Dynamic Model of the Process of Protein Synthesis in Eukaryotic Cells

Protein synthesis is the final step of gene expression in all cells. In order to understand the regulation of this process, it is important to have an accurate model that incorporates the regulatory steps. The model presented in this paper is composed of set of differential equations which describe the dynamics of the initiation process and its control, as well as peptide elongation, starting with the amino acids available for peptide creation. A novel approach for modeling the elongation process permits useful prediction of protein production and consumption of energy and amino acids, as well as ribosome loading rate and ribosome spacing on the mRNA. An erratum to this article can be found at     

抗卵巢癌单链免疫细胞因子真核表达载体的构建及表达

为将细胞因子IL 2靶向卵巢癌局部 ,提高肿瘤局部细胞因子的浓度 ,构建并表达了抗卵巢癌单链免疫细胞因子IL 2 1 83B2scFv .通过基因工程将两段基因IL 2和 1 83B2scFv开放读码框架的编码序列克隆在一起 ,在CHO细胞内人巨细胞病毒启动子的作用下表达可溶性融合蛋白 .酶联免疫吸附法检测其免疫学活性 ,并检测其促淋巴细胞增殖活性 .构建成功的抗体细胞因子融合蛋白能够在哺乳动物细胞内表达并能分泌到细胞外 ,且融合蛋白既能与卵巢癌相关抗原OC1 83B2很好地结合 ,又能刺激IL 2依赖细胞株的增殖 ,为其进一步临床应用打下实验基础     

Complementing the Eukaryotic Protein Interactome

Protein interaction networks are important for the understanding of regulatory mechanisms, for the explanation of experimental data and for the prediction of protein functions. Unfortunately, most interaction data is available only for model organisms. As a possible remedy, the transfer of interactions to organisms of interest is common practice, but it is not clear when interactions can be transferred from one organism to another and, thus, the confidence in the derived interactions is low. Here, we propose to use a rich set of features to train Random Forests in order to score transferred interactions. We evaluated the transfer from a range of eukaryotic organisms to S. cerevisiae using orthologs. Directly transferred interactions to S. cerevisiae are on average only 24% consistent with the current S. cerevisiae interaction network. By using commonly applied filter approaches the transfer precision can be improved, but at the cost of a large decrease in the number of transferred interactions. Our Random Forest approach uses various features derived from both the target and the source network as well as the ortholog annotations to assign confidence values to transferred interactions. Thereby, we could increase the average transfer consistency to 85%, while still transferring almost 70% of all correctly transferable interactions. We tested our approach for the transfer of interactions to other species and showed that our approach outperforms competing methods for the transfer of interactions to species where no experimental knowledge is available. Finally, we applied our predictor to score transferred interactions to 83 targets species and we were able to extend the available interactome of B. taurus, M. musculus and G. gallus with over 40,000 interactions each. Our transferred interaction networks are publicly available via our web interface, which allows to inspect and download transferred interaction sets of different sizes, for various species, and at specified expected precision levels. Availability: http://services.bio.ifi.lmu.de/coin-db/.     

免疫荧光法检测原核和真核细胞中表达的轮状病毒外壳蛋白VP4

目的：用免疫荧光法快速检测原核和真核细胞中表达的轮状病毒（RV）外壳蛋白VP4。方法：以抗VP4的抗体为一抗、FITC标记的羊抗豚鼠IgG为二抗,用免疫荧光方法检测在大肠杆菌BL21（DE3）中重组表达的同源RVVP4;检测SA11或Wa株RV感染MA104细胞后不同时间段病毒VP4的合成及其在感染细胞中的分布情况。结果：用免疫荧光法可直接检测到原核细胞中表达的外源蛋白,也可检测到病毒蛋白在真核细胞中的分布情况。结论：免疫荧光法可特异、方便、快速地检测RV VP4在原核和真核细胞中的表达;来源于RV TB—Chen株的VP4抗体可特异性识别同源病毒VP4,交叉识别SA11或Wa株的VP4。     

RNA Degradation in Eukaryotic Cells

Molecular Biology - RNA is a crucial component of every living organism and is necessary for gene expression and its regulation in the cell. Mechanisms of RNA synthesis (especially mRNA synthesis)...     

