Interaction kinetics of liposome-incorporated unsaturated fatty acids with fatty acid-binding protein 3 by surface plasmon resonance

The role of heart-type fatty acid-binding protein (FABP3) in human physiology as an intracellular carrier of fatty acids (FAs) has been well-documented. In this study, we aimed to develop an analytical method to study real-time interaction kinetics between FABP3 immobilized on the sensor surface and unsaturated C18 FAs using surface plasmon resonance (SPR). To establish the conditions for SPR experiments, we used an FABP3-selective inhibitor 4-(2-(1-(4-bromophenyl)-5-phenyl-1H-pyrazol-3-yl)-phenoxy)-butyric acid. The affinity index thus obtained was comparable to that reported previously, further supporting the usefulness of the SPR-based approach for evaluating interactions between FABPs and hydrophobic ligands. A pseudo-first-order affinity of FABP3 to K⁺ petroselinate (C18:1 Δ6 cis), K⁺ elaidate (C18:1 Δ9 trans), and K⁺ oleate (C18:1 Δ9 cis) was characterized by the dissociation constant (K_d) near micromolar ranges, whereas K⁺ linoleate (C18:2 Δ9,12 cis/cis) and K⁺ α-linolenate (C18:3 Δ9,12,15 cis/cis/cis) showed a higher affinity to FABP3 with K_d around 1 × 10⁻⁶ M. Interactions between FAPB3 and C18 FAs incorporated in large unilamellar vesicles consisting of 1,2-dimyristoyl-sn-glycero-3-phosphocholine and FAs (5:1 molar ratio) were also analysed. Control DMPC liposomes without FA showed only marginal binding to FABP3 immobilized on a sensor chip while liposome-incorporated FA revealed significant responses in sensorgrams, demonstrating that the affinity of FAs to FABP3 could be evaluated by using the liposome-incorporated analytes. Significant affinity to FABP3 was observed for monounsaturated fatty acids (K_d in the range of 1 × 10⁻⁷ M). These experiments demonstrated that highly hydrophobic compounds in a liposome-incorporated form could be subjected to SPR experiments for kinetic analysis.     

用RACE结合cDNA文库筛选的方法获取新的锌指蛋白基因

大多数有重要功能的蛋白质都含相应的由保守氨基酸顺序组成的功能结构域。本文首先根据蛋白质功能结构域保守氨基酸序列设计简并引物,用PCR方法扩增出基因EST序列,再利用改进的快速扩增cDNA末端（RACE）方法从cDNA文库中扩增出基因非同源部位,然后以非同源序列为探针,筛选cDNA文库。利用此方法成功地从人骨髓cDNA文库中克隆到几个编码锌指蛋白并代表原有EST的新的全长cDNA。这一策略也应适用于筛选编码具有其他序列保守性功能结构域蛋白的基因。 Abstract:Most of the important functionally proteins contain the corresponding function domains that consist of conserved amino acid sequences.The study provided a method to identify novel genes that encode proteins containing important functionally domains with conserved sequences.First,primers were designed according to the sequence of the cDNA library vector and the ESTs that have been obtained by reverse PCR and degenerate primers encoding Zinc finger domain.The cDNA library DNA was used as template for PCR amplification.The amplified fragment that contains nonhomologous sequences of the cDNA was inserted into pGEM-T easy vector.The fragment was recovered and used as a probe for screening the cDNA library.Several cDNAs with full length that encode proteins with Zinc finger domain and represent the original ESTs have been successfully cloned from a human bone marrow cDNA library.This strategy can also be used in screening genes that encode proteins containing differential function domains with conserved sequences.     

Crystal structure of axolotl (Ambystoma mexicanum) liver bile acid-binding protein bound to cholic and oleic acid

The family of the liver bile acid-binding proteins (L-BABPs), formerly called liver basic fatty acid-binding proteins (Lb-FABPs) shares fold and sequence similarity with the paralogous liver fatty acid-binding proteins (L-FABPs) but has a different stoichiometry and specificity of ligand binding. This article describes the first X-ray structure of a member of the L-BABP family, axolotl (Ambystoma mexicanum) L-BABP, bound to two different ligands: cholic and oleic acid. The protein binds one molecule of oleic acid in a position that is significantly different from that of either of the two molecules that bind to rat liver FABP. The stoichiometry of binding of cholate is of two ligands per protein molecule, as observed in chicken L-BABP. The cholate molecule that binds buried most deeply into the internal cavity overlaps well with the analogous bound to chicken L-BABP, whereas the second molecule, which interacts with the first only through hydrophobic contacts, is more external and exposed to the solvent.     

