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Sample records for allosteric enzyme imidazole

  1. Glutamine Hydrolysis by Imidazole Glycerol Phosphate Synthase Displays Temperature Dependent Allosteric Activation

    Directory of Open Access Journals (Sweden)

    George P. Lisi

    2018-02-01

    Full Text Available The enzyme imidazole glycerol phosphate synthase (IGPS is a model for studies of long-range allosteric regulation in enzymes. Binding of the allosteric effector ligand N'-[5'-phosphoribulosylformimino]-5-aminoimidazole-4-carboxamide-ribonucleotide (PRFAR stimulates millisecond (ms timescale motions in IGPS that enhance its catalytic function. We studied the effect of temperature on these critical conformational motions and the catalytic mechanism of IGPS from the hyperthermophile Thermatoga maritima in an effort to understand temperature-dependent allostery. Enzyme kinetic and NMR dynamics measurements show that apo and PRFAR-activated IGPS respond differently to changes in temperature. Multiple-quantum Carr-Purcell-Meiboom-Gill (CPMG relaxation dispersion experiments performed at 303, 323, and 343 K (30, 50, and 70°C reveal that millisecond flexibility is enhanced to a higher degree in apo IGPS than in the PRFAR-bound enzyme as the sample temperature is raised. We find that the flexibility of the apo enzyme is nearly identical to that of its PRFAR activated state at 343 K, whereas conformational motions are considerably different between these two forms of the enzyme at room temperature. Arrhenius analyses of these flexible sites show a varied range of activation energies that loosely correlate to allosteric communities identified by computational methods and reflect local changes in dynamics that may facilitate conformational sampling of the active conformation. In addition, kinetic assays indicate that allosteric activation by PRFAR decreases to 65-fold at 343 K, compared to 4,200-fold at 303 K, which mirrors the decreased effect of PRFAR on ms motions relative to the unactivated enzyme. These studies indicate that at the growth temperature of T. maritima, PFRAR is a weaker allosteric activator than it is at room temperature and illustrate that the allosteric mechanism of IGPS is temperature dependent.

  2. Allosteric regulation of epigenetic modifying enzymes.

    Science.gov (United States)

    Zucconi, Beth E; Cole, Philip A

    2017-08-01

    Epigenetic enzymes including histone modifying enzymes are key regulators of gene expression in normal and disease processes. Many drug development strategies to target histone modifying enzymes have focused on ligands that bind to enzyme active sites, but allosteric pockets offer potentially attractive opportunities for therapeutic development. Recent biochemical studies have revealed roles for small molecule and peptide ligands binding outside of the active sites in modulating the catalytic activities of histone modifying enzymes. Here we highlight several examples of allosteric regulation of epigenetic enzymes and discuss the biological significance of these findings. Copyright © 2017 Elsevier Ltd. All rights reserved.

  3. Fumarate analogs act as allosteric inhibitors of the human mitochondrial NAD(P)+-dependent malic enzyme.

    Science.gov (United States)

    Hsieh, Ju-Yi; Liu, Jyung-Hurng; Yang, Pai-Chun; Lin, Chi-Li; Liu, Guang-Yaw; Hung, Hui-Chih

    2014-01-01

    Human mitochondrial NAD(P)+-dependent malic enzyme (m-NAD(P)-ME) is allosterically activated by the four-carbon trans dicarboxylic acid, fumarate. Previous studies have suggested that the dicarboxylic acid in a trans conformation around the carbon-carbon double bond is required for the allosteric activation of the enzyme. In this paper, the allosteric effects of fumarate analogs on m-NAD(P)-ME are investigated. Two fumarate-insensitive mutants, m-NAD(P)-ME_R67A/R91A and m-NAD(P)-ME_K57S/E59N/K73E/D102S, as well as c-NADP-ME, were used as the negative controls. Among these analogs, mesaconate, trans-aconitate, monomethyl fumarate and monoethyl fumarate were allosteric activators of the enzyme, while oxaloacetate, diethyl oxalacetate, and dimethyl fumarate were found to be allosteric inhibitors of human m-NAD(P)-ME. The IC50 value for diethyl oxalacetate was approximately 2.5 mM. This paper suggests that the allosteric inhibitors may impede the conformational change from open form to closed form and therefore inhibit m-NAD(P)-ME enzyme activity.

  4. Fumarate analogs act as allosteric inhibitors of the human mitochondrial NAD(P+-dependent malic enzyme.

    Directory of Open Access Journals (Sweden)

    Ju-Yi Hsieh

    Full Text Available Human mitochondrial NAD(P+-dependent malic enzyme (m-NAD(P-ME is allosterically activated by the four-carbon trans dicarboxylic acid, fumarate. Previous studies have suggested that the dicarboxylic acid in a trans conformation around the carbon-carbon double bond is required for the allosteric activation of the enzyme. In this paper, the allosteric effects of fumarate analogs on m-NAD(P-ME are investigated. Two fumarate-insensitive mutants, m-NAD(P-ME_R67A/R91A and m-NAD(P-ME_K57S/E59N/K73E/D102S, as well as c-NADP-ME, were used as the negative controls. Among these analogs, mesaconate, trans-aconitate, monomethyl fumarate and monoethyl fumarate were allosteric activators of the enzyme, while oxaloacetate, diethyl oxalacetate, and dimethyl fumarate were found to be allosteric inhibitors of human m-NAD(P-ME. The IC50 value for diethyl oxalacetate was approximately 2.5 mM. This paper suggests that the allosteric inhibitors may impede the conformational change from open form to closed form and therefore inhibit m-NAD(P-ME enzyme activity.

  5. Enzyme-substrate complexes of allosteric citrate synthase: evidence for a novel intermediate in substrate binding.

    Science.gov (United States)

    Duckworth, Harry W; Nguyen, Nham T; Gao, Yin; Donald, Lynda J; Maurus, Robert; Ayed, Ayeda; Bruneau, Brigitte; Brayer, Gary D

    2013-12-01

    The citrate synthase (CS) of Escherichia coli is an allosteric hexameric enzyme specifically inhibited by NADH. The crystal structure of wild type (WT) E. coli CS, determined by us previously, has no substrates bound, and part of the active site is in a highly mobile region that is shifted from the position needed for catalysis. The CS of Acetobacter aceti has a similar structure, but has been successfully crystallized with bound substrates: both oxaloacetic acid (OAA) and an analog of acetyl coenzyme A (AcCoA). We engineered a variant of E. coli CS wherein five amino acids in the mobile region have been replaced by those in the A. aceti sequence. The purified enzyme shows unusual kinetics with a low affinity for both substrates. Although the crystal structure without ligands is very similar to that of the WT enzyme (except in the mutated region), complexes are formed with both substrates and the allosteric inhibitor NADH. The complex with OAA in the active site identifies a novel OAA-binding residue, Arg306, which has no functional counterpart in other known CS-OAA complexes. This structure may represent an intermediate in a multi-step substrate binding process where Arg306 changes roles from OAA binding to AcCoA binding. The second complex has the substrate analog, S-carboxymethyl-coenzyme A, in the allosteric NADH-binding site and the AcCoA site is not formed. Additional CS variants unable to bind adenylates at the allosteric site show that this second complex is not a factor in positive allosteric activation of AcCoA binding. © 2013.

  6. Single Enzyme Studies Reveal the Existence of Discrete Functional States for Monomeric Enzymes and How They Are “Selected” upon Allosteric Regulation

    DEFF Research Database (Denmark)

    Hatzakis, Nikos S.; Wei, Li; Jørgensen, Sune Klamer

    2012-01-01

    Allosteric regulation of enzymatic activity forms the basis for controlling a plethora of vital cellular processes. While the mechanism underlying regulation of multimeric enzymes is generally well understood and proposed to primarily operate via conformational selection, the mechanism underlying...

  7. Enzyme activity and allosteric characteristics of gamma-irradiated solid aspartate transcarbamylase

    International Nuclear Information System (INIS)

    Bigler, W.N.; Tolbert, B.M.

    1977-01-01

    Aspartate transcarbamylase purified from E. coli was lyophilized, irradiated in vacuo with γ radiation from a cesium-137 source, redissolved in buffer under a nitrogen atmosphere, and assayed for enzyme activity. Lyophilized and redissolved enzyme had normal catalytic and allosteric kinetic characteristics. The average D 37 observed with saturating substrate, 25 mM aspartate, was 4.1 Mrad. With less than saturating substrate, 5 mM aspartate, the activity increases from zero to 1.6 Mrad and then decreases with a D 37 of 7.2 Mrad. Inclusion of 1 mM CTP, an allosteric inhibitor, in the 5 mM aspartate assays results in a more pronounced maximum in the activity curve occurring at slightly higher dose, 2.2 Mrad. Inhibitability by CTP has a D 37 of 2.3 Mrad with doses below the activity maximum. Enzyme lyophilized in the presence of 1 mM CTP has a D 37 of 2.9 Mrad. ATCase activity changes caused by irradiation of lyophylized bacteria were qualitatively like the changes observed in the detailed studies with the purified enzyme. Apparent radiation sensitivities of ATCase in lyophilized bacteria were observed to vary with the technique used to disrupt the resuspended bacteria

  8. Allosteric ATPase behavior: the onset of laser-sustained enzyme cooperation

    Science.gov (United States)

    Causa, F.; Costato, Michele; Milani, Marziale; Bolognani, Lorenzo

    1995-01-01

    A two level model is considered to describe the dynamics of a biological system undergoing cyclic oscillations from one state to another separated by an energy quantum interval. This is typically met in enzyme activated reactions, involving the ADP-ATP cycle. General results can be obtained analytically, the dynamics of the system being investigated from an energetic point of view. Numerical solutions show how an enzymatic system can be driven across different regimes where cooperation (allostericity) and oscillations appears. The model can be extended to the case of an external energy supply in the form of electromagnetic radiation, providing clues for a physical understanding of nonthermal laser interaction with biosystems.

  9. Allosteric substrate inhibition of Arabidopsis NAD-dependent malic enzyme 1 is released by fumarate.

    Science.gov (United States)

    Tronconi, Marcos Ariel; Wheeler, Mariel Claudia Gerrard; Martinatto, Andrea; Zubimendi, Juan Pablo; Andreo, Carlos Santiago; Drincovich, María Fabiana

    2015-03-01

    Plant mitochondria can use L-malate and fumarate, which accumulate in large levels, as respiratory substrates. In part, this property is due to the presence of NAD-dependent malic enzymes (NAD-ME) with particular biochemical characteristics. Arabidopsis NAD-ME1 exhibits a non-hyperbolic behavior for the substrate L-malate, and its activity is strongly stimulated by fumarate. Here, the possible structural connection between these properties was explored through mutagenesis, kinetics, and fluorescence studies. The results indicated that NAD-ME1 has a regulatory site for L-malate that can also bind fumarate. L-Malate binding to this site elicits a sigmoidal and low substrate-affinity response, whereas fumarate binding turns NAD-ME1 into a hyperbolic and high substrate affinity enzyme. This effect was also observed when the allosteric site was either removed or altered. Hence, fumarate is not really an activator, but suppresses the inhibitory effect of l-malate. In addition, residues Arg50, Arg80 and Arg84 showed different roles in organic acid binding. These residues form a triad, which is the basis of the homo and heterotrophic effects that characterize NAD-ME1. The binding of L-malate and fumarate at the same allosteric site is herein reported for a malic enzyme and clearly indicates an important role of NAD-ME1 in processes that control flow of C4 organic acids in Arabidopsis mitochondrial metabolism. Copyright © 2014 Elsevier Ltd. All rights reserved.

  10. Evidence of Allosteric Enzyme Regulation via Changes in Conformational Dynamics: A Hydrogen/Deuterium Exchange Investigation of Dihydrodipicolinate Synthase.

    Science.gov (United States)

    Sowole, Modupeola A; Simpson, Sarah; Skovpen, Yulia V; Palmer, David R J; Konermann, Lars

    2016-09-27

    Dihydrodipicolinate synthase is a tetrameric enzyme of the diaminopimelate pathway in bacteria and plants. The protein catalyzes the condensation of pyruvate (Pyr) and aspartate semialdehyde en route to the end product lysine (Lys). Dihydrodipicolinate synthase from Campylobacter jejuni (CjDHDPS) is allosterically inhibited by Lys. CjDHDPS is a promising antibiotic target, as highlighted by the recent development of a potent bis-lysine (bisLys) inhibitor. The mechanism whereby Lys and bisLys allosterically inhibit CjDHDPS remains poorly understood. In contrast to the case for other allosteric enzymes, crystallographically detectable conformational changes in CjDHDPS upon inhibitor binding are very minor. Also, it is difficult to envision how Pyr can access the active site; the available X-ray data seemingly imply that each turnover step requires diffusion-based mass transfer through a narrow access channel. This study employs hydrogen/deuterium exchange mass spectrometry for probing the structure and dynamics of CjDHDPS in a native solution environment. The deuteration kinetics reveal that the most dynamic protein regions are in the direct vicinity of the substrate access channel. This finding is consistent with the view that transient opening/closing fluctuations facilitate access of the substrate to the active site. Under saturating conditions, both Lys and bisLys cause dramatically reduced dynamics in the inhibitor binding region. In addition, rigidification extends to regions close to the substrate access channel. This finding strongly suggests that allosteric inhibitors interfere with conformational fluctuations that are required for CjDHDPS substrate turnover. In particular, our data imply that Lys and bisLys suppress opening/closing events of the access channel, thereby impeding diffusion of the substrate into the active site. Overall, this work illustrates why allosteric control does not have to be associated with crystallographically detectable large

  11. Zinc as Allosteric Ion Channel Modulator: Ionotropic Receptors as Metalloproteins

    Science.gov (United States)

    Peralta, Francisco Andrés; Huidobro-Toro, Juan Pablo

    2016-01-01

    Zinc is an essential metal to life. This transition metal is a structural component of many proteins and is actively involved in the catalytic activity of cell enzymes. In either case, these zinc-containing proteins are metalloproteins. However, the amino acid residues that serve as ligands for metal coordination are not necessarily the same in structural proteins compared to enzymes. While crystals of structural proteins that bind zinc reveal a higher preference for cysteine sulfhydryls rather than histidine imidazole rings, catalytic enzymes reveal the opposite, i.e., a greater preference for the histidines over cysteines for catalysis, plus the influence of carboxylic acids. Based on this paradigm, we reviewed the putative ligands of zinc in ionotropic receptors, where zinc has been described as an allosteric modulator of channel receptors. Although these receptors do not strictly qualify as metalloproteins since they do not normally bind zinc in structural domains, they do transitorily bind zinc at allosteric sites, modifying transiently the receptor channel’s ion permeability. The present contribution summarizes current information showing that zinc allosteric modulation of receptor channels occurs by the preferential metal coordination to imidazole rings as well as to the sulfhydryl groups of cysteine in addition to the carboxyl group of acid residues, as with enzymes and catalysis. It is remarkable that most channels, either voltage-sensitive or transmitter-gated receptor channels, are susceptible to zinc modulation either as positive or negative regulators. PMID:27384555

  12. Functional role of fumarate site Glu59 involved in allosteric regulation and subunit-subunit interaction of human mitochondrial NAD(P)+-dependent malic enzyme.

    Science.gov (United States)

    Hsieh, Ju-Yi; Chiang, Yu-Hsiu; Chang, Kuan-Yu; Hung, Hui-Chih

    2009-02-01

    Here we report on the role of Glu59 in the fumarate-mediated allosteric regulation of the human mitochondrial NAD(P)+-dependent malic enzyme (m-NAD-ME). In the present study, Glu59 was substituted by Asp, Gln or Leu. Our kinetic data strongly indicated that the charge properties of this residue significantly affect the allosteric activation of the enzyme. The E59L enzyme shows nonallosteric kinetics and the E59Q enzyme displays a much higher threshold in enzyme activation with elevated activation constants, K(A,Fum) and alphaK(A,Fum). The E59D enzyme, although retaining the allosteric property, is quite different from the wild-type in enzyme activation. The K(A,Fum) and alphaK(A,Fum) of E59D are also much greater than those of the wild-type, indicating that not only the negative charge of this residue but also the group specificity and side chain interactions are important for fumarate binding. Analytical ultracentrifugation analysis shows that both the wild-type and E59Q enzymes exist as a dimer-tetramer equilibrium. In contrast to the E59Q mutant, the E59D mutant displays predominantly a dimer form, indicating that the quaternary stability in the dimer interface is changed by shortening one carbon side chain of Glu59 to Asp59. The E59L enzyme also shows a dimer-tetramer model similar to that of the wild-type, but it displays more dimers as well as monomers and polymers. Malate cooperativity is not significantly notable in the E59 mutant enzymes, suggesting that the cooperativity might be related to the molecular geometry of the fumarate-binding site. Glu59 can precisely maintain the geometric specificity for the substrate cooperativity. According to the sequence alignment analysis and our experimental data, we suggest that charge effect and geometric specificity are both critical factors in enzyme regulation. Glu59 discriminates human m-NAD-ME from mitochondrial NADP+-dependent malic enzyme and cytosolic NADP+-dependent malic enzyme in fumarate activation and

  13. Sequence analysis and molecular characterization of Clonorchis sinensis hexokinase, an unusual trimeric 50-kDa glucose-6-phosphate-sensitive allosteric enzyme.

    Directory of Open Access Journals (Sweden)

    Tingjin Chen

    Full Text Available Clonorchiasis, which is induced by the infection of Clonorchis sinensis (C. sinensis, is highly associated with cholangiocarcinoma. Because the available examination, treatment and interrupting transmission provide limited opportunities to prevent infection, it is urgent to develop integrated strategies to prevent and control clonorchiasis. Glycolytic enzymes are crucial molecules for trematode survival and have been targeted for drug development. Hexokinase of C. sinensis (CsHK, the first key regulatory enzyme of the glycolytic pathway, was characterized in this study. The calculated molecular mass (Mr of CsHK was 50.0 kDa. The obtained recombinant CsHK (rCsHK was a homotrimer with an Mr of approximately 164 kDa, as determined using native PAGE and gel filtration. The highest activity was obtained with 50 mM glycine-NaOH at pH 10 and 100 mM Tris-HCl at pH 8.5 and 10. The kinetics of rCsHK has a moderate thermal stability. Compared to that of the corresponding negative control, the enzymatic activity was significantly inhibited by praziquantel (PZQ and anti-rCsHK serum. rCsHK was homotropically and allosterically activated by its substrates, including glucose, mannose, fructose, and ATP. ADP exhibited mixed allosteric effect on rCsHK with respect to ATP, while inorganic pyrophosphate (PPi displayed net allosteric activation with various allosteric systems. Fructose behaved as a dose-dependent V activator with the substrate glucose. Glucose-6-phosphate (G6P displayed net allosteric inhibition on rCsHK with respect to ATP or glucose with various allosteric systems in a dose-independent manner. There were differences in both mRNA and protein levels of CsHK among the life stages of adult worm, metacercaria, excysted metacercaria and egg of C. sinensis, suggesting different energy requirements during different development stages. Our study furthers the understanding of the biological functions of CsHK and supports the need to screen for small

  14. Multiple allosteric sites are involved in the modulation of insulin-degrading-enzyme activity by somatostatin.

    Science.gov (United States)

    Tundo, Grazia R; Di Muzio, Elena; Ciaccio, Chiara; Sbardella, Diego; Di Pierro, Donato; Polticelli, Fabio; Coletta, Massimo; Marini, Stefano

    2016-10-01

    Somatostatin is a cyclic peptide, released in the gastrointestinal system and the central nervous system, where it is involved in the regulation of cognitive and sensory functions, motor activity and sleep. It is a substrate of insulin-degrading enzyme (IDE), as well as a modulator of its activity and expression. In the present study, we have investigated the modulatory role of somatostatin on IDE activity at 37 °C and pH 7.3 for various substrates [i.e. insulin, β-amyloid (Aβ) 1-40 and bradykinin], aiming to quantitatively characterize the correlation between the specific features of the substrates and the regulatory mechanism. Functional data indicate that somatostatin, in addition to the catalytic site of IDE (being a substrate), is also able to bind to two additional exosites, which play different roles according to the size of the substrate and its binding mode to the IDE catalytic cleft. In particular, one exosite, which displays high affinity for somatostatin, regulates only the interaction of IDE with larger substrates (such as insulin and Aβ 1-40 ) in a differing fashion according to their various modes of binding to the enzyme. A second exosite, which is involved in the regulation of enzymatic processing by IDE of all substrates investigated (including a 10-25 amino acid long amyloid-like peptide, bradykinin and somatostatin itself, which had been studied previously), probably acts through the alteration of an 'open-closed' equilibrium. © 2016 Federation of European Biochemical Societies.

  15. Evaluating hydrogen bond interactions in enzymes containing Mn(III)-histidine complexation using manganese-imidazole complexes.

    Science.gov (United States)

    Rajendiran, M; Caudle, T; Kirk, Martin L; Setyawati, Ika; Kampf, Jeff W; Pecoraro, Vincent L

    2003-02-01

    It is often difficult to control hydrogen bond interactions in small molecule compounds that model metalloenzyme active sites. The imidazole-containing ligands 4,5-dicarboxyimidazole (H(3)DCBI) and 4,5-dicarboxy- N-methylimidazole (H(2)MeDCBI) allow examination of the effects of internal hydrogen bonding between carboxylate and imidazole nitrogen atoms. A new series of mononuclear manganese imidazole complexes have been prepared using these ligands: Mn(III)(salpn)(H(2)DCBI)(DMF) (1), Mn(III)(salpn)(HMeDCBI) (2), Mn(III)(dtsalpn)(HMeDCBI) (3), [Mn(IV)(dtsalpn)(HMeDCBI)]PF(6) (4), Mn(III)(salpn)(H(2)DCBI) (5), Mn(III)(dtsalpn)(H(2)DCBI) (6), and Mn(IV)(dtsalpn)(H(2)DCBI)PF(6) (8). Complexes 1, 2, 3, 5, and 6 have been prepared by direct reaction of salpn [salpn=(salicylideneaminato)-1,3-diaminopropane)] or dtsalpn [dtsalpn=(3,5-di- t-butylsalicylideneaminato)-1,3-diaminopropane)] and H(3)DCBI and H(2)MeDCBI with Mn(III) acetate, while complexes 4 and 8 were made by bulk electrolysis of complex 3 or 6 in dichloromethane. Complexes 1, 2, and 6 were characterized by X-ray diffraction. The impact of hydrogen bonding interactions of the complexes has been demonstrated by X-ray diffraction, cyclic voltammetry, and EPR spectroscopy. In all complexes the central metal ion is present in a six-coordinate geometry. Magnetic susceptibility measurements confirm the spin and oxidation states of the complexes. The cyclic voltammograms of 3 and 6 in dichloromethane reveal single, reversible redox waves with E(1/2)=600 mV and 690 mV, respectively. The X-band EPR spectrum of 4 shows a broad signal around g=4.4, and the corresponding complex 8 possesses a broad signal at slightly lower field ( g=5.5) than 4. These studies demonstrate that even small changes in the effective charge of the imidazole ligand can have a profound impact on the structure, spectroscopy, and magnetism of manganese(IV) complexes. We use these observations to present a model that may explain the origin of the g=4

  16. Allosteric Regulation of Proteins

    Indian Academy of Sciences (India)

    triguingly, the substrate or the product of the inhibited enzyme can be structurally different from the inhibitor. ... ulation of proteins in this fashion as 'allosteric' in the year 1961. [9]. The word allostery originated from the ..... flux occurs via the conformational selec- tion pathway at low concentrations of the ligand, while the trend.

  17. Structure–activity relationships of imidazole-derived 2-[N-carbamoylmethyl-alkylamino]acetic acids, dual binders of human insulin-degrading enzyme

    Energy Technology Data Exchange (ETDEWEB)

    Charton, Julie; Gauriot, Marion; Totobenazara, Jane; Hennuyer, Nathalie; Dumont, Julie; Bosc, Damien; Marechal, Xavier; Elbakali, Jamal; Herledan, Adrien; Wen, Xiaoan; Ronco, Cyril; Gras-Masse, Helene; Heninot, Antoine; Pottiez, Virginie; Landry, Valerie; Staels, Bart; Liang, Wenguang G.; Leroux, Florence; Tang, Wei-Jen; Deprez, Benoit (INSRM-France); (UC); (IP-France)

    2015-10-30

    Insulin degrading enzyme (IDE) is a zinc metalloprotease that degrades small amyloid peptides such as amyloid-â and insulin. So far the dearth of IDE-specific pharmacological inhibitors impacts the understanding of its role in the physiopathology of Alzheimer's disease, amyloid-â clearance, and its validation as a potential therapeutic target. Hit 1 was previously discovered by high-throughput screening. Here we describe the structure-activity study, that required the synthesis of 48 analogues. We found that while the carboxylic acid, the imidazole and the tertiary amine were critical for activity, the methyl ester was successfully optimized to an amide or a 1,2,4-oxadiazole. Along with improving their activity, compounds were optimized for solubility, lipophilicity and stability in plasma and microsomes. The docking or co-crystallization of some compounds at the exosite or the catalytic site of IDE provided the structural basis for IDE inhibition. The pharmacokinetic properties of best compounds 44 and 46 were measured in vivo. As a result, 44 (BDM43079) and its methyl ester precursor 48 (BDM43124) are useful chemical probes for the exploration of IDE's role.

  18. Uracil phosphoribosyltransferase from the extreme thermoacidophilic archaebacterium Sulfolobus shibatae is an allosteric enzyme, activated by GTP and inhibited by CTP

    DEFF Research Database (Denmark)

    Linde, Lise; Jensen, Kaj Frank

    1996-01-01

    and it showed the highest activity at pH 6.4. The specific activity of the enzyme was 50-times higher at 95°C than at 37°C, but the functional half-life was short at 95°C. The activity of uracil phosphoribosyltransferase was strongly activated by GTP, which increased Vmax of the reaction by approximately 20......-fold without much effect on Km for the substrates. The concentration of GTP required for half-maximal activation was about 80 µM. CTP was a strong inhibitor and acted by raising the concentration of GTP needed for half-maximal activation of the enzyme. We conclude that uracil phosphoribosyltransferase......Uracil phosphoribosyltransferase, which catalyses the formation of UMP and pyrophosphate from uracil and 5-phosphoribosyl a-1-pyrophosphate (PRPP), was partly purified from the extreme thermophilic archaebacterium Sulfolobus shibatae. The enzyme required divalent metal ions for activity...

  19. Uracil phosphoribosyltransferase from the extreme thermoacidophilic archaebacterium Sulfolobus shibatae is an allosteric enzyme, activated by GTP and inhibited by CTP

    DEFF Research Database (Denmark)

    Linde, Lise; Jensen, Kaj Frank

    1996-01-01

    -fold without much effect on Km for the substrates. The concentration of GTP required for half-maximal activation was about 80 µM. CTP was a strong inhibitor and acted by raising the concentration of GTP needed for half-maximal activation of the enzyme. We conclude that uracil phosphoribosyltransferase......Uracil phosphoribosyltransferase, which catalyses the formation of UMP and pyrophosphate from uracil and 5-phosphoribosyl a-1-pyrophosphate (PRPP), was partly purified from the extreme thermophilic archaebacterium Sulfolobus shibatae. The enzyme required divalent metal ions for activity...... and it showed the highest activity at pH 6.4. The specific activity of the enzyme was 50-times higher at 95°C than at 37°C, but the functional half-life was short at 95°C. The activity of uracil phosphoribosyltransferase was strongly activated by GTP, which increased Vmax of the reaction by approximately 20...

  20. p97 Composition Changes Caused by Allosteric Inhibition Are Suppressed by an On-Target Mechanism that Increases the Enzyme's ATPase Activity.

    Science.gov (United States)

    Her, Nam-Gu; Toth, Julia I; Ma, Chen-Ting; Wei, Yang; Motamedchaboki, Khatereh; Sergienko, Eduard; Petroski, Matthew D

    2016-04-21

    The AAA ATPase p97/VCP regulates protein homeostasis using a diverse repertoire of cofactors to fulfill its biological functions. Here we use the allosteric p97 inhibitor NMS-873 to analyze its effects on enzyme composition and the ability of cells to adapt to its cytotoxicity. We found that p97 inhibition changes steady state cofactor-p97 composition, leading to the enrichment of a subset of its cofactors and polyubiquitin bound to p97. We isolated cells specifically insensitive to NMS-873 and identified a new mutation (A530T) in p97. A530T is sufficient to overcome the cytotoxicity of NMS-873 and alleviates p97 composition changes caused by the molecule but not other p97 inhibitors. This mutation does not affect NMS-873 binding but increases p97 catalytic efficiency through altered ATP and ADP binding. Collectively, these findings identify cofactor-p97 interactions sensitive to p97 inhibition and reveal a new on-target mechanism to suppress the cytotoxicity of NMS-873. Copyright © 2016 Elsevier Ltd. All rights reserved.

  1. Crystal structure ofClostridium acetobutylicumAspartate kinase (CaAK): An important allosteric enzyme for amino acids production.

    Science.gov (United States)

    Manjasetty, Babu A; Chance, Mark R; Burley, Stephen K; Panjikar, Santosh; Almo, Steven C

    2014-09-01

    Aspartate kinase (AK) is an enzyme which is tightly regulated through feedback control and responsible for the synthesis of 4-phospho-L-aspartate from L-aspartate. This intermediate step is at an important branch point where one path leads to the synthesis of lysine and the other to threonine, methionine and isoleucine. Concerted feedback inhibition of AK is mediated by threonine and lysine and varies between the species. The crystal structure of biotechnologically important Clostridium acetobutylicum aspartate kinase ( Ca AK; E.C. 2.7.2.4; Mw =48,030Da; 437aa; SwissProt: Q97MC0) has been determined to 3Å resolution. Ca AK acquires a protein fold similar to the other known structures of AKs despite the low sequence identity (Clostridium tetani (64% sequence identity) suggesting the potential of the structure solved here to be applied for modeling drug interactions. Ca AK structure may serve as a guide to better understand and engineer lysine biosynthesis for the biotechnology industry.

  2. Crystal structure of Clostridium acetobutylicum aspartate kinase (CaAk: An important allosteric enzyme for amino acids production

    Directory of Open Access Journals (Sweden)

    Babu A. Manjasetty

    2014-09-01

    Full Text Available Aspartate kinase (AK is an enzyme which is tightly regulated through feedback control and responsible for the synthesis of 4-phospho-l-aspartate from l-aspartate. This intermediate step is at an important branch point where one path leads to the synthesis of lysine and the other to threonine, methionine and isoleucine. Concerted feedback inhibition of AK is mediated by threonine and lysine and varies between the species. The crystal structure of biotechnologically important Clostridium acetobutylicum aspartate kinase (CaAK; E.C. 2.7.2.4; Mw = 48,030 Da; 437aa; SwissProt: Q97MC0 has been determined to 3 Å resolution. CaAK acquires a protein fold similar to the other known structures of AKs despite the low sequence identity (<30%. It is composed of two domains: an N-terminal catalytic domain (kinase domain and a C-terminal regulatory domain further comprised of two small domains belonging to the ACT domain family. Pairwise comparison of 12 molecules in the asymmetric unit helped to identify the bending regions which are in the vicinity of ATP binding site involved in domain movements between the catalytic and regulatory domains. All 12 CaAK molecules adopt fully open T-state conformation leading to the formation of three tetramers unique among other similar AK structures. On the basis of comparative structural analysis, we discuss tetramer formation based on the large conformational changes in the catalytic domain associated with the lysine binding at the regulatory domains. The structure described herein is homologous to a target in wide-spread pathogenic (toxin producing bacteria such as Clostridium tetani (64% sequence identity suggesting the potential of the structure solved here to be applied for modeling drug interactions. CaAK structure may serve as a guide to better understand and engineer lysine biosynthesis for the biotechnology industry.

  3. Dual role of imidazole as activator/inhibitor of sweet almond (Prunus dulcis) β-glucosidase.

    Science.gov (United States)

    Caramia, Sara; Gatius, Angela Gala Morena; Dal Piaz, Fabrizio; Gaja, Denis; Hochkoeppler, Alejandro

    2017-07-01

    The activity of Prunus dulcis (sweet almond) β-glucosidase at the expense of p -nitrophenyl-β-d-glucopyranoside at pH 6 was determined, both under steady-state and pre-steady-state conditions. Using crude enzyme preparations, competitive inhibition by 1-5 mM imidazole was observed under both kinetic conditions tested. However, when imidazole was added to reaction mixtures at 0.125-0.250 mM, we detected a significant enzyme activation. To further inspect this effect exerted by imidazole, β-glucosidase was purified to homogeneity. Two enzyme isoforms were isolated, i.e. a full-length monomer, and a dimer containing a full-length and a truncated subunit. Dimeric β-glucosidase was found to perform much better than the monomeric enzyme, independently of the kinetic conditions used to assay enzyme activity. In addition, the sensitivity towards imidazole was found to differ between the two isoforms. While monomeric enzyme was indeed found to be relatively insensitive to imidazole, dimeric β-glucosidase was observed to be significantly activated by 0.125-0.250 mM imidazole under pre-steady-state conditions. Further, steady-state assays revealed that the addition of 0.125 mM imidazole to reaction mixtures increases the K m of dimeric enzyme from 2.3 to 6.7 mM. The activation of β-glucosidase dimer by imidazole is proposed to be exerted via a conformational transition poising the enzyme towards proficient catalysis.

  4. Dual role of imidazole as activator/inhibitor of sweet almond (Prunus dulcis β-glucosidase

    Directory of Open Access Journals (Sweden)

    Sara Caramia

    2017-07-01

    Full Text Available The activity of Prunus dulcis (sweet almond β-glucosidase at the expense of p-nitrophenyl-β-d-glucopyranoside at pH 6 was determined, both under steady-state and pre-steady-state conditions. Using crude enzyme preparations, competitive inhibition by 1–5 mM imidazole was observed under both kinetic conditions tested. However, when imidazole was added to reaction mixtures at 0.125–0.250 mM, we detected a significant enzyme activation. To further inspect this effect exerted by imidazole, β-glucosidase was purified to homogeneity. Two enzyme isoforms were isolated, i.e. a full-length monomer, and a dimer containing a full-length and a truncated subunit. Dimeric β-glucosidase was found to perform much better than the monomeric enzyme, independently of the kinetic conditions used to assay enzyme activity. In addition, the sensitivity towards imidazole was found to differ between the two isoforms. While monomeric enzyme was indeed found to be relatively insensitive to imidazole, dimeric β-glucosidase was observed to be significantly activated by 0.125–0.250 mM imidazole under pre-steady-state conditions. Further, steady-state assays revealed that the addition of 0.125 mM imidazole to reaction mixtures increases the Km of dimeric enzyme from 2.3 to 6.7 mM. The activation of β-glucosidase dimer by imidazole is proposed to be exerted via a conformational transition poising the enzyme towards proficient catalysis.

  5. Imidazole: Having Versatile Biological Activities

    Directory of Open Access Journals (Sweden)

    Amita Verma

    2013-01-01

    Full Text Available Imidazoles have occupied a unique position in heterocyclic chemistry, and its derivatives have attracted considerable interests in recent years for their versatile properties in chemistry and pharmacology. Imidazole is nitrogen-containing heterocyclic ring which possesses biological and pharmaceutical importance. Thus, imidazole compounds have been an interesting source for researchers for more than a century. The imidazole ring is a constituent of several important natural products, including purine, histamine, histidine, and nucleic acid. Being a polar and ionisable aromatic compound, it improves pharmacokinetic characteristics of lead molecules and thus is used as a remedy to optimize solubility and bioavailability parameters of proposed poorly soluble lead molecules. There are several methods used for the synthesis of imidazole-containing compounds, and also their various structure reactions offer enormous scope in the field of medicinal chemistry. The imidazole derivatives possess extensive spectrum of biological activities such as antibacterial, anticancer, antitubercular, antifungal, analgesic, and anti-HIV activities. This paper aims to review the biological activities of imidazole during the past years.

  6. Allosteric Regulation of Proteins

    Indian Academy of Sciences (India)

    For example, the structural changes that allowed for allosteric regulation of haemoglobin were re- vealed through structural elucidation of the protein in free and oxygen-bound forms by X-ray crystallography. Following this,. X-ray crystallography has been utilized to study a variety of al- losteric proteins including ATCase. 2.

  7. Allosteric Regulation of Proteins

    Indian Academy of Sciences (India)

    ... Lecture Workshops · Refresher Courses · Symposia · Live Streaming. Home; Journals; Resonance – Journal of Science Education; Volume 22; Issue 1. Allosteric Regulation of Proteins: A Historical Perspective on the Development of Concepts and Techniques. General Article Volume 22 Issue 1 January 2017 pp 37-50 ...

  8. Enzyme

    Science.gov (United States)

    Enzymes are complex proteins that cause a specific chemical change in all parts of the body. For ... use them. Blood clotting is another example of enzymes at work. Enzymes are needed for all body ...

  9. An electrospray ms-coupled microfluidic device for sub-second hydrogen/deuterium exchange pulse-labelling reveals allosteric effects in enzyme inhibition.

    Science.gov (United States)

    Rob, Tamanna; Gill, Preet Kamal; Golemi-Kotra, Dasantila; Wilson, Derek J

    2013-07-07

    In this work, we introduce an integrated, electrospray mass spectrometry-coupled microfluidic chip that supports the complete workflow for 'bottom up' hydrogen/deuterium exchange (HDX) pulse labelling experiments. HDX pulse labelling is used to measure structural changes in proteins that occur after the initiation of a reaction, most commonly folding. In the present case, we demonstrate the device on the β-lactamase enzyme TEM-1, identifying active site changes that occur upon acylation by a covalent inhibitor and subtle changes in conformational dynamics that occur away from the active site over a period of several second after the inhibitor is bound. Our results demonstrate the power of microfluidics-enabled sub-second HDX pulse labelling as a tool for studying allostery and show some intriguing correlations with mutagenesis studies.

  10. The lattice dynamics of imidazole

    International Nuclear Information System (INIS)

    Link, K.H.

    1983-05-01

    The lattice dynamics of imidazole have been investigated. To this end dispersion curves have been determined at 10 K by inelastic coherent neutron scattering. RAMAN measurements have been done to investigate identical gamma - point modes. The combination of extinction rules for RAMAN - and neutron scattering leads to the symmetry assignment of identical gamma - point modes. The experiment yields a force constant of the streching vibration of the hydrogen bond of 0.33 mdyn/A. A force model has been developed to describe the intermolecular atom - atom Interactions in imidazole. (orig./BHO)

  11. Comprehensive review in current developments of imidazole-based medicinal chemistry.

    Science.gov (United States)

    Zhang, Ling; Peng, Xin-Mei; Damu, Guri L V; Geng, Rong-Xia; Zhou, Cheng-He

    2014-03-01

    Imidazole ring is an important five-membered aromatic heterocycle widely present in natural products and synthetic molecules. The unique structural feature of imidazole ring with desirable electron-rich characteristic is beneficial for imidazole derivatives to readily bind with a variety of enzymes and receptors in biological systems through diverse weak interactions, thereby exhibiting broad bioactivities. The related research and developments of imidazole-based medicinal chemistry have become a rapidly developing and increasingly active topic. Particularly, numerous imidazole-based compounds as clinical drugs have been extensively used in the clinic to treat various types of diseases with high therapeutic potency, which have shown the enormous development value. This work systematically gives a comprehensive review in current developments of imidazole-based compounds in the whole range of medicinal chemistry as anticancer, antifungal, antibacterial, antitubercular, anti-inflammatory, antineuropathic, antihypertensive, antihistaminic, antiparasitic, antiobesity, antiviral, and other medicinal agents, together with their potential applications in diagnostics and pathology. It is hoped that this review will be helpful for new thoughts in the quest for rational designs of more active and less toxic imidazole-based medicinal drugs, as well as more effective diagnostic agents and pathologic probes. © 2013 Wiley Periodicals, Inc.

  12. Kathepsine C : Een allosterisch enzyme

    NARCIS (Netherlands)

    Gorter, Jeannette

    1969-01-01

    In chapter I an introduction into allosteric systems is given. In chapter II is a detailed method is described for the applica of Gly-Phe--p. nitroanilide (GPNA) as a substrate for the activity assay of the lysosomal enzyme cathepsin C. It is an allosteric which is activated by Cl-, Br-, 1-, CNS-,

  13. Evolution of allosteric regulation in chorismate mutases from early plants

    Energy Technology Data Exchange (ETDEWEB)

    Kroll, Kourtney; Holland, Cynthia K.; Starks, Courtney M.; Jez, Joseph M.

    2017-09-28

    Plants, fungi, and bacteria synthesize the aromatic amino acids: l-phenylalanine, l-tyrosine, and l-tryptophan. Chorismate mutase catalyzes the branch point reaction of phenylalanine and tyrosine biosynthesis to generate prephenate. In Arabidopsis thaliana, there are two plastid-localized chorismate mutases that are allosterically regulated (AtCM1 and AtCM3) and one cytosolic isoform (AtCM2) that is unregulated. Previous analysis of plant chorismate mutases suggested that the enzymes from early plants (i.e. bryophytes/moss, lycophytes, and basal angiosperms) formed a clade distinct from the isoforms found in flowering plants; however, no biochemical information on these enzymes is available. To understand the evolution of allosteric regulation in plant chorismate mutases, we analyzed a basal lineage of plant enzymes homologous to AtCM1 based on sequence similarity. The chorismate mutases from the moss/bryophyte Physcomitrella patens (PpCM1 and PpCM2), the lycophyte Selaginella moellendorffii (SmCM), and the basal angiosperm Amborella trichopoda (AmtCM1 and AmtCM2) were characterized biochemically. Tryptophan was a positive effector for each of the five enzymes examined. Histidine was a weak positive effector for PpCM1 and AmtCM1. Neither tyrosine nor phenylalanine altered the activity of SmCM; however, tyrosine was a negative regulator of the other four enzymes. Phenylalanine down-regulates both moss enzymes and AmtCM2. The 2.0 Å X-ray crystal structure of PpCM1 in complex with the tryptophan identified the allosteric effector site and reveals structural differences between the R- (more active) and T-state (less active) forms of plant chorismate mutases. Molecular insight into the basal plant chorismate mutases guides our understanding of the evolution of allosteric regulation in these enzymes.

  14. The structure and allosteric regulation of glutamate dehydrogenase.

    Science.gov (United States)

    Li, Ming; Li, Changhong; Allen, Aron; Stanley, Charles A; Smith, Thomas J

    2011-09-01

    Glutamate dehydrogenase (GDH) has been extensively studied for more than 50 years. Of particular interest is the fact that, while considered by most to be a 'housekeeping' enzyme, the animal form of GDH is heavily regulated by a wide array of allosteric effectors and exhibits extensive inter-subunit communication. While the chemical mechanism for GDH has remained unchanged through epochs of evolution, it was not clear how or why animals needed to evolve such a finely tuned form of this enzyme. As reviewed here, recent studies have begun to elucidate these issues. Allosteric regulation first appears in the Ciliates and may have arisen to accommodate evolutionary changes in organelle function. The occurrence of allosteric regulation appears to be coincident with the formation of an 'antenna' like feature rising off the tops of the subunits that may be necessary to facilitate regulation. In animals, this regulation further evolved as GDH became integrated into a number of other regulatory pathways. In particular, mutations in GDH that abrogate GTP inhibition result in dangerously high serum levels of insulin and ammonium. Therefore, allosteric regulation of GDH plays an important role in insulin homeostasis. Finally, several compounds have been identified that block GDH-mediated insulin secretion that may be to not only find use in treating these insulin disorders but to kill tumors that require glutamine metabolism for cellular energy. Copyright © 2010 Elsevier Ltd. All rights reserved.

  15. Allosteric regulation of metabolism in cancer: endogenous mechanisms and considerations for drug design.

    Science.gov (United States)

    Macpherson, Jamie A; Anastasiou, Dimitrios

    2017-12-01

    Alterations in metabolic processes have been linked to various diseases, including cancer. Although gene expression can dictate long-term metabolic adaptation, many metabolic changes found in cancer are associated with altered allosteric properties of the underlying enzymes. Small molecule-protein interactions and intracellular signalling converge to orchestrate these allosteric mechanisms, which, emerging evidence suggests, constitute a promising therapeutic avenue. In this review we focus on glucose and energy metabolism to illustrate the role of allostery in cancer physiology and we discuss approaches to streamline the process of targeting aberrant allosteric pathways with small molecules. Copyright © 2017 Elsevier Ltd. All rights reserved.

  16. Identification of the Allosteric Regulatory Site of Insulysin

    Energy Technology Data Exchange (ETDEWEB)

    Noinaj, Nicholas; Bhasin, Sonia K.; Song, Eun Suk; Scoggin, Kirsten E.; Juliano, Maria A.; Juliano, Luiz; Hersh, Louis B.; Rodgers, David W. (U. Sao Paulo); (Kentucky)

    2012-05-25

    Insulin degrading enzyme (IDE) is responsible for the metabolism of insulin and plays a role in clearance of the A{beta} peptide associated with Alzheimer's disease. Unlike most proteolytic enzymes, IDE, which consists of four structurally related domains and exists primarily as a dimer, exhibits allosteric kinetics, being activated by both small substrate peptides and polyphosphates such as ATP. The crystal structure of a catalytically compromised mutant of IDE has electron density for peptide ligands bound at the active site in domain 1 and a distal site in domain 2. Mutating residues in the distal site eliminates allosteric kinetics and activation by a small peptide, as well as greatly reducing activation by ATP, demonstrating that this site plays a key role in allostery. Comparison of the peptide bound IDE structure (using a low activity E111F IDE mutant) with unliganded wild type IDE shows a change in the interface between two halves of the clamshell-like molecule, which may enhance enzyme activity by altering the equilibrium between closed and open conformations. In addition, changes in the dimer interface suggest a basis for communication between subunits. Our findings indicate that a region remote from the active site mediates allosteric activation of insulysin by peptides. Activation may involve a small conformational change that weakens the interface between two halves of the enzyme.

  17. Identification of the Allosteric Regulatory Site of Insulysin

    Energy Technology Data Exchange (ETDEWEB)

    Noinaj, Nicholas; Bhasin, Sonia K.; Song, Eun Suk; Scoggin, Kirsten E.; Juliano, Maria A.; Juliano, Luiz; Hersh, Louis B.; Rodgers, David W.; Gerrard, Juliet Ann

    2011-06-24

    Background Insulin degrading enzyme (IDE) is responsible for the metabolism of insulin and plays a role in clearance of the Aβ peptide associated with Alzheimer's disease. Unlike most proteolytic enzymes, IDE, which consists of four structurally related domains and exists primarily as a dimer, exhibits allosteric kinetics, being activated by both small substrate peptides and polyphosphates such as ATP. Principal Findings The crystal structure of a catalytically compromised mutant of IDE has electron density for peptide ligands bound at the active site in domain 1 and a distal site in domain 2. Mutating residues in the distal site eliminates allosteric kinetics and activation by a small peptide, as well as greatly reducing activation by ATP, demonstrating that this site plays a key role in allostery. Comparison of the peptide bound IDE structure (using a low activity E111F IDE mutant) with unliganded wild type IDE shows a change in the interface between two halves of the clamshell-like molecule, which may enhance enzyme activity by altering the equilibrium between closed and open conformations. In addition, changes in the dimer interface suggest a basis for communication between subunits. Conclusions/Significance Our findings indicate that a region remote from the active site mediates allosteric activation of insulysin by peptides. Activation may involve a small conformational change that weakens the interface between two halves of the enzyme.

  18. Small-molecule allosteric activators of sirtuins.

    Science.gov (United States)

    Sinclair, David A; Guarente, Leonard

    2014-01-01

    The mammalian sirtuins (SIRT1-7) are NAD(+)-dependent lysine deacylases that play central roles in cell survival, inflammation, energy metabolism, and aging. Members of this family of enzymes are considered promising pharmaceutical targets for the treatment of age-related diseases including cancer, type 2 diabetes, inflammatory disorders, and Alzheimer's disease. SIRT1-activating compounds (STACs), which have been identified from a variety of chemical classes, provide health benefits in animal disease models. Recent data point to a common mechanism of allosteric activation by natural and synthetic STACs that involves the binding of STACs to a conserved N-terminal domain in SIRT1. Compared with polyphenols such as resveratrol, the synthetic STACs show greater potency, solubility, and target selectivity. Although considerable progress has been made regarding SIRT1 allosteric activation, key questions remain, including how the molecular contacts facilitate SIRT1 activation, whether other sirtuin family members will be amenable to activation, and whether STACs will ultimately prove safe and efficacious in humans.

  19. First steps in the direction of synthetic, allosteric, direct inhibitors of thrombin and factor Xa.

    Science.gov (United States)

    Verghese, Jenson; Liang, Aiye; Sidhu, Preet Pal Singh; Hindle, Michael; Zhou, Qibing; Desai, Umesh R

    2009-08-01

    Designing non-saccharide functional mimics of heparin is a major challenge. In this work, a library of small, aromatic molecules based on the sulfated DHP scaffold was synthesized and screened against thrombin and factor Xa. The results reveal that (i) selected monomeric benzofuran derivatives inhibit the two enzymes, albeit weakly; (ii) the two enzymes recognize different structural features in the benzofurans studied suggesting significant selectivity of recognition; and (iii) the mechanism of inhibition is allosteric. The molecules represent the first allosteric small molecule inhibitors of the two enzymes.

  20. First Steps in the Direction of Synthetic, Allosteric, Direct Inhibitors of Thrombin and Factor Xa

    Science.gov (United States)

    Verghese, Jenson; Liang, Aiye; Sidhu, Preet Pal Singh; Hindle, Michael; Zhou, Qibing; Desai, Umesh R.

    2009-01-01

    Designing non-saccharide functional mimics of heparin is a major challenge. In this work, a library of small, aromatic molecules based on the sulfated DHP scaffold was synthesized and screened against thrombin and factor Xa. The results reveal that i) selected monomeric benzofuran derivatives inhibit the two enzymes, albeit weakly; ii) the two enzymes recognize different structural features in the benzofurans studied suggesting significant selectivity of recognition; and iii) the mechanism of inhibition is allosteric. The molecules represent the first allosteric small molecule inhibitors of the two enzymes. PMID:19540113

  1. cobaloxime by imidazoles and amino acids

    Indian Academy of Sciences (India)

    Unknown

    Substitution reactions of propyl cobaloxime with imidazole, substituted imidazoles, histidine, histamine, glycine and ethyl glycine ester are carried out as a function of pH. ... varying success.7–10 Among the vitamin B12 models, organocobaloximes are noteworthy because of their ability to accommodate a wide variety of ...

  2. The structure and allosteric regulation of mammalian glutamate dehydrogenase.

    Science.gov (United States)

    Li, Ming; Li, Changhong; Allen, Aron; Stanley, Charles A; Smith, Thomas J

    2012-03-15

    Glutamate dehydrogenase (GDH) is a homohexameric enzyme that catalyzes the reversible oxidative deamination of l-glutamate to 2-oxoglutarate. Only in the animal kingdom is this enzyme heavily allosterically regulated by a wide array of metabolites. The major activators are ADP and leucine, while the most important inhibitors include GTP, palmitoyl CoA, and ATP. Recently, spontaneous mutations in the GTP inhibitory site that lead to the hyperinsulinism/hyperammonemia (HHS) syndrome have shed light as to why mammalian GDH is so tightly regulated. Patients with HHS exhibit hypersecretion of insulin upon consumption of protein and concomitantly extremely high levels of ammonium in the serum. The atomic structures of four new inhibitors complexed with GDH complexes have identified three different allosteric binding sites. Using a transgenic mouse model expressing the human HHS form of GDH, at least three of these compounds were found to block the dysregulated form of GDH in pancreatic tissue. EGCG from green tea prevented the hyper-response to amino acids in whole animals and improved basal serum glucose levels. The atomic structure of the ECG-GDH complex and mutagenesis studies is directing structure-based drug design using these polyphenols as a base scaffold. In addition, all of these allosteric inhibitors are elucidating the atomic mechanisms of allostery in this complex enzyme. Copyright © 2011 Elsevier Inc. All rights reserved.

  3. Glutamate dehydrogenase: structure, allosteric regulation, and role in insulin homeostasis.

    Science.gov (United States)

    Li, Ming; Li, Changhong; Allen, Aron; Stanley, Charles A; Smith, Thomas J

    2014-01-01

    Glutamate dehydrogenase (GDH) is a homohexameric enzyme that catalyzes the reversible oxidative deamination of L-glutamate to 2-oxoglutarate. Only in the animal kingdom is this enzyme heavily allosterically regulated by a wide array of metabolites. The major activators are ADP and leucine and inhibitors include GTP, palmitoyl CoA, and ATP. Spontaneous mutations in the GTP inhibitory site that lead to the hyperinsulinism/hyperammonemia (HHS) syndrome have shed light as to why mammalian GDH is so tightly regulated. Patients with HHS exhibit hypersecretion of insulin upon consumption of protein and concomitantly extremely high levels of ammonium in the serum. The atomic structures of four new inhibitors complexed with GDH complexes have identified three different allosteric binding sites. Using a transgenic mouse model expressing the human HHS form of GDH, at least three of these compounds blocked the dysregulated form of GDH in pancreatic tissue. EGCG from green tea prevented the hyper-response to amino acids in whole animals and improved basal serum glucose levels. The atomic structure of the ECG-GDH complex and mutagenesis studies is directing structure-based drug design using these polyphenols as a base scaffold. In addition, all of these allosteric inhibitors are elucidating the atomic mechanisms of allostery in this complex enzyme.

  4. Organism-adapted specificity of the allosteric regulation of pyruvate kinase in lactic acid bacteria.

    Directory of Open Access Journals (Sweden)

    Nadine Veith

    Full Text Available Pyruvate kinase (PYK is a critical allosterically regulated enzyme that links glycolysis, the primary energy metabolism, to cellular metabolism. Lactic acid bacteria rely almost exclusively on glycolysis for their energy production under anaerobic conditions, which reinforces the key role of PYK in their metabolism. These organisms are closely related, but have adapted to a huge variety of native environments. They include food-fermenting organisms, important symbionts in the human gut, and antibiotic-resistant pathogens. In contrast to the rather conserved inhibition of PYK by inorganic phosphate, the activation of PYK shows high variability in the type of activating compound between different lactic acid bacteria. System-wide comparative studies of the metabolism of lactic acid bacteria are required to understand the reasons for the diversity of these closely related microorganisms. These require knowledge of the identities of the enzyme modifiers. Here, we predict potential allosteric activators of PYKs from three lactic acid bacteria which are adapted to different native environments. We used protein structure-based molecular modeling and enzyme kinetic modeling to predict and validate potential activators of PYK. Specifically, we compared the electrostatic potential and the binding of phosphate moieties at the allosteric binding sites, and predicted potential allosteric activators by docking. We then made a kinetic model of Lactococcus lactis PYK to relate the activator predictions to the intracellular sugar-phosphate conditions in lactic acid bacteria. This strategy enabled us to predict fructose 1,6-bisphosphate as the sole activator of the Enterococcus faecalis PYK, and to predict that the PYKs from Streptococcus pyogenes and Lactobacillus plantarum show weaker specificity for their allosteric activators, while still having fructose 1,6-bisphosphate play the main activator role in vivo. These differences in the specificity of allosteric

  5. Imidazole catalyzes chlorination by unreactive primary chloramines

    Science.gov (United States)

    Roemeling, Margo D.; Williams, Jared; Beckman, Joseph S.; Hurst, James K.

    2015-01-01

    Hypochlorous acid and simple chloramines (RNHCl) are stable biologically-derived chlorinating agents. In general, the chlorination potential of HOCl is much greater than that of RNHCl, allowing it to oxidize or chlorinate a much wider variety of reaction partners. However, in this study we demonstrate by kinetic analysis that the reactivity of RNHCl can be dramatically promoted by imidazole and histidyl model compounds via intermediary formation of the corresponding imidazole chloramines. Two biologically relevant reactions were investigated—loss of imidazole-catalyzed chlorinating capacity and phenolic ring chlorination using fluorescein and the tyrosine analog, 4-hydroxyphenylacetic acid (HPA). HOCl reacted stoichiometrically with imidazole, N-acetylhistidine (NAH), or imidazoleacetic acid to generate the corresponding imidazole chloramines which subsequently decomposed. Chloramine (NH2Cl) also underwent a markedly accelerated loss in chlorinating capacity when NAH was present, although in this case NAHCl did not accumulate, indicating that the catalytic intermediate must be highly reactive. Mixing HOCl with 1-methylimidazole (MeIm) led to very rapid loss in chlorinating capacity via formation of a highly reactive chlorinium ion (MeImCl+) intermediate; this behavior suggests that the reactive forms of the analogous imidazole chloramines are their conjugate acids, e.g., the imidazolechlorinium ion (HImCl+). HOCl-generated imidazole chloramine (ImCl) reacted rapidly with fluorescein in a specific acid-catalyzed second order reaction to give 3′-monochloro and 3′,5′-dichloro products. Equilibrium constants for the transchlorination reactions: HOCl + HIm = H2O + ImCl and NH2Cl + HIm = NH3 + ImCl were estimated from the dependence of the rate constants upon [HIm]/[HOCl] and literature data. Acid catalysis again suggests that the actual chlorinating agent is HImCl+; consistent with this interpretation, MeIm markedly catalyzed fluorescein chlorination by HOCl

  6. Allosteric transition: a comparison of two models

    DEFF Research Database (Denmark)

    Bindslev, Niels

    2013-01-01

    Introduction Two recent models are in use for analysis of allosteric drug action at receptor sites remote from orthosteric binding sites. One is an allosteric two-state mechanical model derived in 2000 by David Hall. The other is an extended operational model developed in 2007 by Arthur Christopo...

  7. Bioinformatic scaling of allosteric interactions in biomedical isozymes

    Science.gov (United States)

    Phillips, J. C.

    2016-09-01

    Allosteric (long-range) interactions can be surprisingly strong in proteins of biomedical interest. Here we use bioinformatic scaling to connect prior results on nonsteroidal anti-inflammatory drugs to promising new drugs that inhibit cancer cell metabolism. Many parallel features are apparent, which explain how even one amino acid mutation, remote from active sites, can alter medical results. The enzyme twins involved are cyclooxygenase (aspirin) and isocitrate dehydrogenase (IDH). The IDH results are accurate to 1% and are overdetermined by adjusting a single bioinformatic scaling parameter. It appears that the final stage in optimizing protein functionality may involve leveling of the hydrophobic limits of the arms of conformational hydrophilic hinges.

  8. Epoxy Nanocomposites Containing Zeolitic Imidazolate Framework-8.

    Science.gov (United States)

    Liu, Cong; Mullins, Michael; Hawkins, Spencer; Kotaki, Masaya; Sue, Hung-Jue

    2018-01-10

    Zeolitic imidazole framework-8 (ZIF-8) is utilized as a functional filler and a curing agent in the preparation of epoxy nanocomposites. The imidazole group on the surface of the ZIF-8 initiates epoxy curing, resulting in covalent bonding between the ZIF-8 crystals and epoxy matrix. A substantial reduction in dielectric constant and increase in tensile modulus were observed. The implication of the present study for utilization of metal-organic framework to improve physical and mechanical properties of polymeric matrixes is discussed.

  9. Physicochemical properties of the modeled structure of astacin metalloprotease moulting enzyme NAS-36 and mapping the druggable allosteric space of Heamonchus contortus, Brugia malayi and Ceanorhabditis elegans via molecular dynamics simulation.

    Science.gov (United States)

    Sharma, Om Prakash; Agrawal, Sonali; Kumar, M Suresh

    2013-12-01

    Nematodes represent the second largest phylum in the animal kingdom. It is the most abundant species (500,000) in the planet. It causes chronic, debilitating infections worldwide such as ascariasis, trichuriasis, hookworm, enterobiasis, strongyloidiasis, filariasis and trichinosis, among others. Molecular modeling tools can play an important role in the identification and structural investigation of molecular targets that can act as a vital candidate against filariasis. In this study, sequence analysis of NAS-36 from H. contortus (Heamonchus contortus), B. malayi (Brugia malayi) and C. elegans (Ceanorhabditis elegans) has been performed, in order to identify the conserved residues. Tertiary structure was developed for an insight into the molecular structure of the enzyme. Molecular Dynamics Simulation (MDS) studies have been carried out to analyze the stability and the physical properties of the proposed enzyme models in the H. contortus, B. malayi and C. elegans. Moreover, the drug binding sites have been mapped for inhibiting the function of NAS-36 enzyme. The molecular identity of this protease could eventually demonstrate how ex-sheathment is regulated, as well as provide a potential target of anthelmintics for the prevention of nematode infections.

  10. A small-molecule allosteric inhibitor of Mycobacterium tuberculosis tryptophan synthase

    Energy Technology Data Exchange (ETDEWEB)

    Wellington, Samantha; Nag, Partha P.; Michalska, Karolina; Johnston, Stephen E.; Jedrzejczak, Robert P.; Kaushik, Virendar K.; Clatworthy, Anne E.; Siddiqi, Noman; McCarren, Patrick; Bajrami, Besnik; Maltseva, Natalia I.; Combs, Senya; Fisher, Stewart L.; Joachimiak, Andrzej; Schreiber, Stuart L.; Hung, Deborah T.

    2017-07-03

    New antibiotics with novel targets are greatly needed. Bacteria have numerous essential functions, but only a small fraction of such processes—primarily those involved in macromolecular synthesis—are inhibited by current drugs. Targeting metabolic enzymes has been the focus of recent interest, but effective inhibitors have been difficult to identify. We describe a synthetic azetidine derivative, BRD4592, that kills Mycobacterium tuberculosis (Mtb) through allosteric inhibition of tryptophan synthase (TrpAB), a previously untargeted, highly allosterically regulated enzyme. BRD4592 binds at the TrpAB α–β-subunit interface and affects multiple steps in the enzyme's overall reaction, resulting in inhibition not easily overcome by changes in metabolic environment. We show that TrpAB is required for the survival of Mtb and Mycobacterium marinum in vivo and that this requirement may be independent of an adaptive immune response. This work highlights the effectiveness of allosteric inhibition for targeting proteins that are naturally highly dynamic and that are essential in vivo, despite their apparent dispensability under in vitro conditions, and suggests a framework for the discovery of a next generation of allosteric inhibitors.

  11. Guanine nucleotide binding to the Bateman domain mediates the allosteric inhibition of eukaryotic IMP dehydrogenases

    Science.gov (United States)

    Buey, Rubén M.; Ledesma-Amaro, Rodrigo; Velázquez-Campoy, Adrián; Balsera, Mónica; Chagoyen, Mónica; de Pereda, José M.; Revuelta, José L.

    2015-11-01

    Inosine-5'-monophosphate dehydrogenase (IMPDH) plays key roles in purine nucleotide metabolism and cell proliferation. Although IMPDH is a widely studied therapeutic target, there is limited information about its physiological regulation. Using Ashbya gossypii as a model, we describe the molecular mechanism and the structural basis for the allosteric regulation of IMPDH by guanine nucleotides. We report that GTP and GDP bind to the regulatory Bateman domain, inducing octamers with compromised catalytic activity. Our data suggest that eukaryotic and prokaryotic IMPDHs might have developed different regulatory mechanisms, with GTP/GDP inhibiting only eukaryotic IMPDHs. Interestingly, mutations associated with human retinopathies map into the guanine nucleotide-binding sites including a previously undescribed non-canonical site and disrupt allosteric inhibition. Together, our results shed light on the mechanisms of the allosteric regulation of enzymes mediated by Bateman domains and provide a molecular basis for certain retinopathies, opening the door to new therapeutic approaches.

  12. A dynamically coupled allosteric network underlies binding cooperativity in Src kinase

    Science.gov (United States)

    Foda, Zachariah H.; Shan, Yibing; Kim, Eric T.; Shaw, David E.; Seeliger, Markus A.

    2015-01-01

    Protein tyrosine kinases are attractive drug targets because many human diseases are associated with the deregulation of kinase activity. However, how the catalytic kinase domain integrates different signals and switches from an active to an inactive conformation remains incompletely understood. Here we identify an allosteric network of dynamically coupled amino acids in Src kinase that connects regulatory sites to the ATP- and substrate-binding sites. Surprisingly, reactants (ATP and peptide substrates) bind with negative cooperativity to Src kinase while products (ADP and phosphopeptide) bind with positive cooperativity. We confirm the molecular details of the signal relay through the allosteric network by biochemical studies. Experiments on two additional protein tyrosine kinases indicate that the allosteric network may be largely conserved among these enzymes. Our work provides new insights into the regulation of protein tyrosine kinases and establishes a potential conduit by which resistance mutations to ATP-competitive kinase inhibitors can affect their activity.

  13. A dynamically coupled allosteric network underlies binding cooperativity in Src kinase.

    Science.gov (United States)

    Foda, Zachariah H; Shan, Yibing; Kim, Eric T; Shaw, David E; Seeliger, Markus A

    2015-01-20

    Protein tyrosine kinases are attractive drug targets because many human diseases are associated with the deregulation of kinase activity. However, how the catalytic kinase domain integrates different signals and switches from an active to an inactive conformation remains incompletely understood. Here we identify an allosteric network of dynamically coupled amino acids in Src kinase that connects regulatory sites to the ATP- and substrate-binding sites. Surprisingly, reactants (ATP and peptide substrates) bind with negative cooperativity to Src kinase while products (ADP and phosphopeptide) bind with positive cooperativity. We confirm the molecular details of the signal relay through the allosteric network by biochemical studies. Experiments on two additional protein tyrosine kinases indicate that the allosteric network may be largely conserved among these enzymes. Our work provides new insights into the regulation of protein tyrosine kinases and establishes a potential conduit by which resistance mutations to ATP-competitive kinase inhibitors can affect their activity.

  14. Extreme Flexibility in a Zeolitic Imidazolate Framework

    DEFF Research Database (Denmark)

    Wharmby, M.T.; Henke, S.; Bennett, T.D.

    2015-01-01

    Desolvated zeolitic imidazolate framework ZIF-4(Zn) undergoes a discontinuous porous to dense phase transition on cooling through 140 K, with a 23% contraction in unit cell volume. The structure of the non-porous, low temperature phase was determined from synchrotron X-ray powder diffraction data...

  15. Synthesis, Characterization and Antibacterial Activity of Imidazole ...

    African Journals Online (AJOL)

    NICO

    Synthesis, Characterization and Antibacterial Activity of. Imidazole Derivatives of 1,10-Phenanthroline and their .... Synthesis of Ligands (L1, L2). Ligands (L1. , L2) were synthesized by a method similar to one ... (50 mL). Dropwise addition of concentrated aqueaus ammonia to neutralize gave a yellow precipitate, which was ...

  16. Interactions between oxovanadium (IV), glycylvaline and imidazoles ...

    Indian Academy of Sciences (India)

    Speciation has been determined in aqueous oxovanadium, glycylvaline and imidazoles at 25 ± 1° C and = 0.1M NaClO4 using a combination of potentiometry, and visible and EPR spectroscopy. Results of potentiometric and spectroscopic methods are consistent. Calculations of stability constants have been made using ...

  17. Studies on allosteric phenomena in glycogen phosphorylase b.

    Science.gov (United States)

    Madsen, N B; Avramovic-Zikic, O; Lue, P F; Honikel, K O

    1976-03-26

    This article attempts to trace, from a personal point of view, the history of discoveries of allosteric phenomena in phosphorylase b and the later development of systematic attempts to fit the data into comprehensive theoretical models. Work from our own laboratory is emphasized, but we try to integrate this into the results from other investigators and show their contributions to our ideas and experiments. Finally, some recent unpublished data is presented together with some conclusions and predictions from a new hypothesis. The discoveries by Carl and Gerty Cori of the activation of phosphorylase by AMP, the inhibition of glucose and the enzymatic interconversion of two forms fo the enzyme with different control properties helped lay the foundations of our present understanding of allosteric mechanisms. The later discovery of the oligomeric nature of phosphorylase and its relationship to AMP binding served as a basis for many years of research into the structure-function relationships of phosphorylase and other enzymes. Data showing that AMP lowers the entropy of activation is discussed with respect to the role of the nucleotide and its binding close to the active site. The discovery of the control of phosphorylase b by common metabolites and the impetus this gave to the intensive kinetic studies of the last ten years, wherein fitting to theoretical models has been a common feature, is reviewed.

  18. Chemogenomics of allosteric binding sites in GPCRs

    DEFF Research Database (Denmark)

    Gloriam, David E.

    2013-01-01

    profiling. This review describes recent developments structured into ligand-, target- and combined chemogenomic techniques and applications to allosteric GPCR ligands. It also outlines relative strengths and limitations of these techniques and the impact of the increasing crystallographic data....

  19. One-electron oxidation of iron(II)-imidazole and iron-(II)-bis[imidazol-2-yl]methane complexes: a pulse radiolysis study

    International Nuclear Information System (INIS)

    Parsons, B.J.; Navaratnam, S.; Zhao, Z.; Chen, L.

    1994-01-01

    The radical anion, Br 2 .- , a strong one-electron oxidant, has been used to oxidise iron(II)-imidazole, Fe 11 -ImH, and iron(II)-bis(imidazol-2-yl)methane, Fe 11 -2-BIM, complexes in aqueous solution, the latter being regarded as good models of the iron(II) site in non-haem iron-containing enzymes such as lipoxygenase. The rates of oxidation of Fe 11 -ImH, Fe 11 (ImH) 2 , Fe-2-BIM and Fe 11 (2-BIM) 2 were measured as 1.0 x 10 7 , 2.0 x 10 7 , 1.8 x 10 8 and 3.6 x 10 8 dm 3 mol -1 s -1 . From measurements of the rates of oxidation of the ligand, it is clear that Br 2 .- oxidises the ligand in the metal complexes in the first instance. The same studies also show that the 2-BIM ligand is easier to oxidise than the closely related imidazole ligand by a factor of 10. Measurements of the rate of oxidation of 2-methylimidazole indicate that the difference is attributable to the inductive effect of the -CH 2 -group. (author)

  20. A small-molecule allosteric inhibitor of Mycobacterium tuberculosis tryptophan synthase

    Energy Technology Data Exchange (ETDEWEB)

    Wellington, Samantha; Nag, Partha P.; Michalska, Karolina; Johnston, Stephen E.; Jedrzejczak, Robert P.; Kaushik, Virendar K.; Clatworthy, Anne E.; Siddiqi, Noman; McCarren, Patrick; Bajrami, Besnik; Maltseva, Natalia I.; Combs, Senya; Fisher, Stewart L.; Joachimiak, Andrzej; Schreiber, Stuart L.; Hung, Deborah T.

    2017-07-03

    New antibiotics with novel targets are greatly needed. Bacteria have numerous essential functions, but only a small fraction of such processes—primarily those involved in macromolecular synthesis—are inhibited by current drugs. Targeting metabolic enzymes has been the focus of recent interest, but effective inhibitors have been difficult to identify. We describe a synthetic azetidine derivative, BRD4592, that kills Mycobacterium tuberculosis (Mtb) through allosteric inhibition of tryptophan synthase (TrpAB), a previously untargeted, highly allosterically regulated enzyme. BRD4592 binds at the TrpAB a–b-subunit interface and affects multiple steps in the enzyme’s overall reaction, resulting in inhibition not easily overcome by changes in metabolic environment. We show that TrpAB is required for the survival of Mtb and Mycobacterium marinum in vivo and that this requirement may be independent of an adaptive immune response. This work highlights the effectiveness of allosteric inhibition for targeting proteins that are naturally highly dynamic and that are essential in vivo, despite their apparent dispensability under in vitro conditions, and suggests a framework for the discovery of a next generation of allosteric inhibitors.

  1. Monitoring imidazolů v potravinách

    OpenAIRE

    Le Qui, Khanh Linh

    2016-01-01

    This bachelor thesis deals with the formation, occurrence, and analysis of imidazoles in food. It is mainly devoted to caramel colors and imidazoles contained within. It also describes caramel as a colorant including the process of caramelization and further division of these colors into classes and their usage. Introduces the previously described effect of these substances on human health. The fact that some imidazoles have carcinogenic properties is almost confirmed. In conclusion, there is...

  2. The structure of brain glycogen phosphorylase-from allosteric regulation mechanisms to clinical perspectives.

    Science.gov (United States)

    Mathieu, Cécile; Dupret, Jean-Marie; Rodrigues Lima, Fernando

    2017-02-01

    Glycogen phosphorylase (GP) is the key enzyme that regulates glycogen mobilization in cells. GP is a complex allosteric enzyme that comprises a family of three isozymes: muscle GP (mGP), liver GP (lGP), and brain GP (bGP). Although the three isozymes display high similarity and catalyze the same reaction, they differ in their sensitivity to the allosteric activator adenosine monophosphate (AMP). Moreover, inactivating mutations in mGP and lGP have been known to be associated with glycogen storage diseases (McArdle and Hers disease, respectively). The determination, decades ago, of the structure of mGP and lGP have allowed to better understand the allosteric regulation of these two isoforms and the development of specific inhibitors. Despite its important role in brain glycogen metabolism, the structure of the brain GP had remained elusive. Here, we provide an overview of the human brain GP structure and its relationship with the two other members of this key family of the metabolic enzymes. We also summarize how this structure provides valuable information to understand the regulation of bGP and to design specific ligands of potential pharmacological interest. © 2016 Federation of European Biochemical Societies.

  3. Targeting S-adenosylmethionine biosynthesis with a novel allosteric inhibitor of Mat2A

    Energy Technology Data Exchange (ETDEWEB)

    Quinlan, Casey L.; Kaiser, Stephen E.; Bolaños, Ben; Nowlin, Dawn; Grantner, Rita; Karlicek-Bryant, Shannon; Feng, Jun Li; Jenkinson, Stephen; Freeman-Cook, Kevin; Dann, Stephen G.; Wang, Xiaoli; Wells, Peter A.; Fantin, Valeria R.; Stewart, Al E.; Grant, Stephan K. (Pfizer)

    2017-05-29

    S-Adenosyl-L-methionine (SAM) is an enzyme cofactor used in methyl transfer reactions and polyamine biosynthesis. The biosynthesis of SAM from ATP and L-methionine is performed by the methionine adenosyltransferase enzyme family (Mat; EC 2.5.1.6). Human methionine adenosyltransferase 2A (Mat2A), the extrahepatic isoform, is often deregulated in cancer. We identified a Mat2A inhibitor, PF-9366, that binds an allosteric site on Mat2A that overlaps with the binding site for the Mat2A regulator, Mat2B. Studies exploiting PF-9366 suggested a general mode of Mat2A allosteric regulation. Allosteric binding of PF-9366 or Mat2B altered the Mat2A active site, resulting in increased substrate affinity and decreased enzyme turnover. These data support a model whereby Mat2B functions as an inhibitor of Mat2A activity when methionine or SAM levels are high, yet functions as an activator of Mat2A when methionine or SAM levels are low. The ramification of Mat2A activity modulation in cancer cells is also described.

  4. Zeolitic imidazolate frameworks for kinetic separation of propane and propene

    Science.gov (United States)

    Li, Jing; Li, Kunhao; Olson, David H.

    2014-08-05

    Zeolitic Imidazolate Frameworks (ZIFs) characterized by organic ligands consisting of imidazole ligands that are either essentially all 2-chloroimidazole ligands or essentially all 2-bromoimidazole ligands are disclosed. Methods for separating propane and propene with the ZIFs of the present invention, as well as other ZIFs, are also disclosed.

  5. A trans influence study in propyl (aquo) cobaloxime by imidazoles ...

    Indian Academy of Sciences (India)

    Substitution reactions of propyl cobaloxime with imidazole, substituted imidazoles, histidine, histamine, glycine and ethyl glycine ester are carried out as a function of pH. Trends in the formation constants are explained based on the steric hindrance, extent of -bonding and -donor capacity of the incoming ligand.

  6. Alkylation of imidazole under ultrasound irradiation over alkaline carbons

    Energy Technology Data Exchange (ETDEWEB)

    Costarrosa, L. [Dpto. de Quimica Inorganica y Quimica Tecnica, Facultad de Ciencias, Universidad Nacional de Educacion a Distancia (UNED), C/Senda del Rey, 9, E-28040 Madrid (Spain); Calvino-Casilda, V. [Dpto. de Quimica Inorganica y Quimica Tecnica, Facultad de Ciencias, Universidad Nacional de Educacion a Distancia (UNED), C/Senda del Rey, 9, E-28040 Madrid (Spain); Ferrera-Escudero, S. [Dpto. de Quimica Inorganica y Quimica Tecnica, Facultad de Ciencias, Universidad Nacional de Educacion a Distancia (UNED), C/Senda del Rey, 9, E-28040 Madrid (Spain); Duran-Valle, C.J. [Dpto. de Quimica Inorganica, Facultad de Ciencias, Universidad de Extremadura, Avenida de Elvas s/n, 06071 Badajoz (Spain); Martin-Aranda, R.M. [Dpto. de Quimica Inorganica y Quimica Tecnica, Facultad de Ciencias, Universidad Nacional de Educacion a Distancia (UNED), C/Senda del Rey, 9, E-28040 Madrid (Spain)]. E-mail: rmartin@ccia.uned.es

    2006-06-30

    N-Alkyl-imidazole has been synthesized by sonochemical irradiation of imidazole and 1-bromobutane using alkaline-promoted carbons (exchanged with the binary combinations of Na, K and Cs). The catalysts were characterized by X-ray photoelectron spectroscopy, thermal analysis and N{sub 2} adsorption isotherms. Under the experimental conditions, N-alkyl-imidazoles can be prepared with a high activity and selectivity. It is observed that imidazole conversion increases in parallel with increasing the basicity of the catalyst. The influence of the alkaline promoter, the reaction temperature, and the amount of catalyst on the catalytic activity has been studied. For comparison, the alkylation of imidazole has also been performed in a batch reactor system under thermal activation.

  7. Alkylation of imidazole under ultrasound irradiation over alkaline carbons

    International Nuclear Information System (INIS)

    Costarrosa, L.; Calvino-Casilda, V.; Ferrera-Escudero, S.; Duran-Valle, C.J.; Martin-Aranda, R.M.