真核翻译起始因子5A在蛋白质合成中的功能及机制

在蛋白质合成过程中,除核糖体、氨酰 tRNA和mRNA外,还有多种翻译因子参与其中。真核翻译起始因子5A（eukaryotic translation initiation factor 5A, eIF5A）是维持细胞活性必不可少的翻译因子,在进化上高度保守。eIF5A是真核细胞中唯一含有羟腐胺赖氨酸（hypusine）的蛋白质,该翻译后修饰对eIF5A的活性至关重要。1978年,人们首次鉴定出eIF5A,认为它在翻译起始阶段促进第1个肽键的形成。直到2013年才证实它主要在翻译延伸阶段调控含多聚脯氨酸基序蛋白质的翻译。在经过四十多年研究后,人们对eIF5A的功能有了新的认识。近期基于核糖体图谱数据的分析表明,eIF5A能够缓解翻译延伸过程中核糖体在多种基序处的停滞,并不局限于多聚脯氨酸基序,并且它还能够通过促进肽链的释放增强翻译终止。此外,eIF5A还可以通过调控某些蛋白质的翻译,间接影响细胞内的各种生命活动。本文综述了eIF5A的多种翻译后修饰、在蛋白质合成和细胞自噬过程中的调控作用以及与人类疾病的关系,并与细菌及古细菌中的同源蛋白质进行了比较,探讨了该因子在进化中的保守性,以期为相关领域的研究提供一定的理论基础。     

蜘蛛拖牵丝蛋白基因的克隆与表达

蜘蛛丝具有极高的强度和韧度,工业和医学应用价值很高,但由于蜘蛛的不可驯养性使其应用受到限制.因此,本文尝试利用基因工程的方法获得蛛丝蛋白的表达.我们利用巢式PCR技术从大腹圆蛛Araneus ventricosus基因组中克隆了长度为837 bp的拖牵丝蛋白基因(ASP),并分别将其构建至原核表达载体pGEX-6p-1和真核表达载体pGFP-N2上,分别命名为pASG和pASN.pASG在大肠杆菌中16℃下24 h诱导表达后,经蛋白质印迹证明成功地表达了GST-ASP融合蛋白;pASN转染昆虫sf9细胞48 h后观察到了绿色荧光蛋白GFP的表达,表明ASP基因在大肠杆菌和真核细胞中分别得到了正确表达.本研究为利用基因工程的方法开发蛛丝蛋白的生产途径提供了有益的尝试.     

真核细胞中无义介导的mRNA降解

无义介导的mRNA降解(NMD)作为一种有效的细胞监控机制,主要监测细胞转录产物的提前终止密码子(PTC),并使得含有PTC的mRNA被迅速降解,从而防止其被翻译成为缺陷性的蛋白质.尽管NMD具有一定的保守性,但在酵母、哺乳动物以及后来的果蝇细胞中都发现有所不同.目前对于NMD的研究已进入了结构领域并发现它与端粒调控和RNAi等机制相互关联.     

Modulation of the cAMP Response by G\alpha _i and G\beta \gamma : A Computational Study of G Protein Signaling in Immune Cells

Cyclic AMP is important for the resolution of inflammation, as it promotes anti-inflammatory signaling in several immune cell lines. In this paper, we present an immune cell specific model of the cAMP signaling cascade, paying close attention to the specific isoforms of adenylyl cyclase (AC) and phosphodiesterase that control cAMP production and degradation, respectively, in these cells. The model describes the role that G protein subunits, including G \(\alpha _s\) , G \(\alpha _i\) , and G \(\beta \gamma \) , have in regulating cAMP production. Previously, G \(\alpha _i\) activation has been shown to increase the level of cAMP in certain immune cell types. This increase in cAMP is thought to be mediated by \(\beta \gamma \) subunits which are released upon G \(\alpha \) activation and can directly stimulate specific isoforms of AC. We conduct numerical experiments in order to explore the mechanisms through which G \(\alpha _i\) activation can increase cAMP production. An important conclusion of our analysis is that the relative abundance of different G protein subunits is an essential determinant of the cAMP profile in immune cells. In particular, our model predicts that limited availability of \(\beta \gamma \) subunits may both \((i)\) enable immune cells to link inflammatory G \(\alpha _i\) signaling to anti-inflammatory cAMP production thereby creating a balanced immune response to stimulation with low concentrations of PGE2, and \((ii)\) prohibit robust anti-inflammatory cAMP signaling in response to stimulation with high concentrations of PGE2.     

