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Complex Molecules (complex + molecule)
Kinds of Complex Molecules Selected AbstractsJ -Based Analysis and DFT,NMR Assignments of Natural Complex Molecules: Application to 3,,7-Dihydroxy-5,6-epoxycholestanesEUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 23 2008Jesús Javier Poza Abstract In order to reproduce the stereochemical dispositions of the epoxy and hydroxy functionalities, four 3,,7-hydroxy-5,6-epoxycholestanes were easily prepared from cholesterol, and their NMR spectroscopic data were experimentally obtained from 1D and 2D NMR experiments. An exhaustive QM- J -based analysis was then performed to replicate the experimental H,H and C,H coupling constants as well as the 13C NMR chemical shifts. The B3LYP GIAO methodology with the 6-311-G(d,p) basis set was chosen and showed that the data obtained from rings A and B were sufficient to calculate the correct stereochemistry of the 5,6-epoxy and 7-hydroxy groups. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2008) [source] A New Group Contribution Method based on Equation of State Parameters to Evaluate the Critical Properties of Simple and Complex MoleculesTHE CANADIAN JOURNAL OF CHEMICAL ENGINEERING, Issue 4 2006José O. Valderrama Abstract A new group contribution method to evaluate the critical properties (temperature, pressure and volume) is presented and applied to estimate the critical properties of biomolecules. Similar to other group contribution methods, the one proposed here divides the molecule into conveniently defined groups and evaluates the properties as the sum of the different contributions according to a specified model equation for each of the properties. The proposed method consists of a one-step calculation that uses simple model equations and does not require additional data besides the knowledge of the structure of the molecule, except for isomers. For these substances the normal boiling temperature, the molecular mass and the number of atoms in the molecule are used to distinguish among isomers. The method is applicable to high molecular weight compounds, as most biomolecules and large molecules present in natural products. On présente une nouvelle méthode de contribution de groupe pour évaluer les propriétés critiques (température, pression et volume) de biomolécules. Comme dans le cas d'autres méthodes de contribution de groupe, celle qu'on présente ici divise la molécule en groupes définis de manière pratique et évalue les propriétés comme la somme des différentes contributions selon une équation de modèle spécifique pour chacune des propriétés. La méthode proposée consiste en un calcul en une étape qui utilise des équations de modèle simple et, excepté pour les isomères, ne requiert pas de données supplémentaires hormis la structure de la molécule. Pour ces substances, on utilise la température d'ébullition normale, la masse moléculaire et le nombre d'atomes dans la molécule pour distinguer entre les isomères. La méthode est applicable à des composés de poids moléculaire élevé, comme la plupart des biomolécules et des molécules larges présentes dans les produits naturels. [source] Structure Comparison of Early and Late Lanthanide(III) Homodinuclear Macrocyclic Complexes with the Polyamine Polycarboxylic Ligand H8OHECEUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 19 2004Ulrike A. Böttger Abstract The solid-state structures of two new homodinuclear chelate complexes with the late lanthanide(III) ions Yb and Lu, [Na2(Yb2OHEC)].14.5H2O (1), and [Na2(Lu2OHEC)].14.5H2O (2) (H8OHEC = 1,4,7,10,14,17,20,23-octaazacyclohexacosane- 1,4,7,10,14,17,20,23-octaacetic acid), have been determined by X-ray crystal structure analysis. Each lanthanide(III) ion is coordinated by eight donor atoms of the ligand and the geometry of the coordination polyhedron approaches a bicapped trigonal prism. These structures are compared with those of the homodinuclear chelate complexes with the same ligand and the mid to early lanthanide(III) ions Gd, Eu, La and also Y. A distinctive structural change occurs across the lanthanide series. The centrosymmetric mid to early lanthanide(III) complexes are all ninefold-coordinated in a capped square antiprismatic arrangement with a water molecule coordinated in a prismatic position. This structure is maintained in aqueous solution, together with an asymmetric minor isomer. The late lanthanide(III) OHEC complexes not only lack the inner-sphere water, but the change of coordination sphere also results in a loss of symmetry of the whole complex molecule. The observed change of coordination mode and number of the lanthanide ion may offer a geometric model for the isomerization process in eight- and ninefold-coordinated complex species that are isomers in a possible coordination equilibrium observed by NMR in aqueous solution. This model may also explain the intramolecular rearrangements necessary during water exchange in the inner coordination sphere of the complex [(Gd2OHEC)(H2O)2]2, through a slow dissociative mechanism. Protonation constants of the H8OHEC ligand and complex formation constants of this ligand with GdIII, CaII, CuII and ZnII have been determined by solution thermodynamic studies. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2004) [source] IDENTIFYING COEVOLUTIONARY PATTERNS IN HUMAN LEUKOCYTE ANTIGEN (HLA) MOLECULESEVOLUTION, Issue 5 2010Xiaowei Jiang The antigenic peptide, major histocompatibility complex molecule (MHC; also called human leukocyte antigen, HLA), coreceptor CD8, or CD4 and T-cell receptor (TCR) function as a complex to initiate effectors' mechanisms of the immune system. The tight functional and physical interaction among these molecules may have involved strong coevolution links among domains within and between proteins. Despite the importance of unraveling such dependencies to understand the arms race of host,pathogen interaction, no previous studies have aimed at achieving such an objective. Here, we perform an exhaustive coevolution analysis and show that indeed such dependencies are strongly shaping the evolution and probably the function of these molecules. We identify intramolecular coevolution in HLA class I and II at domains important for their immune activity. Most of the amino acid sites identified to be coevolving in HLAI have been also detected to undergo positive Darwinian selection highlighting therefore their adaptive value. We also identify coevolution among antigen-binding pockets (P1-P9) and among these and TCR-binding sites. Conversely to HLAI, coevolution is weaker in HLAII. Our results support that such coevolutionary patterns are due to selective pressures of host,pathogen coevolution and cooperative binding of TCRs, antigenic peptides, and CD8/CD4 to HLAI and HLAII. [source] X-ray structure study of the light-induced metastable states of the spin-crossover compound [Fe(mtz)6](BF4)2JOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 3 2001Joachim Kusz Iron(II) complexes exhibiting thermal spin-crossover may be converted from the 1A1 low-spin (LS) state to the 5T2 high-spin (HS) state by irradiation with green light (light-induced excited spin-state trapping, LIESST) and from the LS to the HS state by irradiation with red light (reverse LIESST). The lifetime of the metastable LIESST states may be sufficiently long to enable an X-ray diffraction study. The lattice parameters of a single crystal of [Fe(mtz)6](BF4)2 (mtz = methyltetrazole) (space group P21/n) were measured between 300 and 10,K. While one Fe lattice site (A) of the crystal changes from the HS to the LS state near 78,K, the other site (B) remains in the LS state. Using the green light (514,nm) of an argon ion laser the crystal was quantitatively converted to the HS state at 10,K. Irradiation of the crystal at 10,K by red light of a laser diode (820,nm) with site A in the LS and site B in the HS state converts site B almost completely to the LS state. The lattice parameters of both metastable states were measured up to 50,K, where they start to decay on a minute timescale. At 10,K, a full data set for evaluation of the crystal structure was recorded. The volume change of the crystal per complex molecule accompanying the spin transition is 31.5,Å3 at site A and close to zero [,0.21,(14),Å3] at site B. [source] Novel interactions of perlecan: Unraveling perlecan's role in angiogenesisMICROSCOPY RESEARCH AND TECHNIQUE, Issue 5 2008Gregory Bix Abstract Perlecan, a highly conserved and ubiquitous basement membrane heparan sulfate proteoglycan, is essential for life, inasmuch as its absence results in embryonic lethality in mice and C. elegans, and neonatal lethality in humans. Perlecan plays an essential role in vasculogenesis and chondrogenesis, as well as in pathological states where these processes are maladapted. Although a large body of evidence supports a pro-angiogenic role for perlecan, recent findings suggests that portions of the perlecan protein core can be antiangiogenic, requiring a further evaluation of the functioning of this complex molecule. This review is focused on the genetics of mammalian and nonmammalian perlecan, the elucidation of its novel interacting partners and its role in angiogenesis. By more fully understanding perlecan's functioning in angiogenesis, we may gain invaluable insight that could lead to therapeutic interventions in cancer and other pathologic states. Microsc. Res. Tech., 2008. © 2008 Wiley-Liss, Inc. [source] DFT Based Atomic Softness and Its Application in Site SelectivityMOLECULAR INFORMATICS, Issue 8 2003P. Singh Abstract Active site of a complex molecule and mechanism of chemical reaction has been studied with the help of atomic softness values derived from calculation based on Density functional theory. The quantum mechanical equation of Klopman has been solved with the help of AM1 calculation by using Win MOPAC7.21 software. On the basis of chemical potential equalization principle, and Koopmans theorem for frontier orbitals a