Synthesis and characterization of 1-substituted 5-alkylphenazine derivatives carrying functional groups

The following 1-substituted derivatives of 5-methylphenazine and 5-ethylphenazine were synthesized: 1-(3-carboxypropyloxy)-5-methylphenazine (1B), 1-(3-carboxypropyloxy)-5-ethylphenazine (2B), 1-(3-ethoxycarbonylpropyloxy)-5-ethylphenazine (2C) and 1-[N-(2-aminoethyl)carbamoylpropyloxy]-5-ethylphenazine (2D); their spectra, stability and reactivity as electron mediators were investigated, together with those of 5-methylphenazine (1A) and 5-ethylphenazine (2A). The 1-substituted derivatives are all insensitive to light and the derivatives of 5-ethylphenazine are more stable than those of 5-methylphenazine under neutral and alkaline conditions; 2B is the most stable of all the derivatives. The spectral properties of the decomposed compounds showed that photodecomposition of 1A and 2A is associated with hydroxylation at position 1, alkali decomposition of 1A and 1B with elimination of the 5-methyl group and alkali decomposition of 2A, 2B, and 2D with a ring-opening reaction. The second-order rate constant k1 for the reaction of the phenazine derivatives with NADH was measured under steady-state conditions. The k1 values vary depending on the substituents at positions 1 and 5: the values for 1A, 1B, 2A, 2B, 2C and 2D are 1.83 mM-1 s-1, 3.33 mM-1 s-1, 0.75 mM-1 s-1, 1.42 mM-1 s-1, 1.68 mM-1 s-1 and 2.03 mM-1 s-1, respectively. The rate constants, k2 and k3, for the reactions of the reduced form of 2B with oxygen and with 3-(4',5'-dimethylthiazole-2-yl)-2,5-diphenyltetrazolium ion, respectively, were k2 = 1.21 mM-1 s-1 and k3 = 91 mM-1 s-1. These phenazine derivatives have potential applications in the biochemical field.     

Chemical properties of the functional groups of insulin.

The method of competitive binding [Kaplan, Stevenson & Hartley (1971) Biochem. J. 124, 289-299] with 1-fluoro-2,4-dinitrobenzene as the labelling reagent [Duggleby & Kaplan (1975) Biochemistry 14, 5168-5175] was used to determine the chemical properties, namely pK and reactivity, of the amino groups, the histidine residues and the tyrosine residues of the dimeric form of pig zinc-free insulin at 20.0 degrees C. The N-terminal glycine residue of the A-chain has a pK of 7.7 and a slightly higher than normal reactivity. The N-terminal phenylalanine residue of the B-chain has a pK of 6.9 and is approximately an order of magnitude more reactive than a corresponding amino group with the same pK value. The lysine epsilon-amino group has an unusually low pK of 7.0 but has approximately the expected reactivity of such a group. In the case of the two histidine and four tyrosine residues only the average properties of each class were determined. The histidine residues have a pK value of approx. 6.6, but, however, their reactivity is at least an order of magnitude greater than that of a free imidazole group. The tyrosine residues have a pK value of approx. 10, but their average reactivities are substantially less than for a free phenolic group. At alkaline pH values above 8 the reactivity of all the functional groups show sharp discontinuities, indicating that insulin is undergoing a structural change that alters the properties of these groups.     

Effect of functional groups on antioxidant properties of substituted selenoethers

Selenoethers attached to functional groups through propyl chain viz., bis(3-carboxypropyl)selenide (SeBA), bis(3-hydroxypropyl)selenide (SePOH) and bis(3-aminopropyl)selenide dihydrochloride (SePAm), have been examined for their ability to inhibit peroxyl radical mediated DNA damage, peroxyl radical scavenging ability and glutathione peroxidase (GPx) like activity. The DNA damage was monitored by gel electrophoresis, bimolecular rate constants for scavenging of model peroxyl radical were determined by pulse radiolysis and the GPx activity was followed by their ability to reduce hydrogen peroxide in the presence of glutathione utilizing NADPH decay and HPLC analysis. Among these compounds, SeBA showed maximum DNA protecting activity and it was also the most efficient in scavenging peroxyl radicals with the highest GPx mimicking activity. Quantum chemical calculations confirmed that SeBA with the highest energy level of HOMO (highest occupied molecular orbital) is the easiest to undergo oxidation and therefore exhibits better radical scavenging, GPx mimicking and DNA protecting activity than SePOH or SePAm.     

