GST pull-down联合质谱筛选（肌）营养不良短小蛋白结合蛋白1在小鼠睾丸组织中的相互作用蛋白质

（肌）营养不良短小蛋白结合蛋白1（dystrobrevin binding protein 1,dysbindin-1）是溶酶体相关细胞器生物发生复合体-1(biogenesis of lysosome related organelles complex 1, BLOC-1)的1个亚基,在多种组织细胞中广泛表达;然而,其在睾丸组织中的作用至今尚不明确。为寻找（肌）营养不良短小蛋白结合蛋白1在睾丸组织中的相互作用蛋白质,以进一步研究（肌）营养不良短小蛋白结合蛋白1在睾丸中的作用,本研究首先在Rosetta(DE3)菌种中表达可溶性GST-dysbindin-1融合蛋白,经谷胱甘肽 琼脂糖珠亲和纯化后,与小鼠的睾丸组织蛋白质孵育进行GST pull-down实验,并通过液相色谱串联质谱（LC MS/MS）分析筛选（肌）营养不良短小蛋白结合蛋白1在睾丸组织中的相互作用蛋白质。利用BioGPS数据库聚类在睾丸组织中高表达和特异性表达的互作蛋白质,运用DAVID6.8在线分析工具从细胞组分、分子功能、生物学过程和KEGG通路等方面对筛选出的互作蛋白质进行GO（gene ontology）富集分析。本实验共筛选出108个（肌）营养不良短小蛋白结合蛋白1在睾丸组织中的潜在互作蛋白质,其中98个为尚未报道的（肌）营养不良短小蛋白结合蛋白1相互作用蛋白质,7个为睾丸高表达蛋白质,5个为睾丸特异性表达的蛋白质。这些候选蛋白质主要分布在细胞质、细胞核、细胞膜、细胞外泌体等细胞组分中,通过与蛋白质、核酸等分子结合参与蛋白质翻译和转运、囊泡运输及凋亡等生物学过程以及氨基酸生物合成、溶酶体及蛋白酶体等生物学通路。我们推测,在睾丸组织中（肌）营养不良短小蛋白结合蛋白1可能通过与多种蛋白质相互作用参与精子的发生和受精等过程。     

基于质谱技术的蛋白质互作研究进展

蛋白质作为生命活动的执行者,其功能往往体现在与其他蛋白质的相互作用中,研究蛋白-蛋白相互作用对于人们深入了解和预防传染病、靶向治疗多基因疾病、阐明蛋白质的分子作用机制及各种复杂的生命现象具有重要意义。目前,有多种技术被用来研究蛋白间的相互作用,研究难点在于实时捕获瞬时或弱蛋白质间的相互作用,质谱技术（mass spectrometry, MS）可在某种程度上解决该难点。由于质谱技术可研究简单的蛋白质复合物再到大规模的蛋白质组实验,基于质谱技术研究蛋白质间相互作用被越来越多地应用于科学研究中。综述了蛋白质间相互作用检测方法的研究进展,重点介绍了氢氘交换质谱法和化学交联质谱法研究蛋白质间相互作用的优缺点及其应用,最后对基于质谱技术研究蛋白质间相互作用进行了总结与展望,以期为深入开展相关研究提供借鉴。     

亚健康便秘人群结肠黏膜蛋白质组的筛选鉴定与临床应用

筛选亚健康便秘人群结肠黏膜变化的分子标志物,为亚健康便秘人群的结肠黏膜改变机制提供理论依据.采用双向凝胶电泳(two-dimensional electrophoresis,2-DE)对亚健康便秘人群及健康志愿者结肠黏膜组织进行蛋白质分离,ImageMaster2D Elite分析软件进行图像分析,基质辅助激光解吸电离飞行时间质谱(matrix-assisted laser desorption/ionization time of flightmass spectrometry,MALDI-TOF-MS)得到相应的肽质量指纹图(peptide mass fingerprint,PMF),搜索数据库鉴定差异蛋白.建立了亚健康便秘人群及健康志愿者结肠黏膜组织2-DE图谱,分析出其凝胶的平均蛋白质点数(501.00±37.16,536.00±41.63),两者平均差异蛋白质点数为46.00±7.82,取20个表达量明显改变的蛋白质点进行质谱分析,鉴定出17个蛋白质.其中7个蛋白质点表达下调,10个蛋白质点表达上调.差异蛋白质点包括蛋白质合成与分解、分子伴侣、氧化还原调节及信号传导等相关蛋白质.随即应用免疫印迹(Western blot)技术分析差异蛋白β-actin、YWHAZ及PBP-Ⅰ(phosphatidylethanolamine-binding proteinⅠ)在两类组织中的表达水平及临床意义.结果表明,亚健康便秘人群和健康志愿者的结肠黏膜组织蛋白表达存在差异,β-actin、YWHAZ表达下调及PBP-Ⅰ上调参与了亚健康便秘的发生,对此状态进行合理干预,可使身体向健康转化.     

