WorldWideScience

Sample records for proximal ligand interactions

  1. RET Recognition of GDNF-GFRα1 Ligand by a Composite Binding Site Promotes Membrane-Proximal Self-Association

    Directory of Open Access Journals (Sweden)

    Kerry M. Goodman

    2014-09-01

    Full Text Available The RET receptor tyrosine kinase is essential to vertebrate development and implicated in multiple human diseases. RET binds a cell surface bipartite ligand comprising a GDNF family ligand and a GFRα coreceptor, resulting in RET transmembrane signaling. We present a hybrid structural model, derived from electron microscopy (EM and low-angle X-ray scattering (SAXS data, of the RET extracellular domain (RETECD, GDNF, and GFRα1 ternary complex, defining the basis for ligand recognition. RETECD envelopes the dimeric ligand complex through a composite binding site comprising four discrete contact sites. The GFRα1-mediated contacts are crucial, particularly close to the invariant RET calcium-binding site, whereas few direct contacts are made by GDNF, explaining how distinct ligand/coreceptor pairs are accommodated. The RETECD cysteine-rich domain (CRD contacts both ligand components and makes homotypic membrane-proximal interactions occluding three different antibody epitopes. Coupling of these CRD-mediated interactions suggests models for ligand-induced RET activation and ligand-independent oncogenic deregulation.

  2. Ligand interactions with galactose oxidase: mechanistic insights.

    Science.gov (United States)

    Whittaker, M M; Whittaker, J W

    1993-01-01

    Interactions between galactose oxidase and small molecules have been explored using a combination of optical absorption, circular dichroism, and electron paramagnetic resonance (EPR) spectroscopies to detect complex formation and characterize the products. Anions bind directly to the cupric center in both active and inactive galactose oxidase, converting to complexes with optical and EPR spectra that are distinctly different from those of the starting aquo enzyme. Azide binding is coupled to stoichiometric proton uptake by the enzyme, reflecting the generation of a strong base (pKa > 9) in the active site anion adduct. At low temperature, the aquo enzyme converts to a form that exhibits the characteristic optical and EPR spectra of an anion complex, apparently reflecting deprotonation of the coordinated water. Anion binding results in a loss of the optical transition arising from coordinated tyrosine, implying displacement of the axial tyrosine ligand on forming the adduct. Nitric oxide binds to galactose oxidase, forming a specific complex exhibiting an unusual EPR spectrum with all g values below 2. The absence of Cu splitting in this spectrum and the observation that the cupric EPR signal from the active site metal ion is not significantly decreased in the complex suggest a nonmetal interaction site for NO in galactose oxidase. These results have been interpreted in terms of a mechanistic scheme where substrate binding displaces a tyrosinate ligand from the active site cupric ion, generating a base that may serve to deprotonate the coordinated hydroxyl group of the substrate, activating it for oxidation. The protein-NO interactions may probe a nonmetal O2 binding site in this enzyme. PMID:8386015

  3. Roles of the proximal heme thiolate ligand in cytochrome p450(cam).

    Science.gov (United States)

    Auclair, K; Moënne-Loccoz, P; Ortiz de Montellano, P R

    2001-05-30

    To examine the roles of the proximal thiolate iron ligand, the C357H mutant of P450(cam) (CYP101) was characterized by resonance Raman, UV, circular dichroism, and activity measurements. The C357H mutant must be reconstituted with hemin for activity to be observed. The reconstituted enzyme is a mixture of high and low spin species. Low temperature (10 degrees C), low enzyme concentration (1 microM), high camphor concentration (1 mM), and 5--50 mM buffer concentrations increase the high to low spin ratio, but under no conditions examined was the protein more than 60% high spin. The C357H mutant has a poorer K(m) for camphor (23 vs 2 microM) and a poorer K(d) for putidaredoxin (50 vs 20 microM) than wild-type P450(cam). The mutant also exhibits a greatly decreased camphor oxidation rate, elevated uncoupling rate, and much greater peroxidase activity. Electron transfer from putidaredoxin to the mutant is much slower than to the wild-type even though redox potential measurements show that the electron transfer remains thermodynamically favored. These experiments confirm that the thiolate ligand facilitates the O--O bond cleavage by P450 enzymes and also demonstrate that this ligand satisfies important roles in protein folding, substrate binding, and electron transfer.

  4. Visualizing cellular interactions with a generalized proximity reporter.

    Science.gov (United States)

    Sellmyer, Mark A; Bronsart, Laura; Imoto, Hiroshi; Contag, Christopher H; Wandless, Thomas J; Prescher, Jennifer A

    2013-05-21

    Interactions among neighboring cells underpin many physiological processes ranging from early development to immune responses. When these interactions do not function properly, numerous pathologies, including infection and cancer, can result. Molecular imaging technologies, especially optical imaging, are uniquely suited to illuminate complex cellular interactions within the context of living tissues in the body. However, no tools yet exist that allow the detection of microscopic events, such as two cells coming into close proximity, on a global, whole-animal scale. We report here a broadly applicable, longitudinal strategy for probing interactions among cells in living subjects. This approach relies on the generation of bioluminescent light when two distinct cell populations come into close proximity, with the intensity of the optical signal correlating with relative cellular location. We demonstrate the ability of this reporter strategy to gauge cell-cell proximity in culture models in vitro and then evaluate this approach for imaging tumor-immune cell interactions using a murine breast cancer model. In these studies, our imaging strategy enabled the facile visualization of features that are otherwise difficult to observe with conventional imaging techniques, including detection of micrometastatic lesions and potential sites of tumor immunosurveillance. This proximity reporter will facilitate probing of numerous types of cell-cell interactions and will stimulate the development of similar techniques to detect rare events and pathological processes in live animals.

  5. 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.

  6. Ligand binding induces a conformational change in ifnar1 that is propagated to its membrane-proximal domain.

    Science.gov (United States)

    Strunk, Jennifer Julia; Gregor, Ingo; Becker, Yvonne; Li, Zongli; Gavutis, Martynas; Jaks, Eva; Lamken, Peter; Walz, Thomas; Enderlein, Jörg; Piehler, Jacob

    2008-03-28

    The type I interferon (IFN) receptor plays a key role in innate immunity against viral and bacterial infections. Here, we show by intramolecular Förster resonance energy transfer spectroscopy that ligand binding induces substantial conformational changes in the ectodomain of ifnar1 (ifnar1-EC). Binding of IFN alpha 2 and IFN beta induce very similar conformations of ifnar1, which were confirmed by single-particle electron microscopy analysis of the ternary complexes formed by IFN alpha 2 or IFN beta with the two receptor subunits ifnar1-EC and ifnar2-EC. Photo-induced electron-transfer-based fluorescence quenching and single-molecule fluorescence lifetime measurements revealed that the ligand-induced conformational change in the membrane-distal domains of ifnar1-EC is propagated to its membrane-proximal domain, which is not involved in ligand recognition but is essential for signal activation. Temperature-dependent ligand binding studies as well as stopped-flow fluorescence experiments corroborated a multistep conformational change in ifnar1 upon ligand binding. Our results thus suggest that the relatively intricate architecture of the type I IFN receptor complex is designed to propagate the ligand binding event to and possibly even across the membrane by conformational changes.

  7. Calreticulin discriminates the proximal region at the N-glycosylation site of Glc1Man9GlcNAc2 ligand

    Energy Technology Data Exchange (ETDEWEB)

    Hirano, Makoto; Adachi, Yuka [Department of Materials and Life Science, Seikei University, 3-3-1 Kichijoji-kita, Musashino, Tokyo 180-8633 (Japan); Ito, Yukishige [Synthetic Cellular Chemistry Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198 (Japan); ERATO, Japan Science and Technology Agency, Ito Glycotrilogy Project, 2-1 Hirosawa, Wako, Saitama 351-0198 (Japan); Totani, Kiichiro, E-mail: ktotani@st.seikei.ac.jp [Department of Materials and Life Science, Seikei University, 3-3-1 Kichijoji-kita, Musashino, Tokyo 180-8633 (Japan)

    2015-10-23

    Calreticulin (CRT) is well known as a lectin-like chaperone that recognizes Glc1Man9GlcNAc2 (G1M9)-glycoproteins in the endoplasmic reticulum (ER). However, whether CRT can directly interact with the aglycone moiety (protein portion) of the glycoprotein remains controversial. To improve our understanding of CRT interactions, structure-defined G1M9-derivatives with different aglycones (–OH, –Gly–NH{sub 2}, and –Gly–Glu–{sup t}Bu) were used as CRT ligands, and their interactions with recombinant CRT were analyzed using thermal shift analysis. The results showed that CRT binds strongly to a G1M9-ligand in the order –Gly–Glu–{sup t}Bu > –Gly–NH{sub 2} > –OH, which is the same as that of the reglucosylation of Man9GlcNAc2 (M9)-derivatives by the folding sensor enzyme UGGT (UDP-glucose: glycoprotein glucosyltransferase). Our results indicate that, similar to UGGT, CRT discriminates the proximal region at the N-glycosylation site, suggesting a similar mechanism mediating the recognition of aglycone moieties in the ER glycoprotein quality control system. - Highlights: • Glc1Man9GlcNAc2 (G1M9) ligands with different aglycones were chemically prepared. • Calreticulin (CRT) discriminates the aglycone of Glc1Man9GlcNAc2 (G1M9) ligand. • CRT binds with G1M9 ligands in a similar manner to folding sensor enzyme.

  8. Structural Analysis of Chemokine Receptor–Ligand Interactions

    Science.gov (United States)

    2017-01-01

    This review focuses on the construction and application of structural chemokine receptor models for the elucidation of molecular determinants of chemokine receptor modulation and the structure-based discovery and design of chemokine receptor ligands. A comparative analysis of ligand binding pockets in chemokine receptors is presented, including a detailed description of the CXCR4, CCR2, CCR5, CCR9, and US28 X-ray structures, and their implication for modeling molecular interactions of chemokine receptors with small-molecule ligands, peptide ligands, and large antibodies and chemokines. These studies demonstrate how the integration of new structural information on chemokine receptors with extensive structure–activity relationship and site-directed mutagenesis data facilitates the prediction of the structure of chemokine receptor–ligand complexes that have not been crystallized. Finally, a review of structure-based ligand discovery and design studies based on chemokine receptor crystal structures and homology models illustrates the possibilities and challenges to find novel ligands for chemokine receptors. PMID:28165741

  9. Modeling of metal interaction geometries for protein-ligand docking.

    Science.gov (United States)

    Seebeck, Birte; Reulecke, Ingo; Kämper, Andreas; Rarey, Matthias

    2008-05-15

    The accurate modeling of metal coordination geometries plays an important role for structure-based drug design applied to metalloenzymes. For the development of a new metal interaction model, we perform a statistical analysis of metal interaction geometries that are relevant to protein-ligand complexes. A total of 43,061 metal sites of the Protein Data Bank (PDB), containing amongst others magnesium, calcium, zinc, iron, manganese, copper, cadmium, cobalt, and nickel, were evaluated according to their metal coordination geometry. Based on statistical analysis, we derived a model for the automatic calculation and definition of metal interaction geometries for the purpose of molecular docking analyses. It includes the identification of the metal-coordinating ligands, the calculation of the coordination geometry and the superposition of ideal polyhedra to identify the optimal positions for free coordination sites. The new interaction model was integrated in the docking software FlexX and evaluated on a data set of 103 metalloprotein-ligand complexes, which were extracted from the PDB. In a first step, the quality of the automatic calculation of the metal coordination geometry was analyzed. In 74% of the cases, the correct prediction of the coordination geometry could be determined on the basis of the protein structure alone. Secondly, the new metal interaction model was tested in terms of predicting protein-ligand complexes. In the majority of test cases, the new interaction model resulted in an improved docking accuracy of the top ranking placements. 2007 Wiley-Liss, Inc.