斜纹夜蛾3种SlitPBPs的组织表达模式分析

性信息素结合蛋白(pheromone binding proteins,PBPs)能够与性信息素分子结合,从而启动昆虫的寻偶及交配行为。本研究采用半定量RT-PCR技术分别对斜纹夜蛾3种性信息素结合蛋白SlitPBP1、SlitPBP2和SlitPBP3基因在雌、雄虫不同组织的基因表达模式进行了比较分析。组织表达模式结果表明,SlitPBP1基因只在雌、雄虫触角和雌虫前足中表达而在其他组织中无表达;SlitPBP2基因在雌虫的触角、喙、前足、中足、后足、翅膀和雄虫的触角、喙、前足、翅膀中均有表达,且在同一部位,SlitPBP2基因在雌虫的表达量均高于雄虫相应部位的表达量;除雌、雄虫的胸部外,SlitPBP3在雌、雄虫的触角、喙、前足、中足、后足、腹部和翅膀中均有较高水平的表达。可见,SlitPBP1、SlitPBP2和SlitPBP3基因在斜纹夜蛾不同组织的表达模式各不相同。本研究结果可为深入研究不同SlitPBPs蛋白在斜纹夜蛾生长发育过程中的不同生理功能提供科学参考。     

一种新的乙型肝炎病毒表面抗原结合蛋白的筛选、表达及其生物学活性的初步研究

为了研究乙肝病毒侵染肝细胞过程中的功能蛋白 ,通过印迹免疫分析技术从人肝cDNA噬菌体表达库中筛选出一株编码乙肝表面抗原结合蛋白 (hepatitisBsurfaceantigenbindingprotein ,HBsAg BP)的cDNA克隆 .基因测序结果表明 ,该cDNA具有独立的开放阅读框架 ,编码 1个由 344个氨基酸残基构成的可溶性蛋白分子 ,属于免疫球蛋白超家族成员 .将该基因克隆到原核表达载体pTriplEx后 ,在E .coliXL1 Blue菌株中获得 4 4kD的重组蛋白 .重组蛋白经Western印迹和ELISA实验证明具有与乙肝表面抗原特异性结合的能力 .进一步经流式细胞仪实验显示 ,在纯化的重组蛋白存在的情况下 ,天然的HBsAg与肝细胞株HepG2的亲和力显著增高 .结果显示 ,该乙肝表面抗原结合蛋白可能是介导乙肝病毒对肝细胞亲和侵染的可溶性辅助受体 .     

New approaches to target RNA binding proteins

RNA binding proteins (RBPs) are a large and diverse class of proteins that regulate all aspects of RNA biology. As RBP dysregulation has been implicated in a number of human disorders, including cancers and neurodegenerative disease, small molecule chemical probes that target individual RBPs represent useful tools for deciphering RBP function and guiding the production of new therapeutics. While RBPs are often thought of as tough-to-drug, the discovery of a number of small molecules that target RBPs has spurred considerable recent interest in new strategies for RBP chemical probe discovery. Here we review current and emerging technologies for high throughput RBP-small molecule screening that we expect will help unlock the full therapeutic potential of this exciting protein class.     

用抑制差减杂交法分离和克隆梭梭幼苗受渗透胁迫诱导相关基因的cDNA片段

以Hoagland溶液培养的梭梭幼苗(H)为对照群体,甘露醇处理的梭梭幼苗(M)为目标群体,进行抑制差减杂交.用经过H cDNA差减的M cDNA构建了一个含有大约400个独立克隆的差减文库;采用差减前的H cDNA和M cDNA以及正向/反向差减杂交后的cDNA为模板标记探针,对随机挑取的100个重组质粒进行差示筛选,获得了21个阳性候选克隆.从这些阳性候选克隆中随机挑取了8个进行Northern blot分析,证实其中3个候选克隆代表了在M中特异表达或表达增强的基因,序列分析和同源性比较表明它们与逆境胁迫有关;而另外5个候选克隆无Northem杂交信号,推测它们为低丰度转录本.     

