Isolation of rice allergenic cDNA clones from a rice cDNA library by immunoscreening with a polyclonal antibody specific to 16 kD rice allergenic protein

Clinical cases of type-1 hypersensitive reaction to rice (Oryza sativa) have been reported in western countries as well as in Japan. Among rice proteins, 14-16 kD globulin proteins encoded by multiple gene family have been identified as major rice allergens. In this study, a rice cDNA library was constructed using lambda UniZap vector and screened with a rat anti-16 kD globulin protein polyclonal antibody in order to isolate Korean rice allergenic cDNA clones. Five independent cDNA clones, termed RAK1-5, were obtained after second rounds of plaque assay and immunoblot analysis. These clones encoded 13-19 kD recombinant proteins upon IPTG induction, which were identified by the polyclonal antibody in immunoblot analysis. DNA sequencing analysis showed that RAK1-4 have 99% sequence homology with RA5b, and RAK5 is closely related with RA14c. This result indicated that RA5b gene is widely distributed in our cDNA library among other possible rice allergenic genes, and more study is needed to isolate heterogeneous or novel rice allergen genes.     

Location of 43 kD mosquito-larvicidal toxin gene of highly toxic Bacillus sphaericus 10

The direct evidence of the location of the mosquito-larvicidal gene of Bacillus sphaericus 10 (isolated from Jiangsu Province of China) on megaplasmid pFW1 was given by molecular cloning. The clone (pFL109) containing the 1.4 kb HindIII DNA fragment from pFW1 expressed the mosquito-larvicidal toxin protein (43 kD). The location of the gene coding for the 43 kD toxin protein within the XhoI B fragment on the restriction map of pFW1 was confirmed by Southern blotting using the 1.4 kb HindIII DNA fragment as a probe. The non-toxic strains of Bacillus sphaericus were revealed to be 43 kD toxin gene deletion mutants by Southern and Western analyses. The 1.4 kb HindIII fragment of pFL109 can be used as a probe for differentiating the non-toxic strains of Bacillus sphaericus from the toxic ones.     

Mapping chemical exchange in proteins with MW > 50 kD

Chemical exchange reveals motions in proteins that are critical for ligand binding, catalysis, and allosteric regulation at the microsecond to millisecond time scale. The detection of chemical exchange is inherently difficult in large proteins because of the fast transverse relaxation rate (R2) and spectral overlap. Here we report novel pulse sequences for the rapid identification of chemical exchange applicable to large deuterated proteins with MW greater than 30 kD. The success of our method is demonstrated in triosephosphate isomerase (TIM, MW = 54 kD).     

Analysis of the expression of two phosphoglycerate kinase genes in a mouse cultured cell line during activation and inactivation of the c-myc gene

The effect of a change in the concentration of c-myc protein on the expression of genes for two phosphoglycerate kinase isozymes was investigated. The steady state levels of messenger ribonucleic acids (mRNAs) for sperm-type and non-sperm-type proteins were determined by blot hybridization using the RNA of the mouse cell line 38-2 containing the inducible rat c-myc gene cultured under various conditions. Without induction the c-myc gene. mRNA for non-sperm-type protein was detected at a level that remained essentially constant during both activation and inactivation of the c-myc gene. mRNA for sperm-type protein was not detected in 38-2 cells cultured under any conditions used. Change in the amount of c-myc protein alone does not appear to bring about a switch of the expression of the two phosphoglycerate kinase genes during spermatogenesis in mouse testis.     

硫黄素T与侧翼连接双链DNA的G-四链体高特异性作用

富G碱基的DNA序列在离子诱导下可形成G-四链体(G4),基于这一构型转化设计了大量的传感检测平台。其中的荧光检测平台是基于G4与荧光小分子的相互作用。但是,G4与荧光小分子的有效结合依赖于G4构型和体系中存在的离子种类和离子浓度,尤其是高Na⁺浓度(140 mmol·L^-1)。那么如何实现G4与荧光小分子普适性地有效结合,并不依赖于体系中的Na⁺和Na⁺浓度,是一个难题。在本研究中,以最简单的富G DNA序列凝血酶适体链TBA (thrombin binding aptamer)为例,在3’端和5’端分别增加10个碱基(TBA-10 bp),K⁺诱导TBA-10 bp形成K⁺稳定TBA (K⁺-TBA,G4)并衔接含有10个互补碱基对的双链DNA (K⁺-TBA-10 bp)。相较于K⁺-TBA,硫磺素T与K⁺-TBA-10 bp结合后的荧光强度增加了100倍,相互作用强度增加了1000倍,而且与体系中的Na⁺ (5-140 mmol·L^-1)无关。结合荧光光谱,紫外吸收光谱和圆二色光谱发现硫磺素T特异性的嵌合于K⁺-TBA和双链DNA衔接处的空腔内。有趣的是,这一结合模式不受G4构型的影响。该研究结果为研究G4与荧光小分子的有效结合提供了新视角,也为拓展G4在生物功能和生化检测领域的应用提供了实验依据。     