    2006-01-01

    N-Alkyl-imidazole has been synthesized by sonochemical irradiation of imidazole and 1-bromobutane using alkaline-promoted carbons (exchanged with the binary combinations of Na, K and Cs). The catalysts were characterized by X-ray photoelectron spectroscopy, thermal analysis and N 2 adsorption isotherms. Under the experimental conditions, N-alkyl-imidazoles can be prepared with a high activity and selectivity. It is observed that imidazole conversion increases in parallel with increasing the basicity of the catalyst. The influence of the alkaline promoter, the reaction temperature, and the amount of catalyst on the catalytic activity has been studied. For comparison, the alkylation of imidazole has also been performed in a batch reactor system under thermal activation

  8. ALLO: A tool to discriminate and prioritize allosteric pockets.

    Science.gov (United States)

    Akbar, Rahmad; Helms, Volkhard

    2018-04-01

    Allosteric proteins make up a substantial proportion of human drug targets. Thus, rational design of small molecule binders that target these proteins requires the identification of putative allosteric pockets and an understanding of their potential activity. Here, we characterized allosteric pockets using a set of physicochemical descriptors and compared them to pockets that are found on the surface of a protein. Further, we trained predictive models capable of discriminating allosteric pockets from orthosteric pockets and models capable of prioritizing allosteric pockets in a set of pockets found on a given protein. Such models might be useful for identifying novel allosteric sites and in turn, potentially new allosteric drug targets. Datasets along with a Python program encapsulating the predictive models are available at http://github.com/fibonaccirabbits/allo. © 2017 John Wiley & Sons A/S.

  9. Allosteric small-molecule kinase inhibitors

    DEFF Research Database (Denmark)

    Wu, Peng; Clausen, Mads Hartvig; Nielsen, Thomas E.

    2015-01-01

    current barriers of kinase inhibitors, including poor selectivity and emergence of drug resistance. In spite of the small number of identified allosteric inhibitors in comparison with that of inhibitors targeting the ATP pocket, encouraging results, such as the FDA-approval of the first small...

  10. Agonism/antagonism switching in allosteric ensembles.

    Science.gov (United States)

    Motlagh, Hesam N; Hilser, Vincent J

    2012-03-13

    Ligands for several transcription factors can act as agonists under some conditions and antagonists under others. The structural and molecular bases of such effects are unknown. Previously, we demonstrated how the folding of intrinsically disordered (ID) protein sequences, in particular, and population shifts, in general, could be used to mediate allosteric coupling between different functional domains, a model that has subsequently been validated in several systems. Here it is shown that population redistribution within allosteric systems can be used as a mechanism to tune protein ensembles such that a given ligand can act as both an agonist and an antagonist. Importantly, this mechanism can be robustly encoded in the ensemble, and does not require that the interactions between the ligand and the protein differ when it is acting either as an agonist or an antagonist. Instead, the effect is due to the relative probabilities of states prior to the addition of the ligand. The ensemble view of allostery that is illuminated by these studies suggests that rather than being seen as switches with fixed responses to allosteric activation, ensembles can evolve to be "functionally pluripotent," with the capacity to up or down regulate activity in response to a stimulus. This result not only helps to explain the prevalence of intrinsic disorder in transcription factors and other cell signaling proteins, it provides important insights about the energetic ground rules governing site-to-site communication in all allosteric systems.

  11. Metalloregulatory proteins: metal selectivity and allosteric switching.

    Science.gov (United States)

    Reyes-Caballero, Hermes; Campanello, Gregory C; Giedroc, David P

    2011-07-01

    Prokaryotic organisms have evolved the capacity to quickly adapt to a changing and challenging microenvironment in which the availability of both biologically required and non-essential transition metal ions can vary dramatically. In all bacteria, a panel of metalloregulatory proteins controls the expression of genes encoding membrane transporters and metal trafficking proteins that collectively manage metal homeostasis and resistance. These "metal sensors" are specialized allosteric proteins, in which the direct binding of a specific or small number of "cognate" metal ion(s) drives a conformational change in the regulator that allosterically activates or inhibits operator DNA binding, or alternatively, distorts the promoter structure thereby converting a poor promoter to a strong one. In this review, we discuss our current understanding of the features that control metal specificity of the allosteric response in these systems, and the role that structure, thermodynamics and conformational dynamics play in mediating allosteric activation or inhibition of DNA binding. Copyright © 2011 Elsevier B.V. All rights reserved.

  12. Allosteric Modulation of Muscarinic Acetylcholine Receptors

    Czech Academy of Sciences Publication Activity Database

    Jakubík, Jan; El-Fakahany, E. E.

    2010-01-01

    Roč. 3, č. 9 (2010), s. 2838-2860 ISSN 1424-8247 R&D Projects: GA ČR GA305/09/0681 Institutional research plan: CEZ:AV0Z50110509 Keywords : muscarinic acetylcholine receptors * allosteric modulation * Alzheimer ´s disease Subject RIV: CE - Biochemistry

  13. A tailored biocatalyst achieved by the rational anchoring of imidazole groups on a natural polymer: furnishing a potential artificial nuclease by sustainable materials engineering.

    Science.gov (United States)

    Ferreira, José G L; Grein-Iankovski, Aline; Oliveira, Marco A S; Simas-Tosin, Fernanda F; Riegel-Vidotti, Izabel C; Orth, Elisa S

    2015-04-11

    Foreseeing the development of artificial enzymes by sustainable materials engineering, we rationally anchored reactive imidazole groups on gum arabic, a natural biocompatible polymer. The tailored biocatalyst GAIMZ demonstrated catalytic activity (>10(5)-fold) in dephosphorylation reactions with recyclable features and was effective in cleaving plasmid DNA, comprising a potential artificial nuclease.

  14. Allosteric control of internal electron transfer in cytochrome cd1 nitrite reductase

    DEFF Research Database (Denmark)

    Farver, Ole; Kroneck, Peter M H; Zumft, Walter G

    2003-01-01

    Cytochrome cd1 nitrite reductase is a bifunctional multiheme enzyme catalyzing the one-electron reduction of nitrite to nitric oxide and the four-electron reduction of dioxygen to water. Kinetics and thermodynamics of the internal electron transfer process in the Pseudomonas stutzeri enzyme have...... been studied and found to be dominated by pronounced interactions between the c and the d1 hemes. The interactions are expressed both in dramatic changes in the internal electron-transfer rates between these sites and in marked cooperativity in their electron affinity. The results constitute a prime...... example of intraprotein control of the electron-transfer rates by allosteric interactions....

  15. Allosteric Inhibition Through Core Disruption

    Energy Technology Data Exchange (ETDEWEB)

    Horn, James R.; Shoichet, Brian K. (NWU); (UCSF)

    2010-03-05

    Although inhibitors typically bind pre-formed sites on proteins, it is theoretically possible to inhibit by disrupting the folded structure of a protein or, in the limit, to bind preferentially to the unfolded state. Equilibria defining how such molecules act are well understood, but structural models for such binding are unknown. Two novel inhibitors of {beta}-lactamase were found to destabilize the enzyme at high temperatures, but at lower temperatures showed no preference for destabilized mutant enzymes versus stabilized mutants. X-ray crystal structures showed that both inhibitors bound to a cryptic site in {beta}-lactamase, which the inhibitors themselves created by forcing apart helixes 11 and 12. This opened up a portion of the hydrophobic core of the protein, into which these two inhibitors bind. Although this binding site is 16 {angstrom} from the center of the active site, the conformational changes were transmitted through a sequence of linked motions to a key catalytic residue, Arg244, which in the complex adopts conformations very different from those in catalytically competent enzyme conformations. These structures offer a detailed view of what has heretofore been a theoretical construct, and suggest the possibility for further design against this novel site.

  16. Structure Property Relationships in Imidazole-based Deep Eutectic Mixtures

    Science.gov (United States)

    Terheggen, Logan; Cosby, Tyler; Sangoro, Joshua

    2015-03-01

    Deep eutectic mixtures of levulinic acid with a systematic series of imidazoles are measured by broadband dielectric spectroscopy, differential scanning calorimetry, and Fourier transform infrared spectroscopy to investigate the impact of steric interactions on charge transport and structural dynamics. An enhancement of dc conductivity is found in each of the imidazoles upon the addition of levulinic acid. However, the extent of increase is dependent upon the alkyl substitution on the imidazole ring. These results highlight the importance of molecular structure on hydrogen bonding and charge transport in deep eutectic mixtures.

  17. Characterization of the allosteric binding pocket of human liver fructose-1,6-bisphosphatase by protein crystallography and inhibitor activity studies.

    Science.gov (United States)

    Iversen, L F; Brzozowski, M; Hastrup, S; Hubbard, R; Kastrup, J S; Larsen, I K; Naerum, L; Nørskov-Lauridsen, L; Rasmussen, P B; Thim, L; Wiberg, F C; Lundgren, K

    1997-05-01

    The structures of three complexes of human fructose-1,6-bisphosphatase (FB) with the allosteric inhibitor AMP and two AMP analogues have been determined and all fully refined. The data used for structure determination were collected at cryogenic temperature (110 K), and with the use of synchrotron radiation. The structures reveal a common mode of binding for AMP and formycine monophosphate (FMP). 5-Amino-4-carboxamido-1 beta-D-5-phosphate-ribofuranosyl-1H-imidazole (AICAR-P) shows an unexpected mode of binding to FB, different from that of the other two ligands. The imidazole ring of AICAR-P is rotated 180 degrees compared to the AMP and FMP bases. This rotation results in a slightly different hydrogen bonding pattern and minor changes in the water structure in the binding pocket. Common features of binding are seen for the ribose and phosphate moieties of all three compounds. Although binding in a different mode, AICAR-P is still capable of making all the important interactions with the residues building the allosteric binding pocket. The IC50 values of AMP, FMP, and AICAR-P were determined to be 1.7, 1.4, and 20.9 microM, respectively. Thus, the approximately 10 times lower potency of AICAR-P is difficult to explain solely from the variations observed in the binding pocket. Only one water molecule in the allosteric binding pocket was found to be conserved in all four subunits in all three structures. This water molecule coordinates to a phosphate oxygen atom and the N7 atom of the AMP molecule, and to similarly situated atoms in the FMP and AICAR-P complexes. This implies an important role of the conserved water molecule in binding of the ligand.

  18. Allosteric Control of Substrate Specificity of the Escherichia coli ADP-glucose Pyrophosphorylase

    Science.gov (United States)

    Ebrecht, Ana C.; Solamen, Ligin; Hill, Benjamin L.; Iglesias, Alberto A.; Olsen, Kenneth W.; Ballicora, Miguel A.

    2017-06-01

    The substrate specificity of enzymes is crucial to control the fate of metabolites to different pathways. However, there is growing evidence that many enzymes can catalyze alternative reactions. This promiscuous behavior has important implications in protein evolution and the acquisition of new functions. The question is how the undesirable outcomes of in vivo promiscuity can be prevented. ADP-glucose pyrophosphorylase from Escherichia coli is an example of an enzyme that needs to select the correct substrate from a broad spectrum of alternatives. This selection will guide the flow of carbohydrate metabolism towards the synthesis of reserve polysaccharides. Here, we show that the allosteric activator fructose-1,6-bisphosphate plays a role in such selection by increasing the catalytic efficiency of the enzyme towards the use of ATP rather than other nucleotides. In the presence of fructose-1,6-bisphosphate, the kcat/S0.5 for ATP was near 600-fold higher that other nucleotides, whereas in the absence of activator was only 3-fold higher. We propose that the allosteric regulation of certain enzymes is an evolutionary mechanism of adaptation for the selection of specific substrates.

  19. The Structural Basis for Allosteric Inhibition of a Threonine-sensitive Aspartokinase

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Xuying; Pavlovsky, Alexander G.; Viola, Ronald E. (Toledo)

    2008-10-08

    The commitment step to the aspartate pathway of amino acid biosynthesis is the phosphorylation of aspartic acid catalyzed by aspartokinase (AK). Most microorganisms and plants have multiple forms of this enzyme, and many of these isofunctional enzymes are subject to feedback regulation by the end products of the pathway. However, the archeal species Methanococcus jannaschii has only a single, monofunctional form of AK. The substrate l-aspartate binds to this recombinant enzyme in two different orientations, providing the first structural evidence supporting the relaxed regiospecificity previously observed with several alternative substrates of Escherichia coli AK. Binding of the nucleotide substrate triggers significant domain movements that result in a more compact quaternary structure. In contrast, the highly cooperative binding of the allosteric regulator l-threonine to multiple sites on this dimer of dimers leads to an open enzyme structure. A comparison of these structures supports a mechanism for allosteric regulation in which the domain movements induced by threonine binding causes displacement of the substrates from the enzyme, resulting in a relaxed, inactive conformation.

  20. Hydrogen-deuterium exchange study of an allosteric energy cycle.

    Science.gov (United States)

    Beckett, Dorothy

    2012-01-01

    Elucidation of mechanisms of energy transduction through macromolecules in allosteric systems requires application of a broad range of techniques and approaches. High-resolution structures of the end states in an allosteric system provide invaluable clues about allosteric mechanism. Thermodynamic and kinetic studies reveal the rules that govern the transitions between states in the system. Acquisition of detailed molecular level information about allosteric mechanism requires interrogation of the structural and dynamic properties of both intermediates and end states in the allosteric cycle. Many experimental and computational tools have been developed to probe allostery. Among these are hydrogen-deuterium exchange detected by either NMR spectroscopy or mass spectrometry. This article provides a detailed description of application of hydrogen exchange detected by mass spectrometry (HDX-MS) to investigate an allosteric system.

  1. Agonism/antagonism switching in allosteric ensembles

    OpenAIRE

    Motlagh, Hesam N.; Hilser, Vincent J.

    2012-01-01

    Ligands for several transcription factors can act as agonists under some conditions and antagonists under others. The structural and molecular bases of such effects are unknown. Previously, we demonstrated how the folding of intrinsically disordered (ID) protein sequences, in particular, and population shifts, in general, could be used to mediate allosteric coupling between different functional domains, a model that has subsequently been validated in several systems. Here it is shown that pop...

  2. Exploiting protein flexibility to predict the location of allosteric sites

    Directory of Open Access Journals (Sweden)

    Panjkovich Alejandro

    2012-10-01

    Full Text Available Abstract Background Allostery is one of the most powerful and common ways of regulation of protein activity. However, for most allosteric proteins identified to date the mechanistic details of allosteric modulation are not yet well understood. Uncovering common mechanistic patterns underlying allostery would allow not only a better academic understanding of the phenomena, but it would also streamline the design of novel therapeutic solutions. This relatively unexplored therapeutic potential and the putative advantages of allosteric drugs over classical active-site inhibitors fuel the attention allosteric-drug research is receiving at present. A first step to harness the regulatory potential and versatility of allosteric sites, in the context of drug-discovery and design, would be to detect or predict their presence and location. In this article, we describe a simple computational approach, based on the effect allosteric ligands exert on protein flexibility upon binding, to predict the existence and position of allosteric sites on a given protein structure. Results By querying the literature and a recently available database of allosteric sites, we gathered 213 allosteric proteins with structural information that we further filtered into a non-redundant set of 91 proteins. We performed normal-mode analysis and observed significant changes in protein flexibility upon allosteric-ligand binding in 70% of the cases. These results agree with the current view that allosteric mechanisms are in many cases governed by changes in protein dynamics caused by ligand binding. Furthermore, we implemented an approach that achieves 65% positive predictive value in identifying allosteric sites within the set of predicted cavities of a protein (stricter parameters set, 0.22 sensitivity, by combining the current analysis on dynamics with previous results on structural conservation of allosteric sites. We also analyzed four biological examples in detail, revealing

  3. The future of type 1 cannabinoid receptor allosteric ligands.

    Science.gov (United States)

    Alaverdashvili, Mariam; Laprairie, Robert B

    2018-02-01

    Allosteric modulation of the type 1 cannabinoid receptor (CB1R) holds great therapeutic potential. This is because allosteric modulators do not possess intrinsic efficacy, but instead augment (positive allosteric modulation) or diminish (negative allosteric modulation) the receptor's response to endogenous ligand. Consequently, CB1R allosteric modulators have an effect ceiling which allows for the tempering of CB1R signaling without the desensitization, tolerance, dependence, and psychoactivity associated with orthosteric compounds. Pain, movement disorders, epilepsy, obesity are all potential therapeutic targets for CB1R allosteric modulation. Several challenges exist for the development of CB1R allosteric modulators, such as receptor subtype specificity, translation to in vivo systems, and mixed allosteric/agonist/inverse agonist activity. Despite these challenges, elucidation of crystal structures of CB1R and compound design based on structure-activity relationships will advance the field. In this review, we will cover recent progress for CB1R allosteric modulators and discuss the future promise of this research.

  4. Synthesis of Trisubstituted Imidazoles Using Lewis and Bronsted Acid Catalysts

    OpenAIRE

    Hekmatshoar, Rahim; HEKMATSHOAR, Rahim; JAHANBAKHSHI, Hajar; MOUSAVIZADEH, Farnoosh; RAHNAMAFAR, Reyhane

    2010-01-01

    An efficient and one-pot method for the preparation of trisubstituted imidazoles by condensation of benzil, different aldehydes and ammonium acetate in the presence of  a catalytic amount of NiSO4.7H2O or H3BO3 under different conditions is reported.                    Key Words: Trisubstituted imidazoles, Multi-component &a...

  5. Synthesis of Novel Allosteric Agonists and Allosteric Modulators for Nicotinic Acetylcholine Receptors

    OpenAIRE

    Dhankher, P.

    2013-01-01

    In healthy individuals, the α7 and α4β2 nAChRs are concentrated in regions of the brain involved with learning, cognition and memory, which are relevant to diseases such as Alzheimer’s disease. Hence, these receptors have become significant from a pharmacological and drug discovery perspective. The tetrahydroquinoline compound 4BP-TQS has been reported to act as a potent allosteric agonist on the α7 nAChR. The natural product desformylflustrabromine is able to act as a positive allosteric mod...

  6. The contribution of two isozymes to the pyruvate kinase activity of Vibrio cholerae: One K+-dependent constitutively active and another K+-independent with essential allosteric activation.

    Science.gov (United States)

    Guerrero-Mendiola, Carlos; García-Trejo, José J; Encalada, Rusely; Saavedra, Emma; Ramírez-Silva, Leticia

    2017-01-01

    In a previous phylogenetic study of the family of pyruvate kinase EC (2.7.1.40), a cluster with Glu117 and another with Lys117 were found (numbered according to the rabbit muscle enzyme). The sequences with Glu117 have been found to be K+-dependent, whereas those with Lys117 were K+-independent. Interestingly, only γ-proteobacteria exhibit sequences in both branches of the tree. In this context, it was explored whether these phylogenetically distinct pyruvate kinases were both expressed and contribute to the pyruvate kinase activity in Vibrio cholerae. The main findings of this work showed that the isozyme with Glu117 is an active K+-dependent enzyme. At the same substrate concentration, its Vmax in the absence of fructose 1,6 bisphosphate was 80% of that with its effector. This result is in accordance with the non-essential activation described by allosteric ligands for most pyruvate kinases. In contrast, the pyruvate kinase with Lys117 was a K+-independent enzyme displaying an allosteric activation by ribose 5-phosphate. At the same substrate concentration, its activity without the effector was 0.5% of the one obtained in the presence of ribose 5-phosphate, indicating that this sugar monophosphate is a strong activator of this enzyme. This absolute allosteric dependence is a novel feature of pyruvate kinase activity. Interestingly, in the K+-independent enzyme, Mn2+ may "mimic" the allosteric effect of Rib 5-P. Despite their different allosteric behavior, both isozymes display a rapid equilibrium random order kinetic mechanism. The intracellular concentrations of fructose 1,6-bisphosphate and ribose 5-phosphate in Vibrio cholerae have been experimentally verified to be sufficient to induce maximal activation of both enzymes. In addition, Western blot analysis indicated that both enzymes were co-expressed. Therefore, it is concluded that VcIPK and VcIIPK contribute to the activity of pyruvate kinase in this γ-proteobacterium.

  7. Multiple transmembrane binding sites for p-trifluoromethyldiazirinyl-etomidate, a photoreactive Torpedo nicotinic acetylcholine receptor allosteric inhibitor.

    Science.gov (United States)

    Hamouda, Ayman K; Stewart, Deirdre S; Husain, S Shaukat; Cohen, Jonathan B

    2011-06-10

    Photoreactive derivatives of the general anesthetic etomidate have been developed to identify their binding sites in γ-aminobutyric acid, type A and nicotinic acetylcholine receptors. One such drug, [(3)H]TDBzl-etomidate (4-[3-(trifluoromethyl)-3H-diazirin-3-yl]benzyl-[(3)H]1-(1-phenylethyl)-1H-imidazole-5-carboxylate), acts as a positive allosteric potentiator of Torpedo nACh receptor (nAChR) and binds to a novel site in the transmembrane domain at the γ-α subunit interface. To extend our understanding of the locations of allosteric modulator binding sites in the nAChR, we now characterize the interactions of a second aryl diazirine etomidate derivative, TFD-etomidate (ethyl-1-(1-(4-(3-trifluoromethyl)-3H-diazirin-3-yl)phenylethyl)-1H-imidazole-5-carboxylate). TFD-etomidate inhibited acetylcholine-induced currents with an IC(50) = 4 μM, whereas it inhibited the binding of [(3)H]phencyclidine to the Torpedo nAChR ion channel in the resting and desensitized states with IC(50) values of 2.5 and 0.7 mm, respectively. Similar to [(3)H]TDBzl-etomidate, [(3)H]TFD-etomidate bound to a site at the γ-α subunit interface, photolabeling αM2-10 (αSer-252) and γMet-295 and γMet-299 within γM3, and to a site in the ion channel, photolabeling amino acids within each subunit M2 helix that line the lumen of the ion channel. In addition, [(3)H]TFD-etomidate photolabeled in an agonist-dependent manner amino acids within the δ subunit M2-M3 loop (δIle-288) and the δ subunit transmembrane helix bundle (δPhe-232 and δCys-236 within δM1). The fact that TFD-etomidate does not compete with ion channel blockers at concentrations that inhibit acetylcholine responses indicates that binding to sites at the γ-α subunit interface and/or within δ subunit helix bundle mediates the TFD-etomidate inhibitory effect. These results also suggest that the γ-α subunit interface is a binding site for Torpedo nAChR negative allosteric modulators (TFD-etomidate) and for positive

  8. Multiple Transmembrane Binding Sites for p-Trifluoromethyldiazirinyl-etomidate, a Photoreactive Torpedo Nicotinic Acetylcholine Receptor Allosteric Inhibitor*

    Science.gov (United States)

    Hamouda, Ayman K.; Stewart, Deirdre S.; Husain, S. Shaukat; Cohen, Jonathan B.

    2011-01-01

    Photoreactive derivatives of the general anesthetic etomidate have been developed to identify their binding sites in γ-aminobutyric acid, type A and nicotinic acetylcholine receptors. One such drug, [3H]TDBzl-etomidate (4-[3-(trifluoromethyl)-3H-diazirin-3-yl]benzyl-[3H]1-(1-phenylethyl)-1H-imidazole-5-carboxylate), acts as a positive allosteric potentiator of Torpedo nACh receptor (nAChR) and binds to a novel site in the transmembrane domain at the γ-α subunit interface. To extend our understanding of the locations of allosteric modulator binding sites in the nAChR, we now characterize the interactions of a second aryl diazirine etomidate derivative, TFD-etomidate (ethyl-1-(1-(4-(3-trifluoromethyl)-3H-diazirin-3-yl)phenylethyl)-1H-imidazole-5-carboxylate). TFD-etomidate inhibited acetylcholine-induced currents with an IC50 = 4 μm, whereas it inhibited the binding of [3H]phencyclidine to the Torpedo nAChR ion channel in the resting and desensitized states with IC50 values of 2.5 and 0.7 mm, respectively. Similar to [3H]TDBzl-etomidate, [3H]TFD-etomidate bound to a site at the γ-α subunit interface, photolabeling αM2-10 (αSer-252) and γMet-295 and γMet-299 within γM3, and to a site in the ion channel, photolabeling amino acids within each subunit M2 helix that line the lumen of the ion channel. In addition, [3H]TFD-etomidate photolabeled in an agonist-dependent manner amino acids within the δ subunit M2-M3 loop (δIle-288) and the δ subunit transmembrane helix bundle (δPhe-232 and δCys-236 within δM1). The fact that TFD-etomidate does not compete with ion channel blockers at concentrations that inhibit acetylcholine responses indicates that binding to sites at the γ-α subunit interface and/or within δ subunit helix bundle mediates the TFD-etomidate inhibitory effect. These results also suggest that the γ-α subunit interface is a binding site for Torpedo nAChR negative allosteric modulators (TFD-etomidate) and for positive modulators (TDBzl

  9. Allosteric effectors and trehalose protect larval Manduca sexta fat body glycogen phosphorylase B against thermal denaturation.

    Science.gov (United States)

    Meyer-Fernandes, J R; Arrese, E L; Wells, M A

    2000-06-01

    In this paper we assessed the ability of modulators of the activity of glycogen phosphorylase b from the fat body of larval Manduca sexta to stabilize the enzyme against thermal denaturation. This approach has allowed us to distinguish between modulators that stabilize the enzyme, presumably through some conformational effect, from those that do not affect thermal stability. For example, 5'-AMP and 5'-IMP are both positive modulators of the enzyme and the K(m)s for AMP and IMP were similar, 0.71 and 1.09 mM, respectively. However, the V(max) for AMP (123 nmol/mg/min) was 10 times higher than the value found for IMP (12.5 nmol/mg/min) and AMP increased the thermal stability of glycogen phosphorylase b, however IMP did not increase the enzyme's thermal stability. Indeed, IMP decreased both the allosteric activation of the enzyme by AMP and the thermal protection conferred by AMP. The allosteric inhibitors ADP and ATP, which in vertebrate phosphorylase bind to the same site as AMP, both increased the thermal stability of the enzyme, however with less efficiency than AMP. Inorganic phosphate increased thermal stability, but glycogen and amylose did not. Glycerol, at 600 mM, protected the enzyme against thermal inactivation, whereas sorbitol at the same concentration did not show any effect. Among the polyols tested, trehalose was the most effective in conferring thermal stability. In fact, in the presence of 20 mM AMP and 600 mM trehalose, 90% of the enzyme activity remained after 20 min at 60 degrees C.

  10. Structural basis for leucine-induced allosteric activation of glutamate dehydrogenase.

    Science.gov (United States)

    Tomita, Takeo; Kuzuyama, Tomohisa; Nishiyama, Makoto

    2011-10-28

    Glutamate dehydrogenase (GDH) catalyzes reversible conversion between glutamate and 2-oxoglutarate using NAD(P)(H) as a coenzyme. Although mammalian GDH is regulated by GTP through the antenna domain, little is known about the mechanism of allosteric activation by leucine. An extremely thermophilic bacterium, Thermus thermophilus, possesses GDH with a unique subunit configuration composed of two different subunits, GdhA (regulatory subunit) and GdhB (catalytic subunit). T. thermophilus GDH is unique in that the enzyme is subject to allosteric activation by leucine. To elucidate the structural basis for leucine-induced allosteric activation of GDH, we determined the crystal structures of the GdhB-Glu and GdhA-GdhB-Leu complexes at 2.1 and 2.6 Å resolution, respectively. The GdhB-Glu complex is a hexamer that binds 12 glutamate molecules: six molecules are bound at the substrate-binding sites, and the remaining six are bound at subunit interfaces, each composed of three subunits. The GdhA-GdhB-Leu complex is crystallized as a heterohexamer composed of four GdhA subunits and two GdhB subunits. In this complex, six leucine molecules are bound at subunit interfaces identified as glutamate-binding sites in the GdhB-Glu complex. Consistent with the structure, replacement of the amino acid residues of T. thermophilus GDH responsible for leucine binding made T. thermophilus GDH insensitive to leucine. Equivalent amino acid replacement caused a similar loss of sensitivity to leucine in human GDH2, suggesting that human GDH2 also uses the same allosteric site for regulation by leucine.

  11. Allosteric modulation of G-protein coupled receptors

    DEFF Research Database (Denmark)

    Jensen, Anders A.; Spalding, Tracy A

    2004-01-01

    are believed to activate (agonists) or inhibit (competitive antagonists) receptor signalling by binding the receptor at the same site as the endogenous agonist, the orthosteric site. In contrast, allosteric ligands modulate receptor function by binding to different regions in the receptor, allosteric sites....... In recent years, combinatorial chemistry and high throughput screening have helped identify several allosteric GPCR modulators with novel structures, several of which already have become valuable pharmacological tools and may be candidates for clinical testing in the near future. This mini review outlines...... the current status and perspectives of allosteric modulation of GPCR function with emphasis on the pharmacology of endogenous and synthesised modulators, their receptor interactions and the therapeutic prospects of allosteric ligands compared to orthosteric ligands....

  12. Orthosteric and Allosteric Regulation in Trypsin-Like Peptidases

    DEFF Research Database (Denmark)

    Kromann-Tofting, Tobias

    peptides and Camelid derived antibody fragments, so-called nanobodies. Allosteric regulation of activity in trypsin-like serine peptidases is in general poorly understood, as the propagation of the allosteric signal from the ligand binding site to the active site in some cases is subtle and based...... exclusively on a change in side chain and backbone dynamics along the allosteric trajectory. This thesis describes the characterisation of two allosteric monoclonal antibodies and the development and characterisation of an allosteric nanobody against murine uPA. Insights into their binding mechanisms, using X...... approach for molecular intervention with the function of trypsin-like serine peptidases. In the thesis, I also describe the development of nanobodies that specifically target zymogen activation of uPA, by preventing its proteolytic cleavage by plasmin....

  13. ETA-receptor antagonists or allosteric modulators?

    DEFF Research Database (Denmark)

    De Mey, Jo G R; Compeer, Matthijs G; Lemkens, Pieter

    2011-01-01

    . In resistance arteries, the long-lasting contractile effects can only be partly and reversibly relaxed by low-molecular-weight ET(A) antagonists (ERAs). However, the neuropeptide calcitonin-gene-related peptide selectively terminates binding of ET1 to ET(A). We propose that ET1 binds polyvalently to ET......(A) and that ERAs and the physiological antagonist allosterically reduce ET(A) functions. Combining the two-state model and the two-domain model of GPCR function and considering receptor activation beyond agonist binding might lead to better anti-endothelinergic drugs. Future studies could lead to compounds...

  14. A large-scale allosteric transition in cytochrome P450 3A4 revealed by luminescence resonance energy transfer (LRET.

    Directory of Open Access Journals (Sweden)

    Elena V Sineva

    Full Text Available Effector-induced allosteric transitions in cytochrome P450 3A4 (CYP3A4 were investigated by luminescence resonance energy transfer (LRET between two SH-reactive probes attached to various pairs of distantly located cysteine residues, namely the double-cysteine mutants CYP3A4(C64/C468, CYP3A4(C377/C468 and CYP3A4(C64/C121. Successive equimolar labeling of these proteins with the phosphorescent probe erythrosine iodoacetamide (donor and the near-infrared fluorophore DY-731 maleimide (acceptor allowed us to establish donor/acceptor pairs sensitive to conformational motions. The interactions of all three double-labeled mutants with the allosteric activators α-naphthoflavone and testosterone resulted in an increase in the distance between the probes. A similar effect was elicited by cholesterol. These changes in distance vary from 1.3 to 8.5 Å, depending on the position of the donor/acceptor pair and the nature of the effector. In contrast, the changes in the interprobe distance caused by such substrates as bromocriptine or 1-pyrenebutanol were only marginal. Our results provide a decisive support to the paradigm of allosteric modulation of CYP3A4 and indicate that the conformational transition caused by allosteric effectors increases the spatial separation between the beta-domain of the enzyme (bearing residues Cys64 and Cys377 and the alpha-domain, where Cys121 and Cys468 are located.

  15. Preparation of 5-amino-4-imidazole-N-succinocarboxamide ribotide, 5-amino-4-imidazole-N-succinocarboxamide riboside and succinyladenosine, compounds usable in diagnosis and research of adenylosuccinate lyase deficiency.

    Science.gov (United States)

    Zikánová, M; Krijt, J; Hartmannová, H; Kmoch, S

    2005-01-01

    The enzyme adenylosuccinate lyase (ADSL) intervenes twice in the biosynthesis of adenine nucleotides. ADSL deficiency is an inherited metabolic disease characterized by various degrees of psychomotor retardation and accumulation of dephosphorylated enzyme substrates 5-amino-4-imidazole-N-succinocarboxamide riboside (SAICAr) and succinyladenosine (SAdo) in body fluids. Severity of symptoms seems to correlate with residual activity of mutant enzyme and with SAdo/SAICAr concentration ratio in cerebrospinal fluid. To better understand the pathogenetic mechanisms of the disease symptoms, studies of catalytic properties of mutant enzymes together with in vitro and in vivo experiments utilizing SAICAr and SAdo must be performed. Such studies require availability of both ADSL substrates, 5-amino-4-imidazole-N-succinocarboxamide ribotide (SAICAR) and succinyladenosine 5'-monophosphate (SAMP) and their dephosphorylated products in sufficient amounts and purity. Except for SAMP, none of these compounds is commercially available and they must therefore be synthesized. SAICAR was prepared by recombinant human ADSL-catalysed reaction of AICAR (5-aminoimidazole-4-carboxamide) with fumarate and isolated by thin-layer chromatography. SAICAr and SAdo were prepared by calf intestine alkaline phosphatase-catalysed dephosphorylation of SAICAR and SAMP and isolated on cation- and anion-exchange resin columns. The procedures described are easily scalable and provide high yields of sufficiently pure products for use in experiments related to studies of pathogenetic mechanisms in ADSL deficiency.

  16. Optimal allosteric stabilization sites using contact stabilization analysis.

    Science.gov (United States)

    Dickson, Alex; Bailey, Christopher T; Karanicolas, John

    2017-06-05

    Proteins can be destabilized by a number of environmental factors such as temperature, pH, and mutation. The ability to subsequently restore function under these conditions by adding small molecule stabilizers, or by introducing disulfide bonds, would be a very powerful tool, but the physical principles that drive this stabilization are not well understood. The first problem lies is in choosing an appropriate binding site or disulfide bond location to best confer stability to the active site and restore function. Here, we present a general framework for predicting which allosteric binding sites correlate with stability in the active site. Using the Karanicolas-Brooks Gō-like model, we examine the dynamics of the enzyme β-glucuronidase using an Umbrella Sampling method to thoroughly sample the conformational landscape. Each intramolecular contact is assigned a score termed a "stabilization factor" that measures its correlation with structural changes in the active site. We have carried out this analysis for three different scaling strengths for the intramolecular contacts, and we examine how the calculated stabilization factors depend on the ensemble of destabilized conformations. We further examine a locally destabilized mutant of β-glucuronidase that has been characterized experimentally, and show that this brings about local changes in the stabilization factors. We find that the proximity to the active site is not sufficient to determine which contacts can confer active site stability. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  17. Non-imidazole histamine NO-donor H3-antagonists.

    Science.gov (United States)

    Tosco, Paolo; Bertinaria, Massimo; Di Stilo, Antonella; Cena, Clara; Fruttero, Roberta; Gasco, Alberto

    2005-01-01

    Recently a series of H3-antagonists related to Imoproxifan was realised (I); in these products the oxime substructure of the lead was constrained in NO-donor furoxan systems and in the corresponding furazan derivatives. In this paper, a new series of compounds derived from I by substituting the imidazole ring with the ethoxycarbonylpiperazino moiety present in the non-imidazole H3-ligand A-923 is described. For all the products synthesis and preliminary pharmacological characterisation, as well as their hydrophilic-lipophilic balance, are reported. The imidazole ring replacement generally results in a decreased H3-antagonist activity with respect to the analogues of series I and, in some cases, induces relaxing effects on the electrically contracted guinea-pig ileum, probably due to increased affinity for other receptor systems.

  18. Synthesis, characterization and metal coordination of a potential β-lactamase inhibitor: 5-Methyl-2-phenoxymethyl-3-H-imidazole-4-carboxylic acid (PIMA

    Directory of Open Access Journals (Sweden)

    Chiara Romagnoli

    2017-12-01

    Full Text Available Among relevant metal ions in biological systems, zinc and iron play a key role as active partners of the catalytic machinery. In particular, the inhibition of metal enzymes that are involved in physiological and pathological processes has been deeply investigated for the rational design of selective and efficient drugs based on chelators. Since imidazole histidine residue is one of the most versatile sites in proteins, especially in enzymes acting in the presence of metal ions as cofactors, in this work the synthesis and characterization of a new imidazole derivative, namely 5-methyl-2-phenoxymethyl-3-H-imidazole-4-carboxylic acid (PIMA is reported. PIMA was designed as metallo-β-lactamase inhibitor thanks to its similarity with penicillin V, a β-lactam antibiotic inactivated by metallo-β-lactamase, for which there are no commercially available inhibitors. The evaluation of PIMA coordinating ability toward iron, zinc, and gallium, these latter selected as a non-paramagnetic probe for iron, is performed by theoretical DFT calculations and in solution by experimental techniques, i.e. potentiometry, UV–vis and NMR spectroscopy. PIMA exhibits an efficient metal chelating ability; the prevailing species in physiological condition are ML3 for Fe3+ and Ga3+ and ML2 for Zn2+, in which chelation is due to deprotonated carboxylic oxygen and imidazole nitrogen in the N,O donor set. The demonstrated ability of PIMA to chelate zinc ion, combined with its structure similarity with penicillin V, supports further exploration of this imidazole-4-carboxylate as metallo-β-lactamase inhibitor.

  19. Emerging Computational Methods for the Rational Discovery of Allosteric Drugs.

    Science.gov (United States)

    Wagner, Jeffrey R; Lee, Christopher T; Durrant, Jacob D; Malmstrom, Robert D; Feher, Victoria A; Amaro, Rommie E

    2016-06-08

    Allosteric drug development holds promise for delivering medicines that are more selective and less toxic than those that target orthosteric sites. To date, the discovery of allosteric binding sites and lead compounds has been mostly serendipitous, achieved through high-throughput screening. Over the past decade, structural data has become more readily available for larger protein systems and more membrane protein classes (e.g., GPCRs and ion channels), which are common allosteric drug targets. In parallel, improved simulation methods now provide better atomistic understanding of the protein dynamics and cooperative motions that are critical to allosteric mechanisms. As a result of these advances, the field of predictive allosteric drug development is now on the cusp of a new era of rational structure-based computational methods. Here, we review algorithms that predict allosteric sites based on sequence data and molecular dynamics simulations, describe tools that assess the druggability of these pockets, and discuss how Markov state models and topology analyses provide insight into the relationship between protein dynamics and allosteric drug binding. In each section, we first provide an overview of the various method classes before describing relevant algorithms and software packages.

  20. The tertiary origin of the allosteric activation of E. coli glucosamine-6-phosphate deaminase studied by sol-gel nanoencapsulation of its T conformer.

    Directory of Open Access Journals (Sweden)

    Sergio Zonszein

    Full Text Available The role of tertiary conformational changes associated to ligand binding was explored using the allosteric enzyme glucosamine-6-phosphate (GlcN6P deaminase from Escherichia coli (EcGNPDA as an experimental model. This is an enzyme of amino sugar catabolism that deaminates GlcN6P, giving fructose 6-phosphate and ammonia, and is allosterically activated by N-acetylglucosamine 6-phosphate (GlcNAc6P. We resorted to the nanoencapsulation of this enzyme in wet silica sol-gels for studying the role of intrasubunit local mobility in its allosteric activation under the suppression of quaternary transition. The gel-trapped enzyme lost its characteristic homotropic cooperativity while keeping its catalytic properties and the allosteric activation by GlcNAc6P. The nanoencapsulation keeps the enzyme in the T quaternary conformation, making possible the study of its allosteric activation under a condition that is not possible to attain in a soluble phase. The involved local transition was slowed down by nanoencapsulation, thus easing the fluorometric analysis of its relaxation kinetics, which revealed an induced-fit mechanism. The absence of cooperativity produced allosterically activated transitory states displaying velocity against substrate concentration curves with apparent negative cooperativity, due to the simultaneous presence of subunits with different substrate affinities. Reaction kinetics experiments performed at different tertiary conformational relaxation times also reveal the sequential nature of the allosteric activation. We assumed as a minimal model the existence of two tertiary states, t and r, of low and high affinity, respectively, for the substrate and the activator. By fitting the velocity-substrate curves as a linear combination of two hyperbolic functions with Kt and Kr as KM values, we obtained comparable values to those reported for the quaternary conformers in solution fitted to MWC model. These results are discussed in the

  1. Defining the Structural Basis for Allosteric Product Release from E. coli Dihydrofolate Reductase Using NMR Relaxation Dispersion.

    Science.gov (United States)

    Oyen, David; Fenwick, R Bryn; Aoto, Phillip C; Stanfield, Robyn L; Wilson, Ian A; Dyson, H Jane; Wright, Peter E

    2017-08-16

    The rate-determining step in the catalytic cycle of E. coli dihydrofolate reductase is tetrahydrofolate (THF) product release, which can occur via an allosteric or an intrinsic pathway. The allosteric pathway, which becomes accessible when the reduced cofactor NADPH is bound, involves transient sampling of a higher energy conformational state, greatly increasing the product dissociation rate as compared to the intrinsic pathway that obtains when NADPH is absent. Although the kinetics of this process are known, the enzyme structure and the THF product conformation in the transiently formed excited state remain elusive. Here, we use side-chain proton NMR relaxation dispersion measurements, X-ray crystallography, and structure-based chemical shift predictions to explore the structural basis of allosteric product release. In the excited state of the E:THF:NADPH product release complex, the reduced nicotinamide ring of the cofactor transiently enters the active site where it displaces the pterin ring of the THF product. The p-aminobenzoyl-l-glutamate tail of THF remains weakly bound in a widened binding cleft. Thus, through transient entry of the nicotinamide ring into the active site, the NADPH cofactor remodels the enzyme structure and the conformation of the THF to form a weakly populated excited state that is poised for rapid product release.

  2. Not different, Just Better: The Adaptive Evolution of an Enzyme

    Science.gov (United States)

    2015-12-20

    Our program provides a uniquely detailed functional understanding of how evolution by natural selection occurs at the molecular level. Many studies...different, just better: the adaptive evolution of a glycolytic enzyme. Queenstown, New Zealand: Queenstown Molecular Biology Conference, Enzyme Engineering... evolution experiment. This program was aimed at uncovering the molecular basis for a series of adaptive mutations in a key allosteric enzyme. We chose the

  3. Cobalt tetradehydrocorrins coordinated by imidazolate-like histidine in the heme pocket of horseradish peroxidase.

    Science.gov (United States)

    Oohora, Koji; Tang, Ning; Morita, Yoshitsugu; Hayashi, Takashi

    2017-07-01

    Horseradish peroxidase was reconstituted with cobalt tetradehydrocorrin, rHRP(Co(TDHC)), as a structural analog of cobalamin coordinated with an imidazolate-like His residue, which is generally seen in native enzymes. In contrast to the previously reported cobalt tetradehydrocorrin-reconstituted myoglobin, rMb(Co(TDHC)), the HRP matrix was expected to provide strong axial ligation by His170 which has imidazolate character. rHRP(Co II (TDHC)) was characterized by EPR and its reaction with reductants indicates a negative shift of its redox potential compared to rMb(Co(TDHC)). Furthermore, aqua- and CN-forms of Co(III) state were prepared. The former species was obtained by oxidation of rHRP(Co II (TDHC)) with K 3 [Fe(CN) 6 ]. The cyanide-coordinated Co(III) species in the latter was prepared by ligand exchange of rHRP(Co III (OH)(TDHC)) with exogenous cyanide upon addition of KCN. The 13 C NMR chemical shift of cyanide in rHRP(Co III (CN)(TDHC)) was determined to be 121.8 ppm. IR measurements show that the cyanide of rHRP(Co III (CN)(TDHC)) has a stretching frequency peak at 2144 cm -1 . The 13 C NMR and IR measurements indicate strong coordination of cyanide to Co III (TDHC) relative to rMb(Co III (CN)(TDHC)). Thus, the extent of π-back donation from the cobalt ion to the cyanide ion is relatively high in rHRP(Co III (CN)(TDHC)). The pK 1/2 values of rHRP(Co III (OH)(TDHC)) and rHRP(Co III (CN)(TDHC)) are the same (pK 1/2  = 3.2) as determined by a pH titration experiment, indicating that cyanide ligation does not affect Co-His ligation, whereas cyanide ligation weakens the Co-His ligation in rMb(Co III (CN)(TDHC)). Taken together, these results indicate that HRP reconstituted with cobalt tetradehydrocorrin is a suitable cobalamin-dependent enzyme model with imidazolate-like His residue.

  4. Nickel (II) complexes having Imidazol-2-ylidene-N′-phenylurea ...

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Chemical Sciences; Volume 127; Issue 8. Nickel(II) complexes having Imidazol-2-ylidene-N′-phenylurea ligand in the coordination sphere – syntheses and solid state structures. Kishor Naktode Abhinanda Kundu Sudeshna Saha Hari Pada Nayek Tarun K Panda. Regular Articles Volume 127 ...

  5. Topoisomerase II poisoning by indazole and imidazole complexes ...

    Indian Academy of Sciences (India)

    Unknown

    of topoisomerase II by forming a ternary cleavage complex of DNA, drug and topoisomerase II. The thymidine incorporation assays ... sage reaction is central to the various functions of topo II, as well as for targeting the .... or imidazole. These cationic ligands may be released from the main molecules in biological systems.

  6. Synthesis and characterization of 2-mercapto-N-methyl imidazole ...

    African Journals Online (AJOL)

    Among these three compounds, PLBs sections cultured on medium supplemented with nitro compound (5c) at 5 µM concentration produced maximum number (95) of plantlets. Key words: Benzimidazole derivatives, protocorm like bodies, plant growth regulators, 2-mercapto-N-methyl imidazole. Abbreviation: PLBs ...

  7. Allosteric Equilibria in the Binding of Fibrinogen to Platelets

    Science.gov (United States)

    de Cristofaro, Raimondo; Landolfi, Raffaele; de Candia, Erica; Castagnola, Massimo; di Cera, Enrico; Wyman, Jeffries

    1988-11-01

    The binding of fibrinogen to platelets occurs according to the law of mass action. The platelet receptor binds reversibly a single fibrinogen molecule and undergoes a conformational transition between two allosteric states, T and R, that differ in their affinity for fibrinogen. The equilibrium between the two forms is shifted by ADP toward the R (high-affinity) state, thus promoting the aggregation process. This model opens the way to consideration of allosteric modulation of the binding of fibrinogen to its platelet receptor.

  8. From Enzymatic Adaptation to Allosteric Transitions

    Indian Academy of Sciences (India)

    current definition), systems synthesized in the absence of any substrate or exogenous inducer, as is the case, of course, with all the enzymes of intermediate and biosynthetic metabolism. It did not seem unreasonable to suppose that the synthesis of these enzymes was controlled by their endogenous substrate, which would ...

  9. Spectroscopic investigation of Bovine Liver Catalase interactions with a novel phen-imidazole derivative of platinum.

    Science.gov (United States)

    Ghobadi, Roohollah; Divsalar, Adeleh; Harifi-Mood, Ali Reza; Saboury, Ali Akbar

    2018-02-01

    Successful clinical experience of using cisplatin and its derivatives in cancer therapy has encouraged scientists to synthesize new metal complexes with the aim of interacting with special targets such as proteins In this regard, biological effects of [Pt(FIP)(Phen)](NO 3 ) 2 compound which contains a novel phen-imidazole ligand, FIP, was investigated on bovine liver catalase (BLC) structure and function. Various spectroscopic methods such as UV-visible, fluorescence, and circular dichroism (CD) were applied at two temperatures 25 and 37°C for kinetics and structural studies. As a consequence, the enzymatic activity decreased slightly with increasing the platinum compound's concentration up to 30 μM and then remained constant at near 80% after this concentration. On the other hand, the fluorescence quenching measurements revealed that despite slight changes in activity, catalase experiences notable alterations in three-dimensional environment around the chromophores of the enzyme structure with increasing platinum complex concentration. Moreover, quenching data showed that BLC has two binding sites for Pt complex and hydrogen bonding interactions play a major role in the binding process. Furthermore, CD spectroscopy data showed that Pt(II) complex induces significant decrease in α-helix content of the secondary structure of BLC, but notable increase in random coil proportion accompanying a slight decrease in β-sheet content. All in all, hydrogen bonding interactions which are mainly involved in the binding process of the novel phen-imidazole compound to BLC significantly alter the protein structure but slightly change its function. This might be a promising outcome for chemotherapists and medicinal chemists to investigate in vivo properties of this novel metal complex with significant binding tendency to a macromolecule in the low concentrations without decreasing its intrinsic function.

  10. Novel inhibitors complexed with glutamate dehydrogenase: allosteric regulation by control of protein dynamics.

    Science.gov (United States)

    Li, Ming; Smith, Christopher J; Walker, Matthew T; Smith, Thomas J

    2009-08-21

    Mammalian glutamate dehydrogenase (GDH) is a homohexameric enzyme that catalyzes the reversible oxidative deamination of l-glutamate to 2-oxoglutarate using NAD(P)(+) as coenzyme. Unlike its counterparts from other animal kingdoms, mammalian GDH is regulated by a host of ligands. The recently discovered hyperinsulinism/hyperammonemia disorder showed that the loss of allosteric inhibition of GDH by GTP causes excessive secretion of insulin. Subsequent studies demonstrated that wild-type and hyperinsulinemia/hyperammonemia forms of GDH are inhibited by the green tea polyphenols, epigallocatechin gallate and epicatechin gallate. This was followed by high throughput studies that identified more stable inhibitors, including hexachlorophene, GW5074, and bithionol. Shown here are the structures of GDH complexed with these three compounds. Hexachlorophene forms a ring around the internal cavity in GDH through aromatic stacking interactions between the drug and GDH as well as between the drug molecules themselves. In contrast, GW5074 and bithionol both bind as pairs of stacked compounds at hexameric 2-fold axes between the dimers of subunits. The internal core of GDH contracts when the catalytic cleft closes during enzymatic turnover. None of the drugs cause conformational changes in the contact residues, but all bind to key interfaces involved in this contraction process. Therefore, it seems likely that the drugs inhibit enzymatic turnover by inhibiting this transition. Indeed, this expansion/contraction process may play a major role in the inter-subunit communication and allosteric regulation observed in GDH.

  11. Novel Inhibitors Complexed with Glutamate Dehydrogenase: ALLOSTERIC REGULATION BY CONTROL OF PROTEIN DYNAMICS

    Energy Technology Data Exchange (ETDEWEB)

    Li, Ming; Smith, Christopher J.; Walker, Matthew T.; Smith, Thomas J.; (Danforth)

    2009-12-01

    Mammalian glutamate dehydrogenase (GDH) is a homohexameric enzyme that catalyzes the reversible oxidative deamination of L-glutamate to 2-oxoglutarate using NAD(P){sup +} as coenzyme. Unlike its counterparts from other animal kingdoms, mammalian GDH is regulated by a host of ligands. The recently discovered hyperinsulinism/hyperammonemia disorder showed that the loss of allosteric inhibition of GDH by GTP causes excessive secretion of insulin. Subsequent studies demonstrated that wild-type and hyperinsulinemia/hyperammonemia forms of GDH are inhibited by the green tea polyphenols, epigallocatechin gallate and epicatechin gallate. This was followed by high throughput studies that identified more stable inhibitors, including hexachlorophene, GW5074, and bithionol. Shown here are the structures of GDH complexed with these three compounds. Hexachlorophene forms a ring around the internal cavity in GDH through aromatic stacking interactions between the drug and GDH as well as between the drug molecules themselves. In contrast, GW5074 and bithionol both bind as pairs of stacked compounds at hexameric 2-fold axes between the dimers of subunits. The internal core of GDH contracts when the catalytic cleft closes during enzymatic turnover. None of the drugs cause conformational changes in the contact residues, but all bind to key interfaces involved in this contraction process. Therefore, it seems likely that the drugs inhibit enzymatic turnover by inhibiting this transition. Indeed, this expansion/contraction process may play a major role in the inter-subunit communication and allosteric regulation observed in GDH.

  12. Notes on stochastic (bio)-logic gates: computing with allosteric cooperativity

    Science.gov (United States)

    Agliari, Elena; Altavilla, Matteo; Barra, Adriano; Dello Schiavo, Lorenzo; Katz, Evgeny

    2015-05-01

    Recent experimental breakthroughs have finally allowed to implement in-vitro reaction kinetics (the so called enzyme based logic) which code for two-inputs logic gates and mimic the stochastic AND (and NAND) as well as the stochastic OR (and NOR). This accomplishment, together with the already-known single-input gates (performing as YES and NOT), provides a logic base and paves the way to the development of powerful biotechnological devices. However, as biochemical systems are always affected by the presence of noise (e.g. thermal), standard logic is not the correct theoretical reference framework, rather we show that statistical mechanics can work for this scope: here we formulate a complete statistical mechanical description of the Monod-Wyman-Changeaux allosteric model for both single and double ligand systems, with the purpose of exploring their practical capabilities to express noisy logical operators and/or perform stochastic logical operations. Mixing statistical mechanics with logics, and testing quantitatively the resulting findings on the available biochemical data, we successfully revise the concept of cooperativity (and anti-cooperativity) for allosteric systems, with particular emphasis on its computational capabilities, the related ranges and scaling of the involved parameters and its differences with classical cooperativity (and anti-cooperativity).

  13. Characterization and Solubilization of Pyrrole–Imidazole Polyamide Aggregates

    OpenAIRE

    Hargrove, Amanda E.; Raskatov, Jevgenij A.; Meier, Jordan L.; Montgomery, David C.; Dervan, Peter B.

    2012-01-01

    To optimize the biological activity of pyrrole–imidazole polyamide DNA-binding molecules, we characterized the aggregation propensity of these compounds through dynamic light scattering and fractional solubility analysis. Nearly all studied polyamides were found to form measurable particles 50–500 nm in size under biologically relevant conditions, while HPLC-based analyses revealed solubility trends in both core sequences and peripheral substituents that did not correlate with overall ionic c...

  14. Synthesis and Antibacterial Activities of New Metronidazole and Imidazole Derivatives

    Directory of Open Access Journals (Sweden)

    Abdul Jabar Kh. Atia

    2009-07-01

    Full Text Available New imidazole ring derivatives comprising 1,3-oxazoline, Schiff's bases, thiadiazole, oxadiazole and 1,2,4-triazole moieties are reported. 3-Aminobiimidazol-4-one compounds 7a-c were synthesized by the reaction of compounds 6a-c with hydrazine hydrate. Biimidazole esters 9a-c were converted into biimidazole hydrazide esters 10a-c. Compounds 7a-c and 10a-c were converted into a variety of derivatives.

  15. Alcohol and water adsorption in zeolitic imidazolate frameworks

    KAUST Repository

    Zhang, Ke

    2013-01-01

    Alcohol (methanol, ethanol, 1-propanol, 2-propanol and 1-butanol) and water vapor adsorption in zeolitic imidazolate frameworks (ZIF-8, ZIF-71 and ZIF-90) with similar crystal sizes was systematically studied. The feasibility of applying these ZIF materials to the recovery of bio-alcohols is evaluated by estimating the vapor-phase alcohol-water sorption selectivity. © 2013 The Royal Society of Chemistry.

  16. Thermodynamic study of phase transitions of imidazoles and 1-methylimidazoles

    Energy Technology Data Exchange (ETDEWEB)

    Almeida, Ana R.R.P., E-mail: ana.figueira@fc.up.pt [Centro de Investigacao em Quimica, Departamento de Quimica e Bioquimica, Faculdade de Ciencias da Universidade do Porto, Rua do Campo Alegre, 687, P-4169-007 Porto (Portugal); Monte, Manuel J.S., E-mail: mjmonte@fc.up.pt [Centro de Investigacao em Quimica, Departamento de Quimica e Bioquimica, Faculdade de Ciencias da Universidade do Porto, Rua do Campo Alegre, 687, P-4169-007 Porto (Portugal)

    2012-01-15

    Highlights: > Sublimation vapor pressures of imidazole, N-methylimidazole and four derivatives were measured. > Liquid vapor pressures were also measured for four of the compounds studied. > Vapor pressure results enabled determination of sublimation, vaporization, and fusion enthalpy. > From enthalpies of sublimation, enthalpies of intermolecular N-H...N bonds were estimated. - Abstract: The vapor pressures of imidazole, N-methylimidazole and of their dichloro and dicyano substituted compounds were measured at different temperatures, in the crystalline phase for two of them, and in crystalline and liquid phases for the other four. From these measurements, enthalpies and standard entropies of sublimation and vaporization were derived. The results allowed the determination of the triple points (p, T) coordinates of the four compounds studied in both condensed phases as well as the calculation of their enthalpy of fusion. Enthalpies and temperatures of fusion were also determined using d.s.c. The experimental results enabled the estimation of the enthalpy of the intermolecular N-H...N bonds in the imidazoles studied.

  17. Imidazole and Triazole Coordination Chemistry for Antifouling Coatings

    Directory of Open Access Journals (Sweden)

    Markus Andersson Trojer

    2013-01-01

    Full Text Available Fouling of marine organisms on the hulls of ships is a severe problem for the shipping industry. Many antifouling agents are based on five-membered nitrogen heterocyclic compounds, in particular imidazoles and triazoles. Moreover, imidazole and triazoles are strong ligands for Cu2+ and Cu+, which are both potent antifouling agents. In this review, we summarize a decade of work within our groups concerning imidazole and triazole coordination chemistry for antifouling applications with a particular focus on the very potent antifouling agent medetomidine. The entry starts by providing a detailed theoretical description of the azole-metal coordination chemistry. Some attention will be given to ways to functionalize polymers with azole ligands. Then, the effect of metal coordination in azole-containing polymers with respect to material properties will be discussed. Our work concerning the controlled release of antifouling agents, in particular medetomidine, using azole coordination chemistry will be reviewed. Finally, an outlook will be given describing the potential for tailoring the azole ligand chemistry in polymers with respect to Cu2+ adsorption and Cu2+→Cu+ reduction for antifouling coatings without added biocides.

  18. On the mechanism of action of ribonucleases: dinucleotide cleavage catalyzed by imidazole and Zn2+.

    OpenAIRE

    Breslow, R; Huang, D L; Anslyn, E

    1989-01-01

    Cyclization/cleavage of the 2-(p-nitrophenyl) phosphate ester of propylene glycol is catalyzed by imidazole and, much more effectively, by Zn2+ with imidazole. In the latter case, the mechanism involves simultaneous Lewis acid/base catalysis. Similar Zn2+ and imidazole catalysis of cyclization/cleavage is seen with the dinucleotide 3',5'-UpU (uridylyluridine). Again, the zinc system is much more effective than is catalysis by imidazole alone, and in this case simultaneous Lewis acid/base cata...

  19. Imidazole, a New Tunable Reagent for Producing Nanocellulose, Part I: Xylan-Coated CNCs and CNFs

    Directory of Open Access Journals (Sweden)

    Jia Mao

    2017-09-01

    Full Text Available Imidazole is reported to be an effective reactant for the production of nanocellulose from hardwood pulp. The morphologies and surface properties of the nanocellulose can be simply tailored according to the water content in the imidazole system: with pure imidazole, cellulose nanofibrils (CNFs in a yield of 10 wt % can be produced. With 25 wt % of water in imidazole, cellulose nanocrystals (CNCs are obtained in 20 wt % yield. Both nanocelluloses exhibit crystallinity indices in the order of 70%. Interestingly, they retain the original xylan from the pulp with ca. 9–10 wt % of residual xylan content.

  20. Allosterically tunable, DNA-based switches triggered by heavy metals.

    Science.gov (United States)

    Porchetta, Alessandro; Vallée-Bélisle, Alexis; Plaxco, Kevin W; Ricci, Francesco

    2013-09-11

    Here we demonstrate the rational design of allosterically controllable, metal-ion-triggered molecular switches. Specifically, we designed DNA sequences that adopt two low energy conformations, one of which does not bind to the target ion and the other of which contains mismatch sites serving as specific recognition elements for mercury(II) or silver(I) ions. Both switches contain multiple metal binding sites and thus exhibit homotropic allosteric (cooperative) responses. As heterotropic allosteric effectors we employ single-stranded DNA sequences that either stabilize or destabilize the nonbinding state, enabling dynamic range tuning over several orders of magnitude. The ability to rationally introduce these effects into target-responsive switches could be of value in improving the functionality of DNA-based nanomachines.

  1. Targeting PDE10A GAF Domain with Small Molecules: A Way for Allosteric Modulation with Anti-Inflammatory Effects.

    Science.gov (United States)

    García, Ana M; Brea, José; González-García, Alejandro; Pérez, Concepción; Cadavid, María Isabel; Loza, María Isabel; Martinez, Ana; Gil, Carmen

    2017-09-04

    Phosphodiesterase (PDE) enzymes regulate the levels of cyclic nucleotides, cAMP, and/or cGMP, being attractive therapeutic targets. In order to modulate PDE activity in a selective way, we focused our efforts on the search of allosteric modulators. Based on the crystal structure of the PDE10A GAF-B domain, a virtual screening study allowed the discovery of new hits that were also tested experimentally, showing inhibitory activities in the micromolar range. Moreover, these new PDE10A inhibitors were able to decrease the nitrite production in LPS-stimulated cells, thus demonstrating their potential as anti-inflammatory agents.

  2. I₂-catalyzed synthesis of substituted imidazoles from vinyl azides and benzylamines.

    Science.gov (United States)

    Xiang, Likui; Niu, Yanning; Pang, Xiaobo; Yang, Xiaodong; Yan, Rulong

    2015-04-18

    A novel and efficient I2-catalyzed oxidative tandem cyclization of simple vinyl azides and benzylamines has been developed for the synthesis of substituted imidazoles. In this reaction, various substituted groups on vinyl azides and benzylamines proceed smoothly and the desired imidazoles are obtained in moderate to good yields.

  3. Phosphoric acid doped polysulfone membranes with aminopyridine pendant groups and imidazole cross-links

    DEFF Research Database (Denmark)

    Hink, Steffen; Elsøe, Katrine; Cleemann, Lars Nilausen

    2015-01-01

    Udel polysulfone based membranes with 4-aminopyridine pendant groups and cross-linking imidazole units are synthesized in a simple two step reaction. The ratio of 4-aminopyridine and imidazole is varied and the materials are extensively characterized. The average phosphoric acid uptake (in 85 wt%...

  4. An Imidazole based probe for relay recognition of Cu and OH ions ...

    Indian Academy of Sciences (India)

    Abstract. 2-(2-methoxyphenyl)-4,5-diphenyl-1H-imidazole 1, an imidazole-based compound, was found to sense Cu2+ ions via fluorescence and absorption spectroscopy over a number of other metal ions. During Cu2+ sensing, the chemosensor 1 followed a “switch-off” mechanism. Job's plot supported 1:1 stoichiometry of ...

  5. Imidazol-Lipide : zur chemischen Implementierung eines Minimalen Chemotons als Modellsystem für Protozellen

    OpenAIRE

    Hellwig, Nils

    2011-01-01

    Zur chemischen Implementierung eines neuen Konzepts zu synthetischer Zellen - im Rahmen des EU-Projekts PACE - wurden zell-typische Reaktionssysteme (membranformendes-(1), metabolisches-(2) und genetisches-(3) Subsystem) umgesetzt und analysiert. Als zentrale Reaktionskomponenten dienten strukturunterschiedliche Imidazol-Lipide (Zugang über Festphasensynthese). Imidazol-Vesikel wurden über gezielte Selbstaggregationsprozesse hergestellt und mikroskopisch untersucht (Reaktionsconta...

  6. Chiral bicycle imidazole nucleophilic catalysts: rational design, facile synthesis, and successful application in asymmetric Steglich rearrangement.

    Science.gov (United States)

    Zhang, Zhenfeng; Xie, Fang; Jia, Jia; Zhang, Wanbin

    2010-11-17

    A new type of chiral bicycle imidazole nucleophilic catalyst was rationally designed, facilely synthesized, and successfully applied in an asymmetric Steglich rearrangement with good to excellent yield and enantioselectivity at ambient temperature. Moreover, it can be easily recycled with almost no reduction of catalytic efficiency. This is the first example for the successful chiral imidazole nucleophilic catalyst without H-bonding assistance.

  7. Metal ion coupled protein folding and allosteric motions

    Science.gov (United States)

    Wang, Wei

    2014-03-01

    Many proteins need the help of cofactors for their successful folding and functioning. Metal ions, i.e., Zn2+, Ca2+, and Mg2+ etc., are typical biological cofactors. Binding of metal ions can reshape the energy landscapes of proteins, thereby modifying the folding and allosteric motions. For example, such binding may make the intrinsically disordered proteins have funneled energy landscapes, consequently, ensures their spontaneous folding. In addition, the binding may activate certain biological processes by inducing related conformational changes of regulation proteins. However, how the local interactions involving the metal ion binding can induce the global conformational motions of proteins remains elusive. Investigating such question requires multiple models with different details, including quantum mechanics, atomistic models, and coarse grained models. In our recent work, we have been developing such multiscale methods which can reasonably model the metal ion binding induced charge transfer, protonation/deprotonation, and large conformational motions of proteins. With such multiscale model, we elucidated the zinc-binding induced folding mechanism of classical zinc finger and the calcium-binding induced dynamic symmetry breaking in the allosteric motions of calmodulin. In addition, we studied the coupling of folding, calcium binding and allosteric motions of calmodulin domains. In this talk, I will introduce the above progresses on the metal ion coupled protein folding and allosteric motions. We thank the finacial support from NSFC and the 973 project.

  8. The allosteric communication pathways in KIX domain of CBP

    Science.gov (United States)

    Palazzesi, Ferruccio; Barducci, Alessandro; Tollinger, Martin; Parrinello, Michele

    2013-01-01

    Allosteric regulation plays an important role in a myriad of biomacromolecular processes. Specifically, in a protein, the process of allostery refers to the transmission of a local perturbation, such as ligand binding, to a distant site. Decades after the discovery of this phenomenon, models built on static images of proteins are being reconsidered with the knowledge that protein dynamics plays an important role in its function. Molecular dynamics simulations are a valuable tool for studying complex biomolecular systems, providing an atomistic description of their structure and dynamics. Unfortunately, their predictive power has been limited by the complexity of the biomolecule free-energy surface and by the length of the allosteric timescale (in the order of milliseconds). In this work, we are able to probe the origins of the allosteric changes that transcription factor mixed lineage leukemia (MLL) causes to the interactions of KIX domain of CREB-binding protein (CBP) with phosphorylated kinase inducible domain (pKID), by combing all-atom molecular dynamics with enhanced sampling methods recently developed in our group. We discuss our results in relation to previous NMR studies. We also develop a general simulations protocol to study allosteric phenomena and many other biological processes that occur in the micro/milliseconds timescale. PMID:23940332

  9. Conformational Dynamics in Penicillin-Binding Protein 2a of Methicillin-Resistant Staphylococcus aureus, Allosteric Communication Network and Enablement of Catalysis.

    Science.gov (United States)

    Mahasenan, Kiran V; Molina, Rafael; Bouley, Renee; Batuecas, María T; Fisher, Jed F; Hermoso, Juan A; Chang, Mayland; Mobashery, Shahriar

    2017-02-08

    The mechanism of the β-lactam antibacterials is the functionally irreversible acylation of the enzymes that catalyze the cross-linking steps in the biosynthesis of their peptidoglycan cell wall. The Gram-positive pathogen Staphylococcus aureus uses one primary resistance mechanism. An enzyme, called penicillin-binding protein 2a (PBP2a), is brought into this biosynthetic pathway to complete the cross-linking. PBP2a effectively discriminates against the β-lactam antibiotics as potential inhibitors, and in favor of the peptidoglycan substrate. The basis for this discrimination is an allosteric site, distal from the active site, that when properly occupied concomitantly opens the gatekeeper residues within the active site and realigns the conformation of key residues to permit catalysis. We address the molecular basis of this regulation using crystallographic studies augmented by computational analyses. The crystal structures of three β-lactams (oxacillin, cefepime, ceftazidime) complexes with PBP2a-each with the β-lactam in the allosteric site-defined (with preceding PBP2a structures) as the "open" or "partially open" PBP2a states. A particular loop motion adjacent to the active site is identified as the driving force for the active-site conformational change that accompanies active-site opening. Correlation of this loop motion to effector binding at the allosteric site, in order to identify the signaling pathway, was accomplished computationally in reference to the known "closed" apo-PBP2a X-ray crystal structure state. This correlation enabled the computational simulation of the structures coinciding with initial peptidoglycan substrate binding to PBP2a, acyl enzyme formation, and acyl transfer to a second peptidoglycan substrate to attain cross-linking. These studies offer important insights into the structural bases for allosteric site-to-active site communication and for β-lactam mimicry of the peptidoglycan substrates, as foundational to the mechanistic

  10. Benzothiazole Derivative as a Novel Mycobacterium tuberculosis Shikimate Kinase Inhibitor: Identification and Elucidation of Its Allosteric Mode of Inhibition.

    Science.gov (United States)

    Mehra, Rukmankesh; Rajput, Vikrant Singh; Gupta, Monika; Chib, Reena; Kumar, Amit; Wazir, Priya; Khan, Inshad Ali; Nargotra, Amit

    2016-05-23

    Mycobacterium tuberculosis shikimate kinase (Mtb-SK) is a key enzyme involved in the biosynthesis of aromatic amino acids through the shikimate pathway. Since it is proven to be essential for the survival of the microbe and is absent from mammals, it is a promising target for anti-TB drug discovery. In this study, a combined approach of in silico similarity search and pharmacophore building using already reported inhibitors was used to screen a procured library of 20,000 compounds of the commercially available ChemBridge database. From the in silico screening, 15 hits were identified, and these hits were evaluated in vitro for Mtb-SK enzyme inhibition. Two compounds presented significant enzyme inhibition with IC50 values of 10.69 ± 0.9 and 46.22 ± 1.2 μM. The best hit was then evaluated for the in vitro mode of inhibition where it came out to be an uncompetitive and noncompetitive inhibitor with respect to shikimate (SKM) and ATP, respectively, suggesting its binding at an allosteric site. Potential binding sites of Mtb-SK were identified which confirmed the presence of an allosteric binding pocket apart from the ATP and SKM binding sites. The docking simulations were performed at this pocket in order to find the mode of binding of the best hit in the presence of substrates and the products of the enzymatic reaction. Molecular dynamics (MD) simulations elucidated the probability of inhibitor binding at the allosteric site in the presence of ADP and shikimate-3-phosphate (S-3-P), that is, after the formation of products of the reaction. The inhibitor binding may prevent the release of the product from Mtb-SK, thereby inhibiting its activity. The binding stability and the key residue interactions of the inhibitor to this product complex were also revealed by the MD simulations. Residues ARG43, ILE45, and PHE57 were identified as crucial that were involved in interactions with the best hit. This is the first report of an allosteric binding site of Mtb-SK, which

  11. Chemistry and properties of new poly(arylene ether imidazoles)

    Science.gov (United States)

    Connell, J. W.; Hergenrother, P. M.

    1990-01-01

    As part of a program to develop high-temperature high-performance structural resins for aerospace applications, the chemistry and properties of new poly(arylene ether imidazoles) were investigated. The polymers were prepared by the nucleophilic displacement reaction of aromatic bis(imidazolephenols) with activated aromatic difluoro compounds. The amorphous thermoplastic polymers exhibited glass transition temperatures from 230 to 301 C, inherent viscosities from 0.46 to 1.46 dL/g, and number-average molecular weights as high as 59,300 g/mole. The polymers exhibit good toughness, adhesive, composite, and film properties. The chemical, physical, and mechanical properties of these materials are discussed.

  12. Functional Properties and Mechanism of Action of PPTQ, an Allosteric Agonist and Low Nanomolar Positive Allosteric Modulator at GABAA Receptors

    DEFF Research Database (Denmark)

    Madjroh, Nawid; Olander, Emma Rie; Bundgaard, Christoffer

    2018-01-01

    The former sedative-hypnotic and recreational drug methaqualone (Quaalude) is a moderately potent, non-selective positive allosteric modulator (PAM) at GABAA receptors (GABAARs) (Hammer et al., 2015). In the present study, we have identified a novel methaqualone analog, 2-phenyl-3-(p...

  13. Extracellular loop 2 of the free Fatty Acid receptor 2 mediates allosterism of a phenylacetamide ago-allosteric modulator

    DEFF Research Database (Denmark)

    Smith, Nicola J; Ward, Richard J; Stoddart, Leigh A

    2011-01-01

    Allosteric agonists are powerful tools for exploring the pharmacology of closely related G protein-coupled receptors that have nonselective endogenous ligands, such as the short chain fatty acids at free fatty acid receptors 2 and 3 (FFA2/GPR43 and FFA3/GPR41, respectively). We explored the molec...

  14. Rapid access to the core skeleton of the [3 + 2]-type dimeric pyrrole-imidazole alkaloids by triplet ketone-mediated C-H functionalization.

    Science.gov (United States)

    You, Lin; Chen, Chuo

    2018-02-22

    The ability of triplet ketones to abstract a hydrogen atom from hydrocarbons is reminiscent of that of the high-spin metal-oxo complexes in C-H oxidation enzymes. In practice, the reactivity of triplet ketones is easier to control and applicable to promoting a wider range of reactions. We demonstrate herein the synthetic utility of triplet ketone-mediated C -addition of methanol to cyclopentenone derivatives with an expedient synthesis of the core skeleton of the [3+2]-type dimeric pyrrole-imidazole alkaloids. Remarkably, this photochemical C-H functionalization reaction is highly regioselective and can tolerate a good range of functional groups.

  15. Synthesis and biological evaluation of coumarin derivatives containing imidazole skeleton as potential antibacterial agents.

    Science.gov (United States)

    Hu, Yang; Shen, Yufeng; Wu, Xiaohu; Tu, Xiao; Wang, Gao-Xue

    2018-01-01

    Emergence of multidrug-resistant bacteria causes an urgent need for new generation of antibiotics, which may have a different mechanism of inhibition or killing action from the existing. Here, we report on the design, synthesis, and biological evaluation of thirty-nine coumarin derivatives in order to solve the antibacterial resistance by targeting at the inhibition of biosynthesis pathway of fatty acids. Their antibacterial activities against Escherichia coli, Staphylococcus aureus, Streptococcus agalactiae, and Flavobacterium cloumnare are tested and action mechanism against the key enzyme in bacterial fatty acid synthesis pathway are studied. The results show that compounds 13 and 18 have potent and broad spectrum antimicrobial activity. In addition, 9, 14 and 19 show eminent antimicrobial efficacy toward S. aureus, S. agalactiae, and F. cloumnare. Mechanistically, coumarin derivatives display the antibacterial activity via the control of FabI and FabK function. The structure-activity relationship analysis indicate that the length of linker and imidazole substitute group could significantly influence the antimicrobial activity, as well as the inhibitory activity against FabI and FabK. The structural optimization analysis of coumarin suggest that derivatives 9, 13, 14, 18 and 19 could be a viable way of preventing and controlling bacteria and considered as promising lead compounds for the development of commercial drugs. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

  16. Changes in the hydration structure of imidazole upon protonation: Neutron scattering and molecular simulations

    Science.gov (United States)

    Duboué-Dijon, Elise; Mason, Philip E.; Fischer, Henry E.; Jungwirth, Pavel

    2017-05-01

    The imidazole motif is widely encountered in biomolecules, and its biological role, for instance, as a proton relay, is often linked to its ability to form hydrogen bonds with water molecules. The detailed characterization of the hydration pattern of imidazole and of its changes upon protonation is thus of high interest. Here, we combine neutron scattering experiments with force field simulations to provide an unprecedented characterization of the neutral and protonated imidazole solvation at the atomistic level. We show that neutron diffraction data can be used to assess the quality of the imidazole force field in molecular simulations. Simulations using the CHARMM general force field for imidazole are in excellent agreement with the experimental neutron scattering data and we use them to provide an atomic scale interpretation of the neutron scattering patterns. Upon protonation, we clearly identify the signature of the reorganization in the hydration pattern caused by the change from one H-bond donor and one H-bond acceptor group for imidazole to two H-bond donor groups for imidazolium. We also point the limits of the experiment, which are rather insensitive to details of the H-bond geometry at the deprotonated nitrogen of imidazole and further complement the description of the hydration structure with ab initio molecular dynamics simulations.

  17. Photoinduced electron-transfer from imidazole derivative to nano-semiconductors.

    Science.gov (United States)

    Karunakaran, C; Jayabharathi, J; Jayamoorthy, K; Devi, K Brindha

    2012-04-01

    Bioactive imidazole derivative absorbs in the UV region at 305 nm. The interaction of imidazole derivative with nanoparticulate WO3, Fe2O3, Fe3O4, CuO, ZrO2 and Al2O3 has been studied by UV-visible absorption, FT-IR and fluorescence spectroscopies. The imidazole derivative adsorbs strongly on the surfaces of nanosemiconductor, the apparent binding constants for the association between nanomaterials and imidazole derivative have been determined from the fluorescence quenching. In the case of nanocrystalline insulator, fluorescence quenching through electron transfer from the excited state of the imidazole derivative to alumina is not possible. However, a possible mechanism for the quenching of fluorescence by the insulator is energy transfer, that is, energy transferred from the organic molecule to the alumina lattice. Based on Forster's non-radiation energy transfer theory, the distance between the imidazole derivative and nanoparticles (r0∼2.00 nm) as well as the critical energy transfer distance (R0∼1.70 nm) has been calculated. The interaction between the imidazole derivative and nanosurfaces occurs through static quenching mechanism. The free energy change (ΔGet) for electron transfer process has been calculated by applying Rehm-Weller equation. Copyright © 2012 Elsevier B.V. All rights reserved.