  10. Metal ligand aromatic cation-pi interactions in metalloproteins: ligands coordinated to metal interact with aromatic residues.

    Science.gov (United States)

    Zarić, S D; Popović, D M; Knapp, E W

    2000-11-03

    Cation-pi interactions between aromatic residues and cationic amino groups in side chains and have been recognized as noncovalent bonding interactions relevant for molecular recognition and for stabilization and definition of the native structure of proteins. We propose a novel type of cation-pi interaction in metalloproteins; namely interaction between ligands coordinated to a metal cation--which gain positive charge from the metal--and aromatic groups in amino acid side chains. Investigation of crystal structures of metalloproteins in the Protein Data Bank (PDB) has revealed that there exist quite a number of metalloproteins in which aromatic rings of phenylalanine, tyrosine, and tryptophan are situated close to a metal center interacting with coordinated ligands. Among these ligands are amino acids such as asparagine, aspartate, glutamate, histidine, and threonine, but also water and substrates like ethanol. These interactions play a role in the stability and conformation of metalloproteins, and in some cases may also be directly involved in the mechanism of enzymatic reactions, which occur at the metal center. For the enzyme superoxide dismutase, we used quantum chemical computation to calculate that Trp163 has an interaction energy of 10.09 kcal mol(-1) with the ligands coordinated to iron.

  11. Ligand-target interactions: what can we learn from NMR?

    Science.gov (United States)

    Carlomagno, Teresa

    2005-01-01

    The conformation of the ligand in complex with a macromolecular target can be studied by nuclear magnetic resonance (NMR) in solution for both tightly and weakly forming complexes. In the weak binding regime (k(off) > 10(4) Hz), the structure of the bound ligand is accessible also for very large complexes (>100 kDa), which are not amenable to NMR studies in the tight binding regime. Here I review the state-of-the-art NMR methodology used for screening ligands and for the structural investigation of bound ligand conformations, in both tight and weak binding regimes. The advantages and disadvantages of each approach are critically described. The NMR methodology used to investigate transiently forming complexes has expanded considerably in the past few years, opening new possibilities for a detailed description of ligand-target interactions. Novel methods for the determination of the bound ligand conformation, in particular transferred cross-correlated relaxation, are thoroughly reviewed, and their advantages with respect to established methodology are discussed, using the epothilone-tubulin complex as a primary example.

  12. Insights into Protein–Ligand Interactions: Mechanisms, Models, and Methods

    Science.gov (United States)

    Du, Xing; Li, Yi; Xia, Yuan-Ling; Ai, Shi-Meng; Liang, Jing; Sang, Peng; Ji, Xing-Lai; Liu, Shu-Qun

    2016-01-01

    Molecular recognition, which is the process of biological macromolecules interacting with each other or various small molecules with a high specificity and affinity to form a specific complex, constitutes the basis of all processes in living organisms. Proteins, an important class of biological macromolecules, realize their functions through binding to themselves or other molecules. A detailed understanding of the protein–ligand interactions is therefore central to understanding biology at the molecular level. Moreover, knowledge of the mechanisms responsible for the protein-ligand recognition and binding will also facilitate the discovery, design, and development of drugs. In the present review, first, the physicochemical mechanisms underlying protein–ligand binding, including the binding kinetics, thermodynamic concepts and relationships, and binding driving forces, are introduced and rationalized. Next, three currently existing protein-ligand binding models—the “lock-and-key”, “induced fit”, and “conformational selection”—are described and their underlying thermodynamic mechanisms are discussed. Finally, the methods available for investigating protein–ligand binding affinity, including experimental and theoretical/computational approaches, are introduced, and their advantages, disadvantages, and challenges are discussed. PMID:26821017

  13. CREDO: a protein-ligand interaction database for drug discovery.

    Science.gov (United States)

    Schreyer, Adrian; Blundell, Tom

    2009-02-01

    Harnessing data from the growing number of protein-ligand complexes in the Protein Data Bank is an important task in drug discovery. In order to benefit from the abundance of three-dimensional structures, structural data must be integrated with sequence as well as chemical data and the protein-small molecule interactions characterized structurally at the inter-atomic level. In this study, we present CREDO, a new publicly available database of protein-ligand interactions, which represents contacts as structural interaction fingerprints, implements novel features and is completely scriptable through its application programming interface. Features of CREDO include implementation of molecular shape descriptors with ultrafast shape recognition, fragmentation of ligands in the Protein Data Bank, sequence-to-structure mapping and the identification of approved drugs. Selected analyses of these key features are presented to highlight a range of potential applications of CREDO. The CREDO dataset has been released into the public domain together with the application programming interface under a Creative Commons license at http://www-cryst.bioc.cam.ac.uk/credo. We believe that the free availability and numerous features of CREDO database will be useful not only for commercial but also for academia-driven drug discovery programmes.

  14. Isothermal titration calorimetry for studying protein-ligand interactions.

    Science.gov (United States)

    Damian, Luminita

    2013-01-01

    Isothermal titration calorimetry (ITC) is a biophysical technique that allows a thermodynamic characterization of an interactive system. It is a free in solution technique that requires no labeling, using heat as signal. ITC allows simultaneous determination of affinity K a, stoichiometry n, enthalpy change ΔH and calculation of free energy change ΔG and entropy change ΔS in one single experiment. It is the only technique that allows direct enthalpy change measurement. By accessing the enthalpy change, we get a step closer in estimating the driving forces that characterize the interaction of a protein with a ligand, information much needed in the drug discovery process.

  15. Probing interaction of a fluorescent ligand with HIV TAR RNA

    Science.gov (United States)

    Qi, Liang; Zhang, Jing; He, Tian; Huo, Yuan; Zhang, Zhi-Qi

    2017-02-01

    Trans-activator of Transcription (Tat) antagonists could block the interaction between Tat protein and its target, trans-activation responsive region (TAR) RNA, to inhibit Tat function and prevent human immunodeficiency virus type 1 (HIV-1) replication. For the first time, a small fluorescence ligand, ICR 191, was found to interact with TAR RNA at the Tat binding site and compete with Tat. It was also observed that the fluorescence of ICR 191 could be quenched when binding to TAR RNA and recovered when discharged via competition with Tat peptide or a well-known Tat inhibitor, neomycin B. The binding parameters of ICR 191 to TAR RNA were determined through theoretical calculations. Mass spectrometry, circular dichroism and molecular docking were used to further confirm the interaction of ICR 191 with TAR RNA. Inspired by these discoveries, a primary fluorescence model for the discovery of Tat antagonists was built using ICR 191 as a fluorescence indicator and the feasibility of this model was evaluated. This ligand-RNA interaction could provide a new strategy for research aimed at discovering Tat antagonists.

  16. Covalent heme attachment to the protein in human heme oxygenase-1 with selenocysteine replacing the His25 proximal iron ligand.

    Science.gov (United States)

    Jiang, Yongying; Trnka, Michael J; Medzihradszky, Katalin F; Ouellet, Hugues; Wang, Yongqiang; Ortiz de Montellano, Paul R

    2009-03-01

    To characterize heme oxygenase with a selenocysteine (SeCys) as the proximal iron ligand, we have expressed truncated human heme oxygenase-1 (hHO-1) His25Cys, in which Cys-25 is the only cysteine, in the Escherichia coli cysteine auxotroph strain BL21(DE3)cys. Selenocysteine incorporation into the protein was demonstrated by both intact protein mass measurement and mass spectrometric identification of the selenocysteine-containing tryptic peptide. One selenocysteine was incorporated into approximately 95% of the expressed protein. Formation of an adduct with Ellman's reagent (DTNB) indicated that the selenocysteine in the expressed protein was in the reduced state. The heme-His25SeCys hHO-1 complex could be prepared by either (a) supplementing the overexpression medium with heme, or (b) reconstituting the purified apoprotein with heme. Under reducing conditions in the presence of imidazole, a covalent bond is formed by addition of the selenocysteine residue to one of the heme vinyl groups. No covalent bond is formed when the heme is replaced by mesoheme, in which the vinyls are replaced by ethyl groups. These results, together with our earlier demonstration that external selenolate ligands can transfer an electron to the iron [Y. Jiang, P.R. Ortiz de Montellano, Inorg. Chem. 47 (2008) 3480-3482 ], indicate that a selenyl radical is formed in the hHO-1 His25SeCys mutant that adds to a heme vinyl group.

  17. Decoding of lipoprotein-receptor interactions: properties of ligand binding modules governing interactions with apolipoprotein E.

    Science.gov (United States)

    Guttman, Miklos; Prieto, J Helena; Croy, Johnny E; Komives, Elizabeth A

    2010-02-16

    Clusters of complement-type ligand binding repeats in the LDL receptor family are thought to mediate the interactions between these receptors and their various ligands. Apolipoprotein E, a key ligand for cholesterol homeostasis, has been shown to interact with LDLR, LRP, and VLDLR, through these clusters. LDLR and VLDLR each contain a single ligand binding repeat cluster, whereas LRP contains three large clusters of ligand binding repeats, each with ligand binding functions. We show that within sLRP3 the three-repeat subcluster CR16-18 recapitulated ligand binding to the isolated receptor binding portion of ApoE (residues 130-149). Binding experiments with LA3-5 of LDLR and CR16-18 showed that a conserved W25/D30 pair appears to be critical for high-affinity binding to ApoE(130-149). The triple repeat LA3-5 showed the expected interaction with ApoE(1-191).DMPC, but surprisingly CR16-18 did not interact with this form of ApoE. To understand these differences in ApoE binding affinity, we introduced mutations of conserved residues from LA5 into CR18 and produced a CR16-18 variant capable of binding ApoE(1-191).DMPC. This change cannot fully be accounted for by the interaction with the proposed ApoE receptor binding region; therefore, we speculate that LA5 is recognizing a distinct epitope on ApoE that may only exist in the lipid-bound form. The combination of avidity effects with this distinct recognition process likely governs the ApoE-LDL receptor interaction.

  18. Affordable dual-sensing proximity sensor for touchless interactive systems

    KAUST Repository

    Nassar, Joanna M.