formalism has been developed for the calculation of electron affinity of an atom in a molecule EA. The reliability of the EA values have been tested with electron density (obtained from AM1 calculation) and Fukui function values taken from literature. [source] Peptide-induced suppression of collagen-induced arthritis in HLA,DR1 transgenic miceARTHRITIS & RHEUMATISM, Issue 12 2002Linda K. Myers Objective To identify peptides capable of altering the immune response to type II collagen (CII) in the context of HLA,DR. Methods Immunizing mice transgenic for the human HLA,DRB1*0101 immune response gene with CII elicits an arthritis (collagen-induced arthritis [CIA]) that resembles rheumatoid arthritis. We have previously identified an immunodominant determinant of CII, CII (263,270), recognized by T cells in the context of DR1. To produce synthetic peptides with the potential of disrupting the DR1-restricted immune response, synthetic analog peptides were developed that contain site-directed substitutions in critical positions. These peptides were used to treat CIA in DR1 transgenic mice. Results An analog peptide, CII (256,276, N263, D266), that inhibited T cell responses in vitro, was identified. When DR1 mice were coimmunized with CII and CII (256,276, N263, D266), the incidence and severity of arthritis were greatly reduced, as was the antibody response to CII. Moreover, CII (256,276, N263, D266) was effective in down-regulating the immune responses to CII and arthritis, even when administered 2 weeks following immunization with CII. Spleen and lymph node cells from CII-immunized mice cultured with CII (256,276, N263, D266) in vitro produced increased amounts of interleukin-4 (IL-4) compared with cells cultured with the wild-type peptide, CII (256,276). Furthermore, CII (256,276, N263, D266) was incapable of preventing arthritis in DR1 IL-4,/, mice (genetically deficient in IL-4). Conclusion These data establish that CII (256,276, N263, D266) is a potent suppressor of the DR-mediated immune response to CII. Its effect is mediated, at least in part, by IL-4. These experiments represent the first description of an analog peptide of CII recognized by T cells in the context of a human major histocompatibility complex molecule that can suppress autoimmune arthritis. [source] Production of native and modified recombinant Der p 1 molecules in tobacco plantsCLINICAL & EXPERIMENTAL ALLERGY, Issue 5 2009D. Burtin Summary Background As a complex molecule requiring post-translational processing, it has been difficult to produce the Der p 1 major allergen from the Dermatophagoides pteronyssinus house dust mite in a recombinant form. Objective Here, we tested whether transgenic tobacco plants are suitable to express Der p 1, either as a wild-type molecule or as variants lacking N -glycosylation sites (Gly,) and/or cysteine protease activity (Enz,). Methods Using Agrobacterium tumefaciens -based transformation, pro Der p 1 molecules bearing mutations within either the N -glycosylation sites (N34Q, N150Q) and/or the cysteine protease-active site (C132V) were expressed in tobacco plants. After purification by ion exchange chromatography, allergens were characterized using immunoblotting, circular dichroism (CD), as well as basophil and T lymphocyte stimulation assays. Results Four forms of recombinant Der p 1 (i.e. wild-type Gly+/Enz+, as well as Gly,/Enz+, Gly+/Enz, or Gly,/Enz, variants) were successfully expressed in tobacco leaves as pro Der p 1 molecules. Spontaneous cleavage of the pro-peptide was observed in tobacco leaf extracts for all forms of recombinant Der p 1 (r Der p 1). CD confirmed that all r Der p 1 molecules, with the exception of the Gly,/Enz, variant, exhibited secondary structures comparable to the natural protein. A cysteine protease activity was associated only with the Gly+/Enz+ form. All these molecules exhibit a profile similar to natural Der p 1 with respect to IgE immunoreactivity, basophil activation and T cell recognition. Conclusion A tobacco plant expression system allows the production of various forms of mature Der p 1, which could be used for diagnostic or immunotherapeutic purposes. [source] Interplay between T helper type 1 and type 2 cytokines and soluble major histocompatibility complex molecules: a paradigm in pregnancyIMMUNOLOGY, Issue 3 2002I. Athanassakis No abstract is available for this article. [source] Mineral phosphate solubilization by rhizosphere bacteria and scope for manipulation of the direct oxidation pathway involving glucose dehydrogenaseJOURNAL OF APPLIED MICROBIOLOGY, Issue 1 2010B. Sashidhar Summary Microbial biodiversity in the soil plays a significant role in metabolism of complex molecules, helps in plant nutrition and offers countless new genes, biochemical pathways, antibiotics and other metabolites, useful molecules for agronomic productivity. Phosphorus being the second most important macro-nutrient required by the plants, next to nitrogen, its availability in soluble form in the soils