WorldWideScience

Sample records for pseudo-peptide binding mode

  1. Inhibition of Metalloprotease Botulinum Serotype A from a Pseudo-Peptide Binding Mode to a Small Molecule that is Active in Primary Neurons

    Science.gov (United States)

    2007-02-16

    then with laminin. Cultures were incubated overnight at 37 °C prior to intoxication . Microscopy—Autofluorescence was used to examine inhibi- tor entry...488-conjugated goat anti-mouse secondary antibody, 1:25 Texas Red phalloidin, and Hoechst stain (Molecular Probes, Eugene, OR). Intoxication , Inhibitor...pharmacophore. Q2–15 chlorine atoms are light green; all other col- ors are as indicated for B. Small Molecule Inhibition of Botulinum Neurotoxin

  2. Binding mode and affinity studies of DNA-binding agents using topoisomerase I DNA unwinding assay.

    Science.gov (United States)

    McKnight, Ruel E; Gleason, Aaron B; Keyes, James A; Sahabi, Sadia

    2007-02-15

    A topoisomerase I DNA unwinding assay has been used to determine the relative DNA-binding affinities of a model pair of homologous naphthalene diimides. Binding affinity data were corroborated using calorimetric (ITC) and spectrophotometric (titration and T(m)) studies, with substituent size playing a significant role in binding. The assay was also used to investigate the mode of binding adopted by several known DNA-binding agents, including SYBR Green and PicoGreen. Some of the compounds exhibited unexpected binding modes.

  3. Multiple binding modes of ibuprofen in human serum albumin identified by absolute binding free energy calculations

    KAUST Repository

    Evoli, Stefania

    2016-11-10

    Human serum albumin possesses multiple binding sites and transports a wide range of ligands that include the anti-inflammatory drug ibuprofen. A complete map of the binding sites of ibuprofen in albumin is difficult to obtain in traditional experiments, because of the structural adaptability of this protein in accommodating small ligands. In this work, we provide a set of predictions covering the geometry, affinity of binding and protonation state for the pharmaceutically most active form (S-isomer) of ibuprofen to albumin, by using absolute binding free energy calculations in combination with classical molecular dynamics (MD) simulations and molecular docking. The most favorable binding modes correctly reproduce several experimentally identified binding locations, which include the two Sudlow\\'s drug sites (DS2 and DS1) and the fatty acid binding sites 6 and 2 (FA6 and FA2). Previously unknown details of the binding conformations were revealed for some of them, and formerly undetected binding modes were found in other protein sites. The calculated binding affinities exhibit trends which seem to agree with the available experimental data, and drastically degrade when the ligand is modeled in a protonated (neutral) state, indicating that ibuprofen associates with albumin preferentially in its charged form. These findings provide a detailed description of the binding of ibuprofen, help to explain a wide range of results reported in the literature in the last decades, and demonstrate the possibility of using simulation methods to predict ligand binding to albumin.

  4. Interplay between the folding mechanism and binding modes in folding coupled to binding processes.

    Science.gov (United States)

    Sharma, Rajendra; De Sancho, David; Muñoz, Victor

    2017-11-01

    Proteins that fold upon binding to their partners exhibit complex binding behavior such as induced-fit. But the connections between the folding mechanism and the binding mode remain unknown. Here we focus on the high affinity complex between the physiologically and marginally unstable, fast folder PSBD and the E1 subunit of pyruvate dehydrogenase. Using coarse-grained simulations we investigate the binding to E1 of a partially disordered PSBD under two folding scenarios: two-state and downhill. Our simulations show that induced-fit binding requires that PSBD folds-unfolds in the downhill folding regime. In contrast, a two-state folding PSBD must fold completely before it binds. The reason is that effective coupling between folding and binding involves partially folded conformations, which are only sufficiently populated under the downhill folding regime. Our results establish a direct mechanistic link between complex binding and downhill folding, supporting the idea that PSBD operates functionally as a conformational rheostat.

  5. Probing the binding mode of psoralen to calf thymus DNA.

    Science.gov (United States)

    Zhou, Xiaoyue; Zhang, Guowen; Wang, Langhong

    2014-06-01

    The binding properties between psoralen (PSO) and calf thymus DNA (ctDNA) were predicted by molecular docking, and then determined with the use of UV-vis absorption, fluorescence, circular dichroism (CD) and Fourier transform infrared (FT-IR) spectroscopy, coupled with DNA melting and viscosity measurements. The data matrix obtained from UV-vis spectra was resolved by multivariate curve resolution-alternating least squares (MCR-ALS) approach. The pure spectra and the equilibrium concentration profiles for PSO, ctDNA and PSO-ctDNA complex extracted from the highly overlapping composite response were obtained simultaneously to evaluate the PSO-ctDNA interaction. The intercalation mode of PSO binding to ctDNA was supported by the results from the melting studies, viscosity measurements, iodide quenching and fluorescence polarization experiments, competitive binding investigations and CD analysis. The molecular docking prediction showed that the specific binding most likely occurred between PSO and adenine bases of ctDNA. FT-IR spectra studies further confirmed that PSO preferentially bound to adenine bases, and this binding decreased right-handed helicity of ctDNA and enhanced the degree of base stacking with the preservation of native B-conformation. The calculated thermodynamic parameters indicated that hydrogen bonds and van der Waals forces played a major role in the binding process. Copyright © 2014 Elsevier B.V. All rights reserved.

  6. New binding mode to TNF-alpha revealed by ubiquitin-based artificial binding protein.

    Directory of Open Access Journals (Sweden)

    Andreas Hoffmann

    Full Text Available A variety of approaches have been employed to generate binding proteins from non-antibody scaffolds. Utilizing a beta-sheet of the human ubiquitin for paratope creation we obtained binding proteins against tumor necrosis factor (TNF-alpha. The bioactive form of this validated pharmacological target protein is a non-covalently linked homo-trimer. This structural feature leads to the observation of a certain heterogeneity concerning the binding mode of TNF-alpha binding molecules, for instance in terms of monomer/trimer specificity. We analyzed a ubiquitin-based TNF-alpha binder, selected by ribosome display, with a particular focus on its mode of interaction. Using enzyme-linked immunosorbent assays, specific binding to TNF-alpha with nanomolar affinity was observed. In isothermal titration calorimetry we obtained comparable results regarding the affinity and detected an exothermic reaction with one ubiquitin-derived binding molecule binding one TNF-alpha trimer. Using NMR spectroscopy and other analytical methods the 1:3 stoichiometry could be confirmed. Detailed binding analysis showed that the interaction is affected by the detergent Tween-20. Previously, this phenomenon was reported only for one other type of alternative scaffold-derived binding proteins--designed ankyrin repeat proteins--without further investigation. As demonstrated by size exclusion chromatography and NMR spectroscopy, the presence of the detergent increases the association rate significantly. Since the special architecture of TNF-alpha is known to be modulated by detergents, the access to the recognized epitope is indicated to be restricted by conformational transitions within the target protein. Our results suggest that the ubiquitin-derived binding protein targets a new epitope on TNF-alpha, which differs from the epitopes recognized by TNF-alpha neutralizing antibodies.

  7. Nonspecific DNA Binding and Bending by HUαβ: Interfaces of the Three Binding Modes Characterized by Salt Dependent Thermodynamics

    Science.gov (United States)

    Koh, Junseock; Shkel, Irina; Saecker, Ruth M.; Record, M. Thomas

    2011-01-01

    Previous ITC and FRET studies demonstrated that Escherichia coli HUαβ binds nonspecifically to duplex DNA in three different binding modes: a tighter-binding 34 bp mode which interacts with DNA in large (>34 bp) gaps between bound proteins, reversibly bending it 140° and thereby increasing its flexibility, and two weaker, modestly cooperative small-site-size modes (10 bp, 6 bp) useful for filling gaps between bound proteins shorter than 34 bp. Here we use ITC to determine the thermodynamics of these binding modes as a function of salt concentration, and deduce that DNA in the 34 bp mode is bent around but not wrapped on the body of HU, in contrast to specific binding of IHF. Analyses of binding isotherms (8, 15, 34 bp DNA) and initial binding heats (34, 38, 160 bp DNA) reveal that all three modes have similar log-log salt concentration derivatives of the binding constants (Ski) even though their binding site sizes differ greatly; most probable values of Ski on 34 bp or larger DNA are − 7.5 ± 0.5. From the similarity of Ski values, we conclude that binding interfaces of all three modes involve the same region of the arms and saddle of HU. All modes are entropy-driven, as expected for nonspecific binding driven by the polyelectrolyte effect. The bent-DNA 34 bp mode is most endothermic, presumably because of the cost of HU-induced DNA bending, while the 6 bp mode is modestly exothermic at all salt concentrations examined. Structural models consistent with the observed Ski values are proposed. PMID:21513716

  8. Binding modes of thrombin binding aptamers investigated by simulations and experiments

    Science.gov (United States)

    Trapaidze, A.; Bancaud, A.; Brut, M.

    2015-01-01

    Thrombin binding aptamers HD1 and HD22 are the most studied aptamers, both for therapeutic and sensing purposes. Yet, there is still no commercialized aptamer-based sensor device for thrombin detection, suggesting that the binding modes of these aptamers remain to be precisely described. Here, we investigate thrombin-aptamer interactions with molecular dynamics simulations, and show that the different solved structures of HD1-thrombin complex are energetically similar and consequently possibly co-existing. Conversely, HD22 folding is much more stable, and its binding energy with thrombin is significantly larger than that of HD1 complexes. These results are confronted to experiments, which consist in monitoring aggregation of aptamer-functionalized gold nanoparticles triggered by thrombin. HD1 alone, but not HD22, can trigger aggregation, meaning that this aptamer has multiple sites of interactions with thrombin. Furthermore, pre-incubation of HD22 with thrombin impedes HD1 aggregation, suggesting that HD1 and HD22 have competing affinities for the same binding site. Altogether, this study shows that the characterization of aptamer-thrombin interactions by structural and kinetic experiments joined to simulations is necessary for the development of biosensors.

  9. Computer modelling studies on the modes of binding of some of the ...

    Indian Academy of Sciences (India)

    tribpo

    Abstract. The possible modes of binding of kojibiose, nigerose, maltose and ManPα(1. →2)Man to concanavalin A have been investigated using computer modelling studies. While α12 linked disaccharides bind to concanavalin A in two modes, i.e. by placing the reducing as well as non-reducing sugar units in the sugar ...

  10. DNA synthesis determines the binding mode of the human mitochondrial single-stranded DNA-binding protein.

    Science.gov (United States)

    Morin, José A; Cerrón, Fernando; Jarillo, Javier; Beltran-Heredia, Elena; Ciesielski, Grzegorz L; Arias-Gonzalez, J Ricardo; Kaguni, Laurie S; Cao, Francisco J; Ibarra, Borja

    2017-07-07

    Single-stranded DNA-binding proteins (SSBs) play a key role in genome maintenance, binding and organizing single-stranded DNA (ssDNA) intermediates. Multimeric SSBs, such as the human mitochondrial SSB (HmtSSB), present multiple sites to interact with ssDNA, which has been shown in vitro to enable them to bind a variable number of single-stranded nucleotides depending on the salt and protein concentration. It has long been suggested that different binding modes might be used selectively for different functions. To study this possibility, we used optical tweezers to determine and compare the structure and energetics of long, individual HmtSSB-DNA complexes assembled on preformed ssDNA and on ssDNA generated gradually during 'in situ' DNA synthesis. We show that HmtSSB binds to preformed ssDNA in two major modes, depending on salt and protein concentration. However, when protein binding was coupled to strand-displacement DNA synthesis, only one of the two binding modes was observed under all experimental conditions. Our results reveal a key role for the gradual generation of ssDNA in modulating the binding mode of a multimeric SSB protein and consequently, in generating the appropriate nucleoprotein structure for DNA synthetic reactions required for genome maintenance. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  11. A 3D-QSAR-driven approach to binding mode and affinity prediction

    DEFF Research Database (Denmark)

    Tosco, Paolo; Balle, Thomas

    2012-01-01

    A method for predicting the binding mode of a series of ligands is proposed. The procedure relies on three-dimensional quantitative structure-activity relationships (3D-QSAR) and does not require structural knowledge of the binding site. Candidate alignments are automatically built and ranked acc...... according to a consensus scoring function. 3D-QSAR analysis based on the selected binding mode enables affinity prediction of new drug candidates having less than 10 rotatable bonds....

  12. An in silico analysis of the binding modes and binding affinities of small molecule modulators of PDZ-peptide interactions.

    Directory of Open Access Journals (Sweden)

    Garima Tiwari

    Full Text Available Inhibitors of PDZ-peptide interactions have important implications in a variety of biological processes including treatment of cancer and Parkinson's disease. Even though experimental studies have reported characterization of peptidomimetic inhibitors of PDZ-peptide interactions, the binding modes for most of them have not been characterized by structural studies. In this study we have attempted to understand the structural basis of the small molecule-PDZ interactions by in silico analysis of the binding modes and binding affinities of a set of 38 small molecules with known K(i or K(d values for PDZ2 and PDZ3 domains of PSD-95 protein. These two PDZ domains show differential selectivity for these compounds despite having a high degree of sequence similarity and almost identical peptide binding pockets. Optimum binding modes for these ligands for PDZ2 and PDZ3 domains were identified by using a novel combination of semi-flexible docking and explicit solvent molecular dynamics (MD simulations. Analysis of the binding modes revealed most of the peptidomimectic ligands which had high K(i or K(d moved away from the peptide binding pocket, while ligands with high binding affinities remained in the peptide binding pocket. The differential specificities of the PDZ2 and PDZ3 domains primarily arise from differences in the conformation of the loop connecting βB and βC strands, because this loop interacts with the N-terminal chemical moieties of the ligands. We have also computed the MM/PBSA binding free energy values for these 38 compounds with both the PDZ domains from multiple 5 ns MD trajectories on each complex i.e. a total of 228 MD trajectories of 5 ns length each. Interestingly, computational binding free energies show good agreement with experimental binding free energies with a correlation coefficient of approximately 0.6. Thus our study demonstrates that combined use of docking and MD simulations can help in identification of potent inhibitors

  13. Structure-Based Understanding of Binding Affinity and Mode of Estrogen Receptor α Agonists and Antagonists.

    Directory of Open Access Journals (Sweden)

    Sehan Lee

    Full Text Available The flexible hydrophobic ligand binding pocket (LBP of estrogen receptor α (ERα allows the binding of a wide variety of endocrine disruptors. Upon ligand binding, the LBP reshapes around the contours of the ligand and stabilizes the complex by complementary hydrophobic interactions and specific hydrogen bonds with the ligand. Here we present a framework for quantitative analysis of the steric and electronic features of the human ERα-ligand complex using three dimensional (3D protein-ligand interaction description combined with 3D-QSAR approach. An empirical hydrophobicity density field is applied to account for hydrophobic contacts of ligand within the LBP. The obtained 3D-QSAR model revealed that hydrophobic contacts primarily determine binding affinity and govern binding mode with hydrogen bonds. Several residues of the LBP appear to be quite flexible and adopt a spectrum of conformations in various ERα-ligand complexes, in particular His524. The 3D-QSAR was combined with molecular docking based on three receptor conformations to accommodate receptor flexibility. The model indicates that the dynamic character of the LBP allows accommodation and stable binding of structurally diverse ligands, and proper representation of the protein flexibility is critical for reasonable description of binding of the ligands. Our results provide a quantitative and mechanistic understanding of binding affinity and mode of ERα agonists and antagonists that may be applicable to other nuclear receptors.

  14. Structure of Osh3 reveals a conserved mode of phosphoinositide binding in oxysterol-binding proteins.

    Science.gov (United States)

    Tong, Junsen; Yang, Huiseon; Yang, Hongyuan; Eom, Soo Hyun; Im, Young Jun

    2013-07-02

    The oxysterol-binding protein (OSBP)-related proteins (ORPs) are conserved from yeast to humans, and implicated in the regulation of lipid homeostasis and in signaling pathways. Saccharomyces cerevisiae has seven ORPs (Osh1-Osh7) that share one unknown essential function. Here, we report the 1.5-2.3 Å structures of the PH domain and ORD (OSBP-related domain) of yeast Osh3 in apo-form or in complex with phosphatidylinositol 4-phosphate (PI[4]P). Osh3 recognizes PI(4)P by the highly conserved residues in the tunnel of ORD whereas it lacks sterol binding due to the narrow hydrophobic tunnel. Yeast complementation tests suggest that PI(4)P binding to PH and ORD is essential for function. This study suggests that the unifying feature in all ORP homologs is the binding of PI(4)P to ORD and sterol binding is additional to certain homologs. Structural modeling of full-length Osh3 is consistent with the concept that Osh3 is a lipid transfer protein or regulator in membrane contact sites. Copyright © 2013 Elsevier Ltd. All rights reserved.

  15. The structure and binding mode of citrate in the stabilization of gold nanoparticles

    KAUST Repository

    Al-Johani, Hind

    2017-03-27

    Elucidating the binding mode of carboxylate-containing ligands to gold nanoparticles (AuNPs) is crucial to understand their stabilizing role. A detailed picture of the three-dimensional structure and coordination modes of citrate, acetate, succinate and glutarate to AuNPs is obtained by 13C and 23Na solid-state NMR in combination with computational modelling and electron microscopy. The binding between the carboxylates and the AuNP surface is found to occur in three different modes. These three modes are simultaneously present at low citrate to gold ratios, while a monocarboxylate monodentate (1κO1) mode is favoured at high citrate:gold ratios. The surface AuNP atoms are found to be predominantly in the zero oxidation state after citrate coordination, although trace amounts of Auδ+ are observed. 23Na NMR experiments show that Na+ ions are present near the gold surface, indicating that carboxylate binding occurs as a 2e− L-type interaction for each oxygen atom involved. This approach has broad potential to probe the binding of a variety of ligands to metal nanoparticles.

  16. The structure and binding mode of citrate in the stabilization of gold nanoparticles

    Science.gov (United States)

    Al-Johani, Hind; Abou-Hamad, Edy; Jedidi, Abdesslem; Widdifield, Cory M.; Viger-Gravel, Jasmine; Sangaru, Shiv Shankar; Gajan, David; Anjum, Dalaver H.; Ould-Chikh, Samy; Hedhili, Mohamed Nejib; Gurinov, Andrei; Kelly, Michael J.; El Eter, Mohamad; Cavallo, Luigi; Emsley, Lyndon; Basset, Jean-Marie

    2017-09-01

    Elucidating the binding mode of carboxylate-containing ligands to gold nanoparticles (AuNPs) is crucial to understand their stabilizing role. A detailed picture of the three-dimensional structure and coordination modes of citrate, acetate, succinate and glutarate to AuNPs is obtained by 13C and 23Na solid-state NMR in combination with computational modelling and electron microscopy. The binding between the carboxylates and the AuNP surface is found to occur in three different modes. These three modes are simultaneously present at low citrate to gold ratios, while a monocarboxylate monodentate (1κO1) mode is favoured at high citrate:gold ratios. The surface AuNP atoms are found to be predominantly in the zero oxidation state after citrate coordination, although trace amounts of Auδ+ are observed. 23Na NMR experiments show that Na+ ions are present near the gold surface, indicating that carboxylate binding occurs as a 2e- L-type interaction for each oxygen atom involved. This approach has broad potential to probe the binding of a variety of ligands to metal nanoparticles.

  17. Efficient purification of recombinant proteins fused to maltose-binding protein by mixed-mode chromatography.

    Science.gov (United States)

    Cabanne, Charlotte; Pezzini, Jérôme; Joucla, Gilles; Hocquellet, Agnès; Barbot, Caroline; Garbay, Bertrand; Santarelli, Xavier

    2009-05-15

    Two mixed-mode resins were evaluated as an alternative to conventional affinity resins for the purification of recombinant proteins fused to maltose-binding protein (MPB). We purified recombinant MBP, MBP-LacZ and MBP-Leap2 from crude Escherichia coli extracts. Mixed-mode resins allowed the efficient purification of MBP-fused proteins. Indeed, the quantity of purified proteins was significantly higher with mixed-mode resins, and their purity was equivalent to that obtained with affinity resins. By using purified MBP, MBP-LacZ and MBP-Leap2, the dynamic binding capacity of mixed-mode resins was 5-fold higher than that of affinity resins. Moreover, the recovery for the three proteins studied was in the 50-60% range for affinity resins, and in the 80-85% range for mixed-mode resins. Mixed-mode resins thus represent a powerful alternative to the classical amylose or dextrin resins for the purification of recombinant proteins fused to maltose-binding protein.

  18. Structure-based drug design enables conversion of a DFG-in binding CSF-1R kinase inhibitor to a DFG-out binding mode

    Energy Technology Data Exchange (ETDEWEB)

    Meyers, Marvin J.; Pelc, Matthew; Kamtekar, Satwik; Day, Jacqueline; Poda, Gennadiy I.; Hall, Molly K.; Michener, Marshall L.; Reitz, Beverly A.; Mathis, Karl J.; Pierce, Betsy S.; Parikh, Mihir D.; Mischke, Deborah A.; Long, Scott A.; Parlow, John J.; Anderson, David R.; Thorarensen, Atli (Pfizer)

    2010-08-11

    The work described herein demonstrates the utility of structure-based drug design (SBDD) in shifting the binding mode of an HTS hit from a DFG-in to a DFG-out binding mode resulting in a class of novel potent CSF-1R kinase inhibitors suitable for lead development.

  19. Structure-based drug design enables conversion of a DFG-in binding CSF-1R kinase inhibitor to a DFG-out binding mode.

    Science.gov (United States)

    Meyers, Marvin J; Pelc, Matthew; Kamtekar, Satwik; Day, Jacqueline; Poda, Gennadiy I; Hall, Molly K; Michener, Marshall L; Reitz, Beverly A; Mathis, Karl J; Pierce, Betsy S; Parikh, Mihir D; Mischke, Deborah A; Long, Scott A; Parlow, John J; Anderson, David R; Thorarensen, Atli

    2010-03-01

    The work described herein demonstrates the utility of structure-based drug design (SBDD) in shifting the binding mode of an HTS hit from a DFG-in to a DFG-out binding mode resulting in a class of novel potent CSF-1R kinase inhibitors suitable for lead development. Copyright 2010 Elsevier Ltd. All rights reserved.

  20. Reassessment of the unique mode of binding between angiotensin II type 1 receptor and their blockers.

    Directory of Open Access Journals (Sweden)

    Shin-Ichiro Miura

    Full Text Available While the molecular structures of angiotensin II (Ang II type 1 (AT1 receptor blockers (ARBs are very similar, they are also slightly different. Although each ARB has been shown to exhibit a unique mode of binding to AT1 receptor, different positions of the AT1 receptor have been analyzed and computational modeling has been performed using different crystal structures for the receptor as a template and different kinds of software. Therefore, we systematically analyzed the critical positions of the AT1 receptor, Tyr(113, Tyr(184, Lys(199, His(256 and Gln(257 using a mutagenesis study, and subsequently performed computational modeling of the binding of ARBs to AT1 receptor using CXCR4 receptor as a new template and a single version of software. The interactions between Tyr(113 in the AT1 receptor and the hydroxyl group of olmesartan, between Lys(199 and carboxyl or tetrazole groups, and between His(256 or Gln(257 and the tetrazole group were studied. The common structure, a tetrazole group, of most ARBs similarly bind to Lys(199, His(256 and Gln(257 of AT1 receptor. Lys(199 in the AT1 receptor binds to the carboxyl group of EXP3174, candesartan and azilsartan, whereas oxygen in the amidecarbonyl group of valsartan may bind to Lys(199. The benzimidazole portion of telmisartan may bind to a lipophilic pocket that includes Tyr(113. On the other hand, the n-butyl group of irbesartan may bind to Tyr(113. In conclusion, we confirmed that the slightly different structures of ARBs may be critical for binding to AT1 receptor and for the formation of unique modes of binding.

  1. Linear and circular dichroism characterization of thionine binding mode with DNA polynucleotides

    Science.gov (United States)

    Tuite, Eimer Mary; Nordén, Bengt

    2018-01-01

    The binding mode of thionine (3,7-diamino-5-phenothiazinium) with alternating and non-alternating DNA polynucleotides at low binding ratios was conclusively determined using linear and circular dichroism spectroscopies. The binding to [poly(dG-dC)]2 and poly(dG)·poly(dC) was purely intercalative and was insensitive to ionic strength. Intercalative binding to [poly(dA-dT)]2 is observed at low ionic strength, but a shift of some dye to an non-intercalative mode is observed as the background salt concentration increases. With poly(dA)·poly(dT), intercalative binding is unfavourable, although some dye molecules may intercalate at low ionic strength, and groove binding is strongly promoted with increasing concentration of background salt. However, stacking with bases is observed with single-stranded poly(dA) and with triplex poly(dT)*poly(dA)·poly(dT) which suggests that the unusual structure of poly(dA)·poly(dT) precludes intercalation. Thionine behaves similarly to the related dye methylene blue, and small differences may be attributed either to the ability of thionine to form H-bonds that stabilize intercalation or to its improved stacking interactions in the basepair pocket on steric grounds.

  2. Structural insights into the binding mode and conformational changes of BSA induced by bixin and crocin.

    Science.gov (United States)

    Mohan, Sankari; Hemachandran, Hridya; Sneha, P; George Priya Doss, C; Godwin Christopher, J; Jayaraman, Gurunathan; Ramamoorthy, Siva

    2017-06-30

    Bixin and crocin are natural apocarotenoids utilized as food colorants and additives in food industries worldwide. For safety assessment, it is necessary to understand the biological interaction of food colorants. In our present study, we report the interaction of two apocarotenoids with bovine serum albumin (BSA) at physiological pH using spectroscopic techniques and in silico tools. The binding constant and the mode of binding sites have been studied. The enthalpic and entropic contribution to the intermolecular binding event was analyzed and it was found that the contribution of hydrogen bonding and hydrophobic interactions was dominant. The adverse temperature dependence in the unusual static quenching is found to be a reasonable consequence of the large activation energy requirement in the binding process, which is required to overcome the fundamental block and is a direct result of the unique microstructure of the binding sites. To confirm the experimental analysis, we investigated the binding patterns using different in silico tools. A combination of molecular docking, molecular dynamics, and toxicity analysis was performed, and the obtained results revealed that both the apocarotenoids had high binding affinity with a binding energy of -5.44 and -5.93 kcal/mol for bixin and crocin, respectively, with no toxic effects and are in accordance with our experimental analysis. The results directly revealed the flexibility of the protein toward bixin and crocin which has a great impact on the interaction. Thus bixin and crocin can guardedly be used as food colorants in food industries.

  3. Multi-Mode Binding of Cellobiohydrolase Cel7A from Trichoderma reesei to Cellulose

    Science.gov (United States)

    Jalak, Jürgen; Väljamäe, Priit

    2014-01-01

    Enzymatic hydrolysis of recalcitrant polysaccharides like cellulose takes place on the solid-liquid interface. Therefore the adsorption of enzymes to the solid surface is a pre-requisite for catalysis. Here we used enzymatic activity measurements with fluorescent model-substrate 4-methyl-umbelliferyl-β-D-lactoside for sensitive monitoring of the binding of cellobiohydrolase TrCel7A from Trichoderma reesei to bacterial cellulose (BC). The binding at low nanomolar free TrCel7A concentrations was exclusively active site mediated and was consistent with Langmuir's one binding site model with Kd and Amax values of 2.9 nM and 126 nmol/g BC, respectively. This is the strongest binding observed with non-complexed cellulases and apparently represents the productive binding of TrCel7A to cellulose chain ends on the hydrophobic face of BC microfibril. With increasing free TrCel7A concentrations the isotherm gradually deviated from the Langmuir's one binding site model. This was caused by the increasing contribution of lower affinity binding modes that included both active site mediated binding and non-productive binding with active site free from cellulose chain. The binding of TrCel7A to BC was found to be only partially reversible. Furthermore, the isotherm was dependent on the concentration of BC with more efficient binding observed at lower BC concentrations. The phenomenon can be ascribed to the BC concentration dependent aggregation of BC microfibrils with concomitant reduction of specific surface area. PMID:25265511

  4. The Facilitation of Protein-DNA Search and Recognition by Multiple Modes of Binding

    Science.gov (United States)

    Leith, Jason Suh

    The studies discussed in this thesis unify experimental and theoretical techniques, both established and novel, in investigating the problem of how a protein that binds specific sites on DNA translocates to, recognizes, and stably binds to its target site or sites. The thesis is organized into two parts. Part I outlines the history of the problem and the theory and experiments that have addressed the problem and presents an apparent incompatibility between efficient search and stable, specific binding. To address this problem, we elaborate a model of protein-DNA interaction in which the protein may bind DNA in either a search (S) mode or a recognition (R) mode. The former is characterized by zero or weak sequence-dependence in the binding energy, while the latter is highly sequence-dependent. The protein undergoes a random walk along the DNA in the S mode, and if it encounters its target site, must undergo a conformational transition into the R mode. The model resolves the apparent paradox, and accounts for the observed speed, specificity, and stability in protein-DNA interactions. The model shows internal agreement as regards theoretical and simulated results, as well as external agreement with experimental measurements. Part II reports on research that has tested the applicability of the two-mode model to the tumor suppressor transcription factor p53. It describes in greater depth the experimental techinques and findings up to the present work, and introduces the techinques and biological system used in our research. We employ single-molecule optical microscopy in two projects to study the diffusional kinetics of p53 on DNA. The first project measures the diffusion coefficient of p53 and determines that the protein satisfies a number of requirements for the validity of the two-mode model and for efficient target localization. The second project examines the sequence-dependence in p53's sliding kinetics, and explicitly models the energy landscape it experiences on

  5. Exploring the stability of ligand binding modes to proteins by molecular dynamics simulations.

    Science.gov (United States)

    Liu, Kai; Watanabe, Etsurou; Kokubo, Hironori

    2017-02-01

    The binding mode prediction is of great importance to structure-based drug design. The discrimination of various binding poses of ligand generated by docking is a great challenge not only to docking score functions but also to the relatively expensive free energy calculation methods. Here we systematically analyzed the stability of various ligand poses under molecular dynamics (MD) simulation. First, a data set of 120 complexes was built based on the typical physicochemical properties of drug-like ligands. Three potential binding poses (one correct pose and two decoys) were selected for each ligand from self-docking in addition to the experimental pose. Then, five independent MD simulations for each pose were performed with different initial velocities for the statistical analysis. Finally, the stabilities of ligand poses under MD were evaluated and compared with the native one from crystal structure. We found that about 94% of the native poses were maintained stable during the simulations, which suggests that MD simulations are accurate enough to judge most experimental binding poses as stable properly. Interestingly, incorrect decoy poses were maintained much less and 38-44% of decoys could be excluded just by performing equilibrium MD simulations, though 56-62% of decoys were stable. The computationally-heavy binding free energy calculation can be performed only for these survived poses.

  6. Molecular modeling and prediction of binding mode and relative binding affinity of Art-Qui-OH with P. falciparum Histo-Aspartic Protease (HAP).

    Science.gov (United States)

    Mahapatra, Rajani Kanta; Behera, Niranjan; Naik, Pradeep Kumar

    2012-01-01

    The relative binding affinity in terms of ΔΔG (bind-cald) value of the antimalarial compound artemisinin-quinine hybrid is primarily derived and is discussed in this article with reference to the ΔG (bind-cald) values of two known inhibitors Pepstatin-A and KNI-10006 complexed with HAP enzyme. The ΔG (bind-cald) value for KNI-10006 and Pepstatin-A is -14.10 kcal/mol and -13.09 kcal/mol respectively. The MM-GB/SA scoring results in the relative binding energy (ΔΔG (bind-cald)) of the hybrid molecule with respect to Pepstatin-A as 2.43 kcal/mol and 3.44 kcal/mol against KNI-10006. The overall binding mode of Art-Qui-OH resembles that of Pepstatin-A binding in HAP active site. We suggest here that the ΔΔG (bind-cald) value & proposed binding mode of the Art-Qui-OH for HAP enzyme should be considered for further structure-based drug design effort.

  7. Investigation of the binding modes of a positively charged pillar[5]arene: internal and external guest complexation.

    Science.gov (United States)

    Gómez-González, Borja; Francisco, Vitor; Montecinos, Rodrigo; García-Río, Luis

    2017-01-25

    The selective binding behavior of a trimethylammonium-derived pillar[5]arene towards different guests in aqueous media and under neutral conditions is reported. Although it is known that this macrocycle has the capability to form complexes with guests, we anticipate that the intrinsic pillar shape of the macrocycle with two positively charged rims should allow a diversity of binding modes. The three guests were selected based on their charge and size. The inclusion binding modes and the affinity of the macrocycle to form host-guest complexes were determined by ITC and NMR techniques. We reveal the ability of a cationic water soluble pillar[5]arene to effectively complex two guest molecules, one in each rim, evidencing the diversity of binding modes. Two different structures for 1 : 1 and three for 1 : 2 complexes are reported showing the pillararene ability for internal/external binding.

  8. Deciphering the intercalative binding modes of benzoyl peroxide with calf thymus DNA.

    Science.gov (United States)

    Xia, Kaixin; Zhang, Guowen; Gong, Deming

    2017-09-01

    The binding of benzoyl peroxide (BPO), a flour brightener, with calf thymus DNA (ctDNA) was predicted by molecular simulation, and this were confirmed using multi-spectroscopic techniques and a chemometrics algorithm. The molecular docking result showed that BPO could insert into the base pairs of ctDNA, and the adenine bases were the preferential binding sites which were validated by the analysis of Fourier transform infrared spectra. The mode of binding of BPO with ctDNA was an intercalation as supported by the results from ctDNA melting and viscosity measurements, iodide quenching effects and competitive binding investigations. The circular dichroism and DNA cleavage assays indicated that BPO induced a conformational change from B-like DNA structure towards to A-like form, but did not lead to significant damage in the DNA. The complexation was driven mainly by hydrogen bonds and hydrophobic interactions. Moreover, the ultraviolet-visible (UV-vis) spectroscopic data matrix was resolved by a multivariate curve resolution-alternating least-squares algorithm. The equilibrium concentration profiles for the components (BPO, ctDNA and BPO-ctDNA complex) were extracted from the highly overlapping composite response to quantitatively monitor the BPO-ctDNA interaction. This study has provided insights into the mechanism of the interaction of BPO with ctDNA and potential hazards of the food additive. Copyright © 2017 John Wiley & Sons, Ltd.

  9. Exploring the DNA binding mode of transition metal based biologically active compounds

    Science.gov (United States)

    Raman, N.; Sobha, S.

    2012-01-01

    Few novel 4-aminoantipyrine derived Schiff bases and their metal complexes were synthesized and characterized. Their structural features and other properties were deduced from the elemental analysis, magnetic susceptibility and molar conductivity as well as from mass, IR, UV-vis, 1H NMR and EPR spectral studies. The binding of the complexes with CT-DNA was analyzed by electronic absorption spectroscopy, viscosity measurement, and cyclic voltammetry. The interaction of the metal complexes with DNA was also studied by molecular modeling with special reference to docking. The experimental and docking results revealed that the complexes have the ability of interaction with DNA of minor groove binding mode. The intrinsic binding constants ( Kb) of the complexes with CT-DNA were found out which show that they are minor groove binders. Gel electrophoresis assay demonstrated the ability of the complexes to cleave the pUC19 DNA in the presence of AH 2 (ascorbic acid). Moreover, the oxidative cleavage studies using distamycin revealed the minor groove binding for the newly synthesized 4-aminoantipyrine derived Schiff bases and their metal complexes. Evaluation of antibacterial activity of the complexes against Staphylococcus aureus, Pseudomonas aeruginosa, Escherichia coli, Staphylococcus epidermidis, and Klebsiella pneumoniae exhibited that the complexes have potent biocidal activity than the free ligands.

  10. The binding mode of side chain- and C3-modified epothilones to tubulin.

    Science.gov (United States)

    Erdélyi, Máté; Navarro-Vázquez, Armando; Pfeiffer, Bernhard; Kuzniewski, Christian N; Felser, Andrea; Widmer, Toni; Gertsch, Jürg; Pera, Benet; Díaz, José Fernando; Altmann, Karl-Heinz; Carlomagno, Teresa

    2010-06-07

    The tubulin-binding mode of C3- and C15-modified analogues of epothilone A (Epo A) was determined by NMR spectroscopy and computational methods and compared with the existing structural models of tubulin-bound natural Epo A. Only minor differences were observed in the conformation of the macrocycle between Epo A and the C3-modified analogues investigated. In particular, 3-deoxy- (compound 2) and 3-deoxy-2,3-didehydro-Epo A (3) were found to adopt similar conformations in the tubulin-binding cleft as Epo A, thus indicating that the 3-OH group is not essential for epothilones to assume their bioactive conformation. None of the available models of the tubulin-epothilone complex is able to fully recapitulate the differences in tubulin-polymerizing activity and microtubule-binding affinity between C20-modified epothilones 6 (C20-propyl), 7 (C20-butyl), and 8 (C20-hydroxypropyl). Based on the results of transferred NOE experiments in the presence of tubulin, the isomeric C15 quinoline-based Epo B analogues 4 and 5 show very similar orientations of the side chain, irrespective of the position of the nitrogen atom in the quinoline ring. The quinoline side chain stacks on the imidazole moiety of beta-His227 with equal efficiency in both cases, thus suggesting that the aromatic side chain moiety in epothilones contributes to tubulin binding through strong van der Waals interactions with the protein rather than hydrogen bonding involving the heteroaromatic nitrogen atom. These conclusions are in line with existing tubulin polymerization and microtubule-binding data for 4, 5, and Epo B.

  11. Binding mode and free energy prediction of fisetin/β-cyclodextrin inclusion complexes

    Directory of Open Access Journals (Sweden)

    Bodee Nutho

    2014-11-01

    Full Text Available In the present study, our aim is to investigate the preferential binding mode and encapsulation of the flavonoid fisetin in the nano-pore of β-cyclodextrin (β-CD at the molecular level using various theoretical approaches: molecular docking, molecular dynamics (MD simulations and binding free energy calculations. The molecular docking suggested four possible fisetin orientations in the cavity through its chromone or phenyl ring with two different geometries of fisetin due to the rotatable bond between the two rings. From the multiple MD results, the phenyl ring of fisetin favours its inclusion into the β-CD cavity, whilst less binding or even unbinding preference was observed in the complexes where the larger chromone ring is located in the cavity. All MM- and QM-PBSA/GBSA free energy predictions supported the more stable fisetin/β-CD complex of the bound phenyl ring. Van der Waals interaction is the key force in forming the complexes. In addition, the quantum mechanics calculations with M06-2X/6-31G(d,p clearly showed that both solvation effect and BSSE correction cannot be neglected for the energy determination of the chosen system.

  12. DNA binding mode of novel tetradentate amino acid based 2-hydroxybenzylidene-4-aminoantipyrine complexes

    Science.gov (United States)

    Raman, N.; Sobha, S.; Selvaganapathy, M.; Mahalakshmi, R.

    2012-10-01

    Few transition metal complexes of tetradentate N2O2 donor Schiff base ligands containing 2-hydroxybenzylidene-4-aminoantipyrine and amino acids (alanine/valine) abbreviated to KHL1/KHL2 have been synthesized. All the metal complexes have been fully characterized with the help of elemental analyses, molecular weights, molar conductance values, magnetic moments and spectroscopic data. The Schiff bases KHL1/KHL2 are found to act as tetradentate ligands using N2O2 donor set of atoms leading to a square-planar geometry for the complexes around the metal ions. The binding behaviors of the complexes to calf thymus DNA have been investigated by absorption spectra, viscosity measurements and cyclic voltammetry. The DNA binding constants reveal that all these complexes interact with DNA through minor groove binding mode. The studies on mechanism of photocleavage reveal that singlet oxygen (1O2) and superoxide anion radical (O2rad -) may play an important role in the photocleavage. The Schiff bases and their metal complexes have been screened for their in vitro antibacterial activities against Staphylococcus aureus, Pseudomonas aeruginosa, Escherichia coli, Staphylococcus epidermidis, Klebsiella pneumoniae and antifungal activities against Aspergillus niger, Fusarium solani, Culvularia lunata, Rhizoctonia bataicola and Candida albicans by MIC method.

  13. Substituent effect on the preferred DNA binding mode and affinity of a homologous series of naphthalene diimides.

    Science.gov (United States)

    McKnight, Ruel E; Reisenauer, Eric; Pintado, Manuel V; Polasani, Shivani R; Dixon, Dabney W

    2011-07-15

    A combination of isothermal titration calorimetry (ITC), topoisomerase I DNA unwinding assays, and ethidium bromide displacement studies were employed to investigate the binding of a homologous series of naphthalene diimides (NDI) to DNA. Our results suggest that the nature of the substituent plays a significant role in both the preferred binding mode and relative binding affinity of the compounds of this study. Only intercalative-type binding (K=15±3×10(6)M(-1)) was observed for the NDI with the smallest substituent (trimethyl-ethylamino), while larger members of the series (diethylmethyl-, dipropylmethyl- and dibutylmethyl-ethylamino substituents) adopted an additional binding mode of higher affinity (K(1)=31-78×10(6)M(-1)). Copyright © 2011 Elsevier Ltd. All rights reserved.

  14. Cytotoxic protein from the mushroom Coprinus comatus possesses a unique mode for glycan binding and specificity.

    Science.gov (United States)

    Zhang, Peilan; Li, Kunhua; Yang, Guang; Xia, Changqing; Polston, Jane E; Li, Gengnan; Li, Shiwu; Lin, Zhao; Yang, Li-Jun; Bruner, Steven D; Ding, Yousong

    2017-08-22

    Glycans possess significant chemical diversity; glycan binding proteins (GBPs) recognize specific glycans to translate their structures to functions in various physiological and pathological processes. Therefore, the discovery and characterization of novel GBPs and characterization of glycan-GBP interactions are significant to provide potential targets for therapeutic intervention of many diseases. Here, we report the biochemical, functional, and structural characterization of a 130-amino-acid protein, Y3, from the mushroom Coprinus comatus Biochemical studies of recombinant Y3 from a yeast expression system demonstrated the protein is a unique GBP. Additionally, we show that Y3 exhibits selective and potent cytotoxicity toward human T-cell leukemia Jurkat cells compared with a panel of cancer cell lines via inducing caspase-dependent apoptosis. Screening of a glycan array demonstrated GalNAcβ1-4(Fucα1-3)GlcNAc (LDNF) as a specific Y3-binding ligand. To provide a structural basis for function, the crystal structure was solved to a resolution of 1.2 Å, revealing a single-domain αβα-sandwich motif. Two monomers were dimerized to form a large 10-stranded, antiparallel β-sheet flanked by α-helices on each side, representing a unique oligomerization mode among GBPs. A large glycan binding pocket extends into the dimeric interface, and docking of LDNF identified key residues for glycan interactions. Disruption of residues predicted to be involved in LDNF/Y3 interactions resulted in the significant loss of binding to Jurkat T-cells and severely impaired their cytotoxicity. Collectively, these results demonstrate Y3 to be a GBP with selective cytotoxicity toward human T-cell leukemia cells and indicate its potential use in cancer diagnosis and treatment.

  15. Comparing binding modes of analogous fragments using NMR in fragment-based drug design: application to PRDX5.

    Directory of Open Access Journals (Sweden)

    Clémentine Aguirre

    Full Text Available Fragment-based drug design is one of the most promising approaches for discovering novel and potent inhibitors against therapeutic targets. The first step of the process consists of identifying fragments that bind the protein target. The determination of the fragment binding mode plays a major role in the selection of the fragment hits that will be processed into drug-like compounds. Comparing the binding modes of analogous fragments is a critical task, not only to identify specific interactions between the protein target and the fragment, but also to verify whether the binding mode is conserved or differs according to the fragment modification. While X-ray crystallography is the technique of choice, NMR methods are helpful when this fails. We show here how the ligand-observed saturation transfer difference (STD experiment and the protein-observed 15N-HSQC experiment, two popular NMR screening experiments, can be used to compare the binding modes of analogous fragments. We discuss the application and limitations of these approaches based on STD-epitope mapping, chemical shift perturbation (CSP calculation and comparative CSP sign analysis, using the human peroxiredoxin 5 as a protein model.

  16. Determination of binding modes and binding constants for the complexes of 6H-pyrido[4,3-b]carbazole derivatives with DNA.

    Science.gov (United States)

    Shimazu, Akihito; Kawagoshi, Masashi; Takeda, Shoichi; Kurasaki, Haruaki; Kato, Asako; Morii, Nahoko; Sakai, Norio; Konakahara, Takeo

    2017-02-01

    The binding modes and binding constants for the complexes of forty types of pyridocarbazole derivatives 1-40 with double stranded DNAs (dsDNAs) were reported. The binding modes were determined by a combination of a deflection spectroscopy and orientation of the corresponding molecule in the DNA-based film with chain alignment. All of the compounds exhibited the intercalation-binding mode. Its binding constants Ka for the complexes, determined by quartz crystal microbalance (QCM), varied from 1.7×10(5) to 4.5×10(7)M(-1) according to the substituents on the pyridocarbazole framework and the sequences of dsDNA. The binding constants Ka of pyridocarbazole derivatives possessing the 2-(ω-amino)alkyl group and 5-(ω-amino)alkylcarbamyl group were larger than those of the corresponding ω-ureido derivatives. These ω-amino compounds exhibited strong GC base-pair preference in complexation. The Ka values decreased with the increasing NaCl concentration. It was clarified by a molecular modeling that the framework of the 2-tethered ω-amino derivative was completely overlapped with the stacking GC base-pairs leading to the formation of the stable intercalative-complex, and that the framework of the 5-tethered ureido derivative was half overlapped leading to the formation of the unstable complex. Furthermore, there were good linear relationships between lnKa and the relative stabilities Srel of the complexes. Contrary to our expectation, there was no linear relationship between lnKa and IC50 against Sarcoma-180, NIH3T3, and HeLa S-3 cell lines. Copyright © 2016 Elsevier Ltd. All rights reserved.

  17. Docking studies on DNA-ligand interactions: building and application of a protocol to identify the binding mode.

    Science.gov (United States)

    Ricci, Clarisse G; Netz, Paulo A

    2009-08-01

    Despite DNA being an important target for several drugs, most of the docking programs are validated only for proteins and their ligands. In this paper, we used AutoDock 4.0 to perform self-dockings and cross dockings between two DNA ligands (a minor groove binder and an intercalator) and four distinct receptors: 1) crystallographic DNA without intercalation gap; 2) crystallographic DNA with intercalation gap; 3) canonical B-DNA; and 4) modified B-DNA with intercalation gap. Besides being efficient in self-dockings, AutoDock is capable of correctly identifying two of the main DNA binding modes with the condition that the target possesses an artificial intercalation gap. Therefore, we suggest a default protocol to identify DNA binding modes which uses a modified canonical DNA (with gap) as receptor. This protocol was applied to dock two different Troger bases to DNA and the predicted binding modes agree with those suggested, yet not established, by experimental data. We also applied the protocol to dock aflatoxin B(1) exo-8,9-epoxide, and the results are in complete agreement with experimental data from the literature. We propose that this approach can be used to investigate other ligands whose binding mode to DNA remains unknown, yielding a suitable starting point for further theoretical studies such as molecular dynamics simulations.

  18. New insights from molecular dynamic simulation studies of the multiple binding modes of a ligand with G-quadruplex DNA

    Science.gov (United States)

    Hou, Jin-Qiang; Chen, Shuo-Bin; Tan, Jia-Heng; Luo, Hai-Bin; Li, Ding; Gu, Lian-Quan; Huang, Zhi-Shu

    2012-12-01

    G-quadruplexes are higher-order DNA and RNA structures formed from guanine-rich sequences. These structures have recently emerged as a new class of potential molecular targets for anticancer drugs. An understanding of the three-dimensional interactions between small molecular ligands and their G-quadruplex targets in solution is crucial for rational drug design and the effective optimization of G-quadruplex ligands. Thus far, rational ligand design has been focused mainly on the G-quartet platform. It should be noted that small molecules can also bind to loop nucleotides, as observed in crystallography studies. Hence, it would be interesting to elucidate the mechanism underlying how ligands in distinct binding modes influence the flexibility of G-quadruplex. In the present study, based on a crystal structure analysis, the models of a tetra-substituted naphthalene diimide ligand bound to a telomeric G-quadruplex with different modes were built and simulated with a molecular dynamics simulation method. Based on a series of computational analyses, the structures, dynamics, and interactions of ligand-quadruplex complexes were studied. Our results suggest that the binding of the ligand to the loop is viable in aqueous solutions but dependent on the particular arrangement of the loop. The binding of the ligand to the loop enhances the flexibility of the G-quadruplex, while the binding of the ligand simultaneously to both the quartet and the loop diminishes its flexibility. These results add to our understanding of the effect of a ligand with different binding modes on G-quadruplex flexibility. Such an understanding will aid in the rational design of more selective and effective G-quadruplex binding ligands.

  19. An alternate mode of binding of the polyphenol quercetin with serum albumins when complexed with Cu(II)

    Energy Technology Data Exchange (ETDEWEB)

    Singha Roy, Atanu; Tripathy, Debi Ranjan; Ghosh, Arup Kumar [Department of Chemistry, Indian Institute of Technology, Kharagpur 721302 (India); Dasgupta, Swagata, E-mail: swagata@chem.iitkgp.ernet.in [Department of Chemistry, Indian Institute of Technology, Kharagpur 721302 (India)

    2012-11-15

    Polyphenols find wide use as antioxidants, cancer chemopreventive agents and metal chelators. The latter activity has proved interesting in many aspects. We have probed the binding characteristics of the polyphenol quercetin-Cu(II) complex with human serum albumin (HSA) and bovine serum albumin (BSA). Fluorescence studies reveal that the quercetin-Cu(II) complex can quench the fluorescence of the serum albumins. The binding constant (K{sub b}) values are of the order of 10{sup 5} M{sup -1} which increased with rise in temperature in case of HSA and BSA interacting with the quercetin-Cu(II) complex. Displacement studies reveal that both the ligands bind to site 1 (subdomain IIA) of the serum albumins. However, thermodynamic parameters calculated from temperature dependent studies indicated that the mode of interaction of the complexes with the proteins differs. Both {Delta}H Degree-Sign and {Delta}S Degree-Sign were positive for the interaction of the quercetin-Cu(II) complex with both proteins but the value of {Delta}H Degree-Sign was negative in case of the interaction of quercetin with the proteins. This implies that after chelation with metal ions, the polyphenol alters its mode of interaction which could have varying implications on its other physicochemical activities. - Research Highlights: Black-Right-Pointing-Pointer Mode of binding of quercetin with SAs is altered after complexation with Cu(II). Black-Right-Pointing-Pointer Hydrophobic forces play a key role in the binding of the copper complex with SAs. Black-Right-Pointing-Pointer Negative {Delta}G Degree-Sign values indicate the spontaneity of the binding processes. Black-Right-Pointing-Pointer Quercetin and its copper complex bind at the same site of the SAs.

  20. Crystal structure and RNA-binding properties of an Hfq homolog from the deep-branching Aquificae: conservation of the lateral RNA-binding mode

    Energy Technology Data Exchange (ETDEWEB)

    Stanek, Kimberly A.; Patterson-West, Jennifer; Randolph, Peter S.; Mura, Cameron

    2017-03-31

    The host factor Hfq, as the bacterial branch of the Sm family, is an RNA-binding protein involved in the post-transcriptional regulation of mRNA expression and turnover. Hfq facilitates pairing between small regulatory RNAs (sRNAs) and their corresponding mRNA targets by binding both RNAs and bringing them into close proximity. Hfq homologs self-assemble into homo-hexameric rings with at least two distinct surfaces that bind RNA. Recently, another binding site, dubbed the `lateral rim', has been implicated in sRNA·mRNA annealing; the RNA-binding properties of this site appear to be rather subtle, and its degree of evolutionary conservation is unknown. An Hfq homolog has been identified in the phylogenetically deep-branching thermophileAquifex aeolicus(Aae), but little is known about the structure and function of Hfq from basal bacterial lineages such as the Aquificae. Therefore,AaeHfq was cloned, overexpressed, purified, crystallized and biochemically characterized. Structures ofAaeHfq were determined in space groupsP1 andP6, both to 1.5 Å resolution, and nanomolar-scale binding affinities for uridine- and adenosine-rich RNAs were discovered. Co-crystallization with U6RNA reveals that the outer rim of theAaeHfq hexamer features a well defined binding pocket that is selective for uracil. ThisAaeHfq structure, combined with biochemical and biophysical characterization of the homolog, reveals deep evolutionary conservation of the lateral RNA-binding mode, and lays a foundation for further studies of Hfq-associated RNA biology in ancient bacterial phyla.

  1. Tracking binding modes of 1,2,4-trisubstituted imidazolinone P38 MAP kinase and ERK-2 inhibitors.

    Science.gov (United States)

    Rao, Shashidhar N

    2017-09-01

    Putative binding modes of recently reported p38 MAP Kinase and ERK-2 inhibitors containing 1,2,4-tri-substituted imidazolinone have been investigated using molecular docking methods In the case of p38 MAP Kinase, X-ray structures with both DFG-in and DFG-out conformations of the activation loop have been employed for docking studies. The present investigations demonstrate that the DFG-out conformation of the activation loop in p38 MAP Kinase accommodates the 1,2,4-tri-substituted imidazolinones with greater computed binding affinities than the alternative DFG-in conformation. The best scoring binding modes in ERK-2 are distinctly different from those found in the p38 MAP Kinase structures. Both sets of binding modes are characterized by an extensive network of hydrophobic and π-cation interactions, with the hinge region showing little hydrogen bonding propensity with the top-ranked poses. Thus, these docking studies provide a putative pathway for lead optimizations in which hydrogen bonding interactions with the hinge region residues are feasible. Copyright © 2017 Elsevier Inc. All rights reserved.

  2. Cation binding mode of fully oxidised calmodulin explained by the unfolding of the apostate.

    Science.gov (United States)

    Lafitte, Daniel; Tsvetkov, Philippe O; Devred, François; Toci, René; Barras, Frédéric; Briand, Claudette; Makarov, Alexander A; Haiech, Jacques

    2002-11-04

    Calmodulin is the most ubiquitous calcium binding protein. The protein is very sensitive to oxidation and this modification has pronounced effects on calmodulin function. In this work, we decided to fully oxidise calmodulin in order to study the consequences on cation binding, domain stability, and alpha helicity. Oxidation of methionines unfolds completely the apostate of the protein, which upon calcium binding recovers the major part of its secondary and tertiary structure. However, the unstructuring of the apostate results in a protein that binds calcium to any site in an independent manner, does not bind magnesium and does not possess auxiliary sites anymore.

  3. Improving binding mode and binding affinity predictions of docking by ligand-based search of protein conformations: evaluation in D3R grand challenge 2015

    Science.gov (United States)

    Xu, Xianjin; Yan, Chengfei; Zou, Xiaoqin

    2017-08-01

    The growing number of protein-ligand complex structures, particularly the structures of proteins co-bound with different ligands, in the Protein Data Bank helps us tackle two major challenges in molecular docking studies: the protein flexibility and the scoring function. Here, we introduced a systematic strategy by using the information embedded in the known protein-ligand complex structures to improve both binding mode and binding affinity predictions. Specifically, a ligand similarity calculation method was employed to search a receptor structure with a bound ligand sharing high similarity with the query ligand for the docking use. The strategy was applied to the two datasets (HSP90 and MAP4K4) in recent D3R Grand Challenge 2015. In addition, for the HSP90 dataset, a system-specific scoring function (ITScore2_hsp90) was generated by recalibrating our statistical potential-based scoring function (ITScore2) using the known protein-ligand complex structures and the statistical mechanics-based iterative method. For the HSP90 dataset, better performances were achieved for both binding mode and binding affinity predictions comparing with the original ITScore2 and with ensemble docking. For the MAP4K4 dataset, although there were only eight known protein-ligand complex structures, our docking strategy achieved a comparable performance with ensemble docking. Our method for receptor conformational selection and iterative method for the development of system-specific statistical potential-based scoring functions can be easily applied to other protein targets that have a number of protein-ligand complex structures available to improve predictions on binding.

  4. On the verification of binding modes of p-dimethylaminobenzaldehyde thiosemicarbazone with mercury(II). The solid state studies

    Science.gov (United States)

    Trzesowska-Kruszynska, Agata

    2014-08-01

    Two coordination compounds of p-dimethylaminobenzaldehyde thiosemicarbazone, fluorescent chemosensor, have been synthesised from the mercury(II) nitrate and mercury(II) chloride, and subsequently characterised by IR spectroscopy, thermal analysis, as well as single crystal X-ray diffraction technique. The inorganic anion has a distinct influence on binding mode of thiosemicarbazone ligand to Hg(II) ion. In both compounds the metal to ligand stoichiometry is 1:2 and the organic ligands coordinate to Hg ion in the neutral thione form, but they differ in a ligand binding mode and the conformation of the ligand. The crystal packing of mercury(II) nitrate complex with thiosemicarbazone is controlled by the mercury chelate ring-phenylene ring π···π stacking interactions.

  5. Discovery of a Potent Class of PI3Kα Inhibitors with Unique Binding Mode via Encoded Library Technology (ELT).

    Science.gov (United States)

    Yang, Hongfang; Medeiros, Patricia F; Raha, Kaushik; Elkins, Patricia; Lind, Kenneth E; Lehr, Ruth; Adams, Nicholas D; Burgess, Joelle L; Schmidt, Stanley J; Knight, Steven D; Auger, Kurt R; Schaber, Michael D; Franklin, G Joseph; Ding, Yun; DeLorey, Jennifer L; Centrella, Paolo A; Mataruse, Sibongile; Skinner, Steven R; Clark, Matthew A; Cuozzo, John W; Evindar, Ghotas

    2015-05-14

    In the search of PI3K p110α wild type and H1047R mutant selective small molecule leads, an encoded library technology (ELT) campaign against the desired target proteins was performed which led to the discovery of a selective chemotype for PI3K isoforms from a three-cycle DNA encoded library. An X-ray crystal structure of a representative inhibitor from this chemotype demonstrated a unique binding mode in the p110α protein.

  6. Inhibitor-binding mode of homobelactosin C to proteasomes: New insights into class I MHC ligand generation

    Science.gov (United States)

    Groll, Michael; Larionov, Oleg V.; Huber, Robert; de Meijere, Armin

    2006-01-01

    Most class I MHC ligands are generated from the vast majority of cellular proteins by proteolysis within the ubiquitin–proteasome pathway and are presented on the cell surface by MHC class I molecules. Here, we present the crystallographic analysis of yeast 20S proteasome in complex with the inhibitor homobelactosin C. The structure reveals a unique inhibitor-binding mode and provides information about the composition of proteasomal primed substrate-binding sites. IFN-γ inducible substitution of proteasomal constitutive subunits by immunosubunits modulates characteristics of generated peptides, thus producing fragments with higher preference for binding to MHC class I molecules. The structural data for the proteasome:homobelactosin C complex provide an explanation for involvement of immunosubunits in antigen generation and open perspectives for rational design of ligands, inhibiting exclusively constitutive proteasomes or immunoproteasomes. PMID:16537370

  7. Research on anti-HIV-1 agents. Investigation on the CD4-Suradista binding mode through docking experiments

    Science.gov (United States)

    Manetti, Fabrizio; Corelli, Federico; Mongelli, Nicola; Lombardi Borgia, Andrea; Botta, Maurizio

    2000-05-01

    Sulfonated distamycin (Suradista) derivatives exhibit anti-HIV-1 activity by inhibiting the binding of the viral envelope glycoprotein gp120 to its receptor (CD4). With the aim to propose a possible binding mode between Suradistas and the CD4 macromolecule, molecular docking experiments, followed by energy minimization of the complexes thus obtained, were performed. Computational results show that ligand binding at the CD4 surface involves two or three positively charged regions of the macromolecule, in agreement with the results of X-ray crystallographic analysis of a ternary complex (CD4/gp120/neutralizing antibody) recently reported in the literature. Our findings account well for the structure-activity relationship found for Suradista compounds.

  8. The Binding Mode of the Sonic Hedgehog Inhibitor Robotnikinin, a Combined Docking and QM/MM MD Study

    Directory of Open Access Journals (Sweden)

    Manuel Hitzenberger

    2017-10-01

    Full Text Available Erroneous activation of the Hedgehog pathway has been linked to a great amount of cancerous diseases and therefore a large number of studies aiming at its inhibition have been carried out. One leverage point for novel therapeutic strategies targeting the proteins involved, is the prevention of complex formation between the extracellular signaling protein Sonic Hedgehog and the transmembrane protein Patched 1. In 2009 robotnikinin, a small molecule capable of binding to and inhibiting the activity of Sonic Hedgehog has been identified, however in the absence of X-ray structures of the Sonic Hedgehog-robotnikinin complex, the binding mode of this inhibitor remains unknown. In order to aid with the identification of novel Sonic Hedgehog inhibitors, the presented investigation elucidates the binding mode of robotnikinin by performing an extensive docking study, including subsequent molecular mechanical as well as quantum mechanical/molecular mechanical molecular dynamics simulations. The attained configurations enabled the identification of a number of key protein-ligand interactions, aiding complex formation and providing stabilizing contributions to the binding of the ligand. The predicted structure of the Sonic Hedgehog-robotnikinin complex is provided via a PDB file as Supplementary Material and can be used for further reference.

  9. Definition of the binding mode of phosphoinositide 3-kinase α-selective inhibitor A-66S through molecular dynamics simulation.

    Science.gov (United States)

    Bian, Xiaoli; Dong, Wangqing; Zhao, Yang; Sun, Rui; Kong, Wanjun; Li, Yiping

    2014-04-01

    Activation of the phosphatidylinositol 3-kinase α (PI3Kα) is commonly observed in human cancer and is critical for tumor progression, which has made PI3Kα an attractive target for anticancer drug discovery. To systematically investigate the binding mode of A-66S, a new selective PI3Kα inhibitor for PI3Kα, molecular docking, molecular dynamics simulation and ensuing energetic analysis were performed. The binding free energy between PI3Kα and A-66S is -11.27 kcal•mol⁻¹ using MMPBSA method, while -14.67 kcal•mol⁻¹ using MMGBSA method, which is beneficial for the binding, and the van der Waals/hydrophobic and electrostatic interactions are critical for the binding. The conserved hydrophobic adenine region of PI3Kα made up of Met772, Pro778, Ile800, Tyr836, Ile848, Val850, Val851, Met922, Phe930 and Ile932 accommodates the flat 2-tert-butyl-4'-methyl-4,5'-bithiazol moiety of A-66S, and the NH of Val851 forms a hydrogen with the nitrogen atom embedded in the aminothiazole ring of A-66S. The (S)-pyrrolidine carboxamide urea moiety especially extends toward the region of the binding site wall (Ser854-Gln859) defined by the C-terminal lobe, and has three hydrogen-bond arms with the backbone of Ser854 and the side chain of Gln859. Notably the interaction between the non-conserved residue Gln859 and A-66S is responsible for the selectivity profile of A-66S. The binding mode of A-66S for PI3Kα presented in this study should aid in the design of a new highly selective PI3Kα inhibitor.

  10. Structural combination of established 5-HT(2A) receptor ligands: new aspects of the binding mode

    DEFF Research Database (Denmark)

    Kramer, Vasko; Herth, Matthias M; Santini, Martin A

    2010-01-01

    the binding properties of new compounds. Three new derivatives were synthesized with a 4-benzoyl-piperidine moiety as the lead structure. The in vitro affinity of the novel compounds was determined by a [³H]MDL 100907 competition binding assay. The combination of MH.MZ and SR 46349B resulted in a compound (8...

  11. Characterization of the modes of binding between human sweet taste receptor and low-molecular-weight sweet compounds.

    Directory of Open Access Journals (Sweden)

    Katsuyoshi Masuda

    Full Text Available One of the most distinctive features of human sweet taste perception is its broad tuning to chemically diverse compounds ranging from low-molecular-weight sweeteners to sweet-tasting proteins. Many reports suggest that the human sweet taste receptor (hT1R2-hT1R3, a heteromeric complex composed of T1R2 and T1R3 subunits belonging to the class C G protein-coupled receptor family, has multiple binding sites for these sweeteners. However, it remains unclear how the same receptor recognizes such diverse structures. Here we aim to characterize the modes of binding between hT1R2-hT1R3 and low-molecular-weight sweet compounds by functional analysis of a series of site-directed mutants and by molecular modeling-based docking simulation at the binding pocket formed on the large extracellular amino-terminal domain (ATD of hT1R2. We successfully determined the amino acid residues responsible for binding to sweeteners in the cleft of hT1R2 ATD. Our results suggest that individual ligands have sets of specific residues for binding in correspondence with the chemical structures and other residues responsible for interacting with multiple ligands.

  12. Diverse p53/DNA binding modes expand the repertoire of p53 response elements.

    Science.gov (United States)

    Vyas, Pratik; Beno, Itai; Xi, Zhiqun; Stein, Yan; Golovenko, Dmitrij; Kessler, Naama; Rotter, Varda; Shakked, Zippora; Haran, Tali E

    2017-10-03

    The tumor suppressor protein p53 acts as a transcription factor, binding sequence-specifically to defined DNA sites, thereby activating the expression of genes leading to diverse cellular outcomes. Canonical p53 response elements (REs) are made of two decameric half-sites separated by a variable number of base pairs (spacers). Fifty percent of all validated p53 REs contain spacers between 1 and 18 bp; however, their functional significance is unclear at present. Here, we show that p53 forms two different tetrameric complexes with consensus or natural REs, both with long spacers: a fully specific complex where two p53 dimers bind to two specific half-sites, and a hemispecific complex where one dimer binds to a specific half-site and the second binds to an adjacent spacer sequence. The two types of complexes have comparable binding affinity and specificity, as judged from binding competition against bulk genomic DNA. Structural analysis of the p53 REs in solution shows that these sites are not bent in both their free and p53-bound states when the two half-sites are either abutting or separated by spacers. Cell-based assay supports the physiological relevance of our findings. We propose that p53 REs with long spacers comprise separate specific half-sites that can lead to several different tetrameric complexes. This finding expands the universe of p53 binding sites and demonstrates that even isolated p53 half-sites can form tetrameric complexes. Moreover, it explains the manner in which p53 binds to clusters of more than one canonical binding site, common in many natural REs.

  13. Glycosaminoglycans are interactants of Langerin: comparison with gp120 highlights an unexpected calcium-independent binding mode.

    Directory of Open Access Journals (Sweden)

    Eric Chabrol

    Full Text Available Langerin is a C-type lectin specifically expressed in Langerhans cells. As recently shown for HIV, Langerin is thought to capture pathogens and mediate their internalisation into Birbeck Granules for elimination. However, the precise functions of Langerin remain elusive, mostly because of the lack of information on its binding properties and physiological ligands. Based on recent reports that Langerin binds to sulfated sugars, we conducted here a comparative analysis of Langerin interaction with mannose-rich HIV glycoprotein gp120 and glycosaminoglycan (GAGs, a family of sulfated polysaccharides expressed at the surface of most mammalian cells. Our results first revealed that Langerin bound to these different glycans through very distinct mechanisms and led to the identification of a novel, GAG-specific binding mode within Langerin. In contrast to the canonical lectin domain, this new binding site showed no Ca(2+-dependency, and could only be detected in entire, trimeric extracellular domains of Langerin. Interestingly binding to GAGs, did not simply rely on a net charge effect, but rather on more discrete saccharide features, such as 6-O-sulfation, or iduronic acid content. Using molecular modelling simulations, we proposed a model of Langerin/heparin complex, which located the GAG binding site at the interface of two of the three Carbohydrate-recognition domains of the protein, at the edge of the a-helix coiled-coil. To our knowledge, the binding properties that we have highlighted here for Langerin, have never been reported for C-type lectins before. These findings provide new insights towards the understanding of Langerin biological functions.

  14. A comprehensive approach to ascertain the binding mode of curcumin with DNA

    Science.gov (United States)

    Haris, P.; Mary, Varughese; Aparna, P.; Dileep, K. V.; Sudarsanakumar, C.

    2017-03-01

    Curcumin is a natural phytochemical from the rhizoma of Curcuma longa, the popular Indian spice that exhibits a wide range of pharmacological properties like antioxidant, anticancer, anti-inflammatory, antitumor, and antiviral activities. In the published literatures we can see different studies and arguments on the interaction of curcumin with DNA. The intercalative binding, groove binding and no binding of curcumin with DNA were reported. In this context, we conducted a detailed study to understand the mechanism of recognition of dimethylsulfoxide-solubilized curcumin by DNA. The interaction of curcumin with calf thymus DNA (ctDNA) was confirmed by agarose gel electrophoresis. The nature of binding and energetics of interaction were studied by Isothermal Titration Calorimetry (ITC), Differential Scanning Calorimetry (DSC), UV-visible, fluorescence and melting temperature (Tm) analysis. The experimental data were compared with molecular modeling studies. Our investigation confirmed that dimethylsulfoxide-solubilized curcumin binds in the minor groove of the ctDNA without causing significant structural alteration to the DNA.

  15. Binding mode similarity measures for ranking of docking poses: a case study on the adenosine A2A receptor

    Science.gov (United States)

    Anighoro, Andrew; Bajorath, Jürgen

    2016-06-01

    We report an investigation designed to explore alternative approaches for ranking of docking poses in the search for antagonists of the adenosine A2A receptor, an attractive target for structure-based virtual screening. Calculation of 3D similarity of docking poses to crystallographic ligand(s) as well as similarity of receptor-ligand interaction patterns was consistently superior to conventional scoring functions for prioritizing antagonists over decoys. Moreover, the use of crystallographic antagonists and agonists, a core fragment of an antagonist, and a model of an agonist placed into the binding site of an antagonist-bound form of the receptor resulted in a significant early enrichment of antagonists in compound rankings. Taken together, these findings showed that the use of binding modes of agonists and/or antagonists, even if they were only approximate, for similarity assessment of docking poses or comparison of interaction patterns increased the odds of identifying new active compounds over conventional scoring.

  16. A unique binding mode enables MCM2 to chaperone histones H3-H4 at replication forks

    DEFF Research Database (Denmark)

    Huang, Hongda; Strømme, Caroline B; Saredi, Giulia

    2015-01-01

    During DNA replication, chromatin is reassembled by recycling of modified old histones and deposition of new ones. How histone dynamics integrates with DNA replication to maintain genome and epigenome information remains unclear. Here, we reveal how human MCM2, part of the replicative helicase...... for MCM2-7 histone-chaperone function and normal cell proliferation. Further, we show that MCM2 can chaperone both new and old canonical histones H3-H4 as well as H3.3 and CENPA variants. The unique histone-binding mode of MCM2 thus endows the replicative helicase with ideal properties for recycling...... histones genome wide during DNA replication....

  17. Interconvertible geometric isomers of Plasmodium falciparum dihydroorotate dehydrogenase inhibitors exhibit multiple binding modes.

    Science.gov (United States)

    McConkey, Glenn A; Bedingfield, Paul T P; Burrell, David R; Chambers, Nicholas C; Cunningham, Fraser; Prior, Timothy J; Fishwick, Colin W G; Boa, Andrew N

    2017-08-15

    Two new tricyclic β-aminoacrylate derivatives (2e and 3e) have been found to be inhibitors of Plasmodium falciparum dihydroorotate dehydrogenase (PfDHODH) with Ki 0.037 and 0.15μM respectively. 1H and 13C NMR spectroscopic data show that these compounds undergo ready cis-trans isomerisation at room temperature in polar solvents. In silico docking studies indicate that for both molecules there is neither conformation nor double bond configuration which bind preferentially to PfDHODH. This flexibility is favourable for inhibitors of this channel that require extensive positioning to reach their binding site. Copyright © 2017 Elsevier Ltd. All rights reserved.