The putative lead-binding carrier protein in rat epidermis using210Pb

To verify the usefulness of hair as an indicator of²¹⁰Pb and¹⁰⁹Cd accumulation in rats their distribution in different organs were determined. Whereas the radioactivity following²¹⁰Pb i.p. administration after seven days is extremely diminished to compare with that after two days, a considerable accumulation with time of¹⁰⁹Cd was observed under similar experimental conditions. The binding of lead in rat epidermis and hair was investigated and relatively tightly bound²¹⁰Pb to extracted proteins was established. By electrophoretic analysis of epidermal proteins using PAGE-SDS binding of radiolead to a protein carrier with m.w. of about 16 000 was detected. The work was performed in the frame of IAEA Coordinated Research Programme /RC 3673/RB/.     

Formation of complexes of Rubisco-Rubisco activase from La~(3+), Ce~(3+) treatment spinach

It has been proved by many early researches thatrare earth elements (REEs) could improve photosyn-thesis. However, the studies were mainly focused onthe effects of REEs on the absorption of light energy,transforming light energy into electron energy, elec…     

Copper(II) interaction with unstructured prion domain outside the octarepeat region: speciation, stability, and binding details of copper(II) complexes with PrP106-126 peptides

Copper(II) complexes of the neurotoxic peptide fragments of human and chicken prion proteins were studied by potentiometric, UV-vis, CD, and EPR spectroscopic and ESI-MS methods. The peptides included the terminally blocked native and scrambled sequences of HuPrP106-126 (HuPrPAc106-126NH2 and ScrHuPrPAc106-126NH2) and also the nona- and tetrapeptide fragments of both the human and chicken prion proteins (HuPrPAc106-114NH2, ChPrPAc119-127NH2, HuPrPAc109-112NH2, and ChPrPAc122-125NH2). The histidyl imidazole-N donor atoms were found to be the major copper(II) binding sites of all peptides; 3N and 4N complexes containing additional 2 and 3 deprotonated amide-N donors, respectively, are the major species in the physiological pH range. The complex formation processes for nona- and tetrapeptides are very similar, supporting the fact that successive deprotonation and metal ion coordination of amide functions go toward the N-termini in the form of joined six- and five-membered chelates. As a consequence, the peptide sequences investigated here, related to the neurotoxic region of the human PrP106-126 sequence, show a higher metal-binding affinity than the octarepeat fragments. In the case of the HuPrP peptide sequences, a weak pH-dependent binding of the Met109 residue was also detected in the 3N-coordinated complexes.     

Purification of clathrin assembly protein from rat liver

Recently, the gene encoding clathrin assembly protein of lymphoid myeloid leukemia (CALM), which is homologous to the AP180, was cloned from rat brain, and its expression differential to AP180 was reported (Kim and Lee, 1999). This gene product promotes the polymerization of clathrin into clathrin cage and found to be a regulator in membrane trafficking between intracellular compartments in eukaryotic cells (Kim et al., 2000). In this study, we have purified the CALM protein from clathrin-coated vesicles of rat liver using the monoclonal antibody against the recombinant N-terminal region of the CALM. The coated proteins extracted from the coated vesicle fraction was further purified by multi-step procedures involving gel-filtration and ion-exchange chromatography and SDS-PAGE. The purified protein with an apparent molecular weight of 100 kD promoted the assembly of clathrin triskelia into clathrin cage. In this respect the CALM protein bears a functional resemblance to the AP180 that has been previously described.     

Fluoromethylated and hydroxymethylated derivatives of N-methyl-D-aspartate receptor antagonist 1-[1-(2-thienyl)cyclohexyl]piperidine.