  18. Biochemistry and structural studies of kynurenine 3-monooxygenase reveal allosteric inhibition by Ro 61-8048.

    Science.gov (United States)

    Gao, Jingjing; Yao, Licheng; Xia, Tingting; Liao, Xuebin; Zhu, Deyu; Xiang, Ye

    2018-04-01

    The human kynurenine 3-monooxygenase (hKMO) is a potential therapeutic target for neurodegenerative and neurologic disorders. Inhibition of KMO by Ro 61-8048, a potent, selective, and the most widely used inhibitor of KMO, was shown effective in various models of neurodegenerative or neurologic disorders. However, the molecular basis of hKMO inhibition by Ro 61-8048 is not clearly understood. Here, we report biochemistry studies on hKMO and crystal structures of an hKMO homolog, pfKMO from Pseudomonas fluorescens, in complex with the substrate l-kynurenine and Ro 61-8048. We found that the C-terminal ∼110 aa are essential for the enzymatic activity of hKMO and the homologous C-terminal region of pfKMO folds into a distinct, all-α-helical domain, which associates with the N-terminal catalytic domain to form a unique tunnel in proximity to the substrate-binding pocket. The tunnel binds the Ro 61-8048 molecule, which fills most of the tunnel, and Ro 61-8048 is hydrogen bonded with several completely conserved residues, including an essential catalytic residue. Modification of Ro 61-8048 and biochemical studies of the modified Ro 61-8048 derivatives suggested that Ro 61-8048 inhibits the enzyme in an allosteric manner by affecting the conformation of the essential catalytic residue and by blocking entry of the substrate or product release. The unique binding sites distinguish Ro 61-8048 as a noncompetitive and highly selective inhibitor from other competitive inhibitors, which should facilitate further optimization of Ro 61-8048 and the development of new inhibitory drugs to hKMO.-Gao, J., Yao, L., Xia, T., Liao, X., Zhu, D., Xiang, Y. Biochemistry and structural studies of kynurenine 3-monooxygenase reveal allosteric inhibition by Ro 61-8048.

  19. Inhibiting effects of imidazole on copper corrosion in 1 M HNO3 solution

    International Nuclear Information System (INIS)

    Lee, Woo-Jin

    2003-01-01

    The present work deals with the inhibiting effects of imidazole on the pure copper (Cu) corrosion in 1 M HNO 3 solution analysing potentiodynamic polarisation curves, potentiostatic anodic current transient, AC impedance spectra and X-ray photoelectron spectra (XPS). By adding imidazole to HNO 3 solution, the polarisation curves showed decrease in the corrosion current and the cathodic current, suggesting that imidazole acts as an effective cathodic inhibitor to Cu corrosion. From the measured anodic current transients, it is inferred that the protective Cu-imidazole complex film is simultaneously formed with the Cu oxide in the presence of imidazole during the early stage of the anodic polarisation. Analysis of the AC impedance spectra revealed that the values of the charge transfer resistance R ct obtained in imidazole-containing HNO 3 solution were greater than that value in imidazole-free one and at the same time steadily increased with immersion time to the constant value. Contrarily, the capacitance value was abruptly lowered from the double layer capacitance C dl to the complex film capacitance C cf in the progress of immersion time. Furthermore, the Warburg coefficient σ value for the ion diffusion through the complex film was observed to increase with immersion time. This means that the Cu(N-OH) complex film becomes thicker during immersion in the HNO 3 solution with imidazole through the inward growth of the N-rich outer layer to the O-rich inner layer, as well validated by XPS. Based upon the experimental results, it is suggested that the Cu corrosion in 1 M HNO 3 solution is efficiently inhibited with the addition of imidazole by retarding both the charge transfer on cathodic sites of the Cu surface in the early stage of immersion time and the subsequent ion diffusion through the steadily growing complex film

  20. Intermolecular interactions between imidazole derivatives intercalated in layered solids. Substituent group effect

    Energy Technology Data Exchange (ETDEWEB)

    González, M.; Lemus-Santana, A.A. [Centro de Investigación en Ciencia Aplicada y Tecnología Avanzada, Unidad Legaria, Instituto Politécnico Nacional, México, DF (Mexico); Rodríguez-Hernández, J. [Centro de Investigación en Ciencia Aplicada y Tecnología Avanzada, Unidad Legaria, Instituto Politécnico Nacional, México, DF (Mexico); Instituto de Ciencia y Tecnología de Materiales, Universidad de La Habana, Havana (Cuba); Aguirre-Velez, C.I. [Centro de Investigación en Ciencia Aplicada y Tecnología Avanzada, Unidad Legaria, Instituto Politécnico Nacional, México, DF (Mexico); Knobel, M. [Institute of Physics “Gleb Wataghin”, UNICAMP, 13083-970 Campinas, SP (Brazil); Reguera, E., E-mail: edilso.reguera@gmail.com [Centro de Investigación en Ciencia Aplicada y Tecnología Avanzada, Unidad Legaria, Instituto Politécnico Nacional, México, DF (Mexico)

    2013-08-15

    This study sheds light on the intermolecular interactions between imidazole derive molecules (2-methyl-imidazole, 2-ethyl-imidazole and benzimidazole) intercalated in T[Ni(CN){sub 4}] layers to form a solid of formula unit T(ImD){sub 2}[Ni(CN){sub 4}]. These hybrid inorganic–organic solids were prepared by soft chemical routes and their crystal structures solved and refined from X-ray powder diffraction data. The involved imidazole derivative molecules were found coordinated through the pyridinic N atom to the axial positions for the metal T in the T[Ni(CN){sub 4}] layer. In the interlayers region ligand molecules from neighboring layers remain stacked in a face-to-face configuration through dipole–dipole and quadrupole–quadrupole interactions. These intermolecular interactions show a pronounced dependence on the substituent group and are responsible for an ImD-pillaring concatenation of adjacent layers. This is supported by the structural information and the recorded magnetic data in the 2–300 K temperature range. The samples containing Co and Ni are characterized by presence of spin–orbit coupling and pronounced temperature dependence for the effective magnetic moment except for 2-ethyl-imidazole related to the local distortion for the metal coordination environment. For this last one ligand a weak ferromagnetic ordering ascribed to a super-exchange interaction between T metals from neighboring layers through the ligands π–π interaction was detected. - Graphical abstract: In the interlayers region imidazole derivative molecules are oriented according to their dipolar and quadrupolar interactions and minimizing the steric impediment. Highlights: • Imidazole derivatives intercalation compounds. • Intermolecular interaction between intercalated imidazole derivatives. • Hybrid inorganic–organic solids. • Pi–pi interactions and ferromagnetic coupling. • Dipolar and quadrupolar interactions between intercalated imidazole derivatives.

  1. The relative importance of kinetic mechanisms and variable enzyme abundances for the regulation of hepatic glucose metabolism--insights from mathematical modeling.

    Science.gov (United States)

    Bulik, Sascha; Holzhütter, Hermann-Georg; Berndt, Nikolaus

    2016-03-02

    Adaptation of the cellular metabolism to varying external conditions is brought about by regulated changes in the activity of enzymes and transporters. Hormone-dependent reversible enzyme phosphorylation and concentration changes of reactants and allosteric effectors are the major types of rapid kinetic enzyme regulation, whereas on longer time scales changes in protein abundance may also become operative. Here, we used a comprehensive mathematical model of the hepatic glucose metabolism of rat hepatocytes to decipher the relative importance of different regulatory modes and their mutual interdependencies in the hepatic control of plasma glucose homeostasis. Model simulations reveal significant differences in the capability of liver metabolism to counteract variations of plasma glucose in different physiological settings (starvation, ad libitum nutrient supply, diabetes). Changes in enzyme abundances adjust the metabolic output to the anticipated physiological demand but may turn into a regulatory disadvantage if sudden unexpected changes of the external conditions occur. Allosteric and hormonal control of enzyme activities allow the liver to assume a broad range of metabolic states and may even fully reverse flux changes resulting from changes of enzyme abundances alone. Metabolic control analysis reveals that control of the hepatic glucose metabolism is mainly exerted by enzymes alone, which are differently controlled by alterations in enzyme abundance, reversible phosphorylation, and allosteric effects. In hepatic glucose metabolism, regulation of enzyme activities by changes of reactants, allosteric effects, and reversible phosphorylation is equally important as changes in protein abundance of key regulatory enzymes.

  2. Light-activated DNA binding in a designed allosteric protein

    Energy Technology Data Exchange (ETDEWEB)

    Strickland, Devin; Moffat, Keith; Sosnick, Tobin R. (UC)

    2008-09-03

    An understanding of how allostery, the conformational coupling of distant functional sites, arises in highly evolvable systems is of considerable interest in areas ranging from cell biology to protein design and signaling networks. We reasoned that the rigidity and defined geometry of an {alpha}-helical domain linker would make it effective as a conduit for allosteric signals. To test this idea, we rationally designed 12 fusions between the naturally photoactive LOV2 domain from Avena sativa phototropin 1 and the Escherichia coli trp repressor. When illuminated, one of the fusions selectively binds operator DNA and protects it from nuclease digestion. The ready success of our rational design strategy suggests that the helical 'allosteric lever arm' is a general scheme for coupling the function of two proteins.

  3. Macrolide antibiotics allosterically predispose the ribosome for translation arrest.

    Science.gov (United States)

    Sothiselvam, Shanmugapriya; Liu, Bo; Han, Wei; Ramu, Haripriya; Klepacki, Dorota; Atkinson, Gemma Catherine; Brauer, Age; Remm, Maido; Tenson, Tanel; Schulten, Klaus; Vázquez-Laslop, Nora; Mankin, Alexander S

    2014-07-08

    Translation arrest directed by nascent peptides and small cofactors controls expression of important bacterial and eukaryotic genes, including antibiotic resistance genes, activated by binding of macrolide drugs to the ribosome. Previous studies suggested that specific interactions between the nascent peptide and the antibiotic in the ribosomal exit tunnel play a central role in triggering ribosome stalling. However, here we show that macrolides arrest translation of the truncated ErmDL regulatory peptide when the nascent chain is only three amino acids and therefore is too short to be juxtaposed with the antibiotic. Biochemical probing and molecular dynamics simulations of erythromycin-bound ribosomes showed that the antibiotic in the tunnel allosterically alters the properties of the catalytic center, thereby predisposing the ribosome for halting translation of specific sequences. Our findings offer a new view on the role of small cofactors in the mechanism of translation arrest and reveal an allosteric link between the tunnel and the catalytic center of the ribosome.

  4. 2-(4-Methoxyphenylphenanthro[9,10-d]imidazole methanol solvate

    Directory of Open Access Journals (Sweden)

    Fanpeng Kong

    2008-01-01

    Full Text Available The title compound, C22H16N2O·CH4O, is a product of the condensation reaction between phenanthrenequinone and 4-methoxybenzadehyde. There are two imidazole molecules and two methanol molecules in the asymmetric unit. The phenanthryl and imidazole rings are almost parallel in both molecules, with interplanar angles of 6.65 (1 and 5.40 (3°. The dihedral angles between the imidazole and the attached benzene rings are 5.40 (3 and 6.65 (1° in the two molecules. Intermolecular O—H...N and N—H...O hydrogen bonds stabilize the crystal packing.

  5. Pectic enzymes

    NARCIS (Netherlands)

    Benen, J.A.E.; Voragen, A.G.J.; Visser, J.

    2003-01-01

    The pectic enzymes comprise a diverse group of enzymes. They consist of main-chain depolymerases and esterases active on methyl- and acetylesters of galacturonosyl uronic acid residues. The depolymerizing enzymes comprise hydrolases as wel as lyases

  6. Trade-offs and constraints in allosteric sensing.

    Science.gov (United States)

    Martins, Bruno M C; Swain, Peter S

    2011-11-01

    Sensing extracellular changes initiates signal transduction and is the first stage of cellular decision-making. Yet relatively little is known about why one form of sensing biochemistry has been selected over another. To gain insight into this question, we studied the sensing characteristics of one of the biochemically simplest of sensors: the allosteric transcription factor. Such proteins, common in microbes, directly transduce the detection of a sensed molecule to changes in gene regulation. Using the Monod-Wyman-Changeux model, we determined six sensing characteristics--the dynamic range, the Hill number, the intrinsic noise, the information transfer capacity, the static gain, and the mean response time--as a function of the biochemical parameters of individual sensors and of the number of sensors. We found that specifying one characteristic strongly constrains others. For example, a high dynamic range implies a high Hill number and a high capacity, and vice versa. Perhaps surprisingly, these constraints are so strong that most of the space of characteristics is inaccessible given biophysically plausible ranges of parameter values. Within our approximations, we can calculate the probability distribution of the numbers of input molecules that maximizes information transfer and show that a population of one hundred allosteric transcription factors can in principle distinguish between more than four bands of input concentrations. Our results imply that allosteric sensors are unlikely to have been selected for high performance in one sensing characteristic but for a compromise in the performance of many.

  7. On the nature of inhibition performance of imidazole on iron surface

    Energy Technology Data Exchange (ETDEWEB)

    Mendes, Juliana O.; Silva, Edilson C. da [Instituto de Quimica, Departamento de Fisico-Quimica, Universidade Federal do Rio de Janeiro, Cidade Universitaria, CT Bloco A. Rio de Janeiro, 21941-909 Rio de Janeiro (Brazil); Rocha, Alexandre B., E-mail: rocha@iq.ufrj.br [Instituto de Quimica, Departamento de Fisico-Quimica, Universidade Federal do Rio de Janeiro, Cidade Universitaria, CT Bloco A. Rio de Janeiro, 21941-909 Rio de Janeiro (Brazil)

    2012-04-15

    Highlights: Black-Right-Pointing-Pointer Imidazole corrosion inhibition performance. Black-Right-Pointing-Pointer Slab model and periodic DFT. Black-Right-Pointing-Pointer Cooperative effect on adsorption. Black-Right-Pointing-Pointer Polymerization of imidazole molecules at high coverage. Black-Right-Pointing-Pointer Protective film. - Abstract: Quantum mechanical calculations based on the Density Functional Theory under periodic boundary conditions were used to construct a model for the inhibition performance of imidazole on iron surface. It is shown that, at high coverage, imidazole molecules form C-C intermolecular bonds creating a protective film, which constitutes a hydrophobic medium and, consequently, prevents adsorption of water molecules. The establishment of intermolecular bonds leads to a stabilization of the adsorption energy and this cooperative effect is the thermodynamic explanation for the film formation. These results also point out to the limitation of previous studies based on properties of isolated inhibitor molecules.

  8. Titanium-based zeolitic imidazolate framework for chemical fixation of carbon dioxide

    Data.gov (United States)

    U.S. Environmental Protection Agency — A titanium-based zeolitic imidazolate framework (Ti-ZIF) with high surface area and porous morphology has been synthesized and its application as a recyclable...

  9. Titanium-based zeolitic imidazolate framework for chemical fixation of carbon dioxide

    Science.gov (United States)

    A titanium-based zeolitic imidazolate framework (Ti-ZIF) with high surface area and porous morphology was synthesized and itsefficacy was demonstrated in the synthesis of cyclic carbonates from epoxides and carbon dioxide.

  10. Virtual Screening for Potential Allosteric Inhibitors of Cyclin-Dependent Kinase 2 from Traditional Chinese Medicine

    Directory of Open Access Journals (Sweden)

    Fang Lu

    2016-09-01

    Full Text Available Cyclin-dependent kinase 2 (CDK2, a member of Cyclin-dependent kinases (CDKs, plays an important role in cell division and DNA replication. It is regarded as a desired target to treat cancer and tumor by interrupting aberrant cell proliferation. Compared to lower subtype selectivity of CDK2 ATP-competitive inhibitors, CDK2 allosteric inhibitor with higher subtype selectivity has been used to treat CDK2-related diseases. Recently, the first crystal structure of CDK2 with allosteric inhibitor has been reported, which provides new opportunities to design pure allosteric inhibitors of CDK2. The binding site of the ATP-competition inhibitors and the allosteric inhibitors are partially overlapped in space position, so the same compound might interact with the two binding sites. Thus a novel screening strategy was essential for the discovery of pure CDK2 allosteric inhibitors. In this study, pharmacophore and molecular docking were used to screen potential CDK2 allosteric inhibitors and ATP-competition inhibitors from Traditional Chinese Medicine (TCM. In the docking result of the allosteric site, the compounds which can act with the CDK2 ATP site were discarded, and the remaining compounds were regarded as the potential pure allosteric inhibitors. Among the results, prostaglandin E1 and nordihydroguaiaretic acid (NDGA were available and their growth inhibitory effect on human HepG2 cell lines was determined by MTT assay. The two compounds could substantially inhibit the growth of HepG2 cell lines with an estimated IC50 of 41.223 μmol/L and 45.646 μmol/L. This study provides virtual screening strategy of allosteric compounds and a reliable method to discover potential pure CDK2 allosteric inhibitors from TCM. Prostaglandin E1 and NDGA could be regarded as promising candidates for CDK2 allosteric inhibitors.

  11. Imidazole modified g-C3N4 photocatalyst: Structural characterization and versatile energy applications

    Science.gov (United States)

    Zhang, Lu; Liu, Qianqian; Chai, Yuanyuan; Ren, Jia; Dai, Wei-Lin

    2018-02-01

    Novel imidazole modified g-C3N4 were firstly synthesized via a facile one-pot thermo-induced co-condensation method. Characterization results showed that imidazole modification can improve the visible light harvesting, interfacial charge transfer and separation of g-C3N4, without destroying its pristine framework structure. The as-obtained imidazole modified g-C3N4 showed remarkably enhanced and rather stable photocatalytic performance in H2 evolution, photo-degradation of water contaminants and selective photo-oxidation of benzyl alcohol, demonstrating its all-round applications as a versatile photocatalyst. The weight ratio between imidazole and urea was well tuned and the optimal photocatalytic activity was obtained, which shows CNU-I50 sample (50 mg imidazole in 15 g urea) possesses the highest hydrogen evolution rate of 2150 μmol g-1 h-1, superior to most of the previous reported g-C3N4 materials. These results suggest that those imidazole modified g-C3N4 materials are potential photocatalyst when applied to solar energy conversion, water purification and selective photosynthesis reactions.

  12. Structural insight into activity enhancement and inhibition of H64A carbonic anhydrase II by imidazoles.

    Science.gov (United States)

    Aggarwal, Mayank; Kondeti, Bhargav; Tu, Chingkuang; Maupin, C Mark; Silverman, David N; McKenna, Robert

    2014-03-01

    Human carbonic anhydrases (CAs) are zinc metalloenzymes that catalyze the hydration and dehydration of CO2 and HCO3 (-), respectively. The reaction follows a ping-pong mechanism, in which the rate-limiting step is the transfer of a proton from the zinc-bound solvent (OH(-)/H2O) in/out of the active site via His64, which is widely believed to be the proton-shuttling residue. The decreased catalytic activity (∼20-fold lower with respect to the wild type) of a variant of CA II in which His64 is replaced with Ala (H64A CA II) can be enhanced by exogenous proton donors/acceptors, usually derivatives of imidazoles and pyridines, to almost the wild-type level. X-ray crystal structures of H64A CA II in complex with four imidazole derivatives (imidazole, 1--methylimidazole, 2--methylimidazole and 4-methylimidazole) have been determined and reveal multiple binding sites. Two of these imidazole binding sites have been identified that mimic the positions of the 'in' and 'out' rotamers of His64 in wild-type CA II, while another directly inhibits catalysis by displacing the zinc-bound solvent. The data presented here not only corroborate the importance of the imidazole side chain of His64 in proton transfer during CA catalysis, but also provide a complete structural understanding of the mechanism by which imidazoles enhance (and inhibit when used at higher concentrations) the activity of H64A CA II.

  13. Structure of a small-molecule inhibitor complexed with GlmU from Haemophilus influenzae reveals an allosteric binding site

    Energy Technology Data Exchange (ETDEWEB)

    Mochalkin, Igor; Lightle, Sandra; Narasimhan, Lakshmi; Bornemeier, Dirk; Melnick, Michael; VanderRoest, Steven; McDowell, Laura (Pfizer)

    2008-04-02

    N-Acetylglucosamine-1-phosphate uridyltransferase (GlmU) is an essential enzyme in aminosugars metabolism and an attractive target for antibiotic drug discovery. GlmU catalyzes the formation of uridine-diphospho-N-acetylglucosamine (UDP-GlcNAc), an important precursor in the peptidoglycan and lipopolisaccharide biosynthesis in both Gram-negative and Gram-positive bacteria. Here we disclose a 1.9 {angstrom} resolution crystal structure of a synthetic small-molecule inhibitor of GlmU from Haemophilus influenzae (hiGlmU). The compound was identified through a high-throughput screening (HTS) configured to detect inhibitors that target the uridyltransferase active site of hiGlmU. The original HTS hit exhibited a modest micromolar potency (IC{sub 50} - 18 {mu}M in a racemic mixture) against hiGlmU and no activity against Staphylococcus aureus GlmU (saGlmU). The determined crystal structure indicated that the inhibitor occupies an allosteric site adjacent to the GlcNAc-1-P substrate-binding region. Analysis of the mechanistic model of the uridyltransferase reaction suggests that the binding of this allosteric inhibitor prevents structural rearrangements that are required for the enzymatic reaction, thus providing a basis for structure-guided design of a new class of mechanism-based inhibitors of GlmU.

  14. Lid L11 of the glutamine amidotransferase domain of CTP synthase mediates allosteric GTP activation of glutaminase activity

    DEFF Research Database (Denmark)

    Willemoës, Martin; Mølgaard, Anne; Johansson, Eva

    2005-01-01

    GTP is an allosteric activator of CTP synthase and acts to increase the k(cat) for the glutamine-dependent CTP synthesis reaction. GTP is suggested, in part, to optimally orient the oxy-anion hole for hydrolysis of glutamine that takes place in the glutamine amidotransferase class I (GATase) doma...... with lid L11 and indicate that the GTP activation of glutamine dependent CTP synthesis may be explained by structural rearrangements around the oxy-anion hole of the GATase domain......GTP is an allosteric activator of CTP synthase and acts to increase the k(cat) for the glutamine-dependent CTP synthesis reaction. GTP is suggested, in part, to optimally orient the oxy-anion hole for hydrolysis of glutamine that takes place in the glutamine amidotransferase class I (GATase) domain...... of CTP synthase. In the GATase domain of the recently published structures of the Escherichia coli and Thermus thermophilus CTP synthases a loop region immediately proceeding amino acid residues forming the oxy-anion hole and named lid L11 is shown for the latter enzyme to be flexible and change position...

  15. Non equivalence of the chains in the allosteric interaction of the hemoglobin

    International Nuclear Information System (INIS)

    Jacchieri, S.G.

    1983-01-01

    The importance, for the temperature dependence of the cooperative behaviour of hemoglobin, of the functional non equivalence of the polypeptide chains from which the hemoglobin molecule is built is studied. With such purpose thermodynamic allosteric parameters are introduced called 'mean allosteric parameters' which relate the last two oxygen bindings to the firsttwo ones. It is shown that the mean allosteric free energy is strongly correlated to the Hill parameter which is a classic measure of cooperativity; hence, the mean allosteric free energy measures the hemoglobin cooperativity. Recent experimental data show that the mean allosteric free energy decreasses with temperature; this is due to the mean allosteric enthalphy and entropy being positive quantities. To analise such behaviour in terms of thermodynamic's arguments equations are derived for the thermodynamic parameters of oxygen binding to hemoglobin in terms of those of its chains. Since the obtained equations have a great number of terms the same treatment is applied to a hypothetic dimer from which simpler relations are derived. From both cases it is concluded that the positive character of the mean allosteric enthalpy and entropy is due to the presence of cooperative and anticooperative terms. Since the last terms are absent in the equations of allosteric homoproteins, the characteristic temperature-dependence of hemoglobin's cooperativity depends on the presence of non-equivalent chains. (Author) [pt

  16. The therapeutic potential of allosteric ligands for free fatty acid sensitive GPCRs

    DEFF Research Database (Denmark)

    Hudson, Brian D; Ulven, Trond; Milligan, Graeme

    2013-01-01

    of identifying allosteric leads and their often flat or confusing SAR. The present review will consider the advantages and challenges associated with allosteric GPCR ligands, and examine how the particular properties of these ligands may be exploited to uncover the therapeutic potential for free fatty acid...

  17. Stereochemical requirements of chitin synthase for ligand binding at the allosteric site for N-acetylglucosamine.

    Science.gov (United States)

    Horsch, M; Mayer, C; Rast, D M

    1996-04-15

    The substrate kinetics of chitin synthase (CS) were non-Michaelian, irrespective of the type of enzyme preparation studied (105-S chitosomal CS, and 16-S ex walls), even in the presence of saturating GlcNAc. An unexplained idiosyncrasy of this enzyme, which is likely to be responsible for this phenomenon, is evident from the striking non-linearity of product deposition with time at low substrate or low enzyme concentrations, particularly in the absence of GlcNac. The possibility can be excluded that this non-linearity is due to the formation of soluble by-products or intermediates in the form of chito-oligomers, as shown by HPLC/pulsed amperometric detection analysis. Additional evidence was sought for the tenet that CS is homotropically-heterotropically regulated, at least under steady-state reaction conditions. Substrate kinetic curves established from rate data for the linear reaction phase only were used for modelling. These could be reasonably well parameterised on the basis of the Monod mathematical model for co-operative ligand binding. Within a series of test compounds used to assess the stereochemical conditions of the allosteric site of CS for effector binding, N-acetylglucosaminono-1,5-lactone oxime excelled. Requirements for effector binding are as follows: (a) an aminoglucopyranose skeleton with the amino function acetylated, and (b) a single-bonded oxo-function present at C(1), which is preferentially a hydrogen bond donor, that may be equatorially spaced off, but must not be alpha-anomeric. The implications of these findings for chitin synthesis in vivo are discussed in terms of a mechanistically based fitness of CS to operate efficiently under vastly different combinations of substrate could be coordinately linked to the catabolism of chitin.

  18. Allosteric modulators of the hERG K{sup +} channel

    Energy Technology Data Exchange (ETDEWEB)

    Yu, Zhiyi, E-mail: z.yu@lacdr.leidenuniv.nl; Klaasse, Elisabeth, E-mail: elisabethklaasse@hotmail.com; Heitman, Laura H., E-mail: l.h.heitman@lacdr.leidenuniv.nl; IJzerman, Adriaan P., E-mail: ijzerman@lacdr.leidenuniv.nl

    2014-01-01

    Drugs that block the cardiac K{sup +} channel encoded by the human ether-à-go-go gene (hERG) have been associated with QT interval prolongation leading to proarrhythmia, and in some cases, sudden cardiac death. Because of special structural features of the hERG K{sup +} channel, it has become a promiscuous target that interacts with pharmaceuticals of widely varying chemical structures and a reason for concern in the pharmaceutical industry. The structural diversity suggests that multiple binding sites are available on the channel with possible allosteric interactions between them. In the present study, three reference compounds and nine compounds of a previously disclosed series were evaluated for their allosteric effects on the binding of [{sup 3}H]astemizole and [{sup 3}H]dofetilide to the hERG K{sup +} channel. LUF6200 was identified as an allosteric inhibitor in dissociation assays with both radioligands, yielding similar EC{sub 50} values in the low micromolar range. However, potassium ions increased the binding of the two radioligands in a concentration-dependent manner, and their EC{sub 50} values were not significantly different, indicating that potassium ions behaved as allosteric enhancers. Furthermore, addition of potassium ions resulted in a concentration-dependent leftward shift of the LUF6200 response curve, suggesting positive cooperativity and distinct allosteric sites for them. In conclusion, our investigations provide evidence for allosteric modulation of the hERG K{sup +} channel, which is discussed in the light of findings on other ion channels. - Highlights: • Allosteric modulators on the hERG K{sup +} channel were evaluated in binding assays. • LUF6200 was identified as a potent allosteric inhibitor. • Potassium ions were found to behave as allosteric enhancers. • Positive cooperativity and distinct allosteric sites for them were proposed.

  19. Toward controlling water oxidation catalysis: tunable activity of ruthenium complexes with axial imidazole/DMSO ligands.

    Science.gov (United States)

    Wang, Lei; Duan, Lele; Stewart, Beverly; Pu, Maoping; Liu, Jianhui; Privalov, Timofei; Sun, Licheng

    2012-11-14

    Using the combinations of imidazole and dimethyl sulfoxide (DMSO) as axial ligands and 2,2'-bipyridine-6,6'-dicarboxylate (bda) as the equatorial ligand, we have synthesized six novel ruthenium complexes with noticeably different activity as water oxidation catalysts (WOCs). In four C(s) symmetric Ru(II)(κ(3)-bda)(DMSO)L(2) complexes L = imidazole (1), N-methylimidazole (2), 5-methylimidazole (3), and 5-bromo-N-methylimidazole (4). Additionally, in two C(2v) symmetric Ru(II)(κ(4)-bda)L(2) complexes L = 5-nitroimidazole (5) and 5-bromo-N-methylimidazole (6), that is, fully equivalent axial imidazoles. A detailed characterization of all complexes and the mechanistic investigation of the catalytic water oxidation have been carried out with a number of experimental techniques, that is, kinetics, electrochemistry and high resolution mass spectrometry (HR-MS), and density functional theory (DFT) calculations. We have observed the in situ formation of a Ru(II)-complex with the accessible seventh coordination position. The measured catalytic activities and kinetics of complex 1-6 revealed details about an important structure-activity relation: the connection between the nature of axial ligands in the combination and either the increase or decrease of the catalytic activity. In particular, an axial DMSO group substantially increases the turnover frequency of WOCs reported in the article, with the ruthenium-complex having one axial 5-bromo-N-methyl-imidazole and one axial DMSO (4), we have obtained a high initial turnover frequency of ∼180 s(-1). DFT modeling of the binuclear reaction pathway of the O-O bond formation in catalytic water oxidation further corroborated the concept of the mechanistic significance of the axial ligands and rationalized the experimentally observed difference in the activity of complexes with imidazole/DMSO and imidazole/imidazole combinations of axial ligands.

  20. Unexpected Molecular Sieving Properties of Zeolitic Imidazolate Framework-8.

    Science.gov (United States)

    Zhang, Chen; Lively, Ryan P; Zhang, Ke; Johnson, Justin R; Karvan, Oguz; Koros, William J

    2012-08-16

    We studied molecular sieving properties of zeolitic imidazolate framework-8 (ZIF-8) by estimating the thermodynamically corrected diffusivities of probe molecules at 35 °C. From helium (2.6 Å) to iso-C4H10 (5.0 Å), the corrected diffusivity drops 14 orders of magnitude. Our results further suggest that the effective aperture size of ZIF-8 for molecular sieving is in the range of 4.0 to 4.2 Å, which is significantly larger than the XRD-derived value (3.4 Å) and between the well-known aperture size of zeolite 4A (3.8 Å) and 5A (4.3 Å). Interestingly, because of aperture flexibility, the studied C4 hydrocarbon molecules that are larger than this effective aperture size still adsorb in the micropores of ZIF-8 with kinetic selectivities for iso-C4H8/iso-C4H10 of 180 and n-C4H10/iso-C4H10 of 2.5 × 10(6). These unexpected molecular sieving properties open up new opportunities for ZIF materials for separations that cannot be economically achieved by traditional microporous adsorbents such as synthetic zeolites.

  1. Mechanistic Probes of Zeolitic Imidazolate Framework for Photocatalytic Application

    Energy Technology Data Exchange (ETDEWEB)

    Pattengale, Brian [Department; Yang, Sizhuo [Department; Lee, Sungsik [X-ray; Huang, Jier [Department

    2017-11-07

    In this work, we report a zeolitic imidazolate framework (ZIF-67) with remarkable activity for hydrogen evolution reaction (HER) of 40,500 μmol H2/g MOF, which is, to the best of our knowledge, the highest activity achieved by any MOF system. This result necessitated assessment of its atomic-scale mechanistic function for HER using advanced spectroscopy techniques including time-resolved optical (OTA) and in situ X-ray absorption (XAS) spectroscopy. Through the correlation of OTA results with catalytic performance, we demonstrated that the electron transfer (ET) rather than energy transfer (ENT) pathway between photosensitizer and ZIF-67 is the key factor that controls the efficiency of HER activity, as HER activity that undergoes ET pathway is 3 orders of magnitude higher than that of ENT process. Using in situ XAS, we unraveled the spectral features for key intermediate species which are likely responsible for the rate determining process under turn over conditions. This work represents an original approach to study porous ZIF materials at the molecular level using advanced spectroscopic techniques, providing unprecedented insights into the photoactive nature of ZIF frameworks.

  2. Unexpected Molecular Sieving Properties of Zeolitic Imidazolate Framework-8

    KAUST Repository

    Zhang, Chen

    2012-08-16

    We studied molecular sieving properties of zeolitic imidazolate framework-8 (ZIF-8) by estimating the thermodynamically corrected diffusivities of probe molecules at 35 °C. From helium (2.6 Å) to iso-C 4H 10 (5.0 Å), the corrected diffusivity drops 14 orders of magnitude. Our results further suggest that the effective aperture size of ZIF-8 for molecular sieving is in the range of 4.0 to 4.2 Å, which is significantly larger than the XRD-derived value (3.4 Å) and between the well-known aperture size of zeolite 4A (3.8 Å) and 5A (4.3 Å). Interestingly, because of aperture flexibility, the studied C 4 hydrocarbon molecules that are larger than this effective aperture size still adsorb in the micropores of ZIF-8 with kinetic selectivities for iso-C 4H 8/iso-C 4H 10 of 180 and n-C 4H 10/iso-C 4H 10 of 2.5 × 10 6. These unexpected molecular sieving properties open up new opportunities for ZIF materials for separations that cannot be economically achieved by traditional microporous adsorbents such as synthetic zeolites. © 2012 American Chemical Society.

  3. Biological applications of zinc imidazole framework through protein encapsulation

    Science.gov (United States)

    Kumar, Pawan; Bansal, Vasudha; Paul, A. K.; Bharadwaj, Lalit M.; Deep, Akash; Kim, Ki-Hyun

    2016-10-01

    The robustness of biomolecules is always a significant challenge in the application of biostorage in biotechnology or pharmaceutical research. To learn more about biostorage in porous materials, we investigated the feasibility of using zeolite imidazolate framework (ZIF-8) with respect to protein encapsulation. Here, bovine serum albumin (BSA) was selected as a model protein for encapsulation with the synthesis of ZIF-8 using water as a media. ZIF-8 exhibited excellent protein adsorption capacity through successive adsorption of free BSA with the formation of hollow crystals. The loading of protein in ZIF-8 crystals is affected by the molecular weight due to diffusion-limited permeation inside the crystals and also by the affinity of the protein to the pendent group on the ZIF-8 surface. The polar nature of BSA not only supported adsorption on the solid surface, but also enhanced the affinity of crystal spheres through weak coordination interactions with the ZIF-8 framework. The novel approach tested in this study was therefore successful in achieving protein encapsulation with porous, biocompatible, and decomposable microcrystalline ZIF-8. The presence of both BSA and FITC-BSA in ZIF-8 was confirmed consistently by spectroscopy as well as optical and electron microscopy.

  4. Biological applications of zinc imidazole framework through protein encapsulation

    Directory of Open Access Journals (Sweden)

    Pawan Kumar

    2015-12-01

    Full Text Available Abstract The robustness of biomolecules is always a significant challenge in the application of biostorage in biotechnology or pharmaceutical research. To learn more about biostorage in porous materials, we investigated the feasibility of using zeolite imidazolate framework (ZIF-8 with respect to protein encapsulation. Here, bovine serum albumin (BSA was selected as a model protein for encapsulation with the synthesis of ZIF-8 using water as a media. ZIF-8 exhibited excellent protein adsorption capacity through successive adsorption of free BSA with the formation of hollow crystals. The loading of protein in ZIF-8 crystals is affected by the molecular weight due to diffusion-limited permeation inside the crystals and also by the affinity of the protein to the pendent group on the ZIF-8 surface. The polar nature of BSA not only supported adsorption on the solid surface, but also enhanced the affinity of crystal spheres through weak coordination interactions with the ZIF-8 framework. The novel approach tested in this study was therefore successful in achieving protein encapsulation with porous, biocompatible, and decomposable microcrystalline ZIF-8. The presence of both BSA and FITC–BSA in ZIF-8 was confirmed consistently by spectroscopy as well as optical and electron microscopy.

  5. Benzimidazole and imidazole lithium salts for battery electrolytes

    Energy Technology Data Exchange (ETDEWEB)

    Scheers, Johan; Johansson, Patrik; Jacobsson, Per [Department of Applied Physics, Chalmers University of Technology, SE-412 96 Goeteborg (Sweden); Szczecinski, Przemyslaw; Wieczorek, Wladyslaw [Polymer Ionics Research Group, Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, PL-00664 Warsaw (Poland); Armand, Michel [Laboratoire de Reactivite et de Chimie des Solides, Universite de Picardie Jules Verne, 33 rue St. Leu, 80089 Amiens (France)

    2010-09-15

    The intrinsic anion oxidation potential ({delta}E{sub v}) and lithium ion pair dissociation energy ({delta}E{sub d}) are two important properties for predicting the potential use of new lithium salts for battery electrolytes. In this work several cyano substituted fluoroalkylated benzimidazole and imidazole anions have been investigated computationally to obtain {delta}E{sub v} and {delta}E{sub d}. Varying the number and position of cyano substituents results in large effects on the electrochemical stability of the anion and on the possible lithium ion pair configurations. The lengthening of the fluoroalkyl group introduces several new stable ion pair configurations and a small increase in anion oxidation stability. The most promising fluoroalkylated anions in the present work are the 4,5,6,7-tetracyano-2-fluoroalkylated benzimidazolides (TTB and PTB), with oxidation potentials suitable for high voltage Li-ion battery applications (<4.2 V) and much improved {delta}E{sub d} compared to PF{sub 6}{sup -} - a benchmark for commercially available anions. Further improvements in {delta}E{sub d}, with maintained stability towards oxidation, are obtainable by replacing the fluoroalkyl group by an additional cyano group, but possibly demanding increased synthesis efforts. (author)

  6. Liquid electrolytes based on new lithium conductive imidazole salts

    Energy Technology Data Exchange (ETDEWEB)

    Niedzicki, L.; Kasprzyk, M.; Kuziak, K.; Zukowska, G.Z.; Marcinek, M.; Wieczorek, W. [Department of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw (Poland); Armand, M. [LRCS, University de Picardie Jules Verne, UMR 6007 CNRS, 33 rue de Saint-Leu, 80039 Amiens (France)

    2011-02-01

    In the present paper new generation of imidazole-derived lithium salts (LiTDI - lithium 4,5-dicyano-2-(trifluoromethyl)imidazolide, LiPDI - lithium 4,5-dicyano-2-(pentafluoroethyl)imidazolide and LiHDI - lithium 4,5-dicyano-2-(n-heptafluoropropyl)imidazolide) applied in a model liquid electrolyte, with propylene carbonate used as a solvent, is described. Room temperature ionic conductivities measured by Impedance Spectroscopy are as high as 10{sup -2} to 10{sup -3} S cm{sup -1} for the 0.1-1 mol dm{sup -3} salt concentration range. Lithium cation transference numbers calculated using the Bruce-Vincent method exceed 0.4 at salt concentration equal to 1 mol dm{sup -3}. Interface resistance measurements showed good stability at high - 0.5 mol dm{sup -3} or low - 0.01 mol dm{sup -3} salt concentrations. Ionic associations were estimated using Fuoss-Kraus semiempirical method revealing relatively low association rates. The effect of anion structure on ionic interactions and electrochemical characteristics of the studied electrolytes is discussed. (author)

  7. The allosteric transition of GroEL induced by metal fluoride-ADP complexes.

    Science.gov (United States)

    Inobe, Tomonao; Kikushima, Kenji; Makio, Tadashi; Arai, Munehito; Kuwajima, Kunihiro

    2003-05-23

    To understand the mechanism of a functionally important ATP-induced allosteric transition of GroEL, we have studied the effect of a series of metal fluoride-ADP complexes and vanadate-ADP on GroEL by kinetic fluorescence measurement of pyrene-labeled GroEL and by small-angle X-ray scattering measurement of wild-type GroEL. The metal fluorides and vanadate, complexed with ADP, are known to mimic the gamma-phosphate group of ATP, but they differ in geometry and size; it is expected that these compounds will be useful for investigating the strikingly high specificity of GroEL for ATP that enables the induction of the allosteric transition. The kinetic fluorescence measurement revealed that aluminium, beryllium, and gallium ions, when complexed with the fluoride ion and ADP, induced a biphasic fluorescence change of pyrenyl GroEL, while scandium and vanadate ions did not induce any kinetically observed change in fluorescence. The burst phase and the first phase of the fluorescence kinetics were reversible, while the second phase and subsequent changes were irreversible. The dependence of the burst-phase and the first-phase fluorescence changes on the ADP concentration indicated that the burst phase represents non-cooperative nucleotide binding to GroEL, and that the first phase represents the allosteric transition of GroEL. Both the amplitude and the rate constant of the first phase of the fluorescence kinetics were well understood in terms of a kinetic allosteric model, which is a combination of transition state theory and the Monod-Wyman-Changeux allosteric model. From the kinetic allosteric model analysis, the relative free energy of the transition state in the metal fluoride-ADP-induced allosteric transition of GroEL was found to be larger than the corresponding free energy of the ATP-induced allosteric transition by more than 5.5kcal/mol. However, the X-ray scattering measurements indicated that the allosteric state induced by these metal fluoride-ADP complexes is

  8. The allosteric switching mechanism in bacteriophage MS2

    Science.gov (United States)

    Perkett, Matthew R.; Mirijanian, Dina T.; Hagan, Michael F.

    2016-07-01

    We use all-atom simulations to elucidate the mechanisms underlying conformational switching and allostery within the coat protein of the bacteriophage MS2. Assembly of most icosahedral virus capsids requires that the capsid protein adopts different conformations at precise locations within the capsid. It has been shown that a 19 nucleotide stem loop (TR) from the MS2 genome acts as an allosteric effector, guiding conformational switching of the coat protein during capsid assembly. Since the principal conformational changes occur far from the TR binding site, it is important to understand the molecular mechanism underlying this allosteric communication. To this end, we use all-atom simulations with explicit water combined with a path sampling technique to sample the MS2 coat protein conformational transition, in the presence and absence of TR-binding. The calculations find that TR binding strongly alters the transition free energy profile, leading to a switch in the favored conformation. We discuss changes in molecular interactions responsible for this shift. We then identify networks of amino acids with correlated motions to reveal the mechanism by which effects of TR binding span the protein. We find that TR binding strongly affects residues located at the 5-fold and quasi-sixfold interfaces in the assembled capsid, suggesting a mechanism by which the TR binding could direct formation of the native capsid geometry. The analysis predicts amino acids whose substitution by mutagenesis could alter populations of the conformational substates or their transition rates.

  9. Allosteric Inhibition of Macrophage Migration Inhibitory Factor Revealed by Ibudilast

    Energy Technology Data Exchange (ETDEWEB)

    Cho, Y.; Crichlow, G; Vermeire, J; Leng, L; Du, X; Hodsdon, M; Bucala, R; Cappello, M; Gross, M; et al.

    2010-01-01

    AV411 (ibudilast; 3-isobutyryl-2-isopropylpyrazolo-[1,5-a]pyridine) is an antiinflammatory drug that was initially developed for the treatment of bronchial asthma but which also has been used for cerebrovascular and ocular indications. It is a nonselective inhibitor of various phosphodiesterases (PDEs) and has varied antiinflammatory activity. More recently, AV411 has been studied as a possible therapeutic for the treatment of neuropathic pain and opioid withdrawal through its actions on glial cells. As described herein, the PDE inhibitor AV411 and its PDE-inhibition-compromised analog AV1013 inhibit the catalytic and chemotactic functions of the proinflammatory protein, macrophage migration inhibitory factor (MIF). Enzymatic analysis indicates that these compounds are noncompetitive inhibitors of the p-hydroxyphenylpyruvate (HPP) tautomerase activity of MIF and an allosteric binding site of AV411 and AV1013 is detected by NMR. The allosteric inhibition mechanism is further elucidated by X-ray crystallography based on the MIF/AV1013 binary and MIF/AV1013/HPP ternary complexes. In addition, our antibody experiments directed against MIF receptors indicate that CXCR2 is the major receptor for MIF-mediated chemotaxis of peripheral blood mononuclear cells.

  10. The allosteric switching mechanism in bacteriophage MS2

    Energy Technology Data Exchange (ETDEWEB)

    Perkett, Matthew R.; Mirijanian, Dina T.; Hagan, Michael F., E-mail: hagan@brandeis.edu [Martin Fisher School of Physics, Brandeis University, Waltham, Massachusetts 02474 (United States)

    2016-07-21

    We use all-atom simulations to elucidate the mechanisms underlying conformational switching and allostery within the coat protein of the bacteriophage MS2. Assembly of most icosahedral virus capsids requires that the capsid protein adopts different conformations at precise locations within the capsid. It has been shown that a 19 nucleotide stem loop (TR) from the MS2 genome acts as an allosteric effector, guiding conformational switching of the coat protein during capsid assembly. Since the principal conformational changes occur far from the TR binding site, it is important to understand the molecular mechanism underlying this allosteric communication. To this end, we use all-atom simulations with explicit water combined with a path sampling technique to sample the MS2 coat protein conformational transition, in the presence and absence of TR-binding. The calculations find that TR binding strongly alters the transition free energy profile, leading to a switch in the favored conformation. We discuss changes in molecular interactions responsible for this shift. We then identify networks of amino acids with correlated motions to reveal the mechanism by which effects of TR binding span the protein. We find that TR binding strongly affects residues located at the 5-fold and quasi-sixfold interfaces in the assembled capsid, suggesting a mechanism by which the TR binding could direct formation of the native capsid geometry. The analysis predicts amino acids whose substitution by mutagenesis could alter populations of the conformational substates or their transition rates.

  11. Allosteric inhibitors of Coxsackie virus A24 RNA polymerase.

    Science.gov (United States)

    Schein, Catherine H; Rowold, Diane; Choi, Kyung H

    2016-02-15

    Coxsackie virus A24 (CVA24), a causative agent of acute hemorrhagic conjunctivitis, is a prototype of enterovirus (EV) species C. The RNA polymerase (3D(pol)) of CVA24 can uridylylate the viral peptide linked to the genome (VPg) from distantly related EV and is thus, a good model for studying this reaction. Once UMP is bound, VPgpU primes RNA elongation. Structural and mutation data have identified a conserved binding surface for VPg on the RNA polymerase (3D(pol)), located about 20Å from the active site. Here, computational docking of over 60,000 small compounds was used to select those with the lowest (best) specific binding energies (BE) for this allosteric site. Compounds with varying structures and low BE were assayed for their effect on formation of VPgU by CVA24-3D(pol). Two compounds with the lowest specific BE for the site inhibited both uridylylation and formation of VPgpolyU at 10-20μM. These small molecules can be used to probe the role of this allosteric site in polymerase function, and may be the basis for novel antiviral compounds. Copyright © 2015 Elsevier Ltd. All rights reserved.

  12. Profiling of engineering hotspots identifies an allosteric CRISPR-Cas9 switch.

    Science.gov (United States)

    Oakes, Benjamin L; Nadler, Dana C; Flamholz, Avi; Fellmann, Christof; Staahl, Brett T; Doudna, Jennifer A; Savage, David F

    2016-06-01

    The clustered, regularly interspaced, short palindromic repeats (CRISPR)-associated protein Cas9 from Streptococcus pyogenes is an RNA-guided DNA endonuclease with widespread utility for genome modification. However, the structural constraints limiting the engineering of Cas9 have not been determined. Here we experimentally profile Cas9 using randomized insertional mutagenesis and delineate hotspots in the structure capable of tolerating insertions of a PDZ domain without disruption of the enzyme's binding and cleavage functions. Orthogonal domains or combinations of domains can be inserted into the identified sites with minimal functional consequence. To illustrate the utility of the identified sites, we construct an allosterically regulated Cas9 by insertion of the estrogen receptor-α ligand-binding domain. This protein showed robust, ligand-dependent activation in prokaryotic and eukaryotic cells, establishing a versatile one-component system for inducible and reversible Cas9 activation. Thus, domain insertion profiling facilitates the rapid generation of new Cas9 functionalities and provides useful data for future engineering of Cas9.

  13. Enzyme Informatics

    Science.gov (United States)

    Alderson, Rosanna G.; Ferrari, Luna De; Mavridis, Lazaros; McDonagh, James L.; Mitchell, John B. O.; Nath, Neetika

    2012-01-01

    Over the last 50 years, sequencing, structural biology and bioinformatics have completely revolutionised biomolecular science, with millions of sequences and tens of thousands of three dimensional structures becoming available. The bioinformatics of enzymes is well served by, mostly free, online databases. BRENDA describes the chemistry, substrate specificity, kinetics, preparation and biological sources of enzymes, while KEGG is valuable for understanding enzymes and metabolic pathways. EzCatDB, SFLD and MACiE are key repositories for data on the chemical mechanisms by which enzymes operate. At the current rate of genome sequencing and manual annotation, human curation will never finish the functional annotation of the ever-expanding list of known enzymes. Hence there is an increasing need for automated annotation, though it is not yet widespread for enzyme data. In contrast, functional ontologies such as the Gene Ontology already profit from automation. Despite our growing understanding of enzyme structure and dynamics, we are only beginning to be able to design novel enzymes. One can now begin to trace the functional evolution of enzymes using phylogenetics. The ability of enzymes to perform secondary functions, albeit relatively inefficiently, gives clues as to how enzyme function evolves. Substrate promiscuity in enzymes is one example of imperfect specificity in protein-ligand interactions. Similarly, most drugs bind to more than one protein target. This may sometimes result in helpful polypharmacology as a drug modulates plural targets, but also often leads to adverse side-effects. Many cheminformatics approaches can be used to model the interactions between druglike molecules and proteins in silico. We can even use quantum chemical techniques like DFT and QM/MM to compute the structural and energetic course of enzyme catalysed chemical reaction mechanisms, including a full description of bond making and breaking. PMID:23116471

  14. In Vivo Investigation of Escitalopram’s Allosteric Site on the Serotonin Transporter

    Science.gov (United States)

    Murray, Karen E.; Ressler, Kerry J.; Owens, Michael J.

    2015-01-01

    Escitalopram is a commonly prescribed antidepressant of the selective serotonin reuptake inhibitor class. Clinical evidence and mapping of the serotonin transporter (SERT) identified that escitalopram, in addition to its binding to a primary uptake-blocking site, is capable of binding to the SERT via an allosteric site that is hypothesized to alter escitalopram’s kinetics at the SERT. The studies reported here examined the in vivo role of the SERT allosteric site in escitalopram action. A knockin mouse model that possesses an allosteric-null SERT was developed. Autoradiographic studies indicated that the knockin protein was expressed at a lower density than endogenous mouse SERT (approximately 10–30% of endogenous mouse SERT), but the knockin mice are a viable tool to study the allosteric site. Microdialysis studies in the ventral hippocampus found no measurable decrease in extracellular serotonin response after local escitalopram challenge in mice without the allosteric site compared to mice with the site (p = 0.297). In marble burying assays there was a modest effect of the absence of the allosteric site, with a larger systemic dose of escitalopram (10-fold) necessary for the same effect as in mice with intact SERT (p = 0.023). However, there was no effect of the allosteric site in the tail suspension test. Together these data suggest that there may be a regional specificity in the role of the allosteric site. The lack of a robust effect overall suggests that the role of the allosteric site for escitalopram on the SERT may not produce meaningful in vivo effects. PMID:26621784

  15. Surface binding sites in carbohydrate active enzymes: An emerging picture of structural and functional diversity

    DEFF Research Database (Denmark)

    Svensson, Birte; Cockburn, Darrell

    2013-01-01

    identified in enzymes from a wide variety of families, though almost half are found in the α-amylase family GH13. The roles attributed to SBSs are not limited to targeting the enzyme to the substrate, but also include a variety of others such as guiding the substrate into the active site, altering enzyme...... specificity and acting as an allosteric site. Although SBSs share many roles with CBMs they may not simply be an alternative to CBMs, but rather complementary as SBSs and CBMs frequently co-occur in enzymes. Despite a relatively long history, it is only in recent years that SBSs have been studied in great...

  16. Hydrogen/Deuterium Exchange Kinetics Demonstrate Long Range Allosteric Effects of Thumb Site 2 Inhibitors of Hepatitis C Viral RNA-dependent RNA Polymerase.

    Science.gov (United States)

    Deredge, Daniel; Li, Jiawen; Johnson, Kenneth A; Wintrode, Patrick L

    2016-05-06

    New nonnucleoside analogs are being developed as part of a multi-drug regimen to treat hepatitis C viral infections. Particularly promising are inhibitors that bind to the surface of the thumb domain of the viral RNA-dependent RNA polymerase (NS5B). Numerous crystal structures have been solved showing small molecule non-nucleoside inhibitors bound to the hepatitis C viral polymerase, but these structures alone do not define the mechanism of inhibition. Our prior kinetic analysis showed that nonnucleoside inhibitors binding to thumb site-2 (NNI2) do not block initiation or elongation of RNA synthesis; rather, they block the transition from the initiation to elongation, which is thought to proceed with significant structural rearrangement of the enzyme-RNA complex. Here we have mapped the effect of three NNI2 inhibitors on the conformational dynamics of the enzyme using hydrogen/deuterium exchange kinetics. All three inhibitors rigidify an extensive allosteric network extending >40 Å from the binding site, thus providing a structural rationale for the observed disruption of the transition from distributive initiation to processive elongation. The two more potent inhibitors also suppress slow cooperative unfolding in the fingers extension-thumb interface and primer grip, which may contribute their stronger inhibition. These results establish that NNI2 inhibitors act through long range allosteric effects, reveal important conformational changes underlying normal polymerase function, and point the way to the design of more effective allosteric inhibitors that exploit this new information. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

  17. Ethyl 2-(2-methyl-4-nitro-1H-imidazol-1-ylacetate

    Directory of Open Access Journals (Sweden)

    Yassine Hakmaoui

    2016-04-01

    Full Text Available In the title compound, C8H11N3O4, the imidazole ring and the nitro group are nearly coplanar, with the largest deviation from the mean plane being 0.119 (2 Å. The mean plane through the acetate group is approximately perpendicular to the imidazole ring, subtending a dihedral angle of 75.71 (13°. In the crystal, molecules are linked by weak C—H...O and very weak C—H...N hydrogen bonds, forming a three-dimensional network. There is also a weak C—H...π(imidazole interaction, which contributes to the stability of the crystal packing arrangement.

  18. Building blocks for ionic liquids: Vapor pressures and vaporization enthalpies of 1-(n-alkyl)-imidazoles

    International Nuclear Information System (INIS)

    Emel'yanenko, Vladimir N.; Portnova, Svetlana V.; Verevkin, Sergey P.; Skrzypczak, Andrzej; Schubert, Thomas

    2011-01-01

    Highlights: → We measured vapor pressures of the 1-(n-alkyl)-imidazoles by transpiration method. → Variations on the alkyl chain length n were C 3 , C 5 -C 7 , and C 9 -C 10 . → Enthalpies of vaporization were derived from (p, T) dependencies. → Enthalpies of vaporization at 298.15 K were linear dependent on the chain length. - Abstract: Vapor pressures of the linear 1-(n-alkyl)-imidazoles with the alkyl chain C 3 , C 5 -C 7 , and C 9 -C 10 have been measured by the transpiration method. The molar enthalpies of vaporization Δ l g H m of these compounds were derived from the temperature dependencies of vapor pressures. A linear correlation of enthalpies of vaporization Δ l g H m (298.15 K) of the 1-(n-alkyl)-imidazoles with the chain length has been found.

  19. Comparative study between phenol and imidazole derivatives in radiolabeling of some steroid hormones

    International Nuclear Information System (INIS)

    Sallam, Kh.M.

    2010-01-01

    A phenol or imidazole ring is rarely present in steroid hormones, So, the molecule of steroid hormone requires chemical modification by addition of an iodinable residue like phenol or imedazole. So that the comparative study between phenol derivatives, include tyrosine methyl ester (TME) and tyramine, and imidazole derivatives, like histamine and histedine methyl ester (HME), for radiolabeling of some steroid hormones include estradiol and testosterone is the aim of the present study. The conjugation step was carried using mixed anhydride method and followed by radioiodination using iodogen as an oxidizing agent. Purification step was carried out using high performance liquid chromatography (HPLC). Optimization and validation of the tracer were carried out. Immunoreactivity of the all obtained tracers was check by using specific polyclonal antibodies. The results indicated that imidazols derivatives are more suitable from immunoreactivity view and storage period.

  20. Structural insight into activity enhancement and inhibition of H64A carbonic anhydrase II by imidazoles

    Directory of Open Access Journals (Sweden)

    Mayank Aggarwal

    2014-03-01

    Full Text Available Human carbonic anhydrases (CAs are zinc metalloenzymes that catalyze the hydration and dehydration of CO2 and HCO3−, respectively. The reaction follows a ping-pong mechanism, in which the rate-limiting step is the transfer of a proton from the zinc-bound solvent (OH−/H2O in/out of the active site via His64, which is widely believed to be the proton-shuttling residue. The decreased catalytic activity (∼20-fold lower with respect to the wild type of a variant of CA II in which His64 is replaced with Ala (H64A CA II can be enhanced by exogenous proton donors/acceptors, usually derivatives of imidazoles and pyridines, to almost the wild-type level. X-ray crystal structures of H64A CA II in complex with four imidazole derivatives (imidazole, 1-methylimidazole, 2-methylimidazole and 4-methylimidazole have been determined and reveal multiple binding sites. Two of these imidazole binding sites have been identified that mimic the positions of the `in' and `out' rotamers of His64 in wild-type CA II, while another directly inhibits catalysis by displacing the zinc-bound solvent. The data presented here not only corroborate the importance of the imidazole side chain of His64 in proton transfer during CA catalysis, but also provide a complete structural understanding of the mechanism by which imidazoles enhance (and inhibit when used at higher concentrations the activity of H64A CA II.

  1. A Novel Tetrasubstituted Imidazole as a Prototype for the Development of Anti-inflammatory Drugs.

    Science.gov (United States)

    Nascimento, Marcus Vinicius P S; Munhoz, Antonio C M; Theindl, Lais C; Mohr, Eduarda Talita B; Saleh, Najla; Parisotto, Eduardo B; Rossa, Thaís A; Zamoner, Ariane; Creczynski-Pasa, Tania B; Filippin-Monteiro, Fabíola B; Sá, Marcus M; Dalmarco, Eduardo Monguilhott

    2018-04-14

    Although inflammation is a biological phenomenon that exists to protect the host against infections and/or related problems, its unceasing activation results in the aggravation of several medical conditions. Imidazoles, whether natural or synthetic, are molecules related to a broad spectrum of biological effects, including anti-inflammatory properties. In this study, we screened eight novel small molecules of the imidazole class synthesized by our research group for their in vitro anti-inflammatory activity. The effect of the selected molecules was confirmed in an in vivo inflammatory model. We also analyzed whether the effects were caused by inhibition of nuclear factor kappa B (NF-κB) transcription factor transmigration. Of the eight imidazoles tested, methyl 1-allyl-2-(4-fluorophenyl)-5-phenyl-1H-imidazole-4-acetate (8) inhibited nitric oxide metabolites and pro-inflammatory cytokine (TNF-α, IL-6, and IL-1β) secretion in J774 macrophages stimulated with LPS. It also attenuated leukocyte migration and exudate formation in the pleural cavity of mice challenged with carrageenan. Furthermore, imidazole 8 reverted the oxidative stress pattern triggered by carrageenan in the pleural cavity by diminishing myeloperoxidase, superoxide dismutase, catalase, and glutathione S-transferase activities and reducing the production of nitric oxide metabolites and thiobarbituric acid-reactive substances. Finally, these effects can be attributed, at least in part, to the ability of this compound to prevent NF-κB transmigration. In this context, our results demonstrate that imidazole 8 has promising potential as a prototype for the development of a new anti-inflammatory drug to treat inflammatory conditions in which NF-κB and oxidative stress play a prominent role. Graphical Abstract ᅟ.

  2. 2-(2-Methyl-5-nitro-1H-imidazol-1-ylethyl 2-nitrobenzoate

    Directory of Open Access Journals (Sweden)

    Muhammad Raza Shah

    2010-03-01

    Full Text Available In the title compound, C13H12N4O6, the mean plane through the nitrobenzene forms a dihedral angle of 37.38 (15° with the plane through the imidazole ring. The crystal packing is stabilized by weak intermolecular C—H...O and C—H...N interactions together with π–π stacking interactions between nitrobenzene rings [centroid–centroid distance = 3.788 (3 Å] and between imidazole rings [centroid–centroid distance = 3.590 (2 Å].

  3. SYNTHESIS OF METAL-ORGANIC (COMPLEXES) COMPOUNDS COPPER(II)-IMIDAZOLE FOR ANTIVIRAL HIV CANDIDATE

    OpenAIRE

    Sucipto, Teguh Hari; Martak, Fahimah

    2016-01-01

    The human immunodeficiency virus (HIV) is viruses known as rotaviruses. Potential target for therapeutic is reverse transcriptase (RT), possesses an RNA dependent DNA polymerase, DNA-dependent DNA polymerase and ribonuclease H fuctions. Imidazoles have high anti-HIV inhibitory activity, some derivates of imidazole reported drugs. 8-chloro-2,3-dihydroimidazole[1,2-b] [1,4,2]benzodithiazine-5,5-dioxides and 9-chloro-2,3,4-trihydropyri-mido[1,2-b][1,4,2]benzodithi-azine-6,6-dioxides. This compou...

  4. Poly(arylene ether-co-imidazole)s as toughness modifiers for epoxy resins

    Science.gov (United States)

    Mcdaniel, Patricia D. (Inventor); Connell, John W. (Inventor)

    1994-01-01

    A toughened epoxy was prepared by reacting an epoxy resin with a poly(arylene ether-co-imidazole)s (PAEI). The epoxy resin comprises N,N,N',N'tetraglycidyl-4,4'- methylenebisbenzenamine and 4-aminophenyl sulfone. The PAEI was prepared by reacting an aromatic bisphenol, a bisphenol imidazole, and an activated aromatic dihalide or dinitro compound in the presence of potassium carbonate in a polar aprotic solvent at an elevated temperature. The epoxies which were modified with these particular PAEI's showed a significant increase in toughness with only a 10 weight percent loading of the PAEI into the epoxy. These toughened epoxies were used to prepare composites and molded parts.

  5. Structural Basis for Allosteric Regulation of GPCRs by Sodium Ions

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Wei; Chun, Eugene; Thompson, Aaron A.; Chubukov, Pavel; Xu, Fei; Katritch, Vsevolod; Han, Gye Won; Roth, Christopher B.; Heitman, Laura H.; IJzerman, Adriaan P.; Cherezov, Vadim; Stevens, Raymond C. (Scripps); (Leiden/Amsterdam); (Receptos)

    2012-08-31

    Pharmacological responses of G protein-coupled receptors (GPCRs) can be fine-tuned by allosteric modulators. Structural studies of such effects have been limited due to the medium resolution of GPCR structures. We reengineered the human A{sub 2A} adenosine receptor by replacing its third intracellular loop with apocytochrome b{sub 562}RIL and solved the structure at 1.8 angstrom resolution. The high-resolution structure allowed us to identify 57 ordered water molecules inside the receptor comprising three major clusters. The central cluster harbors a putative sodium ion bound to the highly conserved aspartate residue Asp{sup 2.50}. Additionally, two cholesterols stabilize the conformation of helix VI, and one of 23 ordered lipids intercalates inside the ligand-binding pocket. These high-resolution details shed light on the potential role of structured water molecules, sodium ions, and lipids/cholesterol in GPCR stabilization and function.

  6. Enhancing NMDA Receptor Function: Recent Progress on Allosteric Modulators

    Directory of Open Access Journals (Sweden)

    Lulu Yao

    2017-01-01

    Full Text Available The N-methyl-D-aspartate receptors (NMDARs are subtype glutamate receptors that play important roles in excitatory neurotransmission and synaptic plasticity. Their hypo- or hyperactivation are proposed to contribute to the genesis or progression of various brain diseases, including stroke, schizophrenia, depression, and Alzheimer’s disease. Past efforts in targeting NMDARs for therapeutic intervention have largely been on inhibitors of NMDARs. In light of the discovery of NMDAR hypofunction in psychiatric disorders and perhaps Alzheimer’s disease, efforts in boosting NMDAR activity/functions have surged in recent years. In this review, we will focus on enhancing NMDAR functions, especially on the recent progress in the generation of subunit-selective, allosteric positive modulators (PAMs of NMDARs. We shall also discuss the usefulness of these newly developed NMDAR-PAMs.

  7. Enzyme assays.

    Science.gov (United States)

    Brodelius, P E

    1991-02-01

    The past year or so has seen the development of new enzyme assays, as well as the improvement of existing ones. Assays are becoming more rapid and sensitive as a result of modifications such as amplification of the enzyme product(s). Recombinant DNA technology is now being recognized as a particularly useful tool in the search for improved assay systems.

  8. The therapeutic potential of allosteric ligands for free fatty acid sensitive GPCRs

    DEFF Research Database (Denmark)

    Hudson, Brian D; Ulven, Trond; Milligan, Graeme

    2013-01-01

    G protein coupled receptors (GPCRs) are the most historically successful therapeutic targets. Despite this success there are many important aspects of GPCR pharmacology and function that have yet to be exploited to their full therapeutic potential. One in particular that has been gaining attention...... in recent times is that of GPCR ligands that bind to allosteric sites on the receptor distinct from the orthosteric site of the endogenous ligand. As therapeutics, allosteric ligands possess many theoretical advantages over their orthosteric counterparts, including more complex modes of action, improved...... of identifying allosteric leads and their often flat or confusing SAR. The present review will consider the advantages and challenges associated with allosteric GPCR ligands, and examine how the particular properties of these ligands may be exploited to uncover the therapeutic potential for free fatty acid...

  9. Allosteric and orthosteric sites in CC chemokine receptor (CCR5), a chimeric receptor approach

    DEFF Research Database (Denmark)

    Thiele, Stefanie; Steen, Anne; Jensen, Pia C

    2011-01-01

    molecules often act more deeply in an allosteric mode. However, opposed to the well described molecular interaction of allosteric modulators in class C 7-transmembrane helix (7TM) receptors, the interaction in class A, to which the chemokine receptors belong, is more sparsely described. Using the CCR5...... chemokine receptor as a model system, we studied the molecular interaction and conformational interchange required for proper action of various orthosteric chemokines and allosteric small molecules, including the well known CCR5 antagonists TAK-779, SCH-C, and aplaviroc, and four novel CCR5 ago......-allosteric molecules. A chimera was successfully constructed between CCR5 and the closely related CCR2 by transferring all extracellular regions of CCR2 to CCR5, i.e. a Trojan horse that resembles CCR2 extracellularly but signals through a CCR5 transmembrane unit. The chimera bound CCR2 (CCL2 and CCL7), but not CCR5...

  10. Change in Allosteric Network Affects Binding Affinities of PDZ Domains: Analysis through Perturbation Response Scanning

    Science.gov (United States)

    Gerek, Z. Nevin; Ozkan, S. Banu

    2011-01-01

    The allosteric mechanism plays a key role in cellular functions of several PDZ domain proteins (PDZs) and is directly linked to pharmaceutical applications; however, it is a challenge to elaborate the nature and extent of these allosteric interactions. One solution to this problem is to explore the dynamics of PDZs, which may provide insights about how intramolecular communication occurs within a single domain. Here, we develop an advancement of perturbation response scanning (PRS) that couples elastic network models with linear response theory (LRT) to predict key residues in allosteric transitions of the two most studied PDZs (PSD-95 PDZ3 domain and hPTP1E PDZ2 domain). With PRS, we first identify the residues that give the highest mean square fluctuation response upon perturbing the binding sites. Strikingly, we observe that the residues with the highest mean square fluctuation response agree with experimentally determined residues involved in allosteric transitions. Second, we construct the allosteric pathways by linking the residues giving the same directional response upon perturbation of the binding sites. The predicted intramolecular communication pathways reveal that PSD-95 and hPTP1E have different pathways through the dynamic coupling of different residue pairs. Moreover, our analysis provides a molecular understanding of experimentally observed hidden allostery of PSD-95. We show that removing the distal third alpha helix from the binding site alters the allosteric pathway and decreases the binding affinity. Overall, these results indicate that (i) dynamics plays a key role in allosteric regulations of PDZs, (ii) the local changes in the residue interactions can lead to significant changes in the dynamics of allosteric regulations, and (iii) this might be the mechanism that each PDZ uses to tailor their binding specificities regulation. PMID:21998559

  11. Structural characteristics of the nonallosteric human cytosolic malic enzyme.

    Science.gov (United States)

    Hsieh, Ju-Yi; Li, Shao-Yu; Chen, Meng-Chun; Yang, Pai-Chun; Chen, Hui-Yi; Chan, Nei-Li; Liu, Jyung-Hurng; Hung, Hui-Chih

    2014-10-01

    Human cytosolic NADP(+)-dependent malic enzyme (c-NADP-ME) is neither a cooperative nor an allosteric enzyme, whereas mitochondrial NAD(P)(+)-dependent malic enzyme (m-NAD(P)-ME) is allosterically activated by fumarate. This study examines the molecular basis for the different allosteric properties and quaternary structural stability of m-NAD(P)-ME and c-NADP-ME. Multiple residues corresponding to the fumarate-binding site were mutated in human c-NADP-ME to correspond to those found in human m-NAD(P)-ME. Additionally, the crystal structure of the apo (ligand-free) human c-NADP-ME conformation was determined. Kinetic studies indicated no significant difference between the wild-type and mutant enzymes in Km,NADP, Km,malate, and kcat. A chimeric enzyme, [51-105]_c-NADP-ME, was designed to include the putative fumarate-binding site of m-NAD(P)-ME at the dimer interface of c-NADP-ME; however, this chimera remained nonallosteric. In addition to fumarate activation, the quaternary structural stability of c-NADP-ME and m-NAD(P)-ME is quite different; c-NADP-ME is a stable tetramer, whereas m-NAD(P)-ME exists in equilibrium between a dimer and a tetramer. The quaternary structures for the S57K/N59E/E73K/S102D and S57K/N59E/E73K/S102D/H74K/D78P/D80E/D87G mutants of c-NADP-ME are tetrameric, whereas the K57S/E59N/K73E/D102S m-NAD(P)-ME quadruple mutant is primarily monomeric with some dimer formation. These results strongly suggest that the structural features near the fumarate-binding site and the dimer interface are highly related to the quaternary structural stability of c-NADP-ME and m-NAD(P)-ME. In this study, we attempt to delineate the structural features governing the fumarate-induced allosteric activation of malic enzyme. Copyright © 2014 Elsevier B.V. All rights reserved.

  12. Inversion of allosteric effect of arginine on N-acetylglutamate synthase, a molecular marker for evolution of tetrapods

    Directory of Open Access Journals (Sweden)

    Cabrera-Luque Juan

    2008-09-01

    Full Text Available Abstract Background The efficient conversion of ammonia, a potent neurotoxin, into non-toxic metabolites was an essential adaptation that allowed animals to move from the aquatic to terrestrial biosphere. The urea cycle converts ammonia into urea in mammals, amphibians, turtles, snails, worms and many aquatic animals and requires N-acetylglutamate (NAG, an essential allosteric activator of carbamylphosphate synthetase I (CPSI in mammals and amphibians, and carbamylphosphate synthetase III (CPSIII in fish and invertebrates. NAG-dependent CPSI and CPSIII catalyze the formation of carbamylphosphate in the first and rate limiting step of ureagenesis. NAG is produced enzymatically by N-acetylglutamate synthase (NAGS, which is also found in bacteria and plants as the first enzyme of arginine biosynthesis. Arginine is an allosteric inhibitor of microbial and plant NAGS, and allosteric activator of mammalian NAGS. Results Information from mutagenesis studies of E. coli and P. aeruginosa NAGS was combined with structural information from the related bacterial N-acetylglutamate kinases to identify four residues in mammalian NAGS that interact with arginine. Substitutions of these four residues were engineered in mouse NAGS and into the vertebrate-like N-acetylglutamate synthase-kinase (NAGS-K of Xanthomonas campestris, which is inhibited by arginine. All mutations resulted in arginine losing the ability to activate mouse NAGS, and inhibit X. campestris NAGS-K. To examine at what point in evolution inversion of arginine effect on NAGS occur, we cloned NAGS from fish and frogs and examined the arginine response of their corresponding proteins. Fish NAGS were partially inhibited by arginine and frog NAGS were activated by arginine. Conclusion Difference in arginine effect on bacterial and mammalian NAGS most likely stems from the difference in the type of conformational change triggered by arginine binding to these proteins. The change from arginine

  13. Allosteric modulation of PS1/gamma-secretase conformation correlates with amyloid beta(42/40 ratio.

    Directory of Open Access Journals (Sweden)

    Kengo Uemura

    Full Text Available BACKGROUND: Presenilin 1(PS1 is the catalytic subunit of gamma-secretase, the enzyme responsible for the Abeta C-terminal cleavage site, which results in the production of Abeta peptides of various lengths. Production of longer forms of the Abeta peptide occur in patients with autosomal dominant Alzheimer disease (AD due to mutations in presenilin. Many modulators of gamma-secretase function have been described. We hypothesize that these modulators act by a common mechanism by allosterically modifying the structure of presenilin. METHODOLOGY/PRINCIPAL FINDINGS: To test this hypothesis we generated a genetically encoded GFP-PS1-RFP (G-PS1-R FRET probe that allows monitoring of the conformation of the PS1 molecule in its native environment in live cells. We show that G-PS1-R can be incorporated into the gamma-secretase complex, reconstituting its activity in PS1/2 deficient cells. Using Förster resonance energy transfer (FRET-based approaches we show that various pharmacological and genetic manipulations that target either gamma-secretase components (PS1, Pen2, Aph1 or gamma-secretase substrate (amyloid precursor protein, APP and are known to change Abeta(42 production are associated with a consistent conformational change in PS1. CONCLUSIONS/SIGNIFICANCE: These results strongly support the hypothesis that allosteric changes in PS1 conformation underlie changes in the Abeta(42/40 ratio. Direct measurement of physiological and pathological changes in the conformation of PS1/gamma-secretase may provide insight into molecular mechanism of Abeta(42 generation, which could be exploited therapeutically.

  14. Structural Studies and Investigation on the Activity of Imidazole-Derived Thiosemicarbazones and Hydrazones against Crop-Related Fungi

    Directory of Open Access Journals (Sweden)

    Jacqueline A. Takahashi

    2013-10-01

    Full Text Available New imidazole derived thiosemicarbazones and hydrazones were prepared by condensation of 4(5-imidazole carboxaldehyde, 4-(1H-imidazole-1-ylbenzaldehyde and 4-(1H-imidazole-1-ylacetophenone with a thiosemicarbazide or hydrazide. All compounds were characterized by quantitative elemental analysis, IR and NMR techniques. Eight structures were determined by single crystal X-ray diffraction. The antifungal activities of the compounds were evaluated. None of the compounds exhibited significant activity against Aspergillus flavus and Candida albicans, while 4(5-imidazolecarboxaldehyde thiosemicarbazone (ImT and 4-(1H-imidazole-1-ylbenzaldehyde thiosemicabazone (4ImBzT were highly and selectively active against Cladosporium cladosporioides. 4(5-Imidazolecarboxaldehyde benzoyl hydrazone (4(5ImPh, 4(5-imidazolecarboxaldehyde-para-chlorobenzoyl hydrazone (4(5ImpClPh, 4(5-imidazolecarboxaldehyde-para-nitrobenzoyl hydrazone (4(5ImpNO2Ph, 4-(imidazole-1-ylacetophenone-para-chloro-benzoyl hydrazone (4ImAcpClPh and 4-(imidazole-1-ylacetophenone-para-nitro-benzoylhydrazone (4ImAcpNO2Ph were highly active against Candida glabrata. 4(5ImpClPh and 4(5ImpNO2Ph were very effective against C. cladosporioides. In many cases, activity was superior to that of the reference compound nystatin.

  15. Structural studies and investigation on the activity of imidazole-derived thiosemicarbazones and hydrazones against crop-related fungi.

    Science.gov (United States)

    Reis, Débora C; Despaigne, Angel A Recio; Da Silva, Jeferson G; Silva, Nayane F; Vilela, Camila F; Mendes, Isolda C; Takahashi, Jacqueline A; Beraldo, Heloisa

    2013-10-14

    New imidazole derived thiosemicarbazones and hydrazones were prepared by condensation of 4(5)-imidazole carboxaldehyde, 4-(1H-imidazole-1-yl)benzaldehyde and 4-(1H-imidazole-1-yl)acetophenone with a thiosemicarbazide or hydrazide. All compounds were characterized by quantitative elemental analysis, IR and NMR techniques. Eight structures were determined by single crystal X-ray diffraction. The antifungal activities of the compounds were evaluated. None of the compounds exhibited significant activity against Aspergillus flavus and Candida albicans, while 4(5)-imidazolecarboxaldehyde thiosemicarbazone (ImT) and 4-(1H-imidazole-1-yl)benzaldehyde thiosemicabazone (4ImBzT) were highly and selectively active against Cladosporium cladosporioides. 4(5)-Imidazolecarboxaldehyde benzoyl hydrazone (4(5)ImPh), 4(5)-imidazolecarboxaldehyde-para-chlorobenzoyl hydrazone (4(5)ImpClPh), 4(5)-imidazolecarboxaldehyde-para-nitrobenzoyl hydrazone (4(5)ImpNO2Ph), 4-(imidazole-1-yl)acetophenone-para-chloro-benzoyl hydrazone (4ImAcpClPh) and 4-(imidazole-1-yl)acetophenone-para-nitro-benzoylhydrazone (4ImAcpNO2Ph) were highly active against Candida glabrata. 4(5)ImpClPh and 4(5)ImpNO2Ph were very effective against C. cladosporioides. In many cases, activity was superior to that of the reference compound nystatin.

  16. Nickel(II) complexes having Imidazol-2-ylidene-N′-phenylurea ...

    Indian Academy of Sciences (India)

    Nickel(II); imidazol-2-ylidene-N′-phenylurea; hexa-coordination; chelating ligands; hydrogen bonding .... ized by combustion analysis as well as FT-IR technique. .... arrangement of the aniline coordination with respect to the acetylacetonate ligand towards nickel ion. Hydrogen bonding (2.625 Å) was observed between the ...

  17. Poly[bis[μ-1,4-bis(imidazol-1-ylmethylbenzene]dichloridocadmium(II

    Directory of Open Access Journals (Sweden)

    Xinliang Hu

    2008-07-01

    Full Text Available The title compound, [CdCl2(C14H14N42]n, has a slightly distorted octahedral coordination geometry, formed by four N atoms from 1,4-bis(imidazol-1-ylmethylbenzene ligands and two Cl atoms, giving a two-dimensional network. The Cd atom lies on a centre of inversion.