  18. Determination of Vanadium Binding Mode on Seawater-Contacted Polyamidoxime Adsorbents

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Zhicheng [Lawrence Berkeley National Laboratory (LBNL); Rao, Linfeng [Lawrence Berkeley National Laboratory (LBNL); Abney, Carter W. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Bryantsev, Vyacheslav [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Ivanov, Aleksandr [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

    2017-09-01

    Adsorbents developed for the recovery of uranium from seawater display poor selectivity over other transition metals present in the ocean, with vanadium particularly problematic. To improve selectivity, an indispensable step is the positive identification of metal binding environments following actual seawater deployment. In this work we apply x-ray absorption fine structure (XAFS) spectroscopy to directly investigate the vanadium binding environment on seawater-deployed polyamidoxime adsorbents. Comparison of the x-ray absorption near edge spectra (XANES) reveal marked similarities to recently a reported non-oxido vanadium (V) structure formed upon binding with cyclic imidedioxime, a byproduct of generating amidoxime functionalities. Density functional theory (DFT) calculations provided a series of putative vanadium binding environments for both vanadium (IV) and vanadium (V) oxidation states, and with both amidoxime and cyclic imidedioxime. Fits of the extended XAFS (EXAFS) data confirmed vanadium (V) is bound exclusively by the cyclic imidedioxime moiety in a 1:2 metal:ligand fashion, though a modest structural distortion is also observed compared to crystal structure data and computationally optimized geometries which is attributed to morphology effects from the polymer graft chain and the absence of crystal packing interactions. These results demonstrate that improved selectivity for uranium over vanadium can be achieved by suppressing the formation of cyclic imidedioxime during preparation of polyamidoxime adsorbents for seawater uranium recovery.

  19. PEPTIDE BINDING AS A MODE OF ACTION FOR THE CARCINOGENICITY AND TOXICITY OF ARSENIC

    Science.gov (United States)

    Arsenic exposure leads to tumors in human skin, lung, urinary bladder, kidney and liver. Three likely initial stages of arsenical-macromolecular interaction are (1) binding of trivalent arsenicals to the sulfhydryl groups of peptides and proteins, (2) arsenical-induced generation...

  20. Machine Learning Reveals a Non-Canonical Mode of Peptide Binding to MHC class II Molecules

    DEFF Research Database (Denmark)

    Andreatta, Massimo; Jurtz, Vanessa Isabell; Kaever, Thomas

    2017-01-01

    MHC class II molecules play a fundamental role in the cellular immune system: they load short peptide fragments derived from extracellular proteins and present them on the cell surface. It is currently thought that the peptide binds lying more or less flat in the MHC groove, with a fixed distance...

  1. MtrA of the sodium ion pumping methyltransferase binds cobalamin in a unique mode.

    Science.gov (United States)

    Wagner, Tristan; Ermler, Ulrich; Shima, Seigo

    2016-06-21

    In the three domains of life, vitamin B12 (cobalamin) is primarily used in methyltransferase and isomerase reactions. The methyltransferase complex MtrA-H of methanogenic archaea has a key function in energy conservation by catalysing the methyl transfer from methyl-tetrahydromethanopterin to coenzyme M and its coupling with sodium-ion translocation. The cobalamin-binding subunit MtrA is not homologous to any known B12-binding proteins and is proposed as the motor of the sodium-ion pump. Here, we present crystal structures of the soluble domain of the membrane-associated MtrA from Methanocaldococcus jannaschii and the cytoplasmic MtrA homologue/cobalamin complex from Methanothermus fervidus. The MtrA fold corresponds to the Rossmann-type α/β fold, which is also found in many cobalamin-containing proteins. Surprisingly, the cobalamin-binding site of MtrA differed greatly from all the other cobalamin-binding sites. Nevertheless, the hydrogen-bond linkage at the lower axial-ligand site of cobalt was equivalently constructed to that found in other methyltransferases and mutases. A distinct polypeptide segment fixed through the hydrogen-bond linkage in the relaxed Co(III) state might be involved in propagating the energy released upon corrinoid demethylation to the sodium-translocation site by a conformational change.

  2. DNA binding, DNA cleavage and cytotoxicity studies of a new water soluble copper(II) complex: the effect of ligand shape on the mode of binding.

    Science.gov (United States)

    Kashanian, Soheila; Khodaei, Mohammad Mehdi; Roshanfekr, Hamideh; Shahabadi, Nahid; Mansouri, Ghobad

    2012-02-01

    The interaction of native calf thymus DNA (CT-DNA) with [Cu(ph(2)phen)(phen-dione)Cl]Cl was studied at physiological pH by spectrophotometric, spectrofluorometric, circular dichroism, and viscometric techniques. Considerable hypochromicity and red shift are observed in the UV absorption band of the Cu complex. Binding constants (K(b)) of DNA with the complex were calculated at different temperatures. Thermodynamic parameters, enthalpy and entropy changes were calculated according to Van't Hoff equation, which indicated that reaction is predominantly enthalpically driven. All these results indicate that Cu(II) complex interacts with CT-DNA via intercalative mode. Also, this new complex induced cleavage in pUC18 plasmid DNA as indicated in gel electrophoresis and showed excellent antitumor activity against K562 (human chronic myeloid leukemia) and human T lymphocyte carcinoma-Jurkat cell lines. Copyright © 2011 Elsevier B.V. All rights reserved.

  3. Asymmetric binding to NS5A by daclatasvir (BMS-790052) and analogs suggests two novel modes of HCV inhibition.

    Science.gov (United States)

    Nettles, James H; Stanton, Richard A; Broyde, Joshua; Amblard, Franck; Zhang, Hongwang; Zhou, Longhu; Shi, Junxing; McBrayer, Tamara R; Whitaker, Tony; Coats, Steven J; Kohler, James J; Schinazi, Raymond F

    2014-12-11

    Symmetric, dimeric daclatasvir (BMS-790052) is the clinical lead for a class of picomolar inhibitors of HCV replication. While specific, resistance-bearing mutations at positions 31 and 93 of domain I strongly suggest the viral NS5A as target, structural mechanism(s) for the drugs' activities and resistance remains unclear. Several previous models suggested symmetric binding modes relative to the homodimeric target; however, none can fully explain SAR details for this class. We present semiautomated workflows to model potential receptor conformations for docking. Surprisingly, ranking docked hits with our library-derived 3D-pharmacophore revealed two distinct asymmetric binding modes, at a conserved poly-proline region between 31 and 93, consistent with SAR. Interfering with protein-protein interactions at this membrane interface can explain potent inhibition of replication-complex formation, resistance, effects on lipid droplet distribution, and virion release. These detailed interaction models and proposed mechanisms of action will allow structure-based design of new NS5A directed compounds with higher barriers to HCV resistance.

  4. Implications of binding mode and active site flexibility for inhibitor potency against the salicylate synthase from Mycobacterium tuberculosis.

    Science.gov (United States)

    Chi, Gamma; Manos-Turvey, Alexandra; O'Connor, Patrick D; Johnston, Jodie M; Evans, Genevieve L; Baker, Edward N; Payne, Richard J; Lott, J Shaun; Bulloch, Esther M M

    2012-06-19

    MbtI is the salicylate synthase that catalyzes the first committed step in the synthesis of the iron chelating compound mycobactin in Mycobacterium tuberculosis. We previously developed a series of aromatic inhibitors against MbtI based on the reaction intermediate for this enzyme, isochorismate. The most potent of these inhibitors had hydrophobic substituents, ranging in size from a methyl to a phenyl group, appended to the terminal alkene of the enolpyruvyl group. These compounds exhibited low micromolar inhibition constants against MbtI and were at least an order of magnitude more potent than the parental compound for the series, which carries a native enolpyruvyl group. In this study, we sought to understand how the substituted enolpyruvyl group confers greater potency, by determining cocrystal structures of MbtI with six inhibitors from the series. A switch in binding mode at the MbtI active site is observed for inhibitors carrying a substituted enolpyruvyl group, relative to the parental compound. Computational studies suggest that the change in binding mode, and higher potency, is due to the effect of the substituents on the conformational landscape of the core inhibitor structure. The crystal structures and fluorescence-based thermal shift assays indicate that substituents larger than a methyl group are accommodated in the MbtI active site through significant but localized flexibility in the peptide backbone. These findings have implications for the design of improved inhibitors of MbtI, as well as other chorismate-utilizing enzymes from this family.

  5. Multiple DNA-binding modes for the ETS family transcription factor PU.1.

    Science.gov (United States)

    Esaki, Shingo; Evich, Marina G; Erlitzki, Noa; Germann, Markus W; Poon, Gregory M K

    2017-09-29

    The eponymous DNA-binding domain of ETS ( E 26 t ransformation- s pecific) transcription factors binds a single sequence-specific site as a monomer over a single helical turn. Following our previous observation by titration calorimetry that the ETS member PU.1 dimerizes sequentially at a single sequence-specific DNA-binding site to form a 2:1 complex, we have carried out an extensive spectroscopic and biochemical characterization of site-specific PU.1 ETS complexes. Whereas 10 bp of DNA was sufficient to support PU.1 binding as a monomer, additional flanking bases were required to invoke sequential dimerization of the bound protein. NMR spectroscopy revealed a marked loss of signal intensity in the 2:1 complex, and mutational analysis implicated the distal surface away from the bound DNA as the dimerization interface. Hydroxyl radical DNA footprinting indicated that the site-specifically bound PU.1 dimers occupied an extended DNA interface downstream from the 5'-GGAA-3' core consensus relative to its 1:1 counterpart, thus explaining the apparent site size requirement for sequential dimerization. The site-specifically bound PU.1 dimer resisted competition from nonspecific DNA and showed affinities similar to other functionally significant PU.1 interactions. As sequential dimerization did not occur with the ETS domain of Ets-1, a close structural homolog of PU.1, 2:1 complex formation may represent an alternative autoinhibitory mechanism in the ETS family at the protein-DNA level. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  6. Calculating the contribution of different binding modes to Quinacrine - DNA complex formation from polarized fluorescence data

    CERN Document Server

    Voloshin, Igor; Karachevtsev, Victor; Zozulya, Victor

    2013-01-01

    Binding of acridine derivative quinacrine (QA) to chicken erythrocyte DNA was studied by methods of absorption and polarized fluorescent spectroscopy. Measurements were carried out in aqueous buffered solutions (pH 6.9) of different dye concentrations (QA concentration range from $10^{-6}$ till $10^{-4}$ M) and ionic strengths ($Na^{+}$ concentration rang from $10^{-3}$ till 0.15 M) in a wide range of phosphate-to-dye molar ratios ($P/D$). It is established that the minimum of fluorescent titration curve plotted as relative fluorescence intensity $vs$ $P/D$ is conditioned by the competition between the two types of QA binding to DNA which posses by different emission parameters: (i) intercalative one dominating under high $P/D$ values, and (ii) outside electrostatic binding dominating under low $P/D$ values, which is accompanied by the formation of non-fluorescent dye associates on the DNA backbone. Absorption and fluorescent characteristics of complexes formed were determined. The method of calculation of di...

  7. A Novel, “Double-Clamp” Binding Mode for Human Heme Oxygenase-1 Inhibition

    Science.gov (United States)

    Rahman, Mona N.; Vlahakis, Jason Z.; Vukomanovic, Dragic; Lee, Wallace; Szarek, Walter A.; Nakatsu, Kanji; Jia, Zongchao

    2012-01-01

    The development of heme oxygenase (HO) inhibitors is critical in dissecting and understanding the HO system and for potential therapeutic applications. We have established a program to design and optimize HO inhibitors using structure-activity relationships in conjunction with X-ray crystallographic analyses. One of our previous complex crystal structures revealed a putative secondary hydrophobic binding pocket which could be exploited for a new design strategy by introducing a functional group that would fit into this potential site. To test this hypothesis and gain further insights into the structural basis of inhibitor binding, we have synthesized and characterized 1-(1H-imidazol-1-yl)-4,4-diphenyl-2-butanone (QC-308). Using a carbon monoxide (CO) formation assay on rat spleen microsomes, the compound was found to be ∼15 times more potent (IC50 = 0.27±0.07 µM) than its monophenyl analogue, which is already a potent compound in its own right (QC-65; IC50 = 4.0±1.8 µM). The crystal structure of hHO-1 with QC-308 revealed that the second phenyl group in the western region of the compound is indeed accommodated by a definitive secondary proximal hydrophobic pocket. Thus, the two phenyl moieties are each stabilized by distinct hydrophobic pockets. This “double-clamp” binding offers additional inhibitor stabilization and provides a new route for improvement of human heme oxygenase inhibitors. PMID:22276118

  8. A novel, "double-clamp" binding mode for human heme oxygenase-1 inhibition.

    Science.gov (United States)

    Rahman, Mona N; Vlahakis, Jason Z; Vukomanovic, Dragic; Lee, Wallace; Szarek, Walter A; Nakatsu, Kanji; Jia, Zongchao

    2012-01-01

    The development of heme oxygenase (HO) inhibitors is critical in dissecting and understanding the HO system and for potential therapeutic applications. We have established a program to design and optimize HO inhibitors using structure-activity relationships in conjunction with X-ray crystallographic analyses. One of our previous complex crystal structures revealed a putative secondary hydrophobic binding pocket which could be exploited for a new design strategy by introducing a functional group that would fit into this potential site. To test this hypothesis and gain further insights into the structural basis of inhibitor binding, we have synthesized and characterized 1-(1H-imidazol-1-yl)-4,4-diphenyl-2-butanone (QC-308). Using a carbon monoxide (CO) formation assay on rat spleen microsomes, the compound was found to be ∼15 times more potent (IC(50) = 0.27±0.07 µM) than its monophenyl analogue, which is already a potent compound in its own right (QC-65; IC(50) = 4.0±1.8 µM). The crystal structure of hHO-1 with QC-308 revealed that the second phenyl group in the western region of the compound is indeed accommodated by a definitive secondary proximal hydrophobic pocket. Thus, the two phenyl moieties are each stabilized by distinct hydrophobic pockets. This "double-clamp" binding offers additional inhibitor stabilization and provides a new route for improvement of human heme oxygenase inhibitors.

  9. A novel, "double-clamp" binding mode for human heme oxygenase-1 inhibition.

    Directory of Open Access Journals (Sweden)

    Mona N Rahman

    Full Text Available The development of heme oxygenase (HO inhibitors is critical in dissecting and understanding the HO system and for potential therapeutic applications. We have established a program to design and optimize HO inhibitors using structure-activity relationships in conjunction with X-ray crystallographic analyses. One of our previous complex crystal structures revealed a putative secondary hydrophobic binding pocket which could be exploited for a new design strategy by introducing a functional group that would fit into this potential site. To test this hypothesis and gain further insights into the structural basis of inhibitor binding, we have synthesized and characterized 1-(1H-imidazol-1-yl-4,4-diphenyl-2-butanone (QC-308. Using a carbon monoxide (CO formation assay on rat spleen microsomes, the compound was found to be ∼15 times more potent (IC(50 = 0.27±0.07 µM than its monophenyl analogue, which is already a potent compound in its own right (QC-65; IC(50 = 4.0±1.8 µM. The crystal structure of hHO-1 with QC-308 revealed that the second phenyl group in the western region of the compound is indeed accommodated by a definitive secondary proximal hydrophobic pocket. Thus, the two phenyl moieties are each stabilized by distinct hydrophobic pockets. This "double-clamp" binding offers additional inhibitor stabilization and provides a new route for improvement of human heme oxygenase inhibitors.

  10. Binding Mode Analysis of Zerumbone to Key Signal Proteins in the Tumor Necrosis Factor Pathway

    Science.gov (United States)

    Fatima, Ayesha; Abdul, Ahmad Bustamam Hj.; Abdullah, Rasedee; Karjiban, Roghayeh Abedi; Lee, Vannajan Sanghiran

    2015-01-01

    Breast cancer is the second most common cancer among women worldwide. Several signaling pathways have been implicated as causative and progression agents. The tumor necrosis factor (TNF) α protein plays a dual role in promoting and inhibiting cancer depending largely on the pathway initiated by the binding of the protein to its receptor. Zerumbone, an active constituent of Zingiber zerumbet, Smith, is known to act on the tumor necrosis factor pathway upregulating tumour necrosis factor related apoptosis inducing ligand (TRAIL) death receptors and inducing apoptosis in cancer cells. Zerumbone is a sesquiterpene that is able to penetrate into the hydrophobic pockets of proteins to exert its inhibiting activity with several proteins. We found a good binding with the tumor necrosis factor, kinase κB (IKKβ) and the Nuclear factor κB (NF-κB) component proteins along the TNF pathway. Our results suggest that zerumbone can exert its apoptotic activities by inhibiting the cytoplasmic proteins. It inhibits the IKKβ kinase that activates the NF-κB and also binds to the NF-κB complex in the TNF pathway. Blocking both proteins can lead to inhibition of cell proliferating proteins to be downregulated and possibly ultimate induction of apoptosis. PMID:25629232

  11. Binding modes of phosphonic acid derivatives adsorbed on TiO2 surfaces: Assignments of experimental IR and NMR spectra based on DFT/PBC calculations

    Science.gov (United States)

    Geldof, D.; Tassi, M.; Carleer, R.; Adriaensens, P.; Roevens, A.; Meynen, V.; Blockhuys, F.

    2017-01-01

    A DFT study on the adsorption of a series of phosphonic acids (PAs) on the TiO2 anatase (101) and (001) surfaces was performed. The adsorption energies and geometries of the most stable binding modes were compared to literature data and the effect of the inclusion of dispersion forces in the energy calculations was gauged. As the (101) surface is the most exposed surface of TiO2 anatase, the calculated chemical shifts and vibrational frequencies of PAs adsorbed on this surface were compared to experimental 31P and 17O NMR and IR data in order to assign the two possible binding modes (mono- and bidentate) to peaks and bands in these spectra; due to the corrugated nature of anatase (101) tridentate binding is not possible on this surface. Analysis of the calculated and experimental 31P chemical shifts indicates that both monodentate and bidentate binding modes are present. For the reactive (001) surface, the results of the calculations indicate that both bi- and tridentate binding modes result in stable systems. Due to the particular sensitivity of 17O chemical shifts to hydrogen bonding and solvent effects, the model used is insufficient to assign these spectra at present. Comparison of calculated and experimental IR spectra leads to the conclusion that IR spectroscopy is not suitable for the characterization of the different binding modes of the adsorption complexes.

  12. A Comparative Structure/Function Analysis of Two Type IV Pilin DNA Receptors Defines a Novel Mode of DNA Binding.

    Science.gov (United States)

    Berry, Jamie-Lee; Xu, Yingqi; Ward, Philip N; Lea, Susan M; Matthews, Stephen J; Pelicic, Vladimir

    2016-06-07

    DNA transformation is a widespread process allowing bacteria to capture free DNA by using filamentous nano-machines composed of type IV pilins. These proteins can act as DNA receptors as demonstrated by the finding that Neisseria meningitidis ComP minor pilin has intrinsic DNA-binding ability. ComP binds DNA better when it contains the DNA-uptake sequence (DUS) motif abundant in this species genome, playing a role in its trademark ability to selectively take up its own DNA. Here, we report high-resolution structures for meningococcal ComP and Neisseria subflava ComPsub, which recognize different DUS motifs. We show that they are structurally identical type IV pilins that pack readily into filament models and display a unique DD region delimited by two disulfide bonds. Functional analysis of ComPsub defines a new mode of DNA binding involving the DD region, adapted for exported DNA receptors. Copyright © 2016 The Author(s). Published by Elsevier Ltd.. All rights reserved.

  13. Molecular Dynamics Simulations to Investigate the Binding Mode of the Natural Product Liphagal with Phosphoinositide 3-Kinase α

    Directory of Open Access Journals (Sweden)

    Yanjuan Gao

    2016-06-01

    Full Text Available Phosphatidylinositol 3-kinase α (PI3Kα is an attractive target for anticancer drug design. Liphagal, isolated from the marine sponge Aka coralliphaga, possesses the special “liphagane” meroterpenoid carbon skeleton and has been demonstrated as a PI3Kα inhibitor. Molecular docking and molecular dynamics simulations were performed to explore the dynamic behaviors of PI3Kα binding with liphagal, and free energy calculations and energy decomposition analysis were carried out by use of molecular mechanics/Poisson-Boltzmann (generalized Born surface area (MM/PB(GBSA methods. The results reveal that the heteroatom rich aromatic D-ring of liphagal extends towards the polar region of the binding site, and the D-ring 15-hydroxyl and 16-hydroxyl form three hydrogen bonds with Asp810 and Tyr836. The cyclohexyl A-ring projects up into the upper pocket of the lipophilic region, and the hydrophobic/van der Waals interactions with the residues Met772, Trp780, Ile800, Ile848, Val850, Met922, Phe930, Ile932 could be the key interactions for the affinity of liphagal to PI3Kα. Thus, a new strategy for the rational design of more potent analogs of liphagal against PI3Kα is provided. Our proposed PI3Kα/liphagal binding mode would be beneficial for the discovery of new active analogs of liphagal against PI3Kα.

  14. Binding mode prediction and MD/MMPBSA-based free energy ranking for agonists of REV-ERBα/NCoR

    Science.gov (United States)

    Westermaier, Yvonne; Ruiz-Carmona, Sergio; Theret, Isabelle; Perron-Sierra, Françoise; Poissonnet, Guillaume; Dacquet, Catherine; Boutin, Jean A.; Ducrot, Pierre; Barril, Xavier

    2017-08-01

    The knowledge of the free energy of binding of small molecules to a macromolecular target is crucial in drug design as is the ability to predict the functional consequences of binding. We highlight how a molecular dynamics (MD)-based approach can be used to predict the free energy of small molecules, and to provide priorities for the synthesis and the validation via in vitro tests. Here, we study the dynamics and energetics of the nuclear receptor REV-ERBα with its co-repressor NCoR and 35 novel agonists. Our in silico approach combines molecular docking, molecular dynamics (MD), solvent-accessible surface area (SASA) and molecular mechanics poisson boltzmann surface area (MMPBSA) calculations. While docking yielded initial hints on the binding modes, their stability was assessed by MD. The SASA calculations revealed that the presence of the ligand led to a higher exposure of hydrophobic REV-ERB residues for NCoR recruitment. MMPBSA was very successful in ranking ligands by potency in a retrospective and prospective manner. Particularly, the prospective MMPBSA ranking-based validations for four compounds, three predicted to be active and one weakly active, were confirmed experimentally.

  15. Detailed Analysis of the Binding Mode of Vanilloids to Transient Receptor Potential Vanilloid Type I (TRPV1 by a Mutational and Computational Study.

    Directory of Open Access Journals (Sweden)

    Katsuya Ohbuchi

    Full Text Available Transient receptor potential vanilloid type 1 (TRPV1 is a non-selective cation channel and a multimodal sensor protein. Since the precise structure of TRPV1 was obtained by electron cryo-microscopy, the binding mode of representative agonists such as capsaicin and resiniferatoxin (RTX has been extensively characterized; however, detailed information on the binding mode of other vanilloids remains lacking. In this study, mutational analysis of human TRPV1 was performed, and four agonists (capsaicin, RTX, [6]-shogaol and [6]-gingerol were used to identify amino acid residues involved in ligand binding and/or modulation of proton sensitivity. The detailed binding mode of each ligand was then simulated by computational analysis. As a result, three amino acids (L518, F591 and L670 were newly identified as being involved in ligand binding and/or modulation of proton sensitivity. In addition, in silico docking simulation and a subsequent mutational study suggested that [6]-gingerol might bind to and activate TRPV1 in a unique manner. These results provide novel insights into the binding mode of various vanilloids to the channel and will be helpful in developing a TRPV1 modulator.

  16. Diverse modes of binding in structures of Leishmania majorN-myristoyltransferase with selective inhibitors

    Directory of Open Access Journals (Sweden)

    James A. Brannigan

    2014-07-01

    Full Text Available The leishmaniases are a spectrum of global diseases of poverty associated with immune dysfunction and are the cause of high morbidity. Despite the long history of these diseases, no effective vaccine is available and the currently used drugs are variously compromised by moderate efficacy, complex side effects and the emergence of resistance. It is therefore widely accepted that new therapies are needed. N-Myristoyltransferase (NMT has been validated pre-clinically as a target for the treatment of fungal and parasitic infections. In a previously reported high-throughput screening program, a number of hit compounds with activity against NMT from Leishmania donovani have been identified. Here, high-resolution crystal structures of representative compounds from four hit series in ternary complexes with myristoyl-CoA and NMT from the closely related L. major are reported. The structures reveal that the inhibitors associate with the peptide-binding groove at a site adjacent to the bound myristoyl-CoA and the catalytic α-carboxylate of Leu421. Each inhibitor makes extensive apolar contacts as well as a small number of polar contacts with the protein. Remarkably, the compounds exploit different features of the peptide-binding groove and collectively occupy a substantial volume of this pocket, suggesting that there is potential for the design of chimaeric inhibitors with significantly enhanced binding. Despite the high conservation of the active sites of the parasite and human NMTs, the inhibitors act selectively over the host enzyme. The role of conformational flexibility in the side chain of Tyr217 in conferring selectivity is discussed.

  17. Unveiling a novel transient druggable pocket in BACE-1 through molecular simulations: Conformational analysis and binding mode of multisite inhibitors

    Science.gov (United States)

    Di Pietro, Ornella; Laughton, Charles A.

    2017-01-01

    The critical role of BACE-1 in the formation of neurotoxic ß-amyloid peptides in the brain makes it an attractive target for an efficacious treatment of Alzheimer’s disease. However, the development of clinically useful BACE-1 inhibitors has proven to be extremely challenging. In this study we examine the binding mode of a novel potent inhibitor (compound 1, with IC50 80 nM) designed by synergistic combination of two fragments—huprine and rhein—that individually are endowed with very low activity against BACE-1. Examination of crystal structures reveals no appropriate binding site large enough to accommodate 1. Therefore we have examined the conformational flexibility of BACE-1 through extended molecular dynamics simulations, paying attention to the highly flexible region shaped by loops 8–14, 154–169 and 307–318. The analysis of the protein dynamics, together with studies of pocket druggability, has allowed us to detect the transient formation of a secondary binding site, which contains Arg307 as a key residue for the interaction with small molecules, at the edge of the catalytic cleft. The formation of this druggable “floppy” pocket would enable the binding of multisite inhibitors targeting both catalytic and secondary sites. Molecular dynamics simulations of BACE-1 bound to huprine-rhein hybrid compounds support the feasibility of this hypothesis. The results provide a basis to explain the high inhibitory potency of the two enantiomeric forms of 1, together with the large dependence on the length of the oligomethylenic linker. Furthermore, the multisite hypothesis has allowed us to rationalize the inhibitory potency of a series of tacrine-chromene hybrid compounds, specifically regarding the apparent lack of sensitivity of the inhibition constant to the chemical modifications introduced in the chromene unit. Overall, these findings pave the way for the exploration of novel functionalities in the design of optimized BACE-1 multisite inhibitors

  18. In silico characterization of binding mode of CCR8 inhibitor: homology modeling, docking and membrane based MD simulation study.

    Science.gov (United States)

    Gadhe, Changdev G; Balupuri, Anand; Cho, Seung Joo

    2015-01-01

    Human CC-chemokine receptor 8 (CCR8) is a crucial drug target in asthma that belongs to G-protein-coupled receptor superfamily, which is characterized by seven transmembrane helices. To date, there is no X-ray crystal structure available for CCR8; this hampers active research on the target. Molecular basis of interaction mechanism of antagonist with CCR8 remains unclear. In order to provide binding site information and stable binding mode, we performed modeling, docking and molecular dynamics (MD) simulation of CCR8. Docking study of biaryl-ether-piperidine derivative (13C) was performed inside predefined CCR8 binding site to get the representative conformation of 13C. Further, MD simulations of receptor and complex (13C-CCR8) inside dipalmitoylphosphatidylcholine lipid bilayers were performed to explore the effect of lipids. Results analyses showed that the Gln91, Tyr94, Cys106, Val109, Tyr113, Cys183, Tyr184, Ser185, Lys195, Thr198, Asn199, Met202, Phe254, and Glu286 were conserved in both docking and MD simulations. This indicated possible role of these residues in CCR8 antagonism. However, experimental mutational studies on these identified residues could be effective to confirm their importance in CCR8 antagonism. Furthermore, calculated Coulombic interactions represented the crucial roles of Glu286, Lys195, and Tyr113 in CCR8 antagonism. Important residues identified in this study overlap with the previous non-peptide agonist (LMD-009) binding site. Though, the non-peptide agonist and currently studied inhibitor (13C) share common substructure, but they differ in their effects on CCR8. So, to get more insight into their agonist and antagonist effects, further side-by-side experimental studies on both agonist (LMD-009) and antagonist (13C) are suggested.

  19. Salmonella Enterica Serovar Typhimurium BipA Exhibits Two Distinct Ribosome Binding Modes

    Energy Technology Data Exchange (ETDEWEB)

    deLivron, M.; Robinson, V

    2008-01-01

    BipA is a highly conserved prokaryotic GTPase that functions to influence numerous cellular processes in bacteria. In Escherichia coli and Salmonella enterica serovar Typhimurium, BipA has been implicated in controlling bacterial motility, modulating attachment and effacement processes, and upregulating the expression of virulence genes and is also responsible for avoidance of host defense mechanisms. In addition, BipA is thought to be involved in bacterial stress responses, such as those associated with virulence, temperature, and symbiosis. Thus, BipA is necessary for securing bacterial survival and successful invasion of the host. Steady-state kinetic analysis and pelleting assays were used to assess the GTPase and ribosome-binding properties of S. enterica BipA. Under normal bacterial growth, BipA associates with the ribosome in the GTP-bound state. However, using sucrose density gradients, we demonstrate that the association of BipA and the ribosome is altered under stress conditions in bacteria similar to those experienced during virulence. The data show that this differential binding is brought about by the presence of ppGpp, an alarmone that signals the onset of stress-related events in bacteria.

  20. Crystal structure of Arabidopsis thaliana calmodulin7 and insight into its mode of DNA binding.

    Science.gov (United States)

    Kumar, Sanjeev; Mazumder, Mohit; Gupta, Nisha; Chattopadhyay, Sudip; Gourinath, Samudrala

    2016-09-01

    Calmodulin (CaM) is a Ca(2+) sensor that participates in several cellular signaling cascades by interacting with various targets, including DNA. It has been shown that Arabidopsis thaliana CaM7 (AtCaM7) interacts with Z-box DNA and functions as a transcription factor [Kushwaha R et al. (2008) Plant Cell 20, 1747-1759; Abbas N et al. (2014) Plant Cell 26, 1036-1052]. The crystal structure of AtCaM7, and a model of the AtCAM7-Z-box complex suggest that Arg-127 determines the DNA-binding ability by forming crucial interactions with the guanine base. We validated the model using biolayer interferometry, which confirmed that AtCaM7 interacts with Z-box DNA with high affinity. In contrast, the AtCaM2/3/5 isoform does not show any binding, although it differs from AtCaM7 by only a single residue. © 2016 Federation of European Biochemical Societies.

  1. Deoxyribonuclease I footprinting reveals different DNA binding modes of bifunctional platinum complexes.

    Science.gov (United States)

    Chválová, Katerina; Kaspárková, Jana; Farrell, Nicholas; Brabec, Viktor

    2006-08-01

    Deoxyribonuclease I (DNase I) footprinting methodology was used to analyze oligodeoxyribonucleotide duplexes containing unique and single, site-specific adducts of trinuclear bifunctional platinum compound, [{trans-PtCl(NH3)2}2 mu-trans-Pt(NH3)2{H2N(CH2)6NH2}2]4+ (BBR3464) and the results were compared with DNase I footprints of some adducts of conventional mononuclear cis-diamminedichloroplatinum(II) (cisplatin). These examinations took into account the fact that the local conformation of the DNA at the sites of the contacts of DNase I with DNA phosphates, such as the minor groove width and depth, sequence-dependent flexibility and bendability of the double helix, are important determinants of sequence-dependent binding to and cutting of DNA by DNase I. It was shown that various conformational perturbations induced by platinum binding in the major groove translated into the minor groove, allowing their detection by DNase I probing. The results also demonstrate the very high sensitivity of DNase I to DNA conformational alterations induced by platinum complexes so that the platinum adducts which induce specific local conformational alterations in DNA are differently recognized by DNase I.

  2. Interaction of the N-(3-Methylpyridin-2-ylamide Derivatives of Flurbiprofen and Ibuprofen with FAAH: Enantiomeric Selectivity and Binding Mode.

    Directory of Open Access Journals (Sweden)

    Jessica Karlsson

    Full Text Available Combined fatty acid amide hydrolase (FAAH and cyclooxygenase (COX inhibition is a promising approach for pain-relief. The Flu-AM1 and Ibu-AM5 derivatives of flurbiprofen and ibuprofen retain similar COX-inhibitory properties and are more potent inhibitors of FAAH than the parent compounds. However, little is known as to the nature of their interaction with FAAH, or to the importance of their chirality. This has been explored here.FAAH inhibitory activity was measured in rat brain homogenates and in lysates expressing either wild-type or FAAH(T488A-mutated enzyme. Molecular modelling was undertaken using both docking and molecular dynamics. The (R- and (S-enantiomers of Flu-AM1 inhibited rat FAAH with similar potencies (IC50 values of 0.74 and 0.99 μM, respectively, whereas the (S-enantiomer of Ibu-AM5 (IC50 0.59 μM was more potent than the (R-enantiomer (IC50 5.7 μM. Multiple inhibition experiments indicated that both (R-Flu-AM1 and (S-Ibu-AM5 inhibited FAAH in a manner mutually exclusive to carprofen. Computational studies indicated that the binding site for the Flu-AM1 and Ibu-AM5 enantiomers was located between the acyl chain binding channel and the membrane access channel, in a site overlapping the carprofen binding site, and showed a binding mode in line with that proposed for carprofen and other non-covalent ligands. The potency of (R-Flu-AM1 was lower towards lysates expressing FAAH mutated at the proposed carprofen binding area than in lysates expressing wild-type FAAH.The study provides kinetic and structural evidence that the enantiomers of Flu-AM1 and Ibu-AM5 bind in the substrate channel of FAAH. This information will be useful in aiding the design of novel dual-action FAAH: COX inhibitors.

  3. Interaction and Binding Modes of bis-Ruthenium(II Complex to Synthetic DNAs

    Directory of Open Access Journals (Sweden)

    Hasi Rani Barai

    2016-06-01

    Full Text Available [μ-(linkerL2(dipyrido[3,2-a:2′,3′-c]phenazine2(phenanthroline2Ru(II2]2+ with linker: 1,3-bis-(4-pyridyl-propane, L: PF6 (bis-Ru-bpp was synthesized and their binding properties to a various polynucleotides were investigated by spectroscopy, including normal absorption, circular dichroism(CD, linear dichroism(LD, and luminescence techniques in this study. On binding to polynucleotides, the bis-Ru-bpp complex with poly[d(A-T2], and poly[d(I-C2] exhibited a negative LDr signal whose intensity was as large as that in the DNA absorption region, followed by a complicated LDr signal in the metal-to-ligand charge transfer region. Also, the emission intensity and equilibrium constant of the bis-Ru-bpp complex with poly[d(A-T2], and poly[d(I-C2] were enhanced. It was reported that both of dppz ligand of the bis-Ru-bpp complex intercalated between DNA base-pairs when bound to native, mixed sequence DNA. Observed spectral properties resemble to those observed for poly[d(A-T2] and poly[d(I-C2], led us to be concluded that both dppz ligands intercalate between alternated AT and IC bases-pairs In contrast when bis-Ru-bpp complex was bound to poly[d(G-C2], the magnitude of the LDr in the dppz absorption region, as well as the emission intensity, was half in comparison to that of bound to poly[d(A-T2], and poly[d(I-C2]. Therefore the spectral properties of the bis-Ru-bpp-poly[d(G-C2] complex suggested deviation from bis-intercalation model in the poly[d(G-C2] case. These results can be explained by a model whereby one of the dppz ligands is intercalated while the other is exposed to solvent or may exist near to phosphate. Also it is indicative that the amine group of guanine in the minor groove provides the steric hindrance for incoming intercalation binder and it also takes an important role in a difference in binding of bis-Ru-bpp bound to poly[d(A-T2] and poly[d(I-C2].

  4. Pharmacological characterization and binding modes of novel racemic and optically active phenylalanine-based antagonists of AMPA receptors

    DEFF Research Database (Denmark)

    Szymańska, Ewa; Nielsen, Birgitte; Johansen, Tommy Nørskov

    2017-01-01

    In order to map out molecular determinants for the competitive blockade of AMPA receptor subtypes, a series of racemic aryl-substituted phenylalanines was synthesized and pharmacologically characterized in vitro at native rat ionotropic glutamate receptors. Most of the compounds showed micromolar...... affinity and preference for AMPA receptors. Individual stereoisomers of selected compounds were further evaluated at recombinant homomeric rat GluA2 and GluA3 receptors. The most potent compound, (–)-2-amino-3-(6-chloro-2',5'-dihydroxy-5-nitro-[1,1'-biphenyl]-3-yl)propanoic acid, the expected R......-isomer showing Ki of 1.71 µM at the GluA2 subtype, was found to competitively antagonize GluA2(Q)i receptors in TEVC electrophysiological experiments (Kb = 2.13 µM). Molecular docking experiments allowed us to compare two alternative antagonist binding modes for the synthesized phenylalanines at the GluA2...

  5. Molecular dynamic simulations reveal structural insights into substrate and inhibitor binding modes and functionality of Ecto-Nucleoside Triphosphate Diphosphohydrolases.

    Science.gov (United States)

    Iqbal, Jamshed; Shah, Syed Jawad Ali

    2018-02-07

    Ecto-nucleotidase enzymes catalyze the hydrolysis of extracellular nucleotides to their respective nucleosides. Herein, we place the focus on the elucidation of structural features of the cell surface located ecto-nucleoside triphosphate diphosphohydrolases (E-NTPDase1-3 and 8). The physiological role of these isozymes is crucially important as they control purinergic signaling by modulating the extracellular availability of nucleotides. Since, crystal or NMR structure of the human isozymes are not available - structures have been obtained by homology modeling. Refinement of the homology models with poor stereo-chemical quality is of utmost importance in order to derive reliable structures for subsequent studies. Therefore, the resultant models obtained by homology modelling were refined by running molecular dynamic simulation. Binding mode analysis of standard substrates and of competitive inhibitor was conducted to highlight important regions of the active site involved in hydrolysis of the substrates and possible mechanism of inhibition.

  6. A designed inhibitor of a CLC antiporter blocks function through a unique binding mode

    Science.gov (United States)

    Howery, Andrew E.; Elvington, Shelley; Abraham, Sherwin J.; Choi, Kee-Hyun; Phillips, Sabrina; Ryan, Christopher M.; Sanford, R. Lea; Simpson-Dworschak, Sierra; Almqvist, Jonas; Tran, Kevin; Chew, Thomas A.; Zachariae, Ulrich; Andersen, Olaf S.; Whitelegge, Julian; Matulef, Kimberly; Du Bois, Justin; Maduke, Merritt C.

    2012-01-01

    SUMMARY The lack of small-molecule inhibitors for anion-selective transporters and channels has impeded our understanding of the complex mechanisms that underlie ion passage. The ubiquitous CLC “Chloride Channel” family represents a unique target for biophysical and biochemical studies because its distinctive protein fold supports both passive chloride channels and secondary-active chloride-proton transporters. Here, we describe the synthesis and characterization of the first specific small-molecule inhibitor directed against a CLC antiporter (ClC-ec1). This compound, 4,4′-octanamidostilbene-2,2′-disulfonate (OADS), inhibits ClC-ec1 with low micromolar affinity and has no specific effect on a CLC channel (ClC-1). Inhibition of ClC-ec1 occurs by binding to two distinct intracellular sites. The location of these sites and the lipid-dependence of inhibition suggest potential mechanisms of action. The discovery of this compound will empower research to elucidate differences between antiporter and channel mechanisms and to develop treatments for CLC-mediated disorders. PMID:23177200

  7. Selective binding modes and allosteric inhibitory effects of lupane triterpenes on protein tyrosine phosphatase 1B.

    Science.gov (United States)

    Jin, Tiantian; Yu, Haibo; Huang, Xu-Feng

    2016-02-11

    Protein Tyrosine Phosphatase 1B (PTP1B) has been recognized as a promising therapeutic target for treating obesity, diabetes, and certain cancers for over a decade. Previous drug design has focused on inhibitors targeting the active site of PTP1B. However, this has not been successful because the active site is positively charged and conserved among the protein tyrosine phosphatases. Therefore, it is important to develop PTP1B inhibitors with alternative inhibitory strategies. Using computational studies including molecular docking, molecular dynamics simulations, and binding free energy calculations, we found that lupane triterpenes selectively inhibited PTP1B by targeting its more hydrophobic and less conserved allosteric site. These findings were verified using two enzymatic assays. Furthermore, the cell culture studies showed that lupeol and betulinic acid inhibited the PTP1B activity stimulated by TNFα in neurons. Our study indicates that lupane triterpenes are selective PTP1B allosteric inhibitors with significant potential for treating those diseases with elevated PTP1B activity.

  8. Co-solvation effect on the binding mode of the α-mangostin/β-cyclodextrin inclusion complex

    Directory of Open Access Journals (Sweden)

    Chompoonut Rungnim

    2015-11-01

    Full Text Available Cyclodextrins (CDs have been extensively utilized as host molecules to enhance the solubility, stability and bioavailability of hydrophobic drug molecules through the formation of inclusion complexes. It was previously reported that the use of co-solvents in such studies may result in ternary (host:guest:co-solvent complex formation. The objective of this work was to investigate the effect of ethanol as a co-solvent on the inclusion complex formation between α-mangostin (α-MGS and β-CD, using both experimental and theoretical studies. Experimental phase-solubility studies were carried out in order to assess complex formation, with the mechanism of association being probed using a mathematical model. It was found that α-MGS was poorly soluble at low ethanol concentrations (0–10% v/v, but higher concentrations (10–40% v/v resulted in better α-MGS solubility at all β-CD concentrations studied (0–10 mM. From the equilibrium constant calculation, the inclusion complex is still a binary complex (1:1, even in the presence of ethanol. The results from our theoretical study confirm that the binding mode is binary complex and the presence of ethanol as co-solvent enhances the solubility of α-MGS with some effects on the binding affinity with β-CD, depending on the concentration employed.

  9. Evolutionary Limitation and Opportunities for Developing tRNA Synthetase Inhibitors with 5-Binding-Mode Classification

    Directory of Open Access Journals (Sweden)

    Pengfei Fang

    2015-12-01

    Full Text Available Aminoacyl-tRNA synthetases (aaRSs are enzymes that catalyze the transfer of amino acids to their cognate tRNAs as building blocks for translation. Each of the aaRS families plays a pivotal role in protein biosynthesis and is indispensable for cell growth and survival. In addition, aaRSs in higher species have evolved important non-translational functions. These translational and non-translational functions of aaRS are attractive for developing antibacterial, antifungal, and antiparasitic agents and for treating other human diseases. The interplay between amino acids, tRNA, ATP, EF-Tu and non-canonical binding partners, had shaped each family with distinct pattern of key sites for regulation, with characters varying among species across the path of evolution. These sporadic variations in the aaRSs offer great opportunity to target these essential enzymes for therapy. Up to this day, growing numbers of aaRS inhibitors have been discovered and developed. Here, we summarize the latest developments and structural studies of aaRS inhibitors, and classify them with distinct binding modes into five categories.

  10. A unique binding mode enables MCM2 to chaperone histones H3–H4 at replication forks

    Science.gov (United States)

    Huang, Hongda; Strømme, Caroline B; Saredi, Giulia; Hödl, Martina; Strandsby, Anne; González-Aguilera, Cristina; Chen, Shoudeng; Groth, Anja; Patel, Dinshaw J

    2015-01-01

    During DNA replication, chromatin is reassembled by recycling of modified old histones and deposition of new ones. How histone dynamics integrates with DNA replication to maintain genome and epigenome information remains unclear. Here, we reveal how human MCM2, part of the replicative helicase, chaperones histones H3–H4. Our first structure shows an H3–H4 tetramer bound by two MCM2 histone-binding domains (HBDs), which hijack interaction sites used by nucleosomal DNA. Our second structure reveals MCM2 and ASF1 cochaperoning an H3–H4 dimer. Mutational analyses show that the MCM2 HBD is required for MCM2–7 histone-chaperone function and normal cell proliferation. Further, we show that MCM2 can chaperone both new and old canonical histones H3–H4 as well as H3.3 and CENPA variants. The unique histone-binding mode of MCM2 thus endows the replicative helicase with ideal properties for recycling histones genome wide during DNA replication. PMID:26167883

  11. Physical organization of DNA by multiple non-specific DNA-binding modes of integration host factor (IHF.

    Directory of Open Access Journals (Sweden)

    Jie Lin

    Full Text Available The integration host factor (IHF is an abundant nucleoid-associated protein and an essential co-factor for phage λ site-specific recombination and gene regulation in E. coli. Introduction of a sharp DNA kink at specific cognate sites is critical for these functions. Interestingly, the intracellular concentration of IHF is much higher than the concentration needed for site-specific interactions, suggesting that non-specific binding of IHF to DNA plays a role in the physical organization of bacterial chromatin. However, it is unclear how non-specific DNA association contributes to DNA organization. By using a combination of single DNA manipulation and atomic force microscopy imaging methods, we show here that distinct modes of non-specific DNA binding of IHF result in complex global DNA conformations. Changes in KCl and IHF concentrations, as well as tension applied to DNA, dramatically influence the degree of DNA-bending. In addition, IHF can crosslink DNA into a highly compact DNA meshwork that is observed in the presence of magnesium at low concentration of monovalent ions and high IHF-DNA stoichiometries. Our findings provide important insights into how IHF contributes to bacterial chromatin organization, gene regulation, and biofilm formation.

  12. Determination of the binding mode for the cyclopentapeptide CXCR4 antagonist FC131 using a dual approach of ligand modifications and receptor mutagenesis

    DEFF Research Database (Denmark)

    Thiele, Stefanie; Mungalpara, J; Steen, A

    2014-01-01

    BACKGROUND AND PURPOSE: The cyclopentapeptide FC131 (cyclo(-L-Arg(1) -L-Arg(2) -L-2-Nal(3) -Gly(4) -D-Tyr(5) -)) is an antagonist at the CXC chemokine receptor CXCR4, which plays a role in human immunodeficiency virus infection, cancer and stem cell recruitment. Binding modes for FC131 in CXCR4...... activation) of FC131 and three analogues were performed on wild-type CXCR4 and 25 receptor mutants. Computational modelling was used to rationalize the experimental data. KEY RESULTS: The Arg(2) and 2-Nal(3) side chains of FC131 interact with residues in TM-3 (His(113) , Asp(171) ) and TM-5 (hydrophobic......-bond in CXCR4 crystal structures and mutation of either residue to Ala abolishes CXCR4 activity. CONCLUSIONS AND IMPLICATIONS: Ligand modification, receptor mutagenesis and computational modelling approaches were used to identify the binding mode of FC131 in CXCR4, which was in agreement with binding modes...

  13. Homology modeling of Homo sapiens lipoic acid synthase: Substrate docking and insights on its binding mode.

    Science.gov (United States)

    Krishnamoorthy, Ezhilarasi; Hassan, Sameer; Hanna, Luke Elizabeth; Padmalayam, Indira; Rajaram, Rama; Viswanathan, Vijay

    2017-05-07

    Lipoic acid synthase (LIAS) is an iron-sulfur cluster mitochondrial enzyme which catalyzes the final step in the de novo pathway for the biosynthesis of lipoic acid, a potent antioxidant. Recently there has been significant interest in its role in metabolic diseases and its deficiency in LIAS expression has been linked to conditions such as diabetes, atherosclerosis and neonatal-onset epilepsy, suggesting a strong inverse correlation between LIAS reduction and disease status. In this study we use a bioinformatics approach to predict its structure, which would be helpful to understanding its role. A homology model for LIAS protein was generated using X-ray crystallographic structure of Thermosynechococcus elongatus BP-1 (PDB ID: 4U0P). The predicted structure has 93% of the residues in the most favour region of Ramachandran plot. The active site of LIAS protein was mapped and docked with S-Adenosyl Methionine (SAM) using GOLD software. The LIAS-SAM complex was further refined using molecular dynamics simulation within the subsite 1 and subsite 3 of the active site. To the best of our knowledge, this is the first study to report a reliable homology model of LIAS protein. This study will facilitate a better understanding mode of action of the enzyme-substrate complex for future studies in designing drugs that can target LIAS protein. Copyright © 2017 Elsevier Ltd. All rights reserved.

  14. 'In-Crystallo' Capture of a Michaelis Complex And Product Binding Modes of a Bacterial Phosphotriesterase

    Energy Technology Data Exchange (ETDEWEB)

    Jackson, C.J.; Foo, J.-L.; Kim, H.-K.; Carr, P.D.; Liu, J.-W.; Salem, G.; Ollis, D.L.

    2009-05-18

    The mechanism by which the binuclear metallophosphotriesterases (PTEs, E.C. 3.1.8.1) catalyse substrate hydrolysis has been extensively studied. The {mu}-hydroxo bridge between the metal ions has been proposed to be the initiating nucleophile in the hydrolytic reaction. In contrast, analysis of some biomimetic systems has indicated that {mu}-hydroxo bridges are often not themselves nucleophiles, but act as general bases for freely exchangeable nucleophilic water molecules. Herein, we present crystallographic analyses of a bacterial PTE from Agrobacterium radiobacter, OpdA, capturing the enzyme-substrate complex during hydrolysis. This model of the Michaelis complex suggests the alignment of the substrate will favor attack from a solvent molecule terminally coordinated to the {alpha}-metal ion. The bridging of both metal ions by the product, without disruption of the {mu}-hydroxo bridge, is also consistent with nucleophilic attack occurring from the terminal position. When phosphodiesters are soaked into crystals of OpdA, they coordinate bidentately to the {beta}-metal ion, displacing the {mu}-hydroxo bridge. Thus, alternative product-binding modes exist for the PTEs, and it is the bridging mode that appears to result from phosphotriester hydrolysis. Kinetic analysis of the PTE and promiscuous phosphodiesterase activities confirms that the presence of a {mu}-hydroxo bridge during phosphotriester hydrolysis is correlated with a lower pK{sub a} for the nucleophile, consistent with a general base function during catalysis.

  15. Determination of the binding mode for anti-inflammatory natural product xanthohumol with myeloid differentiation protein 2

    Directory of Open Access Journals (Sweden)

    Fu W

    2016-01-01

    Full Text Available Weitao Fu,1,* Lingfeng Chen,1,* Zhe Wang,1 Chengwei Zhao,1 Gaozhi Chen,1 Xing Liu,1 Yuanrong Dai,2 Yuepiao Cai,1 Chenglong Li,1,3 Jianmin Zhou,1 Guang Liang1 1Chemical Biology Research Center, School of Pharmaceutical Sciences, 2Department of Respiratory Medicine, the Second Affiliated Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, People’s Republic of China; 3Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, Ohio State University, Columbus, OH, USA *These authors contributed equally to this work Abstract: It is recognized that myeloid differentiation protein 2 (MD-2, a coreceptor of toll-like receptor 4 (TLR4 for innate immunity, plays an essential role in activation of the lipopolysaccharide signaling pathway. MD-2 is known as a neoteric and suitable therapeutical target. Therefore, there is great interest in the development of a potent MD-2 inhibitor for anti-inflammatory therapeutics. Several studies have reported that xanthohumol (XN, an anti-inflammatory natural product from hops and beer, can block the TLR4 signaling by binding to MD-2 directly. However, the interaction between MD-2 and XN remains unknown. Herein, our work aims at characterizing interactions between MD-2 and XN. Using a combination of experimental and theoretical modeling analysis, we found that XN can embed into the hydrophobic pocket of MD-2 and form two stable hydrogen bonds with residues ARG-90 and TYR-102 of MD-2. Moreover, we confirmed that ARG-90 and TYR-102 were two necessary residues during the recognition process of XN binding to MD-2. Results from this study identified the atomic interactions between the MD-2 and XN, which will contribute to future structural design of novel MD-2-targeting molecules for the treatment of inflammatory diseases. Keywords: myeloid differentiation 2, xanthohumol, binding mode, inflammation, molecular dynamics simulation 

  16. Substrate binding mode and its implication on drug design for botulinum neurotoxin A.

    Directory of Open Access Journals (Sweden)

    Desigan Kumaran

    2008-09-01

    Full Text Available The seven antigenically distinct serotypes of Clostridium botulinum neurotoxins, the causative agents of botulism, block the neurotransmitter release by specifically cleaving one of the three SNARE proteins and induce flaccid paralysis. The Centers for Disease Control and Prevention (CDC has declared them as Category A biowarfare agents. The most potent among them, botulinum neurotoxin type A (BoNT/A, cleaves its substrate synaptosome-associated protein of 25 kDa (SNAP-25. An efficient drug for botulism can be developed only with the knowledge of interactions between the substrate and enzyme at the active site. Here, we report the crystal structures of the catalytic domain of BoNT/A with its uncleavable SNAP-25 peptide (197QRATKM(202 and its variant (197RRATKM(202 to 1.5 A and 1.6 A, respectively. This is the first time the structure of an uncleavable substrate bound to an active botulinum neurotoxin is reported and it has helped in unequivocally defining S1 to S5' sites. These substrate peptides make interactions with the enzyme predominantly by the residues from 160, 200, 250 and 370 loops. Most notably, the amino nitrogen and carbonyl oxygen of P1 residue (Gln197 chelate the zinc ion and replace the nucleophilic water. The P1'-Arg198, occupies the S1' site formed by Arg363, Thr220, Asp370, Thr215, Ile161, Phe163 and Phe194. The S2' subsite is formed by Arg363, Asn368 and Asp370, while S3' subsite is formed by Tyr251, Leu256, Val258, Tyr366, Phe369 and Asn388. P4'-Lys201 makes hydrogen bond with Gln162. P5'-Met202 binds in the hydrophobic pocket formed by the residues from the 250 and 200 loop. Knowledge of interactions between the enzyme and substrate peptide from these complex structures should form the basis for design of potent inhibitors for this neurotoxin.

  17. Identical phosphatase mechanisms achieved through distinct modes of binding phosphoprotein substrate

    Energy Technology Data Exchange (ETDEWEB)

    Pazy, Y.; Motaleb, M.A.; Guarnieri, M.T.; Charon, N.W.; Zhao, R.; Silversmith, R.E. (WVU); (UNC); (Colorado); (EC Uni.)

    2010-04-05

    Two-component signal transduction systems are widespread in prokaryotes and control numerous cellular processes. Extensive investigation of sensor kinase and response regulator proteins from many two-component systems has established conserved sequence, structural, and mechanistic features within each family. In contrast, the phosphatases which catalyze hydrolysis of the response regulator phosphoryl group to terminate signal transduction are poorly understood. Here we present structural and functional characterization of a representative of the CheC/CheX/FliY phosphatase family. The X-ray crystal structure of Borrelia burgdorferi CheX complexed with its CheY3 substrate and the phosphoryl analogue BeF{sub 3}{sup -} reveals a binding orientation between a response regulator and an auxiliary protein different from that shared by every previously characterized example. The surface of CheY3 containing the phosphoryl group interacts directly with a long helix of CheX which bears the conserved (E - X{sub 2} - N) motif. Conserved CheX residues Glu96 and Asn99, separated by a single helical turn, insert into the CheY3 active site. Structural and functional data indicate that CheX Asn99 and CheY3 Thr81 orient a water molecule for hydrolytic attack. The catalytic residues of the CheX-CheY3 complex are virtually superimposable on those of the Escherichia coli CheZ phosphatase complexed with CheY, even though the active site helices of CheX and CheZ are oriented nearly perpendicular to one other. Thus, evolution has found two structural solutions to achieve the same catalytic mechanism through different helical spacing and side chain lengths of the conserved acid/amide residues in CheX and CheZ.

  18. Structural basis of DNA recognition by PCG2 reveals a novel DNA binding mode for winged helix-turn-helix domains

    Science.gov (United States)

    Liu, Junfeng; Huang, Jinguang; Zhao, Yanxiang; Liu, Huaian; Wang, Dawei; Yang, Jun; Zhao, Wensheng; Taylor, Ian A.; Peng, You-Liang

    2015-01-01

    The MBP1 family proteins are the DNA binding subunits of MBF cell-cycle transcription factor complexes and contain an N terminal winged helix-turn-helix (wHTH) DNA binding domain (DBD). Although the DNA binding mechanism of MBP1 from Saccharomyces cerevisiae has been extensively studied, the structural framework and the DNA binding mode of other MBP1 family proteins remains to be disclosed. Here, we determined the crystal structure of the DBD of PCG2, the Magnaporthe oryzae orthologue of MBP1, bound to MCB–DNA. The structure revealed that the wing, the 20-loop, helix A and helix B in PCG2–DBD are important elements for DNA binding. Unlike previously characterized wHTH proteins, PCG2–DBD utilizes the wing and helix-B to bind the minor groove and the major groove of the MCB–DNA whilst the 20-loop and helix A interact non-specifically with DNA. Notably, two glutamines Q89 and Q82 within the wing were found to recognize the MCB core CGCG sequence through making hydrogen bond interactions. Further in vitro assays confirmed essential roles of Q89 and Q82 in the DNA binding. These data together indicate that the MBP1 homologue PCG2 employs an unusual mode of binding to target DNA and demonstrate the versatility of wHTH domains. PMID:25550425

  19. Multiple Modes of Binding Enhance the Affinity of DC-SIGN for High-Mannose N-Linked Glycans Found on Viral Glycoproteins

    Energy Technology Data Exchange (ETDEWEB)

    Feinberg, H.; Castelli, R.; Drickamer, K.; Seeberger, P.H.; Weis, W.I.; /Stanford U., Med. School /Zurich, ETH /Imperial Coll., London

    2007-07-09

    The dendritic cell surface receptor DC-SIGN and the closely related endothelial cell receptor DC-SIGNR specifically recognize high mannose N-linked carbohydrates on viral pathogens. Previous studies have shown that these receptors bind the outer trimannose branch Man{alpha}1-3[Man{alpha}1-6]Man{alpha} present in high mannose structures. Although the trimannoside binds to DC-SIGN or DC-SIGNR more strongly than mannose, additional affinity enhancements are observed in the presence of one or more Man{alpha}1-2Man{alpha} moieties on the nonreducing termini of oligomannose structures. The molecular basis of this enhancement has been investigated by determining crystal structures of DC-SIGN bound to a synthetic six-mannose fragment of a high mannose N-linked oligosaccharide, Man{alpha}1-2Man{alpha}1-3[Man{alpha}1-2Man{alpha}1-6]Man{alpha}1-6Man and to the disaccharide Man{alpha}1-2Man. The structures reveal mixtures of two binding modes in each case. Each mode features typical C-type lectin binding at the principal Ca{sup 2+}-binding site by one mannose residue. In addition, other sugar residues form contacts unique to each binding mode. These results suggest that the affinity enhancement displayed toward oligosaccharides decorated with the Man{alpha}1-2Man{alpha} structure is due in part to multiple binding modes at the primary Ca{sup 2+} site, which provide both additional contacts and a statistical (entropic) enhancement of binding.

  20. Insights into the binding mode of MEK type-III inhibitors. A step towards discovering and designing allosteric kinase inhibitors across the human kinome

    OpenAIRE

    Zhao, Zheng; Xie, Lei; Bourne, Philip E.

    2017-01-01

    Protein kinases are critical drug targets for treating a large variety of human diseases. Type-III kinase inhibitors have attracted increasing attention as highly selective therapeutics. Thus, understanding the binding mechanism of existing type-III kinase inhibitors provides useful insights into designing new type-III kinase inhibitors. In this work, we have systematically studied the binding mode of MEK-targeted type-III inhibitors using structural systems pharmacology and molecular dynamic...

  1. The Drosophila hnRNP F/H Homolog Glorund Uses Two Distinct RNA-Binding Modes to Diversify Target Recognition

    Energy Technology Data Exchange (ETDEWEB)

    Tamayo, Joel V.; Teramoto, Takamasa; Chatterjee, Seema; Hall, Traci M. Tanaka; Gavis, Elizabeth R. (Princeton); (NIH)

    2017-04-01

    The Drosophila hnRNP F/H homolog, Glorund (Glo), regulates nanos mRNA translation by interacting with a structured UA-rich motif in the nanos 3' untranslated region. Glo regulates additional RNAs, however, and mammalian homologs bind G-tract sequences to regulate alternative splicing, suggesting that Glo also recognizes G-tract RNA. To gain insight into how Glo recognizes both structured UA-rich and G-tract RNAs, we used mutational analysis guided by crystal structures of Glo’s RNA-binding domains and identified two discrete RNA-binding surfaces that allow Glo to recognize both RNA motifs. By engineering Glo variants that favor a single RNA-binding mode, we show that a subset of Glo’s functions in vivo is mediated solely by the G-tract binding mode, whereas regulation of nanos requires both recognition modes. Our findings suggest a molecular mechanism for the evolution of dual RNA motif recognition in Glo that may be applied to understanding the functional diversity of other RNA-binding proteins.

  2. Molecular modeling of the dopamine D-2 and serotonin 5-HT1A receptor binding modes of the enantiomers of 5-OMe-BPAT

    NARCIS (Netherlands)

    Homan, EJ; Wikstrom, HV; Grol, CJ

    Molecular modeling studies were undertaken in order to elucidate the possible dopamine D-2 and serotonin 5-HT1A receptor binding modes of the enantiomers of 5-methoxy-2-[N-(2-benzamidoethyl)-N-n-pylamino]tetralin (5-OMe-BPAT, 1). For this purpose, a combination of indirect molecular modeling and

  3. Structural Dynamics Investigation of Human Family 1 & 2 Cystatin-Cathepsin L1 Interaction: A Comparison of Binding Modes.

    Science.gov (United States)

    Nandy, Suman Kumar; Seal, Alpana

    2016-01-01

    Cystatin superfamily is a large group of evolutionarily related proteins involved in numerous physiological activities through their inhibitory activity towards cysteine proteases. Despite sharing the same cystatin fold, and inhibiting cysteine proteases through the same tripartite edge involving highly conserved N-terminal region, L1 and L2 loop; cystatins differ widely in their inhibitory affinity towards C1 family of cysteine proteases and molecular details of these interactions are still elusive. In this study, inhibitory interactions of human family 1 & 2 cystatins with cathepsin L1 are predicted and their stability and viability are verified through protein docking & comparative molecular dynamics. An overall stabilization effect is observed in all cystatins on complex formation. Complexes are mostly dominated by van der Waals interaction but the relative participation of the conserved regions varied extensively. While van der Waals contacts prevail in L1 and L2 loop, N-terminal segment chiefly acts as electrostatic interaction site. In fact the comparative dynamics study points towards the instrumental role of L1 loop in directing the total interaction profile of the complex either towards electrostatic or van der Waals contacts. The key amino acid residues surfaced via interaction energy, hydrogen bonding and solvent accessible surface area analysis for each cystatin-cathepsin L1 complex influence the mode of binding and thus control the diverse inhibitory affinity of cystatins towards cysteine proteases.

  4. Structural Dynamics Investigation of Human Family 1 & 2 Cystatin-Cathepsin L1 Interaction: A Comparison of Binding Modes.

    Directory of Open Access Journals (Sweden)

    Suman Kumar Nandy

    Full Text Available Cystatin superfamily is a large group of evolutionarily related proteins involved in numerous physiological activities through their inhibitory activity towards cysteine proteases. Despite sharing the same cystatin fold, and inhibiting cysteine proteases through the same tripartite edge involving highly conserved N-terminal region, L1 and L2 loop; cystatins differ widely in their inhibitory affinity towards C1 family of cysteine proteases and molecular details of these interactions are still elusive. In this study, inhibitory interactions of human family 1 & 2 cystatins with cathepsin L1 are predicted and their stability and viability are verified through protein docking & comparative molecular dynamics. An overall stabilization effect is observed in all cystatins on complex formation. Complexes are mostly dominated by van der Waals interaction but the relative participation of the conserved regions varied extensively. While van der Waals contacts prevail in L1 and L2 loop, N-terminal segment chiefly acts as electrostatic interaction site. In fact the comparative dynamics study points towards the instrumental role of L1 loop in directing the total interaction profile of the complex either towards electrostatic or van der Waals contacts. The key amino acid residues surfaced via interaction energy, hydrogen bonding and solvent accessible surface area analysis for each cystatin-cathepsin L1 complex influence the mode of binding and thus control the diverse inhibitory affinity of cystatins towards cysteine proteases.

  5. Binding Mode Prediction of 5-Hydroxytryptamine 2C Receptor Ligands by Homology Modeling and Molecular Docking Analysis

    Energy Technology Data Exchange (ETDEWEB)

    Ahmed, Asif; Nagarajan, Shanthi; Doddareddy, Munikumar Reddy; Cho, Yong Seo; Pae, Ae Nim [Korea Institute of Science and Technology, Seoul (Korea, Republic of)

    2011-06-15

    Serotonin or 5-hydroxytryptamine subtype 2C (5-HT{sub 2C}) receptor belongs to class A amine subfamily of Gprotein- coupled receptor (GPCR) super family and its ligands has therapeutic promise as anti-depressant and -obesity agents. So far, bovine rhodopsin from class A opsin subfamily was the mostly used X-ray crystal template to model this receptor. Here, we explained homology model using beta 2 adrenergic receptor (β2AR), the model was energetically minimized and validated by flexible ligand docking with known agonists and antagonists. In the active site Asp134, Ser138 of transmembrane 3 (TM3), Arg195 of extracellular loop 2 (ECL2) and Tyr358 of TM7 were found as important residues to interact with agonists. In addition to these, V208 of ECL2 and N351 of TM7 was found to interact with antagonists. Several conserved residues including Trp324, Phe327 and Phe328 were also found to contribute hydrophobic interaction. The predicted ligand binding mode is in good agreement with published mutagenesis and homology model data. This new template derived homology model can be useful for further virtual screening based lead identification.

  6. Structure of Bacillus subtilis γ-glutamyltranspeptidase in complex with acivicin: diversity of the binding mode of a classical and electrophilic active-site-directed glutamate analogue

    Energy Technology Data Exchange (ETDEWEB)

    Ida, Tomoyo [Osaka University, Toyonaka, Osaka 560-0043 (Japan); Suzuki, Hideyuki [Kyoto Institute of Technology, Goshokaido-cho, Matsugasaki, Sakyo-ku, Kyoto 606-8585 (Japan); Fukuyama, Keiichi [Osaka University, Toyonaka, Osaka 560-0043 (Japan); Hiratake, Jun [Kyoto University, Uji, Kyoto 611-0011 (Japan); Wada, Kei, E-mail: keiwada@med.miyazaki-u.ac.jp [University of Miyazaki, Miyazaki 889-1692 (Japan); Osaka University, Toyonaka, Osaka 560-0043 (Japan)

    2014-02-01

    The binding modes of acivicin, a classical and an electrophilic active-site-directed glutamate analogue, to bacterial γ-glutamyltranspeptidases were found to be diverse. γ-Glutamyltranspeptidase (GGT) is an enzyme that plays a central role in glutathione metabolism, and acivicin is a classical inhibitor of GGT. Here, the structure of acivicin bound to Bacillus subtilis GGT determined by X-ray crystallography to 1.8 Å resolution is presented, in which it binds to the active site in a similar manner to that in Helicobacter pylori GGT, but in a different binding mode to that in Escherichia coli GGT. In B. subtilis GGT, acivicin is bound covalently through its C3 atom with sp{sup 2} hybridization to Thr403 O{sup γ}, the catalytic nucleophile of the enzyme. The results show that acivicin-binding sites are common, but the binding manners and orientations of its five-membered dihydroisoxazole ring are diverse in the binding pockets of GGTs.

  7. Two modes of interaction of the single-stranded DNA-binding protein of bacteriophage T7 with the DNA polymerase-thioredoxin complex

    KAUST Repository

    Ghosh, Sharmistha

    2010-04-06

    The DNA polymerase encoded by bacteriophage T7 has low processivity. Escherichia coli thioredoxin binds to a segment of 76 residues in the thumb subdomain of the polymerase and increases the processivity. The binding of thioredoxin leads to the formation of two basic loops, loops A and B, located within the thioredoxin-binding domain (TBD). Both loops interact with the acidic C terminus of the T7 helicase. A relatively weak electrostatic mode involves the C-terminal tail of the helicase and the TBD, whereas a high affinity interaction that does not involve the C-terminal tail occurs when the polymerase is in a polymerization mode. T7 gene 2.5 single-stranded DNA-binding protein (gp2.5) also has an acidic C-terminal tail. gp2.5 also has two modes of interaction with the polymerase, but both involve the C-terminal tail of gp2.5. An electrostatic interaction requires the basic residues in loops A and B, and gp2.5 binds to both loops with similar affinity as measured by surface plasmon resonance. When the polymerase is in a polymerization mode, the C terminus of gene 2.5 protein interacts with the polymerase in regions outside the TBD.gp2.5 increases the processivity of the polymerase-helicase complex during leading strand synthesis. When loop B of the TBD is altered, abortive DNA products are observed during leading strand synthesis. Loop B appears to play an important role in communication with the helicase and gp2.5, whereas loop A plays a stabilizing role in these interactions. © 2010 by The American Society for Biochemistry and Molecular Biology, Inc.

  8. Validation of tautomeric and protomeric binding modes by free energy calculations. A case study for the structure based optimization of uc(d)-amino acid oxidase inhibitors

    Science.gov (United States)

    Orgován, Zoltán; Ferenczy, György G.; Steinbrecher, Thomas; Szilágyi, Bence; Bajusz, Dávid; Keserű, György M.

    2018-01-01

    Optimization of fragment size uc(d)-amino acid oxidase (DAAO) inhibitors was investigated using a combination of computational and experimental methods. Retrospective free energy perturbation (FEP) calculations were performed for benzo[d]isoxazole derivatives, a series of known inhibitors with two potential binding modes derived from X-ray structures of other DAAO inhibitors. The good agreement between experimental and computed binding free energies in only one of the hypothesized binding modes strongly support this bioactive conformation. Then, a series of 1-H-indazol-3-ol derivatives formerly not described as DAAO inhibitors was investigated. Binding geometries could be reliably identified by structural similarity to benzo[d]isoxazole and other well characterized series and FEP calculations were performed for several tautomers of the deprotonated and protonated compounds since all these forms are potentially present owing to the experimental pKa values of representative compounds in the series. Deprotonated compounds are proposed to be the most important bound species owing to the significantly better agreement between their calculated and measured affinities compared to the protonated forms. FEP calculations were also used for the prediction of the affinities of compounds not previously tested as DAAO inhibitors and for a comparative structure-activity relationship study of the benzo[d]isoxazole and indazole series. Selected indazole derivatives were synthesized and their measured binding affinity towards DAAO was in good agreement with FEP predictions.

