Conformational Flexibility of Cytokine-Like C-Module of Tyrosyl-tRNA Synthetase Monitored by Trp144 Intrinsic Fluorescence

The non-catalytic COOH-terminal module formed after proteolytic cleavage of full-length mammalian tyrosyl-tRNA synthetase displays dual function: tRNA binding ability and cytokine activity. With the aim to explore the intramolecular dynamics of C-module in solution we used fluorescence spectroscopy to study conformational changes of isolated protein. We used information from fluorescence spectra and computational model for characterization of a microenvironment of a single tryptophan residue (Trp144). Its fluorescence parameters and protection from quenching by Cs⁺ ions indicate the internal localization—buried into protein globule. The fluorescence quenching of Trp144 by acrylamide suggests rapid conformation dynamics of the C-module in nanosecond time scale. The temperature-induced conformational changes in the C-module were monitored by the fluorescence measurements of Trp144 emission and by red-edge excitation shift. An emission maximum shift up to ∼349 nm and significant decrease of the red-edge shift effect at 37–52 °C indicated a major conformational transition of Trp144 from buried native state into highly relaxing polar solvent environment.     

In vivo dynamic turnover of cerebral 13C isotopomers from [U-13C]glucose

An INEPT-based (13)C MRS method and a cost-effective and widely available 11.7 Tesla 89-mm bore vertical magnet were used to detect dynamic (13)C isotopomer turnover from intravenously infused [U-(13)C]glucose in a 211 microL voxel located in the adult rat brain. The INEPT-based (1)H-->(13)C polarization transfer method is mostly adiabatic and therefore minimizes signal loss due to B(1) inhomogeneity of the surface coils used. High quality and reproducible data were acquired as a result of combined use of outer volume suppression, ISIS, and the single-shot three-dimensional localization scheme built in the INEPT pulse sequence. Isotopomer patterns of both glutamate C4 at 34.00 ppm and glutamine C4 at 31.38 ppm are dominated first by a doublet originated from labeling at C4 and C5 but not at C3 (with (1)J(C4C5) = 51 Hz) and then by a quartet originated from labeling at C3, C4, and C5 (with (1)J(C3C4) = 35 Hz). A lag in the transition of glutamine C4 pattern from doublet-dominance to quartet dominance as compared to glutamate C4 was observed, which provides an independent verification of the precursor-product relationship between neuronal glutamate and glial glutamine and a significant intercompartmental cerebral glutamate-glutamine cycle between neurons and glial cells.     

新型双功能谷胱甘肽合成酶的真核和原核表达

通过裂解无乳链球菌(Streptococcus agalactiae)菌体细胞得到基因组DNA。根据GenBank上已发表的无乳链球菌(菌种编号ATCC13813)新型双功能谷胱甘肽合成酶基因(gshF)的核酸序列与2种不同表达载体多克隆位点序列,分别设计引物F₁、R₁和F₂、R₂,再以总DNA为模板,经过特异性PCR扩增出长度约为2 200 bp的目的基因。随后分别对目的基因gshF和2种表达载体进行双酶切、连接等操作,得到表达载体pPIC9K-gshF与pET-gshF。用Sal I线性化表达载体pPIC9K-gshF后电转至毕赤酵母GS115中。经MD平板筛选重组子、菌落PCR鉴定阳性菌株、G418抗性梯度平板筛选多拷贝菌株,最终在4.0 mg·mL^-1 G418抗性平板上筛选出阳性菌株。用甲醇终浓度为2%的BMMY培养基诱导该阳性菌株表达,每隔12 h取样并添加甲醇,96 h后离心收集发酵上清,经SDS-PAGE蛋白电泳显示：在85 kDa处出现1条明显蛋白带,大小与预期GshF蛋白一致。重组菌BL21-pET-gshF用IPTG诱导表达,先在37 ℃下培养90 min,再加入IPTG至1 mmol·L^-1后诱导7 h,离心收集表达产物并对重组菌进行超声破碎处理后,进行SDS-PAGE蛋白电泳,同样在85 kDa处有1条蛋白带。采用Bradford法测定2种表达产物上清的蛋白量,其中重组酵母表达上清中蛋白量为0.46 mg·mL^-1,重组大肠杆菌表达产物破壁后的蛋白量为1.46 mg·mL^-1。测定并比较2种不同表达方式所得酶活,发现GshF在毕赤酵母表达中的比酶活仅为14.15 U·mL^-1,经原核表达后比酶活可达62.15 U·mL^-1。     