A convenient route for the preparation of peptide nucleic acid monomers carrying acid-labile groups for the protection of the amino function

A convenient route for the preparation of peptide nucleic acid (PNA) monomers is described. Two different base-labile protecting groups (2-cyanoethyl and 4-nitrophenylethyl) are described for the protection of the carboxylic function of the N-(2-aminoethyl)glycine backbone during the assembly of the monomers. These groups are selectively removed yielding the desired PNA monomers in high yields, the 2-cyanoethyl group being faster and cleaner than the 4-nitrophenylethyl group. The use of PNA monomers for the preparation of DNA–PNA chimeric molecules is also discussed.     

A convenient route for the preparation of peptide nucleic acid monomers carrying acid-labile groups for the protection of the amino function

Summary A convenient route for the preparation of peptide nucleic acid (PNA) monomers is described. Two different baselabile protecting groups (2-cyanoethyl and 4-nitrophenylethyl) are described for the protection of the carboxylic function of theN-(2-aminoethyl)glycine backbone during the assembly of the monomers. These groups are selectively removed yielding the desired PNA monomers in high yields, the 2-cyanoethyl group being faster and cleaner than the 4-nitrophenylethyl group. The use of PNA monomers for the preparation of DNA-PNA chimeric molecules is also discussed.     

The PathoChip,a functional gene array for assessing pathogenic properties of diverse microbial communities

Pathogens present in the environment pose a serious threat to human, plant and animal health as evidenced by recent outbreaks. As many pathogens can survive and proliferate in the environment, it is important to understand their population dynamics and pathogenic potential in the environment. To assess pathogenic potential in diverse habitats, we developed a functional gene array, the PathoChip, constructed with key virulence genes related to major virulence factors, such as adherence, colonization, motility, invasion, toxin, immune evasion and iron uptake. A total of 3715 best probes were selected from 13 virulence factors, covering 7417 coding sequences from 1397 microbial species (2336 strains). The specificity of the PathoChip was computationally verified, and approximately 98% of the probes provided specificity at or below the species level, proving its excellent capability for the detection of target sequences with high discrimination power. We applied this array to community samples from soil, seawater and human saliva to assess the occurrence of virulence genes in natural environments. Both the abundance and diversity of virulence genes increased in stressed conditions compared with their corresponding controls, indicating a possible increase in abundance of pathogenic bacteria under environmental perturbations such as warming or oil spills. Statistical analyses showed that microbial communities harboring virulence genes were responsive to environmental perturbations, which drove changes in abundance and distribution of virulence genes. The PathoChip provides a useful tool to identify virulence genes in microbial populations, examine the dynamics of virulence genes in response to environmental perturbations and determine the pathogenic potential of microbial communities.     

Fine structure and its functional properties of the endostyle of Ascidians,Ciona intestinalis

Summary For the purpose used in understanding thyroid phylogenesis, the fine structure and the iodine metabolism of the endostyle of Ascidians,Ciona intestinalis, was studied by electron microscopy and electron microscopic autoradiography. There are 8 kinds of zones in the endostyle.Zone 1, 3, and 5 cells, especially zone 1 cells, are characterized by numerous long cilia. These cells which show no indications of protein-secretion but numerous small vesicles and cytoplasmic filaments might play a role in catching and transporting food, absorption of liquid and supporting the endostylar construction.Zone 2, 4, and 6 cells are large and characterized by well developed rough endoplasmic reticulum and numerous electron-dense secretory granules which are considered to be synthesized in the rough endoplasmic reticulum and transported to the Golgi apparatus to mature. They, which are somewhat similar to the pancreatic exocrine cells in fine structure, are believed to secrete the proteinous or mucoproteinous substances which might be related to the digestion of food.Zone 7 and 8 cells which might be homologous to the thyroid cell of the higher vertebrate contains poorly developed rough endoplasmic reticulum, small Golgi apparatus, a few multivesicular bodies, a few lysosomes, and numerous small vesicles. In addition zone 8 cells bear cilia on their apical surface. The cytoplasmic characteristics of these cell types, especially of zone 8 cells, are fairly similar to those of type 2C and type 3 cells of the endostyle of a larval lamprey, though the rough endoplasmic reticulum is not so well developed. By electron microscopic autoradiography numerous silver grains were observed on the apical cell membrane region of zone 7 and 8 cells, especially of zone 8 cells, 1, 4, 6, 16 and 24 hours after immersion in sea water containing¹²⁵I. This fact suggests that the iodination takes place in the apical cell membrane region of these cells. The materials in the endostylar lumen is washed away during the fixation and dehydrating processes of the tissue. Therefore, the possibility of iodination of thyroglobulin-like substances taking place within the endostylar lumen cannot be ruled out. Grains were also found in the multivesicular bodies and lysosomes after 4, 6, 16 and 24 hours, especially 16 and 24 hours. It seems that the organic iodine might be reabsorbed into the cytoplasm of these cells.This investigation was supported by research grant from Dr. Henry C. Buswell Research Fellowship.On leave from Department of Anatomy, Hiroshima University, School of Medicine, as a Visiting Research Professor. The authors wish to express their hearty thanks to Dr. Oliver P. Jones for his valuable criticism.     

