蛋白质亚细胞定位预测研究进展

蛋白质的功能与其在细胞中的定位有着密切的联系,新合成的蛋白质必须处于适当的亚细胞位置才能正确的行使其功能．预测蛋白质的亚细胞定位,在确定一个未知蛋白质的功能,了解蛋白质相互作用等方面有着重要的意义．机器学习方法在蛋白质亚细胞定位研究中扮演着一个重要的角色．笔者从数据集的构建、蛋白质序列特征提取方法、蛋白质亚细胞定位预测算法以及预测算法的性能评估等四方面总结了过去十几年间机器学习方法在蛋白质亚细胞定位研究中的应用情况,系统阐述了蛋白质亚细胞定位预测研究的进展．     

蛋白质组学用于疾病特殊蛋白质的鉴定

蛋白质组学是一门新的启动技术.它将便利越过一切生物学系统或疾病的蛋白质系统分析.在疾病特殊蛋白质的鉴别过程蛋白质组学高度补充基因组方法,且第一次提供科学家使蛋白质组信息,表达mRNA,它们各自的蛋白质和亚细胞定位一体化的能力.期望会导致对疾病机制新的重大认识.     

Hypervariable C-terminal domain of rab proteins acts as a targeting signal

Mammalian cells express many ras-like low molecular mass GTP-binding proteins (rab proteins) that are highly homologous to the Ypt1 and Sec4 proteins involved in controlling secretion in yeast. Owing to their structural similarity and to their variety, rab proteins have been postulated to act as specific regulators of membrane traffic in exocytosis and endocytosis, and rab5 has been shown to be involved in early endosome fusion in vitro. In agreement with their postulated functions, all rab proteins studied so far have been found in distinct subcompartments along the exocytic or endocytic pathways. To define the region mediating their specific localization, we transiently expressed rab2, rab5 and rab7 hybrid proteins in BHK cells, and determined their intracellular localization by immunofluorescence confocal microscopy and subcellular fractionation. Here we present evidence that the highly variable C-terminal domain contains structural elements necessary for the association of rab proteins with their specific target membranes in the endocytic pathway.     

嗜水气单胞菌感染暗纹东方鲀脾脏的蛋白质组学分析

为了解暗纹东方鲀(Takifugu obscurus)受到病原菌感染后参与应答的主要蛋白的功能与调控作用,采用TMT标记、高效液相色谱(HPLC)分级技术以及基于质谱的定量蛋白质组学技术,分析了暗纹东方鲀感染嗜水气单胞菌(Aeromonas hydrophila) 12 h后脾脏组织的蛋白表达水平,鉴定差异表达蛋白,并通过亚细胞定位、GO(Gene Oncology)和KEGG(Kyoto Encyclopedia of Genes and Genomes)对差异表达蛋白进行进一步分析.本次实验共鉴定到306个差异表达蛋白,其中120个上调表达蛋白,186个下调表达蛋白;利用平行反应检测实验(PRM)对4个(1个上调,3个下调)与免疫相关的差异蛋白进行验证,其结果与蛋白质测序结果一致;亚细胞定位结果显示:差异表达蛋白主要定位在细胞质、细胞核和胞外; GO分析发现:差异表达蛋白参与的主要生物进程有代谢过程、细胞进程和单一生物进程,主要的分子功能有结合、催化活性和机构分析活性; KEGG通路分析结果显示:差异表达蛋白主要参与了核糖体、视黄醇代谢、卟啉和叶绿素代谢、ECM受体相互作用、吞噬体...     

胃癌下调新基因GDDR表达特性及功能研究

明确胃癌下调新基因GDDR的亚细胞定位、分泌特性及生物学功能研究.与绿色荧光蛋白(GFP)融合表达明确GDDR表达产物亚细胞定位;GES细胞系转染上清检测分泌蛋白表达;胃癌7901细胞系稳定转染GDDR,观察其生物学作用.发现GDDR表达产物定位于胞浆,是一分泌蛋白.四甲基偶氮唑盐比色法(MTT assay)检测描绘生长曲线及流式细胞计数仪(FACS)细胞周期检测表明,GDDR对胃癌7901细胞增值显著抑制(96 h(1.233±0.017) vs (0.618±0.015), t =2.447, P =2.63×10-9),并且可以引起细胞的周期阻滞.说明胃癌下调新基因GDDR产物为胞浆分布,具有分泌特性,能通过阻滞细胞周期显著抑制胃癌细胞生长,可能为新的候选抑癌基因.     