水稻线粒体tRNATrp种属特异性元件研究

为了研究水稻线粒体tRNATrp的种属特异性元件,在野生型水稻线粒体tRNATrp的基础上,设计并完成了3种向人tRNATrp的突变,体外转录并用枯草杆菌和人这两种不同种属来源的色氨酰-tRNA合成酶(TrpRS)测定了这些 tRNATrp 分子的氨酰化活力(Kcat/KM).结果表明,与野生型水稻线粒体tRNATrp相比, 3个突变体被人TrpRS氨酰化的活力分别提高了354、407和803倍,其中以PMPH3(水稻线粒体tRNATrp的氨基酸接受茎的C2-G71和G3-C70都突变为人tRNATrp的氨基酸接受茎的相应部位)的氨酰化活力改变最大.而3个突变体对B.subtilis TrpRS氨酰化活力有进一步负影响,氨酰化活力微弱.说明水稻线粒体tRNATrp氨基酸接受茎上的第2个碱基对C2-G71和第3个碱基对G3-C70在人色氨酰-tRNA合成酶识别过程中有着极为重要的作用,是水稻线粒体tRNATrp的种属特异性元件.     

Molecular Docking of SP40 Peptide towards Cellular Receptors for Enterovirus 71 (EV-A71)

Enterovirus 71 (EV-A71) is one of the predominant etiological agents of hand, foot and mouth disease (HMFD), which can cause severe central nervous system infections in young children. There is no clinically approved vaccine or antiviral agent against HFMD. The SP40 peptide, derived from the VP1 capsid of EV-A71, was reported to be a promising antiviral peptide that targeted the host receptor(s) involved in viral attachment or entry. So far, the mechanism of action of SP40 peptide is unknown. In this study, interactions between ten reported cell receptors of EV-A71 and the antiviral SP40 peptide were evaluated through molecular docking simulations, followed by in vitro receptor blocking with specific antibodies. The preferable binding region of each receptor to SP40 was predicted by global docking using HPEPDOCK and the cell receptor-SP40 peptide complexes were refined using FlexPepDock. Local molecular docking using GOLD (Genetic Optimization for Ligand Docking) showed that the SP40 peptide had the highest binding score to nucleolin followed by annexin A2, SCARB2 and human tryptophanyl-tRNA synthetase. The average GoldScore for 5 top-scoring models of human cyclophilin, fibronectin, human galectin, DC-SIGN and vimentin were almost similar. Analysis of the nucleolin-SP40 peptide complex showed that SP40 peptide binds to the RNA binding domains (RBDs) of nucleolin. Furthermore, receptor blocking by specific monoclonal antibody was performed for seven cell receptors of EV-A71 and the results showed that the blocking of nucleolin by anti-nucleolin alone conferred a 93% reduction in viral infectivity. Maximum viral inhibition (99.5%) occurred when SCARB2 was concurrently blocked with anti-SCARB2 and the SP40 peptide. This is the first report to reveal the mechanism of action of SP40 peptide in silico through molecular docking analysis. This study provides information on the possible binding site of SP40 peptide to EV-A71 cellular receptors. Such information could be useful to further validate the interaction of the SP40 peptide with nucleolin by site-directed mutagenesis of the nucleolin binding site.     

Enhancement ofSpirulina biomass productivity by a protein hydrolysate

The effect of a hydrolyzed protein preparation on the growth and biomass yield of the blue-gree algaSpirulina platensis was studied. At the optimum dosage, the hydrolysate enhancedSpirulina productivity by almost 40% when compared to untreated cultures. This increased productivity correlated with an increase in the level of nitrogen assimilating enzymes, nitrate reductase and glutamine synthetase.     

ARGINYL-tRNA SYNTHETASE FROM Escherichia coli AFFINITY LABELING WITH 3''''-OXIDIZED tRNA~(Arg)

The covalent modification of E. coli arginyl-tRNA synthetase by the 2',3'-dialdehydederivative of tRNA~(Arg) (tRNA_(ox)~(Arg)) resulted in the complete inactivation of the ATP-PPi ex-change and aminoacylation activities of the enzyme. Sodium dodecyl sulfate polyacrylamide gelelectrophoresis of the ArgRS-tRNA_(ox)~(Arg) covalent complexes indicated that two bands simulta-neously appeared on the gel parallel with inactivation corresponding to different higher mo-lecular weights. This result was different from that of the other aminoacyl-tRNA synthetaselabeling systems as previously reported. Upon the ribonuclease treatment of the modifiedArgRS, less than 15% of both the initial ATP-PPi exchange and aminocylation activities wererecovered. During the whole process of labeling and RNase treatment, the two activities ofthe enzyme were closely associated.     