An improved procedure for expression and purification of ribosomal protection protein Tet(O) for high-resolution structural studies

Tetracycline (Tc) is a broad spectrum antibiotic that binds to the A site of the bacterial ribosome inhibiting delivery of aminoacyl-tRNA to the A site for productive protein biosynthesis. Tet(O) is in a class of the ribosomal protection proteins (RPPs) found in many pathogenic bacteria, that dislodges Tc from the A site of 70S ribosome to restore polypeptide elongation and confer Tc resistance to the bacteria. Considerable difficulty has been encountered in overexpressing and purifying Tet(O) from various Escherichia coli strains using lambdaPI, tac or T7 promoters. Here we report molecular cloning, overexpression of His-tagged Tet(O) in E. coli, an improved purification procedure and initial biochemical and biophysical characterization of His-tagged Tet(O).     

法氏囊活性五肽BP5的抗肿瘤作用

【目的】法氏囊活性五肽Bursopentin(BP5)是一种多功能生物学活性因子,不仅具有免疫调节和抗氧化功能,还具有抗肿瘤活性。目前,BP5发挥抗肿瘤生物功能的作用机制尚不清晰。【方法】本研究利用T7噬菌体展示技术构建鸡DT40细胞T7噬菌体c DNA文库,以BP5-BSA为靶分子对文库进行亲和淘选,通过序列测定和生物信息学分析,获得BP5的结合蛋白。通过分析BP5诱导的鸡DT40细胞mRNA基因表达谱和检测BP5对HCT116细胞中p53 Luciferase活性和p53信号通路中相关蛋白表达的影响来探讨BP5抗肿瘤的作用机制。【结果】构建的鸡DT40细胞T7噬菌体c DNA文库原始滴度为1.2×104pfu/m L,重组率为91.7%,扩增后滴度为1.9×109pfu/m L;通过生物淘选获得3条与BP5结合的鸡源蛋白血管内皮生长因子A(vascular endothelial growth factor A)、细胞周期蛋白E1(cyclin E1)和运输蛋白颗粒复合体2(trafficking protein particle complex 2)。基因表达谱分析结果显示,BP5参与调节多条与抗肿瘤功能有关的通路,其中包括p53信号通路,且p53信号通路涉及的5个差异表达基因均与细胞周期调控或抗肿瘤相关,其中SIAH1、TP53(p53)、CIP1(p21)基因被上调,CHEK2、CCNE1基因被下调。RT-PCR方法检测10个表达水平有明显变化的差异基因,其结果与基因芯片分析结果相符;BP5对p53 Luciferase活性的影响实验结果显示,BP5在0.2-20μg/m L浓度下能够明显提高HCT116细胞中p53相对Luciferase活性,Western blotting结果证实,BP5能显著促进p53、p21蛋白的表达水平,而CCNE1和CHEK2蛋白的表达水平则明显降低。【结论】本研究结果表明BP5通过p53信号通路途径发挥其抗肿瘤生物学功能,为进一步研究BP5抗肿瘤具体的分子机制提供了参考依据。     

华北大黑鳃金龟两种围食膜蛋白cDNA的分子克隆与序列分析

本文以华北大黑鳃金龟Holotrichia oblita中肠为材料,依据Stratagene公司文库构建试剂盒方法,构建其中肠cDNA表达文库,该文库滴度为1.9×106 pfu/mL,重组率为99.97%。依据现代免疫学原理,利用棉铃虫Helicoverpa armigera围食膜蛋白多克隆抗体筛选文库,得到两个编码华北大黑鳃金龟围食膜蛋白的cDNA克隆Ho-Peritrophin1与Ho-Peritrophin2,其cDNA长分别为2 385 bp和1 633 bp,在PolyA末端上游各有3个多聚腺苷酸信号序列AATAAA,最长开放阅读框(ORF)分别编码729个和477个氨基酸,与粉纹夜蛾Trichoplusia ni CBP2(chitin binding protein 2)的相似性最高,分别为21.9%和19.1%。结构域分析表明,Ho-Peritrophin1与Ho-Peritrophin2分别具有9个和6个几丁质结合功能域,只含有较少的O-糖基化位点,不含有类粘蛋白结构域。胰蛋白酶和胰凝乳蛋白酶对两种蛋白的作用位点主要位于几丁质结合功能域(chitin binding domain, CBD)内部,而因受几丁质结合功能域保护,这两种蛋白能够抵抗这些蛋白酶的降解。与正常CBD比较,这两种蛋白C端的CBD只含有4个Cys,只在第1与第3、第4与第5个Cys之间形成两对二硫键,缺少由第2与第6个Cys形成的二硫键。推测其N端还应包括信号肽序列和几丁质结合功能域的未知序列。     

