From genomics to proteomics

Proteomics is the study of the function of all expressed proteins. Tremendous progress has been made in the past few years in generating large-scale data sets for protein-protein interactions, organelle composition, protein activity patterns and protein profiles in cancer patients. But further technological improvements, organization of international proteomics projects and open access to results are needed for proteomics to fulfil its potential.     

差异蛋白质组学及其应用

蛋白质组学是后基因组研究中最主要的部分,其研究策略有2种:一种是"完全"蛋白质组学,目的是检测一种细胞类型或一种组织内基因组表达的所有蛋白质; 另一种是"差异"蛋白质组学,主要是筛选和鉴定不同种类或状态下各样本之间蛋白质组的区别与变化.着重介绍了差异蛋白质组学的特点、研究内容和应用前景,简要介绍了适用于差异蛋白质组学研究的相关技术和近期发展概况.     

蛋白质组研究进展

蛋白质组学是在基因组研究由结构基因组学转入到功能基因组学的背景下产生的．蛋白质组是指一个有机物所有的全部蛋白质．蛋白质组研究中使用双向凝胶电泳技术分离蛋白质，质谱技术鉴定蛋白质．蛋白质组研究可应用于基础研究和应用研究，尤其在生物医学领域前景美好．蛋白质组研究将带来生命科学的巨大变化，并将深刻地影响和改变人类的生活．     

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.     

《蛋白质组学》课程教学实践与探讨

《蛋白质组学》作为一门新兴课程,以细胞内的所有蛋白质作为研究对象,系统地揭示生命的过程,为疾病的发病机制、药物的靶向机制等研究提供了新的思路。《蛋白质组学》已经在医学、药理学及微生物学等诸多领域得到了广泛的应用。在该课程教学过程中,作者尝试采用多元化的教学方法,既介绍最新的领域研究进展和新技术,又注重以承担的科研课题为例,让学生参与到具体的实验过程中来,实现理论与实践的有机结合。文中探讨了《蛋白质组学》教学思路和方法,旨在提高蛋白质组学课程的教学质量,激发学生的学习兴趣,并提高学生的创新思维能力。     

Multiple conformations of proteins in native state

Examples of protein sequences that can adopt multiple native states are recently accumulated. Characterization of the protein multiple conformations will have important implications for our understanding of the relationship between structure and function, and their folding kinetics. In present review, the experimental evidence for the existence of multiple conformations in the native state of proteins, the molecular basis and the biological significance of multiple conformations of proteins are focused.     

蛋白质组学及其在布鲁氏菌中的研究进展

蛋白质组学研究蛋白质组成及其活动规律,是对不同时间和空间发挥功能的特定蛋白质群体的研究.本文介绍了蛋白质组学基本概念、研究技术及其在布鲁氏菌致病机理、毒力因子、免疫靶点上的研究与应用.     

Sperm chromatin proteomics identifies evolutionarily conserved fertility factors

Male infertility is a long-standing enigma of significant medical concern. The integrity of sperm chromatin is a clinical indicator of male fertility and in vitro fertilization potential: chromosome aneuploidy and DNA decondensation or damage are correlated with reproductive failure. Identifying conserved proteins important for sperm chromatin structure and packaging can reveal universal causes of infertility. Here we combine proteomics, cytology and functional analysis in Caenorhabditis elegans to identify spermatogenic chromatin-associated proteins that are important for fertility. Our strategy employed multiple steps: purification of chromatin from comparable meiotic cell types, namely those undergoing spermatogenesis or oogenesis; proteomic analysis by multidimensional protein identification technology (MudPIT) of factors that co-purify with chromatin; prioritization of sperm proteins based on abundance; and subtraction of common proteins to eliminate general chromatin and meiotic factors. Our approach reduced 1,099 proteins co-purified with spermatogenic chromatin, currently the most extensive catalogue, to 132 proteins for functional analysis. Reduction of gene function through RNA interference coupled with protein localization studies revealed conserved spermatogenesis-specific proteins vital for DNA compaction, chromosome segregation, and fertility. Unexpected roles in spermatogenesis were also detected for factors involved in other processes. Our strategy to find fertility factors conserved from C. elegans to mammals achieved its goal: of mouse gene knockouts corresponding to nematode proteins, 37% (7/19) cause male sterility. Our list therefore provides significant opportunity to identify causes of male infertility and targets for male contraceptives.     