is of great importance in agriculture. Microbes present in the soil employ different strategies to make use of unavailable forms of phosphate and in turn also help plants making phosphate available for plant use. Azotobacter, a free-living nitrogen fixer, is known to increase the fertility of the soil and in turn the productivity of different crops. The glucose dehydrogenase gene, the first enzyme in the direct oxidation pathway, contributes significantly to mineral phosphate solubilization ability in several Gram-negative bacteria. It is possible to enhance further the biofertilizer potential of plant growth-promoting rhizobacteria by introducing the genes involved mineral phosphate solubilization without affecting their ability to fix nitrogen or produce phytohormones for dual benefit to agricultural crops. Glucose dehydrogenases from Gram-negative bacteria can be engineered to improve their ability to use different substrates, function at higher temperatures and EDTA tolerance, etc., through site-directed mutagenesis. [source] Green chemistry for the second generation biorefinery,sustainable chemical manufacturing based on biomassJOURNAL OF CHEMICAL TECHNOLOGY & BIOTECHNOLOGY, Issue 7 2007James H Clark The material needs of society are reaching a crisis point. The demands of a growing and developing world population will soon exceed the capacity of our present fossil resource based infrastructure. In particular, the chemical industry that underpins most industries needs to respond to these challenges. The chemical manufacturing and user industries face an unprecedented range and intensity of drivers for change, the greatest of which, REACH (Registration, Evaluation and Authorisation of Chemicals) has yet to bite. In order to address the key issues of switching to renewable resources, avoiding hazardous and polluting processes, and manufacturing and using safe and environmentally compatible products, we need to develop sustainable and green chemical product supply chains. For organic chemicals and materials these need to operate under agreed and strict criteria and need to start with widely available, totally renewable and low cost carbon,the only source is biomass and the conversion of biomass into useful products will be carried out in biorefineries. Where these operate at present, their product range is largely limited to simple materials (e.g. cellulose), chemicals (e.g. ethanol) and bioenergy/biofuels. Second generation biorefineries need to build on the need for sustainable chemical products through modern and proven green chemical technologies such as bioprocessing, controlled pyrolysis, catalysis in water and microwave activation, in order to make more complex molecules and materials on which a future sustainable society will be based. Copyright © 2007 Society of Chemical Industry [source] Exquisite specificity and peptide epitope recognition promiscuity, properties shared by antibodies from sharks to humansJOURNAL OF MOLECULAR RECOGNITION, Issue 2 2001John J. Marchalonis Abstract This review considers definitions of the specificity of antibodies including the development of recent concepts of recognition polyspecificity and epitope promiscuity. Using sets of homologous and unrelated peptides derived from the sequences of immunoglobulin and T cell receptor chains we offer operational definitions of cross-reactivity by investigating correlations of either identities in amino acid sequence, or in hydrophobicity/hydrophilicity profiles with degree of binding in enzyme-linked immunosorbent assays. Polyreactivity, or polyspecificity, are terms used to denote binding of a monoclonal antibody or purified antibody preparation to large complex molecules that are structurally unrelated, such as thyroglobulin and DNA. As a first approximation, there is a linear correlation between degree of sequence identity or hydrophobicity/hydrophilicity and antigenic cross-binding. However, catastrophic interchanges of amino acids can occur where changing of one amino acid out of 16 in a synthetic peptide essentially eliminates binding to certain antibodies. An operational definition of epitope promiscuity for peptides is the case where two peptides show little or no identity in amino acid sequence but bind strongly to the same antibody as shown by either direct binding or competitive inhibition. Analysis of antibodies of humans and sharks, the two most divergent species in evolution to express antibodies and the combinatorial immune response, indicates that the capacity for both exquisite specificity and epitope recognition promiscuity are essential conserved features of individual vertebrate antibodies. Copyright © 2001 John Wiley & Sons, Ltd. [source] Sulfoalkyl ether-alkyl ether cyclodextrin derivatives, their synthesis, NMR characterization, and binding of 6,-methylprednisoloneJOURNAL OF PHARMACEUTICAL SCIENCES, Issue 11 2005Serena Tongiani Abstract The objective of this study is to see if random alkyl ethers of various sulfoalkyl ether