  9. Interaction of the amyloid precursor protein-like protein 1 (APLP1) E2 domain with heparan sulfate involves two distinct binding modes

    Energy Technology Data Exchange (ETDEWEB)

    Dahms, Sven O., E-mail: sdahms@fli-leibniz.de [Leibniz Institute for Age Research (FLI), Beutenbergstrasse 11, 07745 Jena (Germany); Mayer, Magnus C. [Freie Universität Berlin, Thielallee 63, 14195 Berlin (Germany); Miltenyi Biotec GmbH, Robert-Koch-Strasse 1, 17166 Teterow (Germany); Roeser, Dirk [Leibniz Institute for Age Research (FLI), Beutenbergstrasse 11, 07745 Jena (Germany); Multhaup, Gerd [McGill University Montreal, Montreal, Quebec H3G 1Y6 (Canada); Than, Manuel E., E-mail: sdahms@fli-leibniz.de [Leibniz Institute for Age Research (FLI), Beutenbergstrasse 11, 07745 Jena (Germany)

    2015-03-01

    Two X-ray structures of APLP1 E2 with and without a heparin dodecasaccharide are presented, revealing two distinct binding modes of the protein to heparan sulfate. The data provide a mechanistic explanation of how APP-like proteins bind to heparan sulfates and how they specifically recognize nonreducing structures of heparan sulfates. Beyond the pathology of Alzheimer’s disease, the members of the amyloid precursor protein (APP) family are essential for neuronal development and cell homeostasis in mammals. APP and its paralogues APP-like protein 1 (APLP1) and APP-like protein 2 (APLP2) contain the highly conserved heparan sulfate (HS) binding domain E2, which effects various (patho)physiological functions. Here, two crystal structures of the E2 domain of APLP1 are presented in the apo form and in complex with a heparin dodecasaccharide at 2.5 Å resolution. The apo structure of APLP1 E2 revealed an unfolded and hence flexible N-terminal helix αA. The (APLP1 E2){sub 2}–(heparin){sub 2} complex structure revealed two distinct binding modes, with APLP1 E2 explicitly recognizing the heparin terminus but also interacting with a continuous heparin chain. The latter only requires a certain register of the sugar moieties that fits to a positively charged surface patch and contributes to the general heparin-binding capability of APP-family proteins. Terminal binding of APLP1 E2 to heparin specifically involves a structure of the nonreducing end that is very similar to heparanase-processed HS chains. These data reveal a conserved mechanism for the binding of APP-family proteins to HS and imply a specific regulatory role of HS modifications in the biology of APP and APP-like proteins.

  10. A new mode of DNA binding distinguishes Capicua from other HMG-box factors and explains its mutation patterns in cancer.

    Science.gov (United States)

    Forés, Marta; Simón-Carrasco, Lucía; Ajuria, Leiore; Samper, Núria; González-Crespo, Sergio; Drosten, Matthias; Barbacid, Mariano; Jiménez, Gerardo

    2017-03-01

    HMG-box proteins, including Sox/SRY (Sox) and TCF/LEF1 (TCF) family members, bind DNA via their HMG-box. This binding, however, is relatively weak and both Sox and TCF factors employ distinct mechanisms for enhancing their affinity and specificity for DNA. Here we report that Capicua (CIC), an HMG-box transcriptional repressor involved in Ras/MAPK signaling and cancer progression, employs an additional distinct mode of DNA binding that enables selective recognition of its targets. We find that, contrary to previous assumptions, the HMG-box of CIC does not bind DNA alone but instead requires a distant motif (referred to as C1) present at the C-terminus of all CIC proteins. The HMG-box and C1 domains are both necessary for binding specific TGAATGAA-like sites, do not function via dimerization, and are active in the absence of cofactors, suggesting that they form a bipartite structure for sequence-specific binding to DNA. We demonstrate that this binding mechanism operates throughout Drosophila development and in human cells, ensuring specific regulation of multiple CIC targets. It thus appears that HMG-box proteins generally depend on auxiliary DNA binding mechanisms for regulating their appropriate genomic targets, but that each sub-family has evolved unique strategies for this purpose. Finally, the key role of C1 in DNA binding also explains the fact that this domain is a hotspot for inactivating mutations in oligodendroglioma and other tumors, while being preserved in oncogenic CIC-DUX4 fusion chimeras associated to Ewing-like sarcomas.

  11. A computational analysis of the binding mode of closantel as inhibitor of the Onchocerca volvulus chitinase: insights on macrofilaricidal drug design

    Science.gov (United States)

    Segura-Cabrera, Aldo; Bocanegra-García, Virgilio; Lizarazo-Ortega, Cristian; Guo, Xianwu; Correa-Basurto, José; Rodríguez-Pérez, Mario A.

    2011-12-01

    Onchocerciasis is a leading cause of blindness with at least 37 million people infected and more than 120 million people at risk of contracting the disease; most (99%) of this population, threatened by infection, live in Africa. The drug of choice for mass treatment is the microfilaricidal Mectizan® (ivermectin); it does not kill the adult stages of the parasite at the standard dose which is a single annual dose aimed at disease control. However, multiple treatments a year with ivermectin have effects on adult worms. The discovery of new therapeutic targets and drugs directed towards the killing of the adult parasites are thus urgently needed. The chitinase of filarial nematodes is a new drug target due to its essential function in the metabolism and molting of the parasite. Closantel is a potent and specific inhibitor of chitinase of Onchocerca volvulus (OvCHT1) and other filarial chitinases. However, the binding mode and specificity of closantel towards OvCHT1 remain unknown. In the absence of a crystallographic structure of OvCHT1, we developed a homology model of OvCHT1 using the currently available X-ray structures of human chitinases as templates. Energy minimization and molecular dynamics (MD) simulation of the model led to a high quality of 3D structure of OvCHIT1. A flexible docking study using closantel as the ligand on the binding site of OvCHIT1 and human chitinases was performed and demonstrated the differences in the closantel binding mode between OvCHIT1 and human chitinase. Furthermore, molecular dynamics simulations and free-energy calculation were employed to determine and compare the detailed binding mode of closantel with OvCHT1 and the structure of human chitinase. This comparative study allowed identification of structural features and properties responsible for differences in the computationally predicted closantel binding modes. The homology model and the closantel binding mode reported herein might help guide the rational development of

  12. Probe the Binding Mode of Aristololactam-β-D-glucoside to Phenylalanine Transfer RNA in Silico

    DEFF Research Database (Denmark)

    Xiao, Xingqing; Zhao, Binwu; Yang, Li

    2016-01-01

    on the tRNAPhe, and atomistic MD simulations were conducted to examine the thermal stability of five predicted binding poses for the complex of ADG and the tRNAPhe. The binding free energies of the five complexes were then calculated using the molecular mechanics/generalized born surface area approach...... with the variable internal dielectric constant model. By comparing computed affinities and experimentally-measured values in the binding free energy, we identified a most likely binding structure of ADG and the tRNAPhe. Further analysis of energy of the ADG-tRNA complex revealed that the aristololactam of ADG...

  13. Search for β2 adrenergic receptor ligands by virtual screening via grid computing and investigation of binding modes by docking and molecular dynamics simulations.

    Directory of Open Access Journals (Sweden)

    Qifeng Bai

    Full Text Available We designed a program called MolGridCal that can be used to screen small molecule database in grid computing on basis of JPPF grid environment. Based on MolGridCal program, we proposed an integrated strategy for virtual screening and binding mode investigation by combining molecular docking, molecular dynamics (MD simulations and free energy calculations. To test the effectiveness of MolGridCal, we screened potential ligands for β2 adrenergic receptor (β2AR from a database containing 50,000 small molecules. MolGridCal can not only send tasks to the grid server automatically, but also can distribute tasks using the screensaver function. As for the results of virtual screening, the known agonist BI-167107 of β2AR is ranked among the top 2% of the screened candidates, indicating MolGridCal program can give reasonable results. To further study the binding mode and refine the results of MolGridCal, more accurate docking and scoring methods are used to estimate the binding affinity for the top three molecules (agonist BI-167107, neutral antagonist alprenolol and inverse agonist ICI 118,551. The results indicate agonist BI-167107 has the best binding affinity. MD simulation and free energy calculation are employed to investigate the dynamic interaction mechanism between the ligands and β2AR. The results show that the agonist BI-167107 also has the lowest binding free energy. This study can provide a new way to perform virtual screening effectively through integrating molecular docking based on grid computing, MD simulations and free energy calculations. The source codes of MolGridCal are freely available at http://molgridcal.codeplex.com.

  14. Molecular modeling reveals the novel inhibition mechanism and binding mode of three natural compounds to staphylococcal α-hemolysin.

    Directory of Open Access Journals (Sweden)

    Jiazhang Qiu

    Full Text Available α-Hemolysin (α-HL is a self-assembling, channel-forming toxin that is produced as a soluble monomer by Staphylococcus aureus strains. Until now, α-HL has been a significant virulence target for the treatment of S. aureus infection. In our previous report, we demonstrated that some natural compounds could bind to α-HL. Due to the binding of those compounds, the conformational transition of α-HL from the monomer to the oligomer was blocked, which resulted in inhibition of the hemolytic activity of α-HL. However, these results have not indicated how the binding of the α-HL inhibitors influence the conformational transition of the whole protein during the oligomerization process. In this study, we found that three natural compounds, Oroxylin A 7-O-glucuronide (OLG, Oroxin A (ORA, and Oroxin B (ORB, when inhibiting the hemolytic activity of α-HL, could bind to the "stem" region of α-HL. This was completed using conventional Molecular Dynamics (MD simulations. By interacting with the novel binding sites of α-HL, the ligands could form strong interactions with both sides of the binding cavity. The results of the principal component analysis (PCA indicated that because of the inhibitors that bind to the "stem" region of α-HL, the conformational transition of α-HL from the monomer to the oligomer was restricted. This caused the inhibition of the hemolytic activity of α-HL. This novel inhibition mechanism has been confirmed by both the steered MD simulations and the experimental data obtained from a deoxycholate-induced oligomerization assay. This study can facilitate the design of new antibacterial drugs against S. aureus.

  15. Insight into the structural similarity between HIV protease and secreted aspartic protease-2 and binding mode analysis of HIV-Candida albicans inhibitors.

    Science.gov (United States)

    Calugi, Chiara; Guarna, Antonio; Trabocchi, Andrea

    2013-10-01

    The analysis of the structural similarity between Candida albicans Sap2 and HIV-1 aspartic proteases by molecular modeling gave insight into the common requirements for inhibition of both targets. Structure superimposition of Sap2 and HIV-1 protease confirmed the similarity between their active sites and flap regions. HIV-1 protease inhibitors herein investigated can fit the active site of Sap2, adopting very similar ligand-backbone conformations. In particular, key anchoring sites consisting of Gly85 in Sap2 and Ile50 in HIV-1 protease, both belonging to their corresponding flap regions, were found as elements of a similar binding-mode interaction. The knowledge of the molecular basis for binding to both Sap2 and HIV-1 proteases may ultimately lead to the development of single inhibitor acting on both targets.

  16. Computational Studies of Difference in Binding Modes of Peptide and Non-Peptide Inhibitors to MDM2/MDMX Based on Molecular Dynamics Simulations

    Directory of Open Access Journals (Sweden)

    Yuxin Zhang

    2012-02-01

    Full Text Available Inhibition of p53-MDM2/MDMX interaction is considered to be a promising strategy for anticancer drug design to activate wild-type p53 in tumors. We carry out molecular dynamics (MD simulations to study the binding mechanisms of peptide and non-peptide inhibitors to MDM2/MDMX. The rank of binding free energies calculated by molecular mechanics generalized Born surface area (MM-GBSA method agrees with one of the experimental values. The results suggest that van der Waals energy drives two kinds of inhibitors to MDM2/MDMX. We also find that the peptide inhibitors can produce more interaction contacts with MDM2/MDMX than the non-peptide inhibitors. Binding mode predictions based on the inhibitor-residue interactions show that the π–π, CH–π and CH–CH interactions dominated by shape complimentarity, govern the binding of the inhibitors in the hydrophobic cleft of MDM2/MDMX. Our studies confirm the residue Tyr99 in MDMX can generate a steric clash with the inhibitors due to energy and structure. This finding may theoretically provide help to develop potent dual-specific or MDMX inhibitors.

  17. Characterization of the differences in the cyclopiazonic acid binding mode to mammalian and P. Falciparum Ca2+ pumps: a computational study.

    KAUST Repository

    Di Marino, Daniele

    2015-03-01

    Despite the investments in malaria research, an effective vaccine has not yet been developed and the causative parasites are becoming increasingly resistant to most of the available drugs. PfATP6, the sarco/endoplasmic reticulum Ca2+ pump (SERCA) of P. falciparum, has been recently genetically validated as a potential antimalarial target and cyclopiazonic acid (CPA) has been found to be a potent inhibitor of SERCAs in several organisms, including P. falciparum. In position 263, PfATP6 displays a leucine residue, whilst the corresponding position in the mammalian SERCA is occupied by a glutamic acid. The PfATP6 L263E mutation has been studied in relation to the artemisinin inhibitory effect on P. falciparum and recent studies have provided evidence that the parasite with this mutation is more susceptible to CPA. Here, we characterized, for the first time, the interaction of CPA with PfATP6 and its mammalian counterpart to understand similarities and differences in the mode of binding of the inhibitor to the two Ca2+ pumps. We found that, even though CPA does not directly interact with the residue in position 263, the presence of a hydrophobic residue in this position in PfATP6 rather than a negatively charged one, as in the mammalian SERCA, entails a conformational arrangement of the binding pocket which, in turn, determines a relaxation of CPA leading to a different binding mode of the compound. Our findings highlight differences between the plasmodial and human SERCA CPA-binding pockets that may be exploited to design CPA derivatives more selective toward PfATP6.

  18. Inhibition and Larvicidal Activity of Phenylpropanoids from Piper sarmentosum on Acetylcholinesterase against Mosquito Vectors and Their Binding Mode of Interaction.

    Directory of Open Access Journals (Sweden)

    Arshia Hematpoor

    Full Text Available Aedes aegypti, Aedes albopictus and Culex quinquefasciatus are vectors of dengue fever and West Nile virus diseases. This study was conducted to determine the toxicity, mechanism of action and the binding interaction of three active phenylpropanoids from Piper sarmentosum (Piperaceae toward late 3rd or early 4th larvae of above vectors. A bioassay guided-fractionation on the hexane extract from the roots of Piper sarmentosum led to the isolation and identification of three active phenylpropanoids; asaricin 1, isoasarone 2 and trans-asarone 3. The current study involved evaluation of the toxicity and acetylcholinesterase (AChE inhibition of these compounds against Aedes aegypti, Aedes albopictus and Culex quinquefasciatus larvae. Asaricin 1 and isoasarone 2 were highly potent against Aedes aegypti, Aedes albopictus and Culex quinquefasciatus larvae causing up to 100% mortality at ≤ 15 μg/mL concentration. The ovicidal activity of asaricin 1, isoasarone 2 and trans-asarone 3 were evaluated through egg hatching. Asaricin 1 and isoasarone 2 showed potent ovicidal activity. Ovicidal activity for both compounds was up to 95% at 25μg/mL. Asaricin 1 and isoasarone 2 showed strong inhibition on acetylcholinesterase with relative IC50 values of 0.73 to 1.87 μg/mL respectively. These findings coupled with the high AChE inhibition may suggest that asaricin 1 and isoasarone 2 are neuron toxic compounds toward Aedes aegypti, Aedes albopictus and Culex quinquefasciatus. Further computational docking with Autodock Vina elaborates the possible interaction of asaricin 1 and isoasarone 2 with three possible binding sites of AChE which includes catalytic triads (CAS: S238, E367, H480, the peripheral sites (PAS: E72, W271 and anionic binding site (W83. The binding affinity of asaricin 1 and isoasarone 2 were relatively strong with asaricin 1 showed a higher binding affinity in the anionic pocket.

  19. Inhibition and Larvicidal Activity of Phenylpropanoids from Piper sarmentosum on Acetylcholinesterase against Mosquito Vectors and Their Binding Mode of Interaction.

    Science.gov (United States)

    Hematpoor, Arshia; Liew, Sook Yee; Chong, Wei Lim; Azirun, Mohd Sofian; Lee, Vannajan Sanghiran; Awang, Khalijah

    2016-01-01

    Aedes aegypti, Aedes albopictus and Culex quinquefasciatus are vectors of dengue fever and West Nile virus diseases. This study was conducted to determine the toxicity, mechanism of action and the binding interaction of three active phenylpropanoids from Piper sarmentosum (Piperaceae) toward late 3rd or early 4th larvae of above vectors. A bioassay guided-fractionation on the hexane extract from the roots of Piper sarmentosum led to the isolation and identification of three active phenylpropanoids; asaricin 1, isoasarone 2 and trans-asarone 3. The current study involved evaluation of the toxicity and acetylcholinesterase (AChE) inhibition of these compounds against Aedes aegypti, Aedes albopictus and Culex quinquefasciatus larvae. Asaricin 1 and isoasarone 2 were highly potent against Aedes aegypti, Aedes albopictus and Culex quinquefasciatus larvae causing up to 100% mortality at ≤ 15 μg/mL concentration. The ovicidal activity of asaricin 1, isoasarone 2 and trans-asarone 3 were evaluated through egg hatching. Asaricin 1 and isoasarone 2 showed potent ovicidal activity. Ovicidal activity for both compounds was up to 95% at 25μg/mL. Asaricin 1 and isoasarone 2 showed strong inhibition on acetylcholinesterase with relative IC50 values of 0.73 to 1.87 μg/mL respectively. These findings coupled with the high AChE inhibition may suggest that asaricin 1 and isoasarone 2 are neuron toxic compounds toward Aedes aegypti, Aedes albopictus and Culex quinquefasciatus. Further computational docking with Autodock Vina elaborates the possible interaction of asaricin 1 and isoasarone 2 with three possible binding sites of AChE which includes catalytic triads (CAS: S238, E367, H480), the peripheral sites (PAS: E72, W271) and anionic binding site (W83). The binding affinity of asaricin 1 and isoasarone 2 were relatively strong with asaricin 1 showed a higher binding affinity in the anionic pocket.

  20. Detection of amyloid-β fibrils using the DNA-intercalating dye YOYO-1: Binding mode and fibril formation kinetics.

    Science.gov (United States)

    Lindberg, David J; Esbjörner, Elin K

    2016-01-08

    Identification of the chemical and biological properties of amyloid fibrils is important for understanding their roles in human diseases and to clarify the mechanisms that govern their formation. In pursuit of these goals, small molecule fluorescent dyes have received increasing attention as probes of amyloid conformations. In this study, we report on the ability of YOYO-1, a homodimeric derivative of oxazole yellow, to detect fibrils formed by the Alzheimer's disease related Aβ(1-42) peptide. We find that YOYO-1 binds to Aβ(1-42) fibrils with the long axes of its oxazole yellow moieties parallel to the fibril axis, resulting in a 200x emission enhancement; a result that shows that YOYO-1 is a sensitive amyloid probe. Further, YOYO-1 exhibits characteristic absorption shifts upon binding to the Aβ(1-42) fibrils that we attribute to a self-stacking to non-stacking transition in its homodimer configuration; herein we show how this phenomenon can be exploited to estimate the degree of dye binding. Furthermore, we show that YOYO-1 can be used to monitor the kinetics of amyloid formation reactions. Taken together, our results show that YOYO-1 is a sensitive amyloid probe that can operate with both absorption and fluorescence read-outs, and this suggests that this commercially available dye could become a useful complement to thioflavin-T for in vitro amyloid-sensing applications. Copyright © 2015 Elsevier Inc. All rights reserved.

  1. Assessing GPCR homology models constructed from templates of various transmembrane sequence identities: Binding mode prediction and docking enrichment.

    Science.gov (United States)

    Loo, Jason S E; Emtage, Abigail L; Ng, Kar Weng; Yong, Alene S J; Doughty, Stephen W

    2018-03-01

    GPCR crystal structures have become more readily accessible in recent years. However, homology models of GPCRs continue to play an important role as many GPCR structures remain unsolved. The new crystal structures now available provide not only additional templates for homology modelling but also the opportunity to assess the performance of homology models against their respective crystal structures and gain insight into the performance of such models. In this study we have constructed homology models from templates of various transmembrane sequence identities for eight GPCR targets to better understand the relationship between transmembrane sequence identity and model quality. Model quality was assessed relative to the crystal structure in terms of structural accuracy as well as performance in two typical structure-based drug design applications: ligand binding pose prediction and docking enrichment in virtual screening. Crystal structures significantly outperformed homology models in both assessments. Accurate ligand binding pose prediction was possible but difficult to achieve using homology models, even with the use of induced fit docking. In virtual screening using homology models still conferred significant enrichment compared to random selection, with a clear benefit also observed in using models optimized through induced fit docking. Our results indicate that while homology models that are reasonably accurate structurally can be constructed, without significant refinement homology models will be outperformed by crystal structures in ligand binding pose prediction and docking enrichment regardless of the template used, primarily due to the extremely high level of structural accuracy needed for such applications. Copyright © 2017 Elsevier Inc. All rights reserved.

  2. Agrobacterium uses a unique ligand-binding mode for trapping opines and acquiring a competitive advantage in the niche construction on plant host.

    Science.gov (United States)

    Lang, Julien; Vigouroux, Armelle; Planamente, Sara; El Sahili, Abbas; Blin, Pauline; Aumont-Nicaise, Magali; Dessaux, Yves; Moréra, Solange; Faure, Denis

    2014-10-01

    By modifying the nuclear genome of its host, the plant pathogen Agrobacterium tumefaciens induces the development of plant tumours in which it proliferates. The transformed plant tissues accumulate uncommon low molecular weight compounds called opines that are growth substrates for A. tumefaciens. In the pathogen-induced niche (the plant tumour), a selective advantage conferred by opine assimilation has been hypothesized, but not experimentally demonstrated. Here, using genetics and structural biology, we deciphered how the pathogen is able to bind opines and use them to efficiently compete in the plant tumour. We report high resolution X-ray structures of the periplasmic binding protein (PBP) NocT unliganded and liganded with the opine nopaline (a condensation product of arginine and α-ketoglurate) and its lactam derivative pyronopaline. NocT exhibited an affinity for pyronopaline (K(D) of 0.6 µM) greater than that for nopaline (KD of 3.7 µM). Although the binding-mode of the arginine part of nopaline/pyronopaline in NocT resembled that of arginine in other PBPs, affinity measurement by two different techniques showed that NocT did not bind arginine. In contrast, NocT presented specific residues such as M117 to stabilize the bound opines. NocT relatives that exhibit the nopaline/pyronopaline-binding mode were only found in genomes of the genus Agrobacterium. Transcriptomics and reverse genetics revealed that A. tumefaciens uses the same pathway for assimilating nopaline and pyronopaline. Fitness measurements showed that NocT is required for a competitive colonization of the plant tumour by A. tumefaciens. Moreover, even though the Ti-plasmid conjugal transfer was not regulated by nopaline, the competitive advantage gained by the nopaline-assimilating Ti-plasmid donors led to a preferential horizontal propagation of this Ti-plasmid amongst the agrobacteria colonizing the plant-tumour niche. This work provided structural and genetic evidences to support the niche

  3. Agrobacterium uses a unique ligand-binding mode for trapping opines and acquiring a competitive advantage in the niche construction on plant host.

    Directory of Open Access Journals (Sweden)

    Julien Lang

    2014-10-01

    Full Text Available By modifying the nuclear genome of its host, the plant pathogen Agrobacterium tumefaciens induces the development of plant tumours in which it proliferates. The transformed plant tissues accumulate uncommon low molecular weight compounds called opines that are growth substrates for A. tumefaciens. In the pathogen-induced niche (the plant tumour, a selective advantage conferred by opine assimilation has been hypothesized, but not experimentally demonstrated. Here, using genetics and structural biology, we deciphered how the pathogen is able to bind opines and use them to efficiently compete in the plant tumour. We report high resolution X-ray structures of the periplasmic binding protein (PBP NocT unliganded and liganded with the opine nopaline (a condensation product of arginine and α-ketoglurate and its lactam derivative pyronopaline. NocT exhibited an affinity for pyronopaline (K(D of 0.6 µM greater than that for nopaline (KD of 3.7 µM. Although the binding-mode of the arginine part of nopaline/pyronopaline in NocT resembled that of arginine in other PBPs, affinity measurement by two different techniques showed that NocT did not bind arginine. In contrast, NocT presented specific residues such as M117 to stabilize the bound opines. NocT relatives that exhibit the nopaline/pyronopaline-binding mode were only found in genomes of the genus Agrobacterium. Transcriptomics and reverse genetics revealed that A. tumefaciens uses the same pathway for assimilating nopaline and pyronopaline. Fitness measurements showed that NocT is required for a competitive colonization of the plant tumour by A. tumefaciens. Moreover, even though the Ti-plasmid conjugal transfer was not regulated by nopaline, the competitive advantage gained by the nopaline-assimilating Ti-plasmid donors led to a preferential horizontal propagation of this Ti-plasmid amongst the agrobacteria colonizing the plant-tumour niche. This work provided structural and genetic evidences to

  4. DNA interaction studies of a copper (II) complex containing an antiviral drug, valacyclovir: the effect of metal center on the mode of binding.

    Science.gov (United States)

    Shahabadi, Nahid; Fatahi, Parvin

    2012-07-01

    The water-soluble complex, [Cu(Val)(2)(NO(3))(2)]; in which Val = valacyclovir, an antiviral drug, has been synthesized and characterized by elemental analysis, furier transfer-infrared, hydrogen nuclear magnetic resonance (H NMR), and UV-Vis techniques. The binding of this Cu (II) complex to calf thymus DNA was investigated using fluorimetry, spectrophotometry, circular dichroism, and viscosimetry. In fluorimetric studies, the enthalpy and entropy of the reaction between the complex and calf-thymus DNA (CT-DNA) showed that the reaction is endothermic (ΔH = 208.22 kJ mol(-1); ΔS = 851.35 J mol(-1)K(-1)). The complex showed the absorption hyperchromism in its ultra violet-visible (UV-Vis) spectrum with DNA. The calculated binding constant, K(b), obtained from UV-Vis absorption studies was 2 × 10(5) M(-1). Moreover, the complex induced detectable changes in the circular dichroism spectrum of CT-DNA, as well as changes in its viscosity. The results suggest that this copper (II) complex interacts with CT-DNA via a groove-binding mode.

  5. Structure of myostatin·follistatin-like 3: N-terminal domains of follistatin-type molecules exhibit alternate modes of binding.

    Science.gov (United States)

    Cash, Jennifer N; Angerman, Elizabeth B; Kattamuri, Chandramohan; Nolan, Kristof; Zhao, Huaying; Sidis, Yisrael; Keutmann, Henry T; Thompson, Thomas B

    2012-01-06

    TGF-β family ligands are involved in a variety of critical physiological processes. For instance, the TGF-β ligand myostatin is a staunch negative regulator of muscle growth and a therapeutic target for muscle-wasting disorders. Therefore, it is important to understand the molecular mechanisms of TGF-β family regulation. One form of regulation is through inhibition by extracellular antagonists such as the follistatin (Fst)-type proteins. Myostatin is tightly controlled by Fst-like 3 (Fstl3), which is the only Fst-type molecule that has been identified in the serum bound to myostatin. Here, we present the crystal structure of myostatin in complex with Fstl3. The structure reveals that the N-terminal domain (ND) of Fstl3 interacts uniquely with myostatin as compared with activin A, because it utilizes different surfaces on the ligand. This results in conformational differences in the ND of Fstl3 that alter its position in the type I receptor-binding site of the ligand. We also show that single point mutations in the ND of Fstl3 are detrimental to ligand binding, whereas corresponding mutations in Fst have little effect. Overall, we have shown that the NDs of Fst-type molecules exhibit distinctive modes of ligand binding, which may affect overall affinity of ligand·Fst-type protein complexes.

  6. X-ray structure of papaya chitinase reveals the substrate binding mode of glycosyl hydrolase family 19 chitinases.

    Science.gov (United States)

    Huet, Joëlle; Rucktooa, Prakash; Clantin, Bernard; Azarkan, Mohamed; Looze, Yvan; Villeret, Vincent; Wintjens, René

    2008-08-12

    The crystal structure of a chitinase from Carica papaya has been solved by the molecular replacement method and is reported to a resolution of 1.5 A. This enzyme belongs to family 19 of the glycosyl hydrolases. Crystals have been obtained in the presence of N-acetyl- d-glucosamine (GlcNAc) in the crystallization solution and two well-defined GlcNAc molecules have been identified in the catalytic cleft of the enzyme, at subsites -2 and +1. These GlcNAc moieties bind to the protein via an extensive network of interactions which also involves many hydrogen bonds mediated by water molecules, underlying their role in the catalytic mechanism. A complex of the enzyme with a tetra-GlcNAc molecule has been elaborated, using the experimental interactions observed for the bound GlcNAc saccharides. This model allows to define four major substrate interacting regions in the enzyme, comprising residues located around the catalytic Glu67 (His66 and Thr69), the short segment E89-R90 containing the second catalytic residue Glu89, the region 120-124 (residues Ser120, Trp121, Tyr123, and Asn124), and the alpha-helical segment 198-202 (residues Ile198, Asn199, Gly201, and Leu202). Water molecules from the crystal structure were introduced during the modeling procedure, allowing to pinpoint several additional residues involved in ligand binding that were not previously reported in studies of poly-GlcNAc/family 19 chitinase complexes. This work underlines the role played by water-mediated hydrogen bonding in substrate binding as well as in the catalytic mechanism of the GH family 19 chitinases. Finally, a new sequence motif for family 19 chitinases has been identified between residues Tyr111 and Tyr125.

  7. The different modes of binding of the dust mite allergens, Der f 7 and Der p 7, on a monoclonal antibody WH9 contribute to the differential reactivity.

    Science.gov (United States)

    Tai, Hsiao-Yun; Zhou, Jia-Kai; Yeh, Chang-Ching; Tam, Ming F; Sheu, Sheh-Yi; Shen, Horng-Der

    2017-06-28

    Der f 7 and Der p 7 are important house dust mite allergens. An IgE-binding inhibition monoclonal antibody WH9 reacts ten folds stronger against Der p 7 than to Der f 7. The purpose of this study is to identify the antigenic determinant(s) and the structural basis of Der f 7 recognize by WH9. WH9-reactive determinant(s) on Der f 7 was identified by immunoblot and immunoblot inhibition. The 3-D binary complex structures of WH9 and the group 7 allergens were simulated with homology modeling and docking methods. WH9 reacted with the Der f 7 f9 fragment. Among the five site-directed Der f 7 mutants, WH9 showed reduced immunoblot reactivity against Der f 7 S156A, D159A and P160A mutants. Only the wild-type protein and the Der f 7 I157A and L158A mutants can inhibit significantly the WH9-binding against Der f 7. The structural model of the Der f 7-WH9 complex suggests residues S156 and D159 of Der f 7 can bind to WH9 via potential hydrogen bonds. The structure models of Der f 7-WH9 and Der p 7-WH9 complexes revealed that the differential modes of binding of Der p 7 and Der f 7 allergens on WH9 contribute to the differential reactivity of WH9 against the Der f 7 and the Der p 7 mite allergens. Copyright © 2017. Published by Elsevier B.V.

  8. Structure of the Human Angiotensin II Type 1 (AT1) Receptor Bound to Angiotensin II from Multiple Chemoselective Photoprobe Contacts Reveals a Unique Peptide Binding Mode*

    Science.gov (United States)

    Fillion, Dany; Cabana, Jérôme; Guillemette, Gaétan; Leduc, Richard; Lavigne, Pierre; Escher, Emanuel

    2013-01-01

    Breakthroughs in G protein-coupled receptor structure determination based on crystallography have been mainly obtained from receptors occupied in their transmembrane domain core by low molecular weight ligands, and we have only recently begun to elucidate how the extracellular surface of G protein-coupled receptors (GPCRs) allows for the binding of larger peptide molecules. In the present study, we used a unique chemoselective photoaffinity labeling strategy, the methionine proximity assay, to directly identify at physiological conditions a total of 38 discrete ligand/receptor contact residues that form the extracellular peptide-binding site of an activated GPCR, the angiotensin II type 1 receptor. This experimental data set was used in homology modeling to guide the positioning of the angiotensin II (AngII) peptide within several GPCR crystal structure templates. We found that the CXC chemokine receptor type 4 accommodated the results better than the other templates evaluated; ligand/receptor contact residues were spatially grouped into defined interaction clusters with AngII. In the resulting receptor structure, a β-hairpin fold in extracellular loop 2 in conjunction with two extracellular disulfide bridges appeared to open and shape the entrance of the ligand-binding site. The bound AngII adopted a somewhat vertical binding mode, allowing concomitant contacts across the extracellular surface and deep within the transmembrane domain core of the receptor. We propose that such a dualistic nature of GPCR interaction could be well suited for diffusible linear peptide ligands and a common feature of other peptidergic class A GPCRs. PMID:23386604

  9. Alkaloid metabolite profiles by GC/MS and acetylcholinesterase inhibitory activities with binding-mode predictions of five Amaryllidaceae plants.

    Science.gov (United States)

    Cortes, Natalie; Alvarez, Rafael; Osorio, Edison H; Alzate, Fernando; Berkov, Strahil; Osorio, Edison

    2015-01-01

    Acetylcholinesterase (AChE) enzymatic inhibition is an important target for the management of Alzheimer disease (AD) and AChE inhibitors are the mainstay drugs for its treatment. In order to discover new sources of potent AChE inhibitors, a combined strategy is presented based on AChE-inhibitory activity and chemical profiles by GC/MS, together with in silico studies. The combined strategy was applied on alkaloid extracts of five Amaryllidaceae species that grow in Colombia. Fifty-seven alkaloids were detected using GC/MS, and 21 of them were identified by comparing their mass-spectral fragmentation patterns with standard reference spectra in commercial and private library databases. The alkaloid extracts of Zephyranthes carinata exhibited a high level of inhibitory activity (IC50 = 5.97 ± 0.24 μg/mL). Molecular modeling, which was performed using the structures of some of the alkaloids present in this extract and the three-dimensional crystal structures of AChE derived from Torpedo californica, disclosed their binding configuration in the active site of this AChE. The results suggested that the alkaloids 3-epimacronine and lycoramine might be of interest for AChE inhibition. Although the galanthamine group is known for its potential utility in treating AD, the tazettine-type alkaloids should be evaluated to find more selective compounds of potential benefit for AD. Copyright © 2014 Elsevier B.V. All rights reserved.

  10. Tetraphenylethylene Foldamers with Double Hairpin-Turn Linkers, TNT-Binding Mode and Detection of Highly Diluted TNT Vapor.

    Science.gov (United States)

    Xiong, Jia-Bin; Feng, Hai-Tao; Wang, Jin-Hua; Zhang, Chun; Li, Bao; Zheng, Yan-Song

    2018-02-06

    Tetraphenylethylene (TPE) foldamers with double hairpin-turn linkers showing an aggregation-induced emission (AIE) effect have been synthesized for the first time. A crystal structure of a foldamer-TNT complex has been obtained, enabling unprecedented direct observation of the interactions between TNT molecules and the chromophores of the foldamer. Instead of π-π stacking interactions, which have often been considered to be the key mechanism in the binding of TNT by chromophoric receptors, strong n-π interactions between the nitro groups of TNT and the aromatic rings of the foldamer have been found. Exceptionally, by addition of 1 % NaF to a suspension of the foldamer in H 2 O/THF (95:5), the fluorescence quenching efficiency by TNT vapor significantly increased from about 20 % to more than 90 %. Even after diluting TNT-saturated air at 25 °C by a factor of 2×10 4 , an obvious quenching response was observed, indicating that ultratrace TNT vapor (down to 3.4 fg per mL of air) could be detected. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. Vitual screening and binding mode elucidation of curcumin analogues on Cyclooxygenase-2 using AYO_COX2_V1.1 protocol

    Science.gov (United States)

    Mulatsari, E.; Mumpuni, E.; Herfian, A.

    2017-05-01

    Curcumin is yellow colored phenolic compounds contained in Curcuma longa. Curcumin is known to have biological activities as anti-inflammatory, antiviral, antioxidant, and anti-infective agent [1]. Synthesis of curcumin analogue compounds has been done and some of them had biological activity like curcumin. In this research, the virtual screening of curcumin analogue compounds has been conducted. The purpose of this research was to determine the activity of these compounds as selective Cyclooxygenase-2inhibitors in in-silico. Binding mode elucidation was made by active and inactive representative compounds to see the interaction of the amino acids in the binding site of the compounds. This research used AYO_COX2_V.1.1, a structure-based virtual screening protocol (SBVS) that has been validated by Mumpuni E et al, 2014 [2]. AYO_COX2_V.1.1 protocol using a variety of integrated applications such as SPORES, PLANTS, BKchem, OpenBabel and PyMOL. The results of virtual screening conducted on 49 curcumin analogue compounds obtained 8 compounds with 4 active amino acid residues (GLY340, ILE503, PHE343, and PHE367) that were considered active as COX-2 inhibitor.

  12. Binding modes of phosphotriesterase-like lactonase complexed with δ-nonanoic lactone and paraoxon using molecular dynamics simulations.

    Science.gov (United States)

    Guan, Shanshan; Zhao, Li; Jin, Hanyong; Shan, Ning; Han, Weiwei; Wang, Song; Shan, Yaming

    2017-02-01

    Phosphotriesterase-like lactonases (PLLs) have received much attention because of their physical and chemical properties. They may have widespread applications in various fields. For example, they show potential for quorum-sensing signaling pathways and organophosphorus (OP) detoxification in agricultural science. However, the mechanism by which PLLs hydrolyze, which involves OP compounds and lactones and a variety of distinct catalytic efficiencies, has only rarely been explored. In the present study, molecular dynamics (MD) simulations were performed to characterize and contrast the structural dynamics of DrPLL, a member of the PLL superfamily in Deinococcus radiodurans, bound to two substrates, δ-nonanoic lactone and paraoxon. It has been observed that there is a 16-fold increase in the catalytic efficiency of the two mutant strains of DrPLL (F26G/C72I) vs. the wild-type enzyme toward the hydrolysis of paraoxon, but an explanation for this behavior is currently lacking. The analysis of the molecular trajectories of DrPLL bound to δ-nonanoic lactone indicated that lactone-induced conformational changes take place in loop 8, which is near the active site. Binding to paraoxon may lead to conformational displacement of loop 1 residues, which could lead to the deformation of the active site and so trigger the entry of the paraoxon into the active site. The efficiency of the F26G/C72I mutant was increased by decreasing the displacement of loop 1 residues and increasing the flexibility of loop 8 residues. These results provide a molecular-level explanation for the experimental behavior.

  13. Effect of axial ligand on the binding mode of M-meso-tetrakis(N-methylpyridinium-4-yl)porphyrin to DNA probed by circular and linear dichroism spectroscopies.

    Science.gov (United States)

    Gong, Lindan; Bae, Inho; Kim, Seog K

    2012-10-18

    The binding modes of cationic porphyrins, namely M-meso-tetrakis(N-methylpyridinium-4-yl)porphyrin (MTMPyP, where M = free base, Cu(II), Ni(II), Co(III), Mn(III), V(IV)═O, and Ti(IV)═O), to native DNA were systematically investigated by polarized light spectroscopies, viz. circular and linear dichroism spectroscopy (CD and LD, respectively). At low [porphyrin]/[DNA] ratio, planar porphyrins including TMPyP, CuTMPyP, and NiTMPyP exhibited a negative CD signal in the Soret region and large negative wavelength-dependent LD(r) signal which is characteristics of their intercalative binding mode. In the intercalation pocket, the molecular plane of porphyrin is skewed to a large extent as it was judged from a large wavelength-dependency of the LD(r) magnitude in the Soret region. As the mixing ratio was increased, a bisignate CD spectrum became apparent for all of the planar porphyrins, while the shape of LD(r) remained the same, indicating the coupling of the electric transition moments of the intercalated porphyrins. Thus, coupling can occur between the porphyrins when they are separated at least two DNA base-pairs according to the nearest neighboring site exclusion model. This coupling interaction was the weakest for NiTMPyP. The porphyrins with axial ligands, namely VOTMPyP, TiOTMPyP, MnTMPyP, and CoTMPyP, bind to the exterior of the DNA at a low [porphyrin]/[DNA] ratio, which is indicated by the positive CD signal in the Soret region. The absorption and LD spectra in the Soret region were treated as the sum of two transitions to calculate the angle between each of the electric transition moments of the porphyrin, i.e., the B(x) and B(y) transitions relative to the local DNA helix axis. The angle of one of the two electric transitions of the porphyrin is in the range of 56°∼59°, whereas the other is in the range of 59°∼65°. Increasing the porphyrin density resulted in the appearance of an interaction between the bound porphyrins, which was indicated by the

  14. New insights into the structure and mode of action of Mo-CBP3, an antifungal chitin-binding protein of Moringa oleifera seeds.

    Directory of Open Access Journals (Sweden)

    Adelina B Batista

    Full Text Available Mo-CBP3 is a chitin-binding protein purified from Moringa oleifera Lam. seeds that displays inhibitory activity against phytopathogenic fungi. This study investigated the structural properties and the antifungal mode of action of this protein. To this end, circular dichroism spectroscopy, antifungal assays, measurements of the production of reactive oxygen species and microscopic analyses were utilized. Mo-CBP3 is composed of 30.3% α-helices, 16.3% β-sheets, 22.3% turns and 30.4% unordered forms. The Mo-CBP3 structure is highly stable and retains its antifungal activity regardless of temperature and pH. Fusarium solani was used as a model organism for studying the mechanisms by which this protein acts as an antifungal agent. Mo-CBP3 significantly inhibited spore germination and mycelial growth at 0.05 mg.mL-1. Mo-CBP3 has both fungistatic and fungicidal effects, depending on the concentration used. Binding of Mo-CBP3 to the fungal cell surface is achieved, at least in part, via electrostatic interactions, as salt was able to reduce its inhibitory effect. Mo-CBP3 induced the production of ROS and caused disorganization of both the cytoplasm and the plasma membrane in F. solani cells. Based on its high stability and specific toxicity, with broad-spectrum efficacy against important phytopathogenic fungi at low inhibitory concentrations but not to human cells, Mo-CBP3 has great potential for the development of new antifungal drugs or transgenic crops with enhanced resistance to phytopathogens.

  15. Functional SNPs of INCENP Affect Semen Quality by Alternative Splicing Mode and Binding Affinity with the Target Bta-miR-378 in Chinese Holstein Bulls.

    Directory of Open Access Journals (Sweden)

    Juan Liu

    Full Text Available Inner centromere protein (INCENP plays an important role in mitosis and meiosis as the main member of chromosomal passenger protein complex (CPC. To investigate the functional markers of the INCENP gene associated with semen quality, the single nucleotide polymorphisms (SNPs g.19970 A>G and g.34078 T>G were identified and analyzed. The new splice variant INCENP-TV is characterized by the deletion of exon 12. The g.19970 A>G in the exonic splicing enhancer (ESE motif region results in an aberrant splice variant by constructing two minigene expression vectors using the pSPL3 exon capturing vector and transfecting vectors into MLTC-1 cells. INCENP-TV was more highly expressed than INCENP-reference in adult bull testes. The g.34078 T>G located in the binding region of bta-miR-378 could affect the expression of INCENP, which was verified by luciferase assay. To analyze comprehensively the correlation of SNPs with sperm quality, haplotype combinations constructed by g.19970 A>G and g.34078 T>G, as well as g.-692 C>T and g.-556 G>T reported in our previous studies, were analyzed. The bulls with H1H12 and H2H2 exhibited a higher ejaculate volume than those with H2H10 and H9H12, respectively (P G and g.34078 T>G in INCENP both of which appear to change the molecular and biological characteristics of the mRNA transcribed from the locus may serve as a biomarkers of male bovine fertility by affecting alternative splicing mode and binding affinity with the target bta-miR-378.

  16. Computational study on the inhibitor binding mode and allosteric regulation mechanism in hepatitis C virus NS3/4A protein.

    Directory of Open Access Journals (Sweden)

    Weiwei Xue

    Full Text Available HCV NS3/4A protein is an attractive therapeutic target responsible for harboring serine protease and RNA helicase activities during the viral replication. Small molecules binding at the interface between the protease and helicase domains can stabilize the closed conformation of the protein and thus block the catalytic function of HCV NS3/4A protein via an allosteric regulation mechanism. But the detailed mechanism remains elusive. Here, we aimed to provide some insight into the inhibitor binding mode and allosteric regulation mechanism of HCV NS3/4A protein by using computational methods. Four simulation systems were investigated. They include: apo state of HCV NS3/4A protein, HCV NS3/4A protein in complex with an allosteric inhibitor and the truncated form of the above two systems. The molecular dynamics simulation results indicate HCV NS3/4A protein in complex with the allosteric inhibitor 4VA adopts a closed conformation (inactive state, while the truncated apo protein adopts an open conformation (active state. Further residue interaction network analysis suggests the communication of the domain-domain interface play an important role in the transition from closed to open conformation of HCV NS3/4A protein. However, the inhibitor stabilizes the closed conformation through interaction with several key residues from both the protease and helicase domains, including His57, Asp79, Asp81, Asp168, Met485, Cys525 and Asp527, which blocks the information communication between the functional domains interface. Finally, a dynamic model about the allosteric regulation and conformational changes of HCV NS3/4A protein was proposed and could provide fundamental insights into the allosteric mechanism of HCV NS3/4A protein function regulation and design of new potent inhibitors.

  17. New insights into the structure and mode of action of Mo-CBP3, an antifungal chitin-binding protein of Moringa oleifera seeds.

    Science.gov (United States)

    Batista, Adelina B; Oliveira, José T A; Gifoni, Juliana M; Pereira, Mirella L; Almeida, Marina G G; Gomes, Valdirene M; Da Cunha, Maura; Ribeiro, Suzanna F F; Dias, Germana B; Beltramini, Leila M; Lopes, José Luiz S; Grangeiro, Thalles B; Vasconcelos, Ilka M

    2014-01-01

    Mo-CBP3 is a chitin-binding protein purified from Moringa oleifera Lam. seeds that displays inhibitory activity against phytopathogenic fungi. This study investigated the structural properties and the antifungal mode of action of this protein. To this end, circular dichroism spectroscopy, antifungal assays, measurements of the production of reactive oxygen species and microscopic analyses were utilized. Mo-CBP3 is composed of 30.3% α-helices, 16.3% β-sheets, 22.3% turns and 30.4% unordered forms. The Mo-CBP3 structure is highly stable and retains its antifungal activity regardless of temperature and pH. Fusarium solani was used as a model organism for studying the mechanisms by which this protein acts as an antifungal agent. Mo-CBP3 significantly inhibited spore germination and mycelial growth at 0.05 mg.mL-1. Mo-CBP3 has both fungistatic and fungicidal effects, depending on the concentration used. Binding of Mo-CBP3 to the fungal cell surface is achieved, at least in part, via electrostatic interactions, as salt was able to reduce its inhibitory effect. Mo-CBP3 induced the production of ROS and caused disorganization of both the cytoplasm and the plasma membrane in F. solani cells. Based on its high stability and specific toxicity, with broad-spectrum efficacy against important phytopathogenic fungi at low inhibitory concentrations but not to human cells, Mo-CBP3 has great potential for the development of new antifungal drugs or transgenic crops with enhanced resistance to phytopathogens.

  18. Homology modeling of T. cruzi and L. major NADH-dependent fumarate reductases: ligand docking, molecular dynamics validation, and insights on their binding modes.

    Science.gov (United States)

    Merlino, Alicia; Vieites, Marisol; Gambino, Dinorah; Coitiño, E Laura

    2014-03-01

    Leishmania major and Trypanosoma cruzi are the main causes of leishmaniasis and Chagas disease, two endemic parasitosis identified as neglected diseases by the World Health Organization. Fumarate reductase (FR) is a central enzyme in the conversion of fumarate to succinate, an energy releasing path essential for the survival of these protozoans which is also absent in their mammalian hosts. FR can thus be considered as a good candidate for targeting specific inhibition by new drugs designed against L. major and T. cruzi. The lack of tertiary structures available for LmFR and TcFR has limited until now the possibility of performing structure-based drug design. Here we used homology modeling combined with enzyme-cofactor docking to propose tertiary structures for NADH-dependent LmFR and TcFR using an homologous X-ray crystallographic structure of flavine-adenine dinucleotide (FAD) dependent FR from Shewanella frigidimarina (PDB ID: 1QO8) as template. These models were refined and stabilized with/without substrate in the active site using classical molecular dynamics simulations under quasi-physiological conditions. Structural features relevant for understanding the mechanism of action of the enzyme were also analyzed, with special attention to the hydrogen bond network involving the cofactor and water molecules present at the binding sites. A small set of compounds previously synthesized and assayed for their inhibitory capacity against TcFR ([M(mpo)₂] metal complexes with M=Pt(II), Pd(II) and V(IV)O and mpo=2-mercaptopyridine N-oxide) and LmFR (licochalcone A) were screened by protein-ligand docking using the NADH-LmFR and NADH-TcFR models here proposed and validated, gaining insight into their binding modes in each enzyme. Copyright © 2013 Elsevier Inc. All rights reserved.

  19. Different binding modes of Cu and Pb vs. Cd, Ni, and Zn with the trihydroxamate siderophore desferrioxamine B at seawater ionic strength

    Energy Technology Data Exchange (ETDEWEB)

    Schijf, Johan; Christenson, Emily A.; Potter, Kailee J.

    2015-07-01

    The solution speciation in seawater of divalent trace metals (Cd, Cu, Ni, Pb, Zn) is dominated by strong, ostensibly metal-specific organic ligands that may play important roles in microbial metal acquisition and/or detoxification processes. We compare the effective stabilities of these metal-organic complexes to the stabilities of their complexes with a model siderophore, desferrioxamine B (DFOB). While metal-DFOB complexation has been studied in various dilute but often moderately coordinating media, for the purpose of this investigation we measured the stability constants in a non-coordinating background electrolyte at seawater ionic strength (0.7 M NaClO4). Potentiometric titrations of single metals (M) were performed in the presence of ligand (L) at different M:L molar ratios, whereupon the stability constants of multiple complexes were simultaneously determined by non-linear regression of the titration curves with FITEQL, using the optimal binding mode for each metal. Cadmium, Ni, and Zn, like trivalent Fe, sequentially form a bi-, tetra-, and hexadentate complex with DFOB as pH increases, consistent with their coordination number of 6 and regular octahedral geometry. Copper has a Jahn-Teller-distorted square-bipyramidal geometry whereas the geometry of Pb is cryptic, involving a range of bond lengths. Supported by a thermodynamic argument, our data suggest that this impedes binding of the third hydroxamate group and that the hexadentate Cu-DFOB and Pb-DFOB complex identified in earlier reports may instead be a deprotonated tetradentate complex. Absence of the hexadentate complex promotes the formation of a dinuclear (bidentate-tetradentate) complex, M2HL2+, albeit not for Pb in 0.7 M NaCl, evidently due to extensive complexation with chloride. Stabilities of the hexadentate Ni-DFOB, Zn-DFOB, and the tetradentate Pb-DFOB complex are nearly equal, yet about 2 orders of magnitude higher and 4 orders of magnitude lower than those of the hexadentate Cd-DFOB and

  20. Binding mode prediction of aplysiatoxin, a potent agonist of protein kinase C, through molecular simulation and structure-activity study on simplified analogs of the receptor-recognition domain.

    Science.gov (United States)

    Ashida, Yoshiki; Yanagita, Ryo C; Takahashi, Chise; Kawanami, Yasuhiro; Irie, Kazuhiro

    2016-09-15

    Aplysiatoxin (ATX) is a naturally occurring tumor promoter isolated from a sea hare and cyanobacteria. ATX binds to, and activates, protein kinase C (PKC) isozymes and shows anti-proliferative activity against human cancer cell lines. Recently, ATX has attracted attention as a lead compound for the development of novel anticancer drugs. In order to predict the binding mode between ATX and protein kinase Cδ (PKCδ) C1B domain, we carried out molecular docking simulation, atomistic molecular dynamics simulation in phospholipid membrane environment, and structure-activity study on a simple acyclic analog of ATX. These studies provided the binding model where the carbonyl group at position 27, the hydroxyl group at position 30, and the phenolic hydroxyl group at position 20 of ATX were involved in intermolecular hydrogen bonding with the PKCδ C1B domain, which would be useful for the rational design of ATX derivatives as anticancer lead compounds. Copyright © 2016 Elsevier Ltd. All rights reserved.

  1. Insight into the binding modes of Lassa nucleoprotein complexed with ssRNA by molecular dynamic simulations and free energy calculations.

    Science.gov (United States)

    Zhang, Ying; Chen, Hang; Han, Ju-Guang

    2015-01-01

    Lassa virus (LASV), an arenavirus known to be responsible for a severe hemorrhagic fever, causes thousands of deaths annually and there is no effective vaccine for it so far. The nucleoprotein (NP) of LASV plays an essential role in the replication and transcription of the viral genome. Recent research shows that viral RNA binds in a deep crevice located within the N-terminal domain of NP and suggests a gating mechanism in which NP transforms from a "closed" position to an "open" position to bind RNA. To characterize the molecular mechanisms of how RNA binds to N-terminal domain of NP, two molecular dynamic (MD) simulations of RNA-binding structure and RNA-free structure have been performed. The simulation results show that an important helix α6 interacts with RNA in the "open" conformation, while helix α6 rotates toward the binding crevice and reduces the space of RNA-binding pocket in the "closed" conformation; it appears that helix α6 would clash with RNA while NP is in a "closed" state. In addition, to characterize the role of residues involved in the binding of RNA, the MD simulations of the double-mutant (W164A/F176A) and the single-mutant (G243P) RNA-binding NP complexes have been performed. Our MD simulations and molecular mechanics-generalized born surface area (MM-GBSA) energy calculations exhibit that the three mutant residues increase the binding affinity. Furthermore, we infer that the defect of the replication and transcription of viral genome is possibly due to the change of structural integrity rather than the reduction of RNA-binding affinity.

  2. Characterization of binding mode of action of a blocking anti-platelet-derived growth factor (PDGF)-B monoclonal antibody, MOR8457, reveals conformational flexibility and avidity needed for PDGF-BB to bind PDGF receptor-β.

    Science.gov (United States)

    Kuai, Jun; Mosyak, Lidia; Brooks, Jon; Cain, Michael; Carven, Gregory J; Ogawa, Shinji; Ishino, Tetsuya; Tam, May; Lavallie, Edward R; Yang, Zhiyong; Ponsel, Dirk; Rauchenberger, Robert; Arch, Robert; Pullen, Nick

    2015-03-17

    Platelet derived growth factor-BB (PDGF-BB) is an important mitogen and cell survival factor during development. PDGF-BB binds PDGF receptor-β (PDGFRβ) to trigger receptor dimerization and tyrosine kinase activation. We present the pharmacological and biophysical characterization of a blocking PDGF-BB monoclonal antibody, MOR8457, and contrast this to PDGFRβ. MOR8457 binds to PDGF-BB with high affinity and selectivity, and prevents PDGF-BB induced cell proliferation competitively and with high potency. The structural characterization of the MOR8457-PDGF-BB complex indicates that MOR8457 binds with a 2:1 stoichiometry, but that binding of a single MOR8457 moiety is sufficient to prevent binding to PDGFRβ. Comparison of the MOR8457-PDGF-BB structure with that of the PDGFRβ-PDGF-BB complex suggested the potential reason for this was a substantial bending and twisting of PDGF-BB in the MOR8457 structure, relative to the structures of PDGF-BB alone, bound to a PDGF-BB aptamer or PDGFRβ, which makes it nonpermissive for PDGFRβ binding. These biochemical and structural data offer insights into the permissive structure of PDGF-BB needed for agonism as well as strategies for developing specific PDGF ligand antagonists.

  3. Alanine mutants of the interface residues of human thymidylate synthase decode key features of the binding mode of allosteric anticancer peptides.

    Science.gov (United States)

    Tochowicz, Anna; Santucci, Matteo; Saxena, Puneet; Guaitoli, Giambattista; Trande, Matteo; Finer-Moore, Janet; Stroud, Robert M; Costi, Maria P

    2015-01-22

    Allosteric peptide inhibitors of thymidylate synthase (hTS) bind to the dimer interface and stabilize the inactive form of the protein. Four interface residues were mutated to alanine, and interaction studies were employed to decode the key role of these residues in the peptide molecular recognition. This led to the identification of three crucial interface residues F59, L198, and Y202 that impart activity to the peptide inhibitors and suggest the binding area for further inhibitor design.

  4. Dissecting the Binding Mode of Low Affinity Phage Display Peptide Ligands to Protein Targets by Hydrogen/Deuterium Exchange Coupled to Mass Spectrometry

    DEFF Research Database (Denmark)

    Leurs, Ulrike; Lohse, Brian; Ming, Shonoi A

    2014-01-01

    of hydrogen/deuterium exchange mass spectrometry (HDX-MS) to characterize interactions of low affinity peptides with their cognate protein targets. The HDX-MS workflow was optimized to accurately detect low-affinity peptide-protein interactions by use of ion mobility, electron transfer dissociation, non......Phage display (PD) is frequently used to discover peptides capable of binding to biological protein targets. The structural characterization of peptide-protein complexes is often challenging due to their low binding affinities and high structural flexibility. Here, we investigate the use...

  5. Tyrosine 105 and threonine 212 at outermost substrate binding subsites -6 and +4 control substrate specificity, oligosaccharide cleavage patterns, and multiple binding modes of barley alpha-amylase 1

    DEFF Research Database (Denmark)

    Bak-Jensen, K.S.; André, G.; Gottschalk, T.E.

    2004-01-01

    and oligosaccharides, respectively. Bond cleavage analysis of oligosaccharide degradation by wild-type and mutant AMY1 supports that Tyr105 is critical for binding at subsite -6. Substrate binding is improved by T212(Y/W) introduced at subsite +4 and the [Y105A/ T212(Y/W)] AMY1 double mutants synergistically enhanced......The role in activity of outer regions in the substrate binding cleft in alpha-amylases is illustrated by mutational analysis of Tyr(105) and Thr(212) localized at subsites - 6 and +4 ( substrate cleavage occurs between subsites -1 and +1) in barley alpha-amylase 1 (AMY1). Tyr(105) is conserved......% activity, respectively. Thus engineering of aromatic stacking interactions at the ends of the 10-subsite long binding cleft affects activity very differently, dependent on the substrate. Y105A dominates in dual subsite -6/+4 [Y105A/T212(Y/W)] AMY1 mutants having almost retained and low activity on starch...

  6. High resolution crystal structures of unliganded and liganded human liver ACBP reveal a new mode of binding for the acyl-CoA ligand

    DEFF Research Database (Denmark)

    Taskinen, Jukka P; van Aalten, Daan M; Knudsen, Jens

    2007-01-01

    The acyl-CoA binding protein (ACBP) is essential for the fatty acid metabolism, membrane structure, membrane fusion, and ceramide synthesis. Here high resolution crystal structures of human cytosolic liver ACBP, unliganded and liganded with a physiological ligand, myristoyl-CoA are described...

  7. Two Distinct Binding Modes Define the Interaction of Brox with the C-Terminal Tails of CHMP5 and CHMP4B

    Energy Technology Data Exchange (ETDEWEB)

    Mu, Ruiling; Dussupt, Vincent; Jiang, Jiansheng; Sette, Paola; Rudd, Victoria; Chuenchor, Watchalee; Bello, Nana F.; Bouamr, Fadila; Xiao, Tsan Sam (NIH)

    2012-05-21

    Interactions of the CHMP protein carboxyl terminal tails with effector proteins play important roles in retroviral budding, cytokinesis, and multivesicular body biogenesis. Here we demonstrate that hydrophobic residues at the CHMP4B C-terminal amphipathic {alpha} helix bind a concave surface of Brox, a mammalian paralog of Alix. Unexpectedly, CHMP5 was also found to bind Brox and specifically recruit endogenous Brox to detergent-resistant membrane fractions through its C-terminal 20 residues. Instead of an {alpha} helix, the CHMP5 C-terminal tail adopts a tandem {beta}-hairpin structure that binds Brox at the same site as CHMP4B. Additional Brox:CHMP5 interface is furnished by a unique CHMP5 hydrophobic pocket engaging the Brox residue Y348 that is not conserved among the Bro1 domains. Our studies thus unveil a {beta}-hairpin conformation of the CHMP5 protein C-terminal tail, and provide insights into the overlapping but distinct binding profiles of ESCRT-III and the Bro1 domain proteins.

  8. Structural insights into the binding mode of flavonols with the active site of matrix metalloproteinase-9 through molecular docking and molecular dynamic simulations studies.

    Science.gov (United States)

    Pradiba, Dhinakararajan; Aarthy, Murali; Shunmugapriya, Velu; Singh, Sanjeev Kumar; Vasanthi, Mani

    2017-11-06

    Cartilage degradation in rheumatoid arthritis is mediated principally by the collagenases and gelatinases. Gelatinase B (also called matrix metalloproteinase 9 - MMP-9), is a valid target molecule which is known to participate in cartilage degradation as well as angiogenesis associated with the disease and inhibition of its activity shall prevent cartilage damage and angiogenesis. The focus of this study is to investigate the possibilities of MMP-9 inhibition by flavonol class of bioflavonoids by studying their crucial binding interactions at the active site of MMP 9 using molecular docking (Glide XP and QPLD) and further improvisation by post-docking MM-GBSA and molecular dynamic (MD) simulations. The results show that flavonols can convincingly bind to active site of MMP-9 as demonstrated by their stable interactions at the S1' specificity pocket and favourable binding energies. Gossypin has emerged as a promising candidate with a docking score of -14.618 kcal/mol, binding energy of -79.97 kcal/mol and a stable MD pattern over 15 ns. In addition, interaction mechanisms with respect to catalytic site zinc are also discussed. Further, the drug-like characters of the ligands were also analysed using ADME analysis.

  9. Epistatic mutations in PUMA BH3 drive an alternate binding mode to potently and selectively inhibit anti-apoptotic Bfl-1

    Energy Technology Data Exchange (ETDEWEB)

    Jenson, Justin M.; Ryan, Jeremy A.; Grant, Robert A.; Letai, Anthony; Keating, Amy E. (DFCI); (MIT)

    2017-06-08

    Overexpression of anti-apoptotic Bcl-2 family proteins contributes to cancer progression and confers resistance to chemotherapy. Small molecules that target Bcl-2 are used in the clinic to treat leukemia, but tight and selective inhibitors are not available for Bcl-2 paralog Bfl-1. Guided by computational analysis, we designed variants of the native BH3 motif PUMA that are > 150-fold selective for Bfl-1 binding. The designed peptides potently trigger disruption of the mitochondrial outer membrane in cells dependent on Bfl-1, but not in cells dependent on other anti-apoptotic homologs. High-resolution crystal structures show that designed peptide FS2 binds Bfl-1 in a shifted geometry, relative to PUMA and other binding partners, due to a set of epistatic mutations. FS2 modified with an electrophile reacts with a cysteine near the peptide-binding groove to augment specificity. Designed Bfl-1 binders provide reagents for cellular profiling and leads for developing enhanced and cell-permeable peptide or small-molecule inhibitors.

  10. Oxygen equilibria and ligand binding kinetics of erythrocruorins from two burrowing polychaetes of different modes of life, Marphysa sanguinea and Diopatra cuprea

    DEFF Research Database (Denmark)

    Weber, Roy E.; Bonaventura, J.; Sullivan, B.

    1978-01-01

    Oxygen equilibria, ligand-binding kinetics and some other physicochemical properties are reported for erythrocruorins of two intertidal polychaetes:Marphysa sanguinea, which inhabits simple, relatively stagnant burrows, andDiopatra cuprea, which inhabits impermeable, parchment-like tubes that are...

  11. Exploratory computational assessment of possible binding modes for small molecule inhibitors of the CD40-CD154 co-stimulatory interaction.

    Science.gov (United States)

    Ganesan, L; Vidović, D; Schürer, S C; Buchwald, P

    2012-05-01

    Protein-protein interactions (PPI) tend to involve extensive, flat, and featureless interfaces that are difficult to disrupt by small molecule binding. However, recently, PPIs are being recognized as increasingly valuable 'druggable' targets. We have identified several small molecule inhibitors of the immunologically relevant CD40-CD154 co-stimulatory interaction that bind to the homotrimeric CD154, a member of the tumor necrosis factor superfamily (TNFSF). Recently, on the basis of the co-crystal structure of CD154 with another small molecule (BIO8898), it has been suggested that these PPIs could be particularly susceptible to small molecule blockade due to a subunit fracture mechanism resulting in a distortion of the trimeric structure. To investigate whether this mechanism can occur with our organic dye-related inhibitors, we performed exploratory computational docking experiments. Possible druggable pockets that can serve as binding sites for small molecule inhibitors were identified with the FFT map algorithm both along the CD154-CD40 binding interface (competitive, orthosteric model) and in the interior core of the CD154 trimer corresponding to the BIO8898 binding site (allosteric model). Docking experiments (using Glide) were performed at these sites using the PDB ID: 3QD6 (CD40-CD154) and 3LKJ (BIO8898-CD154) co-crystal structures, respectively. The docking algorithm was able to better discriminate binders from non-binders at the deeper allosteric site than at the competitive site. Accordingly, an allosteric inhibitory mechanism that involves intercalation between monomeric subunits seems feasible for our small molecules making the constitutively trimeric CD154 a likely druggable target.

  12. Field-Evolved Mode 1 Resistance of the Fall Armyworm to Transgenic Cry1Fa-Expressing Corn Associated with Reduced Cry1Fa Toxin Binding and Midgut Alkaline Phosphatase Expression.

    Science.gov (United States)

    Jakka, Siva R K; Gong, Liang; Hasler, James; Banerjee, Rahul; Sheets, Joel J; Narva, Kenneth; Blanco, Carlos A; Jurat-Fuentes, Juan L

    2015-12-04

    Insecticidal protein genes from the bacterium Bacillus thuringiensis (Bt) are expressed by transgenic Bt crops (Bt crops) for effective and environmentally safe pest control. The development of resistance to these insecticidal proteins is considered the most serious threat to the sustainability of Bt crops. Resistance in fall armyworm (Spodoptera frugiperda) populations from Puerto Rico to transgenic corn producing the Cry1Fa insecticidal protein resulted, for the first time in the United States, in practical resistance, and Bt corn was withdrawn from the local market. In this study, we used a field-collected Cry1Fa corn-resistant strain (456) of S. frugiperda to identify the mechanism responsible for field-evolved resistance. Binding assays detected reduced Cry1Fa, Cry1Ab, and Cry1Ac but not Cry1Ca toxin binding to midgut brush border membrane vesicles (BBMV) from the larvae of strain 456 compared to that from the larvae of a susceptible (Ben) strain. This binding phenotype is descriptive of the mode 1 type of resistance to Bt toxins. A comparison of the transcript levels for putative Cry1 toxin receptor genes identified a significant downregulation (>90%) of a membrane-bound alkaline phosphatase (ALP), which translated to reduced ALP protein levels and a 75% reduction in ALP activity in BBMV from 456 compared to that of Ben larvae. We cloned and heterologously expressed this ALP from susceptible S. frugiperda larvae and demonstrated that it specifically binds with Cry1Fa toxin. This study provides a thorough mechanistic description of field-evolved resistance to a transgenic Bt crop and supports an association between resistance and reduced Cry1Fa toxin binding and levels of a putative Cry1Fa toxin receptor, ALP, in the midguts of S. frugiperda larvae. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

  13. The structure of tubulin-binding cofactor A from Leishmania major infers a mode of association during the early stages of microtubule assembly

    Energy Technology Data Exchange (ETDEWEB)

    Barrack, Keri L.; Fyfe, Paul K.; Hunter, William N., E-mail: w.n.hunter@dundee.ac.uk [University of Dundee, Dow Street, Dundee DD1 5EH, Scotland (United Kingdom)

    2015-04-21

    The structure of a tubulin-binding cofactor from L. major is reported and compared with yeast, plant and human orthologues. Tubulin-binding cofactor A (TBCA) participates in microtubule formation, a key process in eukaryotic biology to create the cytoskeleton. There is little information on how TBCA might interact with β-tubulin en route to microtubule biogenesis. To address this, the protozoan Leishmania major was targeted as a model system. The crystal structure of TBCA and comparisons with three orthologous proteins are presented. The presence of conserved features infers that electrostatic interactions that are likely to involve the C-terminal tail of β-tubulin are key to association. This study provides a reagent and template to support further work in this area.

  14. Structural and Enzymatic Analyses Reveal the Binding Mode of a Novel Series of Francisella tularensis Enoyl Reductase (FabI) Inhibitors

    Energy Technology Data Exchange (ETDEWEB)

    Mehboob, Shahila; Hevener, Kirk E.; Truong, Kent; Boci, Teuta; Santarsiero, Bernard D.; Johnson, Michael E. (UIC)

    2012-10-10

    Because of structural and mechanistic differences between eukaryotic and prokaryotic fatty acid synthesis enzymes, the bacterial pathway, FAS-II, is an attractive target for the design of antimicrobial agents. We have previously reported the identification of a novel series of benzimidazole compounds with particularly good antibacterial effect against Francisella tularensis, a Category A biowarfare pathogen. Herein we report the crystal structure of the F. tularensis FabI enzyme in complex with our most active benzimidazole compound bound with NADH. The structure reveals that the benzimidazole compounds bind to the substrate site in a unique conformation that is distinct from the binding motif of other known FabI inhibitors. Detailed inhibition kinetics have confirmed that the compounds possess a novel inhibitory mechanism that is unique among known FabI inhibitors. These studies could have a strong impact on future antimicrobial design efforts and may reveal new avenues for the design of FAS-II active antibacterial compounds.

  15. Crystal structure of enoyl–acyl carrier protein reductase (FabK) from Streptococcus pneumoniae reveals the binding mode of an inhibitor

    Science.gov (United States)

    Saito, Jun; Yamada, Mototsugu; Watanabe, Takashi; Iida, Maiko; Kitagawa, Hideo; Takahata, Sho; Ozawa, Tomohiro; Takeuchi, Yasuo; Ohsawa, Fukuichi

    2008-01-01

    Enoyl–acyl carrier protein (ACP) reductases are critical for bacterial type II fatty acid biosynthesis and thus are attractive targets for developing novel antibiotics. We determined the crystal structure of enoyl–ACP reductase (FabK) from Streptococcus pneumoniae at 1.7 Å resolution. There was one dimer per asymmetric unit. Each subunit formed a triose phosphate isomerase (TIM) barrel structure, and flavin mononucleotide (FMN) was bound as a cofactor in the active site. The overall structure was similar to the enoyl–ACP reductase (ER) of fungal fatty acid synthase and to 2-nitropropane dioxygenase (2-ND) from Pseudomonas aeruginosa, although there were some differences among these structures. We determined the crystal structure of FabK in complex with a phenylimidazole derivative inhibitor to envision the binding site interactions. The crystal structure reveals that the inhibitor binds to a hydrophobic pocket in the active site of FabK, and this is accompanied by induced-fit movements of two loop regions. The thiazole ring and part of the ureido moiety of the inhibitor are involved in a face-to-face π–π stacking interaction with the isoalloxazine ring of FMN. The side-chain conformation of the proposed catalytic residue, His144, changes upon complex formation. Lineweaver–Burk plots indicate that the inhibitor binds competitively with respect to NADH, and uncompetitively with respect to crotonoyl coenzyme A. We propose that the primary basis of the inhibitory activity is competition with NADH for binding to FabK, which is the first step of the two-step ping-pong catalytic mechanism. PMID:18305197

  16. The 1.3 A crystal structure of human mitochondrial Delta3-Delta2-enoyl-CoA isomerase shows a novel mode of binding for the fatty acyl group.