Dynamics of the Eukaryotic Replicative Helicase at Lagging-Strand Protein Barriers Support the Steric Exclusion Model

1. Download high-res image (161KB)
2. Download full-size image

     

Protein Synthesis in Newcastle Disease Virus-Infected Chicken Embryo Cells

A double-isotopic label difference analysis of polyacrylamide gels has been used to distinguish between cellular and viral protein accumulation in infected cells and to quantify the kinetics of accumulation of viral polypeptides. This technique, coupled with the determination of total radioactive amino acid incorporation in infected cultures, has revealed the following kinetic patterns. Viral polypeptides are first detected in infected cultures 2.0 to 2.5 h postinfection. The rate of accumulation of radioactive amino acids in viral polypeptides increases to a maximum (30 to 35% of the rate of accumulation in uninfected control cultures), whereas the rate of accumulation of radioactive amino acids in host-cell protein decreases to a minimum (20% of the rate of accumulation in uninfected control cultures) by 5 to 6 h postinfection. All of the viral polypeptides detected late in infection are also present at the earlier times, and the major virion structural polypeptides are present in approximately the same (N/G-2, 53K) or slightly increasing (L, G-1, M) relative amounts. One peak area containing a nonstructural glycopeptide with an apparent molecular weight of 66,000 shows significant alterations in rates of accumulation during infection. Inhibition in the rate of radioactive amino acid incorporation into both trichloroacetic acid-soluble and acid-precipitable material during infection has been demonstrated. However, these two inhibition phenomena can be uncoupled temporally by incubating infected cultures at 36 C instead of the usual 40 C, suggesting that they may not be directly related.     

草鱼呼肠孤病毒NS31蛋白在昆虫细胞中表达及互作多肽筛选

草鱼呼肠孤病毒(Grasscarpreovirus,GCRV)是引发病毒性草鱼出血病的主要病原.前期研究证实GCRV-S7基因片段编码NS31蛋白是GCRV的非结构蛋白,在病毒感染的中后期表达.为深入开展NS31的具体生物学功能,本研究从GCRV-JX01株病毒基因组中扩增NS31,克隆至pFastBacHTA载体;利用杆状病毒Bac-to-Bac系统成功表达携带his标签的重组蛋白his-NS31;Western-Blot和IFA实验表明重组杆状病毒能够感染昆虫细胞(Sf9)表达NS31,进一步通过his-Ni2+柱纯化NS31,SDS-PAGE鉴定蛋白约为30KD.运用噬菌体展示技术筛选噬菌体12肽库,研究NS31特异性结合多肽.挑取30个克隆进行DNA序列测定,结果表明NS31主要和2种多肽分子相互作用.进一步结合生物信息学分析表明上述多肽与草鱼基因组中6个基因具有同源性,提示其可能是NS31互作蛋白.本研究为深入探索NS31在病毒感染过程中的生物学功能奠定了重要基础.     

真核表达MERS-CoV刺突蛋白亚单位的信号肽序列优化研究

中东呼吸综合征冠状病毒(Middle East respiratory syndrome coronavirus,MERS-CoV)的刺突蛋白(Spike,S)亚单位1(S1)是引起宿主免疫反应和产生中和抗体的主要靶抗原,也是疫苗研发和病原检测的重要靶标,选用适宜的真核表达系统高效表达S1蛋白是进行相关研究的基础。为确定MERS-CoV S1在哺乳动物细胞中高效分泌性表达的信号肽序列,构建了含高斯荧光素酶(Gaussia luciferase,GLuc)、人组织纤溶酶原激活剂(Tissue plasminogen activator,tPA)及小鼠免疫球蛋白G的2a亚型(Mouse immunoglobular G subtype 2a,MIgG2a)7个信号肽(原始序列和改造序列)序列的MERS-CoV S1表达质粒,瞬时转染细胞后,通过Western Blot检测并比较细胞培养上清和裂解液中S1的表达水平及分泌表达效率(条带密度灰度扫描比),并对哺乳动物细胞表达的S1蛋白的纯度与抗原特性进行了分析。结果表明7种信号肽在293T、BHK21和ExpiCHO-S^TM三种细胞系统中介导MERS-CoV S1的高效分泌表达的效率各有不同,其中tPA-1信号肽介导S1抗原在ExpiCHO-S^TM中具有较高的分泌表达效率与产量,纯化的S1蛋白保持了较好的抗原性。本研究为进一步研发基于MERS-CoV S1的亚单位疫苗及免疫学检测试剂奠定了基础。     

