Reactions of carbohydrate α-nitroepoxides with dimethylamine and with methylmagnesium iodide

Methyl 2,3-anhydro-4,6-O-benzylidene-3-C-nitro-β-d-allopyranoside (1), as well as its β-d-manno (2) and α- d-manno (3) isomers, reacted with dimethylamine to give the same, crystalline 3-(dimethylamino) adduct (4) of 1,5-anhydro-4,6-O-benzylidene-2-deoxy-2-(dimethylamino)-d-erythro-hex-1-en-3-ulose (5). The enulose 5 was obtained from 4 by the action of silica gel. Similarly, the β-d-gulo (6) and α-d-talo (7) stereoisomers of 1–3 afforded a 3-(dimethylamino) adduct (8) of the d-threo isomer (9) of 5. Reaction of dimethylamine with 5,6-anhydro-1,2-O-isopropylidene-6-C-nitro-α-d-glucofuranose (10) yielded a mixture of two diastereoisomeric (possibly anometic at C-6) 5-deoxy-5-(dimethylamino)-1,2-O-isopropylideric-α-d-hexodialdo-1,4:6,3-difuranoses (11). The β-glycoside 1 and the α-glycoside 3 reacted with methylmagnesium iodide to produce methyl 4,6-O-benzylidene-3-deoxy-3-C-methyl-3-(N-hydroxy-N-methylamino)-β- and -α-d-hexopyranosides (12) and (13), respectively; both products had the 1,2-trans configuration, but their configurations at the quaternary center C-3 have not been determined.     

β-structures of polypeptides with L- and D-residues

The possible formation of beta-structures from polypeptide chains with L-and D-Residues randomly distributed was statistically analyzed within the frame of two hypotheses. Firstly, only those segments containing residues of identical chirality can associate to form antiparallel beta-structures, and secondly these segments must have a minimum length. The influence of different factors was examined: initial ratio of the L-and D-monomer, minimum length required for the segments to be incorporated into beta-sheets, average length of the peptide molecules, and stereoselectivity in the course of the polymerization process. The results show that in all cases nuclei of beta-sheets surrounded by random coil segments are formed, the optical activity of which very increases to purity when the initial ratio of monomers deviates from the racemic mixture. This suggests experiments to enrich the system in one enantiomer. Comparison is made with the corresponding behavior and properties of the alpha-helical structure.     

β-structures of polypeptides with L- and D-residues

Summary It was previously shown that nuclei of-sheets surrounded by unordered segments are formed in polypeptide chains built up with alternating hydrophobic and hydrophilic residues and containing both L- and D-enantiomers. It was also established that segments of residues having the same configuration tend to segregate in these nuclei when the starting composition of stereomonomers departs from the racemic mixture.Soft acidic hydrolysis of these polymers has been studied. Kinetic measurements show two pseudo first order rate constants, in agreement with the existence of two conformational species. The unordered part of the chains is hydrolyzed more rapidly, allowing the isolation of a-fraction enriched in one enantiomer. Thus, a plausible process of enrichment in enantiomer during prebiotic evolution has been described, which however does not explain the preference of one enantiomer over the other one.     

β-structures of polypeptides with L- and D-residues

Summary A series of five alternating poly(leucyl-lysyl) samples with varying amounts of L- and D-residues randomly distributed along the chain, but evenly shared out amongst leucyl and lysyl residues were synthesized by condensation of a mixture of the four diastereoisomeric dipeptidep-nitro-phenylesters. Their behavior in aqueous solution at various ionic strengths was studied by infrared spectroscopy which allowed measurement of the total amount of-structures, and by circular dichroism which gives the excess of L-residues over D-residues in the same structures. Comparison with the properties of the all L-poly(Lys-Leu-Lys-Leu) shows that incorporation of a few D-residues in a L-chain seems to reduce the width of the-sheets obtained in presence of salt. Higher proportions of D-isomers prevent the coil transition from occurring when the ionic strength is increased except for segments containing at least 6 to 7 adjacent residues of the same configuration.     