    Science.gov (United States)

    Partanen, Sanna T; Novikov, Dmitry K; Popov, Alexander N; Mursula, Anu M; Hiltunen, J Kalervo; Wierenga, Rik K

    2004-09-24

    The crystal structure of Delta3-Delta2-enoyl-CoA isomerase from human mitochondria (hmEci), complexed with the substrate analogue octanoyl-CoA, has been refined at 1.3 A resolution. This enzyme takes part in the beta-oxidation of unsaturated fatty acids by converting both cis-3 and trans-3-enoyl-CoA esters (with variable length of the acyl group) to trans-2-enoyl-CoA. hmEci belongs to the hydratase/isomerase (crotonase) superfamily. Most of the enzymes belonging to this superfamily are hexamers, but hmEci is shown to be a trimer. The mode of binding of the ligand, octanoyl-CoA, shows that the omega-end of the acyl group binds in a hydrophobic tunnel formed by residues of the loop preceding helix H4 as well as by side-chains of the kinked helix H9. From the structure of the complex it can be seen that Glu136 is the only catalytic residue. The importance of Glu136 for catalysis is confirmed by mutagenesis studies. A cavity analysis shows the presence of two large, adjacent empty hydrophobic cavities near the active site, which are shaped by side-chains of helices H1, H2, H3 and H4. The structure comparison of hmEci with structures of other superfamily members, in particular of rat mitochondrial hydratase (crotonase) and yeast peroxisomal enoyl-CoA isomerase, highlights the variable mode of binding of the fatty acid moiety in this superfamily.

  17. Investigation of the mode of binding of a novel series of N-benzyl-4-heteroaryl-1-(phenylsulfonyl)piperazine-2-carboxamides to the hepatitis C virus polymerase

    Energy Technology Data Exchange (ETDEWEB)

    Gentles, Robert G.; Sheriff, Steven; Beno, Brett R.; Wan, Changhong; Kish, Kevin; Ding, Min; Zheng, Xiaofan; Chupak, Louis; Poss, Michael A.; Witmer, Mark R.; Morin, Paul; Wang, Ying-Kai; Rigat, Karen; Lemm, Julie; Voss, Stacey; Liu, Mengping; Pelosi, Lenore; Roberts, Susan B.; Gao, Min; Kadow, John F. (BMS)

    2013-11-20

    Structure based rationales for the activities of potent N-benzyl-4-heteroaryl-1-(phenylsulfonyl)piperazine-2-carboxamide inhibitors of the hepatitis C viral polymerase are described herein. These compounds bind to the hepatitis C virus non-structural protein 5B (NS5B), and co-crystal structures of select examples from this series with NS5B are reported. Comparison of co-crystal structures of a potent analog with both NS5B genotype 1a and genotype 1b provides a possible explanation for the genotype-selectivity observed with this compound class and suggests opportunities for the further optimization of the series.

  18. Genetic Analysis of the Mode of Interplay between an ATPase Subunit and Membrane Subunits of the Lipoprotein-Releasing ATP-Binding Cassette Transporter LolCDE†

    OpenAIRE

    Ito, Yasuko; Matsuzawa, Hitomi; Matsuyama, Shin-ichi; Narita, Shin-ichiro; Tokuda, Hajime

    2006-01-01

    The LolCDE complex, an ATP-binding cassette (ABC) transporter, releases lipoproteins from the inner membrane, thereby initiating lipoprotein sorting to the outer membrane of Escherichia coli. The LolCDE complex is composed of two copies of an ATPase subunit, LolD, and one copy each of integral membrane subunits LolC and LolE. LolD hydrolyzes ATP on the cytoplasmic side of the inner membrane, while LolC and/or LolE recognize and release lipoproteins anchored to the periplasmic leaflet of the i...

  19. Crystal structures of yeast beta-alanine synthase complexes reveal the mode of substrate binding and large scale domain closure movements.

    Science.gov (United States)

    Lundgren, Stina; Andersen, Birgit; Piskur, Jure; Dobritzsch, Doreen

    2007-12-07

    Beta-alanine synthase is the final enzyme of the reductive pyrimidine catabolic pathway, which is responsible for the breakdown of uracil and thymine in higher organisms. The fold of the homodimeric enzyme from the yeast Saccharomyces kluyveri identifies it as a member of the AcyI/M20 family of metallopeptidases. Its subunit consists of a catalytic domain harboring a di-zinc center and a smaller dimerization domain. The present site-directed mutagenesis studies identify Glu(159) and Arg(322) as crucial for catalysis and His(262) and His(397) as functionally important but not essential. We determined the crystal structures of wild-type beta-alanine synthase in complex with the reaction product beta-alanine, and of the mutant E159A with the substrate N-carbamyl-beta-alanine, revealing the closed state of a dimeric AcyI/M20 metallopeptidase-like enzyme. Subunit closure is achieved by a approximately 30 degrees rigid body domain rotation, which completes the active site by integration of substrate binding residues that belong to the dimerization domain of the same or the partner subunit. Substrate binding is achieved via a salt bridge, a number of hydrogen bonds, and coordination to one of the zinc ions of the di-metal center.

  20. Elucidation of the sequence selective binding mode of the DNA minor groove binder adozelesin, by high-field {sup 1}H NMR and restrained molecular dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Cameron, L

    1999-07-01

    Adozelesin (formerly U73-975, The Upjohn Co.) is a covalent, minor-groove binding analogue of the antitumour antibiotic (+)CC-1065. Adozelesin consists of a cyclopropapyrroloindole alkylating sub-unit identical to (+)CC-1065, plus indole and benzofuran sub-units which replace the more complex pyrroloindole B and C sub-units, respectively, of (+)CC-1065. Adozelesin is a clinically important drug candidate, since it does not contain the ethylene bridge moieties on the B and C sub-units which are thought to be responsible for the unusual delayed hepatotoxicity exhibited by (+)CC-1065. Sequencing techniques identified two consensus sequences for adozelesin binding as p(dA) and 5'(T/A)(T/A)T-A*(C/G)G. This suggests that adozelesinspans a total of five base-pairs and shows a preference for A=T base-pair rich sequences, thus avoiding steric crowding around the exocyclic NH{sub 2} of guanine and a wide minor groove. In this project, the covalent modification of two DNA sequences, i.e. 5'd(CGTAAGCGCTTA*CG){sub 2} and 5'-d(CGAAAAA*CGG){center_dot} 5'-d(CCGTTTTTCG), by adozelesin was examined by high-field NMR and restrained molecular mechanics and dynamics. Previous studies of minor groove binding drugs, using techniques as diverse as NMR, X-ray crystallography and molecular modelling, indicate that the incorporation of a guanine into the consensus sequence sterically hinders binding and, more importantly, produces a wider minor groove which is a 'slack' fit for the ligand. The aim of this investigation was to provide an insight into the sequence selective binding of adozelesin to 5'-AAAAA*CG and 5'-GCTTA*CG. The {sup 1}H NMR data revealed that, in both cases, {beta}-helical structure and Watson-Crick base-pairing was maintained on adduct formation. The 5'-GCTTA*CG adduct displayed significant distortion of the guanine base on the non-covalently modified strand. This distortion resulted from an amalgamation of two factors. Firstly

  1. A mode of error: Immunoglobulin binding protein (a subset of anti-citrullinated proteins can cause false positive tuberculosis test results in rheumatoid arthritis

    Directory of Open Access Journals (Sweden)

    Maria Greenwald

    2017-12-01

    Full Text Available Citrullinated Immunoglobulin Binding Protein (BiP is a newly described autoimmune target in rheumatoid arthritis (RA, one of many cyclic citrullinated peptides(CCP or ACPA. BiP is over-expressed in RA patients causing T cell expansion and increased interferon levels during incubation for the QuantiFERON-Gold tuberculosis test (QFT-G TB. The QFT-G TB has never been validated where interferon is increased by underlying disease, as for example RA.Of ACPA-positive RA patients (n = 126, we found a 13% false-positive TB test rate by QFT-G TB. Despite subsequent biologic therapy for 3 years of all 126 RA patients, none showed evidence of TB without INH. Most of the false-positive RA patients after treatment with biologic therapy reverted to a negative QFT-G test. False TB tests correlated with ACPA level (p < 0.02.Three healthy women without arthritis or TB exposure had negative QFT-G TB. In vitro, all three tested positive every time for TB correlating to the dose of BiP or anti-BiP added, at 2 ug/ml, 5 ug/ml, 10 ug/ml, and 20 ug/ml.BiP naturally found in the majority of ACPA-positive RA patients can result in a false positive QFT-G TB. Subsequent undertreatment of RA, if biologic therapy is withheld, and overtreatment of presumed latent TB may harm patients. Keywords: Tuberculosis, IGRA, Rheumatoid arthritis, Interferon, Anti-citrullinated peptide antibody (ACPA, Immunoglobulin binding protein (BiP

  2. The structure of the exopolyphsophatase (PPX) from Escherchia coli O157:H7 suggests a binding mode for long polyphosphate chains

    Energy Technology Data Exchange (ETDEWEB)

    Rangarajan,E.; Nadeau, G.; Li, Y.; Wagner, J.; Hung, M.; Schrag, J.; Cygler, M.; Matte, A.

    2006-01-01

    Polyphosphate (polyP) is a linear polymer consisting of tens to hundreds of phosphate molecules joined together by high-energy anhydride bonds. These polymers are found in virtually all prokaryotic and eukaryotic cells and perform many functions; prominent among them are the responses to many stresses. Polyphosphate is synthesized by polyP kinase (PPK), using the terminal phosphate of ATP as the substrate, and degraded to inorganic phosphate by both endo- and exopolyphosphatases. Here we report the crystal structure and analysis of the polyphosphate phosphatase PPX from Escherichia coli O157:H7 refined at 2.2 Angstroms resolution. PPX is made of four domains. Domains I and II display structural similarity with one another and share the ribonuclease-H-like fold. Domain III bears structural similarity to the N-terminal, HD domain of SpoT. Domain IV, the smallest domain, has structural counterparts in cold-shock associated RNA-binding proteins but is of unknown function in PPX. The putative PPX active site is located at the interface between domains I and II. In the crystal structure of PPX these two domains are close together and represent the 'closed' state. Comparison with the crystal structure of PPX/GPPA from Aquifex aeolicus reveals close structural similarity between domains I and II of the two enzymes, with the PPX/GPPA representing an 'open' state. A striking feature of the dimer is a deep S-shaped canyon extending along the dimer interface and lined with positively charged residues. The active site region opens to this canyon. We postulate that this is a likely site of polyP binding.

  3. Reactivity of Fe and Ru Complexes of Picolyl-Substituted N-Heterocyclic Carbene Ligand: Diverse Coordination Modes and Small Molecule Binding.

    Science.gov (United States)

    Liang, Qiuming; Song, Datong

    2017-10-02

    Complexes [MClCp*(HL)] (1[Fe]/1[Ru]) (where HL = 1-mesityl-3-(pyridin-2-ylmethyl)imidazol-2-ylidene) were synthesized from the reaction of in situ generated HL ligand and [FeClCp*(TMEDA)] (where TMEDA is N,N,N',N'-tetramethylethylenediamine) or [RuClCp*]4, respectively. The deprotonation of 1[Fe]/1[Ru] with 1 equiv of LiHMDS led to cyclometalation through the o-Me of the mesityl group, forming [MCp*(L-κC,κC',κN)] 2[Fe]/2[Ru]. The coordinatively unsaturated compounds [MCp*(HL)]BPh4 3[Fe]/3[Ru] were prepared from 1[Fe]/1[Ru] and halide scavenger NaBPh4. Complex 3[Ru] showed agostic interactions between the o-Me group of the mesityl moiety and the metal center in solution and the solid state. When the vacant coordination site of 3[Fe]/3[Ru] is occupied by CO, the resulting [MCp*(CO)(HL)]BPh4 4[Fe]/4[Ru] can be deprotonated with 1 equiv of KHMDS at the pyridylic position to afford complexes [MCp*L'(CO)] 5[Fe]/5[Ru], where the L'(-) ligand chelates to the metal center through the nitrogen donor atom of the dearomatized pyridine ring and the carbene carbon. Complex 2[Fe] reacted rapidly with CO to afford the simple ligand substitution product [FeCp*(L-κC,κC')(CO)] 6[Fe], where the L(-) acts as a bidentate chelating ligand through the carbene carbon and benzylic carbon. Under the same condition, the reaction of 2[Ru] with CO forms [RuCp*L″(CO)] 7[Ru], where the L″(-) ligand (an isomer of L(-) and L'(-)) chelates to the metal center through the carbene carbon and a pyridyl carbon. Complexes 3[Fe]/3[Ru] reversibly bind dinitrogen to form [MCp*(HL)(N2)]BPh4 8[Fe]/8[Ru]. 3[Ru] reversibly binds dihydrogen to give [MCp*(H2)(HL)]BPh4 9[Ru], while no reaction was observed between 3[Fe] and H2. The reaction of 3[Ru] with dioxygen led to the isolation of a stable side-on O2 complex [RuCp*(HL)(O2)]BPh4 10[Ru], while the reaction of 3[Fe] with dioxygen led to an intractable mixture of products.

  4. Investigations of binding mode insight in Salmonella typhi type-III secretion system tip protein (SipD: A molecular docking and MD simulation study

    Directory of Open Access Journals (Sweden)

    Gopinath Samykannu

    2017-01-01

    Full Text Available Salmonella typhi is a Gram-negative pathogen that utilizes type three secretion systems (TTSS to translocate virulence factors into host cells. This causes a wide variety of diseases mainly gastroenteritis and typhoid fever in both humans and animals. Salmonella invasive protein D (SipD is a tip protein, attached to the needle protein and interacts with translocon complex. Exploring the molecular mechanisms of SipD may aid in better understanding about secretion, translocators and transmission of environmental signals of Salmonella. In this study, SipD sequence (Q56136 was retrieved from Uniprot for which three-dimensional (3D structure was modelled with the help of I-TASSER server. The modelled structure was subjected to molecular docking using Glide. About 25 compounds of T3SS inhibitors were chosen after literature studies and docking was performed. It was evident that polyol product Caminoside A possessed (≤-5 kcal/mol the best interaction with SipD and therefore this complex was subjected to molecular dynamic simulation for interaction stability analysis. The simulation results showed that Caminoside A binding was highly stable (life time of 80% with SipD and Asn318 interaction was more significant for the protein-ligand complex stability. These results will provide new knowledge for the development of novel therapeutic strategies against Salmonella typhi.

  5. Synthesis and biological evaluation of cationic fullerene quinazolinone conjugates and their binding mode with modeled Mycobacterium tuberculosis hypoxanthine-guanine phosphoribosyltransferase enzyme.

    Science.gov (United States)

    Patel, Manishkumar B; Kumar, Sivakumar Prasanth; Valand, Nikunj N; Jasrai, Yogesh T; Menon, Shobhana K

    2013-08-01

    The present work reports a series of novel cationic fullerene derivatives bearing a substituted-quinazolinone moiety as a side arm. Fullerene-quinazolinone conjugates synthesized using the 1,3-dipolar cycloaddition reaction of C60 with azomethine ylides generated from the corresponding Schiff bases of substituted quinazolinone were characterized by elemental analysis, FT-IR, (1)H NMR, (13)C NMR and ESI-MS and screened for their antibacterial activity against Mycobacterium tuberculosis (H 37 Rv strain). All the compounds exhibited significant activity with the most effective having MIC in the range of 1.562-3.125 μg/mL. Compound 9f exhibited good biological activity compared to standard drugs. We developed a computational strategy based on the modeled M. tuberculosis hypoxanthine-guanine phosphoribosyltransferase (HGPRT) using homology modeling techniques and studied its binding pattern with synthesized fullerene derivatives. We then explored the surface geometry of the protein to place the cage adjacent to the active site while optimizing its quinazolinone side arm to establish H bonding with active site residues.

  6. Elucidation of the CCR1- and CCR5-binding modes of MIP-1α by application of an NMR spectra reconstruction method to the transferred cross-saturation experiments

    Energy Technology Data Exchange (ETDEWEB)

    Yoshiura, Chie; Ueda, Takumi; Kofuku, Yutaka; Matsumoto, Masahiko; Okude, Junya; Kondo, Keita; Shiraishi, Yutaro; Shimada, Ichio, E-mail: shimada@iw-nmr.f.u-tokyo.ac.jp [The University of Tokyo, Graduate School of Pharmaceutical Sciences (Japan)

    2015-12-15

    C–C chemokine receptor 1 (CCR1) and CCR5 are involved in various inflammation and immune responses, and regulate the progression of the autoimmune diseases differently. However, the number of residues identified at the binding interface was not sufficient to clarify the differences in the CCR1- and CCR5-binding modes to MIP-1α, because the NMR measurement time for CCR1 and CCR5 samples was limited to 24 h, due to their low stability. Here we applied a recently developed NMR spectra reconstruction method, Conservation of experimental data in ANAlysis of FOuRier, to the amide-directed transferred cross-saturation experiments of chemokine receptors, CCR1 and CCR5, embedded in lipid bilayers of the reconstituted high density lipoprotein, and MIP-1α. Our experiments revealed that the residues on the N-loop and β-sheets of MIP-1α are close to both CCR1 and CCR5, and those in the C-terminal helix region are close to CCR5. These results suggest that the genetic influence of the single nucleotide polymorphisms of MIP-1α that accompany substitution of residues in the C-terminal helix region, E57 and V63, would provide clues toward elucidating how the CCR5–MIP-1α interaction affects the progress of autoimmune diseases.

  7. An Unexpected Mode Of Binding Defines BMS948 as A Full Retinoic Acid Receptor β (RARβ, NR1B2 Selective Agonist.

    Directory of Open Access Journals (Sweden)

    Eswarkumar Nadendla

    Full Text Available Retinoic acid is an important regulator of cell differentiation which plays major roles in embryonic development and tissue remodeling. The biological action of retinoic acid is mediated by three nuclear receptors denoted RARα, β and γ. Multiple studies support that RARβ possesses functional characteristics of a tumor suppressor and indeed, its expression is frequently lost in neoplastic tissues. However, it has been recently reported that RARβ could also play a role in mammary gland tumorigenesis, thus demonstrating the important but yet incompletely understood function of this receptor in cancer development. As a consequence, there is a great need for RARβ-selective agonists and antagonists as tools to facilitate the pharmacological analysis of this protein in vitro and in vivo as well as for potential therapeutic interventions. Here we provide experimental evidences that the novel synthetic retinoid BMS948 is an RARβ-selective ligand exhibiting a full transcriptional agonistic activity and activating RARβ as efficiently as the reference agonist TTNPB. In addition, we solved the crystal structures of the RARβ ligand-binding domain in complex with BMS948 and two related compounds, BMS641 and BMS411. These structures provided a rationale to explain how a single retinoid can be at the same time an RARα antagonist and an RARβ full agonist, and revealed the structural basis of partial agonism. Finally, in addition to revealing that a flip by 180° of the amide linker, that usually confers RARα selectivity, accounts for the RARβ selectivity of BMS948, the structural analysis uncovers guidelines for the rational design of RARβ-selective antagonists.

  8. Revised stability constant, spectroscopic properties and binding mode of Zn(II) to FluoZin-3, the most common zinc probe in life sciences.

    Science.gov (United States)

    Marszałek, I; Krężel, A; Goch, W; Zhukov, I; Paczkowska, I; Bal, W

    2016-08-01

    2-[2-[2-[2-[bis(carboxylatomethyl)amino]-5-methoxyphenoxy]ethoxy]-4-(2,7-difluoro-3-oxido-6-oxo-4a,9a-dihydroxanthen-9-yl)anilino]acetate (FluoZin-3) is used very broadly in life sciences as intra- and extracellular Zn(II) sensor selective for Zn(II) over Co(II), Ca(II) and Mg(II) ions at their physiological concentrations. It has been used for determination of relative and absolute levels of exchangeable Zn(II) in cells and extracellular fluids. Despite its popularity, the knowledge of its acid/base and Zn(II) coordination abilities and of its spectroscopic properties remained very limited. Also the published conditional dissociation constant ((C)Kd) values at pH7.4 are slightly discrepant, (15nM or 8.9nM). In this work we determined the (C)Kd for Zn(II) complexation by FluoZin-3 at pH7.4 with nitrilotriacetic acid (NTA) as competitor using two independent methods: fluorimetry and UV-Vis spectroscopy. For the first time, we investigated FluoZin-3 alone and complexed with Zn(II) in the wide range of pH, determining the total of eight pKa values from fluorescence spectra and from various regions of UV-Vis spectra. The validated values of (C)Kd (9.1±0.4nM; -log (C)Kd=8.04) and of the absolute (pH-independent) stability constant log βZnL (8.16±0.05) were provided by fluorescence spectroscopy experiments performed at 1μM concentrations. Our experiments demonstrated that both of aminocarboxylate moieties of FluoZin-3 bind the Zn(II) ion synergistically. Copyright © 2016 Elsevier Inc. All rights reserved.

  9. Crystal Structure of the Streptomyces coelicolor Sortase E1 Transpeptidase Provides Insight into the Binding Mode of the Novel Class E Sorting Signal.

    Directory of Open Access Journals (Sweden)

    Michele D Kattke

    Full Text Available Many species of Gram-positive bacteria use sortase transpeptidases to covalently affix proteins to their cell wall or to assemble pili. Sortase-displayed proteins perform critical and diverse functions for cell survival, including cell adhesion, nutrient acquisition, and morphological development, among others. Based on their amino acid sequences, there are at least six types of sortases (class A to F enzymes; however, class E enzymes have not been extensively studied. Class E sortases are used by soil and freshwater-dwelling Actinobacteria to display proteins that contain a non-canonical LAXTG sorting signal, which differs from 90% of known sorting signals by substitution of alanine for proline. Here we report the first crystal structure of a class E sortase, the 1.93 Å resolution structure of the SrtE1 enzyme from Streptomyces coelicolor. The active site is bound to a tripeptide, providing insight into the mechanism of substrate binding. SrtE1 possesses β3/β4 and β6/β7 active site loops that contact the LAXTG substrate and are structurally distinct from other classes. We propose that SrtE1 and other class E sortases employ a conserved tyrosine residue within their β3/β4 loop to recognize the amide nitrogen of alanine at position P3 of the sorting signal through a hydrogen bond, as seen here. Incapability of hydrogen-bonding with canonical proline-containing sorting signals likely contributes to class E substrate specificity. Furthermore, we demonstrate that surface anchoring of proteins involved in aerial hyphae formation requires an N-terminal segment in SrtE1 that is presumably positioned within the cytoplasm. Combined, our results reveal unique features within class E enzymes that enable them to recognize distinct sorting signals, and could facilitate the development of substrate-based inhibitors of this important enzyme family.

  10. Analysis of nidogen-1/laminin γ1 interaction by cross-linking, mass spectrometry, and computational modeling reveals multiple binding modes.

    Directory of Open Access Journals (Sweden)

    Philip Lössl

    Full Text Available We describe the detailed structural investigation of nidogen-1/laminin γ1 complexes using full-length nidogen-1 and a number of laminin γ1 variants. The interactions of nidogen-1 with laminin variants γ1 LEb2-4, γ1 LEb2-4 N836D, γ1 short arm, and γ1 short arm N836D were investigated by applying a combination of (photo-chemical cross-linking, high-resolution mass spectrometry, and computational modeling. In addition, surface plasmon resonance and ELISA studies were used to determine kinetic constants of the nidogen-1/laminin γ1 interaction. Two complementary cross-linking strategies were pursued to analyze solution structures of laminin γ1 variants and nidogen-1. The majority of distance information was obtained with the homobifunctional amine-reactive cross-linker bis(sulfosuccinimidylglutarate. In a second approach, UV-induced cross-linking was performed after incorporation of the diazirine-containing unnatural amino acids photo-leucine and photo-methionine into laminin γ1 LEb2-4, laminin γ1 short arm, and nidogen-1. Our results indicate that Asn-836 within laminin γ1 LEb3 domain is not essential for complex formation. Cross-links between laminin γ1 short arm and nidogen-1 were found in all protein regions, evidencing several additional contact regions apart from the known interaction site. Computational modeling based on the cross-linking constraints indicates the existence of a conformational ensemble of both the individual proteins and the nidogen-1/laminin γ1 complex. This finding implies different modes of interaction resulting in several distinct protein-protein interfaces.

  11. Production in Pichia pastoris, antifungal activity and crystal structure of a class I chitinase from cowpea (Vigna unguiculata): Insights into sugar binding mode and hydrolytic action.

    Science.gov (United States)

    Landim, Patrícia G Castro; Correia, Tuana O; Silva, Fredy D A; Nepomuceno, Denise R; Costa, Helen P S; Pereira, Humberto M; Lobo, Marina D P; Moreno, Frederico B M B; Brandão-Neto, José; Medeiros, Suelen C; Vasconcelos, Ilka M; Oliveira, José T A; Sousa, Bruno L; Barroso-Neto, Ito L; Freire, Valder N; Carvalho, Cristina P S; Monteiro-Moreira, Ana C O; Grangeiro, Thalles B

    2017-04-01

    A cowpea class I chitinase (VuChiI) was expressed in the methylotrophic yeast P. pastoris. The recombinant protein was secreted into the culture medium and purified by affinity chromatography on a chitin matrix. The purified chitinase migrated on SDS-polyacrylamide gel electrophoresis as two closely-related bands with apparent molecular masses of 34 and 37 kDa. The identity of these bands as VuChiI was demonstrated by mass spectrometry analysis of tryptic peptides and N-terminal amino acid sequencing. The recombinant chitinase was able to hydrolyze colloidal chitin but did not exhibit enzymatic activity toward synthetic substrates. The highest hydrolytic activity of the cowpea chitinase toward colloidal chitin was observed at pH 5.0. Furthermore, most VuChiI activity (approximately 92%) was retained after heating to 50 °C for 30 min, whereas treatment with 5 mM Cu 2+ caused a reduction of 67% in the enzyme's chitinolytic activity. The recombinant protein had antifungal activity as revealed by its ability to inhibit the spore germination and mycelial growth of Penicillium herquei. The three-dimensional structure of VuChiI was resolved at a resolution of 1.55 Å by molecular replacement. The refined model had 245 amino acid residues and 381 water molecules, and the final R-factor and R free values were 14.78 and 17.22%, respectively. The catalytic domain of VuChiI adopts an α-helix-rich fold, stabilized by 3 disulfide bridges and possessing a wide catalytic cleft. Analysis of the crystallographic model and molecular docking calculations using chito-oligosaccharides provided evidences about the VuChiI residues involved in sugar binding and catalysis, and a possible mechanism of antifungal action is suggested. Copyright © 2017 Elsevier B.V. and Société Française de Biochimie et Biologie Moléculaire (SFBBM). All rights reserved.

  12. High prevalence of subclass-specific binding and neutralizing antibodies against Clostridium difficile toxins in adult cystic fibrosis sera: possible mode of immunoprotection against symptomatic C. difficile infection

    Directory of Open Access Journals (Sweden)

    Monaghan TM

    2017-07-01

    Full Text Available Tanya M Monaghan,1 Ola H Negm,2,3 Brendon MacKenzie,4 Mohamed R Hamed,2,3 Clifford C Shone,5 David P Humphreys,4 K Ravi Acharya,6 Mark H Wilcox7 1Nottingham Digestive Diseases Centre, NIHR Nottingham Digestive Diseases Biomedical Research Unit, School of Medicine, University of Nottingham, Nottingham, 2Breast Surgery Group, Division of Medical Sciences and Graduate Entry Medicine, School of Medicine, Queen’s Medical Centre, University of Nottingham, Nottingham, UK; 3Medical Microbiology and Immunology Department, Faculty of Medicine, Mansoura University, Mansoura, Egypt; 4Antibody Biology, UCB-New Medicines, UCB Celltech, Slough, UK; 5Toxins Group, National Infection Service, Public Health England, Salisbury, UK; 6Department of Biology and Biochemistry, University of Bath, Bath, UK; 7Leeds Institute of Biomedical and Clinical Sciences, University of Leeds, Leeds, UK Objectives: Despite multiple risk factors and a high rate of colonization for Clostridium difficile, the occurrence of C. difficile infection in patients with cystic fibrosis is rare. The aim of this study was to compare the prevalence of binding C. difficile toxin-specific immunoglobulin (IgA, IgG and anti-toxin neutralizing antibodies in the sera of adults with cystic fibrosis, symptomatic C. difficile infection (without cystic fibrosis and healthy controls. Methods: Subclass-specific IgA and IgG responses to highly purified whole C. difficile toxins A and B (toxinotype 0, strain VPI 10463, ribotype 087, toxin B from a C. difficile toxin-B-only expressing strain (CCUG 20309 and precursor form of B fragment of binary toxin, pCDTb, were determined by protein microarray. Neutralizing antibodies to C. difficile toxins A and B were evaluated using a Caco-2 cell-based neutralization assay. Results: Serum IgA anti-toxin A and B levels and neutralizing antibodies against toxin A were significantly higher in adult cystic fibrosis patients (n=16 compared with healthy controls (n=17 and

  13. Characterization of the active site and insight into the binding mode of the anti-angiogenesis agent fumagillin to the manganese(II)-loaded methionyl aminopeptidase from Escherichia coli.

    Science.gov (United States)

    D'souza, Ventris M; Brown, Robert S; Bennett, Brian; Holz, Richard C

    2005-01-01

    EPR spectra were recorded for methionine aminopeptidase from Escherichia coli (EcMetAP-I) samples (approximately 2.5 mM) to which one and two equivalents of Mn(II) were added (the latter is referred to as [MnMn(EcMetAP-I)]). The spectra for each sample were indistinguishable except that the spectrum of [MnMn(EcMetAP-I)] was twice as intense. The EPR spectrum of [MnMn(EcMetAP-I)] exhibited the characteristic six-line g approximately 2 EPR signal of mononuclear Mn(II) with A(av)((55)Mn)=9.3 mT (93 G) and exhibited Curie-law temperature dependence. This signal is typical of Mn(II) in a ligand sphere comprising oxygen and/or nitrogen atoms. Other features in the spectrum were observed only as the temperature was raised from that of liquid helium. The temperature dependences of these features are consistent with their assignment to excited state transitions in the S=1, 2 ... 5 non-Kramer's doublets, due to two antiferromagnetically coupled Mn(II) ions with an S=0 ground state. This assignment is supported by the observation of a characteristic 4.5 mT hyperfine pattern, and by the presence of signals in the parallel mode consistent with a non-Kramers' spin ladder. Upon the addition of the anti-angiogenesis agent fumagillin to [MnMn(EcMetAP-I)], very small changes were observed in the EPR spectrum. MALDI-TOF mass spectrometry indicated that fumagillin was, however, covalently coordinated to EcMetAP-I. Therefore, the inhibitory action of this anti-angiogenesis agent on EcMetAP-I appears to involve covalent binding to a polypeptide component at or near the active site rather than direct binding to the metal ions.

  14. The structure of an LIM-only protein 4 (LMO4 and Deformed epidermal autoregulatory factor-1 (DEAF1 complex reveals a common mode of binding to LMO4.

    Directory of Open Access Journals (Sweden)

    Soumya Joseph

    Full Text Available LIM-domain only protein 4 (LMO4 is a widely expressed protein with important roles in embryonic development and breast cancer. It has been reported to bind many partners, including the transcription factor Deformed epidermal autoregulatory factor-1 (DEAF1, with which LMO4 shares many biological parallels. We used yeast two-hybrid assays to show that DEAF1 binds both LIM domains of LMO4 and that DEAF1 binds the same face on LMO4 as two other LMO4-binding partners, namely LIM domain binding protein 1 (LDB1 and C-terminal binding protein interacting protein (CtIP/RBBP8. Mutagenic screening analysed by the same method, indicates that the key residues in the interaction lie in LMO4LIM2 and the N-terminal half of the LMO4-binding domain in DEAF1. We generated a stable LMO4LIM2-DEAF1 complex and determined the solution structure of that complex. Although the LMO4-binding domain from DEAF1 is intrinsically disordered, it becomes structured on binding. The structure confirms that LDB1, CtIP and DEAF1 all bind to the same face on LMO4. LMO4 appears to form a hub in protein-protein interaction networks, linking numerous pathways within cells. Competitive binding for LMO4 therefore most likely provides a level of regulation between those different pathways.

  15. Atomistic fingerprint of hyaluronan-CD44 binding

    DEFF Research Database (Denmark)

    Vuorio, Joni; Vattulainen, Ilpo; Martinez-Seara, Hector

    2017-01-01

    that hyaluronan can bind CD44 with three topographically different binding modes that in unison define an interaction fingerprint, thus providing a plausible explanation for the disagreement between the earlier studies. Our results confirm that the known crystallographic mode is the strongest of the three binding...

  16. Failure Modes

    DEFF Research Database (Denmark)

    Jakobsen, K. P.; Burcharth, H. F.; Ibsen, Lars Bo

    1999-01-01

    The present appendix contains the derivation of ten different limit state equations divided on three different failure modes. Five of the limit state equations can be used independently of the characteristics of the subsoil, whereas the remaining five can be used for either drained or undrained s...

  17. Exploration of electrostatic interaction in the hydrophobic pocket of lysozyme: Importance of ligand-induced perturbation of the secondary structure on the mode of binding of exogenous ligand and possible consequences.

    Science.gov (United States)

    Panja, Sudipta; Halder, Mintu

    2016-08-01

    Exogenous ligand binding can be adequate to alter the secondary structure of biomolecules besides other external stimuli. In such cases, structural alterations can complicate on the nature of interaction with the exogenous molecules. In order to accommodate the exogenous ligand, the biomolecule has to unfold resulting in a considerable change to its properties. If the bound ligand can be unbound, the biomolecule gets the opportunity to refold back and return to its native state. Keeping this in mind, we have purposely investigated the interaction of tartrazine (TZ), a well abundant azo food colorant, with two homologous lysozymes, namely, human lysozyme (HLZ) and chicken egg white lysozyme (CEWLZ) in physiological pH condition. The binding of TZ with lysozymes has been identified to accompany a ligand-induced secondary structure alteration as indicated by the circular dichroism spectra, and the reduction of α-helical content is more with HLZ than CEWLZ. Interestingly, the binding is identified to occur in the electronic ground state of TZ with lysozyme in its hydrophobic cavity, containing excess of positive charge, predominantly via electrostatic interaction. With increase of salinity of the medium the protein tends to refold back due to wakening of electrostatic forces and consequent reduction of strength of ligand interaction and unbinding. The entropy enthalpy compensation (EEC) has been probed to understand the binding features and it is found that CEWLZ-TZ shows better compensation than HLZ-TZ complex. This is presumably due to the fact that with CEWLZ the binding does not accompany substantial change in the protein secondary structure and hence ineffective to scramble the EEC. The present study initiates the importance of ligand-perturbed structural alteration of biomolecule in controlling the thermodynamics of binding. If there is a considerable alteration of the protein secondary structure due to binding, it is indicative that such changes should bring in

  18. Retinoid-binding proteins: similar protein architectures bind similar ligands via completely different ways.

    Directory of Open Access Journals (Sweden)

    Yu-Ru Zhang

    Full Text Available BACKGROUND: Retinoids are a class of compounds that are chemically related to vitamin A, which is an essential nutrient that plays a key role in vision, cell growth and differentiation. In vivo, retinoids must bind with specific proteins to perform their necessary functions. Plasma retinol-binding protein (RBP and epididymal retinoic acid binding protein (ERABP carry retinoids in bodily fluids, while cellular retinol-binding proteins (CRBPs and cellular retinoic acid-binding proteins (CRABPs carry retinoids within cells. Interestingly, although all of these transport proteins possess similar structures, the modes of binding for the different retinoid ligands with their carrier proteins are different. METHODOLOGY/PRINCIPAL FINDINGS: In this work, we analyzed the various retinoid transport mechanisms using structure and sequence comparisons, binding site analyses and molecular dynamics simulations. Our results show that in the same family of proteins and subcellular location, the orientation of a retinoid molecule within a binding protein is same, whereas when different families of proteins are considered, the orientation of the bound retinoid is completely different. In addition, none of the amino acid residues involved in ligand binding is conserved between the transport proteins. However, for each specific binding protein, the amino acids involved in the ligand binding are conserved. The results of this study allow us to propose a possible transport model for retinoids. CONCLUSIONS/SIGNIFICANCE: Our results reveal the differences in the binding modes between the different retinoid-binding proteins.

  19. Low nanomolar GABA effects at extrasynaptic a4ß1/ß3delta GABAA receptor subtypes indicate a different binding mode for GABA at these receptors

    DEFF Research Database (Denmark)

    Karim, Nasiara; Wellendorph, Petrine; Absalom, Nathan

    2012-01-01

    the two-electrode voltage clamp technique, and to investigate, using site-directed mutagenesis, the molecular determinants for GABA potency at a4ß3d GABA(A) receptors. a4/d-Containing GABA(A) receptors displayed high sensitivity to GABA, with mid-nanomolar concentrations activating a4ß1d (EC(50)=24n......M) and a4ß3d (EC(50)=12nM) receptors. In the majority of oocytes expressing a4ß3d subtypes, GABA produced a biphasic concentration-response curve, and activated the receptor with low and high concentrations (EC(50)(1)=16nM; EC(50)(2)=1.2µM). At a4ß2d, GABA had low micromolar activity (EC(50)=1µ...... did not significantly affect GABA potency. Mutating the residue R218 of the d-subunit, equivalent to the GABA binding residue R207 of the ß2-subunit, reduced the potency of GABA by 670-fold, suggesting a novel GABA binding site at the d-subunit interface. Taken together, GABA may have different...

  20. Exploration of the binding modes of buffalo PGRP1 receptor complexed with meso-diaminopimelic acid and lysine-type peptidoglycans by molecular dynamics simulation and free energy calculation.

    Science.gov (United States)

    Sahoo, Bikash Ranjan; Dubey, Praveen Kumar; Goyal, Shubham; Bhoi, Gopal Krushna; Lenka, Santosh Kumar; Maharana, Jitendra; Pradhan, Sukanta Kumar; Kataria, Ranjit Singh

    2014-09-05

    The peptidoglycan recognition proteins (PGRPs) are the key components of innate-immunity, and are highly specific for the recognition of bacterial peptidoglycans (PGN). Among different mammalian PGRPs, the PGRP1 binds to murein PGN of Gram-positive bacteria (lysine-type) and also have bactericidal activity towards Gram-negative bacteria (diaminopimelic acid or Dap-type). Buffaloes are the major sources of milk and meat in Asian sub-continents and are highly exposed to bacterial infections. The PGRP activates the innate-immune signaling, but their studies has been confined to limited species due to lack of structural and functional information. So, to understand the structural constituents, 3D model of buffalo PGRP1 (bfPGRP1) was constructed and conformational and dynamics properties of bfPGRP1 was studied. The bfPGRP1 model highly resembled human and camel PGRP structure, and shared a highly flexible N-terminus and centrally placed L-shaped cleft. Docking simulation of muramyl-tripeptide, tetrapeptide, pentapeptide-Dap-(MTP-Dap, MTrP-Dap and MPP-Dap) and lysine-type (MTP-Lys, MTrP-Lys and MPP-Lys) in AutoDock 4.2 and ArgusLab 4.0.1 anticipated β1, α2, α4, β4, and loops connecting β1-α2, α2-β2, β3-β4 and α4-α5 as the key interacting domains. The bfPGRP1-ligand complex molecular dynamics simulation followed by free binding energy (BE) computation conceded BE values of -18.30, -35.53, -41.80, -25.03, -24.62 and -22.30 kJ mol(-1) for MTP-Dap, MTrP-Dap, MPP-Dap, MTP-Lys, MTrP-Lys and MPP-Lys, respectively. The groove-surface and key binding residues involved in PGN-Dap and Lys-type interaction intended by the molecular docking, and were also accompanied by significant BE values directed their importance in pharmacogenomics, and warrants further in vivo studies for drug targeting and immune signaling pathways exploration. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

  1. Immune hierarchy among HIV-1 CD8+ T cell epitopes delivered by dendritic cells depends on MHC-I binding irrespective of mode of loading and immunization in HLA-A*0201 mice

    DEFF Research Database (Denmark)

    Kloverpris, Henrik N; Karlsson, Ingrid; Thorn, Mette

    2009-01-01

    Recent human immunodeficiency virus type 1 (HIV-1) vaccination strategies aim at targeting a broad range of cytotoxic T lymphocyte (CTL) epitopes from different HIV-1 proteins by immunization with multiple CTL epitopes simultaneously. However, this may establish an immune hierarchical response......, where the immune system responds to only a small number of the epitopes administered. To evaluate the feasibility of such vaccine strategies, we used the human leukocyte antigen (HLA)-A*0201 transgenic (tg) HHD murine in vivo model and immunized with dendritic cells pulsed with seven HIV-1-derived HLA......-A*0201 binding CTL epitopes. The seven peptides were simultaneously presented on the same dendritic cell (DC) or on separate DCs before immunization to one or different lymphoid compartments. Data from this study showed that the T-cell response, as measured by cytolytic activity and gamma-interferon (IFN...

  2. Benzoxazepines Achieve Potent Suppression of IL-17 Release in Human T-Helper 17 (TH 17) Cells through an Induced-Fit Binding Mode to the Nuclear Receptor RORγ.

    Science.gov (United States)

    Olsson, Roine I; Xue, Yafeng; von Berg, Stefan; Aagaard, Anna; McPheat, Jane; Hansson, Eva L; Bernström, Jenny; Hansson, Pia; Jirholt, Johan; Grindebacke, Hanna; Leffler, Agnes; Chen, Rongfeng; Xiong, Yao; Ge, Hongbin; Hansson, Thomas G; Narjes, Frank

    2016-01-19

    RORγt, an isoform of the retinoic acid-related orphan receptor gamma (RORc, RORγ), has been identified as the master regulator of T-helper 17 (TH 17) cell function and development, making it an attractive target for the treatment of autoimmune diseases. Validation for this target comes from antibodies targeting interleukin-17 (IL-17), the signature cytokine produced by TH 17 cells, which have shown impressive results in clinical trials. Through focused screening of our compound collection, we identified a series of N-sulfonylated benzoxazepines, which displayed micromolar affinity for the RORγ ligand-binding domain (LBD) in a radioligand binding assay. Optimization of these initial hits resulted in potent binders, which dose-dependently decreased the ability of the RORγ-LBD to interact with a peptide derived from steroid receptor coactivator 1, and inhibited the release of IL-17 secretion from isolated and cultured human TH 17 cells with nanomolar potency. A cocrystal structure of inverse agonist 15 (2-chloro-6-fluoro-N-(4-{[3-(trifluoromethyl)phenyl]sulfonyl}-2,3,4,5-tetrahydro-1,4-benzoxazepin-7-yl)benzamide) bound to the RORγ-LBD illustrated that both hydrophobic interactions, leading to an induced fit around the substituted benzamide moiety of 15, as well as a hydrogen bond from the amide NH to His479 seemed to be important for the mechanism of action. This structure is compared with the structure of agonist 25 (N-(2-fluorophenyl)-4-[(4-fluorophenyl)sulfonyl]-2,3,4,5-tetrahydro-1,4-benzoxazepin-6-amine ) and structures of other known RORγ modulators. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  3. Estimation of the binding modes with important human cytochrome P450 enzymes, drug interaction potential, pharmacokinetics, and hepatotoxicity of ginger components using molecular docking, computational, and pharmacokinetic modeling studies

    Directory of Open Access Journals (Sweden)

    Qiu JX

    2015-02-01

    2, 2C9, 2C19, 2D6, and 3A4 mainly through hydrogen bond formation, to a lesser extent, via π–π stacking. The pharmacokinetic simulation studies showed that the [I]/[Ki] value for CYP2C9, 2C19, and 3A4 ranged from 0.0002 to 19.6 and the R value ranged from 1.0002 to 20.6 and that ginger might exhibit a high risk of drug interaction via inhibition of the activity of human CYP2C9 and CYP3A4, but a low risk of drug interaction toward CYP2C19-mediated drug metabolism. Furthermore, it has been evaluated that the 12 ginger components possessed a favorable ADMET profiles with regard to the solubility, absorption, permeability across the blood–brain barrier, interactions with CYP2D6, hepatotoxicity, and plasma protein binding. The validation results showed that there was no remarkable effect of ginger on the metabolism of warfarin in humans, whereas concurrent use of ginger and nifedipine exhibited a synergistic effect on platelet aggregation in humans. Moreover, ginger components showed a rapid half-life and no to low toxicity in humans. Taken together, this study shows that ginger components may regulate the activity and expression of various human CYPs, probably resulting in alterations in drug clearance and response. More studies are warranted to identify and confirm potential ginger–drug interactions and explore possible interactions of ginger with human CYPs and other functionally important proteins, to reduce and avoid side effects induced by unfavorable ginger–drug interactions.Keywords: CYP, drug metabolism, ginger, drug interaction, docking

  4. SNV's modes of ordering

    NARCIS (Netherlands)

    Hummel, John; Duim, van der Rene

    2016-01-01

    This article adopts an aidnographic approach to examine how internal organizational modes of ordering have influenced tourism development practices of SNV Netherlands Development Organisation (SNV). Our research revealed six modes of ordering: administration, project management, enterprising,

  5. Modes of log gravity

    NARCIS (Netherlands)

    Bergshoeff, Eric A.; Hohm, Olaf; Rosseel, Jan; Townsend, Paul K.

    2011-01-01

    The physical modes of a recently proposed D-dimensional "critical gravity'', linearized about its anti-de Sitter vacuum, are investigated. All "log mode'' solutions, which we categorize as "spin-2'' or "Proca'', arise as limits of the massive spin-2 modes of the noncritical theory. The linearized

  6. Synthesis, DNA binding and cytotoxic evaluation of aminoquinoline ...

    Indian Academy of Sciences (India)

    DNA binding studies of selected isomeric compounds showed interaction withDNA via intercalation mode with higher binding affinity of 4-substituted ... Universiti Sains Malaysia, Minden 11800, Penang, Malaysia; New Drug Discovery Research, Department of Medicinal Chemistry, Alwar Pharmacy College, Alwar, ...

  7. Streaming tearing mode

    Science.gov (United States)

    Shigeta, M.; Sato, T.; Dasgupta, B.

    1985-01-01

    The magnetohydrodynamic stability of streaming tearing mode is investigated numerically. A bulk plasma flow parallel to the antiparallel magnetic field lines and localized in the neutral sheet excites a streaming tearing mode more strongly than the usual tearing mode, particularly for the wavelength of the order of the neutral sheet width (or smaller), which is stable for the usual tearing mode. Interestingly, examination of the eigenfunctions of the velocity perturbation and the magnetic field perturbation indicates that the streaming tearing mode carries more energy in terms of the kinetic energy rather than the magnetic energy. This suggests that the streaming tearing mode instability can be a more feasible mechanism of plasma acceleration than the usual tearing mode instability.

  8. Mode selection laser

    DEFF Research Database (Denmark)

    2014-01-01

    The invention relates to a semiconductor mode selection laser, particularly to a VCSEL laser (200) having mode selection properties. The mode selection capability of the laser is achieved by configuring one of the reflectors (15,51) in the resonance cavity so that a reflectivity of the reflector...... (15) varies spatially in one dimension or two dimensions. Accordingly, the reflector (15) with spatially varying reflectivity is part both of the resonance cavity and the mode selection functionality of the laser. A plurality of the lasers configured with different mode selectors, i.e. different...... spatial reflector variations, may be combined to generate a laser beam containing a plurality of orthogonal modes. The laser beam may be injected into a few- mode optical fiber, e.g. for the purpose of optical communication. The VCSEL may have intra-cavity contacts (31,37) and a Tunnel junction (33...

  9. Dual-Mode Combustor

    Science.gov (United States)

    Trefny, Charles J (Inventor); Dippold, Vance F (Inventor)

    2013-01-01

    A new dual-mode ramjet combustor used for operation over a wide flight Mach number range is described. Subsonic combustion mode is usable to lower flight Mach numbers than current dual-mode scramjets. High speed mode is characterized by supersonic combustion in a free-jet that traverses the subsonic combustion chamber to a variable nozzle throat. Although a variable combustor exit aperture is required, the need for fuel staging to accommodate the combustion process is eliminated. Local heating from shock-boundary-layer interactions on combustor walls is also eliminated.

  10. Molecular aspects of herbicide binding in chloroplasts = [Molekulaire aspekten van herbicide binding in chloroplasten

    NARCIS (Netherlands)

    Naber, D.

    1989-01-01

    Many weed-controlling agents act by inhibiting the process of photosynthesis. Their mode of action is a displacement of the secondary quinone electron acceptor of photosystem II from its proteinaceous binding environment. This results in a blocking of the electron transport. Consequently

  11. Total iron binding capacity

    Science.gov (United States)

    ... page: //medlineplus.gov/ency/article/003489.htm Total iron binding capacity To use the sharing features on this page, please enable JavaScript. Total iron binding capacity (TIBC) is a blood test to ...

  12. DNA binding studies of tartrazine food additive.

    Science.gov (United States)

    Kashanian, Soheila; Zeidali, Sahar Heidary

    2011-07-01

    The interaction of native calf thymus DNA with tartrazine in 10 mM Tris-HCl aqueous solution at neutral pH 7.4 was investigated. Tartrazine is a nitrous derivative and may cause allergic reactions, with a potential of toxicological risk. Also, tartrazine induces oxidative stress and DNA damage. Its DNA binding properties were studied by UV-vis and circular dichroism spectra, competitive binding with Hoechst 33258, and viscosity measurements. Tartrazine molecules bind to DNA via groove mode as illustrated by hyperchromism in the UV absorption band of tartrazine, decrease in Hoechst-DNA solution fluorescence, unchanged viscosity of DNA, and conformational changes such as conversion from B-like to C-like in the circular dichroism spectra of DNA. The binding constants (K(b)) of DNA with tartrazine were calculated at different temperatures. Enthalpy and entropy changes were calculated to be +37 and +213 kJ mol(-1), respectively, according to the Van't Hoff equation, which indicated that the reaction is predominantly entropically driven. Also, tartrazine does not cleave plasmid DNA. Tartrazine interacts with calf thymus DNA via a groove interaction mode with an intrinsic binding constant of 3.75 × 10(4) M(-1).

  13. Interaction of zinc and cobalt with dipeptides and their DNA binding ...

    Indian Academy of Sciences (India)

    Interactions of zinc and cobalt with peptides cysteinylglycine and histidylglycine have been studied. The binding modes were identified and geometry assigned. Stabilities of these complexes and their ability to bind DNA have been investigated. It is demonstrated that only zinc complexes bind DNA as compared to cobalt ...

  14. Noncovalent endo-binding of fullerenes to diprotonated bisporphyrins.

    Science.gov (United States)

    Jung, Sunghan; van Paauwe, John D; Boyd, Peter D W; Shin, Seung Koo

    2011-12-07

    Noncovalent binding of fullerenes to bisporphyrins was studied in the gas phase by energy-dependent collision-induced dissociation (CID) with Xe under single-collision conditions. The electrospray ionization mass spectra of calix[4]arene-linked bisporphyrins show that bisporphyrins take up to 3-4 protons, depending on the type of meso-substituents. Of the protonated bisporphyrins, the diprotonated species form stable 1:1 complexes with fullerenes (C(60) and C(70)). CID cracking patterns of the diprotonated bisporphyrins indicate that each monomeric porphyrin moiety is singly protonated. CID yield-energy curves obtained from the 1:1 diprotonated bisporphyrin-fullerene complexes suggest that a fullerene occupies the endo-binding site intercalated between the two singly protonated porphyrin moieties. In the cases of 1:2 diprotonated bisporphyrin-fullerene complexes, CID results show that one fullerene binds inside (endo-binding) and the other outside (exo-binding). The exo-binding mode is energetically almost identical to the binding of fullerenes to singly protonated porphyrin monomers. The endo-binding energy is at least twice the exo-binding energy. To gain insights into the binding mode, we optimized structures of diprotonated bisporphyrins and their 1:1 endo-complexes with fullerenes, and calculated the endo-binding energy for C(60), C(70) (end-on), and C(70) (side-on). The endo-binding of fullerenes to diprotonated bisporphyrins nearly doubles the π-π interactions while reducing the electrostatic repulsion between the two singly protonated porphyrin moieties. The side-on binding of C(70) is favored over the end-on binding because the former exerts less steric strain to the lower rim of calixarene.

  15. Microbubble Surface Modes

    NARCIS (Netherlands)

    Versluis, Michel; Palanchon, P.; Goertz, D.; van der Meer, S.M.; Chin, C.T.; Lohse, Detlef; de Jong, N.

    2004-01-01

    We have investigated surface vibrations generated by ultrasound excitation of individual unencapsulated micron-sized bubbles. In addition, we present surface modes (n=2 and 3) observed for phospholipid-coated ultrasound contrast agents excited through excitation of radial modes at frequencies

  16. Mode decomposition evolution equations.

    Science.gov (United States)

    Wang, Yang; Wei, Guo-Wei; Yang, Siyang

    2012-03-01

    Partial differential equation (PDE) based methods have become some of the most powerful tools for exploring the fundamental problems in signal processing, image processing, computer vision, machine vision and artificial intelligence in the past two decades. The advantages of PDE based approaches are that they can be made fully automatic, robust for the analysis of images, videos and high dimensional data. A fundamental question is whether one can use PDEs to perform all the basic tasks in the image processing. If one can devise PDEs to perform full-scale mode decomposition for signals and images, the modes thus generated would be very useful for secondary processing to meet the needs in various types of signal and image processing. Despite of great progress in PDE based image analysis in the past two decades, the basic roles of PDEs in image/signal analysis are only limited to PDE based low-pass filters, and their applications to noise removal, edge detection, segmentation, etc. At present, it is not clear how to construct PDE based methods for full-scale mode decomposition. The above-mentioned limitation of most current PDE based image/signal processing methods is addressed in the proposed work, in which we introduce a family of mode decomposition evolution equations (MoDEEs) for a vast variety of applications. The MoDEEs are constructed as an extension of a PDE based high-pass filter (Europhys. Lett., 59(6): 814, 2002) by using arbitrarily high order PDE based low-pass filters introduced by Wei (IEEE Signal Process. Lett., 6(7): 165, 1999). The use of arbitrarily high order PDEs is essential to the frequency localization in the mode decomposition. Similar to the wavelet transform, the present MoDEEs have a controllable time-frequency localization and allow a perfect reconstruction of the original function. Therefore, the MoDEE operation is also called a PDE transform. However, modes generated from the present approach are in the spatial or time domain and can be

  17. Oligosaccharide binding to barley alpha-amylase 1

    DEFF Research Database (Denmark)

    Robert, X.; Haser, R.; Mori, H.

    2005-01-01

    Enzymatic subsite mapping earlier predicted 10 binding subsites in the active site substrate binding cleft of barley alpha-amylase isozymes. The three-dimensional structures of the oligosaccharide complexes with barley alpha-amylase isozyme 1 (AMY1) described here give for the first time a thorough...... in barley alpha-amylase isozyme 2 (AMY2), and the sugar binding modes are compared between the two isozymes. The "sugar tongs" surface binding site discovered in the AMY1-thio-DP4 complex is confirmed in the present work. A site that putatively serves as an entrance for the substrate to the active site...

  18. Shaft mode shape demonstration

    Science.gov (United States)

    Grissom, R.

    1985-01-01

    The dynamic response of a rotating machine is directly influenced by its geometric configuration and all aspects of the rotor construction. These determine two significant parameters, mass distribution and stiffness, which yield a spectrum of natural frequencies and mode shapes. The mode shapes can be presented as snapshots of the characteristic amplitude/phase reponse patterns of the shaft, due to the major forcing function of unbalance, at different rotative speeds. To demonstrate the three shaft mode shapes of the rotor rig using the Shaft Mode Demonstrator and oscilloscopes. The synchronous (1X) amplitude and phase of the rotor vibration in the vertical direction from several points along the shaft is displayed on corresponding points of the demonstrator. Unfiltered vibration from vertical and horizontal probe pairs is displayed on the oscilloscopes in orbit format for a dynamic presentation of the mode shape.

  19. Higher Order Mode Fibers

    DEFF Research Database (Denmark)

    Israelsen, Stine Møller

    This PhD thesis considers higher order modes (HOMs) in optical fibers. That includes their excitation and characteristics. Within the last decades, HOMs have been applied both for space multiplexing in optical communications, group velocity dispersion management and sensing among others....... The research presented in this thesis falls in three parts. In the first part, a first time demonstration of the break of the azimuthal symmetry of the Bessel-like LP0X modes is presented. This effect, known as the bowtie effect, causes the mode to have an azimuthal dependence as well as a quasi......-radial polarization as opposed to the linear polarization of the LP0X modes. The effect is investigated numerically in a double cladding fiber with an outer aircladding using a full vectorial modesolver. Experimentally, the bowtie modes are excited using a long period grating and their free space characteristics...

  20. Mixed-mode sorption of hydroxylated atrazine degradation products to sell: A mechanism for bound residue

    Science.gov (United States)

    Lerch, R.N.; Thurman, E.M.; Kruger, E.L.

    1997-01-01

    This study tested the hypothesis that sorption of hydroxylated atrazine degradation products (HADPs: hydroxyatrazine, HA; deethylhydroxyatrazine, DEHA; and deisopropylhydroxyatrazine, DIHA) to soils occurs by mixed-mode binding resulting from two simultaneous mechanisms: (1) cation exchange and (2) hydrophobic interaction. The objective was to use liquid chromatography and soil extraction experiments to show that mixed-mode binding is the mechanism controlling HADP sorption to soils and is also a mechanism for bound residue. Overall, HADP binding to solid-phase extraction (SPE) sorbents occurred in the order: cation exchange >> octadecyl (C18) >> cyanopropyl. Binding to cation exchange SPE and to a high-performance liquid chromatograph octyl (C8) column showed evidence for mixed-mode binding. Comparison of soil extracted by 0.5 M KH2P04, pH 7.5, or 25% aqueous CH3CN showed that, for HA and DIHA, cation exchange was a more important binding mechanism to soils than hydrophobic interaction. Based on differences between several extractants, the extent of HADP mixed-mode binding to soil occurred in the following order: HA > DIHA > DEHA. Mixed-mode extraction recovered 42.8% of bound atrazine residues from aged soil, and 88% of this fraction was identified as HADPs. Thus, a significant portion of bound atrazine residues in soils is sorbed by the mixed-mode binding mechanisms.

  1. How To Deal with Multiple Binding Poses in Alchemical Relative Protein–Ligand Binding Free Energy Calculations

    Science.gov (United States)

    2016-01-01

    Recent advances in improved force fields and sampling methods have made it possible for the accurate calculation of protein–ligand binding free energies. Alchemical free energy perturbation (FEP) using an explicit solvent model is one of the most rigorous methods to calculate relative binding free energies. However, for cases where there are high energy barriers separating the relevant conformations that are important for ligand binding, the calculated free energy may depend on the initial conformation used in the simulation due to the lack of complete sampling of all the important regions in phase space. This is particularly true for ligands with multiple possible binding modes separated by high energy barriers, making it difficult to sample all relevant binding modes even with modern enhanced sampling methods. In this paper, we apply a previously developed method that provides a corrected binding free energy for ligands with multiple binding modes by combining the free energy results from multiple alchemical FEP calculations starting from all enumerated poses, and the results are compared with Glide docking and MM-GBSA calculations. From these calculations, the dominant ligand binding mode can also be predicted. We apply this method to a series of ligands that bind to c-Jun N-terminal kinase-1 (JNK1) and obtain improved free energy results. The dominant ligand binding modes predicted by this method agree with the available crystallography, while both Glide docking and MM-GBSA calculations incorrectly predict the binding modes for some ligands. The method also helps separate the force field error from the ligand sampling error, such that deviations in the predicted binding free energy from the experimental values likely indicate possible inaccuracies in the force field. An error in the force field for a subset of the ligands studied was identified using this method, and improved free energy results were obtained by correcting the partial charges assigned to the

  2. How to deal with multiple binding poses in alchemical relative protein-ligand binding free energy calculations.

    Science.gov (United States)

    Kaus, Joseph W; Harder, Edward; Lin, Teng; Abel, Robert; McCammon, J Andrew; Wang, Lingle

    2015-06-09

    Recent advances in improved force fields and sampling methods have made it possible for the accurate calculation of protein–ligand binding free energies. Alchemical free energy perturbation (FEP) using an explicit solvent model is one of the most rigorous methods to calculate relative binding free energies. However, for cases where there are high energy barriers separating the relevant conformations that are important for ligand binding, the calculated free energy may depend on the initial conformation used in the simulation due to the lack of complete sampling of all the important regions in phase space. This is particularly true for ligands with multiple possible binding modes separated by high energy barriers, making it difficult to sample all relevant binding modes even with modern enhanced sampling methods. In this paper, we apply a previously developed method that provides a corrected binding free energy for ligands with multiple binding modes by combining the free energy results from multiple alchemical FEP calculations starting from all enumerated poses, and the results are compared with Glide docking and MM-GBSA calculations. From these calculations, the dominant ligand binding mode can also be predicted. We apply this method to a series of ligands that bind to c-Jun N-terminal kinase-1 (JNK1) and obtain improved free energy results. The dominant ligand binding modes predicted by this method agree with the available crystallography, while both Glide docking and MM-GBSA calculations incorrectly predict the binding modes for some ligands. The method also helps separate the force field error from the ligand sampling error, such that deviations in the predicted binding free energy from the experimental values likely indicate possible inaccuracies in the force field. An error in the force field for a subset of the ligands studied was identified using this method, and improved free energy results were obtained by correcting the partial charges assigned to the

  3. Mediaeval manuscript bindings

    Directory of Open Access Journals (Sweden)

    Jedert Vodopivec

    1999-01-01

    Full Text Available The present article represents an excerpt from the final chapters of the research study titled "The development of structures in mediaeval manuscript bindings - interdependence with conservatory methods". In it, aims, methods of work, archive and library materials used and directions for conservatory methods are presented. Besides, the research study includes also a historcial overview of book bindings, detailed analysis of separate structural elements in Slovenian mediaeval bindings, comprehensive presentation of separate structures, the techniques of binding and materials of the preserved mediaeval bindings in Slovenian public archives and libraries, terminological dictionary of specific professional terms related to binding as a segment of a book, and a catalogue of all analysed bindings, containing a survey of ajI detectable data, sketches,graphite prints and photographs.

  4. Mode choice model parameters estimation

    OpenAIRE

    Strnad, Irena

    2010-01-01

    The present work focuses on parameter estimation of two mode choice models: multinomial logit and EVA 2 model, where four different modes and five different trip purposes are taken into account. Mode choice model discusses the behavioral aspect of mode choice making and enables its application to a traffic model. Mode choice model includes mode choice affecting trip factors by using each mode and their relative importance to choice made. When trip factor values are known, it...

  5. Surface modes in physics

    CERN Document Server

    Sernelius, Bo E

    2011-01-01

    Electromagnetic surface modes are present at all surfaces and interfaces between material of different dielectric properties. These modes have very important effects on numerous physical quantities: adhesion, capillary force, step formation and crystal growth, the Casimir effect etc. They cause surface tension and wetting and they give rise to forces which are important e.g. for the stability of colloids.This book is a useful and elegant approach to the topic, showing how the concept of electromagnetic modes can be developed as a unifying theme for a range of condensed matter physics. The

  6. Interaction entropy for protein-protein binding

    Science.gov (United States)

    Sun, Zhaoxi; Yan, Yu N.; Yang, Maoyou; Zhang, John Z. H.

    2017-03-01

    Protein-protein interactions are at the heart of signal transduction and are central to the function of protein machine in biology. The highly specific protein-protein binding is quantitatively characterized by the binding free energy whose accurate calculation from the first principle is a grand challenge in computational biology. In this paper, we show how the interaction entropy approach, which was recently proposed for protein-ligand binding free energy calculation, can be applied to computing the entropic contribution to the protein-protein binding free energy. Explicit theoretical derivation of the interaction entropy approach for protein-protein interaction system is given in detail from the basic definition. Extensive computational studies for a dozen realistic protein-protein interaction systems are carried out using the present approach and comparisons of the results for these protein-protein systems with those from the standard normal mode method are presented. Analysis of the present method for application in protein-protein binding as well as the limitation of the method in numerical computation is discussed. Our study and analysis of the results provided useful information for extracting correct entropic contribution in protein-protein binding from molecular dynamics simulations.

  7. Ligand photo-isomerization triggers conformational changes in iGluR2 ligand binding domain.

    Directory of Open Access Journals (Sweden)

    Tino Wolter

    Full Text Available Neurological glutamate receptors bind a variety of artificial ligands, both agonistic and antagonistic, in addition to glutamate. Studying their small molecule binding properties increases our understanding of the central nervous system and a variety of associated pathologies. The large, oligomeric multidomain membrane protein contains a large and flexible ligand binding domains which undergoes large conformational changes upon binding different ligands. A recent application of glutamate receptors is their activation or inhibition via photo-switchable ligands, making them key systems in the emerging field of optochemical genetics. In this work, we present a theoretical study on the binding mode and complex stability of a novel photo-switchable ligand, ATA-3, which reversibly binds to glutamate receptors ligand binding domains (LBDs. We propose two possible binding modes for this ligand based on flexible ligand docking calculations and show one of them to be analogues to the binding mode of a similar ligand, 2-BnTetAMPA. In long MD simulations, it was observed that transitions between both binding poses involve breaking and reforming the T686-E402 protein hydrogen bond. Simulating the ligand photo-isomerization process shows that the two possible configurations of the ligand azo-group have markedly different complex stabilities and equilibrium binding modes. A strong but slow protein response is observed after ligand configuration changes. This provides a microscopic foundation for the observed difference in ligand activity upon light-switching.

  8. Comparative analyses of the thermodynamic RNA binding signatures of different types of RNA recognition motifs.

    Science.gov (United States)

    Samatanga, Brighton; Cléry, Antoine; Barraud, Pierre; Allain, Frédéric H-T; Jelesarov, Ilian

    2017-06-02

    RNA recognition motifs (RRMs) are structurally versatile domains important in regulation of alternative splicing. Structural mechanisms of sequence-specific recognition of single-stranded RNAs (ssRNAs) by RRMs are well understood. The thermodynamic strategies are however unclear. Therefore, we utilized microcalorimetry and semi-empirical analyses to comparatively analyze the cognate ssRNA binding thermodynamics of four different RRM domains, each with a different RNA binding mode. The different binding modes are: canonical binding to the β-sheet surface; canonical binding with involvement of N- and C-termini; binding to conserved loops; and binding to an α-helix. Our results identify enthalpy as the sole and general force driving association at physiological temperatures. Also, networks of weak interactions are a general feature regulating stability of the different RRM-ssRNA complexes. In agreement, non-polyelectrolyte effects contributed between ∼75 and 90% of the overall free energy of binding in the considered complexes. The various RNA binding modes also displayed enormous heat capacity differences, that upon dissection revealed large differential changes in hydration, conformations and dynamics upon binding RNA. Altogether, different modes employed by RRMs to bind cognate ssRNAs utilize various thermodynamics strategies during the association process. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  9. Mode Gaussian beam tracing

    Science.gov (United States)

    Trofimov, M. Yu.; Zakharenko, A. D.; Kozitskiy, S. B.

    2016-10-01

    A mode parabolic equation in the ray centered coordinates for 3D underwater sound propagation is developed. The Gaussian beam tracing in this case is constructed. The test calculations are carried out for the ASA wedge benchmark and proved an excellent agreement with the source images method in the case of cross-slope propagation. But in the cases of wave propagation at some angles to the cross-slope direction an account of mode interaction becomes necessary.

  10. Evolving nucleotide binding surfaces

    Science.gov (United States)

    Kieber-Emmons, T.; Rein, R.

    1981-01-01

    An analysis is presented of the stability and nature of binding of a nucleotide to several known dehydrogenases. The employed approach includes calculation of hydrophobic stabilization of the binding motif and its intermolecular interaction with the ligand. The evolutionary changes of the binding motif are studied by calculating the Euclidean deviation of the respective dehydrogenases. Attention is given to the possible structural elements involved in the origin of nucleotide recognition by non-coded primordial polypeptides.

  11. RNA recognition by the DNA end-binding Ku heterodimer.

    Science.gov (United States)

    Dalby, Andrew B; Goodrich, Karen J; Pfingsten, Jennifer S; Cech, Thomas R

    2013-06-01

    Most nucleic acid-binding proteins selectively bind either DNA or RNA, but not both nucleic acids. The Saccharomyces cerevisiae Ku heterodimer is unusual in that it has two very different biologically relevant binding modes: (1) Ku is a sequence-nonspecific double-stranded DNA end-binding protein with prominent roles in nonhomologous end-joining and telomeric capping, and (2) Ku associates with a specific stem-loop of TLC1, the RNA subunit of budding yeast telomerase, and is necessary for proper nuclear localization of this ribonucleoprotein enzyme. TLC1 RNA-binding and dsDNA-binding are mutually exclusive, so they may be mediated by the same site on Ku. Although dsDNA binding by Ku is well studied, much less is known about what features of an RNA hairpin enable specific recognition by Ku. To address this question, we localized the Ku-binding site of the TLC1 hairpin with single-nucleotide resolution using phosphorothioate footprinting, used chemical modification to identify an unpredicted motif within the hairpin secondary structure, and carried out mutagenesis of the stem-loop to ascertain the critical elements within the RNA that permit Ku binding. Finally, we provide evidence that the Ku-binding site is present in additional budding yeast telomerase RNAs and discuss the possibility that RNA binding is a conserved function of the Ku heterodimer.

  12. Dendrimers bind antioxidant polyphenols and cisplatin drug.

    Directory of Open Access Journals (Sweden)

    Amine Abderrezak

    Full Text Available Synthetic polymers of a specific shape and size play major role in drug delivery systems. Dendrimers are unique synthetic macromolecules of nanometer dimensions with a highly branched structure and globular shape with potential applications in gene and drug delivery. We examine the interaction of several dendrimers of different compositions mPEG-PAMAM (G3, mPEG-PAMAM (G4 and PAMAM (G4 with hydrophilic and hydrophobic drugs cisplatin, resveratrol, genistein and curcumin at physiological conditions. FTIR and UV-visible spectroscopic methods as well as molecular modeling were used to analyse drug binding mode, the binding constant and the effects of drug complexation on dendrimer stability and conformation. Structural analysis showed that cisplatin binds dendrimers in hydrophilic mode via Pt cation and polymer terminal NH(2 groups, while curcumin, genistein and resveratrol are located mainly in the cavities binding through both hydrophobic and hydrophilic contacts. The overall binding constants of durg-dendrimers are ranging from 10(2 M(-1 to 10(3 M(-1. The affinity of dendrimer binding was PAMAM-G4>mPEG-PAMAM-G4>mPEG-PAMAM-G3, while the order of drug-polymer stability was curcumin>cisplatin>genistein>resveratrol. Molecular modeling showed larger stability for genisten-PAMAM-G4 (ΔG = -4.75 kcal/mol than curcumin-PAMAM-G4 ((ΔG = -4.53 kcal/mol and resveratrol-PAMAM-G4 ((ΔG = -4.39 kcal/mol. Dendrimers might act as carriers to transport hydrophobic and hydrophilic drugs.

