C. elegans cell-signalling gene sem-5 encodes a protein with SH2 and SH3 domains.

The induction of the hermaphrodite vulva and the migration of the sex myoblasts in the nematode Caenorhabditis elegans are both controlled by intercellular signalling. The gonadal anchor cell induces formation of the vulva from nearby hypodermal cells, and a set of somatic gonadal cells attract the migrating sex myoblasts to their final positions. Many genes required for vulval induction have been identified, including the let-23 receptor tyrosine kinase gene and the let-60 ras gene. We report here the identification and characterization of a new gene, sem-5 (sem, sex muscle abnormal), that acts both in vulval induction and in sex myoblast migration. On the basis of its DNA sequence, sem-5 encodes a novel 228-amino-acid protein which consists almost entirely of one SH2 (SH, src homology region) and two SH3 domains. SH2 and SH3 domains are present in many signalling proteins regulated by receptor and non-receptor tyrosine kinases. Mutations that impair sem-5 activity alter residues that are highly conserved among different SH2 and SH3 domains. Our results indicate that the sem-5 gene encodes a novel protein that functions in at least two distinct cell-signalling processes.     

Stabilization of protein structure by interaction of alpha-helix dipole with a charged side chain

The alpha-helix in proteins has a dipole moment resulting from the alignment of dipoles of the peptide bond which can perturb the pKas of ionizing groups. One of the two histidine residues (His18) in barnase, the small ribonuclease from Bacillus amyloliquefaciens, is located at the negatively charged end (C-terminal) of an alpha-helix. From NMR titrations of wild-type and engineered mutants we find that the pKa of His18 is 7.9 in wild-type enzyme, 1.6 units above the value in the urea-denatured enzyme and in model peptides. This implies that there is a favourable interaction between the protonated form of His18 and the alpha-helix that should stabilize the native structure at neutral pH by 2.1 kcal mol-1. Denaturation at various values of pH of wild-type and muant enzymes engineered at position 18 shows that this is so. The increase in stability of the enzyme as the pH changes from 8.5 to 6.3 is attributable to this interaction, and the pH-stability curve fits pKa values for His18 in native and urea-denatured enzymes that are consistent with the NMR data.     

Optimization of specificity in a cellular protein interaction network by negative selection

Most proteins that participate in cellular signalling networks contain modular protein-interaction domains. Multiple versions of such domains are present within a given organism: the yeast proteome, for example, contains 27 different Src homology 3 (SH3) domains. This raises the potential problem of cross-reaction. It is generally thought that isolated domain-ligand pairs lack sufficient information to encode biologically unique interactions, and that specificity is instead encoded by the context in which the interaction pairs are presented. Here we show that an isolated peptide ligand from the yeast protein Pbs2 recognizes its biological partner, the SH3 domain from Sho1, with near-absolute specificity--no other SH3 domain present in the yeast genome cross-reacts with the Pbs2 peptide, in vivo or in vitro. Such high specificity, however, is not observed in a set of non-yeast SH3 domains, and Pbs2 motif variants that cross-react with other SH3 domains confer a fitness defect, indicating that the Pbs2 motif might have been optimized to minimize interaction with competing domains specifically found in yeast. System-wide negative selection is a subtle but powerful evolutionary mechanism to optimize specificity within an interaction network composed of overlapping recognition elements.     

Speech interaction with a rat

This paper presents the first report of a system of human's speech interaction with rats via integration of brain–machine interfaces and automatic speech recognition technologies. We propose a novel human–rat speech interaction paradigm by incorporating speech translator module, which translates human's speech commands into suitable electrical brain stimulation to steer the rat to induce expected locomotor behaviors. The preliminary results show that we can guide a rat's movement by speech commands. We further look into the future application scenarios together with forthcoming challenges facing this newly evolved cyborg intelligent system. This work will pave the way for natural interaction with animal robots.     

基于多窗口不同特征的蛋白质相互作用位点预测

识别蛋白质相互作用位点在蛋白质功能研究中发挥着重要作用.文章从蛋白质序列出发,提取相关特征——序列谱、序列谱+信息熵,分别形成多个滑动窗口,以此构造输入特征向量.采用"留一法"生成训练数据集和测试数据集,使用支持向量机构建6种分类器,预测测试集中的表面残基是否是蛋白质相互作用位点,得到了较好的结果,说明了实验方法的有效性和可行性.     

The structure of ribosomal protein S5 reveals sites of interaction with 16S rRNA.

Understanding the process whereby the ribosome translates the genetic code into protein molecules will ultimately require high-resolution structural information, and we report here the first crystal structure of a protein from the small ribosomal subunit. This protein, S5, has a molecular mass of 17,500 and is highly conserved in all lifeforms. The molecule contains two distinct alpha/beta domains that have structural similarities to several other proteins that are components of ribonucleoprotein complexes. Mutations in S5 result in several phenotypes which suggest that S5 may have a role in translational fidelity and translocation. These include ribosome ambiguity or ram, reversion from streptomycin dependence and resistance to spectinomycin. Also, a cold-sensitive, spectinomycin-resistant mutant of S5 has been identified which is defective in initiation. Here we show that these mutations map to two distinct regions of the molecule which seem to be sites of interaction with ribosomal RNA. A structure/function analysis of the molecule reveals discrepancies with current models of the 30S subunit.     

