WorldWideScience

Sample records for strict ligand specificity

  1. Pseudouridine synthase 1: a site-specific synthase without strict sequence recognition requirements

    Science.gov (United States)

    Sibert, Bryan S.; Patton, Jeffrey R.

    2012-01-01

    Pseudouridine synthase 1 (Pus1p) is an unusual site-specific modification enzyme in that it can modify a number of positions in tRNAs and can recognize several other types of RNA. No consensus recognition sequence or structure has been identified for Pus1p. Human Pus1p was used to determine which structural or sequence elements of human tRNASer are necessary for pseudouridine (Ψ) formation at position 28 in the anticodon stem-loop (ASL). Some point mutations in the ASL stem of tRNASer had significant effects on the levels of modification and compensatory mutation, to reform the base pair, restored a wild-type level of Ψ formation. Deletion analysis showed that the tRNASer TΨC stem-loop was a determinant for modification in the ASL. A mini-substrate composed of the ASL and TΨC stem-loop exhibited significant Ψ formation at position 28 and a number of mutants were tested. Substantial base pairing in the ASL stem (3 out of 5 bp) is required, but the sequence of the TΨC loop is not required for modification. When all nucleotides in the ASL stem other than U28 were changed in a single mutant, but base pairing was retained, a near wild-type level of modification was observed. PMID:22102571

  2. Specific activity of radioiodine-labelled human chorionic gonadotropin ligand

    International Nuclear Information System (INIS)

    Crespi, M.; Kay, G.W.; Van der Walt, L.A.

    1983-01-01

    The article deals with the determination of the specific activity of radioiodine-labbelled human chorionic gonadotropin ligand. The iodiation of human chorionic gonadotropin and the counting efficiency of 125 I are discussed

  3. Molecular mechanism of strict substrate specificity of an extradiol dioxygenase, DesB, derived from Sphingobium sp. SYK-6.

    Directory of Open Access Journals (Sweden)

    Keisuke Sugimoto

    Full Text Available DesB, which is derived from Sphingobium sp. SYK-6, is a type II extradiol dioxygenase that catalyzes a ring opening reaction of gallate. While typical extradiol dioxygenases show broad substrate specificity, DesB has strict substrate specificity for gallate. The substrate specificity of DesB seems to be required for the efficient growth of S. sp. SYK-6 using lignin-derived aromatic compounds. Since direct coordination of hydroxyl groups of the substrate to the non-heme iron in the active site is a critical step for the catalytic reaction of the extradiol dioxygenases, the mechanism of the substrate recognition and coordination of DesB was analyzed by biochemical and crystallographic methods. Our study demonstrated that the direct coordination between the non-heme iron and hydroxyl groups of the substrate requires a large shift of the Fe (II ion in the active site. Mutational analysis revealed that His124 and His192 in the active site are essential to the catalytic reaction of DesB. His124, which interacts with OH (4 of the bound gallate, seems to contribute to proper positioning of the substrate in the active site. His192, which is located close to OH (3 of the gallate, is likely to serve as the catalytic base. Glu377' interacts with OH (5 of the gallate and seems to play a critical role in the substrate specificity. Our biochemical and structural study showed the substrate recognition and catalytic mechanisms of DesB.

  4. Sensitive and specific detection of ligands using engineered riboswitches.

    Science.gov (United States)

    Morse, Daniel P; Nevins, Colin E; Aggrey-Fynn, Joana; Bravo, Rick J; Pfaeffle, Herman O I; Laney, Jess E

    2018-03-05

    Riboswitches are RNA elements found in non-coding regions of messenger RNAs that regulate gene expression through a ligand-triggered conformational change. Riboswitches typically bind tightly and specifically to their ligands, so they have the potential to serve as highly effective sensors in vitro. In B. subtilis and other gram-positive bacteria, purine nucleotide synthesis is regulated by riboswitches that bind to guanine. We modified the xpt-pbuX guanine riboswitch for use in a fluorescence quenching assay that allowed us to specifically detect and quantify guanine in vitro. Using this assay, we reproducibly detected as little as 5 nM guanine. We then produced sensors for 2'-deoxyguanosine and cyclic diguanylate (c-diGMP) by appending the P1 stem of the guanine riboswitch to the ligand-binding domains of a 2'-deoxyguanosine riboswitch and a c-diGMP riboswitch. These hybrid sensors could detect 15 nM 2'-deoxyguanosine and 3 nM c-diGMP, respectively. Each sensor retained the ligand specificity of its corresponding natural riboswitch. In order to extend the utility of our approach, we developed a strategy for the in vitro selection of sensors with novel ligand specificity. Here we report a proof-of-principle experiment that demonstrated the feasibility of our selection strategy. Published by Elsevier B.V.

  5. Evolution of ligand specificity in vertebrate corticosteroid receptors

    Directory of Open Access Journals (Sweden)

    Deitcher David L

    2011-01-01

    Full Text Available Abstract Background Corticosteroid receptors include mineralocorticoid (MR and glucocorticoid (GR receptors. Teleost fishes have a single MR and duplicate GRs that show variable sensitivities to mineralocorticoids and glucocorticoids. How these receptors compare functionally to tetrapod MR and GR, and the evolutionary significance of maintaining two GRs, remains unclear. Results We used up to seven steroids (including aldosterone, cortisol and 11-deoxycorticosterone [DOC] to compare the ligand specificity of the ligand binding domains of corticosteroid receptors between a mammal (Mus musculus and the midshipman fish (Porichthys notatus, a teleost model for steroid regulation of neural and behavioral plasticity. Variation in mineralocorticoid sensitivity was considered in a broader phylogenetic context by examining the aldosterone sensitivity of MR and GRs from the distantly related daffodil cichlid (Neolamprologus pulcher, another teleost model for neurobehavioral plasticity. Both teleost species had a single MR and duplicate GRs. All MRs were sensitive to DOC, consistent with the hypothesis that DOC was the initial ligand of the ancestral MR. Variation in GR steroid-specificity corresponds to nine identified amino acid residue substitutions rather than phylogenetic relationships based on receptor sequences. Conclusion The mineralocorticoid sensitivity of duplicate GRs in teleosts is highly labile in the context of their evolutionary phylogeny, a property that likely led to neo-functionalization and maintenance of two GRs.

  6. Redesigning an FKBP–ligand interface to generate chemical dimerizers with novel specificity

    OpenAIRE

    Clackson, Tim; Yang, Wu; Rozamus, Leonard W.; Hatada, Marcos; Amara, Jane F.; Rollins, Carl T.; Stevenson, Lauren F.; Magari, Shannon R.; Wood, Susan A.; Courage, Nancy L.; Lu, Xiaode; Cerasoli, Franklin; Gilman, Michael; Holt, Dennis A.

    1998-01-01

    FKBP ligand homodimers can be used to activate signaling events inside cells and animals that have been engineered to express fusions between appropriate signaling domains and FKBP. However, use of these dimerizers in vivo is potentially limited by ligand binding to endogenous FKBP. We have designed ligands that bind specifically to a mutated FKBP over the wild-type protein by remodeling an FKBP-ligand interface to introduce a specificity binding pocket. A compound bearing an ethyl substituen...

  7. Ligand specificity of nuclear hormone receptors: sifting through promiscuity.

    Science.gov (United States)

    Noy, Noa

    2007-11-27

    The superfamily of nuclear hormone receptors includes transcription factors that play key roles in regulating multiple biological functions during embryonic development and in adult tissues, as well as in many disease states. The quintessential characteristic of nuclear receptors, and the basis for the name of the family, is that their transcriptional activities can be regulated by small molecules, usually comprised of hydrophobic compounds. However, the endogenous ligands for approximately half of the members of the nuclear receptor family are unknown, and these receptors are thus designated as "orphan receptors". One class of orphan receptors encompasses receptors that display a broad ligand selectivity; i.e., they can promiscuously bind to and may be activated by multiple ligands. This characteristic complicates the identification of physiologically meaningful ligands that activate these receptors in vivo. Here, we discuss a few examples of promiscuous receptors and outline strategies that may be employed in shedding light on the nature of bona fide ligands for such receptors.

  8. Strict confluent drawing

    Directory of Open Access Journals (Sweden)

    David Eppstein

    2016-01-01

    Full Text Available We define strict confluent drawing, a form of confluent drawing in which the existence of an edge is indicated by the presence of a smooth path through a system of arcs and junctions (without crossings, and in which such a path, if it exists, must be unique. We prove that it is NP-complete to determine whether a given graph has a strict confluent drawing but polynomial to determine whether it has an outerplanar strict confluent drawing with a fixed vertex ordering (a drawing within a disk, with the vertices placed in a given order on the boundary.

  9. Ligand-specific conformational changes in the alpha1 glycine receptor ligand-binding domain

    DEFF Research Database (Denmark)

    Pless, Stephan Alexander; Lynch, Joseph W

    2009-01-01

    , and by the antagonist, strychnine. Voltage-clamp fluorometry involves labeling introduced cysteines with environmentally sensitive fluorophores and inferring structural rearrangements from ligand-induced fluorescence changes. In the inner beta-sheet, we labeled residues in loop 2 and in binding domain loops D and E....... At each position, strychnine and glycine induced distinct maximal fluorescence responses. The pre-M1 domain responded similarly; at each of four labeled positions glycine produced a strong fluorescence signal, whereas strychnine did not. This suggests that glycine induces conformational changes...... in the inner beta-sheet and pre-M1 domain that may be important for activation, desensitization, or both. In contrast, most labeled residues in loops C and F yielded fluorescence changes identical in magnitude for glycine and strychnine. A notable exception was H201C in loop C. This labeled residue responded...

  10. Strictly convex renormings

    Czech Academy of Sciences Publication Activity Database

    Moltó, A.; Orihuela, J.; Troyanski, S.; Zizler, Václav

    2007-01-01

    Roč. 75, č. 3 (2007), s. 647-658 ISSN 0024-6107 R&D Projects: GA AV ČR IAA100190502 Institutional research plan: CEZ:AV0Z10190503 Keywords : strictly convex norms * lattice norm * quasi-diagonal sets Subject RIV: BA - General Mathematics Impact factor: 0.733, year: 2007

  11. Quine's "Strictly Vegetarian" Analyticity

    NARCIS (Netherlands)

    Decock, L.B.

    2017-01-01

    I analyze Quine’s later writings on analyticity from a linguistic point of view. In Word and Object Quine made room for a “strictly vegetarian” notion of analyticity. In later years, he developed this notion into two more precise notions, which I have coined “stimulus analyticity” and “behaviorist

  12. Ligand-specific regulation of the extracellular surface of a G-protein-coupled receptor

    DEFF Research Database (Denmark)

    Bokoch, Michael P; Zou, Yaozhong; Rasmussen, Søren Gøgsig Faarup

    2010-01-01

    extending from the orthosteric ligand-binding site in the transmembrane core to the cytoplasmic G-protein-coupling domains. In contrast, the extracellular surface (ECS) of GPCRs is remarkably diverse and is therefore an ideal target for the discovery of subtype-selective drugs. However, little is known...... about the functional role of the ECS in receptor activation, or about conformational coupling of this surface to the native ligand-binding pocket. Here we use NMR spectroscopy to investigate ligand-specific conformational changes around a central structural feature in the ECS of the beta(2) adrenergic...

  13. Redesigning an FKBP-ligand interface to generate chemical dimerizers with novel specificity.

    Science.gov (United States)

    Clackson, T; Yang, W; Rozamus, L W; Hatada, M; Amara, J F; Rollins, C T; Stevenson, L F; Magari, S R; Wood, S A; Courage, N L; Lu, X; Cerasoli, F; Gilman, M; Holt, D A

    1998-09-01

    FKBP ligand homodimers can be used to activate signaling events inside cells and animals that have been engineered to express fusions between appropriate signaling domains and FKBP. However, use of these dimerizers in vivo is potentially limited by ligand binding to endogenous FKBP. We have designed ligands that bind specifically to a mutated FKBP over the wild-type protein by remodeling an FKBP-ligand interface to introduce a specificity binding pocket. A compound bearing an ethyl substituent in place of a carbonyl group exhibited sub-nanomolar affinity and 1,000-fold selectivity for a mutant FKBP with a compensating truncation of a phenylalanine residue. Structural and functional analysis of the new pocket showed that recognition is surprisingly relaxed, with the modified ligand only partially filling the engineered cavity. We incorporated the specificity pocket into a fusion protein containing FKBP and the intracellular domain of the Fas receptor. Cells expressing this modified chimeric protein potently underwent apoptosis in response to AP1903, a homodimer of the modified ligand, both in culture and when implanted into mice. Remodeled dimerizers such as AP1903 are ideal reagents for controlling the activities of cells that have been modified by gene therapy procedures, without interference from endogenous FKBP.

  14. Specific ability of sulfur-ligands on removal of 203Hg-labeled organomercury from hemoglobin in comparison with nitrogen-ligands

    International Nuclear Information System (INIS)

    Hojo, Yasuji; Sugiura, Yukio; Tanaka, Hisashi

    1975-01-01

    Removal of 203 Hg-labeled organomercurials, bound to sulfhydryl groups of hemoglobin, by various chelating agents was investigated by the use of equilibrium dialysis. Organomercurials employed were chlormerodrin, methylmercury, ethylmercury and phenylmercury compounds. Higher and more specific effects of the sulfur-ligands, such as penicillamine and glutathione, on removal of organomercurial were found as compared with those of the nitrogen-ligands such as EDTA, glycine and polymethylenediamines. Linear correlation was observed between the degree of organomercury elimination from hemoglobin and the stability constant (log K 1 ) of 1:1 organomercury complex in both the sulfur- and nitrogen-ligand systems and at the same value of log K 1 , the elimination-effect of sulfur-ligands was extremely greater than that of the nitrogen-ligands. The relationship between the average percentage of removal and the Taft's polar substituent constant of organic moiety of the metal was also linear among the organomercury compounds other than chlormerodrin. The average removal percentage by sulfur-ligands increased in the order, ethylmercury>methylmercury>phenylmercury, while that of the nitrogen-ligands was not different among the organomercurials investigated. In addition, direct ligand-exchange reaction between hemoglobin-SH and the ligand coordinating-atom (S or N) against organomercurials rather than Ssub(N2) reaction via the ternary complex, hemoglobin-S-RHg-ligand, is postulated. (auth.)

  15. Flexible or Strict Taxonomic Organization?

    DEFF Research Database (Denmark)

    Glückstad, Fumiko Kano; Mørup, Morten

    2012-01-01

    This work compares methods for constructing feature-based ontologies that are supposed to be used for culturally-specific knowledge transfer. The methods to be compared are the Terminological Ontology (TO) [1], a method of constructing ontology based on strict principles and rules, and the Infinite...... Relational Model (IRM) [2], a novel unsupervised machine learning method that learns multi-dimensional relations among concepts and features from loosely structured datasets. These methods are combined with a novel cognitive model, the Bayesian Model of Generalization (BMG) [3] that maps culturally...

  16. Multifunctional Transmembrane Protein Ligands for Cell-Specific Targeting of Plasma Membrane-Derived Vesicles.

    Science.gov (United States)

    Zhao, Chi; Busch, David J; Vershel, Connor P; Stachowiak, Jeanne C

    2016-07-01

    Liposomes and nanoparticles that bind selectively to cell-surface receptors can target specific populations of cells. However, chemical conjugation of ligands to these particles is difficult to control, frequently limiting ligand uniformity and complexity. In contrast, the surfaces of living cells are decorated with highly uniform populations of sophisticated transmembrane proteins. Toward harnessing cellular capabilities, here it is demonstrated that plasma membrane vesicles (PMVs) derived from donor cells can display engineered transmembrane protein ligands that precisely target cells on the basis of receptor expression. These multifunctional targeting proteins incorporate (i) a protein ligand, (ii) an intrinsically disordered protein spacer to make the ligand sterically accessible, and (iii) a fluorescent protein domain that enables quantification of the ligand density on the PMV surface. PMVs that display targeting proteins with affinity for the epidermal growth factor receptor (EGFR) bind at increasing concentrations to breast cancer cells that express increasing levels of EGFR. Further, as an example of the generality of this approach, PMVs expressing a single-domain antibody against green fluorescence protein (eGFP) bind to cells expressing eGFP-tagged receptors with a selectivity of ≈50:1. The results demonstrate the versatility of PMVs as cell targeting systems, suggesting diverse applications from drug delivery to tissue engineering. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  17. VASP: a volumetric analysis of surface properties yields insights into protein-ligand binding specificity.

    Directory of Open Access Journals (Sweden)

    Brian Y Chen

    2010-08-01

    Full Text Available Many algorithms that compare protein structures can reveal similarities that suggest related biological functions, even at great evolutionary distances. Proteins with related function often exhibit differences in binding specificity, but few algorithms identify structural variations that effect specificity. To address this problem, we describe the Volumetric Analysis of Surface Properties (VASP, a novel volumetric analysis tool for the comparison of binding sites in aligned protein structures. VASP uses solid volumes to represent protein shape and the shape of surface cavities, clefts and tunnels that are defined with other methods. Our approach, inspired by techniques from constructive solid geometry, enables the isolation of volumetrically conserved and variable regions within three dimensionally superposed volumes. We applied VASP to compute a comparative volumetric analysis of the ligand binding sites formed by members of the steroidogenic acute regulatory protein (StAR-related lipid transfer (START domains and the serine proteases. Within both families, VASP isolated individual amino acids that create structural differences between ligand binding cavities that are known to influence differences in binding specificity. Also, VASP isolated cavity subregions that differ between ligand binding cavities which are essential for differences in binding specificity. As such, VASP should prove a valuable tool in the study of protein-ligand binding specificity.

  18. Evaluation of the ligand specificity of hemolymph hemoagglutinins and hemolysins of gastropod and bivalve molluscs

    NARCIS (Netherlands)

    Baskakov, AV; Polevshchikov, AV; Kharazova, AD

    2000-01-01

    The study deals with evaluation of ligand specificities of hemoagglutinins and hemolysins of hemolymph of three species of gastropods ( Planorbius corneus, Lymnaea stagnalis, and Achatina fu[ica) and one species of bivalve molluscs (Anodonta cygnea). The hemoagglutinin titer was estimated from

  19. The architecture of ligand attachment to nanocarriers controls their specific interaction with target cells

    OpenAIRE

    Sawant, Rupa R.; Sawant, Rishikesh M.; Kale, Amit A.; Torchilin, Vladimir P.

    2008-01-01

    Surface architecture of pharmaceutical nanocarriers (using polymeric micelles as an example) and the length of the spacer group through which specific ligand is attached to the carrier surface determine the interaction of ligand-bearing nanocarrier with cells. We have prepared surface-modified polyethyleneglycol–phosphatidylethanolamine (PEG–PE) micelles containing TATp attached to PEG–PE with a PEG block longer or shorter (TATp–PEG1000–PE or TATp–PEG3400–PE) than the PEG block in the main mi...

  20. A single glycine-alanine exchange directs ligand specificity of the elephant progestin receptor.

    Directory of Open Access Journals (Sweden)

    Michael Wierer

    Full Text Available The primary gestagen of elephants is 5α-dihydroprogesterone (DHP, which is unlike all other mammals studied until now. The level of DHP in elephants equals that of progesterone in other mammals, and elephants are able to bind DHP with similar affinity to progesterone indicating a unique ligand-binding specificity of the elephant progestin receptor (PR. Using site-directed mutagenesis in combination with in vitro binding studies we here report that this change in specificity is due to a single glycine to alanine exchange at position 722 (G722A of PR, which specifically increases DHP affinity while not affecting binding of progesterone. By conducting molecular dynamics simulations comparing human and elephant PR ligand-binding domains (LBD, we observed that the alanine methyl group at position 722 is able to push the DHP A-ring into a position similar to progesterone. In the human PR, the DHP A-ring position is twisted towards helix 3 of PR thereby disturbing the hydrogen bond pattern around the C3-keto group, resulting in a lower binding affinity. Furthermore, we observed that the elephant PR ligand-binding pocket is more rigid than the human analogue, which probably explains the higher affinity towards both progesterone and DHP. Interestingly, the G722A substitution is not elephant-specific, rather it is also present in five independent lineages of mammalian evolution, suggesting a special role of the substitution for the development of distinct mammalian gestagen systems.

  1. Extreme sequence divergence but conserved ligand-binding specificity in Streptococcus pyogenes M protein.

    Directory of Open Access Journals (Sweden)

    2006-05-01

    Full Text Available Many pathogenic microorganisms evade host immunity through extensive sequence variability in a protein region targeted by protective antibodies. In spite of the sequence variability, a variable region commonly retains an important ligand-binding function, reflected in the presence of a highly conserved sequence motif. Here, we analyze the limits of sequence divergence in a ligand-binding region by characterizing the hypervariable region (HVR of Streptococcus pyogenes M protein. Our studies were focused on HVRs that bind the human complement regulator C4b-binding protein (C4BP, a ligand that confers phagocytosis resistance. A previous comparison of C4BP-binding HVRs identified residue identities that could be part of a binding motif, but the extended analysis reported here shows that no residue identities remain when additional C4BP-binding HVRs are included. Characterization of the HVR in the M22 protein indicated that two relatively conserved Leu residues are essential for C4BP binding, but these residues are probably core residues in a coiled-coil, implying that they do not directly contribute to binding. In contrast, substitution of either of two relatively conserved Glu residues, predicted to be solvent-exposed, had no effect on C4BP binding, although each of these changes had a major effect on the antigenic properties of the HVR. Together, these findings show that HVRs of M proteins have an extraordinary capacity for sequence divergence and antigenic variability while retaining a specific ligand-binding function.

  2. Specific noncovalent interactions at protein-ligand interface: implications for rational drug design.

    Science.gov (United States)

    Zhou, P; Huang, J; Tian, F

    2012-01-01

    Specific noncovalent interactions that are indicative of attractive, directional intermolecular forces have always been of key interest to medicinal chemists in their search for the "glue" that holds drugs and their targets together. With the rapid increase in the number of solved biomolecular structures as well as the performance enhancement of computer hardware and software in recent years, it is now possible to give more comprehensive insight into the geometrical characteristics and energetic landscape of certain sophisticated noncovalent interactions present at the binding interface of protein receptors and small ligands based on accumulated knowledge gaining from the combination of two quite disparate but complementary approaches: crystallographic data analysis and quantum-mechanical ab initio calculation. In this perspective, we survey massive body of published works relating to structural characterization and theoretical investigation of three kinds of strong, specific, direct, enthalpy-driven intermolecular forces, including hydrogen bond, halogen bond and salt bridge, involved in the formation of protein-ligand complex architecture in order to characterize their biological functions in conferring affinity and specificity for ligand recognition by host protein. In particular, the biomedical implications of raised knowledge are discussed with respect to potential applications in rational drug design.

  3. Efficient Strictness Analysis of Haskell

    DEFF Research Database (Denmark)

    Jensen, Kristian Damm; Hjæresen, Peter; Rosendahl, Mads

    1994-01-01

    Strictness analysis has been a living field of investigation since Mycroft's original work in 1980, and is getting increasingly significant with the still wider use of lazy functional programming languages. This paper focuses on an actual implementation of a strictness analyser for Haskell...

  4. Ligand-specific allosteric regulation of coactivator functions of androgen receptor in prostate cancer cells

    Science.gov (United States)

    Baek, Sung Hee; Ohgi, Kenneth A.; Nelson, Charles A.; Welsbie, Derek; Chen, Charlie; Sawyers, Charles L.; Rose, David W.; Rosenfeld, Michael G.

    2006-01-01

    The androgen receptor not only mediates prostate development but also serves as a key regulator of primary prostatic cancer growth. Although initially responsive to selective androgen receptor modulators (SARMs), which cause recruitment of the nuclear receptor–corepressor (N-CoR) complex, resistance invariably occurs, perhaps in response to inflammatory signals. Here we report that dismissal of nuclear receptor–corepressor complexes by specific signals or androgen receptor overexpression results in recruitment of many of the cohorts of coactivator complexes that permits SARMs and natural ligands to function as agonists. SARM-bound androgen receptors appear to exhibit failure to recruit specific components of the coactivators generally bound by liganded nuclear receptors, including cAMP response element-binding protein (CBP)/p300 or coactivator-associated arginine methyltransferase 1 (CARM1) to the SARM-bound androgen receptor, although still causing transcriptional activation of androgen receptor target genes. SARM-bound androgen receptors use distinct LXXLL (L, leucine; X, any amino acid) helices in the p160 nuclear receptor interaction domains that may impose selective allosteric effects, providing a component of the molecular basis of differential responses to different classes of ligands by androgen receptor. PMID:16492776

  5. Design of a dual-ligand system using a specific ligand and cell penetrating peptide, resulting in a synergistic effect on selectivity and cellular uptake.

    Science.gov (United States)

    Takara, Kazuhiro; Hatakeyama, Hiroto; Ohga, Noritaka; Hida, Kyoko; Harashima, Hideyoshi

    2010-08-30

    In this study, a dual-ligand liposomal system comprised of a specific ligand and a cell penetrating peptide (CPP) is described to enhance selectivity and cellular uptake. Dual-ligand PEGylated liposomes were prepared by modifying the end of the PEG with an NGR motif peptide, followed by a surface coating of the liposomes with stearylated oligoarginine (STR-RX). The NGR motif recognizes CD13, a marker protein located on tumor endothelial cells. A suitable number of RX units was determined to be R4, since it can be masked by the PEG aqueous layer. Although no enhanced cellular uptake was observed when a single modification of PEGylated liposomes with either NGR- or STR-R4 was used, the dual-modification with NGR and STR-R4 stimulated uptake of PEGylated liposomes by CD13 positive cells, and this uptake was superior to that obtained by PEG-unmodified liposomes modified with STR-R4. The dual-ligand system shows a synergistic effect on cellular uptake. Collectively, the dual-ligand system promises to be useful in the development efficient and specific drug delivery systems. Copyright 2010 Elsevier B.V. All rights reserved.

  6. Anti-metatype peptides, a molecular tool with high sensitivity and specificity to monitor small ligands.

    Science.gov (United States)

    Inaba, Junko; Nakamura, Shugo; Shimizu, Kentaro; Asami, Tadao; Suzuki, Yoshihito

    2009-05-01

    To develop a new immunological detection system of gibberellins (GAs), a class of phytohormones, peptides that interact with an antibody against GA4 in a GA4-dependent manner, were screened from phage display random peptide libraries. The biopanning procedure yielded peptides designated as anti-metatype peptides (AM-peps), which showed specific binding to the complex of the antibody and its ligand GA4; that is, the antibody could not be replaced with the other anti-GA4 antibody, and GA4 could not be replaced with GA1, another ligand of the antibody. Together with computational analyses such as analysis of structural propensity of the AM-peps and docking simulation of the AM-peps and the 8/E9-GA4 complex, it was suggested that AM-peps formed a helix in their central region and interacted with a part of the 8/E9-GA4 complex located in close proximity to the GA4 molecule. Based on the property of AM-peps to make a ternary complex with antibody and its ligand, a noncompetitive enzyme-linked immunosorbent assay (ELISA) system corresponding to sandwich ELISA was developed to detect GA4. GA4 as low as 30 pg, which could not be achieved by conventional competitive ELISA, could be detected by the new system, demonstrating the feasibility of this system.

  7. Ligand-specific regulation of the extracellular surface of a G-protein-coupled receptor

    Energy Technology Data Exchange (ETDEWEB)

    Bokoch, Michael P.; Zou, Yaozhong; Rasmussen, Søren G.F.; Liu, Corey W.; Nygaard, Rie; Rosenbaum, Daniel M.; Fung, Juan José; Choi, Hee-Jung; Thian, Foon Sun; Kobilka, Tong Sun; Puglisi, Joseph D.; Weis, William I.; Pardo, Leonardo; Prosser, R. Scott; Mueller, Luciano; Kobilka, Brian K. (Stanford-MED); (Toronto); (BMS); (UAB, Spain)

    2010-01-14

    G-protein-coupled receptors (GPCRs) are seven-transmembrane proteins that mediate most cellular responses to hormones and neurotransmitters. They are the largest group of therapeutic targets for a broad spectrum of diseases. Recent crystal structures of GPCRs have revealed structural conservation extending from the orthosteric ligand-binding site in the transmembrane core to the cytoplasmic G-protein-coupling domains. In contrast, the extracellular surface (ECS) of GPCRs is remarkably diverse and is therefore an ideal target for the discovery of subtype-selective drugs. However, little is known about the functional role of the ECS in receptor activation, or about conformational coupling of this surface to the native ligand-binding pocket. Here we use NMR spectroscopy to investigate ligand-specific conformational changes around a central structural feature in the ECS of the {beta}{sub 2} adrenergic receptor: a salt bridge linking extracellular loops 2 and 3. Small-molecule drugs that bind within the transmembrane core and exhibit different efficacies towards G-protein activation (agonist, neutral antagonist and inverse agonist) also stabilize distinct conformations of the ECS. We thereby demonstrate conformational coupling between the ECS and the orthosteric binding site, showing that drugs targeting this diverse surface could function as allosteric modulators with high subtype selectivity. Moreover, these studies provide a new insight into the dynamic behaviour of GPCRs not addressable by static, inactive-state crystal structures.

  8. Structural determinant for inducing RORgamma specific inverse agonism triggered by a synthetic benzoxazinone ligand.

    Science.gov (United States)

    Marcotte, Douglas J; Liu, YuTing; Little, Kevin; Jones, John H; Powell, Noel A; Wildes, Craig P; Silvian, Laura F; Chodaparambil, Jayanth V

    2016-06-01

    The nuclear hormone receptor RORγ regulates transcriptional genes involved in the production of the pro-inflammatory interleukin IL-17 which has been linked to autoimmune diseases such as rheumatoid arthritis, multiple sclerosis and inflammatory bowel disease. This transcriptional activity of RORγ is modulated through a protein-protein interaction involving the activation function 2 (AF2) helix on the ligand binding domain of RORγ and a conserved LXXLL helix motif on coactivator proteins. Our goal was to develop a RORγ specific inverse agonist that would help down regulate pro-inflammatory gene transcription by disrupting the protein protein interaction with coactivator proteins as a therapeutic agent. We identified a novel series of synthetic benzoxazinone ligands having an agonist (BIO592) and inverse agonist (BIO399) mode of action in a FRET based assay. We show that the AF2 helix of RORγ is proteolytically sensitive when inverse agonist BIO399 binds. Using x-ray crystallography we show how small modifications on the benzoxazinone agonist BIO592 trigger inverse agonism of RORγ. Using an in vivo reporter assay, we show that the inverse agonist BIO399 displayed specificity for RORγ over ROR sub-family members α and β. The synthetic benzoxazinone ligands identified in our FRET assay have an agonist (BIO592) or inverse agonist (BIO399) effect by stabilizing or destabilizing the agonist conformation of RORγ. The proteolytic sensitivity of the AF2 helix of RORγ demonstrates that it destabilizes upon BIO399 inverse agonist binding perturbing the coactivator protein binding site. Our structural investigation of the BIO592 agonist and BIO399 inverse agonist structures identified residue Met358 on RORγ as the trigger for RORγ specific inverse agonism.

  9. Computational Biology Tools for Identifying Specific Ligand Binding Residues for Novel Agrochemical and Drug Design.

    Science.gov (United States)

    Neshich, Izabella Agostinho Pena; Nishimura, Leticia; de Moraes, Fabio Rogerio; Salim, Jose Augusto; Villalta-Romero, Fabian; Borro, Luiz; Yano, Inacio Henrique; Mazoni, Ivan; Tasic, Ljubica; Jardine, Jose Gilberto; Neshich, Goran

    2015-01-01

    The term "agrochemicals" is used in its generic form to represent a spectrum of pesticides, such as insecticides, fungicides or bactericides. They contain active components designed for optimized pest management and control, therefore allowing for economically sound and labor efficient agricultural production. A "drug" on the other side is a term that is used for compounds designed for controlling human diseases. Although drugs are subjected to much more severe testing and regulation procedures before reaching the market, they might contain exactly the same active ingredient as certain agrochemicals, what is the case described in present work, showing how a small chemical compound might be used to control pathogenicity of Gram negative bacteria Xylella fastidiosa which devastates citrus plantations, as well as for control of, for example, meningitis in humans. It is also clear that so far the production of new agrochemicals is not benefiting as much from the in silico new chemical compound identification/discovery as pharmaceutical production. Rational drug design crucially depends on detailed knowledge of structural information about the receptor (target protein) and the ligand (drug/agrochemical). The interaction between the two molecules is the subject of analysis that aims to understand relationship between structure and function, mainly deciphering some fundamental elements of the nanoenvironment where the interaction occurs. In this work we will emphasize the role of understanding nanoenvironmental factors that guide recognition and interaction of target protein and its function modifier, an agrochemical or a drug. The repertoire of nanoenvironment descriptors is used for two selected and specific cases we have approached in order to offer a technological solution for some very important problems that needs special attention in agriculture: elimination of pathogenicity of a bacterium which is attacking citrus plants and formulation of a new fungicide. Finally

  10. Coupling Protein Side-Chain and Backbone Flexibility Improves the Re-design of Protein-Ligand Specificity.

    Directory of Open Access Journals (Sweden)

    Noah Ollikainen

    Full Text Available Interactions between small molecules and proteins play critical roles in regulating and facilitating diverse biological functions, yet our ability to accurately re-engineer the specificity of these interactions using computational approaches has been limited. One main difficulty, in addition to inaccuracies in energy functions, is the exquisite sensitivity of protein-ligand interactions to subtle conformational changes, coupled with the computational problem of sampling the large conformational search space of degrees of freedom of ligands, amino acid side chains, and the protein backbone. Here, we describe two benchmarks for evaluating the accuracy of computational approaches for re-engineering protein-ligand interactions: (i prediction of enzyme specificity altering mutations and (ii prediction of sequence tolerance in ligand binding sites. After finding that current state-of-the-art "fixed backbone" design methods perform poorly on these tests, we develop a new "coupled moves" design method in the program Rosetta that couples changes to protein sequence with alterations in both protein side-chain and protein backbone conformations, and allows for changes in ligand rigid-body and torsion degrees of freedom. We show significantly increased accuracy in both predicting ligand specificity altering mutations and binding site sequences. These methodological improvements should be useful for many applications of protein-ligand design. The approach also provides insights into the role of subtle conformational adjustments that enable functional changes not only in engineering applications but also in natural protein evolution.

  11. Species Protection in the European Union : How Strict is Strict?

    NARCIS (Netherlands)

    Schoukens, Hendrik; Bastmeijer, Kees; Born et al., Charles-Hubert

    2015-01-01

    European Union law to protect wild species of plants and animals is generally considered as ‘strict’. Opponents of nature conservation law often pick the species protection components of the EU Bird Directive and Habitat Directive as a prime example of an unnecessary strict regulatory scheme that

  12. The architecture of ligand attachment to nanocarriers controls their specific interaction with target cells.

    Science.gov (United States)

    Sawant, Rupa R; Sawant, Rishikesh M; Kale, Amit A; Torchilin, Vladimir P

    2008-08-01

    Surface architecture of pharmaceutical nanocarriers (using polymeric micelles as an example) and the length of the spacer group through which specific ligand is attached to the carrier surface determine the interaction of ligand-bearing nanocarrier with cells. We have prepared surface-modified polyethyleneglycol-phosphatidylethanolamine (PEG-PE) micelles containing TATp attached to PEG-PE with a PEG block longer or shorter (TATp-PEG(1000)-PE or TATp-PEG(3400)-PE) than the PEG block in the main micelle-forming material (PEG(750)-PE and/or PEG(2000)-PE). The length of the PEG spacer in TATp-PEG-PE should allow for a non-hindered interaction of TATp with the cell surface, but it should not be too long to allow for the conformational "folding in" of TATp moiety inside the PEG globule making it unable to interact with the cells. The "folding in" of the ligand attached to an unnecessary long PEG spacer was further supported by the fluorescence resonance energy transfer (FRET) study between fluorescently labeled lipid 1,2-dipalmitoyl-sn-glycero-3-phosphoethanolamine-N-(7-nitro-2-1,3-benzoxadiazol-4-yl) (NBD-PE) inserted into the core of PEG(750)-PE micelles and micelle-incorporated rhodamine-labeled TATp-PEG-PE. Micelles containing rhodamine-labeled TATp-PEG-PE with the longest PEG spacer (3400 Da) demonstrated strongly enhanced quenching of NBD-PE fluorescence with rhodamine-TATp confirming the "folding in" of TATp moiety into PEG globule bringing it closer to the micelle core-incorporated NBD.

  13. Flow Cytometry-Based Bead-Binding Assay for Measuring Receptor Ligand Specificity

    NARCIS (Netherlands)

    Sprokholt, Joris K.; Hertoghs, Nina; Geijtenbeek, Teunis B. H.

    2016-01-01

    In this chapter we describe a fluorescent bead-binding assay, which is an efficient and feasible method to measure interaction between ligands and receptors on cells. In principle, any ligand can be coated on fluorescent beads either directly or via antibodies. Binding between ligand-coated beads

  14. Ligand-specific sequential regulation of transcription factors for differentiation of MCF-7 cells

    Directory of Open Access Journals (Sweden)

    Toyoda Tetsuro

    2009-11-01

    Full Text Available Abstract Background Sharing a common ErbB/HER receptor signaling pathway, heregulin (HRG induces differentiation of MCF-7 human breast cancer cells while epidermal growth factor (EGF elicits proliferation. Although cell fates resulting from action of the aforementioned ligands completely different, the respective gene expression profiles in early transcription are qualitatively similar, suggesting that gene expression during late transcription, but not early transcription, may reflect ligand specificity. In this study, based on both the data from time-course quantitative real-time PCR on over 2,000 human transcription factors and microarray of all human genes, we identified a series of transcription factors which may control HRG-specific late transcription in MCF-7 cells. Results We predicted that four transcription factors including EGR4, FRA-1, FHL2, and DIPA should have responsibility of regulation in MCF-7 cell differentiation. Validation analysis suggested that one member of the activator protein 1 (AP-1 family, FOSL-1 (FRA-1 gene, appeared immediately following c-FOS expression, might be responsible for expression of transcription factor FHL2 through activation of the AP-1 complex. Furthermore, RNAi gene silencing of FOSL-1 and FHL2 resulted in increase of extracellular signal-regulated kinase (ERK phosphorylation of which duration was sustained by HRG stimulation. Conclusion Our analysis indicated that a time-dependent transcriptional regulatory network including c-FOS, FRA-1, and FHL2 is vital in controlling the ERK signaling pathway through a negative feedback loop for MCF-7 cell differentiation.

  15. Affinophoresis in two-dimensional agarose gel electrophoresis: specific separation of biomolecules by a moving affinity ligand.

    Science.gov (United States)

    Shimura, K; Kasai, K

    1987-02-15

    Affinophoresis is an electrophoretic separation technique for biomolecules which uses an affinophore. An affinophore is a macromolecular polyelectrolyte bearing affinity ligands. It migrates rapidly in an electric field, and consequently the electrophoretic mobility of molecules having affinity for the ligand is specifically changed. This technique has now been incorporated in two-dimensional agarose gel electrophoresis in a procedure which utilizes normal electrophoresis in the first dimension and affinophoresis in the second dimension. Proteins which do not have affinity for the ligand migrate to locations along a diagonal line passing through the origin, whereas proteins which have affinity are carried away from the line by the affinophore. Accordingly, molecules having affinity for the ligand can be readily assigned. Trypsins contained in Pronase and pancreatin were separated by this procedure using an affinophore bearing a competitive inhibitor for trypsin, benzamidine, on a polyanionic molecule (a polyacrylic acid derivative).

  16. Strictness Analysis for Attribute Grammars

    DEFF Research Database (Denmark)

    Rosendahl, Mads

    1992-01-01

    interpretation of attribute grammars. The framework is used to construct a strictness analysis for attribute grammars. Results of the analysis enable us to transform an attribute grammar such that attributes are evaluated during parsing, if possible. The analysis is proved correct by relating it to a fixpoint...... semantics for attribute grammars. An implementation of the analysis is discussed and some extensions to the analysis are mentioned....

  17. Changing the insulin receptor to possess insulin-like growth factor I ligand specificity

    International Nuclear Information System (INIS)

    Andersen, A.S.; Kjeldsen, T.; Wiberg, F.C.; Christensen, P.M.; Rasmussen, J.S.; Norris, K.; Moeller, K.B.; Moeller, N.P.H.

    1990-01-01

    To examine the role of the N-terminal part of the insulin-like growth factor I (IGF-I) receptor and insulin receptor in determining ligand specificity, the authors prepared an expression vector encoding a hybrid receptor where exon 1 (encoding the signal peptide and seven amino acids of the α-subunit), exon 2, and exon 3 of the insulin receptor were replaced with the corresponding IGF-I receptor cDNA (938 nucleotides). To allow direct quantitative comparison of the binding capabilities of this hybrid receptor with those of the human IGF-I receptor and the insulin receptor, all three receptors were expressed in baby hamster kidney (BHK) cells as soluble molecules and partially purified before characterization. The hybrid IGF-I/insulin receptor bound IGF-I with an affinity comparable to that of the wild-type IGF-I receptor. In contrast, the hybrid receptor no longer displayed high-affinity binding of insulin. These results directly demonstrate that it is possible to change the specificity of the insulin receptor to that of the IGF-I receptor and, furthermore, that the binding specificity for IGF-I is encoded within the nucleotide sequence from 135 to 938 of the IGF-I receptor cDNA. Since the hybrid receptor only bound insulin with low affinity, the insulin binding region is likely to be located within exons 2 and 3 of the insulin receptor

  18. Changing the insulin receptor to possess insulin-like growth factor I ligand specificity

    Energy Technology Data Exchange (ETDEWEB)

    Andersen, A.S.; Kjeldsen, T.; Wiberg, F.C.; Christensen, P.M.; Rasmussen, J.S.; Norris, K.; Moeller, K.B.; Moeller, N.P.H. (Biopharmaceuticals Div., Bagsvaerd (Denmark))

    1990-08-14

    To examine the role of the N-terminal part of the insulin-like growth factor I (IGF-I) receptor and insulin receptor in determining ligand specificity, the authors prepared an expression vector encoding a hybrid receptor where exon 1 (encoding the signal peptide and seven amino acids of the {alpha}-subunit), exon 2, and exon 3 of the insulin receptor were replaced with the corresponding IGF-I receptor cDNA (938 nucleotides). To allow direct quantitative comparison of the binding capabilities of this hybrid receptor with those of the human IGF-I receptor and the insulin receptor, all three receptors were expressed in baby hamster kidney (BHK) cells as soluble molecules and partially purified before characterization. The hybrid IGF-I/insulin receptor bound IGF-I with an affinity comparable to that of the wild-type IGF-I receptor. In contrast, the hybrid receptor no longer displayed high-affinity binding of insulin. These results directly demonstrate that it is possible to change the specificity of the insulin receptor to that of the IGF-I receptor and, furthermore, that the binding specificity for IGF-I is encoded within the nucleotide sequence from 135 to 938 of the IGF-I receptor cDNA. Since the hybrid receptor only bound insulin with low affinity, the insulin binding region is likely to be located within exons 2 and 3 of the insulin receptor.

  19. Mechanism of selective VEGF-A binding by neuropilin-1 reveals a basis for specific ligand inhibition.

    Directory of Open Access Journals (Sweden)

    Matthew W Parker

    Full Text Available Neuropilin (Nrp receptors function as essential cell surface receptors for the Vascular Endothelial Growth Factor (VEGF family of proangiogenic cytokines and the semaphorin 3 (Sema3 family of axon guidance molecules. There are two Nrp homologues, Nrp1 and Nrp2, which bind to both overlapping and distinct members of the VEGF and Sema3 family of molecules. Nrp1 specifically binds the VEGF-A(164/5 isoform, which is essential for developmental angiogenesis. We demonstrate that VEGF-A specific binding is governed by Nrp1 residues in the b1 coagulation factor domain surrounding the invariant Nrp C-terminal arginine binding pocket. Further, we show that Sema3F does not display the Nrp-specific binding to the b1 domain seen with VEGF-A. Engineered soluble Nrp receptor fragments that selectively sequester ligands from the active signaling complex are an attractive modality for selectively blocking the angiogenic and chemorepulsive functions of Nrp ligands. Utilizing the information on Nrp ligand binding specificity, we demonstrate Nrp constructs that specifically sequester Sema3 in the presence of VEGF-A. This establishes that unique mechanisms are used by Nrp receptors to mediate specific ligand binding and that these differences can be exploited to engineer soluble Nrp receptors with specificity for Sema3.

  20. Nuclear localization and function of polypeptide ligands and their receptors: a new paradigm for hormone specificity within the mammary gland?

    International Nuclear Information System (INIS)

    Clevenger, Charles V

    2003-01-01

    The specific effects triggered by polypeptide hormone/growth factor stimulation of mammary cells were considered mediated solely by receptor-associated signaling networks. A compelling body of new data, however, clearly indicates that polypeptide ligands and/or their receptors are transported into the nucleus, where they function directly to regulate the expression of specific transcription factors and gene loci. The intranuclear function of these complexes may contribute to the explicit functions associated with a given ligand, and may serve as new targets for pharmacologic intervention

  1. Peptide ligands specific to the oxidized form of escherichia coli thioredoxin.

    Energy Technology Data Exchange (ETDEWEB)

    Scholle, M. D.; Banach, B. S.; Hamdan, S. M.; Richardson, C. C.; Kay, B. K.; Biosciences Division; Amunix, Inc.; Univ. of Illinois at Chicago; Harvard Medical School

    2008-11-01

    Thioredoxin (Trx) is a highly conserved redox protein involved in several essential cellular processes. In this study, our goal was to isolate peptide ligands to Escherichia coli Trx that mimic protein-protein interactions, specifically the T7 polymerase-Trx interaction. To do this, we subjected Trx to affinity selection against a panel of linear and cysteine-constrained peptides using M13 phage display. A novel cyclized conserved peptide sequence, with a motif of C(D/N/S/T/G)D(S/T)-hydrophobic-C-X-hydrophobic-P, was isolated to Trx. These peptides bound specifically to the E. coli Trx when compared to the human and spirulina homologs. An alanine substitution of the active site cysteines (CGPC) resulted in a significant loss of peptide binding affinity to the Cys-32 mutant. The peptides were also characterized in the context of Trx's role as a processivity factor of the T7 DNA polymerase (gp5). As the interaction between gp5 and Trx normally takes place under reducing conditions, which might interfere with the conformation of the disulfide-bridged peptides, we made use of a 22 residue deletion mutant of gp5 in the thioredoxin binding domain (gp5{Delta}22) that bypassed the requirements of reducing conditions to interact with Trx. A competition study revealed that the peptide selectively inhibits the interaction of gp5{Delta}22 with Trx, under oxidizing conditions, with an IC50 of {approx} 10 {micro}M.

  2. A chelating dendritic ligand capped quantum dot: preparation, surface passivation, bioconjugation and specific DNA detection

    Science.gov (United States)

    Zhou, Dejian; Li, Yang; Hall, Elizabeth A. H.; Abell, Chris; Klenerman, David

    2011-01-01

    Herein we report the synthesis of a new chelating dendritic ligand (CDL) and its use in the preparation a compact, stable and water-soluble quantum dot (QD), and further development of specific DNA sensor. The CDL, which contains a chelative dihydrolipoic acid moiety for strong QD surface anchoring and four dendritic carboxylic acidgroups, provides a stable, compact and entangled hydrophilic coating around the QD that significantly increases the stability of the resulting water-soluble QD. A CDL-capped CdSe/ZnS core/shell QD (CDL-QD) has stronger fluorescence than that capped by a monodendate single-chain thiol, 3-mercapto-propionic acid (MPA-QD). In addition, the fluorescence of the CDL-QD can be enhanced by 2.5-fold by treatments with Zn2+ or S2- ions, presumably due to effective passivation of the surface defects. This level of fluorescence enhancement obtained for the CDL-QD is much greater than that for the MPA-QD. Further, by coupling a short single-stranded DNA target to the QD via the CDL carboxylic acidgroup, a functional QD-DNA conjugate that can resist non-specific adsorption and hybridize quickly to its complementary DNAprobe has been obtained. This functional QD-DNA conjugate is suitable for specific quantification of short, labelled complementary probes at the low DNAprobe:QD copy numbers via a QD-sensitised dyefluorescence resonance energy transfer (FRET) response with 500 pM sensitivity on a conventional fluorimeter.Herein we report the synthesis of a new chelating dendritic ligand (CDL) and its use in the preparation a compact, stable and water-soluble quantum dot (QD), and further development of specific DNA sensor. The CDL, which contains a chelative dihydrolipoic acid moiety for strong QD surface anchoring and four dendritic carboxylic acidgroups, provides a stable, compact and entangled hydrophilic coating around the QD that significantly increases the stability of the resulting water-soluble QD. A CDL-capped CdSe/ZnS core/shell QD (CDL-QD) has

  3. High affinity, ligand specific uptake of complexed copper-67 by brain tissue incubated in vitro

    International Nuclear Information System (INIS)

    Barnea, A.; Hartter, D.E.

    1987-01-01

    Copper is an essential metal that is highly concentrated in the brain. The blood, the sole source of tissue Cu, contains 16-20 μM Cu, of which >95% is complexed to proteins and 2 was 10 times greater than that of CuAlbumin or Cu(II). Within the range of 0.2-150μM Cu, multiple uptake sites for CuHis were apparent. Increasing the molar ratio of His:Cu had a differential effect on Cu uptake: enhancing uptake at [Cu] 1 μM. Thus, using a His:Cu ratio of 1000, they observed a high affinity process exhibiting saturating and half saturating values of 5 μM and 1.5 μM Cu, respectively; using a His:Cu ratio of 2, they observed a low affinity process exhibiting saturating and half-saturating values of 100 μM and 40 μM Cu, respectively. Both processes required thermic but not metabolic energy, suggestive of facilitated diffusion. Considering the blood brain barrier for proteins, CuHis appears to be the major substrate for Cu uptake by neuronal tissue. They demonstrate the existence of a ligand specific, high affinity (apparent Km about 1.5 μM Cu) uptake process for CuHis in the brain, operative at the physiological concentration range of CuHis and histidine

  4. Orbital-specific mapping of the ligand exchange dynamics of Fe(CO)5 in solution

    Science.gov (United States)

    Wernet, Ph.; Kunnus, K.; Josefsson, I.; Rajkovic, I.; Quevedo, W.; Beye, M.; Schreck, S.; Grübel, S.; Scholz, M.; Nordlund, D.; Zhang, W.; Hartsock, R. W.; Schlotter, W. F.; Turner, J. J.; Kennedy, B.; Hennies, F.; de Groot, F. M. F.; Gaffney, K. J.; Techert, S.; Odelius, M.; Föhlisch, A.

    2015-04-01

    Transition-metal complexes have long attracted interest for fundamental chemical reactivity studies and possible use in solar energy conversion. Electronic excitation, ligand loss from the metal centre, or a combination of both, creates changes in charge and spin density at the metal site that need to be controlled to optimize complexes for photocatalytic hydrogen production and selective carbon-hydrogen bond activation. An understanding at the molecular level of how transition-metal complexes catalyse reactions, and in particular of the role of the short-lived and reactive intermediate states involved, will be critical for such optimization. However, suitable methods for detailed characterization of electronic excited states have been lacking. Here we show, with the use of X-ray laser-based femtosecond-resolution spectroscopy and advanced quantum chemical theory to probe the reaction dynamics of the benchmark transition-metal complex Fe(CO)5 in solution, that the photo-induced removal of CO generates the 16-electron Fe(CO)4 species, a homogeneous catalyst with an electron deficiency at the Fe centre, in a hitherto unreported excited singlet state that either converts to the triplet ground state or combines with a CO or solvent molecule to regenerate a penta-coordinated Fe species on a sub-picosecond timescale. This finding, which resolves the debate about the relative importance of different spin channels in the photochemistry of Fe(CO)5 (refs 4, 16,17,18,19 and 20), was made possible by the ability of femtosecond X-ray spectroscopy to probe frontier-orbital interactions with atom specificity. We expect the method to be broadly applicable in the chemical sciences, and to complement approaches that probe structural dynamics in ultrafast processes.

  5. Strategy and Aspects of Monitoring / Control Strictly in Coordinated Subsystems

    Directory of Open Access Journals (Sweden)

    William José Borges

    2012-06-01

    Full Text Available This paper aims to discuss the approach structures of the strictly coordinated theoretical framework developed by Zylbersztajn and Farina (1999 as an expanded perspective of the firm, taking into account the food supply chains as an extension of the nexus of contracts proposed by Coase (1937 and taken up by Williamson (1985. The structures stand out as strictly coordinated. Zylbersztajn and Farina (1999 turn to identifying points of common interests that encourage firms to promote contracts between themselves in a strictly coordinated way, considering the degree of asset specificity involved in the transaction and the competitive forces that determine the search for strategic positioning organizations to achieve sustainable superior results.

  6. Function-specific virtual screening for GPCR ligands using a combined scoring method.

    Science.gov (United States)

    Kooistra, Albert J; Vischer, Henry F; McNaught-Flores, Daniel; Leurs, Rob; de Esch, Iwan J P; de Graaf, Chris

    2016-06-24

    The ability of scoring functions to correctly select and rank docking poses of small molecules in protein binding sites is highly target dependent, which presents a challenge for structure-based drug discovery. Here we describe a virtual screening method that combines an energy-based docking scoring function with a molecular interaction fingerprint (IFP) to identify new ligands based on G protein-coupled receptor (GPCR) crystal structures. The consensus scoring method is prospectively evaluated by: 1) the discovery of chemically novel, fragment-like, high affinity histamine H1 receptor (H1R) antagonists/inverse agonists, 2) the selective structure-based identification of ß2-adrenoceptor (ß2R) agonists, and 3) the experimental validation and comparison of the combined and individual scoring approaches. Systematic retrospective virtual screening simulations allowed the definition of scoring cut-offs for the identification of H1R and ß2R ligands and the selection of an optimal ß-adrenoceptor crystal structure for the discrimination between ß2R agonists and antagonists. The consensus approach resulted in the experimental validation of 53% of the ß2R and 73% of the H1R virtual screening hits with up to nanomolar affinities and potencies. The selective identification of ß2R agonists shows the possibilities of structure-based prediction of GPCR ligand function by integrating protein-ligand binding mode information.

  7. Specificity of Campylobacter jejuni Adhesin PEB3 for Phosphates and Structural Differences among Its Ligand Complexes

    Energy Technology Data Exchange (ETDEWEB)

    Min, Tongpil; Vedadi, Masoud; Watson, David C.; Wasney, Gregory A.; Munger, Christine; Cygler, Miroslaw; Matte, Allan; Young, N. Martin; (NRCC); (McGill); (Toronto)

    2009-04-22

    PEB3 is a glycoprotein adhesin from Campylobacter jejuni whose structure suggested a role in transport. We have investigated potential ligands for PEB3 and characterized their binding properties using biophysical methods in solution and by X-ray crystallography. A thermal aggregation assay of PEB3 with a library of physiological compounds identified three possible ligands [3-phosphoglycerate (3-PG), phosphoenolpyruvate (PEP), and aconitate], which stabilized wild-type PEB3 but did not stabilize either a PEB3 form containing two mutations at the ligand-binding site, T138A/S139A, or a second PEB3 mutant, K135E, at a site {approx}14 {angstrom} away. Fluorescence titration experiments and cocrystal structures with various ligands were used to characterize the binding of 3-PG, PEP, and phosphate to PEB3. Further, a C. jejuni growth experiment in minimal medium supplemented with 3-PG showed that this molecule enhances the growth of wild-type C. jejuni, but not of the PEB3 mutants. Crystallographic analysis of PEB3 complexes revealed that the Ser171-Gln180 region in the presence of 3-PG or other phosphates is helical and similar to those of other transport proteins, but it is nonhelical when citrate is bound. The K135E mutation resulted in expression of a more highly glycosylated form of PEB3 in vivo, and its crystal structure showed the conformation of the first two residues of the glycan. On the basis of our findings, we suggest that PEB3 is a transport protein that may function in utilization of 3-PG or other phosphate-containing molecules from the host.

  8. Structural determinant for inducing RORgamma specific inverse agonism triggered by a synthetic benzoxazinone ligand

    OpenAIRE

    Marcotte, Douglas J.; Liu, YuTing; Little, Kevin; Jones, John H.; Powell, Noel A.; Wildes, Craig P.; Silvian, Laura F.; Chodaparambil, Jayanth V.

    2016-01-01

    Background The nuclear hormone receptor ROR? regulates transcriptional genes involved in the production of the pro-inflammatory interleukin IL-17 which has been linked to autoimmune diseases such as rheumatoid arthritis, multiple sclerosis and inflammatory bowel disease. This transcriptional activity of ROR? is modulated through a protein-protein interaction involving the activation function 2 (AF2) helix on the ligand binding domain of ROR? and a conserved LXXLL helix motif on coactivator pr...

  9. Target-specific NMR detection of protein-ligand interactions with antibody-relayed 15N-group selective STD.

    Science.gov (United States)

    Hetényi, Anasztázia; Hegedűs, Zsófia; Fajka-Boja, Roberta; Monostori, Éva; Kövér, Katalin E; Martinek, Tamás A

    2016-12-01

    Fragment-based drug design has been successfully applied to challenging targets where the detection of the weak protein-ligand interactions is a key element. 1 H saturation transfer difference (STD) NMR spectroscopy is a powerful technique for this work but it requires pure homogeneous proteins as targets. Monoclonal antibody (mAb)-relayed 15 N-GS STD spectroscopy has been developed to resolve the problem of protein mixtures and impure proteins. A 15 N-labelled target-specific mAb is selectively irradiated and the saturation is relayed through the target to the ligand. Tests on the anti-Gal-1 mAb/Gal-1/lactose system showed that the approach is experimentally feasible in a reasonable time frame. This method allows detection and identification of binding molecules directly from a protein mixture in a multicomponent system.

  10. Segregation of myoblast fusion and muscle-specific gene expression by distinct ligand-dependent inactivation of GSK-3β.

    Science.gov (United States)

    Pansters, N A M; van der Velden, J L J; Kelders, M C J M; Laeremans, H; Schols, A M W J; Langen, R C J

    2011-02-01

    Myogenic differentiation involves myoblast fusion and induction of muscle-specific gene expression, which are both stimulated by pharmacological (LiCl), genetic, or IGF-I-mediated GSK-3β inactivation. To assess whether stimulation of myogenic differentiation is common to ligand-mediated GSK-3β inactivation, myoblast fusion and muscle-specific gene expression were investigated in response to Wnt-3a. Moreover, crosstalk between IGF-I/GSK-3β/NFATc3 and Wnt/GSK-3β/β-catenin signaling was assessed. While both Wnt-3a and LiCl promoted myoblast fusion, muscle-specific gene expression was increased by LiCl, but not by Wnt-3a or β-catenin over-expression. Furthermore, LiCl and IGF-I, but not Wnt-3a, increased NFATc3 transcriptional activity. In contrast, β-catenin-dependent transcriptional activity was increased by Wnt-3a and LiCl, but not IGF-I. These results for the first time reveal a segregated regulation of myoblast fusion and muscle-specific gene expression following stimulation of myogenic differentiation in response to distinct ligand-specific signaling routes of GSK-3β inactivation.

  11. Expression and characterization of an M cell-specific ligand-fused dengue virus tetravalent epitope using Saccharomyces cerevisiae.

    Science.gov (United States)

    Nguyen, Ngoc-Luong; So, Kum-Kang; Kim, Jung-Mi; Kim, Sae-Hae; Jang, Yong-Suk; Yang, Moon-Sik; Kim, Dae-Hyuk

    2015-01-01

    A fusion construct (Tet-EDIII-Co1) consisting of an M cell-specific peptide ligand (Co1) at the C-terminus of a recombinant tetravalent gene encoding the amino acid sequences of dengue envelope domain III (Tet-EDIII) from four serotypes was expressed and tested for binding activity to the mucosal immune inductive site M cells for the development of an oral vaccine. The yeast episomal expression vector, pYEGPD-TER, which was designed to direct gene expression using the glyceraldehyde-3-phosphate dehydrogenase (GPD) promoter, a functional signal peptide of the amylase 1A protein from rice, and the GAL7 terminator, was used to clone the Tet-EDIII-Co1 gene and resultant plasmids were then used to transform Saccharomyces cerevisiae. PCR and back-transformation into Escherichia coli confirmed the presence of the Tet-EDIII-Co1 gene-containing plasmid in transformants. Northern blot analysis of transformed S. cerevisiae identified the presence of the Tet-EDIII-Co1-specific transcript. Western blot analysis indicated that the produced Tet-EDIII-Co1 protein with the expected molecular weight was successfully secreted into the culture medium. Quantitative Western blot analysis and ELISA revealed that the recombinant Tet-EDIII-Co1 protein comprised approximately 0.1-0.2% of cell-free extracts (CFEs). In addition, 0.1-0.2 mg of Tet-EDIII-Co1 protein per liter of culture filtrate was detected on day 1, and this quantity peaked on day 3 after cultivation. In vivo binding assays showed that the Tet-EDIII-Co1 protein was delivered specifically to M cells in Peyer's patches (PPs) while the Tet-EDIII protein lacking the Co1 ligand did not, which demonstrated the efficient targeting of this antigenic protein through the mucosal-specific ligand. Copyright © 2014 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

  12. Design of sequence-specific DNA binding ligands that use a two-stranded peptide motif for DNA sequence recognition.

    Science.gov (United States)

    Nikolaev, V A; Grokhovsky, S L; Surovaya, A N; Leinsoo, T A; Sidorova NYu; Zasedatelev, A S; Zhuze, A L; Strahan, G A; Shafer, R H; Gursky, G V

    1996-08-01

    The design and DNA binding activity of beta-structure-forming peptides and netropsin-peptide conjugates are reported. It is found that a pair of peptides-S,S'-bis(Lys-Gly-Val-Cys-Val-NH-NH-Dns)-bridged by an S-S bond binds at least 10 times more strongly to poly(dG).poly(dC) than to poly(dA).poly(dT). This peptide can also discriminate between 5'-GpG-3' and 5'-GpC-3' steps in the DNA minor groove. Based on these observations, new synthetic ligands, bis-netropsins, were constructed in which two netropsin-like fragments were attached by means of short linkers to a pair of peptides-Gly-Cys-Gly- or Val-Cys-Val-bridged by S-S bonds. These compounds possess a composite binding specificity: the peptide chains recognize 5'-GpG-3' steps on DNA, whereas the netropsin-like fragments bind preferentially to runs of 4 AT base pairs. Our data indicate that combining the AT-base-pair specific properties of the netropsin-type structure with the 5'-GpG-3'-specific properties of certain oligopeptides offers a new approach to the synthesis of ligands capable of recognizing mixed sequences of AT- and GC-base pairs in the DNA minor groove. These compounds are potential models for DNA-binding domains in proteins which specifically recognize base pair sequences in the minor groove of DNA.

  13. Extremely strict ideals in Banach spaces

    Indian Academy of Sciences (India)

    Motivated by the notion of an ideal introduced by Godefroy {\\it et al.} ({\\it Studia Math.} {\\bf 104} (1993) 13–59), in this article, we introduce and study the notion of an extremely strict ideal. For a Poulsen simplex K , we show that the space of affine continuous functions on K is an extremely strict ideal in the space of continuous ...

  14. Hyperbolic spaces are of strictly negative type

    DEFF Research Database (Denmark)

    Hjorth, Poul G.; Kokkendorff, Simon L.; Markvorsen, Steen

    2002-01-01

    We study finite metric spaces with elements picked from, and distances consistent with, ambient Riemannian manifolds. The concepts of negative type and strictly negative type are reviewed, and the conjecture that hyperbolic spaces are of strictly negative type is settled, in the affirmative...

  15. Extremely strict ideals in Banach spaces

    Indian Academy of Sciences (India)

    Abstract. Motivated by the notion of an ideal introduced by Godefroy et al. (Stu- dia Math. 104 (1993) 13–59), in this article, we introduce and study the notion of an extremely strict ideal. For a Poulsen simplex K, we show that the space of affine contin- uous functions on K is an extremely strict ideal in the space of continuous ...

  16. The NKG2D ligand ULBP2 is specifically regulated through an invariant chain-dependent endosomal pathway

    DEFF Research Database (Denmark)

    Uhlenbrock, Franziska Katharina; Hagemann-Jensen, Michael Henrik; Kehlet, Stephanie

    2014-01-01

    by affecting endosomal/lysosomal integrity and protein kinase C activity. The invariant chain was further essential for endosomal transport of ULBP2. This novel pathway was identified through screening experiments by which methylselenic acid was found to possess notable NKG2D ligand regulatory properties....... The protein kinase C inhibitor methylselenic acid induced MICA/B surface expression but dominantly blocked ULBP2 surface transport. Remarkably, by targeting this novel pathway we could specifically block the production of soluble ULBP2 from different, primary melanomas. Our findings strongly suggest...

  17. Thyroid hormone and retinoic acid nuclear receptors: specific ligand-activated transcription factors

    International Nuclear Information System (INIS)

    Brtko, J.

    1998-01-01

    Transcriptional regulation by both the thyroid hormone and the vitamin A-derived 'retinoid hormones' is a critical component in controlling many aspects of higher vertebrate development and metabolism. Their functions are mediated by nuclear receptors, which comprise a large super-family of ligand-inducible transcription factors. Both the thyroid hormone and the retinoids are involved in a complex arrangement of physiological and development responses in many tissues of higher vertebrates. The functions of 3,5,3'-triiodothyronine (T 3 ), the thyromimetically active metabolite of thyroxine as well as all-trans retinoic acid, the biologically active vitamin A metabolite are mediated by nuclear receptor proteins that are members of the steroid/thyroid/retinoid hormone receptor family. The functions of all members of the receptor super family are discussed. (authors)

  18. Specific ligand binding domain residues confer low dioxin responsiveness to AHR1β of Xenopus laevis.

    Science.gov (United States)

    Odio, Camila; Holzman, Sarah A; Denison, Michael S; Fraccalvieri, Domenico; Bonati, Laura; Franks, Diana G; Hahn, Mark E; Powell, Wade H

    2013-03-12

    The aryl hydrocarbon receptor (AHR) is a Per-ARNT-Sim (PAS) family protein that mediates the toxicity of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) in vertebrates. Frogs are remarkably insensitive to TCDD, and AHRs from Xenopus laevis bind TCDD with low affinity. We sought to identify structural features of X. laevis AHR1β associated with low TCDD sensitivity. Substitution of the entire ligand binding domain (LBD) with the corresponding sequence from mouse AHR(b-1) dramatically increased TCDD responsiveness in transactivation assays. To identify the amino acid residues responsible, we constructed a comparative model of the AHR1β LBD using homologous domains of PAS proteins HIF2α and ARNT. The model revealed an internal cavity with dimensions similar to those of the putative binding cavity of mouse AHR(b-1), suggesting the importance of side chain interactions over cavity size. Of residues with side chains clearly pointing into the cavity, only two differed from the mouse sequence. When A354, located within a conserved β-strand, was changed to serine, the corresponding mouse residue, the EC50 for TCDD decreased more than 15-fold. When N325 was changed to serine, the EC50 decreased 3-fold. When the mutations were combined, the EC50 decreased from 18.6 to 0.8 nM, the value nearly matching the TCDD sensitivity of mouse AHR. Velocity sedimentation analysis confirmed that mutant frog AHRs exhibited correspondingly increased levels of TCDD binding. We also assayed mutant AHRs for responsiveness to a candidate endogenous ligand, 6-formylindolo[3,2-b]carbazole (FICZ). Mutations that increased sensitivity to TCDD also increased sensitivity to FICZ. This comparative study represents a novel approach to discerning fundamental information about the structure of AHR and its interactions with biologically important agonists.

  19. Oligoclonal band phenotypes in MS differ in their HLA class II association, while specific KIR ligands at HLA class I show association to MS in general

    DEFF Research Database (Denmark)

    Gustavsen, Marte W; Viken, Marte K; Celius, Elisabeth G

    2014-01-01

    Multiple sclerosis (MS) patients have been reported to have different HLA class II allele profiles depending on oligoclonal bands (OCBs) in the cerebrospinal fluid, but HLA class I alleles and killer cell immunoglobulin-like receptor (KIR) ligands have not been studied. We investigated the associ......Multiple sclerosis (MS) patients have been reported to have different HLA class II allele profiles depending on oligoclonal bands (OCBs) in the cerebrospinal fluid, but HLA class I alleles and killer cell immunoglobulin-like receptor (KIR) ligands have not been studied. We investigated...... the association of HLA alleles and KIR ligands according to OCB status in MS patients (n=3876). Specific KIR ligands were associated with patients when compared to controls (n=3148), supporting a role for NK cells in MS pathogenesis. HLA class I alleles and KIR ligands did not differ between OCB phenotypes...

  20. Dissecting electrostatic screening, specific ion binding, and ligand binding in an energetic model for glycine riboswitch folding

    Energy Technology Data Exchange (ETDEWEB)

    Lipfert, Jan; Sim, Adelene Y.L.; Herschlag, Daniel; Doniach, Sebastian (Stanford)

    2010-09-17

    Riboswitches are gene-regulating RNAs that are usually found in the 5{prime}-untranslated regions of messenger RNA. As the sugar-phosphate backbone of RNA is highly negatively charged, the folding and ligand-binding interactions of riboswitches are strongly dependent on the presence of cations. Using small angle X-ray scattering (SAXS) and hydroxyl radical footprinting, we examined the cation dependence of the different folding stages of the glycine-binding riboswitch from Vibrio cholerae. We found that the partial folding of the tandem aptamer of this riboswitch in the absence of glycine is supported by all tested mono- and divalent ions, suggesting that this transition is mediated by nonspecific electrostatic screening. Poisson-Boltzmann calculations using SAXS-derived low-resolution structural models allowed us to perform an energetic dissection of this process. The results showed that a model with a constant favorable contribution to folding that is opposed by an unfavorable electrostatic term that varies with ion concentration and valency provides a reasonable quantitative description of the observed folding behavior. Glycine binding, on the other hand, requires specific divalent ions binding based on the observation that Mg{sup 2+}, Ca{sup 2+}, and Mn{sup 2+} facilitated glycine binding, whereas other divalent cations did not. The results provide a case study of how ion-dependent electrostatic relaxation, specific ion binding, and ligand binding can be coupled to shape the energetic landscape of a riboswitch and can begin to be quantitatively dissected.