Interactions of β-lactoglobulin with serotonin and arachidonyl serotonin

β‐Lactoglobulin (β‐LG) is a lipocalin, which is the major whey protein of cow's milk and the milk of other mammals. However, it is absent from human milk. The biological function of β‐LG is not clear, but its potential role in carrying fatty acids through the digestive tract has been suggested. β‐LG has been found in complexes with lipids such as butyric and oleic acids and has a high affinity for a wide variety of compounds. Serotonin (5‐hydroxytryptamine, 5‐HT), an important compound found in animals and plants, has various functions, including the regulation of mood, appetite, sleep, muscle contraction, and some cognitive functions such as memory and learning. In this study, the interaction of serotonin and one of its derivatives, arachidonyl serotonin (AA‐5HT), with β‐LG was investigated using circular dichroism (CD) and fluorescence intensity measurements. These two ligands interact with β‐LG forming equimolar complexes. The binding constant for the serotonin/β‐LG interaction is between 10⁵ and 10⁶ M⁻¹, whereas for the AA‐5HT/β‐LG complex it is between 10⁴ and 10⁵ M⁻¹ as determined by measurements of either protein or ligand fluorescence. The observed binding affinities were higher in hydroethanolic media (25% EtOH). The interactions between serotonin/β‐LG and AA‐5HT/β‐LG may compete with self‐association (micellization) of both the ligand and the protein. According to far‐ and near‐UV CD results, these ligands have no apparent influence on β‐LG secondary structure, however they partially destabilize its tertiary structure. Their binding by β‐LG may be one of the peripheral mechanisms of the regulation of the content of serotonin and its derivatives in the bowel of milk‐fed animals. © 2011 Wiley Periodicals, Inc. Biopolymers 95: 871–880, 2011.     

Exploration of the activation pathway of Δα-Chymotrypsin with molecular dynamics simulations and correlation with kinetic experiments

Correlating the experimentally observed kinetics of protein conformational changes with theoretical predictions is a formidable and challenging task, due to the multitude of degrees of freedom (>5,000) in a protein and the huge gap between the timescale of the kinetic event of interest (ms) and the typical timescale of computer simulations (ns). In this study we show that using the targeted molecular dynamics (TMD) method it is possible to simulate conformational changes of the ms time range and to correlate multiple simulations of single pathways with ensemble experiments on both the structural and energetic basis. As a model system we chose to study the conformational change of rat-Δα-chymotrypsin from its inactive to its active conformation. This activation process has been analyzed previously by experimental and theoretical methods, i.e. fluorescence stopped-flow spectroscopy (FSF), molecular dynamics (MD) and TMD. Inspired by the results of these studies on the wild type (WT) enzyme, several mutants were constructed to alter the conformational pathway and studied by FSF measurements. In the present work WT and mutant N18G were subjected to multiple MD and subsequent TMD simulations. We report the existence of two main activation pathways, a feature of chymotrypsin activation that has been hitherto unknown. A method to correlate the energetics of the different pathways calculated by TMD and the kinetic parameters observed by experimental methods such as FSF is presented. Our work is relevant for experimental single molecule studies of enzymes in general. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Model of synthesis and release of insulin from rat islet β-cells and the effect of pretreatment with tolbutamide

A kinetic model involving synthesis of proinsulin in the rough endoplasmic reticulum, maturation through the Golgi apparatus and granules, with conversion to insulin, is proposed to account for data on the amount of insulin and of proinsulin both secreted during various time intervals and remaining in islets. Introducing three compartments for granules makes it possible to account for the measurement of both hot (pulse labeled with tritiated leucine) and cold proinsulin and insulin over a period of 21/2 hr under constant glucose. Data from islets from animals pretreated with tolbutamide are also presented and modeled. The model is then expanded so that it can be successfully applied to available data on the effects of a period of glucose deprivation on secretion of both hot and cold hormone. Parameters have essentially the same values, where they overlap, as were obtained (Landahl and Grodsky, 1982Bull. math. Biol. 44, 399–410) from insulin secretion by perfused rat pancreas stimulated by a variety of temporal patterns of glucose concentration.     