  13. DNS BIND Server Configuration

    Directory of Open Access Journals (Sweden)

    Radu MARSANU

    2011-01-01

    Full Text Available After a brief presentation of the DNS and BIND standard for Unix platforms, the paper presents an application which has a principal objective, the configuring of the DNS BIND 9 server. The general objectives of the application are presented, follow by the description of the details of designing the program.

  14. Melanin-binding radiopharmaceuticals

    Energy Technology Data Exchange (ETDEWEB)

    Packer, S; Fairchild, R G; Watts, K P; Greenberg, D; Hannon, S J

    1980-01-01

    The scope of this paper is limited to an analysis of the factors that are important to the relationship of radiopharmaceuticals to melanin. While the authors do not attempt to deal with differences between melanin-binding vs. melanoma-binding, a notable variance is assumed. (PSB)

  15. Sliding mode control and observation

    CERN Document Server

    Shtessel, Yuri; Fridman, Leonid; Levant, Arie

    2014-01-01

    The sliding mode control methodology has proven effective in dealing with complex dynamical systems affected by disturbances, uncertainties and unmodeled dynamics. Robust control technology based on this methodology has been applied to many real-world problems, especially in the areas of aerospace control, electric power systems, electromechanical systems, and robotics. Sliding Mode Control and Observation represents the first textbook that starts with classical sliding mode control techniques and progresses toward newly developed higher-order sliding mode control and observation algorithms and their applications. The present volume addresses a range of sliding mode control issues, including: *Conventional sliding mode controller and observer design *Second-order sliding mode controllers and differentiators *Frequency domain analysis of conventional and second-order sliding mode controllers *Higher-order sliding mode controllers and differentiators *Higher-order sliding mode observers *Sliding mode disturbanc...

  16. Free boundary ballooning mode representation

    Science.gov (United States)

    Zheng, Linjin

    2012-03-01

    Considerable efforts have been made in this field to develop a free boundary ballooning mode representation, which can incorporate the peeling mode stability criterion. Those efforts have not succeeded, simply because the so-called ballooning mode invariance is broken toward plasma edge. This makes 1D description of high n modes at plasma edge become impossible, where n is toroidal mode number. Nevertheless, we prove that the existence of ``half" ballooning mode invariance toward plasma core enables an 1.δ-dimentional representation of the modes, where δ˜O(1/n). This considerably reduces the complicity in investigating high n modes at plasma edge and can be used to study peeling-ballooning modes. This technique can also be useful to extend the 1D calculation of fixed boundary ballooning modes for free boundary ballooning modes. Numerical example will also be presented together with the topological symmetry analysis.

  17. Topological edge modes in multilayer graphene systems.

    Science.gov (United States)

    Ge, Lixin; Wang, Li; Xiao, Meng; Wen, Weijia; Chan, C T; Han, Dezhuan

    2015-08-24

    Plasmons can be supported on graphene sheets as the Dirac electrons oscillate collectively. A tight-binding model for graphene plasmons is a good description as the field confinement in the normal direction is strong. With this model, the topological properties of plasmonic bands in multilayer graphene systems are investigated. The Zak phases of periodic graphene sheet arrays are obtained for different configurations. Analogous to Su-Schrieffer-Heeger (SSH) model in electronic systems, topological edge plasmon modes emerge when two periodic graphene sheet arrays with different Zak phases are connected. Interestingly, the dispersion of these topological edge modes is the same as that in the monolayer graphene and is invariant as the geometric parameters of the structure such as the separation and period change. These plasmonic edge states in multilayer graphene systems can be further tuned by electrical gating or chemical doping.

  18. Topological edge modes in multilayer graphene systems

    KAUST Repository

    Ge, Lixin

    2015-08-10

    Plasmons can be supported on graphene sheets as the Dirac electrons oscillate collectively. A tight-binding model for graphene plasmons is a good description as the field confinement in the normal direction is strong. With this model, the topological properties of plasmonic bands in multilayer graphene systems are investigated. The Zak phases of periodic graphene sheet arrays are obtained for different configurations. Analogous to Su-Schrieffer-Heeger (SSH) model in electronic systems, topological edge plasmon modes emerge when two periodic graphene sheet arrays with different Zak phases are connected. Interestingly, the dispersion of these topological edge modes is the same as that in the monolayer graphene and is invariant as the geometric parameters of the structure such as the separation and period change. These plasmonic edge states in multilayer graphene systems can be further tuned by electrical gating or chemical doping. © 2015 Optical Society of America.

  19. Modeli diskretne izbire

    Directory of Open Access Journals (Sweden)

    Boštjan Kerbler – Kefo

    2006-01-01

    Full Text Available V članku je sistematično predstavljena posebna oblika regresijskih metod – modelov diskretne izbire –, imenovanih tudi verjetnostni modeli. Poleg njihovega pomena so opisane še metodološke značilnosti pri njihovi izvedbi, natančneje pa so predstavljeni modeli binarne izbire in tisti z omejeno odvisno spremenljivko, logistični model ter modela probit in tobit kot izhodiščni metodološki pristopi k izvedbi modelov.

  20. Mode og mozzarella

    DEFF Research Database (Denmark)

    Nielsen, Jakob Isak

    2013-01-01

    Under en samtale i Paolo Sorrentinos La grande bellezza/da. Den store skønhed (2013) anføres det, at Italiens primære eksportvarer er mode og mozzarella. Selve filmen vidner om, at Italien har andet at byde på – heriblandt filmkunst og Roms righoldige kulturhistorie.......Under en samtale i Paolo Sorrentinos La grande bellezza/da. Den store skønhed (2013) anføres det, at Italiens primære eksportvarer er mode og mozzarella. Selve filmen vidner om, at Italien har andet at byde på – heriblandt filmkunst og Roms righoldige kulturhistorie....

  1. Hydrogen local vibrational modes in semiconductors

    Energy Technology Data Exchange (ETDEWEB)

    McCluskey, Matthew D. [Univ. of California, Berkeley, CA (United States). Dept. of Physics

    1997-06-01

    Following, a review of experimental techniques, theory, and previous work, the results of local vibrational mode (LVM) spectroscopy on hydrogen-related complexes in several different semiconductors are discussed. Hydrogen is introduced either by annealing in a hydrogen ambient. exposure to a hydrogen plasma, or during growth. The hydrogen passivates donors and acceptors in semiconductors, forming neutral complexes. When deuterium is substituted for hydrogen. the frequency of the LVM decreases by approximately the square root of two. By varying the temperature and pressure of the samples, the microscopic structures of hydrogen-related complexes are determined. For group II acceptor-hydrogen complexes in GaAs, InP, and GaP, hydrogen binds to the host anion in a bond-centered orientation, along the [111] direction, adjacent to the acceptor. The temperature dependent shift of the LVMs are proportional to the lattice thermal energy U(T), a consequence of anharmonic coupling between the LVM and acoustical phonons. In the wide band gap semiconductor ZnSe, epilayers grown by metalorganic chemical vapor phase epitaxy (MOCVD) and doped with As form As-H complexes. The hydrogen assumes a bond-centered orientation, adjacent to a host Zn. In AlSb, the DX centers Se and Te are passivated by hydrogen. The second, third, and fourth harmonics of the wag modes are observed. Although the Se-D complex has only one stretch mode, the Se-H stretch mode splits into three peaks. The anomalous splitting is explained by a new interaction between the stretch LVM and multi-phonon modes of the lattice. As the temperature or pressure is varied, and anti-crossing is observed between LVM and phonon modes.

  2. The Escherichia coli modE gene: effect of modE mutations on molybdate dependent modA expression.

    Science.gov (United States)

    McNicholas, P M; Chiang, R C; Gunsalus, R P

    1996-11-15

    The Escherichia coli modABCD operon, which encodes a high-affinity molybdate uptake system, is transcriptionally regulated in response to molybdate availability by ModE. Here we describe a highly effective enrichment protocol, applicable to any gene with a repressor role, and establish its application in the isolation of transposon mutations in modE. In addition we show that disruption of the ModE C-terminus abolishes derepression in the absence of molybdate, implying this region of ModE controls the repressor activity. Finally, a mutational analysis of a proposed molybdate binding motif indicates that this motif does not function in regulating the repressor activity of ModE.

  3. Nonclassicality in two-mode BEC

    OpenAIRE

    Giri, Sandip Kumar; Sen, Biswajit; Ooi, C H Raymond; Pathak, Anirban

    2013-01-01

    The operator solution of a completely quantum mechanical Hamiltonian of the Raman processes is used here to investigate the possibility of obtaining intermodal entanglement between different modes involved in the Raman processes (e.g. pump mode, Stokes mode, vibration (phonon) mode and anti-Stokes mode). Intermodal entanglement is reported between a) pump mode and anti-Stokes mode, b) pump mode and vibration (phonon) mode c) Stokes mode and vibration phonon mode, d) Stokes mode and anti-stoke...

  4. Retinoblastoma-binding Protein 1 Has an Interdigitated Double Tudor Domain with DNA Binding Activity*

    Science.gov (United States)

    Gong, Weibin; Wang, Jinfeng; Perrett, Sarah; Feng, Yingang

    2014-01-01

    Retinoblastoma-binding protein 1 (RBBP1) is a tumor and leukemia suppressor that binds both methylated histone tails and DNA. Our previous studies indicated that RBBP1 possesses a Tudor domain, which cannot bind histone marks. In order to clarify the function of the Tudor domain, the solution structure of the RBBP1 Tudor domain was determined by NMR and is presented here. Although the proteins are unrelated, the RBBP1 Tudor domain forms an interdigitated double Tudor structure similar to the Tudor domain of JMJD2A, which is an epigenetic mark reader. This indicates the functional diversity of Tudor domains. The RBBP1 Tudor domain structure has a significant area of positively charged surface, which reveals a capability of the RBBP1 Tudor domain to bind nucleic acids. NMR titration and isothermal titration calorimetry experiments indicate that the RBBP1 Tudor domain binds both double- and single-stranded DNA with an affinity of 10–100 μm; no apparent DNA sequence specificity was detected. The DNA binding mode and key interaction residues were analyzed in detail based on a model structure of the Tudor domain-dsDNA complex, built by HADDOCK docking using the NMR data. Electrostatic interactions mediate the binding of the Tudor domain with DNA, which is consistent with NMR experiments performed at high salt concentration. The DNA-binding residues are conserved in Tudor domains of the RBBP1 protein family, resulting in conservation of the DNA-binding function in the RBBP1 Tudor domains. Our results provide further insights into the structure and function of RBBP1. PMID:24379399

  5. Retinoblastoma-binding protein 1 has an interdigitated double Tudor domain with DNA binding activity.

    Science.gov (United States)

    Gong, Weibin; Wang, Jinfeng; Perrett, Sarah; Feng, Yingang

    2014-02-21

    Retinoblastoma-binding protein 1 (RBBP1) is a tumor and leukemia suppressor that binds both methylated histone tails and DNA. Our previous studies indicated that RBBP1 possesses a Tudor domain, which cannot bind histone marks. In order to clarify the function of the Tudor domain, the solution structure of the RBBP1 Tudor domain was determined by NMR and is presented here. Although the proteins are unrelated, the RBBP1 Tudor domain forms an interdigitated double Tudor structure similar to the Tudor domain of JMJD2A, which is an epigenetic mark reader. This indicates the functional diversity of Tudor domains. The RBBP1 Tudor domain structure has a significant area of positively charged surface, which reveals a capability of the RBBP1 Tudor domain to bind nucleic acids. NMR titration and isothermal titration calorimetry experiments indicate that the RBBP1 Tudor domain binds both double- and single-stranded DNA with an affinity of 10-100 μM; no apparent DNA sequence specificity was detected. The DNA binding mode and key interaction residues were analyzed in detail based on a model structure of the Tudor domain-dsDNA complex, built by HADDOCK docking using the NMR data. Electrostatic interactions mediate the binding of the Tudor domain with DNA, which is consistent with NMR experiments performed at high salt concentration. The DNA-binding residues are conserved in Tudor domains of the RBBP1 protein family, resulting in conservation of the DNA-binding function in the RBBP1 Tudor domains. Our results provide further insights into the structure and function of RBBP1.

  6. Vibrational modes of nanolines

    Science.gov (United States)

    Heyliger, Paul R.; Flannery, Colm M.; Johnson, Ward L.

    2008-04-01

    Brillouin-light-scattering spectra previously have been shown to provide information on acoustic modes of polymeric lines fabricated by nanoimprint lithography. Finite-element methods for modeling such modes are presented here. These methods provide a theoretical framework for determining elastic constants and dimensions of nanolines from measured spectra in the low gigahertz range. To make the calculations feasible for future incorporation in inversion algorithms, two approximations of the boundary conditions are employed in the calculations: the rigidity of the nanoline/substrate interface and sinusoidal variation of displacements along the nanoline length. The accuracy of these approximations is evaluated as a function of wavenumber and frequency. The great advantage of finite-element methods over other methods previously employed for nanolines is the ability to model any cross-sectional geometry. Dispersion curves and displacement patterns are calculated for modes of polymethyl methacrylate nanolines with cross-sectional dimensions of 65 nm × 140 nm and rectangular or semicircular tops. The vibrational displacements and dispersion curves are qualitatively similar for the two geometries and include a series of flexural, Rayleigh-like, and Sezawa-like modes. This paper is a contribution of the National Institute of Standards and Technology and is not subject to copyright in the United States.

  7. Mode Gaussian beam tracing

    CERN Document Server

    Trofimov, M Yu; Kozitskiy, S B

    2015-01-01

    An adiabatic mode Helmholtz equation for 3D underwater sound propagation is developed. The Gaussian beam tracing in this case is constructed. The test calculations are carried out for the crosswedge benchmark and proved an excellent agreement with the source images method.

  8. New Modes of Citizenship

    DEFF Research Database (Denmark)

    Nickelsen, Niels Christian Mossfeldt

    2017-01-01

    in common that they involve important elements of autonomy and self-care and are part of an international movement toward empowering citizens and patients. This chapter discusses the relation between care innovation and new modes of citizenship in terms of the ‘active’ citizen. By way of an ethnographic...

  9. Thermodynamics of Radiation Modes

    Science.gov (United States)

    Pina, Eduardo; de la Selva, Sara Maria Teresa

    2010-01-01

    We study the equilibrium thermodynamics of the electromagnetic radiation in a cavity of a given volume and temperature. We found three levels of description, the thermodynamics of one mode, the thermodynamics of the distribution of frequencies in a band by summing over the frequencies in it and the global thermodynamics by summing over all the…

  10. Theories and Modes

    Science.gov (United States)

    Apsche, Jack A.

    2005-01-01

    In his work on the Theory of Modes, Beck (1996) suggested that there were flaws with his cognitive theory. He suggested that though there are shortcomings to his cognitive theory, there were not similar shortcomings to the practice of Cognitive Therapy. The author suggests that if there are shortcomings to cognitive theory the same shortcomings…

  11. Binding site and interlobe interactions of the ionotropic glutamate receptor GluK3 ligand binding domain revealed by high resolution crystal structure in complex with (S)-glutamate

    DEFF Research Database (Denmark)

    Venskutonyte, Raminta; Frydenvang, Karla; Gajhede, Michael

    2011-01-01

    present the first X-ray crystal structure of the ligand binding domain of GluK3 in complex with glutamate, determined to 1.6Å resolution. The structure reveals a conserved glutamate binding mode, characteristic for iGluRs, and a water molecule network in the glutamate binding site similar to that seen...

  12. Modes of perceiving and imagining

    OpenAIRE

    Nudds, Matthew

    2000-01-01

    We enjoy modes of sensory imagining corresponding to our five modes of perception - seeing, touching, hearing, smelling and tasting. An account of what constitutes these different modes of perseption needs also to explain what constitutes the corresponding modes of sensory perception. In this paper I argue that we can explain what distinguishes the different modes of sensory imagination in terms of their characteristic experiences without supposing that we must distinguish the senses in terms...

  13. SHBG (Sex Hormone Binding Globulin)

    Science.gov (United States)

    ... Links Patient Resources For Health Professionals Subscribe Search Sex Hormone Binding Globulin (SHBG) Send Us Your Feedback ... As Testosterone-estrogen Binding Globulin TeBG Formal Name Sex Hormone Binding Globulin This article was last reviewed ...

  14. A revisit of the mode of interaction of small transcription inhibitors ...

    Indian Academy of Sciences (India)

    A revisit of the mode of interaction of small transcription inhibitors with genomic DNA. Dipak Dasgupta Parijat ... the associated histone(s). Structural effects of the DNA-binding molecules upon chromatin in light of the above broad categories and the associated biological implications of the two types of binding are discussed.

  15. Whispering Gallery Mode Thermometry.

    Science.gov (United States)

    Corbellini, Simone; Ramella, Chiara; Yu, Lili; Pirola, Marco; Fernicola, Vito

    2016-10-29

    This paper presents a state-of-the-art whispering gallery mode (WGM) thermometer system, which could replace platinum resistance thermometers currently used in many industrial applications, thus overcoming some of their well-known limitations and their potential for providing lower measurement uncertainty. The temperature-sensing element is a sapphire-crystal-based whispering gallery mode resonator with the main resonant modes between 10 GHz and 20 GHz. In particular, it was found that the WGM around 13.6 GHz maximizes measurement performance, affording sub-millikelvin resolution and temperature stability of better than 1 mK at 0 °C. The thermometer system was made portable and low-cost by developing an ad hoc interrogation system (hardware and software) able to achieve an accuracy in the order of a few parts in 10⁸ in the determination of resonance frequencies. Herein we report the experimental assessment of the measurement stability, repeatability and resolution, and the calibration of the thermometer in the temperature range from -74 °C to 85 °C. The combined standard uncertainty for a single temperature calibration point is found to be within 5 mK (i.e., comparable with state-of-the-art for industrial thermometry), and is mainly due to the employed calibration setup. The uncertainty contribution of the WGM thermometer alone is within a millikelvin.

  16. Whispering Gallery Mode Thermometry

    Directory of Open Access Journals (Sweden)

    Simone Corbellini

    2016-10-01

    Full Text Available This paper presents a state-of-the-art whispering gallery mode (WGM thermometer system, which could replace platinum resistance thermometers currently used in many industrial applications, thus overcoming some of their well-known limitations and their potential for providing lower measurement uncertainty. The temperature-sensing element is a sapphire-crystal-based whispering gallery mode resonator with the main resonant modes between 10 GHz and 20 GHz. In particular, it was found that the WGM around 13.6 GHz maximizes measurement performance, affording sub-millikelvin resolution and temperature stability of better than 1 mK at 0 °C. The thermometer system was made portable and low-cost by developing an ad hoc interrogation system (hardware and software able to achieve an accuracy in the order of a few parts in 109 in the determination of resonance frequencies. Herein we report the experimental assessment of the measurement stability, repeatability and resolution, and the calibration of the thermometer in the temperature range from −74 °C to 85 °C. The combined standard uncertainty for a single temperature calibration point is found to be within 5 mK (i.e., comparable with state-of-the-art for industrial thermometry, and is mainly due to the employed calibration setup. The uncertainty contribution of the WGM thermometer alone is within a millikelvin.

  17. How Native and Alien Metal Cations Bind ATP: Implications for Lithium as a Therapeutic Agent

    Science.gov (United States)

    Dudev, Todor; Grauffel, Cédric; Lim, Carmay

    2017-02-01

    Adenosine triphosphate (ATP), the major energy currency of the cell, exists in solution mostly as ATP-Mg. Recent experiments suggest that Mg2+ interacts with the highly charged ATP triphosphate group and Li+ can co-bind with the native Mg2+ to form ATP-Mg-Li and modulate the neuronal purine receptor response. However, it is unclear how the negatively charged ATP triphosphate group binds Mg2+ and Li+ (i.e. which phosphate group(s) bind Mg2+/Li+) and how the ATP solution conformation depends on the type of metal cation and the metal-binding mode. Here, we reveal the preferred ATP-binding mode of Mg2+/Li+ alone and combined: Mg2+ prefers to bind ATP tridentately to each of the three phosphate groups, but Li+ prefers to bind bidentately to the terminal two phosphates. We show that the solution ATP conformation depends on the cation and its binding site/mode, but it does not change significantly when Li+ binds to Mg2+-loaded ATP. Hence, ATP-Mg-Li, like Mg2+-ATP, can fit in the ATP-binding site of the host enzyme/receptor, activating specific signaling pathways.

  18. The human mitochondrial single-stranded DNA-binding protein displays distinct kinetics and thermodynamics of DNA binding and exchange.

    Science.gov (United States)

    Qian, Yufeng; Johnson, Kenneth A

    2017-08-04

    The human mitochondrial ssDNA-binding protein (mtSSB) is a homotetrameric protein, involved in mtDNA replication and maintenance. Although mtSSB is structurally similar to SSB from Escherichia coli (EcoSSB), it lacks the C-terminal disordered domain, and little is known about the biophysics of mtSSB-ssDNA interactions. Here, we characterized the kinetics and thermodynamics of mtSSB binding to ssDNA by equilibrium titrations and stopped-flow kinetic measurements. We show that the mtSSB tetramer can bind to ssDNA in two distinct binding modes: (SSB) 30 and (SSB) 60 , defined by DNA binding site sizes of 30 and 60 nucleotides, respectively. We found that the binding mode is modulated by magnesium ion and NaCl concentration, but unlike EcoSSB, the mtSSB does not show negative intersubunit cooperativity. Global fitting of both the equilibrium and kinetic data afforded estimates for the rate and equilibrium constants governing the formation of (SSB) 60 and (SSB) 30 complexes and for the transitions between the two binding modes. We found that the mtSSB tetramer binds to ssDNA with a rate constant near the diffusion limit (2 × 10 9 m -1 s -1 ) and that longer DNA (≥60 nucleotides) rapidly wraps around all four monomers, as revealed by FRET assays. We also show that the mtSSB tetramer can directly transfer from one ssDNA molecule to another via an intermediate with two DNA molecules bound to the mtSSB. In conclusion, our results indicate that human mtSSB shares many physicochemical properties with EcoSSB and that the differences may be explained by the lack of an acidic, disordered C-terminal tail in human mtSSB protein. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  19. In silico footprinting of ligands binding to the minor groove of DNA.

    Science.gov (United States)

    Anthony, Nahoum G; Huchet, Guillaume; Johnston, Blair F; Parkinson, John A; Suckling, Colin J; Waigh, Roger D; Mackay, Simon P

    2005-01-01

    The sequence selectivity of small molecules binding to the minor groove of DNA can be predicted by "in silico footprinting". Any potential ligand can be docked in the minor groove and then moved along it using simple simulation techniques. By applying a simple scoring function to the trajectory after energy minimization, the preferred binding site can be identified. We show application to all known noncovalent binding modes, namely 1:1 ligand:DNA binding (including hairpin ligands) and 2:1 side-by-side binding, with various DNA base pair sequences and show excellent agreement with experimental results from X-ray crystallography, NMR, and gel-based footprinting.

  20. Mode-to-mode energy transfers in convective patterns

    Indian Academy of Sciences (India)

    Abstract. We investigate the energy transfer between various Fourier modes in a low- dimensional model for thermal convection. We have used the formalism of mode-to-mode energy transfer rate in our calculation. The evolution equations derived using this scheme is the same as those derived using the hydrodynamical ...

  1. SwarmDock and the Use of Normal Modes in Protein-Protein Docking

    Directory of Open Access Journals (Sweden)

    Paul A. Bates

    2010-09-01

    Full Text Available Here is presented an investigation of the use of normal modes in protein-protein docking, both in theory and in practice. Upper limits of the ability of normal modes to capture the unbound to bound conformational change are calculated on a large test set, with particular focus on the binding interface, the subset of residues from which the binding energy is calculated. Further, the SwarmDock algorithm is presented, to demonstrate that the modelling of conformational change as a linear combination of normal modes is an effective method of modelling flexibility in protein-protein docking.

  2. Azimuthal decomposition of optical modes

    CSIR Research Space (South Africa)

    Dudley, Angela L

    2012-07-01

    Full Text Available This presentation analyses the azimuthal decomposition of optical modes. Decomposition of azimuthal modes need two steps, namely generation and decomposition. An azimuthally-varying phase (bounded by a ring-slit) placed in the spatial frequency...

  3. Free boundary ballooning mode representation

    Science.gov (United States)

    Zheng, L. J.

    2012-10-01

    A new type of ballooning mode invariance is found in this paper. Application of this invariance is shown to be able to reduce the two-dimensional problem of free boundary high n modes, such as the peeling-ballooning modes, to a one-dimensional problem. Here, n is toroidal mode number. In contrast to the conventional ballooning representation, which requires the translational invariance of the Fourier components of the perturbations, the new invariance reflects that the independent solutions of the high n mode equations are translationally invariant from one radial interval surrounding a single singular surface to the other intervals. The conventional ballooning mode invariance breaks down at the vicinity of plasma edge, since the Fourier components with rational surfaces in vacuum region are completely different from those with rational surfaces in plasma region. But, the new type of invariance remains valid. This overcomes the limitation of the conventional ballooning mode representation for studying free boundary modes.

  4. Saccharide binding by intelectins.

    Science.gov (United States)

    Sharma, Shailza; Ramya, T N C

    2017-11-04

    This communication probes ligand binding by human Intelectin-1 with several saccharides. Human Intelectin-1 was previously reported to bind to microbial glycans via ribofuranoside or galactofuranoside residues, whereas subsequently, a crystal structure of ligand bound hITLN1 indicated that hITLN1 does not bind to ribofuranoside but distinguishes between microbial and human glycans through a glycan motif - a terminal, acyclic 1,2-diol, which is present on galactofuranose and other microbial saccharides. Here, we demonstrate that besides glycerol and glycerol derivatives (which have an acyclic 1,2-diol), and 2-deoxy-d-galactose, d-ribose and 2-deoxy-d-ribose, which have been previously reported as human Intelectin-1 ligands, 2-C-hydroxymethyl-d-ribose, d-talose, d-idose, d-altrose and sorbitol also elute human Intelectin-1 from Sepharose CL-6B. Interestingly, Sepharose, 2-deoxy-d-galactose (in its pyranose form), 2-C-hydroxymethyl-d-ribose, d-ribose and 2-deoxy d-ribose lack a terminal, acyclic 1,2-diol. We discuss the implications of these observations and rationalize the discrepancies in the apparent affinity of saccharide ligands for hITLN1 with different assay formats. We also report the distinct saccharide binding profiles of the hITLN1 homologues, HaloITLN and XL35ITLN, and demonstrate that hITLN1 binding to a saccharide ligand may modulate binding to its protein ligand, lactoferrin and vice versa. Copyright © 2017 Elsevier B.V. All rights reserved.

  5. Benchmarking ab initio binding energies of hydrogen-bonded molecular clusters based on FTIR spectroscopy

    DEFF Research Database (Denmark)

    Bork, Nicolai Christian; Du, Lin; Reiman, Heidi

    2014-01-01

    of the Gibbs free binding energies in molecular complexes and clusters based on gas phase FTIR spectroscopy. The acetonitrile-HCl molecular complex is identified via its redshifted H-Cl stretching vibrational mode. We determine the Gibbs free binding energy, ΔG°295 K, to between 4.8 and 7.9 kJ mol(-1...

  6. Inhibition of selectin binding

    Energy Technology Data Exchange (ETDEWEB)

    Nagy, Jon O. (Rodeo, CA); Spevak, Wayne R. (Albany, CA); Dasgupta, Falguni (New Delhi, IN); Bertozzi, Carolyn (Albany, CA)

    1999-10-05

    This invention provides a system for inhibiting the binding between two cells, one expressing P- or L-selectin on the surface and the other expressing the corresponding ligand. A covalently crosslinked lipid composition is prepared having saccharides and acidic group on separate lipids. The composition is then interposed between the cells so as to inhibit binding. Inhibition can be achieved at an effective oligosaccharide concentration as low as 10.sup.6 fold below that of the free saccharide. Since selectins are involved in recruiting cells to sites of injury, this system can be used to palliate certain inflammatory and immunological conditions.

  7. Aristotelian Syllogistic, Subalternate Modes, Theophrastus’ Modes and the Fourth Figure

    OpenAIRE

    СЛИНИН Я.А.

    2015-01-01

    In his treatise «New Essays Concerning Human Understanding» Leibniz gives some evidence which suggests that he believed that each of the four figures of Aristotle’s categorical syllogism has 6 correct modes. It is known that Aristotle stated and proved correct syllogisms modes in the three figures, with the fi rst of them having a number of the indirect modes. Why Aristotle did not explicitly introduced into his syllogistic subalternative modes and modes with conversed conclusion? In the pape...

  8. Damage mechanics - failure modes

    Energy Technology Data Exchange (ETDEWEB)

    Krajcinovic, D.; Vujosevic, M. [Arizona State Univ., Tempe, AZ (United States)

    1996-12-31

    The present study summarizes the results of the DOE sponsored research program focused on the brittle failure of solids with disordered microstructure. The failure is related to the stochastic processes on the microstructural scale; namely, the nucleation and growth of microcracks. The intrinsic failure modes, such as the percolation, localization and creep rupture, are studied by emphasizing the effect of the micro-structural disorder. A rich spectrum of physical phenomena and new concepts that emerges from this research demonstrates the reasons behind the limitations of traditional, deterministic, and local continuum models.

  9. Localized Acoustic Surface Modes

    KAUST Repository

    Farhat, Mohamed

    2015-08-04

    We introduce the concept of localized acoustic surface modes (ASMs). We demonstrate that they are induced on a two-dimensional cylindrical rigid surface with subwavelength corrugations under excitation by an incident acoustic plane wave. Our results show that the corrugated rigid surface is acoustically equivalent to a cylindrical scatterer with uniform mass density that can be represented using a Drude-like model. This, indeed, suggests that plasmonic-like acoustic materials can be engineered with potential applications in various areas including sensing, imaging, and cloaking.

  10. Standardization of Keyword Search Mode

    Science.gov (United States)

    Su, Di

    2010-01-01

    In spite of its popularity, keyword search mode has not been standardized. Though information professionals are quick to adapt to various presentations of keyword search mode, novice end-users may find keyword search confusing. This article compares keyword search mode in some major reference databases and calls for standardization. (Contains 3…

  11. Raman amplification of OAM modes

    DEFF Research Database (Denmark)

    Ingerslev, Kasper; Gregg, Patrick; Galili, Michael

    2017-01-01

    The set of fibre modes carrying orbital angular momentum (OAM) is a possible basis for mode division multiplexing. In this regard, fibres supporting OAM modes have been fabricated [1], and optical communication using these fibres, has been demonstrated [2]. A vital part of any long range communic...

  12. Fluxon modes in superconducting multilayers

    DEFF Research Database (Denmark)

    Pedersen, Niels Falsig; Madsen, Søren Peder

    2004-01-01

    We show how to construct fluxon modes from plasma modes in the inductively coupled stacked Josephson junctions, and consider some special cases of these fluxon modes analytically. In some cases we can find exact analytical solutions when we choose the bias current in a special way. We also consid...

  13. Design of large mode area, mode selection fiber

    Science.gov (United States)

    Jin, Liang; Xu, Li; Zhang, He; Zou, Yonggang; Ding, Ye; Ma, Xiaohui

    2014-12-01

    The paper study on the effect of index distribution on the mode field and calculated the mode distribution in various index profiles. A single mode gaussian hybrid multicore fiber with 19 hexagonally arranged high index quartz rods is designed and investigated. Theoretical and simulative results are presented and compared to the conventional large mode area double clad fiber, the fundamental mode (FM) area can be reached 694.28 μm2, the confinement loss of FM and high order modes (HOMs) are 0.186 dB/m and 1.48 dB/m respectively with the bending radius of 20 cm at 1.064 μm wavelength, moreover, the index distribution can resistant the mode field distortion, which caused by fiber bending. So the FM delivery can be formed and the beam quality can be improved.

  14. Mechanics, thermodynamics, and kinetics of ligand binding to biopolymers.

    Science.gov (United States)

    Jarillo, Javier; Morín, José A; Beltrán-Heredia, Elena; Villaluenga, Juan P G; Ibarra, Borja; Cao, Francisco J

    2017-01-01

    Ligands binding to polymers regulate polymer functions by changing their physical and chemical properties. This ligand regulation plays a key role in many biological processes. We propose here a model to explain the mechanical, thermodynamic, and kinetic properties of the process of binding of small ligands to long biopolymers. These properties can now be measured at the single molecule level using force spectroscopy techniques. Our model performs an effective decomposition of the ligand-polymer system on its covered and uncovered regions, showing that the elastic properties of the ligand-polymer depend explicitly on the ligand coverage of the polymer (i.e., the fraction of the polymer covered by the ligand). The equilibrium coverage that minimizes the free energy of the ligand-polymer system is computed as a function of the applied force. We show how ligands tune the mechanical properties of a polymer, in particular its length and stiffness, in a force dependent manner. In addition, it is shown how ligand binding can be regulated applying mechanical tension on the polymer. Moreover, the binding kinetics study shows that, in the case where the ligand binds and organizes the polymer in different modes, the binding process can present transient shortening or lengthening of the polymer, caused by changes in the relative coverage by the different ligand modes. Our model will be useful to understand ligand-binding regulation of biological processes, such as the metabolism of nucleic acid. In particular, this model allows estimating the coverage fraction and the ligand mode characteristics from the force extension curves of a ligand-polymer system.

  15. Mechanics, thermodynamics, and kinetics of ligand binding to biopolymers.

    Directory of Open Access Journals (Sweden)

    Javier Jarillo

    Full Text Available Ligands binding to polymers regulate polymer functions by changing their physical and chemical properties. This ligand regulation plays a key role in many biological processes. We propose here a model to explain the mechanical, thermodynamic, and kinetic properties of the process of binding of small ligands to long biopolymers. These properties can now be measured at the single molecule level using force spectroscopy techniques. Our model performs an effective decomposition of the ligand-polymer system on its covered and uncovered regions, showing that the elastic properties of the ligand-polymer depend explicitly on the ligand coverage of the polymer (i.e., the fraction of the polymer covered by the ligand. The equilibrium coverage that minimizes the free energy of the ligand-polymer system is computed as a function of the applied force. We show how ligands tune the mechanical properties of a polymer, in particular its length and stiffness, in a force dependent manner. In addition, it is shown how ligand binding can be regulated applying mechanical tension on the polymer. Moreover, the binding kinetics study shows that, in the case where the ligand binds and organizes the polymer in different modes, the binding process can present transient shortening or lengthening of the polymer, caused by changes in the relative coverage by the different ligand modes. Our model will be useful to understand ligand-binding regulation of biological processes, such as the metabolism of nucleic acid. In particular, this model allows estimating the coverage fraction and the ligand mode characteristics from the force extension curves of a ligand-polymer system.

  16. Viscoelastic pulsational mode

    Science.gov (United States)

    Dutta, Pranamika; Karmakar, Pralay Kumar

    2017-08-01

    We present a theoretical model analysis to study the linear pulsational mode dynamics in viscoelastic complex self-gravitating infinitely extended clouds in the presence of active frictional coupling and dust-charge fluctuations. The complex cloud consists of uniformly distributed lighter hot mutually thermalized electrons and ions, and heavier cold dust grains amid partial ionization in a homogeneous, quasi-neutral, hydrostatic equilibrium configuration. A normal mode analysis over the closed set of slightly perturbed cloud governing equations is employed to obtain a generalized dispersion relation (septic) of unique analytic construct on the plasma parameters. Two extreme cases of physical interest depending on the perturbation scaling, hydrodynamic limits and kinetic limits are considered. It is shown that the grain mass and viscoelastic relaxation time associated with the charged dust fluid play stabilizing roles to the fluctuations in the hydrodynamic regime. In contrast, however in the kinetic regime, the stabilizing effects are introduced by the dust mass, dust equilibrium density and equilibrium ionic population distribution. Besides, the oscillatory and propagatory features are illustrated numerically and interpreted in detail. The results are in good agreement with the previously reported findings as special corollaries in like situations. Finally, a focalized indication to new implications and applications of the outcomes in the astronomical context is foregrounded.

  17. Carboplatin binding to histidine

    NARCIS (Netherlands)

    Tanley, Simon W M; Diederichs, Kay; Kroon - Batenburg, Louise|info:eu-repo/dai/nl/070944172; Levy, Colin; Schreurs, Antoine M M|info:eu-repo/dai/nl/304847453; Helliwell, John R.

    2014-01-01

    Carboplatin is a second-generation platinum anticancer agent used for the treatment of a variety of cancers. Previous X-ray crystallographic studies of carboplatin binding to histidine (in hen egg-white lysozyme; HEWL) showed the partial conversion of carboplatin to cisplatin owing to the high NaCl

  18. Sequential memory: Binding dynamics

    Science.gov (United States)

    Afraimovich, Valentin; Gong, Xue; Rabinovich, Mikhail

    2015-10-01

    Temporal order memories are critical for everyday animal and human functioning. Experiments and our own experience show that the binding or association of various features of an event together and the maintaining of multimodality events in sequential order are the key components of any sequential memories—episodic, semantic, working, etc. We study a robustness of binding sequential dynamics based on our previously introduced model in the form of generalized Lotka-Volterra equations. In the phase space of the model, there exists a multi-dimensional binding heteroclinic network consisting of saddle equilibrium points and heteroclinic trajectories joining them. We prove here the robustness of the binding sequential dynamics, i.e., the feasibility phenomenon for coupled heteroclinic networks: for each collection of successive heteroclinic trajectories inside the unified networks, there is an open set of initial points such that the trajectory going through each of them follows the prescribed collection staying in a small neighborhood of it. We show also that the symbolic complexity function of the system restricted to this neighborhood is a polynomial of degree L - 1, where L is the number of modalities.

  19. Binding and Bulgarian

    NARCIS (Netherlands)

    Schürcks-Grozeva, Lilia Lubomirova

    2003-01-01

    In haar proefschrift analyseert Lilia Schürcks de anaforische verschijnselen in de Bulgaarse taal. Het gaat dan om wederkerende aspecten, uitgedrukt bij woorden als ‘zich’ en ‘elkaar’. De situatie in het Bulgaars blijkt moeilijk in te passen in de klassieke Binding Theory van Noam Chomsky. Bron: RUG

  20. Monolithic mode-selective few-mode multicore fiber multiplexers.

    Science.gov (United States)

    Riesen, Nicolas; Gross, Simon; Love, John D; Sasaki, Yusuke; Withford, Michael J

    2017-08-01

    With the capacity limits of standard single-mode optical fiber fast approaching, new technologies such as space-division multiplexing are required to avoid an Internet capacity crunch. Few-mode multicore fiber (FM-MCF) could allow for a two orders of magnitude increase in capacity by using the individual spatial modes in the different cores as unique data channels. We report the realization of a monolithic mode-selective few-mode multicore fiber multiplexer capable of addressing the individual modes of such a fiber. These compact multiplexers operate across the S + C + L telecommunications bands and were inscribed into a photonic chip using ultrafast laser inscription. They allow for the simultaneous multiplexing of the LP 01 , LP 11a and LP 11b modes of all cores in a 3-mode, 4-core fiber with excellent mode extinction ratios and low insertion losses. The devices are scalable to more modes and cores and therefore could represent an enabling technology for practical ultra-high capacity dense space-division multiplexing.

  1. Polarization Mode Dispersion

    CERN Document Server

    Galtarossa, Andrea

    2005-01-01

    This book contains a series of tutorial essays on polarization mode dispersion (PMD) by the leading experts in the field. It starts with an introductory review of the basic concepts and continues with more advanced topics, including a thorough review of PMD mitigation techniques. Topics covered include mathematical representation of PMD, how to properly model PMD in numerical simulations, how to accurately measure PMD and other related polarization effects, and how to infer fiber properties from polarization measurements. It includes discussions of other polarization effects such as polarization-dependent loss and the interaction of PMD with fiber nonlinearity. It additionally covers systems issues like the impact of PMD on wavelength division multiplexed systems. This book is intended for research scientists or engineers who wish to become familiar with PMD and its system impacts.

  2. The Integrated Mode Management Interface

    Science.gov (United States)

    Hutchins, Edwin

    1996-01-01

    Mode management is the processes of understanding the character and consequences of autoflight modes, planning and selecting the engagement, disengagement and transitions between modes, and anticipating automatic mode transitions made by the autoflight system itself. The state of the art is represented by the latest designs produced by each of the major airframe manufacturers, the Boeing 747-400, the Boeing 777, the McDonnell Douglas MD-11, and the Airbus A320/A340 family of airplanes. In these airplanes autoflight modes are selected by manipulating switches on the control panel. The state of the autoflight system is displayed on the flight mode annunciators. The integrated mode management interface (IMMI) is a graphical interface to autoflight mode management systems for aircraft equipped with flight management computer systems (FMCS). The interface consists of a vertical mode manager and a lateral mode manager. Autoflight modes are depicted by icons on a graphical display. Mode selection is accomplished by touching (or mousing) the appropriate icon. The IMMI provides flight crews with an integrated interface to autoflight systems for aircraft equipped with flight management computer systems (FMCS). The current version is modeled on the Boeing glass-cockpit airplanes (747-400, 757/767). It runs on the SGI Indigo workstation. A working prototype of this graphics-based crew interface to the autoflight mode management tasks of glass cockpit airplanes has been installed in the Advanced Concepts Flight Simulator of the CSSRF of NASA Ames Research Center. This IMMI replaces the devices in FMCS equipped airplanes currently known as mode control panel (Boeing), flight guidance control panel (McDonnell Douglas), and flight control unit (Airbus). It also augments the functions of the flight mode annunciators. All glass cockpit airplanes are sufficiently similar that the IMMI could be tailored to the mode management system of any modern cockpit. The IMMI does not replace the

  3. Influence of exciton-phonons coupling on the exciton binding energy in monolayer transition metal dichalcogenides

    Science.gov (United States)

    Wang, Zi-Wu; Li, Wei-Ping; Xiao, Yao; Li, Run-Ze; Li, Zhi-Qing

    2017-06-01

    We theoretically investigate the correction of exciton binding energy arising from the exciton-optical phonon coupling in monolayer transition metal dichalcogenides (TMDs) using the linear operator and Lee-Low-Pines unitary transformation methods. We take into account not only the exciton coupling with intrinsic longitudinal optical phonon modes but also the surface optical phonon modes induced by polar substrates supporting monolayer TMDs. We find that the exciton binding energies are corrected on a large scale due to these exciton-optical phonon couplings. We discuss the dependences of exciton binding energy on the cut-off wave vector of optical phonon modes, the polarization strength of substrate materials, and the distance between polar substrates and TMDs. These results provide potential explanations for the divergence of the exciton binding energy between the experiment and theory in TMDs.

  4. In vitro DNA binding studies of Aspartame, an artificial sweetener.

    Science.gov (United States)

    Kashanian, Soheila; Khodaei, Mohammad Mehdi; Kheirdoosh, Fahimeh

    2013-03-05

    A number of small molecules bind directly and selectively to DNA, by inhibiting replication, transcription or topoisomerase activity. In this work the interaction of native calf thymus DNA (CT-DNA) with Aspartame (APM), an artificial sweeteners was studied at physiological pH. DNA binding study of APM is useful to understand APM-DNA interaction mechanism and to provide guidance for the application and design of new and safer artificial sweeteners. The interaction was investigated using spectrophotometric, spectrofluorometric competition experiment and circular dichroism (CD). Hypochromism and red shift are shown in UV absorption band of APM. A strong fluorescence quenching reaction of DNA to APM was observed and the binding constants (Kf) of DNA with APM and corresponding number of binding sites (n) were calculated at different temperatures. Thermodynamic parameters, enthalpy changes (ΔH) and entropy changes (ΔS) were calculated to be +181kJmol(-1) and +681Jmol(-1)K(-1) according to Van't Hoff equation, which indicated that reaction is predominantly entropically driven. Moreover, spectrofluorometric competition experiment and circular dichroism (CD) results are indicative of non-intercalative DNA binding nature of APM. We suggest that APM interacts with calf thymus DNA via groove binding mode with an intrinsic binding constant of 5×10(+4)M(-1). Copyright © 2013 Elsevier B.V. All rights reserved.

  5. Binding leverage as a molecular basis for allosteric regulation.

    Science.gov (United States)

    Mitternacht, Simon; Berezovsky, Igor N

    2011-09-01

    Allosteric regulation involves conformational transitions or fluctuations between a few closely related states, caused by the binding of effector molecules. We introduce a quantity called binding leverage that measures the ability of a binding site to couple to the intrinsic motions of a protein. We use Monte Carlo simulations to generate potential binding sites and either normal modes or pairs of crystal structures to describe relevant motions. We analyze single catalytic domains and multimeric allosteric enzymes with complex regulation. For the majority of the analyzed proteins, we find that both catalytic and allosteric sites have high binding leverage. Furthermore, our analysis of the catabolite activator protein, which is allosteric without conformational change, shows that its regulation involves other types of motion than those modulated at sites with high binding leverage. Our results point to the importance of incorporating dynamic information when predicting functional sites. Because it is possible to calculate binding leverage from a single crystal structure it can be used for characterizing proteins of unknown function and predicting latent allosteric sites in any protein, with implications for drug design.

  6. Waveguides having patterned, flattened modes

    Energy Technology Data Exchange (ETDEWEB)

    Messerly, Michael J.; Pax, Paul H.; Dawson, Jay W.

    2015-10-27

    Field-flattening strands may be added to and arbitrarily positioned within a field-flattening shell to create a waveguide that supports a patterned, flattened mode. Patterning does not alter the effective index or flattened nature of the mode, but does alter the characteristics of other modes. Compared to a telecom fiber, a hexagonal pattern of strands allows for a three-fold increase in the flattened mode's area without reducing the separation between its effective index and that of its bend-coupled mode. Hexagonal strand and shell elements prove to be a reasonable approximation, and, thus, to be of practical benefit vis-a-vis fabrication, to those of circular cross section. Patterned flattened modes offer a new and valuable path to power scaling.

  7. Elastic network normal mode dynamics reveal the GPCR activation mechanism.

    Science.gov (United States)

    Kolan, Dikla; Fonar, Gennadiy; Samson, Abraham O

    2014-04-01

    G-protein-coupled receptors (GPCR) are a family of membrane-embedded metabotropic receptors which translate extracellular ligand binding into an intracellular response. Here, we calculate the motion of several GPCR family members such as the M2 and M3 muscarinic acetylcholine receptors, the A2A adenosine receptor, the β2 -adrenergic receptor, and the CXCR4 chemokine receptor using elastic network normal modes. The normal modes reveal a dilation and a contraction of the GPCR vestibule associated with ligand passage, and activation, respectively. Contraction of the vestibule on the extracellular side is correlated with cavity formation of the G-protein binding pocket on the intracellular side, which initiates intracellular signaling. Interestingly, the normal modes of rhodopsin do not correlate well with the motion of other GPCR family members. Electrostatic potential calculation of the GPCRs reveal a negatively charged field around the ligand binding site acting as a siphon to draw-in positively charged ligands on the membrane surface. Altogether, these results expose the GPCR activation mechanism and show how conformational changes on the cell surface side of the receptor are allosterically translated into structural changes on the inside. Copyright © 2013 Wiley Periodicals, Inc.

  8. Identification of the quinolinedione inhibitor binding site in Cdc25 phosphatase B through docking and molecular dynamics simulations

    Science.gov (United States)

    Ge, Yushu; van der Kamp, Marc; Malaisree, Maturos; Liu, Dan; Liu, Yi; Mulholland, Adrian J.

    2017-10-01

    Cdc25 phosphatase B, a potential target for cancer therapy, is inhibited by a series of quinones. The binding site and mode of quinone inhibitors to Cdc25B remains unclear, whereas this information is important for structure-based drug design. We investigated the potential binding site of NSC663284 [DA3003-1 or 6-chloro-7-(2-morpholin-4-yl-ethylamino)-quinoline-5, 8-dione] through docking and molecular dynamics simulations. Of the two main binding sites suggested by docking, the molecular dynamics simulations only support one site for stable binding of the inhibitor. Binding sites in and near the Cdc25B catalytic site that have been suggested previously do not lead to stable binding in 50 ns molecular dynamics (MD) simulations. In contrast, a shallow pocket between the C-terminal helix and the catalytic site provides a favourable binding site that shows high stability. Two similar binding modes featuring protein-inhibitor interactions involving Tyr428, Arg482, Thr547 and Ser549 are identified by clustering analysis of all stable MD trajectories. The relatively flexible C-terminal region of Cdc25B contributes to inhibitor binding. The binding mode of NSC663284, identified through MD simulation, likely prevents the binding of protein substrates to Cdc25B. The present results provide useful information for the design of quinone inhibitors and their mechanism of inhibition.

  9. Identification of the quinolinedione inhibitor binding site in Cdc25 phosphatase B through docking and molecular dynamics simulations

    Science.gov (United States)

    Ge, Yushu; van der Kamp, Marc; Malaisree, Maturos; Liu, Dan; Liu, Yi; Mulholland, Adrian J.

    2017-11-01

    Cdc25 phosphatase B, a potential target for cancer therapy, is inhibited by a series of quinones. The binding site and mode of quinone inhibitors to Cdc25B remains unclear, whereas this information is important for structure-based drug design. We investigated the potential binding site of NSC663284 [DA3003-1 or 6-chloro-7-(2-morpholin-4-yl-ethylamino)-quinoline-5, 8-dione] through docking and molecular dynamics simulations. Of the two main binding sites suggested by docking, the molecular dynamics simulations only support one site for stable binding of the inhibitor. Binding sites in and near the Cdc25B catalytic site that have been suggested previously do not lead to stable binding in 50 ns molecular dynamics (MD) simulations. In contrast, a shallow pocket between the C-terminal helix and the catalytic site provides a favourable binding site that shows high stability. Two similar binding modes featuring protein-inhibitor interactions involving Tyr428, Arg482, Thr547 and Ser549 are identified by clustering analysis of all stable MD trajectories. The relatively flexible C-terminal region of Cdc25B contributes to inhibitor binding. The binding mode of NSC663284, identified through MD simulation, likely prevents the binding of protein substrates to Cdc25B. The present results provide useful information for the design of quinone inhibitors and their mechanism of inhibition.

  10. Evaluation of binding strength depending on the adhesive binding methods

    OpenAIRE

    Suzana Pasanec Preprotić; Ivan Budimir; Gorana Tomić

    2015-01-01

    A book with a personal value is worth remembering since it represents specific interests of an individual - author of the book. Therefore the original is the first issue of a book which is always bound manually. Due to cost-effectiveness, adhesive binding is most commonly used in author’s edition in paperback and hardback. Adhesive binding methods differ only if a paper leaf is a binding unit in adhesive binding form. The subject of the research is the quality of book block binding for two bi...

  11. Binding properties of palmatine to DNA: spectroscopic and molecular modeling investigations.

    Science.gov (United States)

    Mi, Ran; Tu, Bao; Bai, Xiao-Ting; Chen, Jun; Ouyang, Yu; Hu, Yan-Jun

    2015-12-01

    Palmatine, an isoquinoline alkaloid, is an important medicinal herbal extract with diverse pharmacological and biological properties. In this work, spectroscopic and molecular modeling approaches were employed to reveal the interaction between palmatine and DNA isolated from herring sperm. The absorption spectra and iodide quenching results indicated that groove binding was the main binding mode of palmatine to DNA. Fluorescence studies indicated that the binding constant (K) of palmatine and DNA was ~ 10(4)L·mol(-1). The associated thermodynamic parameters, ΔG, ΔH, and ΔS, indicated that hydrogen bonds and van der Waals forces played major roles in the interaction. The effects of chemical denaturant, thermal denaturation and pH on the interaction were investigated and provided further support for the groove binding mode. In addition to experimental approaches, molecular modeling was conducted to verify binding pattern of palmatine-DNA. Copyright © 2015 John Wiley & Sons, Ltd.

  12. Whispering gallery mode sensors.

    Science.gov (United States)

    Foreman, Matthew R; Swaim, Jon D; Vollmer, Frank

    2015-06-30

    We present a comprehensive overview of sensor technology exploiting optical whispering gallery mode (WGM) resonances. After a short introduction we begin by detailing the fundamental principles and theory of WGMs in optical microcavities and the transduction mechanisms frequently employed for sensing purposes. Key recent theoretical contributions to the modeling and analysis of WGM systems are highlighted. Subsequently we review the state of the art of WGM sensors by outlining efforts made to date to improve current detection limits. Proposals in this vein are numerous and range, for example, from plasmonic enhancements and active cavities to hybrid optomechanical sensors, which are already working in the shot noise limited regime. In parallel to furthering WGM sensitivity, efforts to improve the time resolution are beginning to emerge. We therefore summarize the techniques being pursued in this vein. Ultimately WGM sensors aim for real-world applications, such as measurements of force and temperature, or alternatively gas and biosensing. Each such application is thus reviewed in turn, and important achievements are discussed. Finally, we adopt a more forward-looking perspective and discuss the outlook of WGM sensors within both a physical and biological context and consider how they may yet push the detection envelope further.

  13. Library Binding Manual. Revised Edition.

    Science.gov (United States)

    Lakhanpal, S. K.

    This procedural manual is designed to be used in bindery sections in public, university and special libraries. It briefly discusses these general matters: administrative control; selection of a binder; when and what to bind; conventional binding; routines; missing issues; schedule for shipments; temporary binding; rare books, maps and newspapers;…

  14. In Silico Investigation of the Neurotensin Receptor 1 Binding Site

    DEFF Research Database (Denmark)

    Lückmann, Michael; Holst, Birgitte; Schwartz, Thue W.

    2016-01-01

    structure of NTSR1 in complex with NTS8-13 has been detd., providing novel insights into peptide ligand recognition by 7TM receptors. SR48692, a potent and selective small mol. antagonist has previously been used extensively as a tool compd. to study NTSR1 receptor signaling properties. To investigate...... the binding mode of SR48692 and other small mol. compds. to NTSR1, we applied an Automated Ligand-guided Backbone Ensemble Receptor Optimization protocol (ALiBERO), taking receptor flexibility and ligand knowledge into account. Structurally overlapping binding poses for SR48692 and NTS8-13 were obsd., despite...

  15. Spectrofluorimetric study of the binding of codeine to nucleic acids

    Science.gov (United States)

    Wang, Feng; Huang, Wei; Su, Liang; Dong, Zijia; Zhang, Shuai

    2009-06-01

    The characteristics of the interaction between codeine (CD) and nucleic acids were studied by ultraviolet-visible spectra and fluorescent spectra. It shows that there is a powerful ability in nucleic acids to quench the fluorescence intensity of codeine. The fluorescence quenching data were analyzed according to Stern-Volmer equation and Förster's nonradiative energy transfer mechanism. Thus the binding constant and the thermodynamic parameters between codeine and nucleic acids were obtained. The results show that codeine interacts with nucleic acids in a mode of groove binding and -OCH 3 of the codeine molecular combines with the groove of nucleic acids through hydrogen bond or van der Waals force.

  16. Discovery and Characterization of a Cell-Permeable, Small-Molecule c-Abl Kinase Activator that Binds to the Myristoyl Binding Site

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Jingsong; Campobasso, Nino; Biju, Mangatt P.; Fisher, Kelly; Pan, Xiao-Qing; Cottom, Josh; Galbraith, Sarah; Ho, Thau; Zhang, Hong; Hong, Xuan; Ward, Paris; Hofmann, Glenn; Siegfried, Brett; Zappacosta, Francesca; Washio, Yoshiaki; Cao, Ping; Qu, Junya; Bertrand, Sophie; Wang, Da-Yuan; Head, Martha S.; Li, Hu; Moores, Sheri; Lai, Zhihong; Johanson, Kyung; Burton, George; Erickson-Miller, Connie; Simpson, Graham; Tummino, Peter; Copeland, Robert A.; Oliff, Allen (GSKPA)

    2014-10-02

    c-Abl kinase activity is regulated by a unique mechanism involving the formation of an autoinhibited conformation in which the N-terminal myristoyl group binds intramolecularly to the myristoyl binding site on the kinase domain and induces the bending of the {alpha}I helix that creates a docking surface for the SH2 domain. Here, we report a small-molecule c-Abl activator, DPH, that displays potent enzymatic and cellular activity in stimulating c-Abl activation. Structural analyses indicate that DPH binds to the myristoyl binding site and prevents the formation of the bent conformation of the {alpha}I helix through steric hindrance, a mode of action distinct from the previously identified allosteric c-Abl inhibitor, GNF-2, that also binds to the myristoyl binding site. DPH represents the first cell-permeable, small-molecule tool compound for c-Abl activation.

  17. Intrinsic localized modes and nonlinear impurity modes in curved ...

    Indian Academy of Sciences (India)

    We explore the nature of intrinsic localized modes (ILMs) in a curved Fermi–. Pasta–Ulam (FPU) chain ... We further demonstrate that a nonlinear impurity mode may be treated as a bound state of an ILM with the impurity .... length [14] and see that the particular choice of the chain geometry ensures the DB propagation with ...

  18. Plasmodium vivax Duffy binding protein peptides specifically bind to reticulocytes.

    Science.gov (United States)

    Ocampo, Marisol; Vera, Ricardo; Eduardo Rodriguez, Luis; Curtidor, Hernando; Urquiza, Mauricio; Suarez, Jorge; Garcia, Javier; Puentes, Alvaro; Lopez, Ramsés; Trujillo, Mary; Torres, Elizabeth; Patarroyo, Manuel Elkin

    2002-01-01

    Plasmodium vivax Duffy Binding Protein (Pv-DBP) is essential during merozoite invasion of reticulocytes. Reticulocyte binding region identification is important for understanding Pv-DBP reticulocyte recognition. Fifty 20 mer non-overlapping peptides, spanning Pv-DBP sequences, were tested in erythrocyte and reticulocyte binding assays. Ten HARBPs, mainly located in region II (Kd 50-130 nM), were High Activity Reticulocyte Binding Peptides (HARBPs); one bound to erythrocytes. Reticulocyte trypsin-, chymotrypsin- or neuraminidase- treatment affects HARBP binding differently, suggesting that these peptides have different reticulocyte-binding-sites. Some peptides bound to a Coomasie non-stainable 40 Kda band. Some HARBPs were able to block recombinant PvRII binding (Pv-DBP region II) to Duffy positive reticulocytes.

  19. Mode Launcher Design for the Multi-moded DLDS

    CERN Document Server

    Li, Z

    2003-01-01

    The DLDS (Delay Line Distribution System) power delivery system proposed by KEK combines several klystrons to obtain the high peak power required to drive a TeV scale linear collider. In this system the combined klystron output is subdivided into shorter pulses by proper phasing of the sources, and each subpulse is delivered to various accelerator sections via separate waveguides. A cost-saving improvement suggested by SLAC is to use a single multimoded waveguide to deliver the power of all the subpulses. This scheme requires a mode launcher that can deliver each subpulse by way of a different waveguide mode through selective phasing of the sources when combining their power. We present a compact design for such a mode launcher that converts the power from four rectangular waveguide feeds to separate modes in a multi-moded circular guide through coupling slots. Such a design has been simulated and found to satisfy the requirements for high efficiency and low surface fields.

  20. MANAGING TIGHT BINDING RECEPTORS FOR NEW SPEARATIONS TECHNOLOGIES

    Energy Technology Data Exchange (ETDEWEB)

    DARYLE H BUSCH RICHARD S GIVENS

    2004-12-10

    even more interesting. They convert from rings to structures that wrap around a metal ion to form a cage. These ligands are called cryptands. Switch release is accomplished by photolytic cleavage of a bond to convert a cyclic ligand into a linear ligand or to break similar bonds in a cryptate. Our studies have demonstrated switch binding and switch release with cryptates of calcium. These remarkable cyclic ligands and cage-like ligands are indeed tight-binding and may, in principle, be incorporated in various separations methodologies, including the soil poultice. The soil poultice mimics the way in which microbes secrete extremely powerful ligands into the soil in order to harvest iron. The cellular membrane of the microbe recognizes the iron/ligand complex and admits it into the cell. The soil poultice uses molecularly imprinted polymers (MIPs) to play the role of the cellular membrane. Imprinting involves creation of the polymer in the presence of the metal/ligand complex. In principle, a well design ligand/MIP combination can be highly selective toward almost any targeted metal ion. The principles for that design are the focus of these investigations. An imprinting molecule can interact with the polymer through any, some, or all of the so-called supramolecular modes; e.g., hydrogen bonding, electrostatic charge, minor ligand bonding, Pi-Pi stacking, and hydrophobic and van der Waals interactions. Historically these modes of binding have given MIPs only small re-binding capacities and very limited selectivities. This program has shown that each mode of interaction can be made more powerful than previously suspected and that combinations of different supramolecular interaction modes can produce remarkable synergisms. The results of this systematic study provide a firm foundation for tailoring molecular imprinted polymers for reclamation of specific metal ion, including those important to the DOE EM mission.

  1. Modes of action of anthelmintic drugs.

    Science.gov (United States)

    Martin, R J

    1997-07-01

    Modes of action of anthelmintic drugs are described. Some anthelmintic drugs act rapidly and selectively on neuromuscular transmission of nematodes. Levamisole, pyrantel and morantel are agonists at nicotinic acetylcholine receptors of nematode muscle and cause spastic paralysis. Dichlorvos and haloxon are organophosphorus cholinesterase antagonists. Piperazine is a GABA (gamma-amino-butyric acid) agonist at receptors on nematode muscles and causes flaccid paralysis. The avermectins increase the opening of glutamate-gated chloride (GluCl) channels and produce paralysis of pharyngeal pumping. Praziquantel has a selective effect on the tegument of trematodes and increases permeability of calcium. Other anthelmintics have a biochemical mode of action. The benzimidazole drugs bind selectively to beta-tubulin of nematodes, cestodes and fluke, and inhibit microtubule formation. The salicylanilides: rafoxanide, oxyclozanide, brotianide and closantel and the substituted phenol, nitroxynil, are proton ionophores. Clorsulon is a selective antagonist of fluke phosphoglycerate kinase and mutase. Diethylcarbamazine blocks host, and possibly parasite, enzymes involved in arachidonic acid metabolism, and enhances the innate, nonspecific immune system.

  2. Carboplatin binding to histidine

    Energy Technology Data Exchange (ETDEWEB)

    Tanley, Simon W. M. [University of Manchester, Brunswick Street, Manchester M13 9PL (United Kingdom); Diederichs, Kay [University of Konstanz, D-78457 Konstanz (Germany); Kroon-Batenburg, Loes M. J. [Utrecht University, Padualaan 8, 3584 CH Utrecht (Netherlands); Levy, Colin [University of Manchester, 131 Princess Street, Manchester M1 7DN (United Kingdom); Schreurs, Antoine M. M. [Utrecht University, Padualaan 8, 3584 CH Utrecht (Netherlands); Helliwell, John R., E-mail: john.helliwell@manchester.ac.uk [University of Manchester, Brunswick Street, Manchester M13 9PL (United Kingdom)

    2014-08-29

    An X-ray crystal structure showing the binding of purely carboplatin to histidine in a model protein has finally been obtained. This required extensive crystallization trials and various novel crystal structure analyses. Carboplatin is a second-generation platinum anticancer agent used for the treatment of a variety of cancers. Previous X-ray crystallographic studies of carboplatin binding to histidine (in hen egg-white lysozyme; HEWL) showed the partial conversion of carboplatin to cisplatin owing to the high NaCl concentration used in the crystallization conditions. HEWL co-crystallizations with carboplatin in NaBr conditions have now been carried out to confirm whether carboplatin converts to the bromine form and whether this takes place in a similar way to the partial conversion of carboplatin to cisplatin observed previously in NaCl conditions. Here, it is reported that a partial chemical transformation takes place but to a transplatin form. Thus, to attempt to resolve purely carboplatin binding at histidine, this study utilized co-crystallization of HEWL with carboplatin without NaCl to eliminate the partial chemical conversion of carboplatin. Tetragonal HEWL crystals co-crystallized with carboplatin were successfully obtained in four different conditions, each at a different pH value. The structural results obtained show carboplatin bound to either one or both of the N atoms of His15 of HEWL, and this particular variation was dependent on the concentration of anions in the crystallization mixture and the elapsed time, as well as the pH used. The structural details of the bound carboplatin molecule also differed between them. Overall, the most detailed crystal structure showed the majority of the carboplatin atoms bound to the platinum centre; however, the four-carbon ring structure of the cyclobutanedicarboxylate moiety (CBDC) remained elusive. The potential impact of the results for the administration of carboplatin as an anticancer agent are described.

  3. Lasing mode regulation and single-mode realization in ZnO whispering gallery microcavities by the Vernier effect.

    Science.gov (United States)

    Wang, Y Y; Xu, C X; Jiang, M M; Li, J T; Dai, J; Lu, J F; Li, P L

    2016-10-07

    The wide direct bandgap and strong exciton binding energy of ZnO have inspired examinations of ultraviolet lasing over the previous decades. However, regulation of the lasing mode, especially the realization of single mode lasing, is still a challenge. In this study, a ZnO comb-like structure with an array of microrods was selected to design coupled whispering-gallery-mode cavities, wherein the naturally varied air-gap between the adjacent microrods created a flexible condition for optical field coupling without any complicated micromanipulation. Spectral behaviour of lasing and coupling interaction between coupled ZnO microrods were systematically investigated. By regulating the nano-scale inter-space of dual coupled microrods, stable single-mode lasing with a higher Q factor and lower threshold was obtained successfully based on the Vernier effect. The formation conditions and the mechanism of single-mode lasing derived from the coupled ZnO microrods were discussed in detail. It also demonstrated an approach to construct high quality single-mode lasing by tuning the diameters of the coupled ZnO microrods.

  4. Theory of psychological adaptive modes.

    Science.gov (United States)

    Lehti, Juha

    2016-05-01

    When an individual is facing a stressor and normal stress-response mechanism cannot guarantee sufficient adaptation, special emotional states, adaptive modes, are activated (for example a depressive reaction). Adaptive modes are involuntary states of mind, they are of comprehensive nature, they interfere with normal functioning, and they cannot be repressed or controlled the same way as many emotions. Their transformational nature differentiates them from other emotional states. The object of the adaptive mode is to optimize the problem-solving abilities according to the situation that has provoked the mode. Cognitions and emotions during the adaptive mode are different than in a normal mental state. These altered cognitions and emotional reactions guide the individual to use the correct coping skills in order to deal with the stressor. Successful adaptation will cause the adaptive mode to fade off since the adaptive mode is no longer necessary, and the process as a whole will lead to raised well-being. However, if the adaptation process is inadequate, then the transformation period is prolonged, and the adaptive mode will turn into a dysfunctional state. Many psychiatric disorders are such maladaptive processes. The maladaptive processes can be turned into functional ones by using adaptive skills that are used in functional adaptive processes. Copyright © 2016 Elsevier Ltd. All rights reserved.

  5. Transformation and Modes of Production

    DEFF Research Database (Denmark)

    Høst, Jeppe Engset

    2015-01-01

    modes of production and examine the ways of life that are enabled by the two modes of production. The central questions are around how market-based fisheries management transforms the principal preconditions for the self-employed fishers; and, in turn, why capitalist organized large-scale fisheries...

  6. Evaluation of binding strength depending on the adhesive binding methods

    Directory of Open Access Journals (Sweden)

    Suzana Pasanec Preprotić

    2015-05-01

    Full Text Available A book with a personal value is worth remembering since it represents specific interests of an individual - author of the book. Therefore the original is the first issue of a book which is always bound manually. Due to cost-effectiveness, adhesive binding is most commonly used in author’s edition in paperback and hardback. Adhesive binding methods differ only if a paper leaf is a binding unit in adhesive binding form. The subject of the research is the quality of book block binding for two binding methods with/without mull fabric. The assumption is that double-fan adhesive binding method shows an extraordinary binding quality as compared to the rough spine method. For the needs of this research book block parameters remained unaltered: paper type, size and book volume. The results related to strength were obtained by using an experimental method of tensile strength for individual paper leaves. The rating of book block quality was conducted in accordance with FOGRA Nr.71006 guidelines for page pull-test. Furthermore, strength results for both methods were compared in order to evaluate the importance of changing the quality of adhesive binding. Statistical method ANOVA analysis of variance and Fisher’s F-test were used to evaluate the quality of book block binding.

  7. Mode Combinations and International Operations

    DEFF Research Database (Denmark)

    Benito, Gabriel R. G.; Petersen, Bent; Welch, Lawrence S.

    2011-01-01

    An enduring characteristic of extant literature on foreign operation modes is its discrete choice approach, where companies are assumed to choose one among a small number of distinctive alternatives. In this paper we use detailed information about the operations of six Norwegian companies in three...... key markets (China, UK and USA) as the basis for an exploration of the extent to which, and how and why, companies combine clearly different foreign operation modes. We examine their use of foreign operation mode combinations within given value activities as well as within given countries. The study...... reveals that companies tend to combine modes of operation; thereby producing unique foreign operation mode “packages” for given activities and/or countries, and that the packages are liable to be modified over time – providing a potentially important optional path for international expansion. Our data...

  8. Mode Combinations and International Operations

    DEFF Research Database (Denmark)

    Benito, Gabriel R. G.; Petersen, Bent; Welch, Lawrence S.

    2011-01-01

    An enduring characteristic of extant literature on foreign operation modes is its discrete choice approach, where companies are assumed to choose one among a small number of distinctive alternatives. In this paper, detailed information about the operations of six Norwegian companies in three key...... markets (China, UK and USA) is used as the basis for an exploration of the extent to which, and how and why, companies combine clearly different foreign operation modes. We examine their use of foreign operation mode combinations within given value activities as well as within given countries. The study...... reveals that companies tend to combine modes of operation; thereby producing unique foreign operation mode “packages” for given activities and/or countries, and that the packages are liable to be modified over time—providing a potentially important optional path for international expansion. The data show...

  9. Mode coupling trigger of neoclassical magnetohydrodynamic tearing modes in tokamaks

    Energy Technology Data Exchange (ETDEWEB)

    Gianakon, T.A.; Hegna, C.C.; Callen, J.D.

    1997-05-01

    Numerical studies of the nonlinear evolution of coupled magnetohydrodynamic - type tearing modes in three-dimensional toroidal geometry with neoclassical effects are presented. The inclusion of neoclassical physics introduces an additional free-energy source for the nonlinear formation of magnetic islands through the effects of a bootstrap current in Ohm`s law. The neoclassical tearing mode is demonstrated to be destabilized in plasmas which are otherwise {Delta}{prime} stable, albeit once a threshold island width is exceeded. A possible mechanism for exceeding or eliminating this threshold condition is demonstrated based on mode coupling due to toroidicity with a pre-existing instability at the q = 1 surface.

  10. Mode-by-mode hydrodynamics: Ideas and concepts

    Energy Technology Data Exchange (ETDEWEB)

    Floerchinger, Stefan

    2014-06-15

    The main ideas, technical concepts and perspectives for a mode resolved description of the hydrodynamical regime of relativistic heavy ion collisions are discussed. A background-fluctuation splitting and a Bessel–Fourier expansion for the fluctuating part of the hydrodynamical fields allows for a complete characterization of initial conditions, the fluid dynamical propagation of single modes, the study of interaction effects between modes, the determination of the associated particle spectra and the generalization of the whole program to event-by-event correlations and probability distributions.