Quality Control in Eukaryotic Membrane Protein Overproduction

The overexpression of authentically folded eukaryotic membrane proteins in milligramme quantities is a fundamental prerequisite for structural studies. One of the most commonly used expression systems for the production of mammalian membrane proteins is the baculovirus expression system in insect cells. However, a detailed analysis by radioligand binding and comparative Western blotting of G protein-coupled receptors and a transporter produced in insect cells showed that a considerable proportion of the expressed protein was misfolded and incapable of ligand binding. In contrast, production of the same membrane proteins in stable inducible mammalian cell lines suggested that the majority was folded correctly. It was noted that detergent solubilisation of the misfolded membrane proteins using either digitonin or dodecylmaltoside was considerably less efficient than using sodium dodecyl sulfate or foscholine-12, whilst these detergents were equally efficient at solubilising correctly folded membrane proteins. This provides a simple and rapid test to suggest whether heterologously expressed mammalian membrane proteins are indeed correctly folded, without requiring radioligand binding assays. This will greatly facilitate the high-throughput production of fully functional membrane proteins for structural studies.     

Tinkering with Translation: Protein Synthesis in Virus-Infected Cells

Viruses are obligate intracellular parasites, and their replication requires host cell functions. Although the size, composition, complexity, and functions encoded by their genomes are remarkably diverse, all viruses rely absolutely on the protein synthesis machinery of their host cells. Lacking their own translational apparatus, they must recruit cellular ribosomes in order to translate viral mRNAs and produce the protein products required for their replication. In addition, there are other constraints on viral protein production. Crucially, host innate defenses and stress responses capable of inactivating the translation machinery must be effectively neutralized. Furthermore, the limited coding capacity of the viral genome needs to be used optimally. These demands have resulted in complex interactions between virus and host that exploit ostensibly virus-specific mechanisms and, at the same time, illuminate the functioning of the cellular protein synthesis apparatus.The dependence of viruses on the host translation system imposes constraints that are central to virus biology and have led to specialized mechanisms and intricate regulatory interactions. Failure to translate viral mRNAs and to modulate host mRNA translation would have catastrophic effects on virus replication, spread, and evolution. Accordingly, a wide assortment of virus-encoded functions is dedicated to commandeering and controlling the cellular translation apparatus. Viral strategies to dominate the host translation machinery target the initiation, elongation, and termination steps and include mechanisms ranging from the manipulation of key eukaryotic translation factors to the evolution of specialized cis-acting elements that recruit ribosomes or modify genome-coding capacity. Because many of these strategies have likely been pirated from their hosts and because virus genetic systems can be manipulated with relative ease, the study of viruses has been a preeminent source of information on the mechanism and regulation of the protein synthesis machinery. In this article, we focus on select viruses that infect mammalian or plant cells and review the mechanisms they use to exploit and control the cellular protein synthesis machinery.     

X射线衍射法在研究蛋白质动态过程中的应用

介绍了X射线衍射技术在研究蛋白质动态过程中的应用.首先介绍了用常规X射线衍射法和劳埃X射线衍射法等数据采样法研究反应时间为几分钟的蛋白质催化反应.然后介绍了通过选择不匹配底物,不适宜酸度,选择温度和酸度的跳跃,金属和光化学瞬时激发达到反应的同步来研究反应时间为几秒钟的蛋白质催化反应.     

A Legionella pneumophila Kinase Phosphorylates the Hsp70 Chaperone Family to Inhibit Eukaryotic Protein Synthesis

1. Download high-res image (98KB)
2. Download full-size image