    2016-09-13

    We report an ultra-low cost flexible proximity sensor using only off-the-shelf recyclable materials such as aluminum foil, napkin and double-sided tape. Unlike previous reports, our device structure exhibits two sensing capabilities in one platform, with outstanding long detection range of 20 cm and pressure sensitivity of 0.05 kPa. This is the first ever demonstration of a low-cost, accessible, and batch manufacturing process for pressure and proximity sensing on a singular platform. The mechanical flexibility of the sensor makes it possible to mount on various irregular platforms, which is vital in many areas, such as robotics, machine automation, vehicular technology and inspection tools.

  19. Measuring RNA-Ligand Interactions with Microscale Thermophoresis.

    Science.gov (United States)

    Moon, Michelle H; Hilimire, Thomas; Sanders, Allix M; Schneekloth, John S

    2018-01-12

    In the past twenty years, there has been a dramatic increase in the study of RNA. RNA has gone from being known as an intermediate in the central dogma of molecular biology to a molecule with a large diversity of structure and function that is involved in all aspects of biology. As new functions are rapidly discovered, it has become clear that there is a need for RNA-targeting small molecule probes to investigate RNA biology and clarify the potential for therapeutics based on RNA/small molecule interactions. While a host of techniques exist to measure small molecule/RNA interactions, many of these have drawbacks that make them intractable for routine use and are often not broadly applicable. A newer technology called microscale thermophoresis (MST), which measures the directed migration of a molecule and/or molecule ligand complex along a temperature gradient, can be used to measure binding affinities using very small amounts of sample, greatly reducing cost of materials. Here, we demonstrate how MST can be used to study a range of RNA interactions, including peptide/RNA interactions, RNA/small molecule interactions, and displacement of an RNA bound peptide by a small molecule.

  20. Treeline proximity alters an alpine plant-herbivore interaction.

    Science.gov (United States)

    Illerbrun, Kurt; Roland, Jens

    2011-05-01

    Rising treeline threatens the size and contiguity of alpine meadows worldwide. As trees encroach into previously open habitat, the movement and population dynamics of above-treeline alpine species may be disrupted. This process is well documented in studies of the Rocky Mountain apollo butterfly (Parnassius smintheus). However, subtler consequences of treeline rise remain poorly understood. In this study, we examine whether treeline proximity affects feeding behaviour of P. smintheus larvae, due to altered habitat affecting the distribution and availability of their host plant, lance-leaved stonecrop (Sedum lanceolatum). Understanding differential larval exploitation of food resources in relation to the treeline is an important step in predicting the consequences of continued treeline rise. Parnassius smintheus larvae feed more intensively on S. lanceolatum away from the treeline despite the relative paucity of hosts in these areas, and despite higher fitness penalties associated with the plant's herbivory-induced chemical defenses. Sedum lanceolatum growing near the treeline is less attractive, and therefore represents a less significant resource for P. smintheus larvae than its abundance might imply. If treeline rise continues, we suggest that this pattern of altered resource exploitation may represent a mechanism by which larvae are adversely affected even while adult movement among and within meadows appears sufficient for maintaining population health, and total host availability seems ample.

  1. Interaction Effect of Season, Habitat and Leaf Age on Proximate ...

    African Journals Online (AJOL)

    Data was subjected to ANOVA and LSD at 0.05% for means separation. The results for interaction effect were all statistically significant (P<0.05) in the leaves of the two Senna species and were influenced variedly by the treatment factors. Specifically, rainy subseason, fadama and upland habitats, young and matured ...

  2. 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.

  3. Research Techniques Made Simple: Emerging Methods to Elucidate Protein Interactions through Spatial Proximity.

    Science.gov (United States)

    Che, Yonglu; Khavari, Paul A

    2017-12-01

    Interactions between proteins are essential for fundamental cellular processes, and the diversity of such interactions enables the vast variety of functions essential for life. A persistent goal in biological research is to develop assays that can faithfully capture different types of protein interactions to allow their study. A major step forward in this direction came with a family of methods that delineates spatial proximity of proteins as an indirect measure of protein-protein interaction. A variety of enzyme- and DNA ligation-based methods measure protein co-localization in space, capturing novel interactions that were previously too transient or low affinity to be identified. Here we review some of the methods that have been successfully used to measure spatially proximal protein-protein interactions. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

  4. Structural basis of ligand interaction with atypical chemokine receptor 3

    Science.gov (United States)

    Gustavsson, Martin; Wang, Liwen; van Gils, Noortje; Stephens, Bryan S.; Zhang, Penglie; Schall, Thomas J.; Yang, Sichun; Abagyan, Ruben; Chance, Mark R.; Kufareva, Irina; Handel, Tracy M.

    2017-01-01

    Chemokines drive cell migration through their interactions with seven-transmembrane (7TM) chemokine receptors on cell surfaces. The atypical chemokine receptor 3 (ACKR3) binds chemokines CXCL11 and CXCL12 and signals exclusively through β-arrestin-mediated pathways, without activating canonical G-protein signalling. This receptor is upregulated in numerous cancers making it a potential drug target. Here we collected over 100 distinct structural probes from radiolytic footprinting, disulfide trapping, and mutagenesis to map the structures of ACKR3:CXCL12 and ACKR3:small-molecule complexes, including dynamic regions that proved unresolvable by X-ray crystallography in homologous receptors. The data are integrated with molecular modelling to produce complete and cohesive experimentally driven models that confirm and expand on the existing knowledge of the architecture of receptor:chemokine and receptor:small-molecule complexes. Additionally, we detected and characterized ligand-induced conformational changes in the transmembrane and intracellular regions of ACKR3 that elucidate fundamental structural elements of agonism in this atypical receptor.

  5. Structural basis of ligand interaction with atypical chemokine receptor 3

    Energy Technology Data Exchange (ETDEWEB)

    Gustavsson, Martin; Wang, Liwen; van Gils, Noortje; Stephens, Bryan S.; Zhang, Penglie; Schall, Thomas J.; Yang, Sichun; Abagyan, Ruben; Chance, Mark R.; Kufareva, Irina; Handel, Tracy M.

    2017-01-18

    Chemokines drive cell migration through their interactions with seven-transmembrane (7TM) chemokine receptors on cell surfaces. The atypical chemokine receptor 3 (ACKR3) binds chemokines CXCL11 and CXCL12 and signals exclusively through β-arrestin-mediated pathways, without activating canonical G-protein signalling. This receptor is upregulated in numerous cancers making it a potential drug target. Here we collected over 100 distinct structural probes from radiolytic footprinting, disulfide trapping, and mutagenesis to map the structures of ACKR3:CXCL12 and ACKR3:small-molecule complexes, including dynamic regions that proved unresolvable by X-ray crystallography in homologous receptors. The data are integrated with molecular modelling to produce complete and cohesive experimentally driven models that confirm and expand on the existing knowledge of the architecture of receptor:chemokine and receptor:small-molecule complexes. Additionally, we detected and characterized ligand-induced conformational changes in the transmembrane and intracellular regions of ACKR3 that elucidate fundamental structural elements of agonism in this atypical receptor.

  6. Thermodynamics and solvent linkage of macromolecule-ligand interactions

    Science.gov (United States)

    Duff, Michael R.; Howell, Elizabeth E.

    2014-01-01

    Binding involves two steps, desolvation and association. While water is ubiquitous and occurs at high concentration, it is typically ignored. In vitro experiments typically use infinite dilution conditions, while in vivo, the concentration of water is decreased due to the presence of high concentrations of molecules in the cellular milieu. This review discusses isothermal titration calorimetry approaches that address the role of water in binding. For example, use of D2O allows the contribution of solvent reorganization to the enthalpy component to be assessed. Further, the addition of osmolytes will decrease the water activity of a solution and allow effects on Ka to be determined. In most cases, binding becomes tighter in the presence of osmolytes as the desolvation penalty associated with binding is minimized. In other cases, the osmolytes prefer to interact with the ligand or protein, and if their removal is more difficult than shedding water, then binding can be weakened. These complicating layers can be discerned by different slopes in ln(Ka) vs osmolality plots and by differential scanning calorimetry in the presence of the osmolyte. PMID:25462561

  7. Effect of ligand substitution on the exchange interactions in {Mn12}-type single-molecule magnets

    OpenAIRE

    Boukhvalov, D. W.; Dobrovitski, V. V.; Kögerler, P.; Al-Saqer, M.; Katsnelson, M. I.; Lichtenstein, A. I.; Harmon, B. N.

    2010-01-01

    We investigate how the ligand substitution affects the intra-molecular spin exchange interactions, studying a prototypal family of single-molecule magnets comprising dodecanuclear cluster molecules [Mn12O12(COOR)16]. We identify a simple scheme based on accumulated Pauling electronegativity numbers (a.e.n.) of the carboxylate ligand groups (R). The redistribution of the electron density, controlled by a.e.n. of a ligand, changes the degree of hybridization between 3d electrons of manganese an...

  8. NMR Studies of Protein Hydration and Protein-Ligand Interactions

    Science.gov (United States)

    Chong, Yuan

    Water on the surface of a protein is called hydration water. Hydration water is known to play a crucial role in a variety of biological processes including protein folding, enzymatic activation, and drug binding. Although the significance of hydration water has been recognized, the underlying mechanism remains far from being understood. This dissertation employs a unique in-situ nuclear magnetic resonance (NMR) technique to study the mechanism of protein hydration and the role of hydration in alcohol-protein interactions. Water isotherms in proteins are measured at different temperatures via the in-situ NMR technique. Water is found to interact differently with hydrophilic and hydrophobic groups on the protein. Water adsorption on hydrophilic groups is hardly affected by the temperature, while water adsorption on hydrophobic groups strongly depends on the temperature around 10 C, below which the adsorption is substantially reduced. This effect is induced by the dramatic decrease in the protein flexibility below 10 C. Furthermore, nanosecond to microsecond protein dynamics and the free energy, enthalpy, and entropy of protein hydration are studied as a function of hydration level and temperature. A crossover at 10 C in protein dynamics and thermodynamics is revealed. The effect of water at hydrophilic groups on protein dynamics and thermodynamics shows little temperature dependence, whereas water at hydrophobic groups has stronger effect above 10 C. In addition, I investigate the role of water in alcohol binding to the protein using the in-situ NMR detection. The isotherms of alcohols are first measured on dry proteins, then on proteins with a series of controlled hydration levels. The free energy, enthalpy, and entropy of alcohol binding are also determined. Two distinct types of alcohol binding are identified. On the one hand, alcohols can directly bind to a few specific sites on the protein. This type of binding is independent of temperature and can be

  9. Glucagon-like peptide-1 receptor ligand interactions: structural cross talk between ligands and the extracellular domain.