蛋白质组学的研究进展

蛋白质组学是近几年出现的生物学者研究的热点和新领域.人类基因组"工作框架图"的完成,标志着后基 因组时代的来临,在后基因组时代,研究的中心将从揭示生命的所有遗传信息转移到在整体水平上对功能的研究,主 要以蛋白质组为中心阐述了一些与其相关的概念、研究内容、技术及其应用方面的研究进展;在这其中,蛋白质组学 的相关概念包括结构基因组学和功能蛋白质组学;而研究技术主要有2-DE技术、生物质谱技术、蛋白质芯片技术以及 生物信息学技术等.     

蛋白质组学在植物生命研究中的应用

文章综述了蛋白质组学及蛋白质组学在植物蛋白研究中的应用。重点阐述了植物光合作用蛋白的研究、种子发育时期特异蛋白的研究、逆境条件下蛋白表达的研究、植物次生代谢物的研究。并对未来植物蛋白质组学作了展望。     

蛋白质组学在植物生命研究中的应用

文章综述了蛋白质组学及蛋白质组学在植物蛋白研究中的应用.重点阐述了植物光合作用蛋白的研究、种子发育时期特异蛋白的研究、逆境条件下蛋白表达的研究、植物次生代谢物的研究.并对未来植物蛋白质组学作了展望.     

Strain-resolved community proteomics reveals recombining genomes of acidophilic bacteria

Microbes comprise the majority of extant organisms, yet much remains to be learned about the nature and driving forces of microbial diversification. Our understanding of how microorganisms adapt and evolve can be advanced by genome-wide documentation of the patterns of genetic exchange, particularly if analyses target coexisting members of natural communities. Here we use community genomic data sets to identify, with strain specificity, expressed proteins from the dominant member of a genomically uncharacterized, natural, acidophilic biofilm. Proteomics results reveal a genome shaped by recombination involving chromosomal regions of tens to hundreds of kilobases long that are derived from two closely related bacterial populations. Inter-population genetic exchange was confirmed by multilocus sequence typing of isolates and of uncultivated natural consortia. The findings suggest that exchange of large blocks of gene variants is crucial for the adaptation to specific ecological niches within the very acidic, metal-rich environment. Mass-spectrometry-based discrimination of expressed protein products that differ by as little as a single amino acid enables us to distinguish the behaviour of closely related coexisting organisms. This is important, given that microorganisms grouped together as a single species may have quite distinct roles in natural systems and their interactions might be key to ecosystem optimization. Because proteomic data simultaneously convey information about genome type and activity, strain-resolved community proteomics is an important complement to cultivation-independent genomic (metagenomic) analysis of microorganisms in the natural environment.     

Inverse Thermal-Responsive Glyco-Polypeptide Polymer for One-Pot Glyco-Affinity Proteomic

1 Introduction Proteins are ultimately responsible for the biological processes in cells, body fluids, and tissue specimens. This presents enormous challenges to the field of proteomics, which aims to identify, characterize and assign biological functions of all proteins. Determining individual protein in complex biological samples often requires some type of separation as a prerequisite for its measurement. The complexities of chemical structure and in the physiological function of every prot…     

蛋白质组学及其在神经科学研究中的应用

蛋白质组学是后基因组时代研究中兴起还不到十年的新型学科,但已应用到生命科学与基础医学研究中的各个领域.对蛋白质组进行大规模的分析可使我们更加深入了解生物体的结构与功能.在神经科学研究领域,对于神经突触、受体复合物以及其他的神经元和神经胶质特性的研究因为该学科的渗透,近年来取得了辉煌成就.然而,蛋白质组学相关技术用于神经系统的研究还面临着很多挑战,如脑蛋白样品的准备、脑的复杂性、有限的数据库资源和生物信息学工具等.蛋白质组学技术与其他功能基因组学研究方法,如基因芯片、网络生物学分析技术等相结合,将在基因及其功能、神经生理学与病理学之间架起一道重要的桥梁.     