  11. A unique bivalent binding and inhibition mechanism by the yatapoxvirus interleukin 18 binding protein.

    Directory of Open Access Journals (Sweden)

    Brian Krumm

    Full Text Available Interleukin 18 (IL18 is a cytokine that plays an important role in inflammation as well as host defense against microbes. Mammals encode a soluble inhibitor of IL18 termed IL18 binding protein (IL18BP that modulates IL18 activity through a negative feedback mechanism. Many poxviruses encode homologous IL18BPs, which contribute to virulence. Previous structural and functional studies on IL18 and IL18BPs revealed an essential binding hot spot involving a lysine on IL18 and two aromatic residues on IL18BPs. The aromatic residues are conserved among the very diverse mammalian and poxviruses IL18BPs with the notable exception of yatapoxvirus IL18BPs, which lack a critical phenylalanine residue. To understand the mechanism by which yatapoxvirus IL18BPs neutralize IL18, we solved the crystal structure of the Yaba-Like Disease Virus (YLDV IL18BP and IL18 complex at 1.75 Å resolution. YLDV-IL18BP forms a disulfide bonded homo-dimer engaging IL18 in a 2∶2 stoichiometry, in contrast to the 1∶1 complex of ectromelia virus (ECTV IL18BP and IL18. Disruption of the dimer interface resulted in a functional monomer, however with a 3-fold decrease in binding affinity. The overall architecture of the YLDV-IL18BP:IL18 complex is similar to that observed in the ECTV-IL18BP:IL18 complex, despite lacking the critical lysine-phenylalanine interaction. Through structural and mutagenesis studies, contact residues that are unique to the YLDV-IL18BP:IL18 binding interface were identified, including Q67, P116 of YLDV-IL18BP and Y1, S105 and D110 of IL18. Overall, our studies show that YLDV-IL18BP is unique among the diverse family of mammalian and poxvirus IL-18BPs in that it uses a bivalent binding mode and a unique set of interacting residues for binding IL18. However, despite this extensive divergence, YLDV-IL18BP binds to the same surface of IL18 used by other IL18BPs, suggesting that all IL18BPs use a conserved inhibitory mechanism by blocking a putative receptor-binding

  12. Analysis of high-affinity binding of protein kinase R to double-stranded RNA.

    Science.gov (United States)

    Husain, Bushra; Mukerji, Ishita; Cole, James L

    2012-11-06

    Protein kinase R (PKR) is an interferon-induced kinase that plays a pivotal role in the innate immunity response to viral infection. PKR is activated upon binding to double-stranded RNA (dsRNA). Our previous analysis of binding of PKR to dsRNAs ranging from 20 to 40 bp supports a dimerization model for activation in which 30 bp represents the minimal length required to bind two PKR monomers and activate PKR via autophosphorylation. These studies were complicated by the formation of protein-RNA aggregates, particularly at low salt concentrations using longer dsRNAs. Here, we have taken advantage of the enhanced sensitivity afforded using fluorescence-detected analytical ultracentrifugation to reduce the RNA concentrations from micromolar to nanomolar. Under these conditions, we are able to characterize high-affinity binding of PKR to longer dsRNAs in 75 mM NaCl. The PKR binding stoichiometries are increased at lower salt concentrations but remain lower than those previously obtained for the dsRNA binding domain. The dependence of the limiting PKR binding stoichiometries on dsRNA length does not conform to standard models for nonspecific binding and suggests that binding to longer sequences occurs via a different binding mode with a larger site size. Although dimerization plays a key role in the PKR activation mechanism, the ability of shorter dsRNAs to bind two PKR monomers is not sufficient to induce autophosphorylation. We propose that activation of PKR by longer RNAs is correlated with an alternative binding mode in which both of the dsRNA binding motifs contact the RNA, inducing PKR to dimerize via a direct interaction of the kinase domains.

  13. Pressure locking and thermal binding of gate valves

    Energy Technology Data Exchange (ETDEWEB)

    Kelly, E.M.

    1996-12-01

    Pressure locking and thermal binding represent potential common mode failure mechanisms that can cause safety-related power-operated gate valves to fail in the closed position, thus rendering redundant safety-related systems incapable of performing their safety functions. Supplement 6 to Generic Letter 89-10, {open_quotes}Safety-Related Motor-Operated Gate Valve Testing and Surveillance,{close_quotes} provided an acceptable approach to addressing pressure locking and thermal binding of gate valves. More recently, the NRC has issued Generic Letter 95-07, {open_quotes}Pressure Locking and Thermal Binding of Safety-Related Power-Operated Gate Valves,{close_quotes} to request that licensees take certain actions to ensure that safety-related power-operated gate valves that are susceptible to pressure locking or thermal binding are capable of performing their safety functions within the current licensing bases. Over the past two years, several plants in Region I determined that valves in certain systems were potentially susceptible to pressure locking and thermal binding, and have taken various corrective actions. The NRC Region I Systems Engineering Branch has been actively involved in the inspection of licensee actions in response to the pressure locking and thermal binding issue. Region I continues to maintain an active involvement in this area, including participation with the Office of Nuclear Reactor Regulation in reviewing licensee responses to Generic Letter 95-07.

  14. Megalin binds and mediates cellular internalization of folate binding protein

    DEFF Research Database (Denmark)

    Birn, Henrik; Zhai, Xiaoyue; Holm, Jan

    2005-01-01

    and semen. The function and significance of FBPs are unresolved, however, it has been suggested that they may facilitate folate uptake, e.g. during suckling. The present study shows that megalin, a large, multiligand endocytic receptor and member of the low-density lipoprotein-receptor family, is able...... to bind and mediate cellular uptake of FBP. Surface plasmon resonance analysis shows binding of bovine and human milk FBP to immobilized megalin, but not to low density lipoprotein receptor related protein. Binding of (125)I-labeled folate binding protein (FBP) to sections of kidney proximal tubule, known...

  15. Exotic decay: Transition from cluster mode to fission mode

    Indian Academy of Sciences (India)

    ' reaction were studied taking interacting barrier consisting of Coulomb and proximity potential. Calculated half-life time shows that some modes of decay are well within the present upper limit for measurements (1/2 < 1030 s). Cluster ...

  16. Mode control and mode conversion in nonlinear aluminum nitride waveguides.

    Science.gov (United States)

    Stegmaier, Matthias; Pernice, Wolfram H P

    2013-11-04

    While single-mode waveguides are commonly used in integrated photonic circuits, emerging applications in nonlinear and quantum optics rely fundamentally on interactions between modes of different order. Here we propose several methods to evaluate the modal composition of both externally and device-internally excited guided waves and discuss a technique for efficient excitation of arbitrary modes. The applicability of these methods is verified in photonic circuits based on aluminum nitride. We control modal excitation through suitably engineered grating couplers and are able to perform a detailed study of waveguide-internal second harmonic generation. Efficient and broadband power conversion between orthogonal polarizations is realized within an asymmetric directional coupler to demonstrate selective excitation of arbitrary higher-order modes. Our approach holds promise for applications in nonlinear optics and frequency up/down-mixing in a chipscale framework.

  17. Principal Metabolic Flux Mode Analysis.

    Science.gov (United States)

    Bhadra, Sahely; Blomberg, Peter; Castillo, Sandra; Rousu, Juho; Wren, Jonathan

    2018-02-06

    In the analysis of metabolism, two distinct and complementary approaches are frequently used: Principal component analysis (PCA) and stoichiometric flux analysis. PCA is able to capture the main modes of variability in a set of experiments and does not make many prior assumptions about the data, but does not inherently take into account the flux mode structure of metabolism. Stoichiometric flux analysis methods, such as Flux Balance Analysis (FBA) and Elementary Mode Analysis, on the other hand, are able to capture the metabolic flux modes, however, they are primarily designed for the analysis of single samples at a time, and not best suited for exploratory analysis on a large sets of samples. We propose a new methodology for the analysis of metabolism, called Principal Metabolic Flux Mode Analysis (PMFA), which marries the PCA and stoichiometric flux analysis approaches in an elegant regularized optimization framework. In short, the method incorporates a variance maximization objective form PCA coupled with a stoichiometric regularizer, which penalizes projections that are far from any flux modes of the network. For interpretability, we also introduce a sparse variant of PMFA that favours flux modes that contain a small number of reactions. Our experiments demonstrate the versatility and capabilities of our methodology. The proposed method can be applied to genome-scale metabolic network in efficient way as PMFA does not enumerate elementary modes. In addition, the method is more robust on out-of-steady steady-state experimental data than competing flux mode analysis approaches. Matlab software for PMFA and SPMFA and data set used for experiments are available in https://github.com/aalto-ics-kepaco/PMFA. sahely@iitpkd.ac.in, juho.rousu@aalto.fi, Peter.Blomberg@vtt.fi, Sandra.Castillo@vtt.fi. Detailed results are in Supplementary files. Supplementary data are available at https://github.com/aalto-ics-kepaco/PMFA/blob/master/Results.zip.

  18. Mode synthesizing atomic force microscopy and mode-synthesizing sensing

    Science.gov (United States)

    Passian, Ali; Thundat, Thomas George; Tetard, Laurene

    2013-05-17

    A method of analyzing a sample that includes applying a first set of energies at a first set of frequencies to a sample and applying, simultaneously with the applying the first set of energies, a second set of energies at a second set of frequencies, wherein the first set of energies and the second set of energies form a multi-mode coupling. The method further includes detecting an effect of the multi-mode coupling.

  19. Distributed Mode Filtering Rod Fiber Amplifier With Improved Mode Stability

    DEFF Research Database (Denmark)

    Laurila, Marko; Alkeskjold, Thomas Tanggaard; Broeng, Jes

    2012-01-01

    We report 216W of average output power from a photonic crystal rod fiber amplifier. We demonstrate 44% power improvement before onset of the mode instability by operating the rod fiber in a leaky guiding regime.......We report 216W of average output power from a photonic crystal rod fiber amplifier. We demonstrate 44% power improvement before onset of the mode instability by operating the rod fiber in a leaky guiding regime....

  20. Intelligence and musical mode preference

    DEFF Research Database (Denmark)

    Bonetti, Leonardo; Costa, Marco

    2016-01-01

    The relationship between fluid intelligence and preference for major–minor musical mode was investigated in a sample of 80 university students. Intelligence was assessed by the Raven’s Advanced Progressive Matrices. Musical mode preference was assessed by presenting 14 pairs of musical stimuli...... that varied only in mode. Mood and personality were assessed, respectively, by the Brief Mood Introspection Scale and the Big Five Questionnaire. Preference for minor stimuli was related positively and significantly to fluid intelligence and openness to experience. The results add evidence of individual...

  1. Carboplatin binding to histidine

    Science.gov (United States)

    Tanley, Simon W. M.; Diederichs, Kay; Kroon-Batenburg, Loes M. J.; Levy, Colin; Schreurs, Antoine M. M.; Helliwell, John R.

    2014-01-01

    Carboplatin is a second-generation platinum anticancer agent used for the treatment of a variety of cancers. Previous X-ray crystallographic studies of carboplatin binding to histidine (in hen egg-white lysozyme; HEWL) showed the partial conversion of carboplatin to cisplatin owing to the high NaCl concentration used in the crystallization conditions. HEWL co-crystallizations with carboplatin in NaBr conditions have now been carried out to confirm whether carboplatin converts to the bromine form and whether this takes place in a similar way to the partial conversion of carboplatin to cisplatin observed previously in NaCl conditions. Here, it is reported that a partial chemical transformation takes place but to a transplatin form. Thus, to attempt to resolve purely carboplatin binding at histidine, this study utilized co-crystallization of HEWL with carboplatin without NaCl to eliminate the partial chemical conversion of carboplatin. Tetragonal HEWL crystals co-crystallized with carboplatin were successfully obtained in four different conditions, each at a different pH value. The structural results obtained show carboplatin bound to either one or both of the N atoms of His15 of HEWL, and this particular variation was dependent on the concentration of anions in the crystallization mixture and the elapsed time, as well as the pH used. The structural details of the bound carboplatin molecule also differed between them. Overall, the most detailed crystal structure showed the majority of the carboplatin atoms bound to the platinum centre; however, the four-carbon ring structure of the cyclobutanedicarboxylate moiety (CBDC) remained elusive. The potential impact of the results for the administration of carboplatin as an anticancer agent are described. PMID:25195881

  2. Few-mode fiber technology for mode division multiplexing

    Science.gov (United States)

    Mori, Takayoshi; Sakamoto, Taiji; Wada, Masaki; Yamamoto, Takashi; Nakajima, Kazuhide

    2017-02-01

    We review recent progress on few-mode fiber (FMF) technologies for mode-division multiplexing (MDM) transmission. First, we introduce fibers for use without and with multiple-input multiple-output (MIMO) digital signal processing (DSP) to compensate for modal crosstalk, and briefly report recent work on FMF for use without/with a MIMO DSP system. We next discuss in detail a fiber for MIMO transmission systems, and show numerically that a graded-index core can flexibly tune the differential mode group delay (DMD) and a cladding trench can flexibly control the guiding mode number. We optimized the spacing of the core and trench. Accordingly, we can achieve a 6 LP (10 spatial) mode operation and a low DMD while preventing the high index difference that leads to manufacturing difficulties and any loss increase. We finally describe our experimental results for a 6 LP (10 spatial) mode transmission line for use in a C + L band wavelength-division multiplexing (WDM) MDM transmission with MIMO DSP.

  3. Unraveling the multivalent binding of a marine family 6 carbohydrate-binding module with its native laminarin ligand.

    Science.gov (United States)

    Jam, Murielle; Ficko-Blean, Elizabeth; Labourel, Aurore; Larocque, Robert; Czjzek, Mirjam; Michel, Gurvan

    2016-05-01

    Laminarin is an abundant brown algal storage polysaccharide. Marine microorganisms, such as Zobellia galactanivorans, produce laminarinases for its degradation, which are important for the processing of this organic matter in the ocean carbon cycle. These laminarinases are often modular, as is the case with ZgLamC which has an N-terminal GH16 module, a central family 6 carbohydrate-binding module (CBM) and a C-terminal PorSS module. To date, no studies have characterized a true marine laminarin-binding CBM6 with its natural carbohydrate ligand. The crystal structure of ZgLamCCBM6 indicates that this CBM has two clefts for binding sugar (variable loop site, VLS; and concave face site, CFS). The ZgLamCCBM6 VLS binds in an exo-manner and the CFS interacts in an endo-manner with laminarin. Isothermal titration calorimetry (ITC) experiments on native and mutant ZgLamCCBM6 confirm that these binding sites have different modes of recognition for laminarin, in agreement with the 'regional model' postulated for CBM6-binding modules. Based on ITC data and structural data, we propose a model of ZgLamCCBM6 interacting with different chains of laminarin in a multivalent manner, forming a complex cross-linked protein-polysaccharide network. PDB code 5FUI. © 2016 Federation of European Biochemical Societies.

  4. Fiber cavities with integrated mode matching optics.

    Science.gov (United States)

    Gulati, Gurpreet Kaur; Takahashi, Hiroki; Podoliak, Nina; Horak, Peter; Keller, Matthias

    2017-07-17

    In fiber based Fabry-Pérot Cavities (FFPCs), limited spatial mode matching between the cavity mode and input/output modes has been the main hindrance for many applications. We have demonstrated a versatile mode matching method for FFPCs. Our novel design employs an assembly of a graded-index and large core multimode fiber directly spliced to a single mode fiber. This all-fiber assembly transforms the propagating mode of the single mode fiber to match with the mode of a FFPC. As a result, we have measured a mode matching of 90% for a cavity length of ~400 μm. This is a significant improvement compared to conventional FFPCs coupled with just a single mode fiber, especially at long cavity lengths. Adjusting the parameters of the assembly, the fundamental cavity mode can be matched with the mode of almost any single mode fiber, making this approach highly versatile and integrable.

  5. Adaptive Structural Mode Control Project

    Data.gov (United States)

    National Aeronautics and Space Administration — M4 Engineering proposes the development of an adaptive structural mode control system. The adaptive control system will begin from a "baseline" dynamic model of the...

  6. Rotational Modes in Phononic Crystals

    Science.gov (United States)

    Wu, Ying; Peng, Pai; Mei, Jun

    2014-03-01

    We propose a lumped model for the rotational modes in two-dimensional phononic crystals comprised of square arrays of solid cylindrical scatterers in solid hosts. The model not only can reproduce the dispersion relations in a certain range with one fitted parameter, but also gives simple analytical expressions for the frequencies of the eigenmodes at the high symmetry points in the Brillouin zone. These expressions provide physical understandings of the rotational modes as well as certain translational and hybrid mode, and predict the presence of accidental degeneracy of the rotational and dipolar modes, which leads to a Dirac-like cone in the Brillouin zone center. Supported by KAUST Baseline Research Fund, National Natural Science Foundation of China (Grants No. 10804086 and No. 11274120), and the Fundamental Research Funds for the Central Universities (Grant No. 2012ZZ0077).

  7. Amplitude damping of vortex modes

    CSIR Research Space (South Africa)

    Dudley, Angela L

    2010-09-01

    Full Text Available An interferometer, mimicking an amplitude damping channel for vortex modes, is presented. Experimentally the action of the channel is in good agreement with that predicted theoretically. Since we can characterize the action of the channel on orbital...

  8. Novel Modes Workshop Summary Report

    Science.gov (United States)

    2015-12-01

    On December 2-3, 2014, the Federal Highway Administration's (FHWA's) Exploratory Advanced Research Program, with support from the John A. Volpe National Transportation Systems Center, convened the 2-day workshop "Novel Modes." It was held concurrentl...

  9. The Kuhnian mode of HPS

    DEFF Research Database (Denmark)

    Schindler, Samuel

    2013-01-01

    In this article I argue that a methodological challenge to an integrated history and philosophy of science approach put forth by Ronald Giere almost forty years ago can be met by what I call the Kuhnian mode of History and Philosophy of Science (HPS). Although in the Kuhnian mode of HPS norms about...... science are motivated by historical facts about scientific practice, the justifiers of the constructed norms are not historical facts. The Kuhnian mode of HPS therefore evades the naturalistic fallacy which Giere’s challenge is a version of. Against the backdrop of a discussion of Laudan’s normative...... naturalism I argue that the Kuhnian mode of HPS is a superior form of naturalism: it establishes contact to the practice of science without making itself dependent on its contingencies....

  10. Dendrimers Bind Antioxidant Polyphenols and cisPlatin Drug

    Science.gov (United States)

    Abderrezak, Amine; Bourassa, Philippe; Mandeville, Jean-Sebastian; Sedaghat-Herati, Reza; Tajmir-Riahi, Heidar-Ali

    2012-01-01

    Synthetic polymers of a specific shape and size play major role in drug delivery systems. Dendrimers are unique synthetic macromolecules of nanometer dimensions with a highly branched structure and globular shape with potential applications in gene and drug delivery. We examine the interaction of several dendrimers of different compositions mPEG-PAMAM (G3), mPEG-PAMAM (G4) and PAMAM (G4) with hydrophilic and hydrophobic drugs cisplatin, resveratrol, genistein and curcumin at physiological conditions. FTIR and UV-visible spectroscopic methods as well as molecular modeling were used to analyse drug binding mode, the binding constant and the effects of drug complexation on dendrimer stability and conformation. Structural analysis showed that cisplatin binds dendrimers in hydrophilic mode via Pt cation and polymer terminal NH2 groups, while curcumin, genistein and resveratrol are located mainly in the cavities binding through both hydrophobic and hydrophilic contacts. The overall binding constants of durg-dendrimers are ranging from 102 M−1 to 103 M−1. The affinity of dendrimer binding was PAMAM-G4>mPEG-PAMAM-G4>mPEG-PAMAM-G3, while the order of drug-polymer stability was curcumin>cisplatin>genistein>resveratrol. Molecular modeling showed larger stability for genisten-PAMAM-G4 (ΔG = −4.75 kcal/mol) than curcumin-PAMAM-G4 ((ΔG = −4.53 kcal/mol) and resveratrol-PAMAM-G4 ((ΔG = −4.39 kcal/mol). Dendrimers might act as carriers to transport hydrophobic and hydrophilic drugs. PMID:22427960

  11. Examination of the 'web mode effect'

    DEFF Research Database (Denmark)

    Clement, Sanne Lund; Shamshiri-Petersen, Ditte

    for different modes, and mode differences then are influenced by stratification differences. In both cases the real mode differences are nearly impossible to determine and remains rather speculative. The purpose of this contribution is to examine potential “web mode effects” in mixed-mode surveys. Compared...

  12. The Fifth Mode of Representation

    DEFF Research Database (Denmark)

    Hansen, Per Krogh; Behrendt, Poul Olaf

    2011-01-01

    “The fifth mode of representation: Ambiguous voices in unreliable third person narration”. Sammen med Poul Behrendt. In Per Krogh Hansen, Stefan Iversen, Henrik Skov Nielsen og Rolf Reitan (red.): Strange Voices. Walter de Gruyter, Berlin & New York......“The fifth mode of representation: Ambiguous voices in unreliable third person narration”. Sammen med Poul Behrendt. In Per Krogh Hansen, Stefan Iversen, Henrik Skov Nielsen og Rolf Reitan (red.): Strange Voices. Walter de Gruyter, Berlin & New York...

  13. An interdecadal American rainfall mode

    Science.gov (United States)

    Jury, Mark R.

    2009-04-01

    Low-frequency climate variability across the American continents and surrounding oceans is analyzed by application of singular value decomposition (SVD) to gauge-based rainfall and environmental anomaly fields in the period 1901-2002. A 5-year filter is used to maintain a focus on interdecadal cycles. The rainfall regime of particular interest (mode 1) is when West Africa and the Caribbean share positive loading and North and South America share negative loading. Wavelet cospectral energy is found at ˜8, 24, and 50 years for Caribbean/West African zones and 16 and 32 years for North/South America. West Africa and South America exhibit antiphase multidecadal variability, while North America and the Caribbean rainfall exhibit quasi-decadal cycles. The rainfall associations are nonstationary. In the early 1900s, Caribbean and South American rainfall were antiphase. Since 1930 low-frequency oscillations of North American (West African) rainfall have been positively (negatively) associated with South America. Low-frequency oscillations of North American rainfall have been consistently antiphase with respect to Caribbean rainfall; however, West Africa rainfall fluctuations have been in phase with the Caribbean more in the period 1920-1950 than at other times. Hemispheric-scale environmental SVD patterns and scores were compared with the leading rainfall modes. The north-south gradient modes in temperature are influential in respect of mode 1 rainfall, while east-west gradients relate to mode 2 (northern Brazil) rainfall. The ability of the GFDL2.1 coupled (ocean-atmosphere) general circulation model to represent interdecadal rainfall modes in the 20th century was evaluated. While mode 2 is reproduced, mode 1 remains elusive.

  14. Overall carbohydrate-binding properties of Castanea crenata agglutinin (CCA).

    Science.gov (United States)

    Nomura, Keiichi; Takahashi, Nobuyuki; Hirose, Masaaki; Nakamura, Sachiko; Yagi, Fumio

    2005-09-05

    The carbohydrate-binding properties of Castanea crenata agglutinin (CCA) were investigated by an enzyme-linked lectin absorbent assay. The binding ability of each carbohydrate was compared using IC(50) values. CCA exhibited mannose/glucose specificity, as observed with many mannose-binding jacalin-related lectins. For oligosaccharides containing glucose, it has been shown that the degree of polymerization and the linkage mode of glucose residues have no effect on CCA-carbohydrate interaction; thus, only the non-reducing end glucose unit in glucooligosaccharides may be involved in the interaction with CCA. Among mannooligosaccharides, CCA strongly recognized alpha-(1-->3)-D-Man-[alpha-D-Man-(1-->6)]-D-Man, which is a core in N-linked carbohydrate chains. By considering the results with glycoproteins, it is likely that CCA binds preferentially to mono- or non-sialylated biantennary carbohydrate chains. We also obtained K(d) values by analysis of the dependency of the IC(50) on CCA concentration, based on the hypothesis that CCA has a single binding site or two equivalent binding sites. The estimated K(d) values for mannose, glucose and alpha-(1-->3)-D-Man-[alpha-D-Man-(1-->6)]-D-Man were 2.39, 7.19 and 0.483 mM, respectively. The relative binding abilities showed good agreement with the relative inhibition intensities. Isothermal calorimetric titration was carried out to directly estimate the dissociation constants of CCA for mannose and for alpha-D-Man-(1-->3)-D-Man. The values were 2.34 mM for mannose and 0.507 mM alpha-D-Man-(1-->3)-D-Man. These results suggest that the relative inhibition intensity represents the ratio of K(d) values and that CCA has a single or two equivalent binding sites.

  15. Spectroscopic investigations on the complexation of Cm(III) and Eu(III) with organic model ligands and their binding mode in human urine (in vitro); Spektroskopische Untersuchungen zur Komplexbildung von Cm(III) und Eu(III) mit organischen Modellliganden sowie ihrer chemischen Bindungsform in menschlichem Urin (in vitro)

    Energy Technology Data Exchange (ETDEWEB)

    Heller, Anne

    2011-10-26

    In case of incorporation, trivalent actinides (An(III)) and lanthanides (Ln(III)) pose a serious health risk to humans. An(III) are artificial, highly radioactive elements which are mainly produced during the nuclear fuel cycle in nuclear power plants. Via hazardous accidents or nonprofessional storage of radioactive waste, they can be released in the environment and enter the human food chain. In contrast, Ln(III) are nonradioactive, naturally occurring elements with multiple applications in technique and medicine. Consequently it is possible that humans get in contact and incorporate both, An(III) and Ln(III). Therefore, it is of particular importance to elucidate the behaviour of these elements in the human body. While macroscopic processes such as distribution, accumulation and excretion are studied quite well, knowledge about the chemical binding form (speciation) of An(III) and Ln(III) in various body fluids is still sparse. In the present work, for the first time, the speciation of Cm(III) and Eu(III) in natural human urine (in vitro) has been investigated spectroscopically and the formed complex identified. For this purpose, also basic investigations on the complex formation of Cm(III) and Eu(III) in synthetic model urine as well as with the urinary relevant, organic model ligands urea, alanine, phenylalanine, threonine and citrate have been performed and the previously unknown complex stability constants determined. Finally, all experimental results were compared to literature data and predictions calculated by thermodynamic modelling. Since both, Cm(III) and Eu(III), exhibit unique luminescence properties, particularly the suitability of time-resolved laser-induced fluorescence spectroscopy (TRLFS) could be demonstrated as a method to investigate these metal ions in untreated, complex biofluids. The results of this work provide new scientific findings on the biochemical reactions of An(III) and Ln(III) in human body fluids on a molecular scale and

  16. Induced circular dichroism as a tool to investigate the binding of drugs to carrier proteins: Classic approaches and new trends.

    Science.gov (United States)

    Tedesco, Daniele; Bertucci, Carlo

    2015-09-10

    Induced circular dichroism (ICD) is a spectroscopic phenomenon that provides versatile and useful methods for characterizing the structural and dynamic properties of the binding of drugs to target proteins. The understanding of biorecognition processes at the molecular level is essential to discover and validate new pharmacological targets, and to design and develop new potent and selective drugs. The present article reviews the main applications of ICD to drug binding studies on serum carrier proteins, going from the classic approaches for the derivation of drug binding parameters and the identification of binding sites, to an overview of the emerging trends for the characterization of binding modes by means of quantum chemical (QC) techniques. The advantages and limits of the ICD methods for the determination of binding parameters are critically reviewed; the capability to investigate the binding interactions of drugs and metabolites to their target proteins is also underlined, as well as the possibility of characterizing the binding sites to obtain a complete picture of the binding mechanism and dynamics. The new applications of ICD methods to identify stereoselective binding modes of drug/protein complexes are then reviewed with relevant examples. The combined application of experimental ICD spectroscopy and QC calculations is shown to identify qualitatively the bound conformations of ligands to target proteins even in the absence of a detailed structure of the binding sites, either obtained from experimental X-ray crystallography and NMR measurements or from computational models of the complex. Copyright © 2015 Elsevier B.V. All rights reserved.

  17. Factors influencing the specificity of inhibitor binding to the human and malaria parasite dihydroorotate dehydrogenases.

    Science.gov (United States)

    Bedingfield, Paul T P; Cowen, Deborah; Acklam, Paul; Cunningham, Fraser; Parsons, Mark R; McConkey, Glenn A; Fishwick, Colin W G; Johnson, A Peter

    2012-06-28

    The de novo pyrimidine biosynthesis enzyme dihydroorotate dehydrogenase is an emerging drug target for the treatment of malaria. In this context a key property of Plasmodium falciparum DHODH (PfDHODH) is that it can be selectively inhibited over its human homologue (HsDHODH). However, HsDHODH is also a validated drug target for autoimmune diseases such as arthritis. Here a series of novel inhibitors is described that includes compounds that switch specificity between the two enzymes as a result of small alterations in chemical structure. Structure-activity relationship (SAR), crystallography, docking, and mutagenesis studies are used to examine the binding modes of the compounds within the two enzymes and to reveal structural changes induced by inhibitor binding. Within this series, compounds with therapeutically relevant HsDHODH activity are described and their binding modes characterized using X-ray crystallography, which reveals a novel conformational shift within the inhibitor binding site.

  18. Normal modes and mode transformation of pure electron vortex beams.

    Science.gov (United States)

    Thirunavukkarasu, G; Mousley, M; Babiker, M; Yuan, J

    2017-02-28

    Electron vortex beams constitute the first class of matter vortex beams which are currently routinely produced in the laboratory. Here, we briefly review the progress of this nascent field and put forward a natural quantum basis set which we show is suitable for the description of electron vortex beams. The normal modes are truncated Bessel beams (TBBs) defined in the aperture plane or the Fourier transform of the transverse structure of the TBBs (FT-TBBs) in the focal plane of a lens with the said aperture. As these modes are eigenfunctions of the axial orbital angular momentum operator, they can provide a complete description of the two-dimensional transverse distribution of the wave function of any electron vortex beam in such a system, in analogy with the prominent role Laguerre-Gaussian (LG) beams played in the description of optical vortex beams. The characteristics of the normal modes of TBBs and FT-TBBs are described, including the quantized orbital angular momentum (in terms of the winding number l) and the radial index p>0. We present the experimental realization of such beams using computer-generated holograms. The mode analysis can be carried out using astigmatic transformation optics, demonstrating close analogy with the astigmatic mode transformation between LG and Hermite-Gaussian beams.This article is part of the themed issue 'Optical orbital angular momentum'. © 2017 The Author(s).

  19. Investigating the Mode Structure of the Weakly Coherent Mode

    Science.gov (United States)

    Golfinopoulos, T.; Labombard, B.; Hubbard, A.; Hughes, J. W.; Whyte, D.; Granetz, R.; Davis, E. M.; Edlund, E.; Ennever, P.; Greenwald, M.; Marmar, E.; Porkolab, M.; Wolfe, S. M.; Wukitch, S. J.; Alcator C-Mod Team

    2017-10-01

    The Weakly Coherent Mode (WCM, 200-500 kHz, k⊥ρs < 0.1) is an edge phenomenon associated with I-mode, a steady state, ELM-free confinement regime that has been observed on the Alcator C-Mod, ASDEX-Upgrade, and DIII-D tokamaks. I-mode is characterized by high particle flux, creating a separation of transport channels that leads to the development of a temperature pedestal, but not a density pedestal. The WCM is thought to contribute to this increased particle flux, though its precise role in regulating edge transport is not well-understood. Here, we investigate the structure of the WCM, particularly regarding poloidal asymmetry, using data from poloidally- and toroidally-arrayed Mirnov coils, as well as phase contrast imaging, with radial profiles of Te, ne, and Φ in the scrape-off layer provided by the Mirror Langmuir Probe. The WCM phenomenology is then compared to that of the Quasi-Coherent Mode, the edge fluctuation responsible for exhausting impurities in the Enhanced Dα H-mode. This work is supported by USDoE award DE-FC02-99ER54512.

  20. Empirically Unbinding the Double Bind.

    Science.gov (United States)

    Olson, David H.

    The theoretical concept of the double bind and the possibilities for researching it are discussed. The author has observed that theory and research, which should be reciprocal and mutually beneficial, have been working, as concerns the double bind, at odds with one another. Two approaches to empirically investigating the concept are considered via…

  1. Managing a Library Binding Program.

    Science.gov (United States)

    Merrill-Oldham, Jan

    Library binding is one of the activities typically included in newly created preservation departments, but librarians continue to discover that transforming a traditional binding program into one that better meets preservation objectives requires considerable investment of time. This resource guide is intended to help libraries review their…

  2. The binding sites for benztropines and dopamine in the dopamine transporter overlap

    DEFF Research Database (Denmark)

    Jensen, Heidi Bisgaard; Larsen, M Andreas B; Mazier, Sonia

    2011-01-01

    Analogs of benztropines (BZTs) are potent inhibitors of the dopamine transporter (DAT) but are less effective than cocaine as behavioral stimulants. As a result, there have been efforts to evaluate these compounds as leads for potential medication for cocaine addiction. Here we use computational...... with a larger decrease in the affinity for BZT than for JHW007. Summarized, our data suggest that BZTs display a classical competitive binding mode with binding sites overlapping those of cocaine and dopamine....

  3. Optically Mediated Hybridization Between Two Mechanical Modes

    CERN Document Server

    Shkarin, A B; Hoch, S W; Deutsch, C; Reichel, J; Harris, J G E

    2013-01-01

    In this paper we study a system consisting of two nearly degenerate mechanical modes that couple to a single mode of an optical cavity. We show that this coupling leads to nearly complete (99.5%) hybridization of the two mechanical modes into a bright mode that experiences strong optomechanical interactions and a dark mode that experiences almost no optomechanical interactions. We use this hybridization to transfer energy between the mechanical modes with 40% efficiency.

  4. Challenges in higher order mode Raman amplifiers

    DEFF Research Database (Denmark)

    Rottwitt, Karsten; Nielsen, Kristian; Friis, Søren Michael Mørk

    2015-01-01

    A higher order Raman amplifier model that take random mode coupling into account ispresented. Mode dependent gain and signal power fluctuations at the output of the higher order modeRaman amplifier are discussed......A higher order Raman amplifier model that take random mode coupling into account ispresented. Mode dependent gain and signal power fluctuations at the output of the higher order modeRaman amplifier are discussed...

  5. Tapping mode microwave impedance microscopy

    KAUST Repository

    Lai, K.

    2009-01-01

    We report tapping mode microwave impedance imaging based on atomic force microscope platforms. The shielded cantilever probe is critical to localize the tip-sample interaction near the tip apex. The modulated tip-sample impedance can be accurately simulated by the finite-element analysis and the result agrees quantitatively to the experimental data on a series of thin-film dielectric samples. The tapping mode microwave imaging is also superior to the contact mode in that the thermal drift in a long time scale is totally eliminated and an absolute measurement on the dielectric properties is possible. We demonstrated tapping images on working nanodevices, and the data are consistent with the transport results. © 2009 American Institute of Physics.

  6. Macroscopic (and microscopic massless modes

    Directory of Open Access Journals (Sweden)

    Michael C. Abbott

    2015-05-01

    Full Text Available We study certain spinning strings exploring the flat directions of AdS3×S3×S3×S1, the massless sector cousins of su(2 and sl(2 sector spinning strings. We describe these, and their vibrational modes, using the D(2,1;α2 algebraic curve. By exploiting a discrete symmetry of this structure which reverses the direction of motion on the spheres, and alters the masses of the fermionic modes s→κ−s, we find out how to treat the massless fermions which were previously missing from this formalism. We show that folded strings behave as a special case of circular strings, in a sense which includes their mode frequencies, and we are able to recover this fact in the worldsheet formalism. We use these frequencies to calculate one-loop corrections to the energy, with a version of the Beisert–Tseytlin resummation.

  7. Quasiadiabatic modes from viscous inhomogeneities

    CERN Document Server

    Giovannini, Massimo

    2016-04-20

    The viscous inhomogeneities of a relativistic plasma determine a further class of entropic modes whose amplitude must be sufficiently small since curvature perturbations are observed to be predominantly adiabatic and Gaussian over large scales. When the viscous coefficients only depend on the energy density of the fluid the corresponding curvature fluctuations are shown to be almost adiabatic. After addressing the problem in a gauge-invariant perturbative expansion, the same analysis is repeated at a non-perturbative level by investigating the nonlinear curvature inhomogeneities induced by the spatial variation of the viscous coefficients. It is demonstrated that the quasiadiabatic modes are suppressed in comparison with a bona fide adiabatic solution. Because of its anomalously large tensor to scalar ratio the quasiadiabatic mode cannot be a substitute for the conventional adiabatic paradigm so that, ultimately, the present findings seems to exclude the possibility of a successful accelerated dynamics solely...

  8. A Survey of Plants with Anti-HIV Active Compounds and their Modes ...

    African Journals Online (AJOL)

    Administrator

    jacalin-related lectin that binds to glycosylated viral envelopes blocked HIV-1 entry into cells , and. Phytolacca americana pokeweed antiviral protein (PAP), a 29 KDa ribosome-inactivating protein that. 46 removes adenine from rRNA was found to be a potent microbicide . Table 1: Plants with active compounds and modes ...

  9. Soft mode and acoustic mode ferroelectric properties of deuterated ...

    Indian Academy of Sciences (India)

    SO4 crystal by a theoretical model which is extended with two sublattice pseudospin lattice coupled mode model by adding third, fourth and fifth order phonon anharmonic interaction terms as well as external electric field term in the crystal ...

  10. Thermodynamic description of peptide adsorption on mixed-mode resins.

    Science.gov (United States)

    Chilamkurthi, Sreekanth; Sevillano, David Méndez; Albers, Leonoor H G; Sahoo, Manas Ranjan; Verheijen, Peter J T; van der Wielen, Luuk A M; den Hollander, Jeroen L; Ottens, Marcel

    2014-05-09

    In this work the adsorption of tri-peptides on a mixed-mode resin was studied using isocratic pulse response experiments. Various salt concentration, temperature and pH combinations were used to measure retention times of several tri-peptides. The experiments were evaluated according to an extension of the stoichiometric displacement model and the steric mass action model of protein-ligand binding. The application of this model in the understanding of mixed mode adsorption process is discussed. A unique set of meaningful thermodynamic parameters was obtained for each resin-peptide-temperature and resin-peptide-pH combination. Finally it was shown that these thermodynamic parameters can be used in defining quantitative relationships within the framework of extra thermodynamic relationships. Copyright © 2014 Elsevier B.V. All rights reserved.

  11. Transverse magnetic mode along THz waveguides with biased superlattices

    Energy Technology Data Exchange (ETDEWEB)

    Aceituno, P. [Dpto. Fisica Basica, Universidad de La Laguna, La Laguna, 38206 Tenerife (Spain)], E-mail: paceitun@ull.es; Hernandez-Cabrera, A. [Dpto. Fisica Basica, Universidad de La Laguna, La Laguna, 38206 Tenerife (Spain); Vasko, F.T. [Institute of Semiconductor Physics, NAS Ukraine, Pr. Nauki 41, Kiev 03028 (Ukraine)

    2008-05-15

    We study the propagation of transverse magnetic modes arising from a waveguide consisting on a GaAs-based superlattice located at vacuum-dielectric interface. The transverse mode is generated by the ultrafast intersubband response of the superlattice subjected to a high-frequency electric field. The superlattice is also subjected to a homogeneous bias potential to get a biased superlattice with equipopulated levels. The heterostructure is analyzed through the tight-binding approximation, and considering the level broadening caused by different scattering processes (homogeneous and inhomogeneous broadening mechanisms). We pay special attention to the dispersion relations of the complex dielectric permittivity because of real and imaginary parts of this function play a key role in wide miniband superlattices.

  12. Nonlinear oscillations of TM-mode gyrotrons

    Science.gov (United States)

    Chang, Tsun-Hsu; Yao, Hsin-Yu; Su, Bo-Yuan; Huang, Wei-Chen; Wei, Bo-Yuan

    2017-12-01

    This study investigates the interaction between the relativistic electrons and the waves in cavities with fixed field profiles. Both the transverse electric (TE) and the transverse magnetic (TM) cavity modes are examined, including three first-axial modes, TE011, TM011, and TM111, and two zero-axial modes, TM010 and TM110. The first-axial modes have the same resonant frequency, so a direct comparison can be made. By sweeping the electron pitch factor (α) and the electron transit angle (Θ), the optimal converting efficiency of TM modes occurs at α = 1.5 and Θ = 1.5π, unlike the TE mode of α = 2.0 and Θ = 1.0π. The converting efficiencies of both the first-axial TM modes are much lower than that of TE011 mode. The starting currents of TM011 and TM111 modes are four times higher than that of TE011 mode, indicating that these two TM modes are very difficult to oscillate. This evidences that under the traditional operating conditions, the TM-mode gyrotrons are insignificant. However, the two unique, zero-axial TM modes have relatively high converting efficiency. The highest converting efficiency of TM110 is 27.4%, the same value as that of TE011 mode. The starting currents of TM110 mode and TE011 mode are at the same level. The results suggest that some TM-mode gyrotron oscillators are feasible and deserve further theoretical and experimental studies.

  13. Natural history of S-adenosylmethionine-binding proteins

    Directory of Open Access Journals (Sweden)

    Mushegian Arcady R

    2005-10-01

    Full Text Available Abstract Background S-adenosylmethionine is a source of diverse chemical groups used in biosynthesis and modification of virtually every class of biomolecules. The most notable reaction requiring S-adenosylmethionine, transfer of methyl group, is performed by a large class of enzymes, S-adenosylmethionine-dependent methyltransferases, which have been the focus of considerable structure-function studies. Evolutionary trajectories of these enzymes, and especially of other classes of S-adenosylmethionine-binding proteins, nevertheless, remain poorly understood. We addressed this issue by computational comparison of sequences and structures of various S-adenosylmethionine-binding proteins. Results Two widespread folds, Rossmann fold and TIM barrel, have been repeatedly used in evolution for diverse types of S-adenosylmethionine conversion. There were also cases of recruitment of other relatively common folds for S-adenosylmethionine binding. Several classes of proteins have unique unrelated folds, specialized for just one type of chemistry and unified by the theme of internal domain duplications. In several cases, functional divergence is evident, when evolutionarily related enzymes have changed the mode of binding and the type of chemical transformation of S-adenosylmethionine. There are also instances of functional convergence, when biochemically similar processes are performed by drastically different classes of S-adenosylmethionine-binding proteins. Comparison of remote sequence similarities and analysis of phyletic patterns suggests that the last universal common ancestor of cellular life had between 10 and 20 S-adenosylmethionine-binding proteins from at least 5 fold classes, providing for S-adenosylmethionine formation, polyamine biosynthesis, and methylation of several substrates, including nucleic acids and peptide chain release factor. Conclusion We have observed several novel relationships between families that were not known to be

  14. Equine sperm-neutrophil binding.

    Science.gov (United States)

    Alghamdi, Abdorrahman S; Madill, Scott; Foster, Douglas N; Troedsson, Mats H T

    2015-04-01

    When mares are inseminated repeatedly, protein molecules from the seminal plasma (SP) prevent sperm-neutrophil binding and reduced fertility. The molecule(s) responsible for sperm-neutrophil binding is not known and the identification of beneficial SP proteins is complicated by their large numbers and abundant variation. We examined several important aspects of sperm-neutrophil binding to ultimately facilitate the identification and isolation of the molecule(s) responsible. First, we raised anti-equine P-selectin antibodies to determine the involvement of this adhesion molecule in sperm-neutrophil binding. While these antibodies identified equine P-selectin, they did not inhibit sperm-neutrophil binding. However, acrosome-reacted equine sperm expressed a molecule similar to the ligand recognition unit of P-selectin. Second, we attempted to characterize SP protein binding to equine sperm and gauge their affinity. Biotinylated SP proteins were incubated with fresh sperm, washed over a viscous medium, electrophoresed, and probed with avidin. Several SP proteins bound to sperm with a strong affinity to withstand these treatments. This finding may prove valuable for future attempts to identify and characterize specific SP molecules. Lastly, we compared the secretions from male sex organs/glands on sperm motility, sperm-neutrophil binding, and their protein profile. We expected fewer proteins from individual organs/glands, which would facilitate isolation and identification of target molecules. While each secretion had a varying effect on motility and sperm-neutrophil binding, the protein profile was as complex as that seen in whole SP, indicating that collection of proteins from individual sources will not facilitate this work. Together, these experiments answer several important questions related to sperm-neutrophil binding, sperm-SP proteins interaction, and the complexity of the SP proteome. © 2015 by the Society for the Study of Reproduction, Inc.

  15. Screening and collective modes in disordered graphene antidot lattices

    DEFF Research Database (Denmark)

    Yuan, Shengjun; Jin, Fengping; Roldan, Rafael

    2013-01-01

    The excitation spectrum and the collective modes of graphene antidot lattices (GALs) are studied in the context of a π-band tight-binding model. The dynamical polarizability and dielectric function are calculated within the random-phase approximation. The effect of different kinds of disorder......, such as geometric and chemical disorder, are included in our calculations. We highlight the main differences of GALs with respect to single-layer graphene (SLG). Our results show that, in addition to the well-understood bulk plasmon in doped samples, interband plasmons appear in GALs. We further show...

  16. A modern mode of activation for nucleic acid enzymes.

    Directory of Open Access Journals (Sweden)

    Dominique Lévesque

    2007-07-01

    Full Text Available Through evolution, enzymes have developed subtle modes of activation in order to ensure the sufficiently high substrate specificity required by modern cellular metabolism. One of these modes is the use of a target-dependent module (i.e. a docking domain such as those found in signalling kinases. Upon the binding of the target to a docking domain, the substrate is positioned within the catalytic site. The prodomain acts as a target-dependent module switching the kinase from an off state to an on state. As compared to the allosteric mode of activation, there is no need for the presence of a third partner. None of the ribozymes discovered to date have such a mode of activation, nor does any other known RNA. Starting from a specific on/off adaptor for the hepatitis delta virus ribozyme, that differs but has a mechanism reminiscent of this signalling kinase, we have adapted this mode of activation, using the techniques of molecular engineering, to both catalytic RNAs and DNAs exhibiting various activities. Specifically, we adapted three cleaving ribozymes (hepatitis delta virus, hammerhead and hairpin ribozymes, a cleaving 10-23 deoxyribozyme, a ligating hairpin ribozyme and an artificially selected capping ribozyme. In each case, there was a significant gain in terms of substrate specificity. Even if this mode of control is unreported for natural catalytic nucleic acids, its use needs not be limited to proteinous enzymes. We suggest that the complexity of the modern cellular metabolism might have been an important selective pressure in this evolutionary process.

  17. Binding and thermodynamics of REV peptide-ctDNA interaction.

    Science.gov (United States)

    Upadhyay, Santosh Kumar

    2017-03-01

    The thermodynamics of DNA-ligand binding is important as it provides useful information to understand the details of binding processes. HIV-1 REV response element (RRE) located in the env coding region of the viral genome is reported to be well conserved across different HIV-1 isolates. In this study, the binding characteristics of Calf thymus DNA (ctDNA) and REV peptide from HIV-1 were investigated using spectroscopic (UV-visible, fluorescence, and circular dichroism (CD)) and isothermal titration calorimetric (ITC) techniques. Thermal stability and ligand binding properties of the ctDNA revealed that native ctDNA had a Tm of 75.5 °C, whereas the ctDNA-REV peptide complex exhibited an incremental shift in the Tm by 8 °C, indicating thermal stability of the complex. CD data indicated increased ellipticity due to large conformational changes in ctDNA molecule upon binding with REV peptide and two binding stoichiometric modes are apparent. The ctDNA experienced condensation due to large conformational changes in the presence of REV peptide and positive B→Ψ transition was observed at higher molar charge ratios. Fluorescence studies performed at several ligand concentrations revealed a gradual decrease in the fluorescence intensity of EtBr-bound ctDNA in response to increasing ligand concentrations. The fluorescence data further confirmed two stoichiometric modes of binding for ctDNA-REV peptide complex as previously observed with CD studies. The binding enthalpies were determined using ITC in the temperature range of 293 K-308 K. The ITC binding isotherm was exothermic at all temperatures examined, with low ΔH values indicating that the ctDNA-REV peptide interaction is driven largely by entropy. The heat capacity change (ΔCp ) was insignificant, an unusual finding in the area of DNA-peptide interaction studies. The variation in the values obtained for ΔH, ΔS, and ΔG with temperature further suggests that ctDNA-REV peptide interaction is entropically

  18. Dually-mode-locked ND: YAG laser

    Science.gov (United States)

    Osmundson, J.; Rowe, E.; Santarpia, D.

    1974-01-01

    Mode-locking is stabilized effectively by conventional loss-modulator and phase-modulator, mode-locking elements placed in laser cavity in optical series with one another. Resulting dually-mode-locked system provides pulses with constant phase relative to mode-lock drive signal without presence of relaxation oscillation noise.

  19. Optical binding of two microparticles levitated in vacuum

    Science.gov (United States)

    Arita, Yoshihiko; Wright, Ewan M.; Dholakia, Kishan

    2017-04-01

    Optical binding refers to an optically mediated inter-particle interaction that creates new equilibrium positions for closely spaced particles [1-5]. Optical binding of mesoscopic particles levitated in vacuum can pave the way towards the realisation of a large scale quantum bound array in cavity-optomechanics [6-9]. Recently we have demonstrated trapping and rotation of two mesoscopic particles in vacuum using a spatial-light-modulator-based approach to trap more than one particle, induce controlled rotation of individual particles, and mediate interparticle separation [10]. By trapping and rotating two vaterite particles, we observe intensity modulation of the scattered light at the sum and difference frequencies with respect to the individual rotation rates. This first demonstration of optical interference between two microparticles in vacuum has lead to a platform to explore optical binding. Here we demonstrate for the first time optically bound two microparticles mediated by light scattering in vacuum. We investigate autocorrelations between the two normal modes of oscillation, which are determined by the centre-of-mass and the relative positions of the two-particle system. In situ determination of the optical restoring force acting on the bound particles are based on measurement of the oscillation frequencies of the autocorrelation functions of the two normal modes, thereby providing a powerful and original platform to explore multiparticle entanglement in cavity-optomechanics.

  20. Modeling of ligand binding to dopamine D2 receptor

    Directory of Open Access Journals (Sweden)

    Ostopovici-Halip Liliana

    2014-01-01

    Full Text Available The dopaminic receptors have been for long time the major targets for developing new small molecules with high affinity and selectivity to treat psychiatric disorders, neurodegeneration, drug abuse, and other therapeutic areas. In the absence of a 3D structure for the human D2 dopamine (HDD2 receptor, the efforts for discovery and design of new potential drugs rely on comparative models generation, docking and pharmacophore development studies. To get a better understanding of the HDD2 receptor binding site and the ligand-receptor interactions a homology model of HDD2 receptor based on the X-ray structure of β2-adrenergic receptor has been built and used to dock a set of partial agonists of HDD2 receptor. The main characteristics of the binding mode for the HDD2 partial agonists set are given by the ligand particular folding and a complex network of contacts represented by stacking interactions, salt bridge and hydrogen bond formation. The characterization of the partial agonist binding mode at HDD2 receptor provide the needed information to generate pharmacophore models which represent essential information in the future virtual screening studies in order to identify new potential HDD2 partial agonists.

  1. Rubble Mound Breakwater Failure Modes

    DEFF Research Database (Denmark)

    Burcharth, H. F.; Z., Liu

    1995-01-01

    The RMBFM-Project (Rubble Mound Breakwater Failure Modes) is sponsored by the Directorate General XII of the Commission of the European Communities under the Contract MAS-CT92- 0042, with the objective of contributing to the development of rational methods for the design of rubble mound breakwate...

  2. Mode structure of active resonators

    NARCIS (Netherlands)

    Ernst, G.J.; Witteman, W.J.

    1973-01-01

    An analysis is made of the mode structure of lasers when the interaction with the active medium is taken into account. We consider the combined effect of gain and refractive-index variations for arbitrary mirror configurations. Using a dimensionless round-trip matrix for a medium with a quadratic

  3. Single-mode optical fibres

    CERN Document Server

    Cancellieri, G

    1991-01-01

    This book describes signal propagation in single-mode optical fibres for telecommunication applications. Such description is based on the analysis of field propagation, considering waveguide properties and also some of the particular characteristics of the material fibre. The book covers such recent advances as, coherent transmissions; optical amplification; MIR fibres; polarization maintaining; polarization diversity and photon counting.

  4. Theory of Modes and Impulses

    Science.gov (United States)

    Apsche, Jack A.

    2005-01-01

    In his work on the Theory of Modes, Beck (1996) suggested that there were flaws with his cognitive theory. He suggested that though there are shortcomings to his cognitive theory, there were not similar shortcomings to the practice of Cognitive Therapy. The author suggests that if there are shortcomings to cognitive theory the same shortcomings…

  5. Cap-binding complex (CBC)

    National Research Council Canada - National Science Library

    Gonatopoulos-Pournatzis, Thomas; Cowling, Victoria H

    2014-01-01

    .... One of the most important mediators of 7mG functions is CBC (cap-binding complex). CBC has a key role in several gene expression mechanisms, including transcription, splicing, transcript export and translation...

  6. Integrin binding: Sticking around vessels

    Science.gov (United States)

    Blatchley, Michael R.; Gerecht, Sharon

    2017-09-01

    A study demonstrates that controlled integrin binding on a biomaterial was capable of promoting vascular cell sprouting and formation of a non-leaky blood vessel network in a healthy and diseased state.

  7. HIV: cell binding and entry

    National Research Council Canada - National Science Library

    Wilen, Craig B; Tilton, John C; Doms, Robert W

    2012-01-01

    The first step of the human immunodeficiency virus (HIV) replication cycle-binding and entry into the host cell-plays a major role in determining viral tropism and the ability of HIV to degrade the human immune system...

  8. Creative Double Bind in Oral Interpretation.

    Science.gov (United States)

    Peterson, Eric E.; Langellier, Kristin M.

    1982-01-01

    Explains how oral interpretation is uniquely communicative and how the double bind theory of communication can include creativity. Discusses (1) double bind and oral interpretation, (2) creating aesthetic text, and (3) the performance of double bind. (PD)

  9. Two-mode Nonlinear Coherent States

    OpenAIRE

    Wang, Xiao-Guang

    2000-01-01

    Two-mode nonlinear coherent states are introduced in this paper. The pair coherent states and the two-mode Perelomov coherent states are special cases of the two-mode nonlinear coherent states. The exponential form of the two-mode nonlinear coherent states is given. The photon-added or photon-subtracted two-mode nonlinear coherent states are found to be two-mode nonlinear coherent states with different nonlinear functions. The parity coherent states are introduced as examples of two-mode nonl...

  10. Biodiscovery of Aluminum Binding Peptides

    Science.gov (United States)

    2013-08-01

    conjunction with organic-based targets, such as protein toxins or carbon nanotubes . However, this technology has been expanded for use with inorganic...conjunction with organic-based targets, such as protein toxins or carbon nanotubes . However, this technology has been expanded for use with inorganic targets...8] Rothenstein, D. C., et al., "Isolation of ZnO -binding 12-mer peptides and determination of their binding epitopes by NMR spectroscopy," J. Am

  11. Spectrophotometric analysis of flavonoid-DNA binding interactions at physiological conditions

    Science.gov (United States)

    Janjua, Naveed Kausar; Siddiqa, Asima; Yaqub, Azra; Sabahat, Sana; Qureshi, Rumana; Haque, Sayed ul

    2009-12-01

    Mode of interactions of three flavonoids [morin (M), quercetin (Q), and rutin (R)] with chicken blood ds.DNA (ck.DNA) has been investigated spectrophotometrically at different temperatures including body temperature (310 K) and at two physiological pH values, i.e. 7.4 (human blood pH) and 4.7 (stomach pH). The binding constants, Kf, evaluated using Benesi-Hildebrand equation showed that the flavonoids bind effectively through intercalation at both pH values and body temperature. Quercetin, somehow, showed greater binding capabilities with DNA. The free energies of flavonoid-DNA complexes indicated the spontaneity of their binding. The order of binding constants of three flavonoids at both pH values were found to be Kf(Q) > Kf(R) > Kf(M) and at 310 K.

  12. Crystal structure of the mineralocorticoid receptor DNA binding domain in complex with DNA.

    Science.gov (United States)

    Hudson, William H; Youn, Christine; Ortlund, Eric A

    2014-01-01

    The steroid hormone receptors regulate important physiological functions such as reproduction, metabolism, immunity, and electrolyte balance. Mutations within steroid receptors result in endocrine disorders and can often drive cancer formation and progression. Despite the conserved three-dimensional structure shared among members of the steroid receptor family and their overlapping DNA binding preference, activation of individual steroid receptors drive unique effects on gene expression. Here, we present the first structure of the human mineralocorticoid receptor DNA binding domain, in complex with a canonical DNA response element. The overall structure is similar to the glucocorticoid receptor DNA binding domain, but small changes in the mode of DNA binding and lever arm conformation may begin to explain the differential effects on gene regulation by the mineralocorticoid and glucocorticoid receptors. In addition, we explore the structural effects of mineralocorticoid receptor DNA binding domain mutations found in type I pseudohypoaldosteronism and multiple types of cancer.

  13. Analysis of RNA binding by the dengue virus NS5 RNA capping enzyme.

    Directory of Open Access Journals (Sweden)

    Brittney R Henderson

    Full Text Available Flaviviruses are small, capped positive sense RNA viruses that replicate in the cytoplasm of infected cells. Dengue virus and other related flaviviruses have evolved RNA capping enzymes to form the viral RNA cap structure that protects the viral genome and directs efficient viral polyprotein translation. The N-terminal domain of NS5 possesses the methyltransferase and guanylyltransferase activities necessary for forming mature RNA cap structures. The mechanism for flavivirus guanylyltransferase activity is currently unknown, and how the capping enzyme binds its diphosphorylated RNA substrate is important for deciphering how the flavivirus guanylyltransferase functions. In this report we examine how flavivirus NS5 N-terminal capping enzymes bind to the 5' end of the viral RNA using a fluorescence polarization-based RNA binding assay. We observed that the K(D for RNA binding is approximately 200 nM Dengue, Yellow Fever, and West Nile virus capping enzymes. Removal of one or both of the 5' phosphates reduces binding affinity, indicating that the terminal phosphates contribute significantly to binding. RNA binding affinity is negatively affected by the presence of GTP or ATP and positively affected by S-adensyl methoninine (SAM. Structural superpositioning of the dengue virus capping enzyme with the Vaccinia virus VP39 protein bound to RNA suggests how the flavivirus capping enzyme may bind RNA, and mutagenesis analysis of residues in the putative RNA binding site demonstrate that several basic residues are critical for RNA binding. Several mutants show differential binding to 5' di-, mono-, and un-phosphorylated RNAs. The mode of RNA binding appears similar to that found with other methyltransferase enzymes, and a discussion of diphosphorylated RNA binding is presented.

  14. Artificial zinc finger DNA binding domains: versatile tools for genome engineering and modulation of gene expression.

    Science.gov (United States)

    Hossain, Mir A; Barrow, Joeva J; Shen, Yong; Haq, Md Imdadul; Bungert, Jörg

    2015-11-01

    Genome editing and alteration of gene expression by synthetic DNA binding activities gained a lot of momentum over the last decade. This is due to the development of new DNA binding molecules with enhanced binding specificity. The most commonly used DNA binding modules are zinc fingers (ZFs), TALE-domains, and the RNA component of the CRISPR/Cas9 system. These binding modules are fused or linked to either nucleases that cut the DNA and induce DNA repair processes, or to protein domains that activate or repress transcription of genes close to the targeted site in the genome. This review focuses on the structure, design, and applications of ZF DNA binding domains (ZFDBDs). ZFDBDs are relatively small and have been shown to penetrate the cell membrane without additional tags suggesting that they could be delivered to cells without a DNA or RNA intermediate. Advanced algorithms that are based on extensive knowledge of the mode of ZF/DNA interactions are used to design the amino acid composition of ZFDBDs so that they bind to unique sites in the genome. Off-target binding has been a concern for all synthetic DNA binding molecules. Thus, increasing the specificity and affinity of ZFDBDs will have a significant impact on their use in analytical or therapeutic settings. © 2015 Wiley Periodicals, Inc.

  15. Determining ERβ Binding Affinity to Singly Mutant ERE Using Dual Polarization Interferometry

    Science.gov (United States)

    Song, Hong Yan; Su, Xiaodi

    In a classic mode of estrogen action, estrogen receptors (ERs) bind to estrogen responsive element (ERE) to activate gene transcription. A perfect ERE contains a 13-base pair sequence of a palindromic repeat separated by a three-base spacer, 5‧-GGTCAnnnTGACC-3‧. In addition to the consensus or wild-type ERE (wtERE), naturally occurring EREs often have one or two base pairs’ alternation. Based on the newly constructed Thermodynamic Modeling of ChIP-seq (TherMos) model, binding energy between ERβ and a series of 34-bp mutant EREs (mutERE) was simulated to predict the binding affinity between ERs and EREs with single base pair deviation at different sites of the 13-bp inverted sequence. Experimentally, dual polarization interferometry (DPI) method was developed to measure ERβ-mutEREs binding affinity. On a biotin-NeutrAvidin (NA)-biotin treated DPI chip, wtERE is immobilized. In a direct binding assay, ERβ-wtERE binding affinity is determined. In a competition assay, ERβ was preincubated with mutant EREs before being added for competitive binding to the immobilized wtERE. This competition strategy provided a successful platform to evaluate the binding affinity variation among large number of ERE with different base mutations. The experimental result correlates well with the mathematically predicted binding energy with a Spearman correlation coefficient of 0.97.

  16. Suppression of high order modes employing active self-imaging mode filter in large mode area strongly pumped fiber amplifier

    Science.gov (United States)

    Zhao, Xiang; Bai, Gang; Zheng, Ye; Chen, Xiaolong; Yang, Yifeng; Qi, Yunfeng; He, Bing; Zhou, Jun

    2017-10-01

    To suppress high order modes and improve the beam quality, an active self-imaging mode filter based on multimode interference and self-imaging effect is proposed in large mode area (LMA) fiber amplifier. With this filter structure, transverse mode competition and individual transverse mode power distributions in strongly pumped fiber amplifiers are theoretically demonstrated. Employing this mode selection technique in 30/400 LMA strongly pumped fiber amplifier, the percentage of the fundamental mode rises from 27.8% (without filter) to 96.3%. By the modal power decomposition, the M2 parameter of beam quality decrease dramatically from 2.24 to 1.11 (0 relative phase) and from 3.01 to 1.24 (π/2 relative phase). This study provides a new method to achieve single mode in LMA fiber amplifier and this filter would be extended to larger mode area fiber amplifier to improve the beam quality.

  17. Scaling Fiber Lasers to Large Mode Area: An Investigation of Passive Mode-Locking Using a Multi-Mode Fiber

    Science.gov (United States)

    Ding, Edwin; Lefrancois, Simon; Kutz, Jose Nathan; Wise, Frank W.

    2011-01-01

    The mode-locking of dissipative soliton fiber lasers using large mode area fiber supporting multiple transverse modes is studied experimentally and theoretically. The averaged mode-locking dynamics in a multi-mode fiber are studied using a distributed model. The co-propagation of multiple transverse modes is governed by a system of coupled Ginzburg–Landau equations. Simulations show that stable and robust mode-locked pulses can be produced. However, the mode-locking can be destabilized by excessive higher-order mode content. Experiments using large core step-index fiber, photonic crystal fiber, and chirally-coupled core fiber show that mode-locking can be significantly disturbed in the presence of higher-order modes, resulting in lower maximum single-pulse energies. In practice, spatial mode content must be carefully controlled to achieve full pulse energy scaling. This paper demonstrates that mode-locking performance is very sensitive to the presence of multiple waveguide modes when compared to systems such as amplifiers and continuous-wave lasers. PMID:21731106

  18. All-fiber 6-mode multiplexers based on fiber mode selective couplers.

    Science.gov (United States)

    Chang, Sun Hyok; Moon, Sang-Rok; Chen, Haoshuo; Ryf, Roland; Fontaine, Nicolas K; Park, Kyung Jun; Kim, Kwangjoon; Lee, Joon Ki

    2017-03-06

    All-fiber 6-mode multiplexer composed of two consecutive LP11-mode selective couplers (MSC), two LP21-MSCs and an LP02-MSC is fully characterized by wavelength-swept interferometer technique. The MSCs are fabricated by polished-type fiber couplers coupling LP01 mode of a single mode fiber into a higher-order mode of a few mode fiber. A pair of the mode multiplexers has minimum mode dependent loss of 4 dB and high mode group selectivity of over 15 dB. Mode division multiplexed transmission enabled by the all-fiber mode multiplexers is demonstrated over fiber spans of 117 km employing an in-line multi-mode optical amplifier. 6 modes of 120 Gb/s dual polarization quadrature phase shift keying signals combined with 30 wavelength channels are successfully transmitted.

  19. Synthesis and structure elucidation of a copper(II) Schiff-base complex: in vitro DNA binding, pBR322 plasmid cleavage and HSA binding studies.

    Science.gov (United States)

    Tabassum, Sartaj; Ahmad, Musheer; Afzal, Mohd; Zaki, Mehvash; Bharadwaj, Parimal K

    2014-11-01

    New copper(II) complex with Schiff base ligand 4-[(2-Hydroxy-3-methoxy-benzylidene)-amino]-benzoic acid (H₂L) was synthesized and characterized by spectroscopic and analytical and single crystal X-ray diffraction studies which revealed that the complex 1 exist in a distorted octahedral environment. In vitro CT-DNA binding studies were performed by employing different biophysical technique which indicated that the 1 strongly binds to DNA in comparison to ligand via electrostatic binding mode. Complex 1 cleaves pBR322 DNA via hydrolytic pathway and recognizes minor groove of DNA double helix. The HSA binding results showed that ligand and complex 1 has ability to quench the fluorescence emission intensity of Trp 214 residue available in the subdomain IIA of HSA. Copyright © 2014 Elsevier B.V. All rights reserved.

  20. Modes of an endlessly single-mode photonic crystal fiber: a finite element investigation

    NARCIS (Netherlands)

    Uranus, H.P.; Hoekstra, Hugo; van Groesen, Embrecht W.C.

    2004-01-01

    Using a finite-element mode solver, the modes of a commercial endlessly single-mode photonic crystal fiber (ESM-PCF) were investigated. Based on the loss discrimination between the dominant and the nearest higher order mode, we set-up a criterion for the single-modeness. Using that measure, we

  1. Binding of an anticancer Rutaceae plant flavonoid glycoside with calf thymus DNA: Biophysical and electrochemical studies

    Energy Technology Data Exchange (ETDEWEB)

    Balakrishnan, Sandhya; Jaldappagari, Seetharamappa, E-mail: jseetharam@yahoo.com

    2013-10-15

    In the present work, we report the interaction of a bioactive Rutaceae plant flavonoid glycoside, diosmin (DIO) with calf thymus DNA employing ethidium bromide as a fluorescence probe. The mode of binding between DIO and DNA was investigated by UV absorption, fluorescence, 3D-fluorescence, fluorescence polarization, FT-IR, circular dichroism, melting temperature (T{sub m}) measurements and differential pulse voltammogram studies. The results revealed the intercalative mode of binding between DIO and DNA. Further, the values of thermodynamic parameters, ∆H° (−388.32 kJ mol{sup −1}) and ∆S° (−1.22 kJ mol{sup −1} K{sup −1}) indicated that the van der Waals forces and hydrogen bond played a major role in the binding of DIO to DNA. The observed negative ∆G° values revealed the spontaneity of interaction process. The binding of DIO to DNA–EB was found to be stronger in the presence of coexisting substances. -- Highlights: • Mechanism of interaction of diosmin with DNA was studied by spectroscopic methods. • Ethidium bromide was used as a fluorescence probe in the present study. • The van der Waals forces and hydrogen bond played a significant role in the interaction. • Intercalative mode of binding was proposed between DIO and DNA.

  2. Vainshtein solutions without superluminal modes

    Science.gov (United States)

    Gabadadze, Gregory; Kimura, Rampei; Pirtskhalava, David

    2015-06-01

    The Vainshtein mechanism suppresses the fifth force at astrophysical distances, while enabling it to compete with gravity at cosmological scales. Typically, Vainshtein solutions exhibit superluminal perturbations. However, a restricted class of solutions with special boundary conditions was shown to be devoid of the faster-than-light modes. Here we extend this class by finding solutions in a theory of quasidilaton, amended by derivative terms consistent with its symmetries. Solutions with Minkowski asymptotics are not stable, while the ones that exhibit the Vainshtein mechanism by transitioning to cosmological backgrounds are free of ghosts, tachyons, gradient instability, and superluminality, for all propagating modes present in the theory. These solutions require a special choice of the strength and signs of nonlinear terms, as well as a choice of asymptotic cosmological boundary conditions.

  3. Hypersonic modes in nanophononic semiconductors.

    Science.gov (United States)

    Hepplestone, S P; Srivastava, G P

    2008-09-05

    Frequency gaps and negative group velocities of hypersonic phonon modes in periodically arranged composite semiconductors are presented. Trends and criteria for phononic gaps are discussed using a variety of atomic-level theoretical approaches. From our calculations, the possibility of achieving semiconductor-based one-dimensional phononic structures is established. We present results of the location and size of gaps, as well as negative group velocities of phonon modes in such structures. In addition to reproducing the results of recent measurements of the locations of the band gaps in the nanosized Si/Si{0.4}Ge{0.6} superlattice, we show that such a system is a true one-dimensional hypersonic phononic crystal.

  4. Evaluation of Advanced Bionics high resolution mode.

    Science.gov (United States)

    Buechner, Andreas; Frohne-Buechner, Carolin; Gaertner, Lutz; Lesinski-Schiedat, Anke; Battmer, Rolf-Dieter; Lenarz, Thomas

    2006-07-01

    The objective of this paper is to evaluate the advantages of the Advanced Bionic high resolution mode for speech perception, through a retrospective analysis. Forty-five adult subjects were selected who had a minimum experience of three months' standard mode (mean of 10 months) before switching to high resolution mode. Speech perception was tested in standard mode immediately before fitting with high resolution mode, and again after a maximum of six months high resolution mode usage (mean of two months). A significant improvement was found, between 11 and 17%, depending on the test material. The standard mode preference does not give any indication about the improvement when switching to high resolution. Users who are converted within any study achieve a higher performance improvement than those converted in the clinical routine. This analysis proves the significant benefits of high resolution mode for users, and also indicates the need for guidelines for individual optimization of parameter settings in a high resolution mode program.

  5. Dual Mode Slotted Monopole Antenna

    Science.gov (United States)

    2017-01-05

    of 15 DUAL MODE SLOTTED MONOPOLE ANTENNA STATEMENT OF GOVERNMENT INTEREST [0001] The invention described herein may be manufactured and used by...REFERENCE TO OTHER PATENT APPLICATIONS [0002] None. BACKGROUND OF THE INVENTION (1) Field of the Invention [0003] The present invention is directed...such as this that is capable of radiating at a different frequency below this cutoff. The present invention provides a means by which the overall

  6. Substructuring and Component Mode Synthesis

    Directory of Open Access Journals (Sweden)

    P. Seshu

    1997-01-01

    Full Text Available Substructuring and component mode synthesis (CMS, is a very popular method of model reduction for large structural dynamics problems. Starting from the pioneering works on this technique in the early 1960s, many researchers have studied and used this technique in a variety of applications. Besides model reduction, CMS offers several other crucial advantages. The present work aims to provide a review of the available literature on this important technique.