  1. Transfer of Copper from an Amyloid to a Natural Copper-Carrier Peptide with a Specific Mediating Ligand.

    Science.gov (United States)

    Nguyen, Michel; Bijani, Christian; Martins, Nathalie; Meunier, Bernard; Robert, Anne

    2015-11-16

    The oxidative stress that arises from the catalytic reduction of dioxygen by Cu(II/I)-loaded amyloids is the major pathway for neuron death that occurs in Alzheimer's disease. In this work, we show that bis-8(aminoquinoline) ligands, copper(II) specific chelators, are able to catalytically extract Cu(II) from Cu-Aβ1-16 and then completely release Cu(I) in the presence of glutathione to provide a Cu(I)-glutathione complex, a biological intermediate that is able to deliver copper to apo forms of copper-protein complexes. These data demonstrate that bis-8(aminoquinolines) can perform the transfer of copper ions from the pathological Cu-amyloid complexes to regular copper-protein complexes. These copper-specific ligands assist GSH to recycle Cu(I) in an AD brain and consequently slow down oxidative damage that is due to copper dysregulation in Alzheimer's disease. Under the same conditions, we have shown that the copper complex of PBT2, a mono(8-hydroxyquinoline) previously used as a drug candidate, does not efficiently release copper in the presence of GSH. In addition, we report that GSH itself was unable to fully abstract copper ions from Cu-β-amyloid complexes. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  2. Finite Metric Spaces of Strictly negative Type

    DEFF Research Database (Denmark)

    Hjorth, Poul G.

    If a finite metric space is of strictly negative type then its transfinite diameter is uniquely realized by an infinite extent (“load vector''). Finite metric spaces that have this property include all trees, and all finite subspaces of Euclidean and Hyperbolic spaces. We prove that if the distance...... matrix of a finite metric space is both hypermetric and regular, then it is of strictly negative type. We show that the strictly negative type finite subspaces of spheres are precisely those which do not contain two pairs of antipodal points....

  3. Androgen receptor functional analyses by high throughput imaging: determination of ligand, cell cycle, and mutation-specific effects.

    Directory of Open Access Journals (Sweden)

    Adam T Szafran

    Full Text Available Understanding how androgen receptor (AR function is modulated by exposure to steroids, growth factors or small molecules can have important mechanistic implications for AR-related disease therapies (e.g., prostate cancer, androgen insensitivity syndrome, AIS, and in the analysis of environmental endocrine disruptors.We report the development of a high throughput (HT image-based assay that quantifies AR subcellular and subnuclear distribution, and transcriptional reporter gene activity on a cell-by-cell basis. Furthermore, simultaneous analysis of DNA content allowed determination of cell cycle position and permitted the analysis of cell cycle dependent changes in AR function in unsynchronized cell populations. Assay quality for EC50 coefficients of variation were 5-24%, with Z' values reaching 0.91. This was achieved by the selective analysis of cells expressing physiological levels of AR, important because minor over-expression resulted in elevated nuclear speckling and decreased transcriptional reporter gene activity. A small screen of AR-binding ligands, including known agonists, antagonists, and endocrine disruptors, demonstrated that nuclear translocation and nuclear "speckling" were linked with transcriptional output, and specific ligands were noted to differentially affect measurements for wild type versus mutant AR, suggesting differing mechanisms of action. HT imaging of patient-derived AIS mutations demonstrated a proof-of-principle personalized medicine approach to rapidly identify ligands capable of restoring multiple AR functions.HT imaging-based multiplex screening will provide a rapid, systems-level analysis of compounds/RNAi that may differentially affect wild type AR or clinically relevant AR mutations.

  4. Hyperbolic spaces are of strictly negative type

    DEFF Research Database (Denmark)

    Hjorth, Poul G.; Kokkendorff, Simon L.; Markvorsen, Steen

    2002-01-01

    We study finite metric spaces with elements picked from, and distances consistent with, ambient Riemannian manifolds. The concepts of negative type and strictly negative type are reviewed, and the conjecture that hyperbolic spaces are of strictly negative type is settled, in the affirmative....... The technique of the proof is subsequently applied to show that every compact manifold of negative type must have trivial fundamental group, and to obtain a necessary criterion for product manifolds to be of negative type....

  5. How to awaken your nanomachines: Site-specific activation of focal adhesion kinases through ligand interactions

    KAUST Repository

    Walkiewicz, Katarzyna Wiktoria

    2015-06-17

    The focal adhesion kinase (FAK) and the related protein-tyrosine kinase 2-beta (Pyk2) are highly versatile multidomain scaffolds central to cell adhesion, migration, and survival. Due to their key role in cancer metastasis, understanding and inhibiting their functions are important for the development of targeted therapy. Because FAK and Pyk2 are involved in many different cellular functions, designing drugs with partial and function-specific inhibitory effects would be desirable. Here, we summarise recent progress in understanding the structural mechanism of how the tug-of-war between intramolecular and intermolecular interactions allows these protein ‘nanomachines’ to become activated in a site-specific manner.

  6. Species differences in ligand specificity of auxin-controlled elongation and auxin transport: comparing Zea and Vigna

    Science.gov (United States)

    Zhao, Hu; Hertel, Rainer; Ishikawa, Hideo; Evans, Michael L.

    2002-01-01

    The plant hormone auxin affects cell elongation in both roots and shoots. In roots, the predominant action of auxin is to inhibit cell elongation while in shoots auxin, at normal physiological levels, stimulates elongation. The question of whether the primary receptor for auxin is the same in roots and shoots has not been resolved. In addition to its action on cell elongation in roots and shoots, auxin is transported in a polar fashion in both organs. Although auxin transport is well characterized in both roots and shoots, there is relatively little information on the connection, if any, between auxin transport and its action on elongation. In particular, it is not clear whether the protein mediating polar auxin movement is separate from the protein mediating auxin action on cell elongation or whether these two processes might be mediated by one and the same receptor. We examined the identity of the auxin growth receptor in roots and shoots by comparing the response of roots and shoots of the grass Zea mays L. and the legume Vigna mungo L. to indole-3-acetic acid, 2-naphthoxyacetic acid, 4,6-dichloroindoleacetic acid, and 4,7-dichloroindoleacetic acid. We also studied whether or not a single protein might mediate both auxin transport and auxin action by comparing the polar transport of indole-3-acetic acid and 2-naphthoxyacetic acid through segments from Vigna hypocotyls and maize coleoptiles. For all of the assays performed (root elongation, shoot elongation, and polar transport) the action and transport of the auxin derivatives was much greater in the dicots than in the grass species. The preservation of ligand specificity between roots and shoots and the parallels in ligand specificity between auxin transport and auxin action on growth are consistent with the hypothesis that the auxin receptor is the same in roots and shoots and that this protein may mediate auxin efflux as well as auxin action in both organ types.

  7. Oligoclonal band phenotypes in MS differ in their HLA class II association, while specific KIR ligands at HLA class I show association to MS in general.

    Science.gov (United States)

    Gustavsen, Marte W; Viken, Marte K; Celius, Elisabeth G; Berge, Tone; Mero, Inger-Lise; Berg-Hansen, Pål; Aarseth, Jan H; Myhr, Kjell-Morten; Søndergaard, Helle B; Sellebjerg, Finn; Oturai, Annette B; Hillert, Jan; Alfredsson, Lars; Olsson, Tomas; Kockum, Ingrid; Lie, Benedicte A; Harbo, Hanne F

    2014-09-15

    Multiple sclerosis (MS) patients have been reported to have different HLA class II allele profiles depending on oligoclonal bands (OCBs) in the cerebrospinal fluid, but HLA class I alleles and killer cell immunoglobulin-like receptor (KIR) ligands have not been studied. We investigated the association of HLA alleles and KIR ligands according to OCB status in MS patients (n=3876). Specific KIR ligands were associated with patients when compared to controls (n=3148), supporting a role for NK cells in MS pathogenesis. HLA class I alleles and KIR ligands did not differ between OCB phenotypes, but HLA class II associations were convincingly replicated. Copyright © 2014 Elsevier B.V. All rights reserved.

  8. Miniature protein ligands for EVH1 domains: interplay between affinity, specificity, and cell motility.

    Science.gov (United States)

    Holtzman, Jennifer H; Woronowicz, Kamil; Golemi-Kotra, Dasantila; Schepartz, Alanna

    2007-11-27

    Dynamic rearrangements of the actin cytoskeleton power cell motility in contexts ranging from intracellular microbial pathogenesis to axon guidance. The Ena/VASP family proteins-Mena, VASP, and Evl-are believed to control cell motility by serving as a direct link between signaling events and the actin cytoskeleton. It has previously been reported that a novel miniature protein, pGolemi, binds with high affinity to the EVH1 domain of Mena (Mena1-112) but not to those of VASP (VASP1-115) or Evl (Evl1-115) and also causes an unusual defect in actin-driven Listeria monocytogenes motility. Here, scanning mutagenesis was used to examine the effects of single amino acid changes within pGolemi on EVH1 domain affinity and specificity, miniature protein secondary structure, and L. monocytogenes motility. The data suggest that pGolemi contains the expected aPP-like fold and binds Mena1-112 in a manner highly analogous to the proline-rich repeat region of L. monocytogenes ActA protein. Residues throughout pGolemi contribute to both EVH1 domain affinity and paralog specificity. Moreover, the affinities of pGolemi variants for Mena1-112 correlate with selectivity against the EVH1 domains of VASP and Evl. In L. monocytogenes motility assays, speed and speed variability correlate strongly with EVH1 paralog specificity, suggesting that the Ena/VASP paralogs do not play equivalent roles in the process of L. monocytogenes actin tail maturation.

  9. Specific imaging of inflammation with the 18 kDa translocator protein ligand DPA-714 in animal models of epilepsy and stroke.

    Directory of Open Access Journals (Sweden)

    Denise Harhausen

    Full Text Available Inflammation is a pathophysiological hallmark of many diseases of the brain. Specific imaging of cells and molecules that contribute to cerebral inflammation is therefore highly desirable, both for research and in clinical application. The 18 kDa translocator protein (TSPO has been established as a suitable target for the detection of activated microglia/macrophages. A number of novel TSPO ligands have been developed recently. Here, we evaluated the high affinity TSPO ligand DPA-714 as a marker of brain inflammation in two independent animal models. For the first time, the specificity of radiolabeled DPA-714 for activated microglia/macrophages was studied in a rat model of epilepsy (induced using Kainic acid and in a mouse model of stroke (transient middle cerebral artery occlusion, tMCAO using high-resolution autoradiography and immunohistochemistry. Additionally, cold-compound blocking experiments were performed and changes in blood-brain barrier (BBB permeability were determined. Target-to-background ratios of 2 and 3 were achieved in lesioned vs. unaffected brain tissue in the epilepsy and tMCAO models, respectively. In both models, ligand uptake into the lesion corresponded well with the extent of Ox42- or Iba1-immunoreactive activated microglia/macrophages. In the epilepsy model, ligand uptake was almost completely blocked by pre-injection of DPA-714 and FEDAA1106, another high-affinity TSPO ligand. Ligand uptake was independent of the degree of BBB opening and lesion size in the stroke model. We provide further strong evidence that DPA-714 is a specific ligand to image activated microglia/macrophages in experimental models of brain inflammation.

  10. Strictly convex functions on complete Finsler manifolds

    Indian Academy of Sciences (India)

    ... Refresher Courses · Symposia · Live Streaming. Home; Journals; Proceedings – Mathematical Sciences; Volume 126; Issue 4. Strictly convex functions on complete Finsler manifolds. YOE ITOKAWA KATSUHIRO SHIOHAMA BANKTESHWAR TIWARI. Research Article Volume 126 Issue 4 October 2016 pp 623-627 ...

  11. Finite Metric Spaces of Strictly Negative Type

    DEFF Research Database (Denmark)

    Hjorth, Poul; Lisonek, P.; Markvorsen, Steen

    1998-01-01

    We prove that, if a finite metric space is of strictly negative type, then its transfinite diameter is uniquely realized by the infinite extender (load vector). Finite metric spaces that have this property include all spaces on two, three, or four points, all trees, and all finite subspaces of Eu...

  12. Specific gut commensal flora locally alters T cell tuning to endogenous ligands.

    Science.gov (United States)

    Chappert, Pascal; Bouladoux, Nicolas; Naik, Shruti; Schwartz, Ronald H

    2013-06-27

    Differences in gut commensal flora can dramatically influence autoimmune responses, but the mechanisms behind this are still unclear. We report, in a Th1-cell-driven murine model of autoimmune arthritis, that specific gut commensals, such as segmented filamentous bacteria, have the ability to modulate the activation threshold of self-reactive T cells. In the local microenvironment of gut-associated lymphoid tissues, inflammatory cytokines elicited by the commensal flora dynamically enhanced the antigen responsiveness of T cells that were otherwise tuned down to a systemic self-antigen. Together with subtle differences in early lineage differentiation, this ultimately led to an enhanced recruitment of pathogenic Th1 cells and the development of a more severe form of autoimmune arthritis. These findings define a key role for the gut commensal flora in sustaining ongoing autoimmune responses through the local fine tuning of T-cell-receptor-proximal activation events in autoreactive T cells. Copyright © 2013 Elsevier Inc. All rights reserved.

  13. Structure versus function-The impact of computational methods on the discovery of specific GPCR-ligands.

    Science.gov (United States)

    Bermudez, Marcel; Wolber, Gerhard

    2015-07-15

    Over the past decades, computational methods have become invaluable for drug design campaigns but also as auxiliary tool for structural biology. The combination of experimental and in silico methods in the field of G protein coupled receptors (GPCRs) is indispensable. Despite recent groundbreaking achievements in GPCR crystallography, structural information for the vast majority of this physiologically important protein class is only accessible through homology models. Since the understanding of the conformational changes resulting in multiple activation pathways is incomplete, the design of specific GPCR modulating drugs remains a major challenge. However, due to the highly interdisciplinary requirements for the investigation of receptor function and the necessity of joining scientist from different fields, computational approaches gain importance in rationalizing and illustrating certain specific effects. In silico methods, such as molecular dynamics (MD) simulations, pharmacophore modeling or docking, proved to be suitable to complement experimental approaches. In this review, we highlight recent examples of in silico studies that were successfully applied in the field of GPCR research. Those approaches follow two main goals: Firstly, structural investigations that help to understand the receptor function and the characterization of ligand binding and secondly the identification of novel GPCR modulators as potential drugs. Copyright © 2015 Elsevier Ltd. All rights reserved.

  14. INTERACTION OF IRON(II MIXED-LIGAND COMPLEXES WITH DNA: BASE-PAIR SPECIFICITY AND THERMAL DENATURATION STUDIES

    Directory of Open Access Journals (Sweden)

    Mudasir Mudasir

    2010-06-01

    Full Text Available A research about base-pair specificity of the DNA binding of [Fe(phen3]2+, [Fe(phen2(dip]2+ and [Fe(phen(dip2]2+ complexes and the effect of calf-thymus DNA (ct-DNA binding of these metal complexes on thermal denaturation of ct-DNA has been carried out. This research is intended to evaluate the preferential binding of the complexes to the sequence of DNA (A-T or G-C sequence and to investigate the binding strength and mode upon their interaction with DNA. Base-pair specificity of the DNA binding of the complexes was determined by comparing the equilibrium binding constant (Kb of each complex to polysynthetic DNA that contain only A-T or G-C sequence. The Kb value of the interaction was determined by spectrophotometric titration and thermal denaturation temperature (Tm was determined by monitoring the absorbance of the mixture solution of each complex and ct-DNA at λ =260 nm as temperature was elevated in the range of 25 - 100 oC. Results of the study show that in general all iron(II complexes studied exhibit a base-pair specificity in their DNA binding to prefer the relatively facile A-T sequence as compared to the G-C one. The thermal denaturation experiments have demonstrated that Fe(phen3]2+ and [Fe(phen2(dip]2+ interact weakly with double helical DNA via electrostatic interaction as indicated by insignificant changes in melting temperature, whereas [Fe(phen2(dip]2+  most probably binds to DNA in mixed modes of interaction, i.e.: intercalation and electrostatic interaction. This conclusion is based on the fact that the binding of [Fe(phen2(dip]2+ to ct-DNA moderately increase the Tm value of ct- DNA   Keywords: DNA Binding, mixed-ligand complexes

  15. Extremely strict ideals in Banach spaces

    Indian Academy of Sciences (India)

    the space of regular Borel measures, it is easy to see that with respect to the projection μ → μ|(0, 1), M is an extremely strict ideal in C([0, 1]) but as the Lebesgue measure is non-atomic, M. ∗. 1 is not the norm closed ..... (Grenoble) 28 (1978) 35–65. [10] Rao T S S R K, On ideals in Banach spaces, Rocky Mountain J. Math.

  16. Ligand size is a major determinant of specificity in periplasmic oxyanion-binding proteins: the 1.2 A resolution crystal structure of Azotobacter vinelandii ModA.

    Science.gov (United States)

    Lawson, D M; Williams, C E; Mitchenall, L A; Pau, R N

    1998-12-15

    . Periplasmic receptors constitute a diverse class of binding proteins that differ widely in size, sequence and ligand specificity. Nevertheless, almost all of them display a common beta/alpha folding motif and have similar tertiary structures consisting of two globular domains. The ligand is bound at the bottom of a deep cleft, which lies at the interface between these two domains. The oxyanion-binding proteins are notable in that they can discriminate between very similar ligands. . Azotobacter vinelandii is unusual in that it possesses two periplasmic molybdate-binding proteins. The crystal structure of one of these with bound ligand has been determined at 1.2 A resolution. It superficially resembles the structure of sulphate-binding protein (SBP) from Salmonella typhimurium and uses a similar constellation of hydrogen-bonding interactions to bind its ligand. However, the detailed interactions are distinct from those of SBP and the more closely related molybdate-binding protein of Escherichia coli. . Despite differences in the residues involved in binding, the volumes of the binding pockets in the A. vinelandii and E. coli molybdate-binding proteins are similar and are significantly larger than that of SBP. We conclude that the discrimination between molybdate and sulphate shown by these binding proteins is largely dependent upon small differences in the sizes of these two oxyanions.

  17. On the analysis and comparison of conformer-specific essential dynamics upon ligand binding to a protein

    International Nuclear Information System (INIS)

    Grosso, Marcos; Kalstein, Adrian; Parisi, Gustavo; Fernandez-Alberti, Sebastian; Roitberg, Adrian E.

    2015-01-01

    The native state of a protein consists of an equilibrium of conformational states on an energy landscape rather than existing as a single static state. The co-existence of conformers with different ligand-affinities in a dynamical equilibrium is the basis for the conformational selection model for ligand binding. In this context, the development of theoretical methods that allow us to analyze not only the structural changes but also changes in the fluctuation patterns between conformers will contribute to elucidate the differential properties acquired upon ligand binding. Molecular dynamics simulations can provide the required information to explore these features. Its use in combination with subsequent essential dynamics analysis allows separating large concerted conformational rearrangements from irrelevant fluctuations. We present a novel procedure to define the size and composition of essential dynamics subspaces associated with ligand-bound and ligand-free conformations. These definitions allow us to compare essential dynamics subspaces between different conformers. Our procedure attempts to emphasize the main similarities and differences between the different essential dynamics in an unbiased way. Essential dynamics subspaces associated to conformational transitions can also be analyzed. As a test case, we study the glutaminase interacting protein (GIP), composed of a single PDZ domain. Both GIP ligand-free state and glutaminase L peptide-bound states are analyzed. Our findings concerning the relative changes in the flexibility pattern upon binding are in good agreement with experimental Nuclear Magnetic Resonance data

  18. On the analysis and comparison of conformer-specific essential dynamics upon ligand binding to a protein

    Science.gov (United States)

    Grosso, Marcos; Kalstein, Adrian; Parisi, Gustavo; Roitberg, Adrian E.; Fernandez-Alberti, Sebastian

    2015-06-01

    The native state of a protein consists of an equilibrium of conformational states on an energy landscape rather than existing as a single static state. The co-existence of conformers with different ligand-affinities in a dynamical equilibrium is the basis for the conformational selection model for ligand binding. In this context, the development of theoretical methods that allow us to analyze not only the structural changes but also changes in the fluctuation patterns between conformers will contribute to elucidate the differential properties acquired upon ligand binding. Molecular dynamics simulations can provide the required information to explore these features. Its use in combination with subsequent essential dynamics analysis allows separating large concerted conformational rearrangements from irrelevant fluctuations. We present a novel procedure to define the size and composition of essential dynamics subspaces associated with ligand-bound and ligand-free conformations. These definitions allow us to compare essential dynamics subspaces between different conformers. Our procedure attempts to emphasize the main similarities and differences between the different essential dynamics in an unbiased way. Essential dynamics subspaces associated to conformational transitions can also be analyzed. As a test case, we study the glutaminase interacting protein (GIP), composed of a single PDZ domain. Both GIP ligand-free state and glutaminase L peptide-bound states are analyzed. Our findings concerning the relative changes in the flexibility pattern upon binding are in good agreement with experimental Nuclear Magnetic Resonance data.

  19. Strictness Analysis and Denotational Abstract Interpretation

    DEFF Research Database (Denmark)

    Nielson, Flemming

    1988-01-01

    there and this sufices to make the framework applicable to strictness analysis for the lambda-calculus. This shows the possibility of a general theory for the analysis of functional programs and it gives more insight into the relative precision of the various analyses. In particular it is shown that a collecting (static......A theory of abstract interpretation () is developed for a typed lambda-calculus. The typed lambda-calculus may be viewed as the ''static'' part of a two-level denotational metalanguage for which abstract interpretation was developed by ). The present development relaxes a condition imposed...

  20. 7 CFR 28.441 - Strict Middling Yellow Stained Color.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 2 2010-01-01 2010-01-01 false Strict Middling Yellow Stained Color. 28.441 Section... Strict Middling Yellow Stained Color. Strict Middling Yellow Stained Color is color which is deeper than that of Strict Middling Tinged Color. [57 FR 34498, Aug. 5, 1992] ...

  1. 7 CFR 28.412 - Strict Middling Light Spotted Color.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 2 2010-01-01 2010-01-01 false Strict Middling Light Spotted Color. 28.412 Section 28... Light Spotted Color. Strict Middling Light Spotted Color is color which in spot or color, or both, is between Strict Middling Color and Strict Middling Spotted Color. ...

  2. High Specificity in Circulating Tumor Cell Identification Is Required for Accurate Evaluation of Programmed Death-Ligand 1.

    Directory of Open Access Journals (Sweden)

    Jennifer L Schehr

    Full Text Available Expression of programmed-death ligand 1 (PD-L1 in non-small cell lung cancer (NSCLC is typically evaluated through invasive biopsies; however, recent advances in the identification of circulating tumor cells (CTCs may be a less invasive method to assay tumor cells for these purposes. These liquid biopsies rely on accurate identification of CTCs from the diverse populations in the blood, where some tumor cells share characteristics with normal blood cells. While many blood cells can be excluded by their high expression of CD45, neutrophils and other immature myeloid subsets have low to absent expression of CD45 and also express PD-L1. Furthermore, cytokeratin is typically used to identify CTCs, but neutrophils may stain non-specifically for intracellular antibodies, including cytokeratin, thus preventing accurate evaluation of PD-L1 expression on tumor cells. This holds even greater significance when evaluating PD-L1 in epithelial cell adhesion molecule (EpCAM positive and EpCAM negative CTCs (as in epithelial-mesenchymal transition (EMT.To evaluate the impact of CTC misidentification on PD-L1 evaluation, we utilized CD11b to identify myeloid cells. CTCs were isolated from patients with metastatic NSCLC using EpCAM, MUC1 or Vimentin capture antibodies and exclusion-based sample preparation (ESP technology.Large populations of CD11b+CD45lo cells were identified in buffy coats and stained non-specifically for intracellular antibodies including cytokeratin. The amount of CD11b+ cells misidentified as CTCs varied among patients; accounting for 33-100% of traditionally identified CTCs. Cells captured with vimentin had a higher frequency of CD11b+ cells at 41%, compared to 20% and 18% with MUC1 or EpCAM, respectively. Cells misidentified as CTCs ultimately skewed PD-L1 expression to varying degrees across patient samples.Interfering myeloid populations can be differentiated from true CTCs with additional staining criteria, thus improving the

  3. Identification of amino acid residues in the ligand-binding domain of the aryl hydrocarbon receptor causing the species-specific response to omeprazole: possible determinants for binding putative endogenous ligands.

    Science.gov (United States)

    Shiizaki, Kazuhiro; Ohsako, Seiichiroh; Kawanishi, Masanobu; Yagi, Takashi

    2014-02-01

    Omeprazole (OME) induces the expression of genes encoding drug-metabolizing enzymes, such as CYP1A1, via activation of the aryl hydrocarbon receptor (AhR) both in vivo and in vitro. However, the precise mechanism of OME-mediated AhR activation is still under investigation. While elucidating species-specific susceptibility to dioxin, we found that OME-mediated AhR activation was mammalian species specific. Moreover, we previously reported that OME has inhibitory activity toward CYP1A1 enzymes. From these observations, we speculated that OME-mediated AhR target gene transcription is due to AhR activation by increasing amounts of putative AhR ligands in serum by inhibition of CYP1A1 activity. We compared the amino acid sequences of OME-sensitive rabbit AhR and nonsensitive mouse AhR to identify the residues responsible for the species-specific response. Chimeric AhRs were constructed by exchanging domains between mouse and rabbit AhRs to define the region required for the response to OME. OME-mediated transactivation was observed only with the chimeric AhR that included the ligand-binding domain (LBD) of the rabbit AhR. Site-directed mutagenesis revealed three amino acids (M328, T353, and F367) in the rabbit AhR that were responsible for OME-mediated transactivation. Replacing these residues with those of the mouse AhR abolished the response of the rabbit AhR. In contrast, substitutions of these amino acids with those of the rabbit AhR altered nonsensitive mouse AhR to become sensitive to OME. These results suggest that OME-mediated AhR activation requires a specific structure within LBD that is probably essential for binding with enigmatic endogenous ligands.

  4. Identification of novel peptide ligands for the cancer-specific receptor mutation EFGRvIII using a mixture-based synthetic combinatorial library

    DEFF Research Database (Denmark)

    Denholt, Charlotte Lund; Hansen, Paul Robert; Pedersen, Nina

    2009-01-01

    . This study demonstrates the value of using mixture-based combinatorial positional scanning libraries for the identification of novel peptide ligands targeted against the cancer-specific EGFRvIII. Our best candidate H-FALGEA-NH(2) will be radioactively labeled and evaluated as an imaging agent for positron......We report here, the design and synthesis of a positional scanning synthetic combinatorial library for the identification of novel peptide ligands targeted against the cancer-specific epidermal growth factor tyrosine kinase receptor mutation variant III (EGFRvIII). This receptor is expressed...... in several kinds of cancer, in particular, ovarian, glioblastomas, and breast cancer, but not in normal tissue. The library consisted of six individual positional sublibraries in the format, H-O(1-6)XXXXX-NH(2), O being one of the 19 proteinogenic amino acids (cysteine omitted) and X an equimolar mixture...

  5. Allele-specific recognition by LILRB3 and LILRA6 of a cytokeratin 8-associated ligand on necrotic glandular epithelial cells.

    Science.gov (United States)

    Jones, Des C; Hewitt, Colin R A; López-Álvarez, María R; Jahnke, Martin; Russell, Alasdair I; Radjabova, Valeria; Trowsdale, Alice R Z; Trowsdale, John

    2016-03-29

    The LILRs are a family of receptors that regulate the activities of myelomonocytic cells. We found that specific allelic variants of two related members of the LILR family, LILRB3 and LILRA6, interact with a ligand exposed on necrotic glandular epithelial cells. The extracellular domains of LILRB3 and LILRA6 are very similar and their genes are highly polymorphic. A commonly occurring allele, LILRB3*12, displayed particularly strong binding of these necrotic cells and further screening of the products of LILRB3 alleles identified motifs that correlated with binding. Immunoprecipitation of the ligand from epithelial cell lysates using recombinant LILRB3*12, identified cytokeratins 8, 18 and 19. Purified proteins obtained from epithelial cell lysates, using anti-cytokeratin 8 antibodies, were able to activate LILRB3*12 reporter cells. Knock-down of cytokeratin 8 in epithelial cells abrogated expression of the LILRB3 ligand, while staining with recombinant LILRB3*12 showed co-localisation with cytokeratin 8 and 18 in permeabilised breast cancer cells. Necrosis is a common feature of tumours. The finding of a necrosis-associated ligand for these two receptors raises the possibility of a novel interaction that alters immune responses within the tumour microenvironment. Since LILRB3 and LILRA6 genes are highly polymorphic the interaction may influence an individual's immune response to tumours.

  6. Ligand-specific Deactivation Time Course of GluN1/GluN2D NMDA Receptors

    Energy Technology Data Exchange (ETDEWEB)

    K Vance; N Simorowski; S Traynelis; H Furukawa

    2011-12-31

    N-methyl-D-aspartate (NMDA) receptors belong to the family of ionotropic glutamate receptors that mediate a majority of excitatory synaptic transmission. One unique property of GluN1/GluN2D NMDA receptors is an unusually prolonged deactivation time course following the removal of L-glutamate. Here we show, using x-ray crystallography and electrophysiology, that the deactivation time course of GluN1/GluN2D receptors is influenced by the conformational variability of the ligand-binding domain (LBD) as well as the structure of the activating ligand. L-glutamate and L-CCG-IV induce significantly slower deactivation time courses compared with other agonists. Crystal structures of the isolated GluN2D LBD in complex with various ligands reveal that the binding of L-glutamate induces a unique conformation at the backside of the ligand-binding site in proximity to the region at which the transmembrane domain would be located in the intact receptors. These data suggest that the activity of the GluN1/GluN2D NMDA receptor is controlled distinctively by the endogenous neurotransmitter L-glutamate.

  7. Allele-specific recognition by LILRB3 and LILRA6 of a cytokeratin 8 - associated ligand on necrotic glandular epithelial cells

    OpenAIRE

    Jones, Des C.; Hewitt, Colin R.A.; L?pez-?lvarez, Mar?a R.; Jahnke, Martin; Russell, Alasdair I.; Radjabova, Valeria; Trowsdale, Alice R.Z.; Trowsdale, John

    2016-01-01

    The LILRs are a family of receptors that regulate the activities of myelomonocytic cells. We found that specific allelic variants of two related members of the LILR family, LILRB3 and LILRA6, interact with a ligand exposed on necrotic glandular epithelial cells. The extracellular domains of LILRB3 and LILRA6 are very similar and their genes are highly polymorphic. A commonly occurring allele, LILRB3*12, displayed particularly strong binding of these necrotic cells and further screening of the...

  8. CA-125 of fetal origin can act as a ligand for dendritic cell-specific ICAM-3-grabbing non-integrin.

    Science.gov (United States)

    Mitić, Ninoslav; Milutinović, Bojana; Janković, Miroslava

    2014-06-01

    CA-125 (coelomic epithelium-related antigen) forms the extracellular portion of transmembrane mucin 16 (MUC16). It is shed after proteolytic degradation. Due to structural heterogeneity, CA-125 ligand capacity and biological roles are not yet understood. In this study, we assessed CA-125 as a ligand for dendritic cell-specific ICAM-3-grabbing non-integrin (DC-SIGN), which is a C-type lectin showing specificity for mannosylated and fucosylated structures. It plays a role as a pattern recognition molecule for viral and bacterial glycans or as an adhesion receptor. We probed a human DC-SIGN-Fc chimera with CA-125 of fetal or cancer origin using solid- or fluid-phase binding and inhibition assays. The results showed that DC-SIGN binds to CA-125 of fetal origin and that this interaction is carbohydrate-dependent. By contrast, cancer-derived CA-125 displayed negligible binding. Inhibition assays indicated differences in the potency of CA-125 to interfere with DC-SIGN binding to pathogen-related glycoconjugates, such as mannan and Helicobacter pylori antigens. The differences in ligand properties between CA-125 of fetal and cancer origin may be due to specificities of glycosylation. This might influence various functions of dendritic cells based on their subset diversity and maturation-related functional capacity.

  9. Seeking structural specificity: direct modulation of pentameric ligand-gated ion channels by alcohols and general anesthetics.

    Science.gov (United States)

    Howard, Rebecca J; Trudell, James R; Harris, R Adron

    2014-01-01

    Alcohols and other anesthetic agents dramatically alter neurologic function in a wide range of organisms, yet their molecular sites of action remain poorly characterized. Pentameric ligand-gated ion channels, long implicated in important direct effects of alcohol and anesthetic binding, have recently been illuminated in renewed detail thanks to the determination of atomic-resolution structures of several family members from lower organisms. These structures provide valuable models for understanding and developing anesthetic agents and for allosteric modulation in general. This review surveys progress in this field from function to structure and back again, outlining early evidence for relevant modulation of pentameric ligand-gated ion channels and the development of early structural models for ion channel function and modulation. We highlight insights and challenges provided by recent crystal structures and resulting simulations, as well as opportunities for translation of these newly detailed models back to behavior and therapy.

  10. Geometrical optimization for strictly localized structures

    Science.gov (United States)

    Mo, Yirong

    2003-07-01

    Recently we proposed the block localized wavefunction (BLW) approach which takes the advantages of valence bond theory and molecular orbital theory and defines the wavefunctions for resonance structures based on the assumption that all electrons and orbitals are partitioned into a few subgroups. In this work, we implement the geometrical optimization of the BLW method based on the algorithm proposed by Gianinetti and coworkers. Thus, we can study the conjugation effect on not only the molecular stability, but also the molecular geometry. With this capability, the π conjugation effect in trans-polyenes C2nH2n+2 (n=2-5) as well as in formamide and its analogs are studied by optimizing their delocalized and strictly localized forms with the 6-31G(d) and 6-311+G(d,p) basis sets. Although it has been well presumed that the π resonance shortens the single bonds and lengthens the double bonds with the delocalization of π electrons across the whole line in polyenes, our optimization of the strictly localized structures quantitatively shows that when the conjugation effect is "turned off," the double bond lengths will be identical to the CC bond length in ethylene and the single Csp2-Csp2 bond length will be about 1.513-1.517 Å. In agreement with the classical Hückel theory, the resonance energies in polyenes are approximately in proportion to the number of double bonds. Similarly, resonance is responsible not only for the planarity of formamide, thioformamide, and selenoformamide, but also for the lengthening of the CX (X=O,S,Se) double bond and the shortening of the CN bonds. Although it is assumed that the CX bond polarization decreases in the order of O>S>Se, the π electronic delocalization increases in the opposite order, i.e., formamide

  11. Target-specific NMR detection of protein–ligand interactions with antibody-relayed {sup 15}N-group selective STD

    Energy Technology Data Exchange (ETDEWEB)

    Hetényi, Anasztázia [University of Szeged, Department of Medical Chemistry (Hungary); Hegedűs, Zsófia [University of Szeged, SZTE-MTA Lendület Foldamer Research Group, Institute of Pharmaceutical Analysis Department (Hungary); Fajka-Boja, Roberta; Monostori, Éva [Biological Research Center of the Hungarian Academy of Sciences, Lymphocyte Signal Transduction Laboratory, Institute of Genetics (Hungary); Kövér, Katalin E. [University of Debrecen, Department of Inorganic and Analytical Chemistry (Hungary); Martinek, Tamás A., E-mail: martinek@pharm.u-szeged.hu [University of Szeged, SZTE-MTA Lendület Foldamer Research Group, Institute of Pharmaceutical Analysis Department (Hungary)

    2016-12-15

    Fragment-based drug design has been successfully applied to challenging targets where the detection of the weak protein–ligand interactions is a key element. {sup 1}H saturation transfer difference (STD) NMR spectroscopy is a powerful technique for this work but it requires pure homogeneous proteins as targets. Monoclonal antibody (mAb)-relayed {sup 15}N-GS STD spectroscopy has been developed to resolve the problem of protein mixtures and impure proteins. A {sup 15}N-labelled target-specific mAb is selectively irradiated and the saturation is relayed through the target to the ligand. Tests on the anti-Gal-1 mAb/Gal-1/lactose system showed that the approach is experimentally feasible in a reasonable time frame. This method allows detection and identification of binding molecules directly from a protein mixture in a multicomponent system.

  12. From Regular to Strictly Locally Testable Languages

    Directory of Open Access Journals (Sweden)

    Stefano Crespi Reghizzi

    2011-08-01

    Full Text Available A classical result (often credited to Y. Medvedev states that every language recognized by a finite automaton is the homomorphic image of a local language, over a much larger so-called local alphabet, namely the alphabet of the edges of the transition graph. Local languages are characterized by the value k=2 of the sliding window width in the McNaughton and Papert's infinite hierarchy of strictly locally testable languages (k-slt. We generalize Medvedev's result in a new direction, studying the relationship between the width and the alphabetic ratio telling how much larger the local alphabet is. We prove that every regular language is the image of a k-slt language on an alphabet of doubled size, where the width logarithmically depends on the automaton size, and we exhibit regular languages for which any smaller alphabetic ratio is insufficient. More generally, we express the trade-off between alphabetic ratio and width as a mathematical relation derived from a careful encoding of the states. At last we mention some directions for theoretical development and application.

  13. 7 CFR 28.404 - Strict Low Middling Color.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 2 2010-01-01 2010-01-01 false Strict Low Middling Color. 28.404 Section 28.404... for the Color Grade of American Upland Cotton § 28.404 Strict Low Middling Color. Strict Low Middling Color is color which is within the range represented by a set of samples in the custody of the United...

  14. 7 CFR 28.406 - Strict Good Ordinary Color.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 2 2010-01-01 2010-01-01 false Strict Good Ordinary Color. 28.406 Section 28.406... for the Color Grade of American Upland Cotton § 28.406 Strict Good Ordinary Color. Strict Good Ordinary Color is color which is within the range represented by a set of samples in the custody of the...

  15. 7 CFR 28.402 - Strict Middling Color.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 2 2010-01-01 2010-01-01 false Strict Middling Color. 28.402 Section 28.402... for the Color Grade of American Upland Cotton § 28.402 Strict Middling Color. Strict Middling Color is color which is within the range represented by a set of samples in the custody of the United States...

  16. Identification of cancer specific ligands from one-bead one compound combinatorial libraries to develop theranostics agents against oral squamous cell carcinoma

    Science.gov (United States)

    Yang, Frances Fan

    Background: Oral squamous cell carcinoma (OSCC) is one of the most prevalent disease worldwide. One-bead one-compound (OBOC) combinatorial technology is a powerful method to identify peptidomimetic ligands against a variety of receptors on cell surfaces. We therefore hypothesized that cancer specific ligands against OSCC might be identified and can be conjugated to optical dyes or nanocarriers to develop theranostic agents against OSCC. Material and methods: Different OSCC cell lines were incubated with OBOC libraries and beads with cell binding were sorted and then screened with normal human cells to identify peptide-beads binding to different OSCC cell lines but not binding to normal human cells. The molecular probes of OSCC were developed by biotinylating the carboxyl end of the ligands. OSCC theranostic agents were developed by decorating LLY13 with NPs and evaluated by using orthotopic bioluminescent oral cancer model. Results: Six OSCC specific ligands were discovered. Initial peptide-histochemistry study indicated that LLY12 and LLY13 were able to specifically detect OSCC cells grown on chamber slides at the concentration of 1 muM. In addition, LLY13 was found to penetrate into the OSCC cells and accumulate in the cytoplasm, and nucleus. After screened with a panel of integrin antibodies, only anti-alpha3 antibody was able to block most of OSCC cells binding to the LLY13 beads. OSCC theranostic agents developed using targeting LLY13 micelles (25+/- 4nm in diameter) were more efficient in binding to HSC-3 cancer cells compared to non-targeting micelles. Ex vivo images demonstrated that xenografts from the mice with targeting micelles appeared to have higher signals than the non-targeting groups. Conclusion: LLY13 has promising in vitro and in vivo targeting activity against OSCC. In addition, LLY13 is also able to penetrate into cancer cells via endocytosis. Initial study indicated that alpha3 integrin might partially be the corresponding receptor involved

  17. Mammalian evolution may not be strictly bifurcating.

    Science.gov (United States)

    Hallström, Björn M; Janke, Axel

    2010-12-01

    The massive amount of genomic sequence data that is now available for analyzing evolutionary relationships among 31 placental mammals reduces the stochastic error in phylogenetic analyses to virtually zero. One would expect that this would make it possible to finally resolve controversial branches in the placental mammalian tree. We analyzed a 2,863,797 nucleotide-long alignment (3,364 genes) from 31 placental mammals for reconstructing their evolution. Most placental mammalian relationships were resolved, and a consensus of their evolution is emerging. However, certain branches remain difficult or virtually impossible to resolve. These branches are characterized by short divergence times in the order of 1-4 million years. Computer simulations based on parameters from the real data show that as little as about 12,500 amino acid sites could be sufficient to confidently resolve short branches as old as about 90 million years ago (Ma). Thus, the amount of sequence data should no longer be a limiting factor in resolving the relationships among placental mammals. The timing of the early radiation of placental mammals coincides with a period of climate warming some 100-80 Ma and with continental fragmentation. These global processes may have triggered the rapid diversification of placental mammals. However, the rapid radiations of certain mammalian groups complicate phylogenetic analyses, possibly due to incomplete lineage sorting and introgression. These speciation-related processes led to a mosaic genome and conflicting phylogenetic signals. Split network methods are ideal for visualizing these problematic branches and can therefore depict data conflict and possibly the true evolutionary history better than strictly bifurcating trees. Given the timing of tectonics, of placental mammalian divergences, and the fossil record, a Laurasian rather than Gondwanan origin of placental mammals seems the most parsimonious explanation.

  18. The N2-Src neuronal splice variant of C-Src has altered SH3 domain ligand specificity and a higher constitutive activity than N1-Src

    OpenAIRE

    Keenan, Sarah; Lewis, Philip A.; Wetherill, Sarah J.; Dunning, Christopher J.R.; Evans, Gareth J.O.

    2015-01-01

    N2-Src is a poorly understood neuronal splice variant of the ubiquitous C-Src tyrosine kinase, containing a 17 amino acid insert in its Src homology 3 (SH3) domain. To characterise the properties of N2-Src we directly compared its SH3 domain specificity and kinase activity with C- and N1-Src in vitro. N2- and N1-Src had a similar low affinity for the phosphorylation of substrates containing canonical C-Src SH3 ligands and synaptophysin, an established neuronal substrate for C-Src. N2-Src also...

  19. The ligand specificities of the insulin receptor and the insulin-like growth factor I receptor reside in different regions of a common binding site

    Energy Technology Data Exchange (ETDEWEB)

    Kjeldsen, T.; Andersen, A.S.; Wiberg, F.C.; Rasmussen, J.S.; Schaeffer, L.; Balschmidt, P.; Moller, K.B.; Moller, N.P.H. (Novo Nordisk, Bagsvaerd (Denmark))

    1991-05-15

    To identify the region(s) of the insulin receptor and the insulin-like growth factor I (IGF-I) receptor responsible for ligand specificity (high-affinity binding), expression vectors encoding soluble chimeric insulin/IGF-I receptors were prepared. The chimeric receptors were expressed in mammalian cells and partially purified. Binding studies revealed that a construct comprising an IGF-I receptor in which the 68 N-terminal amino acids of the insulin receptor {alpha}-subunit had replaced the equivalent IGF-I receptor segment displayed a markedly increased affinity for insulin. In contrast, the corresponding IGF-I receptor sequence is not critical for high-affinity IGF-I binding. It is shown that part of the cysteine-rich domain determines IGF-I specificity. The authors have previously shown that exchanging exons 1, 2, and 3 of the insulin receptor with the corresponding IGF-I receptor sequence results in loss of high affinity for insulin and gain of high affinity for IGF-I. Consequently, it is suggested that the ligand specificities of the two receptors (i.e., the sequences that discriminate between insulin and IGF-I) reside in different regions of a binding site with common features present in both receptors.

  20. "Strict" Anadeixis, Discourse Deixis and Text Structuring

    Science.gov (United States)

    Cornish, Francis

    2011-01-01

    Taking English as the example language, the article begins by presenting a Scale of indexicality characterizing context-bound expression types, ranging from those signalling pure deixis at one pole, to ones expressing pure anaphora at the other. On the basis of this Scale, the article attempts to determine the specific way in which demonstratives…

  1. Unique structure and dynamics of the EphA5 ligand binding domain mediate its binding specificity as revealed by X-ray crystallography, NMR and MD simulations.

    Directory of Open Access Journals (Sweden)

    Xuelu Huan

    Full Text Available The 16 EphA and EphB receptors represent the largest family of receptor tyrosine kinases, and their interactions with 9 ephrin-A and ephrin-B ligands initiate bidirectional signals controlling many physiological and pathological processes. Most interactions occur between receptor and ephrins of the same class, and only EphA4 can bind all A and B ephrins. To understand the structural and dynamic principles that enable Eph receptors to utilize the same jellyroll β-sandwich fold to bind ephrins, the VAPB-MSP domain, peptides and small molecules, we have used crystallography, NMR and molecular dynamics (MD simulations to determine the first structure and dynamics of the EphA5 ligand-binding domain (LBD, which only binds ephrin-A ligands. Unexpectedly, despite being unbound, the high affinity ephrin-binding pocket of EphA5 resembles that of other Eph receptors bound to ephrins, with a helical conformation over the J-K loop and an open pocket. The openness of the pocket is further supported by NMR hydrogen/deuterium exchange data and MD simulations. Additionally, the EphA5 LBD undergoes significant picosecond-nanosecond conformational exchanges over the loops, as revealed by NMR and MD simulations, but lacks global conformational exchanges on the microsecond-millisecond time scale. This is markedly different from the EphA4 LBD, which shares 74% sequence identity and 87% homology. Consequently, the unbound EphA5 LBD appears to comprise an ensemble of open conformations that have only small variations over the loops and appear ready to bind ephrin-A ligands. These findings show how two proteins with high sequence homology and structural similarity are still able to achieve distinctive binding specificities through different dynamics, which may represent a general mechanism whereby the same protein fold can serve for different functions. Our findings also suggest that a promising strategy to design agonists/antagonists with high affinity and selectivity

  2. Evidence for ligand and/or receptor-specific mechanisms of internalization and processing in cultured H35 hepatoma cells

    Energy Technology Data Exchange (ETDEWEB)

    Goldberg, R.I.; Smith, R.M.; Jarett, L.

    1987-05-01

    Total cell associated (TC) and intracellularly accumulated (IC) SVI-labeled insulin (INS) or -2-macroglobulin ( 2M) were assessed in cultured H35 hepatoma cells which were preincubated with various agents. Cytochalasin D or sodium azide, which affect microfilament- or energy-dependent receptor internalization, had no significant effects on INS TC or IC but each decreased 2M TC and IC to 50-75% of control. Monensin and chloroquine, acidotrophic agents, each increased INS TC and IC to 150-300% of control yet decreased TC and IC of 2M to 20-50% of control. Only leupeptin, a lysosomal protease inhibitor, caused an increase in both INS and 2M TC and IC. These data suggest significant differences exist in the biochemical regulation or structural routes of INS and 2M receptors and/or receptor-ligand complexes in their (1) internalization, (2) processing in acidic organelles, (3) recycling to the cell surface or in combinations of the above. Biochemical and ultrastructural studies are being performed on the H35 hepatoma cell which will characterize the processing of INS and 2M receptors and provide an explanation for the differences observed.

  3. Evidence for ligand and/or receptor-specific mechanisms of internalization and processing in cultured H35 hepatoma cells

    International Nuclear Information System (INIS)

    Goldberg, R.I.; Smith, R.M.; Jarett, L.

    1987-01-01

    Total cell associated (TC) and intracellularly accumulated (IC) 125 I-labeled insulin (INS) or α-2-macroglobulin (α2M) were assessed in cultured H35 hepatoma cells which were preincubated with various agents. Cytochalasin D or sodium azide, which affect microfilament- or energy-dependent receptor internalization, had no significant effects on INS TC or IC but each decreased α2M TC and IC to 50-75% of control. Monensin and chloroquine, acidotrophic agents, each increased INS TC and IC to 150-300% of control yet decreased TC and IC of α2M to 20-50% of control. Only leupeptin, a lysosomal protease inhibitor, caused an increase in both INS and α2M TC and IC. These data suggest significant differences exist in the biochemical regulation or structural routes of INS and α2M receptors and/or receptor-ligand complexes in their (1) internalization, (2) processing in acidic organelles, (3) recycling to the cell surface or in combinations of the above. Biochemical and ultrastructural studies are being performed on the H35 hepatoma cell which will characterize the processing of INS and α2M receptors and provide an explanation for the differences observed

  4. Deciphering ligand specificity of a Clostridium thermocellum family 35 carbohydrate binding module (CtCBM35 for gluco- and galacto- substituted mannans and its calcium induced stability.

    Directory of Open Access Journals (Sweden)

    Arabinda Ghosh

    Full Text Available This study investigated the role of CBM35 from Clostridium thermocellum (CtCBM35 in polysaccharide recognition. CtCBM35 was cloned into pET28a (+ vector with an engineered His6 tag and expressed in Escherichia coli BL21 (DE3 cells. A homogenous 15 kDa protein was purified by immobilized metal ion chromatography (IMAC. Ligand binding analysis of CtCBM35 was carried out by affinity electrophoresis using various soluble ligands. CtCBM35 showed a manno-configured ligand specific binding displaying significant association with konjac glucomannan (Ka = 14.3×10(4 M(-1, carob galactomannan (Ka = 12.4×10(4 M(-1 and negligible association (Ka = 12 µM(-1 with insoluble mannan. Binding of CtCBM35 with polysaccharides which was calcium dependent exhibited two fold higher association in presence of 10 mM Ca(2+ ion with konjac glucomannan (Ka = 41×10(4 M(-1 and carob galactomannan (Ka = 30×10(4 M(-1. The polysaccharide binding was further investigated by fluorescence spectrophotometric studies. On binding with carob galactomannan and konjac glucomannan the conformation of CtCBM35 changed significantly with regular 21 nm peak shifts towards lower quantum yield. The degree of association (K a with konjac glucomannan and carob galactomannan, 14.3×10(4 M(-1 and 11.4×10(4 M(-1, respectively, corroborated the findings from affinity electrophoresis. The association of CtCBM35with konjac glucomannan led to higher free energy of binding (ΔG -25 kJ mole(-1 as compared to carob galactomannan (ΔG -22 kJ mole(-1. On binding CtCBM35 with konjac glucomannan and carob galactomannan the hydrodynamic radius (RH as analysed by dynamic light scattering (DLS study, increased to 8 nm and 6 nm, respectively, from 4.25 nm in absence of ligand. The presence of 10 mM Ca(2+ ions imparted stiffer orientation of CtCBM35 particles with increased RH of 4.52 nm. Due to such stiffer orientation CtCBM35 became more thermostable and its melting temperature was

  5. Chirality of TLR-2 ligand Pam3CysSK4 in fully synthetic peptide conjugates critically influences the induction of specific CD8+ T-cells.

    Science.gov (United States)

    Khan, Selina; Weterings, Jimmy J; Britten, Cedrik M; de Jong, Ana R; Graafland, Dirk; Melief, Cornelis J M; van der Burg, Sjoerd H; van der Marel, Gijs; Overkleeft, Hermen S; Filippov, Dmitri V; Ossendorp, Ferry

    2009-03-01

    Covalent conjugation of synthetic Toll-like receptor ligands (TLR-L) to synthetic antigenic peptides provides well-defined constructs that have significantly improved capacity to induce efficient priming of CD8(+) T lymphocytes in vivo. We have recently explored the cellular mechanisms underlying the efficient induction of a CD8(+) cytotoxic T lymphocyte response by such synthetic model vaccines [Khan, S., Bijker, M.S., Weterings, J.J., Tanke, H.J., Adema, G.J., van, H.T., Drijfhout, J.W., Melief, C.J., Overkleeft, H.S., van der Marel, G.A., Filippov, D.V., van der Burg, S.H., Ossendorp, F., 2007. Distinct uptake mechanisms but similar intracellular processing of two different toll-like receptor ligand-peptide conjugates in dendritic cells. J. Biol. Chem. 282, 21145-21159.]. In the current study we have investigated the behaviour of two diastereomers of the TLR-2 ligand Pam(3)CSK(4) (Pam) derivatives, namely the R- and S-epimers at C-2 of the glycerol moiety. Other studies have shown that the Pam(3)Cys based lipopeptides of R-configuration (Pam(R)) in the glycerol moiety enhanced macrophage and B-cell activation compared to those with S-configuration (Pam(S)). Here we report that Pam(R)-conjugates lead to better activation of dendritic cells than the Pam(S)-conjugates as judged by higher IL-12 secretion, upregulation of relevant markers for dendritic cell maturation. In contrast both epimers were internalized equally efficient in a clathrin-dependent manner indicating no qualitative difference in the uptake of the two stereoisomeric Pam-conjugates. We conclude that the enhanced DC activation is due to enhanced TLR-2 triggering by the Pam(R)-conjugate in contrast to the Pam(S)-conjugate. Importantly, induction of specific CD8(+) T-cells was significantly higher in mice injected with the Pam(R)-conjugates compared to mice injected with the Pam(S)-conjugate. In summary we show that the favourable effects of the Pam(R)-configuration of TLR-2 ligand can be attributed to

  6. Modal Inclusion Logic: Being Lax is Simpler than Being Strict

    DEFF Research Database (Denmark)

    Hella, Lauri; Kuusisto, Antti Johannes; Meier, Arne

    2015-01-01

    We investigate the computational complexity of the satisfiability problem of modal inclusion logic. We distinguish two variants of the problem: one for strict and another one for lax semantics. The complexity of the lax version turns out to be complete for EXPTIME, whereas with strict semantics...

  7. 7 CFR 28.431 - Strict Middling Tinged Color.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 2 2010-01-01 2010-01-01 false Strict Middling Tinged Color. 28.431 Section 28.431 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards... Color. Strict Middling Tinged Color is color which is better than Middling Tinged Color. ...

  8. 7 CFR 28.433 - Strict Low Middling Tinged Color.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 2 2010-01-01 2010-01-01 false Strict Low Middling Tinged Color. 28.433 Section 28.433 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards... Tinged Color. Strict Low Middling Tinged Color is color which is within the range represented by a set of...

  9. 7 CFR 28.424 - Strict Low Middling Spotted Color.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 2 2010-01-01 2010-01-01 false Strict Low Middling Spotted Color. 28.424 Section 28.424 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards... Spotted Color. Strict Low Middling Spotted Color is color which is within the range represented by a set...

  10. 7 CFR 28.426 - Strict Good Ordinary Spotted Color.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 2 2010-01-01 2010-01-01 false Strict Good Ordinary Spotted Color. 28.426 Section 28.426 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards... Spotted Color. Strict Good Ordinary Spotted Color is color which is within the range represented by a set...

  11. 7 CFR 28.422 - Strict Middling Spotted Color.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 2 2010-01-01 2010-01-01 false Strict Middling Spotted Color. 28.422 Section 28.422 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards... Color. Strict Middling Spotted Color is color which is within the range represented by a set of samples...

  12. Strictly-regular number system and data structures

    DEFF Research Database (Denmark)

    Elmasry, Amr Ahmed Abd Elmoneim; Jensen, Claus; Katajainen, Jyrki

    2010-01-01

    We introduce a new number system that we call the strictly-regular system, which efficiently supports the operations: digit-increment, digit-decrement, cut, concatenate, and add. Compared to other number systems, the strictly-regular system has distinguishable properties. It is superior to the re...

  13. Decitabine immunosensitizes human gliomas to NY-ESO-1 specific T lymphocyte targeting through the Fas/Fas Ligand pathway

    Directory of Open Access Journals (Sweden)

    Konkankit Veerauo V

    2011-11-01

    Full Text Available Abstract Background The lack of effective treatments for gliomas makes them a significant health problem and highlights the need for the development of novel and innovative treatment approaches. Immunotherapy is an appealing strategy because of the potential ability for immune cells to traffic to and destroy infiltrating tumor cells. However, the absence of well-characterized, highly immunogenic tumor-rejection antigens (TRA in gliomas has limited the implementation of targeted immune-based therapies. Methods We hypothesized that treatment with the demethylating agent, decitabine, would upregulate the expression of TRA on tumor cells, thereby facilitating enhanced surveillance by TRA-specific T cells. Results and Discussion Treatment of human glioma cells with decitabine increased the expression of NY-ESO-1 and other well characterized cancer testes antigens. The upregulation of NY-ESO-1 made these tumors susceptible to NY-ESO-1-specific T-cell recognition and lysis. Interestingly, decitabine treatment of T98 glioma cells also sensitized them to Fas-dependent apoptosis with an agonistic antibody, while a Fas blocking antibody could largely prevent the enhanced functional recognition by NY-ESO-1 specific T cells. Thus, decitabine treatment transformed a non-immunogenic glioma cell into an immunogenic target that was efficiently recognized by NY-ESO-1--specific T cells. Conclusions Such data supports the hypothesis that agents which alter epigenetic cellular processes may "immunosensitize" tumor cells to tumor-specific T cell-mediated lysis.

  14. Decitabine immunosensitizes human gliomas to NY-ESO-1 specific T lymphocyte targeting through the Fas/Fas Ligand pathway

    Science.gov (United States)

    2011-01-01

    Background The lack of effective treatments for gliomas makes them a significant health problem and highlights the need for the development of novel and innovative treatment approaches. Immunotherapy is an appealing strategy because of the potential ability for immune cells to traffic to and destroy infiltrating tumor cells. However, the absence of well-characterized, highly immunogenic tumor-rejection antigens (TRA) in gliomas has limited the implementation of targeted immune-based therapies. Methods We hypothesized that treatment with the demethylating agent, decitabine, would upregulate the expression of TRA on tumor cells, thereby facilitating enhanced surveillance by TRA-specific T cells. Results and Discussion Treatment of human glioma cells with decitabine increased the expression of NY-ESO-1 and other well characterized cancer testes antigens. The upregulation of NY-ESO-1 made these tumors susceptible to NY-ESO-1-specific T-cell recognition and lysis. Interestingly, decitabine treatment of T98 glioma cells also sensitized them to Fas-dependent apoptosis with an agonistic antibody, while a Fas blocking antibody could largely prevent the enhanced functional recognition by NY-ESO-1 specific T cells. Thus, decitabine treatment transformed a non-immunogenic glioma cell into an immunogenic target that was efficiently recognized by NY-ESO-1--specific T cells. Conclusions Such data supports the hypothesis that agents which alter epigenetic cellular processes may "immunosensitize" tumor cells to tumor-specific T cell-mediated lysis. PMID:22060015

  15. Understanding the specificity of human Galectin-8C domain interactions with its glycan ligands based on molecular dynamics simulations.

    Science.gov (United States)

    Kumar, Sonu; Frank, Martin; Schwartz-Albiez, Reinhard

    2013-01-01

    Human Galectin-8 (Gal-8) is a member of the galectin family which shares an affinity for β-galactosides. The tandem-repeat Gal-8 consists of a N- and a C-terminal carbohydrate recognition domain (N- and C-CRD) joined by a linker peptide of various length. Despite their structural similarity both CRDs recognize different oligosaccharides. While the molecular requirements of the N-CRD for high binding affinity to sulfated and sialylated glycans have recently been elucidated by crystallographic studies of complexes with several oligosaccharides, the binding specificities of the C-CRD for a different set of oligosaccharides, as derived from experimental data, has only been explained in terms of the three-dimensional structure for the complex C-CRD with lactose. In this study we performed molecular dynamics (MD) simulations using the recently released crystal structure of the Gal-8C-CRD to analyse the three-dimensional conditions for its specific binding to a variety of oligosaccharides as previously defined by glycan-microarray analysis. The terminal β-galactose of disaccharides (LacNAc, lacto-N-biose and lactose) and the internal β-galactose moiety of blood group antigens A and B (BGA, BGB) as well as of longer linear oligosaccharide chains (di-LacNAc and lacto-N-neotetraose) are interacting favorably with conserved amino acids (H53, R57, N66, W73, E76). Lacto-N-neotetraose and di-LacNAc as well as BGA and BGB are well accommodated. BGA and BGB showed higher affinity than LacNAc and lactose due to generally stronger hydrogen bond interactions and water mediated hydrogen bonds with α1-2 fucose respectively. Our results derived from molecular dynamics simulations are able to explain the glycan binding specificities of the Gal-8C-CRD in comparison to those of the Gal-8N -CRD.

  16. Understanding the specificity of human Galectin-8C domain interactions with its glycan ligands based on molecular dynamics simulations.

    Directory of Open Access Journals (Sweden)

    Sonu Kumar

    Full Text Available Human Galectin-8 (Gal-8 is a member of the galectin family which shares an affinity for β-galactosides. The tandem-repeat Gal-8 consists of a N- and a C-terminal carbohydrate recognition domain (N- and C-CRD joined by a linker peptide of various length. Despite their structural similarity both CRDs recognize different oligosaccharides. While the molecular requirements of the N-CRD for high binding affinity to sulfated and sialylated glycans have recently been elucidated by crystallographic studies of complexes with several oligosaccharides, the binding specificities of the C-CRD for a different set of oligosaccharides, as derived from experimental data, has only been explained in terms of the three-dimensional structure for the complex C-CRD with lactose. In this study we performed molecular dynamics (MD simulations using the recently released crystal structure of the Gal-8C-CRD to analyse the three-dimensional conditions for its specific binding to a variety of oligosaccharides as previously defined by glycan-microarray analysis. The terminal β-galactose of disaccharides (LacNAc, lacto-N-biose and lactose and the internal β-galactose moiety of blood group antigens A and B (BGA, BGB as well as of longer linear oligosaccharide chains (di-LacNAc and lacto-N-neotetraose are interacting favorably with conserved amino acids (H53, R57, N66, W73, E76. Lacto-N-neotetraose and di-LacNAc as well as BGA and BGB are well accommodated. BGA and BGB showed higher affinity than LacNAc and lactose due to generally stronger hydrogen bond interactions and water mediated hydrogen bonds with α1-2 fucose respectively. Our results derived from molecular dynamics simulations are able to explain the glycan binding specificities of the Gal-8C-CRD in comparison to those of the Gal-8N -CRD.

  17. Strict finitism and the logic of mathematical applications

    CERN Document Server

    Ye, Feng

    2011-01-01

    Exploring the logic behind applied mathematics to the physical world, this volume illustrates how radical naturalism, nominalism and strict finitism can account for the applications of classical mathematics in current theories about natural phenomena.

  18. Strict monotonicity and unique continuation of the biharmonic operator

    Directory of Open Access Journals (Sweden)

    Najib Tsouli

    2012-01-01

    Full Text Available In this paper, we will show that the strict monotonicity of the eigenvalues of the biharmonic operator holds if and only if some unique continuation property is satisfied by the corresponding eigenfunctions.

  19. Two examples of non strictly convex large deviations

    OpenAIRE

    De Marco, Stefano; Jacquier, Antoine; Roome, Patrick

    2016-01-01

    We present two examples of a large deviations principle where the rate function is not strictly convex. This is motivated by a model used in mathematical finance (the Heston model), and adds a new item to the zoology of non strictly convex large deviations. For one of these examples, we show that the rate function of the Cramer-type of large deviations coincides with that of the Freidlin-Wentzell when contraction principles are applied.

  20. Strictly contractive quantum channels and physically realizable quantum computers

    International Nuclear Information System (INIS)

    Raginsky, Maxim

    2002-01-01

    We study the robustness of quantum computers under the influence of errors modeled by strictly contractive channels. A channel T is defined to be strictly contractive if, for any pair of density operators ρ, σ in its domain, parallel Tρ-Tσ parallel 1 ≤k parallel ρ-σ parallel 1 for some 0≤k 1 denotes the trace norm). In other words, strictly contractive channels render the states of the computer less distinguishable in the sense of quantum detection theory. Starting from the premise that all experimental procedures can be carried out with finite precision, we argue that there exists a physically meaningful connection between strictly contractive channels and errors in physically realizable quantum computers. We show that, in the absence of error correction, sensitivity of quantum memories and computers to strictly contractive errors grows exponentially with storage time and computation time, respectively, and depends only on the constant k and the measurement precision. We prove that strict contractivity rules out the possibility of perfect error correction, and give an argument that approximate error correction, which covers previous work on fault-tolerant quantum computation as a special case, is possible

  1. Strict or graduated punishment? Effect of punishment strictness on the evolution of cooperation in continuous public goods games.

    Directory of Open Access Journals (Sweden)

    Hajime Shimao

    Full Text Available Whether costly punishment encourages cooperation is one of the principal questions in studies on the evolution of cooperation and social sciences. In society, punishment helps deter people from flouting rules in institutions. Specifically, graduated punishment is a design principle for long-enduring common-pool resource institutions. In this study, we investigate whether graduated punishment can promote a higher cooperation level when each individual plays the public goods game and has the opportunity to punish others whose cooperation levels fall below the punisher's threshold. We then examine how spatial structure affects evolutionary dynamics when each individual dies inversely proportional to the game score resulting from the social interaction and another player is randomly chosen from the population to produce offspring to fill the empty site created after a player's death. Our evolutionary simulation outcomes demonstrate that stricter punishment promotes increased cooperation more than graduated punishment in a spatially structured population, whereas graduated punishment increases cooperation more than strict punishment when players interact with randomly chosen opponents from the population. The mathematical analysis also supports the results.

  2. Strict or Graduated Punishment? Effect of Punishment Strictness on the Evolution of Cooperation in Continuous Public Goods Games

    Science.gov (United States)

    Shimao, Hajime; Nakamaru, Mayuko

    2013-01-01

    Whether costly punishment encourages cooperation is one of the principal questions in studies on the evolution of cooperation and social sciences. In society, punishment helps deter people from flouting rules in institutions. Specifically, graduated punishment is a design principle for long-enduring common-pool resource institutions. In this study, we investigate whether graduated punishment can promote a higher cooperation level when each individual plays the public goods game and has the opportunity to punish others whose cooperation levels fall below the punisher’s threshold. We then examine how spatial structure affects evolutionary dynamics when each individual dies inversely proportional to the game score resulting from the social interaction and another player is randomly chosen from the population to produce offspring to fill the empty site created after a player’s death. Our evolutionary simulation outcomes demonstrate that stricter punishment promotes increased cooperation more than graduated punishment in a spatially structured population, whereas graduated punishment increases cooperation more than strict punishment when players interact with randomly chosen opponents from the population. The mathematical analysis also supports the results. PMID:23555826

  3. Development of a Tc-99m labeled sigma-2 receptor-specific ligand as a potential breast tumor imaging agent

    International Nuclear Information System (INIS)

    Choi, Seok-Rye; Yang, Biao; Ploessl, Karl; Chumpradit, Sumalee; Wey, Shiaw-Pyng; Acton, Paul D.; Wheeler, Kenneth; Mach, Robert H.; Kung, Hank F.

    2001-01-01

    A novel in vivo imaging agent, 99m Tc labeled [(N-[2-((3'-N'-propyl-[3,3,1]aza-bicyclononan-3α-yl)(2''-methoxy-5- methyl-phenylcarbamate) (2-mercaptoethyl)amino)acetyl]-2-aminoethanethiolato] technetium(V) oxide), [ 99m Tc]2, displaying specific binding towards sigma-2 receptors was prepared and characterized. In vitro binding assays showed that the rhenium surrogate of [ 99m Tc]2, Re-2, displayed excellent binding affinity and selectivity towards sigma-2 receptors (K i = 2,723 and 22 nM for sigma-1 and sigma-2 receptor, respectively). Preparation of [ 99m Tc]2 was achieved by heating the S-protected starting material, 1, in the presence of acid, reducing agent (stannous glucoheptonate) and sodium [ 99m Tc]pertechnetate. The lipophilic racemic mixture was successfully prepared in 10 to 50% yield and the radiochemical purity was >98%. Separation of the isomers, peak A and peak B, was successfully achieved by using a chiralpak AD column eluted with an isocratic solvent (n-hexane/isopropanol; 3:1; v/v). The peak A and peak B appear to co-elute with the isomers of the surrogate, Re-2, under the same HPLC condition. Biodistribution studies in tumor bearing mice (mouse mammary adenocarcinoma, cell line 66, which is known to over-express sigma-2 receptors) showed that the racemic [ 99m Tc]2 localized in the tumor. Uptake in the tumor was 2.11, 1.30 and 1.11 %dose/gram at 1, 4 and 8 hr post iv injection, respectively, suggesting good uptake and retention in the tumor cells. The tumor uptake was significantly, but incompletely, blocked (about 25-30% blockage) by co-injection of 'cold' (+)pentazocine or haloperidol (1 mg/Kg). A majority of the radioactivity localized in the tumor tissue was extractable (>60%), and the HPLC analysis showed that it is the original compound, racemic [ 99m Tc]2 (>98% pure). The distribution of the purified peak A and peak B was determined in the same tumor bearing mice at 4 hr post iv injection. The tumor uptake was similar for both isomers

  4. 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.

  5. Convergence theorems for strictly hemi-contractive maps

    International Nuclear Information System (INIS)

    Chidume, C.E.; Osilike, M.O.