蛋白质组及其在原虫领域中的研究进展

近十几年来,蛋白质组学的研究技术得到了很大发展。质谱技术,比较蛋白质组方法,研究蛋白质相互作用的酵母双杂交技术等的发展,极大地推进了蛋白质组研究的进程。原虫作为单细胞的真核动物,虽体积微小但能独立完成生命活动的全部生理机能,其中近万种原虫为寄生性原虫,它们常寄生在动物体内或体表使其致病,从而对人类及牲畜造成极大的危害。因此,原虫蛋白质组作为蛋白质组学研究的一个分支也迅速发展起来。到目前为止,世界上已有73种原虫的基因组已完成或正在进行测序工作,并且大部分已经进入了蛋白质组研究的工作。本文综述了一些具有代表性的原虫蛋白质组的研究情况,如：溶组织性阿米巴,布氏锥虫,间日疟原虫等,同时阐述了它们的致病机理、诊断及疫苗等方面的蛋白质组研究。     

蛋白质组学核心技术研究进展

人类基因组计划的完成标志着生命科学已进入后基因组时代,蛋白质组学的研究被提升到了前所未有的高度.对蛋白质组学研究中的三大核心技术——双向电泳、生物质谱、生物信息学技术的进展及其应用进行了概述,重点介绍了双向电泳技术和生物质谱技术.     

The structural basis of yeast prion strain variants

Among the many surprises to arise from studies of prion biology, perhaps the most unexpected is the strain phenomenon whereby a single protein can misfold into structurally distinct, infectious states that cause distinguishable phenotypes. Similarly, proteins can adopt a spectrum of conformations in non-infectious diseases of protein folding; some are toxic and others are well tolerated. However, our understanding of the structural differences underlying prion strains and how these differences alter their physiological impact remains limited. Here we use a combination of solution NMR, amide hydrogen/deuterium (H/D) exchange and mutagenesis to study the structural differences between two strain conformations, termed Sc4 and Sc37 (ref. 5), of the yeast Sup35 prion. We find that these two strains have an overlapping amyloid core spanning most of the Gln/Asn-rich first 40 amino acids that is highly protected from H/D exchange and very sensitive to mutation. These features indicate that the cores are composed of tightly packed beta-sheets possibly resembling 'steric zipper' structures revealed by X-ray crystallography of Sup35-derived peptides. The stable structure is greatly expanded in the Sc37 conformation to encompass the first 70 amino acids, revealing why this strain shows increased fibre stability and decreased ability to undergo chaperone-mediated replication. Our findings establish that prion strains involve large-scale conformational differences and provide a structural basis for understanding a broad range of functional studies, including how conformational changes alter the physiological impact of prion strains.     

蛋白质组学的研究方法

蛋白质组学是后基因组时代出现的一个新兴研究领域,具有巨大的商业应用前景,将会推动整个生命科学的发展．本文对蛋白质组学的定义和主要使用的研究方法作一简要介绍．     

基于双反相二维色谱串联质谱技术的大鼠海马膜蛋白分析

色谱与质谱联用技术在蛋白质组学研究中应用广泛,特别是二维色谱分离技术的发展,为复杂生物样品的分离分析提供了更为精准的技术手段.海马是大脑颞叶内侧的一个重要脑区,主要负责哺乳动物的学习和记忆,实现这些功能的生理过程与海马膜蛋白密切相关,但由于海马膜蛋白具有强疏水性和低丰度的特点,因此在分离和鉴定上难度较高.运用差速离心的方法分离纯化得到成年大鼠的海马膜蛋白,采用双反相二维色谱串联质谱技术进行分离分析.最终鉴定2 502个蛋白,结合生物信息学分析发现,所鉴定到的2 502个蛋白在包含蛋白定位、突触可塑性、蛋白运输以及囊泡转运等在内的与学习记忆功能密切相关的生理过程中均有涉及.这一分析结果为更加全面的揭示海马膜蛋白与脑海马区的特定功能间的具体关系提供了重要的参考.     

蛋白质的磷酸化修饰及其研究方法

蛋白质磷酸化是一种重要的翻译后修饰，它参与和调控生物体内的许多生命活动。随着蛋白质组技术的不断发展，蛋白质磷酸化的研究越来越受到广泛的重视。本文介绍了蛋白质磷酸化修饰的主要类型与功能、磷酸化兰白质及磷酸化肽的标记和分离与富集、磷酸化肽及磷酸化位点分析以及蛋白质的磷酸化改性等方法,并综述了近年来国内外的主要研究进展。