Interaction of zinc finger ZNF191(243—368) and its I323 W and R327W mutants with oligonucleotides by florescence spectrum

Two mutants of the zinc finger protein, ZNF191 (243–368) I323W and R327W, are successfully obtained by site-directed mutagenesis. The fluorescence spectrum is used to study the interaction between these two mutants and the oligonucleotides. The influence of the mutation on the interaction has been studied using ethidium bromide (EB) as the fluorescence probe. The binding constants of the I323W-DNA and R327W-DNA have been calculated and the possible binding models have been discussed.     

Optimized POCl3-assisted synthesis of 2-amino-1,3,4-thiadiazole/1,3,4-oxadiazole derivatives as anti-influenza agents

Although recent decades have witnessed the synthesis of 1,3,4-thiadiazoles via phosphorus POCl₃-promoted cyclization reaction, simultaneous access to 2-amino-1,3,4-thiadiazole and 2-amino-1,3,4-oxadiazole analogs remains unexpected and elusive. Herein, a detailed regiocontrolled synthesis of 2-amino-1,3,4-thiadiazoles in good to high yields with good regioselectivities from readily available thiosemicarbazides using POCl₃ was disclosed. Meantime, to establish a comprehensive structure–activity relationship, 2-amino-1,3,4-oxadiazole derivatives as single regioisomers were prepared via EDCI·HCl-triggered cyclization of the thiosemicarbazide intermediates. The in vitro anti-influenza assays proved that the selected compounds with the pyrazine/pyridine ring exhibited certain inhibitory activities against influenza A virus strains A/HK/68 (H3N2) and A/PR/8/34 (H1N1) in MDCK cells. Among them, N-(adamantan-1-yl)-5-(5-(azepan-1-yl)pyrazin-2-yl)-1,3,4-thiadiazol-2-amine (4j) was the most active compound, and exhibited favorable activity with EC₅₀ values of 3.5 μM and 7.5 μM, respectively. In addition, the molecular docking results explained the reason why compound 4j had dual inhibitory activity and revealed the reasonable binding mode of this compound with the M2-S31N and M2-WT ion channels. This compound had the potential to be further developed as an anti-influenza drug.     

Surface-grafted polystyrene beads with comb-like poly(ethylene glycol) chains: preparation and biological application

We prepared surface-grafted polystyrene (PS) beads with comb-like poly(ethylene glycol) (PEG) chains. To accomplish this, conventional gel-type PS beads (35-75 microm) were treated with ozone gas to introduce hydroperoxide groups onto the surface. Using these hydroperoxide groups, poly(methyl methacrylate) (PMMA, Mn= 22,000-25,000) was grafted onto the surface of the PS beads. The ester groups of the grafted PMMA were reduced to hydroxyl groups with lithium aluminum hydride (LAH). After adding ethylene oxide (EO) to the hydroxyl groups, we obtained the PS-sg-PEG beads, which had a rugged surface and a diameter of 80-150 microm. We could obtain several kinds of the PS-sg-PEG beads by controlling the chain lengths of the grafted PMMA and the molecular weights of the PEG chains. The grafted PEG layer was about 30-50 microm thick, which was verified from the cross-sectioned views of the fluorescamine-labeled beads. These fluorescence images proved that the beads possessed a pellicular structure. Furthermore, we found that the surface-grafted PEG chains had the characteristic property of reducing non-specific protein adsorption on the beads.     

聚合物涂层在毛细管电泳分离蛋白中的研究进展

毛细管电泳具有分析时间短,分离效率高,样品消耗量少等优点,在生物样品分离,特别是蛋白质分析领域有重要应用。然而,毛细管内壁硅羟基的解离给分离结果带来诸多不良影响。聚合物涂层能够抑制蛋白质在毛细管内壁的吸附以及调控电渗流,故对毛细管内壁进行有效修饰能够提高其对蛋白质的分离效率及分离稳定性。该文主要综述了动态及静态聚合物涂层毛细管的最新研究进展,并概述了近些年基于多巴胺/聚多巴胺发展起来的涂层毛细管的研究进展,最后展望了聚合物涂层毛细管的发展趋势。     

Modification of Escherichia coli single-stranded DNA binding protein with gold nanoparticles for electrochemical detection of DNA hybridization

The unique binding event between Escherichia coli single-stranded DNA binding protein (SSB) and single-stranded oligonucleotides conjugated to gold (Au) nanoparticles is utilized for the electrochemical detection of DNA hybridization. SSB was attached onto a self-assembled monolayer (SAM) of single-stranded oligonucleotide modified Au nanoparticle, and the resulting Au-tagged SSB was used as the hybridization label. Changes in the Au oxidation signal was monitored upon binding of Au tagged SSB to probe and hybrid on the electrode surface. The amplified oxidation signal of Au nanoparticles provided a detection limit of 2.17 pM target DNA, which can be applied to genetic diagnosis applications. This work presented here has important implications with regard to combining a biological binding event between a protein and DNA with a solid transducer and metal nanoparticles.     