    1992-04-01

    It is proved that each of two well-known fixed point iteration methods (the Mann and the Ishikawa iteration methods) converges strongly to the fixed point of strictly hemi-contractive map in real Banach spaces with property (U, λ, m+1,m), λ is an element of R, m is an element of IN. The class of strictly hemi-contractive maps includes all strictly pseudo-contractive maps with nonempty fixed point sets; and Banach spaces with property (U, λ, m+1, m), λ is an element of R, m is an element of IN include the L p (or l p ) spaces, p≥2. Our theorems generalize important known results. (author). 22 refs

  6. Mann iteration with errors for strictly pseudo-contractive mappings ...

    African Journals Online (AJOL)

    It is well known that any fixed point of a Lipschitzian strictly pseudo-contractive self mapping of a nonempty closed convex and bounded subset K of a Banach space X is unique [6] and may be norm approximated by an iterative procedure. In this paper, we show that Mann iteration with errors can be used to approximate the ...

  7. Dominated operators, absolutely summing operators and the strict ...

    African Journals Online (AJOL)

    b(X;E) be the space of all E-valued bounded continuous functions on X, equipped with the strict topology β. We study dominated and absolutely summing operators T : Cb(X;E) → F. We derive that if X is a locally compact Hausdorff space and E ...

  8. Convergence of GAOR Iterative Method with Strictly Diagonally Dominant Matrices

    Directory of Open Access Journals (Sweden)

    Guangbin Wang

    2011-01-01

    Full Text Available We discuss the convergence of GAOR method for linear systems with strictly diagonally dominant matrices. Moreover, we show that our results are better than ones of Darvishi and Hessari (2006, Tian et al. (2008 by using three numerical examples.

  9. Runaway selection for cooperation and strict-and-severe punishment.

    Science.gov (United States)

    Nakamaru, Mayuko; Dieckmann, Ulf

    2009-03-07

    Punishing defectors is an important means of stabilizing cooperation. When levels of cooperation and punishment are continuous, individuals must employ suitable social standards for defining defectors and for determining punishment levels. Here we investigate the evolution of a social reaction norm, or psychological response function, for determining the punishment level meted out by individuals in dependence on the cooperation level exhibited by their neighbors in a lattice-structured population. We find that (1) cooperation and punishment can undergo runaway selection, with evolution towards enhanced cooperation and an ever more demanding punishment reaction norm mutually reinforcing each other; (2) this mechanism works best when punishment is strict, so that ambiguities in defining defectors are small; (3) when the strictness of punishment can adapt jointly with the threshold and severity of punishment, evolution favors the strict-and-severe punishment of individuals who offer slightly less than average cooperation levels; (4) strict-and-severe punishment naturally evolves and leads to much enhanced cooperation when cooperation without punishment would be weak and neither cooperation nor punishment are too costly; and (5) such evolutionary dynamics enable the bootstrapping of cooperation and punishment, through which defectors who never punish gradually and steadily evolve into cooperators who punish those they define as defectors.

  10. Dominance on Strict Triangular Norms and Mulholland Inequality

    Czech Academy of Sciences Publication Activity Database

    Petrík, Milan

    2018-01-01

    Roč. 335, 15 March (2018), s. 3-17 ISSN 0165-0114 R&D Projects: GA ČR GJ15-07724Y Institutional support: RVO:67985807 Keywords : dominance relation * Mulholland inequality * strict triangular norm * transitivity Subject RIV: BA - General Mathematics Impact factor: 2.718, year: 2016

  11. Specific sequestering agents for the actinides. 2. A ligand field effect in the crystal and molecular structures of tetrakis(catecholato)uranate(IV) and -thorate(IV)

    International Nuclear Information System (INIS)

    Sofen, S.R.; Abu-Dari, K.; Freyberg, D.P.; Raymond, K.N.

    1978-01-01

    The structures of the title compounds, Na 4 [M(C 6 H 4 O 2 ) 4 ] 21H 2 O,M = Th, U, have been determined by single-crystal x-ray diffraction methods using counter data. These isostructural tetrakis(catecholato) complexes are structural archetypes for actinide-specific macrocyclic sequestering agents. The complexes have D/sub 2d/ molecular symmetry. The M--O bond lengths are 2.417(3) and 2.421(3) A for Th and 2.362(3) and 2.389(4) A for U. The ring O--M--O bond angles are 66.8(1) 0 for Th and 67.7(1) 0 for U. The difference in M--O bond lengths for the uranium complex [0.027(5) A] vs. a difference of 0.004(4) A in the thorium complex is attributed to a ligand field effect of the 5f 2 electronic configuration of U(IV) vs. 5f 0 for Th(IV). Green crystals of the uranium complex, obtained from basic aqueous solution, conform to the space group I anti 4 with a = 14.659(3) and c = 9.984(4) A. For 3660 independent data with F 0 2 > 3 sigma(F 0 2 ) full-matrix least-squares refinement with anisotropic thermal parameters for all nonhydrogen atoms converged to unweighted and weighted R factors of 3.8 and 4.5%, respectively. The colorless thorium compound, also obtained from basic aqueous solution, has a = 14.709(4) and c = 9.978(3) A. For 5038 independent data refinement as above converged to unweighted and weighted R factors of 4.3 and 5.3%, respectively. 3 figures, 8 tables

  12. The TCR ligand-inducible expression of CD73 marks γδ lineage commitment and a metastable intermediate in effector specification

    DEFF Research Database (Denmark)

    Coffey, Francis; Lee, Sang-Yun; Buus, Terkild B

    2014-01-01

    cells, suggesting this is a common occurrence during development. Moreover, CD73 induction appears to mark a metastable intermediate stage before acquisition of effector function, suggesting that γδ lineage and effector fate are specified sequentially. These findings have important implications......Numerous studies indicate that γδ T cell receptor (γδTCR) expression alone does not reliably mark commitment of early thymic progenitors to the γδ fate. This raises the possibility that the γδTCR is unable to intrinsically specify fate and instead requires additional environmental factors......, including TCR-ligand engagement. We use single cell progenitor assays to reveal that ligand acts instructionally to direct adoption of the γδ fate. Moreover, we identify CD73 as a TCR ligand-induced cell surface protein that distinguishes γδTCR-expressing CD4(-)CD8(-) progenitors that have committed...

  13. Molecular recognition of carboxylates in the protein leucine zipper by a multivalent supramolecular ligand: residue-specific, sensitive and label-free probing by UV resonance Raman spectroscopy.

    Science.gov (United States)

    Zakeri, B; Niebling, S; Martinéz, A G; Sokkar, P; Sanchez-Garcia, E; Schmuck, C; Schlücker, S

    2018-01-17

    Ultraviolet resonance Raman (UVRR) spectroscopy is a selective, sensitive and label-free vibrational spectroscopic technique. Here, we demonstrate as proof of concept that UVRR can be used for probing the recognition between a multivalent supramolecular ligand and acidic residues in leucine zipper, an α-helical structural motif of many proteins.

  14. Relaxation Methods for Strictly Convex Regularizations of Piecewise Linear Programs

    International Nuclear Information System (INIS)

    Kiwiel, K. C.

    1998-01-01

    We give an algorithm for minimizing the sum of a strictly convex function and a convex piecewise linear function. It extends several dual coordinate ascent methods for large-scale linearly constrained problems that occur in entropy maximization, quadratic programming, and network flows. In particular, it may solve exact penalty versions of such (possibly inconsistent) problems, and subproblems of bundle methods for nondifferentiable optimization. It is simple, can exploit sparsity, and in certain cases is highly parallelizable. Its global convergence is established in the recent framework of B -functions (generalized Bregman functions)

  15. Clonal analysis of kit ligand a functional expression reveals lineage-specific competence to promote melanocyte rescue in the mutant regenerating caudal fin.

    Directory of Open Access Journals (Sweden)

    Robert C Tryon

    Full Text Available The study of regeneration in an in vivo vertebrate system has the potential to reveal targetable genes and pathways that could improve our ability to heal and repair damaged tissue. We have developed a system for clonal labeling of discrete cell lineages and independently inducing gene expression under control of the heat shock promoter in the zebrafish caudal fin. Consequently we are able to test the affects of overexpressing a single gene in the context of regeneration within each of the nine different cell lineage classes that comprise the caudal fin. This can test which lineage is necessary or sufficient to provide gene function. As a first example to demonstrate this approach, we explored which lineages were competent to functionally express the kit ligand a protein as assessed by the local complementation of the mutation in the sparse-like (kitlgatc244b background. We show that dermal fibroblast expression of kit ligand a robustly supports the rescue of melanocytes in the regenerating caudal fin. kit ligand a expression from skin and osteoblasts results in more modest and variable rescue of melanocytes, while lateral line expression was unable to complement the mutation.

  16. Non-strictly black body spectrum from the tunnelling mechanism

    International Nuclear Information System (INIS)

    Corda, Christian

    2013-01-01

    The tunnelling mechanism is widely used to explain Hawking radiation. However, in many cases the analysis used to obtain the Hawking temperature only involves comparing the emission probability for an outgoing particle with the Boltzmann factor. Banerjee and Majhi improved this approach by explicitly finding a black body spectrum associated with black holes. Their result, obtained using a reformulation of the tunnelling mechanism, is in contrast to that of Parikh and Wilczek, who found an emission probability that is compatible with a non-strictly thermal spectrum. Using the recently identified effective state for a black hole, we solve this contradiction via a slight modification of the analysis by Banerjee and Majhi. The final result is a non-strictly black body spectrum from the tunnelling mechanism. We also show that for an effective temperature, we can express the corresponding effective metric using Hawking’s periodicity arguments. Potential important implications for the black hole information puzzle are discussed. -- Highlights: •We review an important result by Banerjee and Majhi on the tunnelling mechanism in the framework of Hawking radiation. •This result is in contrast to another result reported by Parikh and Wilczek. •We introduce the effective state of a black hole. •We explain the contrast via a slight modification of the analysis by Banerjee and Majhi. •We discuss potential important implications for the black hole information puzzle

  17. A multi-protein receptor-ligand complex underlies combinatorial dendrite guidance choices in C. elegans

    Science.gov (United States)

    Zou, Wei; Shen, Ao; Dong, Xintong; Tugizova, Madina; Xiang, Yang K; Shen, Kang

    2016-01-01

    Ligand receptor interactions instruct axon guidance during development. How dendrites are guided to specific targets is less understood. The C. elegans PVD sensory neuron innervates muscle-skin interface with its elaborate dendritic branches. Here, we found that LECT-2, the ortholog of leukocyte cell-derived chemotaxin-2 (LECT2), is secreted from the muscles and required for muscle innervation by PVD. Mosaic analyses showed that LECT-2 acted locally to guide the growth of terminal branches. Ectopic expression of LECT-2 from seam cells is sufficient to redirect the PVD dendrites onto seam cells. LECT-2 functions in a multi-protein receptor-ligand complex that also contains two transmembrane ligands on the skin, SAX-7/L1CAM and MNR-1, and the neuronal transmembrane receptor DMA-1. LECT-2 greatly enhances the binding between SAX-7, MNR-1 and DMA-1. The activation of DMA-1 strictly requires all three ligands, which establishes a combinatorial code to precisely target and pattern dendritic arbors. DOI: http://dx.doi.org/10.7554/eLife.18345.001 PMID:27705746

  18. Effects of a strict cutoff on Quantum Field Theory

    International Nuclear Information System (INIS)

    Sturnfield, J.F.

    1987-01-01

    Standard Quantum Field Theory has a number of integrals which are infinite. Although these are eliminated for some cases by renormalization, this aspect of the theory is not fully satisfactory. A number of theories with fundamental lengths have been introduced as alternatives and it would be useful to be able to distinguish between them. In particular, the effects that a strict cutoff would have on Quantum Field Theory is studied. It is noted that care must be taken in the method used to apply a strict cutoff. This lead to considering a theory where the cutoffs are defined by restricting each internal line. This theory is only piece-wise analytic. The resulting scattering matrix is frame dependent, yet the theory still satisfies the special relativity view that all frames are subjectively identical. The renormalization of this theory is finite. The change in mass from the electron self-energy will be a spinor operator. The main distinctions of this theory from standard theory will occur at super high energies. New poles and resonances which arise from new endpoint singularities will be found. The locations of these singularities will be frame dependent. Some of these singularities will correspond to creations or interactions of the normal particles with tachyons. It will be shown that for the one loop diagram, the form of the cutoff singularities are closely related to the standard singularities. When there is more than one loop, there can appear some new type of behavior. In particular, a cube root type of behavior in the two loop self-energy diagram will be found. Also the asymptotic behavior of the ladder diagram is studied

  19. Analyses des discours non strictement mathematiques accompagnant des cours de mathematiques (Analysis of Not Strictly Mathematical Discourse in Mathematics Classes).

    Science.gov (United States)

    Robert, Aline

    1995-01-01

    Examines discourse, not strictly mathematical, that teachers might adopt in a mathematics class and presents three major functions of such discourse: communication; structuring and labeling; and reflection. Develops lines for further inquiry, notably on the third function, the most likely focus for specific preparation by the teacher. (13…

  20. 7 CFR 28.414 - Strict Low Middling Light Spotted Color.

    Science.gov (United States)

    2010-01-01

    ... CONTAINER REGULATIONS COTTON CLASSING, TESTING, AND STANDARDS Standards Light Spotted Cotton § 28.414 Strict Low Middling Light Spotted Color. Strict Low Middling Light Spotted Color is color which in spot or...

  1. On N. Chomsky’s strict subcategorization of verbs

    Directory of Open Access Journals (Sweden)

    Janez Orešnik

    1966-12-01

    Full Text Available This paper studies the so-called strict subcategorization rules, and the theory associated with them, in the transformational grammar of. Erigl·ish as proposed by Noarn Chomsky in his Aspects. The syntactic component of English transformational grammar consists of two mutually ordered parts, viz., the base and the transformational subcomponents. The initial part of the base are the so-called categorial rules, which are of almost exclusive interest to us here. Their primary task is to generate what are usually called basic sentence patterns, and will here, with Chomsky (Aspects, p.ll3, be designated with the expression, frames of category symbols.- The rules of the transformational subcomponent modify, in various ways, the frames generated by the base. For several reasons - one of them being that the correct work of the transformational subcomponent quite often depends on the kind of lexical items with which the syntactic positions in the frames of category symbols have been filled, the lexical items must be introduced from the lexicon into the empty positions in the frames before the rules of the transformational subcomponent can be allowed to modify the frames.

  2. Managing Hanford Site solid waste through strict acceptance criteria

    International Nuclear Information System (INIS)

    Jasen, W.G.; Pierce, R.D.; Willis, N.P.

    1993-02-01

    Various types of waste have been generated during the 50-year history of the Hanford Site. Regulatory changes in the last 20 years have provided the emphasis for better management of these wastes. Interpretations of the Atomic Energy Act of 1954 (AEA) and the Resource Conservation and Recovery Act of 1976 (RCRA) have led to the definition of a group of wastes called radioactive mixed wastes (RMW). As a result of the radioactive and hazardous properties of these wastes, strict management programs have been implemented for the management of these wastes. Solid waste management is accomplished through a systems performance approach to waste management that used best-demonstrated available technology (BDAT) and best management practices. The solid waste program at the Hanford Site strives to integrate all aspects of management relative to the treatment, storage and disposal (TSD) of solid waste. Often there are many competing and important needs. It is a difficult task to balance these needs in a manner that is both equitable and productive. Management science is used to help the process of making decisions. Tools used to support the decision making process include five-year planning, cost estimating, resource allocation, performance assessment, waste volume forecasts, input/output models, and waste acceptance criteria. The purpose of this document is to describe how one of these tools, waste acceptance criteria, has helped the Hanford Site manage solid wastes

  3. Effects of strict prolonged bed rest on cardiorespiratory fitness

    DEFF Research Database (Denmark)

    Ried-Larsen, Mathias; Aarts, Hugo M; Joyner, Michael J

    2017-01-01

    with larger declines in V̇o2max). Furthermore, the systematic review revealed a gap in the knowledge about the cardiovascular response to extreme physical inactivity, particularly in older subjects and women of any age group. In addition to its relevance to spaceflight, this lack of data has significant....... Since 1949, 80 studies with a total of 949 participants (>90% men) have been published with data on strict bed rest and V̇o2max The studies were conducted mainly in young participants [median age (interquartile range) 24.5 (22.4-34.0) yr]. The duration of bed rest ranged from 1 to 90 days. V̇o2max...... declined linearly across bed rest duration. No statistical difference in the decline among studies reporting V̇o2max as l/min (-0.3% per day) compared with studies reporting V̇o2max normalized to body weight (ml·kg-1·min-1; -0.43% per day) was observed. Although both total body weight and lean body mass...

  4. Fixed point iterations for strictly hemi-contractive maps in uniformly smooth Banach spaces

    International Nuclear Information System (INIS)

    Chidume, C.E.; Osilike, M.O.

    1993-05-01

    It is proved that the Mann iteration process converges strongly to the fixed point of a strictly hemi-contractive map in real uniformly smooth Banach spaces. The class of strictly hemi-contractive maps includes all strictly pseudo-contractive maps with nonempty fixed point sets. A related result deals with the Ishikawa iteration scheme when the mapping is Lipschitzian and strictly hemi-contractive. Our theorems generalize important known results. (author). 29 refs

  5. Effect of cryopreservation and lyophilization on viability and growth of strict anaerobic human gut microbes.

    Science.gov (United States)

    Bircher, Lea; Geirnaert, Annelies; Hammes, Frederik; Lacroix, Christophe; Schwab, Clarissa

    2018-04-17

    Strict anaerobic gut microbes have been suggested as 'next-generation probiotics' for treating several intestinal disorders. The development of preservation techniques is of major importance for therapeutic application. This study investigated cryopreservation (-80°C) and lyophilization survival and storage stability (4°C for 3 months) of the strict anaerobic gut microbes Bacteroides thetaiotaomicron, Faecalibacterium prausnitzii, Roseburia intestinalis, Anaerostipes caccae, Eubacterium hallii and Blautia obeum. To improve preservation survival, protectants sucrose and inulin (both 5% w/v) were added for lyophilization and were also combined with glycerol (15% v/v) for cryopreservation. Bacterial fitness, evaluated by maximum growth rate and lag phase, viability and membrane integrity were determined using a standardized growth assay and by flow cytometry as markers for preservation resistance. Lyophilization was more detrimental to viability and fitness than cryopreservation, but led to better storage stability. Adding sucrose and inulin enhanced viability and the proportion of intact cells during lyophilization of all strains. Viability of protectant-free B. thetaiotaomicron, A. caccae and F. prausnitzii was above 50% after cryopreservation and storage and increased to above 80% if protectants were present. The addition of glycerol, sucrose and inulin strongly enhanced the viability of B. obeum, E. hallii and R. intestinalis from 0.03-2% in protectant-free cultures to 11-37%. This is the first study that quantitatively compared the effect of cryopreservation and lyophilization and the addition of selected protectants on viability and fitness of six strict anaerobic gut microbes. Our results suggest that efficiency of protectants is process- and species-specific. © 2018 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

  6. Neuronal and glial cell type-specific promoters within adenovirus recombinants restrict the expression of the apoptosis-inducing molecule Fas ligand to predetermined brain cell types, and abolish peripheral liver toxicity.

    Science.gov (United States)

    Morelli, A E; Larregina, A T; Smith-Arica, J; Dewey, R A; Southgate, T D; Ambar, B; Fontana, A; Castro, M G; Lowenstein, P R

    1999-03-01

    Gene therapy using Fas ligand (FasL) for treatment of tumours and protection of transplant rejection is hampered because of the systemic toxicity of FasL. In the present study, recombinant replication-defective adenovirus vectors (RAds) encoding FasL under the control of either the neuronal-specific neuronal-specific enolase (NSE) promoter or the astrocyte-specific glial fibrillary acidic protein (GFAP) promoter have been constructed. The cell type-specific expression of FasL in both neurons and glial cells in primary cultures, and in neuronal and glial cell lines is demonstrated. Furthermore, transgene expression driven by the neuronal and glial promoter was not detected in fibroblastic or epithelial cell lines. Expression of FasL driven by a major immediate early human cytomegalovirus promoter (MIEhCMV) was, however, achieved in all cells tested. As a final test of the stringency of transgene-specific expression, the RAds were injected directly into the bloodstream of mice. The RAds encoding FasL under the control of the non-cell type-specific MIEhCMV promoter induced acute generalized liver haemorrhage with hepatocyte apoptosis, while the RAds containing the NSE or GFAP promoter sequences were completely non-toxic. This demonstrates the specificity of transgene expression, enhanced safety during systemic administration, and tightly regulated control of transgene expression of highly cytotoxic gene products, encoded within transcriptionally targeted RAds.

  7. Bexarotene ligand pharmaceuticals.

    Science.gov (United States)

    Hurst, R E

    2000-12-01

    Bexarotene (LGD-1069), from Ligand, was the first retinoid X receptor (RXR)-selective, antitumor retinoid to enter clinical trials. The company launched the drug for the treatment of cutaneous T-cell lymphoma (CTCL), as Targretin capsules, in the US in January 2000 [359023]. The company filed an NDA for Targretin capsules in June 1999, and for topical gel in December 1999 [329011], [349982] specifically for once-daily oral administration for the treatment of patients with early-stage CTCL who have not tolerated other therapies, patients with refractory or persistent early stage CTCL and patients with refractory advanced stage CTCL. The FDA approved Targretin capsules at the end of December 1999 for once-daily oral treatment of all stages of CTCL in patients refractory to at least one prior systemic therapy, at an initial dose of 300 mg/m2/day. After an NDA was submitted in December 1999 for Targretin gel, the drug received Priority Review status for use as a treatment of cutaneous lesions in patients with stage IA, IB or IIA CTCL [354836]. The FDA issued an approvable letter in June 2000, and granted marketing clearance for CTCL in the same month [370687], [372768], [372769], [373279]. Ligand had received Orphan Drug designation for this indication [329011]. At the request of the FDA, Ligand agreed to carry out certain post-approval phase IV and pharmacokinetic studies [351604]. The company filed an MAA with the EMEA for Targretin Capsules to treat lymphoma in November 1999 [348944]. The NDA for Targretin gel is based on a multicenter phase III trial that was conducted in the US, Canada, Europe and Australia involving 50 patients and a multicenter phase I/II clinical program involving 67 patients. Targretin gel was evaluated for the treatment of patients with early stage CTCL (IA-IIA) who were refractory to, intolerant to, or reached a response plateau for at least 6 months on at least two prior therapies. Efficacy results exceeded the protocol-defined response

  8. Ligand Exchange and 1H NMR Quantification of Single- and Mixed-Moiety Thiolated Ligand Shells on Gold Nanoparticles.

    Science.gov (United States)

    Smith, Ashley M; Millstone, Jill E

    2017-01-01

    The use of nanoparticles in biomedicine critically depends on their surface chemistry. For metal nanoparticles, a common way to tune this surface chemistry is through mass action ligand exchange, where ligand exchange can be used to expand the functionality of the resulting nanoparticle conjugates. Specifically, the quantity, identity, and arrangement of the molecules in the resulting ligand shell each can be tuned significantly. Here, we describe methods to exchange and quantify thiolated and non-thiolated ligands on gold nanoparticle surfaces. Importantly, these strategies allow the quantification of multiple ligand types within a single ligand shell, simultaneously providing ligand composition and ligand density information. These results are crucial for both designing and assigning structure-function relationships in bio-functionalized nanoparticles, and these methods can be applied to a broad range of nanoparticle cores and ligand types including peptides, small molecule drugs, and oligonucleotides.

  9. HIV-mediated phosphatidylinositol 3-kinase/serine-threonine kinase activation in APCs leads to programmed death-1 ligand upregulation and suppression of HIV-specific CD8 T cells.

    Science.gov (United States)

    Muthumani, Karuppiah; Shedlock, Devon J; Choo, Daniel K; Fagone, Paolo; Kawalekar, Omkar U; Goodman, Jonathan; Bian, Chaoran B; Ramanathan, Aarti A; Atman, Parikh; Tebas, Pablo; Chattergoon, Michael A; Choo, Andrew Y; Weiner, David B

    2011-09-15

    Recent evidence demonstrates that HIV-1 infection leads to the attenuation of cellular immune responses, which has been correlated with the increased expression of programmed death (PD)-1 on virus-specific CD8(+) T cells. PD-1 is induced upon T cell activation, and its prolonged expression facilitates CD8(+) T cell inhibitory signals when bound to its B7 family ligands, PD-ligand (L)1/2, which are expressed on APCs. Importantly, early reports demonstrated that blockade of the PD-1/PD-L interaction by Abs may help to counter the development of immune exhaustion driven by HIV viral persistence. To better understand the regulation of the PD-1 pathway during HIV infection, we examined the ability of the virus to induce PD-L expression on macrophages and dendritic cells. We found a direct relationship between the infection of APCs and the expression of PD-L1 in which virus-mediated upregulation induced a state of nonresponsiveness in uninfected HIV-specific T cells. Furthermore, this exhaustion phenotype was revitalized by the blockade of PD-L1, after which T cells regained their capacity for proliferation and the secretion of proinflammatory cytokines IFN-γ, IL-2, and IL-12 upon restimulation. In addition, we identify a critical role for the PI3K/serine-threonine kinase signaling pathway in PD-L1 upregulation of APCs by HIV, because inhibition of these intracellular signal transducer enzymes significantly reduced PD-L1 induction by infection. These data identify a novel mechanism by which HIV exploits the immunosuppressive PD-1 pathway and suggest a new role for virus-infected cells in the local corruption of immune responses required for viral suppression.

  10. The Success Rate of Initial {sup 131I} Ablation in Differentiated Thyroid Cancer: Comparison Between Less strict and Very Strict Low Iodine Diets

    Energy Technology Data Exchange (ETDEWEB)

    Yoo, Ik Dong; Kim, Sung Hoon; Seo, Ye Young; Oh, Jin Kyoung; O, Joo Hyun; Chung, Soo Kyo [The Catholic Univ. of Korea, Seoul (Korea, Republic of)

    2012-03-15

    To decrease the risk of recurrence or metastasis in differentiated thyroid cancer (DTC), selected patients receive radioactive iodine ablation of remnant thyroid tissue or tumor. A low iodine diet can enhance uptake of radioactive iodine. We compared the success rates of radioactive iodine ablation therapy in patients who followed two different low iodine diets (LIDs). The success rates of postsurgical radioactive iodine ablation in DTC patients receiving empiric doses of 150 mCi were retrospectively reviewed. First-time radioactive iodine ablation therapy was done in 71 patients following less strict LID. Less strict LID restricted seafood, iodized salt, egg yolk, dairy products, processed meat, instant prepared meals, and multivitamins. Very strict LID additionally restricted rice, freshwater fish, spinach, and soybean products. Radioactive iodine ablation therapy was considered successful when follow up {sup 123I} whole body scan was negative and stimulated serum thyroglobulin level was less than 2.0 ng/mL. The success rate of patients following less strict LID was 80.3% and for very strict LID 75.6%. There was no statistically significant difference in the success rates between the two LID groups (P=0.48). Very strict LID may not contribute to improving the success rate of initial radioactive iodine ablation therapy at the cost of great inconvenience to the patient.

  11. Ligands in PSI structures

    International Nuclear Information System (INIS)

    Kumar, Abhinav; Chiu, Hsiu-Ju; Axelrod, Herbert L.; Morse, Andrew; Elsliger, Marc-André; Wilson, Ian A.; Deacon, Ashley

    2010-01-01

    A survey of the types and frequency of ligands that are bound to PSI structures is analyzed as well as their utility in functional annotation of previously uncharacterized proteins. Approximately 65% of PSI structures report some type of ligand(s) that is bound in the crystal structure. Here, a description is given of how such ligands are handled and analyzed at the JCSG and a survey of the types, variety and frequency of ligands that are observed in the PSI structures is also compiled and analyzed, including illustrations of how these bound ligands have provided functional clues for annotation of proteins with little or no previous experimental characterization. Furthermore, a web server was developed as a tool to mine and analyze the PSI structures for bound ligands and other identifying features

  12. The extraordinary specificity of xanthine phosphoribosyltransferase from Bacillus subtilis elucidated by reaction kinetics, ligand binding, and crystallography

    DEFF Research Database (Denmark)

    Arent, Susan; Kadziola, Anders; Larsen, Sine

    2006-01-01

    xanthine. The XPRTase is able also to react with guanine and hypoxanthine albeit at much lower (10-4-fold) catalytic efficiency. Different pKa values for the bases and variations in their electrostatic potential can account for these catalytic differences. The unique base specificity of XPRTase has been...

  13. Assessing birth asphyxia using strictly observational signs, the ARC ...

    African Journals Online (AJOL)

    developed by Dr Sultan Omar Sultan was pre-tested at St Francis Hospital Ifakara in 2008 , then tested on 340 newborns in Temeke Hospital and Mnazi Mmoja Hospital. It was found be more sensitive, more specific and more reliable and ultimately ...

  14. Year Class Coexistence or Competitive Exclusion for Strict Biennials?

    NARCIS (Netherlands)

    Davydova, N.V.; Diekmann, O.; van Gils, Stephanus A.

    2001-01-01

    We consider a discrete time model of semelparous biennial population dynamics. Interactions between individuals are modelled with the aid of an 'environmental'' variable I. The impact on and the sensitivity to the environmental condition is age specific. The main result is that competitive exclusion

  15. Year class coexistence or competitive exclusion for strict biennials?

    NARCIS (Netherlands)

    Davydova, N.V.; Diekmann, O.; van Gils, S.A.

    2003-01-01

    We consider a discrete time model of semelparous biennial population dynamics. Interactions between individuals are modelled with the aid of an ``environmental'' variable I. The impact on and the sensitivity to the environmental condition is age specific. The main result is that competitive

  16. Exploiting ligand-protein conjugates to monitor ligand-receptor interactions.

    Directory of Open Access Journals (Sweden)

    Hirohito Haruki

    Full Text Available We introduce three assays for analyzing ligand-receptor interactions based on the specific conjugation of ligands to SNAP-tag fusion proteins. Conjugation of ligands to different SNAP-tag fusions permits the validation of suspected interactions in cell extracts and fixed cells as well as the establishment of high-throughput assays. The different assays allow the analysis of strong and weak interactions. Conversion of ligands into SNAP-tag substrates thus provides access to a powerful toolbox for the analysis of their interactions with proteins.

  17. Strict stoichiometric homeostasis of Cryptomonas pyrenoidifera (Cryptophyceae in relation to N:P supply ratios

    Directory of Open Access Journals (Sweden)

    Eloísa Ramos Rodríguez

    2016-11-01

    Full Text Available A common freshwater cryptophyte, Cryptomonas pyrenoidifera, was cultivated in batch-cultures to analyze intraspecific variation in elemental stoichiometry along a broad gradient of pulsed phosphorus (P enrichment during the early acclimation period and to determine the immediate homeostatic capacity of the nitrogen-to-phosphorus (N:P ratio of this alga when nutrients are at saturating levels. Experimental results revealed that nitrogen (N and P cell quotas significantly increased with increasing P concentration. However, despite the wide range of N:P ratios in the medium, Cryptomonas N:P ratios were highly stable at higher P-level treatments, indicating a highly conservative behavior and suggesting strict elemental homeostasis when nutrients are at saturating levels. The strictly homeostatic N:P ratio appears to be attributable to their high potential for a fast luxury consumption of both N and P after a brief and intense episode of increased resource availability and to physiological limits on their nutrient storage capacity. Most importantly, the N:P biomass ratio at nutrient saturating levels converged around 11:1, which was the observed ratio of maximum internal cell quotas for N and P (i.e. Qmax,N:Qmax,P under the prevailing experimental conditions. This value is particularly informative for C. pyrenoidifera because it represents cell storage quotients and may be a taxon-specific evolutionary optimum, providing a reference point to infer the grade of nutrient-limitation. The experimental data give ranges of variation in C. pyrenoidifera elemental composition permitting, among others, proper parameterization of cryptophyte stoichiometry models.

  18. A novel color change mechanism for breast cancer biomarker detection: naphthoquinones as specific ligands of human arylamine N-acetyltransferase 1.

    Science.gov (United States)

    Laurieri, Nicola; Egleton, James E; Varney, Amy; Thinnes, Cyrille C; Quevedo, Camilo E; Seden, Peter T; Thompson, Sam; Rodrigues-Lima, Fernando; Dairou, Julien; Dupret, Jean-Marie; Russell, Angela J; Sim, Edith

    2013-01-01

    Human arylamine N-acetyltransferase 1 (hNAT1) has become an attractive potential biomarker for estrogen-receptor-positive breast cancers. We describe here the mechanism of action of a selective non-covalent colorimetric biosensor for the recognition of hNAT1 and its murine homologue, mNat2, over their respective isoenzymes, leading to new opportunities in diagnosis. On interaction with the enzyme, the naphthoquinone probe undergoes an instantaneous and striking visible color change from red to blue. Spectroscopic, chemical, molecular modelling and biochemical studies reported here show that the color change is mediated by selective recognition between the conjugate base of the sulfonamide group within the probe and the conjugate acid of the arginine residue within the active site of both hNAT1 and mNat2. This represents a new mechanism for selective biomarker sensing and may be exploited as a general approach to the specific detection of biomarkers in disease.

  19. Validation of an automatic diagnosis of strict left bundle branch block criteria using 12-lead electrocardiograms

    DEFF Research Database (Denmark)

    Xia, Xiaojuan; Ruwald, Anne-Christine; Ruwald, Martin H

    2017-01-01

    AIMS: Strict left bundle branch block (LBBB) criteria were recently proposed to identify LBBB patients to benefit most from cardiac resynchronization therapy (CRT). The aim of our study was to automate identification of strict LBBB in order to facilitate its broader application. METHODS: We devel...

  20. 7 CFR 28.416 - Strict Good Ordinary Light Spotted Color.

    Science.gov (United States)

    2010-01-01

    ... CONTAINER REGULATIONS COTTON CLASSING, TESTING, AND STANDARDS Standards Light Spotted Cotton § 28.416 Strict Good Ordinary Light Spotted Color. Strict Good Ordinary Light Spotted Color is color which in spot or... Cotton Source: 57 FR 34498, Aug. 5, 1992, unless otherwise noted. ...

  1. Substrate coated with receptor and labelled ligand for assays

    International Nuclear Information System (INIS)

    1980-01-01

    Improvements in the procedures for assaying ligands are described. The assay consists of a polystyrene tube on which receptors are present for both the ligand to be assayed and a radioactively labelled form of the ligand. The receptors on the bottom portion of the tube are also coated with labelled ligands, thus eliminating the necessity for separate addition of the labelled ligand and sample during an assay. Examples of ligands to which this method is applicable include polypeptides, nucleotides, nucleosides and proteins. Specific examples are given in which the ligand to be assayed is digoxin, the labelled form of the ligand is 3-0-succinyl digoxyigenin tyrosine ( 125 I) and the receptor is digoxin antibody. (U.K.)

  2. Ligand-Mediated Coating of Liposomes with Human Serum Albumin.

    Science.gov (United States)

    Sato, Hikari; Nakhaei, Elnaz; Kawano, Takahito; Murata, Masaharu; Kishimura, Akihiro; Mori, Takeshi; Katayama, Yoshiki

    2018-02-13

    Coating liposome surfaces with human serum albumin (HSA) can improve the colloidal stability and prevent opsonization. HSA coating via specific binding with alkyl ligands is promising because although the ligand-mediated coating is relatively stable it can spontaneously exchange with fresh HSA. However, to achieve surface coating with HSA, multiple hydrophobic ligands must be exposed to an aqueous medium prior to binding with HSA. This presents a challenge, as hydrophobic ligands tend to be buried in the liposomal membrane. Here we present the first HSA modification of liposome surfaces via alkyl ligands. We found that a relatively short alkyl ligand, or a long alkyl ligand with a terminal carboxylate, could be exposed on the liposome surface without causing aggregation of the liposomes and these ligands could subsequently bind HSA. The resulting HSA-coated liposomes were as inert as conventional PEGylated liposomes in terms of macrophage recognition.

  3. Three-dimensional autoradiographic localization of quench-corrected glycine receptor specific activity in the mouse brain using 3H-strychnine as the ligand

    International Nuclear Information System (INIS)

    White, W.F.; O'Gorman, S.; Roe, A.W.

    1990-01-01

    The autoradiographic analysis of neurotransmitter receptor distribution is a powerful technique that provides extensive information on the localization of neurotransmitter systems. Computer methodologies are described for the analysis of autoradiographic material which include quench correction, 3-dimensional display, and quantification based on anatomical boundaries determined from the tissue sections. These methodologies are applied to the problem of the distribution of glycine receptors measured by 3H-strychnine binding in the mouse CNS. The most distinctive feature of this distribution is its marked caudorostral gradient. The highest densities of binding sites within this gradient were seen in somatic motor and sensory areas; high densities of binding were seen in branchial efferent and special sensory areas. Moderate levels were seen in nuclei related to visceral function. Densities within the reticular formation paralleled the overall gradient with high to moderate levels of binding. The colliculi had low and the diencephalon had very low levels of binding. No binding was seen in the cerebellum or the telencephalon with the exception of the amygdala, which had very low levels of specific binding. This distribution of glycine receptors correlates well with the known functional distribution of glycine synaptic function. These data are illustrated in 3 dimensions and discussed in terms of the significance of the analysis techniques on this type of data as well as the functional significance of the distribution of glycine receptors

  4. HLA-Restricted CTL That Are Specific for the Immune Checkpoint Ligand PD-L1 Occur with High Frequency in Cancer Patients

    DEFF Research Database (Denmark)

    Munir, Shamaila; Andersen, Gitte Holmen; Met, Özcan

    2013-01-01

    PD-L1 (CD274) contributes to functional exhaustion of T cells and limits immune responses in patients with cancer. In this study, we report the identification of an human leukocyte antigen (HLA)-A2-restricted epitope from PD-L1, and we describe natural, cytolytic T-cell reactivity against PD-L1...... in the peripheral blood of patients with cancer and healthy individuals. Notably, PD-L1-specific T cells were able not only to recognize and kill tumor cells but also PD-L1-expressing dendritic cells in a PD-L1-dependent manner, insofar as PD-L1 ablation rescued dendritic cells from killing. Furthermore......, by incubating nonprofessional antigen-presenting cells with long peptides from PD-L1, we found that PD-L1 was rapidly internalized, processed, and cross-presented by HLA-A2 on the cell surface. Apparently, this cross-presentation was TAP-independent, as it was conducted not only by B cells but in addition...

  5. A Novel Color Change Mechanism for Breast Cancer Biomarker Detection: Naphthoquinones as Specific Ligands of Human Arylamine N-Acetyltransferase 1

    Science.gov (United States)

    Varney, Amy; Thinnes, Cyrille C.; Quevedo, Camilo E.; Seden, Peter T.; Thompson, Sam; Rodrigues-Lima, Fernando; Dairou, Julien; Dupret, Jean-Marie; Russell, Angela J.; Sim, Edith

    2013-01-01

    Human arylamine N-acetyltransferase 1 (hNAT1) has become an attractive potential biomarker for estrogen-receptor-positive breast cancers. We describe here the mechanism of action of a selective non-covalent colorimetric biosensor for the recognition of hNAT1 and its murine homologue, mNat2, over their respective isoenzymes, leading to new opportunities in diagnosis. On interaction with the enzyme, the naphthoquinone probe undergoes an instantaneous and striking visible color change from red to blue. Spectroscopic, chemical, molecular modelling and biochemical studies reported here show that the color change is mediated by selective recognition between the conjugate base of the sulfonamide group within the probe and the conjugate acid of the arginine residue within the active site of both hNAT1 and mNat2. This represents a new mechanism for selective biomarker sensing and may be exploited as a general approach to the specific detection of biomarkers in disease. PMID:23940600

  6. A novel color change mechanism for breast cancer biomarker detection: naphthoquinones as specific ligands of human arylamine N-acetyltransferase 1.

    Directory of Open Access Journals (Sweden)

    Nicola Laurieri

    Full Text Available Human arylamine N-acetyltransferase 1 (hNAT1 has become an attractive potential biomarker for estrogen-receptor-positive breast cancers. We describe here the mechanism of action of a selective non-covalent colorimetric biosensor for the recognition of hNAT1 and its murine homologue, mNat2, over their respective isoenzymes, leading to new opportunities in diagnosis. On interaction with the enzyme, the naphthoquinone probe undergoes an instantaneous and striking visible color change from red to blue. Spectroscopic, chemical, molecular modelling and biochemical studies reported here show that the color change is mediated by selective recognition between the conjugate base of the sulfonamide group within the probe and the conjugate acid of the arginine residue within the active site of both hNAT1 and mNat2. This represents a new mechanism for selective biomarker sensing and may be exploited as a general approach to the specific detection of biomarkers in disease.

  7. Pleiotropic effects of Blastocystis spp. Subtypes 4 and 7 on ligand-specific toll-like receptor signaling and NF-κB activation in a human monocyte cell line.

    Directory of Open Access Journals (Sweden)

    Joshua D W Teo

    Full Text Available Blastocystis spp. is a common enteric stramenopile parasite that colonizes the colon of hosts of a diverse array of species, including humans. It has been shown to compromise intestinal epithelial cell barrier integrity and mediate the production of pro-inflammatory cytokines and chemokines. Mucosal epithelial surfaces, including the intestinal epithelium, are increasingly recognized to perform a vital surveillance role in the context of innate immunity, through the expression of pathogen recognition receptors, such as Toll-like receptors (TLRs. In this study, we use the human TLR reporter monocytic cell line, THP1-Blue, which expresses all human TLRs, to investigate effects of Blastocystis on TLR activation, more specifically the activation of TLR-2, -4 and -5. We have observed that live Blastocystis spp. parasites and whole cell lysate (WCL alone do not activate TLRs in THP1-Blue. Live ST4-WR1 parasites inhibited LPS-mediated NF-κB activation in THP1-Blue. In contrast, ST7-B WCL and ST4-WR1 WCL induced pleiotropic modulation of ligand-specific TLR-2 and TLR-4 activation, with no significant effects on flagellin-mediated TLR-5 activation. Real time-qPCR analysis on SEAP reporter gene confirmed the augmenting effect of ST7-B on LPS-mediated NF-κB activation in THP1-Blue. Taken together, this is the first study to characterize interactions between Blastocystis spp. and host TLR activation using an in vitro reporter model.

  8. Tumor targeting via integrin ligands

    Directory of Open Access Journals (Sweden)

    Udaya Kiran eMarelli

    2013-08-01

    Full Text Available Selective and targeted delivery of drugs to tumors is a major challenge for an effective cancer therapy and also to overcome the side effects associated with current treatments. Overexpression of various receptors on tumor cells is a characteristic structural and biochemical aspect of tumors and distinguishes them from physiologically normal cells. This abnormal feature is therefore suitable for selectively directing anticancer molecules to tumors by using ligands that can preferentially recognize such receptors. Several subtypes of integrin receptors that are crucial for cell adhesion, cell signaling, cell viability and motility have been shown to have an upregulated expression on cancer cells. Thus, ligands that recognize specific integrin subtypes represent excellent candidates to be conjugated to drugs or drug carrier systems and be targeted to tumors. In this regard, integrins recognizing the RGD cell adhesive sequence have been extensively targeted for tumor specific drug delivery. Here we review key recent examples on the presentation of RGD-based integrin ligands by means of distinct drug delivery systems, and discuss the prospects of such therapies to specifically target tumor cells.

  9. Immediate effect of instrumentation on the subgingival microflora in deep inflamed pockets under strict plaque control.

    Science.gov (United States)

    Rhemrev, G E; Timmerman, M F; Veldkamp, I; Van Winkelhoff, A J; Van der Velden, U

    2006-01-01

    To investigate (1) reduction in the number of microorganisms obtained directly after subgingival instrumentation, (2) rate of bacterial re-colonization during 2 weeks, under supragingival plaque-free conditions. Effects of subgingival instrumentation were measured at one deep pocket in 22 patients (11 smokers and 11 non-smokers). Immediately after initial therapy, experimental sites, under strict plaque control, were instrumented subgingivally. Microbiological evaluation was performed at pre-instrumentation, immediate post-instrumentation and 1 and 2 weeks post-instrumentation. Mean total anaerobic colony forming units (CFUs) dropped from 3.9 x 10(6) before to 0.09 x 10(6) immediately following instrumentation. Significant reductions were found for Tannerella forsythia, Micromonas micros, Fusobacterium nucleatum and spirochetes. Significant reductions were not observed for Actinobacillus actinomycetemcomitans, Porphyromonas gingivalis, Prevotella intermedia and Campylobacter rectus. Except for spirochetes, no reduction in prevalence of specific periodontal bacteria was found immediately after instrumentation. During follow-up, mean total CFU tended to increase. Prevalence of periodontal bacteria further reduced. No effect of smoking was found. Results indicate that subgingival mechanical cleaning in itself, has a limited effect, in actually removing bacteria. The subsequent reduction in prevalence of specific periodontal bacteria shows that it is apparently difficult for these species to survive in treated pockets.

  10. Controlling Signal Transduction with Synthetic Ligands

    Science.gov (United States)

    Spencer, David M.; Wandless, Thomas J.; Schreiber, Stuart L.; Crabtree, Gerald R.

    1993-11-01

    Dimerization and oligomerization are general biological control mechanisms contributing to the activation of cell membrane receptors, transcription factors, vesicle fusion proteins, and other classes of intra- and extracellular proteins. Cell permeable, synthetic ligands were devised that can be used to control the intracellular oligomerization of specific proteins. To demonstrate their utility, these ligands were used to reduce intracellular oligomerization of cell surface receptors that lacked their transmembrane and extracellular regions but contained intracellular signaling domains. Addition of these ligands to cells in culture resulted in signal transmission and specific target gene activation. Monomeric forms of the ligands blocked the pathway. This method of ligandregulated activation and termination of signaling pathways has the potential to be applied wherever precise control of a signal transduction pathway is desired.

  11. Chemistry of Marine Ligands and Siderophores

    OpenAIRE

    Vraspir, Julia M.; Butler, Alison

    2009-01-01

    Marine microorganisms are presented with unique challenges to obtain essential metal ions required to survive and thrive in the ocean. The production of organic ligands to complex transition metal ions is one strategy to both facilitate uptake of specific metals, such as iron, and to mitigate the potential toxic effects of other metal ions, such as copper. A number of important trace metal ions are complexed by organic ligands in seawater, including iron, cobalt, nickel, copper, zinc, and cad...

  12. Design of targeting ligands in medicinal inorganic chemistry.

    Science.gov (United States)

    Storr, Tim; Thompson, Katherine H; Orvig, Chris

    2006-06-01

    This tutorial review will highlight recent advances in medicinal inorganic chemistry pertaining to the use of multifunctional ligands for enhanced effect. Ligands that adequately bind metal ions and also include specific targeting features are gaining in popularity due to their ability to enhance the efficacy of less complicated metal-based agents. Moving beyond the traditional view of ligands modifying reactivity, stabilizing specific oxidation states, and contributing to substitution inertness, we will discuss recent work involving metal complexes with multifunctional ligands that target specific tissues, membrane receptors, or endogenous molecules, including enzymes.

  13. Synchronization control of cross-strict feedback hyperchaotic system based on cross active backstepping design

    International Nuclear Information System (INIS)

    Wang Jing; Gao Jinfeng; Ma Xikui

    2007-01-01

    This Letter presents a novel cross active backstepping design method for synchronization control of cross-strict feedback hyperchaotic system, in which the ordinary backstepping design is unavailable. The proposed control method, combining backstepping design and active control approach, extends the application of backstepping technique in chaos control. Based on this method, different combinations of controllers can be designed to meet the needs of different applications. The proposed method is applied to achieve chaos synchronization of two identical cross-strict feedback hyperchaotic systems. Also it is used to implement synchronization between cross-strict feedback hyperchaotic system and Roessler hyperchaotic system. Numerical examples illustrate the validity of the control method

  14. The Inhibition of Stat5 by a Peptide Aptamer Ligand Specific for the DNA Binding Domain Prevents Target Gene Transactivation and the Growth of Breast and Prostate Tumor Cells

    Science.gov (United States)

    Weber, Axel; Borghouts, Corina; Brendel, Christian; Moriggl, Richard; Delis, Natalia; Brill, Boris; Vafaizadeh, Vida; Groner, Bernd

    2013-01-01

    The signal transducer and activator of transcription Stat5 is transiently activated by growth factor and cytokine signals in normal cells, but its persistent activation has been observed in a wide range of human tumors. Aberrant Stat5 activity was initially observed in leukemias, but subsequently also found in carcinomas. We investigated the importance of Stat5 in human tumor cell lines. shRNA mediated downregulation of Stat5 revealed the dependence of prostate and breast cancer cells on the expression of this transcription factor. We extended these inhibition studies and derived a peptide aptamer (PA) ligand, which directly interacts with the DNA-binding domain of Stat5 in a yeast-two-hybrid screen. The Stat5 specific PA sequence is embedded in a thioredoxin (hTRX) scaffold protein. The resulting recombinant protein S5-DBD-PA was expressed in bacteria, purified and introduced into tumor cells by protein transduction. Alternatively, S5-DBD-PA was expressed in the tumor cells after infection with a S5-DBD-PA encoding gene transfer vector. Both strategies impaired the DNA-binding ability of Stat5, suppressed Stat5 dependent transactivation and caused its intracellular degradation. Our experiments describe a peptide based inhibitor of Stat5 protein activity which can serve as a lead for the development of a clinically useful compound for cancer treatment. PMID:24276378

  15. The Inhibition of Stat5 by a Peptide Aptamer Ligand Specific for the DNA Binding Domain Prevents Target Gene Transactivation and the Growth of Breast and Prostate Tumor Cells

    Directory of Open Access Journals (Sweden)

    Vida Vafaizadeh

    2013-08-01

    Full Text Available The signal transducer and activator of transcription Stat5 is transiently activated by growth factor and cytokine signals in normal cells, but its persistent activation has been observed in a wide range of human tumors. Aberrant Stat5 activity was initially observed in leukemias, but subsequently also found in carcinomas. We investigated the importance of Stat5 in human tumor cell lines. shRNA mediated downregulation of Stat5 revealed the dependence of prostate and breast cancer cells on the expression of this transcription factor. We extended these inhibition studies and derived a peptide aptamer (PA ligand, which directly interacts with the DNA-binding domain of Stat5 in a yeast-two-hybrid screen. The Stat5 specific PA sequence is embedded in a thioredoxin (hTRX scaffold protein. The resulting recombinant protein S5-DBD-PA was expressed in bacteria, purified and introduced into tumor cells by protein transduction. Alternatively, S5-DBD-PA was expressed in the tumor cells after infection with a S5-DBD-PA encoding gene transfer vector. Both strategies impaired the DNA-binding ability of Stat5, suppressed Stat5 dependent transactivation and caused its intracellular degradation. Our experiments describe a peptide based inhibitor of Stat5 protein activity which can serve as a lead for the development of a clinically useful compound for cancer treatment.

  16. Chemistry of marine ligands and siderophores.

    Science.gov (United States)

    Vraspir, Julia M; Butler, Alison

    2009-01-01

    Marine microorganisms are presented with unique challenges to obtain essential metal ions required to survive and thrive in the ocean. The production of organic ligands to complex transition metal ions is one strategy to both facilitate uptake of specific metals, such as iron, and to mitigate the potential toxic effects of other metal ions, such as copper. A number of important trace metal ions are complexed by organic ligands in seawater, including iron, cobalt, nickel, copper, zinc, and cadmium, thus defining the speciation of these metal ions in the ocean. In the case of iron, siderophores have been identified and structurally characterized. Siderophores are low molecular weight iron-binding ligands produced by marine bacteria. Although progress has been made toward the identity of in situ iron-binding ligands, few compounds have been identified that coordinate the other trace metals. Deciphering the chemical structures and production stimuli of naturally produced organic ligands and the organisms they come from is fundamental to understanding metal speciation and bioavailability. The current evidence for marine ligands, with an emphasis on siderophores, and discussion of the importance and implications of metal-binding ligands in controlling metal speciation and cycling within the world's oceans are presented.

  17. The Effect of Strict Segregation on Pseudomonas aeruginosa in Cystic Fibrosis Patients

    NARCIS (Netherlands)

    van Mansfeld, Rosa; de Vrankrijker, Angelica; Brimicombe, Roland; Heijerman, Harry; Teding van Berkhout, Ferdinand; Spitoni, Cristian|info:eu-repo/dai/nl/304625957; Grave, Sanne; van der Ent, Cornelis; Wolfs, Tom; Willems, Rob; Bonten, Marc

    2016-01-01

    INTRODUCTION: Segregation of patients with cystic fibrosis (CF) was implemented to prevent chronic infection with epidemic Pseudomonas aeruginosa strains with presumed detrimental clinical effects, but its effectiveness has not been carefully evaluated. METHODS: The effect of strict segregation on

  18. Strict deformation quantization for actions of a class of symplectic lie groups

    International Nuclear Information System (INIS)

    Bieliavsky, Pierre; Massar, Marc

    2002-01-01

    We present explicit universal strict deformation quantization formulae for actions of Iwasawa subgroups AN of SN(1, n). This answers a question raised by Rieffel in [Contemp. Math. 228 (1998), 315]. (author)

  19. DNA remodelling by Strict Partial Endoreplication in orchids, an original process in the plant kingdom.

    Science.gov (United States)

    Brown, Spencer C; Bourge, Mickaël; Maunoury, Nicolas; Wong, Maurice; Bianchi, Michele Wolfe; Lepers-Andrzejewski, Sandra; Besse, Pascale; Siljak-Yakovlev, Sonja; Dron, Michel; Satiat-Jeunemaître, Béatrice

    2017-04-13

    DNA remodelling during endoreplication appears to be a strong developmental characteristic in orchids. In this study, we analysed DNA content and nuclei in 41 species of orchids to further map the genome evolution in this plant family. We demonstrate that the DNA remodelling observed in 36 out of 41 orchids studied corresponds to strict partial endoreplication. Such process is developmentally regulated in each wild species studied. Cytometry data analyses allowed us to propose a model where nuclear states 2C, 4E, 8E, etc. form a series comprising a fixed proportion, the euploid genome 2C, plus 2 to 32 additional copies of a complementary part of the genome. The fixed proportion ranged from 89% of the genome in Vanilla mexicana down to 19% in V. pompona, the lowest value for all 148 orchids reported. Insterspecific hybridisation did not suppress this phenomenon. Interestingly, this process was not observed in mass-produced epiphytes. Nucleolar volumes grow with the number of endocopies present, coherent with high transcription activity in endoreplicated nuclei. Our analyses suggest species-specific chromatin rearrangement. Towards understanding endoreplication, V. planifolia constitutes a tractable system for isolating the genomic sequences that confer an advantage via endoreplication from those that apparently suffice at diploid level. © The Author(s) 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  20. Generalized mechanical pain sensitivity over nerve tissues in patients with strictly unilateral migraine.

    Science.gov (United States)

    Fernández-de-las-Peñas, César; Arendt-Nielsen, Lars; Cuadrado, María Luz; Pareja, Juan A

    2009-06-01

    No study has previously analyzed pressure pain sensitivity of nerve trunks in migraine. This study aimed to examine the differences in mechanical pain sensitivity over specific nerves between patients with unilateral migraine and healthy controls. Blinded investigators assessed pressure pain thresholds (PPT) over the supra-orbital nerves (V1) and peripheral nerve trunks of both upper extremities (median, radial, and ulnar nerves) in 20 patients with strictly unilateral migraine and 20 healthy matched controls. Pain intensity after palpation over both supra-orbital nerves was also assessed. A pressure algometer was used to quantify PPT, whereas a 10-point numerical pain rate scale was used to evaluate pain to palpation over the supra-orbital nerve. The analysis of covariance revealed that pain to palpation over the supra-orbital nerve was significantly higher (P0.6). In patients with unilateral migraine, we found increased mechano-sensitivity of the supra-orbital nerve on the symptomatic side of the head. Outside the head, the same patients showed increased mechano-sensitivity of the main peripheral nerves of both upper limbs, without asymmetries. Such diffuse hypersensitivity of the peripheral nerves lends further evidence to the presence of a state of hyperexcitability of the central nervous system in patients with unilateral migraine.

  1. Strict optical orthogonal codes for purely asynchronous code-division multiple-access applications

    Science.gov (United States)

    Zhang, Jian-Guo

    1996-12-01

    Strict optical orthogonal codes are presented for purely asynchronous optical code-division multiple-access (CDMA) applications. The proposed code can strictly guarantee the peaks of its cross-correlation functions and the sidelobes of any of its autocorrelation functions to have a value of 1 in purely asynchronous data communications. The basic theory of the proposed codes is given. An experiment on optical CDMA systems is also demonstrated to verify the characteristics of the proposed code.

  2. A new class of PN3-pincer ligands for metal–ligand cooperative catalysis

    KAUST Repository

    Li, Huaifeng

    2014-12-01

    Work on a new class of PN3-pincer ligands for metal-ligand cooperative catalysis is reviewed. While the field of the pyridine-based PN3-transition metal pincer complexes is still relatively young, many important applications of these complexes have already emerged. In several cases, the PN3-pincer complexes for metal-ligand cooperative catalysis result in significantly improved or unprecedented activities. The synthesis and coordination chemistry of PN3-pincer ligands are briefly summarized first to cover the synthetic routes for their preparation, followed by a focus review on their applications in catalysis. A specific emphasis is placed on the later section about the role of PN3-pincer ligands\\' dearomatization-rearomatization steps during the catalytic cycles. The mechanistic insights from density functional theory (DFT) calculations are also discussed.

  3. Plant use in the medicinal practices known as "strict diets" in Chazuta valley (Peruvian Amazon).

    Science.gov (United States)

    Sanz-Biset, Jaume; Cañigueral, Salvador

    2011-09-01

    Strict diets are traditional medicinal practices where plant remedies are consumed with nearly fasting and with some sort of social seclusion. The aim of this work was to describe these practices of Chazuta and the use of plants within, as well as to analyse the possible functions of the last. The information was obtained through interviews to the 6.3% of the district rural adult population (140 individuals, 75% of which was considered Quechua). In total, 122 strict diets were recorded and 106 different plant species were reported to be used. Strict diets present a characteristic structure and plant use. The main effects reported in strict diets were antinflammatory, antiinfective, brain function alteration and depuration. Strict diets are well structured traditional medicinal practices, also with a symbolic significance in the life cycle of chazutian men. Plants used in strict diets can contribute to the main effects through antinflammation, antiinfective actions, psychoactivity and depurative related activities. The correlation between literature evidence of activity of most used plants and effects reported for the correspondent diet (i.e. in which the plant was used) are 36% for antinflammatory activity, 29% for antimicrobial activity, 18% for psychoactivity and 5% for depurative related activities. The percentages go to 77%, 64%, 73% and 32%, respectively, when literature evidences on related taxa are also considered. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

  4. Radioiodinated ligands for dopamine receptors

    International Nuclear Information System (INIS)

    Kung, H.F.

    1994-01-01

    The dopamine receptor system is important for normal brain function; it is also the apparent action site for various neuroleptic drugs for the treatment of schizophrenia and other metal disorders. In the past few years radioiodinated ligands for single photon emission tomography (SPECT) have been successfully developed and tested in humans: [ 123 I]TISCH for D1 dopamine receptors; [ 123 I]IBZM, epidepride, IBF and FIDA2, four iodobenzamide derivatives, for D2/D3 dopamine receptors. In addition, [ 123 I]β-CIT (RTI-55) and IPT, cocaine derivatives, for the dopamine reuptake site are potentially useful for diagnosis of loss of dopamine neurons. The first iodinated ligand, (R)trans-7-OH-PIPAT, for D3 dopamine receptors, was synthesized and characterized with cloned cell lines (Spodoptera frugiperda, Sf9) expressing the D2 and D3 dopamine receptors and with rat basal forebrain membrane preparations. Most of the known iodobenzamides displayed similar potency in binding to both D2 and D3 dopamine receptors expressed in the cell lines. Initial studies appear to suggest that by fine tuning the structures it may be possible to develop agents specific for D2 and D3 dopamine receptors. It is important to investigate D2/D3 selectivity for this series of potent ligands

  5. Genetic polymorphism rs3760396 of the chemokine (C-C motif) ligand 2 gene (CCL2) associated with the susceptibility of lung cancer in a pathological subtype-specific manner in Han-ancestry Chinese: a case control study

    International Nuclear Information System (INIS)

    Li, Xu; Lin, Fangcai; Zhou, Hong

    2016-01-01

    Chemokines are well known inflammatory factors critical for tumor development in diverse tissues, including lung cancer. Chemokine (C-C motif) Ligand 2 (CCL2) was one of such chemokines important for both primary tumor development and metastasis of various cancers. Polymorphism at rs3760396 of CCL2 genes is associated with the prognosis of non-small cell lung cancer (NSCLC). The goal of our study was to examine the relationship of genetic polymorphisms rs3760396 with the susceptibility of lung cancer and its pathological subtypes in Han-ancestry Chinese population. rs3760396 G/C polymorphism of CCL2 was genotyped using PCR in 394 patients with lung cancer and 545 cancer-free controls from the same Northeast region of China. After controlling for gender, age and smoking status, no significant association was observed between rs3760396 polymorphism and overall lung cancer. However, minor allele G of rs3760396 polymorphism was significantly associated with increased risk of adenosquamous lung carcinoma with either allelic genetic model (OR = 5.29, P < 0.001), or dominant genetic model (OR = 9.88, P < 0.001), or genotypic model (GC genotype vs. CC genotype, OR = 10.73, P < 0.001). Although rs3760396 polymorphism was not significantly associated with increased risk of adenocarcinoma subtype, it was nominally associated with the pooled outcome of either adenocarcinoma or adenosquamous carcinoma under allelic genetic model (OR = 1.54, P = 0.023) or dominant genetic model (OR = 1.57, P = 0.031). Our study suggested rs3760396 polymorphism of CCL2 is associated not only with prognosis of NSCLC, but also with risk of lung cancer in a subtype-specific manner. Our results further supported previous evidence of the important role of CCL2 in lung cancer development

  6. A change of in vivo characteristics depending on specific activity of radioiodinated (+)-2-[4-(4-iodophenyl)piperidino]cyclohexanol [(+)-pIV] as a ligand for sigma receptor imaging.

    Science.gov (United States)

    Akhter, Nasima; Shiba, Kazuhiro; Ogawa, Kazuma; Tsuji, Shiro; Kinuya, Seigo; Nakajima, Kenichi; Mori, Hirofumi

    2008-01-01

    The radioiodinated (+)-p-iodovesamicol [(+)-pIV], which shows a high binding affinity for sigma-1 (sigma-1) receptors, is prepared by an exchange reaction. The specific activity (SA) is fairly low and therefore is insufficient for clinical use. In this study, we prepared (+)-[(125)I]pIV with a high SA from tributylstannyl precursor and compared the in vivo characteristics between high and low SA by imaging sigma-1 receptors in the central nervous system. In the biodistribution study, a difference in brain accumulation was observed between the two methods. At 30 min postinjection, the brain accumulation (1.58%ID/g) of low SA [0.6-1.1 TBq/mmol (16-30 Ci/mmol)] (+)-[(125)I]pIV was higher than that (1.34%ID/g) of high SA [>88.8 TBq/mmol (>2400 Ci/mmol)] (+)-[(125)I]pIV. In the blocking study, the brain uptake of high SA (+)-[(125)I]pIV was reduced more significantly by the coadministration of sigma ligands such as pentazocine, haloperidol or SA4503 than that of low SA (+)-[(125)I]pIV. These results showed that nonspecific binding of high SA (+)-[(125)I]pIV in the brain was lower than that of low SA (+)-[(125)I]pIV, and high SA (+)-[(125)I]pIV bound more specifically to sigma-1 receptors in the brain than low SA (+)-[(125)I]pIV. In contrast, in the blood-binding study, high SA (+)-[(125)I]pIV (58.4%) bound to blood cells with higher affinity than low SA (+)-[(125)I]pIV (46.0%). In metabolite studies, blood metabolites of high SA (+)-[(125)I]pIV (57.3+/-3.5%) were higher than those of low SA (+)-[(125)I]pIV (45.5+/-4.1%) at 30 min postinjection. Higher SA may be apt to bind to blood cells with higher affinity and to be metabolized faster.

  7. A change of in vivo characteristics depending on specific activity of radioiodinated (+)-2-[4-(4-iodophenyl)piperidino]cyclohexanol [(+)-pIV] as a ligand for sigma receptor imaging

    International Nuclear Information System (INIS)

    Akhter, Nasima; Shiba, Kazuhiro; Ogawa, Kazuma; Tsuji, Shiro; Kinuya, Seigo; Nakajima, Kenichi; Mori, Hirofumi

    2008-01-01

    The radioiodinated (+)-p-iodovesamicol [(+)-pIV], which shows a high binding affinity for sigma-1 (σ-1) receptors, is prepared by an exchange reaction. The specific activity (SA) is fairly low and therefore is insufficient for clinical use. In this study, we prepared (+)-[ 125 I]pIV with a high SA from tributylstannyl precursor and compared the in vivo characteristics between high and low SA by imaging σ-1 receptors in the central nervous system. In the biodistribution study, a difference in brain accumulation was observed between the two methods. At 30 min postinjection, the brain accumulation (1.58%ID/g) of low SA [0.6-1.1 TBq/mmol (16-30 Ci/mmol)] (+)-[ 125 I]pIV was higher than that (1.34%ID/g) of high SA [>88.8 TBq/mmol (>2400 Ci/mmol)] (+)-[ 125 I]pIV. In the blocking study, the brain uptake of high SA (+)-[ 125 I]pIV was reduced more significantly by the coadministration of sigma ligands such as pentazocine, haloperidol or SA4503 than that of low SA (+)-[ 125 I]pIV. These results showed that nonspecific binding of high SA (+)-[ 125 I]pIV in the brain was lower than that of low SA (+)-[ 125 I]pIV, and high SA (+)-[ 125 I]pIV bound more specifically to σ-1 receptors in the brain than low SA (+)-[ 125 I]pIV. In contrast, in the blood-binding study, high SA (+)-[ 125 I]pIV (58.4%) bound to blood cells with higher affinity than low SA (+)-[ 125 I]pIV (46.0%). In metabolite studies, blood metabolites of high SA (+)-[ 125 I]pIV (57.3±3.5%) were higher than those of low SA (+)-[ 125 I]pIV (45.5±4.1%) at 30 min postinjection. Higher SA may be apt to bind to blood cells with higher affinity and to be metabolized faster

  8. Strict Host-Symbiont Cospeciation and Reductive Genome Evolution in Insect Gut Bacteria

    Science.gov (United States)

    Hosokawa, Takahiro; Kikuchi, Yoshitomo; Nikoh, Naruo; Shimada, Masakazu; Fukatsu, Takema

    2006-01-01

    Host-symbiont cospeciation and reductive genome evolution have been identified in obligate endocellular insect symbionts, but no such example has been identified from extracellular ones. Here we first report such a case in stinkbugs of the family Plataspidae, wherein a specific gut bacterium is vertically transmitted via “symbiont capsule.” In all of the plataspid species, females produced symbiont capsules upon oviposition and their gut exhibited specialized traits for capsule production. Phylogenetic analysis showed that the plataspid symbionts constituted a distinct group in the γ-Proteobacteria, whose sister group was the aphid obligate endocellular symbionts Buchnera. Removal of the symbionts resulted in retarded growth, mortality, and sterility of the insects. The host phylogeny perfectly agreed with the symbiont phylogeny, indicating strict host-symbiont cospeciation despite the extracellular association. The symbionts exhibited AT-biased nucleotide composition, accelerated molecular evolution, and reduced genome size, as has been observed in obligate endocellular insect symbionts. These findings suggest that not the endocellular conditions themselves but the population genetic attributes of the vertically transmitted symbionts are probably responsible for the peculiar genetic traits of these insect symbionts. We proposed the designation “Candidatus Ishikawaella capsulata” for the plataspid symbionts. The plataspid stinkbugs, wherein the host-symbiont associations can be easily manipulated, provide a novel system that enables experimental approaches to previously untouched aspects of the insect-microbe mutualism. Furthermore, comparative analyses of the sister groups, the endocellular Buchnera and the extracellular Ishikawaella, would lead to insights into how the different symbiotic lifestyles have affected their genomic evolution. PMID:17032065

  9. Actions of a separately strict cpo-monoid on pointed directed complete posets

    Directory of Open Access Journals (Sweden)

    Halimeh Moghbeli Damaneh

    2015-07-01

    Full Text Available ‎ In the present article‎, ‎we study some categorical properties of the category {$bf‎ Cpo_{Sep}$-$S$} of all {separately strict $S$-cpo's}; cpo's equipped with‎ a compatible right action of a separately strict cpo-monoid $S$ which is‎ strict continuous in each component‎. ‎In particular‎, we show that this category is reflective and coreflective in the‎ category of $S$-cpo's‎, ‎find the free and cofree functors‎, characterize products and coproducts‎. ‎Furthermore‎, ‎epimorphisms and‎  monomorphisms in {$bf Cpo_{Sep}$-$S$} are studied‎, ‎and show that‎ {$bf Cpo_{Sep}$-$S$} is not cartesian closed‎.

  10. Switching of bacterial adhesion to a glycosylated surface by reversible reorientation of the carbohydrate ligand

    DEFF Research Database (Denmark)

    Weber, Theresa; Chrasekaran, Vijayan; Stamer, Insa

    2014-01-01

    The surface recognition in many biological systems is guided by the interaction of carbohydrate-specific proteins (lectins) with carbohydrate epitopes (ligands) located within the unordered glycoconjugate layer (glycocalyx) of cells. Thus, for recognition, the respective ligand has to reorient...