壳寡糖及其衍生物对CCl4诱导的小鼠肝损伤的保护作用

研究壳寡糖（COS）、氨基葡萄糖（GlcNH2）和N-乙酰氨基葡萄糖(GlcNAc)对CCl4诱导的雄性昆明种小鼠肝毒性的保护作用,并探讨其可能机制. 小鼠腹腔注射CCl4（20mg/kg体重）24h后,血清天门冬氨酸转氨酶(AST)和丙氨酸转氨酶(ALT)活性明显提高,引起肝脏脂质过氧化反应,巯基含量降低,总抗氧化能力（T-AOC）减弱,诱发基因毒性. 提前连续12天分别灌胃给予COS,GlcNH2 和GlcNAc（1.5g/kg体重）能够显著诱导金属硫蛋白（MT）的表达,体内的抗氧化防御系统随之增强以抵抗CCl4诱导的氧化损伤. 血清AST和ALT活性明显降低,肝脏丙二醛（MDA）生成被抑制,巯基含量,T-AOC明显恢复. 但是,从DNA电泳结果反应出的基因毒性并未减轻. 实验结果证明,提前给予COS,GlcNH2和GlcNAc对CCl4诱导的小鼠肝损伤能够起到有效的保护作用,其中,GlcNH2的作用效果最显著.     

家蚕血液肽聚糖识别蛋白的鉴定和生物信息学分析

采用双向电泳和质谱技术分析、鉴定了家蚕血液中存在的肽聚糖识别蛋白(PGRP).为了进一步研究该蛋白的结构和功能,采用了生物信息学方法对其理化性质、疏水性/亲水性、信号肽、二级结构、三级结构、亚细胞定位和GO功能注释等进行了分析.结果发现,肽聚糖识别蛋白是一种分泌类蛋白,可能具有信号肽.其主要分子功能为肽聚糖受体,在生物学进程中发挥的主要作用为肽聚糖代谢和先天性免疫应答.     

CAP defines a second signalling pathway required for insulin-stimulated glucose transport

Insulin stimulates the transport of glucose into fat and muscle cells. Although the precise molecular mechanisms involved in this process remain uncertain, insulin initiates its actions by binding to its tyrosine kinase receptor, leading to the phosphorylation of intracellular substrates. One such substrate is the Cbl proto-oncogene product. Cbl is recruited to the insulin receptor by interaction with the adapter protein CAP, through one of three adjacent SH3 domains in the carboxy terminus of CAP. Upon phosphorylation of Cbl, the CAP-Cbl complex dissociates from the insulin receptor and moves to a caveolin-enriched, triton-insoluble membrane fraction. Here, to identify a molecular mechanism underlying this subcellular redistribution, we screened a yeast two-hybrid library using the amino-terminal region of CAP and identified the caveolar protein flotillin. Flotillin forms a ternary complex with CAP and Cbl, directing the localization of the CAP-Cbl complex to a lipid raft subdomain of the plasma membrane. Expression of the N-terminal domain of CAP in 3T3-L1 adipocytes blocks the stimulation of glucose transport by insulin, without affecting signalling events that depend on phosphatidylinositol-3-OH kinase. Thus, localization of the Cbl-CAP complex to lipid rafts generates a pathway that is crucial in the regulation of glucose uptake.     

PX domain and CD domain play different roles in localization and vacuolation of Sorting Nexin 10

Sorting nexins （SNXs） are PX domain containing proteins and essential for intracellular protein sorting, trafficking and signal transduction. The PX domains of SNXs can bind to various phosphorelated phosphoinositides （PIs） and target the host proteins to endosomes. Recently, we have reported that overexpression of SNX10 in mammalian cells could induce giant vacuoles. In this study, we aimed to identify regions in SNX10 critical for the vacuolation activity. We found that both the PX domain and the CD1 region were essential for vacuolation. We provided evidence that the PX domain was able to specifically bind to Ptdlns（3）P and target SNX10 to endosomes. A mutation in the 131 region of the PX domain （V15A） disrupted the Ptdlns（3）P binding ability and the endosomal localization of SNX10. However, correct subcellular localization alone was not sufficient for SNX10 to induce vacuoles. We found that the CD1 region, which was not required for the localization, was indispensable for the vacuolation activity of SNX10. In summary, both the PX domain and the CD1 region are necessary for SNX10 to induce vacuoles but they play different roles in this process.     

壳寡糖纳米载体细胞内递送EGFR脱氧核酶的研究

设计靶向EGFR mRNA的脱氧核酶(EGFR DRz),以壳寡糖(COS)为材料,建立了一种有效的纳米基因细胞内传递体系,并研究其介导的靶向EGFR的脱氧核酶在Hela细胞内的生物学效应.流式结果表明COS-EGFR DRz复合体转染效率为88.7%,与脂质体转染试剂的89.7%相比无显著差异.半定量RT-PCR结果显示,经壳寡糖纳米载体递送的EGFR DRz能有效地靶向切割Hela细胞内的EGFR mRNA,使其表达下降.进一步的流式分析显示细胞被阻滞在G0～G1期,并且出现凋亡现象,其中COS组的凋亡率为19.3%,大于对照组脂质体的凋亡率13.0%.研究表明,COS较脂质体有相似的转染效率和更低的毒性,是一种潜在的、有效的脱氧核酶递送载体.     