  18. Synthesis and properties of imidazole-grafted hybrid inorganic-organic polymer membranes

    International Nuclear Information System (INIS)

    Li Siwen; Zhou Zhen; Liu Meilin; Li Wen; Ukai, Junzo; Hase, Kohei; Nakanishi, Masatsugu

    2006-01-01

    Imidazole rings were grafted on alkoxysilane with a simple nucleophilic substitute reaction to form hybrid inorganic-organic polymers with imidazole rings. Proton exchange membranes (PEM) based on these hybrid inorganic-organic polymers and H 3 PO 4 exhibit high proton conductivity and high thermal stability in an atmosphere of low relative humidity. The grafted imidazole rings improved the proton conductivity of the membranes in the high temperature range. It is found that the proton conductivities increase with H 3 PO 4 content and temperature, reaching 3.2 x 10 -3 S/cm at 110 deg. C in a dry atmosphere for a membrane with 1 mole of imidazole ring and 7 moles of H 3 PO 4 . The proton conductivity increases with relative humidity (RH) as well, reaching 4.3 x 10 -2 S/cm at 110 deg. C when the RH is increased to about 20%. Thermogravimetric analysis (TGA) indicates that these membranes are thermally stable up to 250 deg. C in dry air, implying that they have a good potential to be used as the membranes for high-temperature PEM fuel cells

  19. Antibacterial activity of synthesized 2,4,5-trisubstituted imidazole derivatives

    Digital Repository Service at National Institute of Oceanography (India)

    Khan, M.S.; Siddiqui, S.A.; Siddiqui, M.S.R.A.; Goswami, U.; Srinivasan, K.V.; Khan, M.I.

    release or inhibiting the p38 MAP kinase (1), anti-allergic activity (2) and analgesic activity (3). They are also sensitizers of multidrug-resistant cancer cells (4), pesticides (5), antibiotics (6) or sodium-channel mod- ulators (7). Some imidazole...

  20. Recent Advances on Dark and Light-Activated Cytotoxity of Imidazole-Containing Ruthenium Complexes.

    Science.gov (United States)

    Liu, Ping; Jia, Jia; Zhao, Yue; Wang, Ke-Zhi

    2016-01-01

    Imidazole derivatives have known to possess a diverse range of pharmacological activity. In particular, one of ruthenium-based derivatives, imidazolium [trans-RuCl4(1H-imidazole)(DMSOS)] (NAMI-A) which is now in clinical trials, opens a new avenue for developing promising ruthenium-based anticancer drugs alternative to Cisplatin. This mini-review overviews some representative examples of imidazole-containing ruthenium complexes (ICRCs) with in vitro anticancer activities. Special attention is paid on ICRCs with the activities more potent than Cisplatin, and their correlation with their DNA binding properties in the context of possible cancer chemotherapeutic applications. The ICRCs are divided into two main categories according to their dark and light activated cytotoxicity; the former case is further clarified into mononuclear complexes including tris(bidentate polypyridyl) ruthenium complexes and those containing monodentatively coordinative imidazole ligands as well as polynuclear complexes. The perspective, challenges and future efforts for investigations into ICRCs are pointed out or suggested.

  1. Green synthesis of tri/tetrasubstituted 1H-imidazoles and 2,3 ...

    Indian Academy of Sciences (India)

    cosmetics, pesticides, disinfectants, agrochemicals, dy- estuffs and antifreeze.1 In particular, derivatives of imi- dazoles and hydroquinazolins are used as reagents in industry.2 The five-membered imidazole ring is one of the important substructures found in a large number of natural products and pharmacologically active ...

  2. Changes in the hydration structure of imidazole upon protonation: Neutron scattering and molecular simulations

    Czech Academy of Sciences Publication Activity Database

    Duboué-Dijon, Elise; Mason, Philip E.; Fischer, H. E.; Jungwirth, Pavel

    2017-01-01

    Roč. 146, č. 18 (2017), č. článku 185102. ISSN 0021-9606 R&D Projects: GA ČR(CZ) GBP208/12/G016 Institutional support: RVO:61388963 Keywords : imidazole protonation * molecular dynamics * neutron scattering Subject RIV: CF - Physical ; Theoretical Chemistry OBOR OECD: Physical chemistry Impact factor: 2.965, year: 2016

  3. Potential energy surface of the reaction of imidazole with peroxynitrite: Density functional theory study

    Science.gov (United States)

    Gogonea, Valentin

    This article presents a theoretical investigation of the reaction mechanism of imidazole nitration by peroxynitrite using density functional theory calculations. Understanding this reaction mechanism will help in elucidating the mechanism of guanine nitration by peroxynitrite, which is one of the assumed chemical pathways for damaging DNA in cells. This work focuses on the analysis of the potential energy surface (PES) for this reaction in the gas phase. Calculations were carried out using Hartree-Fock (HF) and density functional theory (DFT) Hamiltonians with double-zeta basis sets ranging from 6-31G(d) to 6-31++G(d,p), and the triple-zeta basis set 6-311G(d). The computational results reveal that the reaction of imidazole with peroxynitrite in gas phase produces the following species: (i) hydroxide ion and 2-nitroimidazole, (ii) hydrogen superoxide ion and 2-nitrosoimidazole, and (iii) water and 2-nitroimidazolide. The rate-determining step is the formation of a short-lived intermediate in which the imidazole C2 carbon is covalently bonded to peroxynitrite nitrogen. Three short-lived intermediates were found in the reaction path. These intermediates are involved in a proton-hopping transport from C2 carbon to the terminal oxygen of the OO moiety of peroxynitrite via the nitroso (ON) oxygen. Both HF and DFT calculations (using the Becke3-Lee-Yang-Parr functional) lead to similar reaction paths for proton transport, but the landscape details of the PES for HF and DFT calculations differ. This investigation shows that the reaction of imidazole with peroxynitrite produces essentially the same types of products (nitro- and nitroso-) as observed experimentally in the reaction of guanine with peroxynitrite, which makes the former reaction a good model to study by computation the essential characteristics of the latter reaction. Nevertheless, the computationally determined activation energy for imidazole nitration by peroxynitrite in the gas phase is 84.1 kcal

  4. Testing biochemistry revisited: how in vivo metabolism can be understood from in vitro enzyme kinetics.

    Directory of Open Access Journals (Sweden)

    Karen van Eunen

    Full Text Available A decade ago, a team of biochemists including two of us, modeled yeast glycolysis and showed that one of the most studied biochemical pathways could not be quite understood in terms of the kinetic properties of the constituent enzymes as measured in cell extract. Moreover, when the same model was later applied to different experimental steady-state conditions, it often exhibited unrestrained metabolite accumulation.Here we resolve this issue by showing that the results of such ab initio modeling are improved substantially by (i including appropriate allosteric regulation and (ii measuring the enzyme kinetic parameters under conditions that resemble the intracellular environment. The following modifications proved crucial: (i implementation of allosteric regulation of hexokinase and pyruvate kinase, (ii implementation of V(max values measured under conditions that resembled the yeast cytosol, and (iii redetermination of the kinetic parameters of glyceraldehyde-3-phosphate dehydrogenase under physiological conditions.Model predictions and experiments were compared under five different conditions of yeast growth and starvation. When either the original model was used (which lacked important allosteric regulation, or the enzyme parameters were measured under conditions that were, as usual, optimal for high enzyme activity, fructose 1,6-bisphosphate and some other glycolytic intermediates tended to accumulate to unrealistically high concentrations. Combining all adjustments yielded an accurate correspondence between model and experiments for all five steady-state and dynamic conditions. This enhances our understanding of in vivo metabolism in terms of in vitro biochemistry.

  5. Spectral studies on mixed ligand complexes of sodium dinitro-bis(acetylacetonato) cobaltate(iii) with imida-zole ligands

    Science.gov (United States)

    Roychaudhury, Goutam; Dash, Kailash C.

    1980-11-01

    A number of mixed ligand complexes, nitro(imidazole) bis(acetylacetonato) cobaltate(III), [Co(acac) 2 (NO 2 ) 2 (L)] (L = imidazole or substituted imidazole) have been synthesised and characterised on the basis of chemical analyses, IR, electronic, mass and nuclear ( 1H and 13C) magnetic resonance spectra as well as TGA and DTA data. All complexes are non-electrolytic and possess a trans octahedral structure. The NO 2- group is coordinated through the N atom. Though the 1H NMR data of fresh CDCl 3 solutions of complexes confirm the trans structure, slow isomerisation to the cis configuration is observed at room temperature.

  6. Racing pigeons: a reservoir for nitro-imidazole-resistant Trichomonas gallinae.

    Science.gov (United States)

    Rouffaer, L O; Adriaensen, C; De Boeck, C; Claerebout, E; Martel, A

    2014-06-01

    Trichomonas gallinae , the cause of avian trichomonosis, is most commonly found in the order Columbiformes. Racing pigeons are often treated preventively with nitro-imidazoles, which could result in the emergence of resistant isolates, and these isolates can be a threat to wildlife when exchanges occur. The sequence type of 16 T. gallinae isolates obtained from racing pigeons and 15 isolates from wild pigeons was determined based on the ITS1/5.8S rRNA/ITS2 region sequence. In addition, the resistance profiles of these isolates against 5 different nitro-imidazoles (metronidazole, dimetridazole, ronidazole, tinidazole, and carnidazole) were determined. Two different Trichomonas sequence types were isolated. Sequence type A isolates were recovered from racing and wild pigeons, in contrast to sequence type B, which was only isolated from wild pigeons. Isolates with sequence type B were all susceptible to the tested nitro-imidazoles, except for tinidazole resistance in 3 isolates. Resistance to the nitro-imidazoles was observed more frequently in isolates obtained from racing pigeons than from wild pigeons, with most isolates belonging to sequence type A. A higher percentage of the sequence type A isolated from racing pigeons, in comparison with those isolated from the wild pigeons, were resistant to the nitro-imidazoles and displayed higher mean lethal concentration (MLC) values. Two isolates belonging to sequence type A, 1 recovered from a racing pigeon and 1 from a wild pigeon, displayed a similar resistance pattern, suggesting a potential exchange of resistant isolates between racing pigeons and wild pigeons.

  7. Evidence for allosterism in ribulose-1,5-bisphosphate carboxylase/oxygenase from comfrey

    International Nuclear Information System (INIS)

    Mueller, D.D.; Bolden, T.D.

    1986-01-01

    Evidence has been obtained suggesting that ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) is an allosteric enzyme in the sense that it shows cooperative active site binding, cooperative interactions between the activation and active sites and significant binding of some metabolites at a second site. Investigation of the binding of a potent competitive inhibitor. 2-carboxymannitol-1,6-bisphosphate (CMBP) by 31 P-NMR indicated essentially 1:1 binding with the active sites of comfrey RuBisCo. Among the interactions of competitive inhibitors, as measured by difference UV spectroscopy, the binding curves for ortho-phosphate and ribose-5-phosphate were better fitted by a Monod-Wyman-Changeux model than by an independent site model, whereas the binding of CMBP and 2-phosphoglycolate were not. Difference UV methods also were used to study activation by CO 2 which at pH 7.9 in 10 mM MgCl 2 showed positive cooperativity with k = 100 +/- 3 μM (based on pK/sub a/ = 6.4 for the CO 2 -HCO 3 - equilibrium) and L = 3.5 +/- 0.7. Addition of saturating amounts of CMBP and lowering the MgCl 2 to 2 mM still gave a sigmoidal curve but it was shifted to higher CO 2 concentrations (k = 124 +/- 2 μM and L = 31 +/- 3). In the absence of CMBP the same conditions gave k = 26 +/- 2 μM for L = 3.5. Conversely, k was 0.96 +/- 0.08 μM for CMBP in 0.5 mM MgCl 2 without added NaHCO 3 but was 21 +/- 0.06 μM in 10 MgCl 2 and 2 mM NaHCO 3 , pH 7.3

  8. Stochastic thermodynamics of a chemical nanomachine: The channeling enzyme tryptophan synthase.

    Science.gov (United States)

    Loutchko, Dimitri; Eisbach, Maximilian; Mikhailov, Alexander S

    2017-01-14

    The enzyme tryptophan synthase is characterized by a complex pattern of allosteric interactions that regulate the catalytic activity of its two subunits and opening or closing of their ligand gates. As a single macromolecule, it implements 13 different reaction steps, with an intermediate product directly channeled from one subunit to another. Based on experimental data, a stochastic model for the operation of tryptophan synthase has been earlier constructed [D. Loutchko, D. Gonze, and A. S. Mikhailov, J. Phys. Chem. B 120, 2179 (2016)]. Here, this model is used to consider stochastic thermodynamics of such a chemical nanomachine. The Gibbs energy landscape of the internal molecular states is determined, the production of entropy and its flow within the enzyme are analyzed, and the information exchange between the subunits resulting from allosteric cross-regulations and channeling is discussed.

  9. Coarse-grained molecular simulations of allosteric cooperativity

    Energy Technology Data Exchange (ETDEWEB)

    Nandigrami, Prithviraj; Portman, John J. [Department of Physics, Kent State University, Kent, Ohio 44242 (United States)

    2016-03-14

    Interactions between a protein and a ligand are often accompanied by a redistribution of the population of thermally accessible conformations. This dynamic response of the protein’s functional energy landscape enables a protein to modulate binding affinities and control binding sensitivity to ligand concentration. In this paper, we investigate the structural origins of binding affinity and allosteric cooperativity of binding two Ca{sup 2+} ions to each domain of Calmodulin (CaM) through simulations of a simple coarse-grained model. In this model, the protein’s conformational transitions between open and closed conformational ensembles are simulated explicitly and ligand binding and unbinding are treated implicitly within the grand canonical ensemble. Ligand binding is cooperative because the binding sites are coupled through a shift in the dominant conformational ensemble upon binding. The classic Monod-Wyman-Changeux model of allostery with appropriate binding free energies to the open and closed ensembles accurately describes the simulated binding thermodynamics. The simulations predict that the two domains of CaM have distinct binding affinity and cooperativity. In particular, the C-terminal domain binds Ca{sup 2+} with higher affinity and greater cooperativity than the N-terminal domain. From a structural point of view, the affinity of an individual binding loop depends sensitively on the loop’s structural compatibility with the ligand in the bound ensemble, as well as the conformational flexibility of the binding site in the unbound ensemble.

  10. Allosteric potentiation of quisqualate receptors by a nootropic drug aniracetam.

    Science.gov (United States)

    Ito, I; Tanabe, S; Kohda, A; Sugiyama, H

    1990-05-01

    1. Allosteric potentiation of the ionotropic quisqualate (iQA) receptor by a nootropic drug aniracetam (1-p-anisoyl-2-pyrrolidinone) was investigated using Xenopus oocytes injected with rat brain mRNA and rat hippocampal slices. 2. Aniracetam potentiates the iQA responses induced in Xenopus oocytes by rat brain mRNA in a reversible manner. This effect was observed above the concentrations of 0.1 mM. Kainate. N-methyl-D-aspartate and gamma-aminobutyric acid responses induced in the same oocytes were not affected. 3. The specific potentiation of iQA responses was accompanied by an increase in the conductance change of iQA and alpha-amino-3-hydroxy-5-methyl-4-isoxazole-propionic acid (AMPA) responses, but the affinity of receptors for agonist and the ion-selectivity of the channels (reversal potentials) were not changed. 4. Aniracetam reversibly potentiated the iQA responses recorded intracellularly from the pyramidal cells in the CA1 region of rat hippocampal slices. The excitatory postsynaptic potentials (EPSPs) in Schaffer collateral-commissural-CA1 synapses were also potentiated by aniracetam. 5. Population EPSPs recorded in the mossy fibre-CA3 synapses as well as Schaffer-commissural synapses were also potentiated by aniracetam. The amplitudes of the potentiation were not changed by the formation of long-term potentiation.

  11. Synthesis and characterization of new chiral ketopinic acid-derived catalysts immobilized on polystyrene-bound imidazole

    Directory of Open Access Journals (Sweden)

    Hassan Yusuf

    2017-02-01

    Full Text Available Four new chiral ketopinic acid-derived catalysts were anchored on a polystyrene-bound imidazole via non-covalent bond. The resulting heterogeneous catalysts were successfully characterized using IR, SEM, and TGA analyses.

  12. Structural basis for modulation of a G-protein-coupled receptor by allosteric drugs

    Science.gov (United States)

    Dror, Ron O.; Green, Hillary F.; Valant, Celine; Borhani, David W.; Valcourt, James R.; Pan, Albert C.; Arlow, Daniel H.; Canals, Meritxell; Lane, J. Robert; Rahmani, Raphaël; Baell, Jonathan B.; Sexton, Patrick M.; Christopoulos, Arthur; Shaw, David E.

    2013-11-01

    The design of G-protein-coupled receptor (GPCR) allosteric modulators, an active area of modern pharmaceutical research, has proved challenging because neither the binding modes nor the molecular mechanisms of such drugs are known. Here we determine binding sites, bound conformations and specific drug-receptor interactions for several allosteric modulators of the M2 muscarinic acetylcholine receptor (M2 receptor), a prototypical family A GPCR, using atomic-level simulations in which the modulators spontaneously associate with the receptor. Despite substantial structural diversity, all modulators form cation-π interactions with clusters of aromatic residues in the receptor extracellular vestibule, approximately 15Å from the classical, `orthosteric' ligand-binding site. We validate the observed modulator binding modes through radioligand binding experiments on receptor mutants designed, on the basis of our simulations, either to increase or to decrease modulator affinity. Simulations also revealed mechanisms that contribute to positive and negative allosteric modulation of classical ligand binding, including coupled conformational changes of the two binding sites and electrostatic interactions between ligands in these sites. These observations enabled the design of chemical modifications that substantially alter a modulator's allosteric effects. Our findings thus provide a structural basis for the rational design of allosteric modulators targeting muscarinic and possibly other GPCRs.

  13. Cannabidiol is a negative allosteric modulator of the cannabinoid CB1 receptor.

    Science.gov (United States)

    Laprairie, R B; Bagher, A M; Kelly, M E M; Denovan-Wright, E M

    2015-10-01

    Cannabidiol has been reported to act as an antagonist at cannabinoid CB1 receptors. We hypothesized that cannabidiol would inhibit cannabinoid agonist activity through negative allosteric modulation of CB1 receptors. Internalization of CB1 receptors, arrestin2 recruitment, and PLCβ3 and ERK1/2 phosphorylation, were quantified in HEK 293A cells heterologously expressing CB1 receptors and in the STHdh(Q7/Q7) cell model of striatal neurons endogenously expressing CB1 receptors. Cells were treated with 2-arachidonylglycerol or Δ(9)-tetrahydrocannabinol alone and in combination with different concentrations of cannabidiol. Cannabidiol reduced the efficacy and potency of 2-arachidonylglycerol and Δ(9)-tetrahydrocannabinol on PLCβ3- and ERK1/2-dependent signalling in cells heterologously (HEK 293A) or endogenously (STHdh(Q7/Q7)) expressing CB1 receptors. By reducing arrestin2 recruitment to CB1 receptors, cannabidiol treatment prevented internalization of these receptors. The allosteric activity of cannabidiol depended upon polar residues being present at positions 98 and 107 in the extracellular amino terminus of the CB1 receptor. Cannabidiol behaved as a non-competitive negative allosteric modulator of CB1 receptors. Allosteric modulation, in conjunction with effects not mediated by CB1 receptors, may explain the in vivo effects of cannabidiol. Allosteric modulators of CB1 receptors have the potential to treat CNS and peripheral disorders while avoiding the adverse effects associated with orthosteric agonism or antagonism of these receptors. © 2015 The British Pharmacological Society.

  14. Causality, transfer entropy, and allosteric communication landscapes in proteins with harmonic interactions.

    Science.gov (United States)

    Hacisuleyman, Aysima; Erman, Burak

    2017-06-01

    A fast and approximate method of generating allosteric communication landscapes in proteins is presented by using Schreiber's entropy transfer concept in combination with the Gaussian Network Model of proteins. Predictions of the model and the allosteric communication landscapes generated show that information transfer in proteins does not necessarily take place along a single path, but an ensemble of pathways is possible. The model emphasizes that knowledge of entropy only is not sufficient for determining allosteric communication and additional information based on time delayed correlations should be introduced, which leads to the presence of causality in proteins. The model provides a simple tool for mapping entropy sink-source relations into pairs of residues. By this approach, residues that should be manipulated to control protein activity may be determined. This should be of great importance for allosteric drug design and for understanding the effects of mutations on function. The model is applied to determine allosteric communication in three proteins, Ubiquitin, Pyruvate Kinase, and the PDZ domain. Predictions are in agreement with molecular dynamics simulations and experimental evidence. Proteins 2017; 85:1056-1064. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  15. Binding and discerning interactions of PTP1B allosteric inhibitors: novel insights from molecular dynamics simulations.

    Science.gov (United States)

    Shinde, Ranajit Nivrutti; Sobhia, M Elizabeth

    2013-09-01

    The α7 helix is either disordered or missing in the three co-crystal structures of allosteric inhibitors with protein tyrosine phosphatase 1B (PTP1B). It was modeled in each complex using the open form of PTP1B structure and studied using molecular dynamics (MD) simulations for 25 ns. B-factor analysis of the residues sheds light on its disordered nature in the co-crystal structures. Further, the ability of inhibitors to act as allosteric inhibitor was studied and established using novel hydrogen bond criteria. The MD simulations were utilized to determine the relative importance of electrostatic and hydrophobic component in to the binding of inhibitors. It was revealed that the hydrophobic interactions predominantly drive the molecular recognition of these inhibitors. Per residue energy decomposition analysis attributed dissimilar affinities of three inhibitors to the several hydrogen bonds and non-bonded interactions. Among the secondary structure elements that surround the allosteric site, helices α6, α7 and loop α6-α7 were notorious in providing variable affinities to the inhibitors. A novel hydrophobic pocket lined by the α7 helix residues Val287, Asn289 and Trp291 was identified in the allosteric site. This study provides useful insights for the rational design of high affinity PTP1B allosteric inhibitors. Copyright © 2013 Elsevier Inc. All rights reserved.

  16. Enzyme immunoassay

    DEFF Research Database (Denmark)

    Feldt-Rasmussen, B; Dinesen, B; Deckert, M

    1985-01-01

    An enzyme linked immunoadsorbent assay for urinary albumin using commercially available reagents is described. The assay range is 2.5-120 micrograms/l. When samples are analysed in two standard dilutions, the assayable albumin concentration range is 2.5-240 mg/l, covering the clinical range from...

  17. Synthesis, chemical and biological properties of the new mono- and bis-derivatives of imidazoles

    Directory of Open Access Journals (Sweden)

    E. V. Welchinska

    2014-12-01

    Full Text Available The aim of research. The problem of finding effective antitumour medical preparation with low toxicity is an important issue of medical and pharmaceutical chemistry. Knowledge of cancer cell features and its metabolism enables to predict the direction of chemical and biological research, to conduct a targeted synthesis of potential drugs, and to assess their applicability in oncological practice as antitumor agents. The purpose of work is to explain preformed heterocycles as purines, its synthesis and investigation of chemical and biological properties. After construction of the potential active structures we proposed the new method of original derivatives synthesis which are received on the base of imidazole, from one side, and fluorocontaining common anesthetic halothane (2-bromo-1,1,1-trifluoro-2-chloroethane from other side. Molecular complex of more perspective biologically active bis-imidazole with antitumour bacterial lectine has been received. With the purpose to synthesize potential antitumour compounds on the base of halothane and imidazole, new convenient methods for the preparation of original heterocyclic derivatives of imidazole have been described. The structure and composition of synthesized compound has been confirmed by the methods of elemental analysis, IR- and NMRІН-spectra. Materials and methods. The majority of the absolute organic solvents (benzene, dimethylformamide, ethyl ester employed in the present studies were distilled before their use. Organic solvents were dried over anhydrous magnesium sulfate or metallic sodium. Gas-liquid chromatography was carried out by Perkin Elmer chromatograph with UV-detector ("Perkin", Germany. IR spectra were recorded in a UR-20 spectrometer ("Charles Ceise Hena", Germany. The 1HNMR spectra were recorded in DMSO-d6 on a 200 MHz BrakerWP-200 ("Braker", Switzerland or Varian T-60 spectrometer ("Varian", USA. Investigation of critical toxicity of new compounds was carried out at

  18. Purification, kinetic behavior, and regulation of NAD(P)+ malic enzyme of tumor mitochondria.

    Science.gov (United States)

    Moreadith, R W; Lehninger, A L

    1984-05-25

    The purification and kinetic characterization of an NAD(P)+-malic enzyme from 22aH mouse hepatoma mitochondria are described. The enzyme was purified 328-fold with a final yield of 51% and specific activity of 38.1 units/mg of protein by employing DEAE-cellulose chromatography and an ATP affinity column. Sephadex G-200 chromatography yielded a native Mr = 240,000. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis revealed a major subunit with Mr = 61,000, suggesting a tetrameric structure, and also showed that the preparation contained less than 10% polypeptide impurities. Use of the ATP affinity column required the presence of MnCl2 and fumarate (an allosteric activator) in the elution buffers. In the absence of fumarate, the Michaelis constants for malate, NAD+, and NADP+ were 3.6 mM, 55 microM, and 72 microM, respectively; in the presence of fumarate (2 mM), the constants were 0.34 mM, 9 microM, and 13 microM, respectively. ATP was shown to be an allosteric inhibitor, competitive with malate. However, the inhibition by ATP displayed hyperbolic competitive kinetics with a KI (ATP) of 80 microM (minus fumarate) and 0.5 mM (plus 2 mM fumarate). The allosteric properties of the enzyme are integrated into a rationale for its specific role in the pathways of malate and glutamate oxidation in tumor mitochondria.

  19. Design of Elastic Networks with Evolutionary Optimized Long-Range Communication as Mechanical Models of Allosteric Proteins.

    Science.gov (United States)

    Flechsig, Holger

    2017-08-08

    Allosteric effects often underlie the activity of proteins, and elucidating generic design aspects and functional principles unique to allosteric phenomena represent a major challenge. Here an approach consisting of the in silico design of synthetic structures, which, as the principal element of allostery, encode dynamical long-range coupling among two sites, is presented. The structures are represented by elastic networks, similar to coarse-grained models of real proteins. A strategy of evolutionary optimization was implemented to iteratively improve allosteric coupling. In the designed structures, allosteric interactions were analyzed in terms of strain propagation, and simple pathways that emerged during evolution were identified as signatures through which long-range communication was established. Moreover, robustness of allosteric performance with respect to mutations was demonstrated. As it turned out, the designed prototype structures reveal dynamical properties resembling those found in real allosteric proteins. Hence, they may serve as toy models of complex allosteric systems, such as proteins. Application of the developed modeling scheme to the allosteric transition in the myosin V molecular motor was also demonstrated. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  20. Mitochondria Targeted Nanoscale Zeolitic Imidazole Framework-90 for ATP Imaging in Live Cells.

    Science.gov (United States)

    Deng, Jingjing; Wang, Kai; Wang, Ming; Yu, Ping; Mao, Lanqun

    2017-04-26

    Zeolitic imidazole frameworks (ZIFs) are an emerging class of functional porous materials with promising biomedical applications such as molecular sensing and intracellular drug delivery. We report herein the first example of using nanoscale ZIFs (i.e., ZIF-90), self-assembled from Zn 2+ and imidazole-2-carboxyaldehyde, to target subcellular mitochondria and image dynamics of mitochondrial ATP in live cells. Encapsulation of fluorescent Rhodamine B (RhB) into ZIF-90 suppresses the emission of RhB, while the competitive coordination between ATP and the metal node of ZIF-90 dissembles ZIFs, resulting in the release of RhB for ATP sensing. With this method, we are able to image mitochondrial ATP in live cells and study the ATP level fluctuation in cellular glycolysis and apoptosis processes. The strategy reported here could be further extended to tune nanoscale ZIFs inside live cells for targeted delivery of therapeutics to subcellular organelles for advanced biomedical applications.

  1. Highly-phosphorescent tungsten(0) carbonyl pyridyl-imidazole complexes as photosensitisers.

    Science.gov (United States)

    Lee, Jia Jin; Yap, Chew Pheng; Chwee, Tsz Sian; Fan, Wai Yip

    2017-08-22

    Photoluminescence data are reported for two W(CO) 4 L complexes (L = 2-(1H-imidazol-2-yl)pyridine and 2-(2'-pyridyl)benzimidazole) in room-temperature solutions. The bidentate ligands consist of a pyridine and an imidazole moiety connected by a C-C bond. The complexes have been found to exhibit enhanced phosphorescence from the metal-to-ligand charge transfer (MLCT) excited state with quantum yields in the order of 10 -3 , almost two orders of magnitude higher than those reported for W(CO) 4 (diimine) complexes. One of the complexes W(CO) 4 (2-(2'-pyridyl)benzimidazole) can serve as an efficient visible-light photosensitiser for the isomerisation of aromatic alkenes with efficiency comparable to and even exceeding that of the well-studied ruthenium tris-bipyridine complex, Ru(bpy)Cl 2 .

  2. Allosteric activation of membrane-bound glutamate receptors using coordination chemistry within living cells

    Science.gov (United States)

    Kiyonaka, Shigeki; Kubota, Ryou; Michibata, Yukiko; Sakakura, Masayoshi; Takahashi, Hideo; Numata, Tomohiro; Inoue, Ryuji; Yuzaki, Michisuke; Hamachi, Itaru

    2016-10-01

    The controlled activation of proteins in living cells is an important goal in protein-design research, but to introduce an artificial activation switch into membrane proteins through rational design is a significant challenge because of the structural and functional complexity of such proteins. Here we report the allosteric activation of two types of membrane-bound neurotransmitter receptors, the ion-channel type and the G-protein-coupled glutamate receptors, using coordination chemistry in living cells. The high programmability of coordination chemistry enabled two His mutations, which act as an artificial allosteric site, to be semirationally incorporated in the vicinity of the ligand-binding pockets. Binding of Pd(2,2‧-bipyridine) at the allosteric site enabled the active conformations of the glutamate receptors to be stabilized. Using this approach, we were able to activate selectively a mutant glutamate receptor in live neurons, which initiated a subsequent signal-transduction pathway.

  3. Dynamic Coupling and Allosteric Networks in the α Subunit of Heterotrimeric G Proteins.

    Science.gov (United States)

    Yao, Xin-Qiu; Malik, Rabia U; Griggs, Nicholas W; Skjærven, Lars; Traynor, John R; Sivaramakrishnan, Sivaraj; Grant, Barry J

    2016-02-26

    G protein α subunits cycle between active and inactive conformations to regulate a multitude of intracellular signaling cascades. Important structural transitions occurring during this cycle have been characterized from extensive crystallographic studies. However, the link between observed conformations and the allosteric regulation of binding events at distal sites critical for signaling through G proteins remain unclear. Here we describe molecular dynamics simulations, bioinformatics analysis, and experimental mutagenesis that identifies residues involved in mediating the allosteric coupling of receptor, nucleotide, and helical domain interfaces of Gαi. Most notably, we predict and characterize novel allosteric decoupling mutants, which display enhanced helical domain opening, increased rates of nucleotide exchange, and constitutive activity in the absence of receptor activation. Collectively, our results provide a framework for explaining how binding events and mutations can alter internal dynamic couplings critical for G protein function. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

  4. Discovery and Characterization of Biased Allosteric Agonists of the Chemokine Receptor CXCR3

    DEFF Research Database (Denmark)

    Milanos, Lampros; Brox, Regine; Frank, Theresa

    2016-01-01

    In this work we report a design, synthesis, and detailed functional characterization of unique strongly biased allosteric agonists of CXCR3 that contain tetrahydroisoquinoline carboxamide cores. Compound 11 (FAUC1036) is the first strongly biased allosteric agonist of CXCR3 that selectively induces...... weak chemotaxis and leads to receptor internalization and the β-arrestin 2 recruitment with potency comparable to that of the chemokine CXCL11 without any activation of G proteins. A subtle structural change (addition of a methoxy group, 14 (FAUC1104)) led to a contrasting biased allosteric partial...... agonist that activated solely G proteins, induced chemotaxis, but failed to induce receptor internalization or β-arrestin 2 recruitment. Concomitant structure-activity relationship studies indicated very steep structure-activity relationships, which steer the ligand bias between the β-arrestin 2 and G...

  5. Isotope effect studies of the chemical mechanism of nicotinamide adenine dinucleotide malic enzyme from Crassula

    International Nuclear Information System (INIS)

    Grissom, C.B.; Willeford, O.; Wedding, R.T.

    1987-01-01

    The 13 C primary kinetic isotope effect on the decarboxylation of malate by nicotinamide adenine dinucleotide malic enzyme from Crassula argentea is 1.0199 +/- 0.0006 with proteo L-malate-2-H and 1.0162 +/- 0.0003 with malate-2-d. The primary deuterium isotope effect is 1.45 +/- 0.10 on V/K and 1.93 +/- 0.13 on V/sub max/. This indicates a stepwise conversion of malate to pyruvate and CO 2 with hydride transfer preceding decarboxylation, thereby suggesting a discrete oxaloacetate intermediate. This is in agreement with the stepwise nature of the chemical mechanism of other malic enzymes despite the Crassula enzyme's inability to reduce or decarboxylate oxaloacetate. Differences in morphology and allosteric regulation between enzymes suggest specialization of the Crassula malic enzyme for the physiology of crassulacean and acid metabolism while maintaining the catalytic events founds in malic enzymes from animal sources

  6. Tioconazole, a new imidazole-antifungal agent for the treatment of dermatomycoses. Antifungal and pharmacologic properties.

    Science.gov (United States)

    Marriott, M S; Baird, J R; Brammer, K W; Faulkner, J K; Halliwell, G; Jevons, S; Tarbit, M H

    1983-01-01

    Tioconazole is a new imidazole antifungal agent with broad-spectrum activity. Its in vitro activity against common dermal pathogens is generally better than miconazole by a factor of 2-8. This activity is paralleled by good topical efficacy in a guinea pig dermatomycosis model. Pharmacokinetic studies in animals have demonstrated minimal systemic exposure following dermal application. Acute general pharmacology studies have shown that the compound is well tolerated in animals and unlikely to produce side-effects in man.

  7. cis-Tetra­chloridobis(1H-imidazole-κN 3)platinum(IV)

    Science.gov (United States)

    Bokach, Nadezhda A.; Kukushkin, Vadim Yu.; Izotova, Yulia A.; Usenko, Natalia I.; Haukka, Matti

    2012-01-01

    In the title complex, cis-[PtCl4(C3H4N2)2], the PtIV ion lies on a twofold rotation axis and is coordinated in a slightly distorted octa­hedral geometry. The dihedral angle between the imidazole rings is 69.9 (2)°. In the crystal, mol­ecules are linked by N—H⋯Cl hydrogen bonds, forming a three-dimensional network. PMID:22590070

  8. cis-Tetrachloridobis(1H-imidazole-κN3platinum(IV

    Directory of Open Access Journals (Sweden)

    Vadim Yu. Kukushkin

    2012-05-01

    Full Text Available In the title complex, cis-[PtCl4(C3H4N22], the PtIV ion lies on a twofold rotation axis and is coordinated in a slightly distorted octahedral geometry. The dihedral angle between the imidazole rings is 69.9 (2°. In the crystal, molecules are linked by N—H...Cl hydrogen bonds, forming a three-dimensional network.

  9. Tuning the crystal morphology and size of zeolitic imidazolate framework-8 in aqueous solution by surfactants

    KAUST Repository

    Pan, Yichang

    2011-01-01

    Herein we report a facile synthesis method using surfactant cetyltrimethylammonium bromide (CTAB) as a capping agent for controlling the crystal size and morphology of zeolitic imidazolate framework-8 (ZIF-8) crystals in aqueous systems. The particle sizes can be precisely adjusted from ca. 100 nm to 4 μm, and the morphology can be changed from truncated cubic to rhombic dodecahedron. This journal is © The Royal Society of Chemistry.

  10. Synthesis and antimicrobial activity of amido linked pyrrolyl and pyrazolyl-oxazoles, thiazoles and imidazoles.

    Science.gov (United States)

    Padmavathi, V; Prema Kumari, C; Venkatesh, B C; Padmaja, A

    2011-11-01

    A new class of amido linked bis heterocycles viz., pyrrolyl/pyrazolyl-oxazoles, thiazoles and imidazoles were prepared by 1,3-dipolar cycloaddition of TosMIC and diazomethane to the respective cinnamamide derivatives and screened for antimicrobial activity. The chlorosubstituted imidazolyl cinnamamide (6c) is the most potential antimicrobial agent as it displayed strong antibacterial activity against Bacillus subtilis and antifungal activity against Penicillium chrysogenum. Copyright © 2011 Elsevier Masson SAS. All rights reserved.

  11. Neutral alkaline-metal and alkaline-earth-metal derivatives of imidazole and benzimidazole.

    Science.gov (United States)

    Blanco, Fernando; Lloyd, David G; Alkorta, Ibon; Elguero, José

    2014-06-12

    A theoretical study of the minima and connecting transition states of the neutral complexes formed by alkaline-metal and alkaline-earth-metal derivatives of imidazolate and benzimidazolate anions has been carried out using B3LYP/6-31+G(d,p), B3LYP/6-311+G(3df,2p), and G3B3 methods. Two and three nondegenerated minima and two and four TS structures have been identified for imidazole and benzimidazole derivatives, respectively. The most stable minima of the alkaline-metal derivatives of both systems correspond to the metal interacting with the imidazole ring, whereas in the alkaline-earth-metal derivatives, the preferred minima depend on the substituent. A remarkable feature of some minima is the fact that some of the metal-aromatic interactions follow the classical π-cation pattern, even though the global structure corresponds to a neutral salt, constituting a class of noncovalent interaction of great interest in the chemistry of aromatic and heterocyclic complexes. A CSD search has confirmed that the two bonding modes, N-σ and π, are present in the solid phase. The π mode has been analyzed by comparison with other azoles.

  12. Hydrogen-deuterium exchange in imidazole as a tool for studying histidine phosphorylation.

    Science.gov (United States)

    Cebo, Małgorzata; Kielmas, Martyna; Adamczyk, Justyna; Cebrat, Marek; Szewczuk, Zbigniew; Stefanowicz, Piotr

    2014-12-01

    Isotope exchange at the histidine C2 atom of imidazole in D2O solution is well known to occur at a significantly slower rate than the exchange of amide protons. Analysis of the kinetics of this isotope-exchange reaction is proposed herein as a method of detecting histidine phosphorylation. This modification of His-containing peptides is challenging to pinpoint because of its instability under acidic conditions as well as during CID-MS analysis. In this work, we investigated the effect of phosphorylation of the histidine side chain in peptides on deuterium-hydrogen exchange (DHX) in the imidazole. The results demonstrate that phosphorylation dramatically slows the rate of the DHX reaction. This phenomenon can be applied to detect phosphorylation of peptides at the histidine residue (e.g., in enzymatic digests). We also found that the influence of the peptide sequence on the exchange kinetics is relatively small. A CID fragmentation experiment revealed that there was no detectable hydrogen scrambling in peptides deuterated at C2 of the imidazole ring. Therefore, MS/MS can be used to directly identify the locations of deuterium ions incorporated into peptides containing multiple histidine moieties.

  13. Theoretical prediction of the mechanical properties of zeolitic imidazolate frameworks (ZIFs)

    KAUST Repository

    Zheng, Bin

    2017-08-25

    A good resistance against mechanical stress is essential for the utilization of metal-organic frameworks (MOFs) in practical applications such as gas sorption, separation, catalysis or energy conversion. Here, we report on the successful modification of the mechanical properties of zeolitic imidazolate frameworks (ZIFs) achieved through a substitution of the terminal group. The mechanical modulus of SALEM-2 was found to significantly improve when the -H groups at position 2 of the imidazole linkers were replaced with electron withdrawing groups (-CHO, -Cl, or -Br). The charge distribution and electron density were analyzed to reveal the mechanism behind the observed variation of the elastic stiffness. Furthermore, ZIF-I with a -I group at position 2 of the imidazole linkers was predicted to exhibit an excellent mechanical strength in our study and then prepared experimentally. The results indicate that an inconspicuous change of the structure of ZIFs, i.e., additional groups strengthening the ZnN4 tetrahedron, will lead to a stiffer framework.

  14. SYNTHESIS OF METAL-ORGANIC (COMPLEXES COMPOUNDS COPPER(II-IMIDAZOLE FOR ANTIVIRAL HIV CANDIDATE

    Directory of Open Access Journals (Sweden)

    Teguh Hari Sucipto

    2016-01-01

    Full Text Available The human immunodeficiency virus (HIV is viruses known as rotaviruses. Potential target for therapeutic is reverse transcriptase (RT, possesses an RNA dependent DNA polymerase, DNA-dependent DNA polymerase and ribonuclease H fuctions. Imidazoles have high anti-HIV inhibitory activity, some derivates of imidazole reported drugs. 8-chloro-2,3-dihydroimidazole[1,2-b] [1,4,2]benzodithiazine-5,5-dioxides and 9-chloro-2,3,4-trihydropyri-mido[1,2-b][1,4,2]benzodithi-azine-6,6-dioxides. This compounds succesfully identified anti-HIV activity. Copper is a bio-essential element and copper complexes have been extensively utilized in metal mediated DNA cleavage for the generation of activated oxygen species. It has been reported that teraaza macrocyclic copper coordination compounds have anti-HIV activities. Studies have shown that these macrocyclic complexes can react with DNA in different binding fashions and exhibit effective nuclease activities. Complex compounds are compounds in which there is an atom that acts as the central atom and trotter group of molecules that can be either neutral or charged ions. Application a metal-organic (complex compounds, especially copper metal and derivates of imidazole. So, in this study can explore new anti-HIV candidate.

  15. Understanding reactivity of two newly synthetized imidazole derivatives by spectroscopic characterization and computational study

    Science.gov (United States)

    Hossain, Mossaraf; Thomas, Renjith; Mary, Y. Sheena; Resmi, K. S.; Armaković, Stevan; Armaković, Sanja J.; Nanda, Ashis Kumar; Vijayakumar, G.; Van Alsenoy, C.

    2018-04-01

    Two newly synthetized imidazole derivatives (1-(4-methoxyphenyl)-4,5-dimethyl-1H-imidazole-2-yl acetate (MPDIA) and 1-(4-bromophenyl)-4,5-dimethyl-1H-imidazole-2-yl acetate (BPDIA)) have been prepared by solvent-free synthesis pathway and their specific spectroscopic and reactive properties have been discussed based on combined experimental and computational approaches. Aside of synthesis, experimental part of this work included measurements of IR, FT-Raman and NMR spectra. All of the aforementioned spectra were also obtained computationally, within the framework of density functional theory (DFT) approach. Additionally, DFT calculations have been used in order to investigate local reactivity properties based on molecular orbital theory, molecular electrostatic potential (MEP), average local ionization energy (ALIE), Fukui functions and bond dissociation energy (BDE). Molecular dynamics (MD) simulations have been used in order to obtain radial distribution functions (RDF), which were used for identification of the atoms with pronounced interactions with water molecules. MEP showed negative regions are mainly localized over N28, O29, O35 atoms, it is represent with red colour in rainbow color scheme for MPDIA and BPDIA (which are most reactive sites for electrophilic attack). The first order hyperpolarizabilities of MPDIA and BPDIA are 20.15 and 6.10 times that of the standard NLO material urea. Potential interaction with antihypertensive protein hydrolase.

  16. Study of Antibacterial Effect of Novel Thiazole, Imidazole and Tetrahydropyridine Derivatives against Escherichia coli

    Directory of Open Access Journals (Sweden)

    Behzad Ghasemi

    2016-01-01

    Full Text Available > Introduction: Escherichia coli is one of the important pathogens in human with globalimportance. Because of the necessity for identification and the use of novel antibacterialcompounds against E. coli, in this present study we focused on the antibacterial effects ofsynthesized thiazole, imidazole and tetrahydropyridine derivatives on E. coli.Methods: For evaluation of antibacterial effect, the disk diffusion method was applied to measurethe growth inhibition zone diameter and broth micro-dilution was performed to determine theminimum inhibitory concentration (MIC.Results: Assessing the antibacterial effect showed that only 6d derivative of thiazole hadinhibitory effect on E. coli and the other thiazole, imidazole and tetrahydropyridine derivativeslacked any inhibitory result on this organism. The inhibitory effect of 6d derivative of thiazolewas MIC=125 and growth inhibition zone diameter of 16±0.1.Discussion: The antibacterial effect of thiazole, imidazole and tetrahydropyridine derivativesdiffers from each other and chemical linkages such as oxygen to thiazole ring in 6d derivative,could have reinforced this effect. The next step is determination of the toxicity and therapeuticeffects in the laboratory animals.

  17. Old drug new tricks: Chlorhexidine acts as a potential allosteric inhibitor toward PAK1.

    Science.gov (United States)

    Huang, Han-Wei; Zhang, Xiang-Yu; Song, Pei-Lu; Jiang, Hai-Lun; Li, Wei; Wang, Peng-Liang; Wang, Jian; Liu, Fu-Nan

    2018-01-01

    This paper describes the identification of chlorhexidine, an agent commonly used in clinical as a novel potential allosteric inhibitor of PAK1. In cellular assays, chlorhexidine showed a good inhibitory profile, and its inhibitory profile was even better than IPA-3, a well-known allosteric inhibitor. In pharmacology experiments, chlorhexidine successfully inhibited the relief of PAK1 dimer and inhibited the activation of PAK1. Our findings offer an insight for the new drug development of PAK1 inhibitor. We also provide a possible explanation for the phenomenon that the application of the chlorhexidine in peritoneal lavage inhibited the development of tumor. Copyright © 2017 Elsevier Inc. All rights reserved.

  18. Structure and allosteric effects of low-molecular-weight activators on the protein kinase PDK1

    DEFF Research Database (Denmark)

    Hindie, Valerie; Stroba, Adriana; Zhang, Hua

    2009-01-01

    Protein phosphorylation transduces a large set of intracellular signals. One mechanism by which phosphorylation mediates signal transduction is by prompting conformational changes in the target protein or interacting proteins. Previous work described an allosteric site mediating phosphorylation...... and in solution using a fluorescence-based assay and deuterium exchange experiments. Our results indicate that the binding of the compound produces local changes at the target site, the PIF binding pocket, and also allosteric changes at the ATP binding site and the activation loop. Altogether, we present...

  19. Identification and Structure-Function Study of Positive Allosteric Modulators of Kainate Receptors

    DEFF Research Database (Denmark)

    Larsen, Anja Probst; Fièvre, Sabine; Frydenvang, Karla

    2017-01-01

    as the AMPA receptor subunit GluA1i (5-fold). X-ray structures of the three modulators in the GluK1 ligand-binding domain were determined, locating two modulator-binding sites at the GluK1 dimer interface. In conclusion, this study may enable the design of new positive allosteric modulators selective for KARs......Kainate receptors (KARs) consist of a class of ionotropic glutamate receptors, which exert diverse pre- and postsynaptic functions through complex signaling regulating the activity of neural circuits. Whereas numerous small-molecule positive allosteric modulators of the ligand-binding domain of (S...

  20. Imidazole derivatives as angiotensin II AT1 receptor blockers: Benchmarks, drug-like calculations and quantitative structure-activity relationships modeling

    Science.gov (United States)

    Alloui, Mebarka; Belaidi, Salah; Othmani, Hasna; Jaidane, Nejm-Eddine; Hochlaf, Majdi

    2018-03-01

    We performed benchmark studies on the molecular geometry, electron properties and vibrational analysis of imidazole using semi-empirical, density functional theory and post Hartree-Fock methods. These studies validated the use of AM1 for the treatment of larger systems. Then, we treated the structural, physical and chemical relationships for a series of imidazole derivatives acting as angiotensin II AT1 receptor blockers using AM1. QSAR studies were done for these imidazole derivatives using a combination of various physicochemical descriptors. A multiple linear regression procedure was used to design the relationships between molecular descriptor and the activity of imidazole derivatives. Results validate the derived QSAR model.

  1. Studies on the π-π stacking features of imidazole units present in a series of 5-amino-1-alkylimidazole-4-carboxamides

    Science.gov (United States)

    Ray, Sibdas; Das, Aniruddha

    2015-06-01

    Reaction of 2-ethoxymethyleneamino-2-cyanoacetamide with primary alkyl amines in acetonitrile solvent affords 1-substituted-5-aminoimidazole-4-carboxamides. Single crystal X-ray diffraction studies of these imidazole compounds show that there are both anti-parallel and syn-parallel π-π stackings between two imidazole units in parallel-displaced (PD) conformations and the distance between two π-π stacked imidazole units depends mainly on the anti/ syn-parallel nature and to some extent on the alkyl group attached to N-1 of imidazole; molecules with anti-parallel PD-stacking arrangements of the imidazole units have got vertical π-π stacking distance short enough to impart stabilization whereas the imidazole unit having syn-parallel stacking arrangement have got much larger π-π stacking distances. DFT studies on a pair of anti-parallel imidazole units of such an AICA lead to curves for 'π-π stacking stabilization energy vs. π-π stacking distance' which have got similarity with the 'Morse potential energy diagram for a diatomic molecule' and this affords to find out a minimum π-π stacking distance corresponding to the maximum stacking stabilization energy between the pair of imidazole units. On the other hand, a DFT calculation based curve for 'π-π stacking stabilization energy vs. π-π stacking distance' of a pair of syn-parallel imidazole units is shown to have an exponential nature.

  2. A catalytic and dual recycling amplification ATP sensor based on target-driven allosteric structure switching of aptamer beacons.

    Science.gov (United States)

    Peng, Ying; Li, Daxiu; Yuan, Ruo; Xiang, Yun

    2018-05-15

    Abnormal concentrations of ATP are associated with many diseases and cancers, and quantitative detection of ATP is thus of great importance for disease diagnosis and prognosis. In the present work, we report a new dual recycling amplification sensor integrated with catalytic hairpin assembly (CHA) to achieve high sensitivity for fluorescent detection of ATP. The association of the target ATP with the aptamer beacons causes the allosteric structure switching of the aptamer beacons to expose the toehold regions, which hybridize with and unfold the fluorescently quenched hairpin signal probes (HP1) to recycle the target ATP and to trigger CHA between HP1 and the secondary hairpin probes (HP2) to form HP1/HP2 duplexes. Due to the recycling amplification, the presence of ATP leads to the formation of many HP1/HP2 duplexes, generating dramatically amplified fluorescent signals for sensitive detection of ATP. Under optimal experimental conditions, our sensor linearly responds to ATP in the range from 25 to 600nM with a calculated detection limit of 8.2nM. Furthermore, the sensor shows a high selectivity and can also be used to detect ATP in human serums to realize its application for real samples. With the distinct advantage of significant signal amplification without the involvement of any nanomaterial and enzyme, the developed sensor thus holds great potential for simple and sensitive detection of different small molecules and proteins. Copyright © 2018 Elsevier B.V. All rights reserved.

  3. Enzymes: An integrated view of structure, dynamics and function

    Directory of Open Access Journals (Sweden)

    Agarwal Pratul K

    2006-01-01

    Full Text Available Abstract Microbes utilize enzymes to perform a variety of functions. Enzymes are biocatalysts working as highly efficient machines at the molecular level. In the past, enzymes have been viewed as static entities and their function has been explained on the basis of direct structural interactions between the enzyme and the substrate. A variety of experimental and computational techniques, however, continue to reveal that proteins are dynamically active machines, with various parts exhibiting internal motions at a wide range of time-scales. Increasing evidence also indicates that these internal protein motions play a role in promoting protein function such as enzyme catalysis. Moreover, the thermodynamical fluctuations of the solvent, surrounding the protein, have an impact on internal protein motions and, therefore, on enzyme function. In this review, we describe recent biochemical and theoretical investigations of internal protein dynamics linked to enzyme catalysis. In the enzyme cyclophilin A, investigations have lead to the discovery of a network of protein vibrations promoting catalysis. Cyclophilin A catalyzes peptidyl-prolyl cis/trans isomerization in a variety of peptide and protein substrates. Recent studies of cyclophilin A are discussed in detail and other enzymes (dihydrofolate reductase and liver alcohol dehydrogenase where similar discoveries have been reported are also briefly discussed. The detailed characterization of the discovered networks indicates that protein dynamics plays a role in rate-enhancement achieved by enzymes. An integrated view of enzyme structure, dynamics and function have wide implications in understanding allosteric and co-operative effects, as well as protein engineering of more efficient enzymes and novel drug design.

  4. Evolution of glycaemia in the blood of mice in the presence or absence of imidazole; Evolution de la glycemie sanguine chez la souris protegee ou non par l'imidazole

    Energy Technology Data Exchange (ETDEWEB)

    Polverelli, M.; Teoule, R. [Commissariat a l' Energie Atomique, Grenoble (France). Centre d' Etudes Nucleaires

    1969-07-01

    With respect to the radioprotective properties of the heterocyclic compound, imidazole, the authors followed the action of this product on blood sugar levels of mice X irradiated with a lethal dose. The main results of this work are: probably a hypo-glycemic action of the imidazole; an abolishment of the post-irradiation hyperglycemia by imidazole; an appreciably difference between male and female towards irradiation. (author) [French] Dans le cadre de l'etude des proprietes radioprotectrices de l'imidazole, nous nous sommes attaches a suivre l'action de ce produit sur le taux de glucose sanguin de souris irradiees a dose letale. Les principaux resultats de ce travail sont les suivants: l'action probablement hypoglycemiante de l'imidazole; en tant que radioprotecteur, cet heterocycle azote supprime l'hyperglycemie consecutive a l'irradiation; une difference assez sensible entre males et femelles vis-a-vis de l'irradiation. (auteur)

  5. Evidence for allosterism in ribulose-1,5-bisphosphate carboxylase/oxygenase from comfrey

    Energy Technology Data Exchange (ETDEWEB)

    Mueller, D.D.; Bolden, T.D.

    1986-05-01

    Evidence has been obtained suggesting that ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) is an allosteric enzyme in the sense that it shows cooperative active site binding, cooperative interactions between the activation and active sites and significant binding of some metabolites at a second site. Investigation of the binding of a potent competitive inhibitor. 2-carboxymannitol-1,6-bisphosphate (CMBP) by /sup 31/P-NMR indicated essentially 1:1 binding with the active sites of comfrey RuBisCo. Among the interactions of competitive inhibitors, as measured by difference UV spectroscopy, the binding curves for ortho-phosphate and ribose-5-phosphate were better fitted by a Monod-Wyman-Changeux model than by an independent site model, whereas the binding of CMBP and 2-phosphoglycolate were not. Difference UV methods also were used to study activation by CO/sub 2/ which at pH 7.9 in 10 mM MgCl/sub 2/ showed positive cooperativity with k = 100 +/- 3 ..mu..M (based on pK/sub a/ = 6.4 for the CO/sub 2/-HCO/sub 3//sup -/ equilibrium) and L = 3.5 +/- 0.7. Addition of saturating amounts of CMBP and lowering the MgCl/sub 2/ to 2 mM still gave a sigmoidal curve but it was shifted to higher CO/sub 2/ concentrations (k = 124 +/- 2 ..mu..M and L = 31 +/- 3). In the absence of CMBP the same conditions gave k = 26 +/- 2 ..mu..M for L = 3.5. Conversely, k was 0.96 +/- 0.08 ..mu..M for CMBP in 0.5 mM MgCl/sub 2/ without added NaHCO/sub 3/ but was 21 +/- 0.06 ..mu..M in 10 MgCl/sub 2/ and 2 mM NaHCO/sub 3/, pH 7.3.

  6. Monitoring allostery in D2O: a necessary control in studies using hydrogen/deuterium-exchange to characterize allosteric regulation†

    Science.gov (United States)

    Prasannan, Charulata B.; Artigues, Antonio; Fenton, Aron W.

    2011-01-01

    There is currently a renewed focus aimed at understanding allosteric mechanisms at atomic resolution. This current interest seeks to understand how both changes in protein conformations and changes in protein dynamics contribute to relaying an allosteric signal between two ligand binding sites on a protein (e.g. active site and allosteric site). Both NMR, by monitoring protein dynamics directly, and hydrogen/deuterium exchange, by monitoring solvent accessibility of backbone amides, offer insights into protein dynamics. Unfortunately, many allosteric proteins exceed the size limitations of standard NMR techniques. Although hydrogen/deuterium exchange as detected by mass spectrometry (H/DX-MS) offers an alternative evaluation method, any application of hydrogen/deuterium exchange requires that the property being measured functions in both H2O and D2O. Due to the promising future H/DX-MS has in the evaluation of allosteric mechanisms in large proteins, we demonstrate an evaluation of allosteric regulation in D2O. Exemplified using phenylalanine inhibition of rabbit muscle pyruvate kinase, we find that binding of the inhibitor is greatly reduced in D2O, but the effector continues to elicit an allosteric response. PMID:21701851

  7. Monitoring allostery in D2O: a necessary control in studies using hydrogen/deuterium exchange to characterize allosteric regulation.

    Science.gov (United States)

    Prasannan, Charulata B; Artigues, Antonio; Fenton, Aron W

    2011-08-01

    There is currently a renewed focus aimed at understanding allosteric mechanisms at atomic resolution. This current interest seeks to understand how both changes in protein conformations and changes in protein dynamics contribute to relaying an allosteric signal between two ligand binding sites on a protein (e.g., active and allosteric sites). Both nuclear magnetic resonance (NMR), by monitoring protein dynamics directly, and hydrogen/deuterium exchange, by monitoring solvent accessibility of backbone amides, offer insights into protein dynamics. Unfortunately, many allosteric proteins exceed the size limitations of standard NMR techniques. Although hydrogen/deuterium exchange as detected by mass spectrometry (H/DX-MS) offers an alternative evaluation method, any application of hydrogen/deuterium exchange requires that the property being measured functions in both H(2)O and D(2)O. Due to the promising future H/DX-MS has in the evaluation of allosteric mechanisms in large proteins, we demonstrate an evaluation of allosteric regulation in D(2)O. Exemplified using phenylalanine inhibition of rabbit muscle pyruvate kinase, we find that binding of the inhibitor is greatly reduced in D(2)O, but the effector continues to elicit an allosteric response.

  8. Molecular mechanism of allosteric modulation at GPCRs: insight from a binding kinetics study at the human A1 adenosine receptor.

    Science.gov (United States)

    Guo, Dong; Venhorst, Suzanne N; Massink, Arnault; van Veldhoven, Jacobus P D; Vauquelin, Georges; IJzerman, Adriaan P; Heitman, Laura H

    2014-12-01

    Many GPCRs can be allosterically modulated by small-molecule ligands. This modulation is best understood in terms of the kinetics of the ligand-receptor interaction. However, many current kinetic assays require at least the (radio)labelling of the orthosteric ligand, which is impractical for studying a range of ligands. Here, we describe the application of a so-called competition association assay at the adenosine A1 receptor for this purpose. We used a competition association assay to examine the binding kinetics of several unlabelled orthosteric agonists of the A1 receptor in the absence or presence of two allosteric modulators. We also tested three bitopic ligands, in which an orthosteric and an allosteric pharmacophore were covalently linked with different spacer lengths. The relevance of the competition association assay for the binding kinetics of the bitopic ligands was also explored by analysing simulated data. The binding kinetics of an unlabelled orthosteric ligand were affected by the addition of an allosteric modulator and such effects were probe- and concentration-dependent. Covalently linking the orthosteric and allosteric pharmacophores into one bitopic molecule had a substantial effect on the overall on- or off-rate. The competition association assay is a useful tool for exploring the allosteric modulation of the human adenosine A1 receptor. This assay may have general applicability to study allosteric modulation at other GPCRs as well. © 2014 The British Pharmacological Society.

  9. Reaction of imidazole with toluene-4-sulfonate salts of substituted phenyl N-methylpyridinium-4-carboxylate esters: special base catalysis by imidazole.

    Science.gov (United States)

    Colthurst, Matthew J; Williams, Andrew

    2003-06-07

    The reaction of imidazole in aqueous solution with toluene-4-sulfonate salts of substituted phenyl N-methylpyridinium-4-carboxylate esters obeys the rate law: k(obs) - k(background) = k2[Im] + k3[Im]2 where [Im] is the imidazole concentration present as free base. The parameters k2 and k3 fit Brønsted type free energy correlations against the pKa of the leaving phenol with betaLg values of -0.65 and -0.42 respectively. The imidazolysis is insensitive to catalysis by general bases and yet k3 for the 3-cyanophenyl ester possesses a deuterium oxide solvent isotope effect of 4.43 consistent with rate limiting proton transfer. A special catalytic function is proposed for decomposition of the tetrahedral addition intermediate (T+/-) via k3 whereby the catalytic imidazole interacts electrophilically with the leaving phenolate ion and removes a proton from the nitrogen in the rate limiting step with subsequent non-rate limiting ArO-C bond fission. This is consistent with the change in effective charge on the leaving oxygen in the transition structure of k3 which is more positive (-0.42) than that expected (-0.60) for the equilibrium formation of the zwitterion intermediate. The catalytic function at the leaving oxygen is likely to be an electrophilic role of the NH as a hydrogen bond donor. In the k2 step the deuterium oxide solvent isotope effect of 1.51 for the 3-cyanophenyl ester and the betaLg of -0.65 are consistent with rate limiting expulsion of the phenolate ion from the T+/- intermediate. The absence of general base catalysis of imidazolysis rules out the established mechanism for aminolysis of esters where T+/- is stabilised by a standard rate limiting proton transfer. The kinetically equivalent term for k3 where T- reacts with the imidazolium ion as an acid catalyst would require this step to be rate limiting and involve proton transfer not consistent with departure of the good aryl oxide leaving group.

  10. Selective Negative Allosteric Modulation Of Metabotropic Glutamate Receptors - A Structural Perspective of Ligands and Mutants

    DEFF Research Database (Denmark)

    Harpsøe, Kasper; Isberg, Vignir; Tehan, Benjamin G

    2015-01-01

    The metabotropic glutamate receptors have a wide range of modulatory functions in the central nervous system. They are among the most highly pursued drug targets, with relevance for several neurological diseases, and a number of allosteric modulators have entered clinical trials. However, so far ...

  11. 2013 Philip S. Portoghese Medicinal Chemistry Lectureship: Drug Discovery Targeting Allosteric Sites†

    Science.gov (United States)

    2015-01-01

    The identification of sites on receptors topographically distinct from the orthosteric sites, so-called allosteric sites, has heralded novel approaches and modes of pharmacology for target modulation. Over the past 20 years, our understanding of allosteric modulation has grown significantly, and numerous advantages, as well as caveats (e.g., flat structure–activity relationships, species differences, “molecular switches”), have been identified. For multiple receptors and proteins, numerous examples have been described where unprecedented levels of selectivity are achieved along with improved physiochemical properties. While not a panacea, these novel approaches represent exciting opportunities for tool compound development to probe the pharmacology and therapeutic potential of discrete molecular targets, as well as new medicines. In this Perspective, in commemoration of the 2013 Philip S. Portoghese Medicinal Chemistry Lectureship (LindsleyC. W.Adventures in allosteric drug discovery. Presented at the 246th National Meeting of the American Chemical Society, Indianapolis, IN, September 10, 2013; The 2013 Portoghese Lectureship), several vignettes of drug discovery campaigns targeting novel allosteric mechanisms will be recounted, along with lessons learned and guidelines that have emerged for successful lead optimization. PMID:25180768

  12. "Molecular Switches" on mGluR Allosteric Ligands That Modulate Modes of Pharmacology

    Science.gov (United States)

    Wood, Michael R.; Hopkins, Corey R.; Brogan, John T.; Conn, P. Jeffrey; Lindsley, Craig W.

    2013-01-01

    G-Protein-coupled receptors (GPCRs) represent the largest class of drug targets, accounting for more than 40% of marketed drugs; however, discovery efforts for many GPCRs have failed to provide viable drug candidates. Historically, drug discovery efforts have focused on developing ligands that act at the orthosteric site of the endogenous agonist. Recently, efforts have focused on functional assay paradigms and the discovery of ligands that act at allosteric sites to modulate receptor function in either a positive, negative, or neutral manner. Allosteric modulators have numerous advantages over orthosteric ligands, including high subtype selectivity; the ability to mimic physiological conditions; the lack of densensitization, downregulation, and internalization; and reduced side effects. Despite these virtues, challenging issues have now arisen for allosteric modulators of metabotropic glutamate receptors (mGluRs): shallow SAR, ligand-directed trafficking, and the identification of subtle “molecular switches” that modulate the modes of pharmacology. Here, we will discuss the impact of modest structural changes to multiple mGluR allosteric ligands scaffolds that unexpectedly modulate pharmacology and raise concerns over metabolism and the pharmacology of metabolites. PMID:21341760

  13. The different ways through which specificity works in orthosteric and allosteric drugs.

    Science.gov (United States)

    Nussinov, Ruth; Tsai, Chung-Jung

    2012-01-01

    Currently, there are two types of drugs on the market: orthosteric, which bind at the active site; and allosteric, which bind elsewhere on the protein surface, and allosterically change the conformation of the protein binding site. In this perspective we argue that the different mechanisms through which the two drug types affect protein activity and their potential pitfalls call for different considerations in drug design. The key problem facing orthosteric drugs is side effects which can occur by drug binding to homologous proteins sharing a similar binding site. Hence, orthosteric drugs should have very high affinity to the target; this would allow a low dosage to selectively achieve the goal of target-only binding. By contrast, allosteric drugs work by shifting the free energy landscape. Their binding to the protein surface perturbs the protein surface atoms, and the perturbation propagates like waves, finally reaching the binding site. Effective drugs should have atoms in good contact with the 'right' protein atoms; that is, the contacts should elicit propagation waves optimally reaching the protein binding site target. While affinity is important, the design should consider the protein conformational ensemble and the preferred propagation states. We provide examples from functional in vivo scenarios for both types of cases, and suggest how high potency can be achieved in allosteric drug development.

  14. Divergence of allosteric effects of rapacuronium on binding and function of muscarinic receptors

    Czech Academy of Sciences Publication Activity Database

    Jakubík, Jan; Randáková, Alena; El-Fakahany, E. E.; Doležal, Vladimír

    2009-01-01

    Roč. 9, č. 15 (2009), s. 1-20 ISSN 1471-2210 R&D Projects: GA ČR GA305/09/0681; GA MŠk(CZ) LC554; GA AV ČR(CZ) IAA500110703 Institutional research plan: CEZ:AV0Z50110509 Keywords : muscarinic receptors * allosteric modulation * rapacuronium Subject RIV: ED - Physiology

  15. Allosteric Regulation of the Rotational Speed in a Light-Driven Molecular Motor

    NARCIS (Netherlands)

    Faulkner, Adele; van Leeuwen, Thomas; Feringa, Ben L; Wezenberg, Sander J

    2016-01-01

    The rotational speed of an overcrowded alkene-based molecular rotary motor, having an integrated 4,5-diazafluorenyl coordination motif, can be regulated allosterically via the binding of metal ions. DFT calculations have been used to predict the relative speed of rotation of three different (i.e.

  16. Entropy Transfer between Residue Pairs and Allostery in Proteins: Quantifying Allosteric Communication in Ubiquitin.

    Science.gov (United States)

    Hacisuleyman, Aysima; Erman, Burak

    2017-01-01

    It has recently been proposed by Gunasakaran et al. that allostery may be an intrinsic property of all proteins. Here, we develop a computational method that can determine and quantify allosteric activity in any given protein. Based on Schreiber's transfer entropy formulation, our approach leads to an information transfer landscape for the protein that shows the presence of entropy sinks and sources and explains how pairs of residues communicate with each other using entropy transfer. The model can identify the residues that drive the fluctuations of others. We apply the model to Ubiquitin, whose allosteric activity has not been emphasized until recently, and show that there are indeed systematic pathways of entropy and information transfer between residues that correlate well with the activities of the protein. We use 600 nanosecond molecular dynamics trajectories for Ubiquitin and its complex with human polymerase iota and evaluate entropy transfer between all pairs of residues of Ubiquitin and quantify the binding susceptibility changes upon complex formation. We explain the complex formation propensities of Ubiquitin in terms of entropy transfer. Important residues taking part in allosteric communication in Ubiquitin predicted by our approach are in agreement with results of NMR relaxation dispersion experiments. Finally, we show that time delayed correlation of fluctuations of two interacting residues possesses an intrinsic causality that tells which residue controls the interaction and which one is controlled. Our work shows that time delayed correlations, entropy transfer and causality are the required new concepts for explaining allosteric communication in proteins.

  17. Nootropic α7 nicotinic receptor allosteric modulator derived from GABAA receptor modulators

    Science.gov (United States)

    Ng, Herman J.; Whittemore, Edward R.; Tran, Minhtam B.; Hogenkamp, Derk J.; Broide, Ron S.; Johnstone, Timothy B.; Zheng, Lijun; Stevens, Karen E.; Gee, Kelvin W.

    2007-01-01

    Activation of brain α7 nicotinic acetylcholine receptors (α7 nAChRs) has broad therapeutic potential in CNS diseases related to cognitive dysfunction, including Alzheimer's disease and schizophrenia. In contrast to direct agonist activation, positive allosteric modulation of α7 nAChRs would deliver the clinically validated benefits of allosterism to these indications. We have generated a selective α7 nAChR-positive allosteric modulator (PAM) from a library of GABAA receptor PAMs. Compound 6 (N-(4-chlorophenyl)-α-[[(4-chloro-phenyl)amino]methylene]-3-methyl-5-isoxazoleacet-amide) evokes robust positive modulation of agonist-induced currents at α7 nAChRs, while preserving the rapid native characteristics of desensitization, and has little to no efficacy at other ligand-gated ion channels. In rodent models, it corrects sensory-gating deficits and improves working memory, effects consistent with cognitive enhancement. Compound 6 represents a chemotype for allosteric activation of α7 nAChRs, with therapeutic potential in CNS diseases with cognitive dysfunction. PMID:17470817

  18. Nootropic alpha7 nicotinic receptor allosteric modulator derived from GABAA receptor modulators.

    Science.gov (United States)

    Ng, Herman J; Whittemore, Edward R; Tran, Minhtam B; Hogenkamp, Derk J; Broide, Ron S; Johnstone, Timothy B; Zheng, Lijun; Stevens, Karen E; Gee, Kelvin W

    2007-05-08

    Activation of brain alpha7 nicotinic acetylcholine receptors (alpha7 nAChRs) has broad therapeutic potential in CNS diseases related to cognitive dysfunction, including Alzheimer's disease and schizophrenia. In contrast to direct agonist activation, positive allosteric modulation of alpha7 nAChRs would deliver the clinically validated benefits of allosterism to these indications. We have generated a selective alpha7 nAChR-positive allosteric modulator (PAM) from a library of GABAA receptor PAMs. Compound 6 (N-(4-chlorophenyl)-alpha-[[(4-chloro-phenyl)amino]methylene]-3-methyl-5-isoxazoleacet-amide) evokes robust positive modulation of agonist-induced currents at alpha7 nAChRs, while preserving the rapid native characteristics of desensitization, and has little to no efficacy at other ligand-gated ion channels. In rodent models, it corrects sensory-gating deficits and improves working memory, effects consistent with cognitive enhancement. Compound 6 represents a chemotype for allosteric activation of alpha7 nAChRs, with therapeutic potential in CNS diseases with cognitive dysfunction.

  19. Molecular mechanism of allosteric communication in Hsp70 revealed by molecular dynamics simulations.

    Directory of Open Access Journals (Sweden)

    Federica Chiappori

    Full Text Available Investigating ligand-regulated allosteric coupling between protein domains is fundamental to understand cell-life regulation. The Hsp70 family of chaperones represents an example of proteins in which ATP binding and hydrolysis at the Nucleotide Binding Domain (NBD modulate substrate recognition at the Substrate Binding Domain (SBD. Herein, a comparative analysis of an allosteric (Hsp70-DnaK and a non-allosteric structural homolog (Hsp110-Sse1 of the Hsp70 family is carried out through molecular dynamics simulations, starting from different conformations and ligand-states. Analysis of ligand-dependent modulation of internal fluctuations and local deformation patterns highlights the structural and dynamical changes occurring at residue level upon ATP-ADP exchange, which are connected to the conformational transition between closed and open structures. By identifying the dynamically responsive protein regions and specific cross-domain hydrogen-bonding patterns that differentiate Hsp70 from Hsp110 as a function of the nucleotide, we propose a molecular mechanism for the allosteric signal propagation of the ATP-encoded conformational signal.

  20. Allosteric Modulation of SULT2A1 by Celecoxib and Nimesulide: Computational Analyses

    OpenAIRE

    Yalcin, Emine Bihter; Struzik, Scott M.; King, Roberta S.

    2008-01-01

    We used protein-ligand docking and minimization to identify celecoxib as an allosteric modulator of SULT2A1-catalyzed estradiol sulfonation. Subsequent to celecoxib docking and complex minimization, conformational changes in SULT2A1 allowed estradiol docking to an alternative binding region with predicted preference for 17β-OH-E2 sulfonation over 3-OH-E2 sulfonation.

  1. Screening for Methylated Poly(⌊-histidine with Various Dimethylimidazolium/Methylimidazole/Imidazole Contents as DNA Carrier

    Directory of Open Access Journals (Sweden)

    Shoichiro Asayama

    2015-08-01

    Full Text Available Methylated poly(l-histidine (PLH-Me, our original polypeptide, has controlled the contents of dimethylimidazolium, τ/π-methylimidazole and imidazole groups for efficient gene delivery. The screening for the PLH-Me as DNA carrier has been carried out by use of the PLH with 25 mol% (τ-methyl, 16 mol%; π-methyl, 17 mol%; deprotonated imidazole, 41 mol%, 68 mol% (τ-methyl, 16 mol%; π-methyl, 8 mol%; deprotonated imidazole, 8 mol% and 87 mol% (τ-methyl, 7 mol%; π-methyl, 4 mol%; deprotonated imidazole, 2 mol% dimethylimidazolium groups, that is, PLH-Me(25, PLH-Me(68 and PLH-Me(87, respectively. The screening of the chemical structure of PLH-Me has been carried out for DNA carrier properties, which are the stability of its DNA polyion complexes and gene expression. The DNA complexes with the 25 mol% and 68 mol% dimethylated PLH-Me possessed almost same ability to retain DNA, as compared with the 87 mol% dimethylated PLH-Me, which was examined by competitive exchange with dextran sulfate. From the gene transfection experiment against HepG2 cells, human hepatoma cell line, the PLH-Me(25/DNA complex was revealed to mediate highest gene expression. These results suggest that the dimethyl-imidazolium/methylimidazole/imidazole balance of the PLH-Me is important for DNA carrier design.

  2. Identification of a Novel Allosteric Inhibitory Site on Tryptophan Hydroxylase 1 Enabling Unprecedented Selectivity Over all Related Hydroxylases

    Directory of Open Access Journals (Sweden)

    Mike Petrassi

    2017-05-01

    Full Text Available Pulmonary arterial hypertension (PAH has demonstrated multi-serotonin receptor dependent pathologies, characterized by increased tone (5-HT1B receptor and complex lesions (SERT, 5-HT1B, 5-HT2B receptors of the pulmonary vasculature together with right ventricular hypertrophy, ischemia and fibrosis (5-HT2B receptor. Selective inhibitors of individual signaling elements – SERT, 5-HT2A, 5HT2B, and combined 5-HT2A/B receptors, have all been tested clinically and failed. Thus, inhibition of tryptophan hydroxylase 1 (TPH1, the rate limiting step in 5-HT synthesis, has been suggested as a more broad, and thereby more effective, mode of 5-HT inhibition. However, selectivity over non-pathogenic enzyme family members, TPH2, phenylalanine hydroxylase, and tyrosine hydroxylase has hampered therapeutic development. Here we describe the site/sequence, biochemical, and biophysical characterization of a novel allosteric site on TPH1 through which selectivity over TPH2 and related aromatic amino acid hydroxylases is achieved. We demonstrate the mechanism of action by which novel compounds selectively inhibit TPH1 using surface plasma resonance and enzyme competition assays with both tryptophan ligand and BH4 co-factor. We demonstrate 15-fold greater potency within a human carcinoid cell line versus the most potent known TPH1/2 non-specific inhibitor. Lastly, we detail a novel canine in vivo system utilized to determine effective biologic inhibition of newly synthesized 5-HT. These findings are the first to demonstrate TPH1-selective inhibition and may pave the way to a truly effective means to reduce pathologic 5-HT and thereby treat complex remodeling diseases such as PAH.

  3. 1-[(3-Aryloxy-3-aryl)propyl]-1H-imidazoles, new imidazoles with potent activity against Candida albicans and dermatophytes. Synthesis, structure-activity relationship, and molecular modeling studies.

    Science.gov (United States)

    La Regina, Giuseppe; D'Auria, Felicia Diodata; Tafi, Andrea; Piscitelli, Francesco; Olla, Stefania; Caporuscio, Fabiana; Nencioni, Lucia; Cirilli, Roberto; La Torre, Francesco; De Melo, Nadja Rodrigues; Kelly, Steven L; Lamb, David C; Artico, Marino; Botta, Maurizio; Palamara, Anna Teresa; Silvestri, Romano

    2008-07-10

    New 1-[(3-aryloxy-3-aryl)propyl]-1 H-imidazoles were synthesized and evaluated against Candida albicans and dermatophytes in order to develop structure-activity relationships (SARs). Against C. albicans the new imidazoles showed minimal inhibitory concentrations (MICs) comparable to those of ketoconazole, miconazole, and econazole, and were more potent than fluconazole. Several derivatives ( 10, 12, 14, 18- 20, 24, 28, 29, 30, and 34) turned out to be potent inhibitors of C. albicans strains resistant to fluconazole, with MIC values less than 10 microg/mL. Against dermatophytes strains, compounds 20, 25, and 33 (MIC imidazoles 10- 44 were rationalized with reasonable accuracy by a previously developed quantitative pharmacophore for antifungal agents.