Novel metrics for evaluating the functional coherence of protein groups via protein semantic network

We present the metrics for assessing overall functional coherence of a group of proteins based on associated biomedical literature. A probabilistic topic model is applied to extract biologic concepts from a corpus of protein-related biomedical literature. Bipartite protein semantic networks are constructed, so that the functional coherence of a protein group can be evaluated with metrics that measure the closeness and strength of connectivity of the proteins in the network.     

Controlling light absorption and photoelectric properties of coumarin-triphenylaminedye by different acceptor functional groups

The ground state and excited state properties of three coumarin dyes, ZCJ1, ZCJ2 and ZCJ3, including ground state structures, energy levels, absorption spectra and driving forces of electron injection, were investigated via density functional theory (DFT) and time-dependent density functional theory (TD-DFT). In addition, five new molecules ZCJ3-1, ZCJ3-2, ZCJ3-3, ZCJ3-4 and ZCJ3-5 were designed through the introduction of a –CN group into molecule ZCJ3. The ground state and excited state properties of the five designed molecules were also calculated and compared with that of the original molecule, aiming to investigate the effect of different position of –CN groups on the optical and electrical properties of dye molecules. Moreover, the external electric field was taken into account. The results indicated that all three original molecules have better absorption within the visible-light range, and the molecule with a thiophene–thiophene conjugated bridge enables a red shift of the absorption spectrum. The molecule with a thiophene–benzene ring conjugated bridge enables the increase of driving force of electron injection. The energy levels, spectra and driving force of electron injection for the designed molecules are discussed in terms of studying their potential utility in dye-sensitized solar cells.     

Performance analysis of molecularly imprinted polymers for carboxylate and aminophosphate templates using commercially available basic functional monomers

A survey of commercially available amine-based monomers for binding and selectivity of carboxylate and phosphonic acid templates has revealed that the best selectivity is found for the pyridine-based monomers, while the highest affinity was found for 2-(dimethylamino)ethyl methacrylate (2-DEMA, 1). In fact, a more general finding is that selectivity is higher for aromatic amine-based monomers even though affinity remains higher for aliphatic amine-based monomers. An attempt to combine the optimal properties of these two classes of amine monomers, i.e. 2-vinylpyridine (2-VPY, 2), and 2-DEMA by using both simultaneously in a single imprinted polymer resulted in an MIP whose properties were dominated by the aliphatic amine-based monomer 2-DEMA. A controversy between the two commercially available vinylpyridine monomers, 2-VPY and 4-vinylpyridine (4-VPY, 3), was investigated, revealing that neither monomer is generally better for molecular imprinting; rather, the choice of 2-VPY or 4-VPY is template specific (although the preponderance of data tends to frequently favor 4-VPY). Phosphonic acid templates proved to be less successful as templates for molecular imprinting versus carboxylate functionalized templates, although binding was obtained and shown to be controllable via an ion-exchange process.     

Fine tuning of vesicle assembly and properties using dual hydrophilic triblock copolypeptides

The design, synthesis, and self-assembly of the first dual hydrophilic triblock copolypeptide vesicles, R(H)(m)E(n)L(o) and K(P)(m)R(H)(n)L(o), is reported. Variation of the two distinct hydrophilic domains is used to tune cellular interactions without disrupting the self-assembled structure. The aqueous self-assemblies of these triblock copolypeptides in water are characterized using microscopy and DLS. Cell culture studies are used to evaluate cytotoxicity as well as intracellular uptake of the vesicles. The ability of polypeptides to incorporate ordered chain conformations that direct self-assembly, combined with the facile preparation of functional, multiblock copolypeptide sequences of defined lengths, allow the design of vesicles attractive for development as drug carriers.     