Design,synthesis, biological activity evaluation and mechanism of action of myricetin derivatives containing thioether quinazolinone

Plant bacteria and viruses have a huge negative impact on food crops in the world. Therefore, it is important to create new and efficient green pesticides. In this paper, a series of myricetin derivatives containing quinazolinone sulfide were introduced. Good antibacterial and antiviral activities of the drug molecules 2-((3-((5,7-dimethoxy-4-oxo-2-(3,4,5-trimethoxyphenyl)-4H-chromen-3-yl)oxy)propyl)thio)-6-fluoro-3-phenylquinazolin-4(3H)-one (T5) and 2-((4-((5,7-dimethoxy-4-oxo-2-(3,4,5-trimethoxyphenyl)-4H-chromen-3-yl)oxy)butyl)thio)-6-methyl-3-phenylquinazolin-4(3H)-one (T15) respectively were found by biological activity screening. The value of dissociation constant (K_d) of compound T15 to TMV CP was 0.024 ± 0.006 μM, determined by Microscale thermophoresis (MST), which was far less than the value of 8.491 ± 2.027 μM of commercial drug ningnanmycin (NNM). The interaction between compound T15 and TMV CP was further verified by molecular docking. Compound T15 formed strong hydrogen bonds with residues SER:49 and SER:15 (1.92 Å, 2.20 Å, respectively), which were superior to the traditional hydrogen bonds formed by NNM with residue SER:215 (3.64 Å). In addition, the effects of compound T15 on the contents of chlorophyll and peroxidase (POD) in tobacco were studied, and the results indicated that compound T15 could enhance the disease resistance of tobacco plants to a certain extent.     

Optimization of tetramethoxysilane-derived sol gel entrapment protocol stabilizes highly active chlorophyllase

Entrapment of membrane proteins is a challenging task compared to that involving soluble proteins. Chlorophyllase, a membrane protein, was successfully entrapped in tetramethoxysilane-derived sol-gel. Pre-gel sol typically consists of an aqueous suspension of chlorophyllase, precursors including tetramethoxysilane and/or methytrimethoxysilane, and sodium fluoride as catalyst. To obtain a highly active entrapped enzyme preparation, the effects of various immobilization parameters, including the chemical compositions of pre-gel sol (water/silane ratio, precursor type and proportions, enzyme loading, sodium fluoride concentration), and sol-gel process parameters (aging and drying time and approach) have been investigated. Chlorophyllase demonstrated the highest activity in gel derived from a pre-gel sol with water/silane ratio of 30 and enzyme loading of 0.257 mg_protein/g_gel, and showed moderately lower activity in organically modified sol-gel than that in hydrophilic sol-gel. The effects of water/silane ratio and precursor combinations on the activity of entrapped chlorophyllase were also studied by examining the pore morphology of gel via nitrogen adsorption-desorption. Longer aging time leads to an entrapped chlorophyllase preparation with higher activity. Chlorophyllase preparation demonstrated negligible activity after air-drying for 12 h while lyophilized chlorophyllase preparation demonstrated 8, 4 and 4 times higher activity than air-dried, vacuum-dried and solvent-dried preparations. Chlorophyllase demonstrated 30% higher activity in the improved sol-gel protocol than that from a non-optimized sol-gel protocol developed in a previous study.     

Adaptation of a fast Fourier transform-based docking algorithm for protein design

Designing proteins with novel protein/protein binding properties can be achieved by combining the tools that have been developed independently for protein docking and protein design. We describe here the sequence-independent generation of protein dimer orientations by protein docking for use as scaffolds in protein sequence design algorithms. To dock monomers into sequence-independent dimer conformations, we use a reduced representation in which the side chains are approximated by spheres with atomic radii derived from known C2 symmetry-related homodimers. The interfaces of C2-related homodimers are usually more hydrophobic and protein core-like than the interfaces of heterodimers; we parameterize the radii for docking against this feature to capture and recreate the spatial characteristics of a hydrophobic interface. A fast Fourier transform-based geometric recognition algorithm is used for docking the reduced representation protein models. The resulting docking algorithm successfully predicted the wild-type homodimer orientations in 65 out of 121 dimer test cases. The success rate increases to approximately 70% for the subset of molecules with large surface area burial in the interface relative to their chain length. Forty-five of the predictions exhibited less than 1 A C(alpha) RMSD compared to the native X-ray structures. The reduced protein representation therefore appears to be a reasonable approximation and can be used to position protein backbones in plausible orientations for homodimer design.     

Identification of low molecular weight proteins isolated by 2-D liquid separations

Proteins with molecular mass (M(r)) <20 kDa are often poorly separated in 2-D sodium dodecyl sulfate polyacrylamide gel electrophoresis. In addition, low-M(r) proteins may not be readily identified using peptide mass fingerprinting (PMF) owing to the small number of peptides generated in tryptic digestion. In this work, we used a 2-D liquid separation method based on chromatofocusing and non-porous silica reversed-phase high-performance liquid chromatography to purify proteins for matrix-assisted laser desorption/ionization time-of-flight mass spectrometric (MALDI-TOFMS) analysis and protein identification. Several proteins were identified using the PMF method where the result was supported using an accurate M(r) value obtained from electrospray ionization TOFMS. However, many proteins were not identified owing to an insufficient number of peptides observed in the MALDI-TOF experiments. The small number of peptides detected in MALDI-TOFMS can result from internal fragmentation, the few arginines in its sequence and incomplete tryptic digestion. MALDI-QTOFMS/MS can be used to identify many of these proteins. The accurate experimental M(r) and pI confirm identification and aid in identifying post-translational modifications such as truncations and acetylations. In some cases, high-quality MS/MS data obtained from the MALDI-QTOF spectrometer overcome preferential cleavages and result in protein identification.