人源Fank1蛋白质FN3结构域多肽的原核表达，纯化及晶体筛选

目的纯化人源Fank1（fibronectin type Ⅲ and ankyrin repeat domain1）蛋白质N端FN3（fibronectin typeⅢ,Ⅲ型纤黏连蛋白）结构域蛋白,用于晶体生长的三维结构分析。方法将FN3结构域基因片段克隆至原核表达载体pGEX-6P-1中,将菌落PCR和测序鉴定正确的重组质粒转化E.coli BL21（DE3）后获得表达菌株。该菌株经IPTG诱导高效表达出带有GST标签的可溶性的融合蛋白,经过Glutathione Sepha-rose^TM 4B亲和层析、Hiload16／60 superdex200分子筛层析纯化后,蛋白纯度达到95％以上。结果纯化蛋白采用悬滴气相扩散法得到棒状晶体。结论成功制备了高纯度FN3蛋白,获得FN3蛋白质晶体,为进一步的三维结构解析及Fank1功能研究奠定了基础。     

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.     

双向凝胶电泳-飞行时间质谱技术鉴定食管上皮细胞癌变时14-3-3 protein ε、S100A9的表达

[摘要] 目的：分析食管鳞癌和正常食管上皮细胞蛋白质的表达差异,获取鉴别两者的分子标志物。方法：通过激光捕获显微切割技术分离ESCC肿瘤细胞和癌旁上皮细胞,通过双向电泳和质谱技术鉴定表达异常的蛋白,并通过蛋白免疫印记证实部分差异蛋白的表达。结果：建立了食管癌组织和正常食管上皮蛋白的双向凝胶电泳图谱,通过质谱技术鉴定出14-3-3 protein ε、S100A9等蛋白在食管癌变时差异表达,蛋白印记结果证实14-3-3 protein ε、S100A9的表达量在食管癌变时分别上调和下调。结论：激光捕获显微切割是蛋白质组研究中的一个突破性的技术,可以有效地解决组织异质性的问题;本实验检测到的差异蛋白例如14-3-3 protein ε、S100A9可能成为鉴别食管癌组织和正常食管上皮特异性的分子标记物。     

双孢蘑菇子实体发育不同阶段蛋白质组分析

为探讨双孢蘑菇子实体发育不同阶段的蛋白质表达变化,对双孢蘑菇As2796菌株子实体原基期、幼菇期、采收期、开伞期的蛋白质组进行了二维液相色谱串联质谱（iTRAQ-MS/MS）分析,共获得不同肽段5 869个,鉴定到1 059个蛋白质,其中1 007个具有相对定量信息。与双孢蘑菇原基期相比,幼菇期、采收期和开伞期分别有差异蛋白质242、200、240个,分别占鉴定蛋白质总数的24.0%,19.9%和23.8%。对这些蛋白质及不同阶段之间的差异蛋白质进行了系列生物信息学分析,对8个上、下调表达具有连续性的差异蛋白质相关基因进行了荧光定量PCR验证,其中3个蛋白质（错配碱基识别蛋白、细胞色素C1及某推定的未知蛋白质）基因的转录与蛋白质的表达具有较为一致的趋势。这些结果为后续双孢蘑菇子实体发育相关基因的功能研究奠定了良好的基础。     

