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.     

蛋白质合成中的核糖核酸蛋白质复合物

细胞中的RNA和RNA结合蛋白质(RNA-binding proteins,RBPs)相互作用形成核糖核酸蛋白质(ribonucleoprotein,RNP)复合物。RNP复合物分布广泛,功能众多。蛋白质生物合成包括转录及其调控、mRNA加工转运、tRNA传递、翻译及其调控等,是核酸编码的遗传信息流向活性蛋白质的过程。多种RNA分子参与这一过程,有的与对应的RNA结合蛋白质形成RNP复合物。RNP复合物的多样性和重要功能在此得到了最好的体现。该文以其中起核心作用的RNA分子为主线,对蛋白质合成中的RNP复合物进行了综述。     

蛋白质亚细胞定位的生物信息学研究

细胞中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,如果定位发生偏差,将会对细胞功能甚至生命产生重大影响.蛋白质的亚细胞定位是蛋白质功能研究的重要方面,也是生物信息学中的热点问题,数据库的构建和亚细胞定位分析及预测加速了蛋白质结构和功能的研究.     

通过核质转运调节细胞凋亡的蛋白质

凋亡,也称Ⅰ型程序性细胞死亡,是细胞在面临严重威胁时发起的保护性主动死亡机制. 凋亡对于个体的生长发育及各种生理功能具有不可或缺的作用. 作为涉及整个细胞的复杂过程,凋亡的顺利进行有赖于众多凋亡相关因子的协调合作与精确调控. 细胞受到凋亡刺激后,核内的某些蛋白质转运出核,将凋亡信号传递到核外,胞质内的多种蛋白质则转运入核,在细胞核这一信息整合的大本营直接发挥作用. 这种双向交流机制在胞核与胞质间建立起密切的联系,同时使得相关蛋白质在特定场所发挥促进或抑制凋亡的作用,确保凋亡信号及时、通畅、有序地传递. 因此,蛋白质的核质转运作为介导胞核与胞质物质交换、信号交流的关键机制,在凋亡过程中就显得尤为重要. 本文主要就核质转运的机制、通过核质转运调节凋亡的蛋白质及其作用机理作一综述.     

蛋白质的棕榈酰化修饰

棕榈酰化修饰是蛋白质翻译后脂质修饰的重要形式,是调控蛋白质的转运、稳定、定位和功能的重要机制,同时,棕榈酰化修饰还参与多种细胞生物学进程,与许多疾病的发生发展密切相关。本文主要就蛋白质棕榈酰化及其修饰酶与蛋白质功能、相关疾病的关系做一综述。     

植物病毒蛋白核质转运的研究进展

植物病毒编码一些含有核定位信号(nuclear localization signal,NLS)或者核输出信号(nuclear export signal,NES)的核质转运蛋白,这些已被验证的转运蛋白有三种类型:核输入蛋白、核输出蛋白和核质穿梭蛋白。它们通过识别寄主核质转运受体Importinα和Importinβ,介导含有经典核定位信号的蛋白质入核过程,以及寄主蛋白Ran参与,由XPO1介导的富含亮氨酸核输出信号的蛋白质出核过程。植物病毒核质转运蛋白利用寄主的转运机制,进出细胞核发挥相应功能,如介导病毒基因组的核输入和核输出、介导病毒长距离运输及系统侵染、抵抗寄主细胞启动的RNA沉默、调节寄主细胞转录活性、调控病毒的复制及表达和参与病毒症状的形成等。对植物病毒蛋白核质转运的相关研究进展进行综述,着重介绍植物病毒蛋白核质转运类型、核输入和输出信号、转运机制和生物学意义,以及寄主蛋白介导的互作等研究的最新成果。     

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。     

两种实验技术在蛋白质-蛋白质相互作用检测中的应用

蛋白质是生命活动的主要承担者。蛋白质种类繁多,结构多样,具有十分广泛的生物学功能,可作为载体蛋白、酶蛋白和信号肽等参与调控细胞内的各种代谢活动。生物体内蛋白质与其他分子的相互作用,尤其是蛋白质-蛋白质之间的相互作用,是蛋白质行使这些重要生物学功能的基础。通过研究可以相互作用的蛋白质形成的各种复合体,对揭示蛋白质的功能,更清楚地阐明细胞生长、发育、分化和凋亡的生命活动规律,为重大疾病的预防、治疗和新药开发提供了理论基础。目前科研工作者在基于分子生物学、生物化学、微生物学和生物物理学的基础上已经发展出了许多蛋白质相互作用的研究技术,本文着重对现有研究方法中的生物膜干涉技术和微量热泳动技术进行介绍和综述。     