  11. The photon is no strict particle and nonlocality is far from being proven

    Energy Technology Data Exchange (ETDEWEB)

    Greulich, Karl Otto [Fritz Lipmann Institut, Jena (Germany)

    2010-07-01

    Two aspects of philosophical discussions on physics are the wave particle dualism and non locality including entanglement. However the strict particle aspect of the photon, in the common sense view, has never been proven. The accumulation time argument, the only experimental verification of a strictly particle like photon, has so far not yet been satisfied. Also, experiments thought to prove nonlocality have loophole which have so far not yet been safely closed, and now an even more serious loophole emerges. Thus, also nonlocality cannot be seen as proven. This demands some fine tuning of philosophical discussions on critical experiments in physics.

  12. Characterizing common substructures of ligands for GPCR protein subfamilies.

    Science.gov (United States)

    Erguner, Bekir; Hattori, Masahiro; Goto, Susumu; Kanehisa, Minoru

    2010-01-01

    The G-protein coupled receptor (GPCR) superfamily is the largest class of proteins with therapeutic value. More than 40% of present prescription drugs are GPCR ligands. The high therapeutic value of GPCR proteins and recent advancements in virtual screening methods gave rise to many virtual screening studies for GPCR ligands. However, in spite of vast amounts of research studying their functions and characteristics, 3D structures of most GPCRs are still unknown. This makes target-based virtual screenings of GPCR ligands extremely difficult, and successful virtual screening techniques rely heavily on ligand information. These virtual screening methods focus on specific features of ligands on GPCR protein level, and common features of ligands on higher levels of GPCR classification are yet to be studied. Here we extracted common substructures of GPCR ligands of GPCR protein subfamilies. We used the SIMCOMP, a graph-based chemical structure comparison program, and hierarchical clustering to reveal common substructures. We applied our method to 850 GPCR ligands and we found 53 common substructures covering 439 ligands. These substructures contribute to deeper understanding of structural features of GPCR ligands which can be used in new drug discovery methods.

  13. More strictly protected areas are not necessarily more protective: evidence from Bolivia, Costa Rica, Indonesia, and Thailand

    International Nuclear Information System (INIS)

    Ferraro, Paul J; Hanauer, Merlin M; Miteva, Daniela A; Pattanayak, Subhrendu K; Canavire-Bacarreza, Gustavo Javier; Sims, Katharine R E

    2013-01-01

    National parks and other protected areas are at the forefront of global efforts to protect biodiversity and ecosystem services. However, not all protection is equal. Some areas are assigned strict legal protection that permits few extractive human uses. Other protected area designations permit a wider range of uses. Whether strictly protected areas are more effective in achieving environmental objectives is an empirical question: although strictly protected areas legally permit less anthropogenic disturbance, the social conflicts associated with assigning strict protection may lead politicians to assign strict protection to less-threatened areas and may lead citizens or enforcement agents to ignore the strict legal restrictions. We contrast the impacts of strictly and less strictly protected areas in four countries using IUCN designations to measure de jure strictness, data on deforestation to measure outcomes, and a quasi-experimental design to estimate impacts. On average, stricter protection reduced deforestation rates more than less strict protection, but the additional impact was not always large and sometimes arose because of where stricter protection was assigned rather than regulatory strictness per se. We also show that, in protected area studies contrasting y management regimes, there are y 2 policy-relevant impacts, rather than only y, as earlier studies have implied. (letter)

  14. Strict Monotonicity and Unique Continuation for the Third-Order Spectrum of Biharmonic Operator

    Directory of Open Access Journals (Sweden)

    Khalil Ben Haddouch

    2012-01-01

    Full Text Available We will study the spectrum for the biharmonic operator involving the laplacian and the gradient of the laplacian with weight, which we call third-order spectrum. We will show that the strict monotonicity of the eigenvalues of the operator , where , holds if some unique continuation property is satisfied by the corresponding eigenfunctions.

  15. "Let the Master Respond": Should Schools Be Strictly Liable When Employees Sexually Abuse Children?

    Science.gov (United States)

    Fossey, Richard; DeMitchell, Todd

    Although sexual abuse against children is a problem in the public schools, school officials have generally not acted aggressively to stop it. This paper argues for a strict liability standard--the assessment of liability without fault--against a school district in cases of student sexual abuse by a school employee. Part 1 explores the principle of…

  16. Detection of low numbers of microplastics in North Sea fish using strict quality assurance criteria

    NARCIS (Netherlands)

    Hermsen, E.; Pompe, R.; Besseling, E.; Koelmans, A.A.

    2017-01-01

    We investigated 400 individual fish of four North Sea species: Atlantic Herring, Sprat, Common Dab, and Whiting on ingestion of > 20 μm microplastic. Strict quality assurance criteria were followed in order to control contamination during the study. Two plastic particles were found in only 1 (a

  17. History, administration, goals, values, and long-term data of Russia's strictly protected scientific nature reserves

    Science.gov (United States)

    Martin A. Spetich; Anna E. Kvashnina; Y.D. Nukhimovskya; Olin E. Jr. Rhodes

    2009-01-01

    One of the most comprehensive attempts at biodiversity conservation in Russia and the former Soviet Union has been the establishment of an extensive network of protected natural areas. Among all types of protected areas in Russia, zapovedniks (strictly protected scientific preserve) have been the most effective in protecting biodiversity at the ecosystem scale. Russia...

  18. The Preventive Effect of Strict Gun Control Laws on Suicide and Homicide.

    Science.gov (United States)

    Lester, David; Murrell, Mary E.

    1982-01-01

    Examined state gun control laws and used a multidimensional scaling technique to study the relationship of strictness and death rates. Results showed states with stricter laws had lower suicide rates by firearms but higher rates by other means. No effect on homicide was found. (JAC)

  19. Ligand based pharmacophore modelling of anticancer histone ...

    African Journals Online (AJOL)

    like myocardium damage and bone marrow depression even leading to cell death have been observed in the treatment of caner cells using HDAC inhibitors. The discovery and development of type-specific HDAC inhibitors is of both research and clinical interests. Ligand based pharmacophore modelling is playing a key ...

  20. Sterically demanding iminopyridine ligands

    NARCIS (Netherlands)

    Irrgang, Torsten; Keller, Sandra; Maisel, Heidi; Kretschmer, Winfried; Kempe, Rhett

    Two sterically demanding iminopyridine ligands, (2,6-diisopropylphenyl)[6-(2,4,6-triisopropylphenyl)pyridin-2-ylmeth- ylene]amine and (2,6-diisopropylphenyl)]6-(2,6-dimethylphenyl)pyridin-2-ylmethylene]amine, were prepared by a two-step process: first, condensation of 6-bromopyridine-2-carbaldehyde

  1. Effects of PPARγ ligands on vascular tone.

    Science.gov (United States)

    Salomone, Salvatore; Drago, Filippo

    2012-06-01

    Peroxisome Proliferator-Activated Receptor γ (PPARγ), originally described as a transcription factor for genes of carbohydrate and lipid metabolism, has been more recently studied in the context of cardiovascular pathophysiology. Here, we review the available data on PPARγ ligands as modulator of vascular tone. PPARγ ligands include: thiazolidinediones (used in the treatment of type 2 diabetes mellitus), glitazars (bind and activate both PPARγ and PPARα), and other experimental drugs (still in development) that exploit the chemistry of thiazolidinediones as a scaffold for PPARγ-independent pharmacological properties. In this review, we examine both short (mostly from in vitro data)- and long (mostly from in vivo data)-term effects of PPARγ ligands that extend from PPARγ-independent vascular effects to PPARγ-dependent gene expression. Because endothelium is a master regulator of vascular tone, we have attempted to differentiate between endothelium-dependent and endothelium-independent effects of PPARγ ligands. Based on available data, we conclude that PPARγ ligands appear to influence vascular tone in different experimental paradigms, most often in terms of vasodilatation (potentially increasing blood flow to some tissues). These effects on vascular tone, although potentially beneficial, must be weighed against specific cardiovascular warnings that may apply to some drugs, such as rosiglitazone.

  2. Analysis of macromolecules, ligands and macromolecule-ligand complexes

    Science.gov (United States)

    Von Dreele, Robert B [Los Alamos, NM

    2008-12-23

    A method for determining atomic level structures of macromolecule-ligand complexes through high-resolution powder diffraction analysis and a method for providing suitable microcrystalline powder for diffraction analysis are provided. In one embodiment, powder diffraction data is collected from samples of polycrystalline macromolecule and macromolecule-ligand complex and the refined structure of the macromolecule is used as an approximate model for a combined Rietveld and stereochemical restraint refinement of the macromolecule-ligand complex. A difference Fourier map is calculated and the ligand position and points of interaction between the atoms of the macromolecule and the atoms of the ligand can be deduced and visualized. A suitable polycrystalline sample of macromolecule-ligand complex can be produced by physically agitating a mixture of lyophilized macromolecule, ligand and a solvent.

  3. Radiobiology with DNA ligands

    International Nuclear Information System (INIS)

    Weinreich, R.; Argentini, M.; Guenther, I.; Koziorowski, J.; Larsson, B.; Nievergelt-Egido, M.C.; Salt, C.; Wyer, L.; Dos Santos, D.F.; Hansen, H.J.

    1997-01-01

    The paper deals with the following topics: labelling of DNA ligands and other tumour-affinic compounds with 4.15-d 124 I, radiotoxicity of Hoechst 33258 and 33342 and of iodinated Hoechst 33258 in cell cultures, preparation of 76 Br-, 123 I-, and 221 At-labelled 5-halo-2'-deoxyuridine, chemical syntheses of boron derivatives of Hoechst 33258.III., Gadolinium neutron capture therapy

  4. Therapeutic androgen receptor ligands

    Science.gov (United States)

    Allan, George F.; Sui, Zhihua

    2003-01-01

    In the past several years, the concept of tissue-selective nuclear receptor ligands has emerged. This concept has come to fruition with estrogens, with the successful marketing of drugs such as raloxifene. The discovery of raloxifene and other selective estrogen receptor modulators (SERMs) has raised the possibility of generating selective compounds for other pathways, including androgens (that is, selective androgen receptor modulators, or SARMs). PMID:16604181

  5. Characterization of Ligand Shell for Mixed-Ligand Coated Gold Nanoparticles.

    Science.gov (United States)

    Ong, Quy; Luo, Zhi; Stellacci, Francesco

    2017-08-15

    Gold nanoparticles owe a large number of their properties to their ligand shell. Indeed, many researchers routinely use mixtures of ligand molecules for their nanoparticles to impart complex property sets. It has been shown that the morphology of ligand shells (e.g., Janus, random, stripelike) leads to specific properties. Examples include wettability, solubility, protein nonspecific adsorption, cell penetration, catalysis, and cation-capturing abilities. Yet, it remains a great challenge to evaluate such morphologies in even the most fundamental terms such as dimension and shape. In this Account, we review recent progress in characterization techniques applicable to gold nanoparticles with ligand shells composed of mixed ligands. We divide the characterization into three major categories, namely, microscopy, spectroscopy, and simulation. In microscopy, we review progresses in scanning tunneling microscopy (STM), atomic force microscopy (AFM), and scanning/transmission electron microscopy. In spectroscopy, we mainly highlight recent achievements in nuclear magnetic resonance (NMR), mass spectrometry (MS), small angle neutron scattering (SANS), electron spin resonance (EPR), and adsorption based spectroscopies. In simulation, we point out the latest results in understanding thermodynamic stability of ligand shell morphology and emphasize the role of computer simulation for helping interpretation of experimental data. We conclude with a perspective of future development.

  6. A Criterium for the Strict Positivity of the Density of the Law of a Poisson Process

    Directory of Open Access Journals (Sweden)

    Léandre Rémi

    2011-01-01

    Full Text Available We translate in semigroup theory our result (Léandre, 1990 giving a necessary condition so that the law of a Markov process with jumps could have a strictly positive density. This result express, that we have to jump in a finite number of jumps in a "submersive" way from the starting point to the end point if the density of the jump process is strictly positive in . We use the Malliavin Calculus of Bismut type of (Léandre, (2008;2010 translated in semi-group theory as a tool, and the interpretation in semi-group theory of some classical results of the stochastic analysis for Poisson process as, for instance, the formula giving the law of a compound Poisson process.

  7. The effect of 8 days of strict bed rest on the incretin effect in healthy volunteers

    DEFF Research Database (Denmark)

    Nielsen, Signe Tellerup; Harder-Lauridsen, Nina Majlund; Benatti, Fabiana Braga

    2016-01-01

    in the levels of GLP-1 and Glucagon. Bed rest led to a mean loss of 2.4 kg of fat-free mass, and induced insulin resistance evaluated by the Matsuda index, but did not affect the incretin effect (P = 0.6). In conclusion, 8 days of bed rest induces insulin resistance, but we did not see evidence of an associated......Bed rest and physical inactivity are the consequences of hospital admission for many patients. Physical inactivity induces changes in glucose metabolism, but its effect on the incretin effect, which is reduced in, e.g., Type 2 diabetes, is unknown. To investigate how 8 days of strict bed rest...... affects the incretin effect, 10 healthy nonobese male volunteers underwent 8 days of strict bed rest. Before and after the intervention, all volunteers underwent an oral glucose tolerance test (OGTT) followed by an intravenous glucose infusion (IVGI) on the following day to mimic the blood glucose profile...

  8. Detection of low numbers of microplastics in North Sea fish using strict quality assurance criteria.

    Science.gov (United States)

    Hermsen, Enya; Pompe, Renske; Besseling, Ellen; Koelmans, Albert A

    2017-09-15

    We investigated 400 individual fish of four North Sea species: Atlantic Herring, Sprat, Common Dab, and Whiting on ingestion of >20μm microplastic. Strict quality assurance criteria were followed in order to control contamination during the study. Two plastic particles were found in only 1 (a Sprat) out of 400 individuals (0.25%, with a 95% confidence interval of 0.09-1.1%). The particles were identified to consist of polymethylmethacrylate (PMMA) through FTIR spectroscopy. No contamination occurred during the study, showing the method applied to be suitable for microplastic ingestion studies in biota. We discuss the low particle count for North Sea fish with those in other studies and suggest a relation between reported particle count and degree of quality assurance applied. Microplastic ingestion by fish may be less common than thought initially, with low incidence shown in this study, and other studies adhering to strict quality assurance criteria. Copyright © 2017 Elsevier Ltd. All rights reserved.

  9. A strict anaerobic extreme thermophilic hydrogen-producing culture enriched from digested household waste

    DEFF Research Database (Denmark)

    Karakashev, Dimitar Borisov; Kotay, Shireen Meher; Trably, Eric

    2009-01-01

    sources. Growth on glucose produced acetate, H-2 and carbon dioxide. Maximal H-2 production rate on glucose was 1.1 mmol l(-1) h(-1) with a maximum H-2 yield of 1.9 mole H-2 per mole glucose. 16S ribosomal DNA clone library analyses showed that the culture members were phylogenetically affiliated......The aim of this study was to enrich, characterize and identify strict anaerobic extreme thermophilic hydrogen (H-2) producers from digested household solid wastes. A strict anaerobic extreme thermophilic H-2 producing bacterial culture was enriched from a lab-scale digester treating household...... wastes at 70 degrees C. The enriched mixed culture consisted of two rod-shaped bacterial members growing at an optimal temperature of 80 degrees C and an optimal pH 8.1. The culture was able to utilize glucose, galactose, mannose, xylose, arabinose, maltose, sucrose, pyruvate and glycerol as carbon...

  10. A Hybrid P2P Overlay Network for Non-strictly Hierarchically Categorized Content

    Science.gov (United States)

    Wan, Yi; Asaka, Takuya; Takahashi, Tatsuro

    In P2P content distribution systems, there are many cases in which the content can be classified into hierarchically organized categories. In this paper, we propose a hybrid overlay network design suitable for such content called Pastry/NSHCC (Pastry for Non-Strictly Hierarchically Categorized Content). The semantic information of classification hierarchies of the content can be utilized regardless of whether they are in a strict tree structure or not. By doing so, the search scope can be restrained to any granularity, and the number of query messages also decreases while maintaining keyword searching availability. Through simulation, we showed that the proposed method provides better performance and lower overhead than unstructured overlays exploiting the same semantic information.

  11. Weak asymptotic solution for a non-strictly hyperbolic system of conservation laws-II

    Directory of Open Access Journals (Sweden)

    Manas Ranjan Sahoo

    2016-04-01

    Full Text Available In this article we introduce a concept of entropy weak asymptotic solution for a system of conservation laws and construct the same for a prolonged system of conservation laws which is highly non-strictly hyperbolic. This is first done for Riemann type initial data by introducing $\\delta,\\delta',\\delta''$ waves along a discontinuity curve and then for general initial data by piecing together the Riemann solutions.

  12. Multiple-Set Split Feasibility Problems for κ-Strictly Pseudononspreading Mapping in Hilbert Spaces

    Directory of Open Access Journals (Sweden)

    Jing Quan

    2013-01-01

    Full Text Available The purpose of this paper is to prove some weak and strong convergence theorems for solving the multiple-set split feasibility problems for κ-strictly pseudononspreading mapping in infinite-dimensional Hilbert spaces by using the proposed iterative method. The main results presented in this paper extend and improve the corresponding results of Xu et al. (2006, of Osilike et al. (2011, and of many other authors.

  13. Multiobjective Optimization for the Forecasting Models on the Base of the Strictly Binary Trees

    OpenAIRE

    Nadezhda Astakhova; Liliya Demidova; Evgeny Nikulchev

    2016-01-01

    The optimization problem dealing with the development of the forecasting models on the base of strictly binary trees has been considered. The aim of paper is the comparative analysis of two optimization variants which are applied for the development of the forecasting models. Herewith the first optimization variant assumes the application of one quality indicator of the forecasting model named as the affinity indicator and the second variant realizes the application of two quality indicators ...

  14. Cannabis legalization with strict regulation, the overall superior policy option for public health.

    Science.gov (United States)

    Rehm, J; Fischer, B

    2015-06-01

    Cannabis is the most prevalently used drug globally, with many jurisdictions considering varying reform options to current policies to deal with this substance and associated harm. Three policy options are available: prohibition, decriminalization, and legalization, with prohibition currently the dominant model globally. This contribution gives reasons why legalization with strict regulation should be considered superior to other options with respect to public health in high income countries in North America. © 2015 ASCPT.

  15. related apoptosis-inducing ligand in transplastomic tobacco

    African Journals Online (AJOL)

    -inducing ligand (sTRAIL) can, as the whole length TRAIL protein, bind with its receptors and specifically induce the apoptosis of cancer cells; therefore, it has been developed as a potential therapeutic agent for various cancer treatments.

  16. THERMODYNAMICS OF PROTEIN-LIGAND INTERACTIONS AND THEIR ANALYSIS

    Directory of Open Access Journals (Sweden)

    Rummi Devi Saini

    2017-11-01

    Full Text Available Physiological processes are controlled mainly by intermolecular recognition mechanisms which involve protein–protein and protein–ligand interactions with a high specificity and affinity to form a specific complex. Proteins being an important class of macromolecules in biological systems, it is important to understand their actions through binding to other molecules of proteins or ligands. In fact, the binding of low molecular weight ligands to proteins plays a significant role in regulating biological processes such as cellular metabolism and signal transmission. Therefore knowledge of the protein–ligand interactions and the knowledge of the mechanisms involved in the protein-ligand recognition and binding are key in understanding biology at molecular level which will facilitate the discovery, design, and development of drugs. In this review, the mechanisms involved in protein–ligand binding, the binding kinetics, thermodynamic concepts and binding driving forces are discussed. Thermodynamic mechanisms involved in a few important protein-ligand binding are described. Various spectroscopic, non-spectroscopic and computational method for analysis of protein–ligand binding are also discussed.

  17. Examination of the PCICE method in the nearly incompressible, as well as strictly incompressible, limits

    International Nuclear Information System (INIS)

    Berry, Ray A.; Martineau, Richard C.

    2007-01-01

    The conservative-form, pressure-based PCICE numerical method (Martineau and Berry, 2004) (Berry, 2006), recently developed for computing transient fluid flows of all speeds from very low to very high (with strong shocks), is simplified and generalized. Though the method automatically treats a continuous transition of compressibility, three distinct, limiting compressibility regimes are formally defined for purposes of discussion and comparison with traditional methods - the strictly incompressible limit, the nearly incompressible limit, and the fully compressible limit. The PCICE method's behavior is examined in each limiting regime. In the strictly incompressible limit the PCICE algorithm reduces to the traditional MAC-type method with velocity divergence driving the pressure Poisson equation. In the nearly incompressible limit the PCICE algorithm is found to reduce to a generalization of traditional incompressible methods, i.e. to one in which not only the velocity divergence effect, but also the density gradient effect is included as a driving function in the pressure Poisson equation. This nearly incompressible regime has received little attention, and it appears that in the past, strictly incompressible methods may have been conveniently applied to flows in this regime at the expense of ignoring a potentially important coupling mechanism. This could be significant in many important flows; for example, in natural convection flows resulting from high heat flux. In the fully compressible limit or regime, the algorithm is found to reduce to an expression equivalent to density-based methods for high-speed flow. (author)

  18. Frequency effect on p-nitrophenol degradation under conditions of strict acoustic and electric control

    Directory of Open Access Journals (Sweden)

    Chang-ping Zhu

    2011-03-01

    Full Text Available The process of decomposing p-nitrophenol (PNP with power ultrasound requires strict control of acoustic and electric conditions. In this study, the conditions, including acoustic power and acoustic intensity, but not ultrasonic frequency, were controlled strictly at constant levels. The absorbency and the COD concentrations of the samples were measured in order to show the variation of the sample concentration. The results show significant differences in the trend of the solution degradation rate as acoustic power increases after the PNP solution (with a concentration of 114 mg/L and a pH value of 5.4 is irradiated for 60 min with ultrasonic frequencies of 530.8 kHz, 610.6 kHz, 855.0 kHz, and 1 130.0 kHz. The degradation rate of the solution increases with time and acoustic power (acoustic intensity. On the other hand, the degradation rate of the solution is distinctly dependent on frequency when the acoustic power and intensity are strictly controlled and maintained at constant levels. The degradation rate of the PNP solution declines with ultrasonic frequencies of 530.8 kHz, 610.6 kHz, 855.0 kHz, and 1 130.0 kHz; the COD concentration, on the contrary, increase.

  19. TESTING STRICT HYDROSTATIC EQUILIBRIUM IN SIMULATED CLUSTERS OF GALAXIES: IMPLICATIONS FOR A1689

    International Nuclear Information System (INIS)

    Molnar, S. M.; Umetsu, K.; Chiu, I.-N.; Chen, P.; Hearn, N.; Broadhurst, T.; Bryan, G.; Shang, C.

    2010-01-01

    Accurate mass determination of clusters of galaxies is crucial if they are to be used as cosmological probes. However, there are some discrepancies between cluster masses determined based on gravitational lensing and X-ray observations assuming strict hydrostatic equilibrium (i.e., the equilibrium gas pressure is provided entirely by thermal pressure). Cosmological simulations suggest that turbulent gas motions remaining from hierarchical structure formation may provide a significant contribution to the equilibrium pressure in clusters. We analyze a sample of massive clusters of galaxies drawn from high-resolution cosmological simulations and find a significant contribution (20%-45%) from non-thermal pressure near the center of relaxed clusters, and, in accord with previous studies, a minimum contribution at about 0.1 R vir , growing to about 30%-45% at the virial radius, R vir . Our results strongly suggest that relaxed clusters should have significant non-thermal support in their core region. As an example, we test the validity of strict hydrostatic equilibrium in the well-studied massive galaxy cluster A1689 using the latest high-resolution gravitational lensing and X-ray observations. We find a contribution of about 40% from non-thermal pressure within the core region of A1689, suggesting an alternate explanation for the mass discrepancy: the strict hydrostatic equilibrium is not valid in this region.

  20. Temporary Strict Maternal Avoidance of Cow’s Milk and Infantile Colic

    Directory of Open Access Journals (Sweden)

    Firoozeh Sajedi

    2009-12-01

    Full Text Available Infant colic is a common problem characterized by excessive crying and fussing. We examined whether colic symptoms of exclusively breast-milk-fed infants would be improved by temporary strict maternal avoidance of cows milk. This study is analytic and experimental. Sixty-six subjects were recruited during winter of 2006 from a clinic in Isfahan, Iran. Breast-milk-fed in-fants with "colic", age 3-6 months and to be in otherwise good health were referred by pediatri-cians. The intervention was 1 week period of strict maternal avoidance of cows milk while they continued exclusive breast-milk-feeding. All infants showed improvement in distressed behavior (crying and fussing during intervention. The total recorded crying and fussing time was reduced by an average of 31%. A significant difference was found in cry and fuss time between first and last 2 days of intervention (P = 0.000. Cows milk proteins may play an etiologic role in colic. We propose that a brief intervention with strict maternal avoidance of cows milk may be an effective treatment for colic in some breast-milk-fed infants.

  1. Rate Control Efficacy in Permanent Atrial Fibrillation : Successful and Failed Strict Rate Control Against a Background of Lenient Rate Control

    NARCIS (Netherlands)

    Groenveld, Hessel F.; Tijssen, Jan G. P.; Crijns, Harry J. G. M.; Van den Berg, Maarten P.; Hillege, Hans L.; Alings, Marco; Van Veldhuisen, Dirk J.; Van Gelder, Isabelle C.

    2013-01-01

    Objectives This study sought to investigate differences in outcome between patients treated with successful strict, failed strict, and lenient rate control. Background The RACE II (Rate Control Efficacy in Permanent Atrial Fibrillation) study showed no difference in outcome between lenient and

  2. GLIDA: GPCR-ligand database for chemical genomic drug discovery.

    Science.gov (United States)

    Okuno, Yasushi; Yang, Jiyoon; Taneishi, Kei; Yabuuchi, Hiroaki; Tsujimoto, Gozoh

    2006-01-01

    G-protein coupled receptors (GPCRs) represent one of the most important families of drug targets in pharmaceutical development. GPCR-LIgand DAtabase (GLIDA) is a novel public GPCR-related chemical genomic database that is primarily focused on the correlation of information between GPCRs and their ligands. It provides correlation data between GPCRs and their ligands, along with chemical information on the ligands, as well as access information to the various web databases regarding GPCRs. These data are connected with each other in a relational database, allowing users in the field of GPCR-related drug discovery to easily retrieve such information from either biological or chemical starting points. GLIDA includes structure similarity search functions for the GPCRs and for their ligands. Thus, GLIDA can provide correlation maps linking the searched homologous GPCRs (or ligands) with their ligands (or GPCRs). By analyzing the correlation patterns between GPCRs and ligands, we can gain more detailed knowledge about their interactions and improve drug design efforts by focusing on inferred candidates for GPCR-specific drugs. GLIDA is publicly available at http://gdds.pharm.kyoto-u.ac.jp:8081/glida. We hope that it will prove very useful for chemical genomic research and GPCR-related drug discovery.

  3. Strict versus liberal insulin therapy in the cardiac surgery patient: An evidence-based practice development, implementation and evaluation project.

    Science.gov (United States)

    Gordon, Jacqueline M; Lauver, Lori S; Buck, Harleah G

    2018-02-01

    Hyperglycemia post-cardiac surgery is associated with poor clinical outcomes. Recent studies suggest maintaining liberal glycemic control (liberal CII protocol. Retrospective review of 144 strict CII patient records and 147 liberal CII patient records. Mean blood glucose was 159.8mg/dL (liberal CII) compared to 143.3mg/dL (strict CII) (p≤0.001). No surgical site infections occurred in either group. Mean ICU length of stay was 4.5days (liberal) versus 4.4days (strict) (p=0.74). Two 30-day mortalities occurred for the liberal cohort compared to no deaths in the strict group (p=0.49). Hypoglycemia incidence within 24h after surgery was 0.1% (liberal) compared to 0.3% (strict) compared to (p=0.16). Use of a nurse managed liberal CII resulted in similar outcomes with fewer incidents of hypoglycemia. Copyright © 2017. Published by Elsevier Inc.

  4. Effects of growth temperature and strictly anaerobic recovery on the survival of Listeria monocytogenes during pasteurization.

    Science.gov (United States)

    Knabel, S J; Walker, H W; Hartman, P A; Mendonca, A F

    1990-02-01

    Listeria monocytogenes F5069 was suspended in either Trypticase soy broth-0.6% yeast extract (TSBYE) or sterile, whole milk and heated at 62.8 degrees C in sealed thermal death time tubes. Severely heat-injured cells were recovered in TSBYE within sealed thermal death time tubes because of the formation of reduced conditions in the depths of the TSBYE. Also, the use of strictly anaerobic Hungate techniques significantly increased recovery in TSBYE containing 1.5% agar compared with aerobically incubated controls. The exogenous addition of catalase, but not superoxide dismutase, slightly increased the recovery of heat-injured cells in TSBYE containing 1.5% agar incubated aerobically. Growth of cells at 43 degrees C caused a greater increase in heat resistance as compared with cells heat shocked at 43 degrees C or cells grown at lower temperatures. Growth of L. monocytogenes at 43 degrees C and enumeration by the use of strictly anaerobic Hungate techniques resulted in D62.8 degrees C values that were at least sixfold greater than those previously obtained by using cells grown at 37 degrees C and aerobic plating. Results indicate that, under the conditions of the present study, high levels of L. monocytogenes would survive the minimum low-temperature, long-time treatment required by the U.S. Food and Drug Administration for pasteurizing milk. The possible survival of low levels of L. monocytogenes during high-temperature, short-time pasteurization and enumeration of injured cells by recovery on selective media under strictly anaerobic conditions are discussed.

  5. RelTime Rates Collapse to a Strict Clock When Estimating the Timeline of Animal Diversification.

    Science.gov (United States)

    Lozano-Fernandez, Jesus; Dos Reis, Mario; Donoghue, Philip C J; Pisani, Davide

    2017-05-01

    Establishing an accurate timescale for the history of life is crucial to understand evolutionary processes. For this purpose, relaxed molecular clock models implemented in a Bayesian MCMC framework are generally used. However, these methods are time consuming. RelTime, a non-Bayesian method implementing a fast, ad hoc, algorithm for relative dating, was developed to overcome the computational inefficiencies of Bayesian software. RelTime was recently used to investigate the timing of origin of animals, yielding results consistent with early strict clock studies from the 1980s and 1990s, estimating metazoans to have a Mesoproterozoic origin-over a billion years ago. RelTime results are unexpected and disagree with the largest majority of modern, relaxed, Bayesian molecular clock analyses, which suggest animals originated in the Tonian-Cryogenian (less that 850 million years ago). Here, we demonstrate that RelTime-inferred divergence times for the origin of animals are spurious, a consequence of the inability of RelTime to relax the clock along the internal branches of the animal phylogeny. RelTime-inferred divergence times are comparable to strict-clock estimates because they are essentially inferred under a strict clock. Our results warn us of the danger of using ad hoc algorithms making implicit assumptions about rate changes along a tree. Our study roundly rejects a Mesoproterozoic origin of animals; metazoans emerged in the Tonian-Cryogenian, and diversified in the Ediacaran, in the immediate prelude to the routine fossilization of animals in the Cambrian associated with the emergence of readily preserved skeletons. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  6. Crystal structure of thioflavin T bound to the peripheral site of Torpedo californica acetylcholinesterase reveals how thioflavin T acts as a sensitive fluorescent reporter of ligand binding to the acylation site.

    Science.gov (United States)

    Harel, Michal; Sonoda, Leilani K; Silman, Israel; Sussman, Joel L; Rosenberry, Terrone L

    2008-06-25

    Acetylcholinesterase plays a key role in cholinergic synaptic transmission by hydrolyzing the neurotransmitter acetylcholine with one of the highest known catalytic rate constants. Hydrolysis occurs in a narrow and deep gorge that contains two sites of ligand binding: A peripheral site, or P-site, near the gorge entrance that contributes to catalytic efficiency both by transiently trapping substrate molecules as they enter the gorge and by allosterically accelerating the transfer of the substrate acyl group to a serine hydroxyl in an acylation site or A-site at the base of the gorge. Thioflavin T is a useful reporter of ligand interactions with the A-site. It binds specifically to the P-site with fluorescence that is enhanced approximately 1000-fold over that of unbound thioflavin T, and the enhanced fluorescence is quenched 1.5- to 4-fold when another ligand binds to the A-site in a ternary complex. To clarify the structural basis of this advantageous signal change, we here report the X-ray structure of the complex of thioflavin T with Torpedo californica acetylcholinesterase. The two aromatic rings in thioflavin T are coplanar and are packed snugly parallel to the aromatic side chains of Trp279, Tyr334, and Phe330. Overlays of this structure with the crystal structures of Torpedo californica acetylcholinesterase complexes with either edrophonium or m-( N, N, N-trimethylammonio)-2,2,2-trifluoroacetophenone, two small aromatic ligands that bind specifically to the A-site, indicate that the phenyl side chain of Phe330 must rotate to sterically accommodate both thioflavin T and the A-site ligand in the ternary complex. This rotation may allow some relaxation of the strict coplanarity of the aromatic rings in the bound thioflavin T and result in partial quenching of its fluorescence.

  7. Effects of growth temperature and strictly anaerobic recovery on the survival of Listeria monocytogenes during pasteurization.

    OpenAIRE

    Knabel, S J; Walker, H W; Hartman, P A; Mendonca, A F

    1990-01-01

    Listeria monocytogenes F5069 was suspended in either Trypticase soy broth-0.6% yeast extract (TSBYE) or sterile, whole milk and heated at 62.8 degrees C in sealed thermal death time tubes. Severely heat-injured cells were recovered in TSBYE within sealed thermal death time tubes because of the formation of reduced conditions in the depths of the TSBYE. Also, the use of strictly anaerobic Hungate techniques significantly increased recovery in TSBYE containing 1.5% agar compared with aerobicall...

  8. The Dirichlet problem for the Monge-Ampere equation in convex (but not strictly convex domains

    Directory of Open Access Journals (Sweden)

    David Hartenstine

    2006-10-01

    Full Text Available It is well-known that the Dirichlet problem for the Monge-Amp`ere equation $det D^2 u = mu$ in a bounded strictly convex domain $Omega$ in $mathbb{R}^n$ has a weak solution (in the sense of Aleksandrov for any finite Borel measure $mu$ on $Omega$ and for any continuous boundary data. We consider the Dirichlet problem when $Omega$ is only assumed to be convex, and give a necessary and sufficient condition on the boundary data for solvability.

  9. Selections of the metric projection operator and strict solarity of sets with continuous metric projection

    Science.gov (United States)

    Alimov, A. R.

    2017-07-01

    In a broad class of finite-dimensional Banach spaces, we show that a closed set with lower semicontinuous metric projection is a strict sun, admits a continuous selection of the metric projection operator onto it, has contractible intersections with balls, and its (nonempty) intersection with any closed ball is a retract of this ball. For sets with continuous metric projection, a number of new results relating the solarity of such sets to the stability of the operator of best approximation are obtained. Bibliography 25 titles.

  10. Transplanting Diseases from Organ Donors in Western Europe: Fault Liability or Strict Liability?

    Science.gov (United States)

    Broeckx, Nils; Verhoeven, Dimitri

    2015-06-01

    This article will examine the problem of disease transmission through organ transplantation from a civil liability perspective. Both fault liability and strict product liability might be possible. These two types of liability will be compared, while applying them to the actions of the central parties involved in organ donation and transplantation, namely the physician/hospital, the donor and the organ exchange organisation. While product liability is generally an easier way to obtain compensation than fault liability, it might nevertheless place too heavy a burden on the transplant professionals.

  11. Single molecule experiments challenge the strict wave-particle dualism of light.

    Science.gov (United States)

    Greulich, Karl Otto

    2010-01-21

    Single molecule techniques improve our understanding of the photon and light. If the single photon double slit experiment is performed at the "single photon limit" of a multi-atom light source, faint light pulses with more than one photon hamper the interpretation. Single molecules, quantum dots or defect centres in crystals should be used as light source. "Single photon detectors" do not meet their promise-only "photon number resolving single photon detectors" do so. Particularly, the accumulation time argument, the only safe basis for the postulate of a strictly particle like photon, has so far not yet been verified.

  12. Single Molecule Experiments Challenge the Strict Wave-Particle Dualism of Light

    Directory of Open Access Journals (Sweden)

    Karl Otto Greulich

    2010-01-01

    Full Text Available Single molecule techniques improve our understanding of the photon and light. If the single photon double slit experiment is performed at the “single photon limit” of a multi-atom light source, faint light pulses with more than one photon hamper the interpretation. Single molecules, quantum dots or defect centres in crystals should be used as light source. “Single photon detectors” do not meet their promise―only “photon number resolving single photon detectors” do so. Particularly, the accumulation time argument, the only safe basis for the postulate of a strictly particle like photon, has so far not yet been verified.

  13. Spatio-temporal regulation of Hsp90-ligand complex leads to immune activation.

    Directory of Open Access Journals (Sweden)

    Yasuaki eTamura

    2016-05-01

    Full Text Available Hsp90 is the most abundant cytosolic HSP and is known to act as a molecular chaperone. We found that an Hsp90-cancer antigen peptide complex was efficiently cross-presented by human monocyte-derived dendritic cells and induced peptide-specific cytotoxic T lymphocytes. Furthermore, we observed that the internalized Hsp90-peptide complex was strictly sorted to the Rab5+, EEA1+ static early endosome and the Hsp90-chaperoned peptide was processed and bound to MHC class I molecules through a endosome-recycling pathway. We also found that extracellular Hsp90 complexed with CpG-A or self-DNA stimulates production of a large amount of IFN-α from pDCs via static early endosome targeting. Thus, extracellular Hsp90 can target the antigen or nucleic acid to a static early endosome by spatio-temporal regulation. Moreover, we showed that Hsp90 associates with and delivers TLR7/9 from the ER to early endosomes for ligand recognition. Hsp90 inhibitor, geldanamycin derivative inhibited the Hsp90 association with TLR7/9, resulting in inhibition IFN-α production, leading to improvement of SLE symptoms. Interstingly, we observed that serum Hsp90 is clearly increased in patients with active SLE compared with that in patients with inactive disease. Serum Hsp90 detected in SLE patients binds to self-DNA and/or anti-DNA Ab, thus leading to stimulation of pDCs to produce IFN-α. Thus, Hsp90 plays a crucial role in the pathogenesis of SLE and that an Hsp90 inhibitor will therefore provide a new therapeutic approach to SLE and other nucleic acid-related autoimmune diseases. We will discuss how spatio-temporal regulation of Hsp90-ligand complexes within antigen-presenting cells affects the innate immunity and adaptive immunity.

  14. Ligand Depot: a data warehouse for ligands bound to macromolecules.

    Science.gov (United States)

    Feng, Zukang; Chen, Li; Maddula, Himabindu; Akcan, Ozgur; Oughtred, Rose; Berman, Helen M; Westbrook, John

    2004-09-01

    Ligand Depot is an integrated data resource for finding information about small molecules bound to proteins and nucleic acids. The initial release (version 1.0, November, 2003) focuses on providing chemical and structural information for small molecules found as part of the structures deposited in the Protein Data Bank. Ligand Depot accepts keyword-based queries and also provides a graphical interface for performing chemical substructure searches. A wide variety of web resources that contain information on small molecules may also be accessed through Ligand Depot. Ligand Depot is available at http://ligand-depot.rutgers.edu/. Version 1.0 supports multiple operating systems including Windows, Unix, Linux and the Macintosh operating system. The current drawing tool works in Internet Explorer, Netscape and Mozilla on Windows, Unix and Linux.

  15. Fuzzy Adaptive Decentralized Optimal Control for Strict Feedback Nonlinear Large-Scale Systems.

    Science.gov (United States)

    Sun, Kangkang; Sui, Shuai; Tong, Shaocheng

    2018-04-01

    This paper considers the optimal decentralized fuzzy adaptive control design problem for a class of interconnected large-scale nonlinear systems in strict feedback form and with unknown nonlinear functions. The fuzzy logic systems are introduced to learn the unknown dynamics and cost functions, respectively, and a state estimator is developed. By applying the state estimator and the backstepping recursive design algorithm, a decentralized feedforward controller is established. By using the backstepping decentralized feedforward control scheme, the considered interconnected large-scale nonlinear system in strict feedback form is changed into an equivalent affine large-scale nonlinear system. Subsequently, an optimal decentralized fuzzy adaptive control scheme is constructed. The whole optimal decentralized fuzzy adaptive controller is composed of a decentralized feedforward control and an optimal decentralized control. It is proved that the developed optimal decentralized controller can ensure that all the variables of the control system are uniformly ultimately bounded, and the cost functions are the smallest. Two simulation examples are provided to illustrate the validity of the developed optimal decentralized fuzzy adaptive control scheme.

  16. Melatonin: functions and ligands.

    Science.gov (United States)

    Singh, Mahaveer; Jadhav, Hemant R

    2014-09-01

    Melatonin is a chronobiotic substance that acts as synchronizer by stabilizing bodily rhythms. Its synthesis occurs in various locations throughout the body, including the pineal gland, skin, lymphocytes and gastrointestinal tract (GIT). Its synthesis and secretion is controlled by light and dark conditions, whereby light decreases and darkness increases its production. Thus, melatonin is also known as the 'hormone of darkness'. Melatonin and analogs that bind to the melatonin receptors are important because of their role in the management of depression, insomnia, epilepsy, Alzheimer's disease (AD), diabetes, obesity, alopecia, migraine, cancer, and immune and cardiac disorders. In this review, we discuss the mechanism of action of melatonin in these disorders, which could aid in the design of novel melatonin receptor ligands. Copyright © 2014 Elsevier Ltd. All rights reserved.

  17. Affinity-based methodologies and ligands for antibody purification: advances and perspectives.

    Science.gov (United States)

    Roque, Ana C A; Silva, Cláudia S O; Taipa, M Angela

    2007-08-10

    Many successful, recent therapies for life-threatening diseases such as cancer and rheumatoid arthritis are based on the recognition between native or genetically engineered antibodies and cell-surface receptors. Although naturally produced by the immune system, the need for antibodies with unique specificities and designed for single application, has encouraged the search for novel antibody purification strategies. The availability of these products to the end-consumer is strictly related to manufacture costs, particularly those attributed to downstream processing. Over the last decades, academia and industry have developed different types of interactions and separation techniques for antibody purification, affinity-based strategies being the most common and efficient methodologies. The affinity ligands utilized range from biological to synthetic designed molecules with enhanced resistance and stability. Despite the successes achieved, the purification "paradigm" still moves interests and efforts in the continuous demand for improved separation performances. This review will focus on recent advances and perspectives in antibody purification by affinity interactions using different techniques, with particular emphasis on affinity chromatography.

  18. Database of ligand-induced domain movements in enzymes

    Directory of Open Access Journals (Sweden)

    Hayward Steven

    2009-03-01

    Full Text Available Abstract Background Conformational change induced by the binding of a substrate or coenzyme is a poorly understood stage in the process of enzyme catalysed reactions. For enzymes that exhibit a domain movement, the conformational change can be clearly characterized and therefore the opportunity exists to gain an understanding of the mechanisms involved. The development of the non-redundant database of protein domain movements contains examples of ligand-induced domain movements in enzymes, but this valuable data has remained unexploited. Description The domain movements in the non-redundant database of protein domain movements are those found by applying the DynDom program to pairs of crystallographic structures contained in Protein Data Bank files. For each pair of structures cross-checking ligands in their Protein Data Bank files with the KEGG-LIGAND database and using methods that search for ligands that contact the enzyme in one conformation but not the other, the non-redundant database of protein domain movements was refined down to a set of 203 enzymes where a domain movement is apparently triggered by the binding of a functional ligand. For these cases, ligand binding information, including hydrogen bonds and salt-bridges between the ligand and specific residues on the enzyme is presented in the context of dynamical information such as the regions that form the dynamic domains, the hinge bending residues, and the hinge axes. Conclusion The presentation at a single website of data on interactions between a ligand and specific residues on the enzyme alongside data on the movement that these interactions induce, should lead to new insights into the mechanisms of these enzymes in particular, and help in trying to understand the general process of ligand-induced domain closure in enzymes. The website can be found at: http://www.cmp.uea.ac.uk/dyndom/enzymeList.do

  19. Study on Environment Performance Evaluation and Regional Differences of Strictly-Environmental-Monitored Cities in China

    Directory of Open Access Journals (Sweden)

    Ji Guo

    2017-12-01

    Full Text Available With the rapid economic growth and development, the problem of environmental pollution in China’s cities is becoming increasingly serious, and environmental pollution takes on a regional difference. There is, however, little comprehensive evaluation on the environmental performance and the regional difference of strictly-environmental-monitored cities in China. In this paper, the environmental performance of 109 strictly-environmental-monitored cities in China is evaluated in terms of natural performance, management performance, and scale performance by Data Envelopment Analysis (DEA, incorporating PM2.5 and PM10 as undesirable outputs. The empirical results show that: (1 At present, the natural performance is quite high, while the management performance is noticeably low for most cities. (2 The gap between the level of economic development and environmental protection among cities in China is large, and the scale efficiency of big cities is better than that of smaller cities. The efficiency value of large-scale cities such as Beijing, Shanghai, Guangzhou, Shenzhen, etc. is high, equaling 1; the value of smaller cities such as Sanmenxia, Baoding, Mudanjiang, and Pingdingshan is low, close to 0, indicating that big cities are characterized by high environmental efficiency. (3 From the perspective of region, the level of environmental performance in China is very uneven. For example, the environmental efficiency level of the Pan-Pearl River Delta region is superior to that of the Pan-Yangtze River region and the Bahia Rim region, whose values of environmental efficiency are 0.858, 0.658, and 0.622 respectively. The average efficiency of the Southern Coastal Economic Zone, Eastern Coastal Comprehensive Economic Zone, and the Comprehensive Economic Zone in the middle reaches of the Yangtze River is higher than that of other regions. Finally, corresponding countermeasures and suggestions are put forward. The method used in this paper is applicable

  20. Disordered strictly jammed binary sphere packings attain an anomalously large range of densities

    Science.gov (United States)

    Hopkins, Adam B.; Stillinger, Frank H.; Torquato, Salvatore

    2013-08-01

    Previous attempts to simulate disordered binary sphere packings have been limited in producing mechanically stable, isostatic packings across a broad spectrum of packing fractions. Here we report that disordered strictly jammed binary packings (packings that remain mechanically stable under general shear deformations and compressions) can be produced with an anomalously large range of average packing fractions 0.634≤ϕ≤0.829 for small to large sphere radius ratios α restricted to α≥0.100. Surprisingly, this range of average packing fractions is obtained for packings containing a subset of spheres (called the backbone) that are exactly strictly jammed, exactly isostatic, and also generated from random initial conditions. Additionally, the average packing fractions of these packings at certain α and small sphere relative number concentrations x approach those of the corresponding densest known ordered packings. These findings suggest for entropic reasons that these high-density disordered packings should be good glass formers and that they may be easy to prepare experimentally. We also identify an unusual feature of the packing fraction of jammed backbones (packings with rattlers excluded). The backbone packing fraction is about 0.624 over the majority of the α-x plane, even when large numbers of small spheres are present in the backbone. Over the (relatively small) area of the α-x plane where the backbone is not roughly constant, we find that backbone packing fractions range from about 0.606 to 0.829, with the volume of rattler spheres comprising between 1.6% and 26.9% of total sphere volume. To generate isostatic strictly jammed packings, we use an implementation of the Torquato-Jiao sequential linear programming algorithm [Phys. Rev. EPLEEE81539-375510.1103/PhysRevE.82.061302 82, 061302 (2010)], which is an efficient producer of inherent structures (mechanically stable configurations at the local maxima in the density landscape). The identification and

  1. Disordered strictly jammed binary sphere packings attain an anomalously large range of densities.

    Science.gov (United States)

    Hopkins, Adam B; Stillinger, Frank H; Torquato, Salvatore

    2013-08-01

    Previous attempts to simulate disordered binary sphere packings have been limited in producing mechanically stable, isostatic packings across a broad spectrum of packing fractions. Here we report that disordered strictly jammed binary packings (packings that remain mechanically stable under general shear deformations and compressions) can be produced with an anomalously large range of average packing fractions 0.634≤φ≤0.829 for small to large sphere radius ratios α restricted to α≥0.100. Surprisingly, this range of average packing fractions is obtained for packings containing a subset of spheres (called the backbone) that are exactly strictly jammed, exactly isostatic, and also generated from random initial conditions. Additionally, the average packing fractions of these packings at certain α and small sphere relative number concentrations x approach those of the corresponding densest known ordered packings. These findings suggest for entropic reasons that these high-density disordered packings should be good glass formers and that they may be easy to prepare experimentally. We also identify an unusual feature of the packing fraction of jammed backbones (packings with rattlers excluded). The backbone packing fraction is about 0.624 over the majority of the α-x plane, even when large numbers of small spheres are present in the backbone. Over the (relatively small) area of the α-x plane where the backbone is not roughly constant, we find that backbone packing fractions range from about 0.606 to 0.829, with the volume of rattler spheres comprising between 1.6% and 26.9% of total sphere volume. To generate isostatic strictly jammed packings, we use an implementation of the Torquato-Jiao sequential linear programming algorithm [Phys. Rev. E 82, 061302 (2010)], which is an efficient producer of inherent structures (mechanically stable configurations at the local maxima in the density landscape). The identification and explicit construction of binary packings

  2. Lyme Neuroborreliosis: Preliminary Results from an Urban Referral Center Employing Strict CDC Criteria for Case Selection

    Directory of Open Access Journals (Sweden)

    David S. Younger

    2010-01-01

    Full Text Available Lyme neuroborreliosis or “neurological Lyme disease” was evidenced in 2 of 23 patients submitted to strict criteria for case selection of the Centers for Disease Control and Prevention employing a two-tier test to detect antibodies to Borrelia burgdorferi at a single institution. One patient had symptomatic polyradiculoneuritis, dysautonomia, and serological evidence of early infection; and another had symptomatic small fiber sensory neuropathy, distal polyneuropathy, dysautonomia, and serological evidence of late infection. In the remaining patients symptoms initially ascribed to Lyme disease were probably unrelated to B. burgdorferi infection. Our findings suggest early susceptibility and protracted involvement of the nervous system most likely due to the immunological effects of B. burgdorferi infection, although the exact mechanisms remain uncertain.

  3. On The Integral Representation of Strictly Continuous Set-Valued Maps

    Directory of Open Access Journals (Sweden)

    Anaté K. Lakmon

    2015-11-01

    Full Text Available Let T be a completely regular topological space and C(T be the space of bounded, continuous real-valued functions on T. C(T is endowed with the strict topology (the topology generated by seminorms determined by continuous functions vanishing at in_nity. R. Giles ([13], p. 472, Theorem 4.6 proved in 1971 that the dual of C(T can be identi_ed with the space of regular Borel measures on T. We prove this result for positive, additive set-valued maps with values in the space of convex weakly compact non-empty subsets of a Banach space and we deduce from this result the theorem of R. Giles ([13], theorem 4.6, p.473.

  4. A Total Variation Model Based on the Strictly Convex Modification for Image Denoising

    Directory of Open Access Journals (Sweden)

    Boying Wu

    2014-01-01

    Full Text Available We propose a strictly convex functional in which the regular term consists of the total variation term and an adaptive logarithm based convex modification term. We prove the existence and uniqueness of the minimizer for the proposed variational problem. The existence, uniqueness, and long-time behavior of the solution of the associated evolution system is also established. Finally, we present experimental results to illustrate the effectiveness of the model in noise reduction, and a comparison is made in relation to the more classical methods of the traditional total variation (TV, the Perona-Malik (PM, and the more recent D-α-PM method. Additional distinction from the other methods is that the parameters, for manual manipulation, in the proposed algorithm are reduced to basically only one.

  5. Residual diffeomorphisms and symplectic soft hairs: The need to refine strict statement of equivalence principle

    Science.gov (United States)

    Sheikh-Jabbari, M. M.

    2016-09-01

    General covariance is the cornerstone of Einstein’s general relativity (GR) and implies that any two metrics related by diffeomorphisms are physically equivalent. There are, however, many examples pointing to the fact that this strict statement of general covariance needs refinement. There are a very special (measure-zero) subset of diffeomorphisms, the residual diffeomorphisms, to which one can associate well-defined conserved charges. This would hence render these diffeomorphic geometries physically distinct. We discuss that these symmetries may be appropriately called “symplectic symmetries”. Existence of residual diffeomorphisms and symplectic symmetries can be a quite general feature and not limited to the examples discussed so far in the literature. We propose that, in the context of black holes, these diffeomorphic, but distinct, geometries may be viewed as “symplectic soft hair” on black holes. We comment on how this may remedy black hole microstate problem, which in this context are dubbed as “horizon fluffs”.

  6. Reactions to terror attacks in ultra-orthodox jews: the cost of maintaining strict identity.

    Science.gov (United States)

    Ankri, Yael L E; Bachar, Eytan; Shalev, Arieh Y

    2010-01-01

    Traumatic events can shatter faith and beliefs. The responses of Ultra-Orthodox survivors of deadly terrorist attacks illustrate an effort to reconcile dreadful experiences with deeply embedded beliefs. Qualified clinicians prospectively evaluated self-reported and interviewer-generated posttraumatic stress disorder (PTSD) symptoms and cognitive appraisal in Ultra-Orthodox (n = 20) and non-Ultra-Orthodox (n = 33) survivors of suicide bus-bombing incidents in Jerusalem. Ultra-Orthodox survivors reported higher levels of PTSD symptoms and more personal guilt. Their narratives reflected an unshaken belief in Just Providence, within which being a victim of terror was perceived as a Just retribution for known or unknown wrongdoing. Survivors' reactions to trauma often reflect an effort to reconcile incongruous experiences with previously held beliefs. When treating strict believers, helpers should be sensitive to the identity-preserving function of posttraumatic cognitions.

  7. On a class of adjustable rate mortgage loans subject to a strict balance principle

    DEFF Research Database (Denmark)

    Astrup Jensen, Bjarne

    We describe the background and the basic funding mechanisms for the type of adjustable rate mortgageloans that were introduced in the Danish market in 1996. Each loan is funded separately by tap issuingpass-through mortgage bonds (`strict balance principle'). The novelty is a funding mechanism...... that usesa roll-over strategy, where long term loans are funded by sequentially issuing short term pass-throughbonds, and the first issuer of these loans obtained a patent on the funding principles in 1999. Publiclyavailable descriptions of the principles leave an impression of very complicated numerical...... algorithms.The algorithms described here show that the essentials can be reduced to a `back of an envelope' complexity.Keywords: Adjustable rate mortgages, balance principle, patent, yield curve riding...

  8. A ligand's view of target similarity

    DEFF Research Database (Denmark)

    Garland, Stephen L; Gloriam, David E

    2011-01-01

    -finding and, potentially, to produce ligands for previously intractable receptors. Sequence motifs correlated with ligands can be applied in the design of target-specific focused libraries that are both efficient and cost-effective and should provide increased hit-rates over diversity screening. Furthermore...... shows with several examples how focusing on the binding site(s) has a clear advantage when it comes to establishing sequence-correlated pharmacological profiles. By organizing and comparing sequence and structural data it is possible to "borrow" SAR from similar targets to increase the speed of lead......, in the optimization phase, the binding motif approach offers the possibility to identify quickly the most likely off-target candidates to be chosen for selectivity screening, as well as potentially characterizing those pockets which may best be exploited for improved selectivity....

  9. Nutritionally recommended food for semi- to strict vegetarian diets based on large-scale nutrient composition data.

    Science.gov (United States)

    Kim, Seunghyeon; Fenech, Michael F; Kim, Pan-Jun

    2018-03-12

    Diet design for vegetarian health is challenging due to the limited food repertoire of vegetarians. This challenge can be partially overcome by quantitative, data-driven approaches that utilise massive nutritional information collected for many different foods. Based on large-scale data of foods' nutrient compositions, the recent concept of nutritional fitness helps quantify a nutrient balance within each food with regard to satisfying daily nutritional requirements. Nutritional fitness offers prioritisation of recommended foods using the foods' occurrence in nutritionally adequate food combinations. Here, we systematically identify nutritionally recommendable foods for semi- to strict vegetarian diets through the computation of nutritional fitness. Along with commonly recommendable foods across different diets, our analysis reveals favourable foods specific to each diet, such as immature lima beans for a vegan diet as an amino acid and choline source, and mushrooms for ovo-lacto vegetarian and vegan diets as a vitamin D source. Furthermore, we find that selenium and other essential micronutrients can be subject to deficiency in plant-based diets, and suggest nutritionally-desirable dietary patterns. We extend our analysis to two hypothetical scenarios of highly personalised, plant-based methionine-restricted diets. Our nutrient-profiling approach may provide a useful guide for designing different types of personalised vegetarian diets.

  10. Strict Liability Versus Policy and Regulation for Environmental Protection and Agricultural Waste Management in Malaysia

    Directory of Open Access Journals (Sweden)

    Mohd Bakri Ishak

    2010-01-01

    Full Text Available Basically, strict liability is part of the mechanism for expressing judgment or sentence by using direct evidence. This principle is very useful in order to obtain remedies from any damage either directly or indirectly. The principle in Rylands v Fletcher is responsible on imposing strict liability where if something brought onto land or collected there escapes liability under this rule can include not only the owner of land but also those who control or occupation on it. However, as a matter of fact, policy and regulation are also important in taking any action against any party who are responsible for environmental pollution or damage, which may include mismanagement of waste or industrial waste or agricultural waste. There are certain policies and regulations on environmental protection such as the National Environmental Policy, certain Acts and several regulations under the Environmental Quality Act 1974 (Act 127, which are very useful for agricultural waste management inter alia: Waters Act 1920 (Act 418, Environmental Quality (Prescribed Premises (Crude Palm Oil Regulations 1977, Environmental Quality (Prescribed Premises (Raw Natural Rubber Regulations 1978, Environmental Quality (Sewage and Industrial Effluents Regulations 1979, and Environmental Quality (Compounding of Offences Rules 1978. As a matter of fact, we should realize that time is of an essence for any parties which are involved in court cases and especially in avoiding the element of externality, which is commonly suffered by the government. In making this paper, therefore, some element of comparison with certain developed jurisdiction such as in the United Kingdom and Japan could not be avoided in order to obtain better outcome and to be more practical for the purpose of environmental protection and agricultural waste management.

  11. The Effect of Strict Segregation on Pseudomonas aeruginosa in Cystic Fibrosis Patients.

    Directory of Open Access Journals (Sweden)

    Rosa van Mansfeld

    Full Text Available Segregation of patients with cystic fibrosis (CF was implemented to prevent chronic infection with epidemic Pseudomonas aeruginosa strains with presumed detrimental clinical effects, but its effectiveness has not been carefully evaluated.The effect of strict segregation on the incidence of P. aeruginosa infection in CF patients was investigated through longitudinal protocolized follow-up of respiratory tract infection before and after segregation. In two nested cross-sectional studies in 2007 and 2011 the P. aeruginosa population structure was investigated and clinical parameters were determined in patients with and without infection with the Dutch epidemic P. aeruginosa clone (ST406.Of 784 included patients 315 and 382 were at risk for acquiring chronic P. aeruginosa infection before and after segregation. Acquisition rates were, respectively, 0.14 and 0.05 per 1,000 days at risk (HR: 0.66, 95% CI [0.2548-1.541]; p = 0.28. An exploratory subgroup analysis indicated lower acquisition after segregation in children < 15 years of age (HR: 0.43, 95% CI[0.21-0.95]; p = 0.04. P. aeruginosa population structure did not change after segregation and ST406 was not associated with lung function decline, death or lung transplantation.Strict segregation was not associated with a statistically significant lower acquisition of chronic P. aeruginosa infection and ST406 was not associated with adverse clinical outcome. After segregation there were no new acquisitions of ST406. In an unplanned exploratory analysis chronic acquisition of P. aeruginosa was lower after implementation of segregation in patients under 15 years of age.

  12. Weight of fitness deviation governs strict physical chaos in replicator dynamics

    Science.gov (United States)

    Pandit, Varun; Mukhopadhyay, Archan; Chakraborty, Sagar

    2018-03-01

    Replicator equation—a paradigm equation in evolutionary game dynamics—mathematizes the frequency dependent selection of competing strategies vying to enhance their fitness (quantified by the average payoffs) with respect to the average fitnesses of the evolving population under consideration. In this paper, we deal with two discrete versions of the replicator equation employed to study evolution in a population where any two players' interaction is modelled by a two-strategy symmetric normal-form game. There are twelve distinct classes of such games, each typified by a particular ordinal relationship among the elements of the corresponding payoff matrix. Here, we find the sufficient conditions for the existence of asymptotic solutions of the replicator equations such that the solutions—fixed points, periodic orbits, and chaotic trajectories—are all strictly physical, meaning that the frequency of any strategy lies inside the closed interval zero to one at all times. Thus, we elaborate on which of the twelve types of games are capable of showing meaningful physical solutions and for which of the two types of replicator equation. Subsequently, we introduce the concept of the weight of fitness deviation that is the scaling factor in a positive affine transformation connecting two payoff matrices such that the corresponding one-shot games have exactly same Nash equilibria and evolutionary stable states. The weight also quantifies how much the excess of fitness of a strategy over the average fitness of the population affects the per capita change in the frequency of the strategy. Intriguingly, the weight's variation is capable of making the Nash equilibria and the evolutionary stable states, useless by introducing strict physical chaos in the replicator dynamics based on the normal-form game.

  13. Selvester scoring in patients with strict LBBB using the QUARESS software.

    Science.gov (United States)

    Xia, Xiaojuan; Chaudhry, Uzma; Wieslander, Björn; Borgquist, Rasmus; Wagner, Galen S; Strauss, David G; Platonov, Pyotr; Ugander, Martin; Couderc, Jean-Philippe

    2015-01-01

    Estimation of the infarct size from body-surface ECGs in post-myocardial infarction patients has become possible using the Selvester scoring method. Automation of this scoring has been proposed in order to speed-up the measurement of the score and improving the inter-observer variability in computing a score that requires strong expertise in electrocardiography. In this work, we evaluated the quality of the QuAReSS software for delivering correct Selvester scoring in a set of standard 12-lead ECGs. Standard 12-lead ECGs were recorded in 105 post-MI patients prescribed implantation of an implantable cardiodefibrillator (ICD). Amongst the 105 patients with standard clinical left bundle branch block (LBBB) patterns, 67 had a LBBB pattern meeting the strict criteria. The QuAReSS software was applied to these 67 tracings by two independent groups of cardiologists (from a clinical group and an ECG core laboratory) to measure the Selvester score semi-automatically. Using various level of agreement metrics, we compared the scores between groups and when automatically measured by the software. The average of the absolute difference in Selvester scores measured by the two independent groups was 1.4±1.5 score points, whereas the difference between automatic method and the two manual adjudications were 1.2±1.2 and 1.3±1.2 points. Eighty-two percent score agreement was observed between the two independent measurements when the difference of score was within two point ranges, while 90% and 84% score agreements were reached using the automatic method compared to the two manual adjudications. The study confirms that the QuAReSS software provides valid measurements of the Selvester score in patients with strict LBBB with minimal correction from cardiologists. Copyright © 2015 Elsevier Inc. All rights reserved.

  14. Strict follow-up programme including CT and (18) F-FDG-PET after curative surgery for colorectal cancer

    DEFF Research Database (Denmark)

    Sørensen, N F; Jensen, A B; Wille-Jørgensen, P

    2010-01-01

    Aim  The risk of local recurrence following curative surgery for colorectal cancer (CRC) is up to 50%. A rigorous follow-up program may increase survival. Guidelines on suitable methods for scheduled follow up examinations are needed. This study evaluates a strict follow-up program including...... supported a strict follow-up program following curative surgery for colorectal cancer. FDG-PET combined with CT should be included in control programs....

  15. Glutamate receptor ligands

    DEFF Research Database (Denmark)

    Guldbrandt, Mette; Johansen, Tommy N; Frydenvang, Karla Andrea

    2002-01-01

    Homologation and substitution on the carbon backbone of (S)-glutamic acid [(S)-Glu, 1], as well as absolute stereochemistry, are structural parameters of key importance for the pharmacological profile of (S)-Glu receptor ligands. We describe a series of methyl-substituted 2-aminoadipic acid (AA...... or slightly lower potencies than (S)-AA [e.g., EC(50) = 76 microM for (2S,4S)-4-methyl-AA (5a) as compared to EC(50) = 35 microM for (S)-AA]. The position of the methyl substituent had a profound effect on the observed pharmacology, whereas the absolute stereochemistry at the methylated carbon atom had a very......) analogs, and the synthesis, stereochemistry, and enantiopharmacology of 3-methyl-AA (4a-d), 4-methyl-AA (5a-d), 5-methyl-AA (6a-d), and (E)-Delta(4)-5-methyl-AA (7a and 7b) are reported. The compounds were resolved using chiral HPLC and the configurational assignments of the enantiomers were based on X...

  16. Diagnostic potential of PET/CT using a {sup 68}Ga-labelled prostate-specific membrane antigen ligand in whole-body staging of renal cell carcinoma: initial experience

    Energy Technology Data Exchange (ETDEWEB)

    Sawicki, Lino M.; Buchbender, Christian; Boos, Johannes; Antoch, Gerald [University Dusseldorf, Medical Faculty, Department of Diagnostic and Interventional Radiology, Dusseldorf (Germany); Giessing, Markus [University Dusseldorf, Medical Faculty, Department of Urology, Dusseldorf (Germany); Ermert, Johannes [Juelich Research Center, Institute of Neuroscience and Medicine, INM-5: Nuclear Chemistry, Juelich (Germany); Antke, Christina; Hautzel, Hubertus [University Dusseldorf, Medical Faculty, Department of Nuclear Medicine, Dusseldorf (Germany)

    2017-01-15

    To evaluate the diagnostic potential of whole-body PET/CT using a {sup 68}Ga-labelled PSMA ligand in renal cell carcinoma (RCC). Six patients with histopathologically proven RCC underwent {sup 68}Ga-PSMA PET/CT. Each PET/CT scan was evaluated in relation to lesion count, location and dignity. SUVmax was measured in primary tumours and PET-positive metastases. Tumour-to-background SUVmax ratios (TBR{sub SUVmax}) were calculated for primary RCCs in relation to the surrounding normal renal parenchyma. Metastasis-to-background SUVmax ratios (MBR{sub SUVmax}) were calculated for PET-positive metastases in relation to gluteal muscle. Five primary RCCs and 16 metastases were evaluated. The mean SUVmax of the primary RCCs was 9.9 ± 9.2 (range 1.7 - 27.2). Due to high uptake in the surrounding renal parenchyma, the mean TBR{sub SUVmax} of the primary RCCs was only 0.2 ± 0.3 (range 0.02 - 0.7). Eight metastases showed focal {sup 68}Ga-PSMA uptake (SUVmax 9.9 ± 8.3, range 3.4 - 25.6). The mean MBR{sub SUVmax} of these PET-positive metastases was 11.7 ± 0.2 (range 4.4 - 28.1). All PET-negative metastases were subcentimetre lung metastases. {sup 68}Ga-PSMA PET/CT appears to be a promising method for detecting RCC metastases. However, no additional diagnostic value in assessing the primary tumour was found. (orig.)

  17. Diagnostic potential of PET/CT using a 68Ga-labelled prostate-specific membrane antigen ligand in whole-body staging of renal cell carcinoma: initial experience

    International Nuclear Information System (INIS)

    Sawicki, Lino M.; Buchbender, Christian; Boos, Johannes; Antoch, Gerald; Giessing, Markus; Ermert, Johannes; Antke, Christina; Hautzel, Hubertus

    2017-01-01

    To evaluate the diagnostic potential of whole-body PET/CT using a 68 Ga-labelled PSMA ligand in renal cell carcinoma (RCC). Six patients with histopathologically proven RCC underwent 68 Ga-PSMA PET/CT. Each PET/CT scan was evaluated in relation to lesion count, location and dignity. SUVmax was measured in primary tumours and PET-positive metastases. Tumour-to-background SUVmax ratios (TBR SUVmax ) were calculated for primary RCCs in relation to the surrounding normal renal parenchyma. Metastasis-to-background SUVmax ratios (MBR SUVmax ) were calculated for PET-positive metastases in relation to gluteal muscle. Five primary RCCs and 16 metastases were evaluated. The mean SUVmax of the primary RCCs was 9.9 ± 9.2 (range 1.7 - 27.2). Due to high uptake in the surrounding renal parenchyma, the mean TBR SUVmax of the primary RCCs was only 0.2 ± 0.3 (range 0.02 - 0.7). Eight metastases showed focal 68 Ga-PSMA uptake (SUVmax 9.9 ± 8.3, range 3.4 - 25.6). The mean MBR SUVmax of these PET-positive metastases was 11.7 ± 0.2 (range 4.4 - 28.1). All PET-negative metastases were subcentimetre lung metastases. 68 Ga-PSMA PET/CT appears to be a promising method for detecting RCC metastases. However, no additional diagnostic value in assessing the primary tumour was found. (orig.)

  18. Assessment and Challenges of Ligand Docking into Comparative Models of G-Protein Coupled Receptors

    DEFF Research Database (Denmark)

    Nguyen, E.D.; Meiler, J.; Norn, C.

    2013-01-01

    is increased by one order of magnitude for every 10 residues known to contact the ligand. Additionally, in the case of DOR, knowledge of a single specific ligand-protein contact improved sampling efficiency 7 fold. These findings offer specific guidelines which may lead to increased success in determining...