Binding of α-synuclein with Fe(III) and with Fe(II) and biological implications of the resultant complexes

Parkinson’s disease (PD) is hallmarked by the abnormal intracellular inclusions (Lewy bodies or LBs) in dopaminergic cells. Amyloidogenic protein α-synuclein (α-syn) and iron (including both Fe(III) and Fe(II)) are both found to be present in LBs. The interaction between iron and α-syn might have important biological relevance to PD etiology. Previously, a moderate binding affinity between α-syn and Fe(II) (5.8 × 10³ M⁻¹) has been measured, but studies on the binding between α-syn and Fe(III) have not been reported. In this work, electrospray mass spectrometry (ES-MS), cyclic voltammetry (CV), and fluorescence spectroscopy were used to study the binding between α-syn and Fe(II) and the redox property of the resultant α-syn-Fe(II) complex. The complex is of a 1:1 stoichiometry and can be readily oxidized electrochemically and chemically (by O₂) to the putative α-syn-Fe(III) complex, with H₂O₂ as a co-product. The reduction potential was estimated to be 0.025 V vs. Ag/AgCl, which represents a shift by −0.550 V vs. the standard reduction potential of the free Fe(III)/Fe(II) couple. Such a shift allows a binding constant between α-syn and Fe(III), 1.2 × 10¹³ M⁻¹, to be deduced. Despite the relatively high binding affinity, α-syn-Fe(III) generated from the oxidation of α-syn-Fe(II) still dissociates due to the stronger tendency of Fe(III) to hydrolyze to Fe(OH)₃ and/or ferrihydrite gel. The roles of α-syn and its interaction with Fe(III) and/or Fe(II) are discussed in the context of oxidative stress, metal-catalyzed α-syn aggregation, and iron transfer processes.     

Reaction of Toxic Bicyclic Phosphates with Acetylcholinesterases and α-Chymotrypsin

Some toxic bicyclic phosphates (BPs) inhibited acetylcholinesterases (AChEs), but the activity was very weak. Even the most potent inhibitor, 4-nitro BP, inhibited bovine erythrocyte and housefly head AChEs by only 37 and 38 per cent, respectively, at 1.5 mm. Kinetic analysis indicated that the poor inhibitory activity of 4-nitro BP is ascribed not only to the low affinity for AChEs but also to its poor phosphorylating ability. Similar findings were obtained in the case of the reaction of BPs with the serine enzyme α-chymotrypsin. Despite the relatively high reactivity in an alkaline solution, BPs are much less active than other bioactive organophosphorus esters in phosphorylating a general-base-catalyzed hydroxyl group. This fact suggests that the toxic action of BPs does not result from the phosphorylation of a critical site in biological systems.     

Synergism of 1-β-d-arabinofuranosylcytosine with itself and aphidicolin

JU56 cells have been exposed to 1-β-d-arabinofuranosylcytosine (ara-C) in S phase, and again to aphidicolin (APC) or ara-C during G₂, and examined for chromosomal aberrations at c-metaphase. It was found that the two exposures acted synergistically in the production of chromosomal lesions of both the chromatid and isochromatid type. The results were interpreted as indicating that inhibition of the G₂ repair system prevented the repair of DNA single-strand regions produced by the incorporation of ara-C during semiconservative DNA synthesis.     

Occurrence of Transaminations with Pyruvate andα-Ketoglutarate inAcetobacter suboxydans

Transaminations betweenL-amino acids and pyruvate orα-ketoglutarate(α-KGA) were observed in a cell-free extract ofAcetobacter suboxydans(Gluconobacter suboxydans IFO 3172). The level of the activities of transaminations with pyruvate was greatly influenced by the kinds and amounts of nitrogen sources for growth media. The enzymic activities of transaminations with pyruvate in glutamate-grown cells were extremely higher than in yeast ex- tract-grown cells. Nutritional components decreasing the activities were presumed to be some of amino acids and ammonium ion present in yeast extract. The activities of transaminations withα-KGA were not so variable in the presence or absence of the components.