Fine structure and its functional properties of the ependymal cell in the frog median eminence

Summary Intercellular canaliculi surrounded by several ependymal cells, having numerous microvilli and a few cilia on the apical surface, are present throughout the frog median eminence. The intercellular canaliculi penetrate deeply near the portal vessel from the third ventricle. They are separated from the pericapillary space only by the thin cytoplasm of the ependymal cell.The cytoplasmic protrusions containing a large number of clear vesicles are often found at the apical surface of ependymal cells facing the third ventricle or the lumen of intercellular canaliculus. The ependymal cell shows well developed Golgi apparatus and well developed rough endoplasmic reticulum in its cytoplasm. Dense granules of about 1200–1500 A diameter suggesting secretory materials are found in small number near the Golgi apparatus and abundantly in the ependymal process lying around the portal vessel.Synaptic contacts between the ependymal cell and two different types of the nerve endings, monoaminergic and peptidergic, are frequently observed. A few small flasklike caveolae suggesting micropinocytosis are found in the post-synaptic membrane as well as in the lateral and basal plasma membranes of the ependymal cell. The author consideres that the ependymal cell in this region has secretory and transport (absorption) activities.     

Proteomics analysis of rat brain postsynaptic density. Implications of the diverse protein functional groups for the integration of synaptic physiology

The postsynaptic density contains multiple protein complexes that together relay the presynaptic neurotransmitter input to the activation of the postsynaptic neuron. In the present study we took two independent proteome approaches for the characterization of the protein complement of the postsynaptic density, namely 1) two-dimensional gel electrophoresis separation of proteins in conjunction with mass spectrometry to identify the tryptic peptides of the protein spots and 2) isolation of the trypsin-digested sample that was labeled with isotope-coded affinity tag, followed by liquid chromatography-tandem mass spectrometry for the partial separation and identification of the peptides, respectively. Functional grouping of the identified proteins indicates that the postsynaptic density is a structurally and functionally complex organelle that may be involved in a broad range of synaptic activities. These proteins include the receptors and ion channels for glutamate neurotransmission, proteins for maintenance and modulation of synaptic architecture, sorting and trafficking of membrane proteins, generation of anaerobic energy, scaffolding and signaling, local protein synthesis, and correct protein folding and breakdown of synaptic proteins. Together, these results imply that the postsynaptic density may have the ability to function (semi-) autonomously and may direct various cellular functions in order to integrate synaptic physiology.     

Classification of Reynolds phytoplankton functional groups using individual traits and machine learning techniques

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Fine tuning of physical properties of designed polypeptide multilayer films by control of pH

Adjustment of pH can alter the ensemble of three-dimensional structures of a polypeptide in solution by changing the distribution of charge and Coulombic interactions. The role of pH in layer-by-layer self-assembly (LbL) of designed 32mer peptides containing the amino acid cysteine has been investigated using a combination of physical methods. Results show that pH can have a substantial influence on the mass of adsorbed peptide, surface roughness, and film density over a range of 1.5 pH units. Peptide film thickness depends on the number of layers, as with "conventional" polyelectrolytes. Film density and morphology, however, vary more with pH than does thickness, translating into a change in density on the order of 70% over the pH range 7.4-8.9. Results of this work provide insight on the physical basis of LbL and suggest that peptides are a promising class of polyelectrolytes for the creation of designer thin films for applications in biotechnology and other areas.     

Micropatterning of biomolecules on glass surfaces modified with various functional groups using photoactivatable biotin

Biomolecule patterning by photolithographic methods has considerable advantages because a large number of different biomolecules can be assembled on a spatial area by a combinatorial method and complex biomolecule patterning can be created in situ in closed environments such as microfluidic channels. Here, a photobiotin was used as the photoactivatable reagent to create patterned arrays of biomolecules. The variability of photobiotin deposition on glass substrates modified with a variety of materials having carboxyl, lysine, aldehyde, amine groups, and BSA (bovine serum albumin) was characterized by subsequent derivatization with Cy3-labeled streptavidin. The fluorescence images of the photobiotin patterned glass surfaces showed that the BSA/aldehyde-coated glass could be considered as the most appropriate substrate to immobilize photobiotin, in view of the homogeneous immobilization of biomolecules with high density in defined regions and the reduction of nonspecific binding to the surface. In streptavidin equilibrium adsorption assays, the maximum amount of streptavidin-Cy3 bound to the BSA/aldehyde-coated glass surface continued to rise with increasing streptavidin-Cy3 concentration until 12.0 microg/mL was reached and the surface then became saturated. Also, a line array of biotin-labeled single-strand probe DNAs was created on the BSA/aldehyde-coated glass by photolysis of photobiotin through a slit-type mask and biotin/streptavidin/biotin chemistry, extended to a quantitative measurement of the concentrations of target DNA. The results of target DNA analysis showed linearity over a wide range from 0.5 ng/mL to 5 microg/mL and were reproducible.     