  4. Thermodynamics of organic mixtures containing amines. X. Phase equilibria for binary systems formed by imidazoles and hydrocarbons: Experimental data and modelling using DISQUAC

    International Nuclear Information System (INIS)

    Domanska, Urszula; Zawadzki, Maciej; Gonzalez, Juan Antonio

    2010-01-01

    (Solid + liquid) equilibrium (SLE) temperatures have been determined using a dynamic method for the systems (1H-imidazole, + benzene, + toluene, + hexane, or + cyclohexane; 1-methylimidazole + benzene, or + toluene, 2-methyl-1H-imidazole + benzene, + toluene, or + cyclohexane, and benzimidazole + benzene). In addition (liquid + liquid) equilibrium (LLE) temperatures have been obtained using a cloud point method for (1H-imidazole, + hexane, or + cyclohexane; 1-methylimidazole + toluene, and 2-methyl-1H-imidazole + cyclohexane). The measured systems show positive deviations from the Raoult's law, due to strong dipolar interactions between amine molecules related to the high dipole moment of imidazoles. On the other hand, DISQUAC interaction parameters for the contacts present in these solutions and for the amine/hydroxyl contacts in (1H-imidazole + 1-alkanol) mixtures have been determined. The model correctly represents the available data for the examined systems. Deviations between experimental and calculated SLE temperatures are similar to those obtained using the Wilson or NRTL equations, or the UNIQUAC association solution model. The quasichemical interaction parameters are the same for mixtures containing 1H-imidazole, 1-methylimidazole, or 2-methyl-1H-imidazole and hydrocarbons. This may be interpreted assuming that they are members of a homologous series. Benzimidazole behaves differently.

  5. Investigations on organic fungicides. IX. The antagonistic action of certain imidazole derivatives and of [alpha]-keto acids on the fungitoxicity of dimethyldithiocarbamates

    NARCIS (Netherlands)

    Kaars Sijpesteijn, A.; Kerk, G.J.M. van der

    1. 1. Apart from -histidine a variety of other imidazole derivatives is able to antagonize the inhibiting action of sodium dimethyl dithiocarbamate (NaDDC) on spore germination of moulds in the first zone of inhibition. 2. 2. - and -histidine, -histidinol and imidazole-4-carboxylic acid are of

  6. Thermodynamics of organic mixtures containing amines. X. Phase equilibria for binary systems formed by imidazoles and hydrocarbons: Experimental data and modelling using DISQUAC

    Energy Technology Data Exchange (ETDEWEB)

    Domanska, Urszula; Zawadzki, Maciej [Physical Chemistry Division, Faculty of Chemistry, Warsaw University of Technology, 00-664 Warsaw (Poland); Gonzalez, Juan Antonio, E-mail: jagl@termo.uva.e [G.E.T.E.F., Grupo Especializado en Termodinamica de Equilibrio entre Fases, Departamento de Fisica Aplicada, Facultad de Ciencias, Universidad de Valladolid, E-47071, Valladolid (Spain)

    2010-04-15

    (Solid + liquid) equilibrium (SLE) temperatures have been determined using a dynamic method for the systems (1H-imidazole, + benzene, + toluene, + hexane, or + cyclohexane; 1-methylimidazole + benzene, or + toluene, 2-methyl-1H-imidazole + benzene, + toluene, or + cyclohexane, and benzimidazole + benzene). In addition (liquid + liquid) equilibrium (LLE) temperatures have been obtained using a cloud point method for (1H-imidazole, + hexane, or + cyclohexane; 1-methylimidazole + toluene, and 2-methyl-1H-imidazole + cyclohexane). The measured systems show positive deviations from the Raoult's law, due to strong dipolar interactions between amine molecules related to the high dipole moment of imidazoles. On the other hand, DISQUAC interaction parameters for the contacts present in these solutions and for the amine/hydroxyl contacts in (1H-imidazole + 1-alkanol) mixtures have been determined. The model correctly represents the available data for the examined systems. Deviations between experimental and calculated SLE temperatures are similar to those obtained using the Wilson or NRTL equations, or the UNIQUAC association solution model. The quasichemical interaction parameters are the same for mixtures containing 1H-imidazole, 1-methylimidazole, or 2-methyl-1H-imidazole and hydrocarbons. This may be interpreted assuming that they are members of a homologous series. Benzimidazole behaves differently.

  7. Synthesis and characterization of novel polyamide-ethers based on bis-imidazole containing bulky aryl pendant groups

    Directory of Open Access Journals (Sweden)

    Seyed Mahdi Saadati

    2013-01-01

    Full Text Available A series of novel polyamide-ethers (PAEs based on bis-imidazole containing bulky aryl pendant groups was prepared by direct polycondensation of a diamine, 4-(1-(4-(4-(2-(4-aminophenyl-4,5-diphenyl-1H-imidazol-1-ylphenoxyphenyl-4,5-diphenyl-1H-imidazol-2-ylbenzenamine (DABI, and various dicarboxylic acids. All the resulting polyamide-ethers were amorphous with inherent viscosities ranged from 0.52 to 0.61 dL/g and were readily soluble in many organic solvents which could be solution-cast into transparent and tough films. The glass transition temperatures (Tg of these polymers were affected considerably by their chemical structure and ranged from 230 to 310 ºC. They had useful levels of thermal stability associated with relatively high temperatures of 10% weight loss (T10 in the range of 329-399 ºC in air atmosphere.

  8. Silylation of leached-vermiculites following reaction with imidazole and copper sorption behavior

    Energy Technology Data Exchange (ETDEWEB)

    Santos, Saloana S.G.; Pereira, Mariana B.B. [Chemistry Department of Paraíba Federal University, João Pessoa, Paraíba (Brazil); Almeida, Ramon K.S. [Instituto de Química, Universidade Estadual de Campinas, Caixa Postal 6154, 13083-970 Campinas, São Paulo (Brazil); Souza, Antônio G. [Chemistry Department of Paraíba Federal University, João Pessoa, Paraíba (Brazil); Fonseca, Maria G., E-mail: mgardennia@quimica.ufpb.br [Chemistry Department of Paraíba Federal University, João Pessoa, Paraíba (Brazil); Jaber, M. [Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR 8220, Laboratoire d' archéologie moléculaire et structurale (LAMS), Boîte courrier 225, 4 place Jussieu, 75005 Paris (France)

    2016-04-05

    Highlights: • Silylated vermiculites reacted covalently with imidazole. • Modified vermiculites adsorbed copper from aqueous solution. • Copper retention in all solids occurred at rapid time of 80 min. • Higher organic content on the solid improved the copper adsorption. - Abstract: Organically modified vermiculites were synthesized by previous silylation of three leached vermiculites, V0.3Cl, V0.5Cl and V0.8Cl, under anhydrous conditions following reaction with imidazole (Im), which acted as chelating agent for copper retention. Elemental analysis, X-ray diffraction, infrared spectroscopy, scanning electronic microscopy, transmission electron microscopy, {sup 29}Si and {sup 13}C NMR and nitrogen adsorption/desorption measurements were used to characterize pristine, leached and organofunctionalized solids. X-ray photoelectron spectroscopy (XPS) was used to evaluate the surface after copper sorption. Parameters such as contact time, pH and initial cation concentration for the adsorption of Cu(II) ions were investigated. The adsorption equilibrium data were fitted using the Langmuir isotherm model and the monolayer adsorption capacities were 2.38, 2.52 and 2.69 mmol g{sup −1} for V0.5Cl-Im, V0.3Cl-Im and V0.8Cl-Im, respectively, at pH 6.0 and 298 K for a time reaction of 80 min. The sorption rates were described by pseudo-second-order kinetics. The chloropropyl imidazole vermiculites are promising adsorbents for the rapid removal of Cu(II) ions from aqueous solution.

  9. Tumor Repression of VCaP Xenografts by a Pyrrole-Imidazole Polyamide

    OpenAIRE

    Hargrove, Amanda E.; Martinez, Thomas F.; Hare, Alissa A.; Kurmis, Alexis A.; Phillips, John W.; Sud, Sudha; Pienta, Kenneth J; Dervan, Peter B.

    2015-01-01

    Pyrrole-imidazole (Py-Im) polyamides are high affinity DNA-binding small molecules that can inhibit protein-DNA interactions. In VCaP cells, a human prostate cancer cell line overexpressing both AR and the TMPRSS2-ERG gene fusion, an androgen response element (ARE)-targeted Py-Im polyamide significantly downregulates AR driven gene expression. Polyamide exposure to VCaP cells reduced proliferation without causing DNA damage. Py-Im polyamide treatment also reduced tumor growth in a VCaP mouse ...

  10. Crystal structure of 2-methyl-1H-imidazol-3-ium hydrogen oxalate dihydrate

    Directory of Open Access Journals (Sweden)

    Mouhamadou Birame Diop

    2016-08-01

    Full Text Available Single crystals of the title molecular salt, C4H7N2+·HC2O4−·2H2O, were isolated from the reaction of 2-methyl-1H-imidazole and oxalic acid in a 1:1 molar ratio in water. In the crystal, the cations and anions are positioned alternately along an infinite [010] ribbon and linked together through bifurcated N—H...(O,O hydrogen bonds. The water molecules of crystallization link the chains into (10-1 bilayers, with the methyl groups of the cations organized in an isotactic manner.

  11. New type of imidazole based salts designed specifically for lithium ion batteries

    Energy Technology Data Exchange (ETDEWEB)

    Niedzicki, L., E-mail: asalm@ch.pw.edu.p [Department of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00664 Warsaw (Poland); Zukowska, G.Z.; Bukowska, M.; Szczecinski, P. [Department of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00664 Warsaw (Poland); Grugeon, S.; Laruelle, S.; Armand, M. [Laboratoire de Reactivite et de Chimie des Solides University de Picardie Jules Verne, 33 rue de Saint-Leu, 80039 Amiens (France); Panero, S.; Scrosati, B. [Department of Chemistry, University of Rome ' La Sapienza' , Piazzale Aldo Moro 5, 00185 Rome (Italy); Marcinek, M.; Wieczorek, W. [Department of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00664 Warsaw (Poland)

    2010-01-25

    In this manuscript we announce new type of 'tailored' imidazole-derived salts designed, synthesized and tested for application in lithium conductive electrolytes. Basic characterization of the structure of described materials has been made by Raman, IR and NMR ({sup 13}C NMR, {sup 19}F NMR) techniques. DSC and CV studies showed thermal stability of all salts over 200 deg. C and electrochemical stability in liquid and solid polymer solvents up to +4.6 V vs. metallic lithium anode and Al collectors. Such properties proved applicability of these salts as lithium electrolytes for modern types of lithium ion batteries.

  12. The gdhB gene of Pseudomonas aeruginosa encodes an arginine-inducible NAD(+)-dependent glutamate dehydrogenase which is subject to allosteric regulation.

    Science.gov (United States)

    Lu, C D; Abdelal, A T

    2001-01-01

    The NAD(+)-dependent glutamate dehydrogenase (NAD-GDH) from Pseudomonas aeruginosa PAO1 was purified, and its amino-terminal amino acid sequence was determined. This sequence information was used in identifying and cloning the encoding gdhB gene and its flanking regions. The molecular mass predicted from the derived sequence for the encoded NAD-GDH was 182.6 kDa, in close agreement with that determined from sodium dodecyl sulfate-polyacrylamide gel electrophoresis of the purified enzyme (180 kDa). Cross-linking studies established that the native NAD-GDH is a tetramer of equal subunits. Comparison of the derived amino acid sequence of NAD-GDH from P. aeruginosa with the GenBank database showed the highest homology with hypothetical polypeptides from Pseudomonas putida, Mycobacterium tuberculosis, Rickettsia prowazakii, Legionella pneumophila, Vibrio cholerae, Shewanella putrefaciens, Sinorhizobium meliloti, and Caulobacter crescentus. A moderate degree of homology, primarily in the central domain, was observed with the smaller tetrameric NAD-GDH (protomeric mass of 110 kDa) from Saccharomyces cerevisiae or Neurospora crassa. Comparison with the yet smaller hexameric GDH (protomeric mass of 48 to 55 kDa) of other prokaryotes yielded a low degree of homology that was limited to residues important for binding of substrates and for catalytic function. NAD-GDH was induced 27-fold by exogenous arginine and only 3-fold by exogenous glutamate. Primer extension experiments established that transcription of gdhB is initiated from an arginine-inducible promoter and that this induction is dependent on the arginine regulatory protein, ArgR, a member of the AraC/XyIS family of regulatory proteins. NAD-GDH was purified to homogeneity from a recombinant strain of P. aeruginosa and characterized. The glutamate saturation curve was sigmoid, indicating positive cooperativity in the binding of glutamate. NAD-GDH activity was subject to allosteric control by arginine and citrate, which

  13. Dichloridobis[1-(2,4,6-trimethylphenyl-1H-imidazole-κN3]copper(II

    Directory of Open Access Journals (Sweden)

    Yantao Zhang

    2013-11-01

    Full Text Available In the title complex, [CuCl2(C12H14N22], the Cu2+ cation is situated on an inversion centre and is coordinated by two N atoms from symmetry-related 1-mesityl-1H-imidazole ligands and by two chloride anions in a slightly distorted square-planar geometry. In the organic ligand, the dihedral angle between the benzene ring of the mesityl moiety and the imidazole ring is 76.99 (18°. Weak intramolecular C—H...Cl hydrogen-bonding interactions consolidate the molecular conformation.

  14. Characterization of Zn(q+)-imidazole (q = 0, 1, 2) organometallic complexes: DFT methods vs. standard and explicitly correlated post-Hartree-Fock methods.

    Science.gov (United States)

    Boussouf, K; Boulmene, R; Prakash, M; Komiha, N; Taleb, M; Mogren Al-Mogren, M; Hochlaf, M

    2015-06-14

    In the present work, we investigate the bonding, structures, stability and spectra of the Zn(q+)Im (where q = 0, 1, and 2) complexes, which are zeolitic imidazolate frameworks (ZIFs) and Zn-enzyme sub-units. Through a benchmark work, we used density functional theory (DFT) with dispersion correction and standard and explicitly correlated ab initio methods. For neutral Zn(0)Im, we found two stable weakly bound forms: (i) a stacked ferrocene-like complex and (ii) a planar σ-type complex. This is the first report of the Zn(0) organic compound with a stacked ferrocene-like structure. The most stable isomers of the ionic species consist of σ-type bonded complexes. The role of various types of covalent and noncovalent interactions within these complexes is discussed after performing vibrational, NBO, charge and orbital analyses. For neutral species, van der Waals (vdWs) and charge transfer through covalent as well as noncovalent interactions are in action; whereas the bonding is dominated by charge transfer from Zn to Im within the ionic species. These findings are important to understand, at the microscopic level, the structure and the bonding within the ZIFs and the Zn-enzymes. Moreover, we establish the ability and reliability of M05-2X and PBE0 functionals for the simultaneous correct description of covalent and noncovalent interactions since this DFT leads to a close agreement with post-Hartree-Fock methods. The newly launched M11 functional is also suited for the description of noncovalent interactions. Therefore, M05-2X and PBE0 functionals are recommended for studying the larger complexes formed by Zn and Im, such as the ZIFs and Zn-enzymes.

  15. Benzodiazepine modulation of partial agonist efficacy and spontaneously active GABAA receptors supports an allosteric model of modulation

    OpenAIRE

    Downing, Scott S; Lee, Yan T; Farb, David H; Gibbs, Terrell T

    2005-01-01

    Benzodiazepines (BZDs) have been used extensively for more than 40 years because of their high therapeutic index and low toxicity. Although BZDs are understood to act primarily as allosteric modulators of GABAA receptors, the mechanism of modulation is not well understood.The applicability of an allosteric model with two binding sites for γ-aminobutyric acid (GABA) and one for a BZD-like modulator was investigated.This model predicts that BZDs should enhance the efficacy of partial agonists.C...

  16. Delineation of the functional properties and the mechanism of action of AA29504, an allosteric agonist and positive allosteric modulator of GABAAreceptors.

    Science.gov (United States)

    Olander, Emma Rie; Madjroh, Nawid; Bunch, Lennart; Söderhielm, Pella Cecilia; Jensen, Anders A

    2018-04-01

    The retigabine analog 2-amino-4-[(2,4,6-trimethylbenzylamino)-phenyl]-carbamic acid ethyl ester (AA29504) is a positive allosteric modulator (PAM) of γ-aminobutyric acid A receptors (GABA A Rs), and the modulator has been used in ex vivo/in vivo studies to probe the physiological roles of native δ-containing GABA A Rs. In this study, the functional properties and mode of action of AA29504 were investigated at human GABA A Rs expressed in Xenopus oocytes by two-electrode voltage clamp electrophysiology. AA29504 was found to be an allosteric GABA A R agonist displaying low intrinsic activities at 3-30 μM. AA29504 was essentially equipotent as a PAM at the 13 GABA A R subtypes tested (EC 50 : 0.45-5.2 μM), however GABA EC 5 -evoked currents through αβδ subtypes were modulated to substantially higher levels than those through αβγ 2S subtypes (relative to GABA I max ). While the δ/γ 2S -difference clearly was key for this differential GABA efficacy modulation, studies of the AA29504-mediated modulation of different α 4,5,6 -containing αβ, αβγ 2S and αβδ GABA A Rs revealed the α-subunit identity to be another important determinant. Based on its functional properties at numerous mutant GABA A Rs and on in silico analysis of its low-energy conformations, AA29504 is proposed to act through an allosteric site in the transmembrane β (+) /α (-) interface in the GABA A R also targeted by etomidate and several other modulators. In contrast to these modulators, however, AA29504 did not display substantial β 2 /β 3 -over-β 1 GABA A R preference, which challenges the notion of ligands targeting this site always possessing this subtype-selectivity profile. Hence, the detailed pharmacological profiling of AA29504 both highlights the complexity of allosteric GABA A R modulation and provides valuable information about this modulator as a pharmacological tool. Copyright © 2018 Elsevier Inc. All rights reserved.

  17. Enhancement of proton conduction at low humidity by incorporating imidazole microcapsules into polymer electrolyte membranes

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Jingtao; Yue, Xiujun; Zhang, Zizhuo; Yang, Zheng; Li, Yifan; Wu, Hong; Jiang, Zhongyi [Key Laboratory for Green Chemical Technology, Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072 (China); Zhang, Han; Yang, Xinlin [Key Laboratory of Functional Polymer Materials, Ministry of Education, Institute of Polymer Chemistry, Nankai University, Tianjin 300071 (China)

    2012-11-07

    Design and fabrication of hierarchically structured membranes with high proton conductivity is crucial to many energy-relevant applications including proton exchange membrane fuel cell (PEMFC). Here, a series of imidazole microcapsules (IMCs) with tunable imidazole group loading, shell thickness, and lumen size are synthesized and incorporated into a sulfonated poly(ether ether ketone) (SPEEK) matrix to prepare composite membranes. The IMCs play two roles: i) Improving water retention properties of the membrane. The IMCs, similar to the vacuoles in plant cells, can render membrane a stable water environment. The lumen of the IMCs acts as a water reservoir and the shell of IMCs can manipulate water release. ii) They form anhydrous proton transfer pathways and low energy barrier pathways for proton hopping, imparting an enhanced proton transfer via either a vehicle mechanism or Grotthuss mechanism. In particular, at the relative humidity (RH) as low as 20%, the composite membrane exhibits an ultralow proton conductivity decline and the proton conductivity is one to two orders of magnitude higher than that of SPEEK control membrane. The enhanced proton conductivity affords the composite membrane an elevated peak power density from 69.5 to 104.5 mW cm{sup -2} in a single cell. Moreover, the application potential of the composite membrane for CO{sub 2} capture is explored. (Copyright copyright 2012 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  18. Nonenzymatic electrochemical sensor based on imidazole-functionalized graphene oxide for progesterone detection.

    Science.gov (United States)

    Gevaerd, Ava; Blaskievicz, Sirlon F; Zarbin, Aldo J G; Orth, Elisa S; Bergamini, Márcio F; Marcolino-Junior, Luiz H

    2018-04-21

    The modification of electrode surfaces has been the target of study for many researchers in order to improve the analytical performance of electrochemical sensors. Herein, the use of an imidazole-functionalized graphene oxide (GO-IMZ) as an artificial enzymatic active site for voltammetric determination of progesterone (P4) is described for the first time. The morphology and electrochemical performance of electrode modified with GO-IMZ were characterized by scanning electron microscopy and cyclic voltammetry, respectively. Under optimized conditions, the proposed sensor showed a synergistic effect of the GO sheets and the imidazole groups anchored on its backbone, which promoted a significant enhancement on electrochemical reduction of P4. Figures of merits such as linear dynamic response for P4 concentration ranging from 0.22 to 14.0 μmol L -1 , limit of detection of 68 nmol L -1 and limit of quantification and 210 nmol L -1 were found. In addition, presented a higher sensitivity, 426 nA L µmol -1 , when compared to the unmodified electrode. Overall, the proposed device showed to be a promising platform for a simple, rapid, and direct analysis of progesterone. Copyright © 2018 Elsevier B.V. All rights reserved.

  19. Effect of phenols and carboxylic acids on photochromism of 1-alkyl-2-(arylazo)imidazoles

    International Nuclear Information System (INIS)

    Gayen, Pallab; Sinha, Chittaranjan

    2012-01-01

    Light irradiated trans-to-cis isomerization of 1-alkyl-2-(arylazo)imidazole in the presence of phenol, catechol, benzoic acid and salicylic acid (called co-factors) has been studied in this work. The rate of trans→cis photoisomerization is decreased in the presence of co-factor in the medium and is dependent on the concentration of active quotient about photochrome. The decrease in rate follows catechol>benzoic acid>phenol>salicylic acid. This trend is due to the effects of dissociation ability of –O–H/–COOH, intermolecular association of the molecules etc. The reverse change, cis-to-trans, is very slow in light irradiation and has been carried out by a thermal process in the dark. The quantum yield of isomerization follows the same sequence of effects of co-factors. - Highlights: ► Photoisomerisation of 1-alkyl-2-(arylazo)imidazoles, trans-to-cis, is described in this work. ► The process is sensitive to the environment of the photochrome and the solution. ► The rate of photoisomerization decreases as catechol>benzoic acid>phenol>salicylic acid. ► The reverse isomerization, cis-to-trans is very slow with light and has been carried out with heat. ► The activation energy is less than these values when carried out in fresh solution only.

  20. Imidazole and beta-carotene photoprotection against photodynamic therapy evaluated by synchrotron infrared microscopy

    Science.gov (United States)

    Bosio, Gabriela N.; Parisi, Julieta; García Einschlag, Fernando S.; Mártire, Daniel O.

    2018-04-01

    In order to better understand the role of β-carotene and imidazole on the Photodynamic Therapy (PDT) mechanism, synchrotron infrared microscopy was used to detect the associated intracellular biochemical modifications following the visible light irradiation of HeLa cells incubated with these compounds as typical hydrophobic and hydrophilic singlet oxygen quenchers, respectively. For this purpose, PDT was performed employing the hydrophilic sensitizer 5,10,15,20-Tetrakis (1-methyl-4-pyridinio) porphyrin tetra (p-toluenesulfonate), TMPyP, and the hydrophobic sensitizer 5-(4-Methoxycarboxyphenyl)-10,15,20-triphenyl-21H,23H-porphyrin. The single cell IR spectra of PDT-treated, PDT plus quencher-treated and control HeLa cells were recorded at the SOLEIL Synchrotron Infrared SMIS beamline targeting specifically the cell nucleus. Principal Component Analysis (PCA) was used to assess the IR spectral changes. PCA revealed that there is a frequency shift of the protein Amide I vibrational band for the assays with the TMPyP sensitizer, indicating changes in the protein secondary structures of the PDT-treated cancer cells compared to the controls. In addition, the scores in those cells treated with both quenchers appear to be similar to the controls indicating a photoprotective effect. Comparative experiments carried out with SKMEL-28 and HaCat cells showed non- significant photoprotective effects of β-carotene and imidazole.

  1. Green synthesis of novel quinoline based imidazole derivatives and evaluation of their antimicrobial activity

    Directory of Open Access Journals (Sweden)

    N.C. Desai

    2014-12-01

    Full Text Available We have described the conventional and microwave method for the synthesis of N-(4-((2-chloroquinolin-3-ylmethylene-5-oxo-2-phenyl-4,5-dihydro-1H-imidazol-1-yl(arylamides 3a–l. It is observed that the solvent-free microwave thermolysis is a convenient, rapid, high-yielding, and environmental friendly protocol for the synthesis of quinoline based imidazole derivatives when compared with conventional reaction in a solution phase. Antimicrobial activity of the newly synthesized compounds is screened in vitro on the following microbial cultures: Escherichia coli (MTCC 443, Pseudomonas aeruginosa (MTCC 1688, Staphylococcus aureus (MTCC 96, Streptococcus pyogenes (MTCC 442, Candida albicans (MTCC 227, Aspergillus niger (MTCC 282, Aspergillus clavatus (MTCC 1323. All the synthesized bio-active molecules are tested for their in vitro antimicrobial activity by bioassay namely serial broth dilution. Among these compounds 3c, 3d, 3f, 3h and 3j show significant potency against different microbial strains. All the compounds have been characterized by IR, 1H NMR, 13C NMR and mass spectral data. On the basis of statistical analysis, it is observed that these compounds give significant co-relation.

  2. Acute Toxicity of Imidazole Nitrate Ionic Liquids with Varying Chain Lengths to Earthworms (Eisenia foetida).

    Science.gov (United States)

    Shao, Yuting; Du, Zhongkun; Zhang, Cheng; Zhu, Lusheng; Wang, Jinhua; Wang, Jun

    2017-08-01

    When ionic liquids (ILs) first came into use, we thought that they were safe. However, upon further investigation, researchers found that ILs are not harmless. In this study, the model soil organism, earthworms (Eisenia foetida), were used to study the acute toxicity of imidazole nitrate ionic liquids with varying chain lengths from 2 to 12. The experiment used two different methods, a filter paper contact test (48 h) and an artificial soil test (14 days), to determine the toxicity. These results demonstrated that the toxicity increased with the length of carbon chains until C 8 and that the cut-off effect occurred at 1-octyl-3-methyl imidazole nitrates.Then, the toxicity began to increase again. At the same time, the concentrations of [C 10 mim]NO 3 and [C 12 mim]NO 3 were determined by high performance liquid chromatography and demonstrated that ILs were stable throughout the experiment. The present study revealed the acute toxicity of ILs with varying chain lengths.

  3. The lactose repressor system: paradigms for regulation, allosteric behavior and protein folding.

    Science.gov (United States)

    Wilson, C J; Zhan, H; Swint-Kruse, L; Matthews, K S

    2007-01-01

    In 1961, Jacob and Monod proposed the operon model for gene regulation based on metabolism of lactose in Escherichia coli. This proposal was followed by an explication of allosteric behavior by Monod and colleagues. The operon model rationally depicted how genetic mechanisms can control metabolic events in response to environmental stimuli via coordinated transcription of a set of genes with related function (e.g. metabolism of lactose). The allosteric response found in the lactose repressor and many other proteins has been extended to a variety of cellular signaling pathways in all organisms. These two models have shaped our view of modern molecular biology and captivated the attention of a surprisingly broad range of scientists. More recently, the lactose repressor monomer was used as a model system for experimental and theoretical explorations of protein folding mechanisms. Thus, the lac system continues to advance our molecular understanding of genetic control and the relationship between sequence, structure and function.

  4. Signaling within Allosteric Machines: Signal Transmission Pathways Inside G Protein-Coupled Receptors.

    Science.gov (United States)

    Bartuzi, Damian; Kaczor, Agnieszka A; Matosiuk, Dariusz

    2017-07-15

    In recent years, our understanding of function of G protein-coupled receptors (GPCRs) has changed from a picture of simple signal relays, transmitting only a particular signal to a particular G protein heterotrimer, to versatile machines, capable of various responses to different stimuli and being modulated by various factors. Some recent reports provide not only the data on ligands/modulators and resultant signals induced by them, but also deeper insights into exact pathways of signal migration and mechanisms of signal transmission through receptor structure. Combination of these computational and experimental data sheds more light on underlying mechanisms of signal transmission and signaling bias in GPCRs. In this review we focus on available clues on allosteric pathways responsible for complex signal processing within GPCRs structures, with particular emphasis on linking compatible in silico- and in vitro-derived data on the most probable allosteric connections.

  5. ATP-competitive inhibitors of the mitotic kinesin KSP that function via an allosteric mechanism.

    Science.gov (United States)

    Luo, Lusong; Parrish, Cynthia A; Nevins, Neysa; McNulty, Dean E; Chaudhari, Amita M; Carson, Jeffery D; Sudakin, Valery; Shaw, Antony N; Lehr, Ruth; Zhao, Huizhen; Sweitzer, Sharon; Lad, Latesh; Wood, Kenneth W; Sakowicz, Roman; Annan, Roland S; Huang, Pearl S; Jackson, Jeffrey R; Dhanak, Dashyant; Copeland, Robert A; Auger, Kurt R

    2007-11-01

    The mitotic kinesin KSP (kinesin spindle protein, or Eg5) has an essential role in centrosome separation and formation of the bipolar mitotic spindle. Its exclusive involvement in the mitotic spindle of proliferating cells presents an opportunity for developing new anticancer agents with reduced side effects relative to antimitotics that target tubulin. Ispinesib is an allosteric small-molecule KSP inhibitor in phase 2 clinical trials. Mutations that attenuate ispinesib binding to KSP have been identified, which highlights the need for inhibitors that target different binding sites. We describe a new class of selective KSP inhibitors that are active against ispinesib-resistant forms of KSP. These ATP-competitive KSP inhibitors do not bind in the nucleotide binding pocket. Cumulative data from generation of resistant cells, site-directed mutagenesis and photo-affinity labeling suggest that they compete with ATP binding via a novel allosteric mechanism.

  6. Internalization of the chemokine receptor CCR4 can be evoked by orthosteric and allosteric receptor antagonists.

    Science.gov (United States)

    Ajram, Laura; Begg, Malcolm; Slack, Robert; Cryan, Jenni; Hall, David; Hodgson, Simon; Ford, Alison; Barnes, Ashley; Swieboda, Dawid; Mousnier, Aurelie; Solari, Roberto

    2014-04-15

    The chemokine receptor CCR4 has at least two natural agonist ligands, MDC (CCL22) and TARC (CCL17) which bind to the same orthosteric site with a similar affinity. Both ligands are known to evoke chemotaxis of CCR4-bearing T cells and also elicit CCR4 receptor internalization. A series of small molecule allosteric antagonists have been described which displace the agonist ligand, and inhibit chemotaxis. The aim of this study was to determine which cellular coupling pathways are involved in internalization, and if antagonists binding to the CCR4 receptor could themselves evoke receptor internalization. CCL22 binding coupled CCR4 efficiently to β-arrestin and stimulated GTPγS binding however CCL17 did not couple to β-arrestin and only partially stimulated GTPγS binding. CCL22 potently induced internalization of almost all cell surface CCR4, while CCL17 showed only weak effects. We describe four small molecule antagonists that were demonstrated to bind to two distinct allosteric sites on the CCR4 receptor, and while both classes inhibited agonist ligand binding and chemotaxis, one of the allosteric sites also evoked receptor internalization. Furthermore, we also characterize an N-terminally truncated version of CCL22 which acts as a competitive antagonist at the orthosteric site, and surprisingly also evokes receptor internalization without demonstrating any agonist activity. Collectively this study demonstrates that orthosteric and allosteric antagonists of the CCR4 receptor are capable of evoking receptor internalization, providing a novel strategy for drug discovery against this class of target. Copyright © 2014 The Authors. Published by Elsevier B.V. All rights reserved.

  7. Quantifying Allosteric Communication via Both Concerted Structural Changes and Conformational Disorder with CARDS.

    Science.gov (United States)

    Singh, Sukrit; Bowman, Gregory R

    2017-04-11

    Allosteric (i.e., long-range) communication within proteins is crucial for many biological processes, such as the activation of signaling cascades in response to specific stimuli. However, the physical basis for this communication remains unclear. Existing computational methods for identifying allostery focus on the role of concerted structural changes, but recent experimental work demonstrates that disorder is also an important factor. Here, we introduce the Correlation of All Rotameric and Dynamical States (CARDS) framework for quantifying correlations between both the structure and disorder of different regions of a protein. To quantify disorder, we draw inspiration from methods for quantifying "dynamic heterogeneity" from chemical physics to classify segments of a dihedral's time evolution as being in either ordered or disordered regimes. To demonstrate the utility of this approach, we apply CARDS to the Catabolite Activator Protein (CAP), a transcriptional activator that is regulated by Cyclic Adenosine MonoPhosphate (cAMP) binding. We find that CARDS captures allosteric communication between the two cAMP-Binding Domains (CBDs). Importantly, CARDS reveals that this coupling is dominated by disorder-mediated correlations, consistent with NMR experiments that establish allosteric coupling between the CBDs occurs without a concerted structural change. CARDS also recapitulates an enhanced role for disorder in the communication between the DNA-Binding Domains (DBDs) and CBDs in the S62F variant of CAP. Finally, we demonstrate that using CARDS to find communication hotspots identifies regions of CAP that are in allosteric communication without foreknowledge of their identities. Therefore, we expect CARDS to be of great utility for both understanding and predicting allostery.

  8. Sparse networks of directly coupled, polymorphic, and functional side chains in allosteric proteins.

    Science.gov (United States)

    Soltan Ghoraie, Laleh; Burkowski, Forbes; Zhu, Mu

    2015-03-01

    Recent studies have highlighted the role of coupled side-chain fluctuations alone in the allosteric behavior of proteins. Moreover, examination of X-ray crystallography data has recently revealed new information about the prevalence of alternate side-chain conformations (conformational polymorphism), and attempts have been made to uncover the hidden alternate conformations from X-ray data. Hence, new computational approaches are required that consider the polymorphic nature of the side chains, and incorporate the effects of this phenomenon in the study of information transmission and functional interactions of residues in a molecule. These studies can provide a more accurate understanding of the allosteric behavior. In this article, we first present a novel approach to generate an ensemble of conformations and an efficient computational method to extract direct couplings of side chains in allosteric proteins, and provide sparse network representations of the couplings. We take the side-chain conformational polymorphism into account, and show that by studying the intrinsic dynamics of an inactive structure, we are able to construct a network of functionally crucial residues. Second, we show that the proposed method is capable of providing a magnified view of the coupled and conformationally polymorphic residues. This model reveals couplings between the alternate conformations of a coupled residue pair. To the best of our knowledge, this is the first computational method for extracting networks of side chains' alternate conformations. Such networks help in providing a detailed image of side-chain dynamics in functionally important and conformationally polymorphic sites, such as binding and/or allosteric sites. © 2014 Wiley Periodicals, Inc.

  9. mGluR5 Positive Allosteric Modulation Enhances Extinction Learning Following Cocaine Self-Administration

    OpenAIRE

    Cleva, Richard M.; Hicks, Megan P.; Gass, Justin T.; Wischerath, Kelly C.; Plasters, Elizabeth T.; Widholm, John J.; Olive, M. Foster

    2011-01-01

    Extinction of classically and instrumentally conditioned behaviors, such as conditioned fear and drug-seeking behavior, is a process of active learning, and recent studies indicate that potentiation of glutamatergic transmission facilitates extinction learning. In this study we investigated the effects of the type 5 metabotropic glutamate receptors (mGluR5) positive allosteric modulator 3-cyano-N-(1,3-diphenyl-1H-pyrazol-5-yl)benzamide (CDPPB) on the extinction of cocaine-seeking behavior in ...

  10. Agonist activation of α7 nicotinic acetylcholine receptors via an allosteric transmembrane site

    Science.gov (United States)

    Gill, JasKiran K.; Savolainen, Mari; Young, Gareth T.; Zwart, Ruud; Sher, Emanuele; Millar, Neil S.

    2011-01-01

    Conventional nicotinic acetylcholine receptor (nAChR) agonists, such as acetylcholine, act at an extracellular “orthosteric” binding site located at the interface between two adjacent subunits. Here, we present evidence of potent activation of α7 nAChRs via an allosteric transmembrane site. Previous studies have identified a series of nAChR-positive allosteric modulators (PAMs) that lack agonist activity but are able to potentiate responses to orthosteric agonists, such as acetylcholine. It has been shown, for example, that TQS acts as a conventional α7 nAChR PAM. In contrast, we have found that a compound with close chemical similarity to TQS (4BP-TQS) is a potent allosteric agonist of α7 nAChRs. Whereas the α7 nAChR antagonist metyllycaconitine acts competitively with conventional nicotinic agonists, metyllycaconitine is a noncompetitive antagonist of 4BP-TQS. Mutation of an amino acid (M253L), located in a transmembrane cavity that has been proposed as being the binding site for PAMs, completely blocks agonist activation by 4BP-TQS. In contrast, this mutation had no significant effect on agonist activation by acetylcholine. Conversely, mutation of an amino acid located within the known orthosteric binding site (W148F) has a profound effect on agonist potency of acetylcholine (resulting in a shift of ∼200-fold in the acetylcholine dose-response curve), but had little effect on the agonist dose-response curve for 4BP-TQS. Computer docking studies with an α7 homology model provides evidence that both TQS and 4BP-TQS bind within an intrasubunit transmembrane cavity. Taken together, these findings provide evidence that agonist activation of nAChRs can occur via an allosteric transmembrane site. PMID:21436053

  11. Molecular sites for the positive allosteric modulation of glycine receptors by endocannabinoids.

    Directory of Open Access Journals (Sweden)

    Gonzalo E Yévenes

    Full Text Available Glycine receptors (GlyRs are transmitter-gated anion channels of the Cys-loop superfamily which mediate synaptic inhibition at spinal and selected supraspinal sites. Although they serve pivotal functions in motor control and sensory processing, they have yet to be exploited as drug targets partly because of hitherto limited possibilities for allosteric control. Endocannabinoids (ECs have recently been characterized as direct allosteric GlyR modulators, but the underlying molecular sites have remained unknown. Here, we show that chemically neutral ECs (e.g. anandamide, AEA are positive modulators of α(1, α(2 and α(3 GlyRs, whereas acidic ECs (e.g. N-arachidonoyl-glycine; NA-Gly potentiate α(1 GlyRs but inhibit α(2 and α(3. This subunit-specificity allowed us to identify the underlying molecular sites through analysis of chimeric and mutant receptors. We found that alanine 52 in extracellular loop 2, glycine 254 in transmembrane (TM region 2 and intracellular lysine 385 determine the positive modulation of α(1 GlyRs by NA-Gly. Successive substitution of non-conserved extracellular and TM residues in α(2 converted NA-Gly-mediated inhibition into potentiation. Conversely, mutation of the conserved lysine within the intracellular loop between TM3 and TM4 attenuated NA-Gly-mediated potentiation of α(1 GlyRs, without affecting inhibition of α(2 and α(3. Notably, this mutation reduced modulation by AEA of all three GlyRs. These results define molecular sites for allosteric control of GlyRs by ECs and reveal an unrecognized function for the TM3-4 intracellular loop in the allosteric modulation of Cys-loop ion channels. The identification of these sites may help to understand the physiological role of this modulation and facilitate the development of novel therapeutic approaches to diseases such as spasticity, startle disease and possibly chronic pain.

  12. Allosteric mechanisms within the adenosine A2A-dopamine D2 receptor heterotetramer

    Science.gov (United States)

    Ferré, Sergi; Bonaventura, Jordi; Tomasi, Dardo; Navarro, Gemma; Moreno, Estefanía; Cortés, Antonio; Lluís, Carme; Casadó, Vicent; Volkow, Nora D.

    2017-01-01

    The structure constituted by a G protein coupled receptor (GPCR) homodimer and a G protein provides a main functional unit and oligomeric entities can be viewed as multiples of dimers. For GPCR heteromers, experimental evidence supports a tetrameric structure, comprised of two different homodimers, each able to signal with its preferred G protein. GPCR homomers and heteromers can act as the conduit of allosteric interactions between orthosteric ligands. The well-known agonist/agonist allosteric interaction in the adenosine A2A receptor (A2AR)-dopamine D2 receptor (D2R) heteromer, by which A2AR agonists decrease the affinity of D2R agonists, gave the first rationale for the use of A2AR antagonists in Parkinson’s disease. We review new pharmacological findings that can be explained in the frame of a tetrameric structure of the A2AR-D2R heteromer: first, ligand-independent allosteric modulations by the D2R that result in changes of the binding properties of A2AR ligands; second, differential modulation of the intrinsic efficacy of D2R ligands for G protein-dependent and independent signaling; third, the canonical antagonistic Gs-Gi interaction within the frame of the heteromer; and fourth, the ability of A2AR antagonists, including caffeine, to also exert the same allosteric modulations of D2R ligands than A2AR agonists, while A2AR agonists and antagonists counteract each other’s effects. These findings can have important clinical implications when evaluating the use of A2AR antagonists. They also call for the need of monitoring caffeine intake when evaluating the effect of D2R ligands, when used as therapeutic agents in neuropsychiatric disorders or as probes in imaging studies. PMID:26051403

  13. Allosteric ligands and their binding sites define γ-aminobutyric acid (GABA) type A receptor subtypes.

    Science.gov (United States)

    Olsen, Richard W

    2015-01-01

    GABAA receptors (GABA(A)Rs) mediate rapid inhibitory transmission in the brain. GABA(A)Rs are ligand-gated chloride ion channel proteins and exist in about a dozen or more heteropentameric subtypes exhibiting variable age and brain regional localization and thus participation in differing brain functions and diseases. GABA(A)Rs are also subject to modulation by several chemotypes of allosteric ligands that help define structure and function, including subtype definition. The channel blocker picrotoxin identified a noncompetitive channel blocker site in GABA(A)Rs. This ligand site is located in the transmembrane channel pore, whereas the GABA agonist site is in the extracellular domain at subunit interfaces, a site useful for low energy coupled conformational changes of the functional channel domain. Two classes of pharmacologically important allosteric modulatory ligand binding sites reside in the extracellular domain at modified agonist sites at other subunit interfaces: the benzodiazepine site and the high-affinity, relevant to intoxication, ethanol site. The benzodiazepine site is specific for certain GABA(A)R subtypes, mainly synaptic, while the ethanol site is found at a modified benzodiazepine site on different, extrasynaptic, subtypes. In the transmembrane domain are allosteric modulatory ligand sites for diverse chemotypes of general anesthetics: the volatile and intravenous agents, barbiturates, etomidate, propofol, long-chain alcohols, and neurosteroids. The last are endogenous positive allosteric modulators. X-ray crystal structures of prokaryotic and invertebrate pentameric ligand-gated ion channels, and the mammalian GABA(A)R protein, allow homology modeling of GABA(A)R subtypes with the various ligand sites located to suggest the structure and function of these proteins and their pharmacological modulation. © 2015 Elsevier Inc. All rights reserved.

  14. An allosteric model of the molecular interactions of excitation- contraction coupling in skeletal muscle

    OpenAIRE

    1993-01-01

    A contact interaction is proposed to exist between the voltage sensor of the transverse tubular membrane of skeletal muscle and the calcium release channel of the sarcoplasmic reticulum. This interaction is given a quantitative formulation inspired in the Monod, Wyman, and Changeux model of allosteric transitions in hemoglobin (Monod, J., J. Wyman, and J.-P. Changeux. 1965. Journal of Molecular Biology. 12:88- 118), and analogous to one proposed by Marks and Jones for voltage- dependent Ca ch...

  15. Discovery of a novel allosteric modulator of 5-HT3 receptor

    DEFF Research Database (Denmark)

    Trattnig, Sarah M; Harpsøe, Kasper; Thygesen, Sarah B

    2012-01-01

    class of negative allosteric modulators of the 5HT3 receptors (5HT3Rs). PU02 (6[(1naphthylmethyl)thio]9Hpurine) is a potent and selective antagonist displaying IC50 values ~1 µM at 5-HT3Rs and substantially lower activities at other Cys-loop receptors. In an elaborate mutagenesis study of the 5HT3A...

  16. Substituted benzoxazinones as potent positive allosteric AMPA receptor modulators: part II.

    Science.gov (United States)

    Mueller, Rudolf; Rachwal, Stanislaw; Tedder, Martina E; Li, Yong-Xin; Zhong, Sheng; Hampson, Aidan; Ulas, Jolanta; Varney, Mark; Nielsson, Lena; Rogers, Gary

    2011-07-01

    AMPA receptors (AMPARs) are an important therapeutic target in the CNS. A series of substituted benzoxazinone derivatives with good to very good in vitro activity as positive allosteric AMPAR modulators was synthesized and evaluated. The appropriate substituent choice on the benzoxazinone fragment improved the affinity towards the AMPA receptor significantly in comparison to our lead molecule CX614. Copyright © 2011 Elsevier Ltd. All rights reserved.

  17. Benzotriazinone and benzopyrimidinone derivatives as potent positive allosteric AMPA receptor modulators.

    Science.gov (United States)

    Mueller, Rudolf; Rachwal, Stanislaw; Lee, Steven; Zhong, Sheng; Li, Yong-Xin; Haroldsen, Peter; Herbst, Todd; Tanimura, Susan; Varney, Mark; Johnson, Steven; Rogers, Gary; Street, Leslie J

    2011-10-15

    AMPA receptors (AMPARs) have been demonstrated to be an important therapeutic CNS target. A series of substituted benzotriazinone and benzopyrimidinone derivatives were prepared with the aim to improve in vivo activity over the previously reported bis-benzoxazinone based AMPAKINE series from our laboratory. These compounds were shown to be potent, positive allosteric AMPAR modulators that have better in vivo activity and improved metabolic stability over the analogous benzoxazinone derivatives. Copyright © 2011 Elsevier Ltd. All rights reserved.

  18. High–resolution crystal structure of deoxy hemoglobin complexed with a potent allosteric effector

    OpenAIRE

    Safo, Martin K.; Moure, Carmen M.; Burnett, James C.; Joshi, Gajanan S.; Abraham, Donald J.

    2001-01-01

    The crystal structure of human deoxy hemoglobin (Hb) complexed with a potent allosteric effector (2-[4-[[(3,5-dimethylanilino)carbonyl]methyl]phenoxy]-2-methylpropionic acid) = RSR-13) is reported at 1.85 Å resolution. Analysis of the hemoglobin:effector complex indicates that two of these molecules bind to the central water cavity of deoxy Hb in a symmetrical fashion, and that each constrains the protein by engaging in hydrogen bonding and hydrophobic interactions with three of its four subu...

  19. Enzyme detection by microfluidics

    DEFF Research Database (Denmark)

    2013-01-01

    Microfluidic-implemented methods of detecting an enzyme, in particular a DNA-modifying enzyme, are provided, as well as methods for detecting a cell, or a microorganism expressing said enzyme. The enzyme is detected by providing a nucleic acid substrate, which is specifically targeted...... by that enzyme...

  20. Synthesis and evaluation of 1-hydroxy/methoxy-4-methyl-2-phenyl-1H-imidazole-5-carboxylic acid derivatives as non-purine xanthine oxidase inhibitors.

    Science.gov (United States)

    Chen, Shaolei; Zhang, Tingjian; Wang, Jian; Wang, Fangyang; Niu, Handong; Wu, Chunfu; Wang, Shaojie

    2015-10-20

    Xanthine oxidase is a key enzyme that catalyses hypoxanthine and xanthine to uric acid, whose overproduction leads to the gout-causing hyperuricemia. In this study, a series of 1-hydroxy/methoxy-4-methyl-2-phenyl-1H-imidazole-5-carboxylic acid derivatives (4a-4k and 6a-6k) was synthesized and evaluated for their inhibitory potency against xanthine oxidase. The 1-hydroxyl substituted derivatives 4a-4k showed excellent inhibitory potency with IC50 values ranging from 0.003 μM to 1.2 μM, with compounds 4d (IC₅₀ = 0.003 μM), 4e (IC₅₀ = 0.003 μM), and 4f (IC₅₀ = 0.006 μM) manifesting the most potent xanthine oxidase inhibitory potency that were comparable with that of Febuxostat (IC₅₀ = 0.01 μM). Lineweaver-Burk plot analysis revealed that representative compound 4f acted as a mixed-type inhibitor for xanthine oxidase. The basis of significant inhibition of xanthine oxidase by 4f was rationalized by its molecular docking into the active site of xanthine dehydrogenase. Copyright © 2015 Elsevier Masson SAS. All rights reserved.

  1. Allosteric Mutant IDH1 Inhibitors Reveal Mechanisms for IDH1 Mutant and Isoform Selectivity

    Energy Technology Data Exchange (ETDEWEB)

    Xie, Xiaoling; Baird, Daniel; Bowen, Kimberly; Capka, Vladimir; Chen, Jinyun; Chenail, Gregg; Cho, YoungShin; Dooley, Julia; Farsidjani, Ali; Fortin, Pascal; Kohls, Darcy; Kulathila, Raviraj; Lin, Fallon; McKay, Daniel; Rodrigues, Lindsey; Sage, David; Touré, B. Barry; van der Plas, Simon; Wright, Kirk; Xu, Ming; Yin, Hong; Levell, Julian; Pagliarini, Raymond A. (Novartis)

    2017-03-01

    Oncogenic IDH1 and IDH2 mutations contribute to cancer via production of R-2-hydroxyglutarate (2-HG). Here, we characterize two structurally distinct mutant- and isoform-selective IDH1 inhibitors that inhibit 2-HG production. Both bind to an allosteric pocket on IDH1, yet shape it differently, highlighting the plasticity of this site. Oncogenic IDH1R132H mutation destabilizes an IDH1 “regulatory segment,” which otherwise restricts compound access to the allosteric pocket. Regulatory segment destabilization in wild-type IDH1 promotes inhibitor binding, suggesting that destabilization is critical for mutant selectivity. We also report crystal structures of oncogenic IDH2 mutant isoforms, highlighting the fact that the analogous segment of IDH2 is not similarly destabilized. This intrinsic stability of IDH2 may contribute to observed inhibitor IDH1 isoform selectivity. Moreover, discrete residues in the IDH1 allosteric pocket that differ from IDH2 may also guide IDH1 isoform selectivity. These data provide a deeper understanding of how IDH1 inhibitors achieve mutant and isoform selectivity.

  2. Tuning Transcriptional Regulation through Signaling: A Predictive Theory of Allosteric Induction.

    Science.gov (United States)

    Razo-Mejia, Manuel; Barnes, Stephanie L; Belliveau, Nathan M; Chure, Griffin; Einav, Tal; Lewis, Mitchell; Phillips, Rob

    2018-04-25

    Allosteric regulation is found across all domains of life, yet we still lack simple, predictive theories that directly link the experimentally tunable parameters of a system to its input-output response. To that end, we present a general theory of allosteric transcriptional regulation using the Monod-Wyman-Changeux model. We rigorously test this model using the ubiquitous simple repression motif in bacteria by first predicting the behavior of strains that span a large range of repressor copy numbers and DNA binding strengths and then constructing and measuring their response. Our model not only accurately captures the induction profiles of these strains, but also enables us to derive analytic expressions for key properties such as the dynamic range and [EC 50 ]. Finally, we derive an expression for the free energy of allosteric repressors that enables us to collapse our experimental data onto a single master curve that captures the diverse phenomenology of the induction profiles. Copyright © 2018 The Author(s). Published by Elsevier Inc. All rights reserved.

  3. Identification of an allosteric binding site for RORγt inhibition

    Energy Technology Data Exchange (ETDEWEB)

    Scheepstra, Marcel; Leysen, Seppe; vanAlmen, Geert C.; Miller, J. Richard; Piesvaux, Jennifer; Kutilek, Victoria; van Eenennaam, Hans; Zhang, Hongjun; Barr, Kenneth; Nagpal, Sunil; Soisson, Stephen M.; Kornienko, Maria; Wiley, Kristen; Elsen, Nathaniel; Sharma, Sujata; Correll, Craig C.; Trotter, B. Wesley; van der Stelt, Mario; Oubrie, Arthur; Ottmann, Christian; Parthasarathy, Gopal; Brunsveld, Luc (Merck); (Eindhoven)

    2015-12-07

    RORγt is critical for the differentiation and proliferation of Th17 cells associated with several chronic autoimmune diseases. We report the discovery of a novel allosteric binding site on the nuclear receptor RORγt. Co-crystallization of the ligand binding domain (LBD) of RORγt with a series of small-molecule antagonists demonstrates occupancy of a previously unreported allosteric binding pocket. Binding at this non-canonical site induces an unprecedented conformational reorientation of helix 12 in the RORγt LBD, which blocks cofactor binding. The functional consequence of this allosteric ligand-mediated conformation is inhibition of function as evidenced by both biochemical and cellular studies. RORγt function is thus antagonized in a manner molecularly distinct from that of previously described orthosteric RORγt ligands. This brings forward an approach to target RORγt for the treatment of Th17-mediated autoimmune diseases. The elucidation of an unprecedented modality of pharmacological antagonism establishes a mechanism for modulation of nuclear receptors.

  4. Activation of Hsp90 Enzymatic Activity and Conformational Dynamics through Rationally Designed Allosteric Ligands.

    Science.gov (United States)

    Sattin, Sara; Tao, Jiahui; Vettoretti, Gerolamo; Moroni, Elisabetta; Pennati, Marzia; Lopergolo, Alessia; Morelli, Laura; Bugatti, Antonella; Zuehlke, Abbey; Moses, Mike; Prince, Thomas; Kijima, Toshiki; Beebe, Kristin; Rusnati, Marco; Neckers, Len; Zaffaroni, Nadia; Agard, David A; Bernardi, Anna; Colombo, Giorgio

    2015-09-21

    Hsp90 is a molecular chaperone of pivotal importance for multiple cell pathways. ATP-regulated internal dynamics are critical for its function and current pharmacological approaches block the chaperone with ATP-competitive inhibitors. Herein, a general approach to perturb Hsp90 through design of new allosteric ligands aimed at modulating its functional dynamics is proposed. Based on the characterization of a first set of 2-phenylbenzofurans showing stimulatory effects on Hsp90 ATPase and conformational dynamics, new ligands were developed that activate Hsp90 by targeting an allosteric site, located 65 Å from the active site. Specifically, analysis of protein responses to first-generation activators was exploited to guide the design of novel derivatives with improved ability to stimulate ATP hydrolysis. The molecules' effects on Hsp90 enzymatic, conformational, co-chaperone and client-binding properties were characterized through biochemical, biophysical and cellular approaches. These designed probes act as allosteric activators of the chaperone and affect the viability of cancer cell lines for which proper functioning of Hsp90 is necessary. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  5. Bioavailability of the imidazole antifungal agent clotrimazole and its effects on key biotransformation genes in the common carp (Cyprinus carpio).

    Science.gov (United States)

    Corcoran, Jenna; Lange, Anke; Cumming, Rob I; Owen, Stewart F; Ball, Jonathan S; Tyler, Charles R; Winter, Matthew J

    2014-07-01

    Clotrimazole (CTZ) is a persistent imidazole antifungal agent which is frequently detected in the aquatic environment and predicted to bio-concentrate in fish. Common carp (Cyprinus carpio) were exposed to mean measured concentrations of either 1.02 or 14.63μgl(-1) CTZ for 4 and 10 days, followed by a depuration period of 4 days in a further group of animals. Following each exposure regimen, plasma and liver CTZ concentrations were measured. Mean measured plasma concentrations of CTZ in animals exposed to the lower concentration of CTZ were 30 and 44μgl(-1) on days 4 and 10, respectively, and in the higher concentration were 318 and 336μgl(-1). Mean measured liver levels in the same animals were 514, 1725, 2111 and 7017μgl(-1) suggesting progressive hepatic accumulation. Measurement of CTZ in plasma after depuration suggested efficient elimination within 4 days, but appreciable levels of CTZ remained in the liver after depuration suggesting a degree of persistence in this tissue. In addition we measured responses of a number of key hepatic detoxification gene targets in the liver associated with the transcription factor pregnane X receptor (PXR); namely cyp450s 2k and 3a, glutathione-S-transferases a and p (gsta and p), and drug transporters multidrug resistance protein1 (mdr1), and MDR-related protein2 (mrp2). CTZ is a potent ligand of the PXR in humans and there is some evidence of PXR activation following exposure to CTZ in fish. The highest concentration of CTZ was adopted to explore the potential for alterations to detoxification gene expression in fish at a pharmacologically relevant dose level, and the lower concentration is within the range reported in effluents from waste water treatment works (WWTW). The genes for all biotransformation enzymes were up-regulated after exposure to the higher concentration of CTZ for 10 days, and alterations in expression occurred for the drug transporter genes mdr1 and mrp2 following exposure to the lower concentration

  6. Tyrosinase and catechol oxidase activity of copper(I) complexes supported by imidazole-based ligands: structure-reactivity correlations.

    Science.gov (United States)

    Wendt, Franziska; Näther, Christian; Tuczek, Felix

    2016-09-01

    Four new imidazole-based ligands, 4-((1H-imidazol-4-yl)methyl)-2-phenyl-4,5-dihydrooxyzole (L OL 1), 4-((1H-imidazol-4-yl)methyl)-2-(tert-butyl)-4,5-dihydrooxyzole (L OL 2), 4-((1H-imidazol-4-yl)methyl)-2-methyl-4,5-dihydrooxyzole (L OL 3), and N-(2,2-dimethylpropylidene)-2-(1-trityl-1H-imidazol-4-yl-)ethyl amine (L imz 1), have been synthesized. The corresponding copper(I) complexes [Cu(I)(L OL 1)(CH3CN)]PF6 (CuL OL 1), [Cu(I)(L OL 2)(CH3CN)]PF6 (CuL OL 2), [Cu(I)(L OL 3)(CH3CN)]PF6 (CuL OL 3), [Cu(I)(L imz 1)(CH3CN)2]PF6 (CuL imz 1) as well as the Cu(I) complex derived from the known ligand bis(1-methylimidazol-2-yl)methane (BIMZ), [Cu(I)(BIMZ)(CH3CN)]PF6 (CuBIMZ), are screened as catalysts for the oxidation of 3,5-di-tert-butylcatechol (3,5-DTBC-H2) to 3,5-di-tert-butylquinone (3,5-DTBQ). The primary reaction product of these oxidations is 3,5-di-tert-butylsemiquinone (3,5-DTBSQ) which slowly converts to 3,5-DTBQ. Saturation kinetic studies reveal a trend of catalytic activity in the order CuL OL 3 ≈ CuL OL 1 > CuBIMZ > CuL OL 2 > CuL imz 1. Additionally, the catalytic activity of the copper(I) complexes towards the oxygenation of monophenols is investigated. As substrates 2,4-di-tert-butylphenol (2,4-DTBP-H), 3-tert-butylphenol (3-TBP-H), 4-methoxyphenol (4-MeOP-H), N-acetyl-L-tyrosine ethyl ester monohydrate (NATEE) and 8-hydroxyquinoline are employed. The oxygenation products are identified and characterized with the help of UV/Vis and NMR spectroscopy, mass spectrometry, and fluorescence measurements. Whereas the copper complexes with ligands containing combinations of imidazole and imine functions or two imidazole units (CuL imz 1 and CuBIMZ) are found to exhibit catalytic tyrosinase activity, the systems with ligands containing oxazoline just mediate a stoichiometric conversion. Correlations between the structures of the complexes and their reactivities are discussed.

  7. Caricain: A basis for enzyme therapy for coeliac disease

    Directory of Open Access Journals (Sweden)

    Hugh J. Cornell

    2011-09-01

    Full Text Available Gliadin, a glycoprotein present in wheat and other grass cereals, is a causative agent in coeliac disease. It is therefore important to find methods for the detoxification of gliadin. Lysosomal integrity is lost in patients with active coeliac disease but restored when gliadin is removed from the diet. We employed a rat liver lysosome assay to monitor the extent of detoxification of a gliadin digest by caricain, a protein enzyme found in papaya. Pre-incubating the gliadin digest for different durations with caricain allowed the kinetics of the detoxification process to be studied. A significant degree of protection (80% of the lysosomes was achieved with 1.7% w/w of caricain on substrate after incubation for 2 h at 37 °C. The detoxification followed first-order kinetics with a rate constant of 1.7 x 10-4/s. The enzyme was strongly inhibited by imidazole, but weakly by phenylmethyl sulphonyl fluoride, as was also a caricain-enriched fraction from ion-exchange chromatography of papaya oleo-resin. The value of caricain in the detoxification of gliadin was confirmed in the present studies and this enzyme shows promise for enzyme therapy in coeliac disease.

  8. Elevated Liver Enzymes

    Science.gov (United States)

    Symptoms Elevated liver enzymes By Mayo Clinic Staff Elevated liver enzymes may indicate inflammation or damage to cells in the liver. Inflamed or ... than normal amounts of certain chemicals, including liver enzymes, into the bloodstream, which can result in elevated ...

  9. Synthesis and characterization of some complexes with imidazole and pyrazole from saccharinate transition ions in oxidation state (II)

    International Nuclear Information System (INIS)

    Pineda Cedeno, Leslie William

    2001-01-01

    The synthesis and characterization of metal ions saccharinate of the first serie of transition with the imidazole and pyrazole molecules in water and absolute ethanol were studied. In general, it found that in this series of saccharinate of coordinated water molecules are replaced by imidazole and pyrazole molecules with different substitution patterns, generating neutral complex of molecular formula [M(Sac) 2 (L) n (H 2 O) n-4 ] and cationic complex of molecular formula [M(L) n (H 2 O) 2 ]x2Sac, [M(L) n (H 2 O) 3 ]x2Sac, [M(L) n ]x2Sac, where M = V(II), Cr(II), Mc(II), Fe(II), Co(II), Ni(II) y Zn(II); Sac = saccharinate ion; L = imidazole (imd) and pyrazole (pir) and n = 6,4,3 and 2. These compounds are soluble in DMF and insoluble in all other common solvents. In turn, synthesized compounds in water were characterized by X ray crystallography, where preliminary data of refinement cycles, generate formulas of isostructural type [M(imd) 4 (H 2 O) 2 ]x2Sac and [M(Sac) 2 (pir) 2 (H 2 O) 2 ] where M = Co(II), Ni(II). The imidazole complex crystallize in the triclinic crystal system and space group P-1, while the pyrazole complexes crystallize in the monoclinic crystal system and space group P2 (1)/n. Gradual diminution was observed in the bond distances of M-N (saccharinate ion), M-N (imidazole) and M-N (pyrazole). The complex was characterized by spectroscopic methods, magnetic and electrochemical. (author) [es

  10. An allosteric model of the molecular interactions of excitation-contraction coupling in skeletal muscle.

    Science.gov (United States)

    Ríos, E; Karhanek, M; Ma, J; González, A

    1993-09-01

    A contact interaction is proposed to exist between the voltage sensor of the transverse tubular membrane of skeletal muscle and the calcium release channel of the sarcoplasmic reticulum. This interaction is given a quantitative formulation inspired in the Monod, Wyman, and Changeux model of allosteric transitions in hemoglobin (Monod, J., J. Wyman, and J.-P. Changeux. 1965. Journal of Molecular Biology. 12:88-118), and analogous to one proposed by Marks and Jones for voltage-dependent Ca channels (Marks, T. N., and S. W. Jones. 1992. Journal of General Physiology. 99:367-390). The allosteric protein is the calcium release channel, a homotetramer, with two accessible states, closed and open. The kinetics and equilibrium of this transition are modulated by voltage sensors (dihydropyridine receptors) pictured as four units per release channel, each undergoing independent voltage-driven transitions between two states (resting and activating). For each voltage sensor that moves to the activating state, the tendency of the channel to open increases by an equal (large) factor. The equilibrium and kinetic equations of the model are solved and shown to reproduce well a number of experimentally measured relationships including: charge movement (Q) vs. voltage, open probability of the release channel (Po) vs. voltage, the transfer function relationship Po vs. Q, and the kinetics of charge movement, release activation, and deactivation. The main consequence of the assumption of allosteric coupling is that primary effects on the release channel are transmitted backward to the voltage sensor and give secondary effects. Thus, the model reproduces well the effects of perchlorate, described in the two previous articles, under the assumption that the primary effect is to increase the intrinsic tendency of the release channel to open, with no direct effects on the voltage sensor. This modification of the open-closed equilibrium of the release channel causes a shift in the equilibrium

  11. Synthetic polyspermine imidazole-4, 5-amide as an efficient and cytotoxicity-free gene delivery system

    Directory of Open Access Journals (Sweden)

    Duan S

    2012-07-01

    Full Text Available Shi-Yue Duan, Xue-Mei Ge, Nan Lu, Fei Wu, Weien Yuan, Tuo JinSchool of Pharmacy, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of ChinaAbstract: A chemically dynamic spermine-based polymer: polyspermine imidazole-4, 5-amide (PSIA, Mw > 7 kDa was designed, synthesized, and evaluated in terms of its ability to deliver nucleic acids. This polymer was made from an endogenous monomer professionally condensing genes in sperms, spermine, and a known safety drug metabolite, imidazole-4, 5-dicarboxylic acid, through a bis-amide bond conjugated with the imidazole ring. This polymer can condense pDNA at a W/W ratio above 10 to form polyplexes (100–200 nm in diameter, which is consistent with the observation by transmission electron microscopy (TEM, and the zeta potential was in the range of 10–20 mV. The pDNA packaged polymer was stable in phosphate buffer solution (PBS at pH 7.4 (simulated body fluid while the polyplexes were releasing pDNA into the solution at pH 5.8 (simulated endo-lysosomes due to the degradation of the bis-amide linkages in response to changes in pH values. PSIA-polyplexes were able to achieve efficient cellular uptake and luciferase gene silencing by co-transfection of pDNA and siRNA in COS-7 cells and HepG2 cells with negligible cytotoxicity. Biodistribution of Rhodamine B-labeled PSIA-polyplexes after being systemically injected in BALB/c nude-mice showed that the polyplexes circulated throughout the body, accumulated mainly in the kidney at 4 hours of sample administration, and moved to the liver and spleen after 24 hours. All the results suggested that PSIA offered a promising example to balance the transfection efficiency and toxicity of a synthetic carrier system for the delivery of therapeutic nucleic acids.Keywords: gene delivery, polyspermine, cytotoxicity, transfection efficiency, biodistribution

  12. Characterization and application of zeolitic imidazolate framework-8@polyvinyl alcohol nanofibers mats prepared by electrospinning

    Science.gov (United States)

    Fan, Xiaoxiao; Yu, Linling; Li, Lianghao; Yang, Cao; Wen, Junjie; Ye, Xiaokun; Cheng, Jianhua; Hu, Yongyou

    2017-02-01

    In this study, Zeolitic imidazolate framework-8@polyvinyl alcohol (ZIF-8@PVA) nanofibers were creatively fabricated by electrospinning technique, and the nanofibers membranes were characterized by SEM, TEM, XRD, FTIR, TG, DSC, DTA, BET. Its thermal stability, mechanical property, water stability and adsorption nature were also performed. The optimized fabrication parameter of the ZIF-8@PVA was 10 wt% and the uniform diameters of the nanofibers has been obtained. In addition, the ZIF-8@PVA nanofibers displayed unique properties such as a water stable and flexible structure. The adsorption test for Congo red treatment revealed that the nanofibers had a great adsorption performance. The results indicated that the nonwoven fiber mats had a great potential as a new type of membrane adsorbents in wastewater purification. The possible mechanism of CR adsorption onto ZIF-8@PVA was researched.

  13. Zeolitic Imidazolate Framework-8 (ZIF-8) Membranes for Kr/Xe Separation

    Energy Technology Data Exchange (ETDEWEB)

    Wu, Ting; Feng, Xuhui; Elsaidi, Sameh K.; Thallapally, Praveen K.; Carreon, Moises A.

    2017-01-30

    Herein, we demonstrate that a prototypical type of metal organic framework, zeolitic imidazolate framework-8 (ZIF-8), in membrane form, can effectively separate Kr/Xe gas mixtures at industrially relevant compositions. The best membranes separated Kr/Xe mixtures with average Kr permeances as high as 1.5 × 10-8 ± 0.2 mol/m2 s Pa and average separation selectivities of 14.2 ± 1.9 for molar feed compositions corresponding to Kr/Xe ratio encountered typically in air. Molecular sieving, competitive adsorption, and differences in diffusivities were identified as the prevailing separation mechanisms. These membranes potentially represent a less-energy-intensive alternative to cryogenic distillation, which is the benchmark technology used to separate this challenging gas mixture. To our best knowledge, this is the first example of any metal organic membrane composition displaying separation ability for Kr/Xe gas mixtures.

  14. High-Flux Zeolitic Imidazolate Framework Membranes for Propylene/Propane Separation by Postsynthetic Linker Exchange.

    Science.gov (United States)

    Lee, Moon Joo; Kwon, Hyuk Taek; Jeong, Hae-Kwon

    2018-01-02

    While zeolitic imidazolate framework, ZIF-8, membranes show impressive propylene/propane separation, their throughput needs to be greatly improved for practical applications. A method is described that drastically reduces the effective thickness of ZIF-8 membranes, thereby substantially improving their propylene permeance (that is, flux). The new strategy is based on a controlled single-crystal to single-crystal linker exchange of 2-methylimidazole in ZIF-8 membrane grains with 2-imidazolecarboxaldehyde (ZIF-90 linker), thereby enlarging the effective aperture size of ZIF-8. The linker-exchanged ZIF-8 membranes showed a drastic increase in propylene permeance by about four times, with a negligible loss in propylene/propane separation factor when compared to as-prepared membranes. The linker-exchange effect depends on the membrane synthesis method. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  15. Investigation of Synthesis and some Properties of the Copper Complexes Containing Imidazole Ligand

    Directory of Open Access Journals (Sweden)

    Emin Erdem

    2016-06-01

    Full Text Available The copper(II complexes bearing tetrasubstituted imidazole derivatives containing oxygen donor as ligands (L1-6 were synthesized and characterized by spectroscopic methods, magnetic measurements, elemental and thermogravimetric analyses. The fluorescence efficiency of the ligands (L1-6 and their copper(II complexes were investigated at r.t. in DMF solution. Theoretical calculations were performed for the copper(II complex of L4 ligand, in this study. The molecular geometry, bond lengths, bond angles and vibrational wave numbers were calculated by using ab initio calculations based on the Hartree-Fock{HF/6-31G(d} and the density functional theory {B3LYP/6-31G(d} in the ground state. This work is licensed under a Creative Commons Attribution 4.0 International License.

  16. Investigation of the Linker Swing Motion in the Zeolitic Imidazolate Framework ZIF-90

    KAUST Repository

    Zheng, Bin

    2018-03-13

    The linker swing motion in the zeolitic imidazolate framework ZIF-90 is investigated by density functional theory (DFT) calculation, molecular dynamics (MD) and grand-canonical Monte Carlo (GCMC) simulations. The relation between the terminal aldehyde group rotation and the linker swing motion is revealed. The extremely high activation energy of the linker swing motion in ZIF-90 can be attributed to the asymmetric geometry and electron distribution of aldehyde groups. The change in the gate structure resulting from the linker rotation is used to understand the guest adsorption in ZIF-90. This study shows that it is possible to tune the linker swing motion and then the properties of ZIF-90 by manipulating the terminal group rotation. The results highlight the importance of considering the internal freedom effects to correctly describe the linker swing motion and the flexibility of metal-organic frameworks (MOFs).

  17. Carbon dioxide selective adsorption within a highly stable mixed-ligand Zeolitic Imidazolate Framework

    KAUST Repository

    Huang, Lin

    2014-08-01

    A new mixed-ligand Zeolitic Imidazolate Framework Zn4(2-mbIm) 3(bIm)5·4H2O (named JUC-160, 2-mbIm = 2-methylbenzimidazole, bIm = benzimidazole and JUC = Jilin University China) was synthesized with a solvothermal reaction of Zn(NO3) 2·6H2O, bIm and 2-mbIm in DMF solution at 180 °C. Topological analysis indicated that JUC-160 has a zeolite GIS (gismondine) topology. Study of the gas adsorption and thermal and chemical stability of JUC-160 demonstrated its selective adsorption property for carbon dioxide, high thermal stability, and remarkable chemical resistance to boiling alkaline water and organic solvent for up to one week. © 2014 Elsevier B.V.

  18. Electric properties and fabrication of IMI-O LB films containing the imidazole group

    CERN Document Server

    Yoo, S Y; Kwon, Y S; Park, J C

    1999-01-01

    We fabricated an IMI-O polymer containing an imidazole group that could form a complex structure between the monolayer and the metal ions at the air-water interface. Also, the monolayer behavior at the air-water interface and the electrical properties of metal-complexed Langmuir-Blodgett (LB) films were investigated by using Brewster angle microscopy (BAM) and current-voltage(I-V) measurements. The difference in the BAM images between the pure water and the aqueous metal ions is attributed to the interactions of the copolymers with the metal ions at the interface and the consequent change of the monolayer organization. In the I-V characteristics, the current for LB films with different metal ion depended on the quantity of the metal-ion complexed with the LB film due to the interaction between the metal ion and the IMI-O polymer.

  19. A monomeric variant of insulin degrading enzyme (IDE loses its regulatory properties.

    Directory of Open Access Journals (Sweden)

    Eun Suk Song

    2010-03-01

    Full Text Available Insulin degrading enzyme (IDE is a key enzyme in the metabolism of both insulin and amyloid beta peptides. IDE is unique in that it is subject to allosteric activation which is hypothesized to occur through an oligomeric structure.IDE is known to exist as an equilibrium mixture of monomers, dimers, and higher oligomers, with the dimer being the predominant form. Based on the crystal structure of IDE we deleted the putative dimer interface in the C-terminal region, which resulted in a monomeric variant. Monomeric IDE retained enzymatic activity, however instead of the allosteric behavior seen with wild type enzyme it displayed Michaelis-Menten kinetic behavior. With the substrate Abz-GGFLRKHGQ-EDDnp, monomeric IDE retained approximately 25% of the wild type activity. In contrast with the larger peptide substrates beta-endorphin and amyloid beta peptide 1-40, monomeric IDE retained only 1 to 0.25% of wild type activity. Unlike wild type IDE neither bradykinin nor dynorphin B-9 activated the monomeric variant of the enzyme. Similarly, monomeric IDE was not activated by polyphosphates under conditions in which the activity of wild type enzyme was increased more than 50 fold.These findings serve to establish the dimer interface in IDE and demonstrate the requirement for an oligomeric form of the enzyme for its regulatory properties. The data support a mechanism where the binding of activators to oligomeric IDE induces a conformational change that cannot occur in the monomeric variant. Since a conformational change from a closed to a more open structure is likely the rate-determining step in the IDE reaction, the subunit induced conformational change likely shifts the structure of the oligomeric enzyme to a more open conformation.

  20. Gas-Phase Thermal Tautomerization of Imidazole-Acetic Acid: Theoretical and Computational Investigations

    Directory of Open Access Journals (Sweden)

    Saadullah G. Aziz

    2015-11-01

    Full Text Available The gas-phase thermal tautomerization reaction between imidazole-4-acetic (I and imidazole-5-acetic (II acids was monitored using the traditional hybrid functional (B3LYP and the long-range corrected functionals (CAM-B3LYP and ωB97XD with 6-311++G** and aug-cc-pvdz basis sets. The roles of the long-range and dispersion corrections on their geometrical parameters, thermodynamic functions, kinetics, dipole moments, Highest Occupied Molecular Orbital–Lowest Unoccupied Molecular Orbital (HOMO–LUMO energy gaps and total hyperpolarizability were investigated. All tested levels of theory predicted the preference of I over II by 0.750–0.877 kcal/mol. The origin of predilection of I is assigned to the H-bonding interaction (nN8→σ*O14–H15. This interaction stabilized I by 15.07 kcal/mol. The gas-phase interconversion between the two tautomers assumed a 1,2-proton shift mechanism, with two transition states (TS, TS1 and TS2, having energy barriers of 47.67–49.92 and 49.55–52.69 kcal/mol, respectively, and an sp3-type intermediate. A water-assisted 1,3-proton shift route brought the barrier height down to less than 20 kcal/mol in gas-phase and less than 12 kcal/mol in solution. The relatively high values of total hyperpolarizability of I compared to II were interpreted and discussed.

  1. On the kinetic and allosteric regulatory properties of the ADP-glucose pyrophosphorylase from Rhodococcus jostii: An approach to evaluate glycogen metabolism in oleaginous bacteria

    Directory of Open Access Journals (Sweden)

    Antonela Estefanía Cereijo

    2016-06-01

    Full Text Available Rhodococcus spp. are oleaginous bacteria that accumulate glycogen during exponential growth. Despite the importance of these microorganisms in biotechnology, little is known about the regulation of carbon and energy storage, mainly the relationship between glycogen and triacilglycerols metabolisms. Herein we report the molecular cloning and heterologous expression of the gene coding for ADP-glucose pyrophosphorylase (EC 2.7.7.27 of Rhodococcus jostii, strain RHA1. The recombinant enzyme was purified to electrophoretic homogeneity to accurately characterize its oligomeric, kinetic and regulatory properties. The R. jostii ADP-glucose pyrophosphorylase is a homotetramer of 190 kDa exhibiting low basal activity to catalyze synthesis of ADP-glucose, which is markedly influenced by different allosteric effectors. Glucose-6P, mannose-6P, fructose-6P, ribose-5P and phosphoenolpyruvate were major activators; whereas NADPH and 6P-gluconate behaved as main inhibitors of the enzyme. The combination of glucose-6P and other effectors (activators or inhibitors showed a cross-talk effect suggesting that the different metabolites could orchestrate a fine regulation of ADP-glucose pyrophosphorylase in R. jostii. The enzyme exhibited some degree of affinity toward ATP, GTP, CTP, and other sugar 1P substrates. Remarkably, the use of glucosamine-1P was sensitive to allosteric activation. The relevance of the fine regulation of R. jostii ADP-glucose pyrophosphorylase is further analyzed in the framework of proteomic studies already determined for the bacterium. Results support a critical role for glycogen as a temporal reserve that provides a pool of carbon able of be re-routed to produce long-term storage of lipids under certain conditions.

  2. Dual roles of Lys(57) at the dimer interface of human mitochondrial NAD(P)+-dependent malic enzyme.

    Science.gov (United States)

    Hsieh, Ju-Yi; Liu, Jyung-Hurng; Fang, Yi-Wen; Hung, Hui-Chih

    2009-05-13

    Human m-NAD(P)-ME [mitochondrial NAD(P)+-dependent ME (malic enzyme)] is a homotetramer, which is allosterically activated by the binding of fumarate. The fumarate-binding site is located at the dimer interface of the NAD(P)-ME. In the present study, we decipher the functional role of the residue Lys57, which resides at the fumarate-binding site and dimer interface, and thus may be involved in the allosteric regulation and subunit-subunit interaction of the enzyme. In the present study, Lys57 is replaced with alanine, cysteine, serine and arginine residues. Site-directed mutagenesis and kinetic analysis strongly suggest that Lys57 is important for the fumarate-induced activation and quaternary structural organization of the enzyme. Lys57 mutant enzymes demonstrate a reduction of Km and an elevation of kcat following induction by fumarate binding, and also display a much higher maximal activation threshold than WT (wild-type), indicating that these Lys57 mutant enzymes have lower affinity for the effector fumarate. Furthermore, mutation of Lys57 in m-NAD(P)-ME causes the enzyme to become less active and lose co-operativity. It also increased K0.5,malate and decreased kcat values, indicating that the catalytic power of these mutant enzymes was significantly impaired following mutation of Lys57. Analytical ultracentrifugation analysis demonstrates that the K57A, K57S and K57C mutant enzymes dissociate predominantly into dimers, with some monomers present, whereas the K57R mutant forms a mixture of dimers and tetramers, with a small amount of the enzyme in monomeric form. The dimeric form of these Lys57 mutants, however, cannot be reconstituted into tetramers with the addition of fumarate. Modelling structures of the Lys57 mutant enzymes show that the hydrogen bond network in the dimer interface where Lys57 resides may be reduced compared with WT. Although the fumarate-induced activation effects are partially maintained in these Lys57 mutant enzymes, the mutant enzymes

  3. A study of the allosteric inhibition of HCV RNA-dependent RNA polymerase and implementing virtual screening for the selection of promising dual-site inhibitors with low resistance potential.