    Directory of Open Access Journals (Sweden)

    Graham M West

    Full Text Available Activation of the glucagon-like peptide-1 receptor (GLP-1R in pancreatic β-cells potentiates insulin production and is a current therapeutic target for the treatment of type 2 diabetes mellitus (T2DM. Like other class B G protein-coupled receptors (GPCRs, the GLP-1R contains an N-terminal extracellular ligand binding domain. N-terminal truncations on the peptide agonist generate antagonists capable of binding to the extracellular domain, but not capable of activating full length receptor. The main objective of this study was to use Hydrogen/deuterium exchange (HDX to identify how the amide hydrogen bonding network of peptide ligands and the extracellular domain of GLP-1R (nGLP-1R were altered by binding interactions and to then use this platform to validate direct binding events for putative GLP-1R small molecule ligands. The HDX studies presented here for two glucagon-like peptide-1 receptor (GLP-1R peptide ligands indicates that the antagonist exendin-4[9-39] is significantly destabilized in the presence of nonionic detergents as compared to the agonist exendin-4. Furthermore, HDX can detect stabilization of exendin-4 and exendin-4[9-39] hydrogen bonding networks at the N-terminal helix [Val19 to Lys27] upon binding to the N-terminal extracellular domain of GLP-1R (nGLP-1R. In addition we show hydrogen bonding network stabilization on nGLP-1R in response to ligand binding, and validate direct binding events with the extracellular domain of the receptor for putative GLP-1R small molecule ligands.

  10. Targeting Protein-Protein Interactions with Trimeric Ligands: High Affinity Inhibitors of the MAGUK Protein Family

    DEFF Research Database (Denmark)

    Nissen, Klaus B; Kedström, Linda Maria Haugaard; Wilbek, Theis S

    2015-01-01

    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...

  11. Controlling Nanocrystal Superlattice Symmetry and Shape-Anisotropic Interactions through Variable Ligand Surface Coverage

    KAUST Repository

    Choi, Joshua J.

    2011-03-09

    The assembly of colloidal nanocrystals (NCs) into superstructures with long-range translational and orientational order is sensitive to the molecular interactions between ligands bound to the NC surface. We illustrate how ligand coverage on colloidal PbS NCs can be exploited as a tunable parameter to direct the self-assembly of superlattices with predefined symmetry. We show that PbS NCs with dense ligand coverage assemble into face-centered cubic (fcc) superlattices whereas NCs with sparse ligand coverage assemble into body-centered cubic (bcc) superlattices which also exhibit orientational ordering of NCs in their lattice sites. Surface chemistry characterization combined with density functional theory calculations suggest that the loss of ligands occurs preferentially on {100} than on reconstructed {111} NC facets. The resulting anisotropic ligand distribution amplifies the role of NC shape in the assembly and leads to the formation of superlattices with translational and orientational order. © 2011 American Chemical Society.

  12. Synchronization of proximal intratubular pressure oscillations: evidence for interaction between nephrons

    DEFF Research Database (Denmark)

    Holstein-Rathlou, N H

    1987-01-01

    the greater homogeneity in frequency in group A. Furthermore, nephrons having synchronized pressure oscillations were found to interact with each other. Thus, perturbation of the proximal tubular pressure oscillations in one nephron by loop microperfusion affected the amplitude of the pressure oscillations...... of synchronized, interacting nephrons could be detected. In group A nephrons, i.e., nephrons with a high probability of having their afferent arterioles arising from the same interlobular artery, 29 out of 33 pairs of nephrons were found to show synchronized pressure oscillations. In group B nephrons...... are synchronized. This synchronization is a result of interaction between the different nephrons.(ABSTRACT TRUNCATED AT 250 WORDS)...

  13. Kinetics and mechanism of interaction of some bioactive ligands ...

    Indian Academy of Sciences (India)

    The association equilibrium constant (KE) for the outer sphere complex formation has been evaluated together with rate constants for the two subsequent steps. The rate constants increase with increasing ligand concentration and the evaluated activation parameters for all reactions suggest an associative substitution ...

  14. 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.

  15. Aromatic interactions at the ligand-protein interface: Implications for the development of docking scoring functions.

    Science.gov (United States)

    Brylinski, Michal

    2018-02-01

    The ability to design and fine-tune non-covalent interactions between organic ligands and proteins is indispensable to rational drug development. Aromatic stacking has long been recognized as one of the key constituents of ligand-protein interfaces. In this communication, we employ a two-parameter geometric model to conduct a large-scale statistical analysis of aromatic contacts in the experimental and computer-generated structures of ligand-protein complexes, considering various combinations of aromatic amino acid residues and ligand rings. The geometry of interfacial π-π stacking in crystal structures accords with experimental and theoretical data collected for simple systems, such as the benzene dimer. Many contemporary ligand docking programs implicitly treat aromatic stacking with van der Waals and Coulombic potentials. Although this approach generally provides a sufficient specificity to model aromatic interactions, the geometry of π-π contacts in high-scoring docking conformations could still be improved. The comprehensive analysis of aromatic geometries at ligand-protein interfaces lies the foundation for the development of type-specific statistical potentials to more accurately describe aromatic interactions in molecular docking. A Perl script to detect and calculate the geometric parameters of aromatic interactions in ligand-protein complexes is available at https://github.com/michal-brylinski/earomatic. The dataset comprising experimental complex structures and computer-generated models is available at https://osf.io/rztha/. © 2017 John Wiley & Sons A/S.

  16. Antibody-ligand interactions for hydrophobic charge-induction chromatography: a surface plasmon resonance study.

    Science.gov (United States)

    Cheng, Fang; Li, Ming-Yang; Wang, Han-Qi; Lin, Dong-Qiang; Qu, Jing-Ping

    2015-03-24

    This article describes the use of surface plasmon resonance (SPR) spectroscopy to study antibody-ligand interactions for hydrophobic charge-induction chromatography (HCIC) and its versatility in investigating the surface and solution factors affecting the interactions. Two density model surfaces presenting the HCIC ligand (mercapto-ethyl-pyridine, MEP) were prepared on Au using a self-assembly technique. The surface chemistry and structure, ionization, and protein binding of such model surfaces were characterized by X-ray photoelectron spectroscopy (XPS), near-edge X-ray absorption fine structure (NEXAFS), contact-angle titration, and SPR, respectively. The influences of the surface and solution factors, e.g., ligand density, salt concentration, and solution pH, on protein adsorption were determined by SPR. Our results showed that ligand density affects both equilibrium and dynamic aspects of the interactions. Specifically, a dense ligand leads to an increase in binding strength, rapid adsorption, slow desorption, and low specificity. In addition, both hydrophobic interactions and hydrogen bonding contribute significantly to the protein adsorption at neutral pH, while the electrostatic repulsion is overwhelmed under acidic conditions. The hydrophobic interaction at a high concentration of lyotropic salt would cause drastic conformational changes in the adsorbed protein. Combined with the self-assembly technique, SPR proves to be a powerful tool for studying the interactions between an antibody and a chromatographic ligand.

  17. Effective interactions in a graphene layer induced by the proximity to a ferromagnet

    Science.gov (United States)

    Tiến Phong, Võ; Walet, Niels R.; Guinea, Francisco

    2018-01-01

    The nature of the induced couplings in graphene due its proximity to a ferromagnetic insulator is analysed. We combine general symmetry principles and simple tight-binding descriptions to study different orientations of the magnetization. We find that, in addition to a simple exchange field, a number of other terms arise. Some of these terms act as magnetic orbital couplings, and others are proximity-induced spin–orbit interactions. We find different sets of couplings depending on the orientation of the magnetization. Typically, the magnitudes of all the studied couplings are similar, and the individual strengths are very sensitive to the details of the structure. Depending on these values, we show that a variety of phases, including anomalous Hall effect regimes, are possible.

  18. Proximity Labeling of Interacting Proteins: Application of BioID as a Discovery Tool.

    Science.gov (United States)

    Li, Peipei; Li, Jingjing; Wang, Li; Di, Li-Jun

    2017-10-01

    Proteins perform biochemical functions by forming complexes, or protein-protein interactions (PPIs). Many different approaches such as phage display, yeast hybridization, etc. were developed to illustrate the PPIs, and disclose the composition and organization of protein complexes. However, none of these approaches are based on the real-time and in vivo PPI analysis. Proximity-dependent labeling (PDL) of interacting proteins has recently been proposed by taking advantage of several enzymes, which are capable of attaching the known reactive groups to the nearby proteins covalently. Among the PDL methods, BioID is the earliest and the most widely used one and has been upgraded from its prototype, making it an extremely convenient research tool. In this review, we describe the BioID technology development, its potential applications according to the nature of the target protein, and some recent efforts to circumvent the technical limitations. Moreover, some comparable PDL methods are introduced, including selective proteomic proximity labeling assay using tyramide, enzyme-mediated activation of radical sources, Proximity Labeling with Ascorbate Peroxidase, in vivo proximal labeling, etc., and we propose that systematic comparison of the working radius of these methods may be helpful to develop a tool box, from which the right method can be selected for a given target protein for PPI research. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  19. Interaction of calreticulin with CD40 ligand, TRAIL and Fas ligand

    DEFF Research Database (Denmark)

    Duus, K; Pagh, R T; Holmskov, U

    2007-01-01

    found to bind calreticulin strongly. A low level or no binding was observed for adiponectin, tumour necrosis factor-alpha (TNF-alpha), CD30L, surfactant protein-A and -D and collagen VIII. The interaction with calreticulin required a conformational change in CD40L, TRAIL and FasL and showed the same...

  20. Atomic force microscopy: a multifaceted tool to study membrane proteins and their interactions with ligands.

    Science.gov (United States)

    Whited, Allison M; Park, Paul S-H

    2014-01-01

    Membrane proteins are embedded in lipid bilayers and facilitate the communication between the external environment and the interior of the cell. This communication is often mediated by the binding of ligands to the membrane protein. Understanding the nature of the interaction between a ligand and a membrane protein is required to both understand the mechanism of action of these proteins and for the development of novel pharmacological drugs. The highly hydrophobic nature of membrane proteins and the requirement of a lipid bilayer for native function have hampered the structural and molecular characterizations of these proteins under physiologically relevant conditions. Atomic force microscopy offers a solution to studying membrane proteins and their interactions with ligands under physiologically relevant conditions and can provide novel insights about the nature of these critical molecular interactions that facilitate cellular communication. In this review, we provide an overview of the atomic force microscopy technique and discuss its application in the study of a variety of questions related to the interaction between a membrane protein and a ligand. This article is part of a Special Issue entitled: Structural and biophysical characterization of membrane protein-ligand binding. Copyright © 2013 Elsevier B.V. All rights reserved.

  1. 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.