Extraction of watermelon seed proteins with enhanced functional properties using ultrasound

Abstract

Watermelon seed is the potential source of value-added proteins, oils, and carbohydrates. The present study evaluates the extraction, and functional properties of watermelon seed protein (WMSP) obtained by ultrasound-assisted extraction (UAE) method from watermelon seed (WMS). The optimization of various operating parameters, such as pH (9), WMS powder to solvent ratio (1:50 w/v), temperature (30?±?2?°C), ultrasound power (90?W), frequency (25?kHz), and duty cycle (75%) has been carried out. The extraction yield obtained was 87% and the extraction time was lowered down to 9?min from 120?min of conventional batch extraction. It contains all essential amino acids in an adequate amount required for adults as per FAO/WHO guidelines while for 2–5?years old children, the content of valine and isoleucine are above the required range. Methionine and lysine contents are adequate for both children and adults. Functional properties of ultrasonic extracted proteins were found superior to conventionally extracted proteins.

• highlights

• The UAE method is more efficient for watermelon seed protein extraction.

• Impact of extraction parameters on the extraction yield was studied.

• Protein isolate with enhanced functional properties was obtained.

• Essential amino acid content was determined.

     

Effect of glycoinositolphospholipid anchor lipid groups on functional properties of decay-accelerating factor protein in cells.

The inositol ring in the glycoinositolphospholipid (GPI) anchor of human decay-accelerating factor (DAF) is unmodified in nucleated cells, whereas it is fatty acid acylated in erythrocytes (Ehu). To assess the effect of this and of the glycerol sn-2-associated acyl substituent on the abilities of DAF to cell membrane incorporate and function, 1) endogenous (physiologically anchored) DAF proteins bearing three- and two-"footed" GPI anchors were purified from Ehu and HeLa cells and 2) synthetic DAF variants bearing alternative one- "footed" anchors (retaining either the sn-1 glycerol- or inositol-associated lipid) were prepared by alkaline hydroxylamine treatment and phosphatidylinositol-specific phospholipase D digestion of Ehu DAF, respectively. The different DAF species were added to antibody-sensitized sheep erythrocytes (EshA) and their abilities to insert into the plasma membranes of the cells and control subsequent complement activation on their surfaces were compared. DAF proteins bearing all four GPI anchor structures adhered to the Esh hemolytic intermediates and inhibited expression of C3 convertase (C4b2a) activity. However, mixing of DAF-treated EshA with untreated EshAC142 and stripping of cell-associated DAF proteins with vesicles showed that only the physiologically anchored proteins remained stably associated with the lipid bilayer and functioned intrinsically. Both three- and two-"footed" Ehu and HeLa DAF proteins exhibited comparable ability to incorporate and function in the intermediates as well as to accumulate to levels 1000-fold higher/cell in Schistosoma mansoni schistosomula. These findings indicate that 1) an intact inositolphospholipid-containing GPI anchor is necessary for stable membrane integration and intrinsic function, 2) endogenous GPI anchors (with either unsubstituted and acylated inositol) incorporate and function with comparable efficiency, and 3) the transfer of either endogenous DAF form can account for the previously described circumvented uptake of human C3b by blood stage schistosomula.     

Directed modification of the Tcr gene region of the plasmid pBR322 using complementary single-stranded DNA fragments carrying alkylating groups

A method is suggested for chemical modification of preselected regions of plasmid DNA by complementary single-stranded restriction fragments of DNA (srf DNA), carrying alkylating reagents. The gene coding for tetracycline resistance of plasmid pBR322 was used as a target. Srf DNA was prepared by a partial digestion of a double-stranded EcoRI-BamHI restriction fragment (377 base pairs) from Tcr by E. coli exonuclease III. The residues of an alkylating reagent N,N,N'-tri(beta-chlorethyl)-N'-(p-formylphenyl) propylenediamine 1,3 (TFP) were attached covalently to 4-5% of sfr DNA bases. The alkylating derivative of the sfr DNA was hybridized with supercoiled pBR322 plasmid DNA. The hybridization conditions (37 degrees C, 40% formamide, 0,2 M NaCl, 0,1 M Tris-HCl pH 7,5, 0,001 M EDTA) under which the bases carrying TFP residues are not eliminated from the sfr DNA, and transforming activity of pBR322 DNA does not decrease were established. It was shown that about 20% of plasmid pBR322 molecules form D-loops with alkylating sfr DNA under these conditions. It was shown that sfr DNA, carrying TFP can alkylate the complementary region of plasmid DNA, forming cross-linked D-loops. A method for the site-directed mutagenesis of switching off the preselected genes or non-transcribed DNA functional regions (promotors, introns etc) integrated into plasmids of other vectors is suggested.