SOL-1 is a CUB-domain protein required for GLR-1 glutamate receptor function in C. elegans

Ionotropic glutamate receptors (iGluRs) mediate most excitatory synaptic signalling between neurons. Binding of the neurotransmitter glutamate causes a conformational change in these receptors that gates open a transmembrane pore through which ions can pass. The gating of iGluRs is crucially dependent on a conserved amino acid that was first identified in the 'lurcher' ataxic mouse. Through a screen for modifiers of iGluR function in a transgenic strain of Caenorhabditis elegans expressing a GLR-1 subunit containing the lurcher mutation, we identify suppressor of lurcher (sol-1). This gene encodes a transmembrane protein that is predicted to contain four extracellular beta-barrel-forming domains known as CUB domains. SOL-1 and GLR-1 are colocalized at the cell surface and can be co-immunoprecipitated. By recording from neurons expressing GLR-1, we show that SOL-1 is an accessory protein that is selectively required for glutamate-gated currents. We propose that SOL-1 participates in the gating of non-NMDA (N-methyl-D-aspartate) iGluRs, thereby providing a previously unknown mechanism of regulation for this important class of neurotransmitter receptor.     

Role of thrombin signalling in platelets in haemostasis and thrombosis.

Platelets are critical in haemostasis and in arterial thrombosis, which causes heart attacks and other events triggered by abnormal clotting. The coagulation protease thrombin is a potent activator of platelets ex vivo. However, because thrombin also mediates fibrin deposition and because multiple agonists can trigger platelet activation, the relative importance of platelet activation by thrombin in haemostasis and thrombosis is unknown. Thrombin triggers cellular responses at least in part through protease-activated receptors (PARs). Mouse platelets express PAR3 and PAR4 (ref. 9). Here we show that platelets from PAR4-deficient mice failed to change shape, mobilize calcium, secrete ATP or aggregate in response to thrombin. This result demonstrates that PAR signalling is necessary for mouse platelet activation by thrombin and supports the model that mouse PAR3 (mPAR3) does not by itself mediate transmembrane signalling but instead acts as a cofactor for thrombin cleavage and activation of mPAR4 (ref. 10). Importantly, PAR4-deficient mice had markedly prolonged bleeding times and were protected in a model of arteriolar thrombosis. Thus platelet activation by thrombin is necessary for normal haemostasis and may be an important target in the treatment of thrombosis.     

Primary structure of helix C to helix G of a new retinal protein in H.sp.xz515

The gene fragment encoding the retinal protein from helix C to helix G in a new strain of halobacteria, H.sp.xz515 has been amplified by PCR method. The nucleotide sequence of this fragment has been determined. The deduced amino acid sequence has been compared with halobium br and other two br-like proteins, ar-1 and ar-2. Results show that those amino acid residues in br, essential for proton pumping and binding to retinal, are conserved. The residue M145 in br may be important for isomerization reaction of retinal.     

含外显子8的prosaposin蛋白亚型与Rhox5蛋白间的相互作用

研究含外显子8的prosaposin蛋白亚型(PsapE8)与同源异型框蛋白Rhox5蛋白间的相互作用. 重叠延伸PCR法扩增PsapE8的cDNA序列,将其按照通读框方式分别克隆至pGBKT7和pGADT7酵母双杂交载体中构建pGBKT7-PsapE8和 pGADT7-PsapE8重组质粒. 酵母双杂交实验检测PsapE8与Rhox5蛋白在酵母体内的结合;体外转录翻译S35标记的PsapE8蛋白,GST pull-down实验检测PsapE8与Rhox5蛋白在体外的结合情况. 成功地构建了pGBKT7-PsapE8和 pGADT7-PsapE8重组质粒,酵母双杂交实验表明PsapE8蛋白在酵母体内可以结合Rhox5蛋白;GST pull-down实验再次验证了两者在体外的结合;表明含有外显子8的prosaposin蛋白亚型PsapE8可以与Rhox5蛋白相结合.     