  2. Synergistic Regulation of Coregulator/Nuclear Receptor Interaction by Ligand and DNA.

    Science.gov (United States)

    de Vera, Ian Mitchelle S; Zheng, Jie; Novick, Scott; Shang, Jinsai; Hughes, Travis S; Brust, Richard; Munoz-Tello, Paola; Gardner, William J; Marciano, David P; Kong, Xiangming; Griffin, Patrick R; Kojetin, Douglas J

    2017-10-03

    Nuclear receptor (NR) transcription factors bind various coreceptors, small-molecule ligands, DNA response element sequences, and transcriptional coregulator proteins to affect gene transcription. Small-molecule ligands and DNA are known to influence receptor structure, coregulator protein interaction, and function; however, little is known on the mechanism of synergy between ligand and DNA. Using quantitative biochemical, biophysical, and solution structural methods, including 13C-detected nuclear magnetic resonance and hydrogen/deuterium exchange (HDX) mass spectrometry, we show that ligand and DNA cooperatively recruit the intrinsically disordered steroid receptor coactivator-2 (SRC-2/TIF2/GRIP1/NCoA-2) receptor interaction domain to peroxisome proliferator-activated receptor gamma-retinoid X receptor alpha (PPARγ-RXRα) heterodimer and reveal the binding determinants of the complex. Our data reveal a thermodynamic mechanism by which DNA binding propagates a conformational change in PPARγ-RXRα, stabilizes the receptor ligand binding domain dimer interface, and impacts ligand potency and cooperativity in NR coactivator recruitment. Copyright © 2017 Elsevier Ltd. All rights reserved.

  3. Longitudinal effects of contextual and proximal factors on mother-infant interactions among Brazilian adolescent mothers.

    Science.gov (United States)

    Diniz, Eva; DeSousa, Diogo; Koller, Silvia H; Volling, Brenda L

    2016-05-01

    Adolescent mothers often come from vulnerable backgrounds which might impact the quality of both maternal and infant behavior. Despite the negative impact of adolescent motherhood for maternal and infant behavior, social support may decrease the risks and promote maternal behavior toward the infant. The aim of this study was to investigate longitudinally the effects of proximal (maternal behavior) and distal (mother's perceived social support) variables on infant development in a sample of Brazilian adolescent mothers and their infants. Thirty-nine adolescent mothers (Mage=17.26years; SD=1.71) were observed interacting with their infants at 3 and 6 months postpartum and reported on social support. Results revealed that maternal and infant behavior were associated within and across times. Mothers' perceived social support at 3 months had an indirect effect on infant behavior at 6 months, totally mediated by maternal behavior at 6 months. Our findings revealed the mutual influence between maternal and infant behavior, revealing a proximal process. The results also underscored the importance of the passage of time in the interplay between mother-infant interactions and their developmental context. Copyright © 2016 Elsevier Inc. All rights reserved.

  4. A ligand-reversible dimerization system for controlling protein-protein interactions.

    Science.gov (United States)

    Rollins, C T; Rivera, V M; Woolfson, D N; Keenan, T; Hatada, M; Adams, S E; Andrade, L J; Yaeger, D; van Schravendijk, M R; Holt, D A; Gilman, M; Clackson, T

    2000-06-20

    Chemically induced dimerization provides a general way to gain control over intracellular processes. Typically, FK506-binding protein (FKBP) domains are fused to a signaling domain of interest, allowing crosslinking to be initiated by addition of a bivalent FKBP ligand. In the course of protein engineering studies on human FKBP, we discovered that a single point mutation in the ligand-binding site (Phe-36 --> Met) converts the normally monomeric protein into a ligand-reversible dimer. Two-hybrid, gel filtration, analytical ultracentrifugation, and x-ray crystallographic studies show that the mutant (F(M)) forms discrete homodimers with micromolar affinity that can be completely dissociated within minutes by addition of monomeric synthetic ligands. These unexpected properties form the basis for a "reverse dimerization" regulatory system involving F(M) fusion proteins, in which association is the ground state and addition of ligand abolishes interactions. We have used this strategy to rapidly and reversibly aggregate fusion proteins in different cellular compartments, and to provide an off switch for transcription. Reiterated F(M) domains should be generally useful as conditional aggregation domains (CADs) to control intracellular events where rapid, reversible dissolution of interactions is required. Our results also suggest that dimerization is a latent property of the FKBP fold: the crystal structure reveals a remarkably complementary interaction between the monomer binding sites, with only subtle changes in side-chain disposition accounting for the dramatic change in quaternary structure.

  5. A general and fast scoring function for protein-ligand interactions: a simplified potential approach.

    Science.gov (United States)

    Muegge, I; Martin, Y C

    1999-03-11

    A fast, simplified potential-based approach is presented that estimates the protein-ligand binding affinity based on the given 3D structure of a protein-ligand complex. This general, knowledge-based approach exploits structural information of known protein-ligand complexes extracted from the Brookhaven Protein Data Bank and converts it into distance-dependent Helmholtz free interaction energies of protein-ligand atom pairs (potentials of mean force, PMF). The definition of an appropriate reference state and the introduction of a correction term accounting for the volume taken by the ligand were found to be crucial for deriving the relevant interaction potentials that treat solvation and entropic contributions implicitly. A significant correlation between experimental binding affinities and computed score was found for sets of diverse protein-ligand complexes and for sets of different ligands bound to the same target. For 77 protein-ligand complexes taken from the Brookhaven Protein Data Bank, the calculated score showed a standard deviation from observed binding affinities of 1.8 log Ki units and an R2 value of 0.61. The best results were obtained for the subset of 16 serine protease complexes with a standard deviation of 1.0 log Ki unit and an R2 value of 0.86. A set of 33 inhibitors modeled into a crystal structure of HIV-1 protease yielded a standard deviation of 0.8 log Ki units from measured inhibition constants and an R2 value of 0.74. In contrast to empirical scoring functions that show similar or sometimes better correlation with observed binding affinities, our method does not involve deriving specific parameters that fit the observed binding affinities of protein-ligand complexes of a given training set. We compared the performance of the PMF score, Böhm's score (LUDI), and the SMOG score for eight different test sets of protein-ligand complexes. It was found that for the majority of test sets the PMF score performs best. The strength of the new approach

  6. NMR and computational methods in the structural and dynamic characterization of ligand-receptor interactions.

    Science.gov (United States)

    Ghitti, Michela; Musco, Giovanna; Spitaleri, Andrea

    2014-01-01

    The recurrent failures in drug discovery campaigns, the asymmetry between the enormous financial investments and the relatively scarce results have fostered the development of strategies based on complementary methods. In this context in recent years the rigid lock-and-key binding concept had to be revisited in favour of a dynamic model of molecular recognition accounting for conformational changes of both the ligand and the receptor. The high level of complexity required by a dynamic description of the processes underlying molecular recognition requires a multidisciplinary investigation approach. In this perspective, the combination of nuclear magnetic resonance spectroscopy with molecular docking, conformational searches along with molecular dynamics simulations has given new insights into the dynamic mechanisms governing ligand receptor interactions, thus giving an enormous contribution to the identification and design of new and effective drugs. Herein a succinct overview on the applications of both NMR and computational methods to the structural and dynamic characterization of ligand-receptor interactions will be presented.

  7. NNAlign: a platform to construct and evaluate artificial neural network models of receptor-ligand interactions

    DEFF Research Database (Denmark)

    Nielsen, Morten; Andreatta, Massimo

    2017-01-01

    Peptides are extensively used to characterize functional or (linear) structural aspects of receptor-ligand interactions in biological systems, e.g. SH2, SH3, PDZ peptide-recognition domains, the MHC membrane receptors and enzymes such as kinases and phosphatases. NNAlign is a method for the ident...

  8. Unnatural amino acids as probes of ligand-receptor interactions and their conformational consequences

    DEFF Research Database (Denmark)

    Pless, Stephan Alexander; Ahern, Christopher A

    2013-01-01

    -edge synthetic and chemical biological approaches. Here we summarize recent advances in the use of site-directed incorporation of unnatural amino acids and chemical probes to study ligand-receptor interactions, determine the location of binding sites, and examine the downstream conformational consequences...

  9. A BRET assay for monitoring insulin receptor interactions and ligand pharmacology

    DEFF Research Database (Denmark)

    Kulahin, Nikolaj; Sanni, Samra J; Slaaby, Rita

    2012-01-01

    homology-2-containing proteins (Src). Here, we applied the bioluminescence resonance energy transfer 2 (BRET2) technique to study the IR signaling pathways. The interaction between the IR and the substrates IRS1, IRS4 and Shc was examined in response to ligands with different signaling properties...

  10. Interpolation method for accurate affinity ranking of arrayed ligand analyte interactions

    NARCIS (Netherlands)

    Schasfoort, Richardus B.M.; Andree, Kiki Carlijn; van der Velde, N.; van der Kooi, A.; Stojanovic, Ivan; Terstappen, Leonardus Wendelinus Mathias Marie

    2016-01-01

    The values of the affinity constants (kd, ka, and KD) that are determined by label-free interaction analysis methods are affected by the ligand density. This article outlines a surface plasmon resonance (SPR) imaging method that yields high-throughput globally fitted affinity ranking values using a

  11. Characterization of mRNA-Cytoskeleton Interactions In Situ Using FMTRIP and Proximity Ligation

    Science.gov (United States)

    Jung, Jeenah; Lifland, Aaron W.; Alonas, Eric J.; Zurla, Chiara; Santangelo, Philip J.

    2013-01-01

    Many studies have demonstrated an association between the cytoskeleton and mRNA, as well as the asymmetric distribution of mRNA granules within the cell in response to various signaling events. It is likely that the extensive cytoskeletal network directs mRNA transport and localization, with different cytoskeletal elements having their own specific roles. In order to understand the spatiotemporal changes in the interactions between the mRNA and the cytoskeleton as a response to a stimulus, a technique that can visualize and quantify these changes across a population of cells while capturing cell-to-cell variations is required. Here, we demonstrate a method for imaging and quantifying mRNA-cytoskeleton interactions on a per cell basis with single-interaction sensitivity. Using a proximity ligation assay with flag-tagged multiply-labeled tetravalent RNA imaging probes (FMTRIP), we quantified interactions between mRNAs and β-tubulin, vimentin, or filamentous actin (F-actin) for two different mRNAs, poly(A) + and β-actin mRNA, in two different cell types, A549 cells and human dermal fibroblasts (HDF). We found that the mRNAs interacted predominantly with F-actin (>50% in HDF, >20% in A549 cells), compared to β-tubulin (cytoskeleton itself and mRNA localization. Both perturbations led to a decrease in poly(A) + mRNA interactions with F-actin and an increase in the interactions with microtubules, in a time dependent manner. PMID:24040294

  12. 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...