cyclodextrins can be synthesized and characterized. The purpose of the alkylation was to test the hypothesis that an increase in the "height" of a cyclodextrins cavity would help in the binding/complexation of larger more structurally complex molecules. The synthesis of new cyclodextrin derivatives comprising a mixture of sulfoalkyl ether and alkyl ether substituents on the same cyclodextrin ring was performed in aqueous alkaline solutions using various sultones and alkylsulfates. The method presented provided an easy and efficient way to modify cyclodextrins avoiding the use of organic solvents and high quantities of alkylating agents and could be carried out in either a two step or "one pot" single step process. Purification was by neutralization followed by ultrafiltration. The derivatives were characterized by 1D, (1H and 13C), and a 2D NMR technique (HMQC, Heteronuclear Multiple Quantum Coherence). The combination of these techniques allowed an analysis of the degree of substitution and the site of substitution on the cyclodextrin (CD) nucleus. For both ,- and ,-CD, sulfoakylation was preferred on the 2,>,3,>,6 hydroxyls while alkylation was preferred 6,>,2,>,3. Due to the simultaneous presence of short alkyl ether chains and negatively charged sulfoalkyl ether chains, these mixed water-soluble cyclodextrin derivatives, especially those of ,-cyclodextrin, should be able to bind more complex drugs. The improved binding capacity of these new modified CDs with the model drug 6,-methylprednisolone is reported. © 2005 Wiley-Liss, Inc. and the American Pharmacists Association J Pharm Sci 94:2380-2392, 2005 [source] Canine diabetes mellitus: from phenotype to genotypeJOURNAL OF SMALL ANIMAL PRACTICE, Issue 1 2008B. Catchpole Breed differences in susceptibility to diabetes mellitus in dogs suggest an underlying genetic component to the pathogenesis of the disease. There is little evidence for an equivalent of human type 2 diabetes in dogs, and it has been proposed that canine diabetes is more comparable to the type 1 form of the disease. Certain immune response genes, particularly those encoding major histocompatibility complex molecules involved in antigen presentation, are important in determining susceptibility to human type 1 diabetes. We tested the hypothesis that canine major histocompatibility complex genes (known as the dog leucocyte antigen) are associated with diabetes in dogs. A total of 530 diabetic dogs and more than 1000 controls were typed for dog leucocyte antigen, and associations were found with three specific haplotypes. The DLA-DRB1*009/DQA1*001/DQB1*008 haplotype shows the strongest association with diabetes in the UK dog population. This haplotype is common in diabetes-prone breeds (Samoyed, cairn terrier and Tibetan terrier) but rare in diabetes-resistant breeds (boxer, German shepherd dog and golden retriever), which could explain differences in the prevalence of diabetes in these different breeds. There is evidence that the DLA-DQA1*001 allele is also associated with hypothyroidism, suggesting that this could represent a common susceptibility allele for canine immune-mediated endocrinopathies. [source] Activation of large lons in FT-ICR mass spectrometryMASS SPECTROMETRY REVIEWS, Issue 2 2005Julia Laskin Abstract The advent of soft ionization techniques, notably electrospray and laser desorption ionization methods, has enabled the extension of mass spectrometric methods to large molecules and molecular complexes. This both greatly extends the applications of mass spectrometry and makes the activation and dissociation of complex ions an integral part of these applications. This review emphasizes the most promising methods for activation and dissociation of complex ions and presents this discussion in the context of general knowledge of reaction kinetics and dynamics largely established for small ions. We then introduce the characteristic differences associated with the higher number of internal degrees of freedom and high density of states associated with molecular complexity. This is reflected primarily in the kinetics of unimolecular dissociation of complex ions, particularly their slow decay and the higher energy content required to induce decomposition,the kinetic shift (KS). The longer trapping time of Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) significantly reduces the KS, which presents several advantages over other methods for the investigation of dissociation of complex molecules. After discussing general principles of reaction dynamics related to collisional activation of ions, we describe conventional ways to achieve single- and multiple-collision activation in FT-ICR MS. Sustained off-resonance irradiation (SORI),the simplest and most robust means of introducing the multiple collision activation process,is discussed in greatest detail. Details of implementation of this technique, required control of experimental parameters, limitations, and examples of very successful application of SORI-CID