Expression of E1 gene of a hepatitis C virus inE. coli and protein purification

The cDNA containing full encoding region of E1 antigen of HCV was cloned into an expression plasmid pRSETHisB. The recombinant plasmid pRSETE1 was introduced into the BL21 (DE3) strain ofE. coli. The engineering bacteria harbouring the pRSETE1 was cultivated in 2YT medium at 37°C. When the Expression of E1 protein was induced by 1 mmol IPTG, the bacteria was killed and the number of living cell was droped down from 10⁷ to 10³ cell/mL one hour post induction. Suggest that E1 protein is poisoned toE. coli. However, the 26kD polypeptide of E1 fussion protein still synthesized in appropriate condition. The expression level was about 10% of total protein 4 h after inducing. The E1 protin was purified by Ni²⁺-NTA-Agarose column chromatography to homogeneous. The purified E1 protein was sensitive and specific in reaction with anti-HCV antibody in sera. Supported by the Science Committec of Hubei Province Ye Linbai: born in Feb. 1948. Professor     

The mechanosensory protein MEC-6 is a subunit of the C. elegans touch-cell degenerin channel

Mechanosensory transduction in touch receptor neurons is believed to be mediated by DEG/ENaC (degenerin/epithelial Na+ channel) proteins in nematodes and mammals. In the nematode Caenorhabditis elegans, gain-of-function mutations in the degenerin genes mec-4 and mec-10 (denoted mec-4(d) and mec-10(d), respectively) cause degeneration of the touch cells. This phenotype is completely suppressed by mutation in a third gene, mec-6 (refs 3, 4), that is needed for touch sensitivity. This last gene is also required for the function of other degenerins. Here we show that mec-6 encodes a single-pass membrane-spanning protein with limited similarity to paraoxonases, which are implicated in human coronary heart disease. This gene is expressed in muscle cells and in many neurons, including the six touch receptor neurons. MEC-6 increases amiloride-sensitive Na+ currents produced by MEC-4(d)/MEC-10(d) by approximately 30-fold, and functions synergistically with MEC-2 (a stomatin-like protein that regulates MEC-4(d)/MEC-10(d) channel activity) to increase the currents by 200-fold. MEC-6 physically interacts with all three channel proteins. In vivo, MEC-6 co-localizes with MEC-4, and is required for punctate MEC-4 expression along touch-neuron processes. We propose that MEC-6 is a part of the degenerin channel complex that may mediate mechanotransduction in touch cells.     

MARCKS is an actin filament crosslinking protein regulated by protein kinase C and calcium-calmodulin.

AGONISTS that stimulate protein kinase C (PKC) induce profound changes in cell morphology correlating with the reorganization of submembranous actin, but no direct connection between PKC and actin assembly has been identified. The myristoylated, alanine-rich C kinase substrate (MARCKS) binds calmodulin and is a predominant, specific substrate of PKC which is phosphorylated during macrophage and neutrophil activation , growth factor-dependent mitogenesis and neurosecretion; it is redistributed from plasma membrane to cytoplasm when phosphorylated and is involved in leukocyte motility. Here we report that MARCKS is a filamentous (F) actin crosslinking protein, with activity that is inhibited by PKC-mediated phosphorylation and by binding to calcium-calmodulin. MARCKS may be a regulated crossbridge between actin and the plasma membrane, and modulation of the actin crosslinking activity of the MARCKS protein by calmodulin and phosphorylation represents a potential convergence of the calcium-calmodulin and PKC signal transduction pathways in the regulation of the actin cytoskeleton.     

Stimulus-dependent myristoylation of a major substrate for protein kinase C

Bacterial lipopolysaccharide (LPS), the major surface component of gram-negative bacteria, exerts a profound effect on the immune system by enhancing the release of proteins and arachidonic acid metabolites from macrophages (for review see ref. 1). The molecular mechanism(s) by which LPS induces these various secretory responses is unknown. We previously reported that LPS promotes the myristoylation of several macrophage proteins including one with a relative molecular mass (Mr) of 68K2. We have now found that by several criteria the 68K myristoylated protein is similar or identical to the 80/87K protein, a major specific substrate for protein kinase C (PKC) found in brain and fibroblasts (for review see refs 7,8). We have also found that the myristoylated PKC substrate is quantitatively associated with the membrane fraction. Myristoylation of the PKC substrate may target it to the membrane and constitute a transduction pathway for stimulus-response coupling.     

Curcin和curcin C与腺嘌呤互作位点的比较分析

麻疯树核糖体失活蛋白curcin和curcin C均具有抗肿瘤活性,但后者的活性水平显著高于前者,为了探索造成这一差异的结构基础,本文采用在线的同源建模预测软件SWISSMODEL,对两种麻疯树核糖体失活蛋白curcin、curcin C的三维结构模型进行预测,采用SYBYL对预测模型进行能量最小化优化,采用PROCHECK、VERIFY 3D和ERRAT软件对优化前后的模型进行质量评估,随后采用AutoDock软件将预测的模型与腺嘌呤进行分子对接分析.结果显示,两种蛋白采用与Ricin A类似的方式与腺嘌呤相互作用,但在相互作用的氨基酸残基种类、数量以及形成的氢键和疏水相互作用上还是存在差异,其中,curcin C与腺嘌呤具有最强的结合能力,curcin则最低.     

PAS domain of the deduced Org35 protein mediates the interaction with NifA

PAS domains are sensory input domains and pro- tein-protein interaction sites that have been identified recently in a family of sensory proteins from all king-doms of life[1,2]. A variety of environmental stimuli such as light, oxygen, redox potential, an…