  13. Immunophilins interact with calcineurin in the absence of exogenous immunosuppressive ligands.

    Science.gov (United States)

    Cardenas, M E; Hemenway, C; Muir, R S; Ye, R; Fiorentino, D; Heitman, J

    1994-01-01

    The peptidyl-prolyl isomerases FKBP12 and cyclophilin A (immunophilins) form complexes with the immunosuppressants FK506 and cyclosporin A that inhibit the phosphatase calcineurin. With the yeast two hybrid system, we detect complexes between FKBP12 and the calcineurin A catalytic subunit in both the presence and absence of FK506. Mutations in FKBP12 surface residues or the absence of the calcineurin B regulatory subunit perturb the FK506-dependent, but not the ligand-independent, FKBP12-calcineurin complex. By affinity chromatography, both FKBP12 and cyclophilin A bind calcineurin A in the absence of ligand, and FK506 and cyclosporin A respectively potentiate these interactions. Both in vivo and in vitro, the peptidyl-prolyl isomerase active sites are dispensable for ligand-independent immunophilin-calcineurin complexes. Lastly, by genetic analyses we demonstrate that FKBP12 modulates calcineurin functions in vivo. These findings reveal that immunophilins interact with calcineurin in the absence of exogenous ligands and suggest that immunosuppressants may take advantage of the inherent ability of immunophilins to interact with calcineurin. Images PMID:7529175

  14. An interaction-motif-based scoring function for protein-ligand docking

    Directory of Open Access Journals (Sweden)

    Xie Zhong-Ru

    2010-06-01

    Full Text Available Abstract Background A good scoring function is essential for molecular docking computations. In conventional scoring functions, energy terms modeling pairwise interactions are cumulatively summed, and the best docking solution is selected. Here, we propose to transform protein-ligand interactions into three-dimensional geometric networks, from which recurring network substructures, or network motifs, are selected and used to provide probability-ranked interaction templates with which to score docking solutions. Results A novel scoring function for protein-ligand docking, MotifScore, was developed. It is non-energy-based, and docking is, instead, scored by counting the occurrences of motifs of protein-ligand interaction networks constructed using structures of protein-ligand complexes. MotifScore has been tested on a benchmark set established by others to assess its ability to identify near-native complex conformations among a set of decoys. In this benchmark test, 84% of the highest-scored docking conformations had root-mean-square deviations (rmsds below 2.0 Å from the native conformation, which is comparable with the best of several energy-based docking scoring functions. Many of the top motifs, which comprise a multitude of chemical groups that interact simultaneously and make a highly significant contribution to MotifScore, capture recurrent interacting patterns beyond pairwise interactions. Conclusions While providing quite good docking scores, MotifScore is quite different from conventional energy-based functions. MotifScore thus represents a new, network-based approach for exploring problems associated with molecular docking.

  15. Influence of Alkylammonium Acetate Buffers on Protein-Ligand Noncovalent Interactions Using Native Mass Spectrometry

    Science.gov (United States)

    Zhuang, Xiaoyu; Gavriilidou, Agni F. M.; Zenobi, Renato

    2017-02-01

    We investigate the influence of three volatile alkylammonium acetate buffers on binding affinities for protein-ligand interactions determined by native electrospray ionization-mass spectrometry (ESI-MS). Four different types of proteins were chosen for this study. A charge-reduction effect was observed for all the cases studied, in comparison to the ions formed in ammonium acetate solution. When increasing the collision energy, the complexes of trypsin and the ligand were found to be more stable when sprayed from alkylammonium acetate buffers than from ammonium acetate. The determined dissociation constant (Kd) also exhibited a drop (up to 40%) when ammonium acetate was replaced by alkylammonium acetate buffers for the case of lysozyme and the ligand. The prospective uses of these ammonium acetate analogs in native ESI-MS are discussed in this paper as well.

  16. Combined modeling of cell aggregation and adhesion mediated by receptor–ligand interactions under shear flow

    Directory of Open Access Journals (Sweden)

    Yu Du

    2015-11-01

    Full Text Available Blood cell aggregation and adhesion to endothelial cells under shear flow are crucial to many biological processes such as thrombi formation, inflammatory cascade, and tumor metastasis, in which these cellular interactions are mainly mediated by the underlying receptor–ligand bindings. While theoretical modeling of aggregation dynamics and adhesion kinetics of interacting cells have been well studied separately, how to couple these two processes remains unclear. Here we develop a combined model that couples cellular aggregation dynamics and adhesion kinetics under shear flow. The impacts of shear rate (or shear stress and molecular binding affinity were elucidated. This study provides a unified model where the action of a fluid flow drives cell aggregation and adhesion under the modulations of the mechanical shear flow and receptor–ligand interaction kinetics. It offers an insight into understanding the relevant biological processes and functions.

  17. Knowledge-based scoring function to predict protein-ligand interactions.

    Science.gov (United States)

    Gohlke, H; Hendlich, M; Klebe, G

    2000-01-14

    The development and validation of a new knowledge-based scoring function (DrugScore) to describe the binding geometry of ligands in proteins is presented. It discriminates efficiently between well-docked ligand binding modes (root-mean-square deviation Definition of an appropriate reference state and accounting for inaccuracies inherently present in experimental data is required to achieve good predictive power. The sum of the pair preferences and the singlet preferences is calculated based on the 3D structure of protein-ligand binding modes generated by docking tools. For two test sets of 91 and 68 protein-ligand complexes, taken from the Protein Data Bank (PDB), the calculated score recognizes poses generated by FlexX deviating <2 A from the crystal structure on rank 1 in three quarters of all possible cases. Compared to FlexX, this is a substantial improvement. For ligand geometries generated by DOCK, DrugScore is superior to the "chemical scoring" implemented into this tool, while comparable results are obtained using the "energy scoring" in DOCK. None of the presently known scoring functions achieves comparable power to extract binding modes in agreement with experiment. It is fast to compute, regards implicitly solvation and entropy contributions and produces correctly the geometry of directional interactions. Small deviations in the 3D structure are tolerated and, since only contacts to non-hydrogen atoms are regarded, it is independent from assumptions of protonation states. Copyright 2000 Academic Press.

  18. Multivalent ligand-receptor-mediated interaction of small filled vesicles with a cellular membrane

    Science.gov (United States)

    Zhdanov, Vladimir P.

    2017-07-01

    The ligand-receptor-mediated contacts of small sub-100-nm-sized lipid vesicles (or nanoparticles) with the cellular membrane are of interest in the contexts of cell-to-cell communication, endocytosis of membrane-coated virions, and drug (RNA) delivery. In all these cases, the interior of vesicles is filled by biologically relevant content. Despite the diversity of such systems, the corresponding ligand-receptor interaction possesses universal features. One of them is that the vesicle-membrane contacts can be accompanied by the redistribution of ligands and receptors between the contact and contact-free regions. In particular, the concentrations of ligands and receptors may become appreciably higher in the contact regions and their composition may there be different compared to that in the suspended state in the solution. A statistical model presented herein describes the corresponding distribution of various ligands and receptors and allows one to calculate the related change of the free energy with variation of the vesicle-engulfment extent. The results obtained are used to clarify the necessary conditions for the vesicle-assisted pathway of drug delivery.

  19. Quantitation of free energy profiles in RNA–ligand interactions by nucleotide analog interference mapping

    Science.gov (United States)

    COCHRANE, JESSE C.; BATEY, ROBERT T.; STROBEL, SCOTT A.

    2003-01-01

    RNA interactions with protein and small molecule ligands serve a wide variety of biochemical functions in the cell. To best understand the specificity and affinity of these interactions, the free energy contribution made by individual function groups in the RNA must be determined. As an efficient method for obtaining such energetic profiles, we report quantitative nucleotide analog interference mapping (QNAIM). This extension of the NAIM methodology uses the magnitude of analog interference as a function of ligand concentration to calculate binding constants for RNA with individual analog substitutions. In this way, QNAIM not only defines which functional groups are important to an interaction but simultaneously determines the energetic contribution made by each occurrence of that functional group within the RNA polymer. To establish the utility of this approach, QNAIM was used to quantify functional group interactions within the signal recognition particle (SRP), specifically the 4.5S RNA with the M domain of Ffh. In each of the cases in which energetic data were available from previous site-specific substitution analyses, QNAIM provided nearly equivalent results. These experiments on a model system demonstrate that QNAIM is an efficient method to establish a chemically detailed free energy profile for a wide variety of RNA–ligand interactions. PMID:13130142

  20. Fluorinated Carbohydrates as Lectin Ligands: Dissecting Glycan-Cyanovirin Interactions by 19F-NMR

    Science.gov (United States)

    Matei, Elena; André, Sabine; Glinschert, Anja; Infantino, Angela Simona; Oscarson, Stefan; Gabius, Hans-Joachim

    2013-01-01

    NMR spectroscopy and ITC are powerful methods to investigate ligand-protein interactions. Here, we present a versatile and sensitive fluorine NMR approach that exploits the 19F nucleus of 19F labeled carbohydrates as a sensor to study glycan binding to lectins. Our approach is illustrated with the 11 kDa Cyanovirin-N, a mannose binding anti-HIV lectin. Two fluoro-deoxy sugar derivatives, methyl 2-deoxy-2-fluoro-α-D-mannopyranosyl-(1→2)-α-D-mannopyranoside and methyl 2-deoxy-2-fluoro-α-D-mannopyranosyl-(1→2)-α-D-mannopyranosyl-(1→2)-α-D-mannopyranoside were utilized. Binding was studied by 19F-NMR spectroscopy of the ligand and 1H-15N HSQC NMR spectroscopy of the protein. The NMR data agree well with those obtained from the equivalent reciprocal and direct ITC titrations. Our study shows that strategic design of fluorinated ligands and fluorine NMR spectroscopy for ligand screening holds great promise for easy and fast identification of glycan binding as well as for their use in reporting structural and/or electronic perturbations that ensue upon interaction with a cognate lectin. PMID:23447543

  1. The FunFOLD2 server for the prediction of protein–ligand interactions

    Science.gov (United States)

    Roche, Daniel B.; Buenavista, Maria T.; McGuffin, Liam J.

    2013-01-01

    The FunFOLD2 server is a new independent server that integrates our novel protein–ligand binding site and quality assessment protocols for the prediction of protein function (FN) from sequence via structure. Our guiding principles were, first, to provide a simple unified resource to make our function prediction software easily accessible to all via a simple web interface and, second, to produce integrated output for predictions that can be easily interpreted. The server provides a clean web interface so that results can be viewed on a single page and interpreted by non-experts at a glance. The output for the prediction is an image of the top predicted tertiary structure annotated to indicate putative ligand-binding site residues. The results page also includes a list of the most likely binding site residues and the types of predicted ligands and their frequencies in similar structures. The protein–ligand interactions can also be interactively visualized in 3D using the Jmol plug-in. The raw machine readable data are provided for developers, which comply with the Critical Assessment of Techniques for Protein Structure Prediction data standards for FN predictions. The FunFOLD2 webserver is freely available to all at the following web site: http://www.reading.ac.uk/bioinf/FunFOLD/FunFOLD_form_2_0.html. PMID:23761453

  2. Interactions of human hemoglobin with charged ligand-functionalized iron oxide nanoparticles and effect of counterions

    Energy Technology Data Exchange (ETDEWEB)

    Ghosh, Goutam, E-mail: ghoshg@yahoo.com [UGC-DAE Consortium for Scientific Research, Mumbai Centre (India); Panicker, Lata [Bhabha Atomic Research Centre, Solid State Physics Division (India)

    2014-12-15

    Human hemoglobin is an important metalloprotein. It has tetrameric structure with each subunit containing a ‘heme’ group which carries oxygen and carbon dioxide in blood. In this work, we have investigated the interactions of human hemoglobin (Hb) with charged ligand-functionalized iron oxide nanoparticles and the effect of counterions, in aqueous medium. Several techniques like DLS and ζ-potential measurements, UV–vis, fluorescence, and CD spectroscopy have been used to characterize the interaction. The nanoparticle size was measured to be in the range of 20–30 nm. Our results indicated the binding of Hb with both positively as well as negatively charged ligand-functionalized iron oxide nanoparticles in neutral aqueous medium which was driven by the electrostatic and the hydrophobic interactions. The electrostatic binding interaction was not seen in phosphate buffer at pH 7.4. We have also observed that the ‘heme’ groups of Hb remained unaffected on binding with charged nanoparticles, suggesting the utility of the charged ligand-functionalized nanoparticles in biomedical applications.