小鼠晶体蛋白质组的双向电泳和质谱鉴定研究

目的应用双向电泳和质谱技术研究5周龄小鼠晶体蛋白质组。方法提取小鼠晶体总蛋白,进行固相pH梯度（IPG）等电聚焦双向电泳,胶体考马斯亮蓝R-250染色,使用PDQuest7．30图像分析软件分析电泳图像。选择主要蛋白点胶上酶解,应用基质辅助激光解析电离飞行时间／飞行时间（MALDI—TOF／TOF）仪器进行串联质谱（MS／MS）鉴定。结果上样量为882μg和190μg时,分别检测370±41蛋白点（n=3）和57±5个蛋白点（n=3）。高上样量能够较好地分离晶体低丰度蛋白,如念珠状纤维结构蛋白BFSP;低上样量可很好地分离高丰度蛋白-晶体蛋白（包括αA、αB;βA1～βA4;βB1～βB3;γA～γF和γS等）。质谱鉴定得到1种细胞骨架蛋白和16种高丰度晶体蛋白。结论双向电泳和质谱技术有效考察了晶体总蛋白质,为分析白内障形成过程中蛋白质的表达改变提供了新的方法和途径。     

热蛋白质组学分析：一种全面评估蛋白质状态的技术

热蛋白质组学分析（thermal proteome profiling,TPP）是细胞热漂移测定（cellular thermal shift assay,CETSA）与定量质谱（quantitative mass spectrometry,MS）的结合,所以也称为MS-CETSA。热蛋白质组学分析通过测量不同加热温度下细胞或细胞裂解物中可溶蛋白的含量来确定整个蛋白质组的稳定性。蛋白质可以在与药物或代谢物等小分子、核酸或其他蛋白质相互作用或在翻译后修饰时改变其热稳定性,而热蛋白质组学分析可以根据有无配体结合蛋白质的热稳定性差异来确定靶蛋白。目前热蛋白质组学分析已成功应用于识别药物的靶点和脱靶点,探究蛋白质-代谢物和蛋白质-蛋白质的相互作用。总体上,国内对这个技术的了解仍然欠缺,对此,文中对热蛋白质组学分析的原理、方法、应用以及优势与局限性进行了综述。     

酵母双杂交系统筛选GATA-1相互作用蛋白质及功能验证

目的 利用酵母双杂交技术从人脑cDNA文库中筛选与人GATA-1相互作用的蛋白质.方法 从人K562细胞中扩增出全长GATA1基因,设计引物将其3段截断体亚克隆入酵母表达载体pDBLeu中,转化至AH109感受态酵母中,利用酵母双杂交技术筛选人脑cDNA文库中与其相互作用的蛋白质,阳性克隆通过回转及免疫共沉淀试验进行验证,利用3xGATA荧光素酶报告基因对相互作用蛋白质进行功能验证.结果 成功构建出酵母诱饵蛋白表达质粒pDBLeu-GATA1（1）,pDBLeu-GATA1（2）,pDBLeu-GATA1（3）,筛到34个阳性克隆,用生物信息学分析及回转验证得到5个与GATA-1相互作用的候选蛋白,通过免疫共沉淀试验进一步验证,获得3个蛋白质能与GATA-1相互作用,分别是ECSIT,EFEMP1和GPS2.荧光素酶试验表明这3个蛋白质均能对GATA1的转录活性产生影响,证实它们之间的相互作用具有影响GATA1转录的功能.结论 应用酵母双杂交技术及免疫共沉淀试验,从人脑cDNA文库中成功获得3个与GATA-1相互作用并对其转录活性具有调节作用的蛋白质,为研究GATA1蛋白质的功能提供了新的线索.     

Proteomic analysis of infiltrating ductal carcinoma tissues by coupled 2-D DIGE/MS/MS analysis

There is a growing interest in protein expression profiling aiming to identify novel diagnostic markers in breast cancer. Proteomic approaches such as two-dimensional differential gel electrophoresis coupled with tandem mass spectrometry analysis (2-D DIGE/MS/MS) have been used successfully for the identification of candidate biomarkers for screening, diagnosis, prognosis and monitoring of treatment response in various types of cancer. Identifying previously unknown proteins of potential clinical relevance will ultimately help in reaching effective ways to manage the disease. We analyzed breast cancer tissues from five tumor and five normal tissue samples from ten breast cancer subjects with infiltrating ductal carcinoma (IDC) by 2-D DIGE using two types of immobilized pH gradient (IPG) strips: pH 3-10 and pH 4-7. From all the spots detected, differentially expressed (p < 0.05 and ratio > 2) were 50 spots. Of these, 39 proteins were successfully identified by MS, representing 29 different proteins. Ten proteins were overexpressed in the tumor samples. The 2-D DIGE/MS/MS analysis revealed an increase in the expression levels in tumor samples of several proteins not previously associated with breast cancer, such as: macrophage-capping protein (CAPG), phosphomannomutase 2 (PMM2), ATPase ASN1, methylthioribose-1-phosphate isomerase (MRI1), peptidyl-prolyl cis-trans isomerase FKBP4, cellular retinoic acid-binding protein 2 (CRABP2), lamin B1 and keratin, type II cytoskeletal 8 (KRT8). Ingenuity Pathway Analysis (IPA) revealed highly significant (p = 10(-26)) interactions between the identified proteins and their association with cancer. These proteins are involved in many diverse pathways and have established roles in cellular metabolism. It remains the goal of future work to test the suitability of the identified proteins in samples of larger and independent patient groups.     