are described. The advantages of high mass resolving power and the ability to carry out several stages of mass selection and activation intrinsic to FT-ICR MS are demonstrated in several examples. Photodissociation of ions from small molecules can be effected using IR or UV/vis lasers and generally requires tuning lasers to specific wavelengths and/or utilizing high flux, multiphoton excitation to match energy levels in the ion. Photodissociation of complex ions is much easier to accomplish from the basic physics perspective. The quasi-continuum of vibrational states at room temperature makes it very easy to pump relatively large amounts of energy into complex ions and infrared multiphoton dissociation (IRMPD) is a powerful technique for characterizing large ions, particularly biologically relevant molecules. Since both SORI-CID and IRMPD are slow activation methods they have many common characteristics. They are also distinctly different because SORI-CID is intrinsically selective (only ions that have a cyclotron frequency close to the frequency of the excitation field are excited), whereas IRMPD is not (all ions that reside on the optical path of the laser are excited). There are advantages and disadvantages to each technique and in many applications they complement each other. In contrast with these slow activation methods, the less widely appreciated activation method of surface induced dissociation (SID) appears to offer unique advantages because excitation in SID occurs on a sub-picosecond time scale, instantaneously relative to the observation time of any mass spectrometer. Internal energy deposition is quite efficient and readily adjusted by altering the kinetic energy of the impacting ion. The shattering transition,instantaneous decomposition of the ion on the surface,observed at high collision energies enables access to dissociation channels that are not accessible using SORI-CID or IRMPD. Finally, we discuss some approaches for tailoring the surface to achieve particular aims in SID. © 2004 Wiley Periodicals, Inc., Mass Spec Rev 24:135,167, 2005 [source] Arginase activity in a murine macrophage cell line (RAW264.7) stimulated with lipopolysaccharide from Actinobacillus actinomycetemcomitansMOLECULAR ORAL MICROBIOLOGY, Issue 3 2006W. Sosroseno Aims:, The aim of the present study was to determine whether or not lipopolysaccharide from Actinobacillus actinomycetemcomitans could stimulate arginase activity in a murine macrophage cell line (RAW264.7 cells). Methods:, RAW264.7 cells were treated with A. actinomycetemcomitans- lipopolysaccharide or lipopolysaccharide from Escherichia coli for 24 h. The effect of polymyxin B, l -norvaline, dl -norvaline, dexamethasone and cytokines (interferon-, and interleukin-4) on arginase activity in A. actinomycetemcomitans- lipopolysaccharide-stimulated cells was also determined. The cells were pretreated with anti-CD14, anti -toll-like receptor 2, or anti-toll-like receptor 4 antibody prior to stimulation with A. actinomycetemcomitans- lipopolysaccharide. Arginase activity was determined by a colorimetric assay. Results:,A. actinomycetemcomitans- lipopolysaccharide stimulated arginase activity in RAW264.7 cells in a dose-dependent manner, but was less potent than E. coli- lipopolysaccharide. Polymyxin B and l -norvaline, but not dl -norvaline, blocked the arginase activity in A. actinomycetemcomitans- lipopolysaccharide-stimulated cells. Dexamethasone and interleukin-4 but not interferon-, augmented arginase activity in A. actinomycetemcomitans- lipopolysaccharide-stimulated cells. Treatment of the cells with anti-CD14 and anti-toll-like receptor 4 but not anti-toll-like receptor 2 antibody decreased arginase activity in A. actinomycetemcomitans- lipopolysaccharide-stimulated cells. Conclusion:, The results of the present study suggest that lipopolysaccharide from A. actinomycetemcomitans via CD14/toll-like receptor 4 complex molecules and the regulatory control of glucocorticoid and cytokines may stimulate arginase activity in RAW264.7 cells. [source] Structural analysis of oligosaccharides by atmospheric pressure matrix-assisted laser desorption/ionisation quadrupole ion trap mass spectrometryRAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 3 2002Colin S. Creaser An ion source incorporating a fibre optic interface has been constructed for atmospheric pressure matrix-assisted laser desorption/ionisation quadrupole ion trap mass spectrometry. The configuration has been applied to the study of linear and complex oligosaccharides. Multi-stage tandem mass spectrometry (MSn, n,=,2,4) experiments carried out in the ion trap enable extended fragmentation pathways to be investigated that yield structural information. Collisional activation of sodiated oligosaccharides, as demonstrated on the model compound maltoheptaose, produces primarily B and Y fragments resulting from cleavage of glycosidic bonds; fragments from cross-ring cleavages are also observed following further stages of tandem