In vivo labeling method of cyclosporin A with [14C-methyl]-S-adenosyl-L-methionine can evaluate a potency of cyclosporin A-producing mutant

Cyclosporin A synthetase activity ofTolypocladium inflatum can be estimated by measuring its N-methyltransferase activity. In vivo N-methyltransferase activity of cyclosporin A synthetase of cells was measured by in vivo [¹⁴C-methyl] labeling assay, which was designed for actively growing cells. After the cells were incubated with 0.025 μCi of [¹⁴C-methyl]-S-adenosyl-l-methionine, [¹⁴C-methyl] labelled cyclosporin A and its analogs inside the cells were extracted with ethylacetate and¹⁴C radioactivity of the ethylacetate extract of the cells was counted. When various mutant cells grown on agar plate medium after ultraviolet irradiation or N-methyl-N’-nitroso-guanidine treatment were applied to in vivo [¹⁴C-methyl] labeling assay, these mutants showed a broad range of in vivo N-methyltransferase activity. Poor correlation was found between in vivo N-methyltransferase activity of cyclosporin A synthetase of the mutant grown on agar plate and the actual amount of cyclosporin A production in shake-flask culture. However, when the cells grown on the shake-flask culture were applied in the in vivo [¹⁴C-methyl] labeling assay, a better correlation was resulted. In vivo N-methyltransferase activity reached the maximum value at about 150 h, and then declined quickly, but cyclosporin A was synthesized for 200 h during fermentation. Specific in vivo N-methyltransferase activity was not greatly influenced by culture age during fermentation. The major product of in vivo [¹⁴C-methyl] labeling assay was identified as cyclosporin A, and only trace amounts of other cyclosporin analogues were detected. Therefore, the results suggest that in vivo labeling method with [C¹⁴-methyl]-S-adenosyl-l-methionine can easily compare a potency of cyclosporin A-producing mutant during fermentation.     

Protein:Ligand binding free energies: A stringent test for computational protein design

A computational protein design method is extended to allow Monte Carlo simulations where two ligands are titrated into a protein binding pocket, yielding binding free energy differences. These provide a stringent test of the physical model, including the energy surface and sidechain rotamer definition. As a test, we consider tyrosyl‐tRNA synthetase (TyrRS), which has been extensively redesigned experimentally. We consider its specificity for its substrate l ‐tyrosine (l ‐Tyr), compared to the analogs d ‐Tyr, p‐acetyl‐, and p‐azido‐phenylalanine (ac‐Phe, az‐Phe). We simulate l ‐ and d ‐Tyr binding to TyrRS and six mutants, and compare the structures and binding free energies to a more rigorous “MD/GBSA” procedure: molecular dynamics with explicit solvent for structures and a Generalized Born + Surface Area model for binding free energies. Next, we consider l ‐Tyr, ac‐ and az‐Phe binding to six other TyrRS variants. The titration results are sensitive to the precise rotamer definition, which involves a short energy minimization for each sidechain pair to help relax bad contacts induced by the discrete rotamer set. However, when designed mutant structures are rescored with a standard GBSA energy model, results agree well with the more rigorous MD/GBSA. As a third test, we redesign three amino acid positions in the substrate coordination sphere, with either l ‐Tyr or d ‐Tyr as the ligand. For two, we obtain good agreement with experiment, recovering the wildtype residue when l ‐Tyr is the ligand and a d ‐Tyr specific mutant when d ‐Tyr is the ligand. For the third, we recover His with either ligand, instead of wildtype Gln. © 2015 Wiley Periodicals, Inc.     

Benzimidazole-Derived ATP Analogues as Potential Glutamine Synthetase Inhibitors

A series of mono- and dihydroxyalkyl- and -alkyloxybenzimidazoles and their phosphorylated derivatives have been prepared as adenosine triphoshate analogues for investigation as potential M. Tb. glutamine synthetase inhibitors.