    Science.gov (United States)

    Ismail, Nasser S M; Elzahabi, Heba S A; Sabry, Peter; Baselious, Fady N; AbdelMalak, Andrew Samy; Hanna, Fady

    2017-08-01

    Structure-based pharmacophores were generated and validated using the bioactive conformations of different co-crystallized enzyme-inhibitor complexes for allosteric palm-1 and thumb-2 inhibitors of NS5B. Two pharmacophore models were obtained, one for palm-1 inhibitors with sensitivity = 0.929 and specificity = 0.983, and the other for thumb-2 inhibitors with sensitivity = 1 and specificity = 0.979. In addition, a quantitative structure activity relationship (QSAR) models were developed based on using the values of different scoring functions as descriptors predicting the activity on both allosteric binding sites (palm-1 and thumb-2). QSAR studies revealed good predictive and statistically significant two descriptor models (r 2  = .837, r 2 adjusted  = .792 and r 2 prediction  = .688 for palm-1 model and r 2  = .927, r 2 adjusted  = .908 and r 2 prediction  = .779 for thumb-2 model). External validation for the QSAR models assured their prediction power with r 2 ext  = .72 and .89 for palm-1 and thumb-2, respectively. Different docking protocols were examined for their validity to predict the correct binding poses of inhibitors inside their respective binding sites. Virtual screening was carried out on ZINC database using the generated pharmacophores, the selected valid docking algorithms and QSAR models to find compounds that could theoretically bind to both sites simultaneously.

  4. HPC Analysis of Multiple Binding Sites Communication and Allosteric Modulations in Drug Design: The HSP Case Study.

    Science.gov (United States)

    Chiappori, Federica; Milanesi, Luciano; Merelli, Ivan

    2016-01-01

    Allostery is a long-range macromolecular mechanism of internal regulation, in which the binding of a ligand in an allosteric site induces distant conformational changes in a distant portion of the protein, modifying its activity. From the drug design point of view, this mechanism can be exploited to achieve important therapeutic effects, since ligands able to bind allosteric sites may be designed to regulate target proteins. Computational tools are a valid support in this sense, since they allow the characterization of allosteric communications within proteins, which are essential to design modulator ligands. While considering long-range interactions in macromolecules, the principal drug design tool available to researcher is molecular dynamics, and related applications, since it allows the evaluation of conformational changes of a protein bound to a ligand. In particular, all-atoms molecular dynamics is suitable to verify the internal mechanisms that orchestrate allosteric communications, in order to identify key residues and internal pathways that modify the protein behaviour. The problem is that these techniques are heavily time-consuming and computationally intensive, thus high performance computing systems, including parallel computing and GPU-accelerated computations, are necessary to achieve results in a reasonable time. In this review, we will discuss how it is possible to exploit in silico approaches to characterize allosteric modulations and long-range interactions within proteins, describing the case study of the Heat Shock Proteins, a class of chaperons regulated by stress conditions, which is particularly important since it is involved in many cancers and neurodegenerative diseases.

  5. Allosteric regulation of 6-phosphofructo-1-kinase activity of fat body and flight muscle from the bloodsucking bug Rhodnius prolixus

    Directory of Open Access Journals (Sweden)

    Gutemberg G. Alves

    2007-03-01

    Full Text Available 6-phosphofructo-1-kinase (phosphofructokinase; PFK activity from Rhodnius prolixus, a haematophagous insect which is usually a poor flyer, was measured and compared in two metabolically active tissues - flight muscle and fat body. The activity of this important regulatory glycolytic enzyme was much more pronounced in muscle (15.1 ± 1.4 U/mg than in fat body extracts (3.6±0.4 U/mg, although the latter presented higher levels of enzyme per protein content, as measured by western-blotting. Muscle extracts are more responsible than fat body to ATP and fructose 6-phosphate, both substrates of PFK. Allosteric regulation exerted by different effectors such as ADP, AMP and fructose 2,6-phosphate presented a singular pattern for each tissue. Optimal pH (8.0-8.5 and sensitivity to pH variation was very similar, and citrate was unable to inhibit PFK activity in both extracts. Our results suggest the existence of a particular PFK activity for each tissue, with regulatory patterns that are consistent with their physiological roles.A atividade da fosfofrutocinase (PFK de Rodnius prolixus, um inseto hematófago, o qual vôa somente pequenas distâncias, foi medida e comparada em dois tecidos metabolicamente ativos - músculo de asa e corpo gorduroso. A atividade desta importante enzima glicolítica regulatória foi muito mais pronunciada em músculo de asa (15,1 ±1,4 U/mg do que em extrato de corpo gorduroso (3,6 ±0,4 U/mg embora este último tenha apresentado níveis mais altos da enzima por quantidade de proteína, como medido por western-blotting. Extratos de músculo foram mais responsivos do que corpo gorduroso para ATP e frutose-6-fosfato, ambos substratos da PFK. A regulação alostérica exercida por diferentes efetores tais como ADP, AMP, frutose-2,6-bisfosfato apresentou um padrão singular para cada tecido. O pH ótimo (8,0-8,5 e a sensibilidade a variações de pH, foram muito similares e o citrato foi incapaz de inibir a atividade da PFK em

  6. Zeolitic imidazolate framework membranes and methods of making and using same for separation of c2- and c3+ hydrocarbons and separation of propylene and propane mixtures

    KAUST Repository

    Lai, Zhiping

    2012-12-06

    Certain embodiments are directed to processes for fabrication of zeolitic imidazolate framework (ZIF) membranes. These ZIF membranes can be used in separating C2-hydrocarbons from C3+ hydrocarbons and propylene/propane mixtures.

  7. Biocatalytic Single Enzyme Nanoparticles

    Energy Technology Data Exchange (ETDEWEB)

    Grate, Jay W.; Kim, Jungbae

    2004-03-31

    As an innovative way of enzyme stabilization, we recently developed a new enzyme composite of nano-meter scale that we call "single-enzyme nanoparticles (SENs)" (9). Each enzyme molecule is surrounded with a porous composite organic/inorganic network of less than a few nanometers think. This approach represents a new type of enzyme-containing nanostructure. In experiments with perotease (chymotrypsin, CT), the activity of single enzyme nanoparticle form of the enzyme was greatly stabilized compared to the free form, without imposing a serious mass transfer limitation of substrates. In this chapter we will describe the synthesis, characterization and catalytic activity of the new SENs.

  8. Copper(II) imidazolate frameworks as highly efficient photocatalysts for reduction of CO2 into methanol under visible light irradiation

    International Nuclear Information System (INIS)

    Li, Jingtian; Luo, Deliang; Yang, Chengju; He, Shiman; Chen, Shangchao; Lin, Jiawei; Zhu, Li; Li, Xin

    2013-01-01

    Three copper(II) imidazolate frameworks were synthesized by a hydrothermal (or precipitation) reaction. The catalysts were characterized by X-ray diffraction (XRD), nitrogen adsorption, transmission electron microscopy (TEM), ultraviolet–visible spectroscopy (UV–vis), Fourier transform infrared spectra (FTIR), thermogravimetry (TG). Meanwhile, the photocatalytic activities of the samples for reduction of CO 2 into methanol and degradation of methylene blue (MB) under visible light irradiation were also investigated. The results show that the as-prepared samples exhibit better photocatalytic activities for the reduction of carbon dioxide into methanol with water and degradation of MB under visible light irradiation. The orthorhombic copper(II) imidazolate frameworks with a band gap of 2.49 eV and green (G) color has the best photocatalytic activity for reduction of CO 2 into methanol, 1712.7 μmol/g over 5 h, which is about three times as large as that of monoclinic copper(II) imidazolate frameworks with a band gap 2.70 eV and blue (J) color. The degradation kinetics of MB over three photocatalysts fitted well to the apparent first-order rate equation and the apparent rate constants for the degradation of MB over G, J and P (with pink color) are 0.0038, 0.0013 and 0.0016 min −1 , respectively. The synergistic effects of smallest band gap and orthorhombic crystal phase structure are the critical factors for the better photocatalytic activities of G. Moreover, three frameworks can also be stable up to 250 °C. The investigation of Cu-based zeolitic imidazolate frameworks maybe provide a design strategy for a new class of photocatalysts applied in degradation of contaminations, reduction of CO 2 , and even water splitting into hydrogen and oxygen under visible light. - Graphical abstract: Carbon dioxide was reduced into methanol with water over copper(II) imidazolate frameworks under visible light irradiation. - Highlights: • Three copper(II) imidazolate

  9. Synthesis of sulfonyl azides via diazotransfer using an imidazole-1-sulfonyl azide salt: scope and ¹⁵N NMR labeling experiments.

    Science.gov (United States)

    Stevens, Marc Y; Sawant, Rajiv T; Odell, Luke R

    2014-06-06

    Imidazole-1-sulfonyl azide hydrogen sulfate is presented as an efficient reagent for the synthesis of sulfonyl azides from primary sulfonamides. The described method is experimentally simple and high-yielding and does not require the addition of Cu salts. Furthermore, (15)N NMR mechanistic studies show the reaction proceeds via a diazo transfer mechanism. Imidazole-1-sulfonyl azide hydrogen sulfate provides a considerable advantage over existing diazo transfer reagents in terms of impact stability, cost, and ease of use.

  10. Synthesis and antimicrobial evaluation of 2-(2-butyl- 4-chloro-1H-imidazol-5-yl-methylene-substituted-benzofuran-3-ones

    Directory of Open Access Journals (Sweden)

    Bhaskar S. Dawane

    2010-05-01

    Full Text Available In the present study, the oxidation of 3-(4-chloro-1H-imidazol-5-yl-1-(2-hydroxyphenylprop-2-en-1-ones with mercuric(II acetate in in polyethylene glycol (PEG-400 gave the corresponding 2-((4-chloro-1H-imidazol-5-ylmethylenebenzofuran-3(2H-ones. Newly synthesized compounds were tested for their in vitro antimicrobial activity.

  11. Steric hindrance mutagenesis in the conserved extracellular vestibule impedes allosteric binding of antidepressants to the serotonin transporter

    DEFF Research Database (Denmark)

    Plenge, Per; Shi, Lei; Beuming, Thijs

    2012-01-01

    The serotonin transporter (SERT) controls synaptic serotonin levels and is the primary target for antidepressants, including selective serotonin reuptake inhibitors (e.g. (S)-citalopram) and tricyclic antidepressants (e.g. clomipramine). In addition to a high affinity binding site, SERT possesses...... a low affinity allosteric site for antidepressants. Binding to the allosteric site impedes dissociation of antidepressants from the high affinity site, which may enhance antidepressant efficacy. Here we employ an induced fit docking/molecular dynamics protocol to identify the residues that may...... effects of Zn(2+) binding in an engineered site and the covalent attachment of benzocaine-methanethiosulfonate to a cysteine introduced in the extracellular vestibule. The data provide a mechanistic explanation for the allosteric action of antidepressants at SERT and suggest that the role of the vestibule...

  12. Mutations that silence constitutive signaling activity in the allosteric ligand-binding site of the thyrotropin receptor.

    Science.gov (United States)

    Haas, Ann-Karin; Kleinau, Gunnar; Hoyer, Inna; Neumann, Susanne; Furkert, Jens; Rutz, Claudia; Schülein, Ralf; Gershengorn, Marvin C; Krause, Gerd

    2011-01-01

    The thyrotropin receptor (TSHR) exhibits elevated cAMP signaling in the basal state and becomes fully activated by thyrotropin. Previously we presented evidence that small-molecule ligands act allosterically within the transmembrane region in contrast to the orthosteric extracellular hormone-binding sites. Our goal in this study was to identify positions that surround the allosteric pocket and that are sensitive for inactivation of TSHR. Homology modeling combined with site-directed mutagenesis and functional characterization revealed seven mutants located in the allosteric binding site that led to a decrease of basal cAMP signaling activity. The majority of these silencing mutations, which constrain the TSHR in an inactive conformation, are found in two clusters when mapped onto the 3D structural model. We suggest that the amino acid positions identified herein are indicating locations where small-molecule antagonists, both neutral antagonists and inverse agonists, might interfere with active TSHR conformations.

  13. Targeting the Akt1 allosteric site to identify novel scaffolds through virtual screening.

    Science.gov (United States)

    Yilmaz, Oya Gursoy; Olmez, Elif Ozkirimli; Ulgen, Kutlu O

    2014-02-01

    Preclinical data and tumor specimen studies report that AKT kinases are related to many human cancers. Therefore, identification and development of small molecule inhibitors targeting AKT and its signaling pathway can be therapeutic in treatment of cancer. Numerous studies report inhibitors that target the ATP-binding pocket in the kinase domains, but the similarity of this site, within the kinase family makes selectivity a major problem. The sequence identity amongst PH domains is significantly lower than that in kinase domains and developing more selective inhibitors is possible if PH domain is targeted. This in silico screening study is the first time report toward the identification of potential allosteric inhibitors expected to bind the cavity between kinase and PH domains of Akt1. Structural information of Akt1 was used to develop structure-based pharmacophore models comprising hydrophobic, acceptor, donor and ring features. The 3D structural information of previously identified allosteric Akt inhibitors obtained from literature was employed to develop a ligand-based pharmacophore model. Database was generated with drug like subset of ZINC and screening was performed based on 3D similarity to the selected pharmacophore hypotheses. Binding modes and affinities of the ligands were predicted by Glide software. Top scoring hits were further analyzed considering 2D similarity between the compounds, interactions with Akt1, fitness to pharmacophore models, ADME, druglikeness criteria and Induced-Fit docking. Using virtual screening methodologies, derivatives of 3-methyl-xanthine, quinoline-4-carboxamide and 2-[4-(cyclohexa-1,3-dien-1-yl)-1H-pyrazol-3-yl]phenol were proposed as potential leads for allosteric inhibition of Akt1. Copyright © 2013 Elsevier Ltd. All rights reserved.

  14. Intra-subunit flexibility underlies activation and allosteric modulation of neuronal nicotinic acetylcholine receptors.

    Science.gov (United States)

    Chrisman, Paul A; Podair, Julie I; Jobe, Emily M; Levandoski, Mark M

    2014-04-01

    Allosteric modulation is a general feature of nicotinic acetylcholine receptors, yet the structural components and movements important for conversions among functional states are not well understood. In this study, we examine the communication between the binding sites for agonist and the modulator morantel (Mor) of neuronal α3β2 receptors, measuring evoked currents of receptors expressed in Xenopus oocytes with the two-electrode voltage-clamp method. We hypothesized that movement along an interface of β sheets connecting the agonist and modulator sites is necessary for allosteric modulation. To address this, we created pairs of substituted cysteines that span the cleft formed where the outer β sheet meets the β sheet constituting the (-)-face of the α3 subunit; the three pairs were L158C-A179C, L158C-G181C and L158C-K183C. Employing a disulfide trapping approach in which bonds are formed between neighboring cysteines under oxidation conditions, we found that oxidation treatments decreased the amplitude of currents evoked by either the agonist (ACh) or co-applied agonist and modulator (ACh + Mor), by as much as 51%, consistent with the introduced bond decreasing channel efficacy. Reduction treatment increased evoked currents up to 89%. The magnitude of the oxidation effects depended on whether agonists were present during oxidation and on the cysteine pair. Additionally, the cysteine mutations themselves decreased Mor potentiation, implicating these residues in modulation. Our findings suggest that these β sheets in the α3 subunit move with respect to each other during activation and modulation, and the residues studied highlight the contribution of this intramolecular allosteric pathway to receptor function. Copyright © 2013 Elsevier Ltd. All rights reserved.

  15. Disruption of integrin-fibronectin complexes by allosteric but not ligand-mimetic inhibitors.

    Science.gov (United States)

    Mould, A Paul; Craig, Susan E; Byron, Sarah K; Humphries, Martin J; Jowitt, Thomas A

    2014-12-15

    Failure of Arg-Gly-Asp (RGD)-based inhibitors to reverse integrin-ligand binding has been reported, but the prevalence of this phenomenon among integrin heterodimers is currently unknown. In the present study we have investigated the interaction of four different RGD-binding integrins (α5β1, αVβ1, αVβ3 and αVβ6) with fibronectin (FN) using surface plasmon resonance. The ability of inhibitors to reverse ligand binding was assessed by their capacity to increase the dissociation rate of pre-formed integrin-FN complexes. For all four receptors we showed that RGD-based inhibitors (such as cilengitide) were completely unable to increase the dissociation rate. Formation of the non-reversible state occurred very rapidly and did not rely on the time-dependent formation of a high-affinity state of the integrin, or the integrin leg regions. In contrast with RGD-based inhibitors, Ca2+ (but not Mg2+) was able to greatly increase the dissociation rate of integrin-FN complexes, with a half-maximal response at ~0.4 mM Ca2+ for αVβ3-FN. The effect of Ca2+ was overcome by co-addition of Mn2+, but not Mg2+. A stimulatory anti-β1 monoclonal antibody (mAb) abrogated the effect of Ca2+ on α5β1-FN complexes; conversely, a function-blocking mAb mimicked the effect of Ca2+. These results imply that Ca2+ acts allosterically, probably through binding to the adjacent metal-ion-dependent adhesion site (ADMIDAS), and that the α1 helix in the β subunit I domain is the key element affected by allosteric modulators. The data suggest an explanation for the limited clinical efficacy of RGD-based integrin antagonists, and we propose that allosteric antagonists could prove to be of greater therapeutic benefit.

  16. Allosteric activation of sodium-calcium exchange by picomolar concentrations of cadmium.

    Science.gov (United States)

    Le, Hoa Dinh; Omelchenko, Alexander; Hryshko, Larry V; Uliyanova, Alexandra; Condrescu, Madalina; Reeves, John P

    2005-02-15

    Chinese hamster ovary cells expressing the bovine cardiac Na+-Ca2+ exchanger (NCX1.1) accumulated Cd2+ after a lag period of several tens of seconds. The lag period reflects the progressive allosteric activation of exchange activity by Cd2+ as it accumulates within the cytosol. The lag period was greatly reduced in cells expressing a mutant exchanger, Delta(241-680), that does not require allosteric activation by Ca2+ for activity. Non-transfected cells did not show Cd2+ uptake under the same conditions. In cells expressing NCX1.1, the lag period was nearly abolished following an elevation of the cytosolic Ca2+ concentration. Cytosolic Cd2+ concentrations estimated at 0.5-2 pm markedly stimulated the subsequent uptake of Ca2+ by Na+-Ca2+ exchange. Outward exchange currents in membrane patches from Xenopus oocytes expressing the canine NCX1.1 were rapidly and reversibly stimulated by 3 pm Cd2+ applied at the cytosolic membrane surface. Exchange currents activated by 3 pm Cd2+ were 40% smaller than currents activated by 1 mum cytosolic Ca2+. Current amplitudes declined by 30% and the rate of current development fell sharply upon repetitive applications of Na+ in the presence of 3 pm Cd2+. Cd2+ mimicked the anomalous inhibitory effects of Ca2+ on outward exchange currents generated by the Drosophila exchanger CALX1.1. We conclude that the regulatory sites responsible for allosteric Ca2+ activation bind Cd2+ with high affinity and that Cd2+ mimics the regulatory effects of Ca2+ at concentrations 5 orders of magnitude lower than Ca2+.

  17. Convergent transmission of RNAi guide-target mismatch information across Argonaute internal allosteric network.

    Directory of Open Access Journals (Sweden)

    Thomas T Joseph

    Full Text Available In RNA interference, a guide strand derived from a short dsRNA such as a microRNA (miRNA is loaded into Argonaute, the central protein in the RNA Induced Silencing Complex (RISC that silences messenger RNAs on a sequence-specific basis. The positions of any mismatched base pairs in an miRNA determine which Argonaute subtype is used. Subsequently, the Argonaute-guide complex binds and silences complementary target mRNAs; certain Argonautes cleave the target. Mismatches between guide strand and the target mRNA decrease cleavage efficiency. Thus, loading and silencing both require that signals about the presence of a mismatched base pair are communicated from the mismatch site to effector sites. These effector sites include the active site, to prevent target cleavage; the binding groove, to modify nucleic acid binding affinity; and surface allosteric sites, to control recruitment of additional proteins to form the RISC. To examine how such signals may be propagated, we analyzed the network of internal allosteric pathways in Argonaute exhibited through correlations of residue-residue interactions. The emerging network can be described as a set of pathways emanating from the core of the protein near the active site, distributed into the bulk of the protein, and converging upon a distributed cluster of surface residues. Nucleotides in the guide strand "seed region" have a stronger relationship with the protein than other nucleotides, concordant with their importance in sequence selectivity. Finally, any of several seed region guide-target mismatches cause certain Argonaute residues to have modified correlations with the rest of the protein. This arises from the aggregation of relatively small interaction correlation changes distributed across a large subset of residues. These residues are in effector sites: the active site, binding groove, and surface, implying that direct functional consequences of guide-target mismatches are mediated through the

  18. Internalization of the chemokine receptor CCR4 can be evoked by orthosteric and allosteric receptor antagonists

    OpenAIRE

    Ajram, Laura; Begg, Malcolm; Slack, Robert; Cryan, Jenni; Hall, David; Hodgson, Simon; Ford, Alison; Barnes, Ashley; Swieboda, Dawid; Mousnier, Aurelie; Solari, Roberto

    2014-01-01

    The chemokine receptor CCR4 has at least two natural agonist ligands, MDC (CCL22) and TARC (CCL17) which bind to the same orthosteric site with a similar affinity. Both ligands are known to evoke chemotaxis of CCR4-bearing T cells and also elicit CCR4 receptor internalization. A series of small molecule allosteric antagonists have been described which displace the agonist ligand, and inhibit chemotaxis. The aim of this study was to determine which cellular coupling pathways are involved in in...

  19. Preferential binding of allosteric modulators to active and inactive conformational states of metabotropic glutamate receptors

    Directory of Open Access Journals (Sweden)

    Klein-Seetharaman Judith

    2008-02-01

    Full Text Available Abstract Metabotropic glutamate receptors (mGluRs are G protein coupled receptors that play important roles in synaptic plasticity and other neuro-physiological and pathological processes. Allosteric mGluR ligands are particularly promising drug targets because of their modulatory effects – enhancing or suppressing the response of mGluRs to glutamate. The mechanism by which this modulation occurs is not known. Here, we propose the hypothesis that positive and negative modulators will differentially stabilize the active and inactive conformations of the receptors, respectively. To test this hypothesis, we have generated computational models of the transmembrane regions of different mGluR subtypes in two different conformations. The inactive conformation was modeled using the crystal structure of the inactive, dark state of rhodopsin as template and the active conformation was created based on a recent model of the light-activated state of rhodopsin. Ligands for which the nature of their allosteric effects on mGluRs is experimentally known were docked to the modeled mGluR structures using ArgusLab and Autodock softwares. We find that the allosteric ligand binding pockets of mGluRs are overlapping with the retinal binding pocket of rhodopsin, and that ligands have strong preferences for the active and inactive states depending on their modulatory nature. In 8 out of 14 cases (57%, the negative modulators bound the inactive conformations with significant preference using both docking programs, and 6 out of 9 cases (67%, the positive modulators bound the active conformations. Considering results by the individual programs only, even higher correlations were observed: 12/14 (86% and 8/9 (89% for ArgusLab and 10/14 (71% and 7/9 (78% for AutoDock. These findings strongly support the hypothesis that mGluR allosteric modulation occurs via stabilization of different conformations analogous to those identified in rhodopsin where they are induced by

  20. Muscarinic receptor M4 positive allosteric modulators attenuate central effects of cocaine

    DEFF Research Database (Denmark)

    Dall, Camilla; Weikop, Pia; Dencker, Ditte

    2017-01-01

    allosteric modulators VU0152100 and VU0467154 in a drug discrimination assay and a conditioned place preference assay, including extinction and reinstatement of place preference. Specificity of the cocaine discrimination effect was verified using knockout mice lacking either M1or M4receptors (M1-/-, M4....... As previously shown with VU0152100, VU0467154 almost eliminated cocaine-induced hyperactivity and striatal dopamine efflux. VU0467154 failed to attenuate acquisition of cocaine-conditioned place preference, but facilitated extinction and prevented reinstatement of the conditioned place preference. CONCLUSIONS...

  1. Substituted 3-Benzylcoumarins as Allosteric MEK1 Inhibitors: Design, Synthesis and Biological Evaluation as Antiviral Agents

    Directory of Open Access Journals (Sweden)

    Ping Xu

    2013-05-01

    Full Text Available In order to find novel antiviral agents, a series of allosteric MEK1 inhibitors were designed and synthesized. Based on docking results, multiple optimizations were made on the coumarin scaffold. Some of the derivatives showed excellent MEK1 binding affinity in the appropriate enzymatic assays and displayed obvious inhibitory effects on the ERK pathway in a cellular assay. These compounds also significantly inhibited virus (EV71 replication in HEK293 and RD cells. Several compounds showed potential as agents for the treatment of viral infective diseases, with the most potent compound 18 showing an IC50 value of 54.57 nM in the MEK1 binding assay.

  2. Biased signaling of lipids and allosteric actions of synthetic molecules for GPR119

    DEFF Research Database (Denmark)

    Hassing, Helle A; Fares, Suzan; Larsen, Olav

    2016-01-01

    GPR119 is a Gαs-coupled lipid-sensor in the gut, where it mediates release of incretin hormones from the enteroendocrine cells and in pancreatic α-cells, where it releases insulin. Naturally occurring lipids such as monoacylglycerols (MAGs) and N-acylethanolamines (NAEs), like oleoylethanolamide...... for 2h with the 2-MAG-lipase inhibitor JZL84 doubled the constitutive activity, indicating that endogenous lipids contribute to the apparent constitutive activity. Finally, besides being an agonist, AR231453 acted as a positive allosteric modulator of OEA and increased its potency by 54-fold at 100nM AR...

  3. Structural insight to mutation effects uncover a common allosteric site in class C GPCRs

    DEFF Research Database (Denmark)

    Harpsøe, Kasper; Boesgaard, Michael W; Munk, Christian

    2017-01-01

    MOTIVATION: Class C G protein-coupled receptors (GPCRs) regulate important physiological functions and allosteric modulators binding to the transmembrane domain constitute an attractive and, due to a lack of structural insight, a virtually unexplored potential for therapeutics and the food industry....... Combining pharmacological site-directed mutagenesis data with the recent class C GPCR experimental structures will provide a foundation for rational design of new therapeutics. RESULTS: We uncover one common site for both positive and negative modulators with different amino acid layouts that can...

  4. Cu(II) coordination polymers constructed by tetrafluoroterephthalic acid and varied imidazole-containing ligands: Syntheses, structures and properties

    Science.gov (United States)

    Liu, Kang; Sun, Yayong; Deng, Liming; Cao, Fan; Han, Jishu; Wang, Lei

    2018-02-01

    Six new copper(II) coordination polymers combining 2,3,5,6-tetrafluoroterephthalatic acid (H2tfBDC) and diverse imidazole-containing ligands, {[Cu(tfBDC)(1,2-bix)2]·2(H2O)}n (1), {Cu(tfBDC)(Im)2}n (2), {[Cu(1,4-bmimb)2(H2O)]·(tfBDC)·2(H2O)}n (3), {Cu(1,4-bimb)2(H2O)2·(tfBDC)}n (4), {[Cu(1,3-bix)2(H2O)2]·(tfBDC)·6(H2O)}n (5) and {[Cu(1,4-bix)2(H2O)2]·(tfBDC)·(1,4-bix)·4(H2O)}n (6) (1,2-bix = 1,2-bis(imidazole-1-ylmethyl)-benzene, Im = imidazole, 1,4-bmimb = 1,4-bis((2-methyl-1H-imidazol-1-yl)methyl)benzene, 1,4-bimb = 1,4-bis(imidazol-1-yl)-butane, 1,3-bix = 1,3-bis(imidazole-1-ylmethyl)-benzene, 1,4-bix = 1,4-bis(imidazole-1-ylmethyl)-benzene), have been obtained and structurally verified by single-crystal X-ray diffraction analyses and further characterized by powder X-ray diffraction (PXRD), elemental analyses and infrared spectroscopy (IR). Single crystal X-ray diffraction analysis revealed that 1 is 2D 4-connected sql topology (point symbol: {44·62}) based on a single metal ion node. Compound 2 is characterized as an infinite 1D chain structure, which is further extended into a 2D layer through N-H···O hydrogen bonds and then a 3D supramolecular architecture via π···π stacking interactions. Note that 2 was prepared through an in situ ligand reaction in which N,N'-carbonyldiimidazole (cdi) broke up into imidazole ligand. Compound 3 possesses a 3D 4-fold interpenetrated architecture with 4-connected dia topology (Schläfli symbol: {66}) in which tfBDC2- is stabilized in the channel by hydrogen bonds. Compounds 4-6 are all linear 1D coordination polymers. In 4, the free tfBDC2- ligand acts as a μ4-bridge to link four coordinated water molecules from the chain to construct a 2D structure via hydrogen bonds. While in 5 and 6, the uncoordinated tfBDC2- ligands and multimeric water clusters is responsible for the conversion of these 1D coordination polymers into 3D supramolecular assemblies through O-H⋯O hydrogen bonding interactions. Moreover

  5. Solidification of liquid electrolyte with imidazole polymers for quasi-solid-state dye-sensitized solar cells

    International Nuclear Information System (INIS)

    Wang Miao; Lin Yuan; Zhou Xiaowen; Xiao Xurui; Yang Lei; Feng Shujing; Li Xueping

    2008-01-01

    Quasi-solid-state electrolytes were prepared by employing the imidazole polymers to solidify the liquid electrolyte containing lithium iodide, iodine and ethylene carbonate (EC)/propylene carbonate (PC) mixed solvent. The ionic conductivity and diffusion behavior of triiodide in the quasi-solid-state electrolytes were examined in terms of the polymer content. Application of the quasi-solid-state electrolytes to the dye-sensitized solar cells, the maximum energy conversion efficiency of 7.6% (AM 1.5, 100 mW cm -2 ) was achieved. The dependence of the photovoltaic performance on the polymer content and on the different anions of the imidazole polymers was studied by electrochemical impedance spectroscopy and cyclic voltammetry. The results indicate the charge transfer behaviors occurred at nanocrystalline TiO 2 /electrolyte and Pt/electrolyte interface play an important role in influencing the photovoltaic performance of quasi-solid-state dye-sensitized solar cells

  6. Endosomal Escape and Delivery of CRISPR/Cas9 Genome Editing Machinery Enabled by Nanoscale Zeolitic Imidazolate Framework

    KAUST Repository

    Alsaiari, Shahad K.

    2017-12-22

    CRISPR/Cas9 is a combined protein (Cas9) and an engineered single guide RNA (sgRNA) genome editing platform that offers revolutionary solutions to genetic diseases. It has, however, a double delivery problem owning to the large protein size and the highly charged RNA component. In this work, we report the first example of CRISPR/Cas9 encapsulated by nanoscale zeolitic imidazole frameworks (ZIFs) with a loading efficiency of 17% and enhanced endosomal escape promoted by the protonated imidazole moieties. The gene editing potential of CRISPR/Cas9 encapsulated by ZIF-8 (CC-ZIFs) is further verified by knocking down the gene expression of green fluorescent protein by 37% over 4 days employing CRISPR/Cas9 machinery. The nanoscale CC-ZIFs are biocompatible and easily scaled-up offering excellent loading capacity and controlled co-delivery of intact Cas9 protein and sgRNA.

  7. Synthesis, Crystal Structure and Luminescent Property of A Novel Cd(II) Coordination Polymer with Bis-imidazole Ligand

    Energy Technology Data Exchange (ETDEWEB)

    Zhou, Yong Hong [Huaibei Normal Univ., Huaibei (China)

    2013-04-15

    The key to the successful design of metal-organic coordination polymers is the judicious selection of organic ligand. Recently, polydentate aromatic nitrogen heterocyclic ligands with five-membered rings have been well-studied in the construction of supramolecular structure for their N-coordinated sites apt to coordinating to transition metals. Similar to six-membered N-heterocyclic ligands, the azole-based five-membered N-heterocyclic ligands, such as imidazoles, triazoles and tetrazoles have been extensively employed in the construction of various coordination polymers with diverse topologies and interesting properties. The bis(azole) ligands in which N-donor azole rings (imidazole, triazole, or tetrazole) are separated by alkyl, (CH{sub 2}){sub n}, spacers are good choices for flexible bridging ligands. The conformational flexibility of the spacers makes the ligands adaptable to various coordination networks with one-, two-, and three dimensional structures.

  8. The ENZYME data bank.

    Science.gov (United States)

    Bairoch, A

    1994-09-01

    The ENZYME data bank is a repository of information relative to the nomenclature of enzymes. It is primarily based on the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (IUBMB) and it contains the following data for each type of characterized enzyme for which an EC (Enzyme Commission) number has been provided: EC number Recommended name Alternative names (if any) Catalytic activity Cofactors (if any) Pointers to the SWISS-PROT protein sequence entrie(s) that correspond to the enzyme (if any) Pointers to human disease(s) associated with a deficiency of the enzyme (if any).

  9. Tuning the Annulation Reactivity of Vinyl Azides and Carbazates: A Divergent Synthesis of Aza-pyrimidinones and Imidazoles.

    Science.gov (United States)

    Shao, Jiaan; Liu, Xingyu; Shu, Ke; Tang, Pai; Luo, Jing; Chen, Wenteng; Yu, Yongping

    2015-09-18

    A divergent cascade annulation has been developed using readily available vinyl azides and carbazates with a wide range of substituents. Vinyl azides were successfully applied as bifunctional partners to prepare aza-pyrimidinones via 6-ring closure with carbazates as well as to construct polyfunctionalized imidazoles via 5-ring closure with N-substituted carbazates. The aza-heterocycles were obtained with high levels of chemoselectivity and excellent yields.

  10. Zwitterionic 4-carboxy-2-(1-methylpyridin-1-ium-4-yl-1H-imidazole-5-carboxylate

    Directory of Open Access Journals (Sweden)

    Dao-Sen Liu

    2012-02-01

    Full Text Available In the title zwitterionic molecule, C11H9N3O4, the imidazole and pyridine rings form a dihedral angle of 2.60 (2°. An intramolecular O—H...O hydrogen bond occurs. In the crystal, pairs of N—H...O hydrogen bonds link the molecules into inversion dimers. Weak intermolecular C—H...O interactions further consolidate the crystal packing.

  11. Spectroscopic analysis and molecular docking of imidazole derivatives and investigation of its reactive properties by DFT and molecular dynamics simulations

    Science.gov (United States)

    Thomas, Renjith; Hossain, Mossaraf; Mary, Y. Sheena; Resmi, K. S.; Armaković, Stevan; Armaković, Sanja J.; Nanda, Ashis Kumar; Ranjan, Vivek Kumar; Vijayakumar, G.; Van Alsenoy, C.

    2018-04-01

    Solvent-free synthesis pathway for obtaining two imidazole derivatives (2-chloro-1-(4-methoxyphenyl)-4,5-dimethyl-1H-imidazole (CLMPDI) and 1-(4-bromophenyl)-2-chloro-4,5-dimethyl-1H-imidazole (BPCLDI) has been reported in this work, followed by detailed experimental and computational spectroscopic characterization and reactivity study. Spectroscopic methods encompassed IR, FT-Raman and NMR techniques, with the mutual comparison of experimentally and computationally obtained results at DFT/B3LYP level of theory. Reactivity study based on DFT calculations encompassed molecular orbitals analysis, followed by calculations of molecular electrostatic potential (MEP) and average local ionization energy (ALIE) values, Fukui functions and bond dissociation energies (BDE). Additionally, the stability of title molecules in water has been investigated via molecular dynamics (MD) simulations, while interactivity with aspulvinonedimethylallyl transferase protein has been evaluated by molecular docking procedure. CLMPDI compound showed antimicrobial activity against all four bacterial strain in both gram positive and gram negative bacteria while, BPCLDI showed only in gram positive bacteria, Staphylococcus Aureus (MTCC1144). The first order hyperpolarizability of CLMPDI and BPCLDI are 20.15 and 6.10 times that of the standard NLO material urea.

  12. Synthesis, spectroscopic, computational (DFT/B3LYP), AChE inhibition and antioxidant studies of imidazole derivative

    Science.gov (United States)

    Ahmad, Faheem; Alam, Mohammad Jane; Alam, Mahboob; Azaz, Shaista; Parveen, Mehtab; Park, Soonheum; Ahmad, Shabbir

    2018-01-01

    The present study reports the synthesis and evaluation of biological properties of 3a,8a-dihydroxy-8-oxo-1,3,3a,8a-tetrahydroindeno[1,2-d]imidazol-2(1H)-iminium chloride (3). The structure was confirmed by the FTIR, NMR, MS, CHN microanalysis and X-ray crystallographic analysis. Quantum chemical calculations have been performed at B3LYP-D3/6-311++G(d,p) level of theory to study the molecular geometry, IR, (1H and 13C) NMR, UV/Vis spectra and other molecular parameters of the asymmetric unit of crystal of imidazole compound (3). An empirical dispersion correction to hybrid functional (B3LYP-D3) has been incorporated in the present calculations due to presence of non-covalent interaction, Cl⋯H-O, in the present compound. The remarkable agreement has been observed between theoretical data and those measured experimentally. Moreover, the Hirshfeld analysis was carried out to ascertain the secondary interactions and associated 2D fingerprint plots. The synthesized imidazole derivative showed promising antioxidant property and inhibitory activity against acetylcholinesterase (AChE). Molecular docking was also performed in order to explain in silico antioxidant studies and to ascertain the probable binding mode of compound with the amino acid residues of protein.

  13. Allosteric Inhibition of SHP2: Identification of a Potent, Selective, and Orally Efficacious Phosphatase Inhibitor

    Energy Technology Data Exchange (ETDEWEB)

    Fortanet, Jorge Garcia; Chen, Christine Hiu-Tung; Chen, Ying-Nan P.; Chen, Zhouliang; Deng, Zhan; Firestone, Brant; Fekkes, Peter; Fodor, Michelle; Fortin, Pascal D.; Fridrich, Cary; Grunenfelder, Denise; Ho, Samuel; Kang, Zhao B.; Karki, Rajesh; Kato, Mitsunori; Keen, Nick; LaBonte, Laura R.; Larrow, Jay; Lenoir, Francois; Liu, Gang; Liu, Shumei; Lombardo, Franco; Majumdar, Dyuti; Meyer, Matthew J.; Palermo, Mark; Perez, Lawrence; Pu, Minying; Ramsey, Timothy; Sellers, William R.; Shultz, Michael D.; Stams, Travis; Towler, Christopher; Wang, Ping; Williams, Sarah L.; Zhang, Ji-Hu; LaMarche, Matthew J. (Novartis)

    2016-09-08

    SHP2 is a nonreceptor protein tyrosine phosphatase (PTP) encoded by the PTPN11 gene involved in cell growth and differentiation via the MAPK signaling pathway. SHP2 also purportedly plays an important role in the programmed cell death pathway (PD-1/PD-L1). Because it is an oncoprotein associated with multiple cancer-related diseases, as well as a potential immunomodulator, controlling SHP2 activity is of significant therapeutic interest. Recently in our laboratories, a small molecule inhibitor of SHP2 was identified as an allosteric modulator that stabilizes the autoinhibited conformation of SHP2. A high throughput screen was performed to identify progressable chemical matter, and X-ray crystallography revealed the location of binding in a previously undisclosed allosteric binding pocket. Structure-based drug design was employed to optimize for SHP2 inhibition, and several new protein–ligand interactions were characterized. These studies culminated in the discovery of 6-(4-amino-4-methylpiperidin-1-yl)-3-(2,3-dichlorophenyl)pyrazin-2-amine (SHP099, 1), a potent, selective, orally bioavailable, and efficacious SHP2 inhibitor.

  14. Conformationally constrained peptides target the allosteric kinase dimer interface and inhibit EGFR activation.

    Science.gov (United States)

    Fulton, Melody D; Hanold, Laura E; Ruan, Zheng; Patel, Sneha; Beedle, Aaron M; Kannan, Natarajan; Kennedy, Eileen J

    2018-03-15

    Although EGFR is a highly sought-after drug target, inhibitor resistance remains a challenge. As an alternative strategy for kinase inhibition, we sought to explore whether allosteric activation mechanisms could effectively be disrupted. The kinase domain of EGFR forms an atypical asymmetric dimer via head-to-tail interactions and serves as a requisite for kinase activation. The kinase dimer interface is primarily formed by the H-helix derived from one kinase monomer and the small lobe of the second monomer. We hypothesized that a peptide designed to resemble the binding surface of the H-helix may serve as an effective disruptor of EGFR dimerization and activation. A library of constrained peptides was designed to mimic the H-helix of the kinase domain and interface side chains were optimized using molecular modeling. Peptides were constrained using peptide "stapling" to structurally reinforce an alpha-helical conformation. Peptide stapling was demonstrated to notably enhance cell permeation of an H-helix derived peptide termed EHBI2. Using cell-based assays, EHBI2 was further shown to significantly reduce EGFR activity as measured by EGFR phosphorylation and phosphorylation of the downstream signaling substrate Akt. To our knowledge, this is the first H-helix-based compound targeting the asymmetric interface of the kinase domain that can successfully inhibit EGFR activation and signaling. This study presents a novel, alternative targeting site for allosteric inhibition of EGFR. Copyright © 2017 Elsevier Ltd. All rights reserved.

  15. Identification of novel allosteric modulator binding sites in NMDA receptors: A molecular modeling study.

    Science.gov (United States)

    Kane, Lucas T; Costa, Blaise M

    2015-09-01

    The dysfunction of N-methyl-d-Aspartate receptors (NMDARs), a subtype of glutamate receptors, is correlated with schizophrenia, stroke, and many other neuropathological disorders. However, not all NMDAR subtypes equally contribute towards these disorders. Since NMDARs composed of different GluN2 subunits (GluN2A-D) confer varied physiological properties and have different distributions in the brain, pharmacological agents that target NMDARs with specific GluN2 subunits have significant potential for therapeutic applications. In our previous research, we have identified a family of novel allosteric modulators that differentially potentiate and/or inhibit NMDARs of differing GluN2 subunit composition. To further elucidate their molecular mechanisms, in the present study, we have identified four potential binding sites for novel allosteric modulators by performing molecular modeling, docking, and in silico mutations. The molecular determinants of the modulator binding sites (MBS), analysis of particular MBS electrostatics, and the specific loss or gain of binding after mutations have revealed modulators that have strong potential affinities for specific MBS on given subunits and the role of key amino acids in either promoting or obstructing modulator binding. These findings will help design higher affinity GluN2 subunit-selective pharmaceuticals, which are currently unavailable to treat psychiatric and neurological disorders. Copyright © 2015 Elsevier Inc. All rights reserved.

  16. Mechanism of allosteric regulation of β2-adrenergic receptor by cholesterol

    Science.gov (United States)

    Manna, Moutusi; Niemelä, Miia; Tynkkynen, Joona; Javanainen, Matti; Kulig, Waldemar; Müller, Daniel J; Rog, Tomasz; Vattulainen, Ilpo

    2016-01-01

    There is evidence that lipids can be allosteric regulators of membrane protein structure and activation. However, there are no data showing how exactly the regulation emerges from specific lipid-protein interactions. Here we show in atomistic detail how the human β2-adrenergic receptor (β2AR) – a prototypical G protein-coupled receptor – is modulated by cholesterol in an allosteric fashion. Extensive atomistic simulations show that cholesterol regulates β2AR by limiting its conformational variability. The mechanism of action is based on the binding of cholesterol at specific high-affinity sites located near the transmembrane helices 5–7 of the receptor. The alternative mechanism, where the β2AR conformation would be modulated by membrane-mediated interactions, plays only a minor role. Cholesterol analogues also bind to cholesterol binding sites and impede the structural flexibility of β2AR, however cholesterol generates the strongest effect. The results highlight the capacity of lipids to regulate the conformation of membrane receptors through specific interactions. DOI: http://dx.doi.org/10.7554/eLife.18432.001 PMID:27897972

  17. Discovery of Peptidomimetic Ligands of EED as Allosteric Inhibitors of PRC2

    Energy Technology Data Exchange (ETDEWEB)

    Barnash, Kimberly D.; The, Juliana; Norris-Drouin, Jacqueline L.; Cholensky, Stephanie H.; Worley, Beau M.; Li, Fengling; Stuckey, Jacob I.; Brown, Peter J.; Vedadi, Masoud; Arrowsmith, Cheryl H.; Frye, Stephen V.; James, Lindsey I. (UNC); (Toronto)

    2017-02-06

    The function of EED within polycomb repressive complex 2 (PRC2) is mediated by a complex network of protein–protein interactions. Allosteric activation of PRC2 by binding of methylated proteins to the embryonic ectoderm development (EED) aromatic cage is essential for full catalytic activity, but details of this regulation are not fully understood. EED’s recognition of the product of PRC2 activity, histone H3 lysine 27 trimethylation (H3K27me3), stimulates PRC2 methyltransferase activity at adjacent nucleosomes leading to H3K27me3 propagation and, ultimately, gene repression. By coupling combinatorial chemistry and structure-based design, we optimized a low-affinity methylated jumonji, AT-rich interactive domain 2 (Jarid2) peptide to a smaller, more potent peptidomimetic ligand (Kd = 1.14 ± 0.14 μM) of the aromatic cage of EED. Our strategy illustrates the effectiveness of applying combinatorial chemistry to achieve both ligand potency and property optimization. Furthermore, the resulting ligands, UNC5114 and UNC5115, demonstrate that targeted disruption of EED’s reader function can lead to allosteric inhibition of PRC2 catalytic activity.

  18. Allosteric mechanism of action of the therapeutic anti-IgE antibody omalizumab.

    Science.gov (United States)

    Davies, Anna M; Allan, Elizabeth G; Keeble, Anthony H; Delgado, Jean; Cossins, Benjamin P; Mitropoulou, Alkistis N; Pang, Marie O Y; Ceska, Tom; Beavil, Andrew J; Craggs, Graham; Westwood, Marta; Henry, Alistair J; McDonnell, James M; Sutton, Brian J

    2017-06-16

    Immunoglobulin E and its interactions with receptors FcϵRI and CD23 play a central role in allergic disease. Omalizumab, a clinically approved therapeutic antibody, inhibits the interaction between IgE and FcϵRI, preventing mast cell and basophil activation, and blocks IgE binding to CD23 on B cells and antigen-presenting cells. We solved the crystal structure of the complex between an omalizumab-derived Fab and IgE-Fc, with one Fab bound to each Cϵ3 domain. Free IgE-Fc adopts an acutely bent structure, but in the complex it is only partially bent, with large-scale conformational changes in the Cϵ3 domains that inhibit the interaction with FcϵRI. CD23 binding is inhibited sterically due to overlapping binding sites on each Cϵ3 domain. Studies of omalizumab Fab binding in solution demonstrate the allosteric basis for FcϵRI inhibition and, together with the structure, reveal how omalizumab may accelerate dissociation of receptor-bound IgE from FcϵRI, exploiting the intrinsic flexibility and allosteric potential of IgE. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  19. Characterization of an allosteric citalopram-binding site at the serotonin transporter

    DEFF Research Database (Denmark)

    Chen, Fenghua; Breum Larsen, Mads; Neubauer, Henrik Amtoft

    2005-01-01

          rate, of [3H]S-citalopram from human SERT, is retarded by the presence of       serotonin, as well as by several antidepressants, when present in the       dissociation buffer. Dissociation of [3H]S-citalopram from SERT is most       potently inhibited by S-citalopram followed by R...... is independent of       temperature, or the presence of Na+ in the dissociation buffer.       Dissociation of [3H]S-citalopram from a complex with the SERT       double-mutant, N208Q/N217Q, which has been suggested to be unable to       self-assemble into oligomeric complexes, is retarded to an extent similar......       to that found with the wild-type, raising the possibility that the       allosteric mechanism is mediated within a single subunit. A       species-scanning mutagenesis study comparing human and bovine SERT       revealed that Met180, Tyr495 and Ser513 are important residues in       mediating the allosteric...

  20. Molecular mechanism of allosteric modification of voltage-dependent sodium channels by local anesthetics.

    Science.gov (United States)

    Arcisio-Miranda, Manoel; Muroi, Yukiko; Chowdhury, Sandipan; Chanda, Baron

    2010-11-01

    The hallmark of many intracellular pore blockers such as tetra-alkylammonium compounds and local anesthetics is their ability to allosterically modify the movement of the voltage sensors in voltage-dependent ion channels. For instance, the voltage sensor of domain III is specifically stabilized in the activated state when sodium currents are blocked by local anesthetics. The molecular mechanism underlying this long-range interaction between the blocker-binding site in the pore and voltage sensors remains poorly understood. Here, using scanning mutagenesis in combination with voltage clamp fluorimetry, we systematically evaluate the role of the internal gating interface of domain III of the sodium channel. We find that several mutations in the S4-S5 linker and S5 and S6 helices dramatically reduce the stabilizing effect of lidocaine on the activation of domain III voltage sensor without significantly altering use-dependent block at saturating drug concentrations. In the wild-type skeletal muscle sodium channel, local anesthetic block is accompanied by a 21% reduction in the total gating charge. In contrast, point mutations in this critical intracellular region reduce this charge modification by local anesthetics. Our analysis of a simple model suggests that these mutations in the gating interface are likely to disrupt the various coupling interactions between the voltage sensor and the pore of the sodium channel. These findings provide a molecular framework for understanding the mechanisms underlying allosteric interactions between a drug-binding site and voltage sensors.

  1. The Allosterically Unregulated Isoform of ADP-Glucose Pyrophosphorylase from Barley Endosperm Is the Most Likely Source of ADP-Glucose Incorporated into Endosperm Starch1

    Science.gov (United States)

    Doan, Danny N.P.; Rudi, Heidi; Olsen, Odd-Arne

    1999-01-01

    We present the results of studies of an unmodified version of the recombinant major barley (Hordeum vulgare) endosperm ADP-glucose pyrophoshorylase (AGPase) expressed in insect cells, which corroborate previous data that this isoform of the enzyme acts independently of the allosteric regulators 3-phosphoglycerate and inorganic phosphate. We also present a characterization of the individual subunits expressed separately in insect cells, showing that the SS AGPase is active in the presence of 3-phosphoglycerate and is inhibited by inorganic phosphate. As a step toward the elucidation of the role of the two AGPase isoforms in barley, the temporal and spatial expression profile of the four barley AGPase transcripts encoding these isoforms were studied. The results show that the steady-state level of beps and bepl, the transcripts encoding the major endosperm isoform, correlated positively with the rate of endosperm starch accumulation. In contrast, blps and blpl, the transcripts encoding the major leaf isoform, were constitutively expressed at a very low steady-state level throughout the barley plant. The implications of these findings for the evolution of plant AGPases are discussed. PMID:10557246

  2. The Allosterically Unregulated Isoform of ADP-Glucose Pyrophosphorylase from Barley Endosperm Is the Most Likely Source of ADP-Glucose Incorporated into Endosperm Starch.

    Science.gov (United States)

    Doan; Rudi; Olsen

    1999-11-01

    We present the results of studies of an unmodified version of the recombinant major barley (Hordeum vulgare) endosperm ADP-glucose pyrophoshorylase (AGPase) expressed in insect cells, which corroborate previous data that this isoform of the enzyme acts independently of the allosteric regulators 3-phosphoglycerate and inorganic phosphate. We also present a characterization of the individual subunits expressed separately in insect cells, showing that the SS AGPase is active in the presence of 3-phosphoglycerate and is inhibited by inorganic phosphate. As a step toward the elucidation of the role of the two AGPase isoforms in barley, the temporal and spatial expression profile of the four barley AGPase transcripts encoding these isoforms were studied. The results show that the steady-state level of beps and bepl, the transcripts encoding the major endosperm isoform, correlated positively with the rate of endosperm starch accumulation. In contrast, blps and blpl, the transcripts encoding the major leaf isoform, were constitutively expressed at a very low steady-state level throughout the barley plant. The implications of these findings for the evolution of plant AGPases are discussed.

  3. Enzyme inhibition by iminosugars

    DEFF Research Database (Denmark)

    López, Óscar; Qing, Feng-Ling; Pedersen, Christian Marcus

    2013-01-01

    Imino- and azasugar glycosidase inhibitors display pH dependant inhibition reflecting that both the inhibitor and the enzyme active site have groups that change protonation state with pH. With the enzyme having two acidic groups and the inhibitor one basic group, enzyme-inhibitor complexes...

  4. Poly[tetradecaaquatetrakis(μ3-1H-imidazole-4,5-dicarboxylatotetra-μ3-sulfato-cobalt(IIhexagadolinium(III

    Directory of Open Access Journals (Sweden)

    Li-Cai Zhu

    2011-08-01

    Full Text Available The asymmetric unit of the title compound, [CoGd6(C5H2N2O44(SO46(H2O14]n, contains a CoII ion (site symmetry overline1, three GdIII ions, two imidazole-4,5-dicarboxylate ligands, three SO42− anions, and seven coordinated water molecules. The CoII ion is six-coordinated by two O atoms from water molecules, two O atoms and two N atoms from two imidazole-4,5-dicarboxylate ligands, giving a slightly distorted octahedral geometry. The GdIII ions exhibit three types of coordination environments. One Gd ion is eight-coordinated in a bicapped trigonal–prismatic geometry by four O atoms from two imidazole-4,5-dicarboxylate ligands, two O atoms from two SO42− anions and two coordinated water molecules. The other Gd ions are nine-coordinated in a tricapped trigonal–prismatic geometry; one of these Gd ions is bonded to four O atoms from two imidazole-4,5-dicarboxylate ligands, three O atoms from three SO42− anions and two water O atoms and the other Gd ion is coordinated by one O atom and one N atom from one imidazole-4, 5-dicarboxylate ligand, five O atoms from three SO42− anions as well as two coordinated water molecules. These metal coordination units are connected by bridging imidazole-4,5-dicarboxylate and sulfate ligands, generating a three-dimensional network. The crystal structure is further stabilized by N—H...O, O—H...O, and C—H...O hydrogen-bonding interactions between water molecules, SO42− anions, and imidazole-4,5-dicarboxylate ligands.

  5. Mycobacterium tuberculosis phosphoribosylpyrophosphate synthetase: biochemical features of a crucial enzyme for mycobacterial cell wall biosynthesis.

    Directory of Open Access Journals (Sweden)

    Anna P Lucarelli

    Full Text Available The selection and soaring spread of Mycobacterium tuberculosis multidrug-resistant (MDR-TB and extensively drug-resistant strains (XDR-TB is a severe public health problem. Currently, there is an urgent need for new drugs for tuberculosis treatment, with novel mechanisms of action and, moreover, the necessity to identify new drug targets. Mycobacterial phosphoribosylpyrophosphate synthetase (MtbPRPPase is a crucial enzyme involved in the biosynthesis of decaprenylphosphoryl-arabinose, an essential precursor for the mycobacterial cell wall biosynthesis. Moreover, phosphoribosylpyrophosphate, which is the product of the PRPPase catalyzed reaction, is the precursor for the biosynthesis of nucleotides and of some amino acids such as histidine and tryptophan. In this context, the elucidation of the molecular and functional features of MtbPRPPase is mandatory. MtbPRPPase was obtained as a recombinant form, purified to homogeneity and characterized. According to its hexameric form, substrate specificity and requirement of phosphate for activity, the enzyme proved to belong to the class I of PRPPases. Although the sulfate mimicked the phosphate, it was less effective and required higher concentrations for the enzyme activation. MtbPRPPase showed hyperbolic response to ribose 5-phosphate, but sigmoidal behaviour towards Mg-ATP. The enzyme resulted to be allosterically activated by Mg(2+ or Mn(2+ and inhibited by Ca(2+ and Cu(2+ but, differently from other characterized PRPPases, it showed a better affinity for the Mn(2+ and Cu(2+ ions, indicating a different cation binding site geometry. Moreover, the enzyme from M. tuberculosis was allosterically inhibited by ADP, but less sensitive to inhibition by GDP. The characterization of M. tuberculosis PRPPase provides the starting point for the development of inhibitors for antitubercular drug design.

  6. A3 Adenosine Receptor Allosteric Modulator Induces an Anti-Inflammatory Effect: In Vivo Studies and Molecular Mechanism of Action

    Directory of Open Access Journals (Sweden)

    Shira Cohen

    2014-01-01

    Full Text Available The A3 adenosine receptor (A3AR is overexpressed in inflammatory cells and in the peripheral blood mononuclear cells of individuals with inflammatory conditions. Agonists to the A3AR are known to induce specific anti-inflammatory effects upon chronic treatment. LUF6000 is an allosteric compound known to modulate the A3AR and render the endogenous ligand adenosine to bind to the receptor with higher affinity. The advantage of allosteric modulators is their capability to target specifically areas where adenosine levels are increased such as inflammatory and tumor sites, whereas normal body cells and tissues are refractory to the allosteric modulators due to low adenosine levels. LUF6000 administration induced anti-inflammatory effect in 3 experimental animal models of rat adjuvant induced arthritis, monoiodoacetate induced osteoarthritis, and concanavalin A induced liver inflammation in mice. The molecular mechanism of action points to deregulation of signaling proteins including PI3K, IKK, IκB, Jak-2, and STAT-1, resulting in decreased levels of NF-κB, known to mediate inflammatory effects. Moreover, LUF6000 induced a slight stimulatory effect on the number of normal white blood cells and neutrophils. The anti-inflammatory effect of LUF6000, mechanism of action, and the differential effects on inflammatory and normal cells position this allosteric modulator as an attractive and unique drug candidate.

  7. Positive allosteric modulation of the human metabotropic glutamate receptor 4 (hmGluR4) by SIB-1893 and MPEP

    DEFF Research Database (Denmark)

    Mathiesen, Jesper Mosolff; Svendsen, Nannette; Bräuner-Osborne, Hans

    2003-01-01

    We have identified 2-methyl-6-(2-phenylethenyl)pyridine (SIB-1893) and 2-methyl-6-phenylethynyl pyridine hydrochloride (MPEP) as positive allosteric modulators for the hmGluR4. SIB-1893 and MPEP enhanced the potency and efficacy of L-2-amino-4-phophonobutyrate (L-AP4) in guanosine 5'-O-(3-[(35)S...

  8. Discovery of Potential Orthosteric and Allosteric Antagonists of P2Y1R from Chinese Herbs by Molecular Simulation Methods

    Science.gov (United States)

    Lu, Fang; Jiang, Lu-di; Qiao, Lian-sheng; Xiang, Yu-hong

    2016-01-01

    P2Y1 receptor (P2Y1R), which belongs to G protein-coupled receptors (GPCRs), is an important target in ADP-induced platelet aggregation. The crystal structure of P2Y1R has been solved recently, which revealed orthosteric and allosteric ligand-binding sites with the details of ligand-protein binding modes. And it suggests that P2Y1R antagonists, which recognize two distinct sites, could potentially provide an efficacious and safe antithrombotic profile. In present paper, 2D similarity search, pharmacophore based screening, and molecular docking were used to explore the potential natural P2Y1R antagonists. 2D similarity search was used to classify orthosteric and allosteric antagonists of P2Y1R. Based on the result, pharmacophore models were constructed and validated by the test set. Optimal models were selected to discover potential P2Y1R antagonists of orthosteric and allosteric sites from Traditional Chinese Medicine (TCM). And the hits were filtered by Lipinski's rule. Then molecular docking was used to refine the results of pharmacophore based screening and analyze the binding mode of the hits and P2Y1R. Finally, two orthosteric and one allosteric potential compounds were obtained, which might be used in future P2Y1R antagonists design. This work provides a reliable guide for discovering natural P2Y1R antagonists acting on two distinct sites from TCM. PMID:27635149

  9. Polyacrylonitrile nanofibers with added zeolitic imidazolate frameworks (ZIF-7) to enhance mechanical and thermal stability

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Min Wook [Department of Mechanical and Industrial Engineering, University of Illinois at Chicago, 842 W. Taylor St., Chicago, Illinois 60607-7022 (United States); An, Seongpil; Song, Kyo Yong; Joshi, Bhavana N.; Jo, Hong Seok; Yoon, Sam S., E-mail: skyoon@korea.ac.kr, E-mail: ayarin@uic.edu [School of Mechanical Engineering, Korea University, Seoul 136-713 (Korea, Republic of); Al-Deyab, Salem S. [Department of Chemistry, King Saud University, Riyadh 11451 (Saudi Arabia); Yarin, Alexander L., E-mail: skyoon@korea.ac.kr, E-mail: ayarin@uic.edu [Department of Mechanical and Industrial Engineering, University of Illinois at Chicago, 842 W. Taylor St., Chicago, Illinois 60607-7022 (United States); School of Mechanical Engineering, Korea University, Seoul 136-713 (Korea, Republic of)

    2015-12-28

    Zeolitic imidazolate framework 7/polyacrylonitrile (ZIF-7/PAN) nanofiber mat of high porosity and surface area can be used as a flexible fibrous filtration membrane that is subjected to various modes of mechanical loading resulting in stresses and strains. Therefore, the stress-strain relation of ZIF-7/PAN nanofiber mats in the elastic and plastic regimes of deformation is of significant importance for numerous practical applications, including hydrogen storage, carbon dioxide capture, and molecular sensing. Here, we demonstrated the fabrication of ZIF-7/PAN nanofiber mats via electrospinning and report their mechanical properties measured in tensile tests covering the elastic and plastic domains. The effect of the mat fabrication temperature on the mechanical properties is elucidated. We showed the superior mechanical strength and thermal stability of the compound ZIF-7/PAN nanofiber mats in comparison with that of pure PAN nanofiber mats. Material characterization including scanning electron microscope, energy-dispersive X-ray spectroscopy, tensile tests, differential scanning calorimetry, and Fourier transform infrared spectroscopy revealed the enhanced chemical bonds of the ZIF-7/PAN complex.

  10. Fine-scale tribological performance of zeolitic imidazolate framework (ZIF-8 based polymer nanocomposite membranes

    Directory of Open Access Journals (Sweden)

    Nay Win Khun

    2014-12-01

    Full Text Available We combined zeolitic imidazolate framework nanoparticles (ZIF-8: ˜150 nm diameter with Matrimid® 5218 polymer to form permeable mixed matrix membranes, featuring different weight fractions of nanoparticles (up to 30 wt. % loading. We used ball-on-disc micro-tribological method to measure the frictional coefficient of the nanocomposite membranes, as a function of nanoparticle loading and annealing heat treatment. The tribological results reveal that the friction and wear of the unannealed samples rise steadily with greater nanoparticle loading because ZIF-8 is relatively harder than the matrix, thus promoting abrasive wear mechanism. After annealing, however, we discover that the nanocomposites display an appreciably lower friction and wear damage compared with the unannealed counterparts. Evidence shows that the major improvement in tribological performance is associated with the greater amounts of wear debris derived from the annealed nanocomposite membranes. We propose that detached Matrimid-encapsulated ZIF-8 nanoparticles could function as “spacers,” which are capable of not only reducing direct contact between two rubbing surfaces but also enhancing free-rolling under the action of lateral forces.

  11. Hybrid imidazole (benzimidazole)/pyridine (quinoline) derivatives and evaluation of their anticancer and antimycobacterial activity.

    Science.gov (United States)

    Mantu, Dorina; Antoci, Vasilichia; Moldoveanu, Costel; Zbancioc, Gheorghita; Mangalagiu, Ionel I

    2016-01-01

    The design, synthesis, structure, and in vitro anticancer and antimycobacterial activity of new hybrid imidazole (benzimidazole)/pyridine (quinoline) derivatives are described. The strategy adopted for synthesis is straight and efficient, involving a three-step setup procedure: N-acylation, N-alkylation, and quaternization of nitrogen heterocycle. The solubility in microbiological medium and anticancer and antimycobacterial activity of a selection of new synthesized compounds were evaluated. The hybrid derivatives have an excellent solubility in microbiological medium, which make them promising from the pharmacological properties point of view. One of the hybrid compounds, 9 (with a benzimidazole and 8-aminoquinoline skeleton), exhibits a very good and selective antitumor activity against Renal Cancer A498 and Breast Cancer MDA-MB-468. Moreover, the anticancer assay suggests that the hybrid Imz (Bimz)/2-AP (8-AQ) compounds present a specific affinity to Renal Cancer A498. Concerning the antimycobacterial activity, only the hybrid compound, 9, has a significant activity. SAR correlations have been performed.

  12. Novel Zeolitic Imidazolate Framework/Polymer Membranes for Hydrogen Separations in Coal Processing

    Energy Technology Data Exchange (ETDEWEB)

    Musselman, Inga H.

    2013-01-31

    Nanoparticles of zeolitic imidazolate frameworks and other related hybrid materials were prepared by modifying published synthesis procedures by introducing bases, changing stoichiometric ratios, or adjusting reaction conditions. These materials were stable at temperatures >300 °C and were compatible with the polymer matrices used to prepare mixed-matrix membranes (MMMs). MMMs tested at 300 °C exhibited a >30 fold increase in permeability, compared to those measured at 35 °C, while maintaining H{sub 2}/CO{sub 2} selectivity. Measurements at high pressure (up to 30 atm) and high temperature (up to 300 °C) resulted in an increase in gas flux across the membrane with retention of selectivity. No variations in permeability were observed at high pressures at either 35 or 300 °C. CO{sub 2}-induced plasticization was not observed for Matrimid®, VTEC, and PBI polymers or their MMMs at 30 atm and 300 °C. Membrane surface modification by cross-linking with ethylenediamine resulted in an increase in H{sub 2}/CO{sub 2} selectivity at 35 °C. Spectrometric analysis showed that the cross-linking was effective to temperatures <150 °C. At higher temperatures, the cross-linked membranes exhibit a H2/CO2 selectivity similar to the uncrosslinked polymer.

  13. Heterogeneous photochemistry of imidazole-2-carboxaldehyde: HO2 radical formation and aerosol growth

    Science.gov (United States)

    González Palacios, Laura; Corral Arroyo, Pablo; Aregahegn, Kifle Z.; Steimer, Sarah S.; Bartels-Rausch, Thorsten; Nozière, Barbara; George, Christian; Ammann, Markus; Volkamer, Rainer

    2016-09-01

    The multiphase chemistry of glyoxal is a source of secondary organic aerosol (SOA), including its light-absorbing product imidazole-2-carboxaldehyde (IC). IC is a photosensitizer that can contribute to additional aerosol ageing and growth when its excited triplet state oxidizes hydrocarbons (reactive uptake) via H-transfer chemistry. We have conducted a series of photochemical coated-wall flow tube (CWFT) experiments using films of IC and citric acid (CA), an organic proxy and H donor in the condensed phase. The formation rate of gas-phase HO2 radicals (PHO2) was measured indirectly by converting gas-phase NO into NO2. We report on experiments that relied on measurements of NO2 formation, NO loss and HONO formation. PHO2 was found to be a linear function of (1) the [IC] × [CA] concentration product and (2) the photon actinic flux. Additionally, (3) a more complex function of relative humidity (25 % reaction of NO with HO2 in the gas phase. Further, seed aerosols containing IC and ammonium sulfate were exposed to gas-phase limonene and NOx in aerosol flow tube experiments, confirming significant PHO2 from aerosol surfaces. Our results indicate a potentially relevant contribution of triplet state photochemistry for gas-phase HO2 production, aerosol growth and ageing in the atmosphere.

  14. Synthesis of zeolitic imidazolate framework-69 for adsorption separation of ethane and ethylene

    Science.gov (United States)

    Yuan, Wenhui; Zhang, Xiaotao; Li, Li

    2017-07-01

    The zeolitic imidazolate framework ZIF-69 with topology of GME has been synthesized successfully via a facile hydrothermal synthetic method, and characterized by X-ray diffraction (XRD), scanning electron microscopy (SEM), transmission electron microscopy (TEM), nitrogen adsorption-desorption measurements, thermal gravimetric analysis (TGA) and X-ray photoelectron spectroscopy (XPS). The ethane/ethylene separation potential was measured by single-component adsorption isotherms, and the selectivity was calculated based on the ideal adsorbed solution theory (IAST). SEM and TEM images confirmed that the as-synthesized seeds possessed a well-crystallized and uniform morphology, appearing as a flat hexagonal prism with double hexagonal pyramid heads. The obtained ZIF-69 exhibited a higher adsorption capacity of C2H6 over C2H4 at 100 kPa, and the C2H6/C2H4 adsorption selectivity was about 1.7 at below 100 kPa. The outcome would provide a new insight into the study on the effective separation of ethane/ethylene using different topological structures of ZIFs.

  15. Blue-light emitting electrochemical cells comprising pyrene-imidazole derivatives

    Science.gov (United States)

    Lee, Hyeonji; Sunesh, Chozhidakath Damodharan; Subeesh, Madayanad Suresh; Choe, Youngson

    2018-04-01

    Light-emitting electrochemical cells (LECs), the next-generation lighting sources are the potential replacements for organic light-emitting diodes (OLEDs). In recent years, organic small molecules (SMs) have established the applicability in solid-state lighting, and considered as prospective active materials for LECs with higher device performance. Here, we describe the synthesis of pyrene-imidazole based SMs, PYR1, and PYR2 that differ by one pyrene unit and their characterization by various spectroscopic methods. To investigate the thermal, photophysical, and electrochemical properties of the two synthesized compounds, we performed thermogravimetric, UV-visible, photoluminescence (PL), and voltammetric measurements. The photoluminescence (PL) emission spectra of PYR1 and PYR2 measured in the acetonitrile solution, where PYR1 and PYR2 emit in the blue spectral region with peaks aligned at 383 nm and 389 nm, respectively. The fabricated LEC devices exhibited broader electroluminescence (EL) spectra with a significant red shift of the emission maxima to 446 nm and 487 nm, with CIE coordinates of (0.17, 0.18) and (0.18, 0.25) for PYR1 and PYR2, respectively. The LECs based on PYR1 and PYR2 produced maximum brightness values of 180 and 72 cd m-2 and current densities of 55 and 27 mA cm-2, respectively.

  16. Hydrothermal Synthesis of Zeolitic Imidazolate Frameworks-8 (ZIF-8) Crystals with Controllable Size and Morphology

    KAUST Repository

    Lestari, Gabriella

    2012-05-01

    Zeolitic imidazolate frameworks (ZIFs) is a new class of metal-organic frameworks (MOFs) with zeolite-like properties such as permanent porosity, uniform pore size, and exceptional thermal and chemical stability. Until recently, ZIF materials have been mostly synthesized by solvothermal method. In this thesis, further analysis to tune the size and morphology of ZIF-8 is done upon our group’s recent success in preparing ZIF-8 crystals in pure aqueous solutions. Compositional parameters (molar ratio of 2-methylimidazole/Zn2+, type of zinc salt reagents, reagent concentrations, addition of surfactants) as well as process parameters (temperature and time) were systematically investigated. Upon characterizations of as-synthesized samples by X-ray powder diffraction, thermal gravimetric analysis, N2 adsorption, and field-emission scanning electron microscope, the results show that the particle size and morphology of ZIF-8 crystals are extremely sensitive to the compotional parameters of reagent concentration and addition of surfactants. The particle size and morphology of hydrothermally synthesized ZIF-8 crystals can be finely tuned; with the size ranging from 90 nm to 4 μm and the shape from truncated cubic to rhombic dodecahedron.

  17. Tunable CO 2 Adsorbents by Mixed-Linker Synthesis and Postsynthetic Modification of Zeolitic Imidazolate Frameworks

    KAUST Repository

    Thompson, Joshua A.

    2013-04-25

    The incorporation of accessible amine functionality in zeolitic imidazolate frameworks (ZIFs) is used to improve the adsorption selectivity for CO 2/CH4 gas separation applications. Two synthetic approaches are described in this work to introduce functionality into the ZIF: (i) mixed-linker ZIF synthesis with 2-aminobenzimidazole as a substitution linker and (ii) postsynthetic modification of a mixed-linker ZIF with ethylenediamine. Using 2-aminobenzimidazole, a linker with a primary amine functional group, substitution of the ZIF-8 linker during synthesis allows for control over the adsorption properties while maintaining the ZIF-8 structure with up to nearly 50% substitution in the mixed-linker ZIF framework, producing a material with tunable pore size and amine functionality. Alternatively, postsynthetic modification of a mixed-linker ZIF containing an aldehyde functional group produces a ZIF material with a primary amine without detrimental loss of micropore volume by controlling the amount of functional group sites for modification. Both approaches using mixed-linker ZIFs yield new materials that show improvement in adsorption selectivity for the CO 2/CH4 gas pair over ZIF-8 and commercially available adsorbents as well as an increase in the heat of adsorption for CO2 without significant changes to the crystal structure. These results indicate that tuning the surface properties of ZIFs by either mixed-linker synthesis and/or postsynthetic modification may generate new materials with improved gas separation properties, thereby providing a new method for tailoring metal-organic frameworks. © 2013 American Chemical Society.

  18. Synthesis of triazole-based and imidazole-based zinc catalysts

    Energy Technology Data Exchange (ETDEWEB)

    Valdez, Carlos A.; Satcher, Jr., Joe H.; Aines, Roger D.; Baker, Sarah E.

    2013-03-12

    Various methods and structures of complexes and molecules are described herein related to a zinc-centered catalyst for removing carbon dioxide from atmospheric or aqueous environments. According to one embodiment, a method for creating a tris(triazolyl)pentaerythritol molecule includes contacting a pentaerythritol molecule with a propargyl halide molecule to create a trialkyne molecule, and contacting the trialkyne molecule with an azide molecule to create the tris(triazolyl)pentaerythritol molecule. In another embodiment, a method for creating a tris(imidazolyl)pentaerythritol molecule includes alkylating an imidazole 2-carbaldehyde molecule to create a monoalkylated aldehyde molecule, reducing the monoalkylated aldehyde molecule to create an alcohol molecule, converting the alcohol molecule to create an alkyl halide molecule using thionyl halide, and reacting the alkyl halide molecule with a pentaerythritol molecule to create a tris(imidazolyl)pentaerythritol molecule. In another embodiment, zinc is bound to the tris(triazolyl)pentaerythritol molecule to create a zinc-centered tris(triazolyl)pentaerythritol catalyst for removing carbon dioxide from atmospheric or aqueous environments.

  19. Hybrid Zeolitic Imidazolate Frameworks: Controlling Framework Porosity and Functionality by Mixed-Linker Synthesis

    KAUST Repository

    Thompson, Joshua A.

    2012-05-22

    Zeolitic imidazolate frameworks (ZIFs) are a subclass of nanoporous metal-organic frameworks (MOFs) that exhibit zeolite-like structural topologies and have interesting molecular recognition properties, such as molecular sieving and gate-opening effects associated with their pore apertures. The synthesis and characterization of hybrid ZIFs with mixed linkers in the framework are described in this work, producing materials with properties distinctly different from the parent frameworks (ZIF-8, ZIF-90, and ZIF-7). NMR spectroscopy is used to assess the relative amounts of the different linkers included in the frameworks, whereas nitrogen physisorption shows the evolution of the effective pore size distribution in materials resulting from the framework hybridization. X-ray diffraction shows these hybrid materials to be crystalline. In the case of ZIF-8-90 hybrids, the cubic space group of the parent frameworks is continuously maintained, whereas in the case of the ZIF-7-8 hybrids there is a transition from a cubic to a rhombohedral space group. Nitrogen physisorption data reveal that the hybrid materials exhibit substantial changes in gate-opening phenomena, either occurring at continuously tunable partial pressures of nitrogen (ZIF-8-90 hybrids) or loss of gate-opening effects to yield more rigid frameworks (ZIF-7-8 hybrids). With this synthetic approach, significant alterations in MOF properties may be realized to suit a desired separation or catalytic process. © 2012 American Chemical Society.

  20. Heteroepitaxially grown zeolitic imidazolate framework membranes with unprecedented propylene/propane separation performances.

    Science.gov (United States)

    Kwon, Hyuk Taek; Jeong, Hae-Kwon; Lee, Albert S; An, He Seong; Lee, Jong Suk

    2015-09-30

    Propylene/propane separation is one of the most challenging separations, currently achieved by energy-intensive cryogenic distillation. Despite the great potential for energy-efficient membrane-based separations, no commercial membranes are currently available due to the limitations of current polymeric materials. Zeolitic imidazolate framework, ZIF-8, with the effective aperture size of ∼4.0 Å, has been shown to be very promising for propylene/propane separation. Despite the extensive research on ZIF-8 membranes, only a few reported ZIF-8 membranes have displayed good propylene/propane separation performances presumably due to the challenges of controlling the microstructures of polycrystalline membranes. Here we report the first well-intergrown membranes of ZIF-67 (Co-substituted ZIF-8) by heteroepitaxially growing ZIF-67 on ZIF-8 seed layers. The ZIF-67 membranes exhibited impressively high propylene/propane separation capabilities. Furthermore, when a tertiary growth of ZIF-8 layers was applied to heteroepitaxially grown ZIF-67 membranes, the membranes exhibited unprecedentedly high propylene/propane separation factors of ∼200 possibly due to enhanced grain boundary structure.