细胞蛋白质相互作用的结构基础

随着人类基因组计划的进行 ,大量基因被发现和定位 ,基因的功能问题将成为今后研究的热点。大多数基因的最终产物是相应的蛋白质 ,因此要认识基因的功能 ,必然要研究基因所表达的蛋白质。蛋白质的功能往往体现在与其他蛋白质及 /或核酸的相互作用之中。细胞各种重要的生理过程 ,包括信号的转导 ,细胞对外界环境及内环境变化的反应等 ,都是以蛋白质间相互作用为纽带 ,并形成网络。所以 ,近年来 ,蛋白质间相互作用的研究逐渐得到重视。蛋白质分子的结构域有很多种 ,但是现在明确作为为介导蛋白质 蛋白质间相互作用的结构域并不多 ,这里取已明…     

蛋白质入核转运的机制和研究进展

细胞核膜是由外膜和内膜组成的磷脂双分子层结构,同时镶嵌一些核孔复合体（NPC）.核孔复合体是胞浆和胞核之间主动和被动转运的生理屏障.核内功能蛋白在胞浆内合成后通过核孔复合体进入胞核,这个过程除了需要NPC上核孔蛋白、胞浆内核转运受体和RanGTP等蛋白的参与外, 货物蛋白本身的结构特征在其入核转运过程中亦发挥重要作用.本文着重就蛋白入核转运的机制及近年来取得的相关进展进行综述.     

Mechanisms of receptor-mediated nuclear import and nuclear export

Nuclear transport of proteins and RNA occurs through the nuclear pore complex and is mediated by a superfamily of transport receptors known collectively as karyopherins. Karyopherins bind to their cargoes by recognition of specific nuclear localization signals or nuclear export signals. Transport through the nuclear pore complex is facilitated by transient interactions between the karyopherins and the nuclear pore complex. The interactions of karyopherins with their cargoes are regulated by the Ras-related GTPase Ran. Ran is assisted in this process by proteins that regulate its GTPase cycle and subcellular localization. In this review, we describe several of the major transport pathways that are conserved in higher and lower eukaryotes, with particular emphasis on the role of Ran. We highlight the latest advances in the structure and function of transport receptors and discuss recent examples of steroid hormone receptor import and regulation by signal transduction pathways. Understanding the molecular basis of nuclear transport may provide insight into human diseases by revealing how nucleocytoplasmic trafficking regulates protein activity.     

The karyopherin Kap95 and the C-termini of Rfa1, Rfa2, and Rfa3 are necessary for efficient nuclear import of functional RPA complex proteins in Saccharomyces cerevisiae

Nuclear protein import in eukaryotic cells is mediated by karyopherin proteins, which bind to specific nuclear localization signals on substrate proteins and transport them across the nuclear envelope and into the nucleus. Replication protein A (RPA) is a nuclear protein comprised of three subunits (termed Rfa1, Rfa2, and Rfa3 in Saccharomyces cerevisiae) that binds single-stranded DNA and is essential for DNA replication, recombination, and repair. RPA associates with two different karyopherins in yeast, Kap95, and Msn5/Kap142. However, it is unclear which of these karyopherins is responsible for RPA nuclear import. We have generated GFP fusion proteins with each of the RPA subunits and demonstrate that these Rfa-GFP chimeras are functional in yeast cells. The intracellular localization of the RPA proteins in live cells is similar in wild-type and msn5Δ deletion strains but becomes primarily cytoplasmic in cells lacking functional Kap95. Truncating the C-terminus of any of the RPA subunits results in mislocalization of the proteins to the cytoplasm and a loss of protein-protein interactions between the subunits. Our data indicate that Kap95 is likely the primary karyopherin responsible for RPA nuclear import in yeast and that the C-terminal regions of Rfa1, Rfa2, and Rfa3 are essential for efficient nucleocytoplasmic transport of each RPA subunit.     