梨小食心虫气味结合蛋白GmolOBP3的cDNA克隆、表达谱及结合特性分析

【目的】为了更好地了解昆虫气味结合蛋白（odorant binding proteins, OBPs）在梨小食心虫Grapholita molesta（Busck）嗅觉识别中的作用,并明确其与寄主挥发物的结合特性。【方法】利用RT-PCR和RACE技术克隆梨小食心虫OBP基因;采用RT-PCR和实时定量PCR对该基因在成虫不同组织和羽化后不同日龄成虫中的表达情况进行了测定;以N-phenyl-1-naphthylamine（1-NPN）为荧光探针,采用荧光竞争结合试验对GmolOBP3蛋白的结合特性进行了分析。【结果】得到梨小食心虫一个新的气味结合蛋白基因,命名为GmolOBP3（GenBank登录号：KF395363）。GmolOBP3开放阅读框全长492 bp,编码163个氨基酸残基,预测分子量和等电点分别为18.72 kDa和4.93,呈酸性,具有典型的6个半胱氨酸位点。GmolOBP3在雌、雄成虫触角和腹部均有表达,成虫在羽化后5 d内,雌蛾触角中GmolOBP3表达量随羽化后日龄而增加,但雄蛾在羽化后第5天触角中 GmolOBP3表达量显著降低。通过构建GmolOBP3原核表达载体,在大肠杆菌Escherichia coli中诱导表达并获得了GmolOBP3重组蛋白。荧光竞争结合实验对GmolOBP3蛋白与16种寄主挥发物及4种性信息素类似物的结合力发现,在供试的4种梨小食心虫性信息素类似物中,GmolOBP3蛋白与反-8-十二碳烯醋酸酯和十二烷-1-醇不结合,而与顺-8-十二碳烯醋酸酯和顺-8-十二碳烯醇结合,但结合力较弱,结合常数分别为83.00和103.70 μmol/L;与16种寄主挥发物结合能力也不强,其中结合最强的是β 紫罗酮,结合常数为49.36 μmol/L。【结论】由此推断,GmolOBP3具有选择性识别和结合各种配基的特性。     

Cardiac myosin-binding protein C interaction with actin is inhibited by compounds identified in a high-throughput fluorescence lifetime screen

Cardiac myosin-binding protein C (cMyBP-C) interacts with actin and myosin to modulate cardiac muscle contractility. These interactions are disfavored by cMyBP-C phosphorylation. Heart failure patients often display decreased cMyBP-C phosphorylation, and phosphorylation in model systems has been shown to be cardioprotective against heart failure. Therefore, cMyBP-C is a potential target for heart failure drugs that mimic phosphorylation or perturb its interactions with actin/myosin. Here we have used a novel fluorescence lifetime-based assay to identify small-molecule inhibitors of actin-cMyBP-C binding. Actin was labeled with a fluorescent dye (Alexa Fluor 568, AF568) near its cMyBP-C binding sites; when combined with the cMyBP-C N-terminal fragment, C0-C2, the fluorescence lifetime of AF568-actin decreases. Using this reduction in lifetime as a readout of actin binding, a high-throughput screen of a 1280-compound library identified three reproducible hit compounds (suramin, NF023, and aurintricarboxylic acid) that reduced C0-C2 binding to actin in the micromolar range. Binding of phosphorylated C0-C2 was also blocked by these compounds. That they specifically block binding was confirmed by an actin-C0-C2 time-resolved FRET (TR-FRET) binding assay. Isothermal titration calorimetry (ITC) and transient phosphorescence anisotropy (TPA) confirmed that these compounds bind to cMyBP-C, but not to actin. TPA results were also consistent with these compounds inhibiting C0-C2 binding to actin. We conclude that the actin-cMyBP-C fluorescence lifetime assay permits detection of pharmacologically active compounds that affect cMyBP-C-actin binding. We now have, for the first time, a validated high-throughput screen focused on cMyBP-C, a regulator of cardiac muscle contractility and known key factor in heart failure.     