  1. Magnetocaloric effect and critical behavior in Mn2-imidazole-[Nb(CN)8] molecular magnetic sponge

    Science.gov (United States)

    Fitta, Magdalena; Pełka, Robert; Gajewski, Marcin; Mihalik, Marian; Zentkova, Maria; Pinkowicz, Dawid; Sieklucka, Barbara; Bałanda, Maria

    2015-12-01

    A comprehensive study of magnetocaloric effect (MCE) and critical behavior in the {Mn2(imH)2(H2O)4[Nb(CN)8]·4H2O}n molecular magnet is reported. The compound is an example of a magnetic sponge, where structural changes provoked by dehydration process lead to the increase of Tc critical temperature from 25 K for the as-synthesized sample (1) up to 60 K for the anhydrous one (2). MCE and critical behavior were investigated by magnetization measurements. The maximum value of magnetic entropy change ΔS, determined by the magnetization measurements for 1 is 6.70 J mol-1 K-1 (8.95 J kg-1 K-1) at μ0ΔH=5 T, while for 2 it is equal to 4.02 J mol-1 K-1 (7.73 J kg-1 K-1) at the same magnetic field change. The field dependence of MCE at Tc for 1 and 2 was consistent with critical exponents, which allowed to classify both phases to 3D Heisenberg universality class. The Tc-2/3 dependence of the maximum entropy change has been tested using data of 1 and 2 together with MCE data previously reported for other members of the ferrimagnetic Mn2-L-[Nb(CN)8] (L=imidazole, pyridazine and pyrazole) series. Experimental MCE results have been compared with the spin contribution to the magnetic entropy change estimated using a molecular field approximation.

  2. Adsorptive removal of 1-naphthol from water with Zeolitic imidazolate framework-67

    Science.gov (United States)

    Yan, Xinlong; Hu, Xiaoyan; Chen, Tao; Zhang, Shiyu; Zhou, Min

    2017-08-01

    1-Naphthol is widely used as an intermediate in the plastics, dyes, fibers and rubbers production areas, leading to the increasing detection of 1-naphthol in the soil and water environment, which is of particular concern due to its acute toxicity and negative environmental impacts. Considering the high surface area and good stability of ZIFs (zeolitic imidazole frameworks) material, ZIF-67 (a representative cobalt-based ZIFs material) was synthesized and applied as an adsorbent for removal of 1-naphthol from aqueous solution. The obtained ZIF-67 was characterized by XRD, TEM, XPS, N2 physisorption and TG, and the adsorption isotherm, kinetics, and regeneration of the adsorbent were studied in detail. The adsorption of 1-naphthol on ZIF-67 followed a pseudo-second-order equation kinetics and fitted Langmuir adsorption model with a maximum adsorption capacity of 339 mg/g at 313 K, which is much higher than that of the common adsorbents reported such as activated carbon and carbon nanotubes et al. The solution pH was found to be an important factor influencing the adsorption process, which could be explained by the predominant mechanism controlling the process, i.e. electrostatic attraction. In addition, the ZIF-67 showed desirable reusability toward 1-naphthol removal from alkaline aqueous solution.

  3. Co-grafting of acrylamide and vinyl imidazole onto EB pre-irradiated silanized silica gel

    International Nuclear Information System (INIS)

    Xu Ling; Sun Jian; Zhao Long

    2011-01-01

    Silica-based adsorbent was prepared by radiation-induced grafting of acrylamide (AAM) and vinyl imidazole (VIM) onto the silanized silica. The silanized silica was pre-irradiated by electron beam and then reacted with AAM/VIM mixture solution under various conditions. FTIR, TG-DTA and XPS spectra manifested that AAM and VIM were successfully grafted onto the silica surface. The effects of monomer composition, absorbed dose, reaction time and reaction temperature on the grafting yield were investigated to optimize the reaction conditions. The results showed that the optimal reaction conditions were as follows: AAM/VIM mole ratio 6:4 with a total concentration of 4 mol/L, absorbed dose 100 kGy, reaction temperature 60 o C and reaction time 18 h. The SS-g-AAM/VIM adsorbent is expected to be useful for the removal of heavy-metal-ions from wastewater. - Highlights: → AAM and VIM were co-grafted to silanized silica by EB pre-irradiation grafting. → The grafted chain was characterized by thermo-analysis, FTIR and XPS. → Physical adsorption of monomer to silica plays an important role in radiation grafting.

  4. Antifungal activity of tioconazole (UK-20,349), a new imidazole derivative.

    Science.gov (United States)

    Jevons, S; Gymer, G E; Brammer, K W; Cox, D A; Leeming, M R

    1979-04-01

    Tioconazole (UK-20,349), a new antifungal imidazole derivative, was compared with miconazole for activity in vitro against Candida spp., Torulopsis glabrata, Cryptococcus neoformans, Aspergillus spp., and dermatophyte fungi (Trichophyton spp. and Microsporum spp.). Tioconazole was more active than miconazole against all the fungal species examined except Aspergillus, against which both agents showed similar activity. Both tioconazole and miconazole inhibited the growth of all fungi examined at concentrations well below their quoted minimum inhibitory concentrations. Their activity against fungi in vivo was investigated in mice infected systemically with Candida albicans. Both agents significantly reduced the numbers of viable Candida cells recoverable from the kidneys of infected animals, with tioconazole producing a generally more marked reduction. After administration of a single oral dose (25 mg/kg) to beagle dogs or white mice, higher and more sustained circulating levels of bioactive drug were detectable of tioconazole than of miconazole. These observations suggest that tioconazole may have potential in the treatment of both superficial and systemic mycoses in humans.

  5. Imidazole Alkaloids from the South China Sea Sponge Pericharax heteroraphis and Their Cytotoxic and Antiviral Activities

    Directory of Open Access Journals (Sweden)

    Kai-Kai Gong

    2016-01-01

    Full Text Available Marine sponges continue to serve as a rich source of alkaloids possessing interesting biological activities and often exhibiting unique structural frameworks. In the current study, chemical investigation on the marine sponge Pericharax heteroraphis collected from the South China Sea yielded one new imidazole alkaloid named naamidine J (1 along with four known ones (2–5. Their structures were established by extensive spectroscopic methods and comparison of their data with those of the related known compounds. All the isolates possessed a central 2-aminoimidazole ring, substituted by one or two functionalized benzyl groups in some combination of the C4 and C5 positions. The cytotoxicities against selected HL-60, HeLa, A549 and K562 tumor cell lines and anti-H1N1 (Influenza a virus (IAV activity for the isolates were evaluated. Compounds 1 and 2 exhibited cytotoxicities against the K562 cell line with IC50 values of 11.3 and 9.4 μM, respectively. Compound 5 exhibited weak anti-H1N1 (influenza a virus, IAV activity with an inhibition ratio of 33%.

  6. Efficient adsorptive removal of Congo red from aqueous solution by synthesized zeolitic imidazolate framework-8

    Directory of Open Access Journals (Sweden)

    Canlan Jiang

    2016-10-01

    Full Text Available Dyes exposure in aquatic environment creates risks to human health and biota due to their intrinsic toxic mutagenic and carcinogenic characteristics. In this work, a metal-organic frameworks materials, zeolitic imidazolate framework-8 (ZIF-8, was synthesized through hydrothermal reaction for the adsorptive removal of harmful Congo red (CR from aqueous solution. Results showed that the maximum adsorption capacity of CR onto ZIF-8 was ultrahigh as 1250 mg g−1. Adsorption behaviors can be successfully fitted by the pseudo-second order kinetic model and the Langmuir isotherm equation. Solution conditions (pH condition and the co-exist anions may influent the adsorption behaviors. The adsorption performance at various temperatures indicated the process was a spontaneous and endothermic adsorption reaction. The enhanced adsorption capacity was determined due to large surface area of ZIF-8 and the strong interactions between surface groups of ZIF-8 and CR molecules including the electrostatic interaction between external active sites Zn−OH on ZIF-8 -and −SO3 or –N=N– sites in CR molecule, and the π–π interaction.

  7. High-Pressure Chemistry of a Zeolitic Imidazolate Framework Compound in the Presence of Different Fluids.

    Science.gov (United States)

    Im, Junhyuck; Yim, Narae; Kim, Jaheon; Vogt, Thomas; Lee, Yongjae

    2016-09-14

    Pressure-dependent structural and chemical changes of the zeolitic imidazolate framework compound ZIF-8 have been investigated using different pressure transmitting media (PTM) up to 4 GPa. The unit cell of ZIF-8 expands and contracts under hydrostatic pressure depending on the solvent molecules used as PTM. When pressurized in water up to 2.2(1) GPa, the unit cell of ZIF-8 reveals a gradual contraction. In contrast, when alcohols are used as PTM, the ZIF-8 unit cell volume initially expands by 1.2% up to 0.3(1) GPa in methanol, and by 1.7% up to 0.6(1) GPa in ethanol. Further pressure increase then leads to a discontinuous second volume expansion by 1.9% at 1.4(1) GPa in methanol and by 0.3% at 2.3(1) GPa in ethanol. The continuous uptake of molecules under pressure, modeled by the residual electron density derived from Rietveld refinements of X-ray powder diffraction, reveals a saturation pressure near 2 GPa. In non-penetrating PTM (silicone oil), ZIF-8 becomes amorphous at 0.9(1) GPa. The structural changes observed in the ZIF-8-PTM system under pressure point to distinct molecular interactions within the pores.

  8. Investigating Metabotropic Glutamate Receptor 5 Allosteric Modulator Cooperativity, Affinity, and Agonism: Enriching Structure-Function Studies and Structure-Activity Relationships

    Science.gov (United States)

    Gregory, Karen J.; Noetzel, Meredith J.; Rook, Jerri M.; Vinson, Paige N.; Stauffer, Shaun R.; Rodriguez, Alice L.; Emmitte, Kyle A.; Zhou, Ya; Chun, Aspen C.; Felts, Andrew S.; Chauder, Brian A.; Lindsley, Craig W.; Niswender, Colleen M.

    2012-01-01

    Drug discovery programs increasingly are focusing on allosteric modulators as a means to modify the activity of G protein-coupled receptor (GPCR) targets. Allosteric binding sites are topographically distinct from the endogenous ligand (orthosteric) binding site, which allows for co-occupation of a single receptor with the endogenous ligand and an allosteric modulator that can alter receptor pharmacological characteristics. Negative allosteric modulators (NAMs) inhibit and positive allosteric modulators (PAMs) enhance the affinity and/or efficacy of orthosteric agonists. Established approaches for estimation of affinity and efficacy values for orthosteric ligands are not appropriate for allosteric modulators, and this presents challenges for fully understanding the actions of novel modulators of GPCRs. Metabotropic glutamate receptor 5 (mGlu5) is a family C GPCR for which a large array of allosteric modulators have been identified. We took advantage of the many tools for probing allosteric sites on mGlu5 to validate an operational model of allosterism that allows quantitative estimation of modulator affinity and cooperativity values. Affinity estimates derived from functional assays fit well with affinities measured in radioligand binding experiments for both PAMs and NAMs with diverse chemical scaffolds and varying degrees of cooperativity. We observed modulation bias for PAMs when we compared mGlu5-mediated Ca2+ mobilization and extracellular signal-regulated kinase 1/2 phosphorylation data. Furthermore, we used this model to quantify the effects of mutations that reduce binding or potentiation by PAMs. This model can be applied to PAM and NAM potency curves in combination with maximal fold-shift data to derive reliable estimates of modulator affinities. PMID:22863693

  9. Modeling the Contribution of Allosteric Regulation for Flux Control in the Central Carbon Metabolism of E. coli

    DEFF Research Database (Denmark)

    Machado, Daniel; Herrgard, Markus; Rocha, Isabel

    2015-01-01

    contribution to the metabolic flux changes. Inspired by these results, we develop a constraint-based method (arFBA) for simulation of metabolic flux distributions that accounts for allosteric interactions. This method can be used for systematic prediction of potential allosteric regulation under the given...... the metabolic flux. Accounting for allosteric interactions in metabolic reconstructions reveals a hidden topology in metabolic networks, improving our understanding of cellular metabolism and fostering the development of novel simulation methods that account for this type of regulation....

  10. Consequences of Energetic Frustration on the Ligand-Coupled Folding/Dimerization Dynamics of Allosteric Protein S100A12.

    Science.gov (United States)

    Ren, Weitong; Li, Wenfei; Wang, Jun; Zhang, Jian; Wang, Wei

    2017-10-26

    Allosteric proteins are featured by energetic degeneracy of two (or more) functionally relevant conformations, therefore their energy landscapes are often locally frustrated. How such frustration affects the protein folding/binding dynamics is not well understood. Here, by using molecular simulations we study the consequences of local frustration in the dimerization dynamics of allosteric proteins based on a homodimer protein S100A12. Despite of the structural symmetry of the two EF-hand motifs in the three-dimensional structures, the S100A12 homodimer shows allosteric behaviors and local frustration only in half of its structural elements, i.e., the C-terminal EF-hand. We showed that such spatially asymmetric location of frustration leads to asymmetric dimerization pathways, in which the dimerization is dominantly initiated by the interchain binding of the minimally frustrated N-terminal EF-hands, achieving optimal balance between the requirements of rapid conformational switching and interchain assembling to the energy landscapes. We also showed that the local frustration, as represented by the double-basin topography of the energy landscape, gives rise to multiple cross-linked dimerization pathways, in which the dimerization is coupled with the allosteric motions of the C-terminal EF-hands. Binding of metal ions tends to reshape the energy landscape and modulate the dimerization pathways. In addition, by employing the frustratometer method, we showed that the highly frustrated residue-pairs in the C-terminal EF-hand are partially unfolded during the conformational transitions of the native homodimer, leading to lowing of free energy barrier. Our results revealed tight interplay between the local frustration of the energy landscape and the dimerization dynamics for allosteric proteins.

  11. Modulation of global low-frequency motions underlies allosteric regulation: demonstration in CRP/FNR family transcription factors.

    Directory of Open Access Journals (Sweden)

    Thomas L Rodgers

    2013-09-01

    Full Text Available Allostery is a fundamental process by which ligand binding to a protein alters its activity at a distinct site. There is growing evidence that allosteric cooperativity can be communicated by modulation of protein dynamics without conformational change. The mechanisms, however, for communicating dynamic fluctuations between sites are debated. We provide a foundational theory for how allostery can occur as a function of low-frequency dynamics without a change in structure. We have generated coarse-grained models that describe the protein backbone motions of the CRP/FNR family transcription factors, CAP of Escherichia coli and GlxR of Corynebacterium glutamicum. The latter we demonstrate as a new exemplar for allostery without conformation change. We observe that binding the first molecule of cAMP ligand is correlated with modulation of the global normal modes and negative cooperativity for binding the second cAMP ligand without a change in mean structure. The theory makes key experimental predictions that are tested through an analysis of variant proteins by structural biology and isothermal calorimetry. Quantifying allostery as a free energy landscape revealed a protein "design space" that identified the inter- and intramolecular regulatory parameters that frame CRP/FNR family allostery. Furthermore, through analyzing CAP variants from diverse species, we demonstrate an evolutionary selection pressure to conserve residues crucial for allosteric control. This finding provides a link between the position of CRP/FNR transcription factors within the allosteric free energy landscapes and evolutionary selection pressures. Our study therefore reveals significant features of the mechanistic basis for allostery. Changes in low-frequency dynamics correlate with allosteric effects on ligand binding without the requirement for a defined spatial pathway. In addition to evolving suitable three-dimensional structures, CRP/FNR family transcription factors have

  12. Modulation of global low-frequency motions underlies allosteric regulation: demonstration in CRP/FNR family transcription factors.

    Science.gov (United States)

    Rodgers, Thomas L; Townsend, Philip D; Burnell, David; Jones, Matthew L; Richards, Shane A; McLeish, Tom C B; Pohl, Ehmke; Wilson, Mark R; Cann, Martin J

    2013-09-01

    Allostery is a fundamental process by which ligand binding to a protein alters its activity at a distinct site. There is growing evidence that allosteric cooperativity can be communicated by modulation of protein dynamics without conformational change. The mechanisms, however, for communicating dynamic fluctuations between sites are debated. We provide a foundational theory for how allostery can occur as a function of low-frequency dynamics without a change in structure. We have generated coarse-grained models that describe the protein backbone motions of the CRP/FNR family transcription factors, CAP of Escherichia coli and GlxR of Corynebacterium glutamicum. The latter we demonstrate as a new exemplar for allostery without conformation change. We observe that binding the first molecule of cAMP ligand is correlated with modulation of the global normal modes and negative cooperativity for binding the second cAMP ligand without a change in mean structure. The theory makes key experimental predictions that are tested through an analysis of variant proteins by structural biology and isothermal calorimetry. Quantifying allostery as a free energy landscape revealed a protein "design space" that identified the inter- and intramolecular regulatory parameters that frame CRP/FNR family allostery. Furthermore, through analyzing CAP variants from diverse species, we demonstrate an evolutionary selection pressure to conserve residues crucial for allosteric control. This finding provides a link between the position of CRP/FNR transcription factors within the allosteric free energy landscapes and evolutionary selection pressures. Our study therefore reveals significant features of the mechanistic basis for allostery. Changes in low-frequency dynamics correlate with allosteric effects on ligand binding without the requirement for a defined spatial pathway. In addition to evolving suitable three-dimensional structures, CRP/FNR family transcription factors have been selected to

  13. Allosteric Inhibition of Factor XIIIa. Non-Saccharide Glycosaminoglycan Mimetics, but Not Glycosaminoglycans, Exhibit Promising Inhibition Profile.

    Directory of Open Access Journals (Sweden)

    Rami A Al-Horani

    Full Text Available Factor XIIIa (FXIIIa is a transglutaminase that catalyzes the last step in the coagulation process. Orthostery is the only approach that has been exploited to design FXIIIa inhibitors. Yet, allosteric inhibition of FXIIIa is a paradigm that may offer a key advantage of controlled inhibition over orthosteric inhibition. Such an approach is likely to lead to novel FXIIIa inhibitors that do not carry bleeding risks. We reasoned that targeting a collection of basic amino acid residues distant from FXIIIa's active site by using sulfated glycosaminoglycans (GAGs or non-saccharide GAG mimetics (NSGMs would lead to the discovery of the first allosteric FXIIIa inhibitors. We tested a library of 22 variably sulfated GAGs and NSGMs against human FXIIIa to discover promising hits. Interestingly, although some GAGs bound to FXIIIa better than NSGMs, no GAG displayed any inhibition. An undecasulfated quercetin analog was found to inhibit FXIIIa with reasonable potency (efficacy of 98%. Michaelis-Menten kinetic studies revealed an allosteric mechanism of inhibition. Fluorescence studies confirmed close correspondence between binding affinity and inhibition potency, as expected for an allosteric process. The inhibitor was reversible and at least 9-fold- and 26-fold selective over two GAG-binding proteins factor Xa (efficacy of 71% and thrombin, respectively, and at least 27-fold selective over a cysteine protease papain. The inhibitor also inhibited the FXIIIa-mediated polymerization of fibrin in vitro. Overall, our work presents the proof-of-principle that FXIIIa can be allosterically modulated by sulfated non-saccharide agents much smaller than GAGs, which should enable the design of selective and safe anticoagulants.

  14. Synthesis, Crystal Structure, and Luminescent Properties of New Zinc(II and Cadmium(II Metal-Organic Frameworks Based on Flexible Bis(imidazol-1-ylalkane Ligands

    Directory of Open Access Journals (Sweden)

    Marina Barsukova

    2016-10-01

    Full Text Available New metal-organic frameworks (MOFs based on zinc and cadmium ions, terephthalic acid, and flexible ligands 1,5-bis(imidazol-1-ylpentane or 1,6-bis(imidazol-1-ylhexane were prepared and characterized by X-ray diffraction, thermorgavimetric analysis and IR spectroscopy. The imidazolyl ligands were prepared by a new robust procedure involving the reaction between imidazole and 1,5-dibromopentane or 1,6-dibromohexane in a superbasic medium (KOH in DMSO. MOFs based on 1,5-bis(imidazol-1-ylpentane had diamond topology (dia and are triply interpenetrated. Ligands with longer spacer 1,6-bis(imidazol-1-ylhexane, terephthalate ions and zinc(II ions formed five-fold interpenetrated metal-organic framework also with dia topology, while cadmium(II ions with the same ligands formed eight-connected uninodal net with a very rare self-penetrated topological type ilc and a point symbol 424.5.63. The influence of the chemical composition of MOFs on their photoluminescent properties is investigated and discussed in detail.

  15. Ibuprofen Impairs Allosterically Peroxynitrite Isomerization by Ferric Human Serum Heme-Albumin*

    Science.gov (United States)

    Ascenzi, Paolo; di Masi, Alessandra; Coletta, Massimo; Ciaccio, Chiara; Fanali, Gabriella; Nicoletti, Francesco P.; Smulevich, Giulietta; Fasano, Mauro

    2009-01-01

    Human serum albumin (HSA) participates in heme scavenging; in turn, heme endows HSA with myoglobin-like reactivity and spectroscopic properties. Here, the allosteric effect of ibuprofen on peroxynitrite isomerization to NO3− catalyzed by ferric human serum heme-albumin (HSA-heme-Fe(III)) is reported. Data were obtained at 22.0 °C. HSA-heme-Fe(III) catalyzes peroxynitrite isomerization in the absence and presence of CO2; the values of the second order catalytic rate constant (kon) are 4.1 × 105 and 4.5 × 105 m−1 s−1, respectively. Moreover, HSA-heme-Fe(III) prevents peroxynitrite-mediated nitration of free added l-tyrosine. The pH dependence of kon (pKa = 6.9) suggests that peroxynitrous acid reacts preferentially with the heme-Fe(III) atom, in the absence and presence of CO2. The HSA-heme-Fe(III)-catalyzed isomerization of peroxynitrite has been ascribed to the reactive pentacoordinated heme-Fe(III) atom. In the absence and presence of CO2, ibuprofen impairs dose-dependently peroxynitrite isomerization by HSA-heme-Fe(III) and facilitates the nitration of free added l-tyrosine; the value of the dissociation equilibrium constant for ibuprofen binding to HSA-heme-Fe(III) (L) ranges between 7.7 × 10−4 and 9.7 × 10−4 m. Under conditions where [ibuprofen] is ≫L, the kinetics of HSA-heme-Fe(III)-catalyzed isomerization of peroxynitrite is superimposable to that obtained in the absence of HSA-heme-Fe(III) or in the presence of non-catalytic HSA-heme-Fe(III)-cyanide complex and HSA. Ibuprofen binding impairs allosterically peroxynitrite isomerization by HSA-heme-Fe(III), inducing the hexacoordination of the heme-Fe(III) atom. These results represent the first evidence for peroxynitrite isomerization by HSA-heme-Fe(III), highlighting the allosteric modulation of HSA-heme-Fe(III) reactivity by heterotropic interaction(s), and outlining the role of drugs in modulating HSA functions. The present results could be relevant for the drug-dependent protective role

  16. Enzymes for improved biomass conversion

    Science.gov (United States)

    Brunecky, Roman; Himmel, Michael E.

    2016-02-02

    Disclosed herein are enzymes and combinations of the enzymes useful for the hydrolysis of cellulose and the conversion of biomass. Methods of degrading cellulose and biomass using enzymes and cocktails of enzymes are also disclosed.

  17. Magnetically responsive enzyme powders

    Science.gov (United States)

    Pospiskova, Kristyna; Safarik, Ivo

    2015-04-01

    Powdered enzymes were transformed into their insoluble magnetic derivatives retaining their catalytic activity. Enzyme powders (e.g., trypsin and lipase) were suspended in various liquid media not allowing their solubilization (e.g., saturated ammonium sulfate and highly concentrated polyethylene glycol solutions, ethanol, methanol, 2-propanol) and subsequently cross-linked with glutaraldehyde. Magnetic modification was successfully performed at low temperature in a freezer (-20 °C) using magnetic iron oxides nano- and microparticles prepared by microwave-assisted synthesis from ferrous sulfate. Magnetized cross-linked enzyme powders were stable at least for two months in water suspension without leakage of fixed magnetic particles. Operational stability of magnetically responsive enzymes during eight repeated reaction cycles was generally without loss of enzyme activity. Separation of magnetically modified cross-linked powdered enzymes from reaction mixtures was significantly simplified due to their magnetic properties.

  18. Enzymes in animal nutrition

    OpenAIRE

    Scientific Committee on Animal Nutrition

    2011-01-01

    This report brings overview of endogenous as well as exogenous enzymes and their role and importance in animal nutrition. Enzymes for animal nutrition have been systematically developed since 1980´s. Phytase, xylanase and β-glucanase are used in poultry-rising, pig breeding, aquaculture and begin to push to the ruminant nutrition. Phytase increase availability of P, Ca, Zn, digestibility of proteins and fats. Its positive effect on the environment is well described – enzymes decrease the cont...

  19. Profiling the orphan enzymes

    Science.gov (United States)

    2014-01-01

    The emergence of Next Generation Sequencing generates an incredible amount of sequence and great potential for new enzyme discovery. Despite this huge amount of data and the profusion of bioinformatic methods for function prediction, a large part of known enzyme activities is still lacking an associated protein sequence. These particular activities are called “orphan enzymes”. The present review proposes an update of previous surveys on orphan enzymes by mining the current content of public databases. While the percentage of orphan enzyme activities has decreased from 38% to 22% in ten years, there are still more than 1,000 orphans among the 5,000 entries of the Enzyme Commission (EC) classification. Taking into account all the reactions present in metabolic databases, this proportion dramatically increases to reach nearly 50% of orphans and many of them are not associated to a known pathway. We extended our survey to “local orphan enzymes” that are activities which have no representative sequence in a given clade, but have at least one in organisms belonging to other clades. We observe an important bias in Archaea and find that in general more than 30% of the EC activities have incomplete sequence information in at least one superkingdom. To estimate if candidate proteins for local orphans could be retrieved by homology search, we applied a simple strategy based on the PRIAM software and noticed that candidates may be proposed for an important fraction of local orphan enzymes. Finally, by studying relation between protein domains and catalyzed activities, it appears that newly discovered enzymes are mostly associated with already known enzyme domains. Thus, the exploration of the promiscuity and the multifunctional aspect of known enzyme families may solve part of the orphan enzyme issue. We conclude this review with a presentation of recent initiatives in finding proteins for orphan enzymes and in extending the enzyme world by the discovery of new

  20. The EBI enzyme portal

    OpenAIRE

    Alc?ntara, Rafael; Onwubiko, Joseph; Cao, Hong; de Matos, Paula; Cham, Jennifer A.; Jacobsen, Jules; Holliday, Gemma L.; Fischer, Julia D.; Rahman, Syed Asad; Jassal, Bijay; Goujon, Mikael; Rowland, Francis; Velankar, Sameer; L?pez, Rodrigo; Overington, John P.

    2012-01-01

    The availability of comprehensive information about enzymes plays an important role in answering questions relevant to interdisciplinary fields such as biochemistry, enzymology, biofuels, bioengineering and drug discovery. At the EMBL European Bioinformatics Institute, we have developed an enzyme portal (http://www.ebi.ac.uk/enzymeportal) to provide this wealth of information on enzymes from multiple in-house resources addressing particular data classes: protein sequence and structure, reacti...

  1. Enzyme catalysed tandem reactions

    OpenAIRE

    Oroz-Guinea, Isabel; García-Junceda, Eduardo

    2013-01-01

    To transfer to the laboratory, the excellent efficiency shown by enzymes in Nature, biocatalysis, had to mimic several synthetic strategies used by the living organisms. Biosynthetic pathways are examples of tandem catalysis and may be assimilated in the biocatalysis field for the use of isolated multi-enzyme systems in the homogeneous phase. The concurrent action of several enzymes that work sequentially presents extraordinary advantages from the synthetic point of view, since it permits a r...

  2. Kinetic and photochemical studies and alteration of ultraviolet sensitivity of Escherichia coli thymidine kinase of halogenated allosteric regulators and substrate analogues

    International Nuclear Information System (INIS)

    Chen, M.S.; Prusoff, W.H.

    1977-01-01

    The effect of various halogenated and nonhalogenated allosteric effectors on the sensitivity of Escherichia coli thymidine kinase to ultraviolet radiations (uv,253.7 nm) was investigated. All naturally occurring dNTPs convert the monomeric form of the enzyme into the dimeric form which is less sensitive to uv inactivation. Whereas 5-iodo-2'-deoxycytidine triphosphate (IdCTP) and 5-iodo-2' deoxyuridine triphosphate (IdUTP) enhance the uv inactivation of the enzyme, 5-bromo-2'-deoxyuridine triphosphate and 5-bromo-2'-deoxycytidine triphosphate exert a protective effect similar to that produced by the corresponding naturally occurring effectors, dTTP and dCTP. The enhanced uv inactivation by IdUTP is prevented totally by dTTP, but only partially by dCTP or dThd, whereas the enhanced sensitization by IdCTP is prevented almost totally by dCTP, partially by dTTP, and not at all by dThd. The uv sensitization of thymidine kinase by IdCTP appears to be at the regulatory site since a maximum saturation effect is observed, and the concentration required to exert a 50% maximal uv sensitization is similar to its K/sub m/ for enhancement of catalytic activity. When the enzyme was irradiated in the presence of either [2- 14 C]IdUTP or [2- 14 C]IdUrd, zone sedimentation analysis in sucrose density gradients showed the sedimentation coefficient of the radioactive labeled proteins to be the same, 3.8 S. Hence uv irradiation of the effector-induced dimer resulted in not only dissociation to the monomer, but also complete loss of catalytic activity. The substitution of an azido group for the 5'-OH group of 5-iodo-, 5-bromo-, 5-chloro-, or 5-fluorodeoxyuridine greatly decreased their affinity for thymidine kinase, and in addition the kinetics of inhibition changed from a competitive to a noncompetitive pattern. The presence of the azido moiety in the 5' position of the halogenated nucleosides did not enhance the rate of uv inactivation of the enzyme

  3. Robust Stimulation of W1282X-CFTR Channel Activity by a Combination of Allosteric Modulators.

    Directory of Open Access Journals (Sweden)

    Wei Wang

    Full Text Available W1282X is a common nonsense mutation among cystic fibrosis patients that results in the production of a truncated Cystic Fibrosis Transmembrane Conductance Regulator (CFTR channel. Here we show that the channel activity of the W1282X-CFTR polypeptide is exceptionally low in excised membrane patches at normally saturating doses of ATP and PKA (single channel open probability (PO 0.9 when treated with both modulators. VX-770 and curcumin also additively stimulated W1282X-CFTR mediated currents in polarized FRT epithelial monolayers. In this setting, however, the stimulated W1282X-CFTR currents were smaller than those mediated by wild type CFTR (3-5% due presumably to lower expression levels or cell surface targeting of the truncated protein. Combining allosteric modulators of different mechanistic classes is worth considering as a treatment option for W1282X CF patients perhaps when coupled with maneuvers to increase expression of the truncated protein.

  4. A2A adenosine receptor ligand binding and signalling is allosterically modulated by adenosine deaminase.

    Science.gov (United States)

    Gracia, Eduard; Pérez-Capote, Kamil; Moreno, Estefanía; Barkešová, Jana; Mallol, Josefa; Lluís, Carme; Franco, Rafael; Cortés, Antoni; Casadó, Vicent; Canela, Enric I

    2011-05-01

    A2ARs (adenosine A2A receptors) are highly enriched in the striatum, which is the main motor control CNS (central nervous system) area. BRET (bioluminescence resonance energy transfer) assays showed that A2AR homomers may act as cell-surface ADA (adenosine deaminase; EC 3.5.4.4)-binding proteins. ADA binding affected the quaternary structure of A2ARs present on the cell surface. ADA binding to adenosine A2ARs increased both agonist and antagonist affinity on ligand binding to striatal membranes where these proteins are co-expressed. ADA also increased receptor-mediated ERK1/2 (extracellular-signal-regulated kinase 1/2) phosphorylation. Collectively, the results of the present study show that ADA, apart from regulating the concentration of extracellular adenosine, may behave as an allosteric modulator that markedly enhances ligand affinity and receptor function. This powerful regulation may have implications for the physiology and pharmacology of neuronal A2ARs.

  5. Small Molecule-Induced Allosteric Activation of the Vibrio Cholerae RTX Cysteine Protease Domain

    Energy Technology Data Exchange (ETDEWEB)

    Lupardus, P.J.; Shen, A.; Bogyo, M.; Garcia, K.C.

    2009-05-19

    Vibrio cholerae RTX (repeats in toxin) is an actin-disrupting toxin that is autoprocessed by an internal cysteine protease domain (CPD). The RTX CPD is efficiently activated by the eukaryote-specific small molecule inositol hexakisphosphate (InsP{sub 6}), and we present the 2.1 angstrom structure of the RTX CPD in complex with InsP{sub 6}. InsP{sub 6} binds to a conserved basic cleft that is distant from the protease active site. Biochemical and kinetic analyses of CPD mutants indicate that InsP{sub 6} binding induces an allosteric switch that leads to the autoprocessing and intracellular release of toxin-effector domains.

  6. Mechanism of allosteric regulation of β2-adrenergic receptor by cholesterol

    DEFF Research Database (Denmark)

    Manna, Moutusi; Niemelä, Miia; Tynkkynen, Joona

    2016-01-01

    ) - a prototypical G protein-coupled receptor - is modulated by cholesterol in an allosteric fashion. Extensive atomistic simulations show that cholesterol regulates b2AR by limiting its conformational variability. The mechanism of action is based on the binding of cholesterol at specific high-affinity sites located...... near the transmembrane helices 5-7 of the receptor. The alternative mechanism, where the β2AR conformation would be modulated by membrane-mediated interactions, plays only a minor role. Cholesterol analogues also bind to cholesterol binding sites and impede the structural flexibility of β2AR, however...... cholesterol generates the strongest effect. The results highlight the capacity of lipids to regulate the conformation of membrane receptors through specific interactions....

  7. Evidence for a Common Mechanism of SIRT1 Regulation by Allosteric Activators

    Science.gov (United States)

    Hubbard, Basil P.; Gomes, Ana P.; Dai, Han; Li, Jun; Case, April W.; Considine, Thomas; Riera, Thomas V.; Lee, Jessica E.; Sook Yen, E; Lamming, Dudley W.; Pentelute, Bradley L.; Schuman, Eli R.; Stevens, Linda A.; Ling, Alvin J. Y.; Armour, Sean M.; Michan, Shaday; Zhao, Huizhen; Jiang, Yong; Sweitzer, Sharon M.; Blum, Charles A.; Disch, Jeremy S.; Ng, Pui Yee; Howitz, Konrad T.; Rolo, Anabela P.; Hamuro, Yoshitomo; Moss, Joel; Perni, Robert B.; Ellis, James L.; Vlasuk, George P.; Sinclair, David A.

    2013-01-01

    A molecule that treats multiple age-related diseases would have a major impact on global health and economics. The SIRT1 deacetylase has drawn attention in this regard as a target for drug design. Yet controversy exists around the mechanism of sirtuin-activating compounds (STACs). We found that specific hydrophobic motifs found in SIRT1 substrates such as PGC-1α and FOXO3a facilitate SIRT1 activation by STACs. A single amino acid in SIRT1, Glu230, located in a structured N-terminal domain, was critical for activation by all previously reported STAC scaffolds and a new class of chemically distinct activators. In primary cells reconstituted with activation-defective SIRT1, the metabolic effects of STACs were blocked. Thus, SIRT1 can be directly activated through an allosteric mechanism common to chemically diverse STACs. PMID:23471411

  8. Optimization of Allosteric With-No-Lysine (WNK) Kinase Inhibitors and Efficacy in Rodent Hypertension Models

    Energy Technology Data Exchange (ETDEWEB)

    Yamada, Ken; Levell, Julian; Yoon, Taeyong; Kohls, Darcy; Yowe, David; Rigel, Dean F.; Imase, Hidetomo; Yuan, Jun; Yasoshima, Kayo; DiPetrillo, Keith; Monovich, Lauren; Xu, Lingfei; Zhu, Meicheng; Kato, Mitsunori; Jain, Monish; Idamakanti, Neeraja; Taslimi, Paul; Kawanami, Toshio; Argikar, Upendra A.; Kunjathoor, Vidya; Xie, Xiaoling; Yagi, Yukiko I.; Iwaki, Yuki; Robinson, Zachary; Park, Hyi-Man (Novartis)

    2017-08-03

    The observed structure–activity relationship of three distinct ATP noncompetitive With-No-Lysine (WNK) kinase inhibitor series, together with a crystal structure of a previously disclosed allosteric inhibitor bound to WNK1, led to an overlay hypothesis defining core and side-chain relationships across the different series. This in turn enabled an efficient optimization through scaffold morphing, resulting in compounds with a good balance of selectivity, cellular potency, and pharmacokinetic profile, which were suitable for in vivo proof-of-concept studies. When dosed orally, the optimized compound reduced blood pressure in mice overexpressing human WNK1, and induced diuresis, natriuresis and kaliuresis in spontaneously hypertensive rats (SHR), confirming that this mechanism of inhibition of WNK kinase activity is effective at regulating cardiovascular homeostasis.

  9. Dual Allosteric Effect in Glycine/NMDA Receptor Antagonism: A Comparative QSAR Approach

    Directory of Open Access Journals (Sweden)

    Vipin B. Gupta

    2010-10-01

    Full Text Available A comparative Hantzsch type QSAR study was conducted using multiple regression analysis on various sets of quinoxalines, quinoxalin-4-ones, quinazoline-2-carboxylates, 4-hydroxyquinolin-2(1H-ones, 2-carboxytetrahydroquinolines, phenyl-hydroxy-quinolones, nitroquinolones and 4-substituted-3-phenylquinolin-2(1H-ones as selective glycine/NMDA site antagonists. Ten statistically validated equations were developed, which indicated the importance of CMR, Verloop’s sterimol L1 and ClogP parameters in contributing towards biological activity. Interestingly, normal and inverse parabolic relationships were found with CMR in different series, indicating a dual allosteric binding mode in glycine/NMDA antagonism. Equations reveal an optimum CMR of 10 ± 10% is required for good potency of antagonists. Other equations indicate the presence of anionic functionality at 4-position of quinoline/quinolone ring system is not absolutely required for effective binding. The observations are laterally validated and in accordance with previous studies.

  10. Chemogenomic discovery of allosteric antagonists at the GPRC6A receptor

    DEFF Research Database (Denmark)

    Gloriam, David E.; Wellendorph, Petrine; Johansen, Lars Dan

    2011-01-01

    , calindol and NPS 2143, which both display ~30-fold selectivity for the calcium-sensing receptor compared to GPRC6A. The antagonists constitute novel research tools toward investigating the signaling mechanism of the GPRC6A receptor at the cellular level and serve as initial ligands for further optimization...... and pharmacological character: (1) chemogenomic lead identification through the first, to our knowledge, ligand inference between two different GPCR families, Families A and C; and (2) the discovery of the most selective GPRC6A allosteric antagonists discovered to date. The unprecedented inference of...... pharmacological activity across GPCR families provides proof-of-concept for in silico approaches against Family C targets based on Family A templates, greatly expanding the prospects of successful drug design and discovery. The antagonists were tested against a panel of seven Family A and C G protein-coupled receptors...

  11. Molecular Basis for Allosteric Inhibition of Acid-Sensing Ion Channel 1a by Ibuprofen

    DEFF Research Database (Denmark)

    Lynagh, Timothy; Romero-Rojo, José Luis; Lund, Camilla

    2017-01-01

    A growing body of evidence links certain aspects of nonsteroidal anti-inflammatory drug (NSAID) pharmacology with acid-sensing ion channels (ASICs), a small family of excitatory neurotransmitter receptors implicated in pain and neuroinflammation. The molecular basis of NSAID inhibition of ASICs has......-clamp fluorometry. Our results show that ibuprofen is an allosteric inhibitor of ASIC1a, which binds to a crucial site in the agonist transduction pathway and causes conformational changes that oppose channel activation. Ibuprofen inhibits several ASIC subtypes, but certain ibuprofen derivatives show some...... selectivity for ASIC1a over ASIC2a and vice versa. These results thus define the NSAID/ASIC interaction and pave the way for small-molecule drug design targeting pain and inflammation....

  12. Structural insight to mutation effects uncover a common allosteric site in class C GPCRs.

    Science.gov (United States)

    Harpsøe, Kasper; Boesgaard, Michael W; Munk, Christian; Bräuner-Osborne, Hans; Gloriam, David E

    2017-04-15

    Class C G protein-coupled receptors (GPCRs) regulate important physiological functions and allosteric modulators binding to the transmembrane domain constitute an attractive and, due to a lack of structural insight, a virtually unexplored potential for therapeutics and the food industry. Combining pharmacological site-directed mutagenesis data with the recent class C GPCR experimental structures will provide a foundation for rational design of new therapeutics. We uncover one common site for both positive and negative modulators with different amino acid layouts that can be utilized to obtain selectivity. Additionally, we show a large potential for structure-based modulator design, especially for four orphan receptors with high similarity to the crystal structures. All collated mutagenesis data is available in the GPCRdb mutation browser at http://gpcrdb.org/mutations/ and can be analyzed online or downloaded in excel format. david.gloriam@sund.ku.dk. Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

  13. Enzymes from extremophiles.

    Science.gov (United States)

    Demirjian, D C; Morís-Varas, F; Cassidy, C S

    2001-04-01

    The industrial application of enzymes that can withstand harsh conditions has greatly increased over the past decade. This is mainly a result of the discovery of novel enzymes from extremophilic microorganisms. Recent advances in the study of extremozymes point to the acceleration of this trend. In particular, enzymes from thermophilic organisms have found the most practical commercial use to date because of their overall inherent stability. This has also led to a greater understanding of stability factors involved in adaptation of these enzymes to their unusual environments.

  14. Artificial Enzymes, "Chemzymes"

    DEFF Research Database (Denmark)

    Bjerre, Jeannette; Rousseau, Cyril Andre Raphaël; Pedersen, Lavinia Georgeta M

    2008-01-01

    "Chemzymes", based on cyclodextrins and other molecules. Only the chemzymes that have shown enzyme-like activity that has been quantified by different methods will be mentioned. This review will summarize the work done in the field of artificial glycosidases, oxidases, epoxidases, and esterases, as well......Enzymes have fascinated scientists since their discovery and, over some decades, one aim in organic chemistry has been the creation of molecules that mimic the active sites of enzymes and promote catalysis. Nevertheless, even today, there are relatively few examples of enzyme models...

  15. Theoretical Analysis of Allosteric and Operator Binding for Cyclic-AMP Receptor Protein Mutants

    Science.gov (United States)

    Einav, Tal; Duque, Julia; Phillips, Rob

    2018-02-01

    Allosteric transcription factors undergo binding events both at their inducer binding sites as well as at distinct DNA binding domains, and it is often difficult to disentangle the structural and functional consequences of these two classes of interactions. In this work, we compare the ability of two statistical mechanical models - the Monod-Wyman-Changeux (MWC) and the Koshland-N\\'emethy-Filmer (KNF) models of protein conformational change - to characterize the multi-step activation mechanism of the broadly acting cyclic-AMP receptor protein (CRP). We first consider the allosteric transition resulting from cyclic-AMP binding to CRP, then analyze how CRP binds to its operator, and finally investigate the ability of CRP to activate gene expression. In light of these models, we examine data from a beautiful recent experiment that created a single-chain version of the CRP homodimer, thereby enabling each subunit to be mutated separately. Using this construct, six mutants were created using all possible combinations of the wild type subunit, a D53H mutant subunit, and an S62F mutant subunit. We demonstrate that both the MWC and KNF models can explain the behavior of all six mutants using a small, self-consistent set of parameters. In comparing the results, we find that the MWC model slightly outperforms the KNF model in the quality of its fits, but more importantly the parameters inferred by the MWC model are more in line with structural knowledge of CRP. In addition, we discuss how the conceptual framework developed here for CRP enables us to not merely analyze data retrospectively, but has the predictive power to determine how combinations of mutations will interact, how double mutants will behave, and how each construct would regulate gene expression.

  16. Computational redesign reveals allosteric mutation hotspots of organophosphate hydrolase that enhance organophosphate hydrolysis

    Energy Technology Data Exchange (ETDEWEB)

    Jacob, Reed B. [Univ. of North Carolina, Chapel Hill, NC (United States); Ding, Feng [Clemson Univ., SC (United States); Ye, Dongmei [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Ackerman, Eric [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Dokholyan, Nikolay V. [Univ. of North Carolina, Chapel Hill, NC (United States)

    2015-04-01

    Organophosphates are widely used for peaceful (agriculture) and military purposes (chemical warfare agents). The extraordinary toxicity of organophosphates and the risk of deployment, make it critical to develop means for their rapid and efficient deactivation. Organophosphate hydrolase (OPH) already plays an important role in organophosphate remediation, but is insufficient for therapeutic or prophylactic purposes primarily due to low substrate affinity. Current efforts focus on directly modifying the active site to differentiate substrate specificity and increase catalytic activity. Here, we present a novel strategy for enhancing the general catalytic efficiency of OPH through computational redesign of the residues that are allosterically coupled to the active site and validated our design by mutagenesis. Specifically, we identify five such hot-spot residues for allosteric regulation and assay these mutants for hydrolysis activity against paraoxon, a chemical-weapons simulant. A high percentage of the predicted mutants exhibit enhanced activity over wild-type (kcat =16.63 s-1), such as T199I/T54I (899.5 s-1) and C227V/T199I/T54I (848 s-1), while the Km remains relatively unchanged in our high-throughput cell-free expression system. Further computational studies of protein dynamics reveal four distinct distal regions coupled to the active site that display significant changes in conformation dynamics upon these identified mutations. These results validate a computational design method that is both efficient and easily adapted as a general procedure for enzymatic enhancement.

  17. Structure of CC chemokine receptor 2 with orthosteric and allosteric antagonists

    Energy Technology Data Exchange (ETDEWEB)

    Zheng, Yi; Qin, Ling; Ortiz Zacarías, Natalia V.; de Vries, Henk; Han, Gye Won; Gustavsson, Martin; Dabros, Marta; Zhao, Chunxia; Cherney, Robert J.; Carter, Percy; Stamos, Dean; Abagyan, Ruben; Cherezov, Vadim; Stevens, Raymond C.; IJzerman, Adriaan P.; Heitman, Laura H.; Tebben, Andrew; Kufareva, Irina; Handel , Tracy M. (Vertex Pharm); (Leiden-MC); (USC); (BMS); (UCSD)

    2016-12-07

    CC chemokine receptor 2 (CCR2) is one of 19 members of the chemokine receptor subfamily of human class A G-protein-coupled receptors. CCR2 is expressed on monocytes, immature dendritic cells, and T-cell subpopulations, and mediates their migration towards endogenous CC chemokine ligands such as CCL2 (ref. 1). CCR2 and its ligands are implicated in numerous inflammatory and neurodegenerative diseases2 including atherosclerosis, multiple sclerosis, asthma, neuropathic pain, and diabetic nephropathy, as well as cancer3. These disease associations have motivated numerous preclinical studies and clinical trials4 (see http://www.clinicaltrials.gov) in search of therapies that target the CCR2–chemokine axis. To aid drug discovery efforts5, here we solve a structure of CCR2 in a ternary complex with an orthosteric (BMS-681 (ref. 6)) and allosteric (CCR2-RA-[R]7) antagonist. BMS-681 inhibits chemokine binding by occupying the orthosteric pocket of the receptor in a previously unseen binding mode. CCR2-RA-[R] binds in a novel, highly druggable pocket that is the most intracellular allosteric site observed in class A G-protein-coupled receptors so far; this site spatially overlaps the G-protein-binding site in homologous receptors. CCR2-RA-[R] inhibits CCR2 non-competitively by blocking activation-associated conformational changes and formation of the G-protein-binding interface. The conformational signature of the conserved microswitch residues observed in double-antagonist-bound CCR2 resembles the most inactive G-protein-coupled receptor structures solved so far. Like other protein–protein interactions, receptor–chemokine complexes are considered challenging therapeutic targets for small molecules, and the present structure suggests diverse pocket epitopes that can be exploited to overcome obstacles in drug design.

  18. Signaling-sensitive amino acids surround the allosteric ligand binding site of the thyrotropin receptor.

    Science.gov (United States)

    Kleinau, Gunnar; Haas, Ann-Karin; Neumann, Susanne; Worth, Catherine L; Hoyer, Inna; Furkert, Jens; Rutz, Claudia; Gershengorn, Marvin C; Schülein, Ralf; Krause, Gerd

    2010-07-01

    The thyrotropin receptor [thyroid-stimulating hormone receptor (TSHR)], a G-protein-coupled receptor (GPCR), is endogenously activated by thyrotropin, which binds to the extracellular region of the receptor. We previously identified a low-molecular-weight (LMW) agonist of the TSHR and predicted its allosteric binding pocket within the receptor's transmembrane domain. Because binding of the LMW agonist probably disrupts interactions or leads to formation of new interactions among amino acid residues surrounding the pocket, we tested whether mutation of residues at these positions would lead to constitutive signaling activity. Guided by molecular modeling, we performed site-directed mutagenesis of 24 amino acids in this spatial region, followed by functional characterization of the mutant receptors in terms of expression and signaling, measured as cAMP accumulation. We found that mutations V421I, Y466A, T501A, L587V, M637C, M637W, S641A, Y643F, L645V, and Y667A located in several helices exhibit constitutive activity. Of note is mutation M637W at position 6.48 in transmembrane helix 6, which has a significant effect on the interaction of the receptor with the LMW agonist. In summary, we found that a high proportion of residues in several helices surrounding the allosteric binding site of LMW ligands in the TSHR when mutated lead to constitutively active receptors. Our findings of signaling-sensitive residues in this region of the transmembrane bundle may be of general importance as this domain appears to be evolutionarily retained among GPCRs.

  19. 1,4-Bis(4,5-dihydro-1H-imidazol-2-ylbenzene–4-aminobenzenesulfonic acid–water (1/2/2

    Directory of Open Access Journals (Sweden)

    Shao-Ming Shang

    2009-09-01

    Full Text Available The asymmetric unit of the title compound, C12H14N4·2C6H7NO3S·2H2O, contains one half of a centrosymmetric 1,4-bis(4,5-dihydro-1H-imidazol-2-ylbenzene (bib molecule, one 4-aminobenzenesulfonic acid molecule and one water molecule. In the bib molecule, the imidazole ring adopts an envelope conformation. The benzene rings of bib and 4-aminobenzenesulfonic acid are oriented at a dihedral angle of 21.89 (4°. In the crystal structure, intermolecular N—H...O, O—H...N and O—H...O interactions link the molecules into a three-dimensional network. Weak π–π contacts between the benzene and imidazole rings and between the benzene rings [centroid–centroid distances = 3.895 (1 and 3.833 (1 Å, respectively] may further stabilize the structure.

  20. Racemic cobalt phosphonates incorporating flexible bis(imidazole) co-ligands.

    Science.gov (United States)

    Feng, Jian-Shen; Cai, Zhong-Sheng; Ren, Min; Bao, Song-Song; Zheng, Li-Min

    2015-11-07

    By incorporating flexible bis(imidazol-1-ylmethyl)benzene (bix) co-ligands, four new racemic cobalt phosphonates with formulae Co3(3-ppap)2(1,4-bix)2(H2O)4·4H2O (1), Co3(3-ppap)2(1,3-bix)2(H2O)4·5H2O (2), Co3(3-ppap)2(1,2-bix)2(H2O)4·4H2O (3) and Co3(ppa)2(1,2-bix)2·4H2O (4) are isolated, where 3-ppapH3 represents 3-phenyl-3-((phosphonomethyl)amino)propanoic acid and ppaH3 is 2-phenyl-2-(phosphonomethylamino)acetic acid. Compounds 1-3 crystallize in the monoclinic space group P21/c and show two-dimensional structures in which the Co3(3-ppap)2 chains are bridged by 1,4-bix, 1,3-bix and 1,2-bix ligands in trans-modes, respectively. Within the chain, a racemic dimer of Co2(3-ppap)2(2-) is found, where the Co atoms are doubly bridged by O-P-O units from the (S)- and (R)-3-ppap(3-) ligands. The dimers are connected by another crystallographically independent Co atom through O-P-O linkages to form an infinite racemic chain. The packing modes of the layers in 1-3 are quite different, however, which are ABAB in the cases of 1 and 3 while ABCDABCD in the case of 2, attributed to the positional isomerism of the bix co-ligands. Compound 4 displays a chain structure in which the 1,2-bix bridges the Co atoms in cis-mode within the chain. Magnetic properties are investigated for all compounds.

  1. Polarographic study of simple and mixed ligand complexes of Eu(III) with imidazole and succinate

    International Nuclear Information System (INIS)

    Shivhare, Madhu; Singh, Mukhtar

    1982-01-01

    The formation of simple and mixed ligand complexes of Eu(III) with imidazole (Im) and succinate (Succ 2- ) has been studied polarographically at 25deg C+-0.1deg C, μ=1.0 (NaClO 4 ) and pH=6. The reduction of the complexes at d.m.e. is quasi-reversible and diffusion-controlled. Eu(III) forms six successive complexes with Im, viz. [Eu(Im)] 3+ , [Eu(Im) 2 ] 3+ , [Eu(Im) 2 ] 3+ , [Eu(Im) 3 ] 3+ , [Eu(Im) 4 ] 3+ , [Eu(Im) 5 ] 3+ , and[Eu(Im) 6 ] 3+ . Their stability constant values are: logβ 10 =3.6, logβ 20 =4.6, logβ 30 =6.5, logβ 40 =7.8, logβ 50 =8.4 and logβ 60 =9.6 respectively. With succ 2- , Eu(III) forms four successive complexes; [Eu(Succ)] + , [Eu(Succ) 2 ] - , [Eu(Succ) 3 ] 3- and [Eu(Succ) 4 ] 5- with the stability constants, logβ 01 =3.8, logβ 02 =4.6, logβ 03 =5.3 and logβ 04 =6.9 respectively. Eu(III) forms five mixed ligand complexes; [Eu(Im)(Succ) 2 ] - , Eu(Im) 2 (Succ) 2 ] - , [Eu(Im) 3 (Succ) 2 ], [Eu(Im) 4 (Succ) 2 ] and [Eu(Im) 5 (Succ)] + with stability constants, logβ 12 =6.1, logβ 22 =8.0, logβ 32 =9.5, logβ 42 =10.9 and logβ 51 =10.2 respectively. (author)

  2. Antitumor activity of sequence-specific alkylating agents: pyrolle-imidazole CBI conjugates with indole linker.

    Science.gov (United States)

    Shinohara, Ken-ichi; Bando, Toshikazu; Sasaki, Shunta; Sakakibara, Yogo; Minoshima, Masafumi; Sugiyama, Hiroshi

    2006-03-01

    DNA-targeting agents, including cisplatin, bleomycin and mitomycin C, are used routinely in cancer treatments. However, these drugs are extremely toxic, attacking normal cells and causing severe side effects. One important question to consider in designing anticancer agents is whether the introduction of sequence selectivity to DNA-targeting agents can improve their efficacy as anticancer agents. In the present study, the growth inhibition activities of an indole-seco 1,2,9,9a-tetrahydrocyclopropa[1,2-c]benz[1,2-e]indol-4-one (CBI) (1) and five conjugates with hairpin pyrrole-imidazole polyamides (2-6), which have different sequence specificities for DNA alkylation, were compared using 10 different cell lines. The average values of -log GI50 (50% growth inhibition concentration) for compounds 1-6 against the 10 cell lines were 8.33, 8.56, 8.29, 8.04, 8.23 and 8.83, showing that all of these compounds strongly inhibit cell growth. Interestingly, each alkylating agent caused significantly different growth inhibition patterns with each cell line. In particular, the correlation coefficients between the -log GI50 of compound 1 and its conjugates 2-6 showed extremely low values (Ralkylation lead to marked differences in biological activity. Comparison of the correlation coefficients between compounds 6 and 7, with the same sequence specificity as 6, and MS-247, with sequence specificity different from 6, when used against a panel of 37 human cancer cell lines further confirmed the above hypothesis.

  3. Metal-organic and zeolite imidazolate frameworks (MOFs and ZIFs) for highly selective separations

    Energy Technology Data Exchange (ETDEWEB)

    Yaghi, Omar M

    2012-09-17

    Metal-organic and zeolite imidazolate frameworks (MOFs and ZIFs) have been investigated for the realization as separation media with high selectivity. These structures are held together with strong bonds, making them architecturally, chemically, and thermally stable. Therefore, employing well designed building units, it is possible to discover promising materials for gas and vapor separation. This grant was focused on the study of MOFs and ZIFs with these specific objectives: (i) to develop a strategy for producing MOFs and ZIFs that combine high surface areas with active sites for their use in gas adsorption and separation of small organic compounds, (ii) to introduce active sites in the framework by a post-synthetic modification and metalation of MOFs and ZIFs, and (iii) to design and synthesize MOFs with extremely high surface areas and large pore volumes to accommodate large amounts of guest molecules. By the systematic study, this effort demonstrated how to introduce active functional groups in the frameworks, and this is also the origin of a new strategy, which is termed isoreticular functionalization and metalation. However, a large pore volume is still a prerequisite feature. One of the solutions to overcome this challenge is an isoreticular expansion of a MOF's structure. With triangular organic linker and square building units, we demonstrated that MOF-399 has a unit cell volume 17 times larger than that of the first reported material isoreticular to it, and it has the highest porosity (94%) and lowest density (0.126 g cm-3) of any MOF reported to date. MOFs are not just low density materials; the guest-free form of MOF-210 demonstrates an ultrahigh porosity, whose BET surface area was estimated to be 6240 m2 g-1 by N2 adsorption measurements.

  4. Structural Contraction of Zeolitic Imidazolate Frameworks: Membrane Application on Porous Metallic Hollow Fibers for Gas Separation.

    Science.gov (United States)

    Cacho-Bailo, Fernando; Etxeberría-Benavides, Miren; David, Oana; Téllez, Carlos; Coronas, Joaquín

    2017-06-21

    Positive thermal expansion coefficients (TECs) of 52 × 10 -6 and 35 × 10 -6 K -1 were experimentally calculated in the -116 to 250 °C range for the III-phases of zeolitic imidazolate frameworks (ZIF) ZIF-9(Co) and ZIF-7(Zn), respectively, by means of the unit cell dimensions and volume of the materials in the monoclinic crystal system calculated from the XRD patterns. The unit cell dimensions and volume showed a significant expansion phenomenon as the temperature increased, by as much as 5.5% for ZIF-9-III in the studied range. To exploit the advantages of such thermal behavior, a new approach to the fabrication of ZIF-9-III membranes on thin, flexible, and highly porous nickel hollow fiber (Ni HF) supports by a versatile and easy-controllable microfluidic setup is herein reported. These Ni HF supports result from the sintering of 25-μm Ni particles and display very positive mechanical properties and bending resistance. As compared to the traditional polymer-based HF membranes, the ZIF metal-supported membrane exhibited good durability and robustness throughout its operation in a wide temperature range and after heating and cooling cycles. These benefits derive from (1) the pore-plugging membrane configuration resulting from the high porosity of the support and (2) the similarity between the TECs of the ZIF and the metallic support, both positive, which enhances their mutual compatibility. An increase in the H 2 /CO 2 separation selectivity at low temperatures (as high as 22.2 at -10 °C, along with 102 GPU permeance of H 2 ) was achieved, in agreement with the structural variations observed in the ZIF material.

  5. Characterisation of the first enzymes committed to lysine biosynthesis in Arabidopsis thaliana.

    Directory of Open Access Journals (Sweden)

    Michael D W Griffin

    Full Text Available In plants, the lysine biosynthetic pathway is an attractive target for both the development of herbicides and increasing the nutritional value of crops given that lysine is a limiting amino acid in cereals. Dihydrodipicolinate synthase (DHDPS and dihydrodipicolinate reductase (DHDPR catalyse the first two committed steps of lysine biosynthesis. Here, we carry out for the first time a comprehensive characterisation of the structure and activity of both DHDPS and DHDPR from Arabidopsis thaliana. The A. thaliana DHDPS enzyme (At-DHDPS2 has similar activity to the bacterial form of the enzyme, but is more strongly allosterically inhibited by (S-lysine. Structural studies of At-DHDPS2 show (S-lysine bound at a cleft between two monomers, highlighting the allosteric site; however, unlike previous studies, binding is not accompanied by conformational changes, suggesting that binding may cause changes in protein dynamics rather than large conformation changes. DHDPR from A. thaliana (At-DHDPR2 has similar specificity for both NADH and NADPH during catalysis, and has tighter binding of substrate than has previously been reported. While all known bacterial DHDPR enzymes have a tetrameric structure, analytical ultracentrifugation, and scattering data unequivocally show that At-DHDPR2 exists as a dimer in solution. The exact arrangement of the dimeric protein is as yet unknown, but ab initio modelling of x-ray scattering data is consistent with an elongated structure in solution, which does not correspond to any of the possible dimeric pairings observed in the X-ray crystal structure of DHDPR from other organisms. This increased knowledge of the structure and function of plant lysine biosynthetic enzymes will aid future work aimed at improving primary production.

  6. Mutagenicity of 1-Ethyl-2,4,5-triphenyl-1H-imidazole and Six Derivatives in Salmonella typhimurium

    OpenAIRE

    KORKMAZ, Ferhan; Korkmaz, Ferhan; MERCANGOZ, Ayse

    2010-01-01

     Newly synthesized 1-Ethyl-2,4,5-triphenyl-1H-imidazole and its six derivatives were tested by Ames assay. In order to reveal the mutagenic activities of the compounds, two different mutant strains of Salmonella typhimurium (TA98 and TA100) were used in an Ames assay with/without S9 microsomal fraction from rat liver. It was found that the compounds have no mutagenic activities.          &nb...

  7. Stacking Faults and Mechanical Behavior beyond the Elastic Limit of an Imidazole-Based Metal Organic Framework: ZIF-8.

    Science.gov (United States)

    Hegde, Vinay I; Tan, Jin-Chong; Waghmare, Umesh V; Cheetham, Anthony K

    2013-10-17

    We determine the nonlinear mechanical behavior of a prototypical zeolitic imidazolate framework (ZIF-8) along two modes of mechanical failure in response to tensile and shear forces using first-principles simulations. Our generalized stacking fault energy surface reveals an intrinsic stacking fault of surprisingly low energy comparable to that in copper, though the energy barrier associated with its formation is much higher. The lack of vibrational spectroscopic evidence for such faults in experiments can be explained with the structural instability of the barrier state to form a denser and disordered state of ZIF-8 seen in our analysis, that is, large shear leads to its amorphization rather than formation of faults.

  8. Piracetam Defines a New Binding Site for Allosteric Modulators of α-amino-3-hydroxy-5-methyl-4-isoxazole-propionic acid (AMPA) receptors§

    OpenAIRE

    Ahmed, Ahmed H.; Oswald, Robert E.

    2010-01-01

    Glutamate receptors are the most prevalent excitatory neurotransmitter receptors in the vertebrate central nervous system and are important potential drug targets for cognitive enhancement and the treatment of schizophrenia. Allosteric modulators of AMPA receptors promote dimerization by binding to a dimer interface and reducing desensitization and deactivation. The pyrrolidine allosteric modulators, piracetam and aniracetam, were among the first of this class of drugs to be discovered. We ha...

  9. Virtual screening with AutoDock Vina and the common pharmacophore engine of a low diversity library of fragments and hits against the three allosteric sites of HIV integrase: participation in the SAMPL4 protein-ligand binding challenge

    Science.gov (United States)

    Perryman, Alexander L.; Santiago, Daniel N.; Forli, Stefano; Santos-Martins, Diogo; Olson, Arthur J.

    2014-04-01

    To rigorously assess the tools and protocols that can be used to understand and predict macromolecular recognition, and to gain more structural insight into three newly discovered allosteric binding sites on a critical drug target involved in the treatment of HIV infections, the Olson and Levy labs collaborated on the SAMPL4 challenge. This computational blind challenge involved predicting protein-ligand binding against the three allosteric sites of HIV integrase (IN), a viral enzyme for which two drugs (that target the active site) have been approved by the FDA. Positive control cross-docking experiments were utilized to select 13 receptor models out of an initial ensemble of 41 different crystal structures of HIV IN. These 13 models of the targets were selected using our new "Rank Difference Ratio" metric. The first stage of SAMPL4 involved using virtual screens to identify 62 active, allosteric IN inhibitors out of a set of 321 compounds. The second stage involved predicting the binding site(s) and crystallographic binding mode(s) for 57 of these inhibitors. Our team submitted four entries for the first stage that utilized: (1) AutoDock Vina (AD Vina) plus visual inspection; (2) a new common pharmacophore engine; (3) BEDAM replica exchange free energy simulations, and a Consensus approach that combined the predictions of all three strategies. Even with the SAMPL4's very challenging compound library that displayed a significantly lower amount of structural diversity than most libraries that are conventionally employed in prospective virtual screens, these approaches produced hit rates of 24, 25, 34, and 27 %, respectively, on a set with 19 % declared binders. Our only entry for the second stage challenge was based on the results of AD Vina plus visual inspection, and it ranked third place overall according to several different metrics provided by the SAMPL4 organizers. The successful results displayed by these approaches highlight the utility of the computational

  10. 4,5-Dihydro-1H-imidazol-2-yl)-[4-(4-isopropoxy-benzyl)-phenyl]-amine (RO1138452) is a selective, pseudo-irreversible orthosteric antagonist at the prostacyclin (IP)-receptor expressed by human airway epithelial cells: IP-receptor-mediated inhibition of CXCL9 and CXCL10 release.

    Science.gov (United States)

    Ayer, Linda M; Wilson, Sylvia M; Traves, Suzanne L; Proud, David; Giembycz, Mark A

    2008-02-01

    The extent to which the prostacyclin (IP) receptor regulates the release of two proinflammatory chemokines from human airway epithelial cells was investigated using the novel and competitive IP-receptor antagonist 4,5-dihydro-1H-imidazol-2-yl)-[4-(4-isopropoxy-benzyl)-phenyl]-amine (RO1138452). In BEAS-2B human airway epithelial cells, taprostene, a selective IP-receptor agonist, suppressed interferon-gamma-induced CXCL9 and CXCL10 release in a concentration-dependent manner. These effects were mimicked by 8-bromo-cAMP, and they were abolished in cells infected with an adenovirus vector encoding a highly selective inhibitor of cAMP-dependent protein kinase (PKA). RO1138452 blocked the inhibitory effect of taprostene on chemokine output in a manner inconsistent with surmountable competitive antagonism. Comparable results were obtained using primary cultures of human airway epithelial cells. The basis of the antagonism imposed by RO1138452 was studied further using BEAS-2B cells stably transfected with a cAMP-response element (CRE) luciferase reporter. On this output, RO1138452 also behaved insurmountably. Mechanistically, this could not be attributed to covalent receptor inactivation, allosterism, or a state of hemiequilibrium. Other studies established that the degree by which RO1138452 antagonized taprostene-induced CRE-dependent transcription was not reversed over a 20-h "washout" period. This pharmacological profile is consistent with the behavior of a pseudo-irreversible antagonist where dissociation from its cognate receptor is so slow that re-equilibration is not achieved at the time the response is measured. Collectively, these data provide compelling evidence that human airway epithelial cells express inhibitory IP-receptors linked to the activation of PKA. Moreover, contrary to existing literature, RO1138452 behaved pseudoirreversibly, emphasizing the need, in drug discovery, to screen potential new medicines in the target tissue(s) of interest.

  11. Poly[bis(1H-imidazole(μ3-7-oxabicyclo[2.2.1]heptane-2,3-dicarboxylatocadmium(II

    Directory of Open Access Journals (Sweden)

    Na Wang

    2009-07-01

    Full Text Available The title compound, [Cd(C8H8O5(C3H4N22]n, was synthesized by the reaction of 7-oxabicyclo[2.2.1]heptane-2,3-dicarboxylic anhydride, cadmium acetate and imidazole. The CdII atom is seven-coordinated in a distorted pentagonal-bipyramidal configuration by five O atoms from carboxylate groups of three 7-oxabicyclo[2.2.1]heptane-2,3-dicarboxylate ligands and two N atoms from two imidazole ligands. The crystal structure is stabilized by N—H...O and C—H...O hydrogen-bonding and C—H...π interactions.

  12. Sequential one-pot synthesis of imidazoles and 2H-imidazolones from β-ketoamines, acylating agents and ammonium acetate

    Energy Technology Data Exchange (ETDEWEB)

    Jalani, Hitesh B.; Venkateswararao, Edda; Manickam, Manoj; Jung, Sang Hun [College of Pharmacy and Institute of Drug Research and Development, Chungnam National University, Daejeon (Korea, Republic of)

    2016-12-15

    An efficient, practical, straight forward, and transition metal-free three-component synthesis of diversely substituted imidazoles and 2H-imidazolones from β-ketoamines, acylating agents, and ammonium acetate has been described herein. This approach involves [3+1+1] cyclization through consecutive formation of three C–N bonds as a sequence of initial amidation of β-ketoamines with acylating agent, β-iminoketoamide formation with ammonia, and acid catalyzed concomitant cyclodehydration to afford the imidazoles and 2H-imidazolones. This methodology has advantages such as single flask operation, readily available starting materials, mild conditions, broad functional groups tolerance, and simple work-up procedure.

  13. Comparative Corrosion Inhibition Effect of Imidazole Compounds and of Trichodesma indicum (Linn R. Br. on C38 Steel in 1 M HCl Medium

    Directory of Open Access Journals (Sweden)

    S. Alarmal Mangai

    2013-01-01

    Full Text Available Corrosion inhibition effect of alkaloid extract part of the plant Trichodesma indicum (Linn R. Br. of Boraginaceae family was studied and compared with that of imidazole compounds (imidazole, benzimidazole on C38 steel in 1 M HCl solution by weight loss method at various temperatures. The study showed that the alkaloid part of the plant extract acts as a better inhibitor in comparison to the selected organic inhibitors. The maximum inhibition efficiency of the extract of Trichodesma indicum R. Br. was found to be 94.5% at a concentration of 75 mg/L at 30°C.

  14. Investigation of Oxygen Reduction Activity of Catalysts Derived from Co and Co/Zn Methyl-Imidazolate Frameworks in Proton Exchange Membrane Fuel Cells

    Energy Technology Data Exchange (ETDEWEB)

    Chong, Lina [Chemical Sciences and Engineering Division, Argonne National Laboratory, Argonne IL 60439 USA; Engineering Research Center of Light Alloy Net Forming and State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, Shanghai P.R. China; Goenaga, Gabriel A. [Chemical and Biomolecular Engineering Department, University of Tennessee, Knoxville, TN 37996 USA; Williams, Kia [University of South Florida, Tampa FL 33620 USA; Barkholtz, Heather M. [Chemical Sciences and Engineering Division, Argonne National Laboratory, Argonne IL 60439 USA; Grabstanowicz, Lauren R. [Alcoa Technical Center, New Kensington PA 15068 USA; Brooksbank, Jeremy A. [Chemical and Biomolecular Engineering Department, University of Tennessee, Knoxville, TN 37996 USA; Papandrew, Alex B. [Chemical and Biomolecular Engineering Department, University of Tennessee, Knoxville, TN 37996 USA; Elzein, Radwan [University of South Florida, Tampa FL 33620 USA; Schlaf, Rudiger [University of South Florida, Tampa FL 33620 USA; Zawodzinski, Thomas A. [Chemical and Biomolecular Engineering Department, University of Tennessee, Knoxville, TN 37996 USA; Zou, Jianxin [Engineering Research Center of Light Alloy Net Forming and State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, Shanghai P.R. China; Ma, Shengqian [University of South Florida, Tampa FL 33620 USA; Liu, Di-Jia [Chemical Sciences and Engineering Division, Argonne National Laboratory, Argonne IL 60439 USA

    2016-05-31

    We demonstrated that the oxygen reduction reaction (ORR) activity over the catalysts derived from pyrolyzed cobalt zeolitic imidazolate frameworks depends strongly on the imidazole ligand structure and cobalt content. The activity and durability of these catalysts were tested in the proton exchange membrane fuel cell for the first time. The membrane electrode assembly containing a catalyst derived from Co/Zn bimetallic ZIF at cathode achieved an open circuit voltage of 0.93 V, a current density of 28 mA cm-2 at 0.8 ViR-free and a peak power density of 374 mW cm-2.

  15. Magnetically responsive enzyme powders

    International Nuclear Information System (INIS)

    Pospiskova, Kristyna; Safarik, Ivo

    2015-01-01

    Powdered enzymes were transformed into their insoluble magnetic derivatives retaining their catalytic activity. Enzyme powders (e.g., trypsin and lipase) were suspended in various liquid media not allowing their solubilization (e.g., saturated ammonium sulfate and highly concentrated polyethylene glycol solutions, ethanol, methanol, 2-propanol) and subsequently cross-linked with glutaraldehyde. Magnetic modification was successfully performed at low temperature in a freezer (−20 °C) using magnetic iron oxides nano- and microparticles prepared by microwave-assisted synthesis from ferrous sulfate. Magnetized cross-linked enzyme powders were stable at least for two months in water suspension without leakage of fixed magnetic particles. Operational stability of magnetically responsive enzymes during eight repeated reaction cycles was generally without loss of enzyme activity. Separation of magnetically modified cross-linked powdered enzymes from reaction mixtures was significantly simplified due to their magnetic properties. - Highlights: • Cross-linked enzyme powders were prepared in various liquid media. • Insoluble enzymes were magnetized using iron oxides particles. • Magnetic iron oxides particles were prepared by microwave-assisted synthesis. • Magnetic modification was performed under low (freezing) temperature. • Cross-linked powdered trypsin and lipase can be used repeatedly for reaction

  16. Enzymes in Fermented Fish.

    Science.gov (United States)

    Giyatmi; Irianto, H E

    Fermented fish products are very popular particularly in Southeast Asian countries. These products have unique characteristics, especially in terms of aroma, flavor, and texture developing during fermentation process. Proteolytic enzymes have a main role in hydrolyzing protein into simpler compounds. Fermentation process of fish relies both on naturally occurring enzymes (in the muscle or the intestinal tract) as well as bacteria. Fermented fish products processed using the whole fish show a different characteristic compared to those prepared from headed and gutted fish. Endogenous enzymes like trypsin, chymotrypsin, elastase, and aminopeptidase are the most involved in the fermentation process. Muscle tissue enzymes like cathepsins, peptidases, transaminases, amidases, amino acid decarboxylases, glutamic dehydrogenases, and related enzymes may also play a role in fish fermentation. Due to the decreased bacterial number during fermentation, contribution of microbial enzymes to proteolysis may be expected prior to salting of fish. Commercial enzymes are supplemented during processing for specific purposes, such as quality improvement and process acceleration. In the case of fish sauce, efforts to accelerate fermentation process and to improve product quality have been studied by addition of enzymes such as papain, bromelain, trypsin, pepsin, and chymotrypsin. © 2017 Elsevier Inc. All rights reserved.

  17. Enzyme Vs. Extremozyme -32 ...

    Indian Academy of Sciences (India)

    Enzyme Vs. Extremozyme. What Makes Extremozymes Function Under Harsh Conditions? Santosh Kumar is ... extremozymes to high temperature or pH so that enzymes from mesophiles can be engineered to behave .... alkalinity (above pH 10, soda lake) from which extremozymes have been isolated. F C Lowyer of the ...

  18. Industrial Enzymes and Biocatalysis

    Science.gov (United States)

    McAuliffe, Joseph C.; Aehle, Wolfgang; Whited, Gregory M.; Ward, Donald E.

    All life processes are the result of enzyme activity. In fact, life itself, whether plant or animal, involves a complex network of enzymatic reactions. An enzyme is a protein that is synthesized in a living cell. It catalyzes a thermodynamically possible reaction so that the rate of the reaction is compatible with the numerous biochemical processes essential for the growth and maintenance of a cell. The synthesis of an enzyme thus is under tight metabolic regulations and controls that can be genetically or environmentally manipulated sometimes to cause the overproduction of an enzyme by the cell. An enzyme, like chemical catalysts, in no way modifies the equilibrium constant or the free energy change of a reaction.

  19. Biochemical, Biomedical and Metabolic Aspects of Imidazole-Containing Dipeptides with the Inherent Complexity to Neurodegenerative Diseases and Various States of Mental Well-Being: A Challenging Correction and Neurotherapeutic Pharmaceutical Biotechnology for Treating Cognitive Deficits, Depression and Intellectual Disabilities.

    Science.gov (United States)

    Babizhayev, Mark A

    2014-01-01

    The activities of carnosine (β-alanyl-L-histidine), carnosine imidazole containing dipeptide based derivatives (N-acetylcarnosine, carcinine, homocarnosine) and a carnosine degrading enzyme (serum carnosinase (EC 3.4.13.20); [human tissue carnosinase (EC 3.4.13.3), CN2 (CNDP2)] ) activities have been discrepantly linked to neuropathophysiological processes. Approximately 82% of the U.S. population will experience normal age-related cognitive decline, as compared to the precipitous losses that are associated with dementing disorders. Interventions designed to promote health and function through everyday activity and specific pharmaco-nutritional therapeutic treatments may enhance brain plasticity in key regions that support executive function. Cognitive health is multidimensional cascade of functions. It encompasses an array of functions, including general intellectual ability, memory, language, allowing a person to interact effectively and appropriately with the environment. The risk factors for reduced physical and cognitive functions in elderly people, as identified in longitudinal studies, relate to comorbidities, critical care situations, physical and psychosocial health, environmental conditions, social circumstances, nutrition, and lifestyle. Depression and dementia are both common in older adults; cognitive functioning declines slightly with normal aging; depression itself can be associated with cognitive impairment and dementia. In this study the role of carnosine and related neuron specific naturally-occurring endogenous imidazole-containing dipeptide pharmacoperones (N-acetylcarnosine, carcinine) is revealed presently in a surprisingly large amounts in long-lived human tissues to correct conformational abnormalities leading to distinct neurodegeneration and age-related disease states, treating cognitive deficits, depression and intellectual disabilities. Carnosine serves as a physiological buffering agent and a metal ion (e.g., zinc and copper) chelator

  20. Reversible uptake of molecular oxygen by heteroligand Co(II)-L-α-amino acid-imidazole systems: equilibrium models at full mass balance.