The optimum pH of transaminations with pyruvate was in the range of 5.0 ~ 5.5 and that of the reaction withα-KGA in 8.0 ~ 8.5. The optimum temperature of the former was 65°C and that of the latter about 45°C. Some other different properties were also recognized between the two kinds of reactions.     

Isolation of mutants of Penicillium purpurogenum with enhanced xylanase and β-xylosidase production

Penicillium purpurogenum was mutated with u.v. light to increase xylanase production. The best mutant, UV-64, was treated with N-methyl-N'-nitro-N-nitrosoguanidine and a second generation of mutants was obtained (NG-188 and NG-737). NG-737 produced 125 U of xylanase/ml when grown on oat spelts xylan supplemented with wheat bran compared with 69 U/ml for the wild-type strain. The mutants also showed a 2.2-fold increase in -xylosidase as compared with the wild-type.     

Physicochemical Aspects of Reaction of Ozone with Galactolipid and Galactolipid–Tocopherol Layers

The impact of reaction of galactolipids with ozone on the physicochemical properties of their monolayers was examined. In Megli and Russo (Biochim Biophys Acta, 1778:143–152, 2008), Cwiklik and Jungwirth (Chem Phys Lett, 486:99–103, 2010), Jurkiewicz et al. (Biochim Biophys Acta, 1818:2388–2402, 2012), Khabiri et al. (Chem Phys Lett, 519:93–99, 2012), and Conte et al. (Biochim Biophys Acta, 1828:510–517, 2013), the properties of layers formed from model mixtures composed of chosen lipids and selected oxidation products were studied, whereas in this work, question was raised as to how the oxidation reactions taking place in situ affect the physical properties of the galactolipid layers. So, set experiment should take into account the effect of all reaction products. The mechanical characteristics of monolayers of monogalactosyldiacyl-glycerol (MGDG) and digalactosyldiacylglycerol (DGDG) were determined by Langmuir trough technique, and the electrical properties of liposomes formed from these lipids by measuring their electrophoretic mobility. Considerable loss of galactolipid molecules forming monolayers was found at ozone concentrations (in aqueous medium) higher than 0.1 ppm with a stronger effect measured for MGDG. That goes along with the greater amounts of MDA found in the extracts of oxidized MGDG films compared with DGDG. Based on this, it was concluded that an additional galactose group present in DGDG molecules acts protectively under oxidative conditions. The surface tension of the solutions (of small volume) contacting the oxidized galactolipids films was significantly reduced, indicating the presence of soluble in polar media, surface active reaction products. The presence of α-tocopherol in mixtures with tested galactolipids at a molar ratio of lipid to tocopherol equal to 1.7:1 caused some inhibition of lipid oxidation, reducing the decrease of amount of lipid particles forming the monolayer. Here, also protective effect of α-tocopherol was greater for the MGDG compared to DGDG.     

Characterisation and properties of the inclusion complex of 24-epibrassinolide with β-cyclodextrin

This paper reports the first study of an inclusion complex of abrassinosteroid with -cyclodextrin. The formation of inclusion complexesbetween 24-epibrassinolide and -cyclodextrin was confirmed by theirphysicochemical properties and the compounds were analysed by differentialscanning calorimetry, powder X-ray diffraction, nuclear magnetic resonancespectrometry and scanning electron microscopy. Theoretical calculations usingthe MM+ HyperChem force field showed a preference for inclusion of thesidechain of the epibrassinolide molecule into the -cyclodextrin cavity toform a 1:1 inclusion complex, although complexes involving inclusion ofthe steroidal nucleus also possess a favourable interaction energy. Rice laminainclination assay, employing IAC-103 and IAC-104 cultivars, showed an improvedactivity for the epibrassinolide-cyclodextrin complex compared to theepibrassinolide itself. The results suggest that brassinosteroid complexationwith cyclodextrins may enhance the biological activity of these plant growthregulators.     