  7. The binding of botulinum neurotoxins to different peripheral neurons.

    Science.gov (United States)

    Rossetto, O

    2017-10-16

    Botulinum neurotoxins are the most potent toxins known. The double receptor binding modality represents one of the most significant properties of botulinum neurotoxins and largely accounts for their incredible potency and lethality. Despite the high affinity and the very specific binding, botulinum neurotoxins are versatile and multi-tasking toxins. Indeed they are able to act both at the somatic and at the autonomic nervous system. In spite of the preference for cholinergic nerve terminals botulinum neurotoxins have been shown to inhibit to some extent also the noradrenergic postganglionic sympathetic nerve terminals and the afferent nerve terminals of the sensory neurons inhibiting the release of neuropeptides and glutamate, which are responsible of nociception. Therefore, there is increasing evidence that the therapeutic effect in both motor and autonomic disorders is based on a complex mode of botulinum neurotoxin action modulating the activity of efferent as well as afferent nerve fibres. Copyright © 2017 Elsevier Ltd. All rights reserved.

  8. Mode pumping experiments on biomolecules

    Energy Technology Data Exchange (ETDEWEB)

    Austin, R.H.; Erramilli, S. [Princeton Univ., NJ (United States); Xie, A.; Schramm, A.

    1995-12-31

    We will explore several aspects of protein dynamics and energy transfer that can be explored by using the intense, picosecond, tunable mid-IR output of the FEL. In order of appearance they are: (1) Saturation recovery and inter-level coupling of the low temperature amide-I band in acetanilide. This is a continuation of earlier experiments to test soliton models in crystalline hydrogen bonded solids. In this experiment we utilize the sub-picosecond time resolution and low repetition rate of the Stanford SCLA FEL to do both T{sub 1} and T{sub 2} relaxation measurements at 1650 cm{sup -1}. (2) Probing the influence of collective dynamics in sensory rhodopsin. In this experiment we use the FIR output of the Stanford FIREFLY FEL to determine the lifetime of collective modes in the photo-active protein sensory rhodopsin, and begin experiments on the influence of collective modes on retinal reaction dynamics. (3) Probing the transition states of enzymes. This experiment, in the initial stages, attempts to use the intense IR output of the FEL to probe and influence the reaction path of a transition state analog for the protein nucleoside hydrolase. The transition state of the inosine substrate is believed to have critical modes softened by the protein so that bond-breaking paths show absorption at approximately 800 cm{sup -1}. A form of action spectrum using FEL excitation will be used to probe this state.

  9. A History of Emerging Modes?

    Directory of Open Access Journals (Sweden)

    Schmitz Michael

    2016-03-01

    Full Text Available In this paper I first introduce Tomasello’s notion of thought and his account of its emergence and development through differentiation, arguing that it calls into question the theory bias of the philosophical tradition on thought as well as its frequent atomism. I then raise some worries that he may be overextending the concept of thought, arguing that we should recognize an area of intentionality intermediate between action and perception on the one hand and thought on the other. After that I argue that the co-operative nature of humans is reflected in the very structure of their intentionality and thought: in co-operative modes such as the mode of joint attention and action and the we-mode, they experience and represent others as co-subjects of joint relations to situations in the world rather than as mere objects. In conclusion, I briefly comment on what Tomasello refers to as one of two big open questions in the theory of collective intentionality, namely that of the irreducibility of jointness.

  10. Protected Edge Modes without Symmetry

    Directory of Open Access Journals (Sweden)

    Michael Levin

    2013-05-01

    Full Text Available We discuss the question of when a gapped two-dimensional electron system without any symmetry has a protected gapless edge mode. While it is well known that systems with a nonzero thermal Hall conductance, K_{H}≠0, support such modes, here we show that robust modes can also occur when K_{H}=0—if the system has quasiparticles with fractional statistics. We show that some types of fractional statistics are compatible with a gapped edge, while others are fundamentally incompatible. More generally, we give a criterion for when an electron system with Abelian statistics and K_{H}=0 can support a gapped edge: We show that a gapped edge is possible if and only if there exists a subset of quasiparticle types M such that (1 all the quasiparticles in M have trivial mutual statistics, and (2 every quasiparticle that is not in M has nontrivial mutual statistics with at least one quasiparticle in M. We derive this criterion using three different approaches: a microscopic analysis of the edge, a general argument based on braiding statistics, and finally a conformal field theory approach that uses constraints from modular invariance. We also discuss the analogous result for two-dimensional boson systems.

  11. β -Cyclodextrin polymer binding to DNA: Modulating the physicochemical parameters

    Science.gov (United States)

    Rocha, J. C. B.; Silva, E. F.; Oliveira, M. F.; Sousa, F. B.; Teixeira, A. V. N. C.; Rocha, M. S.

    2017-05-01

    Cyclodextrins and cyclodextrins-modified molecules have interesting and appealing properties due to their capacity to host components that are normally insoluble or poorly soluble in water. In this work, we investigate the interaction of a β -cyclodextrin polymer (poly-β -CD) with λ -DNA. The polymers are obtained by the reaction of β -CD with epichlorohydrin in alkaline conditions. We have used optical tweezers to characterize the changes of the mechanical properties of DNA molecules by increasing the concentration of poly-β -CD in the sample. The physical chemistry of the interaction is then deduced from these measurements by using a recently developed quenched-disorder statistical model. It is shown that the contour length of the DNA does not change in the whole range of poly-β -CD concentration (binding modes corresponding to the clustering of ˜2.6 and ˜14 polymer molecules along the DNA double helix, depending on the polymer concentration. Comparing these results with the ones obtained for monomeric β -CD, it was observed that the concentration of CD that alters the DNA persistence length is considerably smaller when in the polymeric form. Also, the binding constant of the polymer-DNA interaction is three orders of magnitude higher than the one found for native (monomeric) β -CD. These results show that the polymerization of the β -CD strongly increases its binding affinity to the DNA molecule. This property can be wisely used to modulate the binding of cyclodextrins to the DNA double helix.

  12. Cholesterol binding to ion channels

    Directory of Open Access Journals (Sweden)

    Irena eLevitan

    2014-02-01

    Full Text Available Numerous studies demonstrated that membrane cholesterol is a major regulator of ion channel function. The goal of this review is to discuss significant advances that have been recently achieved in elucidating the mechanisms responsible for cholesterol regulation of ion channels. The first major insight that comes from growing number of studies that based on the sterol specificity of cholesterol effects, show that several types of ion channels (nAChR, Kir, BK, TRPV are regulated by specific sterol-protein interactions. This conclusion is supported by demonstrating direct saturable binding of cholesterol to a bacterial Kir channel. The second major advance in the field is the identification of putative cholesterol binding sites in several types of ion channels. These include sites at locations associated with the well-known cholesterol binding motif CRAC and its reversed form CARC in nAChR, BK, and TRPV, as well as novel cholesterol binding regions in Kir channels. Notably, in the majority of these channels, cholesterol is suggested to interact mainly with hydrophobic residues in non-annular regions of the channels being embedded in between transmembrane protein helices. We also discuss how identification of putative cholesterol binding sites is an essential step to understand the mechanistic basis of cholesterol-induced channel regulation. Clearly, however, these are only the first few steps in obtaining a general understanding of cholesterol-ion channels interactions and their roles in cellular and organ functions.

  13. Understanding the inhibitory effect of highly potent and selective archazolides binding to the vacuolar ATPase.

    Science.gov (United States)

    Dreisigacker, Sandra; Latek, Dorota; Bockelmann, Svenja; Huss, Markus; Wieczorek, Helmut; Filipek, Slawomir; Gohlke, Holger; Menche, Dirk; Carlomagno, Teresa

    2012-08-27

    Vacuolar ATPases are a potential therapeutic target because of their involvement in a variety of severe diseases such as osteoporosis or cancer. Archazolide A (1) and related analogs have been previously identified as selective inhibitors of V-ATPases with potency down to the subnanomolar range. Herein we report on the determination of the ligand binding mode by a combination of molecular docking, molecular dynamics simulations, and biochemical experiments, resulting in a sound model for the inhibitory mechanism of this class of putative anticancer agents. The binding site of archazolides was confirmed to be located in the equatorial region of the membrane-embedded V(O)-rotor, as recently proposed on the basis of site-directed mutagenesis. Quantification of the bioactivity of a series of archazolide derivatives, together with the docking-derived binding mode of archazolides to the V-ATPase, revealed favorable ligand profiles, which can guide the development of a simplified archazolide analog with potential therapeutic relevance.

  14. Mixed-Mode-Bending Delamination Apparatus

    Science.gov (United States)

    Crews, John H., Jr.; Reeder, James R.

    1991-01-01

    Mixed-mode-bending delamination apparatus generates two types of delamination stress simultaneously in specimen from single externally applied point load. In technique, indivial mode I and mode II contributions to delamination in specimen analyzed by use of simple beam-theory equations, eliminating need for time-consuming, difficult numerical analysis. Allows wider range of mode I/mode II ratios than possible with many other methods. Mixed-mode delamination testing of interest in all fields utilizing composite materials, used mostly in aerospace field, but also used in automobiles, lightweight armored military vehicles, boats, and sporting equipment. Useful in general lumber, plywood, and adhesive industries, as well.

  15. Digital holograms for laser mode multiplexing

    CSIR Research Space (South Africa)

    Mhlanga, T

    2014-10-02

    Full Text Available the sensitivity of the setup to misalignment, that leads to mode-coupling. It is also important that the injected modes ha a uniform power spectrum so that are weighted equally. The size of the multi-modes is highly dependent on the resolution of the SLM. Keywords...: spatial modes, multiplex, mode coupling 1. INTRODUCTION Optical networks form a foundation of modern communications networks since the replacement of copper wires with optical fibres in the 1980’s. This fibre technology has been based on single mode fibres...

  16. Predicting the Diversity of Foreign Entry Modes

    DEFF Research Database (Denmark)

    Hashai, Niron; Geisler Asmussen, Christian; Benito, Gabriel

    2007-01-01

    This paper expands entry mode literature by referring to multiple modes exerted in different value chain activities within and across host markets, rather than to a single entry mode at the host market level. Scale of operations and knowledge intensity are argued to affect firms' entry mode...... diversity across value chain activities and host markets. Analyzing a sample of Israeli based firms we show that larger firms exhibit a higher degree of entry mode diversity both across value chain activities and across host markets. Higher levels of knowledge intensity are also associated with more...... diversity in firms' entry modes across both dimensions....

  17. Mixed-Mode Crack Growth in Wood

    Directory of Open Access Journals (Sweden)

    Octavian POP

    2012-09-01

    Full Text Available In timber elements the mixed mode dependsessentially of wood anatomy and load configuration.In these conditions, in order to evaluate the materialbehavior and the fracture process, it’s necessary toseparate the part of each mode. The mixed modeseparation allows evaluating the amplitude offracture mode. In the present paper, using a mixedmodecrack growth specimen made in Douglas fir,the mixed mode crack growth process is studythanks to marks tracking method. Using the markstracking method the characteristic displacementsassociated to opening and shear mode aremeasured. From the experimental measurements,the energy release rate associated to opening andshear modes is calculated into to account the crackadvancement during the test.

  18. Identification of a Potent Synthetic FXR Agonist with an Unexpected Mode of Binding and Activation

    National Research Council Canada - National Science Library

    Stephen M. Soisson; Gopalakrishnan Parthasarathy; Alan D. Adams; Soumya Sahoo; Ayesha Sitlani; Carl Sparrow; Jisong Cui; Joseph W. Becker

    2008-01-01

    The farnesoid X receptor (FXR), a member of the nuclear hormone receptor family, plays important roles in the regulation of bile acid and cholesterol homeostasis, glucose metabolism, and insulin sensitivity...

  19. Structural basis for PPAR partial or full activation revealed by a novel ligand binding mode

    Science.gov (United States)

    Capelli, Davide; Cerchia, Carmen; Montanari, Roberta; Loiodice, Fulvio; Tortorella, Paolo; Laghezza, Antonio; Cervoni, Laura; Pochetti, Giorgio; Lavecchia, Antonio

    2016-10-01

    The peroxisome proliferator-activated receptors (PPARs) are nuclear receptors involved in the regulation of the metabolic homeostasis and therefore represent valuable therapeutic targets for the treatment of metabolic diseases. The development of more balanced drugs interacting with PPARs, devoid of the side-effects showed by the currently marketed PPARγ full agonists, is considered the major challenge for the pharmaceutical companies. Here we present a structure-based virtual screening approach that let us identify a novel PPAR pan-agonist with a very attractive activity profile and its crystal structure in the complex with PPARα and PPARγ, respectively. In PPARα this ligand occupies a new pocket whose filling is allowed by the ligand-induced switching of the F273 side chain from a closed to an open conformation. The comparison between this pocket and the corresponding cavity in PPARγ provides a rationale for the different activation of the ligand towards PPARα and PPARγ, suggesting a novel basis for ligand design.

  20. A Novel Bipartite Mode of Binding of M.smegmatis Topoisomerase I to its Recognition Sequence

    OpenAIRE

    Sikder, Devanjan; Nagaraja, Valakunja

    2001-01-01

    We have investigated interaction of Mycobacterium smegmatis topoisomerase I at its specific recognition sequence. DNase I foot printing demonstrates a large region of protection on both the scissile and non-scissile strands of DNA. Methylation protection and interference analyses reveal base-specific contacts within the recognition sequence. Missing contact analyses reveal additional interactions with the residues in both single and double-stranded DNA, and hence underline the role for the fu...

  1. Identification of a Common Binding Mode for Imaging Agents to Amyloid Fibrils from Molecular Dynamics Simulations

    DEFF Research Database (Denmark)

    Skeby, Katrine Kirkeby; Sørensen, Jesper; Schiøtt, Birgit

    2013-01-01

    experimentally due to the insoluble nature of amyloid fibrils. This study uses molecular dynamics simulations to investigate the interactions between 13 aromatic amyloid imaging agents, entailing 4 different organic scaffolds, and a model of an amyloid fibril. Clustering analysis combined with free energy......Amyloid diseases are characterized by the misfolding and deposition of proteins in the body in the form of insoluble amyloid fibrils. Alzheimer’s disease and type 2 diabetes mellitus are two examples of amyloid diseases which are closely related both with respect to the atomic structures...

  2. Metal binding by food components

    DEFF Research Database (Denmark)

    Tang, Ning

    , synergistic effect in calcium binding was found for the small glycine peptide rather than amino acids mixtures with the enhanced driving force up to -6 kJ/mol. Such study provides useful information for the future development of calcium supplements. For zinc binding: Isothermal titration calorimetry...... between the above selected food components and zinc citrate or zinc phytate will lead to the enhanced solubility of zinc citrate or zinc phytate. The main driving force for this observed solubility enhancement is the complex formation between zinc and investigated food components as revealed by isothermal...... titration calorimetry and quantum mechanical calculations. This is due to the zinc binding affinity of the relatively softer ligands (investigated food components) will become much stronger than citrate or phytate when they present together in aqueous solution. This mechanism indicates these food components...

  3. Computational Prediction of RNA-Binding Proteins and Binding Sites

    Directory of Open Access Journals (Sweden)

    Jingna Si

    2015-11-01

    Full Text Available Proteins and RNA interaction have vital roles in many cellular processes such as protein synthesis, sequence encoding, RNA transfer, and gene regulation at the transcriptional and post-transcriptional levels. Approximately 6%–8% of all proteins are RNA-binding proteins (RBPs. Distinguishing these RBPs or their binding residues is a major aim of structural biology. Previously, a number of experimental methods were developed for the determination of protein–RNA interactions. However, these experimental methods are expensive, time-consuming, and labor-intensive. Alternatively, researchers have developed many computational approaches to predict RBPs and protein–RNA binding sites, by combining various machine learning methods and abundant sequence and/or structural features. There are three kinds of computational approaches, which are prediction from protein sequence, prediction from protein structure, and protein-RNA docking. In this paper, we review all existing studies of predictions of RNA-binding sites and RBPs and complexes, including data sets used in different approaches, sequence and structural features used in several predictors, prediction method classifications, performance comparisons, evaluation methods, and future directions.

  4. Optically controllable dual-mode switching in single-mode Fabry-Pérot laser diode subject to one side-mode feedback and external single mode injection

    Science.gov (United States)

    Wu, Jian-Wei; Won, Yong Hyub

    2017-06-01

    In this paper, broadly tunable dual-mode lasing system is presented and demonstrated based on single-mode Fabry-Pérot laser diode subject to the feedback of one side mode amplified by an erbium-doped fiber amplifier in the external feedback cavity. The spacing between two resonance modes in output lasing spectrum is broadly tuned by introducing differently amplified side mode into the single-mode laser via the external cavity consisted of amplifier, filter, and polarization controller so that two difference frequencies of 1 THz and 0.6 THz are given to display the tunable behavior of dual-mode emission in this work. Therefore, under an external injection mode into the laser condition, the power dependent injection locking and optical bistability of generated dual-mode emission are discussed in detail. At different wavelength detunings, the emitted two resonance modes including the dominant and feedback modes are switched to on- or off-state by selecting proper high-low power level of the external injection mode. As a consequence, the maximum value of achieved dual-mode on-off ratio is as high as up to 45 dB.

  5. Competition and evolution of dielectric waveguide mode and plasmonic waveguide mode

    Science.gov (United States)

    Yuan, Sheng-Nan; Fang, Yun-Tuan

    2017-10-01

    In order to study the coupling and evolution law of the waveguide mode and two plasmonic surface modes, we construct a line defect waveguide based on hexagonal honeycomb plasmonic photonic crystal. Through adjusting the radius of the edge dielectric rods, the competition and evolution behaviors occur between dielectric waveguide mode and plasmonic waveguide mode. There are three status: only plasmonic waveguide modes occur for rA 0.25a; two kinds of modes coexist for 0.09a slow light.

  6. All-fiber mode selective couplers for mode-division-multiplexed optical transmission

    Science.gov (United States)

    Chang, Sun Hyok; Kim, Kwangjoon; Lee, Joon Ki

    2017-01-01

    All-fiber mode selective coupler (MSC) is comprised of a few mode fiber (FMF) and a single mode fiber (SMF), coupling the LP01 mode of the SMF to a specific higher-order mode (HOM) of the FMF. In order to achieve high coupling ratio and low insertion loss, phase-matching condition between the LP01 mode of SMF arm and the HOM of FMF arm should be satisfied. A polished-type MSC is made by getting their cores into intimate contact. Prism coupling with a polished coupler block can measure the effective refractive index of the mode accurately. We propose and demonstrate three kinds of allfiber mode multiplexer that is composed of consecutive MSCs. 4-mode multiplexer can multiplex 4 modes of LP01, LP11, LP21, and LP02 by cascading LP11, LP21, and LP02 MSCs. It is used for MDM transmission of three modes with 120 Gb/s DP-QPSK signals. In order to enhance the signal transmission performance by receiving degenerate LP modes simultaneously, a mode multiplexer to utilize two-fold degenerate LP11 modes is proposed. It is composed of two consecutive LP11 MSCs that allows the multiplexing of LP01 mode and two orthogonal LP11 modes. We demonstrates WDM transmission of 30 wavelength channels with 33.3 GHz spacing, each carrying 3 modes, over 560 km of FMF. 6- mode multiplexer can multiplex 6 modes of LP01, LP11a, LP11b, LP21a, LP21b, LP02 modes. We demonstrated WDM-MDM transmission with the all-fiber 6-mode multiplexer. In this paper, the manufacturing method and the recent advancements of the all-fiber mode multiplexer based on the MSCs are reviewed. Long-distance mode division multiplexing (MDM) optical signal transmissions with the all-fiber mode multiplexer are experimentally demonstrated.

  7. Mapping the binding site for gossypol-like inhibitors of Plasmodium falciparum lactate dehydrogenase.

    Science.gov (United States)

    Conners, Rebecca; Schambach, Felix; Read, Jon; Cameron, Angus; Sessions, Richard B; Vivas, Livia; Easton, Anna; Croft, Simon L; Brady, R Leo

    2005-08-01

    Gossypol is a di-sesquiterpene natural-product in the form of a functionalised binaphthyl and is isolated from cotton plants. The compound has long been known to exhibit anti-malarial and other biological activities. Previous studies have indicated that compounds of this type target Plasmodium falciparum lactate dehydrogenase (pfLDH), an essential enzyme for energy generation within the parasite. In this study, we report that simple naphthalene-based compounds, the core of the gossypol structure, exhibit weak inhibition of the parasite lactate dehydrogenase. Crystal structures of the complexes formed by binding of these naphthalene-based compounds to their target enzyme have been used to delineate the molecular features likely to form the gossypol binding site. Two modes of binding are observed: one overlapping the pyruvate but not the co-factor site, the other bridging the binding sites for the co-factor nicontinamide group and pyruvate substrate. This latter site encompasses molecular features unique to Plasmodium forms of LDH and is likely to represent the mode of binding for gossypol derivatives that show selectivity for the parasite enzymes. We also report a substrate analogue that unexpectedly binds within the adenine pocket of the co-factor groove. Although these core pharmacophore-like molecules only exhibit low levels of inhibitory activity, these molecular snapshots provide a rational basis for renewed structure-based development of naphthalene-based compounds as anti-malarial agents.

  8. Investigation of binding behaviour of procainamide hydrochloride with human serum albumin using synchronous, 3D fluorescence and circular dichroism

    Directory of Open Access Journals (Sweden)

    Kirthi Byadagi

    2017-04-01

    Full Text Available Interaction of procainamide hydrochloride (PAH with human serum albumin (HSA is of great significance in understanding the pharmacokinetic and pharmacodynamic mechanisms of the drug. Multi-spectroscopic techniques were used to investigate the binding mode of PAH to HSA and results revealed the presence of static type of quenching mechanism. The number of binding sites, binding constants and thermodynamic parameters were calculated. The results showed a spontaneous binding of PAH to HSA and hydrophobic interactions played a major role. In addition, the distance between PAH and the Trp–214 was estimated employing the Förster's theory. Site marker competitive experiments indicated that the binding of PAH to HSA primarily took place in subdomain IIA (Sudlow's site I. The influence of interference of some common metal ions on the binding of PAH to HSA was studied. Synchronous fluorescence spectra (SFS, 3D fluorescence spectra and circular dichroism (CD results indicated the conformational changes in the structure of HSA.

  9. Automobile Road Vibration Reproduction using Sliding Modes

    NARCIS (Netherlands)

    Monsees, G.; Scherpen, J.M.A.

    2001-01-01

    Sliding mode controllers have a reputation for their robustness against parameter variations, modeling errors and disturbances. They have been successfully applied in several practical situations which demonstrated the potential of sliding mode control for other control problems. However research

  10. Higher order mode optical fiber Raman amplifiers

    DEFF Research Database (Denmark)

    Rottwitt, Karsten; Friis, Søren Michael Mørk; Usuga Castaneda, Mario A.

    2016-01-01

    We review higher order mode Raman amplifiers and discuss recent theoretical as well as experimental results including system demonstrations.......We review higher order mode Raman amplifiers and discuss recent theoretical as well as experimental results including system demonstrations....

  11. Bookmarking by specific and nonspecific binding of FoxA1 pioneer factor to mitotic chromosomes.

    Science.gov (United States)

    Caravaca, Juan Manuel; Donahue, Greg; Becker, Justin S; He, Ximiao; Vinson, Charles; Zaret, Kenneth S

    2013-02-01

    While most transcription factors exit the chromatin during mitosis and the genome becomes silent, a subset of factors remains and "bookmarks" genes for rapid reactivation as cells progress through the cell cycle. However, it is unknown whether such bookmarking factors bind to chromatin similarly in mitosis and how different binding capacities among them relate to function. We compared a diverse set of transcription factors involved in liver differentiation and found markedly different extents of mitotic chromosome binding. Among them, the pioneer factor FoxA1 exhibits the greatest extent of mitotic chromosome binding. Genomically, ~15% of the FoxA1 interphase target sites are bound in mitosis, including at genes that are important for liver differentiation. Biophysical, genome mapping, and mutagenesis studies of FoxA1 reveals two different modes of binding to mitotic chromatin. Specific binding in mitosis occurs at sites that continue to be bound from interphase. Nonspecific binding in mitosis occurs across the chromosome due to the intrinsic chromatin affinity of FoxA1. Both specific and nonspecific binding contribute to timely reactivation of target genes post-mitosis. These studies reveal an unexpected diversity in the mechanisms by which transcription factors help retain cell identity during mitosis.

  12. Transverse mode-locking in microcavity lasers

    Science.gov (United States)

    Gordon, R.; Heberle, A. P.; Cleaver, J. R. A.

    2002-12-01

    We experimentally demonstrate mode-locking between the transverse modes of a laser. A vertical-cavity surface-emitting laser with evenly-spaced transverse modes is shown to emit a train of 2.1±0.1 ps pulses with an 11 ps repetition rate and a timing jitter of 235±30 fs. Transverse mode-locking in microcavity lasers has potential to improve the compactness, stability, integrability, repetition rate tunability, and efficiency of ultrafast optical communication sources.

  13. Language Differences and Operation Mode

    DEFF Research Database (Denmark)

    Dasi, Angels; Pedersen, Torben

    2013-01-01

    Language serves different purposes depending on the international activity in question. Language has many dimensions and firms’ communicative requirements vary by operational platform. We argue that different dimensions of language vary in their importance depending on the operation mode chosen...... for a foreign market, so that language distance matters in the case of a home-based sales force, while language incidence is key when operating through a local agent. The hypotheses are tested on a large data set encompassing 462 multinational corporations headquartered in Finland, South Korea, New Zealand......, and Sweden that have undertaken a business operation in a foreign country....

  14. Applications of sliding mode control

    CERN Document Server

    Ghommam, Jawhar; Zhu, Quanmin

    2017-01-01

    This book presents essential studies and applications in the context of sliding mode control, highlighting the latest findings from interdisciplinary theoretical studies, ranging from computational algorithm development to representative applications. Readers will learn how to easily tailor the techniques to accommodate their ad hoc applications. To make the content as accessible as possible, the book employs a clear route in each paper, moving from background to motivation, to quantitative development (equations), and lastly to case studies/illustrations/tutorials (simulations, experiences, curves, tables, etc.). Though primarily intended for graduate students, professors and researchers from related fields, the book will also benefit engineers and scientists from industry. .

  15. Squint mode SAR processing algorithms

    Science.gov (United States)

    Chang, C. Y.; Jin, M.; Curlander, J. C.

    1989-01-01

    The unique characteristics of a spaceborne SAR (synthetic aperture radar) operating in a squint mode include large range walk and large variation in the Doppler centroid as a function of range. A pointing control technique to reduce the Doppler drift and a new processing algorithm to accommodate large range walk are presented. Simulations of the new algorithm for squint angles up to 20 deg and look angles up to 44 deg for the Earth Observing System (Eos) L-band SAR configuration demonstrate that it is capable of maintaining the resolution broadening within 20 percent and the ISLR within a fraction of a decibel of the theoretical value.

  16. Alcohol binding to the odorant binding protein LUSH: multiple factors affecting binding affinities.

    Science.gov (United States)

    Ader, Lauren; Jones, David N M; Lin, Hai

    2010-07-27

    Density function theory (DFT) calculations have been carried out to investigate the binding of alcohols to the odorant binding protein LUSH from Drosophila melanogaster. LUSH is one of the few proteins known to bind to ethanol at physiologically relevant concentrations and where high-resolution structural information is available for the protein bound to alcohol at these concentrations. The structures of the LUSH-alcohol complexes identify a set of specific hydrogen-bonding interactions as critical for optimal binding of ethanol. A set of truncated models based on the structure of the LUSH-butanol complex were constructed for the wild-type and mutant (T57S, S52A, and T57A) proteins in complexes with a series of n-alcohols and for the apoprotein bound to water and for the ligand-free protein. Using both gas-phase calculations and continuum solvation model calculations, we found that the widely used DFT model, B3LYP, failed to reproduce the experimentally observed trend of increasing binding affinity with the increasing length of the alkyl chain in the alcohol. In contrast, the recently developed M05-2X DFT model successfully reproduced this subtle trend. Analysis of the results indicated that multiple factors contribute to the differences in alcohol binding affinity: the H-bonding with Thr57 and Ser52 (4-5 kcal/mol per H-bond), the desolvation contribution (4-6 kcal/mol for alcohols and 8-10 kcal/mol for water), and the other noncovalent interaction (1.2 kcal/mol per CH(2) group of the alcohol alkyl chain). These results reveal the outstanding potential for using the M05-2X model in calculations of protein-substrate complexes where noncovalent interactions are important.

  17. Anticancer drug mithramycin interacts with core histones: An additional mode of action of the DNA groove binder

    Directory of Open Access Journals (Sweden)

    Amrita Banerjee

    2014-01-01

    Full Text Available Mithramycin (MTR is a clinically approved DNA-binding antitumor antibiotic currently in Phase 2 clinical trials at National Institutes of Health for treatment of osteosarcoma. In view of the resurgence in the studies of this generic antibiotic as a human medicine, we have examined the binding properties of MTR with the integral component of chromatin – histone proteins – as a part of our broad objective to classify DNA-binding molecules in terms of their ability to bind chromosomal DNA alone (single binding mode or both histones and chromosomal DNA (dual binding mode. The present report shows that besides DNA, MTR also binds to core histones present in chromatin and thus possesses the property of dual binding in the chromatin context. In contrast to the MTR–DNA interaction, association of MTR with histones does not require obligatory presence of bivalent metal ion like Mg2+. As a consequence of its ability to interact with core histones, MTR inhibits histone H3 acetylation at lysine 18, an important signature of active chromatin, in vitro and ex vivo. Reanalysis of microarray data of Ewing sarcoma cell lines shows that upon MTR treatment there is a significant down regulation of genes, possibly implicating a repression of H3K18Ac-enriched genes apart from DNA-binding transcription factors. Association of MTR with core histones and its ability to alter post-translational modification of histone H3 clearly indicates an additional mode of action of this anticancer drug that could be implicated in novel therapeutic strategies.

  18. A comparison of short distance transport modes

    NARCIS (Netherlands)

    Bouwman, M.E.; Sucharov, LJ

    2000-01-01

    This paper presents a comparison of seven transport modes in both urban and rural settings, based on four characteristics of transport modes: space use, energy use, costs and travel time. The characteristics are calculated with a computer model and based on these results the modes can be ranked.

  19. MDM: A Mode Diagram Modeling Framework

    DEFF Research Database (Denmark)

    Wang, Zheng; Pu, Geguang; Li, Jianwen

    2012-01-01

    Periodic control systems used in spacecrafts and automotives are usually period-driven and can be decomposed into different modes with each mode representing a system state observed from outside. Such systems may also involve intensive computing in their modes. Despite the fact that such control...

  20. Silicon Photonic Integrated Circuit Mode Multiplexer

    DEFF Research Database (Denmark)

    Ding, Yunhong; Ou, Haiyan; Xu, Jing

    2013-01-01

    We propose and demonstrate a novel silicon photonic integrated circuit enabling multiplexing of orthogonal modes in a few-mode fiber (FMF). By selectively launching light to four vertical grating couplers, all six orthogonal spatial and polarization modes supported by the FMF are successfully exc...

  1. Viscoelastic modes in chiral liquid crystals

    Indian Academy of Sciences (India)

    amit@fs.rri.local.net (Amit Kumar Agarwal)

    our studies on the viscoelastic modes of some chiral liquid crystals using dynamic light scattering. We discuss viscoelastic modes corresponding to the C director fluctuations in the chiral smectic C phase and the behaviour of the Goldstone-mode near the chiral smectic C–smectic A phase transition. In cholesteric liquid ...

  2. PLC-based mode multi/demultiplexers for mode division multiplexing

    Science.gov (United States)

    Saitoh, Kunimasa; Hanzawa, Nobutomo; Sakamoto, Taiji; Fujisawa, Takeshi; Yamashita, Yoko; Matsui, Takashi; Tsujikawa, Kyozo; Nakajima, Kazuhide

    2017-02-01

    Recently developed PLC-based mode multi/demultiplexers (MUX/DEMUXs) for mode division multiplexing (MDM) transmission are reviewed. We firstly show the operation principle and basic characteristics of PLC-based MUX/DEMUXs with an asymmetric directional coupler (ADC). We then demonstrate the 3-mode (2LP-mode) multiplexing of the LP01, LP11a, and LP11b modes by using fabricated PLC-based mode MUX/DEMUX on one chip. In order to excite LP11b mode in the same plane, a PLC-based LP11 mode rotator is introduced. Finally, we show the PLC-based 6-mode (4LP-mode) MUX/DEMUX with a uniform height by using ADCs, LP11 mode rotators, and tapered waveguides. It is shown that the LP21a mode can be excited from the LP11b mode by using ADC, and the two nearly degenerated LP21b and LP02 modes can be (de)multiplexed separately by using tapered mode converter from E13 (E31) mode to LP21b (LP02) mode.

  3. Conservation of carbohydrate binding interfaces: evidence of human HBGA selection in norovirus evolution.

    Directory of Open Access Journals (Sweden)

    Ming Tan

    Full Text Available Human noroviruses are the major viral pathogens of epidemic acute gastroenteritis. These genetically diverse viruses comprise two major genogroups (GI and GII and approximately 30 genotypes. Noroviruses recognize human histo-blood group antigens (HBGAs in a diverse, strain-specific manner. Recently the crystal structures of the HBGA-binding interfaces of the GI Norwalk virus and the GII VA387 have been determined, which allows us to examine the genetic and structural relationships of the HBGA-binding interfaces of noroviruses with variable HBGA-binding patterns. Our hypothesis is that, if HBGAs are the viral receptors necessary for norovirus infection and spread, their binding interfaces should be under a selection pressure in the evolution of noroviruses.Structural comparison of the HBGA-binding interfaces of the two noroviruses has revealed shared features but significant differences in the location, sequence composition, and HBGA-binding modes. On the other hand, the primary sequences of the HBGA-binding interfaces are highly conserved among strains within each genogroup. The roles of critical residues within the binding sites have been verified by site-directed mutagenesis followed by functional analysis of strains with variable HBGA-binding patterns.Our data indicate that the human HBGAs are an important factor in norovirus evolution. Each of the two major genogroups represents an evolutionary lineage characterized by distinct genetic traits. Functional convergence of strains with the same HBGA targets subsequently resulted in acquisition of analogous HBGA binding interfaces in the two genogroups that share an overall structural similarity, despite their distinct locations and amino acid compositions. On the other hand, divergent evolution may have contributed to the observed overall differences between and within the two lineages. Thus, both divergent and convergent evolution, as well as the polymorphic human HBGAs, likely contribute to

  4. Protein binding assay for hyaluronate

    Energy Technology Data Exchange (ETDEWEB)

    Lacy, B.E.; Underhill, C.B.

    1986-11-01

    A relatively quick and simple assay for hyaluronate was developed using the specific binding protein, hyaluronectin. The hyaluronectin was obtained by homogenizing the brains of Sprague-Dawley rats, and then centrifuging the homogenate. The resulting supernatant was used as a source of crude hyaluronectin. In the binding assay, the hyaluronectin was mixed with (/sup 3/H)hyaluronate, followed by an equal volume of saturated (NH/sub 4/)/sub 2/SO/sub 4/, which precipitated the hyaluronectin and any (/sup 3/H)hyaluronate associated with it, but left free (/sup 3/H)hyaluronate in solution. The mixture was then centrifuged, and the amount of bound (/sup 3/H)hyaluronate in the precipitate was determined. Using this assay, the authors found that hyaluronectin specifically bound hyaluronate, since other glycosaminoglycans failed to compete for the binding protein. In addition, the interaction between hyaluronectin and hyaluronate was of relatively high affinity, and the size of the hyaluronate did not appear to substantially alter the amount of binding. To determine the amount of hyaluronate in an unknown sample, they used a competition assay in which the binding of a set amount of (/sup 3/H)hyaluronate was blocked by the addition of unlabeled hyaluronate. By comparing the degree of competition of the unknown samples with that of known amounts of hyaluronate, it was possible to determine the amount of hyaluronate in the unknowns. They have found that this method is sensitive to 1 ..mu..g or less of hyaluronate, and is unaffected by the presence of proteins.

  5. Adaptive Batch Mode Active Learning.

    Science.gov (United States)

    Chakraborty, Shayok; Balasubramanian, Vineeth; Panchanathan, Sethuraman

    2015-08-01

    Active learning techniques have gained popularity to reduce human effort in labeling data instances for inducing a classifier. When faced with large amounts of unlabeled data, such algorithms automatically identify the exemplar and representative instances to be selected for manual annotation. More recently, there have been attempts toward a batch mode form of active learning, where a batch of data points is simultaneously selected from an unlabeled set. Real-world applications require adaptive approaches for batch selection in active learning, depending on the complexity of the data stream in question. However, the existing work in this field has primarily focused on static or heuristic batch size selection. In this paper, we propose two novel optimization-based frameworks for adaptive batch mode active learning (BMAL), where the batch size as well as the selection criteria are combined in a single formulation. We exploit gradient-descent-based optimization strategies as well as properties of submodular functions to derive the adaptive BMAL algorithms. The solution procedures have the same computational complexity as existing state-of-the-art static BMAL techniques. Our empirical results on the widely used VidTIMIT and the mobile biometric (MOBIO) data sets portray the efficacy of the proposed frameworks and also certify the potential of these approaches in being used for real-world biometric recognition applications.

  6. Free energy profiles of cocaine esterase-cocaine binding process by molecular dynamics and potential of mean force simulations.

    Science.gov (United States)

    Zhang, Yuxin; Huang, Xiaoqin; Han, Keli; Zheng, Fang; Zhan, Chang-Guo

    2016-11-25

    The combined molecular dynamics (MD) and potential of mean force (PMF) simulations have been performed to determine the free energy profile of the CocE)-(+)-cocaine binding process in comparison with that of the corresponding CocE-(-)-cocaine binding process. According to the MD simulations, the equilibrium CocE-(+)-cocaine binding mode is similar to the CocE-(-)-cocaine binding mode. However, based on the simulated free energy profiles, a significant free energy barrier (∼5 kcal/mol) exists in the CocE-(+)-cocaine binding process whereas no obvious free energy barrier exists in the CocE-(-)-cocaine binding process, although the free energy barrier of ∼5 kcal/mol is not high enough to really slow down the CocE-(+)-cocaine binding process. In addition, the obtained free energy profiles also demonstrate that (+)-cocaine and (-)-cocaine have very close binding free energies with CocE, with a negligible difference (∼0.2 kcal/mol), which is qualitatively consistent with the nearly same experimental KM values of the CocE enzyme for (+)-cocaine and (-)-cocaine. The consistency between the computational results and available experimental data suggests that the mechanistic insights obtained from this study are reasonable. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  7. LIGAND-BINDING SITES ON THE MYCOBACTERIUM TUBERCULOSIS UREASE

    Directory of Open Access Journals (Sweden)

    Lisnyak Yu. V.

    2017-10-01

    Full Text Available Introduction. Mycobacterium tuberculosis is the causative agent of tuberculosis that remains a serious medical and social health problem. Despite intensive efforts have been made in the past decade, there are no new efficient anti-tuberculosis drugs today, and that need is growing due to the spread of drug-resistant strains of M.tuberculosis. M. tuberculosis urease (MTU, being an important factor of the bacterium viability and virulence, is an attractive target for anti-tuberculosis drugs acting by inhibition of urease activity. However, the commercially available urease inhibitors are toxic and unstable, that prevent their clinical use. Therefore, new more potent anti-tuberculosis drugs inhibiting new targets are urgently needed. A useful tool for the search of novel inhibitors is a computational drug design. The inhibitor design is significantly easier if binding sites on the enzyme are identified in advance. This paper aimed to determine the probable ligand binding sites on the surface of M. tuberculosis urease. Methods. To identify ligand binding sites on MTU surface, сomputational solvent mapping method FTSite was applied by the use of MTU homology model we have built earlier. The method places molecular probes (small organic molecules containing various functional groups on a dense grid defined around the enzyme, and for each probe finds favorable positions. The selected poses are refined by free energy minimization, the low energy conformations are clustered, and the clusters are ranked on the basis of the average free energy. FTSite server outputs the protein residues delineating a binding sites and the probe molecules representing each cluster. To predict allosteric pockets on MTU, AlloPred and AlloSite servers were applied. AlloPred uses the normal mode analysis (NMA and models how the dynamics of a protein would be altered in the presence of a modulator at a specific pocket. Pockets on the enzyme are predicted using the Fpocket

  8. Sampling and energy evaluation challenges in ligand binding protein design

    Science.gov (United States)

    Dou, Jiayi; Doyle, Lindsey; Jr. Greisen, Per; Schena, Alberto; Park, Hahnbeom; Johnsson, Kai; Stoddard, Barry L.

    2017-01-01

    Abstract The steroid hormone 17α‐hydroxylprogesterone (17‐OHP) is a biomarker for congenital adrenal hyperplasia and hence there is considerable interest in development of sensors for this compound. We used computational protein design to generate protein models with binding sites for 17‐OHP containing an extended, nonpolar, shape‐complementary binding pocket for the four‐ring core of the compound, and hydrogen bonding residues at the base of the pocket to interact with carbonyl and hydroxyl groups at the more polar end of the ligand. Eight of 16 designed proteins experimentally tested bind 17‐OHP with micromolar affinity. A co‐crystal structure of one of the designs revealed that 17‐OHP is rotated 180° around a pseudo‐two‐fold axis in the compound and displays multiple binding modes within the pocket, while still interacting with all of the designed residues in the engineered site. Subsequent rounds of mutagenesis and binding selection improved the ligand affinity to nanomolar range, while appearing to constrain the ligand to a single bound conformation that maintains the same “flipped” orientation relative to the original design. We trace the discrepancy in the design calculations to two sources: first, a failure to model subtle backbone changes which alter the distribution of sidechain rotameric states and second, an underestimation of the energetic cost of desolvating the carbonyl and hydroxyl groups of the ligand. The difference between design model and crystal structure thus arises from both sampling limitations and energy function inaccuracies that are exacerbated by the near two‐fold symmetry of the molecule. PMID:28980354

  9. Sampling and energy evaluation challenges in ligand binding protein design.

    Science.gov (United States)

    Dou, Jiayi; Doyle, Lindsey; Jr Greisen, Per; Schena, Alberto; Park, Hahnbeom; Johnsson, Kai; Stoddard, Barry L; Baker, David

    2017-12-01

    The steroid hormone 17α-hydroxylprogesterone (17-OHP) is a biomarker for congenital adrenal hyperplasia and hence there is considerable interest in development of sensors for this compound. We used computational protein design to generate protein models with binding sites for 17-OHP containing an extended, nonpolar, shape-complementary binding pocket for the four-ring core of the compound, and hydrogen bonding residues at the base of the pocket to interact with carbonyl and hydroxyl groups at the more polar end of the ligand. Eight of 16 designed proteins experimentally tested bind 17-OHP with micromolar affinity. A co-crystal structure of one of the designs revealed that 17-OHP is rotated 180° around a pseudo-two-fold axis in the compound and displays multiple binding modes within the pocket, while still interacting with all of the designed residues in the engineered site. Subsequent rounds of mutagenesis and binding selection improved the ligand affinity to nanomolar range, while appearing to constrain the ligand to a single bound conformation that maintains the same "flipped" orientation relative to the original design. We trace the discrepancy in the design calculations to two sources: first, a failure to model subtle backbone changes which alter the distribution of sidechain rotameric states and second, an underestimation of the energetic cost of desolvating the carbonyl and hydroxyl groups of the ligand. The difference between design model and crystal structure thus arises from both sampling limitations and energy function inaccuracies that are exacerbated by the near two-fold symmetry of the molecule. © 2017 The Authors Protein Science published by Wiley Periodicals, Inc. on behalf of The Protein Society.

  10. Forms of knowledge and modes of innovation

    DEFF Research Database (Denmark)

    Jensen, Morten Berg; Johnson, Björn; Lorenz, Edward

    2007-01-01

    This paper contrasts two modes of innovation. One, the Science, Technology and Innovation (STI) mode, is based on the production and use of codified scientific and technical knowledge. The other, the Doing, Using and Interacting (DUI) mode, relies on informal processes of learning and experience......-based know-how. Drawing on the results of the 2001 Danish DISKO Survey, latent class analysis is used to identify groups of firms that practice the two modes with different intensities. Logit regression analysis is used to show that firms combining the two modes are more likely to innovate new products...

  11. Parametric Landau damping of space charge modes

    Energy Technology Data Exchange (ETDEWEB)

    Macridin, Alexandru [Fermilab; Burov, Alexey [Fermilab; Stern, Eric [Fermilab; Amundson, James [Fermilab; Spentzouris, Panagiotis [Fermilab

    2016-09-23

    Landau damping is the mechanism of plasma and beam stabilization; it arises through energy transfer from collective modes to the incoherent motion of resonant particles. Normally this resonance requires the resonant particle's frequency to match the collective mode frequency. We have identified an important new damping mechanism, parametric Landau damping, which is driven by the modulation of the mode-particle interaction. This opens new possibilities for stability control through manipulation of both particle and mode-particle coupling spectra. We demonstrate the existence of parametric Landau damping in a simulation of transverse coherent modes of bunched accelerator beams with space charge.

  12. On-chip mode division multiplexing technologies

    DEFF Research Database (Denmark)

    Ding, Yunhong; Frellsen, Louise Floor; Guan, Xiaowei

    2016-01-01

    modes are critical for SDM applications. Here we present such building blocks implemented on the silicon-on-insulator (SOI) platform. These include fabrication tolerant wideband (de) multiplexers, ultra-compact mode converters and (de) multiplexers designed by topology optimization, and mode filters...... using one-dimensional (1D) photonic crystal silicon waveguides. We furthermore use the fabricated devices to demonstrate on-chip point-to-point mode division multiplexing transmission, and all-optical signal processing by mode-selective wavelength conversion. Finally, we report an efficient silicon...

  13. DNA binding by the plant-specific NAC transcription factors in crystal and solution

    DEFF Research Database (Denmark)

    Welner, Ditte Hededam; Lindemose, Søren; Grossmann, J. Günter

    2012-01-01

    angle X-ray scattering on complexes with oligonucleotides, mutagenesis and (DNase I and uranyl photo-) footprinting, is combined to form a structural view of DNA-binding, and for the first time provide experimental evidence for the speculated relationship between plant-specific NAC proteins, WRKY....... The structure of the DNA-binding NAC domain of ANAC019 has previously been determined by X-ray crystallography, revealing a dimeric and predominantly ß-fold structure, but the mode of binding to cognate DNA has remained elusive. In the present study, information from low resolution X-ray structures and small...... transcription factors and the mammalian GCM (Glial cell missing) transcription factors, which all use a ß-strand motif for DNA-binding. The structure shows that the NAC domain inserts the edge of its core ß-sheet into the major groove, while leaving the DNA largely undistorted. The structure of the NAC-DNA...

  14. 3D-QSAR model of flavonoids binding at benzodiazepine site in GABAA receptors.

    Science.gov (United States)

    Huang, X; Liu, T; Gu, J; Luo, X; Ji, R; Cao, Y; Xue, H; Wong, J T; Wong, B L; Pei, G; Jiang, H; Chen, K

    2001-06-07

    With flavone as a structural template, three-dimensional quantitative structure-activity relationship (3D-QSAR) studies and ab initio calculations were performed on a series of flavonoids. A reasonable pharmacophore model was built through CoMFA, CoMSIA, and HQSAR analyses and electrostatic potential calculations. A plausible binding mode for flavonoids with GABA(A) receptors was rationalized. On the basis of the commonly recognized binding site, the specific S1 and S2 subsites relating to substituent positions were proposed. The different binding affinities could be explained according to the frontier orbitals and electrostatic potential (ESP) maps. The ESP could be used as a novel starting point for designing more selective BZ-binding-site ligands.

  15. Characterization of a Single-Stranded DNA-Binding-Like Protein from Nanoarchaeum equitans--A Nucleic Acid Binding Protein with Broad Substrate Specificity.

    Directory of Open Access Journals (Sweden)

    Marcin Olszewski

    Full Text Available SSB (single-stranded DNA-binding proteins play an essential role in all living cells and viruses, as they are involved in processes connected with ssDNA metabolism. There has recently been an increasing interest in SSBs, since they can be applied in molecular biology techniques and analytical methods. Nanoarchaeum equitans, the only known representative of Archaea phylum Nanoarchaeota, is a hyperthermophilic, nanosized, obligatory parasite/symbiont of Ignicoccus hospitalis.This paper reports on the ssb-like gene cloning, gene expression and characterization of a novel nucleic acid binding protein from Nanoarchaeum equitans archaeon (NeqSSB-like protein. This protein consists of 243 amino acid residues and one OB fold per monomer. It is biologically active as a monomer like as SSBs from some viruses. The NeqSSB-like protein displays a low sequence similarity to the Escherichia coli SSB, namely 10% identity and 29% similarity, and is the most similar to the Sulfolobus solfataricus SSB (14% identity and 32% similarity. The NeqSSB-like protein binds to ssDNA, although it can also bind mRNA and, surprisingly, various dsDNA forms, with no structure-dependent preferences as evidenced by gel mobility shift assays. The size of the ssDNA binding site, which was estimated using fluorescence spectroscopy, is 7 ± 1 nt. No salt-dependent binding mode transition was observed. NeqSSB-like protein probably utilizes a different model for ssDNA binding than the SSB proteins studied so far. This protein is highly thermostable; the half-life of the ssDNA binding activity is 5 min at 100 °C and melting temperature (T(m is 100.2 °C as shown by differential scanning calorimetry (DSC analysis.NeqSSB-like protein is a novel highly thermostable protein which possesses a unique broad substrate specificity and is able to bind all types of nucleic acids.

  16. Crystal structure of the neutralizing Llama V(HH D7 and its mode of HIV-1 gp120 interaction.

    Directory of Open Access Journals (Sweden)

    Andreas Hinz

    2010-05-01

    Full Text Available HIV-1 entry into host cells is mediated by the sequential binding of the envelope glycoprotein gp120 to CD4 and a chemokine receptor. Antibodies binding to epitopes overlapping the CD4-binding site on gp120 are potent inhibitors of HIV entry, such as the llama heavy chain antibody fragment V(HH D7, which has cross-clade neutralizing properties and competes with CD4 and mAb b12 for high affinity binding to gp120. We report the crystal structure of the D7 V(HH at 1.5 A resolution, which reveals the molecular details of the complementarity determining regions (CDR and substantial flexibility of CDR3 that could facilitate an induced fit interaction with gp120. Structural comparison of CDRs from other CD4 binding site antibodies suggests diverse modes of interaction. Mutational analysis identified CDR3 as a key component of gp120 interaction as determined by surface plasmon resonance. A decrease in affinity is directly coupled to the neutralization efficiency since mutations that decrease gp120 interaction increase the IC50 required for HIV-1 IIIB neutralization. Thus the structural study identifies the long CDR3 of D7 as the key determinant of interaction and HIV-1 neutralization. Furthermore, our data confirm that the structural plasticity of gp120 can accommodate multiple modes of antibody binding within the CD4 binding site.

  17. Influence of the linear mode coupling on the nonlinear impairments in few-mode fibers

    DEFF Research Database (Denmark)

    Kutluyarov, R.V.; Lyubopytov, V.S.; Bagmanov, V.Kh

    2017-01-01

    This paper is focused on the influence of the linear mode coupling caused by the fiber bending on the nonlinear distortions in a mode-division multiplexed system. The system under test utilizes the fundamental Gaussian mode and the conjugated first-order vortex modes propagating in the step-index...

  18. Distributed mode filtering rod fiber amplifier delivering 292W with improved mode stability

    DEFF Research Database (Denmark)

    Laurila, Marko; Jørgensen, Mette Marie; Hansen, Kristian Rymann

    2012-01-01

    We demonstrate a high power fiber (85μm core) amplifier delivering up to 292Watts of average output power using a mode-locked 30ps source at 1032nm. Utilizing a single mode distributed mode filter bandgap rod fiber, we demonstrate 44% power improvement before the threshold-like onset of mode...

  19. Intermodal Raman Scattering between Full Vectorial Modes in Few Moded Fiber

    DEFF Research Database (Denmark)

    Rishøj, Lars Søgaard; Ramachandran, Siddharth; Rottwitt, Karsten

    2013-01-01

    We experimentally investigate intermodal Raman interaction. The pump is in the fundamental mode, HE11, and the signal is in either of two full vectorial modes, TM01 or TE01. The on-off gain is approximately 3 dB for both modes, using 4 km of few-moded fiber and 400 mW of pump power....

  20. Identifying modes of large whispering-gallery mode resonators from the spectrum and emission pattern

    DEFF Research Database (Denmark)

    Schunk, Gerhard; Fuerst, Josef U.; Förtsch, Michael

    2014-01-01

    Identifying the mode numbers in whispering-gallery mode resonators (WGMRs) is important for tailoring them to experimental needs. Here we report on a novel experimental mode analysis technique based on the combination of frequency analysis and far-field imaging for high mode numbers of large WGMR...

  1. GATS Mode 4 Negotiation and Policy Options

    Directory of Open Access Journals (Sweden)

    Kil-Sang Yoo

    2004-06-01

    Full Text Available This study reviews the characteristics and issues of GATS Mode 4 and guesses the effects of Mode 4 liberalization on Korean economy and labor market to suggest policy options to Korea. Mode 4 negotiation started from the trade perspective, however, since Mode 4 involves international labor migration, it also has migration perspective. Thus developed countries, that have competitiveness in service sector, are interested in free movement of skilled workers such as intra-company transferees and business visitors. On the other hand, developing countries, that have little competitiveness in service sector, are interested in free movement of low-skilled workers. Empirical studies predict that the benefits of Mode 4 liberalization will be focused on developed countries rather than developing countries. The latter may suffer from brain drain and reduction of labor supply. Nevertheless developed countries are reluctant to Mode 4 negotiation because they can utilize skilled workers from developing countries by use of their own temporary visa programs. They are interested in Mode 4 related with Mode 3 in order to ease direct investment and movement of natural persons to developing countries. Regardless of the direction of a single undertaking of Mode 4 negotiation, the net effects of Mode 4 liberalization on Korean economy and labor market may be negative. The Korean initial offer on Mode 4 is the same as the UR offer. Since Korean position on Mode 4 is most defensive, it is hard to expect that Korean position will be accepted as the single undertaking of Mode 4 negotiation. Thus Korea has to prepare strategic package measures to minimize the costs of Mode 4 liberalization and improve competitiveness of service sector.

  2. Wake mode sidebands and instability in mode-locked lasers with slow saturable absorbers.

    Science.gov (United States)

    Wang, Shaokang; Droste, Stefan; Sinclair, Laura C; Coddington, Ian; Newbury, Nathan R; Carruthers, Thomas F; Menyuk, Curtis R

    2017-06-15

    Passively mode-locked lasers with semiconductor saturable absorption mirrors are attractive comb sources due to their simplicity, excellent self-starting properties, and their environmental robustness. These lasers, however, can have an increased noise level and wake mode instabilities. Here, we investigate the wake mode dynamics in detail using a combination of evolutionary and dynamical methods. We describe the mode-locked pulse generation from noise when a stable pulse exists and the evolution of the wake mode instability when no stable pulse exists. We then calculate the dynamical spectrum of the mode-locked pulse, and we show that it has six discrete eigenmodes, two of which correspond to wake modes. The wake modes are unstable when the wake mode eigenvalues have a positive real part. We also show that even when the laser is stable, the wake modes lead to experimentally observed sidebands.

  3. Characterization of the Copper(II) Binding Sites in Human Carbonic Anhydrase II

    Science.gov (United States)

    Nettles, Whitnee L.; Song, He; Farquhar, Erik R.; Fitzkee, Nicholas C.; Emerson, Joseph P.

    2015-01-01

    Human carbonic anhydrase (CA) is a well-studied, robust, mononuclear Zn-containing metalloprotein that serves as an excellent biological ligand system to study the thermodynamics associated with metal ion coordination chemistry in aqueous solution. The apo-form of human carbonic anhydrase II (CA) binds two equivalents of copper(II) with high affinity. The Cu2+ ions bind independently forming two non-coupled type-II copper centers in CA (CuA and CuB). However, the location and coordination mode of the CuA site in solution is unclear, compared to the CuB site that has been well characterized. Using paramagnetic NMR techniques and X-ray absorption spectroscopy we have identified an N-terminal Cu2+ binding location and collected information on the coordination mode of the CuA site in CA, which is consistent with a four to five coordinate N-terminal Cu2+ binding site reminiscent to a number of N-terminal copper(II) binding sites including the copper(II)-ATCUN and copper(II)-beta-amyloid complexes. Additionally, we report a more detailed analysis of the thermodynamics associated with copper(II) binding to CA. Although we are still unable to fully deconvolute Cu2+ binding data to the high-affinity CuA site, we have derived pH- and buffer-independent values for the thermodynamics parameters K and ΔH associated with Cu2+ binding to the CuB site of CA to be 2 × 109 and −17.4 kcal/mol, respectively. PMID:26010488

  4. Low-collective scissors mode

    Energy Technology Data Exchange (ETDEWEB)

    Nojarov, R.; Faessler, A. (Tuebingen Univ. (Germany, F.R.). Inst. fuer Theoretische Physik)

    1990-06-01

    Realistic microscopic RPA calculations for {sup 156}Gd with a deformed Woods-Saxon mean field, quadrupole-quadrupole, spin-spin and symmetry-restoring residual interactions show that the purely collective scissors mode of the two-rotor model is fragmented over orbital isovector 1{sup +} states, lying at 2-7 MeV. The strongest experimentally observed magnetic dipole state is interpreted as performing a low-collective scissors-type of geometrical motion. This conclusion evolves from the identification of the above state with the strongest RPA excitation, which reproduces well the experimental energy, B(M1) value and (e, e') form factor, has the largest overlap with the scissors state and can be represented as a low-collective scissors type vibration. (orig.).

  5. High-energy scissors mode

    Energy Technology Data Exchange (ETDEWEB)

    Nojarov, R.; Faessler, A.; Dingfelder, M. [Institut fuer Theoretische Physik, Universitaet Tuebingen, Auf der Morgenstelle 14, D-72076 Tuebingen (Germany)

    1995-05-01

    All the orbital {ital M}1 excitations, at both low and high energies, obtained from a rotationally invariant quasiparticle random-phase approximation, represent the fragmented scissors mode. The high-energy {ital M}1 strength is almost purely orbital and resides in the region of the isovector giant quadrupole resonance. In heavy deformed nuclei the high-energy scissors model is strongly fragmented between 17 and 25 MeV (with uncertainties arising from the poor knowledge of the isovector potential). The coherent scissors motion is hindered by the fragmentation and {ital B}({ital M}1){lt}0.25{mu}{sub {ital N}}{sup 2} for single transitions in this region. The ({ital e},{ital e}{prime}) cross sections for excitations above 17 MeV are one order of magnitude larger for {ital E}2 than for {ital M}1 excitations even at backward angles.

  6. Filamentation as primitive growth mode?

    Science.gov (United States)

    Bigan, Erwan; Steyaert, Jean-Marc; Douady, Stéphane

    2015-12-01

    Osmotic pressure influences cellular shape. In a growing cell, chemical reactions and dilution induce changes in osmolarity, which in turn influence the cellular shape. Using a protocell model relying upon random conservative chemical reaction networks with arbitrary stoichiometry, we find that when the membrane is so flexible that its shape adjusts itself quasi-instantaneously to balance the osmotic pressure, the protocell either grows filamentous or fails to grow. This behavior is consistent with a mathematical proof. This suggests that filamentation may be a primitive growth mode resulting from the simple physical property of balanced osmotic pressure. We also find that growth is favored if some chemical species are only present inside the protocell, but not in the outside growth medium. Such an insulation requires specific chemical schemes. Modern evolved cells such as E. coli meet these requirements through active transport mechanisms such as the phosphotransferase system.

  7. A characteristic back support structure in the bisphenol A-binding pocket in the human nuclear receptor ERRγ.

    Directory of Open Access Journals (Sweden)

    Xiaohui Liu

    Full Text Available The endocrine disruptor bisphenol A (BPA affects various genes and hormones even at merely physiological levels. We recently demonstrated that BPA binds strongly to human nuclear receptor estrogen-related receptor (ERR γ and that the phenol-A group of BPA is in a receptacle pocket with essential amino acid residues to provide structural support at the backside. This led BPA to bind to ERRγ in an induced-fit-type binding mode, for example, with a rotated motion of Val313 to support the Tyr326-binding site. A similar binding mechanism appears to occur at the binding site of the BPA phenol-B ring. X-ray crystal analysis of the ERRγ-ligand-binding domain/BPA complex suggested that the ERRγ receptor residues Leu342, Leu345, Asn346, and Ile349 function as intrinsic binding sites of the BPA phenol-B, whereas Leu265, Leu268, Ile310, Val313, Leu324, Tyr330, Lys430, Ala431, and His434 work as structural elements to assist these binding sites. In the present study, by evaluating the mutant receptors replaced by a series of amino acids, we demonstrated that a finely assembled structural network indeed exists around the two adjacent Leu342-Asn346 and Leu345-Ile349 ridges on the same α-helix 7 (H7, constructing a part of the binding pocket structure with back support residues for the BPA phenol-B ring. The results reveal that the double-layer binding sites, namely, the ordinary ligand binding sites and their back support residues, substantiate the strong binding of BPA to ERRγ. When ERRγ-Asn346 was replaced by the corresponding Gly and Tyr in ERRα and ERRβ, respectively, the binding affinity of BPA and even 4-hydroxytamxifen (4-OHT is much reduced. Asn346 was found to be one of the residues that make ERRγ to be exclusive to BPA.

  8. Revealing the mechanisms of protein disorder and N-glycosylation in CD44-hyaluronan binding using molecular simulation

    Directory of Open Access Journals (Sweden)

    Olgun eGuvench

    2015-06-01

    Full Text Available The extracellular N-terminal hyaluronan binding domain (HABD of CD44 is a small globular domain that confers hyaluronan (HA binding functionality to this large transmembrane glycoprotein. When recombinantly expressed by itself, HABD exists as a globular water-soluble protein that retains the capacity to bind HA. This has enabled atomic-resolution structural biology experiments that have revealed the structure of HABD and its binding mode with oligomeric HA. Such experiments have also pointed to an order-to-disorder transition in HABD that is associated with HA binding. However, it had remained unclear how this structural transition was involved in binding since it occurs in a region of HABD distant from the HA-binding site. Furthermore, HABD is known to be N-glycosylated, and such glycosylation can diminish HA binding when the associated N-glycans are capped with sialic acid residues. The intrinsic flexibility of disordered proteins and of N-glycans makes it difficult to apply experimental structural biology approaches to probe the molecular mechanisms of how the order-to-disorder transition and N-glycosylation can modulate HA binding by HABD. We review recent results from molecular dynamics simulations that provide atomic-resolution mechanistic understanding of such modulation to help bridge gaps between existing experimental binding and structural biology data. Findings from these simulations include: Tyr42 may function as a molecular switch that converts the HA binding site from a low affinity to a high affinity state; in the partially-disordered form of HABD, basic amino acids in the C-terminal region can gain sufficient mobility to form direct contacts with bound HA to further stabilize binding; and terminal sialic acids on covalently-attached N-glycans can form charge-paired hydrogen bonding interactions with basic amino acids that could otherwise bind to HA, thereby blocking HA binding to glycosylated CD44 HABD.

  9. Asymmetric cation-binding catalysis

    DEFF Research Database (Denmark)

    Oliveira, Maria Teresa; Lee, Jiwoong

    2017-01-01

    The employment of metal salts is quite limited in asymmetric catalysis, although it would provide an additional arsenal of safe and inexpensive reagents to create molecular functions with high optical purity. Cation chelation by polyethers increases the salts' solubility in conventional organic...... solvents, thus increasing their applicability in synthesis. The expansion of this concept to chiral polyethers led to the emergence of asymmetric cation-binding catalysis, where chiral counter anions are generated from metal salts, particularly using BINOL-based polyethers. Alkali metal salts, namely KF...... and KCN, are selectively bound to the catalyst, providing exceptionally high enantioselectivities for kinetic resolutions, elimination reactions (fluoride base), and Strecker synthesis (cyanide nucleophile). Asymmetric cation-binding catalysis was recently expanded to silicon-based reagents, enabling...

  10. Anion binding in biological systems

    Science.gov (United States)

    Feiters, Martin C.; Meyer-Klaucke, Wolfram; Kostenko, Alexander V.; Soldatov, Alexander V.; Leblanc, Catherine; Michel, Gurvan; Potin, Philippe; Küpper, Frithjof C.; Hollenstein, Kaspar; Locher, Kaspar P.; Bevers, Loes E.; Hagedoorn, Peter-Leon; Hagen, Wilfred R.

    2009-11-01

    We compare aspects of biological X-ray absorption spectroscopy (XAS) studies of cations and anions, and report on some examples of anion binding in biological systems. Brown algae such as Laminaria digitata (oarweed) are effective accumulators of I from seawater, with tissue concentrations exceeding 50 mM, and the vanadate-containing enzyme haloperoxidase is implicated in halide accumulation. We have studied the chemical state of iodine and its biological role in Laminaria at the I K edge, and bromoperoxidase from Ascophyllum nodosum (knotted wrack) at the Br K edge. Mo is essential for many forms of life; W only for certain archaea, such as Archaeoglobus fulgidus and the hyperthermophilic archaeon Pyrococcus furiosus, and some bacteria. The metals are bound and transported as their oxo-anions, molybdate and tungstate, which are similar in size. The transport protein WtpA from P. furiosus binds tungstate more strongly than molybdate, and is related in sequence to Archaeoglobus fulgidus ModA, of which a crystal structure is known. We have measured A. fulgidus ModA with tungstate at the W L3 (2p3/2) edge, and compared the results with the refined crystal structure. XAS studies of anion binding are feasible even if only weak interactions are present, are biologically relevant, and give new insights in the spectroscopy.

  11. Anion binding in biological systems

    Energy Technology Data Exchange (ETDEWEB)

    Feiters, Martin C [Department of Organic Chemistry, Institute for Molecules and Materials, Faculty of Science, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ Nijmegen (Netherlands); Meyer-Klaucke, Wolfram [EMBL Hamburg Outstation at DESY, Notkestrasse 85, D-22607 Hamburg (Germany); Kostenko, Alexander V; Soldatov, Alexander V [Faculty of Physics, Southern Federal University, Sorge 5, Rostov-na-Donu, 344090 (Russian Federation); Leblanc, Catherine; Michel, Gurvan; Potin, Philippe [Centre National de la Recherche Scientifique and Universite Pierre et Marie Curie Paris-VI, Station Biologique de Roscoff, Place Georges Teissier, BP 74, F-29682 Roscoff cedex, Bretagne (France); Kuepper, Frithjof C [Scottish Association for Marine Science, Dunstaffnage Marine Laboratory, Oban, Argyll PA37 1QA, Scotland (United Kingdom); Hollenstein, Kaspar; Locher, Kaspar P [Institute of Molecular Biology and Biophysics, ETH Zuerich, Schafmattstrasse 20, Zuerich, 8093 (Switzerland); Bevers, Loes E; Hagedoorn, Peter-Leon; Hagen, Wilfred R, E-mail: m.feiters@science.ru.n [Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft (Netherlands)

    2009-11-15

    We compare aspects of biological X-ray absorption spectroscopy (XAS) studies of cations and anions, and report on some examples of anion binding in biological systems. Brown algae such as Laminaria digitata (oarweed) are effective accumulators of I from seawater, with tissue concentrations exceeding 50 mM, and the vanadate-containing enzyme haloperoxidase is implicated in halide accumulation. We have studied the chemical state of iodine and its biological role in Laminaria at the I K edge, and bromoperoxidase from Ascophyllum nodosum (knotted wrack) at the Br K edge. Mo is essential for many forms of life; W only for certain archaea, such as Archaeoglobus fulgidus and the hyperthermophilic archaeon Pyrococcus furiosus, and some bacteria. The metals are bound and transported as their oxo-anions, molybdate and tungstate, which are similar in size. The transport protein WtpA from P. furiosus binds tungstate more strongly than molybdate, and is related in sequence to Archaeoglobus fulgidus ModA, of which a crystal structure is known. We have measured A. fulgidus ModA with tungstate at the W L{sub 3} (2p{sub 3/2}) edge, and compared the results with the refined crystal structure. XAS studies of anion binding are feasible even if only weak interactions are present, are biologically relevant, and give new insights in the spectroscopy.

  12. Material Binding Peptides for Nanotechnology

    Directory of Open Access Journals (Sweden)

    Urartu Ozgur Safak Seker

    2011-02-01

    Full Text Available Remarkable progress has been made to date in the discovery of material binding peptides and their utilization in nanotechnology, which has brought new challenges and opportunities. Nowadays phage display is a versatile tool, important for the selection of ligands for proteins and peptides. This combinatorial approach has also been adapted over the past decade to select material-specific peptides. Screening and selection of such phage displayed material binding peptides has attracted great interest, in particular because of their use in nanotechnology. Phage display selected peptides are either synthesized independently or expressed on phage coat protein. Selected phage particles are subsequently utilized in the synthesis of nanoparticles, in the assembly of nanostructures on inorganic surfaces, and oriented protein immobilization as fusion partners of proteins. In this paper, we present an overview on the research conducted on this area. In this review we not only focus on the selection process, but also on molecular binding characterization and utilization of peptides as molecular linkers, molecular assemblers and material synthesizers.

  13. The landscape of cytokinin binding by a plant nodulin

    Energy Technology Data Exchange (ETDEWEB)

    Ruszkowski, M.; Szpotkowski, K.; Sikorski, M. [Polish Academy of Sciences, Poznan (Poland); Jaskolski, M., E-mail: mariuszj@amu.edu.pl [Polish Academy of Sciences, Poznan (Poland); A. Mickiewicz University, Poznan (Poland)

    2013-12-01

    The crystal structures of complexes of M. truncatula nodulin 13 with four cytokinins, trans-zeatin, N{sup 6}-isopentenyladenine, kinetin and N{sup 6}-benzyladenine, show an unusual mode of dimerization of this PR-10-fold plant protein. The cytokinin-binding mode in the internal cavity of the protein is the same in each complex and resembles the pattern found in the cytokinin receptor protein. Nodulation is an extraordinary symbiotic interaction between leguminous plants and nitrogen-fixing bacteria (rhizobia) that assimilate atmospheric nitrogen (in root nodules) and convert it into compounds suitable for the plant host. A class of plant hormones called cytokinins are involved in the nodulation process. In the model legume Medicago truncatula, nodulin 13 (MtN13), which belongs to the pathogenesis-related proteins of class 10 (PR-10), is expressed in the outer cortex of the nodules. In general, PR-10 proteins are small and monomeric and have a characteristic fold with an internal hydrophobic cavity formed between a seven-stranded antiparallel β-sheet and a C-terminal α-helix. Previously, some PR-10 proteins not related to nodulation were found to bind cytokinins such as trans-zeatin. Here, four crystal structures of the MtN13 protein are reported in complexes with several cytokinins, namely trans-zeatin, N{sup 6}-isopentenyladenine, kinetin and N{sup 6}-benzyladenine. All four phytohormones are bound in the hydrophobic cavity in the same manner and have excellent definition in the electron-density maps. The binding of the cytokinins appears to be strong and specific and is reinforced by several hydrogen bonds. Although the binding stoichiometry is 1:1, the complex is actually dimeric, with a cytokinin molecule bound in each subunit. The ligand-binding site in each cavity is formed with the participation of a loop element from the other subunit, which plugs the only entrance to the cavity. Interestingly, a homodimer of MtN13 is also formed in solution, as confirmed

  14. A histone-mimicking interdomain linker in a multidomain protein modulates multivalent histone binding.

    Science.gov (United States)

    Kostrhon, Sebastian; Kontaxis, Georg; Kaufmann, Tanja; Schirghuber, Erika; Kubicek, Stefan; Konrat, Robert; Slade, Dea

    2017-10-27

    N-terminal histone tails are subject to many posttranslational modifications that are recognized by and interact with designated reader domains in histone-binding proteins. BROMO domain adjacent to zinc finger 2B (BAZ2B) is a multidomain histone-binding protein that contains two histone reader modules, a plant homeodomain (PHD) and a bromodomain (BRD), linked by a largely disordered linker. Although previous studies have reported specificity of the PHD domain for the unmodified N terminus of histone H3 and of the BRD domain for H3 acetylated at Lys14 (H3K14ac), the exact mode of H3 binding by BAZ2B and its regulation are underexplored. Here, using isothermal titration calorimetry and NMR spectroscopy, we report that acidic residues in the BAZ2B PHD domain are essential for H3 binding and that BAZ2B PHD-BRD establishes a polyvalent interaction with H3K14ac. Furthermore, we provide evidence that the disordered interdomain linker modulates the histone-binding affinity by interacting with the PHD domain. In particular, lysine-rich stretches in the linker, which resemble the positively charged N terminus of histone H3, reduce the binding affinity of the PHD finger toward the histone substrate. Phosphorylation, acetylation, or poly(ADP-ribosyl)ation of the linker residues may therefore act as a cellular mechanism to transiently tune BAZ2B histone-binding affinity. Our findings further support the concept of interdomain linkers serving a dual role in substrate binding by appropriately positioning the adjacent domains and by electrostatically modulating substrate binding. Moreover, inhibition of histone binding by a histone-mimicking interdomain linker represents another example of regulation of protein-protein interactions by intramolecular mimicry. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  15. Investigate the binding of catechins to trypsin using docking and molecular dynamics simulation.