Derivatives with fluoromethyl and hydroxymethyl groups on the cyclohexyl ring of 1-[1-(2-thienyl)cyclohexyl]piperidine (TCP), a noncompetitive antagonist of N-methyl-D-aspartate (NMDA) receptor, were tested in a radioligand binding assay to evaluate their ability to inhibit [3H]TCP binding by rat brain homogenates. The potencies of these compounds as antagonists of NMDA and L-glutamate responses were also compared using a rat cortical slice preparation. One of the analogs, cis-2-hydroxymethyl-r-1-(N-piperidyl)-1-(2-thienyl) cyclohexane (5) was found to show a high affinity (IC50 = 16 nM) for the phencyclidine (PCP) binding sites, very close to that of TCP, and to be 38-fold more potent in binding than its trans isomer. Fluoromethyl and hydroxymethyl substitutions at C4 position of the cyclohexyl ring of TCP clearly reduced the affinity by at least one order of magnitude relative to TCP.     

Bilirubin/rat serum albumin interaction

Essential differences are demonstrated between bilirubin binding to rat serum proteins and to albumin in human serum. Acidimetric titration of rat serum with and without added bilirubin shows that binding of bilirubin acid in the range of pH from 6.8 to 8.8 takes place with release of less than one hydrogen ion per molecule of bound bilirubin. With human serum, two hydrogen ions are released, indicating binding of bilirubin dianion. The binding equilibrium of N-[4-[(4-aminophenyl)-sulfonyl]phenyl]-acetamide (MADDS) to rat serum albumin is influenced slightly by cobinding of bilirubin whereas MADDS and bilirubin bind competitively to human serum albumin. Finally, the rate of oxidation of bilirubin with hydrogen peroxide and peroxidase is decreased moderately by addition of rat serum albumin and strongly by the human protein, indicating that biliribin in its complex with rat serum albumin is subject to oxidation while the complex with human serum albumin is protected. These differences should be considered when rats are used as a model in experimental studies aiming at prevention of bilirubin encephalopathy in human neonates.     

Molecular cloning of clathrin assembly protein gene (rCALM) and its differential expression to AP180 in rat brain

Binding of clathrin assembly protein to clathrin triskelia induces their assembly into clathrin-coated vesicle (CCV) in neurons. The clathrin assembly protein gene (rCALM) was cloned from rat brain cDNA library. rCALM deduced 69 kD molecule has overall 73% amino acid homology compared with that of AP180 protein. The N-terminal domain, where amino acid sequences are very similar with AP180, harbours binding sites for clathrin and inositides, as well as possible phosphorylation sites, but the proline rich C-terminal domain is different from that of AP180. The mRNA expression of rCALM and AP180 by in situ hybridization histochemistry revealed that the rCALM mRNA was more intensely expressed than that of AP180, and the distribution patterns were different from each other. These results suggest that the rCALM mediates the assembly of clathrin in neural and supporting cells of brain, and regulates the clathrin coated-vesicle formation through phosphorylation and inositide metabolism.     

Molecular dynamics simulation and free energy calculation studies of the binding mechanism of allosteric inhibitors with p38α MAP kinase

p38 MAP kinase is a promising target for anti-inflammatory treatment. The classical kinase inhibitors imatinib and sorafenib as well as BI-1 and BIRB-796 were reported to bind in the DFG-out form of human p38α, known as type II or allosteric kinase inhibitors. Although DFG-out conformation has attracted great interest in the design of type II kinase inhibitors, the structural requirements for binding and mechanism of stabilization of DFG-out conformation remain unclear. As allosteric inhibition is important to the selectivity of kinase inhibitor, herein the binding modes of imatinib, sorafenib, BI-1 and BIRB-796 to p38α were investigated by molecular dynamics simulation. Binding free energies were calculated by molecular mechanics/Poisson-Boltzmann surface area method. The predicted binding affinities can give a good explanation of the activity difference of the studied inhibitors. Furthermore, binding free energies decomposition analysis and further structural analysis indicate that the dominating effect of van der Waals interaction drives the binding process, and key residues, such as Lys53, Gly71, Leu75, Ile84, Thr106, Met109, Leu167, Asp168, and Phe169, play important roles by forming hydrogen bond, salt bridge, and hydrophobic interactions with the DFG-out conformation of p38α. Finally, we also conducted a detailed analysis of BI-1, imatinib, and sorafenib binding to p38α in comparison with BIRB-796 exploited for gaining potency as well as selectivity of p38 inhibitors. These results are expected to be useful for future rational design of novel type II p38 inhibitors.