  19. Complex Relationship between Ligand Binding and Dimerization in the Epidermal Growth Factor Receptor

    Directory of Open Access Journals (Sweden)

    Nicholas J. Bessman

    2014-11-01

    Full Text Available The epidermal growth factor receptor (EGFR plays pivotal roles in development and is mutated or overexpressed in several cancers. Despite recent advances, the complex allosteric regulation of EGFR remains incompletely understood. Through efforts to understand why the negative cooperativity observed for intact EGFR is lost in studies of its isolated extracellular region (ECR, we uncovered unexpected relationships between ligand binding and receptor dimerization. The two processes appear to compete. Surprisingly, dimerization does not enhance ligand binding (although ligand binding promotes dimerization. We further show that simply forcing EGFR ECRs into preformed dimers without ligand yields ill-defined, heterogeneous structures. Finally, we demonstrate that extracellular EGFR-activating mutations in glioblastoma enhance ligand-binding affinity without directly promoting EGFR dimerization, suggesting that these oncogenic mutations alter the allosteric linkage between dimerization and ligand binding. Our findings have important implications for understanding how EGFR and its relatives are activated by specific ligands and pathological mutations.

  20. Biosensors engineered from conditionally stable ligand-binding domains

    Energy Technology Data Exchange (ETDEWEB)

    Church, George M.; Feng, Justin; Mandell, Daniel J.; Baker, David; Fields, Stanley; Jester, Benjamin Ward; Tinberg, Christine Elaine

    2017-09-19

    Disclosed is a biosensor engineered to conditionally respond to the presence of specific small molecules, the biosensors including conditionally stable ligand-binding domains (LBDs) which respond to the presence of specific small molecules, wherein readout of binding is provided by reporter genes or transcription factors (TFs) fused to the LBDs.

  1. Ligand-guided receptor optimization.

    Science.gov (United States)

    Katritch, Vsevolod; Rueda, Manuel; Abagyan, Ruben

    2012-01-01

    Receptor models generated by homology or even obtained by crystallography often have their binding pockets suboptimal for ligand docking and virtual screening applications due to insufficient accuracy or induced fit bias. Knowledge of previously discovered receptor ligands provides key information that can be used for improving docking and screening performance of the receptor. Here, we present a comprehensive ligand-guided receptor optimization (LiBERO) algorithm that exploits ligand information for selecting the best performing protein models from an ensemble. The energetically feasible protein conformers are generated through normal mode analysis and Monte Carlo conformational sampling. The algorithm allows iteration of the conformer generation and selection steps until convergence of a specially developed fitness function which quantifies the conformer's ability to select known ligands from decoys in a small-scale virtual screening test. Because of the requirement for a large number of computationally intensive docking calculations, the automated algorithm has been implemented to use Linux clusters allowing easy parallel scaling. Here, we will discuss the setup of LiBERO calculations, selection of parameters, and a range of possible uses of the algorithm which has already proven itself in several practical applications to binding pocket optimization and prospective virtual ligand screening.

  2. Structural Characterization of Natural Nickel and Copper Binding Ligands along the US GEOTRACES Eastern Pacific Zonal Transect

    OpenAIRE

    Boiteau, Rene M.; Till, Claire P.; Ruacho, Angel; Bundy, Randelle M.; Hawco, Nicholas J.; McKenna, Amy M.; Barbeau, Katherine A.; Bruland, Kenneth W.; Saito, Mak A.; Repeta, Daniel J.

    2016-01-01

    Organic ligands form strong complexes with many trace elements in seawater. Various metals can compete for the same ligand chelation sites, and the final speciation of bound metals is determined by relative binding affinities, concentrations of binding sites, uncomplexed metal concentrations, and association/dissociation kinetics. Different ligands have a wide range of metal affinities and specificities. However, the chemical composition of these ligands in the marine environment remains poor...

  3. Structural characterization of natural nickel and copper binding ligands along the US GEOTRACES Eastern Pacific Zonal transect

    OpenAIRE

    Rene M Boiteau; Rene M Boiteau; Claire P Till; Angel Ruacho; Randelle M Bundy; Nicholas J Hawco; Nicholas J Hawco; Amy M. McKenna; Katherine Barbeau; Kenneth Bruland; Mak Saito; Daniel James Repeta

    2016-01-01

    Organic ligands form strong complexes with many trace elements in seawater. Various metals can compete for the same ligand chelation sites, and the final speciation of bound metals is determined by relative binding affinities, concentrations of binding sites, uncomplexed metal concentrations, and association/dissociation kinetics. Different ligands have a wide range of metal affinities and specificities. However, the chemical composition of these ligands in the marine environment remains poor...

  4. Targeting Selectins and Their Ligands in Cancer

    Directory of Open Access Journals (Sweden)

    Alessandro eNatoni

    2016-04-01

    Full Text Available Aberrant glycosylation is a hallmark of cancer cells with increased evidence pointing to a role in tumor progression. In particular, aberrant sialylation of glycoproteins and glycolipids have been linked to increased immune cell evasion, drug evasion, drug resistance, tumor invasiveness, and vascular dissemination leading to metastases. Hypersialylation of cancer cells is largely the result of overexpression of sialyltransferases. Humans differentially express twenty different sialyltransferases in a tissue-specific manner, each of which catalyze the attachment of sialic acids via different glycosidic linkages (2-3; 2-6 or 2-8 to the underlying glycan chain. One important mechanism whereby overexpression of sialyltransferases contributes to an enhanced metastatic phenotype is via the generation of selectin ligands. Selectin ligand function requires the expression of sialyl-Lewis X and its structural-isomer sialyl-Lewis A, which are synthesized by the combined action of alpha 1-3-fucosyltransferases, 2-3-sialyltransferases, 1-4-galactosyltranferases, and N-acetyl--glucosaminyltransferases. The α2-3-sialyltransferases ST3Gal4 and ST3Gal6 are critical to the generation of functional E- and P-selectin ligands and overexpression of these sialyltransferases have been linked to increased risk of metastatic disease in solid tumors and poor outcome in multiple myeloma. Thus, targeting selectins and their ligands as well as the enzymes involved in their generation, in particular sialyltransferases, could be beneficial to many cancer patients. Potential strategies include sialyltransferase inhibition and the use of selectin antagonists, such as glycomimetic drugs and antibodies. Here, we review ongoing efforts to optimize the potency and selectivity of sialyltransferase inhibitors, including the potential for targeted delivery approaches, as well as evaluate the potential utility of selectin inhibitors, which are now in early clinical

  5. Novel olfactory ligands via terpene synthases.

    Science.gov (United States)

    Touchet, Sabrina; Chamberlain, Keith; Woodcock, Christine M; Miller, David J; Birkett, Michael A; Pickett, John A; Allemann, Rudolf K

    2015-05-01

    A synthetic biology approach to the rational design of analogues of olfactory ligands by providing unnatural substrates for the enzyme synthesising (S)-germacrene D, an olfactory ligand acting as a plant derived insect repellent, to produce novel ligands is described as a viable alternative to largely unsuccessful ligand docking studies. (S)-14,15-Dimethylgermacrene D shows an unexpected reversal in behavioural activity.

  6. Magnetic resonance imaging quantitation of changes in muscle volume during 7 days of strict bed rest.

    Science.gov (United States)

    Ferrando, A A; Stuart, C A; Brunder, D G; Hillman, G R

    1995-10-01

    Prolonged bed rest results in a loss of leg lean body mass. Previous studies using bed rest as a model for microgravity have shown decreases in leg mass after 12 and 14 d, 5 and 17 wk. As magnetic resonance imaging (MRI) can provide a precise and non-invasive means of determining muscle volume, we sought to determine if changes in leg muscle volume could be detected in bed rest periods as short as 7 d. Five young, healthy, male volunteers were subjected to 7 d of absolute bed rest. Each subject underwent MRI quantitation of segmental muscle volumes of the calves and thighs before and after bed rest. Eleven (calf) and nine (thigh) contiguous 1-cm thick transaxial images were generated over prescribed regions using a Technicare MRI imager with a 0.6T superconducting magnet and body coil. Image processing was performed using a generalized 8-bit medical image analysis package developed at University of Texas Medical Branch. Images were analyzed for muscle and non-muscle volumes (including fat, blood vessel, and bone marrow volumes). The MRI quantitation demonstrated bed rest-induced significant decreases in segmental thigh muscle (approximately 3.0%, p image analysis of MRI images provides a sensitive tool capable of detecting leg volume changes of as little as 3.0% over a 7-d period of strict bed rest.

  7. Managing curriculum transformation within strict university governance structures: an example from Damascus University Medical School.

    Science.gov (United States)

    Kayyal, Mohammad; Gibbs, Trevor

    2012-01-01

    As the world of medical education moves forward, it becomes increasingly clear that the transformative process is not as easy a process for all. Across the globe, there appears to be many barriers that obstruct or threaten innovation and change, most of which cause almost insurmountable problems to many schools. If transformative education is to result in an equitable raising of standards across such an unlevel playing field, schools have to find ways in overcoming these barriers. One seemingly common barrier to development occurs when medical schools are trapped within strict University governance structures; rules and regulations which are frequently inappropriate and obstructive to the transformation that must occur in today's medical educational paradigm. The Faculty of Medicine at Damascus University, one of the oldest and foremost medical schools in the Middle East, is one such school where rigid rules and regulations and traditional values are obstructing transformative change. This paper describes the problems, which the authors believe to be common to many, and explores how attempts have been made to overcome them and move the school into the twenty-first century. It is the ultimate purpose of this paper to raise awareness of the issue, share the lessons learned in order to assist others who are experiencing similar problems and possibly create opportunities for dialogue between schools.

  8. On a holomorphic Lefschetz formula in strictly pseudoconvex subdomains of complex manifolds

    International Nuclear Information System (INIS)

    Kytmanov, A M; Myslivets, S G; Tarkhanov, N N

    2004-01-01

    The classical Lefschetz formula expresses the number of fixed points of a continuous map f:M→M in terms of the transformation induced by f on the cohomology of M. In 1966, Atiyah and Bott extended this formula to elliptic complexes over a compact closed manifold. In particular, they obtained a holomorphic Lefschetz formula on compact complex manifolds without boundary. Brenner and Shubin (1981, 1991) extended the Atiyah-Bott theory to compact manifolds with boundary. On compact complex manifolds with boundary the Dolbeault complex is not elliptic, therefore the Atiyah-Bott theory is not applicable. Bypassing difficulties related to the boundary behaviour of Dolbeault cohomology, Donnelly and Fefferman (1986) obtained a formula for the number of fixed points in terms of the Bergman metric. The aim of this paper is to obtain a Lefschetz formula on relatively compact strictly pseudoconvex subdomains of complex manifolds X with smooth boundary, that is, to find the total Lefschetz number for a holomorphic endomorphism f * of the Dolbeault complex and to express it in terms of local invariants of the fixed points of f.

  9. Divergent changes in serum sterols during a strict uncooked vegan diet in patients with rheumatoid arthritis.

    Science.gov (United States)

    Agren, J J; Tvrzicka, E; Nenonen, M T; Helve, T; Hänninen, O

    2001-02-01

    The effects of a strict uncooked vegan diet on serum lipid and sterol concentrations were studied in patients with rheumatoid arthritis. The subjects were randomized into a vegan diet group (n 16), who consumed a vegan diet for 2-3 months, or into a control group (n 13), who continued their usual omnivorous diets. Serum total and LDL-cholesterol and -phospholipid concentrations were significantly decreased by the vegan diet. The levels of serum cholestanol and lathosterol also decreased, but serum cholestanol:total cholesterol and lathosterol:total cholesterol did not change. The effect of a vegan diet on serum plant sterols was divergent as the concentration of campesterol decreased while that of sitosterol increased. This effect resulted in a significantly greater sitosterol:campesterol value in the vegan diet group than in the control group (1.48 (SD 0.39) v. 0.72 (SD 0.14); P vegan diet changes the relative absorption rates of these sterols and/or their biliary clearance.

  10. Model-Based Adaptive Event-Triggered Control of Strict-Feedback Nonlinear Systems.

    Science.gov (United States)

    Li, Yuan-Xin; Yang, Guang-Hong

    2018-04-01

    This paper is concerned with the adaptive event-triggered control problem of nonlinear continuous-time systems in strict-feedback form. By using the event-sampled neural network (NN) to approximate the unknown nonlinear function, an adaptive model and an associated event-triggered controller are designed by exploiting the backstepping method. In the proposed method, the feedback signals and the NN weights are aperiodically updated only when the event-triggered condition is violated. A positive lower bound on the minimum intersample time is guaranteed to avoid accumulation point. The closed-loop stability of the resulting nonlinear impulsive dynamical system is rigorously proved via Lyapunov analysis under an adaptive event sampling condition. In comparing with the traditional adaptive backstepping design with a fixed sample period, the event-triggered method samples the state and updates the NN weights only when it is necessary. Therefore, the number of transmissions can be significantly reduced. Finally, two simulation examples are presented to show the effectiveness of the proposed control method.

  11. Strictly hyperbolic models of co-current three-phase flow withgravity

    Energy Technology Data Exchange (ETDEWEB)

    Juanes, Ruben; Patzek, Tadeusz W.

    2002-11-18

    We study the character of the equations in the traditional formulation of one-dimensional immiscible three-phase flow with gravity, in the limit of negligible capillarity. We restrict our analysis to co-current flow required for a displacement process; in cases of mixed co-current and counter-current flow, capillarity effects cannot be dropped from the formulation. The model makes use of the classical multiphase extension of Darcy's equation. It is well known that, if relative permeabilities are taken as fixed functions of saturations, the model yields regions in the saturation space where the system of equations is locally elliptic. We regard elliptic behavior as a nonphysical artifact of an incomplete formulation, and derive conditions on the relative permeabilities that ensure strict hyperbolicity of the governing equations. The key point is to acknowledge that a Darcy-type formulation is insufficient to capture all the physics of three-phase flow and that, consequently, the relative permeabilities are functionals that depend on the fluid viscosity ratio and the gravity number. The derived conditions are consistent with the type of displacements that take place in porous media. By means of an illustrative example, we show how elliptic behavior can be removed, even when using simplistic relative permeability models.

  12. Clinical impact of strict criteria for selectivity and lateralization in adrenal vein sampling.

    Science.gov (United States)

    Gasparetto, Alessandro; Angle, John F; Darvishi, Pasha; Freeman, Colbey W; Norby, Ray G; Carey, Robert M

    2015-04-01

    Selectivity index (SI) and lateralization index (LI) thresholds determine the adequacy of adrenal vein sampling (AVS) and the degree of lateralization. The purpose of this study was investigate the clinical outcome of patients whose adrenal vein sampling was interpreted using "strict criteria" (SC) (SIpre-stimuli≥3, SIpost-stimuli≥5 and LIpre-stimuli≥4, LIpost-stimuli≥4). A retrospective review of 73 consecutive AVS procedures was performed and 67 were technically successful. Forty-three patients showed lateralization and underwent surgery, while 24 did not lateralize and were managed conservatively. Systolic blood pressure (SBP), diastolic blood pressure (DBP), kalemia (K(+)), and the change in number of blood pressure (BP) medications were recorded for each patient before and after AVS and potential surgery were performed. In the surgery group, BP and K(+) changed respectively from 160±5.3/100±2.0 mmHg to 127±3.3/80±1.9 (p blood pressure medications were six (14.0%) in the lateralized group and 22 (91.7%) in the non-lateralized group (p <0.001). AVS interpretation with SC leads to significant clinical improvement in both patients who underwent surgery and those managed conservatively.

  13. Sporothrix schenckii (sensu strict S. globosa) mating type 1-2 (MAT1-2) gene.

    Science.gov (United States)

    Kano, Rui; Anzawa, Kazushi; Mochizuki, Takashi; Nishimoto, Katsutaro; Hiruma, Masataro; Kamata, Hiroshi; Hasegawa, Atsuhiko

    2013-09-01

    Sporotix schenckii is a pathogenic fungus that causes human and animal sporotrichosis, and based on morphology of the sessile conidia and molecular analysis, it was recently recognized as a species complex comprising at least the following six sibling species: S. albicans, S. brasiliensis, S. globosa, S. luriei, S. mexicana and S. schenckii. However, apart from S. schenckii sensu strict, only S. brasiliensis, S. globosa and S. luriei are associated with human and animal infection. S. globosa has been most commonly isolated in Asia, Europe and the USA; therefore, molecular epidemiological study for S. globosa is important in relation to human sporotrichosis in Japan. To the best of our knowledge, this is the first study to determine the mating type 1-2 (MAT1-2) gene of Sporothrix schenckii with the aim of understanding the taxonomy of the genus Sporothrix. The MAT1-2 gene (1618 bp) encodes a protein sequence of 198 amino acids. Reverse transcription polymerase chain reaction analysis also detected MAT1-2 gene mRNA expression in all of the S. schenckii strains examined, indicating that this gene is expressed in S. schenckii cells. Phylogenetic analysis of the MAT1-2 gene fragments of Ophiostoma himal-ulmi, O. novo-ulmi, O. ulmi and S. schenckii indicated that these isolates could be classified into four clusters. MAT1-1 gene-specific polymerase chain reaction was positive in 15 isolates, but negative in four human isolates and one feline isolate. © 2013 Japanese Dermatological Association.

  14. Reversible Size Control of Silver Nanoclusters via Ligand-exchange

    KAUST Repository

    Bootharaju, Megalamane Siddaramappa

    2015-05-21

    The properties of atomically monodisperse noble metal nanoclusters (NCs) are intricately intertwined with their precise molecular formula. The vast majority of size-specific NC syntheses start from the reduction of the metal salt and thiol ligand mixture. Only in gold was it recently shown that ligand-exchange could induce the growth of NCs from one atomically precise species to another; a process of yet unknown reversibility. Here, we present a process for the ligand-exchange-induced growth of atomically precise silver NCs, in a biphasic liquid-liquid system, which is particularly of interest because of its complete reversibility and ability to occur at room temperature. We explore this phenomenon in-depth using Ag35(SG)18 [SG= glutathionate] and Ag44(4-FTP)30 [4-FTP= 4-fluorothiophenol] as model systems. We show that the ligand-exchange conversion of Ag35(SG)18 into Ag44(4-FTP)30 is rapid (< 5 min) and direct, while the reverse process proceeds slowly through intermediate cluster sizes. We adapt a recently developed theory of reverse Ostwald ripening to model the NCs’ interconvertibility. The model’s predictions are in good agreement with the experimental observations, and they highlight the importance of small changes in the ligand-metal binding energy in determining the final equilibrium NC size. Based on the insight provided by this model, we demonstrated experimentally that by varying the choice of ligands, ligand-exchange can be used to obtain different sized NCs. The findings in this work establish ligand-exchange as a versatile tool for tuning cluster sizes.

  15. Strict Criteria for Selection of Laparoscopy for Women with Adnexal Mass

    Science.gov (United States)

    Sallum, Luis Felipe; Sarian, Luis Otávio; Bastos, Joana Fróes Bragança; Derchain, Sophie

    2014-01-01

    Objectives: We compared the indication of laparoscopy for treatment of adnexal masses based on the risk scores and tumor diameters with the indication based on gynecology-oncologists' experience. Methods: This was a prospective study of 174 women who underwent surgery for adnexal tumors (116 laparotomies, 58 laparoscopies). The surgeries begun and completed by laparoscopy, with benign pathologic diagnosis, were considered successful. Laparoscopic surgeries that required conversion to laparotomy, led to a malignant diagnosis, or facilitated cyst rupture were considered failures. Two groups were defined for laparoscopy indication: (1) absence of American College of Obstetrics and Gynecology (ACOG) guideline for referral of high-risk adnexal masses criteria (ACOG negative) associated with 3 different tumor sizes (10, 12, and 14 cm); and (2) Index of Risk of Malignancy (IRM) with cutoffs at 100, 200, and 300, associated with the same 3 tumor sizes. Both groups were compared with the indication based on the surgeon's experience to verify whether the selection based on strict rules would improve the rate of successful laparoscopy. Results: ACOG-negative and tumors ≤10 cm and IRM with a cutoff at 300 points and tumors ≤10cm resulted in the same best performance (78% success = 38/49 laparoscopies). However, compared with the results of the gynecology-oncologists' experience, those were not statistically significant. Discussion: The selection of patients with adnexal mass to laparoscopy by the use of the ACOG guideline or IRM associated with tumor diameter had similar performance as the experience of gynecology-oncologists. Both methods are reproducible and easy to apply to all women with adnexal masses and could be used by general gynecologists to select women for laparoscopic surgery; however, referral to a gynecology-oncologist is advisable when there is any doubt. PMID:25392617

  16. An Analysis of Central Residues Between Ligand-Bound and Ligand-Free Protein Structures Based on Network Approach.

    Science.gov (United States)

    Amala, Arumugam; Emerson, Isacc Arnold

    2017-08-01

    Depiction of protein structures as networks of interacting residues has enabled us to understand the structure and function of the protein. Previous investigations on closeness centrality have identified protein functional sites from three- dimensional structures. It is well recognized that ligand binding to a receptor protein induces a wide range of structural changes. An interesting question is how central residues function during conformational changes triggered during ligand binding? The aim of this study is to comprehend at what extent central residues change during ligand binding to receptor proteins. To determine this, we examined 37 pairs of protein structures consisting of ligand-bound and ligand-free forms. These protein structures were modelled as an undirected network and significant central residues were obtained using residue centrality measures. In addition to these, the basic network parameters were also analysed. On analysing the residue centrality measures, we observed that 60% of central residues were common in both the ligand-bound and ligand-free states. The geometry of the central residues revealed that they were situated closer to the protein center of the mass. Finally, we demonstrated the effectiveness of central residues in amino acids substitutions and in the evolution itself. The closeness centrality was also analyzed among different protein domain sizes and the values gradually declined from single-domains to multi-domain proteins suggesting that the network has potential for hierarchical organization. Betweenness centrality measure was also used to determine the central residues and 31% of these residues were common between the holo/apo states. Findings reveal that central residues play a significant role in determining the functional properties of proteins. These results have implications in predicting binding/active site residues, specifically in the context of drug designing, if additional information concerning ligand binding is

  17. Cd44 Is a Major E-Selectin Ligand on Human Hematopoietic Progenitor Cells

    OpenAIRE

    Dimitroff, Charles J.; Lee, Jack Y.; Rafii, Shahin; Fuhlbrigge, Robert C.; Sackstein, Robert

    2001-01-01

    E-selectin plays a critical role in mediating tissue-specific homing of T cells into skin, and of primitive hematopoietic progenitor cells (HPCs) into bone marrow (BM). Though it is known that a glycoform of PSGL-1 (CLA) functions as the principal E-selectin ligand on human T lymphocytes, the E-selectin ligand(s) of human HPCs has not been identified. We used a shear-based adherence assay to analyze and define the E-selectin ligand activity of membrane proteins from human HPCs. Our data show ...

  18. Properties of N-person axiomatic bargaining solutions if the Pareto frontier is twice differentiable and strictly concave

    NARCIS (Netherlands)

    Douven, R.C.M.H.; Engwerda, J.C.

    1995-01-01

    In this paper we discuss properties of N-person axiomatic bargaining problems, where the Pareto frontier of S can be described by a strictly concave and twice differentiable function. These type of problems are characteristic for the empirical policy coordination literature. In that literature the

  19. Convergence of Implicit and Explicit Schemes for an Asymptotically Nonexpansive Mapping in -Uniformly Smooth and Strictly Convex Banach Spaces

    Directory of Open Access Journals (Sweden)

    Meng Wen

    2012-01-01

    Full Text Available We introduce a new iterative scheme with Meir-Keeler contractions for an asymptotically nonexpansive mapping in -uniformly smooth and strictly convex Banach spaces. We also proved the strong convergence theorems of implicit and explicit schemes. The results obtained in this paper extend and improve many recent ones announced by many others.

  20. A non-permselective membrane reactor for chemical processes normally requiring strict stoichiometric feed rates of reactants

    NARCIS (Netherlands)

    Sloot, H.J.; Versteeg, Geert; van Swaaij, Willibrordus Petrus Maria

    1990-01-01

    A novel type of membrane reactor with separated feeding of the reactants is presented for chemical processes normally requiring strict stoichiometric feed rates of premixed reactants. The reactants are fed in the reactor to the different sides of a porous membrane which is impregnated with a

  1. Strict Fathers, Competing Culture(s), and Racialized Poverty: White South African Teachers' Conceptions of Themselves as Racialized Actors

    Science.gov (United States)

    Casey, Zachary A.

    2016-01-01

    This article focuses in particular on four white South African female practicing P-12 teachers' narratives about their own racialized understanding of their classroom practice(s) and their (racio-cultural) self-identity. Each of the four participants reported growing up with what they described as "strict fathers" and shared ways in…

  2. Rosetta Ligand docking with flexible XML protocols.

    Science.gov (United States)

    Lemmon, Gordon; Meiler, Jens

    2012-01-01

    RosettaLigand is premiere software for predicting how a protein and a small molecule interact. Benchmark studies demonstrate that 70% of the top scoring RosettaLigand predicted interfaces are within 2Å RMSD from the crystal structure [1]. The latest release of Rosetta ligand software includes many new features, such as (1) docking of multiple ligands simultaneously, (2) representing ligands as fragments for greater flexibility, (3) redesign of the interface during docking, and (4) an XML script based interface that gives the user full control of the ligand docking protocol.

  3. Galaxy7TM: flexible GPCR-ligand docking by structure refinement.

    Science.gov (United States)

    Lee, Gyu Rie; Seok, Chaok

    2016-07-08

    G-protein-coupled receptors (GPCRs) play important physiological roles related to signal transduction and form a major group of drug targets. Prediction of GPCR-ligand complex structures has therefore important implications to drug discovery. With previously available servers, it was only possible to first predict GPCR structures by homology modeling and then perform ligand docking on the model structures. However, model structures generated without explicit consideration of specific ligands of interest can be inaccurate because GPCR structures can be affected by ligand binding. The Galaxy7TM server, freely accessible at http://galaxy.seoklab.org/7TM, improves an input GPCR structure by simultaneous ligand docking and flexible structure refinement using GALAXY methods. The server shows better performance in both ligand docking and GPCR structure refinement than commonly used programs AutoDock Vina and Rosetta MPrelax, respectively. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  4. Quantitative chemogenomics: machine-learning models of protein-ligand interaction.

    Science.gov (United States)

    Andersson, Claes R; Gustafsson, Mats G; Strömbergsson, Helena

    2011-01-01

    Chemogenomics is an emerging interdisciplinary field that lies in the interface of biology, chemistry, and informatics. Most of the currently used drugs are small molecules that interact with proteins. Understanding protein-ligand interaction is therefore central to drug discovery and design. In the subfield of chemogenomics known as proteochemometrics, protein-ligand-interaction models are induced from data matrices that consist of both protein and ligand information along with some experimentally measured variable. The two general aims of this quantitative multi-structure-property-relationship modeling (QMSPR) approach are to exploit sparse/incomplete information sources and to obtain more general models covering larger parts of the protein-ligand space, than traditional approaches that focuses mainly on specific targets or ligands. The data matrices, usually obtained from multiple sparse/incomplete sources, typically contain series of proteins and ligands together with quantitative information about their interactions. A useful model should ideally be easy to interpret and generalize well to new unseen protein-ligand combinations. Resolving this requires sophisticated machine-learning methods for model induction, combined with adequate validation. This review is intended to provide a guide to methods and data sources suitable for this kind of protein-ligand-interaction modeling. An overview of the modeling process is presented including data collection, protein and ligand descriptor computation, data preprocessing, machine-learning-model induction and validation. Concerns and issues specific for each step in this kind of data-driven modeling will be discussed. © 2011 Bentham Science Publishers

  5. Copper binding ligands: production by marine plankton and characterization by ESI-MS

    Science.gov (United States)

    Orians, K.; Ross, A.; Lawrence, M.; Ikonomou, M.

    2003-04-01

    Organic complexation affects the bioavailability and distribution of copper in the surface ocean. The cyanobacterium Synechococcus sp. PCC 7002 was cultured in the lab and subjected to near-toxic Cu concentrations. Strong Cu-binding ligands were produced under these conditions, as found for other species of Synechococcus. The copper-binding ligand produced had a log K'cond. (log conditional stability constant) of 12.2, similar to the natural ligands found in the surface ocean. The amount of ligand produced was proportional to the amount of copper present. Isolation and concentration of these compounds for characterization by electrospray mass spectrometry (ESI-MS) provides information about the structure of the organic ligands and their metal-ion complexes. Using model ligands, we'll show that ligands can be characterized by ESI-MS and that the location of the copper binding site can be determined in complex molecules. We'll also present results of copper-complexing ligands extracted from the coastal waters of British Columbia. Ligand concentrations are higher at low salinity and in surface waters, indicating that these ligands are produced in surface waters and/or delivered to the region via the Fraser River. Analysis of the extracts with highest UV absorbance identified two Cu2+ ligands of molecular weight 259 and 264. The mass and isotopic distributions are consistent with dipeptides and tripeptides containing two metal-binding amino groups. This result is consistent with the findings of other studies attempting to characterize Cu2+ ligands in seawater. The structure of the identified ligand is similar to that of rhodotorulic acid (a microbial siderophore), glutathione, and phytochelatins, indicating that small peptides and related compounds can act as strong, specific metal chelators in natural waters

  6. Maintenance of Taste Organs Is Strictly Dependent on Epithelial Hedgehog/GLI Signaling.

    Science.gov (United States)

    Ermilov, Alexandre N; Kumari, Archana; Li, Libo; Joiner, Ariell M; Grachtchouk, Marina A; Allen, Benjamin L; Dlugosz, Andrzej A; Mistretta, Charlotte M

    2016-11-01

    For homeostasis, lingual taste papilla organs require regulation of epithelial cell survival and renewal, with sustained innervation and stromal interactions. To investigate a role for Hedgehog/GLI signaling in adult taste organs we used a panel of conditional mouse models to manipulate GLI activity within epithelial cells of the fungiform and circumvallate papillae. Hedgehog signaling suppression rapidly led to taste bud loss, papilla disruption, and decreased proliferation in domains of papilla epithelium that contribute to taste cells. Hedgehog responding cells were eliminated from the epithelium but retained in the papilla stromal core. Despite papilla disruption and loss of taste buds that are a major source of Hedgehog ligand, innervation to taste papillae was maintained, and not misdirected, even after prolonged GLI blockade. Further, vimentin-positive fibroblasts remained in the papilla core. However, retained innervation and stromal cells were not sufficient to maintain taste bud cells in the context of compromised epithelial Hedgehog signaling. Importantly taste organ disruption after GLI blockade was reversible in papillae that retained some taste bud cell remnants where reactivation of Hedgehog signaling led to regeneration of papilla epithelium and taste buds. Therefore, taste bud progenitors were either retained during epithelial GLI blockade or readily repopulated during recovery, and were poised to regenerate taste buds once Hedgehog signaling was restored, with innervation and papilla connective tissue elements in place. Our data argue that Hedgehog signaling is essential for adult tongue tissue maintenance and that taste papilla epithelial cells represent the key targets for physiologic Hedgehog-dependent regulation of taste organ homeostasis. Because disruption of GLI transcriptional activity in taste papilla epithelium is sufficient to drive taste organ loss, similar to pharmacologic Hedgehog pathway inhibition, the findings suggest that taste

  7. New strategies for designing inexpensive but selective bioadsorbants for environmental pollutants: Selection of specific ligands and their cell surface expression. Technical progress report, September 15, 1996 -September 14, 1997

    International Nuclear Information System (INIS)

    Iverson, B.

    1997-01-01

    'Progress for the last twelve months has revolved around setting up an antibody engineering and surface display system for use with a metal-complex binding antibody. (1) The author has isolated genes for the V regions of the heavy and light chains for the Ru(bpy)3 specific monoclonal AC1106 (Shreder, K S., Hariman, A., and Iverson, B.L., J. Am. Chem. Soc. 1996, 118, 3192-3201). This antibody binds Ru(bpy), derivatives with better than nanomolar affinity, and will serve as the generic metal-complex binding pocket. Cloning antibody genes from hybridomas is complicated by the fact that primers must be found that amplify the particular heavy and light chain genes in the hybridoma of interest. Antibody gene amplification primers are generally designed to amplify antibody repertoires from lymphocyte mRNA isolated from animals. While cloning repertoires from animals is routinely successful due to the diverse population of target m RNA, hybridomas have a single target sequence. Therefore, multiple primers and conditions must be tried before the correct primer combination is identified.'

  8. THERMODYNAMIC ASSESSMENT OF ANIONIC LIGANDS ...

    African Journals Online (AJOL)

    DJFLEX

    2010-06-30

    Jun 30, 2010 ... The presence of the ligands (ethylenediaminettraacetic acid, EDTA, enthylenediamine, en,and chloride ion, Cl-) generally improved the sorption capacity for the adsorbent, the best being. Cl- at optimum pH of 2.0 (for Co2+) and 5.0 (for Ni2+ and Cd2+). The thermodynamic studies reveal that the adsorption.

  9. NKG2D and Its Ligands: “One for All, All for One”

    Directory of Open Access Journals (Sweden)

    Alessandra Zingoni

    2018-03-01

    Full Text Available The activating receptor NKG2D is peculiar in its capability to bind to numerous and highly diversified MHC class I-like self-molecules. These ligands are poorly expressed on normal cells but can be induced on damaged, transformed or infected cells, with the final NKG2D ligand expression resulting from multiple levels of regulation. Although redundant molecular mechanisms can converge in the regulation of all NKG2D ligands, different stimuli can induce specific cellular responses, leading to the expression of one or few ligands. A large body of evidence demonstrates that NK cell activation can be triggered by different NKG2D ligands, often expressed on the same cell, suggesting a functional redundancy of these molecules. However, since a number of evasion mechanisms can reduce membrane expression of these molecules both on virus-infected and tumor cells, the co-expression of different ligands and/or the presence of allelic forms of the same ligand guarantee NKG2D activation in various stressful conditions and cell contexts. Noteworthy, NKG2D ligands can differ in their ability to down-modulate NKG2D membrane expression in human NK cells supporting the idea that NKG2D transduces different signals upon binding various ligands. Moreover, whether proteolytically shed and exosome-associated soluble NKG2D ligands share with their membrane-bound counterparts the same ability to induce NKG2D-mediated signaling is still a matter of debate. Here, we will review recent studies on the NKG2D/NKG2D ligand biology to summarize and discuss the redundancy and/or diversity in ligand expression, regulation, and receptor specificity.

  10. A thermal responsive affinity ligand for precipitation of sialylated proteins

    Directory of Open Access Journals (Sweden)

    Lindsay Arnold

    2016-01-01

    Full Text Available We report here the development of a thermal responsive affinity ligand specific to sialic acid, sialic acid containing oligosaccharides, glycoproteins, and other sialylated glycoconjugates. The ligand is a fusion protein of 40 repeats of pentapeptide of an elastin like polymer (ELP and the 21 kD sialic acid binding domain of a Vibrio cholera neuraminidase (VCNA. For cost-effective synthesis, the fusion protein was targeted to the periplasmic space of an E. coli lpp deletion mutant, resulting in its secretion to the growth medium. A pre-induction heat-shock step at 42 ˚C for 20 minutes was necessary to achieve high level expression of the ligand. Under optimized induction condition (18 ˚C, 0.1 mM IPTG and 48 hours of post-induction cultivation, the ligand was produced to about 100 mg/L. The ligand exhibited a transition temperature of 52 ˚C, which could be depressed to 37 ˚C with the addition of 0.5 M NaCl. Using fetuin as a model sialylated protein, the ligand was applied in an affinity precipitation process to illustrate its potential application in glycoprotein isolation. The ligand captured 100% fetuin from an aqueous solution when the molar ratio of ligand to fetuin was 10 to 1, which was lower than the expected for full titration of sialic acid on the glycoprotein by the lectin. Elution of fetuin from ligand was achieved with PBS buffer containing 2 mM sialic acid. To evaluate how protein and other contaminants influence the recovery of sialylated proteins, CHO medium was spiked into the fetuin solution. The predominant protein species in CHO medium was found to be albumin. Although its removal of over 94% was evident, purified fetuin contained some albumin due to its over-abundance. Additional experiments with albumin contaminant of varying concentrations showed that below 1 mg/L, albumin had no impact on the affinity precipitation, whereas above 10 mg/L, some albumin was co-purified with fetuin. However, even at 50 mg/ml, fetuin

  11. Crystallization of protein–ligand complexes

    International Nuclear Information System (INIS)

    Hassell, Anne M.; An, Gang; Bledsoe, Randy K.; Bynum, Jane M.; Carter, H. Luke III; Deng, Su-Jun J.; Gampe, Robert T.; Grisard, Tamara E.; Madauss, Kevin P.; Nolte, Robert T.; Rocque, Warren J.; Wang, Liping; Weaver, Kurt L.; Williams, Shawn P.; Wisely, G. Bruce; Xu, Robert; Shewchuk, Lisa M.

    2007-01-01

    Methods presented for growing protein–ligand complexes fall into the categories of co-expression of the protein with the ligands of interest, use of the ligands during protein purification, cocrystallization and soaking the ligands into existing crystals. Obtaining diffraction-quality crystals has long been a bottleneck in solving the three-dimensional structures of proteins. Often proteins may be stabilized when they are complexed with a substrate, nucleic acid, cofactor or small molecule. These ligands, on the other hand, have the potential to induce significant conformational changes to the protein and ab initio screening may be required to find a new crystal form. This paper presents an overview of strategies in the following areas for obtaining crystals of protein–ligand complexes: (i) co-expression of the protein with the ligands of interest, (ii) use of the ligands during protein purification, (iii) cocrystallization and (iv) soaks

  12. Identité stricte ou partielle et identification dans les phrases à copule. Comment les identifier ?

    Directory of Open Access Journals (Sweden)

    Amary-Coudreau Valérie

    2014-07-01

    éristiques propres à l’identité, ainsi que celles propres à la spécification et à l’identification, pour lesquelles X et Y ont des degrés de référentialité et/ou de prédicativité différents. Enfin, cette hypothèse nous amène à distinguer l’identité de l’identification, sur la base de tests qui, à l’inverse de Larreya (2003, différencient l’identité stricte de l’identité partielle.

  13. A liposomal drug platform overrides peptide ligand targeting to a cancer biomarker, irrespective of ligand affinity or density.

    Directory of Open Access Journals (Sweden)

    Bethany Powell Gray

    Full Text Available One method for improving cancer treatment is the use of nanoparticle drugs functionalized with targeting ligands that recognize receptors expressed selectively by tumor cells. In theory such targeting ligands should specifically deliver the nanoparticle drug to the tumor, increasing drug concentration in the tumor and delivering the drug to its site of action within the tumor tissue. However, the leaky vasculature of tumors combined with a poor lymphatic system allows the passive accumulation, and subsequent retention, of nanosized materials in tumors. Furthermore, a large nanoparticle size may impede tumor penetration. As such, the role of active targeting in nanoparticle delivery is controversial, and it is difficult to predict how a targeted nanoparticle drug will behave in vivo. Here we report in vivo studies for αvβ6-specific H2009.1 peptide targeted liposomal doxorubicin, which increased liposomal delivery and toxicity to lung cancer cells in vitro. We systematically varied ligand affinity, ligand density, ligand stability, liposome dosage, and tumor models to assess the role of active targeting of liposomes to αvβ6. In direct contrast to the in vitro results, we demonstrate no difference in in vivo targeting or efficacy for H2009.1 tetrameric peptide liposomal doxorubicin, compared to control peptide and no peptide liposomes. Examining liposome accumulation and distribution within the tumor demonstrates that the liposome, and not the H2009.1 peptide, drives tumor accumulation, and that both targeted H2009.1 and untargeted liposomes remain in perivascular regions, with little tumor penetration. Thus H2009.1 targeted liposomes fail to improve drug efficacy because the liposome drug platform prevents the H2009.1 peptide from both actively targeting the tumor and binding to tumor cells throughout the tumor tissue. Therefore, using a high affinity and high specificity ligand targeting an over-expressed tumor biomarker does not guarantee

  14. Metabolic Value Chemoattractants Are Preferentially Recognized at Broad Ligand Range Chemoreceptor of Pseudomonas putida KT2440

    Directory of Open Access Journals (Sweden)

    Matilde Fernández

    2017-05-01

    Full Text Available Bacteria have evolved a wide range of chemoreceptors with different ligand specificities. Typically, chemoreceptors bind ligands with elevated specificity and ligands serve as growth substrates. However, there is a chemoreceptor family that has a broad ligand specificity including many compounds that are not of metabolic value. To advance the understanding of this family, we have used the PcaY_PP (PP2643 chemoreceptor of Pseudomonas putida KT2440 as a model. Using Isothermal Titration Calorimetry we showed here that the recombinant ligand binding domain (LBD of PcaY_PP recognizes 17 different C6-ring containing carboxylic acids with KD values between 3.7 and 138 μM and chemoeffector affinity correlated with the magnitude of the chemotactic response. Mutation of the pcaY_PP gene abolished chemotaxis to these compounds; phenotype that was restored following gene complementation. Growth experiments using PcaY_PP ligands as sole C-sources revealed functional relationships between their metabolic potential and affinity for the chemoreceptor. Thus, only 7 PcaY_PP ligands supported growth and their KD values correlated with the length of the bacterial lag phase. Furthermore, PcaY_PP ligands that did not support growth had significantly higher KD values than those that did. The receptor has thus binds preferentially compounds that serve as C-sources and amongst them those that rapidly promote growth. Tightest binding compounds were quinate, shikimate, 3-dehydroshikimate and protocatechuate, which are at the interception of the biosynthetic shikimate and catabolic quinate pathways. Analytical ultracentrifugation studies showed that ligand free PcaY_PP-LBD is present in a monomer-dimer equilibrium (KD = 57.5 μM. Ligand binding caused a complete shift to the dimeric state, which appears to be a general feature of four-helix bundle LBDs. This study indicates that the metabolic potential of compounds is an important parameter in the molecular recognition

  15. Optimization of an effective growth medium for culturing probiotic bacteria for applications in strict vegetarian food products

    Directory of Open Access Journals (Sweden)

    Manju Pathak

    2012-10-01

    Full Text Available Background: This study aimed to modify de Man Rogosa Sharpe culture medium (termed MRS for selective cultivation of probiotics strain for the consumption by the strictly vegetarian human population. Vegetarian probiotic foods by definition must be free from all animal-derived ingredients. This not only includes the product ingredients but the probiotic inoculum as well. Probiotic starter cultures are traditionally grown and stored in media containing milk or meatderived ingredients. The presence of these ingredients makes the probiotic cell concentrates unsuitable for use in vegetarian products and thus creates the need for a growth medium which isfree from animal-derived ingredients. Present study investigated the growth of a strain of Lactobacillus lactis in MRS. The present invention relates in general to a bacterial culture media,and more specifically a complex microbial culture media, based on plant seed powder extract in place of animal extract for probiotic bacterial growth.Methods: Lactobacillus lactis, a probiotic, was grown in standard MRS culture medium as well as in our various test media (TM containing various vegetal source in place of beef extract, yeast extract and peptone as in case of MRS. The inoculated culture mediums were incubated at 37C for 72 hours and growth of probiotic is recorded at regular intervals. The growth was recorded as Colony Forming Units (CFUs.Results: The best growth of probiotic is observed in TM 2. TM 2 is the leguminous seed extract. Starter culture mediums for probiotics or other bacteria primarily contain protein from animal source. The possibility of using vegetal protein from TM 2 extract in place of peptones and meat extract for the nitrogen supplementation of culture media for the growth of lactic acid bacteria has been demonstrated.Functional Foods in Health and Disease 2012, 2(10:369-378 Conclusion: The absolute vegetarian culture medium containing TM 2 is better than standard MRS for the

  16. Xanthene and Xanthone Derivatives as G-Quadruplex Stabilizing Ligands

    Directory of Open Access Journals (Sweden)

    Alessandro Altieri

    2013-10-01

    Full Text Available Following previous studies on anthraquinone and acridine-based G-quadruplex ligands, here we present a study of similar aromatic cores, with the specific aim of increasing G-quadruplex binding and selectivity with respect to duplex DNA. Synthesized compounds include two and three-side chain xanthone and xanthene derivatives, as well as a dimeric “bridged” form. ESI and FRET measurements suggest that all the studied molecules are good G-quadruplex ligands, both at telomeres and on G-quadruplex forming sequences of oncogene promoters. The dimeric compound and the three-side chain xanthone derivative have been shown to represent the best compounds emerging from the different series of ligands presented here, having also high selectivity for G-quadruplex structures with respect to duplex DNA. Molecular modeling simulations are in broad agreement with the experimental data.

  17. GPCR biased ligands as novel heart failure therapeutics.

    Science.gov (United States)

    Violin, Jonathan D; Soergel, David G; Boerrigter, Guido; Burnett, John C; Lark, Michael W

    2013-10-01

    G protein-coupled receptors have been successfully targeted by numerous therapeutics including drugs that have transformed the management of cardiovascular disease. However, many GPCRs, when activated or blocked by drugs, elicit both beneficial and adverse pharmacology. Recent work has demonstrated that in some cases, the salutary and deleterious signals linked to a specific GPCR can be selectively targeted by "biased ligands" that entrain subsets of a receptor's normal pharmacology. This review briefly summarizes the advances and current state of the biased ligand field, focusing on an example: biased ligands targeting the angiotensin II type 1 receptor. These compounds exhibit unique pharmacology, distinct from classic agonists or antagonists, and one such molecule is now in clinical development for the treatment of acute heart failure. Copyright © 2013 Elsevier Inc. All rights reserved.

  18. -Pincer Ligand Family through Ligand Post-Modification

    KAUST Repository

    Huang, Mei-Hui

    2017-10-02

    A series of air-stable nickel complexes containing triazine-based PN3P-pincer ligands were synthesized and fully characterized. Complex 3 contains a de-aromatized central triazine ring from the deprotonation of one of the N–H arms. With a post-modification strategy, the Me-PN3P*NiCl complex (3) could be converted into a new class of diimine–traizine PN3P-pincer nickel complexes.

  19. Chelating ligands for nanocrystals' surface functionalization

    NARCIS (Netherlands)

    Querner, Claudia; Reiss, Peter; Bleuse, Joël; Pron, Adam

    2004-01-01

    A new family of ligands for the surface functionalization of CdSe nanocrystals is proposed, namely alkyl or aryl derivatives of carbodithioic acids (R-C(S)SH). The main advantages of these new ligands are as follows: they nearly quantitatively exchange the initial surface ligands (TOPO) in very mild

  20. Development of radioiodinated receptor ligands for cerebral single photon emission tomography

    International Nuclear Information System (INIS)

    Knapp, F.F. Jr.; McPherson, D.W.

    1992-01-01

    In the last decade the use of radiolabeled ligands for the imaging of cerebral receptors by emission computed tomography (ECT) has seen rapid growth. The opportunity to routinely perform cerebral single photon emission tomography (SPET) with iodine-123-labeled ligands depends on the availability of receptor ligands into which iodine can be introduced without decreasing the required high target receptor specificity. The use of iodine-123-labeled receptor-specific ligands also depends on the availability of high purity iodine-123 at reasonable costs and the necessary imaging instrumentation. In this paper, the development and current stage of evaluation of various iodine-123-labeled ligands for SPET imaging of dopaminergic, serotonergic and muscarinic acetylcholinergic receptor classes are discussed

  1. Selection of ligands for affinity chromatography using quartz crystal biosensor.

    Science.gov (United States)

    Liu, Yang; Tang, Xiaoling; Liu, Feng; Li, Ke'an

    2005-07-01

    This paper described a new strategy for rapid selecting ligands for application in affinity chromatography using a quartz crystal microbalance (QCM) biosensor. An aminoglycoside antibiotic drug, kanamycin (KM), was immobilized on the gold electrodes of the QCM sensor chip. The binding interactions of the immobilized KM with various proteins in solution were monitored as the variations of the resonant frequency of the modified sensor. Such a rapid screen analysis of interactions indicated clearly that KM-immobilized sensor showed strong specific interaction only with lysozyme (LZM). The resultant sensorgrams were rapidly analyzed by using a kinetic analysis software based on a genetic algorithm to derive both the kinetic rate constants (k(ass) and k(diss)) and equilibrium dissociation constants (K(D)) for LZM-KM interactions. The immobilized KM showed higher affinity to LZM with a dissociation constant on the order of 10(-5) M, which is within the range of 10(-4)-10(-8) M and suitable for an affinity ligand. Therefore, KM was demonstrated for the first time as a novel affinity ligand for purification of LZM and immobilized onto the epoxy-activated silica in the presence of a high potassium phosphate concentration. The KM immobilized affinity column has proved useful for a very convenient purification of LZM from chicken egg white. The purity of LZM obtained was higher than 90%, as determined by densitometric scanning of sodium dodecyl sulfate-polyacrylamide gel electrophoresis of purified fraction. These results confirmed that the selected KM ligand is indeed a valuable affinity ligand for purification of LZM. The new screening strategy based on a QCM biosensor is expected to be a promising way for rapid selecting specific ligands for purifying other valuable proteins.

  2. Residue preference mapping of ligand fragments in the Protein Data Bank.

    Science.gov (United States)

    Wang, Lirong; Xie, Zhaojun; Wipf, Peter; Xie, Xiang-Qun

    2011-04-25

    The interaction between small molecules and proteins is one of the major concerns for structure-based drug design because the principles of protein-ligand interactions and molecular recognition are not thoroughly understood. Fortunately, the analysis of protein-ligand complexes in the Protein Data Bank (PDB) enables unprecedented possibilities for new insights. Herein, we applied molecule-fragmentation algorithms to split the ligands extracted from PDB crystal structures into small fragments. Subsequently, we have developed a ligand fragment and residue preference mapping (LigFrag-RPM) algorithm to map the profiles of the interactions between these fragments and the 20 proteinogenic amino acid residues. A total of 4032 fragments were generated from 71 798 PDB ligands by a ring cleavage (RC) algorithm. Among these ligand fragments, 315 unique fragments were characterized with the corresponding fragment-residue interaction profiles by counting residues close to these fragments. The interaction profiles revealed that these fragments have specific preferences for certain types of residues. The applications of these interaction profiles were also explored and evaluated in case studies, showing great potential for the study of protein-ligand interactions and drug design. Our studies demonstrated that the fragment-residue interaction profiles generated from the PDB ligand fragments can be used to detect whether these fragments are in their favorable or unfavorable environments. The algorithm for a ligand fragment and residue preference mapping (LigFrag-RPM) developed here also has the potential to guide lead chemistry modifications as well as binding residues predictions.

  3. Ligand-directed trafficking of receptor stimulus.

    Science.gov (United States)

    Chilmonczyk, Zdzisław; Bojarski, Andrzej J; Sylte, Ingebrigt

    2014-12-01

    GPCRs are seven transmembrane-spanning receptors that convey specific extracellular stimuli to intracellular signalling. They represent the largest family of cell surface proteins that are therapeutically targeted. According to the traditional two-state model of receptor theory, GPCRs were considered as operating in equilibrium between two functional conformations, an active (R*) and inactive (R) state. Thus, it was assumed that a GPCR can exist either in an "off" or "on" conformation causing either no activation or equal activation of all its signalling pathways. Over the past several years it has become evident that this model is too simple and that GPCR signalling is far more complex. Different studies have presented a multistate model of receptor activation in which ligand-specific receptor conformations are able to differentiate between distinct signalling partners. Recent data show that beside G proteins numerous other proteins, such as β-arrestins and kinases, may interact with GPCRs and activate intracellular signalling pathways. GPCR activation may therefore involve receptor desensitization, coupling to multiple G proteins, Gα or Gβγ signalling, and pathway activation that is independent of G proteins. This latter effect leads to agonist "functional selectivity" (also called ligand-directed receptor trafficking, stimulus trafficking, biased agonism, biased signalling), and agonist intervention with functional selectivity may improve the therapy. Many commercially available drugs with beneficial efficacy also show various undesirable side effects. Further studies of biased signalling might facilitate our understanding of the side effects of current drugs and take us to new avenues to efficiently design pathway-specific medications. Copyright © 2014 Institute of Pharmacology, Polish Academy of Sciences. Published by Elsevier Urban & Partner Sp. z o.o. All rights reserved.

  4. Strict liability as a legal mechanism protecting the aggrieved parties' interests within the nuclear liability regime

    International Nuclear Information System (INIS)

    Novotna, Marianna

    2016-01-01

    The no-fault liability principle of nuclear liability regime, its compensation schemes, sociological and legal grounds of its construction as well as liberation grounds are analysed. The simple existence of causation of damage and nuclear accident without necessity of proving negligence or any other type of fault on the part of the operator as an adequate basis for the operator’s strict liability is highlighted thus simplifying the litigation process eliminating potential obstacles, especially such as might exist with the burden of proof. The question of weighing the interests of society in the development of nuclear industry, the necessary extent of protection of victims of nuclear accidents and the interests of operators of nuclear facilities as main determinants of the strict nature of nuclear liability is also described. (orig.)

  5. Alternative Affinity Ligands for Immunoglobulins.

    Science.gov (United States)

    Kruljec, Nika; Bratkovič, Tomaž

    2017-08-16

    The demand for recombinant therapeutic antibodies and Fc-fusion proteins is expected to increase in the years to come. Hence, extensive efforts are concentrated on improving the downstream processing. In particular, the development of better-affinity chromatography matrices, supporting robust time- and cost-effective antibody purification, is warranted. With the advances in molecular design and high-throughput screening approaches from chemical and biological combinatorial libraries, novel affinity ligands representing alternatives to bacterial immunoglobulin (Ig)-binding proteins have entered the scene. Here, we review the design, development, and properties of diverse classes of alternative antibody-binding ligands, ranging from engineered versions of Ig-binding proteins, to artificial binding proteins, peptides, aptamers, and synthetic small-molecular-weight compounds. We also provide examples of applications for the novel affinity matrices in chromatography and beyond.

  6. Heterobifunctional crosslinkers for tethering single ligand molecules to scanning probes

    International Nuclear Information System (INIS)

    Riener, Christian K.; Kienberger, Ferry; Hahn, Christoph D.; Buchinger, Gerhard M.; Egwim, Innocent O.C.; Haselgruebler, Thomas; Ebner, Andreas; Romanin, Christoph; Klampfl, Christian; Lackner, Bernd; Prinz, Heino; Blaas, Dieter; Hinterdorfer, Peter; Gruber, Hermann J.

    2003-01-01

    Single molecule recognition force microscopy (SMRFM) is a versatile atomic force microscopy (AFM) method to probe specific interactions of cognitive molecules on the single molecule level. It allows insights to be gained into interaction potentials and kinetic barriers and is capable of mapping interaction sites with nm positional accuracy. These applications require a ligand to be attached to the AFM tip, preferably by a distensible poly(ethylene glycol) (PEG) chain between the measuring tip and the ligand molecule. The PEG chain greatly facilitates specific binding of the ligand to immobile receptor sites on the sample surface. The present study contributes to tip-PEG-ligand tethering in three ways: (i) a convenient synthetic route was found to prepare NH 2 -PEG-COOH which is the key intermediate for long heterobifunctional crosslinkers; (ii) a variety of heterobifunctional PEG derivatives for tip-PEG-ligand linking were prepared from NH 2 -PEG-COOH; (iii) in particular, a new PEG crosslinker with one thiol-reactive end and one terminal nitrilotriacetic acid (NTA) group was synthesized and successfully used to tether His 6 -tagged protein molecules to AFM tips via noncovalent NTA-Ni 2+ -His 6 bridges. The new crosslinker was applied to link a recombinant His 6 -tagged fragment of the very-low density lipoprotein receptor to the AFM tip whereupon specific docking to the capsid of human rhinovirus particles was observed by force microscopy. In a parallel study, the specific interaction of the small GTPase Ran with the nuclear import receptor importin β1 was studied in detail by SMRFM, using the new crosslinker to link His 6 -tagged Ran to the measuring tip [Nat. Struct. Biol. (2003), 10, 553-557

  7. The impact of Sleep Time-Related Information and Communication Technology (STRICT) on sleep patterns and daytime functioning in American adolescents.

    Science.gov (United States)

    Polos, Peter G; Bhat, Sushanth; Gupta, Divya; O'Malley, Richard J; DeBari, Vincent A; Upadhyay, Hinesh; Chaudhry, Saqib; Nimma, Anitha; Pinto-Zipp, Genevieve; Chokroverty, Sudhansu

    2015-10-01

    This cross-sectional study explored the extent and impact of mobile device-based Sleep Time-Related Information and Communication Technology (STRICT) use among American adolescents (N = 3139, 49.3% female, mean age = 13.3 years). Nearly 62% used STRICT after bedtime, 56.7% texted/tweeted/messaged in bed, and 20.8% awoke to texts. STRICT use was associated with insomnia, daytime sleepiness, eveningness, academic underperformance, later bedtimes and shorter sleep duration. Moderation analysis demonstrated that the association between STRICT use and insomnia increased with age, the association between STRICT use and daytime sleepiness decreased with age, and the association between STRICT use and shorter sleep duration decreased with age and was stronger in girls. Insomnia and daytime sleepiness partially mediated the relationship between STRICT use and academic underperformance. Our results illustrate the adverse interactions between adolescent STRICT use and sleep, with deleterious effects on daytime functioning. These worrisome findings suggest that placing reasonable limitations on adolescent STRICT use may be appropriate. Copyright © 2015 The Foundation for Professionals in Services for Adolescents. Published by Elsevier Ltd. All rights reserved.

  8. Ligand binding by PDZ domains

    DEFF Research Database (Denmark)

    Chi, Celestine N.; Bach, Anders; Strømgaard, Kristian

    2012-01-01

    The postsynaptic density protein-95/disks large/zonula occludens-1 (PDZ) protein domain family is one of the most common protein-protein interaction modules in mammalian cells, with paralogs present in several hundred human proteins. PDZ domains are found in most cell types, but neuronal proteins...... as pathological conditions have been reviewed recently. In this review, we focus on the molecular details of how PDZ domains bind their protein ligands and their potential as drug targets in this context....

  9. Bitopic Ligands and Metastable Binding Sites

    DEFF Research Database (Denmark)

    Fronik, Philipp; Gaiser, Birgit I; Sejer Pedersen, Daniel

    2017-01-01

    of orthosteric binding sites. Bitopic ligands have been employed to address the selectivity problem by combining (linking) an orthosteric ligand with an allosteric modulator, theoretically leading to high-affinity subtype selective ligands. However, it remains a challenge to identify suitable allosteric binding...... that have been reported to date, this type of bitopic ligands would be composed of two identical pharmacophores. Herein, we outline the concept of bitopic ligands, review metastable binding sites, and discuss their potential as a new source of allosteric binding sites....

  10. Using chemical shift perturbation to characterise ligand binding.

    Science.gov (United States)

    Williamson, Mike P

    2013-08-01

    Chemical shift perturbation (CSP, chemical shift mapping or complexation-induced changes in chemical shift, CIS) follows changes in the chemical shifts of a protein when a ligand is added, and uses these to determine the location of the binding site, the affinity of the ligand, and/or possibly the structure of the complex. A key factor in determining the appearance of spectra during a titration is the exchange rate between free and bound, or more specifically the off-rate koff. When koff is greater than the chemical shift difference between free and bound, which typically equates to an affinity Kd weaker than about 3μM, then exchange is fast on the chemical shift timescale. Under these circumstances, the observed shift is the population-weighted average of free and bound, which allows Kd to be determined from measurement of peak positions, provided the measurements are made appropriately. (1)H shifts are influenced to a large extent by through-space interactions, whereas (13)Cα and (13)Cβ shifts are influenced more by through-bond effects. (15)N and (13)C' shifts are influenced both by through-bond and by through-space (hydrogen bonding) interactions. For determining the location of a bound ligand on the basis of shift change, the most appropriate method is therefore usually to measure (15)N HSQC spectra, calculate the geometrical distance moved by the peak, weighting (15)N shifts by a factor of about 0.14 compared to (1)H shifts, and select those residues for which the weighted shift change is larger than the standard deviation of the shift for all residues. Other methods are discussed, in particular the measurement of (13)CH3 signals. Slow to intermediate exchange rates lead to line broadening, and make Kd values very difficult to obtain. There is no good way to distinguish changes in chemical shift due to direct binding of the ligand from changes in chemical shift due to allosteric change. Ligand binding at multiple sites can often be characterised, by

  11. Strict versus liberal target range for perioperative glucose in patients undergoing coronary artery bypass grafting: a prospective randomized controlled trial.

    Science.gov (United States)

    Desai, Shalin P; Henry, Linda L; Holmes, Sari D; Hunt, Sharon L; Martin, Chidima T; Hebsur, Shrinivas; Ad, Niv

    2012-02-01

    The purpose of this study was to test the hypothesis that a liberal blood glucose strategy (121-180 mg/dL) is not inferior to a strict blood glucose strategy (90-120 mg/dL) for outcomes in patients after first-time isolated coronary artery bypass grafting and is superior for glucose control and target blood glucose management. A total of 189 patients undergoing coronary artery bypass grafting were investigated in this prospective randomized study to compare 2 glucose control strategies on patient perioperative outcomes. Three methods of analyses (intention to treat, completer, and per protocol) were conducted. Observed power was robust (>80%) for significant results. The groups were similar on preoperative hemoglobin A(1c) and number of diabetic patients. The liberal group was found to be noninferior to the strict group for perioperative complications and superior on glucose control and target range management. The liberal group had significantly fewer patients with hypoglycemic events (liberal range after coronary artery bypass grafting led to similar outcomes compared with a strict target range and was superior in glucose control and target range management. On the basis of the results of this study, a target blood glucose range of 121 to 180 mg/dL is recommended for patients after coronary artery bypass grafting as advocated by the Society of Thoracic Surgeons. Copyright © 2012 The American Association for Thoracic Surgery. Published by Mosby, Inc. All rights reserved.

  12. Incorporation of protein flexibility and conformational energy penalties in docking screens to improve ligand discovery

    Science.gov (United States)

    Fischer, Marcus; Coleman, Ryan G.; Fraser, James S.; Shoichet, Brian K.

    2014-07-01

    Proteins fluctuate between alternative conformations, which presents a challenge for ligand discovery because such flexibility is difficult to treat computationally owing to problems with conformational sampling and energy weighting. Here we describe a flexible docking method that samples and weights protein conformations using experimentally derived conformations as a guide. The crystallographically refined occupancies of these conformations, which are observable in an apo receptor structure, define energy penalties for docking. In a large prospective library screen, we identified new ligands that target specific receptor conformations of a cavity in cytochrome c peroxidase, and we confirm both ligand pose and associated receptor conformation predictions by crystallography. The inclusion of receptor flexibility led to ligands with new chemotypes and physical properties. By exploiting experimental measures of loop and side-chain flexibility, this method can be extended to the discovery of new ligands for hundreds of targets in the Protein Data Bank for which similar experimental information is available.

  13. Potential ligand-binding residues in rat olfactory receptors identified by correlated mutation analysis

    Science.gov (United States)

    Singer, M. S.; Oliveira, L.; Vriend, G.; Shepherd, G. M.

    1995-01-01

    A family of G-protein-coupled receptors is believed to mediate the recognition of odor molecules. In order to identify potential ligand-binding residues, we have applied correlated mutation analysis to receptor sequences from the rat. This method identifies pairs of sequence positions where residues remain conserved or mutate in tandem, thereby suggesting structural or functional importance. The analysis supported molecular modeling studies in suggesting several residues in positions that were consistent with ligand-binding function. Two of these positions, dominated by histidine residues, may play important roles in ligand binding and could confer broad specificity to mammalian odor receptors. The presence of positive (overdominant) selection at some of the identified positions provides additional evidence for roles in ligand binding. Higher-order groups of correlated residues were also observed. Each group may interact with an individual ligand determinant, and combinations of these groups may provide a multi-dimensional mechanism for receptor diversity.

  14. Effectiveness of strict vs. multiple use protected areas in reducing tropical forest fires: a global analysis using matching methods.

    Directory of Open Access Journals (Sweden)

    Andrew Nelson

    Full Text Available Protected areas (PAs cover a quarter of the tropical forest estate. Yet there is debate over the effectiveness of PAs in reducing deforestation, especially when local people have rights to use the forest. A key analytic problem is the likely placement of PAs on marginal lands with low pressure for deforestation, biasing comparisons between protected and unprotected areas. Using matching techniques to control for this bias, this paper analyzes the global tropical forest biome using forest fires as a high resolution proxy for deforestation; disaggregates impacts by remoteness, a proxy for deforestation pressure; and compares strictly protected vs. multiple use PAs vs indigenous areas. Fire activity was overlaid on a 1 km map of tropical forest extent in 2000; land use change was inferred for any point experiencing one or more fires. Sampled points in pre-2000 PAs were matched with randomly selected never-protected points in the same country. Matching criteria included distance to road network, distance to major cities, elevation and slope, and rainfall. In Latin America and Asia, strict PAs substantially reduced fire incidence, but multi-use PAs were even more effective. In Latin America, where there is data on indigenous areas, these areas reduce forest fire incidence by 16 percentage points, over two and a half times as much as naïve (unmatched comparison with unprotected areas would suggest. In Africa, more recently established strict PAs appear to be effective, but multi-use tropical forest protected areas yield few sample points, and their impacts are not robustly estimated. These results suggest that forest protection can contribute both to biodiversity conservation and CO2 mitigation goals, with particular relevance to the REDD agenda. Encouragingly, indigenous areas and multi-use protected areas can help to accomplish these goals, suggesting some compatibility between global environmental goals and support for local livelihoods.

  15. Hydroxycinnamic acids used as external acceptors of electrons: an energetic advantage for strictly heterofermentative lactic acid bacteria.

    Science.gov (United States)

    Filannino, Pasquale; Gobbetti, Marco; De Angelis, Maria; Di Cagno, Raffaella

    2014-12-01

    The metabolism of hydroxycinnamic acids by strictly heterofermentative lactic acid bacteria (19 strains) was investigated as a potential alternative energy route. Lactobacillus curvatus PE5 was the most tolerant to hydroxycinnamic acids, followed by strains of Weissella spp., Lactobacillus brevis, Lactobacillus fermentum, and Leuconostoc mesenteroides, for which the MIC values were the same. The highest sensitivity was found for Lactobacillus rossiae strains. During growth in MRS broth, lactic acid bacteria reduced caffeic, p-coumaric, and ferulic acids into dihydrocaffeic, phloretic, and dihydroferulic acids, respectively, or decarboxylated hydroxycinnamic acids into the corresponding vinyl derivatives and then reduced the latter compounds to ethyl compounds. Reductase activities mainly emerged, and the activities of selected strains were further investigated in chemically defined basal medium (CDM) under anaerobic conditions. The end products of carbon metabolism were quantified, as were the levels of intracellular ATP and the NAD(+)/NADH ratio. Electron and carbon balances and theoretical ATP/glucose yields were also estimated. When CDM was supplemented with hydroxycinnamic acids, the synthesis of ethanol decreased and the concentration of acetic acid increased. The levels of these metabolites reflected on the alcohol dehydrogenase and acetate kinase activities. Overall, some biochemical traits distinguished the common metabolism of strictly heterofermentative strains: main reductase activity toward hydroxycinnamic acids, a shift from alcohol dehydrogenase to acetate kinase activities, an increase in the NAD(+)/NADH ratio, and the accumulation of supplementary intracellular ATP. Taken together, the above-described metabolic responses suggest that strictly heterofermentative lactic acid bacteria mainly use hydroxycinnamic acids as external acceptors of electrons. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

  16. Fermentative Degradation of Polyethylene Glycol by a Strictly Anaerobic, Gram-Negative, Nonsporeforming Bacterium, Pelobacter venetianus sp. nov

    OpenAIRE

    1983-01-01

    The synthetic polyether polyethylene glycol (PEG) with a molecular weight of 20,000 was anaerobically degraded in enrichment cultures inoculated with mud of limnic and marine origins. Three strains (Gra PEG 1, Gra PEG 2, and Ko PEG 2) of rod-shaped, gram-negative, nonsporeforming, strictly anaerobic bacteria were isolated in mineral medium with PEG as the sole source of carbon and energy. All strains degraded dimers, oligomers, and polymers of PEG up to a molecular weight of 20,000 completely...

  17. An Iterative Algorithm Combining Viscosity Method with Parallel Method for a Generalized Equilibrium Problem and Strict Pseudocontractions

    Directory of Open Access Journals (Sweden)

    2009-03-01

    Full Text Available We introduce a new approximation scheme combining the viscosity method with parallel method for finding a common element of the set of solutions of a generalized equilibrium problem and the set of fixed points of a family of finitely strict pseudocontractions. We obtain a strong convergence theorem for the sequences generated by these processes in Hilbert spaces. Based on this result, we also get some new and interesting results. The results in this paper extend and improve some well-known results in the literature.

  18. Effect of scanner acoustic background noise on strict resting-state fMRI

    Directory of Open Access Journals (Sweden)

    C. Rondinoni

    2013-04-01

    Full Text Available Functional MRI (fMRI resting-state experiments are aimed at identifying brain networks that support basal brain function. Although most investigators consider a ‘resting-state' fMRI experiment with no specific external stimulation, subjects are unavoidably under heavy acoustic noise produced by the equipment. In the present study, we evaluated the influence of auditory input on the resting-state networks (RSNs. Twenty-two healthy subjects were scanned using two similar echo-planar imaging sequences in the same 3T MRI scanner: a default pulse sequence and a reduced “silent” pulse sequence. Experimental sessions consisted of two consecutive 7-min runs with noise conditions (default or silent counterbalanced across subjects. A self-organizing group independent component analysis was applied to fMRI data in order to recognize the RSNs. The insula, left middle frontal gyrus and right precentral and left inferior parietal lobules showed significant differences in the voxel-wise comparison between RSNs depending on noise condition. In the presence of low-level noise, these areas Granger-cause oscillations in RSNs with cognitive implications (dorsal attention and entorhinal, while during high noise acquisition, these connectivities are reduced or inverted. Applying low noise MR acquisitions in research may allow the detection of subtle differences of the RSNs, with implications in experimental planning for resting-state studies, data analysis, and ergonomic factors.

