基于序列保守性和蛋白质相互作用的真核蛋白质亚细胞定位预测

蛋白质的亚细胞定位是进行蛋白质功能研究的重要信息.蛋白质合成后被转运到特定的细胞器中,只有转运到正确的部位才能参与细胞的各种生命活动,有效地发挥功能.尝试了将保守序列及蛋白质相互作用数据的编码信息结合传统的氨基酸组成编码,采用支持向量机进行蛋白质亚细胞定位预测,在真核生物中5轮交叉验证精度达到91.8%,得到了显著的提高.     

蛋白质亚叶绿体和亚线粒体定位预测研究进展

蛋白质合成后被转运到特定的细胞器中,只有转运到正确的部位才能参与细胞的各种生命活动,有效地发挥功能,因此蛋白质的功能与其亚细胞定位有着密切的联系,通过确定蛋白质在细胞中的位置可以获取蛋白质功能和结构的信息。在近二十年中,蛋白质亚细胞定位预测算法研究已经取得很大的成绩,在此基础上,蛋白质在细胞器内亚结构的定位预测研究,如对蛋白质亚线粒体和亚叶绿体定位的研究成为更深层次的问题,本文简要介绍国内外在蛋白质亚叶绿体和亚线粒体定位预测方面的研究进展。     

蛋白质相互作用调控蛋白质核转运及其功能

蛋白质的核转运是真核生物细胞内发生的重要过程之一,是一大群蛋白质发挥其功能的前提,与细胞正常功能的维持密切相关。蛋白质的核运输通常采用核受体介导的方式进行。此过程非常复杂,需要多种蛋白质的参与,涉及到大量的蛋白质相互作用。本文将综合近年来本领域取得的进展,就蛋白质相互作用参与蛋白质核转运来调节蛋白质的亚细胞定位,进一步在多方面影响细胞以及生物体生理功能的变化进行阐述。     

细胞内蛋白质转运及其在医学中的应用——1999年诺贝尔生理学或医学奖介绍及其相关研究进展

细胞表达出大量的蛋白质,分布到细胞不同的部位执行相应的功能,其中多数被转运到细胞外和细胞核,或定位于细胞内不同的细胞器.新合成的蛋白质是如何跨过膜性结构被转运到相应正确位置的呢? 细胞生物学家Günter Blobel对此给出了答案.     

植物细胞外源蛋白亚细胞定位的机制及其应用

为将不同的生理功能区隔化,植物细胞分化出具有特异性结构特征的细胞器.分化的细胞内膜系统和分子水平的蛋白质转运调控机制为外源蛋白亚细胞定位表达提供了显著的有利条件.当蛋白质被加载适当的定位信号或启动子时,蛋白质的分选途径便确定下来,同时决定蛋白质的表达终点.本文根据相关研究主题分析了蛋白质亚细胞定位机制,重点阐述包括ER腔、质外体、液泡、蛋白体等细胞器和内膜结构在内的蛋白定位因素,同时探讨了目前蛋白定位因素的应用情况.本文确定亚细胞定位因素将成为植物基因工程领域控制亚细胞水平表达的重要技术策略.     

蛋白质体积对其亚细胞定位的影响

蛋白质亚细胞定位信息对深入研究蛋白质的细胞生物学功能十分重要.通过Helix Systems在线计算程序和Vor计算程序两种方法讨论了蛋白质的体积对其亚细胞定位的影响,发现定位于细胞外的蛋白质体积显著小于定位于细胞核、细胞膜和细胞质的蛋白体积,证实了体积参数对区分蛋白质的亚细胞定位是有效的.     

拟南芥膜联蛋白2的亚细胞定位研究

膜联蛋白(annexin)是一类依赖钙离子的多功能磷脂结合蛋白家族,在进化上高度保守,但不同的膜联蛋白基因的表达模式和蛋白质的亚细胞定位具有特异性。拟南芥中已经鉴定出8个编码膜联蛋白的基因,在生长发育和对逆境胁迫响应过程中起作用。已知拟南芥膜联蛋白2参与根的分泌活动和生长素介导的根的向地性反应,但作用机制不清楚。蛋白质的亚细胞定位能为研究其功能和作用机制提供重要参考信息。将编码膜联蛋白2的序列克隆到植物双元表达载体p CAMBIA1300-m Cherry上,在拟南芥中表达Ann At2-m Cherry。利用荧光蛋白技术、m Cherry与绿色荧光蛋白标记的细胞器标记物共定位技术以及细胞器特异性荧光染料染色技术,作者研究了膜联蛋白2的亚细胞定位。结果显示,膜联蛋白2定位于细胞质、细胞核、高尔基体和内质网中,表明该蛋白质可能具有非常重要的功能和复杂的蛋白质翻译与转运调控机制。更多结果发现,转基因拟南芥中膜联蛋白2与绿色荧光蛋白标记的微丝骨架存在共定位现象,推测该蛋白可能通过微丝骨架调节及微丝骨架介导的囊泡运输参与细胞分泌活动。该文为进一步研究膜联蛋白2蛋白质的翻译与转运调控以及作用机制提供了实验依据。     