A complex of nuclear pore proteins required for pore function

A family of proteins bearing novel N-acetylglucosamine residues has previously been found to be required to form functional nuclear pores. To begin to determine which of the proteins in this family are essential for pore function, antisera were raised to each of three members of the family, p62, p58, and p54. With these antisera, it was possible to deplete nuclear reconstitution extracts of the proteins and to test the depleted nuclei for nuclear transport. In the course of the experiments, it was found that the three proteins exist as a complex; antisera to any one, while specific on a protein blot, coimmunoprecipitated all three proteins. This complex of pore proteins is stable to 2 M salt, 2 M urea, and the detergent Mega 10, indicating the presence of specific and tight protein-protein interactions. By gel filtration, the complex has a molecular mass of 550-600 kD. Nuclei containing pores depleted of the complex are found to be defective for nuclear transport; moreover, we observe a strict linear correlation between the amount of complex present in nuclei and the amount of nuclear transport of which those nuclei are capable. Thus, the p62-p58-p54 complex defines a group of proteins with strong protein-protein interactions that form a unit of pore structure essential for pore function.     

The role of nuclear pores in gene regulation,development and disease

Nuclear‐pore complexes (NPCs) are large protein channels that span the nuclear envelope (NE), which is a double membrane that encloses the nuclear genome of eukaryotes. Each of the typically 2,000–4,000 pores in the NE of vertebrate cells is composed of multiple copies of 30 different proteins known as nucleoporins. The evolutionarily conserved NPC proteins have the well‐characterized function of mediating the transport of molecules between the nucleoplasm and the cytoplasm. Mutations in nucleoporins are often linked to specific developmental defects and disease, and the resulting phenotypes are usually interpreted as the consequences of perturbed nuclear transport activity. However, recent evidence suggests that NPCs have additional functions in chromatin organization and gene regulation, some of which might be independent of nuclear transport. Here, we review the transport‐dependent and transport‐independent roles of NPCs in the regulation of nuclear function and gene expression.     

A protein recognized by antibodies to Asp-Asp-Asp-Glu-Asp shows specific binding activity to heterogeneous nuclear transport signals

Nuclear proteins contain a signal, termed the nuclear transport signal, that specifies their selective transport into the nucleus. Previously we reported that antibodies to Asp-Asp-Asp-Glu-Asp (DDDED) inhibited nuclear transport of nuclear proteins in vivo. We therefore tried to detect a cellular receptor of nuclear transport signals as a protein that reacted with both anti-DDDED antibody and nuclear transport signal sequences. Using two steps of affinity chromatography, anti-DDDED-Sepharose and nucleoplasmin-Sepharose, we obtained a protein of 69 kDa (p69) from the nuclear pore fraction that showed these characters. This p69 recognized by anti-DDDED antibody interacted specifically with SV40 large T antigen and nucleoplasmin transport signals.     

核定位信号及其在病毒感染机制中的研究进展

核定位信号介导的蛋白入核是细胞内信号传递网络中核内外物质信息交流的重要一环,绝大多数病毒蛋白进入细胞核均需要核质转运受体识别和结合入核蛋白携带的核定位信号序列。病毒蛋白的入核转运机制在病毒感染过程中起着至关重要的作用,对于病毒的复制、毒力具有重要意义,针对该机制的研究有利于新的抗病毒靶点的发现。本文对核定位信号的分类信息进行了总结,并对不同的核质转运受体及其介导的入核机制进行了比较分析,概述了病毒入核蛋白及其核定位信号在病毒感染机制中的研究发现。     

Computational and biochemical identification of a nuclear pore complex binding site on the nuclear transport carrier NTF2

Nuclear transport carriers interact with proteins of the nuclear pore complex (NPC) to transport their cargo across the nuclear envelope. One such carrier is nuclear transport factor 2 (NTF2), whose import cargo is the small GTPase Ran. A domain highly homologous to the small NTF2 protein (14kDa) is also found in a number of additional proteins, which together make up the NTF2 domain containing superfamily of proteins. Using structural, computational and biochemical analysis we have identified a functional site that is present throughout this superfamily, and our results indicate that this site functions as an NPC binding site in NTF2. Previously we showed that a D23A mutant of NTF2 exhibits increased affinity for the NPC. The mechanism of this mutation, however, was unknown as this region of NTF2 had not been implicated in binding to NPC proteins. Here we show that the D23A mutation in NTF2 does not result in gross structural changes affecting other known NPC binding sites. Instead, the D23 residue is located in an evolutionarily important region in the NTF2 domain containing superfamily, that in NTF2, is involved in binding to the NPC.