    Science.gov (United States)

    Pająk, Marek; Woźniczka, Magdalena; Vogt, Andrzej; Kufelnicki, Aleksander

    2017-09-19

    The paper examines Co(II)-amino acid-imidazole systems (where amino acid = L-α-amino acid: alanine, asparagine, histidine) which, when in aqueous solutions, activate and reversibly take up dioxygen, while maintaining the structural scheme of the heme group (imidazole as axial ligand and O 2 uptake at the sixth, trans position) thus imitating natural respiratory pigments such as myoglobin and hemoglobin. The oxygenated reaction shows higher reversibility than for Co(II)-amac systems with analogous amino acids without imidazole. Unlike previous investigations of the heteroligand Co(II)-amino acid-imidazole systems, the present study accurately calculates all equilibrium forms present in solution and determines the [Formula: see text]equilibrium constants without using any simplified approximations. The equilibrium concentrations of Co(II), amino acid, imidazole and the formed complex species were calculated using constant data obtained for analogous systems under oxygen-free conditions. Pehametric and volumetric (oxygenation) studies allowed the stoichiometry of O 2 uptake reaction and coordination mode of the central ion in the forming oxygen adduct to be determined. The values of dioxygen uptake equilibrium constants [Formula: see text] were evaluated by applying the full mass balance equations. Investigations of oxygenation of the Co(II)-amino acid-imidazole systems indicated that dioxygen uptake proceeds along with a rise in pH to 9-10. The percentage of reversibility noted after acidification of the solution to the initial pH ranged within ca 30-60% for alanine, 40-70% for asparagine and 50-90% for histidine, with a rising tendency along with the increasing share of amino acid in the Co(II): amino acid: imidazole ratio. Calculations of the share of the free Co(II) ion as well as of the particular complex species existing in solution beside the oxygen adduct (regarding dioxygen bound both reversibly and irreversibly) indicated quite significant values for the

  1. Allosteric modulation of the effect of escitalopram, paroxetine and fluoxetine: in-vitro and in-vivo studies

    DEFF Research Database (Denmark)

    Mansari, Mostafa El; Wiborg, Ove; Mnie-Filali, Ouissame

    2006-01-01

    of escitalopram. This effect was suggested to occur via an allosteric modulation at the level of the 5-HT transporter. Using in-vitro binding assays at membranes from COS-1 cells expressing the human 5-HT transporter (hSERT) and in-vivo electrophysiological and microdialysis techniques in rats, the present study...... was directed at determining whether R-citalopram modifies the action of selective serotonin reuptake inhibitors (SSRIs) known to act on allosteric sites namely escitalopram, and to a lesser extent paroxetine, compared to fluoxetine, which has no affinity for these sites. In-vitro binding studies showed that R......-citalopram attenuated the association rates of escitalopram and paroxetine to the 5-HT transporter, but had no effect on the association rates of fluoxetine, venlafaxine or sertraline. In the rat dorsal raphe nucleus, R-citalopram (250 microg/kg i.v.) blocked the suppressant effect on neuronal firing activity of both...

  2. Identification of halosalicylamide derivatives as a novel class of allosteric inhibitors of HCV NS5B polymerase.

    Science.gov (United States)

    Liu, Yaya; Donner, Pamela L; Pratt, John K; Jiang, Wen W; Ng, Teresa; Gracias, Vijaya; Baumeister, Steve; Wiedeman, Paul E; Traphagen, Linda; Warrior, Usha; Maring, Clarence; Kati, Warren M; Djuric, Stevan W; Molla, Akhteruzzaman

    2008-06-01

    Halosalicylamide derivatives were identified from high-throughput screening as potent inhibitors of HCV NS5B polymerase. The subsequent structure and activity relationship revealed the absolute requirement of the salicylamide moiety for optimum activity. Methylation of either the hydroxyl group or the amide group of the salicylamide moiety abolished the activity while the substitutions on both phenyl rings are acceptable. The halosalicylamide derivatives were shown to be non-competitive with respect to elongation nucleotide and demonstrated broad genotype activity against genotype 1-3 HCV NS5B polymerases. Inhibitor competition studies indicated an additive binding mode to the initiation pocket that is occupied by the thiadiazine class of compounds and an additive binding mode to the elongation pocket that is occupied by diketoacids, but a mutually exclusive binding mode with respect to the allosteric thumb pocket that is occupied by the benzimidazole class of inhibitors. Therefore, halosalicylamides represent a novel class of allosteric inhibitors of HCV NS5B polymerase.

  3. Imidazole C-2 Hydrogen/Deuterium Exchange Reaction at Histidine for Probing Protein Structure and Function with MALDI Mass Spectrometry

    Science.gov (United States)

    Hayashi, Naoka; Kuyama, Hiroki; Nakajima, Chihiro; Kawahara, Kazuki; Miyagi, Masaru; Nishimura, Osamu; Matsuo, Hisayuki; Nakazawa, Takashi

    2015-01-01

    We present a mass spectrometric method for analyzing protein structure and function, based on the imidazole C-2 or histidine Cε1 hydrogen/deuterium (H/D) exchange reaction, which is intrinsically second order with respect to the concentrations of the imidazolium cation and OD− in D2O. The second-order rate constant (k2) of this reaction was calculated from the pH-dependency of the pseudo-first-order rate constant (kφ) obtained from the change of average mass ΔMr (0 ≤ ΔMr exchange rate in terms of log(k2max/k2) representing the deviation of k2 from k2max. In the catalytic site of bovine ribonuclease A, His12 showed much larger change in log(k2max/k2) compared with His119 upon binding with cytidine 3′-monophosphate, as anticipated from the X-ray structures and the possible change in solvent accessibility. However, there is a need of considering the hydrogen bonds of the imidazole group with non-dissociable groups to interpret an extremely slow H/D exchange rate of His48 in partially solvent-exposed situation. PMID:24606199

  4. Luminescent pH sensor of a novel imidazole-containing hexanuclear Ru(II) polypyridyl complex

    Science.gov (United States)

    Cheng, Feixiang; Tang, Ning; Chen, Jishu; Chen, Guang

    2013-10-01

    Hexapodal ligand H6L containing imidazole rings has been prepared by the reaction of 1,10-phenanthroline-5,6-dione with 1,2,3,4,5,6-hexakis[(3-formylphenoxy)methyl]benzene. The Ru(II) polypyridyl complex [{Ru(bpy)2}6(μ6-H6L)](PF6)12 (bpy = 2,2'-bipyridine) has been synthesized by the reaction of Ru(bpy)2Cl2·2H2O with ligand H6L. The pH effects on the UV-vis absorption and emission spectra of the complex have been studied. The ground- and excited-state ionization constants of the acid-base equilibria have been calculated according to the absorbance and emission data. The complex acts as an off-on-off luminescent pH sensor through two successive deprotonation processes of imidazole rings, with a maximum on-off ratio of 5 in buffer solution.

  5. Synthesis of Iron Doped Zeolite Imidazolate Framework-8 and Its Remazol Deep Black RGB Dye Adsorption Ability

    Directory of Open Access Journals (Sweden)

    Mai Thi Thanh

    2017-01-01

    Full Text Available Zeolite imidazole framework-8 (ZIF-8 and the iron doped ZIF-8 (Fe-ZIF-8 were synthesized by the hydrothermal process. The obtained materials were characteristic of X-ray diffraction (XRD, X-ray photoelectron spectroscopy (XPS, scanning electron microscope (SEM, nitrogen adsorption/desorption isotherms, and atomic absorption spectroscopy (AAS. The results showed that the obtained Fe-ZIF-8 possessed the ZIF-8 structure with a large specific area. ZIF-8 and Fe-ZIF-8 were used for the removal of Remazol Deep Black (RDB RGB dye from aqueous solutions. The various factors affecting adsorption such as pH, initial concentration, contact time, and temperature were investigated. The results showed that the introduction of iron into ZIF-8 provided a much larger adsorption capacity and faster adsorption kinetics than ZIF-8 without iron. The electrostatic interaction and π-π interaction between the aromatic rings of the RDB dye and the aromatic imidazolate rings of the adsorbent were responsible for the RDB adsorption. Moreover, the coordination of the nitrogen atoms and oxygen in carboxyl group in RDB molecules with the Fe2+ ions in the ZIF-8 framework played a vital role for the effective removal of RDB from aqueous solution.

  6. Molecularly imprinted poly(N-vinyl imidazole) based polymers grafted onto nonwoven fabrics for recognition/removal of phloretic acid

    International Nuclear Information System (INIS)

    Llorina Rañada, Ma.; Akbulut, Meshude; Abad, Lucille; Güven, Olgun

    2014-01-01

    A solution of N-vinyl imidazole (VIm), ethylene glycol dimethylacrylate (EGDMA), and phloretic acid (p-hydroxyphenylpropionic acid, HPPA) as functional monomer, crosslinker and template, respectively, were used to graft molecularly imprinted polymer (MIP) onto polyethylene/polypropylene (PE/PP) nonwoven fabric via gamma radiation at room temperature. Control grafted films were also synthesized using the same procedure in the absence of HPPA. Binding performance of the MIP grafts was investigated for different template molecule concentrations and contact time. An imprinting factor for the sample prepared at 5 kGy dose was determined as 2.41 for 50 ppm HPPA solution for 3-h incubation. MIP graft layers were investigated by positron annihilation lifetime spectroscopy (PALS) as well as SEM. - Highlights: • Molecularly imprinted matrices (MIP) of phloretic acid were prepared by radiation polymerization of N-vinyl imidazole. • Polymerization and crosslinking were achieved as a thin grafted layer on the surface of PE/PP nonwoven fabric. • Binding performance of MIP graft layers were found to show an imprinting factor of 2.41 for this template. • Grafted layers were characterized by SEM and PALS techniques. • Binding isotherms were found to follow double Langmuir isotherms

  7. Stepwise Two-Photon-Gated Photochemical Reaction in Photochromic [2.2]Paracyclophane-Bridged Bis(imidazole dimer).

    Science.gov (United States)

    Mutoh, Katsuya; Nakagawa, Yuki; Sakamoto, Akira; Kobayashi, Yoichi; Abe, Jiro

    2015-05-06

    Stepwise two-photon processes not only have great potential for efficient light harvesting but also can provide valuable insights into novel photochemical sciences. Here we have designed a [2.2]paracyclophane-bridged bis(imidazole dimer), a molecule that is composed of two photochromic units and absorbs two photons in a stepwise manner. The absorption of the first photon leads to the formation of a short-lived biradical species (half-life = 88 ms at 298 K), while the absorption of the additional photon by the biradical species triggers a subsequent photochromic reaction to afford a long-lived quinoid species. The short-lived biradical species and the long-lived quinoid species display significantly different absorption spectra and rates of the thermal back-reaction. The stepwise two-photon excitation process in this photochromic system can be initiated even by incoherent continuous-wave light irradiation, indicating that this two-photon reaction is highly efficient. Our molecule based on the bridged bis(imidazole dimer) unit should be a good candidate for multiphoton-gated optical materials.

  8. Virtual Screening and Molecular Dynamics Study of Potential Negative Allosteric Modulators of mGluR1 from Chinese Herbs

    Directory of Open Access Journals (Sweden)

    Ludi Jiang

    2015-07-01

    Full Text Available The metabotropic glutamate subtype 1 (mGluR1, a member of the metabotropic glutamate receptors, is a therapeutic target for neurological disorders. However, due to the lower subtype selectivity of mGluR1 orthosteric compounds, a new targeted strategy, known as allosteric modulators research, is needed for the treatment of mGluR1-related diseases. Recently, the structure of the seven-transmembrane domain (7TMD of mGluR1 has been solved, which reveals the binding site of allosteric modulators and provides an opportunity for future subtype-selectivity drug design. In this study, a series of computer-aided drug design methods were utilized to discover potential mGluR1 negative allosteric modulators (NAMs. Pharmacophore models were constructed based on three different structure types of mGluR1 NAMs. After validation using the built-in parameters and test set, the optimal pharmacophore model of each structure type was selected and utilized as a query to screen the Traditional Chinese Medicine Database (TCMD. Then, three different hit lists of compounds were obtained. Molecular docking was used based on the latest crystal structure of mGluR1-7TMD to further filter these hits. As a compound with high QFIT and LibDock Score was preferred, a total of 30 compounds were retained. MD simulation was utilized to confirm the stability of potential compounds binding. From the computational results, thesinine-4ʹ-O-β-d-glucoside, nigrolineaxanthone-P and nodakenin might exhibit negative allosteric moderating effects on mGluR1. This paper indicates the applicability of molecular simulation technologies for discovering potential natural mGluR1 NAMs from Chinese herbs.

  9. Determinants of positive cooperativity between strychnine-like allosteric modulators and N-methylscopolamine at muscarinic receptors

    Czech Academy of Sciences Publication Activity Database

    Jakubík, Jan; Doležal, Vladimír

    2006-01-01

    Roč. 30, č. 1-2 (2006), s. 111-112 ISSN 0895-8696 R&D Projects: GA ČR(CZ) GA305/05/0452; GA MŠk(CZ) LC554 Institutional research plan: CEZ:AV0Z50110509 Keywords : muscarinic receptors * strychnine -like allosteric modulators * cooperativity Subject RIV: ED - Physiology Impact factor: 2.965, year: 2006

  10. Antipsychotic Drug-Like Effects of the Selective M4 Muscarinic Acetylcholine Receptor Positive Allosteric Modulator VU0152100

    OpenAIRE

    Byun, Nellie E; Grannan, Michael; Bubser, Michael; Barry, Robert L; Thompson, Analisa; Rosanelli, John; Gowrishankar, Raajaram; Kelm, Nathaniel D; Damon, Stephen; Bridges, Thomas M; Melancon, Bruce J; Tarr, James C; Brogan, John T; Avison, Malcolm J; Deutch, Ariel Y

    2014-01-01

    Accumulating evidence suggests that selective M4 muscarinic acetylcholine receptor (mAChR) activators may offer a novel strategy for the treatment of psychosis. However, previous efforts to develop selective M4 activators were unsuccessful because of the lack of M4 mAChR subtype specificity and off-target muscarinic adverse effects. We recently developed VU0152100, a highly selective M4 positive allosteric modulator (PAM) that exerts central effects after systemic administration. We now repor...

  11. Heterogeneous photochemistry of imidazole-2-carboxaldehyde: HO2 radical formation and aerosol growth

    Directory of Open Access Journals (Sweden)

    L. González Palacios

    2016-09-01

    Full Text Available The multiphase chemistry of glyoxal is a source of secondary organic aerosol (SOA, including its light-absorbing product imidazole-2-carboxaldehyde (IC. IC is a photosensitizer that can contribute to additional aerosol ageing and growth when its excited triplet state oxidizes hydrocarbons (reactive uptake via H-transfer chemistry. We have conducted a series of photochemical coated-wall flow tube (CWFT experiments using films of IC and citric acid (CA, an organic proxy and H donor in the condensed phase. The formation rate of gas-phase HO2 radicals (PHO2 was measured indirectly by converting gas-phase NO into NO2. We report on experiments that relied on measurements of NO2 formation, NO loss and HONO formation. PHO2 was found to be a linear function of (1 the [IC]  ×  [CA] concentration product and (2 the photon actinic flux. Additionally, (3 a more complex function of relative humidity (25 %  <  RH  <  63 % and of (4 the O2 ∕ N2 ratio (15 %  <  O2 ∕ N2  <  56 % was observed, most likely indicating competing effects of dilution, HO2 mobility and losses in the film. The maximum PHO2 was observed at 25–55 % RH and at ambient O2 ∕ N2. The HO2 radicals form in the condensed phase when excited IC triplet states are reduced by H transfer from a donor, CA in our system, and subsequently react with O2 to regenerate IC, leading to a catalytic cycle. OH does not appear to be formed as a primary product but is produced from the reaction of NO with HO2 in the gas phase. Further, seed aerosols containing IC and ammonium sulfate were exposed to gas-phase limonene and NOx in aerosol flow tube experiments, confirming significant PHO2 from aerosol surfaces. Our results indicate a potentially relevant contribution of triplet state photochemistry for gas-phase HO2 production, aerosol growth and ageing in the atmosphere.

  12. Synthesis of amine-modified zeolitic imidazolate framework-8, ultrasound-assisted dye removal and modeling.

    Science.gov (United States)

    Abdi, Jafar; Vossoughi, Manouchehr; Mahmoodi, Niyaz Mohammad; Alemzadeh, Iran

    2017-11-01

    The present research is focused on the ultrasound assisted adsorption of Acid blue 92 (AB92) and Direct red 80 (DR80) as anionic dyes in single and binary systems onto zeolitic imidazolate framework (ZIF-8) functionalized with 3-Aminopropyltrimethoxysilane (APTES). Different techniques such as Fourier transform infrared (FTIR), scanning electron microscope (SEM), field emission scanning electron microscopy (FE-SEM), X-ray diffraction (XRD), Brunauer-Emmett-Teller (BET) and thermogravimetric analyses (TGA) were used to characterize the prepared adsorbent. The individual effects and possible interactions between the various parameters including adsorbent dosage, sonication time, initial dye concentrations and pH on dyes removal efficiency were investigated by response surface methodology (RSM). The optimized experimental conditions were fixed at adsorbent dosage 0.005g for AB92 and 0.01g for DR80, pH 2.1, sonication time 15min, and initial dyes concentration 15mgL -1 to get maximum removal percentage (>95.0%). A reliable and intelligent model based on least-squares support vector machine (LS-SVM) was developed to predict dye removal efficiency. The root mean square error (RMSE) of 0.604, 0.734 and 1.549 with high determination coefficient (R 2 ) of 0.999, 0.996 and 0.997 for AB92, DR80 and binary system, respectively, were able to predict and model the adsorption process. The presented model illustrates better performance in predicting dye removal efficiency compared to the kinetic models. The results showed that the adsorption process had better conformation with pseudo-second order model. The adsorption equilibrium data was investigated by Langmuir, Freundlich, Tempkin and Dubinin-Radushkevich isotherm models and the data were well fitted by Langmuir model with maximum adsorption capacity of 633.4 and 500.2mgg -1 for AB92 and DR80 dyes, respectively. APTES@ZIF-8 was regenerated and found to be reusable after four successive cycles without considerable loss in

  13. Allosteric interactions between agonists and antagonists within the adenosine A2A receptor-dopamine D2 receptor heterotetramer.

    Science.gov (United States)

    Bonaventura, Jordi; Navarro, Gemma; Casadó-Anguera, Verònica; Azdad, Karima; Rea, William; Moreno, Estefanía; Brugarolas, Marc; Mallol, Josefa; Canela, Enric I; Lluís, Carme; Cortés, Antoni; Volkow, Nora D; Schiffmann, Serge N; Ferré, Sergi; Casadó, Vicent

    2015-07-07

    Adenosine A2A receptor (A2AR)-dopamine D2 receptor (D2R) heteromers are key modulators of striatal neuronal function. It has been suggested that the psychostimulant effects of caffeine depend on its ability to block an allosteric modulation within the A2AR-D2R heteromer, by which adenosine decreases the affinity and intrinsic efficacy of dopamine at the D2R. We describe novel unsuspected allosteric mechanisms within the heteromer by which not only A2AR agonists, but also A2AR antagonists, decrease the affinity and intrinsic efficacy of D2R agonists and the affinity of D2R antagonists. Strikingly, these allosteric modulations disappear on agonist and antagonist coadministration. This can be explained by a model that considers A2AR-D2R heteromers as heterotetramers, constituted by A2AR and D2R homodimers, as demonstrated by experiments with bioluminescence resonance energy transfer and bimolecular fluorescence and bioluminescence complementation. As predicted by the model, high concentrations of A2AR antagonists behaved as A2AR agonists and decreased D2R function in the brain.

  14. Enzymic lactose hydrolysis

    Energy Technology Data Exchange (ETDEWEB)

    Miller, J.J.; Brand, J.C.

    1980-01-01

    Acid or enzymic hydrolysis can be used to hydrolyze lactose. Advantages of both are compared and details of enzymic hydrolysis using yeast or fungal enzymes given. The new scheme outlined involves recycling lactase. Because lactose and lactase react to ultrafiltration (UF) membranes differently separation is possible. Milk or milk products are ultrafiltered to separate a concentrate from a lactose-rich permeate which is treated with lactase in a reactor until hydrolysis reaches a required level. The lactase can be removed by UF as it does not permeate the membrane, and it is recycled back to the reactor. Permeate from the second UF stage may or may not be recombined with the concentrate from the first stage to produce a low lactose product (analysis of a typical low-lactose dried whole milk is given). Batch or continuous processes are explained and a batch process without enzyme recovery is discussed. (Refs. 4).

  15. Indicators: Sediment Enzymes

    Science.gov (United States)

    Sediment enzymes are proteins that are produced by microorganisms living in the sediment or soil. They are indicators of key ecosystem processes and can help determine which nutrients are affecting the biological community of a waterbody.

  16. Enzymes in Analytical Chemistry.

    Science.gov (United States)

    Fishman, Myer M.

    1980-01-01

    Presents tabular information concerning recent research in the field of enzymes in analytic chemistry, with methods, substrate or reaction catalyzed, assay, comments and references listed. The table refers to 128 references. Also listed are 13 general citations. (CS)

  17. Enzyme Vs. Extremozyme -32 ...

    Indian Academy of Sciences (India)

    Enzyme Vs. Extremozyme. What Makes Extremozymes Function Under Harsh Conditions? Santosh Kumar is doing his Ph D at Biotechnology. Centre, Indian Institute of. Technology, Bombay. His research interests include: enzymology, metabolism, metabolic regulation and metabolic engineering of a filamentous fungi,.

  18. Membrane Assisted Enzyme Fractionation

    DEFF Research Database (Denmark)

    Yuan, Linfeng

    . In this thesis, separations using crossflow elecro-membrane filtration (EMF) of amino acids, bovine serum albumin (BSA) and industrial enzymes from Novozymes were performed. The main objective of this study was to investigate the technological feasibility of EMF in the application of industrial enzyme...... fractionation, such as removal of a side activity from the main enzyme activity. As a proof-of-concept, amino acids were used as model solution to test the feasibility of EMF in the application of amphoteric molecule separation. A single amino acid was used to illustrate the effect of an electric field...... on the separation performance were very small in the investigated range. The mass transport of each enzyme can be well explained by the Extended-Nernst-Planck equation. Better separation was observed at lower feed concentration, higher solution pH in the investigated range and with a polysulfone (PS) MF membrane...

  19. Advances in enzyme immobilisation

    CSIR Research Space (South Africa)

    Brady, D

    2009-07-10

    Full Text Available improved protein binding capacity. Novel methods of enzyme self immobilisation have been developed (CLEC, CLEA, Spherezyme), as well as carrier materials (Dendrispheres), encapsulation (PEI Microspheres), and entrapment. Apart from retention, recovery...

  20. Enzyme catalysed tandem reactions.

    Science.gov (United States)

    Oroz-Guinea, Isabel; García-Junceda, Eduardo

    2013-04-01

    To transfer to the laboratory, the excellent efficiency shown by enzymes in Nature, biocatalysis, had to mimic several synthetic strategies used by the living organisms. Biosynthetic pathways are examples of tandem catalysis and may be assimilated in the biocatalysis field for the use of isolated multi-enzyme systems in the homogeneous phase. The concurrent action of several enzymes that work sequentially presents extraordinary advantages from the synthetic point of view, since it permits a reversible process to become irreversible, to shift the equilibrium reaction in such a way that enantiopure compounds can be obtained from prochiral or racemic substrates, reduce or eliminate problems due to product inhibition or prevent the shortage of substrates by dilution or degradation in the bulk media, etc. In this review we want to illustrate the developments of recent studies involving in vitro multi-enzyme reactions for the synthesis of different classes of organic compounds. Copyright © 2013 Elsevier Ltd. All rights reserved.

  1. Biology-oriented drug synthesis (BIODS) of 2-(2-methyl-5-nitro-1H-imidazol-1-yl)ethyl aryl ether derivatives, in vitro α-amylase inhibitory activity and in silico studies.

    Science.gov (United States)

    Taha, Muhammad; Imran, Syahrul; Ismail, Nor Hadiani; Selvaraj, Manikandan; Rahim, Fazal; Chigurupati, Sridevi; Ullah, Hayat; Khan, Fahad; Salar, Uzma; Javid, Muhammad Tariq; Vijayabalan, Shantini; Zaman, Khalid; Khan, Khalid Mohammed

    2017-10-01

    A new library of 2-(2-methyl-5-nitro-1H-imidazol-1-yl)ethyl aryl ether derivatives (1-23) were synthesized and characterized by EI-MS and 1 H NMR, and screened for their α-amylase inhibitory activity. Out of twenty-three derivatives, two molecules 19 (IC 50 =0.38±0.82µM) and 23 (IC 50 =1.66±0.14µM), showed excellent activity whereas the remaining compounds, except 10 and 17, showed good to moderate inhibition in the range of IC 50 =1.77-2.98µM when compared with the standard acarbose (IC 50 =1.66±0.1µM). A plausible structure-activity relationship has also been presented. In addition, in silico studies was carried out in order to rationalize the binding interaction of compounds with the active site of enzyme. Copyright © 2017 Elsevier Inc. All rights reserved.

  2. Overproduction of ligninolytic enzymes

    Science.gov (United States)

    Elisashvili, Vladimir; Kachlishvili, Eva; Torok, Tamas

    2014-06-17

    Methods, compositions, and systems for overproducing ligninolytic enzymes from the basidiomycetous fungus are described herein. As described, the method can include incubating a fungal strain of Cerrena unicolor IBB 303 in a fermentation system having growth medium which includes lignocellulosic material and then cultivating the fungal strain in the fermentation system under conditions wherein the fungus expresses the ligninolytic enzymes. In some cases, the lignocellulosic material is mandarin peel, ethanol production residue, walnut pericarp, wheat bran, wheat straw, or banana peel.

  3. Positive allosteric modulation of TRPV1 as a novel analgesic mechanism

    Directory of Open Access Journals (Sweden)

    Lebovitz Evan E

    2012-09-01

    Full Text Available Abstract Background The prevalence of long-term opiate use in treating chronic non-cancer pain is increasing, and prescription opioid abuse and dependence are a major public health concern. To explore alternatives to opioid-based analgesia, the present study investigates a novel allosteric pharmacological approach operating through the cation channel TRPV1. This channel is highly expressed in subpopulations of primary afferent unmyelinated C- and lightly-myelinated Aδ-fibers that detect low and high rates of noxious heating, respectively, and it is also activated by vanilloid agonists and low pH. Sufficient doses of exogenous vanilloid agonists, such as capsaicin or resiniferatoxin, can inactivate/deactivate primary afferent endings due to calcium overload, and we hypothesized that positive allosteric modulation of agonist-activated TRPV1 could produce a selective, temporary inactivation of nociceptive nerve terminals in vivo. We previously identified MRS1477, a 1,4-dihydropyridine that potentiates vanilloid and pH activation of TRPV1 in vitro, but displays no detectable intrinsic agonist activity of its own. To study the in vivo effects of MRS1477, we injected the hind paws of rats with a non-deactivating dose of capsaicin, MRS1477, or the combination. An infrared diode laser was used to stimulate TRPV1-expressing nerve terminals and the latency and intensity of paw withdrawal responses were recorded. qRT-PCR and immunohistochemistry were performed on dorsal root ganglia to examine changes in gene expression and the cellular specificity of such changes following treatment. Results Withdrawal responses of the capsaicin-only or MRS1477-only treated paws were not significantly different from the untreated, contralateral paws. However, rats treated with the combination of capsaicin and MRS1477 exhibited increased withdrawal latency and decreased response intensity consistent with agonist potentiation and inactivation or lesion of TRPV1-containing

  4. Reactivity of Hydroxy and Amino Derivatives of 2-Phenyl-1H-imidazoline and 2-Phenyl-1H-imidazole toward Isocyanates: Synthesis of Appropriate Carbamates and Ureas

    Czech Academy of Sciences Publication Activity Database

    Pařík, P.; Jansa, J.; Holešová, S.; Marek, Aleš; Klimešová, V.

    2013-01-01

    Roč. 50, č. 4 (2013), s. 903-910 ISSN 0022-152X Grant - others:GA ČR(CZ) GA205/08/0869 Institutional support: RVO:61388963 Keywords : elevated-temperature * hydrolysis * imidazoles * alkylation Subject RIV: CC - Organic Chemistry Impact factor: 0.873, year: 2013

  5. The metabolic response in fish to mildly elevated water temperature relates to species-dependent muscular concentrations of imidazole compounds and free amino acids.

    Science.gov (United States)

    Geda, Fikremariam; Declercq, Annelies M; Remø, Sofie C; Waagbø, Rune; Lourenço, Marta; Janssens, Geert P J

    2017-04-01

    Fish species show distinct differences in their muscular concentrations of imidazoles and free amino acids (FAA). This study was conducted to investigate whether metabolic response to mildly elevated water temperature (MEWT) relates to species-dependent muscular concentrations of imidazoles and FAA. Thirteen carp and 17 Nile tilapia, housed one per aquarium, were randomly assigned to either acclimation (25°C) or MEWT (30°C) for 14 days. Main muscular concentrations were histidine (HIS; P0.05), (NAH+HIS)/TAU ratio was markedly higher in carp versus tilapia, and decreased with MEWT only in carp (Pacids in carp metabolism (Pacids (NEFA) in carp (P=0.001), the latter shows that carp, being a fatter fish, more readily mobilises fat than tilapia at MEWT, which coincides with more intensive muscular mobilization of imidazoles. This study demonstrates that fish species differ in their metabolic response to MEWT, which is associated with species-dependent changes in muscle imidazole to taurine ratio. Copyright © 2017 Elsevier Ltd. All rights reserved.

  6. Synthesis and Characterization of 9-Phenyl-9H-purin-6-amines from 5-Amino-1-phenyl-1H-imidazole-4-carbonitriles

    Directory of Open Access Journals (Sweden)

    Asieh Yahyazadeh

    2007-01-01

    Full Text Available 9-Phenyl-9H-purin-6-amine derivatives have been synthesized in high yields by reaction between 5-amino-1-phenyl-1H-imidazole-4-carbonitrile with HC(OEt3 and Ac2O followed by reaction with ammonia.

  7. Measurement of enzyme activity.

    Science.gov (United States)

    Harris, T K; Keshwani, M M

    2009-01-01

    To study and understand the nature of living cells, scientists have continually employed traditional biochemical techniques aimed to fractionate and characterize a designated network of macromolecular components required to carry out a particular cellular function. At the most rudimentary level, cellular functions ultimately entail rapid chemical transformations that otherwise would not occur in the physiological environment of the cell. The term enzyme is used to singularly designate a macromolecular gene product that specifically and greatly enhances the rate of a chemical transformation. Purification and characterization of individual and collective groups of enzymes has been and will remain essential toward advancement of the molecular biological sciences; and developing and utilizing enzyme reaction assays is central to this mission. First, basic kinetic principles are described for understanding chemical reaction rates and the catalytic effects of enzymes on such rates. Then, a number of methods are described for measuring enzyme-catalyzed reaction rates, which mainly differ with regard to techniques used to detect and quantify concentration changes of given reactants or products. Finally, short commentary is given toward formulation of reaction mixtures used to measure enzyme activity. Whereas a comprehensive treatment of enzymatic reaction assays is not within the scope of this chapter, the very core principles that are presented should enable new researchers to better understand the logic and utility of any given enzymatic assay that becomes of interest.

  8. Assessing the structural conservation of protein pockets to study functional and allosteric sites: implications for drug discovery

    Directory of Open Access Journals (Sweden)

    Daura Xavier

    2010-03-01

    Full Text Available Abstract Background With the classical, active-site oriented drug-development approach reaching its limits, protein ligand-binding sites in general and allosteric sites in particular are increasingly attracting the interest of medicinal chemists in the search for new types of targets and strategies to drug development. Given that allostery represents one of the most common and powerful means to regulate protein function, the traditional drug discovery approach of targeting active sites can be extended by targeting allosteric or regulatory protein pockets that may allow the discovery of not only novel drug-like inhibitors, but activators as well. The wealth of available protein structural data can be exploited to further increase our understanding of allosterism, which in turn may have therapeutic applications. A first step in this direction is to identify and characterize putative effector sites that may be present in already available structural data. Results We performed a large-scale study of protein cavities as potential allosteric and functional sites, by integrating publicly available information on protein sequences, structures and active sites for more than a thousand protein families. By identifying common pockets across different structures of the same protein family we developed a method to measure the pocket's structural conservation. The method was first parameterized using known active sites. We characterized the predicted pockets in terms of sequence and structural conservation, backbone flexibility and electrostatic potential. Although these different measures do not tend to correlate, their combination is useful in selecting functional and regulatory sites, as a detailed analysis of a handful of protein families shows. We finally estimated the numbers of potential allosteric or regulatory pockets that may be present in the data set, finding that pockets with putative functional and effector characteristics are widespread across

  9. Electronic structure and (1)H NMR chemical shifts in host-guest complexes of cucurbit[6]uril and sym-tetramethyl cucurbit[6]uril with imidazole derivatives.

    Science.gov (United States)

    Dixit, Priyanka H; Pinjari, Rahul V; Gejji, Shridhar P

    2010-10-14

    Binding patterns and (1)H NMR chemical shifts in the complexes of protonated N-(4-hydroxylphenyl)imidazole (g1), N-(4-aminophenyl)imidazole (g2), 2-phenylimidazole (g3) guests with cucurbit[6]uril (CB[6]), and sym-substituted tetramethyl cucurbit[6]uril (TMeCB[6]) in the gas phase as well as in water have been investigated using the density functional theory. It has been shown that the inclusion complexes of g1 and g2 with CB[6] or TMeCB[6] exhibit selective encapsulation of the phenyl moiety with its substituents binding to portal oxygens on the lower rim of the host and imidazole protons facilitate C-H···O interactions externally with upper rim ureido oxygens. On the other hand, the lowest-energy g3 complex encapsulates the imidazole ring within the host, engendering N-H···O interactions with portal oxygens on the upper rim of the host with the phenyl ring residing outside the cavity owing to an absence of para-substituent and show qualitatively different host-guest binding patterns. Calculated (1)H NMR spectra of the complexes in water reveal shielding of phenyl ring protons within the host cavity which exhibit signals at 0.2-0.5 ppm, whereas the protons of the imidazole ring participating in hydrogen bonded interactions exhibit deshielding, and the corresponding (1)H NMR signals are downshifted by 1.1-1.5 ppm in the spectra compared to those in the unbound guest. (1)H NMR chemical shifts of inclusion complexes thus obtained are in consonant with δ(H) patterns observed in experiments reported in the literature.

  10. Deoxyribonucleotide pool analysis: functional association of thymidylate synthase with the other enzymes of DNA biosynthesis in mammalian cells

    International Nuclear Information System (INIS)

    Reddy, G.P.V.; Christiansen, E.

    1986-01-01

    Allosteric interaction between thymidylate synthase (TS) and the other enzymes of DNA biosynthesis was suggested from the authors observation that inhibitors of ribonucleotide reductase, topoisomerase of DNA polymerase-α inhibit TS in intact S phase CHEF/18 cells, but not in their soluble extracts. In addition the authors observed that 4'-(9-acridinylamino)-methanesulfon-m-anisidide (m-AMSA), a poison of topoisomerase II, had similar effects on TS activity in mammalian cells. They have examined if the inhibitory effects of these antimetabolites on TS is due to the accumulation of thymidine nucleotide(s) in intact cells, rather than to an allosteric interaction in the replitase complex. A novel method of nucleotide pool analysis revealed that in the presence of these antimetabolites the incorporation of radioactivity from 3 H-deoxyuridine (dUrd) into thymidine nucleotide pools inside the cell did not increase as compared to the control. Furthermore, TS activity as measured in-vitro was not inhibited by supraphysiological concentrations (50μM) of thymidine mono- or tri-phosphates. None of these antimetabolites dramatically influenced the uptake of dUrd and its subsequent phosphorylation to deoxyuridine monophosphate. Therefore, they suggest that the inhibitory effect of these antimetabolites is due to the functional association of their target enzymes with TS

  11. Intracellular calcium levels determine differential modulation of allosteric interactions within G protein-coupled receptor heteromers.

    Science.gov (United States)

    Navarro, Gemma; Aguinaga, David; Moreno, Estefania; Hradsky, Johannes; Reddy, Pasham P; Cortés, Antoni; Mallol, Josefa; Casadó, Vicent; Mikhaylova, Marina; Kreutz, Michael R; Lluís, Carme; Canela, Enric I; McCormick, Peter J; Ferré, Sergi

    2014-11-20

    The pharmacological significance of the adenosine A2A receptor (A2AR)-dopamine D2 receptor (D2R) heteromer is well established and it is being considered as an important target for the treatment of Parkinson’s disease and other neuropsychiatric disorders. However, the physiological factors that control its distinctive biochemical properties are still unknown. We demonstrate that different intracellular Ca2+ levels exert a differential modulation of A2AR-D2R heteromer-mediated adenylyl-cyclase and MAPK signaling in striatal cells. This depends on the ability of low and high Ca2+ levels to promote a selective interaction of the heteromer with the neuronal Ca2+-binding proteins NCS-1 and calneuron-1, respectively. These Ca2+-binding proteins differentially modulate allosteric interactions within the A2AR-D2R heteromer, which constitutes a unique cellular device that integrates extracellular (adenosine and dopamine) and intracellular (Ca+2) signals to produce a specific functional response.

  12. Structural basis for the cooperative allosteric activation of the free fatty acid receptor GPR40

    Energy Technology Data Exchange (ETDEWEB)

    Lu, Jun; Byrne, Noel; Wang, John; Bricogne, Gerard; Brown, Frank K.; Chobanian, Harry R.; Colletti, Steven L.; Di Salvo, Jerry; Thomas-Fowlkes, Brande; Guo, Yan; Hall, Dawn L.; Hadix, Jennifer; Hastings, Nicholas B.; Hermes, Jeffrey D.; Ho, Thu; Howard, Andrew D.; Josien, Hubert; Kornienko, Maria; Lumb, Kevin J.; Miller, Michael W.; Patel, Sangita B.; Pio, Barbara; Plummer, Christopher W.; Sherborne, Bradley S.; Sheth, Payal; Souza, Sarah; Tummala, Srivanya; Vonrhein, Clemens; Webb, Maria; Allen, Samantha J.; Johnston, Jennifer M.; Weinglass, Adam B.; Sharma, Sujata; Soisson, Stephen M. (Merck); (Globel Phasing)

    2017-06-05

    Clinical studies indicate that partial agonists of the G-protein-coupled, free fatty acid receptor 1 GPR40 enhance glucose-dependent insulin secretion and represent a potential mechanism for the treatment of type 2 diabetes mellitus. Full allosteric agonists (AgoPAMs) of GPR40 bind to a site distinct from partial agonists and can provide additional efficacy. We report the 3.2-Å crystal structure of human GPR40 (hGPR40) in complex with both the partial agonist MK-8666 and an AgoPAM, which exposes a novel lipid-facing AgoPAM-binding pocket outside the transmembrane helical bundle. Comparison with an additional 2.2-Å structure of the hGPR40–MK-8666 binary complex reveals an induced-fit conformational coupling between the partial agonist and AgoPAM binding sites, involving rearrangements of the transmembrane helices 4 and 5 (TM4 and TM5) and transition of the intracellular loop 2 (ICL2) into a short helix. These conformational changes likely prime GPR40 to a more active-like state and explain the binding cooperativity between these ligands.

  13. Characterization of an allosteric citalopram-binding site at the serotonin transporter

    DEFF Research Database (Denmark)

    Chen, Fenghua; Breum Larsen, Mads; Neubauer, Henrik Amtoft

    2005-01-01

    The serotonin transporter (SERT), which belongs to a family of       sodium/chloride-dependent transporters, is the major pharmacological       target in the treatment of several clinical disorders, including       depression and anxiety. In the present study we show that the dissociation......       rate, of [3H]S-citalopram from human SERT, is retarded by the presence of       serotonin, as well as by several antidepressants, when present in the       dissociation buffer. Dissociation of [3H]S-citalopram from SERT is most       potently inhibited by S-citalopram followed by R......-citalopram, sertraline,       serotonin and paroxetine. EC50 values for S- and R-citalopram are 3.6 +/-       0.4 microm and 19.4 +/- 2.3 microm, respectively. Fluoxetine, venlafaxine       and duloxetine have no significant effect on the dissociation of       [3H]S-citalopram. Allosteric modulation of dissociation...

  14. Conformational changes and allosteric communications in human serum albumin due to ligand binding.

    Science.gov (United States)

    Ahalawat, Navjeet; Murarka, Rajesh K

    2015-01-01

    It is well recognized that knowledge of structure alone is not sufficient to understand the fundamental mechanism of biomolecular recognition. Information of dynamics is necessary to describe motions involving relevant conformational states of functional importance. We carried out principal component analysis (PCA) of structural ensemble, derived from 84 crystal structures of human serum albumin (HSA) with different ligands and/or different conditions, to identify the functionally important collective motions, and compared with the motions along the low-frequency modes obtained from normal mode analysis of the elastic network model (ENM) of unliganded HSA. Significant overlap is observed in the collective motions derived from PCA and ENM. PCA and ENM analysis revealed that ligand selects the most favored conformation from accessible equilibrium structures of unliganded HSA. Further, we analyzed dynamic network obtained from molecular dynamics simulations of unliganded HSA and fatty acids- bound HSA. Our results show that fatty acids-bound HSA has more robust community network with several routes to communicate among different parts of the protein. Critical nodes (residues) identified from dynamic network analysis are in good agreement with allosteric residues obtained from sequence-based statistical coupling analysis method. This work underscores the importance of intrinsic structural dynamics of proteins in ligand recognition and can be utilized for the development of novel drugs with optimum activity.

  15. Allosteric modulation of alpha4beta2 nicotinic acetylcholine receptors by HEPES.

    Science.gov (United States)

    Weltzin, Maegan M; Huang, Yanzhou; Schulte, Marvin K

    2014-06-05

    A number of new positive allosteric modulators (PAMs) have been reported that enhance responses of neuronal alpha7 and alpha4beta2 nicotinic acetylcholine receptor subtypes to orthosteric ligands. PAMs represent promising new leads for the development of therapeutic agents for disorders involving alterations in nicotinic neurotransmission including Autism, Alzheimer's and Parkinson's disease. During our recent studies of alpha4beta2 PAMs, we identified a novel effect of 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (HEPES). The effects of HEPES were evaluated in a phosphate buffered recording solution using two-electrode voltage clamp techniques and alpha4beta2 and alpha7 nicotinic acetylcholine receptor subtypes expressed in Xenopus laevis oocytes. Acetylcholine induced responses of high-sensitivity alpha4beta2 receptors were potentiated 190% by co-exposure to HEPES. Responses were inhibited at higher concentrations (bell-shaped concentration/response curve). Coincidentally, at concentrations of HEPES typically used in oocyte recording (5-10mM), the potentiating effects of HEPES are matched by its inhibitory effects, thus producing no net effect. Mutagenesis results suggest HEPES potentiates the high-sensitivity stoichiometry of the alpha4beta2 receptors through action at the beta2+/beta2- interface and is dependent on residue beta2D218. HEPES did not potentiate low-sensitivity alpha4beta2 receptors and did not produce any observable effect on acetylcholine induced responses on alpha7 nicotinic acetylcholine receptors. Copyright © 2012 Elsevier B.V. All rights reserved.

  16. Allosteric modulation of alpha4beta2 nicotinic acetylcholine receptors by HEPES✩

    Science.gov (United States)

    Weltzin, Maegan M; Huang, Yanzhou; Schulte, Marvin K

    2013-01-01

    A number of new positive allosteric modulators (PAMs) have been reported that enhance responses of neuronal alpha7 and alpha4beta2 nicotinic acetylcholine receptor subtypes to orthosteric ligands. PAMs represent promising new leads for the development of therapeutic agents for disorders involving alterations in nicotinic neurotransmission including Autism, Alzheimer's and Parkinson's disease. During our recent studies of alpha4beta2 PAMs, we identified a novel effect of 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (HEPES). The effects of HEPES were evaluated in a phosphate buffered recording solution using two-electrode voltage clamp techniques and alpha4beta2 and alpha7 nicotinic acetylcholine receptor subtypes expressed in Xenopus laevis oocytes. Acetylcholine induced responses of high-sensitivity alpha4beta2 receptors were potentiated 190% by co-exposure to HEPES. Responses were inhibited at higher concentrations (bell-shaped concentration/response curve). Coincidentally, at concentrations of HEPES typically used in oocyte recording (5–10 mM), the potentiating effects of HEPES are matched by its inhibitory effects, thus producing no net effect. Mutagenesis results suggest HEPES potentiates the high-sensitivity stoichiometry of the alpha4beta2 receptors through action at the beta2+/beta2− interface and is dependent on residue beta2D218. HEPES did not potentiate low-sensitivity alpha4beta2 receptors and did not produce any observable effect on acetylcholine induced responses on alpha7 nicotinic acetylcholine receptors. PMID:22732654

  17. Models, theory structure and mechanisms in biochemistry: The case of allosterism.

    Science.gov (United States)

    Alleva, Karina; Díez, José; Federico, Lucia

    2017-06-01

    From the perspective of the new mechanistic philosophy, it has been argued that explanatory causal mechanisms in some special sciences such as biochemistry and neurobiology cannot be captured by any useful notion of theory, or at least by any standard notion. The goal of this paper is to show that a model-theoretic notion of theory, and in particular the structuralist notion of a theory-net already applied to other unified explanatory theories, adequately suits the MWC allosteric mechanism explanatory set-up. We also argue, contra some mechanistic claims questioning the use of laws in biological explanations, that the theory reconstructed in this way essentially contains non-accidental regularities that qualify as laws, and that taking into account these lawful components, it is possible to explicate the unified character of the theory. Finally, we argue that, contrary to what some mechanists also claim, functional explanations that do not fully specify the mechanistic structure are not defective or incomplete in any relevant sense, and that functional components are perfectly explanatory. The conclusion is that, as some authors have emphasized in other fields (Walmsley 2008), particular elements of traditional approaches do not contradict but rather complement the new mechanist philosophy, and taken together they may offer a more complete understanding of special sciences and the variety of explanations they provide. Copyright © 2017 Elsevier Ltd. All rights reserved.

  18. RET Functions as a Dual-Specificity Kinase that Requires Allosteric Inputs from Juxtamembrane Elements

    Directory of Open Access Journals (Sweden)

    Iván Plaza-Menacho

    2016-12-01

    Full Text Available Receptor tyrosine kinases exhibit a variety of activation mechanisms despite highly homologous catalytic domains. Such diversity arises through coupling of extracellular ligand-binding portions with highly variable intracellular sequences flanking the tyrosine kinase domain and specific patterns of autophosphorylation sites. Here, we show that the juxtamembrane (JM segment enhances RET catalytic domain activity through Y687. This phospho-site is also required by the JM region to rescue an otherwise catalytically deficient RET activation-loop mutant lacking tyrosines. Structure-function analyses identified interactions between the JM hinge, αC helix, and an unconventional activation-loop serine phosphorylation site that engages the HRD motif and promotes phospho-tyrosine conformational accessibility and regulatory spine assembly. We demonstrate that this phospho-S909 arises from an intrinsic RET dual-specificity kinase activity and show that an equivalent serine is required for RET signaling in Drosophila. Our findings reveal dual-specificity and allosteric components for the mechanism of RET activation and signaling with direct implications for drug discovery.

  19. Profiling of engineering hotspots identifies an allosteric CRISPR-Cas9 switch

    Science.gov (United States)

    Oakes, Benjamin L; Nadler, Dana C.; Flamholz, Avi; Fellmann, Christof; Staahl, Brett T.; Doudna, Jennifer A.; Savage, David F.

    2016-01-01

    The CRISPR-associated protein Cas9 from Streptococcus pyogenes is an RNA-guided DNA endonuclease with widespread utility for genome modification. However, the structural constraints limiting the engineering of Cas9 have not been determined. Here we experimentally profile Cas9 using randomized insertional mutagenesis and delineate hotspots in the structure capable of tolerating insertions of a PDZ domain without disrupting the enzyme’s binding and cleavage functions. Orthogonal domains or combinations of domains can be inserted into the identified sites with minimal functional consequence. To illustrate the utility of the identified sites, we construct an allosterically regulated Cas9 by insertion of the Estrogen Receptor α Ligand Binding Domain. This protein displayed robust, ligand-dependent activation in prokaryotic and eukaryotic cells, establishing a versatile one-component system for inducible and reversible Cas9 activation. Thus, domain insertion profiling facilitates the rapid generation of new Cas9 functionalities and provides useful data for future engineering of Cas9. PMID:27136077

  20. Structural Dynamics Control Allosteric Activation of Cytohesin Family Arf GTPase Exchange Factors

    Energy Technology Data Exchange (ETDEWEB)

    Malaby, Andrew W.; Das, Sanchaita; Chakravarthy, Srinivas; Irving, Thomas C.; Bilsel, Osman; Lambright, David G.

    2018-01-01

    Membrane dynamic processes including vesicle biogenesis depend on Arf guanosine triphosphatase (GTPase) activation by guanine nucleotide exchange factors (GEFs) containing a catalytic Sec7 domain and a membrane-targeting module such as a pleckstrin homology (PH) domain. The catalytic output of cytohesin family Arf GEFs is controlled by autoinhibitory interactions that impede accessibility of the exchange site in the Sec7 domain. These restraints can be relieved through activator Arf-GTP binding to an allosteric site comprising the PH domain and proximal autoinhibitory elements (Sec7-PH linker and C-terminal helix). Small-angle X-ray scattering and negative-stain electron microscopy were used to investigate the structural organization and conformational dynamics of cytohesin-3 (Grp1) in autoinhibited and active states. The results support a model in which hinge dynamics in the autoinhibited state expose the activator site for Arf-GTP binding, while subsequent C-terminal helix unlatching and repositioning unleash conformational entropy in the Sec7-PH linker to drive exposure of the exchange site.

  1. GABAB receptors as a therapeutic strategy in substance use disorders: focus on positive allosteric modulators.

    Science.gov (United States)

    Filip, Małgorzata; Frankowska, Małgorzata; Sadakierska-Chudy, Anna; Suder, Agata; Szumiec, Lukasz; Mierzejewski, Paweł; Bienkowski, Przemyslaw; Przegaliński, Edmund; Cryan, John F

    2015-01-01

    γ-Aminobutyric acid B (GABAB) receptors and their ligands are postulated as potential therapeutic targets for the treatment of several brain disorders, including drug dependence. Over the past fifteen years positive allosteric modulators (PAMs) have emerged that enhance the effects of GABA at GABAB receptors and which may have therapeutic effects similar to those of agonists but with superior side-effect profiles. This review summarizes current preclinical evidence supporting a role of GABAB receptor PAMs in drug addiction in several paradigms with relevance to reward processes and drug abuse liability. Extensive behavioral research in recent years has indicated that PAMs of GABAB receptors may have a therapeutic efficacy in cocaine, nicotine, amphetamine and alcohol dependence. The magnitude of the effects observed are similar to that of the clinically approved drug baclofen, an agonist at GABAB receptors. Moreover, given that anxiolytic effects are also reported with such ligands they may also benefit in mitigating the withdrawal from drugs of abuse. In summary, a wealth of data now supports the benefits of GABAB receptor PAMs and clinical validation is now warranted. Copyright © 2014. Published by Elsevier Ltd.

  2. Allosteric heat shock protein 70 inhibitors block hepatitis C virus assembly

    Science.gov (United States)

    Khachatoorian, Ronik; Riahi, Rana; Ganapathy, Ekambaram; Shao, Hao; Wheatley, Nicole M.; Sundberg, Christopher; Jung, Chun-Ling; Ruchala, Piotr; Dasgupta, Asim; Arumugaswami, Vaithilingaraja; Gestwicki, Jason E.; French, Samuel W.

    2016-01-01

    The human molecular chaperones heat shock protein 70 (Hsp70) and heat shock cognate protein 70 (Hsc70) bind to the hepatitis C viral nonstructural protein 5A (NS5A) and regulate its activity. Specifically, Hsp70 is involved in NS5A-augmented internal ribosomal entry site (IRES)-mediated translation of the viral genome, whilst Hsc70 appears to be primarily important for intracellular infectious virion assembly. To better understand the importance of these two chaperones in the viral life cycle, infected human cells were treated with allosteric Hsp70/Hsc70 inhibitors (AHIs). Treatment with AHIs significantly reduced the production of intracellular virus at concentrations that were non-toxic to human hepatoma Huh7.5 cells. The supernatant of treated cultures was then used to infect naïve cells, revealing that AHIs also lowered levels of secreted virus. In contrast to their effects on virion assembly, AHIs did not impact the stability of NS5A or viral protein translation in IRES assays. These results suggest that Hsc70 plays a particularly important and sensitive role in virion assembly. Indeed, it was found that combination of AHIs with a peptide-based viral translation inhibitor exhibited additive antiviral activity. Together these results suggest that the host Hsc70 is a new antiviral target and that its inhibitors utilise a new mechanism of action. PMID:27013001

  3. Thiophene antibacterials that allosterically stabilize DNA-cleavage complexes with DNA gyrase.

    Science.gov (United States)

    Chan, Pan F; Germe, Thomas; Bax, Benjamin D; Huang, Jianzhong; Thalji, Reema K; Bacqué, Eric; Checchia, Anna; Chen, Dongzhao; Cui, Haifeng; Ding, Xiao; Ingraham, Karen; McCloskey, Lynn; Raha, Kaushik; Srikannathasan, Velupillai; Maxwell, Anthony; Stavenger, Robert A

    2017-05-30

    A paucity of novel acting antibacterials is in development to treat the rising threat of antimicrobial resistance, particularly in Gram-negative hospital pathogens, which has led to renewed efforts in antibiotic drug discovery. Fluoroquinolones are broad-spectrum antibacterials that target DNA gyrase by stabilizing DNA-cleavage complexes, but their clinical utility has been compromised by resistance. We have identified a class of antibacterial thiophenes that target DNA gyrase with a unique mechanism of action and have activity against a range of bacterial pathogens, including strains resistant to fluoroquinolones. Although fluoroquinolones stabilize double-stranded DNA breaks, the antibacterial thiophenes stabilize gyrase-mediated DNA-cleavage complexes in either one DNA strand or both DNA strands. X-ray crystallography of DNA gyrase-DNA complexes shows the compounds binding to a protein pocket between the winged helix domain and topoisomerase-primase domain, remote from the DNA. Mutations of conserved residues around this pocket affect activity of the thiophene inhibitors, consistent with allosteric inhibition of DNA gyrase. This druggable pocket provides potentially complementary opportunities for targeting bacterial topoisomerases for antibiotic development.

  4. Modular Assembly of Allosteric MEK Inhibitor Structural Elements Unravels Potency and Feedback-Modulation Handles.

    Science.gov (United States)

    Hartung, Ingo V; Pühler, Florian; Neuhaus, Roland; Scholz, Arne; Siemeister, Gerhard; Geisler, Jens; Hillig, Roman C; von Ahsen, Oliver; Hitchcock, Marion

    2015-12-01

    Having recently identified a so-far unexplored area adjacent to the known binding site of allosteric mitogen-activated protein kinase kinase (MEK) inhibitors, we now report an extension of these studies by combining our new side chains with different MEK inhibitor cores in a modular manner. Replacement of the amide headgroup with inverse sulfonamides resulted in the identification of new MEK inhibitors with at least 10-fold higher cellular potency against K-Ras-mutated tumor cells. A selected inhibitor from this new series retained the favorable pharmacokinetic profile of its predecessor in rodent and non-rodent species and displayed significant in vivo efficacy at once-daily oral doses of 0.25-1 mg kg(-1) in a K-Ras-mutated xenograft model. The brain penetration potential of this analogue was significantly attenuated relative to PD325901. In a second series, the central fluorophenyl core was replaced by a pyridine moiety which gave rise to a similar boost in cellular potency. Most notably, analogues from this second series do not show MEK feedback phosphorylation in K-Ras-mutated A549 cells. Our results complement recent reports on the structural intricacies of MEK-Raf feedback interactions. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  5. A Positive Allosteric Modulator of the Serotonin 5-HT2C Receptor for Obesity.

    Science.gov (United States)

    García-Cárceles, Javier; Decara, Juan M; Vázquez-Villa, Henar; Rodríguez, Ramón; Codesido, Eva; Cruces, Jacobo; Brea, José; Loza, María I; Alén, Francisco; Botta, Joaquin; McCormick, Peter J; Ballesteros, Juan A; Benhamú, Bellinda; Rodríguez de Fonseca, Fernando; López-Rodríguez, María L

    2017-12-14

    The 5-HT 2C R agonist lorcaserin, clinically approved for the treatment of obesity, causes important side effects mainly related to subtype selectivity. In the search for 5-HT 2C R allosteric modulators as safer antiobesity drugs, a chemical library from Vivia Biotech was screened using ExviTech platform. Structural modifications of identified hit VA240 in synthesized analogues 6-41 afforded compound 11 (N-[(1-benzyl-1H-indol-3-yl)methyl]pyridin-3-amine, VA012), which exhibited dose-dependent enhancement of serotonin efficacy, no significant off-target activities, and low binding competition with serotonin or other orthosteric ligands. PAM 11 was very active in feeding inhibition in rodents, an effect that was not related to the activation of 5-HT 2A R. A combination of 11 with the SSRI sertraline increased the anorectic effect. Subchronic administration of 11 reduced food intake and body weight gain without causing CNS-related malaise. The behavior of compound 11 identified in this work supports the interest of a serotonin 5-HT 2C R PAM as a promising therapeutic approach for obesity.

  6. Ligand-specific allosteric regulation of coactivator functions of androgen receptor in prostate cancer cells

    Science.gov (United States)

    Baek, Sung Hee; Ohgi, Kenneth A.; Nelson, Charles A.; Welsbie, Derek; Chen, Charlie; Sawyers, Charles L.; Rose, David W.; Rosenfeld, Michael G.

    2006-01-01

    The androgen receptor not only mediates prostate development but also serves as a key regulator of primary prostatic cancer growth. Although initially responsive to selective androgen receptor modulators (SARMs), which cause recruitment of the nuclear receptor–corepressor (N-CoR) complex, resistance invariably occurs, perhaps in response to inflammatory signals. Here we report that dismissal of nuclear receptor–corepressor complexes by specific signals or androgen receptor overexpression results in recruitment of many of the cohorts of coactivator complexes that permits SARMs and natural ligands to function as agonists. SARM-bound androgen receptors appear to exhibit failure to recruit specific components of the coactivators generally bound by liganded nuclear receptors, including cAMP response element-binding protein (CBP)/p300 or coactivator-associated arginine methyltransferase 1 (CARM1) to the SARM-bound androgen receptor, although still causing transcriptional activation of androgen receptor target genes. SARM-bound androgen receptors use distinct LXXLL (L, leucine; X, any amino acid) helices in the p160 nuclear receptor interaction domains that may impose selective allosteric effects, providing a component of the molecular basis of differential responses to different classes of ligands by androgen receptor. PMID:16492776

  7. High-resolution crystal structure of deoxy hemoglobin complexed with a potent allosteric effector.

    Science.gov (United States)

    Safo, M K; Moure, C M; Burnett, J C; Joshi, G S; Abraham, D J

    2001-05-01

    The crystal structure of human deoxy hemoglobin (Hb) complexed with a potent allosteric effector (2-[4-[[(3,5-dimethylanilino)carbonyl]methyl]phenoxy]-2-methylpropionic acid) = RSR-13) is reported at 1.85 A resolution. Analysis of the hemoglobin:effector complex indicates that two of these molecules bind to the central water cavity of deoxy Hb in a symmetrical fashion, and that each constrains the protein by engaging in hydrogen bonding and hydrophobic interactions with three of its four subunits. Interestingly, we also find that water-mediated interactions between the bound effectors and the protein make significant contributions to the overall binding. Physiologically, the interaction of RSR-13 with Hb results in increased oxygen delivery to peripheral tissues. Thus, this compound has potential therapeutic application in the treatment of hypoxia, ischemia, and trauma-related blood loss. Currently, RSR-13 is in phase III clinical trials as a radiosensitizing agent in the treatment of brain tumors. A detailed structural analysis of this compound complexed with deoxy Hb has important implications for the rational design of future analogs.

  8. An allosteric model of the inositol trisphosphate receptor with nonequilibrium binding

    Science.gov (United States)

    Jia, Chen; Jiang, Daquan; Qian, Minping

    2014-10-01

    The inositol trisphosphate receptor (IPR) is a crucial ion channel that regulates the Ca2+ influx from the endoplasmic reticulum (ER) to the cytoplasm. A thorough study of the IPR channel contributes to a better understanding of calcium oscillations and waves. It has long been observed that the IPR channel is a typical biological system which performs adaptation. However, recent advances on the physical essence of adaptation show that adaptation systems with a negative feedback mechanism, such as the IPR channel, must break detailed balance and always operate out of equilibrium with energy dissipation. Almost all previous IPR models are equilibrium models assuming detailed balance and thus violate the dissipative nature of adaptation. In this article, we constructed a nonequilibrium allosteric model of single IPR channels based on the patch-clamp experimental data obtained from the IPR in the outer membranes of isolated nuclei of the Xenopus oocyte. It turns out that our model reproduces the patch-clamp experimental data reasonably well and produces both the correct steady-state and dynamic properties of the channel. Particularly, our model successfully describes the complicated bimodal [Ca2+] dependence of the mean open duration at high [IP3], a steady-state behavior which fails to be correctly described in previous IPR models. Finally, we used the patch-clamp experimental data to validate that the IPR channel indeed breaks detailed balance and thus is a nonequilibrium system which consumes energy.

  9. D-glucose-6-phosphate dehydrogenase (Entner-Doudoroff enzyme) from Pseudomonas fluorescens

    International Nuclear Information System (INIS)

    Lessmann, D.; Schimz, K.L.; Kurz, G.

    1975-01-01

    The existence of two different D-glucose-6-phosphate dehydrogenases in Pseudomonas fluorescens has been demonstrated. Based on their different specificity and their different metabolic regulation one enzyme is appointed to the Entner-Doudoroff pathway and the other to the hexose monophosphate pathway. A procedure is described for the isolation of that D-glucose-6-phosphate dehydrogenase which forms part of the Entner-Doudoroff pathway (Entner-Doudoroff enzyme). A 950-fold purification was achieved with an overall yield of 44%. The final preparation, having a specific activity of about 300μmol NADH formed per min per mg protein, was shown to be homogeneous. The molecular weight of the Entner-Doudoroff enzyme has been determined to be 220,000 by gel permeation chromatography, and that of the other enzyme (Zwischenferment) has been shown to be 265,000. The pI of the Entner-Doudoroff enzyme has been shown to be 5.24 and that of the Zwischenferment 4.27. The Entner-Doudoroff enzyme is stable in the range of pH 6 to 10.5 and shows its maximal acivity at pH 8.9. The Entner-Doudoroff enzyme showed specificity for NAD + as well as for NADP + and exhibited homotropic effects for D-glucose 6-phosphate. It is inhibited by ATP which acts as a negative allosteric effector. Other nucleoside triphosphates as well as ADP are also inhibitory. The enzyme catalyzes the transfer of the axial hydrogen at carbon-1 of β-D-glucopyranose 6-phosphate to the si face of carbon-4 of the nicotinamide ring and must be classified as B-side stereospecific dehydrogenase. (orig.) [de

  10. Syntheses and structure characterization of ten acid-base hybrid crystals based on imidazole derivatives and mineral acids

    Science.gov (United States)

    Hu, Kaikai; Deng, Bowen; Jin, Shouwen; Ding, Aihua; Jin, Shide; Zhu, Jin; Zhang, Huan; Wang, Daqi

    2018-04-01

    Cocrystallization of the imidazole derivatives with a series of mineral acids gave a total of ten hybrid salts with the compositions: [(H2bzm)(Cl)2·3H2O] (1), [(H2bzm)(ClO4)2] (2), [(H2bze)(Cl)2·2H2O] (3), [(H2bze)(Br)2·2H2O] (4), [(H2bzp)(Cl)2·4H2O] (5), [(H2bzp)(Br)2·4H2O] (6), (2-(imidazol-1-yl)-1-phenylethanone): (phosphoric acid) [(Himpeta)+(H2PO4)-] (7), [(H2impd)(Br)2] (8), [(H2impd)(ClO4)2] (9), and [(Hbzml)(Cl)] (10). The ten salts have been characterised by X-ray diffraction analysis, IR, and elemental analysis, and the melting points of all the salts were also reported. And their structural and supramolecular aspects are fully analyzed. The result reveals that among the ten investigated crystals the ring N atoms of the imidazole are protonated when the acids are deprotonated, and the crystal packing is interpreted in terms of the strong charge-assisted classical H-bonds between the NH+ and deprotonated acidic groups. Further analysis of the crystal packing of the salts indicated that a different set of additional CHsbnd O, CH2sbnd O, CHsbnd Cl, CH2sbnd Cl, CHsbnd N, CHsbnd Br, CH2sbnd Br, Osbnd O, O-π, Br-π, CH-π, and π-π associations contribute to the stabilization and expansion of the total high-dimensional frameworks. For the coexistence of the various weak nonbonding interactions these structures adopted homo or hetero supramolecular synthons or both. Some classical supramolecular synthons, such as R21(7), R22(7), R22(8), and R42(8), usually observed in the organic solids, were again shown to be involved in constructing some of these H-bonding networks.

  11. Random-walk enzymes

    Science.gov (United States)

    Mak, Chi H.; Pham, Phuong; Afif, Samir A.; Goodman, Myron F.

    2015-01-01

    Enzymes that rely on random walk to search for substrate targets in a heterogeneously dispersed medium can leave behind complex spatial profiles of their catalyzed conversions. The catalytic signatures of these random-walk enzymes are the result of two coupled stochastic processes: scanning and catalysis. Here we develop analytical models to understand the conversion profiles produced by these enzymes, comparing an intrusive model, in which scanning and catalysis are tightly coupled, against a loosely coupled passive model. Diagrammatic theory and path-integral solutions of these models revealed clearly distinct predictions. Comparison to experimental data from catalyzed deaminations deposited on single-stranded DNA by the enzyme activation-induced deoxycytidine deaminase (AID) demonstrates that catalysis and diffusion are strongly intertwined, where the chemical conversions give rise to new stochastic trajectories that were absent if the substrate DNA was homogeneous. The C → U deamination profiles in both analytical predictions and experiments exhibit a strong contextual dependence, where the conversion rate of each target site is strongly contingent on the identities of other surrounding targets, with the intrusive model showing an excellent fit to the data. These methods can be applied to deduce sequence-dependent catalytic signatures of other DNA modification enzymes, with potential applications to cancer, gene regulation, and epigenetics. PMID:26465508

  12. Random-walk enzymes

    Science.gov (United States)

    Mak, Chi H.; Pham, Phuong; Afif, Samir A.; Goodman, Myron F.

    2015-09-01

    Enzymes that rely on random walk to search for substrate targets in a heterogeneously dispersed medium can leave behind complex spatial profiles of their catalyzed conversions. The catalytic signatures of these random-walk enzymes are the result of two coupled stochastic processes: scanning and catalysis. Here we develop analytical models to understand the conversion profiles produced by these enzymes, comparing an intrusive model, in which scanning and catalysis are tightly coupled, against a loosely coupled passive model. Diagrammatic theory and path-integral solutions of these models revealed clearly distinct predictions. Comparison to experimental data from catalyzed deaminations deposited on single-stranded DNA by the enzyme activation-induced deoxycytidine deaminase (AID) demonstrates that catalysis and diffusion are strongly intertwined, where the chemical conversions give rise to new stochastic trajectories that were absent if the substrate DNA was homogeneous. The C →U deamination profiles in both analytical predictions and experiments exhibit a strong contextual dependence, where the conversion rate of each target site is strongly contingent on the identities of other surrounding targets, with the intrusive model showing an excellent fit to the data. These methods can be applied to deduce sequence-dependent catalytic signatures of other DNA modification enzymes, with potential applications to cancer, gene regulation, and epigenetics.

  13. Enhancement of photoassimilate utilization by manipulation of starch regulatory enzymes

    Energy Technology Data Exchange (ETDEWEB)

    Okita, Thomas W. [Washington State Univ., Pullman, WA (United States)

    2016-05-11

    ADPglucose pyrophosphorylase (AGPase) and the plastidial starch phosphorylase1 (Pho1) are two regulatory enzymes whose catalytic activities are essential for starch granule synthesis. Conversion of the pre-starch granule to the mature form is dependent on AGPase, which produces ADPglucose, the substrate used by starch synthases. The catalytic activity of AGPase is controlled by small effector molecules and a prime goal of this project was to decipher the role of the two subunit types that comprise the heterotetrameric enzyme structure. Extensive genetic and biochemical studies showed that catalysis was contributed mainly by the small subunit although the large subunit was required for maximum activity. Both subunits were needed for allosteric regulatory properties. We had also demonstrated that the AGPase catalyzed reaction limits the amount of starch accumulation in developing rice seeds and that carbon flux into rice seed starch can be increased by expression of a cytoplasmic-localized, up-regulated bacterial AGPase enzyme form. Results of subsequent physiological and metabolite studies showed that the AGPase reaction is no longer limiting in the AGPase transgenic rice lines and that one or more downstream processes prevent further increases in starch biosynthesis. Further studies showed that over-production of ADPglucose dramatically alters the gene program during rice seed development. Although the expression of nearly all of the genes are down-regulated, levels of a starch binding domain containing protein (SBDCP) are elevated. This SBDCP was found to bind to and inhibit the catalytic activity of starch synthase III and, thereby preventing maximum starch synthesis from occurring. Surprisingly, repression of SBDCP elevated expression of starch synthase III resulting in increasing rice grain weight. A second phase of this project examined the structure-function of Pho1, the enzyme required during the initial phase of pre-starch granule formation and its

  14. Computational Analysis of Residue Interaction Networks and Coevolutionary Relationships in the Hsp70 Chaperones: A Community-Hopping Model of Allosteric Regulation and Communication.

    Directory of Open Access Journals (Sweden)

    Gabrielle Stetz

    2017-01-01

    Full Text Available Allosteric interactions in the Hsp70 proteins are linked with their regulatory mechanisms and cellular functions. Despite significant progress in structural and functional characterization of the Hsp70 proteins fundamental questions concerning modularity of the allosteric interaction networks and hierarchy of signaling pathways in the Hsp70 chaperones remained largely unexplored and poorly understood. In this work, we proposed an integrated computational strategy that combined atomistic and coarse-grained simulations with coevolutionary analysis and network modeling of the residue interactions. A novel aspect of this work is the incorporation of dynamic residue correlations and coevolutionary residue dependencies in the construction of allosteric interaction networks and signaling pathways. We found that functional sites involved in allosteric regulation of Hsp70 may be characterized by structural stability, proximity to global hinge centers and local structural environment that is enriched by highly coevolving flexible residues. These specific characteristics may be necessary for regulation of allosteric structural transitions and could distinguish regulatory sites from nonfunctional conserved residues. The observed confluence of dynamics correlations and coevolutionary residue couplings with global networking features may determine modular organization of allosteric interactions and dictate localization of key mediating sites. Community analysis of the residue interaction networks revealed that concerted rearrangements of local interacting modules at the inter-domain interface may be responsible for global structural changes and a population shift in the DnaK chaperone. The inter-domain communities in the Hsp70 structures harbor the majority of regulatory residues involved in allosteric signaling, suggesting that these sites could be integral to the network organization and coordination of structural changes. Using a network-based formalism of

  15. Enzyme recycling in lignocellulosic biorefineries

    DEFF Research Database (Denmark)

    Jørgensen, Henning; Pinelo, Manuel

    2017-01-01

    platform. Cellulases are the most important enzymes required in this process, but the complex nature of lignocellulose requires several other enzymes (hemicellulases and auxiliary enzymes) for efficient hydrolysis. Enzyme recycling increases the catalytic productivity of the enzymes by reusing them...... upscaled and tested in industrial settings, mainly because of many difficulties with recycling of enzymes from the complex lignocellulose hydrolyzate at industrially relevant conditions, i.e., high solids loadings. The challenges are associated with the large number of different enzymes required...... for efficient hydrolysis, enzyme stability, and the detrimental interaction between enzyme and lignin. This review provides a comprehensive overview of the various methods for enzyme recovery and recycling, for example recycling of free enzymes, readsorption to fresh material, recycling of solids, membrane...

  16. Cytoprotection of human endothelial cells against oxidative stress by 1-[2-cyano-3,12-dioxooleana-1,9(11)-dien-28-oyl]imidazole (CDDO-Im): application of systems biology to understand the mechanism of action.

    Science.gov (United States)

    Wang, Xinyu; Bynum, James A; Stavchansky, Solomon; Bowman, Phillip D

    2014-07-05

    Cellular damage from oxidative stress, in particular following ischemic injury, occurs during heart attack, stroke, or traumatic injury, and is potentially reducible with appropriate drug treatment. We previously reported that caffeic acid phenethyl ester (CAPE), a plant-derived polyphenolic compound, protected human umbilical vein endothelial cells (HUVEC) from menadione-induced oxidative stress and that this cytoprotective effect was correlated with the capacity to induce heme oxygenase-1 (HMOX1) and its protein product, a phase II cytoprotective enzyme. To further improve this cytoprotective effect, we studied a synthetic triterpenoid, 1-[2-cyano-3,12-dioxooleana-1,9(11)-dien-28-oyl]imidazole (CDDO-Im), which is known as a potent phase II enzyme inducer with antitumor and anti-inflammatory activities, and compared it to CAPE. CDDO-Im at 200nM provided more protection to HUVEC against oxidative stress than 20μM CAPE. We explored the mechanism of CDDO-Im cytoprotection with gene expression profiling and pathway analysis and compared to that of CAPE. In addition to potent up-regulation of HMOX1, heat shock proteins (HSP) were also found to be highly induced by CDDO-Im in HUVEC. Pathway analysis results showed that transcription factor Nrf2-mediated oxidative stress response was among the top canonical pathways commonly activated by both CDDO-Im and CAPE. Compared to CAPE, CDDO-Im up-regulated more HSP and some of them to a much higher extent. In addition, CDDO-Im treatment affected Nrf2 pathway more significantly. These findings may provide an explanation why CDDO-Im is a more potent cytoprotectant than CAPE against oxidative stress in HUVEC. Copyright © 2014 Elsevier B.V. All rights reserved.

  17. COMPLEXES DE CUIVRE D’INTERET BIOINORGANIQUE MODELISANT LES METALLO-ENZYMES : SYNTHESE ET CARACTERISATION DES COMPLEXES DE CUIVRE(II) AVEC DES LIGANDS DERIVES DES IMIDAZOLES

    OpenAIRE

    BELFILALI, Imane

    2010-01-01

    La chimie de coordination est une discipline qui fait l’interface entre la chimie organique et la chimie inorganique. Elle a connue un développement tant dans le domaine de la chimie structurale et analytique que dans celui des applications biologiques.

  18. INHIBITORY ACTIVITY OF AN IMIDAZOLE COMPOUND ON ECDYSIOSYNTHETIC ORGANS IN MEALWORMS UNDER IN VIVO AND IN VITRO CONDITIONS

    Directory of Open Access Journals (Sweden)

    N SOLTANI-MAZOUNI

    2000-12-01

    Full Text Available KK-42, an imidazole derivative was tested on adult females of Tenebrio molitor L. (Insecta: Coleoptera. The compound was applied topically (1, 5, 10 mg/insect on 0- or 2-day old adult females or added to the culture medium (1 and 10 mM of abdominal sternites explanted from newly ecdysed pupae or ovaries removed from 2- and 4-day old adult females. Ecdysteroid measurements using an enzymo-immunoassay demonstrated that this compound applied on newly emerged adult females reduced the hormonal amounts in ovaries. However, when applied later, i.e. on 2-day old females corresponding to the beginning of the vitellogenesis, it had no significant effect on the amount of ovarian ecdysteroids with the lowest dose. Finally, the compound was also tested on the in vitro production of ecdysteroids. The amount of ecdysteroid released into the culture medium by ovaries or integumental explants were significantly reduced by KK-42.

  19. Poly[diaquabis[μ-1-hydroxy-2-(imidazol-3-ium-1-ylethane-1,1-diyldiphosphonato]tricopper(II

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    Guanfang Su

    2010-12-01

    Full Text Available In the title coordination polymer, [Cu3(C5H7N2O7P22(H2O2]n, one CuII atom is five-coordinated by five O atoms from three 1-hydroxy-2-(imidazol-3-ium-1-ylethane-1,1-diyldiphosphonate (L ligands in a distorted square-pyramidal geometry. The other CuII atom, lying on an inversion center, is six-coordinated in a distorted octahedral geometry by four O atoms from two L ligands and two O atoms from two water molecules. The five-coordinated CuII atoms are linked by phosphonate O atoms of the L ligands, forming a polymeric chain. These chains are further linked by the six-coordinated Cu atoms into a layer parallel to (overline{1}01. N—H...O and O—H...O hydrogen bonds connect the layers into a three-dimensional supramolecular structure.

  20. SYNTHESIS AND STUDY OF ANTIOXIDANT ACTIVITY OF [(1-ARYL-5-FORMYL-1H-IMIDAZOLE-4-ILTHIO]PROPIONIC ACIDS

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    A. O. Palamar

    2014-12-01

    Full Text Available Introduction. Derivatives of imidazole belong to the promising group of compounds for antioxidant activity study, due to the series of recent publications. This is defined by special features of their structure, specific reactivity and significant potential of pharmacological action. Earlier during process of looking for new antioxidants we studied significant amount of imidazole derivatives, among which the [(1-aryl-5-formylimidazole-4-ilthio]acetic acids structurally modified by the formyl group and thioacetic acid fragment, are especially worth noting. The purpose of the study. Synthesis of [(1-aryl-5-formylimidazole-4-ilthio]propionic acids and comparison of their antioxidant effect with [(1-aryl-5-formylimidazole-4-ilthio]acetic acids with to identify prospects of in-depth study of the most active compounds as antioxidants. Materials and methods. The method based on interaction of available 4-chloro-5-formylimidazoles with thiopropionic acid was proposed for the synthesis of [(1-aryl-5-formylimidazole-4-ilthio]propionic acids. The reaction takes place in ethanol in presence of potassium hydroxide and leads to the target compounds with yields of 81-86%. The study of antioxidant activity of synthesized compounds was conducted in vitro by speed inhibition value of rats’ liver endogenous lipids ascorbate-dependent peroxide oxidation. It was determined by concentration of one of the final products of free radical oxidation of lipids (FROL – maleic aldehyde (MA in the investigated sample. Concentrations of synthesized compounds were chosen within concentrations which were studied for thiotriazolin (manufactured by corporation “Arterium”, Ukraine, solution for injection, 25 mg/ml. The results of the study and their discussion. Preparative method for the synthesis of [(1-aryl-5-formylimidazole-4-ilthio]propionic acids has been designed. Imidazolylthiopropionic acids have been synthesized; they are crystalline compounds, of light