  3. The Fragment Molecular Orbital Method Reveals New Insight into the Chemical Nature of GPCR-Ligand Interactions.

    Science.gov (United States)

    Heifetz, Alexander; Chudyk, Ewa I; Gleave, Laura; Aldeghi, Matteo; Cherezov, Vadim; Fedorov, Dmitri G; Biggin, Philip C; Bodkin, Mike J

    2016-01-25

    Our interpretation of ligand-protein interactions is often informed by high-resolution structures, which represent the cornerstone of structure-based drug design. However, visual inspection and molecular mechanics approaches cannot explain the full complexity of molecular interactions. Quantum Mechanics approaches are often too computationally expensive, but one method, Fragment Molecular Orbital (FMO), offers an excellent compromise and has the potential to reveal key interactions that would otherwise be hard to detect. To illustrate this, we have applied the FMO method to 18 Class A GPCR-ligand crystal structures, representing different branches of the GPCR genome. Our work reveals key interactions that are often omitted from structure-based descriptions, including hydrophobic interactions, nonclassical hydrogen bonds, and the involvement of backbone atoms. This approach provides a more comprehensive picture of receptor-ligand interactions than is currently used and should prove useful for evaluation of the chemical nature of ligand binding and to support structure-based drug design.

  4. Observation of long-range tertiary interactions during ligand binding by the TPP riboswitch aptamer.

    Science.gov (United States)

    Duesterberg, Van K; Fischer-Hwang, Irena T; Perez, Christian F; Hogan, Daniel W; Block, Steven M

    2015-12-28

    The thiamine pyrophosphate (TPP) riboswitch is a cis-regulatory element in mRNA that modifies gene expression in response to TPP concentration. Its specificity is dependent upon conformational changes that take place within its aptamer domain. Here, the role of tertiary interactions in ligand binding was studied at the single-molecule level by combined force spectroscopy and Förster resonance energy transfer (smFRET), using an optical trap equipped for simultaneous smFRET. The 'Force-FRET' approach directly probes secondary and tertiary structural changes during folding, including events associated with binding. Concurrent transitions observed in smFRET signals and RNA extension revealed differences in helix-arm orientation between two previously-identified ligand-binding states that had been undetectable by spectroscopy alone. Our results show that the weaker binding state is able to bind to TPP, but is unable to form a tertiary docking interaction that completes the binding process. Long-range tertiary interactions stabilize global riboswitch structure and confer increased ligand specificity.

  5. Spatio-temporal Characterization of Ligand-Receptor Interactions in Blood Stem-Cell Rolling

    KAUST Repository

    Al Alwan, Bader

    2017-08-16

    One of the most important issues in the research on hematopoietic stem/progenitor cells (HSPCs) is to understand the mechanism of the homing process of these cells to the bone marrow after being transplanted into patients and establish the production of various blood cell types. The HSPCs first come in contact with the endothelial cells. This contact is known as adhesion and occurs through a multi-step paradigm ending with transmigration to the bone marrow niche. The initial step of the homing, tethering and rolling of HSPCs is mediated by P- and E-Selectins expressed on the endothelial cell surface through their interactions with the ligands expressed by HSPCs. Here we developed a novel experimental method to unravel the molecular mechanisms of the selectin-ligands interactions in vitro at the single molecule level by combining microfluidics and single-molecule fluorescence imaging. Our method enables direct visualization of the nanoscale spatiotemporal dynamics of the E-selectin-ligand (PSGL-1) interactions under conditions of shear stress acting on the cells at the molecular level in real time.

  6. The interactions between lipase and pyridinium ligands investigated by electrochemical and spectrophotometric methods

    Directory of Open Access Journals (Sweden)

    Simona Patriche

    2016-04-01

    Full Text Available The interaction between pyridinium ligands derived from 4,4’-bipyridine (N,N’-bis(p-bromophenacyl-4,4’-bipyridinium dibromide – Lr and (N,N’-bis(p-bromophenacyl-1,2-bis (4-pyridyl ethane dibromide – Lm with lipase enzyme was evaluated. The stability of the pyridinium ligands, having an essential role in biological systems, in 0.1 M KNO3 as supporting electrolyte is influenced by the lipase concentration added. The pH and conductometry measurements in aqueous solution suggest a rapid ionic exchange process. The behavior of pyridinium ligands in the presence of lipase is investigated by cyclic voltammetry and UV/Vis spectroscopy, which indicated bindings and changes from the interaction between them. The voltammograms recorded on the glassy carbon electrode showed a more intense electronic transfer for the Lr interaction with lipase compared to Lm, which is due to the absence of mobile ethylene groups from Lr structure.

  7. Proximal Sensing of Plant-Pathogen Interactions in Spring Barley with Three Fluorescence Techniques

    Directory of Open Access Journals (Sweden)

    Georg Leufen

    2014-06-01

    Full Text Available In the last years fluorescence spectroscopy has come to be viewed as an essential approach in key research fields of applied plant sciences. However, the quantity and particularly the quality of information produced by different equipment might vary considerably. In this study we investigate the potential of three optical devices for the proximal sensing of plant-pathogen interactions in four genotypes of spring barley. For this purpose, the fluorescence lifetime, the image-resolved multispectral fluorescence and selected indices of a portable multiparametric fluorescence device were recorded at 3, 6, and 9 days after inoculation (dai from healthy leaves as well as from leaves inoculated with powdery mildew (Blumeria graminis or leaf rust (Puccinia hordei. Genotype-specific responses to pathogen infections were revealed already at 3 dai by higher fluorescence mean lifetimes in the spectral range from 410 to 560 nm in the less susceptible varieties. Noticeable pathogen-induced modifications were also revealed by the ‘Blue-to-Far-Red Fluorescence Ratio’ and the ‘Simple Fluorescence Ratio’. Particularly in the susceptible varieties the differences became more evident in the time-course of the experiment i.e., following the pathogen development. The relevance of the blue and green fluorescence to exploit the plant-pathogen interaction was demonstrated by the multispectral fluorescence imaging system. As shown, mildewed leaves were characterized by exceptionally high blue fluorescence, contrasting the values observed in rust inoculated leaves. Further, we confirm that the intensity of green fluorescence depends on the pathogen infection and the stage of disease development; this information might allow a differentiation of both diseases. Moreover, our results demonstrate that the detection area might influence the quality of the information, although it had a minor impact only in the current study. Finally, we highlight the relevance of

  8. Phospholemman regulates cardiac Na+/Ca2+ exchanger by interacting with the exchanger's proximal linker domain.

    Science.gov (United States)

    Zhang, Xue-Qian; Wang, Jufang; Carl, Lois L; Song, Jianliang; Ahlers, Belinda A; Cheung, Joseph Y

    2009-04-01

    Phospholemman (PLM) belongs to the FXYD family of small ion transport regulators. When phosphorylated at Ser(68), PLM inhibits cardiac Na(+)/Ca(2+) exchanger (NCX1). We previously demonstrated that the cytoplasmic tail of PLM interacts with the proximal intracellular loop (residues 218-358), but not the transmembrane (residues 1-217 and 765-938) or Ca(2+)-binding (residues 371-508) domains, of NCX1. In this study, we used intact Na(+)/Ca(2+) exchanger with various deletions in the intracellular loop to map the interaction sites with PLM. We first demonstrated by Western blotting and confocal immunofluorescence microscopy that wild-type (WT) NCX1 and its deletion mutants were expressed in transfected HEK-293 cells. Cotransfection with PLM and NCX1 (or its deletion mutants) in HEK-293 cells did not decrease expression of NCX1 (or its deletion mutants). Coexpression of PLM with WT NCX1 inhibited NCX1 current (I(NaCa)). Deletion of residues 240-679, 265-373, 250-300, or 300-373 from WT NCX1 resulted in loss of inhibition of I(NaCa) by PLM. Inhibition of I(NaCa) by PLM was preserved when residues 229-237, 270-300, 328-330, or 330-373 were deleted from the intracellular loop of NCX1. These results suggest that PLM mediated inhibition of I(NaCa) by interacting with two distinct regions (residues 238-270 and 300-328) of NCX1. Indeed, I(NaCa) measured in mutants lacking residues 238-270, 300-328, or 238-270 + 300-328 was not affected by PLM. Glutathione S-transferase pull-down assays confirmed that PLM bound to fragments corresponding to residues 218-371, 218-320, 218-270, 238-371, and 300-373, but not to fragments encompassing residues 250-300 and 371-508 of NCX1, indicating that residues 218-270 and 300-373 physically associated with PLM. Finally, acute regulation of I(NaCa) by PLM phosphorylation observed with WT NCX1 was absent in 250-300 deletion mutant but preserved in 229-237 deletion mutant. We conclude that PLM mediates its inhibition of NCX1 by interacting with

  9. 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.

  10. Interaction of pyrrolobenzodiazepine (PBD) ligands with parallel intermolecular G-quadruplex complex using spectroscopy and ESI-MS

    National Research Council Canada - National Science Library

    Raju, Gajjela; Srinivas, Ragampeta; Reddy, Vangala Santhosh; Idris, Mohammed M; Kamal, Ahmed; Nagesh, Narayana

    2012-01-01

    .... Electrospray ionization mass spectrometry (ESI-MS) and spectroscopic studies in solution were used to evaluate the interaction of PBD and TMPyP4 ligands, stoichiometry and selectivity to G-quadruplex DNA...

  11. Lack of functional selectin ligand interactions compromises long term tumor protection by CD8+ T cells.

    Directory of Open Access Journals (Sweden)

    Felicity C Stark

    Full Text Available Central memory CD8(+ T cells expressing the adhesion molecule CD62L (L-selectin are potent mediators of anti-cancer immunity due to their ability to proliferate extensively upon antigen re-stimulation. The interaction of selectin with its ligands mediates leukocyte rolling along high endothelial venules. Mice deficient in α(1,3 Fucosyltransferase IV and VII (FtDKO lack functional L, P and E selectin ligands. Thus, we addressed whether the lack of selectin ligand interactions alters tumor protection by CD8(+ T cells in FtDKO mice. Listeria monocytogenes-OVA (LM-OVA infection evoked potent OVA-specific CD8(+ T cells that proliferated and contracted at similar kinetics and phenotype in FtDKO and wild-type mice. Additionally, OVA-specific CD8(+ T cells in both mouse strains exhibited similar phenotypic differentiation, in vivo cytolytic activity and IFN-γ expression. However, FtDKO mice succumbed to B16-OVA tumors significantly earlier than wild-type mice. In contrast, FtDKO mice evoked strong recall memory CD8(+ T cell responses and protection to systemic LM-OVA re-challenge. The diminished tumor protection in FtDKO mice was not related to defective antigen presentation by dendritic cells or reduced proliferation of antigen-specific CD8(+ T cells. However, WT or FtDKO OVA-specific CD8(+ T cells showed significantly reduced ability to traffic to lymph nodes upon adoptive transfer into naïve FtDKO recipients. Furthermore, FtDKO OVA-specific CD8(+ T cells displayed poor ability to infiltrate tumors growing in WT mice. These results reveal that selectin ligand expression on host endothelium as well CD8(+ T cells may be important for their efficient and continued extravasation into peripheral tumors.