Cuticular strength and pigmentation of rust-red and black strains of Tribolium castaneum: Correlation with catecholamine and β-alanine content

Rust-red wild and black mutant strains of the red flour beetle, Tribolium castaneum, were used to investigate temporal patterns of catecholamine and β-alanine content during sclerotization and pigmentation of adult cuticle and to relate these patterns to corresponding changes in cuticle resistance to puncture. Rust-red elytral cuticle sclerotized more rapidly than black cuticle until 6 days after adult eclosion when both became equal in puncture resistance. The cuticular concentrations of $\text{N-β-}\text{alanyldopamine}$ (NBAD), β-alanine and 3,4-dihydroxyphenylacetic acid (DOPAC) increased more rapidly in the rust-red strain than in the black strain during the first 7 days following adult eclosion. Conversely, cuticular dopamine increased more rapidly in black than in the red strain. Thus the rust-red pigmentation and rapid sclerotization appear to be related to the availability of β-alanine, $\text{N-β-}\text{alanyldopamine}$ and DOPAC. Melanization was prevented and rust-red pigmentation induced by injections of β-alanine or NBAD into newly ecdysed black mutant beetles. Crosses of the two strains generally had intermediate levels of cuticular dopamine and β-alanine, but the NBAD levels were similar to those of the rust-red strain. Dopamine, NBAD and DOPAC levels became similar in both black and rust-red strains about 6 days after adult ecdysis as did resistance to puncture. Therefore, dopamine appears to be directed initially into the melanin pathway in black adults due to a temporary lack of $\text{N-}\text{acylation}$ with β-alanine. After the melanization phase, dopamine is metabolized to sclerotization precursors eventually resulting in normal physical properties of the exoskeleton.     

Interaction of Tetrahydrocortisol–Apolipoprotein A-I Complex with Eukaryotic DNA and with Single-Stranded Oligonucleotides

The complex formed by tetrahydrocortisol (THC) and apolipoprotein A-I (ApoAI) specifically interacts with eukaryotic DNA from rat liver. Taken together, physical and chemical data and the results of small-angle X-ray scattering analysis show that interaction of the THC–ApoAI complex with eukaryotic DNA results in deformation of the DNA double helix. Single-stranded fragments were demonstrated to cause deformation of the double helix. In this state DNA forms complexes with DNA-dependent RNA polymerase. This interaction is cooperative and of saturating type; up to six enzyme molecules bind with one DNA molecule. The putative site of complex binding with DNA is the sequence CC(GCC)_n found in many genes including the human ApoAI gene. An oligonucleotide of this type was synthesized. Its association constant (K _a) was 1.66·10⁶ M^–1. Substitution of THC with cortisol considerably decreases the K _a. We suggest that THC interacting with GC pairs of the binding site forms hydrogen bonds with cytosine, inducing rupture of the bonds within the complementary nucleic base pair.     

Isolation and identification of a staphylococal strain with an anti-mycobacterial activity and study of it’s mode of action

The resistance of mycobacteria to the clinical applied antibiotics poses a serious problem to deal with the infections they cause. So, the search for new antibiotics active against these bacteria becomes urgent. We report here the isolation from a Moroccan biotope of a bacterial strain secreting an active substance of protein nature that inhibits the growth of several mycobacterial species (Mycobacterium smegmatis; M. aurum A+;M. vaccae; M. bovis BCG andM. kansasii). PCR amplification and DNA sequecing of the 16S ribosomal RNA gene allowed the identification of this strain asStaphylococcus haemolyticus. Moreover, the substance produced by this strain was able to lyse the wall ofM. smegmatis and to extract its genomic DNA indicating that it acts probably, like others anti-mycobacterial antibiotics, on this envelope. The identification and characterisation of the active substance would open the way for further technological and therapeutic investigations.     