mass spectrometry, providing additional linkage information. The analyses of mixtures of complex oligosaccharides are demonstrated for N-linked glycans from chicken egg glycoproteins and a ribonuclease glycan mixture. Mass spectrometric and tandem mass spectrometric data for sugars with molecular weights up to 4000,Da is shown for mixtures of linear dextrans and N-linked glycans. The use of MSn (n,=,3,,4) on these complex molecules enabled structural information to be elucidated that confirms data observed in the MS/MS spectra. Copyright © 2001 John Wiley & Sons, Ltd. [source] Two two-dimensional hydrogen-bonded coordination networks: bis(3-carboxybenzoato-,O)bis(4-methyl-1H -imidazole-,N3)copper(II) and bis(3-methylbenzoato-,N)bis(4-methyl-1H -imidazole-,N3)copper(II) monohydrateACTA CRYSTALLOGRAPHICA SECTION C, Issue 12 2009Ziliang Wang The title two-dimensional hydrogen-bonded coordination compounds, [Cu(C8H5O4)2(C4H6N2)2], (I), and [Cu(C8H7O2)2(C4H6N2)2]·H2O, (II), have been synthesized and structurally characterized. The molecule of complex (I) lies across an inversion centre, and the Cu2+ ion is coordinated by two N atoms from two 4-methyl-1H -imidazole (4-MeIM) molecules and two O atoms from two 3-carboxybenzoate (HBDC,) anions in a square-planar geometry. Adjacent molecules are linked through intermolecular N,H...O and O,H...O hydrogen bonds into a two-dimensional sheet with (4,4) topology. In the asymmetric part of the unit cell of (II) there are two symmetry-independent molecules, in which each Cu2+ ion is also coordinated by two N atoms from two 4-MeIM molecules and two O atoms from two 3-methylbenzoate (3-MeBC,) anions in a square-planar coordination. Two neutral complex molecules are held together via N,H...O(carboxylate) hydrogen bonds to generate a dimeric pair, which is further linked via discrete water molecules into a two-dimensional network with the Schläfli symbol (43)2(46,66,83). In both compounds, as well as the strong intermolecular hydrogen bonds, ,,, interactions also stabilize the crystal stacking. [source] Trinitratobis{N,-[1-(2-pyridyl)ethylidene]isonicotinohydrazide}cerium(III): a three-dimensional cerium,organic supramolecular structureACTA CRYSTALLOGRAPHICA SECTION C, Issue 7 2009Ying-Ying Zhang The CeIII ion in the title complex, [Ce(NO3)3(C13H12N4O)2], is 12-coordinated by six chelating nitrate O atoms and six donors (2 O and 4 N atoms) of two N,-[1-(2-pyridyl)ethylidene]isonicotinohydrazide ligands, exhibiting a bicapped pentagonal-antiprism-type coordination geometry. The title complex possesses C2 point symmetry and is located on a twofold crystallographic axis. Each molecule is linked with four surrounding molecules by four N,H...N hydrogen bonds, resulting in an extended two-dimensional layer parallel to the ab plane, while ,,, interactions between pyridine rings from neighboring complex molecules connect the two-dimensional layers into a three-dimensional cerium,organic supramolecular structure. [source] Dimeric (isoquinoline)(N -salicylidene- d,l -glutamato)copper(II) ethanol solvateACTA CRYSTALLOGRAPHICA SECTION C, Issue 5 2009Vratislav Langer The title racemic complex, bis[,- N -(2-oxidobenzylidene)- d,l -glutamato(2,)]bis[(isoquinoline)copper(II)] ethanol disolvate, [Cu2(C12H11NO5)2(C9H7N)2]·2C2H6O, adopts a square-pyramidal CuII coordination mode with a tridentate N -salicylideneglutamato Schiff base dianion and an isoquinoline ligand bound in the basal plane. The apex of the pyramid is occupied by a phenolic O atom from the adjacent chelate molecule at an apical distance of 2.487,(3),Å, building a dimer located on the crystallographic inversion center. The Cu...Cu spacing within the dimers is 3.3264,(12),Å. The ethanol solvent molecules are hydrogen bonded to the dimeric complex molecules, forming infinite chains in the a direction. The biological activity of the title complex has been studied. [source] How to outwit the enemy: dendritic cells face Salmonella,APMIS, Issue 9 2006Review article Salmonella enterica serovar Typhi causes typhoid fever, a serious life-threatening systemic infection. In mice, a similar disease is caused by Salmonella enterica serovar Typhimurium. During typhoid fever, soon after attachment to the mucosal surface of the gut, bacteria come into contact with the dendritic cells (DCs). The ability to sample antigens, process and present them to na,Ðve and mature T cells, in the context of major histocompatibility complex molecules, makes DCs indispensable for mounting a specific and efficient immune response to invading pathogens. These bacteria, however, have evolved a number of mechanisms to interfere with or subvert DC functions. This review aims to describe how Salmonella clashes with dendritic cells at different stages of infection as well as the war strategies of these two opposing sides. [source] Evaluation of software for introducing protein structureBIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION, Issue 5 2010Visualization, simulation Abstract