in nuclei from proliferative cells. Comparison of nuclear proteomes from proliferative or differentiated cells by differential display resulted in the identification of differentially expressed proteins such as nucleolin, hnRNP A2/B1 and hnRNP A1. By using Western blot analysis, we found that the expression and number of specific isoforms of these nuclear proteins decreased in differentiated cells. Immunocytochemistry experiments also showed that in proliferative cells nucleolin was distributed in nucleoli-like bodies. In contrast, hnRNPs A2/B1 and A1 were dispersed throughout the nucleus. This study of the nuclear proteome from intestinal epithelial cells represents the first step towards the establishment of a protein database which will be a valuable resource in future studies on the differential expression of nuclear proteins in response to physiological, pharmacological and pathological modulations.     

A proteomic analysis of thioacetamide-induced hepatotoxicity and cirrhosis in rat livers

Thioacetamide (TAA) administration is an established technique for generating rat models of liver fibrosis and cirrhosis. Oxidative stress is believed to be involved as TAA-induced liver fibrosis is initiated by thioacetamide S-oxide, which is derived from the biotransformation of TAA by the microsomal flavine-adenine dinucleotide (FAD)-containing monooxygense (FMO) and cytochrome P450 systems. A two-dimensional gel electrophoresis-mass spectrometry approach was applied to analyze the protein profiles of livers of rats administered with sublethal doses of TAA for 3, 6 and 10 weeks respectively. With this approach, 59 protein spots whose expression levels changed significantly upon TAA administration were identified, including three novel proteins. These proteins were then sorted according to their common biochemical properties and functions, so that pathways involved in the pathogenesis of rat liver fibrosis due to TAA-induced toxicity could be elucidated. As a result, it was found that TAA-administration down-regulated the enzymes of the primary metabolic pathways such as fatty acid beta-oxidation, branched chain amino acids and methionine breakdown. This phenomenon is suggestive of the depletion of succinyl-CoA which affects heme and iron metabolism. Up-regulated proteins, on the other hand, are related to oxidative stress and lipid peroxidation. Finally, these proteomics data and the data obtained from the scientific literature were integrated into an "overview model" for TAA-induced liver cirrhosis. This model could now serve as a useful resource for researchers working in the same area.     

大豆种子萌发过程中的差异蛋白质组研究

运用蛋白质组学技术对大豆(Glycinemax)N2899种子萌发0h、8h、36h、60h4个时期蛋白质的差异表达情况进行了研究.结果发现,在考马斯亮蓝染色的双向电泳pH3～10胶上,PDQuest图像分析软件可识别的点约350个,其中表达量变化2.5倍以上的蛋白质点有24个,而绝大部分大豆种子贮藏蛋白在萌发期尚未降解.在萌发的第一阶段,24个差异表达蛋白中有10个蛋白质的丰度发生变化.第二阶段,差异表达蛋白的种类和量增加,其中15个蛋白质是动态变化的,14个蛋白质在胚根突破种皮时表达量达到峰值,表明吸胀后种子内的生命活动越来越强.对这24个蛋白质点进行胶内酶解,用基质辅助激光解析电离飞行时间质谱测定均获得肽质量指纹图谱.搜索大豆的UniGene库初步鉴定出6个蛋白质,分别是核苷二磷酸激酶、热激蛋白、硫氧还蛋白、35ku种子成熟蛋白及种子成熟蛋白PM36.对这些蛋白质在种子萌发过程中可能的作用进行了讨论.     

Identification of differentially expressed proteins in poplar leaves induced by Marssonina brunnea f. Sp. Multigermtubi

Black spot disease in poplar is a disease of the leaf caused by fungus. The major pathogen is Marssonina brunnea f. sp. multigermtubi. To date, little is known about the molecular mechanism of poplar （M. brunnea） interaction. In order to identify the proteins related to disease resistance and understand its molecular basis, the clone ＂NL895＂ （P. euramericana CL＂NL895＂）, which is highly resistant to M. brunnea f. sp. multigermtubi, was used in this study. We used two-dimensional gel electrophoresis （2-DE） and mass spectrometry （MS） to identify the proteins in poplar leaves that were differentially expressed in response to black spot disease pathogen, M. brunnea f. sp. multigermtubi. Proteins extracted from poplar leaves at 0, 12, 24, 48, and 72 h after pathogen-inoculation were separated by 2-DE, About 500 reproducible protein spots were detected, of which 40 protein spots displayed differential expression in levels and were subjected to Matrix assisted laser desorption/ionization time of flight mass spectrometry （MALDI-TOF MS） followed by database searching. According to the function, the identified proteins were sorted into five categories, that is, protein synthesis, metabolism, defense response and unclassified proteins.     

A combination of protein profiling and isotopomer analysis using matrix-assisted laser desorption/ionization-time of flight mass spectrometry reveals an active metabolism of the extracellular matrix of 3T3-L1 adipocytes

Differential gel electrophoresis followed by matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) mass spectrometry (MS) is a commonly used protein profiling method. However, observed changes can be explained in multiple ways, one of which is by the protein turnover rate. In order to easily and rapidly obtain information on both the identity and turnover of individual proteins, we applied a combination of protein labeling with L-(ring-2,3,4,5,6 2H5) phenylalanine and MALDI-TOF MS. While the spectrum reveals the identity of a protein, mass isotopomer analysis provides information about the rate of protein labeling as a measure of synthesis or turnover. Using this approach on mature 3T3-L1 adipocytes, we were able to discriminate between rapidly and slowly metabolised proteins. In our isolate, proteins of the cytoskeleton appeared to be slowly metabolised, whereas components of the extracellular matrix, in particular collagen type I alpha 1 (COL1A1) and collagen type I alpha 2 (COL1A2) showed rapid accumulation of newly synthesized proteins. Both proteins appeared to be metabolised in the same ratio as they are present in collagen fibers, i.e. 2:1 (COL1A1: COL1A2). In addition, functionally related proteins were also readily labeled. Taken together, we have shown that a combination of stable isotope labeling and protein profiling by gel electrophoresis and MALDI-TOF analysis can simultaneously provide information on the identity and relative metabolic rate of proteins in eukaryotic cells in a simple, nonhazardous and rapid-throughput way.