Subgroups of Tcr α chains and correlation with T-cell function

T-cell receptor (Tcr) chains are classified into four subgroups (I, II, III, and miscellaneous) based on the amino acid residues at positions 61 and 62. Subgroup I has Gly Phe at these positions, subgroup II has Arg Phe, subgroup III has Arg Leu, and subgroup miscellaneous has several other combinations. Variability plots for subgroups I, II, and III sequences show higher values around positions 93–103, 105, 108, 111, 113, and 115, suggesting that these positions may interact with the processed antigen molecules. Smaller peaks are present at various other regions which may bind the major histocompatibility complex class I or II molecules. The patterns of variability within one subgroup are similar for all species, for human alone, and for mouse alone. These subgroup patterns appear much less complicated than patterns for sequences in all subgroups taken together, implying that subgroups may be related to Tcr functions. Among 83 mouse chains, 15 are from cytotoxic cells and 40 from helper cells. Of the 15 from cytotoxic cells, 11, 2, 0, and 2 are in subgroups I, II, III, and miscellaneous; and of the 40 from helper cells, 9, 16, 12, ans 3 are in subgroups I, II, III, and miscellaneous, respectively. Thus, a correlation between sequence and function of Tcr chains seems possible. Address correspondence and offprint requests to: M. Schiffer.     

Coordination of magnesium with adenosine 5′-diphosphate and triphosphate

³¹P NMR chemical shifts of salts of adenosine 5′-triphosphate and diphosphate: ATPH^2?₂2(Me₄N⁺) · H₂O, ATPH^2?₂2 Na⁺ · 3.5 H₂O, ATPH^2?₂Mg²⁺ · 4 H₂O, ATPH^2?₂Ca²⁺ · 2 H₂O, ADPH^2?2(Me₄N⁺) · H₂O and ADPH^2?Mg²⁺ · 4 H₂O have been measured in 0.02 M ²H₂O solutions at 145.7 MHz (22° C) at constant p²H values (8.20 and 6.20). The results are compared with those obtained from salts of adenosine 5′-monophosphate and other simpler phosphomonoesters, e.g. AMP^2?2(Me₄N⁺), AMP^2?Mg²⁺, AMPH^?Me₄N⁺ and (AMPH^?)₂Mg²⁺. It is concluded that the effects exerted by Mg²⁺ and Ca²⁺ on the ³¹P NMR shifts of dipoly- and tripolyphosphates relative to monovalent cations are due mainly to changes in conformation of the polyphosphate chain rather than to purely electronic factors associated with the binding of divalent cations to the phospho-oxyanions. The data are consistent with the existence of the following complexes at p²H 8.20: (MgP_αP_β)ADP^? and (MgP_αP_γ)ATP^2?af (MgP_αP_β)ATP^2?af (MgP_βP_γ)ATP^2? with the latter equilibrium relatively fast in the NMR time scale. Monoprotonation of the terminal phosphate appears to weaken the Mg²⁺-polyphosphate binding, particularly at P_β of MgADPH and at P_β and P_γ of MgATPH^?. The Mg²⁺-polyphosphate binding weakens further at p²H 3.70, i.e. in MgATPH₂. Possible implications of the results in the mechanism of actomyosin Mg²⁺-ATPase in muscle contraction are discussed.     

Computer modeling of δ opioid receptor and interaction with ligands

Summary Human σ opioid receptor (σOR), a G-protein-coupled receptor, has been modeled using the helix axes as revealed by the crystallographic structure of bacteriorhodopsin and ligand binding profiles of single-point mutants of σOR. The model revealed feasibility of existence of a second disulfide bridge between the transmembrane helices (TMHs) 6 and 7, Cys²⁷³-Cys³⁰³. A common binding site has been suggested for high-affinity selective agonists DPDPE, DPLPE, DTLET, BW373U86 and antagonist Naltrindole. Docking calculations have shown that the amino group of the ligands forms a hydrogen bond with the imidazole ring of His³⁰¹ (TMH7) rather than with Asp¹²⁸ (TMH3) and is not a cation counterpart of this highly conserved aspartyl residue. All the findings and the model shed light on the putative structure and functioning of opioid receptors and can be used for designing further mutagenesis experiments.