Serum differential protein identification of Xinjiang Kazakh esophageal cancer patients based on the two-dimensional liquid-phase chromatography and LTQ MS

The aim of this study was to investigate the impact of chemo-radiotherapy on serum protein expression of the esophageal cancer patients and discover potential biomarkers by detecting serum proteins mass spectrometry of the healthy Kazakh people in Xinjiang as well as the patients before and after their chemo-radiotherapy. In order to separate and compare the three serum samples (the healthy group’s, the patients’ before and after chemo-radiotherapy) with two-dimensional protein liquid chromatography system (Proteome LabTM PF-2D), then detect the differential protein spots with linear trap quadruple mass spectrometer (LTQ MS/MS). (1) The Kazakh esophageal cancer patients got 21 expressed protein spots peaks with significant difference after chemo-radiotherapy compared with before; before the treatment there were 10 different expressed protein spots compared with the healthy group, and after it there were four peaks in the expression of protein spots compared with the healthy group. (2) After LTQ mass spectrometric detection, 22 proteins were up-regulated in serum samples of the healthy group, 22 were up-regulated of the patients before medical treatment and 5 were up-regulated after chemo-radiotherapy. (3) 8 proteins including APOA1 can be served as serum markers in Kazakh esophageal cancer diagnosis, and proteins like CLU can be served as serum markers in judging the resistance and sensitivity towards chemo-radiotherapy. (4) The abnormal expressions of APOC2, APOC3, Antithrombin-III in esophageal cancer were discovered for the first time. Specific protein spots related to Xinjiang Kazakh esophageal cancer diagnosis and chemo-radiotherapy can be identified in the serum, which will probably become a maker in Kazakh esophageal cancer diagnosis and therapeutic evaluation.     

基于蛋白互作网络识别非小细胞肺癌相关基因功能模块

本研究对非小细胞肺癌(non-small cell lung carcinoma,NSCLC)基因表达数据进行差异表达分析,并与蛋白质相互作用网络(PPIN)数据进行整合,进一步利用Heinz搜索算法识别NSCLC相关的基因功能模块,并对模块中的基因进行功能(GO term)和通路(KEGG)富集分析,旨在探究肺癌发病分子机制。蛋白互作网络分析得到一个包含96个基因和117个相互作用的功能模块,以及8个对NSCLC的发生和发展起到关键作用候选基因标志物。富集分析结果表明,这些基因主要富集于基因转录催化及染色质调控等生物学过程,并在基础转录因子、黏着连接、细胞周期、Wnt信号通路及HTLV-Ⅰ感染等生物学通路中发挥重要作用。本研究对非小细胞肺癌相关的基因和生物学通路进行预测,可用于肺癌的早期诊断和早期治疗,以降低肺癌死亡率。     

Subproteomic analysis of the cellular proteins associated with the 3' untranslated region of the hepatitis C virus genome in human liver cells

The 3' untranslated region (UTR) of the hepatitis C virus (HCV) is believed to function in the initiation and regulation of viral RNA replication and protein translation by interacting with the viral and host components. To examine host proteins interacting with the HCV 3'UTR, biotinylated 3'(+)UTR, and its reverse complementary 5'(-)UTR were used in RNA pull-down assay. Cellular proteins from Huh7 cells pulled down by biotinylated RNAs were identified by 2DE/MALDI-TOF MS and 1DE/LC/MS methods. Totally, 10 proteins could be identified from both methods, among which six bound specifically to the 3'(+)UTR, three proteins to the 5'(-)UTR only, and one protein bound to both. Three identified proteins (PCBP2, G3BP1, and DDX1) were selected for further investigation into their possible roles on the HCV replication. Differently regulating effects on HCV replication by siRNA-mediated silencing of these proteins were observed, indicating a complex role of 3'UTR binding proteins on HCV replication.     