MIXTA/MIXTA-like基因特征及其对植物表皮细胞分化的调控

植物表皮细胞是植物最外层直接与环境相互作用的细胞,依据其不同功能,分化形成多种具有防卫功能的特化细胞结构,在植物防御、减少蒸腾、授粉媒介吸引、种子散布、次生代谢产物合成与贮存等方面起着重要作用。研究发现MIXTA/MIXTA-like是多种植物表皮细胞分化的关键调控因子。在不同植物中,MIXTA/MIXTA-like作用部位(主要集中在花瓣、叶片、胚珠和子房)和调节方式不同,但最终都是通过调控表皮细胞分化发挥作用。MIXTA/MIXTA-like在表皮毛的形成、角质层生物合成、锥形表皮细胞的分化过程中起着重要的调节作用,其中植物表皮毛发育是一个研究热点。植物表皮毛有多种不同的功能:如叶片被毛是植物抵御取食昆虫的重要表型特征;法国梧桐、杨树、柳树飞絮都是种子成熟过程中表皮毛发育的结果;而黄花蒿中,青蒿素主要在腺毛中合成和储存。因此,开展植物表皮毛发育和调控机制研究具有重要意义。笔者梳理了MIXTA/MIXTA-like基因的特征及其在不同植物表皮细胞分化过程中的生物学功能,阐述了木本植物表皮毛发育调控的分子机制,为加速林木表皮毛发育相关性状的新品种培育提供借鉴。     

Research progress in quantifying the mechanical properties of single living cells using atomic force microscopy

The advent of atomic force microscopy （AFM） provides a powerful tool for investigating the behaviors of single living cells under near physiological conditions. Besides acquiring the images of cellular ultra-microstruc- tures with nanometer resolution, the most remarkable advances are achieved on the use of AFM indenting tech- nique to quantify the mechanical properties of single living ceils. By indenting single living cells with AFM tip, we can obtain the mechanical properties of cells and monitor their dynamic changes during the biological processes （e.g., after the stimulation of drugs）. AFM indentation-based mechan- ical analysis of single cells provides a novel approach to characterize the behaviors of cells from the perspective of biomechanics, considerably complementing the traditional biological experimental methods. Now, AFM indentation technique has been widely used in the life sciences, yielding a large amount of novel information that is meaningful to our understanding of the underlying mechanisms that govern the cellular biological functions. Here, based on the authors＇ own researches on AFM measurement of cellular mechani- cal properties, the principle and method of AFM indentationtechnique was presented, the recent progress of measuring the cellular mechanical properties using AFM was summa- rized, and the challenges of AFM single-cell nanomechani- cal analysis were discussed.     

一种基于最优局部信息融合的蛋白质-亚细胞定位预测方法

 基于蛋白质的合成及分选机制,提出了一种新的蛋白质亚细胞定位预测方法。先采用遍历搜索技术,找出各种亚细胞蛋白质序列分选信号和成熟蛋白质之间的最佳分割位点,把蛋白质序列分为两条子序列,计算这两条子序列中的氨基酸组份并将它们融合起来作为整条蛋白质序列的特征,然后构造用于识别每类蛋白质的最佳子分类器,再根据最大化原则组建集成分类器。在NNPSL数据集上,采用5重交叉验证方法对本文方法进行测试,原核和真核两个蛋白质序列子集分别取得94.1%和87.5%的总体预测精度。同时,此方法在一些蛋白质序列中找到的分割位点与真实生物现象相吻合,能为预测蛋白质序列的剪切位点提供参考信息。     

柴胡皂苷d对肝星状细胞的作用分析

从传统药物中寻找生物活性成分是开发抗肝纤维化药物的重要途径。人们发现中药柴胡成份柴胡皂苷d（SSd）可以抑制肝星状细胞（HSC）活化，但是相关生物学机制的研究较少。本研究以体外诱导活化的HSC为肝纤维化细胞模型，探究SSd抗肝纤维化效果及其分子机制。结果显示，SSd能够抑制HSC增殖和纤维化相关基因转录，并且可能通过激活细胞凋亡通路和抑制线粒体能量代谢两条途径诱导HSC发生凋亡。本研究表明，SSd有希望成为抗肝纤维化的潜在药物。