Communicating an understanding of the forces and factors that determine a protein's structure is an important goal of many biology and biochemistry courses at a variety of levels. Many educators use computer software that allows visualization of these complex molecules for this purpose. Although visualization is in wide use and has been associated with student learning, it is quite challenging to develop visualizations that allow students to interactively observe the effects of altered amino acid sequence on protein structure. A software simulation, the protein investigator (PI), has been developed to specifically facilitate this type of exploration. When using the PI, students enter or edit an amino acid sequence; the software then simulates its folding in two dimensions using the major forces involved in protein structure. This study explores freshman undergraduate students' use of visualization and simulation when learning about protein structure. It also evaluates some of the learning outcomes from these two approaches. Our results show that simulation leads to similar learning outcomes as visualization. Because simulation allows a more interactive exploration, a combination of the two approaches may be an effective approach to introducing the basic principles of protein structure. [source] High-level production of amorpha-4,11-diene in a two-phase partitioning bioreactor of metabolically engineered Escherichia coliBIOTECHNOLOGY & BIOENGINEERING, Issue 4 2006Jack D. Newman Abstract Reconstructing synthetic metabolic pathways in microbes holds great promise for the production of pharmaceuticals in large-scale fermentations. By recreating biosynthetic pathways in bacteria, complex molecules traditionally harvested from scarce natural resources can be produced in microbial cultures. Here we report on a strain of Escherichia coli containing a heterologous, nine-gene biosynthetic pathway for the production of the terpene amorpha-4,11-diene, a precursor to the anti-malarial drug artemisinin. Previous reports have underestimated the productivity of this strain due to the volatility of amorphadiene. Here we show that amorphadiene evaporates from a fermentor with a half-life of about 50 min. Using a condenser, we take advantage of this volatility by trapping the amorphadiene in the off-gas. Amorphadiene was positively identified using nuclear magnetic resonance spectroscopy and determined to be 89% pure as collected. We captured amorphadiene as it was produced in situ by employing a two-phase partitioning bioreactor with a dodecane organic phase. Using a previously characterized caryophyllene standard to calibrate amorphadiene production and capture, the concentration of amorphadiene produced was determined to be 0.5 g/L of culture medium. A standard of amorphadiene collected from the off-gas showed that the caryophyllene standard overestimated amorphadiene production by approximately 30%. © 2006 Wiley Periodicals, Inc. [source] Formation of ,-Lithio Siloles from Silylated 1,4-Dilithio-1,3-Butadienes: Mechanism and ApplicationsCHEMISTRY - AN ASIAN JOURNAL, Issue 5 2010Qian Luo Abstract A full account of a useful transformation from silylated 1,4-dilithio-1,3-butadienes to ,-lithio siloles is described. These lithio siloles formed by this procedure are general, in terms of substitution patterns and synthetic methods, affording diversified silole derivatives. Notably, some structurally complex molecules, such as bridged bis-silole compounds, have been synthesized easily and successfully by applying our protocol. The structure of the ,-lithio silole, which adopts a dimeric fashion through two lithium bridges, was confirmed by X-ray analysis. Furthermore, a possible mechanism of the skeleton rearrangements via E/Z isomerization of 1-silyl-1-lithio alkene and nucleophilic attack on silicon is proposed, and is also proved by experimental investigations. [source] Influence of Cluster Size on the Structures and Stability of Trimetallic Nitride Fullerenes M3N@C80CHEMPHYSCHEM, Issue 6 2006Li-Hua Gan Dr. Abstract To provide insight into the influence of encaged clusters on the structures and stability of trimetallic nitride fullerenes (TNFs), extensive density functional theory calculations were performed on Sc3N@C80, Y3N@C80, and La3N@C80 as well as their encaged clusters. The calculated results demonstrated that both Sc3N and Y3N units are planar, whereas La3N units are pyramidal inside C80 -Ih, and that both of the Y3N@C80 and La3N@C80 cages deform considerably in the planes of Y3 and La3. The calculated results suggest that M,cage attraction/repulsion and M,M repulsion interactions determine the geometries of these three complex molecules and the dynamics of the corresponding encaged clusters. These calculated findings distinctly reveal the influence of the size of the encaged clusters on the structures and stability of TNFs and may rationalize their significant differences in yields and chemical reactivity. [source] | ||||||||||||||||||||||||||||