  19. Sponge-associated bacteria are strictly maintained in two closely related but geographically distant sponge hosts.

    Science.gov (United States)

    Montalvo, Naomi F; Hill, Russell T

    2011-10-01

    The giant barrel sponges Xestospongia muta and Xestospongia testudinaria are ubiquitous in tropical reefs of the Atlantic and Pacific Oceans, respectively. They are key species in their respective environments and are hosts to diverse assemblages of bacteria. These two closely related sponges from different oceans provide a unique opportunity to examine the evolution of sponge-associated bacterial communities. Mitochondrial cytochrome oxidase subunit I gene sequences from X. muta and X. testudinaria showed little divergence between the two species. A detailed analysis of the bacterial communities associated with these sponges, comprising over 900 full-length 16S rRNA gene sequences, revealed remarkable similarity in the bacterial communities of the two species. Both sponge-associated communities include sequences found only in the two Xestospongia species, as well as sequences found also in other sponge species and are dominated by three bacterial groups, Chloroflexi, Acidobacteria, and Actinobacteria. While these groups consistently dominate the bacterial communities revealed by 16S rRNA gene-based analysis of sponge-associated bacteria, the depth of sequencing undertaken in this study revealed clades of bacteria specifically associated with each of the two Xestospongia species, and also with the genus Xestospongia, that have not been found associated with other sponge species or other ecosystems. This study, comparing the bacterial communities associated with closely related but geographically distant sponge hosts, gives new insight into the intimate relationships between marine sponges and some of their bacterial symbionts.

  20. 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.

  1. Ligand binding affinity and changes in the lateral diffusion of receptor for advanced glycation endproducts (RAGE).

    Science.gov (United States)

    Syed, Aleem; Zhu, Qiaochu; Smith, Emily A

    2016-12-01

    The effect of ligand on the lateral diffusion of receptor for advanced glycation endproducts (RAGE), a receptor involved in numerous pathological conditions, remains unknown. Single particle tracking experiments that use quantum dots specifically bound to hemagglutinin (HA)-tagged RAGE (HA-RAGE) are reported to elucidate the effect of ligand binding on HA-RAGE diffusion in GM07373 cell membranes. The ligand used in these studies is methylglyoxal modified-bovine serum albumin (MGO-BSA) containing advanced glycation end products modifications. The binding affinity between soluble RAGE and MGO-BSA increases by 1.8 to 9.7-fold as the percent primary amine modification increases from 24 to 74% and with increasing negative charge on the MGO-BSA. Ligand incubation affects the HA-RAGE diffusion coefficient, the radius of confinement, and duration of confinement. There is, however, no correlation between MGO-BSA ligand binding affinity with soluble RAGE and the extent of the changes in HA-RAGE lateral diffusion. The ligand induced changes to HA-RAGE lateral diffusion do not occur when cholesterol is depleted from the cell membrane, indicating the mechanism for ligand-induced changes to HA-RAGE diffusion is cholesterol dependent. The results presented here serve as a first step in unraveling how ligand influences RAGE lateral diffusion. Copyright © 2016. Published by Elsevier B.V.

  2. AFAL: a web service for profiling amino acids surrounding ligands in proteins

    Science.gov (United States)

    Arenas-Salinas, Mauricio; Ortega-Salazar, Samuel; Gonzales-Nilo, Fernando; Pohl, Ehmke; Holmes, David S.; Quatrini, Raquel

    2014-11-01

    With advancements in crystallographic technology and the increasing wealth of information populating structural databases, there is an increasing need for prediction tools based on spatial information that will support the characterization of proteins and protein-ligand interactions. Herein, a new web service is presented termed amino acid frequency around ligand (AFAL) for determining amino acids type and frequencies surrounding ligands within proteins deposited in the Protein Data Bank and for assessing the atoms and atom-ligand distances involved in each interaction (availability: http://structuralbio.utalca.cl/AFAL/index.html). AFAL allows the user to define a wide variety of filtering criteria (protein family, source organism, resolution, sequence redundancy and distance) in order to uncover trends and evolutionary differences in amino acid preferences that define interactions with particular ligands. Results obtained from AFAL provide valuable statistical information about amino acids that may be responsible for establishing particular ligand-protein interactions. The analysis will enable investigators to compare ligand-binding sites of different proteins and to uncover general as well as specific interaction patterns from existing data. Such patterns can be used subsequently to predict ligand binding in proteins that currently have no structural information and to refine the interpretation of existing protein models. The application of AFAL is illustrated by the analysis of proteins interacting with adenosine-5'-triphosphate.

  3. Conformational dynamics of L-lysine, L-arginine, L-ornithine binding protein reveals ligand-dependent plasticity.

    Science.gov (United States)

    Silva, Daniel-Adriano; Domínguez-Ramírez, Lenin; Rojo-Domínguez, Arturo; Sosa-Peinado, Alejandro

    2011-07-01

    The molecular basis of multiple ligand binding affinity for amino acids in periplasmic binding proteins (PBPs) and in the homologous domain for class C G-protein coupled receptors is an unsolved question. Here, using unrestrained molecular dynamic simulations, we studied the ligand binding mechanism present in the L-lysine, L-arginine, L-ornithine binding protein. We developed an analysis based on dihedral angles for the description of the conformational changes upon ligand binding. This analysis has an excellent correlation with each of the two main movements described by principal component analysis (PCA) and it's more convenient than RMSD measurements to describe the differences in the conformational ensembles observed. Furthermore, an analysis of hydrogen bonds showed specific interactions for each ligand studied as well as the ligand interaction with the aromatic residues Tyr-14 and Phe-52. Using uncharged histidine tautomers, these interactions are not observed. On the basis of these results, we propose a model in which hydrogen bond interactions place the ligand in the correct orientation to induce a cation-π interaction with Tyr-14 and Phe-52 thereby stabilizing the closed state. Our results also show that this protein adopts slightly different closed conformations to make available specific hydrogen bond interactions for each ligand thus, allowing a single mechanism to attain multiple ligand specificity. These results shed light on the experimental evidence for ligand-dependent conformational plasticity not explained by the previous crystallographic data. Copyright © 2011 Wiley-Liss, Inc.

  4. Ruthenium Cumulenylidene Complexes Bearing Heteroscorpionate Ligands

    OpenAIRE

    Strinitz, Frank

    2014-01-01

    In previous work of the BURZLAFF group, the design of suitable N,N,O ligands for a wide variety of applications ranging from catalysis to bioinorganic model compounds has been extensively investigated. Especially the methyl substituted bis(3,5-dimethylpyrazol-1-yl) acetate (bdmpza) ligand has shown manifold chemistry, comparable to the anionic cyclopentadienyl (Cp) and hydridotris(pyrazol-1-yl)borato (Tp) ligand. In the first part of this thesis the new tricarbonylmanganese(I) complexes be...

  5. Synergistic Effects of PPARγ Ligands and Retinoids in Cancer Treatment

    Directory of Open Access Journals (Sweden)

    Masahito Shimizu

    2008-01-01

    Full Text Available Peroxisome proliferator-activated receptors (PPARs are members of the nuclear receptor superfamily. The activation of PPARs by their specific ligands is regarded as one of the promising strategies to inhibit cancer cell growth. However, recent clinical trials targeting several common cancers showed no beneficial effect when PPAR ligands are used as a monotherapy. Retinoid X receptors (RXRs, which play a critical role in normal cell proliferation as a master regulator for nuclear receptors, preferentially form heterodimers with PPARs. A malfunction of RXRα due to phosphorylation by the Ras/MAPK signaling pathway is associated with the development of certain types of human malignancies. The activation of PPARγ/RXR heterodimer by their respective ligands synergistically inhibits cell growth, while inducing apoptosis in human colon cancer cells when the phosphorylation of RXRα was inhibited. We herein review the synergistic antitumor effects produced by the combination of the PPAR, especially PPARγ, ligands plus other agents, especially retinoids, in a variety of human cancers. We also focus on the phosphorylation of RXRα because the inhibition of RXRα phosphorylation and the restoration of its physiological function may activate PPAR/RXR heterodimer and, therefore, be a potentially effective and critical strategy for the inhibition of cancer cell growth.

  6. Development of immobilized ligands for actinide separations

    International Nuclear Information System (INIS)

    Paine, R.T.

    1994-01-01

    Primary goals during this grant period were to (1) synthesize new bifunctional chelating ligands, (2) characterize the structural features of the Ln and An coordination complexes formed by these ligands, (3) use structural data to iteratively design new classes of multifunctional ligands, and (4) explore additional routes for attachment of key ligands to solid supports that could be useful for chromatographic separations. Some highlights of recently published work as well as a summary of submitted, unpublished and/or still in progress research are outlined

  7. Adaptive terminal sliding mode control for hypersonic flight vehicles with strictly lower convex function based nonlinear disturbance observer.

    Science.gov (United States)

    Wu, Yun-Jie; Zuo, Jing-Xing; Sun, Liang-Hua

    2017-11-01

    In this paper, the altitude and velocity tracking control of a generic hypersonic flight vehicle (HFV) is considered. A novel adaptive terminal sliding mode controller (ATSMC) with strictly lower convex function based nonlinear disturbance observer (SDOB) is proposed for the longitudinal dynamics of HFV in presence of both parametric uncertainties and external disturbances. First, for the sake of enhancing the anti-interference capability, SDOB is presented to estimate and compensate the equivalent disturbances by introducing a strictly lower convex function. Next, the SDOB based ATSMC (SDOB-ATSMC) is proposed to guarantee the system outputs track the reference trajectory. Then, stability of the proposed control scheme is analyzed by the Lyapunov function method. Compared with other HFV control approaches, key novelties of SDOB-ATSMC are that a novel SDOB is proposed and drawn into the (virtual) control laws to compensate the disturbances and that several adaptive laws are used to deal with the differential explosion problem. Finally, it is illustrated by the simulation results that the new method exhibits an excellent robustness and a better disturbance rejection performance than the convention approach. Copyright © 2017 ISA. Published by Elsevier Ltd. All rights reserved.

  8. Strictly monolayer large continuous MoS{sub 2} films on diverse substrates and their luminescence properties

    Energy Technology Data Exchange (ETDEWEB)

    Mohapatra, P. K.; Deb, S.; Singh, B. P.; Vasa, P.; Dhar, S., E-mail: dhar@phy.iitb.ac.in [Department of Physics, Indian Institute of Technology Bombay, Mumbai 400076 (India)

    2016-01-25

    Despite a tremendous interest on molybdenum disulfide as a thinnest direct band gap semiconductor, single step synthesis of a large area purely monolayer MoS{sub 2} film has not yet been reported. Here, we report a CVD route to synthesize a continuous film of strictly monolayer MoS{sub 2} covering an area as large as a few cm{sup 2} on a variety of different substrates without using any seeding material or any elaborate pretreatment of the substrate. This is achieved by allowing the growth to take place in the naturally formed gap between a piece of SiO{sub 2} coated Si wafer and the substrate, when the latter is placed on top of the former inside a CVD reactor. We propose a qualitative model to explain why the MoS{sub 2} films are always strictly monolayer in this method. The photoluminescence study of these monolayers shows the characteristic excitonic and trionic features associated with monolayer MoS{sub 2}. In addition, a broad defect related luminescence band appears at ∼1.7 eV. As temperature decreases, the intensity of this broad feature increases, while the band edge luminescence reduces.

  9. Event-Sampled Direct Adaptive NN Output- and State-Feedback Control of Uncertain Strict-Feedback System.

    Science.gov (United States)

    Szanto, Nathan; Narayanan, Vignesh; Jagannathan, Sarangapani

    2017-04-12

    In this paper, a novel event-triggered implementation of a tracking controller for an uncertain strict-feedback system is presented. Neural networks (NNs) are utilized in the backstepping approach to design a control input by approximating unknown dynamics of the strict-feedback nonlinear system with event-sampled inputs. The system state vector is assumed to be unknown and an NN observer is used to estimate the state vector. By using the estimated state vector and backstepping design approach, an event-sampled controller is introduced. As part of the controller design, first, input-to-state-like stability for a continuously sampled controller that has been injected with bounded measurement errors is demonstrated, and subsequently, an event-execution control law is derived, such that the measurement errors are guaranteed to remain bounded. Lyapunov theory is used to demonstrate that the tracking errors, the observer estimation errors, and the NN weight estimation errors for each NN are locally uniformly ultimately bounded in the presence bounded disturbances, NN reconstruction errors, as well as errors introduced by event sampling. Simulation results are provided to illustrate the effectiveness of the proposed controllers.

  10. High-Throughput Identification of Combinatorial Ligands for DNA Delivery in Cell Culture

    Science.gov (United States)

    Svahn, Mathias G.; Rabe, Kersten S.; Barger, Geoffrey; EL-Andaloussi, Samir; Simonson, Oscar E.; Didier, Boturyn; Olivier, Renaudet; Dumy, Pascal; Brandén, Lars J.; Niemeyer, Christof M.; Smith, C. I. Edvard

    2008-10-01

    Finding the optimal combinations of ligands for tissue-specific delivery is tedious even if only a few well-established compounds are tested. The cargo affects the receptor-ligand interaction, especially when it is charged like DNA. The ligand should therefore be evaluated together with its cargo. Several viruses have been shown to interact with more than one receptor, for efficient internalization. We here present a DNA oligonucleotide-based method for inexpensive and rapid screening of biotin labeled ligands for combinatorial effects on cellular binding and uptake. The oligonucleotide complex was designed as a 44 bp double-stranded DNA oligonucleotide with one central streptavidin molecule and a second streptavidin at the terminus. The use of a highly advanced robotic platform ensured stringent processing and execution of the experiments. The oligonucleotides were fluorescently labeled and used for detection and analysis of cell-bound, internalized and intra-cellular compartmentalized constructs by an automated line-scanning confocal microscope, IN Cell Analyzer 3000. All possible combinations of 22 ligands were explored in sets of 2 and tested on 6 different human cell lines in triplicates. In total, 10 000 transfections were performed on the automation platform. Cell-specific combinations of ligands were identified and their relative position on the scaffold oligonucleotide was found to be of importance. The ligands were found to be cargo dependent, carbohydrates were more potent for DNA delivery whereas cell penetrating peptides were more potent for delivery of less charged particles.

  11. Neutral tridentate PNP ligands and their hybrid analogues: versatile non-innocent scaffolds for homogeneous catalysis.

    Science.gov (United States)

    van der Vlugt, Jarl Ivar; Reek, Joost N H

    2009-01-01

    Ligands in coordination chemistry and homogeneous catalysis are traditionally "static" spectators that do not actively participate in the catalytic cycle. However, such classic systems do not provide additional "handles" that could facilitate or trigger alternative productive reaction pathways. Recent advances in the use of novel nitrogen-centered pincer systems have unveiled interesting opportunities for cooperative catalysis. The chemistry of pyridine-derived, neutral ligands is discussed, with a specific focus on their non-innocent behavior and potential as facilitators for metal-mediated organic transformations. This overview should provide inspiration and an incentive to incorporate non-innocent ligands and their metal complexes within old and new homogeneously catalyzed reactions.

  12. A sequence-based dynamic ensemble learning system for protein ligand-binding site prediction

    KAUST Repository

    Chen, Peng

    2015-12-03

    Background: Proteins have the fundamental ability to selectively bind to other molecules and perform specific functions through such interactions, such as protein-ligand binding. Accurate prediction of protein residues that physically bind to ligands is important for drug design and protein docking studies. Most of the successful protein-ligand binding predictions were based on known structures. However, structural information is not largely available in practice due to the huge gap between the number of known protein sequences and that of experimentally solved structures

  13. MHC ligand generation in T cell-mediated immunity and MHC multimer technologies for T cell detection

    NARCIS (Netherlands)

    Bakker, Arnold Hendrik

    2009-01-01

    This thesis focuses on the generation of MHC ligands and their use in analyzing T cell immunity, both in mouse and men. It is roughly split into two sections: the first part deals specifically with the rules governing the generation of MHC ligands, while the second part describes technological

  14. Macrocyclic ligands for uranium complexation

    Energy Technology Data Exchange (ETDEWEB)

    Potts, K.T.

    1991-04-01

    A highly preorganized 24-macrocycle containing biuret, thiobiuret and pyridine subunits has been prepared by high dilution ring-closure procedures. Intermediate products to this macrocycle have been utilized to extend this synthetic route to include further representatives where solubility and stability will be influenced by substituent variation. A 1:1 complex has been formed from uranyl acetate and a quinquepyridine derivative, this representing a new type of ligand for the uranyl ion. A very convenient synthetic procedure that will allow the incorporation of these macrocycles into polymeric systems has been developed for the introduction of a vinyl substituent into the 4-position of the pyridine ring. Using triflate, vinyltributyltin and Pd{sup 0} chemistry, this procedure should make a variety of substituted 4-vinylpyridines available for the first time. 3 refs.

  15. Macrocyclic ligands for uranium complexation

    International Nuclear Information System (INIS)

    Potts, K.T.

    1991-04-01

    A highly preorganized 24-macrocycle containing biuret, thiobiuret and pyridine subunits has been prepared by high dilution ring-closure procedures. Intermediate products to this macrocycle have been utilized to extend this synthetic route to include further representatives where solubility and stability will be influenced by substituent variation. A 1:1 complex has been formed from uranyl acetate and a quinquepyridine derivative, this representing a new type of ligand for the uranyl ion. A very convenient synthetic procedure that will allow the incorporation of these macrocycles into polymeric systems has been developed for the introduction of a vinyl substituent into the 4-position of the pyridine ring. Using triflate, vinyltributyltin and Pd 0 chemistry, this procedure should make a variety of substituted 4-vinylpyridines available for the first time. 3 refs

  16. Targeting protein-protein interactions with trimeric ligands: high affinity inhibitors of the MAGUK protein family.

    Science.gov (United States)

    Nissen, Klaus B; Haugaard-Kedström, Linda M; Wilbek, Theis S; Nielsen, Line S; Åberg, Emma; Kristensen, Anders S; Bach, Anders; Jemth, Per; Strømgaard, Kristian

    2015-01-01

    PDZ domains in general, and those of PSD-95 in particular, are emerging as promising drug targets for diseases such as ischemic stroke. We have previously shown that dimeric ligands that simultaneously target PDZ1 and PDZ2 of PSD-95 are highly potent inhibitors of PSD-95. However, PSD-95 and the related MAGUK proteins contain three consecutive PDZ domains, hence we envisioned that targeting all three PDZ domains simultaneously would lead to more potent and potentially more specific interactions with the MAGUK proteins. Here we describe the design, synthesis and characterization of a series of trimeric ligands targeting all three PDZ domains of PSD-95 and the related MAGUK proteins, PSD-93, SAP-97 and SAP-102. Using our dimeric ligands targeting the PDZ1-2 tandem as starting point, we designed novel trimeric ligands by introducing a PDZ3-binding peptide moiety via a cysteine-derivatized NPEG linker. The trimeric ligands generally displayed increased affinities compared to the dimeric ligands in fluorescence polarization binding experiments and optimized trimeric ligands showed low nanomolar inhibition towards the four MAGUK proteins, thus being the most potent inhibitors described. Kinetic experiments using stopped-flow spectrometry showed that the increase in affinity is caused by a decrease in the dissociation rate of the trimeric ligand as compared to the dimeric ligands, likely reflecting the lower probability of simultaneous dissociation of all three PDZ ligands. Thus, we have provided novel inhibitors of the MAGUK proteins with exceptionally high affinity, which can be used to further elucidate the therapeutic potential of these proteins.

  17. Structural and Electrochemical Consequences of [Cp*] Ligand Protonation.

    Science.gov (United States)

    Peng, Yun; Ramos-Garcés, Mario V; Lionetti, Davide; Blakemore, James D

    2017-09-05

    There are few examples of the isolation of analogous metal complexes bearing [η 5 -Cp*] and [η 4 -Cp*H] (Cp* = pentamethylcyclopentadienyl) complexes within the same metal/ligand framework, despite the relevance of such structures to catalytic applications. Recently, protonation of Cp*Rh(bpy) (bpy = 2,2'-bipyridyl) has been shown to yield a complex bearing the uncommon [η 4 -Cp*H] ligand, rather than generating a [Rh III -H] complex. We now report the purification and isolation of this protonated species, as well as characterization of analogous complexes of 1,10-phenanthroline (phen). Specifically, reaction of Cp*Rh(bpy) or Cp*Rh(phen) with 1 equiv of Et 3 NH + Br - affords rhodium compounds bearing endo-η 4 -pentamethylcyclopentadiene (η 4 -Cp*H) as a ligand. NMR spectroscopy and single-crystal X-ray diffraction studies confirm protonation of the Cp* ligand, rather than formation of metal hydride complexes. Analysis of new structural data and electronic spectra suggests that phen is significantly reduced in Cp*Rh(phen), similar to the case of Cp*Rh(bpy). Backbonding interactions with olefinic motifs are activated by formation of [η 4 -Cp*H]; protonation of [Cp*] stabilizes the low-valent metal center and results in loss of reduced character on the diimine ligands. In accord with these changes in electronic structure, electrochemical studies reveal a distinct manifold of redox processes that are accessible in the [Cp*H] complexes in comparison with their [Cp*] analogues; these processes suggest new applications in catalysis for the complexes bearing endo-η 4 -Cp*H.

  18. MICB Allele Genotyping on Microarrays by Improving the Specificity of Extension Primers.

    Directory of Open Access Journals (Sweden)

    In-Cheol Baek

    Full Text Available Major histocompatibility complex (MHC class I chain-related gene B (MICB encodes a ligand for activating NKG2D that expressed in natural killer cells, γδ T cells, and αβ CD8+ T cells, which is associated with autoimmune diseases, cancer, and infectious diseases. Here, we have established a system for genotyping MICB alleles using allele-specific primer extension (ASPE on microarrays. Thirty-six high quality, allele-specific extension primers were evaluated using strict and reliable cut-off values using mean fluorescence intensity (MFI, whereby an MFI >30,000 represented a positive signal and an MFI <10,000 represented a negative signal. Eight allele-specific extension primers were found to be false positives, five of which were improved by adjusting their length, and three of which were optimized by refractory modification. The MICB alleles (*002:01, *003, *005:02/*010, *005:03, *008, *009N, *018, and *024 present in the quality control panel could be exactly defined by 22 allele-specific extension primers. MICB genotypes that were identified by ASPE on microarrays were in full concordance with those identified by PCR-sequence-based typing. In conclusion, we have developed a method for genotyping MICB alleles using ASPE on microarrays; which can be applicable for large-scale single nucleotide polymorphism typing studies of population and disease associations.

  19. Ligand based pharmacophore modelling of anticancer histone ...

    African Journals Online (AJOL)

    USER

    2010-06-21

    Jun 21, 2010 ... HDAC ligands (Chen et al., 2008b). The knowledge of common properties of the binding group is essential for the determination of the type of inhibitor binding the target. Major goal of modern drug design is identification and development of new ligands with high affinity of binding toward a given protein.

  20. Organometallic chemistry of chiral diphosphazane ligands ...

    Indian Academy of Sciences (India)

    Unknown

    1. Introduction. Diphosphazanes constitute a class of versatile short-bite bidentate P-donor ligands that have given rise to a varied and extensive transition metal organometallic chemistry. The organometallic chemistry of diphosphazane ligands with almost every transition metal in the periodic table is well documented1–3.

  1. Cofactor-Controlled Chirality of Tropoisomeric Ligand

    NARCIS (Netherlands)

    Théveau, L.; Bellini, R.; Dydio, P.; Szabo, Z.; van der Werf, A.; Sander, R.A.; Reek, J.N.H.; Moberg, C.

    2016-01-01

    A new tropos ligand with an integrated anion receptor receptor site has been prepared. Chiral carboxylate and phosphate anions that bind in the anion receptor unit proved capable of stabilizing chiral conformations of the achiral flexible bidentate biaryl phosphite ligand, as shown by variable

  2. Ligand modification for mono- and biphasic oxosynthesis

    Energy Technology Data Exchange (ETDEWEB)

    Haerter, P.; Herrmann, W.A.; Baskakov, D. [Technische Univ. Muenchen (Germany). Dept. Chemie

    2006-07-01

    The use of aqueous/organic biphasic systems has attracted huge interest in catalytic reactions by transition metal complexes. [1,2,3] The biphasic systems have benefits in catalyst separation and recycling, and the reduction or elimination of organic solvents is also advantageous for the development of economical and environmentally friendly processes. The key for such biphasic catalysis is the use of water soluble phosphines as ligands. Since the launch of the commercial propylene hydroformylation process by Ruhrchemie/Rhone-Poulenc, sulfonated ligands such as TPPTS (1), and BINAS (2) have been widely used as ligands in hydroformylation, hydrogenation and related reactions catalyzed by transition metals. One of the draw backs of ligands 1 and 2 are corrosive production conditions and therefore unfavorable costs. With the synthesis of aminoacid based trishydroxymethylphosphine derivatives (THMP-aminoacid) we introduce to our knowledge a new group of water soluble and cheap to produce ligands [8]. The properties of catalysts based on these compounds in the hydroformylation reaction of propene are discussed in comparison to normally used catalyst systems. In a second part the performance of catalysts containing NHC-ligands in the hydroformylation of 1-octene is discussed [9]. These investigations show, that the activity can be influenced by the electron donating ability of the NHC ligand. Sterical variations on the NHC ligands have no effect on the selectivity performance of the the catalysts. (orig.)

  3. Organometallic chemistry of chiral diphosphazane ligands ...

    Indian Academy of Sciences (India)

    Unknown

    organometallic chemistry of diphosphazane ligands with almost every transition metal in the periodic table is well documented1–3. A very attractive feature of diphosphazane ligands is that 'chirality' can be incorporated at the phosphorus centres as well as at the substituents attached to the nitrogen and the two phosphorus ...

  4. Ligand sphere conversions in terminal carbide complexes

    DEFF Research Database (Denmark)

    Morsing, Thorbjørn Juul; Reinholdt, Anders; Sauer, Stephan P. A.

    2016-01-01

    Metathesis is introduced as a preparative route to terminal carbide complexes. The chloride ligands of the terminal carbide complex [RuC(Cl)2(PCy3)2] (RuC) can be exchanged, paving the way for a systematic variation of the ligand sphere. A series of substituted complexes, including the first exam...

  5. Assessing potential peptide targeting ligands by quantification of cellular adhesion of model nanoparticles under flow conditions.

    Science.gov (United States)

    Broda, Ellen; Mickler, Frauke Martina; Lächelt, Ulrich; Morys, Stephan; Wagner, Ernst; Bräuchle, Christoph

    2015-09-10

    Sophisticated drug delivery systems are coated with targeting ligands to improve the specific adhesion to surface receptors on diseased cells. In our study, we developed a method with which we assessed the potential of peptide ligands to specifically bind to receptor overexpressing target cells. Therefore, a microfluidic setup was used where the cellular adhesion of nanoparticles with ligand and of control nanoparticles was observed in parallel under the same experimental conditions. The effect of the ligand on cellular binding was quantified by counting the number of adhered nanoparticles with ligand and differently labeled control nanoparticles on single cells after incubation under flow conditions. To provide easy-to-synthesize, stable and reproducible nanoparticles which mimic the surface characteristics of drug delivery systems and meet the requirements for quantitative analysis, latex beads based on amine-modified polystyrene were used as model nanoparticles. Two short peptides were tested to serve as targeting ligand on the beads by increasing the specific binding to HuH7 cells. The c-Met binding peptide cMBP2 was used for hepatocyte growth factor receptor (c-Met) targeting and the peptide B6 for transferrin receptor (TfR) targeting. The impact of the targeting peptide on binding was investigated by comparing the beads with ligand to different internal control beads: 1) without ligand and tailored surface charge (electrostatic control) and 2) with scrambled peptide and similar surface charge, but a different amino acid sequence (specificity control). Our results demonstrate that the method is very useful to select suitable targeting ligands for specific nanoparticle binding to receptor overexpressing tumor cells. We show that the cMBP2 ligand specifically enhances nanoparticle adhesion to target cells, whereas the B6 peptide mediates binding to tumor cells mainly by nonspecific interactions. All together, we suggest that cMBP2 is a suitable choice for

  6. Docking Validation Resources: Protein Family and Ligand Flexibility Experiments

    Science.gov (United States)

    Mukherjee, Sudipto; Balius, Trent E.; Rizzo, Robert C.

    2010-01-01

    A database consisting of 780 ligand-receptor complexes, termed SB2010, has been derived from the Protein Databank to evaluate the accuracy of docking protocols for regenerating bound ligand conformations. The goal is to provide easily accessible community resources for development of improved procedures to aid virtual screening for ligands with a wide range of flexibilities. Three core experiments using the program DOCK, which employ rigid (RGD), fixed anchor (FAD), and flexible (FLX) protocols, were used to gauge performance by several different metrics: (1) global results, (2) ligand flexibility, (3) protein family, and (4) crossdocking. Global spectrum plots of successes and failures vs rmsd reveal well-defined inflection regions, which suggest the commonly used 2 Å criteria is a reasonable choice for defining success. Across all 780 systems, success tracks with the relative difficulty of the calculations: RGD (82.3%) > FAD (78.1%) > FLX (63.8%). In general, failures due to scoring strongly outweigh those due to sampling. Subsets of SB2010 grouped by ligand flexibility (7-or-less, 8-to-15, and 15-plus rotatable bonds) reveal success degrades linearly for FAD and FLX protocols, in contrast to RGD which remains constant. Despite the challenges associated with FLX anchor orientation and on-the-fly flexible growth, success rates for the 7-or-less (74.5%), and in particular the 8-to-15 (55.2%) subset, are encouraging. Poorer results for the very flexible 15-plus set (39.3%) indicate substantial room for improvement. Family-based success appears largely independent of ligand flexibility suggesting a strong dependence on the binding site environment. For example, zinc-containing proteins are generally problematic despite moderately flexible ligands. Finally, representative crossdocking examples, for carbonic anhydrase, thermolysin, and neuraminidase families, show the utility of family-based analysis for rapid identification of particularly good or bad docking trends

  7. Biomimetic affinity ligands for protein purification.

    Science.gov (United States)

    Sousa, Isabel T; Taipa, M Angela

    2014-01-01

    The development of sophisticated molecular modeling software and new bioinformatic tools, as well as the emergence of data banks containing detailed information about a huge number of proteins, enabled the de novo intelligent design of synthetic affinity ligands. Such synthetic compounds can be tailored to mimic natural biological recognition motifs or to interact with key surface-exposed residues on target proteins and are designated as "biomimetic ligands." A well-established methodology for generating biomimetic or synthetic affinity ligands integrates rational design with combinatorial solid-phase synthesis and screening, using the triazine scaffold and analogues of amino acids side chains to create molecular diversity.Triazine-based synthetic ligands are nontoxic, low-cost, highly stable compounds that can replace advantageously natural biological ligands in the purification of proteins by affinity-based methodologies.

  8. Strict fibonacci heaps

    DEFF Research Database (Denmark)

    Brodal, Gerth Stølting; Lagogiannis, George; Tarjan, Robert E.

    2012-01-01

    We present the first pointer-based heap implementation with time bounds matching those of Fibonacci heaps in the worst case. We support make-heap, insert, find-min, meld and decrease-key in worst-case O(1) time, and delete and delete-min in worst-case O(lg n) time, where n is the size of the heap...... of the smaller heap when doing a meld. We use the pigeonhole principle in place of the redundant counter mechanism. We present the first pointer-based heap implementation with time bounds matching those of Fibonacci heaps in the worst case. We support make-heap, insert, find-min, meld and decrease-key in worst...

  9. Online Recorded Data-Based Composite Neural Control of Strict-Feedback Systems With Application to Hypersonic Flight Dynamics.

    Science.gov (United States)

    Xu, Bin; Yang, Daipeng; Shi, Zhongke; Pan, Yongping; Chen, Badong; Sun, Fuchun

    2017-09-25

    This paper investigates the online recorded data-based composite neural control of uncertain strict-feedback systems using the backstepping framework. In each step of the virtual control design, neural network (NN) is employed for uncertainty approximation. In previous works, most designs are directly toward system stability ignoring the fact how the NN is working as an approximator. In this paper, to enhance the learning ability, a novel prediction error signal is constructed to provide additional correction information for NN weight update using online recorded data. In this way, the neural approximation precision is highly improved, and the convergence speed can be faster. Furthermore, the sliding mode differentiator is employed to approximate the derivative of the virtual control signal, and thus, the complex analysis of the backstepping design can be avoided. The closed-loop stability is rigorously established, and the boundedness of the tracking error can be guaranteed. Through simulation of hypersonic flight dynamics, the proposed approach exhibits better tracking performance.

  10. Global neural dynamic surface tracking control of strict-feedback systems with application to hypersonic flight vehicle.

    Science.gov (United States)

    Xu, Bin; Yang, Chenguang; Pan, Yongping

    2015-10-01

    This paper studies both indirect and direct global neural control of strict-feedback systems in the presence of unknown dynamics, using the dynamic surface control (DSC) technique in a novel manner. A new switching mechanism is designed to combine an adaptive neural controller in the neural approximation domain, together with the robust controller that pulls the transient states back into the neural approximation domain from the outside. In comparison with the conventional control techniques, which could only achieve semiglobally uniformly ultimately bounded stability, the proposed control scheme guarantees all the signals in the closed-loop system are globally uniformly ultimately bounded, such that the conventional constraints on initial conditions of the neural control system can be relaxed. The simulation studies of hypersonic flight vehicle (HFV) are performed to demonstrate the effectiveness of the proposed global neural DSC design.

  11. Iterative algorithms for the input and state recovery from the approximate inverse of strictly proper multivariable systems

    Science.gov (United States)

    Chen, Liwen; Xu, Qiang

    2018-02-01

    This paper proposes new iterative algorithms for the unknown input and state recovery from the system outputs using an approximate inverse of the strictly proper linear time-invariant (LTI) multivariable system. One of the unique advantages from previous system inverse algorithms is that the output differentiation is not required. The approximate system inverse is stable due to the systematic optimal design of a dummy feedthrough D matrix in the state-space model via the feedback stabilization. The optimal design procedure avoids trial and error to identify such a D matrix which saves tremendous amount of efforts. From the derived and proved convergence criteria, such an optimal D matrix also guarantees the convergence of algorithms. Illustrative examples show significant improvement of the reference input signal tracking by the algorithms and optimal D design over non-iterative counterparts on controllable or stabilizable LTI systems, respectively. Case studies of two Boeing-767 aircraft aerodynamic models further demonstrate the capability of the proposed methods.

  12. Monolithic InP strictly non-blocking 8×8 switch for high-speed WDM optical interconnection.

    Science.gov (United States)

    Kwack, Myung-Joon; Tanemura, Takuo; Higo, Akio; Nakano, Yoshiaki

    2012-12-17

    A strictly non-blocking 8 × 8 switch for high-speed WDM optical interconnection is realized on InP by using the phased-array scheme for the first time. The matrix switch architecture consists of over 200 functional devices such as star couplers, phase-shifters and so on without any waveguide cross-section. We demonstrate ultra-broad optical bandwidth covering the entire C-band through several Input/Output ports combination with extinction ratio performance of more than 20dB. Also, nanoseconds reconfiguration time was successfully achieved by dynamic switching experiment. Error-free transmission was verified for 40-Gbps (10-Gbps × 4ch) WDM signal.

  13. The LHC Continuous Cryostat Interconnections The Organization of a Logistically Complex Worksite Requiring Strict Quality Standards and High Output

    CERN Document Server

    Fessia, P; Bozzini, D; Cruikshank, P; Jacquemod, A; Maan, W; Musso, A; Oberli, L; Poncet, A; Russenschuck, Stephan; Savary, F; Struik, M; Tock, J Ph; Tommasini, D; Völlinger, C; Kotarba, A; Olek, S; Sulek, Z; Grimaud, A; Vaudaux, L

    2008-01-01

    The interconnections of the Large Hadron Collider (LHC) continuous cryostat have been completed in fall 2007: 1695 interconnections magnet to magnet and 224 interconnections between the continuous cryostat and the cryogenic distribution line have been executed along the 27 km of the LHC. The very tight schedule, the complexity of the interconnection sequence, the strict quality standards applied have required the creation of an ad hoc organization in order to steer and coordinate the activities on the worksite dispersed along the whole accelerator ring. The concatenation of construction and test phases carried out by CERN staff, CERN collaborating institutes and contractors have led to the necessity of a common approach and of a very effective information flow. In this paper, after having recalled the main technical challenges, we review the organizational choices that have been taken and we briefly analyze the development of the worksite in term of allocated resources and production.

  14. Analysis of strictly bound modes in photonic crystal fibers by use of a source-model technique.

    Science.gov (United States)

    Hochman, Amit; Leviatan, Yehuda

    2004-06-01

    We describe a source-model technique for the analysis of the strictly bound modes propagating in photonic crystal fibers that have a finite photonic bandgap crystal cladding and are surrounded by an air jacket. In this model the field is simulated by a superposition of fields of fictitious electric and magnetic current filaments, suitably placed near the media interfaces of the fiber. A simple point-matching procedure is subsequently used to enforce the continuity conditions across the interfaces, leading to a homogeneous matrix equation. Nontrivial solutions to this equation yield the mode field patterns and propagation constants. As an example, we analyze a hollow-core photonic crystal fiber. Symmetry characteristics of the modes are discussed and exploited to reduce the computational burden.

  15. Development of a PCR assay based on the 16S-23S rDNA internal transcribed spacer for identification of strictly anaerobic bacterium Zymophilus

    Czech Academy of Sciences Publication Activity Database

    Felsberg, Jürgen; Jelínková, Markéta; Kubizniaková, P.; Matoulková, D.

    2015-01-01

    Roč. 33, June (2015), s. 85-89 ISSN 1075-9964 Institutional support: RVO:61388971 Keywords : Brewing microbiology * Strictly anaerobic bacteria * Yeast contamination Subject RIV: GM - Food Processing Impact factor: 2.424, year: 2015

  16. Strict blood glucose control by an artificial endocrine pancreas during hepatectomy may prevent postoperative acute kidney injury.

    Science.gov (United States)

    Mita, Naoji; Kawahito, Shinji; Soga, Tomohiro; Takaishi, Kazumi; Kitahata, Hiroshi; Matsuhisa, Munehide; Shimada, Mitsuo; Kinoshita, Hiroyuki; Tsutsumi, Yasuo M; Tanaka, Katsuya

    2017-03-01

    The aim of the present study was to evaluate the usefulness of a closed-loop system (STG-55; Nikkiso, Tokyo, Japan), a type of artificial endocrine pancreas for the continuous monitoring and control of intraoperative blood glucose, for preventing postoperative acute kidney injury (AKI) in patients undergoing hepatectomy. Thirty-eight patients were enrolled in this study. Glucose concentrations were controlled with either a manual injection of insulin based on a commonly used sliding scale (manual insulin group, n = 19) or the programmed infusion of insulin determined by the control algorithm of the artificial endocrine pancreas (programmed insulin group, n = 19). After the induction of anesthesia, a 20-G intravenous catheter was inserted into the peripheral forearm vein of patients in the programmed insulin group and connected to an artificial endocrine pancreas (STG-55). The target range for glucose concentrations was set to 100-150 mg/dL. The mean serum creatinine concentrations of preoperative, postoperative 24 and 48 h were 0.72, 0.78, and 0.79 mg/dL in the programmed insulin group, and 0.81, 0.95, and 1.03 mg/dL in the manual insulin group, respectively. Elevations in serum creatinine concentrations postoperative 48 h were significantly suppressed in the programmed insulin group. The STG-55 closed-loop system was effective for maintaining strict blood glucose control during hepatectomy with minimal variability in blood glucose concentrations and for suppressing elevations in serum creatinine concentrations. Strict blood glucose control by an artificial endocrine pancreas during hepatectomy may prevent postoperative AKI.

  17. GLASS: a comprehensive database for experimentally validated GPCR-ligand associations.

    Science.gov (United States)

    Chan, Wallace K B; Zhang, Hongjiu; Yang, Jianyi; Brender, Jeffrey R; Hur, Junguk; Özgür, Arzucan; Zhang, Yang

    2015-09-15

    G protein-coupled receptors (GPCRs) are probably the most attractive drug target membrane proteins, which constitute nearly half of drug targets in the contemporary drug discovery industry. While the majority of drug discovery studies employ existing GPCR and ligand interactions to identify new compounds, there remains a shortage of specific databases with precisely annotated GPCR-ligand associations. We have developed a new database, GLASS, which aims to provide a comprehensive, manually curated resource for experimentally validated GPCR-ligand associations. A new text-mining algorithm was proposed to collect GPCR-ligand interactions from the biomedical literature, which is then crosschecked with five primary pharmacological datasets, to enhance the coverage and accuracy of GPCR-ligand association data identifications. A special architecture has been designed to allow users for making homologous ligand search with flexible bioactivity parameters. The current database contains ∼500 000 unique entries, of which the vast majority stems from ligand associations with rhodopsin- and secretin-like receptors. The GLASS database should find its most useful application in various in silico GPCR screening and functional annotation studies. The website of GLASS database is freely available at http://zhanglab.ccmb.med.umich.edu/GLASS/. zhng@umich.edu Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  18. PANP is a novel O-glycosylated PILR{alpha} ligand expressed in neural tissues

    Energy Technology Data Exchange (ETDEWEB)

    Kogure, Amane [Department of Immunochemistry, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871 (Japan); Laboratory of Immunochemistry, WPI Immunology Frontier Research Center, Osaka University, Osaka 565-0871 (Japan); Shiratori, Ikuo [Department of Immunochemistry, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871 (Japan); Wang, Jing [Department of Immunochemistry, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871 (Japan); Laboratory of Immunochemistry, WPI Immunology Frontier Research Center, Osaka University, Osaka 565-0871 (Japan); Lanier, Lewis L. [Department of Microbiology and Immunology and the Cancer Research Institute, University of California San Francisco, San Francisco, CA 94143 (United States); Arase, Hisashi, E-mail: arase@biken.osaka-u.ac.jp [Department of Immunochemistry, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871 (Japan); Laboratory of Immunochemistry, WPI Immunology Frontier Research Center, Osaka University, Osaka 565-0871 (Japan); JST CREST, Saitama 332-0012 (Japan)

    2011-02-18

    Research highlights: {yields} A Novel molecule, PANP, was identified to be a PILR{alpha} ligand. {yields} Sialylated O-glycan structures on PANP were required for PILR{alpha} recognition. {yields} Transcription of PANP was mainly observed in neural tissues. {yields} PANP seems to be involved in immune regulation as a ligand for PILR{alpha}. -- Abstract: PILR{alpha} is an immune inhibitory receptor possessing an immunoreceptor tyrosine-based inhibitory motif (ITIM) in its cytoplasmic domain enabling it to deliver inhibitory signals. Binding of PILR{alpha} to its ligand CD99 is involved in immune regulation; however, whether there are other PILR{alpha} ligands in addition to CD99 is not known. Here, we report that a novel molecule, PILR-associating neural protein (PANP), acts as an additional ligand for PILR{alpha}. Transcription of PANP was mainly observed in neural tissues. PILR{alpha}-Ig fusion protein bound cells transfected with PANP and the transfectants stimulated PILR{alpha} reporter cells. Specific O-glycan structures on PANP were found to be required for PILR recognition of this ligand. These results suggest that PANP is involved in immune regulation as a ligand of the PILR{alpha}.

  19. Physics-based scoring of protein-ligand interactions: explicit polarizability, quantum mechanics and free energies.

    Science.gov (United States)

    Bryce, Richard A

    2011-04-01

    The ability to accurately predict the interaction of a ligand with its receptor is a key limitation in computer-aided drug design approaches such as virtual screening and de novo design. In this article, we examine current strategies for a physics-based approach to scoring of protein-ligand affinity, as well as outlining recent developments in force fields and quantum chemical techniques. We also consider advances in the development and application of simulation-based free energy methods to study protein-ligand interactions. Fuelled by recent advances in computational algorithms and hardware, there is the opportunity for increased integration of physics-based scoring approaches at earlier stages in computationally guided drug discovery. Specifically, we envisage increased use of implicit solvent models and simulation-based scoring methods as tools for computing the affinities of large virtual ligand libraries. Approaches based on end point simulations and reference potentials allow the application of more advanced potential energy functions to prediction of protein-ligand binding affinities. Comprehensive evaluation of polarizable force fields and quantum mechanical (QM)/molecular mechanical and QM methods in scoring of protein-ligand interactions is required, particularly in their ability to address challenging targets such as metalloproteins and other proteins that make highly polar interactions. Finally, we anticipate increasingly quantitative free energy perturbation and thermodynamic integration methods that are practical for optimization of hits obtained from screened ligand libraries.

  20. The Foundations of Protein-Ligand Interaction

    Science.gov (United States)

    Klebe, Gerhard

    For the specific design of a drug we must first answer the question: How does a drug achieve its activity? An active ingredient must, in order to develop its action, bind to a particular target molecule in the body. Usually this is a protein, but also nucleic acids in the form of RNA and DNA can be target structures for active agents. The most important condition for binding is at first that the active agent exhibits the correct size and shape in order to optimally fit into a cavity exposed to the surface of the protein, the "bindingpocket". It is further necessary for the surface properties of the ligand and protein to be mutually compatible to form specific interactions. In 1894 Emil Fischer compared the exact fit of a substrate for the catalytic centre of an enzyme with the picture of a "lock-and-key". Paul Ehrlich coined in 1913 "Corpora non agunt nisi fixata", literally "bodies do not work when they are not bound". He wanted to imply that active agents that are meant to kill bacteria or parasites must be "fixed" by them, i.e. linked to their structures. Both concepts form the starting point for any rational concept in the development of active pharmaceutical ingredients. In many respects they still apply today. A drug must, after being administered, reach its target and interact with a biological macromolecule. Specific agents have a large affinity and sufficient selectivity to bind to the macromolecule's active site. This is the only way they can develop the desired biological activity without side-effects.

  1. Correcting ligands, metabolites, and pathways

    Directory of Open Access Journals (Sweden)

    Vriend Gert

    2006-11-01

    Full Text Available Abstract Background A wide range of research areas in bioinformatics, molecular biology and medicinal chemistry require precise chemical structure information about molecules and reactions, e.g. drug design, ligand docking, metabolic network reconstruction, and systems biology. Most available databases, however, treat chemical structures more as illustrations than as a datafield in its own right. Lack of chemical accuracy impedes progress in the areas mentioned above. We present a database of metabolites called BioMeta that augments the existing pathway databases by explicitly assessing the validity, correctness, and completeness of chemical structure and reaction information. Description The main bulk of the data in BioMeta were obtained from the KEGG Ligand database. We developed a tool for chemical structure validation which assesses the chemical validity and stereochemical completeness of a molecule description. The validation tool was used to examine the compounds in BioMeta, showing that a relatively small number of compounds had an incorrect constitution (connectivity only, not considering stereochemistry and that a considerable number (about one third had incomplete or even incorrect stereochemistry. We made a large effort to correct the errors and to complete the structural descriptions. A total of 1468 structures were corrected and/or completed. We also established the reaction balance of the reactions in BioMeta and corrected 55% of the unbalanced (stoichiometrically incorrect reactions in an automatic procedure. The BioMeta database was implemented in PostgreSQL and provided with a web-based interface. Conclusion We demonstrate that the validation of metabolite structures and reactions is a feasible and worthwhile undertaking, and that the validation results can be used to trigger corrections and improvements to BioMeta, our metabolite database. BioMeta provides some tools for rational drug design, reaction searches, and

  2. Molecular determinants of ligand binding modes in the histamine H(4) receptor: linking ligand-based three-dimensional quantitative structure-activity relationship (3D-QSAR) models to in silico guided receptor mutagenesis studies.

    Science.gov (United States)

    Istyastono, Enade P; Nijmeijer, Saskia; Lim, Herman D; van de Stolpe, Andrea; Roumen, Luc; Kooistra, Albert J; Vischer, Henry F; de Esch, Iwan J P; Leurs, Rob; de Graaf, Chris

    2011-12-08

    The histamine H(4) receptor (H(4)R) is a G protein-coupled receptor (GPCR) that plays an important role in inflammation. Similar to the homologous histamine H(3) receptor (H(3)R), two acidic residues in the H(4)R binding pocket, D(3.32) and E(5.46), act as essential hydrogen bond acceptors of positively ionizable hydrogen bond donors in H(4)R ligands. Given the symmetric distribution of these complementary pharmacophore features in H(4)R and its ligands, different alternative ligand binding mode hypotheses have been proposed. The current study focuses on the elucidation of the molecular determinants of H(4)R-ligand binding modes by combining (3D) quantitative structure-activity relationship (QSAR), protein homology modeling, molecular dynamics simulations, and site-directed mutagenesis studies. We have designed and synthesized a series of clobenpropit (N-(4-chlorobenzyl)-S-[3-(4(5)-imidazolyl)propyl]isothiourea) derivatives to investigate H(4)R-ligand interactions and ligand binding orientations. Interestingly, our studies indicate that clobenpropit (2) itself can bind to H(4)R in two distinct binding modes, while the addition of a cyclohexyl group to the clobenpropit isothiourea moiety allows VUF5228 (5) to adopt only one specific binding mode in the H(4)R binding pocket. Our ligand-steered, experimentally supported protein modeling method gives new insights into ligand recognition by H(4)R and can be used as a general approach to elucidate the structure of protein-ligand complexes.

  3. Autocrine signal transmission with extracellular ligand degradation

    International Nuclear Information System (INIS)

    Muratov, C B; Posta, F; Shvartsman, S Y

    2009-01-01

    Traveling waves of cell signaling in epithelial layers orchestrate a number of important processes in developing and adult tissues. These waves can be mediated by positive feedback autocrine loops, a mode of cell signaling where binding of a diffusible extracellular ligand to a cell surface receptor can lead to further ligand release. We formulate and analyze a biophysical model that accounts for ligand-induced ligand release, extracellular ligand diffusion and ligand–receptor interaction. We focus on the case when the main mode for ligand degradation is extracellular and analyze the problem with the sharp threshold positive feedback nonlinearity. We derive expressions that link the speed of propagation and other characteristics of traveling waves to the parameters of the biophysical processes, such as diffusion rates, receptor expression level, etc. Analyzing the derived expressions we found that traveling waves in such systems can exhibit a number of unusual properties, e.g. non-monotonic dependence of the speed of propagation on ligand diffusivity. Our results for the fully developed traveling fronts can be used to analyze wave initiation from localized perturbations, a scenario that frequently arises in the in vitro models of epithelial wound healing, and guide future modeling studies of cell communication in epithelial layers

  4. Radiation induced ligand loss from cobalt complexes

    International Nuclear Information System (INIS)

    Funston, A. M.; McFadyen, W.D.; Tregloan, P.A.

    2000-01-01

    Full text: Due to the rapid nature of ligand dissociation from cobalt(II) complexes the study of the rate of ligand dissociation necessitates the use of a technique such as pulse radiolysis. This allows the rapid reduction of the corresponding cobalt(III) complex by a reducing radical, such as the aquated electron, to form the cobalt(II) complex. However, to date, no systematic study of either the mechanism of reduction or the influence of the electronic structure on the rate of ligand dissociation has been carried out. In order to understand these processes more fully the mechanism of reduction of a range of related cobalt(III) complexes by the aquated electron and the subsequent rate of ligand dissociation from the resulting cobalt(II) complexes is being investigated. It has been found that a number of processes are observed following the initial rapid reaction of the cobalt(III) complex with the aquated electron. Ultimately ligand loss is observed. Depending upon the complex, the initial processes observed may include the formation of coordinated radicals and electron transfer within the complex. For complexes containing aromatic ligands such as 2,2'-bipyridine, 1,10-phenanthroline and dipyrido[3,2-a:2',3'-c]phenazine the formation of a coordinated radical is observed as the initial reduction step. The kinetics of ligand dissociation of these complexes has been determined. The loss of monodentate ligands is fast and has been indistinguishable from the reduction processes when aromatic ligands are also present in the complex. However, for diamine chelates and diimine chelates spectra of the transient species can be resolved

  5. Bifidobacterium longum CCM 7952 Promotes Epithelial Barrier Function and Prevents Acute DSS-Induced Colitis in Strictly Strain-Specific Manner

    Czech Academy of Sciences Publication Activity Database

    Šrůtková, Dagmar; Schwarzer, Martin; Hudcovic, Tomáš; Zákostelská, Zuzana; Dráb, V.; Španová, A.; Rittich, B.; Kozáková, Hana; Schabussova, I.

    2015-01-01

    Roč. 10, č. 7 (2015) E-ISSN 1932-6203 R&D Projects: GA ČR GA303/09/0449; GA ČR(CZ) GAP303/12/0535 Institutional support: RVO:61388971 Keywords : INFLAMMATORY BOWEL DISEASES * DEXTRAN SULFATE SODIUM Subject RIV: EC - Immunology Impact factor: 3.057, year: 2015

  6. Stabilization of enzyme by using hydrophobic ligands

    Energy Technology Data Exchange (ETDEWEB)

    Ota, H.; Yamahara, K.; Kuboi, R. [Osaka University, Osaka (Japan)

    1998-02-01

    The protection (stabilization) effect of various hydrophobic ligands on the denaturation and aggregation of carbonic anhydrase from bovine (CAB) has been quantitatively investigated under various heat stress conditions. In a limited temperature range (40-60degC), where the protein was only partially denatured and the local hydrophobicities (LH) of CAB were positive effective stabilization of the protein is achieved by the addition of various ligands. The importance of balance between hydrophobic head and hydrophilic tail of the ligands is hypothesized. 18 refs., 5 figs.

  7. A versatile dinucleating ligand containing sulfonamide groups

    DEFF Research Database (Denmark)

    Sundberg, Jonas; Witt, Hannes; Cameron, Lisa

    2014-01-01

    ligand can be prepared in aqueous solutions using only divalent metal ions. Two of the copper(II) complexes, [Cu2(psmp)(OH)] and [Cu2(psmp)(OAc)2]-, demonstrate the anticipated 1:2 ligand/metal stoichiometry and show that the dimetallic binding site created for exogenous ligands possesses high inherent...... of antiferromagnetic coupling. This is corroborated computationally by broken-symmetry density functional theory, which for isotropic modeling of the coupling predicts an antiferromagnetic coupling strength of J = 70.5 cm-1....

  8. Heterogeneity and dynamics of the ligand recognition mode in purine-sensing riboswitches.

    Science.gov (United States)

    Jain, Niyati; Zhao, Liang; Liu, John D; Xia, Tianbing

    2010-05-04

    High-resolution crystal structures and biophysical analyses of purine-sensing riboswitches have revealed that a network of hydrogen bonding interactions appear to be largey responsible for discrimination of cognate ligands against structurally related compounds. Here we report that by using femtosecond time-resolved fluorescence spectroscopy to capture the ultrafast decay dynamics of the 2-aminopurine base as the ligand, we have detected the presence of multiple conformations of the ligand within the binding pockets of one guanine-sensing and two adenine-sensing riboswitches. All three riboswitches have similar conformational distributions of the ligand-bound state. The known crystal structures represent the global minimum that accounts for 50-60% of the population, where there is no significant stacking interaction between the ligand and bases of the binding pocket, but the hydrogen-bonding cage collectively provides an electronic environment that promotes an ultrafast ( approximately 1 ps) charge transfer pathway. The ligand also samples multiple conformations in which it significantly stacks with either the adenine or the uracil bases of the A21-U75 and A52-U22 base pairs that form the ceiling and floor of the binding pocket, respectively, but favors the larger adenine bases. These alternative conformations with well-defined base stacking interactions are approximately 1-1.5 kcal/mol higher in DeltaG degrees than the global minimum and have distinct charge transfer dynamics within the picosecond to nanosecond time regime. Inside the pocket, the purine ligand undergoes dynamic motion on the low nanosecond time scale, sampling the multiple conformations based on time-resolved anisotropy decay dynamics. These results allowed a description of the energy landscape of the bound ligand with intricate details and demonstrated the elastic nature of the ligand recognition mode by the purine-sensing riboswitches, where there is a dynamic balance between hydrogen bonding

  9. The mammalian tachykinin ligand-receptor system: an emerging target for central neurological disorders.

    Science.gov (United States)

    Pantaleo, Nick; Chadwick, Wayne; Park, Sung-Soo; Wang, Liyun; Zhou, Yu; Martin, Bronwen; Maudsley, Stuart

    2010-11-01

    Our understanding of the complex signaling neurophysiology of the central nervous system has facilitated the exploration of potential novel receptor-ligand system targets for disorders of this most complex organ. In recent years, many relatively neglected receptor-ligand systems have been re-evaluated with respect to their ability to potently modulate discrete tracts in the central nervous system. One such system is the tachykinin (previously neurokinin) system. The multiple heptahelical G protein-coupled receptors and neuropeptide ligands that comprise this system may be significantly involved in more central nervous systems actions than previously thought, including sleep disorders, amyotrophic lateral sclerosis, Alzheimer's disease and Machado-Joseph disease. The development of our understanding of the role of the tachykinin receptor-ligand system in higher order central functions is likely to allow the creation of more specific and selective tachykinin-related neurotherapeutics.

  10. Understanding ligand effects in gold clusters using mass spectrometry

    Energy Technology Data Exchange (ETDEWEB)

    Johnson, Grant E.; Laskin, Julia

    2016-01-01

    -defined surfaces may be explored using ion soft landing (SL) in a custom-built instrument combined with in situ time of flight secondary ion mass spectrometry (TOF-SIMS). Jointly, this multipronged experimental approach allows characterization of the full spectrum of relevant phenomena including cluster synthesis, ligand exchange, thermochemistry, surface immobilization, and reactivity. The fundamental insights obtained from this work will facilitate the directed synthesis of gold clusters with predetermined size and properties for specific applications.

  11. Understanding ligand effects in gold clusters using mass spectrometry.

    Science.gov (United States)

    Johnson, Grant E; Laskin, Julia

    2016-06-21

    -built instrument combined with in situ time of flight secondary ion mass spectrometry (TOF-SIMS). Jointly, this multipronged experimental approach allows characterization of the full spectrum of relevant phenomena including cluster synthesis, ligand exchange, thermochemistry, surface immobilization, and reactivity. The fundamental insights obtained from this work will facilitate the directed synthesis of gold clusters with predetermined size and properties for specific applications.

  12. Intra-Genomic Heterogeneity in 16S rRNA Genes in Strictly Anaerobic Clinical Isolates from Periodontal Abscesses

    Science.gov (United States)

    Chen, Jiazhen; Miao, Xinyu; Xu, Meng; He, Junlin; Xie, Yi; Wu, Xingwen; Chen, Gang; Yu, Liying; Zhang, Wenhong

    2015-01-01

    Background Members of the genera Prevotella, Veillonella and Fusobacterium are the predominant culturable obligate anaerobic bacteria isolated from periodontal abscesses. When determining the cumulative number of clinical anaerobic isolates from periodontal abscesses, ambiguous or overlapping signals were frequently encountered in 16S rRNA gene sequencing chromatograms, resulting in ambiguous identifications. With the exception of the genus Veillonella, the high intra-chromosomal heterogeneity of rrs genes has not been reported. Methods The 16S rRNA genes of 138 clinical, strictly anaerobic isolates and one reference strain were directly sequenced, and the chromatograms were carefully examined. Gene cloning was performed for 22 typical isolates with doublet sequencing signals for the 16S rRNA genes, and four copies of the rrs-ITS genes of 9 Prevotella intermedia isolates were separately amplified by PCR, sequenced and compared. Five conserved housekeeping genes, hsp60, recA, dnaJ, gyrB1 and rpoB from 89 clinical isolates of Prevotella were also amplified by PCR and sequenced for identification and phylogenetic analysis along with 18 Prevotella reference strains. Results Heterogeneity of 16S rRNA genes was apparent in clinical, strictly anaerobic oral bacteria, particularly in the genera Prevotella and Veillonella. One hundred out of 138 anaerobic strains (72%) had intragenomic nucleotide polymorphisms (SNPs) in multiple locations, and 13 strains (9.4%) had intragenomic insertions or deletions in the 16S rRNA gene. In the genera Prevotella and Veillonella, 75% (67/89) and 100% (19/19) of the strains had SNPs in the 16S rRNA gene, respectively. Gene cloning and separate amplifications of four copies of the rrs-ITS genes confirmed that 2 to 4 heterogeneous 16S rRNA copies existed. Conclusion Sequence alignment of five housekeeping genes revealed that intra-species nucleotide similarities were very high in the genera Prevotella, ranging from 94.3–100%. However, the

  13. Allyl functionalized phosphinite and phosphonite ligands: Synthesis ...

    Indian Academy of Sciences (India)

    Allyl functionalized phosphinite and phosphonite ligands: Synthesis, transition metal chemistry and orthopalladation reactions. SINGAPPAGUDEM GOVINDARAJUa, GUDDEKOPPA S ANANTHNAGa, SUSMITA NAIKa,. SHAIKH M MOBINb and MARAVANJI S BALAKRISHNAa,∗. aPhosphorus Laboratory, Department of ...

  14. Organometallic chemistry of chiral diphosphazane ligands ...

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Chemical Sciences; Volume 114; Issue 4. Organometallic chemistry of chiral diphosphazane ligands: Synthesis and structural characterisation. Kannan Raghuraman Swadhin K Mandal T S Venkatakrishnan Setharampattu S Krishnamurthy Munirathinam Nethaji. Volume 114 Issue 4 August 2002 ...

  15. EGFR Activation by Spatially Restricted Ligands

    National Research Council Canada - National Science Library

    Clouse, Katherine N; Goodrich, Jennifer S

    2006-01-01

    ...) activity has been associated with an increased prognosis of breast cancer. During cogenesis in Drosophila melanogaster local Egfr activation by the spatially-restricted TGFalpha-like ligand Gurken (Grk...

  16. EGFR Activation by Spatially Restricted Ligands

    National Research Council Canada - National Science Library

    Goodrich, Jennifer S

    2005-01-01

    ...) activity has been associated with an increased prognosis of breast cancer. During oogenesis in Drosophila melanogaster, local EGFR activation by the spatially restricted TGF alpha-like ligand, Gurken (Grk...

  17. Protein-Ligand Empirical Interaction Components for Virtual Screening.

    Science.gov (United States)

    Yan, Yuna; Wang, Weijun; Sun, Zhaoxi; Zhang, John Z H; Ji, Changge

    2017-08-28

    A major shortcoming of empirical scoring functions is that they often fail to predict binding affinity properly. Removing false positives of docking results is one of the most challenging works in structure-based virtual screening. Postdocking filters, making use of all kinds of experimental structure and activity information, may help in solving the issue. We describe a new method based on detailed protein-ligand interaction decomposition and machine learning. Protein-ligand empirical interaction components (PLEIC) are used as descriptors for support vector machine learning to develop a classification model (PLEIC-SVM) to discriminate false positives from true positives. Experimentally derived activity information is used for model training. An extensive benchmark study on 36 diverse data sets from the DUD-E database has been performed to evaluate the performance of the new method. The results show that the new method performs much better than standard empirical scoring functions in structure-based virtual screening. The trained PLEIC-SVM model is able to capture important interaction patterns between ligand and protein residues for one specific target, which is helpful in discarding false positives in postdocking filtering.

  18. Designer TGFβ superfamily ligands with diversified functionality.

    Directory of Open Access Journals (Sweden)

    George P Allendorph

    Full Text Available Transforming Growth Factor--beta (TGFβ superfamily ligands, including Activins, Growth and Differentiation Factors (GDFs, and Bone Morphogenetic Proteins (BMPs, are excellent targets for protein-based therapeutics because of their pervasiveness in numerous developmental and cellular processes. We developed a strategy termed RASCH (Random Assembly of Segmental Chimera and Heteromer, to engineer chemically-refoldable TGFβ superfamily ligands with unique signaling properties. One of these engineered ligands, AB208, created from Activin-βA and BMP-2 sequences, exhibits the refolding characteristics of BMP-2 while possessing Activin-like signaling attributes. Further, we find several additional ligands, AB204, AB211, and AB215, which initiate the intracellular Smad1-mediated signaling pathways more strongly than BMP-2 but show no sensitivity to the natural BMP antagonist Noggin unlike natural BMP-2. In another design, incorporation of a short N-terminal segment from BMP-2 was sufficient to enable chemical refolding of BMP-9, without which was never produced nor refolded. Our studies show that the RASCH strategy enables us to expand the functional repertoire of TGFβ superfamily ligands through development of novel chimeric TGFβ ligands with diverse biological and clinical values.

  19. Li+-ligand binding energies and the effect of ligand fluorination on the binding energies

    Science.gov (United States)

    Bauschlicher, Charles W.

    2018-02-01

    The Li+-ligand binding energies are computed for seven ligands and their perfluoro analogs using Density Functional Theory. The bonding is mostly electrostatic in origin. Thus the size of the binding energy tends to correlate with the ligand dipole moment, however, the charge-induced dipole contribution can be sufficiently large to affect the dipole-binding energy correlation. The perfluoro species are significantly less strongly bound than their parents, because the electron withdrawing power of the fluorine reduces the ligand dipole moment.

  20. LigandRFs: random forest ensemble to identify ligand-binding residues from sequence information alone

    KAUST Repository

    Chen, Peng

    2014-12-03

    Background Protein-ligand binding is important for some proteins to perform their functions. Protein-ligand binding sites are the residues of proteins that physically bind to ligands. Despite of the recent advances in computational prediction for protein-ligand binding sites, the state-of-the-art methods search for similar, known structures of the query and predict the binding sites based on the solved structures. However, such structural information is not commonly available. Results In this paper, we propose a sequence-based approach to identify protein-ligand binding residues. We propose a combination technique to reduce the effects of different sliding residue windows in the process of encoding input feature vectors. Moreover, due to the highly imbalanced samples between the ligand-binding sites and non ligand-binding sites, we construct several balanced data sets, for each of which a random forest (RF)-based classifier is trained. The ensemble of these RF classifiers forms a sequence-based protein-ligand binding site predictor. Conclusions Experimental results on CASP9 and CASP8 data sets demonstrate that our method compares favorably with the state-of-the-art protein-ligand binding site prediction methods.

  1. Fermentative degradation of polyethylene glycol by a strictly anaerobic, gram-negative, nonsporeforming bacterium, Pelobacter venetianus sp. nov.

    Science.gov (United States)

    Schink, B; Stieb, M

    1983-06-01

    The synthetic polyether polyethylene glycol (PEG) with a molecular weight of 20,000 was anaerobically degraded in enrichment cultures inoculated with mud of limnic and marine origins. Three strains (Gra PEG 1, Gra PEG 2, and Ko PEG 2) of rod-shaped, gram-negative, nonsporeforming, strictly anaerobic bacteria were isolated in mineral medium with PEG as the sole source of carbon and energy. All strains degraded dimers, oligomers, and polymers of PEG up to a molecular weight of 20,000 completely by fermentation to nearly equal amounts of acetate and ethanol. The monomer ethylene glycol was not degraded. An ethylene glycol-fermenting anaerobe (strain Gra EG 12) isolated from the same enrichments was identified as Acetobacterium woodii. The PEG-fermenting strains did not excrete extracellular depolymerizing enzymes and were inhibited by ethylene glycol, probably owing to a blocking of the cellular uptake system. PEG, some PEG-containing nonionic detergents, 1,2-propanediol, 1,2-butanediol, glycerol, and acetoin were the only growth substrates utilized of a broad variety of sugars, organic acids, and alcohols. The isolates did not reduce sulfate, sulfur, thiosulfate, or nitrate and were independent of growth factors. In coculture with A. woodii or Methanospirillum hungatei, PEGs and ethanol were completely fermented to acetate (and methane). A marine isolate is described as the type strain of a new species, Pelobacter venetianus sp. nov. Its physiology and ecological significance, as well as the importance and possible mechanism of anaerobic polyether degradation, are discussed.

  2. Effect of nonsurgical periodontal therapy and strict plaque control on preterm/low birth weight: a randomized controlled clinical trial.

    Science.gov (United States)

    Weidlich, Patricia; Moreira, Carlos Heitor C; Fiorini, Tiago; Musskopf, Marta L; da Rocha, José M; Oppermann, Maria Lucia R; Aass, Anne M; Gjermo, Per; Susin, Cristiano; Rösing, Cassiano K; Oppermann, Rui V

    2013-01-01

    This randomized controlled clinical trial was carried out to assess the effect of comprehensive nonsurgical periodontal treatment and strict plaque control performed during pregnancy on the reduction of preterm and/or low birth weight rates (PTLBW). Three hundred and three women were randomly allocated to receive periodontal treatment either during pregnancy (n = 147, test group) or after delivery (n = 156, control group). During pregnancy, the control group received only one session of supragingival scaling and oral hygiene instruction. In contrast, the test group received comprehensive periodontal treatment including multiple sessions of scaling and root planing, oral hygiene instructions, and frequent maintenance visits. At baseline, periodontal inflammation was observed in approximately 50% of sites and attachment loss affected controls, women in the test group had significant reductions in the percentage of sites with plaque (48.5% vs. 10.3%, p control significantly improved periodontal health; however, no reduction of PTLBW rates was observed. Thus, remaining periodontal inflammation posttreatment cannot explain the lack of effect of periodontal treatment on PTLBW. Clinical relevance This study demonstrated that periodontal diseases may be successfully treated during pregnancy. Our results do not support a potential beneficial effect of periodontal treatment on PTLBW.

  3. Lack of evidence for phase-only control of retinal photoisomerization in the strict one-photon limit

    Science.gov (United States)

    Liebel, M.; Kukura, P.