Genome-wide identification of protein binding sites on RNAs in mammalian cells

RNA-binding proteins (RBPs) are proteins that bind to the RNA and participate in forming ribonucleoprotein complexes. They have crucial roles in various biological processes such as RNA splicing, editing, transport, maintenance, degradation, intracellular localization and translation. The RBPs bind RNA with different RNA-sequence specificities and affinities, thus, identification of protein binding sites on RNAs (R-PBSs) will deeper our understanding of RNA-protein interactions. Currently, high-throughput sequencing of RNA isolated by crosslinking immunoprecipitation (HITS-CLIP, also known as CLIP-Seq) is one of the most powerful methods to map RNA-protein binding sites or RNA modification sites. However, this method is only used for identification of single known RBPs and antibodies for RBPs are required. Here we developed a novel method, called capture of protein binding sites on RNAs (RPBS-Cap) to identify genome-wide protein binding sites on RNAs without using antibodies. Double click strategy is used for the RPBS-Cap assay. Proteins and RNAs are UV-crosslinked in vivo first, then the proteins are crosslinked to the magnetic beads. The RNA elements associated with proteins are captured, reverse transcribed and sequenced. Our approach has potential applications for studying genome-wide RNA-protein interactions.     

中华蜜蜂信息素结合蛋白ASP1 cDNA的克隆及时空表达

信息素结合蛋白（pheromone binding proteins, PBPs）在昆虫信息素的识别、传递和处理过程中具有重要作用。本研究首次克隆了中华蜜蜂Apis cerana cerana的一个PBP基因Ac-ASP1（GenBank序列号为DQ449670）,其预测蛋白具有典型的气味结合蛋白（OBPs）标志（即成熟肽含有6个保守的半胱氨酸）。利用real-time PCR技术对Ac-ASP1在中蜂不同组织和发育历期的时空表达谱进行了鉴定。绝对定量结果显示Ac-ASP1高丰度地表达于工蜂触角（2.07×10⁶ 拷贝数/μg）,而在其他组织（如头、胸、腹、翅及足）中呈低丰度表达（10²拷贝数/μg）; 相对定量结果显示Ac-ASP1在各发育历期如幼虫、蛹以及成虫发育早期（1～6日龄）均有大量表达,而在21日龄前后具有另外一个高丰度表达时期。这些结果可为明确Ac-ASP1在中蜂蜂王信息素信号识别传递过程中的作用提供参考。     

A quantitative characterization of interaction between prion protein with nucleic acids

Binding of recombinant prion protein with small highly structured RNAs, prokaryotic and eukaryotic prion protein mRNA pseudoknots, tRNA and polyA has been studied by the change in fluorescence anisotropy of the intrinsic tryptophan groups of the protein. The affinities of these RNAs to the prion protein and the number of sites where the protein binds to the nucleic acids do not vary appreciably although the RNAs have very different compositions and structures. The binding parameters do not depend upon pH of the solution and show a poor co-operativity. The reactants form larger nucleoprotein complexes at pH 5 compared to that at neutral pH. The electrostatic force between the protein and nucleic acids dominates the binding interaction at neutral pH. In contrast, nucleic acid interaction with the incipient nonpolar groups exposed from the structured region of the prion protein dominates the reaction at pH 5. Prion protein of a particular species forms larger complexes with prion protein mRNA pseudoknots of the same species. The structure of the pseudoknots and not their base sequences probably dominates their interaction with prion protein. Possibilities of the conversion of the prion protein to its infectious form in the cytoplasm by nucleic acids have been discussed.     

Screening of T7 phage displayed Bactrocera dorsalis (Hendel) antenna cDNA library against chemosensory protein

Recent studies have shown that chemosensory proteins (CSPs) were involved in diverse life activities such as insect feeding, development, mating, immune regulation, as well as other important circadian rhythms, etc. To screen the proteins involved in the BdorCSP-related physiological activity, a cDNA library of the Bactrocera dorsalis (Hendel) antenna expressed on the surface of T7 phage was screened against BdorCSP. After four rounds of screening, ELISA-positive samples of selected phages were sequenced and identified as protein disulfide isomerase (PDI), trypsin-like serine protease (Ser), TakeOut (TO), and a new protein by GenBank blast, respectively. Real-time quantitative PCR results showed that the expression levels of Ser, TO, and the new protein were the highest in antenna, sharing similar expression pattern with BdorCSP. These results reveal that these proteins might be involved in the BdorCSP-related physiological or metabolic activities. This work paves a new way for exploring the function of CSPs.