Characterization of the Proteome of Theobroma cacao Beans by Nano‐UHPLC‐ESI MS/MS

Cocoa seed storage proteins play an important role in flavour development as aroma precursors are formed from their degradation during fermentation. Major proteins in the beans of Theobroma cacao are the storage proteins belonging to the vicilin and albumin classes. Although both these classes of proteins have been extensively characterized, there is still limited information on the expression and abundance of other proteins present in cocoa beans. This work is the first attempt to characterize the whole cocoa bean proteome by nano‐UHPLC‐ESI MS/MS analysis using tryptic digests of cocoa bean protein extracts. The results of this analysis show that >1000 proteins could be identified using a species‐specific Theobroma cacao database. The majority of the identified proteins were involved with metabolism and energy. Additionally, a significant number of the identified proteins were linked to protein synthesis and processing. Several proteins were also involved with plant response to stress conditions and defence. Albumin and vicilin storage proteins showed the highest intensity values among all detected proteins, although only seven entries were identified as storage proteins. A comparison of MS/MS data searches carried out against larger non‐specific databases confirmed that using a species‐specific database can increase the number of identified proteins, and at the same time reduce the number of false positives. The results of this work will be useful in developing tools that can allow the comparison of the proteomic profile of cocoa beans from different genotypes and geographic origins. Data are available via ProteomeXchange with identifier PXD005586.     

Proteomics analysis of mature seed of four peanut cultivars using two-dimensional gel electrophoresis reveals distinct differential expression of storage, anti-nutritional, and allergenic proteins

Profiles of total seed proteins isolated from mature seeds of four peanut cultivars, New Mexico Valencia C (NM Valencia C), Tamspan 90, Georgia Green, and NC-7, were studied using two-dimensional gel electrophoresis coupled with nano-electrospray ionization liquid chromatography tandem mass spectrometry (nESI-LC–MS/MS). Two-dimensional gels stained with silver nitrate revealed a total of 457, 516, 556, and 530 protein spots in NM Valencia C, Tamspan 90, Georgia Green, and NC-7, respectively. Twenty abundant protein spots showing differences in relative abundance among these cultivars were analyzed by nESI-LC–MS/MS, resulting in identification of 14 non-redundant proteins. The majority of these proteins belonged to the globulin fraction consisting of arachin (glycinin and Arah3/4) and conarachin seed storage proteins as well as other allergen proteins. The expression of some of these identified protein spots was cultivar-specific. For example, allergen Arah3/Arah4 and conarachin protein spots were only detected in Tamspan 90 and NC-7, whereas the Gly1 protein spot was detected only in NM Valencia C and NC-7. Moreover, a galactose-binding lectin protein spot with anti-nutritive properties was only present in Tamspan 90. Other proteins showing differences in relative abundance among the four cultivars included 13-lipoxygenase, fructose-biphosphate aldolase, and glyceraldehyde 3-phosphate dehydrogenase. Together, these results suggest that identified proteins might serve as potential markers for cultivar differentiation and may be associated with underlying sensory and nutritional traits of peanut cultivars.     

Study of rat hypothalamic proteome by HPLC/ESI ion trap and HPLC/ESI‐Q‐TOF MS

The proteomic profile of hypothalamus, a key organ of CNS, is explored here by employing two widely used MS techniques, i.e. HPLC/ESI‐ion trap and HPLC/ESI‐quadrupole‐TOF MS. Strong cation exchange is used for the fractionation of peptides and protein search engine MASCOT is employed for data query. One hundred and thirty six proteins with 10 973 peptides were identified by HPLC/ESI‐ion trap MS, while 140 proteins with 32 183 peptides were characterized by HPLC/ESI‐quadrupole‐TOF MS. Among the total 198 proteins identified in both experiments, 78 proteins were common in both sets of conditions. The rest of the 120 proteins were identified distinctly in both MS strategies, i.e. 58 unique proteins were found using the quadrupole‐TOF while 62 were found with the HPLC/ESI‐ion trap. Moreover, these proteins were classified into groups based on their functions performed in the body. Results presented here identified some important signal and cellular defense proteins inevitable for survival in stressed conditions. Additionally, it is also shown that any single MS strategy is not reliable for good results due to loss of data depending on sensitivity of the instrument used.