    2017-01-01

    The concept of shaping electric fields to steer light-induced processes coherently has fascinated scientists for decades. Despite early theoretical considerations that ruled out one-photon coherent control (CC), several experimental studies reported that molecular responses are sensitive to the shape of the excitation field in the weak-field limit. These observations were largely attributed to the presence of rapid-decay channels, but experimental verification is lacking. Here, we test this hypothesis by investigating the degree of achievable control over the photoisomerization of the retinal protonated Schiff-base in bacteriorhodopsin, isorhodopsin and rhodopsin, all of which exhibit similar chromophores but different isomerization yields and excited-state lifetimes. Irrespective of the system studied, we find no evidence for dissipation-dependent behaviour, nor for any CC in the strict one-photon limit. Our results question the extent to which a photochemical process at ambient conditions can be controlled at the amplitude level, and how the underlying molecular potential-energy surfaces and dynamics may influence this controllability.

  4. Effect of strict metabolic control on regulation of subcutaneous blood flow in insulin-dependent diabetic patients

    DEFF Research Database (Denmark)

    Kastrup, J; Mathiesen, E R; Saurbrey, Nina

    1987-01-01

    washout technique. Mean arterial blood pressure was reduced by a maximum of 23 mmHg by elevating the limb above heart level and elevated to a maximum of 65 mmHg by head-up tilt; in the latter position venous pressure was kept constantly low by activation of the leg muscle vein pump (heel raising......The effect of 10 weeks of improved metabolic control on the impaired autoregulation of the subcutaneous blood flow was studied at the level of the lateral malleolus in eight long-term insulin-dependent diabetic patients with clinical microangiopathy. Blood flow was measured by the local 133-Xenon......). Improved metabolic control was achieved using either continuous subcutaneous insulin infusion or multiple insulin injections. The blood glucose concentration declined from (median) 12.7 to 6.8 mmol/l and the HbA1C level from 10.1 to 7.5% during strict metabolic control (p less than 0.01 and p less than 0...

  5. Multiscale simulations of ligand adsorption and exchange on gold nanoparticles.

    Science.gov (United States)

    Gao, Hui-Min; Liu, Hong; Qian, Hu-Jun; Jiao, Gui-Sheng; Lu, Zhong-Yuan

    2018-01-17

    We have developed a multiscale model that combines first-principles methods with atomistic and mesoscopic simulations to explore the molecular structures and packing density of the ligands present on the gold nanoparticle (AuNP) surface, as well as the adsorption/exchange reaction kinetics of cetyltrimethylammonium bromide (CTAB)/PEG-SH ligands on different facets of gold, namely, Au(111), Au(100), and Au(110). Our model predicts that on clean gold surfaces, CTAB adsorption is diffusion limited. Specifically, CTAB has the preferentially higher adsorption rate and coverage density on Au(100) and Au(110) surfaces, forming a more compact layer with respect to that on the Au(111) surface, which could result in greater growth of gold nanoparticles along the (111) direction. As opposed to CTAB adsorption, the exchange reaction between PEG-SH with CTAB shows no selectivity to different crystal faces, and the reaction process follows Langmuir diffusion kinetics. Kinetic analysis reveals that, in water, the exchange reaction is zeroth order with respect to the concentration of an incoming PEG-SH, indicative of a dissociative exchange mechanism. The observed rate constant decreases exponentially with the PEG-SH chain length, consistent with a diffusion process for the free PEG-SH in water. In particular, we show that the exchange efficiency increases as the chain rigidness and size of the incoming ligand and/or steric bulk of the initial protecting ligand shell are decreased. Our objectives are to provide a model to assess the kinetics and thermodynamics of the adsorption/exchange reaction process, and we expect that these findings will have important implications for routine surface characterization of AuNPs.

  6. Synthesis and characterization of mixed ligand chiral nanoclusters

    KAUST Repository

    Guven, Zekiye P.

    2016-06-22

    Chiral mixed ligand silver nanoclusters were synthesized in the presence of a chiral and an achiral ligand. While the chiral ligand led mostly to the formation of nanoparticles, the presence of the achiral ligand drastically increased the yield of nanoclusters with enhanced chiral properties. © 2016 The Royal Society of Chemistry.

  7. Domain interplay in the urokinase receptor. Requirement for the third domain in high affinity ligand binding and demonstration of ligand contact sites in distinct receptor domains

    DEFF Research Database (Denmark)

    Behrendt, N; Ronne, E; Dano, K

    1996-01-01

    The urokinase plasminogen activator receptor (uPAR) is a membrane protein comprised of three extracellular domains. In order to study the importance of this domain organization in the ligand-binding process of the receptor we subjected a recombinant, soluble uPAR (suPAR) to specific proteolytic...

  8. Impact of protein and ligand impurities on ITC-derived protein-ligand thermodynamics.

    Science.gov (United States)

    Grüner, Stefan; Neeb, Manuel; Barandun, Luzi Jakob; Sielaff, Frank; Hohn, Christoph; Kojima, Shun; Steinmetzer, Torsten; Diederich, François; Klebe, Gerhard

    2014-09-01

    The thermodynamic characterization of protein-ligand interactions by isothermal titration calorimetry (ITC) is a powerful tool in drug design, giving valuable insight into the interaction driving forces. ITC is thought to require protein and ligand solutions of high quality, meaning both the absence of contaminants as well as accurately determined concentrations. Ligands synthesized to deviating purity and protein of different pureness were titrated by ITC. Data curation was attempted also considering information from analytical techniques to correct stoichiometry. We used trypsin and tRNA-guanine transglycosylase (TGT), together with high affinity ligands to investigate the effect of errors in protein concentration as well as the impact of ligand impurities on the apparent thermodynamics. We found that errors in protein concentration did not change the thermodynamic properties obtained significantly. However, most ligand impurities led to pronounced changes in binding enthalpy. If protein binding of the respective impurity is not expected, the actual ligand concentration was corrected for and the thus revised data compared to thermodynamic properties obtained with the respective pure ligand. Even in these cases, we observed differences in binding enthalpy of about 4kJ⋅mol(-1), which is considered significant. Our results indicate that ligand purity is the critical parameter to monitor if accurate thermodynamic data of a protein-ligand complex are to be recorded. Furthermore, artificially changing fitting parameters to obtain a sound interaction stoichiometry in the presence of uncharacterized ligand impurities may lead to thermodynamic parameters significantly deviating from the accurate thermodynamic signature. Copyright © 2014 Elsevier B.V. All rights reserved.

  9. Agronomic traits and deoxynivalenol contamination of two tetraploid wheat species (Triticum turgidum spp. durum, Triticum turgidum spp. turanicum grown strictly under low input conditions

    Directory of Open Access Journals (Sweden)

    Giovanni Dinelli

    2014-09-01

    Full Text Available An evaluation of the agronomic performance of two tetraploid wheat varieties (Triticum turgidum spp. durum, Claudio; Triticum turgidum spp. turanicum, Kamut® grown strictly under low input conditions was carried out over three consecutive cropping years. The study reported grain yield values ranging from 1.8 to 2.6 t ha-1. Productivity showed to be primarily affected by environmental conditions, while no differences were observed between the two genotypes. The study of the yield components highlighted that the durum wheat variety had a higher plant density than Kamut®, but this discrepancy was offset by a greater number of kernels per spike and the kernel weight of khorasan wheat. The investigated wheat genotypes were also analysed to assess the mycotoxin (DON levels of wholegrain semolina and the efficiency of cleaning treatments to reduce contamination. Results showed that both wheat varieties had a good hygienic and sanitary quality with a DON content ranging from 0.35 to 1.31 mg kg-1, which was lower than the maximum acceptable level set by the European regulation at 1.75 mg kg-1. In addition, our research work investigated the effects of premilling cleaning procedures, such as water washing and brushing, on mycotoxin levels, which yielded interesting results in terms of decontamination efficiency. These methods were particularly efficient with Kamut® semolina (46-93% DON reduction, suggesting that mycotoxins accumulate in this variety at more superficial levels than in the durum wheat variety. On the whole, our study provided additional knowledge on the traits to be further improved to respond to low input requirements and to enhance the potential adaptability of wheat genotypes to organic agriculture. Our results emphasized the need to develop wheat varieties that can provide adequate performance without high levels of nitrogen inputs by selecting specific traits, such as kernel weight, spike length and kernel/spike. This may help

  10. LS-align: an atom-level, flexible ligand structural alignment algorithm for high-throughput virtual screening.

    Science.gov (United States)

    Hu, Jun; Liu, Zi; Yu, Dong-Jun; Zhang, Yang

    2018-02-15

    Sequence-order independent structural comparison, also called structural alignment, of small ligand molecules is often needed for computer-aided virtual drug screening. Although many ligand structure alignment programs are proposed, most of them build the alignments based on rigid-body shape comparison which cannot provide atom-specific alignment information nor allow structural variation; both abilities are critical to efficient high-throughput virtual screening. We propose a novel ligand comparison algorithm, LS-align, to generate fast and accurate atom-level structural alignments of ligand molecules, through an iterative heuristic search of the target function that combines inter-atom distance with mass and chemical bond comparisons. LS-align contains two modules of Rigid-LS-align and Flexi-LS-align, designed for rigid-body and flexible alignments, respectively, where a ligand-size independent, statistics-based scoring function is developed to evaluate the similarity of ligand molecules relative to random ligand pairs. Large-scale benchmark tests are performed on prioritizing chemical ligands of 102 protein targets involving 1,415,871 candidate compounds from the DUD-E (Database of Useful Decoys: Enhanced) database, where LS-align achieves an average enrichment factor (EF) of 22.0 at the 1% cutoff and the AUC score of 0.75, which are significantly higher than other state-of-the-art methods. Detailed data analyses show that the advanced performance is mainly attributed to the design of the target function that combines structural and chemical information to enhance the sensitivity of recognizing subtle difference of ligand molecules and the introduces of structural flexibility that help capture the conformational changes induced by the ligand-receptor binding interactions. These data demonstrate a new avenue to improve the virtual screening efficiency through the development of sensitive ligand structural alignments. http

  11. Influence of CCR7 ligand DNA preexposure on the magnitude and duration of immunity

    International Nuclear Information System (INIS)

    Lee, Yunsang; Seong, Kug Eo; Rouse, Richard J.D.; Rouse, Barry T.

    2003-01-01

    The CC chemokine receptor (CCR) 7 ligands CCL21 and CCL19 were recently described as essential elements for establishing the microenvironment needed to initiate optimal immune responses in secondary lymphoid tissues. In the present study we have kinetically investigated the primary responses of naive DO11.10 TCR-transgenic CD4+ T cells (OVA323-339 peptide specific) adoptively transferred into normal BALB/c mice given plasmid DNA encoding CCR7 ligands. The primary responses of CD4+ Tg-T cells in CCR7 ligand DNA recipients occurred more promptly, reaching levels higher than those observed in vector controls. In line with enhanced specific immunity, the T-cell population in CCR7 ligand recipients underwent more in vivo cell division following Ag stimulation, and a higher percentage of Ag-specific T cells expressed an activation phenotype. Moreover, the enhanced primary responses of naive CD4+ T cells appeared to act via affects on migration and maturation of CD11c+ dendritic cells in the draining lymph nodes. In addition following mucosal challenge of herpes simplex virus-immune mice with virus, those that had received CCL21 or CCL19 during priming contained a higher frequency of responding CD4 T cells in lymph nodes and the site of infection. Moreover, CCL21- and CCL19-treated mice showed less severe disease and better survival following challenge. Our results are discussed in terms of the relevance of CCR7 ligand preimmunization to improve vaccine

  12. Engineering periplasmic ligand binding proteins as glucose nanosensors

    Directory of Open Access Journals (Sweden)

    Constance J. Jeffery

    2011-01-01

    Full Text Available Diabetes affects over 100 million people worldwide. Better methods for monitoring blood glucose levels are needed for improving disease management. Several labs have previously made glucose nanosensors by modifying members of the periplasmic ligand binding protein superfamily. This minireview summarizes recent developments in constructing new versions of these proteins that are responsive within the physiological range of blood glucose levels, employ new reporter groups, and/or are more robust. These experiments are important steps in the development of novel proteins that have the characteristics needed for an implantable glucose nanosensor for diabetes management: specificity for glucose, rapid response, sensitivity within the physiological range of glucose concentrations, reproducibility, and robustness.

  13. IDENTIFICATION OF CATALYTIC METAL ION LIGANDS IN RIBOZYMES

    Science.gov (United States)

    Frederiksen, John K.; Piccirilli, Joseph A.

    2012-01-01

    Site-bound metal ions participate in the catalytic mechanisms of many ribozymes. Understanding these mechanisms therefore requires knowledge of the specific ligands on both substrate and ribozyme that coordinate these catalytic metal ions. A number of different structural and biochemical strategies have been developed and refined for identifying metal ion binding sites within ribozymes, and for assessing the catalytic contributions of the metal ions bound at those sites. We review these approaches and provide examples of their application, focusing in particular on metal ion rescue experiments and their roles in the construction of the transition state models for the Tetrahymena group I and RNase P ribozymes. PMID:19651216

  14. A novel strictly anaerobic recovery and enrichment system incorporating lithium for detection of heat-injured Listeria monocytogenes in pasteurized milk containing background microflora.

    Science.gov (United States)

    Mendonca, A F; Knabel, S J

    1994-11-01

    Heat-injured cells of Listeria monocytogenes were recovered from heated raw milk containing noninjured Enterococcus faecium by combining a simple method for obtaining strict anaerobiosis with a novel enrichment broth, Penn State University broth (PSU broth). Strictly anaerobic conditions were rapidly achieved by adding 0.5 g of filter-sterilized cysteine per liter to PSU broth and then purging the preparation with N2 gas. Little resuscitation or growth occurred in strictly anaerobic PSU broth without lithium chloride because of overgrowth by E. faecium. The growth of E. faecium decreased dramatically with increasing LiCl concentration; LiCl concentrations of 8 and 10 g/liter were completely bacteriostatic. The mechanism of inhibition by LiCl appeared to involve competition with the divalent cations Ca2+ and Mg2+. Heat-injured L. monocytogenes consistently recovered and grew rapidly in strictly anaerobic PSU broth containing 4, 6, or 7 g of LiCl per liter. The use of strictly anaerobic PSU broth containing 7 g of LiCl per liter permitted detection of severely heat-injured L. monocytogenes in one simple recovery-enrichment step by eliminating oxygen toxicity and inhibiting the growth of background microflora, without preventing the resuscitation and subsequent growth of heat-injured L. monocytogenes. L. monocytogenes heated in raw milk at 62.8 degrees C for 10, 15, and 20 min could be consistently recovered from strictly anaerobic PSU broth enrichment cultures at 30 degrees C after 48, 96, and 144 h, respectively, and hence, use of PSU broth may result in better recovery of both injured and noninjured cells from foods than currently used U.S. Department of Agriculture and Food and Drug Administration preenrichment procedures.

  15. Protein stabilization with a dipeptide-mimic triazine-scaffolded synthetic affinity ligand.

    Science.gov (United States)

    Sousa, I T; Lourenço, N M T; Afonso, C A M; Taipa, M A

    2013-02-01

    Protein stabilization was achieved by a novel approach based on the adsorption and establishment of affinity-like interactions with a biomimetic triazine-scaffolded ligand. A synthetic lead compound (ligand 3'/11, K(a) ≈ 10(4) M(-1)) was selected from a previously screened solid-phase library of affinity ligands for studies of adsorption and stabilization of cutinase from Fusarium solani pisi used as a model system. This ligand, directly synthesized in agarose by a well-established solid-phase synthesis method, was able to strongly bind cutinase and led to impressive half-lives of more than 8 h at 70 °C, and of approximately 34 h at 60 °C for bound protein (a 25- and 57-fold increase as compared with the free enzyme, respectively). The ligand density in the solid matrix was found to be a determinant parameter for cutinase stabilization. It is conceivable that the highly stabilizing effect observed results from the binding of more than one ligand residue to the enzyme, creating specific macromolecular configurations that lock structural mobility thus improving molecular stability. Copyright © 2013 John Wiley & Sons, Ltd.

  16. Inhibition of mushroom tyrosinase by a newly synthesized ligand: inhibition kinetics and computational simulations.

    Science.gov (United States)

    Alijanianzadeh, Mahdi; Saboury, Ali Akbar; Ganjali, Mohammad Reza; Hadi-Alijanvand, Hamid; Moosavi-Movahedi, Ali Akbar

    2012-01-01

    Alterations in the synthesis of melanin contribute to a number of diseases; therefore, the design of new tyrosinase inhibitors is very important. Mushroom tyrosinase (MT) is a metalloenzyme, which plays an important role in melanin biosynthesis. In this study, the inhibitory effect of a novel designed compound, i.e. 2-((1Z)-(2-(2,4-dinitrophenyl)hydrazin-1-ylidene)methyl)phenol, as a specific ligand which can bind to the copper ion of MT, has been assessed. The ligand was found to competitively inhibit both the cresolase and catecholase activities of MT, with small inhibition constants of 2.8 and 2.6 μM, respectively. Intrinsic fluorescence studies were performed to gain more information on the binding constants. Docking results indicated that the ligand binds to copper ions in the active site of MT via the OH group of the ligand. The ligand makes four hydrogen bonds with aspartic acid and one hydrogen bond with the histidine residue in the active site. Molecular dynamics results show that ligand binds to the MT via both electrostatic and hydrophobic interactions with its different parts.

  17. Generation, Characterization, and Tunable Reactivity of Organometallic Fragments Bound to a Protein Ligand.

    Science.gov (United States)

    Key, Hanna M; Clark, Douglas S; Hartwig, John F

    2015-07-01

    Organotransition metal complexes catalyze important synthetic transformations, and the development of these systems has rested on the detailed understanding of the structures and elementary reactions of discrete organometallic complexes bound to organic ligands. One strategy for the creation of new organometallic systems is to exploit the intricate and highly structured ligands found in natural metalloproteins. We report the preparation and characterization of discrete rhodium and iridium fragments bound site-specifically in a κ(2)-fashion to the protein carbonic anhydrase as a ligand. The reactions of apo human carbonic anhydrase with [Rh(nbd)2]BF4 or [M(CO)2(acac)] (M=Rh, Ir) form proteins containing Rh or Ir with organometallic ligands. A colorimetric assay was developed to quantify rapidly the metal occupancy at the native metal-binding site, and (15)N-(1)H NMR spectroscopy was used to establish the amino acids to which the metal is bound. IR spectroscopy and EXAFS revealed the presence and number of carbonyl ligands and the number total ligands, while UV-vis spectroscopy provided a signature to readily identify species that had been fully characterized. Exploiting these methods, we observed fundamental stoichiometric reactions of the artificial organometallic site of this protein, including reactions that simultaneously form and cleave metal-carbon bonds. The preparation and reactivity of these artificial organometallic proteins demonstrate the potential to study a new genre of organometallic complexes for which the rates and outcomes of organometallic reactions can be controlled by genetic manipulation of the protein scaffold.

  18. Novel microsatellite DNA markers indicate strict parthenogenesis and few genotypes in the invasive willow sawfly Nematus oligospilus.

    Science.gov (United States)

    Caron, V; Norgate, M; Ede, F J; Nyman, T; Sunnucks, P

    2013-02-01

    Invasive organisms can have major impacts on the environment. Some invasive organisms are parthenogenetic in their invasive range and, therefore, exist as a number of asexual lineages (=clones). Determining the reproductive mode of invasive species has important implications for understanding the evolutionary genetics of such species, more especially, for management-relevant traits. The willow sawfly Nematus oligospilus Förster (Hymenoptera: Tenthredinidae) has been introduced unintentionally into several countries in the Southern Hemisphere where it has subsequently become invasive. To assess the population expansion, reproductive mode and host-plant relationships of this insect, microsatellite markers were developed and applied to natural populations sampled from the native and expanded range, along with sequencing of the cytochrome-oxidase I mitochondrial DNA (mtDNA) region. Other tenthredinids across a spectrum of taxonomic similarity to N. oligospilus and having a range of life strategies were also tested. Strict parthenogenesis was apparent within invasive N. oligospilus populations throughout the Southern Hemisphere, which comprised only a small number of genotypes. Sequences of mtDNA were identical for all individuals tested in the invasive range. The microsatellite markers were used successfully in several sawfly species, especially Nematus spp. and other genera of the Nematini tribe, with the degree of success inversely related to genetic divergence as estimated from COI sequences. The confirmation of parthenogenetic reproduction in N. oligospilus and the fact that it has a very limited pool of genotypes have important implications for understanding and managing this species and its biology, including in terms of phenotypic diversity, host relationships, implications for spread and future adaptive change. It would appear to be an excellent model study system for understanding evolution of invasive parthenogens that diverge without sexual reproduction and

  19. Changes in Frequency Intake of Foods in Patients Undergoing Sleeve Gastrectomy and Following a Strict Dietary Control.

    Science.gov (United States)

    Ruiz-Tovar, Jaime; Bozhychko, Maryana; Del-Campo, Jone Miren; Boix, Evangelina; Zubiaga, Lorea; Muñoz, Jose Luis; Llavero, Carolina

    2017-12-17

    Dietary intake and food preferences change after bariatric surgery, secondary to gastrointestinal symptoms and dietitian counseling. The aim of this study was to evaluate the changes in the frequency intake of different foods in patients undergoing sleeve gastrectomy and following a strict dietary control. A prospective observational study of all the morbidly obese patients undergoing laparoscopic sleeve gastrectomy as bariatric procedure between 2007 and 2012 was performed. Dietary assessment was performed using the Alimentary Frequency Questionnaire 1991-2002, developed and validated by the Department of Epidemiology of Miguel Hernandez University (Elche, Alicante Spain). Ninety-three patients were included for analysis, 73 females and 20 males, with a mean preoperative BMI of 46.4 ± 7.9 kg/m 2 . One year after surgery, excess weight loss was 81.1 ± 8.3% and 5 years after surgery, 79.9 ± 6.4%. Total weight loss at 1 year was 38.8 ± 5.3% and at 5 years, 35.4 ± 4.9%. Postoperatively, a reduction in the intake of dairy products, red meat, deli meat products, shellfish, fried potatoes, sweets, rice, pasta, beer, and processed foods was observed. Vegetables, fruits, and legumes intake increased after surgery. In the first postoperative year, there was a slight intolerance to red meat, fruits, vegetables and legumes, dairy products, pasta, and rice that mostly disappeared 5 years after surgery. One year after sleeve gastrectomy, calibrated with a 50-French bougie, there are not important problems in the intake of foods a priori difficult to digest. These problems mostly disappeared 5 years after surgery. The decrease intake of other unhealthy foods is mostly based on the dietary counseling.

  20. Immobilisation of ligands by radio-derivatized polymers; Immobilisering av ligander med radioderiverte polymerer

    Energy Technology Data Exchange (ETDEWEB)

    Varga, J.M.; Fritsch, P.

    1995-01-30

    The invention relates to radio-derivatized polymers and a method of producing them by contacting non-polymerizable conjugands with radiolysable polymers in the presence of irradiation. The resulting radio-derivatized polymers can be further linked with ligand of organic or inorganic nature to immobilize such ligands. 2 figs., 5 tabs.

  1. PoLi: A Virtual Screening Pipeline Based on Template Pocket and Ligand Similarity.

    Science.gov (United States)

    Roy, Ambrish; Srinivasan, Bharath; Skolnick, Jeffrey

    2015-08-24

    Often in pharmaceutical research the goal is to identify small molecules that can interact with and appropriately modify the biological behavior of a new protein target. Unfortunately, most proteins lack both known structures and small molecule binders, prerequisites of many virtual screening, VS, approaches. For such proteins, ligand homology modeling, LHM, that copies ligands from homologous and perhaps evolutionarily distant template proteins, has been shown to be a powerful VS approach to identify possible binding ligands. However, if we want to target a specific pocket for which there is no homologous holo template protein structure, then LHM will not work. To address this issue, in a new pocket-based approach, PoLi, we generalize LHM by exploiting the fact that the number of distinct small molecule ligand-binding pockets in proteins is small. PoLi identifies similar ligand-binding pockets in a holo template protein library, selectively copies relevant parts of template ligands, and uses them for VS. In practice, PoLi is a hybrid structure and ligand-based VS algorithm that integrates 2D fingerprint-based and 3D shape-based similarity metrics for improved virtual screening performance. On standard DUD and DUD-E benchmark databases, using modeled receptor structures, PoLi achieves an average enrichment factor of 13.4 and 9.6, respectively, in the top 1% of the screened library. In contrast, traditional docking-based VS using AutoDock Vina and homology-based VS using FINDSITE(filt) have an average enrichment of 1.6 (3.0) and 9.0 (7.9) on the DUD (DUD-E) sets, respectively. Experimental validation of PoLi predictions on dihydrofolate reductase, DHFR, using differential scanning fluorimetry, DSF, identifies multiple ligands with diverse molecular scaffolds, thus demonstrating the advantage of PoLi over current state-of-the-art VS methods.

  2. A General Ligand Design for Gold Catalysis allowing Ligand-Directed Anti Nucleophilic Attack of Alkynes

    Science.gov (United States)

    Wang, Yanzhao; Wang, Zhixun; Li, Yuxue; Wu, Gongde; Cao, Zheng; Zhang, Liming

    2014-01-01

    Most homogenous gold catalyses demand ≥0.5 mol % catalyst loading. Due to the high cost of gold, these reactions are unlikely to be applicable in medium or large scale applications. Here we disclose a novel ligand design based on the privileged biphenyl-2-phosphine framework that offers a potentially general approach to dramatically lowering catalyst loading. In this design, an amide group at the 3’ position of the ligand framework directs and promotes nucleophilic attack at the ligand gold complex-activated alkyne, which is unprecedented in homogeneous gold catalysis considering the spatial challenge of using ligand to reach antiapproaching nucleophile in a linear P-Au-alkyne centroid structure. With such a ligand, the gold(I) complex becomes highly efficient in catalyzing acid addition to alkynes, with a turnover number up to 99,000. Density functional theory calculations support the role of the amide moiety in directing the attack of carboxylic acid via hydrogen bonding. PMID:24704803

  3. LIBRA: LIgand Binding site Recognition Application.

    Science.gov (United States)

    Hung, Le Viet; Caprari, Silvia; Bizai, Massimiliano; Toti, Daniele; Polticelli, Fabio

    2015-12-15

    In recent years, structural genomics and ab initio molecular modeling activities are leading to the availability of a large number of structural models of proteins whose biochemical function is not known. The aim of this study was the development of a novel software tool that, given a protein's structural model, predicts the presence and identity of active sites and/or ligand binding sites. The algorithm implemented by ligand binding site recognition application (LIBRA) is based on a graph theory approach to find the largest subset of similar residues between an input protein and a collection of known functional sites. The algorithm makes use of two predefined databases for active sites and ligand binding sites, respectively, derived from the Catalytic Site Atlas and the Protein Data Bank. Tests indicate that LIBRA is able to identify the correct binding/active site in 90% of the cases analyzed, 90% of which feature the identified site as ranking first. As far as ligand binding site recognition is concerned, LIBRA outperforms other structure-based ligand binding sites detection tools with which it has been compared. The application, developed in Java SE 7 with a Swing GUI embedding a JMol applet, can be run on any OS equipped with a suitable Java Virtual Machine (JVM), and is available at the following URL: http://www.computationalbiology.it/software/LIBRAv1.zip. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  4. Dockomatic - automated ligand creation and docking.

    Science.gov (United States)

    Bullock, Casey W; Jacob, Reed B; McDougal, Owen M; Hampikian, Greg; Andersen, Tim

    2010-11-08

    The application of computational modeling to rationally design drugs and characterize macro biomolecular receptors has proven increasingly useful due to the accessibility of computing clusters and clouds. AutoDock is a well-known and powerful software program used to model ligand to receptor binding interactions. In its current version, AutoDock requires significant amounts of user time to setup and run jobs, and collect results. This paper presents DockoMatic, a user friendly Graphical User Interface (GUI) application that eases and automates the creation and management of AutoDock jobs for high throughput screening of ligand to receptor interactions. DockoMatic allows the user to invoke and manage AutoDock jobs on a single computer or cluster, including jobs for evaluating secondary ligand interactions. It also automates the process of collecting, summarizing, and viewing results. In addition, DockoMatic automates creation of peptide ligand .pdb files from strings of single-letter amino acid abbreviations. DockoMatic significantly reduces the complexity of managing multiple AutoDock jobs by facilitating ligand and AutoDock job creation and management.

  5. Dockomatic - automated ligand creation and docking

    Directory of Open Access Journals (Sweden)

    Hampikian Greg

    2010-11-01

    Full Text Available Abstract Background The application of computational modeling to rationally design drugs and characterize macro biomolecular receptors has proven increasingly useful due to the accessibility of computing clusters and clouds. AutoDock is a well-known and powerful software program used to model ligand to receptor binding interactions. In its current version, AutoDock requires significant amounts of user time to setup and run jobs, and collect results. This paper presents DockoMatic, a user friendly Graphical User Interface (GUI application that eases and automates the creation and management of AutoDock jobs for high throughput screening of ligand to receptor interactions. Results DockoMatic allows the user to invoke and manage AutoDock jobs on a single computer or cluster, including jobs for evaluating secondary ligand interactions. It also automates the process of collecting, summarizing, and viewing results. In addition, DockoMatic automates creation of peptide ligand .pdb files from strings of single-letter amino acid abbreviations. Conclusions DockoMatic significantly reduces the complexity of managing multiple AutoDock jobs by facilitating ligand and AutoDock job creation and management.

  6. Chelating ligands for nanocrystals' surface functionalization.

    Science.gov (United States)

    Querner, Claudia; Reiss, Peter; Bleuse, Joël; Pron, Adam

    2004-09-22

    A new family of ligands for the surface functionalization of CdSe nanocrystals is proposed, namely alkyl or aryl derivatives of carbodithioic acids (R-C(S)SH). The main advantages of these new ligands are as follows: they nearly quantitatively exchange the initial surface ligands (TOPO) in very mild conditions; they significantly improve the resistance of nanocrystals against photooxidation because of their ability of strong chelate-type binding to metal atoms; their relatively simple preparation via Grignard intermediates facilitates the development of new bifunctional ligands containing, in addition to the anchoring carbodithioate group, a second function, which enables the grafting of molecules or macromolecules of interest on the nanocrystal surface. To give an example of this approach, we report, for the first time, the grafting of an electroactive oligomer from the polyaniline family-aniline tetramer-on CdSe nanocrystals after their functionalization with 4-formyldithiobenzoic acid. The grafting proceeds via a condensation reaction between the aldehyde group of the ligand and the terminal primary amine group of the tetramer. The resulting organic/inorganic hybrid exhibits complete extinction of the fluorescence of its constituents, indicating efficient charge or energy transfer between the organic and the inorganic semiconductors.

  7. Ligand identification using electron-density map correlations

    International Nuclear Information System (INIS)

    Terwilliger, Thomas C.; Adams, Paul D.; Moriarty, Nigel W.; Cohn, Judith D.

    2007-01-01

    An automated ligand-fitting procedure is applied to (F o − F c )exp(iϕ c ) difference density for 200 commonly found ligands from macromolecular structures in the Protein Data Bank to identify ligands from density maps. A procedure for the identification of ligands bound in crystal structures of macromolecules is described. Two characteristics of the density corresponding to a ligand are used in the identification procedure. One is the correlation of the ligand density with each of a set of test ligands after optimization of the fit of that ligand to the density. The other is the correlation of a fingerprint of the density with the fingerprint of model density for each possible ligand. The fingerprints consist of an ordered list of correlations of each the test ligands with the density. The two characteristics are scored using a Z-score approach in which the correlations are normalized to the mean and standard deviation of correlations found for a variety of mismatched ligand-density pairs, so that the Z scores are related to the probability of observing a particular value of the correlation by chance. The procedure was tested with a set of 200 of the most commonly found ligands in the Protein Data Bank, collectively representing 57% of all ligands in the Protein Data Bank. Using a combination of these two characteristics of ligand density, ranked lists of ligand identifications were made for representative (F o − F c )exp(iϕ c ) difference density from entries in the Protein Data Bank. In 48% of the 200 cases, the correct ligand was at the top of the ranked list of ligands. This approach may be useful in identification of unknown ligands in new macromolecular structures as well as in the identification of which ligands in a mixture have bound to a macromolecule

  8. Peptides identify multiple hotspots within the ligand binding domain of the TNF receptor 2

    Directory of Open Access Journals (Sweden)

    Lennick Michael

    2003-01-01

    Full Text Available Abstract Background Hotspots are defined as the minimal functional domains involved in protein:protein interactions and sufficient to induce a biological response. Results Here we describe the use of complex and high diversity phage display libraries to isolate peptides (called Hotspot Ligands or HSPLs which sub-divide the ligand binding domain of the tumor necrosis factor receptor 2 (TNFR2; p75 into multiple hotspots. We have shown that these libraries could generate HSPLs which not only subdivide hotspots on protein and non-protein targets but act as agonists or antagonists. Using this approach, we generated peptides which were specific for human TNFR2, could be competed by the natural ligands, TNFα and TNFβ and induced an unexpected biological response in a TNFR2-specific manner. Conclusions To our knowledge, this is the first report describing the dissection of the TNFR2 into biologically active hotspots with the concomitant identification of a novel and unexpected biological activity.

  9. Activation of autoreactive B cells by endogenous TLR7 and TLR3 RNA ligands.

    Science.gov (United States)

    Green, Nathaniel M; Moody, Krishna-Sulayman; Debatis, Michelle; Marshak-Rothstein, Ann

    2012-11-16

    The key step in the activation of autoreactive B cells is the internalization of nucleic acid containing ligands and delivery of these ligands to the Toll-like Receptor (TLR) containing endolysosomal compartment. Ribonucleoproteins represent a large fraction of autoantigens in systemic autoimmune diseases. Here we demonstrate that many uridine-rich mammalian RNA sequences associated with common autoantigens effectively activate autoreactive B cells. Priming with type I IFN increased the magnitude of activation, and the range of which RNAs were stimulatory. A subset of RNAs that contain a high degree of self-complementarity also activated B cells through TLR3. For the RNA sequences that activated predominantly through TLR7, the activation is proportional to uridine-content, and more precisely defined by the frequency of specific uridine-containing motifs. These results identify parameters that define specific mammalian RNAs as ligands for TLRs.

  10. Characteristic molecular vibrations of adenosine receptor ligands.

    Science.gov (United States)

    Chee, Hyun Keun; Yang, Jin-San; Joung, Je-Gun; Zhang, Byoung-Tak; Oh, S June

    2015-02-13

    Although the regulation of membrane receptor activation is known to be crucial for molecular signal transduction, the molecular mechanism underlying receptor activation is not fully elucidated. Here we study the physicochemical nature of membrane receptor behavior by investigating the characteristic molecular vibrations of receptor ligands using computational chemistry and informatics methods. By using information gain, t-tests, and support vector machines, we have identified highly informative features of adenosine receptor (AdoR) ligand and corresponding functional amino acid residues such as Asn (6.55) of AdoR that has informative significance and is indispensable for ligand recognition of AdoRs. These findings may provide new perspectives and insights into the fundamental mechanism of class A G protein-coupled receptor activation. Copyright © 2015 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

  11. Effects of PPARγ Ligands on Leukemia

    Directory of Open Access Journals (Sweden)

    Yoko Tabe

    2012-01-01

    Full Text Available Peroxisome proliferator-activated receptors (PPARs and retinoic acid receptors (RARs, members of the nuclear receptor superfamily, are transcription factors that regulate a variety of important cellular functions. PPARs form heterodimers retinoid X receptor (RXR, an obligate heterodimeric partner for other nuclear receptors. Several novel links between retinoid metabolism and PPAR responses have been identified, and activation of PPAR/RXR expression has been shown to increase response to retinoids. PPARγ has emerged as a key regulator of cell growth and survival, whose activity is modulated by a number of synthetic and natural ligands. While clinical trials in cancer patients with thiazolidinediones (TZD have been disappointing, novel structurally different PPARγ ligands, including triterpenoids, have entered clinical arena as therapeutic agents for epithelial and hematopoietic malignancies. Here we shall review the antitumor advances of PPARγ, alone and in combination with RARα ligands in control of cell proliferation, differentiation, and apoptosis and their potential therapeutic applications in hematological malignancies.

  12. Ligand selectivity in tachykinin and natalisin neuropeptidergic systems of the honey bee parasitic mite Varroa destructor.

    Science.gov (United States)

    Jiang, Hongbo; Kim, Donghun; Dobesh, Sharon; Evans, Jay D; Nachman, Ronald J; Kaczmarek, Krzysztof; Zabrocki, Janusz; Park, Yoonseong

    2016-01-28

    The varroa mite, Varroa destructor, is a devastating ectoparasite of the honey bees Apis mellifera and A. cerana. Control of these mites in beehives is a challenge in part due to the lack of toxic agents that are specific to mites and not to the host honey bee. In searching for a specific toxic target of varroa mites, we investigated two closely related neuropeptidergic systems, tachykinin-related peptide (TRP) and natalisin (NTL), and their respective receptors. Honey bees lack both NTL and the NTL receptor in their genome sequences, providing the rationale for investigating these receptors to understand their specificities to various ligands. We characterized the receptors for NTL and TRP of V. destructor (VdNTL-R and VdTRP-R, respectively) and for TRP of A. mellifera (AmTRP-R) in a heterologous reporter assay system to determine the activities of various ligands including TRP/NTL peptides and peptidomimetics. Although we found that AmTRP-R is highly promiscuous, activated by various ligands including two VdNTL peptides when a total of 36 ligands were tested, we serendipitously found that peptides carrying the C-terminal motif -FWxxRamide are highly specific to VdTRP-R. This motif can serve as a seed sequence for designing a VdTRP-R-specific agonist.

  13. Lenient vs. strict rate control in patients with atrial fibrillation and heart failure: a post-hoc analysis of the RACE II study

    NARCIS (Netherlands)

    Mulder, Bart A.; van Veldhuisen, Dirk J.; Crijns, Harry J. G. M.; Tijssen, Jan G. P.; Hillege, Hans L.; Alings, Marco; Rienstra, Michiel; Groenveld, Hessel F.; van den Berg, Maarten P.; van Gelder, Isabelle C.

    2013-01-01

    It is unknown whether lenient rate control is an acceptable strategy in patients with AF and heart failure. We evaluated differences in outcome in patients with AF and heart failure treated with lenient or strict rate control. This post-hoc analysis of the RACE II trial included patients with an

  14. A Banach-Dieudonné theorem for the space of bounded continuous functions on a separable metric space with the strict topology

    NARCIS (Netherlands)

    Kraaij, R.C.

    2016-01-01

    Let X be a separable metric space and let β be the strict topology on the space of bounded continuous functions on X, which has the space of τ-additive Borel measures as a continuous dual space. We prove a Banach-Dieudonné type result for the space of bounded continuous functions equipped with β:

  15. An Analysis of Trafficking Receptors Shows that CD44 and P-Selectin Glycoprotein Ligand-1 Collectively Control the Migration of Activated Human T-Cells

    KAUST Repository

    Ali, Amal J.

    2017-05-03

    Selectins guide the traffic of activated T-cells through the blood stream by mediating their tethering and rolling onto inflamed endothelium, in this way acting as beacons to help navigate them to sites of inflammation. Here, we present a comprehensive analysis of E-selectin ligands expressed on activated human T-cells. We identified several novel glycoproteins that function as E-selectin ligands. Specifically, we compared the role of P-selectin glycoprotein ligand-1 (PSGL-1) and CD43, known E-selectin ligands, to CD44, a ligand that has not previously been characterized as an E-selectin ligand on activated human T-cells. We showed that CD44 acts as a functional E-selectin ligand when expressed on both CD4+ and CD8+ T-cells. Moreover, the CD44 protein carries a binding epitope identifying it as hematopoietic cell E- and/or L-selectin ligand (HCELL). Furthermore, by knocking down these ligands individually or together in primary activated human T-cells, we demonstrated that CD44/HCELL, and not CD43, cooperates with PSGL-1 as a major E-selectin ligand. Additionally, we demonstrated the relevance of our findings to chronic autoimmune disease, by showing that CD44/HCELL and PSGL-1, but not CD43, from T-cells isolated from psoriasis patients, bind E-selectin.

  16. 01-ERD-111 - The Development of Synthetic High Affinity Ligands

    Energy Technology Data Exchange (ETDEWEB)

    Perkins, J; Balhorn, R; Cosman, M; Lightstone, F; Zeller, L

    2004-02-05

    The aim of this project was to develop Synthetic High-Affinity Ligands (SHALs), which bind with high affinity and specificity to proteins of interest for national security and cancer therapy applications. The aim of producing synthetic ligands for sensory devices as an alternative to antibody-based detection assays and therapeutic agents is to overcome the drawbacks associated with antibody-based in next-generation sensors and systems. The focus area of the project was the chemical synthesis of the SHALs. The project concentrated on two different protein targets. (a) The C fragment of tetanus and botulinum toxin, potential biowarfare agents. A SHAL for tetanus or botulinum toxin would be incorporated into a sensory device for the toxins. (b) HLA-DR10, a protein found in high abundance on the surface of Non-Hodgkins Lymphoma. A SHAL specific to a tumor marker, labeled with a radionuclide, would enable the targeted delivery of radiation therapy to metastatic disease. The technical approach used to develop a SHAL for each protein target will be described in more detail below. However, in general, the development of a SHAL requires a combination of computational modeling techniques, modern nuclear magnetic resonance spectroscopy (NMR) and synthetic chemistry.

  17. (+)-camphor-derived tri- and tetradentate amino alcohols; synthesis and application as ligands in the nickel catalyzed enantioselective conjugate addition of diethylzinc

    NARCIS (Netherlands)

    Vries, André H.M. de; Imbos, Rosalinde; Feringa, Bernard

    1997-01-01

    Several novel tri- and tetradentate amino alcohol ligands, all derived from (+)-camphor, have been synthesized by using specific N-alkylation procedures. The amino alcohols were employed as chiral ligands in the nickel catalyzed conjugate additions of diethylzine to chalcone and cyclohexenone as

  18. A2AR Binding Kinetics in the Ligand Depletion Regime.

    Science.gov (United States)

    McNeely, Patrick M; Naranjo, Andrea N; Forsten-Williams, Kimberly; Robinson, Anne Skaja

    2017-02-01

    Ligand binding plays a fundamental role in stimulating the downstream signaling of membrane receptors. Here, ligand-binding kinetics of the full-length human adenosine A 2A receptor (A 2A R) reconstituted in detergent micelles were measured using a fluorescently labeled ligand via fluorescence anisotropy. Importantly, to optimize the signal-to-noise ratio, these experiments were conducted in the ligand depletion regime. In the ligand depletion regime, the assumptions used to determine analytical solutions for one-site binding models for either one or two ligands in competition are no longer valid. We therefore implemented a numerical solution approach to analyze kinetic binding data as experimental conditions approach the ligand depletion regime. By comparing the results from the numerical and the analytical solutions, we highlight the ligand-receptor ratios at which the analytical solution begins to lose predictive accuracy. Using the numerical solution approach, we determined the kinetic rate constants of the fluorescent ligand, FITC-APEC, and those for three unlabeled ligands using competitive association experiments. The association and dissociation rate constants of the unlabeled ligands determined from the competitive association experiments were then independently validated using competitive dissociation data. Based on this study, a numerical solution is recommended to determine kinetic ligand-binding parameters for experiments conducted in the ligand-depletion regime.

  19. CHELATING LIGANDS: ENHANCERS OF QUALITY AND PURITY ...

    African Journals Online (AJOL)

    Nwokem et al.

    ABSTRACT. The quality of biogas depends largely on the percentage of methane and hydrogen sulphide gas present. High concentration of hydrogen sulphide results in low quality biogas. This work employed the use of chelating ligands in scrubbing hydrogen sulphide gas while improving the yield of methane gas.

  20. Ligand iron catalysts for selective hydrogenation

    Science.gov (United States)

    Casey, Charles P.; Guan, Hairong

    2010-11-16

    Disclosed are iron ligand catalysts for selective hydrogenation of aldehydes, ketones and imines. A catalyst such as dicarbonyl iron hydride hydroxycyclopentadiene) complex uses the OH on the five member ring and hydrogen linked to the iron to facilitate hydrogenation reactions, particularly in the presence of hydrogen gas.

  1. Versatile phosphite ligands based on silsesquioxane backbones

    NARCIS (Netherlands)

    van der Vlugt, JI; Ackerstaff, J; Dijkstra, TW; Mills, AM; Kooijman, H; Spek, AL; Meetsma, A; Abbenhuis, HCL; Vogt, D

    Silsesquioxanes are employed as ligand backbones for the synthesis of novel phosphite compounds with 3,3'-5,5'-tetrakis(tert-butyl)-2,2'-di-oxa-1,1'-biphenyl substituents. Both mono- and bidentate phosphites are prepared in good yields. Two types of silsesquioxanes are employed as starting

  2. Constitutive and ligand-induced TCR degradation

    DEFF Research Database (Denmark)

    von Essen, Marina; Bonefeld, Charlotte Menné; Siersma, Volkert

    2004-01-01

    divergent models for TCR down-regulation and degradation have been suggested. The aims of this study were to determine the rate constants for constitutive and ligand-induced TCR degradation and to determine whether the TCR subunits segregate or are processed as an intact unit during TCR down...

  3. Ligand Exchange Kinetics of Environmentally Relevant Metals

    Energy Technology Data Exchange (ETDEWEB)

    Panasci, Adele Frances [Univ. of California, Davis, CA (United States)

    2014-07-15

    The interactions of ground water with minerals and contaminants are of broad interest for geochemists but are not well understood. Experiments on the molecular scale can determine reaction parameters (i.e. rates of ligand exchange, activation entropy, activation entropy, and activation volume) that can be used in computations to gain insight into reactions that occur in natural groundwaters. Experiments to determine the rate of isotopic ligand exchange for three environmentally relevant metals, rhodium (Rh), iron (Fe), and neptunium (Np), are described. Many environmental transformations of metals (e.g. reduction) in soil occur at trivalent centers, Fe(III) in particular. Contaminant ions absorb to mineral surfaces via ligand exchange, and the reversal of this reaction can be dangerous, releasing contaminants into the environment. Ferric iron is difficult to study spectroscopically because most of its complexes are paramagnetic and are generally reactive toward ligand exchange; therefore, Rh(III), which is diamagnetic and less reactive, was used to study substitution reactions that are analogous to those that occur on mineral oxide surfaces. Studies on both Np(V) and Np(VI) are important in their own right, as 237Np is a radioactive transuranic element with a half-life of 2 million years.

  4. Dynamic Ligand Based Pharmacophore Modeling and Virtual ...

    Indian Academy of Sciences (India)

    user

    ChEMBL-HIV https://www.ebi.ac.uk/chembl/index.php/assay/results (ChEMBL Bioassay was searched with the key word “Human. Immunodefficiency virus”, display bioactivity option was chosen and then “Download All Bioactivity Data” was ... Ligand based pharmacophore models generated from the crystal structure and.

  5. Mixed-ligand binuclear copper(II)

    Indian Academy of Sciences (India)

    A new mixed-ligand binuclear copper(II) complex [Cu(MS)(bpy)]2.(ClO4)2, built of 5-methylsalicylaldehyde and 2,2'-bipyridyl has been synthesized and characterized by using elemental analysis, IR and UV-Vis spectroscopy. Crystal structure of the complex shows that copper(II) ion lies in a square pyramidal coordination ...

  6. A versatile dinucleating ligand containing sulfonamide groups

    DEFF Research Database (Denmark)

    Sundberg, Jonas; Witt, Hannes; Cameron, Lisa

    2014-01-01

    Copper, iron, and gallium coordination chemistries of the new pentadentate bis-sulfonamide ligand 2,6-bis(N-2-pyridylmethylsulfonamido)-4-methylphenol (psmpH3) were investigated. PsmpH3 is capable of varying degrees of deprotonation, and notably, complexes containing the fully trideprotonated...

  7. Amidinate Ligands in Zinc coordination sphere

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Chemical Sciences; Volume 128; Issue 6. Amidinate Ligands in Zinc coordination sphere: Synthesis and structural diversity. SRINIVAS ANGA INDRANI BANERJEE TARUN K PANDA. Regular Article Volume 128 Issue 6 June 2016 pp ... Keywords. Zinc; carbodiimides; amidinate; alkyl migration.

  8. Simple tertiary phosphines to hexaphosphane ligands: Syntheses ...

    Indian Academy of Sciences (India)

    In this context, we have developed new synthetic methodologies for making unusual inorganic ring systems containing trivalent phosphorus centres, novel phosphorus-based multidentate and hybrid ligands and explored their rich transition metal chemistry and catalytic applications. We have also fine tuned a few existing ...

  9. Investigation of atomic level patterns in protein--small ligand interactions.

    Directory of Open Access Journals (Sweden)

    Ke Chen

    Full Text Available BACKGROUND: Shape complementarity and non-covalent interactions are believed to drive protein-ligand interaction. To date protein-protein, protein-DNA, and protein-RNA interactions were systematically investigated, which is in contrast to interactions with small ligands. We investigate the role of covalent and non-covalent bonds in protein-small ligand interactions using a comprehensive dataset of 2,320 complexes. METHODOLOGY AND PRINCIPAL FINDINGS: We show that protein-ligand interactions are governed by different forces for different ligand types, i.e., protein-organic compound interactions are governed by hydrogen bonds, van der Waals contacts, and covalent bonds; protein-metal ion interactions are dominated by electrostatic force and coordination bonds; protein-anion interactions are established with electrostatic force, hydrogen bonds, and van der Waals contacts; and protein-inorganic cluster interactions are driven by coordination bonds. We extracted several frequently occurring atomic-level patterns concerning these interactions. For instance, 73% of investigated covalent bonds were summarized with just three patterns in which bonds are formed between thiol of Cys and carbon or sulfur atoms of ligands, and nitrogen of Lys and carbon of ligands. Similar patterns were found for the coordination bonds. Hydrogen bonds occur in 67% of protein-organic compound complexes and 66% of them are formed between NH- group of protein residues and oxygen atom of ligands. We quantify relative abundance of specific interaction types and discuss their characteristic features. The extracted protein-organic compound patterns are shown to complement and improve a geometric approach for prediction of binding sites. CONCLUSIONS AND SIGNIFICANCE: We show that for a given type (group of ligands and type of the interaction force, majority of protein-ligand interactions are repetitive and could be summarized with several simple atomic-level patterns. We summarize

  10. The "high solubility" definition of the current FDA Guidance on Biopharmaceutical Classification System may be too strict for acidic drugs.

    Science.gov (United States)

    Yazdanian, Mehran; Briggs, Katherine; Jankovsky, Corinne; Hawi, Amale

    2004-02-01

    The purpose of this study was to assess if the definition of high solubility as proposed in the FDA Guidance on Biopharmaceutical Classification System (BCS) is too strict for highly permeable acidic drugs. The solubility and permeability values of 20 (18 acidic and 2 non-acidic) nonsteroidal anti-inflammatory drugs (NSAID) were determined. The NSAIDs were grouped into three different sets having acetic acid, propionic acid, or other acidic moieties such as fenamate, oxicam, and salicylate. Two nonacidic NSAIDs (celecoxib and rofecoxib) were also included for comparison purposes. Equilibrium solubility values were determined at pH 1.2, 5.0, 7.4, and in biorelevant media simulating fed intestinal fluid at pH 5.0. For a select number of acids, we also measured solubility values in media simulating gastric and fasted intestinal fluids. Permeability classification was established relative to that of reference drugs in the Caco-2 cell permeability model. Permeability coefficients for all drugs were measured at concentrations corresponding to the lowest and highest marketed dose strengths dissolved in 250 ml volume, and their potential interaction with cellular efflux pumps was investigated. All NSAIDs with different acidic functional groups were classified as highly permeable based on their Caco-2 cell permeability. Only ketorolac appeared to have a potential for interaction with cellular efflux pumps. Solubility classification was based on comparison of equilibrium solubility at pH 1.2, 5.0. and 7.4 relative to marketed dose strengths in 250 ml. The pKa values for the acidic NSAIDs studied were between 3.5 and 5.1. and, as expected, their solubility increased dramatically at pH 7.4 compared to pH 1.2. Only three NSAIDs, ketorolac, ketoprofen. and acetyl salicylic acid, meet the current criteria for high solubility over the entire pH range. However, with the exception of ibuprofen, oxaprozin, and mefenamic acid, the remaining compounds can be classified as Class I drugs

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

    Science.gov (United States)

    Olsen, Richard W

    2015-01-01

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

  12. Improving the binding capacities of protein A chromatographic materials by means of ligand polymerization.

    Science.gov (United States)

    Freiherr von Roman, Matthias; Berensmeier, Sonja

    2014-06-20

    Protein A chromatography is one of the most important techniques used in the purification of monoclonal antibodies. Due to the low dynamic binding capacity of protein A chromatographic materials compared to other stationary phases, protein A chromatography is often discussed to be the bottleneck among current purification processes. Several approaches were tested within this study in order to maximize IgG binding capacities of current acrylamido-based based resins. Genetic engineering techniques were used in order to polymerize one of the IgG binding domains (B-domain) of protein A from Staphylococcus aureus (SpA) to achieve ligands with an increased length. The solution-binding ratio and the total size of ligand-antibody complexes were used to characterize the interaction potential of novel ligands, revealing a relatively linear dependency between the number of binding domains upon the amount of bound antibody molecules. This relationship was also valid up to a ligand which was comprised of 8 B-domains after attaching them onto acrylamido-based based stationary phases using epoxy coupling techniques. Equilibrium binding capacities of more than 80mghIgGmL(-1) were achieved using the B8 ligand. Furthermore, static binding capacities, especially for smaller ligands comprised of fewer B-domains, were improved up to 87mghIgGmL(-1) using site-specific coupling chemistry, which is an improvement of more than 20% compared to commercially available materials. In order to evaluate pore exclusion effects due to the use of prolonged affinity ligands, prepared materials were characterized regarding their effective intraparticle porosity and breakthrough capacity. Copyright © 2014 Elsevier B.V. All rights reserved.

  13. Ammonia formation by metal-ligand cooperative hydrogenolysis of a nitrido ligand

    Science.gov (United States)

    Askevold, Bjorn; Nieto, Jorge Torres; Tussupbayev, Samat; Diefenbach, Martin; Herdtweck, Eberhardt; Holthausen, Max C.; Schneider, Sven

    2011-07-01

    Bioinspired hydrogenation of N2 to ammonia at ambient conditions by stepwise nitrogen protonation/reduction with metal complexes in solution has experienced remarkable progress. In contrast, the highly desirable direct hydrogenation with H2 remains difficult. In analogy to the heterogeneously catalysed Haber-Bosch process, such a reaction is conceivable via metal-centred N2 splitting and unprecedented hydrogenolysis of the nitrido ligands to ammonia. We report the synthesis of a ruthenium(IV) nitrido complex. The high nucleophilicity of the nitrido ligand is demonstrated by unusual N-C coupling with π-acidic CO. Furthermore, the terminal nitrido ligand undergoes facile hydrogenolysis with H2 at ambient conditions to produce ammonia in high yield. Kinetic and quantum chemical examinations of this reaction suggest cooperative behaviour of a phosphorus-nitrogen-phosphorus pincer ligand in rate-determining heterolytic hydrogen splitting.

  14. Wnt ligands signal in a cooperative manner to promote foregut organogenesis

    OpenAIRE

    Miller, Mayumi F.; Cohen, Ethan David; Baggs, Julie E.; Lu, Min Min; Hogenesch, John B.; Morrisey, Edward E.

    2012-01-01

    Endoderm-mesenchyme cross-talk is a central process in the development of foregut-derived organs. How signaling pathways integrate the activity of multiple ligands to guide organ development is poorly understood. We show that two Wnt ligands, Wnt2 and Wnt7b, cooperatively induce Wnt signaling without affecting the stabilization of the Wnt canonical effector β-catenin despite it being necessary for Wnt2–Wnt7b cooperativity. Wnt2–Wnt7b cooperation is specific for mesenchymal cell lineages and t...

  15. Genetic study of KIR and HLA ligands in 235 individuals from Northeastern Thailand.

    Science.gov (United States)

    Chaisri, Suwit; Leelayuwat, Chanvit; Romphruk, Amornrat

    The diversity of 17 KIR and HLA ligands (HLA-C1, C2, Bw4, A11) were investigated in two hundred and thirty-five unrelated healthy donors in Northeastern Thais (NETs) by the polymerase chain reaction with sequence-specific primer (PCR-SSP) method. The Hardy-Weinberg Equilibrium (HWE) was used to verify genotyping method for dimorphic KIR and HLA. They were in HWE (p>0.05). KIR and HLA ligands frequencies, genotypes, haplotypes and linkage disequilibrium (LD) were presented. The genetic data are available in allele Frequencies Net Database. Copyright © 2017. Published by Elsevier Inc.

  16. Entropic Control of Receptor Recycling Using Engineered Ligands.

    Science.gov (United States)

    DeGroot, Andre C M; Busch, David J; Hayden, Carl C; Mihelic, Samuel A; Alpar, Aaron T; Behar, Marcelo; Stachowiak, Jeanne C

    2018-03-27

    Receptor internalization by endocytosis regulates diverse cellular processes, from the rate of nutrient uptake to the timescale of essential signaling events. The established view is that internalization is tightly controlled by specific protein-binding interactions. However, recent work suggests that physical aspects of receptors influence the process in ways that cannot be explained by biochemistry alone. Specifically, work from several groups suggests that increasing the steric bulk of receptors may inhibit their uptake by multiple types of trafficking vesicles. How do biochemical and biophysical factors work together to control internalization? Here, we show that receptor uptake is well described by a thermodynamic trade-off between receptor-vesicle binding energy and the entropic cost of confining receptors within endocytic vesicles. Specifically, using large ligands to acutely increase the size of engineered variants of the transferrin receptor, we demonstrate that an increase in the steric bulk of a receptor dramatically decreases its probability of uptake by clathrin-coated structures. Further, in agreement with a simple thermodynamic analysis, all data collapse onto a single trend relating fractional occupancy of the endocytic structure to fractional occupancy of the surrounding plasma membrane, independent of receptor size. This fundamental scaling law provides a simple tool for predicting the impact of receptor expression level, steric bulk, and the size of endocytic structures on receptor uptake. More broadly, this work suggests that bulky ligands could be used to drive the accumulation of specific receptors at the plasma membrane surface, providing a biophysical tool for targeted modulation of signaling and metabolism from outside the cell. Copyright © 2018 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  17. Role of Lanthanide-Ligand bonding in the magnetization relaxation ...

    Indian Academy of Sciences (India)

    Ligand bonding. Our calculations transpire comparatively improved Single-Ion Magnet (SIM) behaviour for carbene analogues due to the more axially compressed trigonal prismatic ligand environment. Furthermore, our detailed Mulliken charge, ...

  18. Quantum.Ligand.Dock: protein-ligand docking with quantum entanglement refinement on a GPU system.

    Science.gov (United States)

    Kantardjiev, Alexander A

    2012-07-01

    Quantum.Ligand.Dock (protein-ligand docking with graphic processing unit (GPU) quantum entanglement refinement on a GPU system) is an original modern method for in silico prediction of protein-ligand interactions via high-performance docking code. The main flavour of our approach is a combination of fast search with a special account for overlooked physical interactions. On the one hand, we take care of self-consistency and proton equilibria mutual effects of docking partners. On the other hand, Quantum.Ligand.Dock is the the only docking server offering such a subtle supplement to protein docking algorithms as quantum entanglement contributions. The motivation for development and proposition of the method to the community hinges upon two arguments-the fundamental importance of quantum entanglement contribution in molecular interaction and the realistic possibility to implement it by the availability of supercomputing power. The implementation of sophisticated quantum methods is made possible by parallelization at several bottlenecks on a GPU supercomputer. The high-performance implementation will be of use for large-scale virtual screening projects, structural bioinformatics, systems biology and fundamental research in understanding protein-ligand recognition. The design of the interface is focused on feasibility and ease of use. Protein and ligand molecule structures are supposed to be submitted as atomic coordinate files in PDB format. A customization section is offered for addition of user-specified charges, extra ionogenic groups with intrinsic pK(a) values or fixed ions. Final predicted complexes are ranked according to obtained scores and provided in PDB format as well as interactive visualization in a molecular viewer. Quantum.Ligand.Dock server can be accessed at http://87.116.85.141/LigandDock.html.

  19. Quantum.Ligand.Dock: protein–ligand docking with quantum entanglement refinement on a GPU system

    Science.gov (United States)

    Kantardjiev, Alexander A.

    2012-01-01

    Quantum.Ligand.Dock (protein–ligand docking with graphic processing unit (GPU) quantum entanglement refinement on a GPU system) is an original modern method for in silico prediction of protein–ligand interactions via high-performance docking code. The main flavour of our approach is a combination of fast search with a special account for overlooked physical interactions. On the one hand, we take care of self-consistency and proton equilibria mutual effects of docking partners. On the other hand, Quantum.Ligand.Dock is the the only docking server offering such a subtle supplement to protein docking algorithms as quantum entanglement contributions. The motivation for development and proposition of the method to the community hinges upon two arguments—the fundamental importance of quantum entanglement contribution in molecular interaction and the realistic possibility to implement it by the availability of supercomputing power. The implementation of sophisticated quantum methods is made possible by parallelization at several bottlenecks on a GPU supercomputer. The high-performance implementation will be of use for large-scale virtual screening projects, structural bioinformatics, systems biology and fundamental research in understanding protein–ligand recognition. The design of the interface is focused on feasibility and ease of use. Protein and ligand molecule structures are supposed to be submitted as atomic coordinate files in PDB format. A customization section is offered for addition of user-specified charges, extra ionogenic groups with intrinsic pKa values or fixed ions. Final predicted complexes are ranked according to obtained scores and provided in PDB format as well as interactive visualization in a molecular viewer. Quantum.Ligand.Dock server can be accessed at http://87.116.85.141/LigandDock.html. PMID:22669908

  20. Synthesis of new oxovanadium (IV) complexes of potential insulinmimetic activity with coumarin-3-carboxylic acid ligands and substituted derivatives

    International Nuclear Information System (INIS)

    Salas Fernandez, Paloma; Alvino de la Sota, Nora; Galli Rigo-Righi, Carla

    2013-01-01

    This work comprises the design and synthesis of four new oxovanadium (IV) complexes, a metal which possesses insulin-mimetic action. Coumarin-3-carboxylic acid and three of its 6 -and 6,8- derivatives were used as ligands. Coumarins are of interest due to their well-known biological properties and pharmacological applications; these include the insulino-sensibilizing effect of certain alcoxy-hydroxy-derivatives which might lead to the eventual existence of a synergetic effect with the active metal center. The synthesis of the vanadyl complexes was preceded by the synthesis of the coumarin-3-carboxylic acid and its 6-bromo- derivative, as well as the syntheses of three derivatives not previously reported: 6-bromo-8-metoxi-, 6-bromo-8-nitro-, and 6-bromo-8-hydroxy-, which were prepared by a Knoevenagel condensation reaction. The complexes, on their part, were prepared by a metathesis reaction between VOSO 4 and the corresponding ligands, on the basis of methods reported for other vanadyl complexes and under strict pH control. The coumarin-3-carboxylic ligands and the derivatives were characterized by 1 H-NMR-, FTIR- and UV-Vis-spectroscopy. In the case of the complexes, their paramagnetic character did not allow for NMR characterization, being thus identified by FT-IR-spectroscopy and by the quantitative determination of their vanadium contents. (author)

  1. GLIDA: GPCR-ligand database for chemical genomic drug discovery

    OpenAIRE

    Okuno, Yasushi; Yang, Jiyoon; Taneishi, Kei; Yabuuchi, Hiroaki; Tsujimoto, Gozoh

    2005-01-01

    G-protein coupled receptors (GPCRs) represent one of the most important families of drug targets in pharmaceutical development. GPCR-LIgand DAtabase (GLIDA) is a novel public GPCR-related chemical genomic database that is primarily focused on the correlation of information between GPCRs and their ligands. It provides correlation data between GPCRs and their ligands, along with chemical information on the ligands, as well as access information to the various web databases regarding GPCRs. Thes...

  2. Modulation of estrogen receptor α levels by endogenous and exogenous ligands

    Directory of Open Access Journals (Sweden)

    P. La Rosa

    2011-01-01

    Full Text Available ERα is a ligand-activated transcription factor, member of the nuclear receptor superfamily. Regulation of ERα levels is intrinsically required for its transcriptional activity and thus for the modulation of the physiological actions of the cognate hormone 17β-estradiol (E2. Indeed, ERα exogenous ligands that target this molecular circuitry are used as drugs in clinical practice. Interestingly, some natural and synthetic molecules, which human beings are commonly exposed to, interfere with the endocrine system and operate through ERα by selectively modifying its signalling. In addition, these molecules may also modulate ERα cellular content. Here, we report the recent advances in our understanding of how exogenous ERα ligands impact on receptor levels and change the physiological E2-dipendent modulation of specific cellular function.

  3. Hydrophobic interaction membrane chromatography for bioseparation and responsive polymer ligands involved

    Science.gov (United States)

    Chen, Jingling; Peng, Rong; Chen, Xiaonong

    2017-09-01

    Hydrophobic interaction chromatography (HIC) is a rapid growing bioseparation technique, which separates biomolecules, such as therapeutic proteins and antibodys, based on the reversible hydrophobic interaction between immobilized hydrophobic ligands on chromatographic resin spheres and non-polar regions of solute molecule. In this review, the fundamental concepts of HIC and the factors that may affect purification efficiency of HIC is summarized, followed by the comparison of HIC with affinity chromatography and ion-exchange chromatography. Hydrophobic interaction membrane chromatography (HIMC) combines the advantages of HIC and membrane process and has showed great potential in bioseparation. For better understanding of HIMC, this review presents an overview of two main concerns about HIMC, i.e. membrane materials and hydrophobic ligands. Specifically, cellulose fiber-based membrane substrate and environment-responsive ligands are emphasized.

  4. AutoSite: an automated approach for pseudo-ligands prediction—from ligand-binding sites identification to predicting key ligand atoms

    Science.gov (United States)

    Ravindranath, Pradeep Anand; Sanner, Michel F.

    2016-01-01

    Motivation: The identification of ligand-binding sites from a protein structure facilitates computational drug design and optimization, and protein function assignment. We introduce AutoSite: an efficient software tool for identifying ligand-binding sites and predicting pseudo ligand corresponding to each binding site identified. Binding sites are reported as clusters of 3D points called fills in which every point is labelled as hydrophobic or as hydrogen bond donor or acceptor. From these fills AutoSite derives feature points: a set of putative positions of hydrophobic-, and hydrogen-bond forming ligand atoms. Results: We show that AutoSite identifies ligand-binding sites with higher accuracy than other leading methods, and produces fills that better matches the ligand shape and properties, than the fills obtained with a software program with similar capabilities, AutoLigand. In addition, we demonstrate that for the Astex Diverse Set, the feature points identify 79% of hydrophobic ligand atoms, and 81% and 62% of the hydrogen acceptor and donor hydrogen ligand atoms interacting with the receptor, and predict 81.2% of water molecules mediating interactions between ligand and receptor. Finally, we illustrate potential uses of the predicted feature points in the context of lead optimization in drug discovery projects. Availability and Implementation: http://adfr.scripps.edu/AutoDockFR/autosite.html Contact: sanner@scripps.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27354702

  5. Barley as a green factory for the production of functional Flt3 ligand.

    Science.gov (United States)

    Erlendsson, Lýdur S; Muench, Marcus O; Hellman, Ulf; Hrafnkelsdóttir, Soffía M; Jonsson, Anders; Balmer, Yves; Mäntylä, Einar; Orvar, Björn L

    2010-02-01

    Biologically active recombinant human Flt3 ligand was expressed and isolated from transgenic barley seeds. Its expression is controlled by a tissue specific promoter that confines accumulation of the recombinant protein to the endosperm tissue of the seed. The recombinant Flt3 ligand variant expressed in the seeds contains an HQ-tag for affinity purification on immobilized metal ion affinity chromatography (IMAC) resin. The tagged protein was purified from seed extracts to near homogeneity using sequential chromatography on IMAC affinity resin and cation exchange resin. We also show that the recombinant Flt3 ligand protein undergoes posttranslational modifications: it is a glycoprotein containing alpha-1,3-fucose and alpha-1,2-xylose. The HQ-tagged Flt3 ligand variant exhibits comparable biological activity to commercial Flt3 ligand. This is the first report showing expression and accumulation of recombinant human growth factor in barley seeds with a yield of active protein similar to a bacterial expression system. The present results demonstrate that plant molecular farming is a viable approach for the bioproduction of human-derived growth factors.

  6. Identification of small molecular ligands as potent inhibitors of fatty acid metabolism in Mycobacterium tuberculosis

    Science.gov (United States)

    Malikanti, Ramesh; Vadija, Rajender; Veeravarapu, Hymavathi; Mustyala, Kiran Kumar; Malkhed, Vasavi; Vuruputuri, Uma

    2017-12-01

    Tuberculosis (Tb) is one of the major health challenges for the global scientific community. The 3-hydroxy butyryl-CoA dehydrogenase (Fad B2) protein belongs to 3-hydroxyl acetyl-CoA dehydrogenase family, which plays a key role in the fatty acid metabolism and β-oxidation in the cell membrane of Mycobacterium tuberculosis (Mtb). In the present study the Fad B2 protein is targeted for the identification of potential drug candidates for tuberculosis. The 3D model of the target protein Fad B2, was generated using homology modeling approach and was validated. The plausible binding site of the Fad B2 protein was identified from computational binding pocket prediction tools, which ranges from ASN120 to VAL150 amino acid residues. Virtual screening was carried out with the databases, Ligand box UOS and hit definder, at the binding site region. 133 docked complex structures were generated as an output. The identified ligands show good glide scores and glide energies. All the ligand molecules contain benzyl amine pharmacophore in common, which show specific and selective binding interactions with the SER122 and ASN146 residues of the Fad B2 protein. The ADME properties of all the ligand molecules were observed to be within the acceptable range. It is suggested from the result of the present study that the docked molecular structures with a benzyl amine pharmacophore act as potential ligands for Fad B2 protein binding and as leads in Tb drug discovery.