植物蛋白质亚细胞定位相关研究概述

蛋白质在植物细胞内的定位是了解蛋白质功能、基因调控和蛋白质-蛋白质相互作用的关键。近年来随着各种蛋白质亚细胞定位方法的快速发展和技术的不断提升,蛋白质亚细胞定位实现了高通量、活体动态研究。本文总结了植物蛋白质亚细胞定位的常用技术,以及常用细胞器特异性标记的研究进展,并对此领域研究的发展前景做出了展望。     

大肠杆菌周质和外膜蛋白的定位

大肠杆菌周质和外膜蛋白发挥功能必须首先到达其特定亚细胞分区.大肠杆菌通过一系列与蛋白质分泌有关的蛋白（Sec蛋白）将周质和外膜蛋白转运至内膜.在切除了信号肽后,与周质蛋白的定位不同的是,外膜蛋白的最终定位还需要其他因子的协助.外膜蛋白的定位近来认为是以周质作为中介的.     

快速发展的亚细胞蛋白质组学

亚细胞蛋白质组是蛋白质组学领域中的一支新生力量 ,已成为蛋白质组学新的主流方向 ,通过多种策略和技术方法 ,一些重要的亚细胞结构的蛋白质组不断的得到分析 ,到目前为止 ,几乎所有亚细胞结构的蛋白质组学研究都有报道 ,而且已经深入到亚细胞器和复合体水平 ;另外 ,不仅局限于对亚细胞结构的蛋白组成进行简单分析 ,而且更注重功能性分析 ,将定量技术和差异分析引入亚细胞蛋白质组学 ,来观察此亚细胞结构的蛋白质组在某些生理或病理条件下的变化 ,这已经成为亚细胞蛋白质组学新的发展方向 .亚细胞蛋白质组学最大的困难在于怎样确认鉴定出来蛋白质的定位 ,是在提取过程中的污染还是真正在此亚细胞结构中有定位 ?这将是亚细胞蛋白质组学需要努力解决的挑战 .文章全面介绍了亚细胞蛋白质组学的最新研究进展 ,阐述了亚细胞蛋白质组学面临的挑战 ,并对亚细胞蛋白质组学的发展方向作了展望 .     

Predicting subcellular localization with AdaBoost Learner

Protein subcellular localization, which tells where a protein resides in a cell, is an important characteristic of a protein, and relates closely to the function of proteins. The prediction of their subcellular localization plays an important role in the prediction of protein function, genome annotation and drug design. Therefore, it is an important and challenging role to predict subcellular localization using bio-informatics approach. In this paper, a robust predictor, AdaBoost Learner is introduced to predict protein subcellular localization based on its amino acid composition. Jackknife cross-validation and independent dataset test were used to demonstrate that Adaboost is a robust and efficient model in predicting protein subcellular localization. As a result, the correct prediction rates were 74.98% and 80.12% for the Jackknife test and independent dataset test respectively, which are higher than using other existing predictors. An online server for predicting subcellular localization of proteins based on AdaBoost classifier was available on http://chemdata.shu. edu.cn/sl12.     

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。     

Localization of organelle proteins by isotope tagging (LOPIT)

We describe a proteomics method for determining the subcellular localization of membrane proteins. Organelles are partially separated using centrifugation through self-generating density gradients. Proteins from each organelle co-fractionate and therefore exhibit similar distributions in the gradient. Protein distributions can be determined through a series of pair-wise comparisons of gradient fractions, using cleavable ICAT to enable relative quantitation of protein levels by MS. The localization of novel proteins is determined using multivariate data analysis techniques to match their distributions to those of proteins that are known to reside in specific organelles. Using this approach, we have simultaneously demonstrated the localization of membrane proteins in both the endoplasmic reticulum and the Golgi apparatus in Arabidopsis. Localization of organelle proteins by isotope tagging is a new tool for high-throughput protein localization, which is applicable to a wide range of research areas such as the study of organelle function and protein trafficking.     