    Science.gov (United States)

    Cui, Fengchao; Yang, Kecheng; Li, Yunqi

    2015-01-01

    To explore the inhibitory mechanism of catechins for digestive enzymes, we investigated the binding mode of catechins to a typical digestive enzyme-trypsin and analyzed the structure-activity relationship of catechins, using an integration of molecular docking, molecular dynamics simulation and binding free energy calculation. We found that catechins with different structures bound to a conservative pocket S1 of trypsin, which is comprised of residues 189-195, 214-220 and 225-228. In the trypsin-catechin complexes, Asp189 by forming strong hydrogen bonding, and Gln192, Trp215 and Gly216 through hydrophobic interactions, all significantly contribute to the binding of catechins. The number and the position of hydroxyl and aromatic groups, the structure of stereoisomers, and the orientation of catechins in the binding pocket S1 of trypsin all affect the binding affinity. The binding affinity is in the order of Epigallocatechin gallate (EGCG) > Epicatechin gallate (ECG) > Epicatechin (EC) > Epigallocatechin (EGC), and 2R-3R EGCG shows the strongest binding affinity out of other stereoisomers. Meanwhile, the synergic conformational changes of residues and catechins were also analyzed. These findings will be helpful in understanding the knowledge of interactions between catechins and trypsin and referable for the design of novel polyphenol based functional food and nutriceutical formulas.

  16. Six independent fucose-binding sites in the crystal structure of Aspergillus oryzae lectin

    Energy Technology Data Exchange (ETDEWEB)

    Makyio, Hisayoshi [Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki, 305-0801 (Japan); Shimabukuro, Junpei; Suzuki, Tatsuya [Department of Applied Bioorganic Chemistry, Gifu University, 1-1 Yanagido, Gifu-shi, Gifu 501-1193 (Japan); Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida Ushinomiya-cho, Sakyo-ku, Kyoto 606-8501 (Japan); Imamura, Akihiro; Ishida, Hideharu [Department of Applied Bioorganic Chemistry, Gifu University, 1-1 Yanagido, Gifu-shi, Gifu 501-1193 (Japan); Kiso, Makoto [Department of Applied Bioorganic Chemistry, Gifu University, 1-1 Yanagido, Gifu-shi, Gifu 501-1193 (Japan); Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida Ushinomiya-cho, Sakyo-ku, Kyoto 606-8501 (Japan); Ando, Hiromune, E-mail: hando@gifu-u.ac.jp [Department of Applied Bioorganic Chemistry, Gifu University, 1-1 Yanagido, Gifu-shi, Gifu 501-1193 (Japan); Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida Ushinomiya-cho, Sakyo-ku, Kyoto 606-8501 (Japan); Kato, Ryuichi, E-mail: ryuichi.kato@kek.jp [Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki, 305-0801 (Japan)

    2016-08-26

    The crystal structure of AOL (a fucose-specific lectin of Aspergillus oryzae) has been solved by SAD (single-wavelength anomalous diffraction) and MAD (multi-wavelength anomalous diffraction) phasing of seleno-fucosides. The overall structure is a six-bladed β-propeller similar to that of other fucose-specific lectins. The fucose moieties of the seleno-fucosides are located in six fucose-binding sites. Although the Arg and Glu/Gln residues bound to the fucose moiety are common to all fucose-binding sites, the amino-acid residues involved in fucose binding at each site are not identical. The varying peak heights of the seleniums in the electron density map suggest that each fucose-binding site has a different carbohydrate binding affinity. - Highlights: • The six-bladed β-propeller structure of AOL was solved by seleno-sugar phasing. • The mode of fucose binding is essentially conserved at all six binding sites. • The seleno-fucosides exhibit slightly different interactions and electron densities. • These findings suggest that the affinity for fucose is not identical at each site.

  17. Identification of Aminopeptidase-N2 as a Cry2Ab binding protein in Manduca sexta.

    Science.gov (United States)

    Onofre, Janette; Gaytán, Meztlli O; Peña-Cardeña, Arlen; García-Gomez, Blanca I; Pacheco, Sabino; Gómez, Isabel; Bravo, Alejandra; Soberón, Mario

    2017-12-01

    Bacillus thuringiensis Cry2Ab toxin has been used in combination with Cry1Ac for resistance management on the Bt-cotton that is widely planted worldwide. However, little is known regarding Cry2Ab mode of action. Particularly, there is a gap of knowledge on the identification of insect midgut proteins that bind Cry2Ab and mediate toxicity. In the case of Cry1Ab toxin, a transmembrane cadherin protein and glycosyl-phosphatidylinositol (GPI) anchored proteins like aminopeptidase-N1 (APN1) or alkaline-phosphatase (ALP) from Manduca sexta, have been shown to be important for oligomer formation and insertion into the membrane. Binding competition experiments showed that Cry2Ab toxin does not share binding sites with Cry1Ab toxin in M. sexta brush border membrane vesicles (BBMV). Also, that Cry2Ab shows reduced binding to the Cry1Ab binding molecules cadherin, APN1 or ALP. Finally, ligand blot experiments and protein sequence by LC-MS/MS identified APN2 isoform as a Cry2Ab binding protein. Cloning and expression of APN2 confirmed that APN2 is a Cry2Ab binding protein. Copyright © 2017 Elsevier Inc. All rights reserved.

  18. Binding of the multimodal antidepressant drug vortioxetine to the human serotonin transporter.

    Science.gov (United States)

    Andersen, Jacob; Ladefoged, Lucy Kate; Wang, Danyang; Kristensen, Trine N Bjerre; Bang-Andersen, Benny; Kristensen, Anders S; Schiøtt, Birgit; Strømgaard, Kristian

    2015-11-18

    Selective inhibitors of the human serotonin transporter (hSERT) have been first-line treatment against depression for several decades. Recently, vortioxetine was approved as a new therapeutic option for the treatment of depression. Vortioxetine represents a new class of antidepressant drugs with a multimodal pharmacological profile that in addition to potent inhibition of hSERT include agonistic or antagonistic effects at different serotonin receptors. We used a combination of computational, chemical, and biological methods to decipher the molecular basis for high affinity binding of vortioxetine in hSERT. X-ray crystal structures of the bacterial amino acid transporter LeuT and the Drosophila melanogaster dopamine transporter were used to build homology models of hSERT. Comparative modeling and ligand docking suggest that vortioxetine can adopt several distinct binding modes within the central binding site of hSERT. To distinguish between the identified binding modes, we determined the effect of 57 functional hSERT point mutants on vortioxetine potency and characterized seven structurally related analogs of vortioxetine in a subset of the point mutants. This allowed us to determine the orientation of vortioxetine within the central binding site and showed that only one of the proposed binding modes is functionally relevant. The findings provide important new insight about the molecular basis for high affinity recognition of vortioxetine in hSERT, which is essential for future structure-based drug discovery of novel multimodal drugs with fine-tuned selectivity across different transporter and receptor proteins in the human brain.

  19. Developing Network Location Model in Uncertainty Mode (Robust Mode

    Directory of Open Access Journals (Sweden)

    AMINI Mousa

    2013-01-01

    Full Text Available In this research, facility location problem - network design under uncertainty robust mode has been discussed. In this regard a model will be developed, so that the uncertainty in parameters such as demand and problem’s various costs considered. Facility location- network design, unlike classical facility location models, which are assumed that network structure is pre-defined and specified- will also decide on the structure of the network. This has been in many actual applications such as road network, communication systems and etc and finding facility location and main network designing simultaneously has deemed important and the need for simultaneous design and optimization models to meet the mentioned items is felt. Different approaches have been developed in the uncertainty optimization literature. Amongst them, robust and stochastic optimizations are well- known. To deal with uncertainty and problem modeling, in this research robust optimization approach have been used. In addition, by using generated random samples, the proposed model has been tested and computational analysis is presented for various parameters.

  20. Polyethyleneimine anchored copper(II) complexes: synthesis, characterization, in vitro DNA binding studies and cytotoxicity studies.

    Science.gov (United States)

    Lakshmipraba, Jagadeesan; Arunachalam, Sankaralingam; Riyasdeen, Anvarbatcha; Dhivya, Rajakumar; Akbarsha, Mohammad Abdulkader

    2015-01-01

    The water soluble polyethyleneimine-copper(II) complexes, [Cu(phen)(L-tyr)BPEI]ClO4 (where phen=1,10-phenanthroline, L-tyr=L-tyrosine and BPEI=branched polyethyleneimine) with various degree of copper(II) complex units in the polymer chain were synthesized and characterized by elemental analysis and electronic, FT-IR, EPR spectroscopic techniques. The binding of these complexes with CT-DNA was studied using UV-visible absorption titration, thermal denaturation, emission, circular dichroism spectroscopy and cyclic voltammetric methods. The changes observed in the physicochemcial properties indicated that the binding between the polymer-copper complexes and DNA was mostly through electrostatic mode of binding. Among these complexes, the polymer-copper(II) complex with the highest degrees of copper(II) complex units (higher degrees of coordination) showed higher binding constant than those with lower copper(II) complex units (lower degrees of coordination) complexes. The complex with the highest number of metal centre bound strongly due to the cooperative binding effect. Therefore, anticancer study was carried out using this complex. The cytotoxic activity for this complex on MCF-7 breast cancer cell line was determined adopting MTT assay, acridine orange/ethidium bromide (AO/EB) staining and comet assay techniques, which revealed that the cells were committed to specific mode of cell death either apoptosis or necrosis. Copyright © 2014 Elsevier B.V. All rights reserved.

  1. Cu(II Complexes of Isoniazid Schiff Bases: DNA/BSA Binding and Cytotoxicity Studies on A549 Cell Line

    Directory of Open Access Journals (Sweden)

    Pulipaka Ramadevi

    2014-01-01

    Full Text Available A series of isonicotinoyl hydrazones have been synthesized via template method and were complexed to Cu(II. The ligands are coordinated to Cu(II ion through the enolic oxygen and azomethine nitrogen resulting in a square planar geometry. The CT-DNA and bovine serum albumin binding propensities of the compounds were determined spectrophotometrically, the results of which indicate good binding propensity of complexes to DNA and BSA with high binding constant values. Furthermore, the compounds have been investigated for their cytotoxicities on A549 human lung cancer cell. Also the mode of cell death was examined employing various staining techniques and was found to be apoptotic.

  2. Mosquitocidal bacterial toxins: diversity, mode of action and resistance phenomena

    Directory of Open Access Journals (Sweden)

    Charles Jean-François

    2000-01-01

    Full Text Available Bacteria active against dipteran larvae (mosquitoes and black flies include a wide variety of Bacillus thuringiensis and B. sphaericus strains, as well as isolates of Brevibacillus laterosporus and Clostridium bifermentans. All display different spectra and levels of activity correlated with the nature of the toxins, mainly produced during the sporulation process. This paper describes the structure and mode of action of the main mosquitocidal toxins, in relationship with their potential use in mosquito and/or black fly larvae control. Investigations with laboratory and field colonies of mosquitoes that have become highly resistant to the B. sphaericus Bin toxin have shown that several mechanisms of resistance are involved, some affecting the toxin/receptor binding step, others unknown.

  3. Acyl-coenzyme A binding protein (ACBP)

    DEFF Research Database (Denmark)

    Kragelund, B B; Knudsen, J; Poulsen, F M

    1999-01-01

    Acyl-coenzyme A binding proteins are known from a large group of eukaryote species and to bind a long chain length acyl-CoA ester with very high affinity. Detailed biochemical mapping of ligand binding properties has been obtained as well as in-depth structural studies on the bovine apo-protein a...

  4. Binding of quasi two-dimensional biexcitons

    DEFF Research Database (Denmark)

    Birkedal, Dan; Singh, J; Vadim, Lyssenko

    1996-01-01

    Summary form only given. In this presentation we report on a determination of the biexciton binding energies in GaAs-AlGaAs quantum wells of different widths and the results of a theoretical calculation of the ratio of the biexciton binding energy to that of the exciton. We determine the binding ...

  5. binding protein gene from Dasypyrum Villosum

    African Journals Online (AJOL)

    Jane

    2011-07-20

    Jul 20, 2011 ... common wheat. Blue copper-binding protein (BCB) can bind a single copper atom (Ryden and Hunt, 1993). The copper binding sites consist of two ..... Moerschbacher BM, Noll U, Gorrichon L, Reisener HJ (1990). Specific inhibition of lignification breaks hypersensitive resistance of wheat to stem rust.

  6. Identifying modes of large whispering-gallery mode resonators from the spectrum and emission pattern.

    Science.gov (United States)

    Schunk, Gerhard; Fürst, Josef U; Förtsch, Michael; Strekalov, Dmitry V; Vogl, Ulrich; Sedlmeir, Florian; Schwefel, Harald G L; Leuchs, Gerd; Marquardt, Christoph

    2014-12-15

    Identifying the mode numbers in whispering-gallery mode resonators (WGMRs) is important for tailoring them to experimental needs. Here we report on a novel experimental mode analysis technique based on the combination of frequency analysis and far-field imaging for high mode numbers of large WGMRs. The radial mode numbers q and the angular mode numbers p = ℓ-m are identified and labeled via far-field imaging. The polar mode numbers ℓ are determined unambiguously by fitting the frequency differences between individual whispering gallery modes (WGMs). This allows for the accurate determination of the geometry and the refractive index at different temperatures of the WGMR. For future applications in classical and quantum optics, this mode analysis enables one to control the narrow-band phase-matching conditions in nonlinear processes such as second-harmonic generation or parametric down-conversion.

  7. Moving target detection in flash mode against stroboscopic mode by active range-gated laser imaging

    Science.gov (United States)

    Zhang, Xuanyu; Wang, Xinwei; Sun, Liang; Fan, Songtao; Lei, Pingshun; Zhou, Yan; Liu, Yuliang

    2018-01-01

    Moving target detection is important for the application of target tracking and remote surveillance in active range-gated laser imaging. This technique has two operation modes based on the difference of the number of pulses per frame: stroboscopic mode with the accumulation of multiple laser pulses per frame and flash mode with a single shot of laser pulse per frame. In this paper, we have established a range-gated laser imaging system. In the system, two types of lasers with different frequency were chosen for the two modes. Electric fan and horizontal sliding track were selected as the moving targets to compare the moving blurring between two modes. Consequently, the system working in flash mode shows more excellent performance in motion blurring against stroboscopic mode. Furthermore, based on experiments and theoretical analysis, we presented the higher signal-to-noise ratio of image acquired by stroboscopic mode than flash mode in indoor and underwater environment.

  8. A Maltose-Binding Protein Fusion Construct Yields a Robust Crystallography Platform for MCL1.

    Directory of Open Access Journals (Sweden)

    Matthew C Clifton

    Full Text Available Crystallization of a maltose-binding protein MCL1 fusion has yielded a robust crystallography platform that generated the first apo MCL1 crystal structure, as well as five ligand-bound structures. The ability to obtain fragment-bound structures advances structure-based drug design efforts that, despite considerable effort, had previously been intractable by crystallography. In the ligand-independent crystal form we identify inhibitor binding modes not observed in earlier crystallographic systems. This MBP-MCL1 construct dramatically improves the structural understanding of well-validated MCL1 ligands, and will likely catalyze the structure-based optimization of high affinity MCL1 inhibitors.

  9. Electrostatic Control of Isoform Selective Inhibitor Binding in Nitric Oxide Synthase.

    Science.gov (United States)

    Li, Huiying; Wang, Heng-Yen; Kang, Soosung; Silverman, Richard B; Poulos, Thomas L

    2016-07-05

    Development of potent and isoform selective nitric oxide synthase (NOS) inhibitors is challenging because of the structural similarity in the heme active sites. One amino acid difference between NOS isoforms, Asp597 in rat neuronal NOS (nNOS) versus Asn368 in bovine endothelial NOS (eNOS), has been identified as the structural basis for why some dipeptide amide inhibitors bind more tightly to nNOS than to eNOS. We now have found that the same amino acid variation is responsible for substantially different binding modes and affinity for a new class of aminopyridine-based inhibitors.

  10. Mixed-mode fracture of ceramics

    Energy Technology Data Exchange (ETDEWEB)

    Petrovic, J.J.

    1985-01-01

    The mixed-mode fracture behavior of ceramic materials is of importance for monolithic ceramics in order to predict the onset of fracture under generalized loading conditions and for ceramic composites to describe crack deflection toughening mechanisms. Experimental data on surface flaw mixed-mode fracture in various ceramics indicate that the flaw-plane normal stress at fracture decreases with increasing in-flaw-plane shear stress, although present data exhibit a fairly wide range in details of this sigma - tau relationship. Fracture from large cracks suggests that Mode II has a greater effect on Mode I fracture than Mode III. A comparison of surface flaw and large crack mixed-mode I-II fracture responses indicated that surface flaw behavior is influenced by shear resistance effects.

  11. Effect of survey mode on response patterns

    DEFF Research Database (Denmark)

    Christensen, Anne Illemann; Ekholm, Ola; Glümer, Charlotte

    2014-01-01

    .7%). Marital status, ethnic background and highest completed education were associated with non-response in both modes. Furthermore, sex and age were associated with non-response in the self-administered mode. No significant mode effects were observed for indicators related to use of health services...... administrative registers and linked to survey data at individual level. Multiple logistic regression analyses were used to examine the effect of survey mode on response patterns. RESULTS: The non-response rate was higher in the self-administered survey (37.9%) than in the face-to-face interview survey (23......, but significant mode effects were observed for indicators related to self-reported health-related quality of life, health behaviour, social relations and morbidity (long-standing illness). CONCLUSIONS: The same factors were generally associated with non-response in both modes. Indicators based on factual...

  12. Spatial mode discrimination using second harmonic generation

    DEFF Research Database (Denmark)

    Delaubert, Vincent; Lassen, Mikael Østergaard; Pulford, David

    2007-01-01

    -Kleinmann analysis, taking into account the full description of the multi-mode field inside the nonlinear crystal in a type I phase-maching condition. The good agreement between experiments and theory shows that the effect is well understood and that we have reliable models required for the design of novel photonics......Second harmonic generation can be used as a technique for controlling the spatial mode structure of optical beams. We demonstrate experimentally the generation of higher order spatial modes, and that it is possible to use nonlinear phase matching as a predictable and robust technique...... for the conversion of transverse electric modes of the second harmonic output. For a given TEMn0 pump mode the output mode can be altered continuously by adjusting the laser wavelength, the focusing of the pump or the temperature of the nonlinear medium. We make quantitative comparisons with a generalized Boyd...

  13. Semiconductor laser with longitudinal-mode selection

    Science.gov (United States)

    Masloboev, Iu. P.; Poltoratskii, E. A.; Suris, R. A.; Shtofich, S. V.

    1980-06-01

    A new method for longitudinal-mode selection in a semiconductor laser is proposed, based on the conversion of such modes into higher-order transverse modes which can subsequently be filtered out. The key element of this design is an interference cell that is based on an active waveguide, consisting of two branches of different length. If this interference cell is placed between the mirrors of a resonator, and if the emission in higher-order modes is suppressed by some device, the new type of laser with longitudinal-mode selection results. Such a laser would emit in a single mode over a broad range of pump currents, and could be used as an exceptionally good light source for integrated optics and high-speed fiber-optics communications.

  14. Deep Space Mission Emergency Mode Downlink

    Science.gov (United States)

    Kantak, Anil V.

    2008-01-01

    This paper investigates telecommunications between a deep space mission satellite and the ground station during an emergency mode. Once emergency is detected, spacecraft is put into a safe mode, i.e., antenna to be used for emergency mode communications is pointed towards the sun and use total available power to transmit. There are many parameters affecting communications in this mode and these should be properly balanced to produce desired results. This paper explores the effectiveness of spacecraft antenna gain pattern in the emergency mode with respect to positions of the spacecraft, earth, Sun Earth Probe (SEP) angle at the receiving antenna, and the range of the spacecraft with respect to the ground station. The paper also provides parabolic reflector antenna diameter that should be used for emergency mode as a function of the satellite to sun range in the solar system.

  15. Laser modes with helical wave fronts

    Science.gov (United States)

    Harris, M.; Hill, C. A.; Tapster, P. R.; Vaughan, J. M.

    1994-04-01

    We report the operation of an argon-ion laser in pure (single-frequency) ``doughnut'' modes of order m=1, 2, and 3. The phase discontinuity at the center of these modes leads to striking two-beam interference patterns that clearly demonstrate the existence of a helical cophasal surface (wave front). The doughnut mode with m=1 (usually called TEM*01) displays a forking interference fringe pattern characteristic of a pure single helix. The m=2 mode shows a pattern with four extra prongs, establishing that the cophasal surface is a two-start or double helix; the m=3 mode is a triple helix with a six-extra-pronged pattern. Each pure doughnut mode is shown to have two possible states corresponding to output wave fronts of opposite helicity.

  16. Mode propagation and attenuation in lined ducts

    CERN Document Server

    BI, Wenping

    2014-01-01

    Optimal impedance for each mode is an important concept in an infinitely long duct lined with uniform absorption material. However it is not valid for finite length linings. This is because that the modes in lined ducts are not power-orthogonal; the total sound power is not equal to the sum of the sound power of each mode; cross-power terms may play important roles. In this paper, we study sound propagation and attenuation in an infinite rigid duct lined with a finite length of lining impedance. The lining impedance may be axial segments and circumferentially non-uniform. We propose two new physical quantities Kp and S to describe the self-overlap of the left eigenfunction and right eigenfunction of one mode and the normalized overlap between modes, respectively. The two new physical quantities describe totally the mode behaviors in lined ducts.

  17. Structural basis for binding of fluorinated glucose and galactose to Trametes multicolor pyranose 2-oxidase variants with improved galactose conversion.

    Directory of Open Access Journals (Sweden)

    Tien Chye Tan

    Full Text Available Each year, about six million tons of lactose are generated from liquid whey as industrial byproduct, and optimally this large carbohydrate waste should be used for the production of value-added products. Trametes multicolor pyranose 2-oxidase (TmP2O catalyzes the oxidation of various monosaccharides to the corresponding 2-keto sugars. Thus, a potential use of TmP2O is to convert the products from lactose hydrolysis, D-glucose and D-galactose, to more valuable products such as tagatose. Oxidation of glucose is however strongly favored over galactose, and oxidation of both substrates at more equal rates is desirable. Characterization of TmP2O variants (H450G, V546C, H450G/V546C with improved D-galactose conversion has been given earlier, of which H450G displayed the best relative conversion between the substrates. To rationalize the changes in conversion rates, we have analyzed high-resolution crystal structures of the aforementioned mutants with bound 2- and 3-fluorinated glucose and galactose. Binding of glucose and galactose in the productive 2-oxidation binding mode is nearly identical in all mutants, suggesting that this binding mode is essentially unaffected by the mutations. For the competing glucose binding mode, enzyme variants carrying the H450G replacement stabilize glucose as the α-anomer in position for 3-oxidation. The backbone relaxation at position 450 allows the substrate-binding loop to fold tightly around the ligand. V546C however stabilize glucose as the β-anomer using an open loop conformation. Improved binding of galactose is enabled by subtle relaxation effects at key active-site backbone positions. The competing binding mode for galactose 2-oxidation by V546C stabilizes the β-anomer for oxidation at C1, whereas H450G variants stabilize the 3-oxidation binding mode of the galactose α-anomer. The present study provides a detailed description of binding modes that rationalize changes in the relative conversion rates of D

  18. Jurassic climate mode governed by ocean gateway

    OpenAIRE

    Korte, Christoph; Hesselbo, Stephen P.; Ullmann, Clemens Vinzenz; Dietl, Gerd; Ruhl, Micha; Schweigert, Guenter; Thibault, Nicolas

    2015-01-01

    The Jurassic (?201?145?Myr ago) was long considered a warm ?greenhouse' period; more recently cool, even ?icehouse' episodes have been postulated. However, the mechanisms governing transition between so-called Warm Modes and Cool Modes are poorly known. Here we present a new large high-quality oxygen-isotope dataset from an interval that includes previously suggested mode transitions. Our results show an especially abrupt earliest Middle Jurassic (?174?Ma) mid-latitude cooling of seawater by ...

  19. Coupled mode theory of periodic waveguides arrays

    DEFF Research Database (Denmark)

    Lavrinenko, Andrei; Chigrin, Dmitry N.

    We apply the scalar coupled mode theory to the case of waveguides array consisting om two periodic waveguides. One of the waveguides is arbitrary shifted along another. A longitudinal shift acts as a parameter in the coupled mode theory. The proposed theory explains peculiarities of modes dispers...... dispersion and transmission in coupled periodic waveguides systems. Analytical results are compared with the numerical ones obtained by the plane wave expansion and FDTD methods....

  20. Few Mode Multicore Photonic Lantern Multiplexer

    Science.gov (United States)

    2016-01-01

    Zahoora@knights.ucf.edu Abstract: We demonstrate an all-fiber multi-mode, multi-core photonic lantern mode multiplexer for SDM applications ...into a structured capillary consisting of 7 low refractive index fluorine doped capillaries. The device efficiently excites the first three modes (LP01...outer diameter of 125μm. A structured preform consisting of 7 fluorine doped capillaries with Δn=- 9×10-3 and 2 mm outer diameter was used to

  1. Structural basis for the ligand-binding specificity of fatty acid-binding proteins (pFABP4 and pFABP5) in gentoo penguin.

    Science.gov (United States)

    Lee, Chang Woo; Kim, Jung Eun; Do, Hackwon; Kim, Ryeo-Ok; Lee, Sung Gu; Park, Hyun Ho; Chang, Jeong Ho; Yim, Joung Han; Park, Hyun; Kim, Il-Chan; Lee, Jun Hyuck

    2015-09-11

    Fatty acid-binding proteins (FABPs) are involved in transporting hydrophobic fatty acids between various aqueous compartments of the cell by directly binding ligands inside their β-barrel cavities. Here, we report the crystal structures of ligand-unbound pFABP4, linoleate-bound pFABP4, and palmitate-bound pFABP5, obtained from gentoo penguin (Pygoscelis papua), at a resolution of 2.1 Å, 2.2 Å, and 2.3 Å, respectively. The pFABP4 and pFABP5 proteins have a canonical β-barrel structure with two short α-helices that form a cap region and fatty acid ligand binding sites in the hydrophobic cavity within the β-barrel structure. Linoleate-bound pFABP4 and palmitate-bound pFABP5 possess different ligand-binding modes and a unique ligand-binding pocket due to several sequence dissimilarities (A76/L78, T30/M32, underlining indicates pFABP4 residues) between the two proteins. Structural comparison revealed significantly different conformational changes in the β3-β4 loop region (residues 57-62) as well as the flipped Phe60 residue of pFABP5 than that in pFABP4 (the corresponding residue is Phe58). A ligand-binding study using fluorophore displacement assays shows that pFABP4 has a relatively strong affinity for linoleate as compared to pFABP5. In contrast, pFABP5 exhibits higher affinity for palmitate than that for pFABP4. In conclusion, our high-resolution structures and ligand-binding studies provide useful insights into the ligand-binding preferences of pFABPs based on key protein-ligand interactions. Copyright © 2015 Elsevier Inc. All rights reserved.

  2. Coarse-grained molecular dynamics of ligands binding into protein: The case of HIV-1 protease inhibitors

    Science.gov (United States)

    Li, Dechang; Liu, Ming S.; Ji, Baohua; Hwang, Kehchih; Huang, Yonggang

    2009-06-01

    Binding dynamics and pathways of ligands or inhibitors to target proteins are challenging both experimental and theoretical biologists. A dynamics understanding of inhibitors interacting with protein is essential for the design of novel potent drugs. In this work we applied a coarse-grained molecular dynamics method for simulating inhibitors entering the binding cavity of human immunodeficiency virus type 1 protease (PR). It shows that the coarse-grained dynamics, consistent with the experimental results, can capture the essential molecular dynamics of various inhibitors binding into PR. The primary driving force for the binding processes is the nonbond interaction between inhibitors and PR. The size and topology of inhibitors and the interacting strength between inhibitors and PR have great influence on the binding mode and processes. The interaction strength between the PR and various inhibitors is also analyzed by atomistic molecular mechanics and Poisson-Boltzmann solvation area method.

  3. Research of the Power Plant Operational Modes

    Directory of Open Access Journals (Sweden)

    Koismynina Nina M.

    2017-01-01

    Full Text Available In this article the algorithm of the power plant operational modes research is offered. According to this algorithm the program for the modes analysis and connection power transformers choice is developed. The program can be used as educational means for studying of the power plant electric part, at the same time basic data are provided. Also the program can be used for the analysis of the working power plants modes. Checks of the entered data completeness and a choice correctness of the operational modes are provided in the program; in all cases of a deviation from the correct decisions to the user the relevant information is given.

  4. Suspensions with reduced violin string modes

    Energy Technology Data Exchange (ETDEWEB)

    Lee, B H; Ju, L; Blair, D G [School of Physics, University of Western Australia, Crawley 6009, WA (Australia)

    2006-03-02

    We discuss the possibility of significantly reducing the number and Q-factor of violin string modes in the mirror suspension. Simulations of a bar-flexure suspension and an orthogonal ribbon have shown a reduction in the number of violin string modes when compared to a normal ribbon suspension. By calculating the expected suspension thermal noise, we find that the orthogonal ribbon provides a promising suspension alternative. A lower number of violin modes oscillating in the direction of the laser and a reduction in violin mode peak values of at least 23dB can be achieved with a slight increase in thermal noise above 40Hz.

  5. Sliding mode control for synchronous electric drives

    CERN Document Server

    Ryvkin, Sergey E

    2011-01-01

    This volume presents the theory of control systems with sliding mode applied to electrical motors and power converters. It demonstrates the methodology of control design and the original algorithms of control and observation. Practically all semiconductor devices are used in power converters, that feed electrical motors, as power switches. A switching mode offers myriad attractive, inherent properties from a control viewpoint, especially a sliding mode. Sliding mode control supplies high dynamics to systems, invariability of systems to changes of their parameters and of exterior loads in combi

  6. Strip-slot direct mode coupler.

    Science.gov (United States)

    Han, Kyunghun; Kim, Sangsik; Wirth, Justin; Teng, Min; Xuan, Yi; Niu, Ben; Qi, Minghao

    2016-03-21

    We present a direct strip-slot waveguide mode coupler without any auxiliary structures. Contrary to popular belief, an apparent mode mismatch between strip and slot waveguide does not deteriorate conversion efficiency. Separated electric and magnetic field distributions in a slot waveguide lead to highly efficient modal coupling in the direct strip-slot coupler and result in high conversion efficiency. Accurate experimental characterization shows that the direct strip-slot waveguide mode coupler is capable of up to 96% conversion efficiency with a broad bandwidth. Being simplest and of high efficiency, the direct strip-slot waveguide mode coupler can encourage potential applications of slot waveguides.

  7. Multi-mode bosonic Gaussian channels

    Energy Technology Data Exchange (ETDEWEB)

    Caruso, F; Giovannetti, V [NEST CNR-INFM and Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa (Italy); Eisert, J [Institute for Mathematical Sciences, Imperial College London, London SW7 2PE (United Kingdom); Holevo, A S [Steklov Mathematical Institute, Gubkina 8, 119991 Moscow (Russian Federation)], E-mail: filippo.caruso@sns.it

    2008-08-15

    A complete analysis of multi-mode bosonic Gaussian channels (BGCs) is proposed. We clarify the structure of unitary dilations of general Gaussian channels involving any number of bosonic modes and present a normal form. The maximum number of auxiliary modes that is needed is identified, including all rank deficient cases, and the specific role of additive classical noise is highlighted. By using this analysis, we derive a canonical matrix form of the noisy evolution of n-mode BGCs and of their weak complementary counterparts, based on a recent generalization of the normal mode decomposition for non-symmetric or locality constrained situations. This allows us to simplify the weak-degradability classification. Moreover, we investigate the structure of some singular multi-mode channels, like the additive classical noise channel that can be used to decompose a noisy channel in terms of a less noisy one in order to find new sets of maps with zero quantum capacity. Finally, the two-mode case is analyzed in detail. By exploiting the composition rules of two-mode maps and the fact that anti-degradable channels cannot be used to transfer quantum information, we identify sets of two-mode bosonic channels with zero capacity.

  8. Multi-mode bosonic Gaussian channels

    Science.gov (United States)

    Caruso, F.; Eisert, J.; Giovannetti, V.; Holevo, A. S.

    2008-08-01

    A complete analysis of multi-mode bosonic Gaussian channels (BGCs) is proposed. We clarify the structure of unitary dilations of general Gaussian channels involving any number of bosonic modes and present a normal form. The maximum number of auxiliary modes that is needed is identified, including all rank deficient cases, and the specific role of additive classical noise is highlighted. By using this analysis, we derive a canonical matrix form of the noisy evolution of n-mode BGCs and of their weak complementary counterparts, based on a recent generalization of the normal mode decomposition for non-symmetric or locality constrained situations. This allows us to simplify the weak-degradability classification. Moreover, we investigate the structure of some singular multi-mode channels, like the additive classical noise channel that can be used to decompose a noisy channel in terms of a less noisy one in order to find new sets of maps with zero quantum capacity. Finally, the two-mode case is analyzed in detail. By exploiting the composition rules of two-mode maps and the fact that anti-degradable channels cannot be used to transfer quantum information, we identify sets of two-mode bosonic channels with zero capacity.

  9. Correlations between locked modes and impurity influxes

    Energy Technology Data Exchange (ETDEWEB)

    Fishpool, G.M. [Commission of the European Communities, Abingdon (United Kingdom). JET Joint Undertaking; Lawson, K.D. [UKAEA Culham Lab., Abingdon (United Kingdom)

    1994-07-01

    An analysis of pulses that were disturbed by medium Z impurity influxes (Cl, Cr, Fe and Ni) recorded during the 91/92 JET operations, has demonstrated that such influxes can result in MHD modes which subsequently ``lock``. A correlation is found between the power radiated by the influx and the time difference between the start of the influx and the beginning of the locked mode. The growth in the amplitude of the locked mode itself can lead to further impurity influxes. A correlation is noted between intense influxes (superior to 10 MW) and the mode ``unlocking``. (authors). 4 refs., 4 figs.

  10. Drug-binding properties of rat alpha-foetoprotein. Specificities of the phenylbutazone-binding and warfarin-binding sites.

    Science.gov (United States)

    Hervé, F; Rajkowski, K M; Martin, M T; Dessen, P; Cittanova, N

    1986-01-01

    Rat alpha-foetoprotein (alpha-FP) strongly binds the drugs warfarin and phenylbutazone, as does albumin; however, the binding sites for the two drugs seemed to be different. This possibility and the specificity of this/these drug-binding site(s) of rat alpha-FP were investigated by competitive protein-binding experiments with a variety of drugs, representing different pharmacological groups, and biomolecules that are strongly bound by the foetal protein and that are suspected to play a specific role during foetal development. The binding mechanisms were further investigated by using comparisons between computer-derived theoretical displacement curves and experimental points in order to distinguish different possible binding models. The results indicate: that warfarin and phenylbutazone are bound at two distinct sites on rat alpha-FP and that a negative modulatory effect is exerted between the two sites; that the degree of specificity of these two drug-binding sites is different, since the warfarin-binding site appears to be specific for the binding of coumarinic and anthranilic drugs whereas that for phenylbutazone is able to bind substances of very varied chemical structure and is more hydrophobic; that the phenylbutazone-binding site is the site that binds oestrogens that thyroid hormones and, probably, fatty acids and bilirubin are bound at (an)other site(s) but exert negative modulatory effects on phenylbutazone binding. The nature of the different binding areas of rat alpha-FP is compared with that of those already proposed for albumin. The potential risks of toxicity of such interactions between drugs and/or biomolecules on foetal development are also discussed. PMID:2434073

  11. Majorana Zero Modes in Graphene

    Directory of Open Access Journals (Sweden)

    P. San-Jose

    2015-12-01

    Full Text Available A clear demonstration of topological superconductivity (TS and Majorana zero modes remains one of the major pending goals in the field of topological materials. One common strategy to generate TS is through the coupling of an s-wave superconductor to a helical half-metallic system. Numerous proposals for the latter have been put forward in the literature, most of them based on semiconductors or topological insulators with strong spin-orbit coupling. Here, we demonstrate an alternative approach for the creation of TS in graphene-superconductor junctions without the need for spin-orbit coupling. Our prediction stems from the helicity of graphene’s zero-Landau-level edge states in the presence of interactions and from the possibility, experimentally demonstrated, of tuning their magnetic properties with in-plane magnetic fields. We show how canted antiferromagnetic ordering in the graphene bulk close to neutrality induces TS along the junction and gives rise to isolated, topologically protected Majorana bound states at either end. We also discuss possible strategies to detect their presence in graphene Josephson junctions through Fraunhofer pattern anomalies and Andreev spectroscopy. The latter, in particular, exhibits strong unambiguous signatures of the presence of the Majorana states in the form of universal zero-bias anomalies. Remarkable progress has recently been reported in the fabrication of the proposed type of junctions, which offers a promising outlook for Majorana physics in graphene systems.

  12. Transverse multibunch modes for non-rigid bunches, including mode coupling

    Energy Technology Data Exchange (ETDEWEB)

    Berg, J.S.; Ruth, R.D. [Stanford Linear Accelerator Center, Menlo Park, CA (United States)

    1996-08-01

    A method for computing transverse multibunch growth rates and frequency shifts in rings, which has been described previously, is applied to the PEP-II B factory. The method allows multibunch modes with different internal-bunch oscillation modes to couple to one another, similar to single-bunch mode coupling. Including coupling between the multibunch modes gives effects similar to those seen in single-bunch mode coupling. These effects occur at currents that are lower than the single-bunch mode coupling threshold. (author)

  13. Intermodal Nonlinear Effects between Full Vectorial Modes in Few Moded Fiber

    DEFF Research Database (Denmark)

    Rishøj, Lars Søgaard; Rottwitt, Karsten

    2013-01-01

    We experimentally investigate intermodal nonlinear mixing, such as Raman and four wave mixing. This is obtained by pumping in the fundamental mode, or either of the two full vectorial modes, TM01 and TE01 in a specialty designed few moded fiber.......We experimentally investigate intermodal nonlinear mixing, such as Raman and four wave mixing. This is obtained by pumping in the fundamental mode, or either of the two full vectorial modes, TM01 and TE01 in a specialty designed few moded fiber....

  14. A new design of a directional coupler for high order mode multiplexing in few mode fibers

    Science.gov (United States)

    Trichili, Abderrahmen; Ben Salem, Amine; Cherif, Rim; Zghal, Mourad; Forbes, Andrew

    2014-05-01

    We propose a new and versatile design of a directional coupler able to generate and multiplex high order modes in few mode fibers. The designed device can selectively generate five high order modes and multiplex them in a few mode fiber with an overall insertion loss not exceeding 3dB at the telecommunication wavelength λ = 1550 nm. The mode dependent loss is found to be weakly dependent to the wavelength. The proposed device is very promising for high order mode multiplexing and suitable for high bit-rate optical communication systems.

  15. Discrimination of orbital angular momentum modes of the terahertz vortex beam using a diffractive mode transformer.

    Science.gov (United States)

    Liu, Changming; Wei, Xuli; Niu, Liting; Wang, Kejia; Yang, Zhengang; Liu, Jinsong

    2016-06-13

    We present an efficient method to discriminate orbital angular momentum (OAM) of the terahertz (THz) vortex beam using a diffractive mode transformer. The mode transformer performs a log-polar coordinate transformation of the input THz vortex beam, which consists of two 3D-printed diffractive elements. A following lens separates each transformed OAM mode to a different lateral position in its focal plane. This method enables a simultaneous measurement over multiple OAM modes of the THz vortex beam. We experimentally demonstrate the measurement of seven individual OAM modes and two multiplexed OAM modes, which is in good agreement with simulations.

  16. Improved purification of immunoglobulin G from plasma by mixed-mode chromatography.

    Science.gov (United States)

    Chai, Dong-Sheng; Sun, Yan; Wang, Xiao-Ning; Shi, Qing-Hong

    2014-12-01

    Efficient loading of immunoglobulin G in mixed-mode chromatography is often a serious bottleneck in the chromatographic purification of immunoglobulin G. In this work, a mixed-mode ligand, 4-(1H-imidazol-1-yl) aniline, was coupled to Sepharose Fast Flow to fabricate AN SepFF adsorbents with ligand densities of 15-64 mmol/L, and the chromatographic performances of these adsorbents were thoroughly investigated to identify a feasible approach to improve immunoglobulin G purification. The results indicate that a critical ligand density exists for immunoglobulin G on the AN SepFF adsorbents. Above the critical ligand density, the adsorbents showed superior selectivity to immunoglobulin G at high salt concentrations, and also exhibited much higher dynamic binding capacities. For immunoglobulin G purification, both the yield and binding capacity increased with adsorbent ligand density along with a decrease in purity. It is difficult to improve the binding capacity, purity, and yield of immunoglobulin G simultaneously in AN SepFF chromatography. By using tandem AN SepFF chromatography, a threefold increase in binding capacity as well as high purity and yield of immunoglobulin G were achieved. Therefore, the tandem chromatography demonstrates that AN SepFF adsorbent is a practical and feasible alternative to MEP HyperCel adsorbents for immunoglobulin G purification. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  17. Isolation of Prunin from the fruit shell of Bixa orellana and the effect of β-cyclodextrin on its binding with calf thymus DNA.

    Science.gov (United States)

    Yousuf, Sameena; Sudha, N; Murugesan, G; Enoch, Israel V M V

    2013-01-10

    Naringenin-7-O-glucoside [Prunin (Pru)] was isolated from the fruit shell of Bixa orellana L. The binding of Pru with calf thymus DNA (ctDNA) and the influence of cyclomaltoheptaose (β-cyclodextrin, β-CD) on the binding were studied by absorption and fluorescence spectroscopic techniques. The comparison of the binding modes of Pru/β-CD and ctDNA-Pru/β-CD suggested that β-CD extracted Pru from DNA for forming inclusion complex. Molecular modeling gave added support to the above results. Fluorescence microscopy was used to visualize the effect of β-CD on the bindings. Copyright © 2012 Elsevier Ltd. All rights reserved.

  18. Capping of Silybin with β-Cyclodextrin Influences its Binding with Bovine Serum Albumin: A Study by Fluorescence Spectroscopy and Molecular Modeling

    Energy Technology Data Exchange (ETDEWEB)

    Natesan, Sudha; Sowrirajan, Chandrasekaran; Dhanaraj, Premnath; Enoch, Israel V. M. V. [Karunya Univ., Tamil Nadu (India)

    2014-07-15

    The association of silybin with β-cyclodextrin and its influence on silybin's binding with bovine serum albumin are reported. The stoichiometry, binding constant, and the structure of silybin-β-cyclodextrin inclusion complex are reported. The titrations of silybin with bovine serum albumin in the absence and presence of β-cyclodextrin are carried out and the differences in binding strengths are discussed. Molecular modeling is used to optimize the sites and mode of binding of silybin with bovine serum albumin. Forster resonance energy transfer is calculated and the proximity of interacting molecules is reported in the presence and absence of β-cyclodextrin.

  19. Bitopic Ligands and Metastable Binding Sites

    DEFF Research Database (Denmark)

    Fronik, Philipp; Gaiser, Birgit I; Sejer Pedersen, Daniel

    2017-01-01

    G protein-coupled receptors (GPCRs) belong to a large superfamily of membrane receptors mediating a variety of physiological functions. As such they are attractive targets for drug therapy. However, it remains a challenge to develop subtype selective GPCR ligands due to the high conservation...... sites. Computational studies on ligand binding to GPCRs have revealed transient, low-affinity binding sites, termed metastable binding sites. Metastable binding sites may provide a new source of allosteric binding sites that could be exploited in the design of bitopic ligands. Unlike the bitopic ligands...

  20. Cap-binding complex (CBC)

    Science.gov (United States)

    Gonatopoulos-Pournatzis, Thomas; Cowling, Victoria H.

    2013-01-01

    The 7mG (7-methylguanosine cap) formed on mRNA is fundamental to eukaryotic gene expression. Protein complexes recruited to 7mG mediate key processing events throughout the lifetime of the transcript. One of the most important mediators of 7mG functions is CBC (cap-binding complex). CBC has a key role in several gene expression mechanisms, including transcription, splicing, transcript export and translation. Gene expression can be regulated by signalling pathways which influence CBC function. The aim of the present review is to discuss the mechanisms by which CBC mediates and co-ordinates multiple gene expression events. PMID:24354960

  1. DNA damaging, cell cytotoxicity and serum albumin binding efficacy of the rutin-Cu(ii) complex.

    Science.gov (United States)

    Roy, Atanu Singha; Tripathy, Debi Ranjan; Samanta, Sintu; Ghosh, Sudip K; Dasgupta, Swagata

    2016-04-26

    Flavonoids are widely used as anti-oxidants, anti-cancer agents and possess metal ion chelation properties. In this report we have investigated the DNA binding (and damaging), cell cytotoxicity and serum albumin (SA) binding efficacy of the rutin-Cu(ii) complex using differential spectroscopic methods. The rutin-Cu(ii) complex was able to intercalate into calf thymus DNA (ct-DNA) at lower concentrations and its DNA damaging properties were also confirmed from the agarose gel based assay, fluorescence and UV-vis studies. The copper complex was found to be effective against the growth of HeLa cells in vivo. The binding constants (Kb) of the rutin-Cu(ii) complex towards HSA and BSA were found to be (0.98 ± 0.03) and (1.05 ± 0.02) × 10(5) M(-1), respectively, at 299 K and observed to increase with the increase in temperature. Site selectivity studies revealed that the rutin-Cu(ii) complex binds near site 1 (subdomain IIA) of SAs. Thermodynamic parameters indicated that the mode of interaction of rutin and its copper complex with SAs are different from each other. Both ΔH° and ΔS° were observed to be positive for the interaction of the rutin-Cu(ii) complex with SAs, indicating the presence of hydrophobic association in binding. The values of ΔH° were estimated to be negative (-42.07 ± 2.92 and -23.29 ± 2.33 kJ mol(-1) for HSA and BSA respectively) in the binding of rutin with SAs. It implies that after chelation with Cu(ii) ion, rutin alters its binding mode which could have varying applications to its other physicochemical activities.

  2. Binding of 8-methoxypsoralen to DNA in vitro: Monitoring by spectroscopic and chemometrics approaches

    Energy Technology Data Exchange (ETDEWEB)

    Zhou, Xiaoyue; Zhang, Guowen, E-mail: gwzhang@ncu.edu.cn; Wang, Langhong

    2014-10-15

    8-Methoxypsoralen (8-MOP) is a naturally occurring furanocoumarin with a variety of biological and pharmacological activities. The binding mechanism of 8-MOP to calf thymus DNA (ctDNA) at physiological pH was investigated by multi-spectroscopic techniques including UV–vis absorption, fluorescence, circular dichroism (CD) and Fourier transform infrared (FT-IR) spectroscopy along with DNA melting studies and viscosity measurements. The multivariate curve resolution-alternating least squares (MCR-ALS) chemometrics approach was introduced to resolve the expanded UV–vis spectral data matrix, and both the pure spectra and the equilibrium concentration profiles for the components (8-MOP, ctDNA and 8-MOP-ctDNA complex) in the system were successfully obtained to monitor the 8-MOP-ctDNA interaction. The results suggested that 8-MOP could bind to ctDNA via intercalation binding as evidenced by significant increases in melting and relative viscosity of ctDNA and competitive study using acridine orange (AO) as a fluorescence probe. The positive values of enthalpy and entropy change suggested that hydrogen bonds and van der Waals forces played a predominant role in the binding process. Further, FT-IR and CD spectra analysis indicated that 8-MOP preferentially bound to A–T base pairs with no major perturbation in ctDNA double helix conformation. Moreover, molecular docking was employed to exhibit the specific binding mode of 8-MOP to ctDNA intuitively. - Highlights: • The interaction processes of 8-MOP with ctDNA was monitored by MCR-ALS approach. • The binding mode of 8-MOP to ctDNA was an intercalation. • 8-MOP most likely bound to adenine and thymine base pairs of ctDNA. • Molecular docking illustrated the specific binding.

  3. Multiple modes of chromatin remodeling by Forkhead box proteins.

    Science.gov (United States)

    Lalmansingh, Avin S; Karmakar, Sudipan; Jin, Yetao; Nagaich, Akhilesh K

    2012-07-01

    Forkhead box (FOX) proteins represent a large family of transcriptional regulators unified by their DNA binding domain (DBD) known as a 'forkhead' or 'winged helix' domain. Over 40 FOX genes have been identified in the mammalian genome. FOX proteins share significant sequence similarities in the DBD which allow them to bind to a consensus DNA response element. However, their modes of action are quite diverse as they regulate gene expression by acting as pioneer factors, transcription factors, or both. This review focuses on the mechanisms of chromatin remodeling with an emphasis on three sub-classes-FOXA, FOXO, and FOXP members. FOXA proteins serve as pioneer factors to open up local chromatin structure and thereby increase accessibility of chromatin to factors regulating transcription. FOXP proteins, in contrast, function as classic transcription factors to recruit a variety of chromatin modifying enzymes to regulate gene expression. FOXO proteins represent a hybrid subclass having dual roles as pioneering factors and transcription factors. A subset of FOX proteins interacts with condensed mitotic chromatin and may function as 'bookmarking' agents to maintain transcriptional competence at specific genomic sites. The overall diversity in chromatin remodeling function by FOX proteins is related to unique structural motifs present within the DBD flanking regions that govern selective interactions with core histones and/or chromatin coregulatory proteins. This article is part of a Special Issue entitled: Chromatin in time and space. Published by Elsevier B.V.

  4. An alternative mode of microRNA target recognition

    Science.gov (United States)

    Chi, Sung Wook; Hannon, Gregory J.; Darnell, Robert B.

    2012-01-01

    MicroRNAs (miRNAs) regulate mRNA targets through perfect pairing with their seed region (position 2-7). Recently, a precise genome-wide map of miRNA interaction sites in mouse brain was generated by high-throughput sequencing of clusters of ~50 nucleotide RNA tags associated with Argonaute (Ago HITS-CLIP). By analyzing Ago HITS-CLIP “orphan clusters” – Ago binding regions from HITS-CLIP that cannot be explained by canonical seed matches – we have identified an alternative binding mode used by miRNAs. Specifically, G-bulge sites (position 5-6) are often bound and regulated by miR-124 in brain. More generally, bulged sites comprise ≥ 15% (≥ 1441 sites) of all Ago-miRNA interactions in mouse brain and are evolutionally conserved. We have termed position 6 the “pivot” nucleotide and suggest a model in which a transitional “nucleation-bulge” leads to functional bulge mRNA-miRNA interactions, expanding the number of potential miRNA regulatory sites. PMID:22343717

  5. Guiding, bending, and splitting of coupled defect surface modes in a surface-wave photonic crystal

    Energy Technology Data Exchange (ETDEWEB)

    Gao, Zhen; Gao, Fei [Division of Physics and Applied Physics, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, Singapore 637371 (Singapore); Zhang, Baile, E-mail: blzhang@ntu.edu.sg [Division of Physics and Applied Physics, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, Singapore 637371 (Singapore); Centre for Disruptive Photonic Technologies, Nanyang Technological University, Singapore, Singapore 637371 (Singapore)

    2016-01-25

    We experimentally demonstrate a type of waveguiding mechanism for coupled surface-wave defect modes in a surface-wave photonic crystal. Unlike conventional spoof surface plasmon waveguides, waveguiding of coupled surface-wave defect modes is achieved through weak coupling between tightly localized defect cavities in an otherwise gapped surface-wave photonic crystal, as a classical wave analogue of tight-binding electronic wavefunctions in solid state lattices. Wave patterns associated with the high transmission of coupled defect surface modes are directly mapped with a near-field microwave scanning probe for various structures including a straight waveguide, a sharp corner, and a T-shaped splitter. These results may find use in the design of integrated surface-wave devices with suppressed crosstalk.

  6. A unified model of the GABA(A receptor comprising agonist and benzodiazepine binding sites.

    Directory of Open Access Journals (Sweden)

    Rikke Bergmann

    Full Text Available We present a full-length α(1β(2γ(2 GABA receptor model optimized for agonists and benzodiazepine (BZD allosteric modulators. We propose binding hypotheses for the agonists GABA, muscimol and THIP and for the allosteric modulator diazepam (DZP. The receptor model is primarily based on the glutamate-gated chloride channel (GluCl from C. elegans and includes additional structural information from the prokaryotic ligand-gated ion channel ELIC in a few regions. Available mutational data of the binding sites are well explained by the model and the proposed ligand binding poses. We suggest a GABA binding mode similar to the binding mode of glutamate in the GluCl X-ray structure. Key interactions are predicted with residues α(1R66, β(2T202, α(1T129, β(2E155, β(2Y205 and the backbone of β(2S156. Muscimol is predicted to bind similarly, however, with minor differences rationalized with quantum mechanical energy calculations. Muscimol key interactions are predicted to be α(1R66, β(2T202, α(1T129, β(2E155, β(2Y205 and β(2F200. Furthermore, we argue that a water molecule could mediate further interactions between muscimol and the backbone of β(2S156 and β(2Y157. DZP is predicted to bind with interactions comparable to those of the agonists in the orthosteric site. The carbonyl group of DZP is predicted to interact with two threonines α(1T206 and γ(2T142, similar to the acidic moiety of GABA. The chlorine atom of DZP is placed near the important α(1H101 and the N-methyl group near α(1Y159, α(1T206, and α(1Y209. We present a binding mode of DZP in which the pending phenyl moiety of DZP is buried in the binding pocket and thus shielded from solvent exposure. Our full length GABA(A receptor is made available as Model S1.

  7. Exploration of binding of bisphenol A and its analogues with calf thymus DNA by optical spectroscopic and molecular docking methods.

    Science.gov (United States)

    Wang, Yan-Qing; Zhang, Hong-Mei

    2015-08-01

    Bisphenol A and its analogues have carcinogenic potentials and toxicities. However, there are lacks of studies elucidating gene toxic interactions of bisphenols with DNA. In this work, the binding modes of five bisphenol compounds with calf thymus DNA were characterized. The multi-spectroscopic experimental results indicated that the fluorescence quenching of bisphenols by calf thymus DNA point to groove binding. The ultraviolet visible and circular dichroism spectral data displayed that bisphenols partly induced conformational changes of calf thymus DNA. In addition, the binding constants of bisphenol A, diphenolic acid, bisphenol AF, bisphenol AP, bisphenol fluorine with calf thymus DNA obtained from fluorescence emission spectra were 1.09×10(4), 3.65×10(4), 4.46×10(4), 1.69×10(4), 4.49×10(4)Lmol(-1) at 298.15K, which indicated that the multi-noncovalent binding forces were involved in the binding processes. In silico investigations indicated that DNA has the preferable binding sites binding with bisphenols by minor groove binding and electrons transfer from DNA bases to bisphenols occurred. In addition, the structural differences of these five bisphenols partly affected the binding ability of them with DNA. Copyright © 2015 Elsevier B.V. All rights reserved.

  8. Engineering RNA-binding proteins for biology.

    Science.gov (United States)

    Chen, Yu; Varani, Gabriele

    2013-08-01

    RNA-binding proteins play essential roles in the regulation of gene expression. Many have modular structures and combine relatively few common domains in various arrangements to recognize RNA sequences and/or structures. Recent progress in engineering the specificity of the PUF class RNA-binding proteins has shown that RNA-binding domains may be combined with various effector or functional domains to regulate the metabolism of targeted RNAs. Designer RNA-binding proteins with tailored sequence specificity will provide valuable tools for biochemical research as well as potential therapeutic applications. In this review, we discuss the suitability of various RNA-binding domains for engineering RNA-binding specificity, based on the structural basis for their recognition. We also compare various protein engineering and design methods applied to RNA-binding proteins, and discuss future applications of these proteins. © 2013 FEBS.

  9. Interaction of Lamb modes with an inclusion.

    Science.gov (United States)

    Shkerdin, G; Glorieux, C

    2013-01-01

    The interaction of Lamb modes propagating in a steel plate containing a thin inclusion is analyzed for cases where the inclusion material has elastic parameters similar to the ones of the plate, and where the inclusion is in perfect mechanical contact with the surrounding plate material. A modal decomposition method is used to calculate the conversion of an incident Lamb mode to other modes. Hence, the influence of the type of incident mode, of the location and geometry of the inclusion, and of the elastic parameters of the inclusion and plate material on the mode conversion coefficients is analyzed. Besides the expected increase of the conversion efficiency with increasing cross section of the inclusion, it is found that due to reasons of symmetry, the presence of an inclusion leads to an efficient conversion of an incident S0 mode into reflected and transmitted A0 modes, unless the inclusion is located very close to the plate center. On the other hand, the conversion efficiency of an incident A0 mode into a reflected A0 mode is found to be strongly dependent on the depth of the inclusion, this conversion even disappearing for some location depths. For the cases studied, the inclusion location dependence of the mode conversion seems to be correlated with the normal profile of the longitudinal normal stress component σ(yy)(y). As intuitively expected, the mode conversion efficiency increases with the mismatch of an acoustic impedance like factor between the uniform plate and the inclusion region. Copyright © 2012 Elsevier B.V. All rights reserved.

  10. Mode Transitions in Hall Effect Thrusters

    Science.gov (United States)

    Sekerak, Michael J.; Longmier, Benjamin W.; Gallimore, Alec D.; Brown, Daniel L.; Hofer, Richard R.; Polk, James E.

    2013-01-01

    Mode transitions have been commonly observed in Hall Effect Thruster (HET) operation where a small change in a thruster operating parameter such as discharge voltage, magnetic field or mass flow rate causes the thruster discharge current mean value and oscillation amplitude to increase significantly. Mode transitions in a 6-kW-class HET called the H6 are induced by varying the magnetic field intensity while holding all other operating parameters constant and measurements are acquired with ion saturation probes and ultra-fast imaging. Global and local oscillation modes are identified. In the global mode, the entire discharge channel oscillates in unison and azimuthal perturbations (spokes) are either absent or negligible. Downstream azimuthally spaced probes show no signal delay between each other and are very well correlated to the discharge current signal. In the local mode, signals from the azimuthally spaced probes exhibit a clear delay indicating the passage of "spokes" and are not well correlated to the discharge current. These spokes are localized oscillations propagating in the ExB direction that are typically 10-20% of the mean value. In contrast, the oscillations in the global mode can be 100% of the mean value. The transition between global and local modes occurs at higher relative magnetic field strengths for higher mass flow rates or higher discharge voltages. The thrust is constant through mode transition but the thrust-to-power decreased by 25% due to increasing discharge current. The plume shows significant differences between modes with the global mode significantly brighter in the channel and the near-field plasma plume as well as exhibiting a luminous spike on thruster centerline. Mode transitions provide valuable insight to thruster operation and suggest improved methods for thruster performance characterization.

  11. Statistical dynamo theory: Mode excitation.

    Science.gov (United States)

    Hoyng, P

    2009-04-01

    We compute statistical properties of the lowest-order multipole coefficients of the magnetic field generated by a dynamo of arbitrary shape. To this end we expand the field in a complete biorthogonal set of base functions, viz. B= summation operator_{k}a;{k}(t)b;{k}(r) . The properties of these biorthogonal function sets are treated in detail. We consider a linear problem and the statistical properties of the fluid flow are supposed to be given. The turbulent convection may have an arbitrary distribution of spatial scales. The time evolution of the expansion coefficients a;{k} is governed by a stochastic differential equation from which we infer their averages a;{k} , autocorrelation functions a;{k}(t)a;{k *}(t+tau) , and an equation for the cross correlations a;{k}a;{l *} . The eigenfunctions of the dynamo equation (with eigenvalues lambda_{k} ) turn out to be a preferred set in terms of which our results assume their simplest form. The magnetic field of the dynamo is shown to consist of transiently excited eigenmodes whose frequency and coherence time is given by Ilambda_{k} and -1/Rlambda_{k} , respectively. The relative rms excitation level of the eigenmodes, and hence the distribution of magnetic energy over spatial scales, is determined by linear theory. An expression is derived for |a;{k}|;{2}/|a;{0}|;{2} in case the fundamental mode b;{0} has a dominant amplitude, and we outline how this expression may be evaluated. It is estimated that |a;{k}|;{2}/|a;{0}|;{2} approximately 1/N , where N is the number of convective cells in the dynamo. We show that the old problem of a short correlation time (or first-order smoothing approximation) has been partially eliminated. Finally we prove that for a simple statistically steady dynamo with finite resistivity all eigenvalues obey Rlambda_{k}<0 .

  12. Phosphatidylethanolamine-binding is a common feature for cyclotide-membrane interactions

    DEFF Research Database (Denmark)

    Henriques, Sonia; Huang, Yen-Hua; Castanho, Miguel

    2012-01-01

    subfamilies, Möbius and bracelet, and an all-d mirror image form, were examined to determine their mode of action. Their lipid selectivity and membrane affinity were determined, as were their toxicities against a range of targets (red blood cells, bacteria, and HIV particles). Although they had different...... membrane-binding affinities, all of the tested cyclotides targeted membranes through binding to phospholipids containing phosphatidylethanolamine headgroups. Furthermore, the biological potency of the tested cyclotides broadly correlated with their ability to target and disrupt cell membranes. The finding...... are regarded as a combinatorial peptide template with potential applications in drug design. The mode of action of cyclotides remains elusive, but all reported biological activities are consistent with a mechanism involving membrane interactions. In this study, a diverse set of cyclotides from the two major...

  13. Multimodal chromatography: Characterization of protein binding and selectivity enhancement through mobile phase modulators.

    Science.gov (United States)

    Wolfe, Leslie S; Barringer, Cartney P; Mostafa, Sigma S; Shukla, Abhinav A

    2014-05-02

    The unique selectivity of mixed mode chromatography resins is driving increasing utilization of these novel selectivities into bioprocess applications. There is a need for improved fundamental understanding of protein binding to these stationary phases to enable the development of efficient and robust purification processes. A panel of four monoclonal antibodies and two model proteins were employed to characterize protein interaction with a mixed-mode chromatographic resin comprising a hydrophobic ligand with cation-exchange functionality. Binding of these proteins was studied as a function of salt concentration and pH in the presence of various mobile phase modulators. This knowledge was applied towards screening mobile phase modulators that could selectively decrease host cell protein levels during monoclonal antibody purification. Copyright © 2014 Elsevier B.V. All rights reserved.

  14. Human plasminogen binding protein tetranectin

    DEFF Research Database (Denmark)

    Kastrup, J S; Rasmussen, H; Nielsen, B B

    1997-01-01

    The recombinant human plasminogen binding protein tetranectin (TN) and the C-type lectin CRD of this protein (TN3) have been crystallized. TN3 crystallizes in the tetragonal space group P4(2)2(1)2 with cell dimensions a = b = 64.0, c = 75.7 A and with one molecule per asymmetric unit. The crystals...... to at least 2.5 A. A full data set has been collected to 3.0 A. The asymmetric unit contains one monomer of TN. Molecular replacement solutions for TN3 and TN have been obtained using the structure of the C-type lectin CRD of rat mannose-binding protein as search model. The rhombohedral space group indicates...... diffract X-rays to at least 2.0 A resolution. A complete diffraction data set has been collected to 2.7 A resolution. The crystals of TN, obtained by the vapour-diffusion reverse salting-in method at 280 K, are rhombohedral, space group R3, with the hexagonal axes a = b = 89.1, c = 75.8 A, and diffract...

  15. Structure and stability of an unusual zinc-binding protein from Bacteroides thetaiotaomicron.

    Science.gov (United States)

    Knaus, Tanja; Uhl, Michael K; Monschein, Stefanie; Moratti, Sabrina; Gruber, Karl; Macheroux, Peter

    2014-12-01

    The crystal structure of a putative protease from Bacteroides thetaiotaomicron (ppBat) suggested the presence of a zinc ion in each protomer of the dimer as well as a flavin in the dimer interface. Since the chemical identity of the flavin and the exact mode of binding remained unclear, we have determined the crystal structure of ppBat in complex with riboflavin. The obtained structure revealed that the isoalloxazine ring is sandwiched between two tryptophan residues (Trp164) from both chains and adopts two alternate orientations with the N(10)-ribityl side chain protruding from the binding site in opposite directions. In order to characterize the zinc-binding site, we generated two single variants and one double variant in which the two coordinating cysteine residues (Cys74 and Cys111) were replaced by alanine. All three variants were unable to bind zinc demonstrating that both cysteine residues are essential for binding. Moreover, the lack of zinc binding also resulted in drastically reduced thermal stability (11-15°C). A similar effect was obtained when wild-type protein was incubated with EDTA supporting the conclusion that the zinc-binding site plays an important structural role in ppBat. On the other hand, attempts to identify proteolytic activity failed suggesting that the zinc may not act as a catalytic center in ppBat. Structurally similar zinc binding motives in other proteins were also found to play a structural rather than catalytic role and hence it appears that neither the flavin nor the zinc binding sites possess a catalytic function in ppBat. Copyright © 2014 Elsevier B.V. All rights reserved.

  16. Switchable dual-mode all-fiber laser with few-mode fiber Bragg grating

    Science.gov (United States)

    Jin, Wenxing; Qi, Yanhui; Yang, Yuguang; Jiang, Youchao; Wu, Yue; Xu, Yao; Yao, Shuzhi; Jian, Shuisheng

    2017-09-01

    We propose a new approach to realize switchable mode operation in a few-mode erbium-doped fiber laser. The ring fiber laser structure is constructed with a core-offset splicing between single-mode fiber and dual-mode fiber. Stable operating on the fundamental mode laser and second-order mode laser individually or simultaneously is realized by appropriately adjusting the state of the polarization controller and bending status of the few-mode fiber Bragg grating. The narrow 3 dB linewidth less than 0.02 nm and high optical signal to noise ratio more than 42 dB are obtained for both modes in either separate laser or simultaneous laser operating conditions.

  17. New Edge Coherent Mode Providing Continuous Transport in Long Pulse H-mode Plasmas

    DEFF Research Database (Denmark)

    Wang, H.Q.; Xu, G.S.; Wan, B.N.

    2014-01-01

    An electrostatic coherent mode near the electron diamagnetic frequency (20–90 kHz) is observed in the steep-gradient pedestal region of long pulse H-mode plasmas in the Experimental Advanced Super-conducting Tokamak, using a newly developed dual gas-puff-imaging system and diamond-coated reciproc......An electrostatic coherent mode near the electron diamagnetic frequency (20–90 kHz) is observed in the steep-gradient pedestal region of long pulse H-mode plasmas in the Experimental Advanced Super-conducting Tokamak, using a newly developed dual gas-puff-imaging system and diamond......-coated reciprocating probes. The mode propagates in the electron diamagnetic direction in the plasma frame with poloidal wavelength of ∼8 cm. The mode drives a significant outflow of particles and heat as measured directly with the probes, thus greatly facilitating long pulse H-mode sustainment. This mode shows...

  18. Multiwavelength mode-locked cylindrical vector beam fiber laser based on mode selective coupler

    Science.gov (United States)

    Huang, Ping; Cai, Yu; Wang, Jie; Wan, Hongdan; Zhang, Zuxing; Zhang, Lin

    2017-10-01

    We propose and demonstrate a multiwavelength mode-locked fiber laser with cylindrical vector beam generation for the first time, to the best of our knowledge. The mode-locking mechanism is based on a nonlinear polarization rotation effect in fiber, and the multiwavelength operation is contributed to by an in-line birefringence fiber filter with periodic multiple passbands, formed by incorporating a section of polarization maintaining fiber into the laser cavity with a fiber polarizer. Furthermore, by using a home-made mode selective coupler, which acts as both a mode converter from fundamental mode to higher-order mode and an output coupler, multiwavelength mode-locked cylindrical vector beams have been obtained. This may have potential applications in mode-division multiplexing optical fiber communication and material processing.

  19. High efficiency mode-locked, cylindrical vector beam fiber laser based on a mode selective coupler.

    Science.gov (United States)

    Wan, Hongdan; Wang, Jie; Zhang, Zuxing; Cai, Yu; Sun, Bin; Zhang, Lin

    2017-05-15

    We propose and demonstrate an all-fiber passively mode-locked laser with a figure-8 cavity, which generates pulsed cylindrical vector beam output based on a mode selective coupler (MSC). The MSC made of a two mode fiber and a standard single mode fiber is used as both the intracavity transverse mode converter and mode splitter with a low insertion loss of about 0.65 dB. The slope efficiency of the fiber laser is > 3%. Through adjusting the polarization state in the laser cavity, both radially and azimuthally polarized beams have been obtained with high mode purity which are measured to be > 94%. The laser operates at 1556.3 nm with a spectral bandwidth of 3.2 nm. The mode-locked pulses have duration of 17 ns and a repetition rate of 0.66 MHz.

  20. Direct experimental measurement of single-mode and mode-hopping dynamics in frequency swept lasers.

    Science.gov (United States)

    Butler, T P; Goulding, D; Kelleher, B; O'Shaughnessy, B; Slepneva, S; Hegarty, S P; Huyet, G

    2017-10-30

    A time-resolved study is presented of the single-mode and mode-switching dynamics observed in swept source vertical cavity surfing emitting lasers and swept wavelength short external cavity lasers. A self-delayed interferometric technique is used to experimentally measure the phase and intensity of these frequency swept lasers, allowing direct examination of the modal dynamics. Visualisation of the instantaneous optical spectrum reveals mode-hop free single mode lasing in the case of the vertical cavity laser, with a tuning rate of 6.3 GHz/ns. More complex mode-switching behaviour occurs in the external cavity laser, with the mode-hopping dynamics found to be dominated by the deterministic movement of the spectral filter. Evidence of transient multi-mode operation and mode-pulling is also presented.