  7. Luminescent solutions and powders of new samarium complexes with N,N',O,O'-chelating ligands

    Science.gov (United States)

    Kharcheva, Anastasia V.; Nikolskiy, Kirill S.; Borisova, Nataliya E.; Ivanov, Alexey V.; Reshetova, Marina D.; Yuzhakov, Viktor I.; Patsaeva, Svetlana V.

    2016-04-01

    Imaging techniques in biology and medicine are crucial tools to obtain information on structural and functional properties of living cells and organisms. To fulfill the requirements associated with application of these techniques it appears necessary to design markers with specific characteristics. Luminescent complexes of trivalent lanthanide ions with chelating ligands are of increasing importance in biomedical applications because of their millisecond luminescence lifetime, narrow emission band, high signal-to-noise ratio and minimal photodamage to biological samples. In order to extend the available emission wavelength range the luminescent samarium chelates are highly desirable. In this study the ligands with diamides of 2,2'-bipyridin-6,6'-dicarboxylic acid were used to improve photophysical characteristics of samarium complexes. We report the luminescence characteristics of samarium complexes with novel ligands. All complexes exhibited the characteristic emission of Sm (III) ion with the lines at 565, 597, 605, 645 and 654 nm, the intensity strongly depended on the ligand. Absorption and luminescence excitation spectra of Sm (III) complexes showed main peaks in the UV range demonstrating lanthanide coordination to the ligand. The absolute lumenescence quantum yield was measured for solutions in acetonitrile with excitation at 350 nm. The largest luminescence quantum yield was found for the samarium complex Bipy 6MePy Sm (3%) being much higher that for samarium complexes reported in the literature earlier. These results prove as well that samarium chelates are potential markers for multiparametric imaging techniques.

  8. Integrating structural and mutagenesis data to elucidate GPCR ligand binding

    DEFF Research Database (Denmark)

    Munk, Christian; Harpsøe, Kasper; Hauser, Alexander S

    2016-01-01

    G protein-coupled receptors (GPCRs) represent the largest family of human membrane proteins, as well as drug targets. A recent boom in GPCR structural biology has provided detailed images of receptor ligand binding sites and interactions on the molecular level. An ever-increasing number of ligands...... elucidate new GPCR ligand binding sites, and ultimately design drugs with tailored pharmacological activity....

  9. New pinene-derived pyridines as bidentate chiral ligands

    Czech Academy of Sciences Publication Activity Database

    Malkov, A. V.; Stewart-Liddon, A.; Teplý, Filip; Kobr, L.; Muir, K. W.; Haigh, D.; Kočovský, P.

    2008-01-01

    Roč. 64, č. 18 (2008), s. 4011-4025 ISSN 0040-4020 Institutional research plan: CEZ:AV0Z40550506 Keywords : chiral ligands * transition metal catalysis * asymmetric catalysis * pyridine ligands * oxazoline ligands Subject RIV: CC - Organic Chemistry Impact factor: 2.897, year: 2008

  10. Study of the spectroscopic characteristics of methyl (ligand ...

    Indian Academy of Sciences (India)

    TECS

    Abstract. Spectroscopic characterization (IR, NMR and electronic spectra) of methyl (ligand) coba- loxime was done, where ligand = pyrazole, dimethyl pyrazole, alanine and alanine methyl ester. The fre- quency changes in the IR spectra and shifts in the NMR were explained on the basis of basicity of the ligand, steric ...

  11. Equilibrium and kinetic studies on ligand substitution reactions of ...

    Indian Academy of Sciences (India)

    Unknown

    The rate constants and equilibrium constants are correlated to the hardness and softness of the ligands and the Co(III) of cobaloxime. Keywords. Alkylcobaloximes; ligand substitution reactions; hard and soft ligands. 1. Introduction. B12-based enzymes are among the few cofactors known till now contain a metal–carbon.

  12. Design and use of conditional MHC class I ligands

    NARCIS (Netherlands)

    Toebes, Mireille; Coccoris, Miriam; Bins, Adriaan; Rodenko, Boris; Gomez, Raquel; Nieuwkoop, Nella J.; van de Kasteele, Willeke; Rimmelzwaan, Guus F.; Haanen, John B. A. G.; Ovaa, Huib; Schumacher, Ton N. M.

    2006-01-01

    Major histocompatibility complex (MHC) class I molecules associate with a variety of peptide ligands during biosynthesis and present these ligands on the cell surface for recognition by cytotoxic T cells. We have designed conditional MHC ligands that form stable complexes with MHC molecules but

  13. Hydrogen exchange and ligand binding: Ligand-dependent and ligand-independent protection in the Src SH3 domain

    OpenAIRE

    Wildes, David; Marqusee, Susan

    2005-01-01

    Amide hydrogen-deuterium exchange has proven to be a powerful tool for detecting and characterizing high-energy conformations in protein ensembles. Since interactions with ligands can modulate these high-energy conformations, hydrogen exchange appears to be an ideal experimental probe of the physical mechanisms underlying processes like allosteric regulation. The chemical mechanism of hydrogen exchange, however, can complicate such studies. Here, we examine hydrogen exchange rates in a simple...

  14. Nonlinearly Additive Forces in Multivalent Ligand Binding to a Single Protein Revealed with Force Spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Ratto, T V; Rudd, R E; Langry, K C; Balhorn, R L; McElfresh, M W

    2005-07-15

    We present evidence of multivalent interactions between a single protein molecule and multiple carbohydrates at a pH where the protein can bind four ligands. The evidence is based not only on measurements of the force required to rupture the bonds formed between ConcanavalinA (ConA) and {alpha}-D-mannose, but also on an analysis of the polymer-extension force curves to infer the polymer architecture that binds the protein to the cantilever and the ligands to the substrate. We find that although the rupture forces for multiple carbohydrate connections to a single protein are larger than the rupture force for a single connection, they do not scale additively with increasing number. Specifically, the most common rupture forces are approximately 46, 66, and 85 pN, which we argue corresponds to 1, 2, and 3 ligands being pulled simultaneously from a single protein as corroborated by an analysis of the linkage architecture. As in our previous work polymer tethers allow us to discriminate between specific and non-specific binding. We analyze the binding configuration (i.e. serial versus parallel connections) through fitting the polymer stretching data with modified Worm-Like Chain (WLC) models that predict how the effective stiffness of the tethers is affected by multiple connections. This analysis establishes that the forces we measure are due to single proteins interacting with multiple ligands, the first force spectroscopy study that establishes single-molecule multivalent binding unambiguously.

  15. Toward improving selectivity in affinity chromatography with PEGylated affinity ligands: the performance of PEGylated protein A.

    Science.gov (United States)

    González-Valdez, José; Yoshikawa, Alex; Weinberg, Justin; Benavides, Jorge; Rito-Palomares, Marco; Przybycien, Todd M

    2014-01-01

    Chemical modification of macromolecular affinity chromatography ligands with polyethylene glycol chains or "PEGylation" can potentially improve selectivity by sterically suppressing non-specific binding interactions without sacrificing binding capacity. For a commercial protein A affinity media and with yeast extract (YE) and fetal bovine serum (FBS) serving as mock contaminants, we found that the ligand accounted for more than 90% of the media-associated non-specific binding, demonstrating an opportunity for improvement. The IgG static binding affinity of protein A mono-PEGylated with 5.0 and 20.7 kDa poly(ethylene glycol) chains was found to be preserved using a biomolecular interaction screening platform. Similar in situ PEGylations of the commercial protein A media were conducted and the modified media was functionally characterized with IgG solutions spiked with YE and FBS. Ligand PEGylation reduced the mass of media-associated contaminants by a factor of two to three or more. Curiously, we also found an increase of up to 15% in the average recovery of IgG on elution after PEGylation. Combined, these effects produced an order of magnitude increase in the IgG selectivity on average when spiked with YE and a two- to three-fold increase when spiked with FBS relative to the commercial media. Dynamic binding capacity and mass-transfer resistance measurements revealed a reduction in dynamic capacity attributed to a decrease in IgG effective pore diffusivity and possibly slower IgG association kinetics for the PEGylated protein A ligands. Ligand PEGylation is a viable approach to improving selectivity in affinity chromatography with macromolecular ligands. © 2014 American Institute of Chemical Engineers.

  16. Structural characterization of natural nickel and copper binding ligands along the US GEOTRACES Eastern Pacific Zonal transect

    Directory of Open Access Journals (Sweden)

    Rene M Boiteau

    2016-11-01

    Full Text Available Organic ligands form strong complexes with many trace elements in seawater. Various metals can compete for the same ligand chelation sites, and the final speciation of bound metals is determined by relative binding affinities, concentrations of binding sites, uncomplexed metal concentrations, and association/dissociation kinetics. Different ligands have a wide range of metal affinities and specificities. However, the chemical composition of these ligands in the marine environment remains poorly constrained, which has hindered progress in modeling marine metal speciation. In this study, we detected and characterized natural ligands that bind copper (Cu and nickel (Ni in the eastern South Pacific Ocean with liquid chromatography tandem inductively coupled plasma mass spectrometry (LC-ICPMS, and high resolution electrospray ionization mass spectrometry (ESIMS. Dissolved Cu, Ni, and ligand concentrations were highest near the coast. Chromatographically unresolved polar compounds dominated ligands isolated near the coast by solid phase extraction. Offshore, metal and ligand concentrations decreased, but several new ligands appeared. One major ligand was detected that bound both Cu2+ and Ni2+. Based on accurate mass and fragmentation measurements, this compound has a molecular formula of C20H21N4O8S2 + M+ (M = metal isotope and contains several azole-like metal binding groups. Additional lipophilic Ni complexes were also present only in oligotrophic waters, with masses of 649, 698, and 712 m/z (corresponding to the 58Ni metal complex. Molecular formulae of C32H54N3O6S2Ni+ and C33H56N3O6S2Ni+ were determined for two of these compounds. Addition of Cu and Ni to the samples also revealed the presence of additional compounds that can bind both Ni and Cu. Although these specific compounds represent a small fraction of the total dissolved Cu and Ni pool, they highlight the compositional diversity and spatial heterogeneity of marine Ni and Cu ligands, as

  17. Protein-ligand interfaces are polarized: discovery of a strong trend for intermolecular hydrogen bonds to favor donors on the protein side with implications for predicting and designing ligand complexes

    Science.gov (United States)

    Raschka, Sebastian; Wolf, Alex J.; Bemister-Buffington, Joseph; Kuhn, Leslie A.

    2018-02-01

    Understanding how proteins encode ligand specificity is fascinating and similar in importance to deciphering the genetic code. For protein-ligand recognition, the combination of an almost infinite variety of interfacial shapes and patterns of chemical groups makes the problem especially challenging. Here we analyze data across non-homologous proteins in complex with small biological ligands to address observations made in our inhibitor discovery projects: that proteins favor donating H-bonds to ligands and avoid using groups with both H-bond donor and acceptor capacity. The resulting clear and significant chemical group matching preferences elucidate the code for protein-native ligand binding, similar to the dominant patterns found in nucleic acid base-pairing. On average, 90% of the keto and carboxylate oxygens occurring in the biological ligands formed direct H-bonds to the protein. A two-fold preference was found for protein atoms to act as H-bond donors and ligand atoms to act as acceptors, and 76% of all intermolecular H-bonds involved an amine donor. Together, the tight chemical and geometric constraints associated with satisfying donor groups generate a hydrogen-bonding lock that can be matched only by ligands bearing the right acceptor-rich key. Measuring an index of H-bond preference based on the observed chemical trends proved sufficient to predict other protein-ligand complexes and can be used to guide molecular design. The resulting Hbind and Protein Recognition Index software packages are being made available for rigorously defining intermolecular H-bonds and measuring the extent to which H-bonding patterns in a given complex match the preference key.

  18. Proximity labeling of cis-ligands of CD22/Siglec-2 reveals stepwise α2,6 sialic acid-dependent and -independent interactions.

    Science.gov (United States)

    Alborzian Deh Sheikh, Amin; Akatsu, Chizuru; Imamura, Akihiro; Abdu-Allah, Hajjaj H M; Takematsu, Hiromu; Ando, Hiromune; Ishida, Hideharu; Tsubata, Takeshi

    2018-01-01

    Lectins expressed on the cell surface are often bound and regulated by the membrane molecules containing the glycan ligands on the same cell (cis-ligands). However, molecular nature and function of cis-ligands are generally poorly understood partly because of weak interaction between lectins and glycan ligands. Cis-ligands are most extensively studied in CD22 (also known as Siglec-2), an inhibitory B lymphocyte receptor specifically recognizing α2,6 sialic acids. CD22, CD45 and IgM are suggested to be ligands of CD22. Here we labeled molecules in the proximity of CD22 in situ on B cell surface using biotin-tyramide. Molecules including CD22, CD45 and IgM were labeled in wild-type but not ST6GalI -/- B cells that lack α2,6 sialic acids, indicating that these molecules associate with CD22 by lectin-glycan interaction, and are therefore cis-ligands. In ST6GalI -/- B cells, these cis-ligands are located in a slightly more distance from CD22. Thus, the lectin-glycan interaction recruits cis-ligands already located in the relative proximity of CD22 through non-lectin-glycan interaction to the close proximity. Moreover, cis-ligands are labeled in Cmah -/- B cells that lack Neu5Gc preferred by mouse CD22 as efficiently as in wild-type B cells, indicating that very low affinity lectin-glycan interaction is sufficient for recruiting cis-ligands, and can be detected by proximity labeling. Thus, proximity labeling with tyramide appears to be a useful method to identify cis-ligands and to analyze their interaction with the lectins. Copyright © 2017 Elsevier Inc. All rights reserved.

  19. Complexes of .beta.-galactosidase with ligands

    Czech Academy of Sciences Publication Activity Database

    Štěpánková, Andrea; Skálová, Tereza; Dohnálek, Jan; Dušková, Jarmila; Koval, Tomáš; Hašek, Jindřich; Lipovová, P.

    2010-01-01

    Roč. 17, 1a (2010), b54 ISSN 1211-5894. [Discussions in Structural Molecular Biology /8./. 18.03.2010-20.03.2010, Nové Hrady] R&D Projects: GA ČR GA305/07/1073 Institutional research plan: CEZ:AV0Z40500505; CEZ:AV0Z10100521 Keywords : ligands * enzyme * galactosidase Subject RIV: CD - Macromolecular Chemistry

  20. Polyfluoroalkylated tripyrazolylmethane ligands: Synthesis and complexes

    Czech Academy of Sciences Publication Activity Database

    Skalická, V.; Rybáčková, M.; Skalický, M.; Kvíčalová, Magdalena; Cvačka, Josef; Březinová, Anna; Čejka, J.; Kvíčala, J.

    2011-01-01

    Roč. 132, č. 7 (2011), s. 434-440 ISSN 0022-1139 R&D Projects: GA MŠk ME 857; GA MŠk ME09114 Institutional research plan: CEZ:AV0Z40320502; CEZ:AV0Z40550506 Keywords : tripyrazolylmethane * Tpm * tripyrazolylethanol * fluorinated * perfluoroalkylation * ligand Subject RIV: CC - Organic Chemistry Impact factor: 2.033, year: 2011

  1. Organotellurium ligands – designing and complexation reactions

    Indian Academy of Sciences (India)

    Unknown

    which can be compared to the values of 82⋅0(3) and 79⋅6(3)° for Te–Pd–Te angles in the complexes 9 and 10. However in the complex 11 the ditelluroether ligand is not in meso form. The distortions from all 90° angles in the octahedron about ruthenium are apparently not equally shared between the two tellurium atoms.

  2. Displacement of aqua ligands from the hydroxopentaaquarhodium ...

    Indian Academy of Sciences (India)

    cis-Pt(NH3)2Cl2 (cisplatin) is well-known as an anti- tumour drug.1,2 However, there are still difficulties related to its use, ... Cisplatin is not very soluble in water and tends to hydrolyse at neutral pH. Replacement ... cancer agents, but some of them exhibited marked toxic effects.17,18 For certain ligands, the anation reaction.

  3. Hydrogenation and dehydrogenation iron pincer catalysts capable of metal-ligand cooperation by aromatization/dearomatization.

    Science.gov (United States)

    Zell, Thomas; Milstein, David

    2015-07-21

    The substitution of expensive and potentially toxic noble-metal catalysts by cheap, abundant, environmentally benign, and less toxic metals is highly desirable and in line with green chemistry guidelines. We have recently discovered a new type of metal-ligand cooperation, which is based on the reversible dearomatization/aromatization of different heteroaromatic ligand cores caused by deprotonation/protonation of the ligand. More specifically, we have studied complexes of various transition metals (Ru, Fe, Co, Rh, Ir, Ni, Pd, Pt, and Re) bearing pyridine- and bipyridine-based PNP and PNN pincer ligands, which have slightly acidic methylene protons. In addition, we have discovered long-range metal-ligand cooperation in acridine-based pincer ligands, where the cooperation takes place at the electrophilic C-9 position of the acridine moiety leading to dearomatization of its middle ring. This type of metal-ligand cooperation was used for the activation of chemical bonds, including H-H, C-H (sp(2) and sp(3)), O-H, N-H, and B-H bonds. This unusual reactivity likely takes place in various catalytic hydrogenation, dehydrogenation, and related reactions. In this Account, we summarize our studies on novel bifunctional iron PNP and PNN pincer complexes, which were designed on the basis of their ruthenium congeners. Iron PNP pincer complexes serve as efficient (pre)catalysts for hydrogenation and dehydrogenation reactions under remarkably mild conditions. Their catalytic applications include atom-efficient and industrially important hydrogenation reactions of ketones, aldehydes, and esters to the corresponding alcohols. Moreover, they catalyze the hydrogenation of carbon dioxide to sodium formate in the presence of sodium hydroxide, the selective decomposition of formic acid to carbon dioxide and hydrogen, and the E-selective semihydrogenation of alkynes to give E-alkenes. These catalysts feature, compared to other iron-based catalysts, very high catalytic activities which in

  4. Polar self-assembly: steric effects leading to polar mixed-ligand coordination cages.

    Science.gov (United States)

    Zhang, Jianyong; Miller, Philip W; Nieuwenhuyzen, Mark; James, Stuart L

    2006-03-08

    We present a highly unusual example of self-assembly, specifically a polar, mixed-ligand cage which forms in preference to symmetrical homo-ligand products, and which suggests that steric effects can be exploited to obtain novel non-uniform polyhedral cages. In particular, reaction between the bulky tripodal triphosphine 2,4,6-tris(diphenylphosphino)triazine, L1, the non-bulky tripodal trinitrile 2,4,6-tris(cyanomethyl)trimethylbenzene, L2 and silver hexafluoroantimonate, AgSbF6, in a 3:1:4 ratio gives the mixed-ligand aggregate [Ag4(L1)3(L2)(SbF6)]3+, 1-SbF6, instantly as the only product in quantitative yield. The X-ray crystal structure of complex 1-SbF6 is consistent with the suspected solution-state structure. The cage derives from trigonal-pyramidal geometry, the basal vertices of which are defined by three bulky triphosphines, L1, and the apical vertex by the non-bulky trinitrile, L2. There is apical elongation amounting to 19% in comparison to the ideal uniform tetrahedron. The cage also encapsulates an SbF6 anion. 19F NMR spectra in solution for the analogous PF6 complex [Ag4(L1)3(L2)(PF6)]3+, 1-PF6, confirm that one anion is also encapsulated in solution. The synthesis of the analogous CF3SO3(-) complex, [Ag4(L1)3(L2)(OTf)]3+, 1-OTf, in solution is also described, although 1-PF6 and 1-OTf could not be isolated due to slow decomposition in solution. The selective formation of these mixed-ligand cages is discussed in terms of ligand-ligand and ligand-included anion steric repulsions, which we propose prevent the formation of the competing hypothetical homo-ligand tetrahedral structure [Ag4(L1)4(SbF6)]3+, and thus favour the mixed ligand cage. "Cage cone angles" for L1 and L2 are estimated at 115 degrees and 101 degrees, respectively. Variable-temperature 31P NMR spectroscopy shows that complex 1-SbF6 and the related previously reported partial tetrahedral complex [Ag4(L1)3(anion)]3+ undergo dynamic twisting processes in solution between enantiomeric C3

  5. Access Path to the Ligand Binding Pocket May Play a Role in Xenobiotics Selection by AhR

    Science.gov (United States)

    Szöllősi, Dániel; Erdei, Áron; Gyimesi, Gergely; Magyar, Csaba; Hegedűs, Tamás

    2016-01-01

    Understanding of multidrug binding at the atomic level would facilitate drug design and strategies to modulate drug metabolism, including drug transport, oxidation, and conjugation. Therefore we explored the mechanism of promiscuous binding of small molecules by studying the ligand binding domain, the PAS-B domain of the aryl hydrocarbon receptor (AhR). Because of the low sequence identities of PAS domains to be used for homology modeling, structural features of the widely employed HIF-2α and a more recent suitable template, CLOCK were compared. These structures were used to build AhR PAS-B homology models. We performed molecular dynamics simulations to characterize dynamic properties of the PAS-B domain and the generated conformational ensembles were employed in in silico docking. In order to understand structural and ligand binding features we compared the stability and dynamics of the promiscuous AhR PAS-B to other PAS domains exhibiting specific interactions or no ligand binding function. Our exhaustive in silico binding studies, in which we dock a wide spectrum of ligand molecules to the conformational ensembles, suggest that ligand specificity and selection may be determined not only by the PAS-B domain itself, but also by other parts of AhR and its protein interacting partners. We propose that ligand binding pocket and access channels leading to the pocket play equally important roles in discrimination of endogenous molecules and xenobiotics. PMID:26727491

  6. Access Path to the Ligand Binding Pocket May Play a Role in Xenobiotics Selection by AhR.

    Directory of Open Access Journals (Sweden)

    Dániel Szöllősi

    Full Text Available Understanding of multidrug binding at the atomic level would facilitate drug design and strategies to modulate drug metabolism, including drug transport, oxidation, and conjugation. Therefore we explored the mechanism of promiscuous binding of small molecules by studying the ligand binding domain, the PAS-B domain of the aryl hydrocarbon receptor (AhR. Because of the low sequence identities of PAS domains to be used for homology modeling, structural features of the widely employed HIF-2α and a more recent suitable template, CLOCK were compared. These structures were used to build AhR PAS-B homology models. We performed molecular dynamics simulations to characterize dynamic properties of the PAS-B domain and the generated conformational ensembles were employed in in silico docking. In order to understand structural and ligand binding features we compared the stability and dynamics of the promiscuous AhR PAS-B to other PAS domains exhibiting specific interactions or no ligand binding function. Our exhaustive in silico binding studies, in which we dock a wide spectrum of ligand molecules to the conformational ensembles, suggest that ligand specificity and selection may be determined not only by the PAS-B domain itself, but also by other parts of AhR and its protein interacting partners. We propose that ligand binding pocket and access channels leading to the pocket play equally important roles in discrimination of endogenous molecules and xenobiotics.

  7. Quantified Binding Scale of Competing Ligands at the Surface of Gold Nanoparticles: The Role of Entropy and Intermolecular Forces.

    Science.gov (United States)

    Goldmann, Claire; Ribot, François; Peiretti, Leonardo F; Quaino, Paola; Tielens, Frederik; Sanchez, Clément; Chanéac, Corinne; Portehault, David

    2017-05-01

    A basic understanding of the driving forces for the formation of multiligand coronas or self-assembled monolayers over metal nanoparticles is mandatory to control and predict the properties of ligand-protected nanoparticles. Herein, 1 H nuclear magnetic resonance experiments and advanced density functional theory (DFT) modeling are combined to highlight the key parameters defining the efficiency of ligand exchange on dispersed gold nanoparticles. The compositions of the surface and of the liquid reaction medium are quantitatively correlated for bifunctional gold nanoparticles protected by a range of competing thiols, including an alkylthiol, arylthiols of varying chain length, thiols functionalized by ethyleneglycol units, and amide groups. These partitions are used to build scales that quantify the ability of a ligand to exchange dodecanethiol. Such scales can be used to target a specific surface composition by choosing the right exchange conditions (ligand ratio, concentrations, and particle size). In the specific case of arylthiols, the exchange ability scale is exploited with the help of DFT modeling to unveil the roles of intermolecular forces and entropic effects in driving ligand exchange. It is finally suggested that similar considerations may apply to other ligands and to direct biligand synthesis. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  8. Access Path to the Ligand Binding Pocket May Play a Role in Xenobiotics Selection by AhR.

    Science.gov (United States)

    Szöllősi, Dániel; Erdei, Áron; Gyimesi, Gergely; Magyar, Csaba; Hegedűs, Tamás

    2016-01-01

    Understanding of multidrug binding at the atomic level would facilitate drug design and strategies to modulate drug metabolism, including drug transport, oxidation, and conjugation. Therefore we explored the mechanism of promiscuous binding of small molecules by studying the ligand binding domain, the PAS-B domain of the aryl hydrocarbon receptor (AhR). Because of the low sequence identities of PAS domains to be used for homology modeling, structural features of the widely employed HIF-2α and a more recent suitable template, CLOCK were compared. These structures were used to build AhR PAS-B homology models. We performed molecular dynamics simulations to characterize dynamic properties of the PAS-B domain and the generated conformational ensembles were employed in in silico docking. In order to understand structural and ligand binding features we compared the stability and dynamics of the promiscuous AhR PAS-B to other PAS domains exhibiting specific interactions or no ligand binding function. Our exhaustive in silico binding studies, in which we dock a wide spectrum of ligand molecules to the conformational ensembles, suggest that ligand specificity and selection may be determined not only by the PAS-B domain itself, but also by other parts of AhR and its protein interacting partners. We propose that ligand binding pocket and access channels leading to the pocket play equally important roles in discrimination of endogenous molecules and xenobiotics.

  9. Improved pan-specific prediction of MHC class I peptide binding using a novel receptor clustering data partitioning strategy

    DEFF Research Database (Denmark)

    Mattsson, Andreas Holm; Kringelum, Jens Vindahl; Garde, C.

    2016-01-01

    Pan-specific prediction of receptor-ligand interaction is conventionally done using machine-learning methods that integrates information about both receptor and ligand primary sequences. To achieve optimal performance using machine learning, dealing with overfitting and data redundancy is critical...... strategy with the aim of altering this and construct data sets optimal for training of pan-specific receptor-ligand predictions focusing on receptor similarity rather than ligand similarity. We show that this receptor clustering method consistently in benchmarks covering affinity predictions, MHC ligand....... Most often so-called ligand clustering methods have been used to deal with these issues in the context of pan-specific receptor-ligand predictions, and the MHC system the approach has proven highly effective for extrapolating information from a limited set of receptors with well characterized binding...

  10. Sorption-induced reversible oxidation of Fe(2) at the smectite/water interface under strictly anoxic conditions. A Moessbauer spectroscopy study

    Energy Technology Data Exchange (ETDEWEB)

    Gehin, A.; Charlet, L. [Laboratoire de Geophysique Interne et Tectonophysique (LGIT), Universite de Grenoble, 38 - Grenoble (France); Gehin, A. [Agence Nationale pour la Gestion des Dechets Radioactifs, ANDRA, 92 - Chatenay Malabry (France); Greneche, J.M. [Laboratoire de Physique de l' Etat Condense, UMR-CNRS 6087, 72 - Le Mans (France); Brendle, J. [Universite de Haute Alsace, Lab. des Materiaux Mineraux (LMM), 68 - Mulhouse (France); Rancourt, D.G. [Ottawa Univ., Dept. of Physics, Ontario (Canada)

    2005-07-01

    Previous studies of Fe(II) sorption onto montmorillonite have been performed with the mineral extracted from the MX80 bentonite. These studies have shown that Fe(II) can be sorbed onto clay minerals in cation exchange position. The affinity of montmorillonite for Fe(II) and Ca(II) is identical. Fe(II) may also be specifically adsorbed onto montmorillonite clay edges. Moessbauer spectroscopy confirmed the high affinity of clay surfaces for Fe(II) sorption and showed that this sorption is mainly due to a two step mechanism: Fe(II) specific adsorption, followed by oxidation of the Fe(II) sorbed. The identification of the oxidizing agent was prohibited due to the complex chemistry of the natural MX80 montmorillonite. Thus, synthetic iron-free montmorillonite was used (chemical formula: Ca{sub 0.3} (A{sub 1.4}Mg{sub 0.6}) (Si{sub 4}) O{sub 10}(OH){sub 2} ). {sup 57}Fe(II) sorption experiments were conducted in a N{sub 2} atmosphere gloves-box, in strictly anoxic conditions. Solid samples were synthesized in order to confirm the clay high affinity for Fe(II), in absence of structural oxidant, and to have a better comprehension of the sorption mechanism. Moessbauer spectra were recorded for each sample. Whereas no Fe(III) is detected in solution as pH was increased and then, a significant amount of surface sorbed Fe(III) was found to be reversibly produced, which amounts for 0-3% of total Fe in the pre-sorption edge acid region, up to 7% of total Fe when all Fe is sorbed in the neutral to alkaline pH range. From pH {approx_equal} 2 to pH {approx_equal} 7, a sorption edge plateau is observed. In this plateau, the sorbed-Fe(III)/sorbed-Fe ratio increases with pH, up to 45% at pH 7. Moessbauer spectra comparison with ferrous hydroxide, synthesized in the same redox conditions at higher pH, show that this oxidation can not be due to the trace amounts Oz in the suspension. The Moessbauer spectra components of both Fe(II) and Fe(III) appears as paramagnetic doublets: iron has

  11. Changes in Smoking Behavior Following a Strict No-Smoking Policy in U.S. Navy Recruit Training

    Science.gov (United States)

    1993-08-01

    Smoking and Health. DHHS Publication No. (CDC) 87-8396, 1990. Wilcox, N.S., Prochaska , J.D., Velicer, W.F., & DiClemente , C.C. •1985). Subject...the "entry" survey and had an expanded section on attitudes regarding Na,, y smoking policy. Specific questionnaire measures are described below...not expected, given the number of studies that have associated education level with smoking status (US DHI-iS, 1990; Wilcox, Prochaska , Velicer

  12. Study of killer cell immunoglobulin-like receptor genes and HLA C ligands in hematopoietic stem cell transplantation pairs in Vojvodina

    Directory of Open Access Journals (Sweden)

    Ademović-Sazdanić Dušica S.

    2016-01-01

    Full Text Available Objective: The aim of the study was to analyse KIR/HLA profiles and to create the predictive probabilities for the selection of the most suitable Hematopoietic Stem Cell Transplantation (HSCT donor. Materials and Methods: The study was conducted on 92 patients with malignant hematological deseases and 181 their first degree relatives, from the region of Vojvodina. HLA and KIR genotyping was performed by polymerase chain reaction-sequence specific primers (PCR-SSP assay. The analysis included the degree of HLA matching between transplant pairs, number of missing ligands for inhibitory KIR genes, existence of GvH / HvG ligand-ligand mismatches (specific for C1, C2 or Bw4 ligands and distribution of C1/C1, C1/C2, C2/C2 HLA ligand groups in patients. Results: There was no significant differences in HLA frequencies between donors and recipients as analyzed by pairwise comparison, the probability of finding HLA identical donor is only 0.154, the probability of finding the donor with ≥ 1 KIR-ligand mismatch is 0.939, the probability of finding the donor with KIR-ligand mismatch for the KIR 2DL1 gene is 0.298, probability of having favorable C1/C1 and C2/C2 HLA ligand groups is 0.565. Conclusion: The results of our study could be used as a basis for the HSCT outcome prediction representing a powerful tool for choosing the most suitable donor.

  13. Crystal Structure of Epiphyas Postvittana Takeout 1 With Bound Ubiquinone Supports a Role As Ligand Carriers for Takeout Proteins in Insects

    Energy Technology Data Exchange (ETDEWEB)

    Hamiaux, C.; Stanley, D.; Greenwood, D.R.; Baker, E.N.; Newcomb, R.D.

    2009-05-19

    Takeout (To) proteins are found exclusively in insects and have been proposed to have important roles in various aspects of their physiology and behavior. Limited sequence similarity with juvenile hormone-binding proteins (JHBPs), which specifically bind and transport juvenile hormones in Lepidoptera, suggested a role for To proteins in binding hydrophobic ligands. We present the first crystal structure of a To protein, EpTo1 from the light brown apple moth Epiphyas postvittana, solved in-house by the single-wavelength anomalous diffraction technique using sulfur anomalous dispersion, and refined to 1.3 {angstrom} resolution. EpTo1 adopts the unusual {alpha}/{beta}-wrap fold, seen only for JHBP and several mammalian lipid carrier proteins, a scaffold tailored for the binding and/or transport of hydrophobic ligands. EpTo1 has a 45 {angstrom} long, purely hydrophobic, internal tunnel that extends for the full length of the protein and accommodates a bound ligand. The latter was shown by mass spectrometry to be ubiquinone-8 and is probably derived from Escherichia coli. The structure provides the first direct experimental evidence that To proteins are ligand carriers; gives insights into the nature of endogenous ligand(s) of EpTo1; shows, by comparison with JHBP, a basis for different ligand specificities; and suggests a mechanism for the binding/release of ligands.

  14. Assessment and challenges of ligand docking into comparative models of G-protein coupled receptors.

    Directory of Open Access Journals (Sweden)

    Elizabeth Dong Nguyen

    Full Text Available The rapidly increasing number of high-resolution X-ray structures of G-protein coupled receptors (GPCRs creates a unique opportunity to employ comparative modeling and docking to provide valuable insight into the function and ligand binding determinants of novel receptors, to assist in virtual screening and to design and optimize drug candidates. However, low sequence identity between receptors, conformational flexibility, and chemical diversity of ligands present an enormous challenge to molecular modeling approaches. It is our hypothesis that rapid Monte-Carlo sampling of protein backbone and side-chain conformational space with Rosetta can be leveraged to meet this challenge. This study performs unbiased comparative modeling and docking methodologies using 14 distinct high-resolution GPCRs and proposes knowledge-based filtering methods for improvement of sampling performance and identification of correct ligand-receptor interactions. On average, top ranked receptor models built on template structures over 50% sequence identity are within 2.9 Å of the experimental structure, with an average root mean square deviation (RMSD of 2.2 Å for the transmembrane region and 5 Å for the second extracellular loop. Furthermore, these models are consistently correlated with low Rosetta energy score. To predict their binding modes, ligand conformers of the 14 ligands co-crystalized with the GPCRs were docked against the top ranked comparative models. In contrast to the comparative models themselves, however, it remains difficult to unambiguously identify correct binding modes by score alone. On average, sampling performance was improved by 10(3 fold over random using knowledge-based and energy-based filters. In assessing the applicability of experimental constraints, we found that sampling performance is increased by one order of magnitude for every 10 residues known to contact the ligand. Additionally, in the case of DOR, knowledge of a single specific

  15. Structural studies of Ca2+-ATPase ligand and regulatory complexes

    DEFF Research Database (Denmark)

    Drachmann, Nikolaj Düring

    2015-01-01

    , the surrounding membrane itself has a huge influence on SERCA structure and function. Changes in the membrane thickness can alter the activity of the ATPase significantly, and even cause changes in the stoichiometry of ion transport. Structural studies on SERCA in the presence of four different phosphatidyl...... choline lipids with different aliphatic chain length and saturation show three specific lipid binding sites. The four different lipids analysed bind to the same binding sites with varying degrees of disorder. The study contributes to understanding the complex interplay between the surrounding membrane...... to explore the possibilities for an efficient screening of ligand-bound SERCA structures, serial femtosecond crystallography experiments of microcrystals of SERCA1a in the Ca2+ bound state and in a vanadate stabilised E2 state was conducted. A structure obtained at 2.8 Å maximum resolution of the proof...

  16. NMR studies of DNA oligomers and their interactions with minor groove binding ligands

    Energy Technology Data Exchange (ETDEWEB)

    Fagan, Patricia A. [Univ. of California, Berkeley, CA (United States). Dept. of Chemistry

    1996-05-01

    The cationic peptide ligands distamycin and netropsin bind noncovalently to the minor groove of DNA. The binding site, orientation, stoichiometry, and qualitative affinity of distamycin binding to several short DNA oligomers were investigated by NMR spectroscopy. The oligomers studied contain A,T-rich or I,C-rich binding sites, where I = 2-desaminodeoxyguanosine. I•C base pairs are functional analogs of A•T base pairs in the minor groove. The different behaviors exhibited by distamycin and netropsin binding to various DNA sequences suggested that these ligands are sensitive probes of DNA structure. For sites of five or more base pairs, distamycin can form 1:1 or 2:1 ligand:DNA complexes. Cooperativity in distamycin binding is low in sites such as AAAAA which has narrow minor grooves, and is higher in sites with wider minor grooves such as ATATAT. The distamycin binding and base pair opening lifetimes of I,C-containing DNA oligomers suggest that the I,C minor groove is structurally different from the A,T minor groove. Molecules which direct chemistry to a specific DNA sequence could be used as antiviral compounds, diagnostic probes, or molecular biology tools. The author studied two ligands in which reactive groups were tethered to a distamycin to increase the sequence specificity of the reactive agent.

  17. Targeting of Immune Cells by Dual TLR2/7 Ligands Suppresses Features of Allergic Th2 Immune Responses in Mice

    Directory of Open Access Journals (Sweden)

    Jonathan Laiño

    2017-01-01

    Full Text Available Background. TLR ligands can promote Th1-biased immune responses, mimicking potent stimuli of viruses and bacteria. Aim. To investigate the adjuvant properties of dual TLR2/7 ligands compared to those of the mixture of both single ligands. Methods. Dual TLR2/7 ligands: CL401, CL413, and CL531, including CL264 (TLR7-ligand and Pam2CysK4 (TLR2-ligand, were used. Immune-modulatory capacity of the dual ligands with the individual ligands alone or as a mixture in mouse BMmDCs, BMmDC:TC cocultures, or BMCMCs was compared and assessed in naïve mice and in a mouse model of OVA-induced intestinal allergy. Results. CL413 and CL531 induced BMmDC-derived IL-10 secretion, suppressed rOVA-induced IL-5 secretion from OVA-specific DO11.10 CD4+ TCs, and induced proinflammatory cytokine secretion in vivo. In contrast, CL401 induced considerably less IL-10 secretion and led to IL-17A production in BMmDC:TC cocultures, but not BMCMC IL-6 secretion, or IL-6 or TNF-α production in vivo. No immune-modulating effects were observed with single ligands. All dual TLR2/7 ligands suppressed DNP-induced IgE-and-Ag-specific mast cell degranulation. Compared to vaccination with OVA, vaccination with the mixture CL531 and OVA, significantly suppressed OVA-specific IgE production in the intestinal allergy model. Conclusions. Based on beneficial immune-modulating properties, CL413 and CL531 may have utility as potential adjuvants for allergy treatment.

  18. Abundance of Flt3 and its ligand in astrocytic tumors

    Directory of Open Access Journals (Sweden)

    Eßbach C

    2013-05-01

    Full Text Available C Eßbach,1 N Andrae,1 D Pachow,1 J-P Warnke,2 A Wilisch-Neumann,1 E Kirches,1 C Mawrin11Department of Neuropathology, Otto-von-Guericke University, Magdeburg, 2Department of Neurosurgery, Paracelsus Hospital, Zwickau, GermanyBackground: Molecular targeted therapies for astrocytic tumors are the subject of growing research interest, due to the limited response of these tumors, especially glioblastoma multiforme, to conventional chemotherapeutic regimens. Several of these approaches exploit the inhibition of receptor tyrosine kinases. To date, it has not been elucidated if fms-like tyrosine kinase-3 (Flt3 and its natural ligand (Flt3L are expressed in astrocytic tumors, although some of the clinically intended small-molecule receptor tyrosine kinase inhibitors affect Flt3, while others do not. More importantly, the recent proof of principle for successful stimulation of the immune system against gliomas in preclinical models via local Flt3L application requires elucidation of this receptor tyrosine kinase pathway in these tumors in more detail. This therapy is based on recruitment of Flt3-positive dendritic cells, but may be corroborated by activity of this signaling pathway in glioma cells.Methods: Receptor and ligand expression was analyzed by real-time polymerase chain reaction in 31 astrocytic tumors (six diffuse and 11 anaplastic astrocytomas, 14 glioblastomas derived from patients of both genders and in glioblastoma cell lines. The two most common activating mutations of the Flt3 gene, ie, internal tandem duplication and D835 point mutation, were assessed by specific polymerase chain reaction.Results: A relatively high abundance of Flt3L mRNA (4%–6% of the reference, β2 microglobulin could be demonstrated in all tumor samples. Flt3 expression could generally be demonstrated by 40 specific polymerase chain reaction cycles and gel electrophoresis in 87% of the tumors, including all grades, although the small quantities of the receptor did

  19. Ligand and proton exchange dynamics in recombinant human myoglobin mutants.

    Science.gov (United States)

    Lambright, D G; Balasubramanian, S; Boxer, S G

    1989-05-05

    Site-specific mutants of human myoglobin have been prepared in which lysine 45 is replaced by arginine (K45R) and aspartate 60 by glutamate (D60E), in order to examine the influence of these residues and their interaction on the dynamics of the protein. These proteins were studied by a variety of methods, including one and two-dimensional proton nuclear magnetic resonance spectroscopy, exchange kinetics for the distal and proximal histidine NH protons as a function of pH in the met cyano forms, flash photolysis of the CO forms, and ligand replacement kinetics. The electronic absorption and proton nuclear magnetic resonance spectra of the CO forms of these proteins are virtually identical, indicating that the structure of the heme pocket is unaltered by these mutations. There are, however, substantial changes in the dynamics of both CO binding and proton exchange for the mutant K45R, whereas the mutant D60E exhibits behavior indistinguishable from the reference human myoglobin. K45R has a faster CO bimolecular recombination rate and slower CO off-rate relative to the reference. The kinetics for CO binding are independent of pH (6.5 to 10) as well as ionic strength (0 to 1 M-NaCl). The exchange rate for the distal histidine NH is substantially lower for K45R than the reference, whereas the proximal histidine NH exchange rate is unaltered. The exchange behavior of the human proteins is similar to that reported for a comparison of the exchange rates for myoglobins having lysine at position 45 with sperm whale myoglobin, which has arginine at this position. This indicates that the differences in exchange rates reflects largely the Lys----Arg substitution. The lack of a simple correlation for the CO kinetics with this substitution means that these are sensitive to other factors as well. Specific kinetic models, whereby substitution of arginine for lysine at position 45 can affect ligand binding dynamics, are outlined. These experiments demonstrate that a relatively

  20. Steroid signaling: ligand-binding promiscuity, molecular symmetry, and the need for gating.

    Science.gov (United States)

    Lathe, Richard; Kotelevtsev, Yuri

    2014-04-01

    Steroid/sterol-binding receptors and enzymes are remarkably promiscuous in the range of ligands they can bind to and, in the case of enzymes, modify - raising the question of how specific receptor activation is achieved in vivo. Estrogen receptors (ER) are modulated by 27-hydroxycholesterol and 5α-androstane-3β,17β-diol (Adiol), in addition to estradiol (E2), and respond to diverse small molecules such as bisphenol A. Steroid-modifying enzymes are also highly promiscuous in ligand binding and metabolism. The specificity problem is compounded by the fact that the steroid core (hydrogenated cyclopentophenanthrene ring system) has several planes of symmetry. Ligand binding can be in symmetrical East-West (rotation) and North-South (inversion) orientations. Hydroxysteroid dehydrogenases (HSDs) can modify symmetrical 7 and 11, also 3 and 17/20, positions, exemplified here by yeast 3α,20β-HSD and mammalian 11β-HSD and 17β-HSD enzymes. Faced with promiscuity and symmetry, other strategies are clearly necessary to promote signaling selectivity in vivo. Gating regulates hormone access via enzymes that preferentially inactivate (or activate) a subclass of ligands, thereby governing which ligands gain receptor access - exemplified by 11β-HSD gating cortisol access to the mineralocorticoid receptor, and P450 CYP7B1 gating Adiol access to ER. Counter-intuitively, the specificity of steroid/sterol action is achieved not by intrinsic binding selectivity but by the combination of local metabolism and binding affinity. Copyright © 2014 Elsevier Inc. All rights reserved.

  1. ProBiS-ligands: a web server for prediction of ligands by examination of protein binding sites.

    Science.gov (United States)

    Konc, Janez; Janežič, Dušanka

    2014-07-01

    The ProBiS-ligands web server predicts binding of ligands to a protein structure. Starting with a protein structure or binding site, ProBiS-ligands first identifies template proteins in the Protein Data Bank that share similar binding sites. Based on the superimpositions of the query protein and the similar binding sites found, the server then transposes the ligand structures from those sites to the query protein. Such ligand prediction supports many activities, e.g. drug repurposing. The ProBiS-ligands web server, an extension of the ProBiS web server, is open and free to all users at http://probis.cmm.ki.si/ligands. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  2. Ligand activation of the prokaryotic pentameric ligand-gated ion channel ELIC.

    Directory of Open Access Journals (Sweden)

    Iwan Zimmermann

    2011-06-01

    Full Text Available While the pentameric ligand-gated ion channel ELIC has recently provided first insight into the architecture of the family at high resolution, its detailed investigation was so far prevented by the fact that activating ligands were unknown. Here we describe a study on the functional characterization of ELIC by electrophysiology and X-ray crystallography. ELIC is activated by a class of primary amines that include the neurotransmitter GABA at high micro- to millimolar concentrations. The ligands bind to a conserved site and evoke currents that slowly desensitize over time. The protein forms cation selective channels with properties that resemble the nicotinic acetylcholine receptor. The high single channel conductance and the comparably simple functional behavior make ELIC an attractive model system to study general mechanisms of ion conduction and gating in this important family of neurotransmitter receptors.

  3. Secreted and transmembrane 1A is a novel co-stimulatory ligand.

    Directory of Open Access Journals (Sweden)

    Duncan Howie

    Full Text Available Most T cell responses to pathogens or self antigens are modulated through the action of regulatory T cells and tissue-specific inhibitory mechanisms. To this end, several receptor-ligand pairs have evolved which either augment or diminish T cell function. Here we describe the tissue ligand SECTM1A (Secreted and transmembrane1A as an alternative murine CD7 ligand. We show that SECTM1A, like SECTM1B, binds strongly to CD7, and that SECTM1B was able to compete with SECTM1A for CD7 binding. SECTM1A is ubiquitously expressed and has two major alternative transcripts which differ in expression between tissues. Both immobilised soluble forms of SECTM1A and SECTM1B and cell surface anchored forms demonstrated opposing effects on CD4+ T cell activation. Whereas SECTM1A acted as a co-stimulator of T cells, enhancing IL-2 production and proliferation, SECTM1B proved inhibitory to TCR mediated T cell activation. Surprisingly, both functional outcomes proved to be CD7-independent, indicating the existence of alternative receptors for both ligands. We used a SECTM1A-Fc fusion protein to immunoprecipitate potential alternative ligands from detergent lysates of CD7(-/- T cells and, using mass spectrometry, identified GITR as a SECTM1A binder. SECTM1A was found to bind to activated CD4+ and CD8+ T cells as well as to CHO cells expressing cell surface GITR. Binding of SECTM1A to activated primary T cells was inhibited by either GITRL-Fc or anti GITR antibodies. Thus SECTM1A and SECTM1B represent novel reciprocal alternative ligands which may function to modulate the activation of effector and regulatory T cells. The ability of SECTM1A to activate T cells may be explained by its ability to bind to GITR.

  4. Doubling the Size of the Glucocorticoid Receptor Ligand Binding Pocket by Deacylcortivazol

    Energy Technology Data Exchange (ETDEWEB)

    Suino-Powell, Kelly; Xu, Yong; Zhang, Chenghai; Tao, Yong-guang; Tolbert, W. David; Simons, Jr., S. Stoney; Xu, H. Eric (NIH)

    2010-03-08

    A common feature of nuclear receptor ligand binding domains (LBD) is a helical sandwich fold that nests a ligand binding pocket within the bottom half of the domain. Here we report that the ligand pocket of glucocorticoid receptor (GR) can be continuously extended into the top half of the LBD by binding to deacylcortivazol (DAC), an extremely potent glucocorticoid. It has been puzzling for decades why DAC, which contains a phenylpyrazole replacement at the conserved 3-ketone of steroid hormones that are normally required for activation of their cognate receptors, is a potent GR activator. The crystal structure of the GR LBD bound to DAC and the fourth LXXLL motif of steroid receptor coactivator 1 reveals that the GR ligand binding pocket is expanded to a size of 1,070 {angstrom}{sup 3}, effectively doubling the size of the GR dexamethasone-binding pocket of 540 {angstrom}{sup 3} and yet leaving the structure of the coactivator binding site intact. DAC occupies only {approx}50% of the space of the pocket but makes intricate interactions with the receptor around the phenylpyrazole group that accounts for the high-affinity binding of DAC. The dramatic expansion of the DAC-binding pocket thus highlights the conformational adaptability of GR to ligand binding. The new structure also allows docking of various nonsteroidal ligands that cannot be fitted into the previous structures, thus providing a new rational template for drug discovery of steroidal and nonsteroidal glucocorticoids that can be specifically designed to reach the unoccupied space of the expanded pocket.

  5. Spectrophotometric method for determination of bifunctional macrocyclic ligands in macrocyclic ligand-protein conjugates

    International Nuclear Information System (INIS)

    Dadachova, E.; Chappell, L.L.; Brechbiel, M.W.

    1999-01-01

    A simple spectrophotometric assay for determination of bifunctional polyazacarboxylate-macrocyclic ligands of different sizes that are conjugated to proteins has been developed for: 12-membered macrocycle DOTA (2-[4-nitrobenzyl]-1, 4, 7, 10-tetraazacyclododecane-N,N',N'',N'''-tetraacetic acid) and analogs, the 15-membered PEPA macrocycle (2-[4-nitrobenzyl]-1,4,7,10,13-pentaazacyclopentadecane-N,N',N'',N''',N'''' -pentaacetic acid), and the large 18-membered macrocycle HEHA (1,4,7,10,13,16-hexaazacyclooctadecane-N,N',N'',N''',N''''-hexaacetic acid). The method is based on titration of the blue-colored 1:1 Pb(II)-Arsenazo III (AAIII) complex with the polyazacarboxylate macrocyclic ligand in the concentration range of 0-2.5 μM, wherein color change occurring upon transchelation of the Pb(II) from the AAIII to the polyazamacrocyclic ligand is monitored at 656 nm. The assay is performed at ambient temperature within 20 min without any interfering interaction between the protein and Pb(II)-AA(III) complex. Thus, this method also provides a ligand-to-protein ratio (L/P ratio) that reflects the effective number of ligands per protein molecule available to radiolabeling. The method is not suitable for 14-membered TETA macrocycle (2-[4-nitrobenzyl]-1, 4, 8, 11-tetraazacyclotetradecane N,N',N'',N'''-tetraacetic acid) because of low stability constant of Pb(II)-TETA complex. The method is rapid, simple and may be customized for other polyazacarboxylate macrocyclic ligands

  6. Synthetic Peptide Ligands of the Antigen Binding Receptor Induce Programmed Cell Death in a Human B-Cell Lymphoma

    Science.gov (United States)

    Renschler, Markus F.; Bhatt, Ramesh R.; Dower, William J.; Levy, Ronald

    1994-04-01

    Peptide ligands for the antigen binding site of the surface immunoglobulin receptor of a human B-cell lymphoma cell line were identified with the use of filamentous phage libraries displaying random 8- and 12-amino acid peptides. Corresponding synthetic peptides bound specifically to the antigen binding site of this immunoglobulin receptor and blocked the binding of an anti-idiotype antibody. The ligands, when conjugated to form dimers or tetramers, induced cell death by apoptosis in vitro with an IC50 between 40 and 200 nM. This effect was associated with specific stimulation of intracellular protein tyrosine phosphorylation.

  7. Peculiarities of one-carbon metabolism in the strict carnivorous cat and the role in feline hepatic lipidosis.

    Science.gov (United States)

    Verbrugghe, Adronie; Bakovic, Marica

    2013-07-19

    Research in various species has indicated that diets deficient in labile methyl groups (methionine, choline, betaine, folate) produce fatty liver and links to steatosis and metabolic syndrome, but also provides evidence of the importance of labile methyl group balance to maintain normal liver function. Cats, being obligate carnivores, rely on nutrients in animal tissues and have, due to evolutionary pressure, developed several physiological and metabolic adaptations, including a number of peculiarities in protein and fat metabolism. This has led to specific and unique nutritional requirements. Adult cats require more dietary protein than omnivorous species, maintain a consistently high rate of protein oxidation and gluconeogenesis and are unable to adapt to reduced protein intake. Furthermore, cats have a higher requirement for essential amino acids and essential fatty acids. Hastened use coupled with an inability to conserve certain amino acids, including methionine, cysteine, taurine and arginine, necessitates a higher dietary intake for cats compared to most other species. Cats also seemingly require higher amounts of several B-vitamins compared to other species and are predisposed to depletion during prolonged inappetance. This carnivorous uniqueness makes cats more susceptible to hepatic lipidosis.

  8. Peculiarities of One-Carbon Metabolism in the Strict Carnivorous Cat and the Role in Feline Hepatic Lipidosis

    Directory of Open Access Journals (Sweden)

    Marica Bakovic

    2013-07-01

    Full Text Available Research in various species has indicated that diets deficient in labile methyl groups (methionine, choline, betaine, folate produce fatty liver and links to steatosis and metabolic syndrome, but also provides evidence of the importance of labile methyl group balance to maintain normal liver function. Cats, being obligate carnivores, rely on nutrients in animal tissues and have, due to evolutionary pressure, developed several physiological and metabolic adaptations, including a number of peculiarities in protein and fat metabolism. This has led to specific and unique nutritional requirements. Adult cats require more dietary protein than omnivorous species, maintain a consistently high rate of protein oxidation and gluconeogenesis and are unable to adapt to reduced protein intake. Furthermore, cats have a higher requirement for essential amino acids and essential fatty acids. Hastened use coupled with an inability to conserve certain amino acids, including methionine, cysteine, taurine and arginine, necessitates a higher dietary intake for cats compared to most other species. Cats also seemingly require higher amounts of several B-vitamins compared to other species and are predisposed to depletion during prolonged inappetance. This carnivorous uniqueness makes cats more susceptible to hepatic lipidosis.

  9. Gene function analysis in environmental isolates: The nif regulon of the strict iron oxidizing bacterium Leptospirillum ferrooxidans

    Science.gov (United States)

    Parro, Víctor; Moreno-Paz, Mercedes

    2003-01-01

    A random genomic library from an environmental isolate of the Gram-negative bacterium Leptospirillum ferrooxidans has been printed on a microarray. Gene expression analysis was carried out with total RNA extracted from L. ferrooxidans cultures in the presence or absence of ammonium as nitrogen source under aerobic conditions. Although practically nothing is known about the genome sequence of this bacterium, this approach allowed us the selection and sequencing of only those clones bearing genes that showed an altered expression pattern. By sequence comparison, we have identified most of the genes of nitrogen fixation regulon in L. ferrooxidans, like the nifHDKENX operon, encoding the structural components of Mo-Fe nitrogenase; nifSU-hesB-hscBA-fdx operon, for Fe-S cluster assembly; the amtB gene (ammonium transporter); modA (molybdenum ABC type transporter); some regulatory genes like ntrC, nifA (the specific activator of nif genes); or two glnB-like genes (encoding the PII regulatory protein). Our results show that shotgun DNA microarrays are very powerful tools to accomplish gene expression studies with environmental bacteria whose genome sequence is still unknown, avoiding the time and effort necessary for whole genome sequencing projects. PMID:12808145

  10. Sponge-Associated Bacteria Are Strictly Maintained in Two Closely Related but Geographically Distant Sponge Hosts ▿ † ‡ §

    Science.gov (United States)

    Montalvo, Naomi F.; Hill, Russell T.

    2011-01-01

    The giant barrel sponges Xestospongia muta and Xestospongia testudinaria are ubiquitous in tropical reefs of the Atlantic and Pacific Oceans, respectively. They are key species in their respective environments and are hosts to diverse assemblages of bacteria. These two closely related sponges from different oceans provide a unique opportunity to examine the evolution of sponge-associated bacterial communities. Mitochondrial cytochrome oxidase subunit I gene sequences from X. muta and X. testudinaria showed little divergence between the two species. A detailed analysis of the bacterial communities associated with these sponges, comprising over 900 full-length 16S rRNA gene sequences, revealed remarkable similarity in the bacterial communities of the two species. Both sponge-associated communities include sequences found only in the two Xestospongia species, as well as sequences found also in other sponge species and are dominated by three bacterial groups, Chloroflexi, Acidobacteria, and Actinobacteria. While these groups consistently dominate the bacterial communities revealed by 16S rRNA gene-based analysis of sponge-associated bacteria, the depth of sequencing undertaken in this study revealed clades of bacteria specifically associated with each of the two Xestospongia species, and also with the genus Xestospongia, that have not been found associated with other sponge species or other ecosystems. This study, comparing the bacterial communities associated with closely related but geographically distant sponge hosts, gives new insight into the intimate relationships between marine sponges and some of their bacterial symbionts. PMID:21856832

  11. Molecular Hybridization of Potent and Selective γ-Hydroxybutyric Acid (GHB) Ligands: Design, Synthesis, Binding Studies, and Molecular Modeling of Novel 3-Hydroxycyclopent-1-enecarboxylic Acid (HOCPCA) and trans-γ-Hydroxycrotonic Acid (T-HCA) Analogs

    DEFF Research Database (Denmark)

    Krall, Jacob; Jensen, Claus Hatt; Bavo, Francesco

    2017-01-01

    γ-Hydroxybutyric acid (GHB) is a neuroactive substance with specific high-affinity binding sites. To facilitate target identification and ligand optimization, we herein report a comprehensive structure–affinity relationship study for novel ligands targeting these binding sites. A molecular hybrid...... important for high-affinity binding, with high predictive validity. These findings will be valuable in the further processes of both target characterization and ligand identification for the high-affinity GHB binding sites....

  12. Metal isotope coded profiling of organic ligands by mass spectrometry in aquatic environments

    Science.gov (United States)

    Wichard, Thomas; Deicke, Michael; Frieder Mohr, Jan; Klein, Martin

    2017-04-01

    Metal isotope coded profiling (MICP) introduces a universal discovery platform for metal chelating natural products that act as metallophores, ion buffers or sequestering agents. The detection of cation and oxoanion complexing ligands is facilitated by the identification of unique isotopic signatures created by the application of isotopically pure metals. We present a targeted analysis of low-molecular-weight organic ligands based on fast UHPLC-ESI-MS measurements. Replacement of, for example, natural iron or molybdenum with isotopically pure 54Fe/58Fe (ratio 1:1) or 95Mo/98Mo (ratio 1:1) causes easily detectable unique isotopic signatures in the mass spectra of potential metal-complexing ligands. This can be achieved under laboratory conditions not only in growth media, but also by spiking directly aqueous samples or solid-phase extracts. Importantly, as the relative affinity of the metallophores for e.g., Mo or Fe is dependent on the pH, all experiments needs to be conducted under pH-controlled conditions. The improved ionization efficiency of some metal complexes helps to enhance the signal-to-noise ratio compared to the free ligand at the same chromatographic conditions. The methodology does not necessarily depend on HR-ESI-MS measurements (e.g., Q-Exactive Orbitrap) and can be applied to any mass spectrometer. With MICP, two birds can be killed with one stone: (i) the identification of metallophores (e.g., siderophores, molybdophores) for metal uptake by any organism and (ii) organic ligands which solely work as metal buffer in dissolved organic matter (DOM). We currently address following two main research lines: First, DOM has often been used as a proxy for bio-productivity in terms of a carbon source; however, the specific impact of DOM as a "metal buffer" for biological processes is still under-investigated. Upon the administration of individual isotopes or isotopic pairs, for example, 54Fe/58Fe, 63Cu/65Cu, 66Zn/68Zn, or 95Mo/98Mo and subsequent

  13. Structural studies of P-type ATPase–ligand complexes using an X-ray free-electron laser

    Energy Technology Data Exchange (ETDEWEB)

    Bublitz, Maike; Nass, Karol; Drachmann, Nikolaj D.; Markvardsen, Anders J.; Gutmann, Matthias J.; Barends, Thomas R. M.; Mattle, Daniel; Shoeman, Robert L.; Doak, R. Bruce; Boutet, Sébastien; Messerschmidt, Marc; Seibert, Marvin M.; Williams, Garth J.; Foucar, Lutz; Reinhard, Linda; Sitsel, Oleg; Gregersen, Jonas L.; Clausen, Johannes D.; Boesen, Thomas; Gotfryd, Kamil; Wang, Kai-Tuo; Olesen, Claus; Møller, Jesper V.; Nissen, Poul; Schlichting, Ilme

    2015-06-11

    Membrane proteins are key players in biological systems, mediating signalling events and the specific transport ofe.g.ions and metabolites. Consequently, membrane proteins are targeted by a large number of currently approved drugs. Understanding their functions and molecular mechanisms is greatly dependent on structural information, not least on complexes with functionally or medically important ligands. Structure determination, however, is hampered by the difficulty of obtaining well diffracting, macroscopic crystals. Here, the feasibility of X-ray free-electron-laser-based serial femtosecond crystallography (SFX) for the structure determination of membrane protein–ligand complexes using microcrystals of various native-source and recombinant P-type ATPase complexes is demonstrated. The data reveal the binding sites of a variety of ligands, including lipids and inhibitors such as the hallmark P-type ATPase inhibitor orthovanadate. By analyzing the resolution dependence of ligand densities and overall model qualities, SFX data quality metrics as well as suitable refinement procedures are discussed. Even at relatively low resolution and multiplicity, the identification of ligands can be demonstrated. This makes SFX a useful tool for ligand screening and thus for unravelling the molecular mechanisms of biologically active proteins.

  14. Structural studies of P-type ATPase–ligand complexes using an X-ray free-electron laser

    Directory of Open Access Journals (Sweden)

    Maike Bublitz

    2015-07-01

    Full Text Available Membrane proteins are key players in biological systems, mediating signalling events and the specific transport of e.g. ions and metabolites. Consequently, membrane proteins are targeted by a large number of currently approved drugs. Understanding their functions and molecular mechanisms is greatly dependent on structural information, not least on complexes with functionally or medically important ligands. Structure determination, however, is hampered by the difficulty of obtaining well diffracting, macroscopic crystals. Here, the feasibility of X-ray free-electron-laser-based serial femtosecond crystallography (SFX for the structure determination of membrane protein–ligand complexes using microcrystals of various native-source and recombinant P-type ATPase complexes is demonstrated. The data reveal the binding sites of a variety of ligands, including lipids and inhibitors such as the hallmark P-type ATPase inhibitor orthovanadate. By analyzing the resolution dependence of ligand densities and overall model qualities, SFX data quality metrics as well as suitable refinement procedures are discussed. Even at relatively low resolution and multiplicity, the identification of ligands can be demonstrated. This makes SFX a useful tool for ligand screening and thus for unravelling the molecular mechanisms of biologically active proteins.

  15. Nanoparticle orientation to control RNA loading and ligand display on extracellular vesicles for cancer regression.

    Science.gov (United States)

    Pi, Fengmei; Binzel, Daniel W; Lee, Tae Jin; Li, Zhefeng; Sun, Meiyan; Rychahou, Piotr; Li, Hui; Haque, Farzin; Wang, Shaoying; Croce, Carlo M; Guo, Bin; Evers, B Mark; Guo, Peixuan

    2018-01-01

    Nanotechnology offers many benefits, and here we report an advantage of applying RNA nanotechnology for directional control. The orientation of arrow-shaped RNA was altered to control ligand display on extracellular vesicle membranes for specific cell targeting, or to regulate intracellular trafficking of small interfering RNA (siRNA) or microRNA (miRNA). Placing membrane-anchoring cholesterol at the tail of the arrow results in display of RNA aptamer or folate on the outer surface of the extracellular vesicle. In contrast, placing the cholesterol at the arrowhead results in partial loading of RNA nanoparticles into the extracellular vesicles. Taking advantage of the RNA ligand for specific targeting and extracellular vesicles for efficient membrane fusion, the resulting ligand-displaying extracellular vesicles were capable of specific delivery of siRNA to cells, and efficiently blocked tumour growth in three cancer models. Extracellular vesicles displaying an aptamer that binds to prostate-specific membrane antigen, and loaded with survivin siRNA, inhibited prostate cancer xenograft. The same extracellular vesicle instead displaying epidermal growth-factor receptor aptamer inhibited orthotopic breast cancer models. Likewise, survivin siRNA-loaded and folate-displaying extracellular vesicles inhibited patient-derived colorectal cancer xenograft.

  16. Nanoparticle orientation to control RNA loading and ligand display on extracellular vesicles for cancer regression

    Science.gov (United States)

    Pi, Fengmei; Binzel, Daniel W.; Lee, Tae Jin; Li, Zhefeng; Sun, Meiyan; Rychahou, Piotr; Li, Hui; Haque, Farzin; Wang, Shaoying; Croce, Carlo M.; Guo, Bin; Evers, B. Mark; Guo, Peixuan

    2018-01-01

    Nanotechnology offers many benefits, and here we report an advantage of applying RNA nanotechnology for directional control. The orientation of arrow-shaped RNA was altered to control ligand display on extracellular vesicle membranes for specific cell targeting, or to regulate intracellular trafficking of small interfering RNA (siRNA) or microRNA (miRNA). Placing membrane-anchoring cholesterol at the tail of the arrow results in display of RNA aptamer or folate on the outer surface of the extracellular vesicle. In contrast, placing the cholesterol at the arrowhead results in partial loading of RNA nanoparticles into the extracellular vesicles. Taking advantage of the RNA ligand for specific targeting and extracellular vesicles for efficient membrane fusion, the resulting ligand-displaying extracellular vesicles were capable of specific delivery of siRNA to cells, and efficiently blocked tumour growth in three cancer models. Extracellular vesicles displaying an aptamer that binds to prostate-specific membrane antigen, and loaded with survivin siRNA, inhibited prostate cancer xenograft. The same extracellular vesicle instead displaying epidermal growth-factor receptor aptamer inhibited orthotopic breast cancer models. Likewise, survivin siRNA-loaded and folate-displaying extracellular vesicles inhibited patient-derived colorectal cancer xenograft.

  17. Prediction of GPCR-Ligand Binding Using Machine Learning Algorithms

    Directory of Open Access Journals (Sweden)

    Sangmin Seo

    2018-01-01

    Full Text Available We propose a novel method that predicts binding of G-protein coupled receptors (GPCRs and ligands. The proposed method uses hub and cycle structures of ligands and amino acid motif sequences of GPCRs, rather than the 3D structure of a receptor or similarity of receptors or ligands. The experimental results show that these new features can be effective in predicting GPCR-ligand binding (average area under the curve [AUC] of 0.944, because they are thought to include hidden properties of good ligand-receptor binding. Using the proposed method, we were able to identify novel ligand-GPCR bindings, some of which are supported by several studies.

  18. Predicting Nanocrystal Shape through Consideration of Surface-Ligand Interactions

    KAUST Repository

    Bealing, Clive R.

    2012-03-27

    Density functional calculations for the binding energy of oleic acid-based ligands on Pb-rich {100} and {111} facets of PbSe nanocrystals determine the surface energies as a function of ligand coverage. Oleic acid is expected to bind to the nanocrystal surface in the form of lead oleate. The Wulff construction predicts the thermodynamic equilibrium shape of the PbSe nanocrystals. The equilibrium shape is a function of the ligand surface coverage, which can be controlled by changing the concentration of oleic acid during synthesis. The different binding energy of the ligand on the {100} and {111} facets results in different equilibrium ligand coverages on the facets, and a transition in the equilibrium shape from octahedral to cubic is predicted when increasing the ligand concentration during synthesis. © 2012 American Chemical Society.

  19. The autoxidation activity of new mixed-ligand manganese and iron complexes with tripodal ligands

    NARCIS (Netherlands)

    van Gorkum, R.; Berding, J.; Tooke, D.M.; Spek, A.L.|info:eu-repo/dai/nl/156517566; Reedijk, J.; Bouwman, E.

    2007-01-01

    The activity of new manganese and iron complexes of dianionic tripodal ligands in the autoxidation of ethyl linoleate (EL) is reported. EL consumption rates were monitored using time-resolved FTIR and the degree of oligomerisation was determined by SEC. Almost all complexes showed the same trend in

  20. LASSO-ligand activity by surface similarity order: a new tool for ligand based virtual screening.

    Science.gov (United States)

    Reid, Darryl; Sadjad, Bashir S; Zsoldos, Zsolt; Simon, Aniko

    2008-01-01

    Virtual Ligand Screening (VLS) has become an integral part of the drug discovery process for many pharmaceutical companies. Ligand similarity searches provide a very powerful method of screening large databases of ligands to identify possible hits. If these hits belong to new chemotypes the method is deemed even more successful. eHiTS LASSO uses a new interacting surface point types (ISPT) molecular descriptor that is generated from the 3D structure of the ligand, but unlike most 3D descriptors it is conformation independent. Combined with a neural network machine learning technique, LASSO screens molecular databases at an ultra fast speed of 1 million structures in under 1 min on a standard PC. The results obtained from eHiTS LASSO trained on relatively small training sets of just 2, 4 or 8 actives are presented using the diverse directory of useful decoys (DUD) dataset. It is shown that over a wide range of receptor families, eHiTS LASSO is consistently able to enrich screened databases and provides scaffold hopping ability.