Quantitative Protein Localization Signatures Reveal an Association between Spatial and Functional Divergences of Proteins

Protein subcellular localization is a major determinant of protein function. However, this important protein feature is often described in terms of discrete and qualitative categories of subcellular compartments, and therefore it has limited applications in quantitative protein function analyses. Here, we present Protein Localization Analysis and Search Tools (PLAST), an automated analysis framework for constructing and comparing quantitative signatures of protein subcellular localization patterns based on microscopy images. PLAST produces human-interpretable protein localization maps that quantitatively describe the similarities in the localization patterns of proteins and major subcellular compartments, without requiring manual assignment or supervised learning of these compartments. Using the budding yeast Saccharomyces cerevisiae as a model system, we show that PLAST is more accurate than existing, qualitative protein localization annotations in identifying known co-localized proteins. Furthermore, we demonstrate that PLAST can reveal protein localization-function relationships that are not obvious from these annotations. First, we identified proteins that have similar localization patterns and participate in closely-related biological processes, but do not necessarily form stable complexes with each other or localize at the same organelles. Second, we found an association between spatial and functional divergences of proteins during evolution. Surprisingly, as proteins with common ancestors evolve, they tend to develop more diverged subcellular localization patterns, but still occupy similar numbers of compartments. This suggests that divergence of protein localization might be more frequently due to the development of more specific localization patterns over ancestral compartments than the occupation of new compartments. PLAST enables systematic and quantitative analyses of protein localization-function relationships, and will be useful to elucidate protein functions and how these functions were acquired in cells from different organisms or species. A public web interface of PLAST is available at http://plast.bii.a-star.edu.sg.     

Protein subcellular localization prediction based on compartment-specific features and structure conservation

Background  

Protein subcellular localization is crucial for genome annotation, protein function prediction, and drug discovery. Determination of subcellular localization using experimental approaches is time-consuming; thus, computational approaches become highly desirable. Extensive studies of localization prediction have led to the development of several methods including composition-based and homology-based methods. However, their performance might be significantly degraded if homologous sequences are not detected. Moreover, methods that integrate various features could suffer from the problem of low coverage in high-throughput proteomic analyses due to the lack of information to characterize unknown proteins.     

蛋白质通量化定位体系的建立及初步应用

目的:对于蛋白质功能而言,蛋白质定位与蛋白质的表达和修饰等同等重要。传统的蛋白质定位一直沿用单个基因、逐个的研究方法,本实验拟建立一种通量蛋白质定位研究体系。方法:采用并优化了细胞微阵列技术,结合绿色荧光蛋白(GFP)标签、激光扫描共聚焦显微镜及反转染技术,用于大规模蛋白质定位研究。结果:初步建立的蛋白质定位微阵列包含107个GFP标记的cDNA表达载体,分别编码107个重要细胞信号传导通路的蛋白质,并与定位数据库中的已知结果进行了比对;对该系统的有效性进行了验证评价。结论:本定位系统可有效地用于通量化蛋白质定位研究,并可以发展用于蛋白质相互作用、泛素-蛋白酶体通路底物筛选等进一步的功能研究。     

The sequences of MinE responsible for its subcellular localization analyzed by competitive binding method in <Emphasis Type="Italic">Escherichia coli</Emphasis>

The subcellular localization of a protein is important for its proper function. Escherichia coli MinE is a small protein with clear subcellular localization, which provides a good model to study protein localization mechanism. In the present study, a series of recombinant minEs truncated in one end or in the middle regions, fused with egfp, was constructed, and these recombinant proteins could compete to function with the chromosomal MinE. Our results showed that the sequences related to the subcellular localization of MinE span several functional domains, demonstrating that MinE positioning in cells depends on multiple factors. The eGFP fusions with some truncated MinE from N-terminal resulted in different cell phenotypes and localization features, implying that these fusions can interfere chromosomal MinE’s function, similar to MinE^36–88 phenotype in the previous report. The amino acid in the region (32–48) is sensitive to change MinE conformation and influence its dimerization. Some truncated protein structure could be unstable. Thus, the MinE localization is prerequisite for its proper anti-MinCD function and some new features of MinE were demonstrated. This approach can be extended for subcellular localization research for other essential proteins.     

PBX1 nuclear export is regulated independently of PBX-MEINOX interaction by PKA phosphorylation of the PBC-B domain

The regulation of PBC protein function through subcellular distribution is a crucial evolutionarily conserved mechanism for appendage patterning. We investigated the processes controlling PBX1 nuclear export. Here we show that in the absence of MEINOX proteins nuclear export is not a default pathway for PBX1 subcellular localization. In different cell backgrounds, PBX1 can be imported or exported from the nucleus independently of its capacity to interact with MEINOX proteins. The cell context-specific balance between nuclear export and import of PBX1 is controlled by the PBC-B domain, which contains several conserved serine residues corresponding to phosphorylation sites for Ser/Thr kinases. PBX1 subcellular localization correlates with the phosphorylation state of these residues whose dephosphorylation induces nuclear export. Protein kinase A (PKA) specifically phosphorylates PBX1 at these serines, and stimulation of endogenous PKA activity in vivo blocks PBX1 nuclear export in distal limb mesenchymal cells. Our results reveal a novel mechanism for the control of PBX1 nuclear export in addition to the absence of MEINOX protein, which involves the inhibition of PKA-mediated phosphorylation at specific sites within the PBC-B domain.