  12. Descriptor Data Bank (DDB): A Cloud Platform for Multiperspective Modeling of Protein-Ligand Interactions.

    Science.gov (United States)

    Ashtawy, Hossam M; Mahapatra, Nihar R

    2018-01-22

    Protein-ligand (PL) interactions play a key role in many life processes such as molecular recognition, molecular binding, signal transmission, and cell metabolism. Examples of interaction forces include hydrogen bonding, hydrophobic effects, steric clashes, electrostatic contacts, and van der Waals attractions. Currently, a large number of hypotheses and perspectives to model these interaction forces are scattered throughout the literature and largely forgotten. Instead, had they been assembled and utilized collectively, they would have substantially improved the accuracy of predicting binding affinity of protein-ligand complexes. In this work, we present Descriptor Data Bank (DDB), a data-driven platform on the cloud for facilitating multiperspective modeling of PL interactions. DDB is an open-access hub for depositing, hosting, executing, and sharing descriptor extraction tools and data for a large number of interaction modeling hypotheses. The platform also implements a machine-learning (ML) toolbox for automatic descriptor filtering and analysis and scoring function (SF) fitting and prediction. The descriptor filtering module is used to filter out irrelevant and/or noisy descriptors and to produce a compact subset from all available features. We seed DDB with 16 diverse descriptor extraction tools developed in-house and collected from the literature. The tools altogether generate over 2700 descriptors that characterize (i) proteins, (ii) ligands, and (iii) protein-ligand complexes. The in-house descriptors we extract are protein-specific which are based on pairwise primary and tertiary alignment of protein structures followed by clustering and trilateration. We built and used DDB's ML library to fit SFs to the in-house descriptors and those collected from the literature. We then evaluated them on several data sets that were constructed to reflect real-world drug screening scenarios. We found that multiperspective SFs that were constructed using a large number

  13. Predicting Allosteric Effects from Orthosteric Binding in Hsp90-Ligand Interactions: Implications for Fragment-Based Drug Design.

    Directory of Open Access Journals (Sweden)

    Arun Chandramohan

    2016-06-01

    Full Text Available A key question in mapping dynamics of protein-ligand interactions is to distinguish changes at binding sites from those associated with long range conformational changes upon binding at distal sites. This assumes a greater challenge when considering the interactions of low affinity ligands (dissociation constants, KD, in the μM range or lower. Amide hydrogen deuterium Exchange mass spectrometry (HDXMS is a robust method that can provide both structural insights and dynamics information on both high affinity and transient protein-ligand interactions. In this study, an application of HDXMS for probing the dynamics of low affinity ligands to proteins is described using the N-terminal ATPase domain of Hsp90. Comparison of Hsp90 dynamics between high affinity natural inhibitors (KD ~ nM and fragment compounds reveal that HDXMS is highly sensitive in mapping the interactions of both high and low affinity ligands. HDXMS reports on changes that reflect both orthosteric effects and allosteric changes accompanying binding. Orthosteric sites can be identified by overlaying HDXMS onto structural information of protein-ligand complexes. Regions distal to orthosteric sites indicate long range conformational changes with implications for allostery. HDXMS, thus finds powerful utility as a high throughput method for compound library screening to identify binding sites and describe allostery with important implications for fragment-based ligand discovery (FBLD.

  14. Accuracy and precision of protein-ligand interaction kinetics determined from chemical shift titrations.

    Science.gov (United States)

    Markin, Craig J; Spyracopoulos, Leo

    2012-12-01

    NMR-monitored chemical shift titrations for the study of weak protein-ligand interactions represent a rich source of information regarding thermodynamic parameters such as dissociation constants (K ( D )) in the micro- to millimolar range, populations for the free and ligand-bound states, and the kinetics of interconversion between states, which are typically within the fast exchange regime on the NMR timescale. We recently developed two chemical shift titration methods wherein co-variation of the total protein and ligand concentrations gives increased precision for the K ( D ) value of a 1:1 protein-ligand interaction (Markin and Spyracopoulos in J Biomol NMR 53: 125-138, 2012). In this study, we demonstrate that classical line shape analysis applied to a single set of (1)H-(15)N 2D HSQC NMR spectra acquired using precise protein-ligand chemical shift titration methods we developed, produces accurate and precise kinetic parameters such as the off-rate (k ( off )). For experimentally determined kinetics in the fast exchange regime on the NMR timescale, k ( off ) ~ 3,000 s(-1) in this work, the accuracy of classical line shape analysis was determined to be better than 5 % by conducting quantum mechanical NMR simulations of the chemical shift titration methods with the magnetic resonance toolkit GAMMA. Using Monte Carlo simulations, the experimental precision for k ( off ) from line shape analysis of NMR spectra was determined to be 13 %, in agreement with the theoretical precision of 12 % from line shape analysis of the GAMMA simulations in the presence of noise and protein concentration errors. In addition, GAMMA simulations were employed to demonstrate that line shape analysis has the potential to provide reasonably accurate and precise k ( off ) values over a wide range, from 100 to 15,000 s(-1). The validity of line shape analysis for k ( off ) values approaching intermediate exchange (~100 s(-1)), may be facilitated by more accurate K ( D ) measurements

  15. Unconventional interaction forces in protein and protein-ligand systems and their impacts to drug design.

    Science.gov (United States)

    Wang, Qing-Yan; Lu, Jian; Liao, Si-Ming; Du, Qi-Shi; Huang, Ri-Bo

    2013-01-01

    In drug design and enzyme engineering, the information of interactions between receptors and ligands is crucially important. In many cases, the protein structures and drug-target complex structures are determined by a delicate balance of several weak molecular interaction types. Among these interaction forces several unconventional interactions play important roles, however, less familiar for researchers. The cation-π interaction is a unique noncovalent interaction only acting between aromatic amino acids and organic cations (protonated amino acids) and inorganic cations (proton and metallic). This article reports new study results in the interaction strength, the behaviors and the structural characters of cation-π interactions between aromatic amino acids (Phe, Tyr, and Trp) and organic and inorganic cations (Lys(+), Arg(+), H(+), H3O(+), Li(+), Na(+), K(+), Ca(2+), and Zn(2+)) in gas phase and in solutions (water, acetonitrile, and cyclohexane). Systematical research revealed that the cation-π interactions are point-to-plane (aromatic group) interactions, distance and orientationdependent, and the interaction energies change in a broad range. In gas phase the cation-π interaction energies between aromatic amino acids (Phe, Tyr, and Trp) and metallic cations (Li(+), Na(+), K(+), Ca(2+), and Zn(2+)) are in the range -12 to -160 kcal/mol, and the interaction energies of protonated amino acids (Arg(+) and Lys(+)) are in the range from -9 to -18 kcal/mol. In solutions the cation-π energies decrease with the dielectric constant ε of solvents. However, in aqueous solution the cation-π energies of H3O(+) and protonated amino acids are less affected by solvation effects. The applications of unconventional interaction forces in drug design and in protein engineering are introduced.

  16. PL-PatchSurfer: A Novel Molecular Local Surface-Based Method for Exploring Protein-Ligand Interactions

    Directory of Open Access Journals (Sweden)

    Bingjie Hu

    2014-08-01

    Full Text Available Structure-based computational methods have been widely used in exploring protein-ligand interactions, including predicting the binding ligands of a given protein based on their structural complementarity. Compared to other protein and ligand representations, the advantages of a surface representation include reduced sensitivity to subtle changes in the pocket and ligand conformation and fast search speed. Here we developed a novel method named PL-PatchSurfer (Protein-Ligand PatchSurfer. PL-PatchSurfer represents the protein binding pocket and the ligand molecular surface as a combination of segmented surface patches. Each patch is characterized by its geometrical shape and the electrostatic potential, which are represented using the 3D Zernike descriptor (3DZD. We first tested PL-PatchSurfer on binding ligand prediction and found it outperformed the pocket-similarity based ligand prediction program. We then optimized the search algorithm of PL-PatchSurfer using the PDBbind dataset. Finally, we explored the utility of applying PL-PatchSurfer to a larger and more diverse dataset and showed that PL-PatchSurfer was able to provide a high early enrichment for most of the targets. To the best of our knowledge, PL-PatchSurfer is the first surface patch-based method that treats ligand complementarity at protein binding sites. We believe that using a surface patch approach to better understand protein-ligand interactions has the potential to significantly enhance the design of new ligands for a wide array of drug-targets.

  17. Ion-π interactions in ligand design for anions and main group cations.

    Science.gov (United States)

    Watt, Michelle M; Collins, Mary S; Johnson, Darren W

    2013-04-16

    Interactions between ions and aromatic rings are now a mainstay in the field of supramolecular chemistry. The prototypical cation-π interaction, first characterized in the gas phase, is now well-known as an important contributor to protein structure and enzyme function and as a noncovalent force found in many synthetic systems. The complementary "anion-π interaction"-defined as an electrostatic attraction between an anion positioned over the centroid of an aromatic ring-has recently emerged as another reversible ion-π interaction in supramolecular systems. This type of interaction could offer new selectivity in binding poorly basic, strongly solvated anions and may also affect structure, biological function, and anion transport. This Account describes our group's efforts in ion-π interactions in two areas. We first describe a series of self-assembled Group 15 (pnictogen)-thiolate complexes, all featuring prominent cation-π interactions between the trivalent pnictogen and an aromatic ring of the ligand. This structural feature appears to stabilize a variety of self-assembled dinuclear macrocycles, dinuclear M2L3 cryptand-analogues, and a tetranuclear As4L2 metallocyclophane. These complexes are all remarkably robust and feature intramolecular cation-π interactions, which suggest that these interactions could be an important feature in ligand design for the Group 15 elements. We also highlight our efforts to characterize the interaction between anions and electron-deficient aromatic rings in solution. Complementary crystallographic and computational studies suggest that off-center weak-σ interactions play the dominant role in stabilizing the anion-arene adducts unless an acidic CH bond is present to participate in favorable CH···anion hydrogen bonds. In solution the weak-σ complexes show downfield shifts of the proton resonances in their NMR spectra. With more polarizable anions such as bromide and iodide, we also observe anion binding by UV

  18. Predicting Ligand Binding Sites on Protein Surfaces by 3-Dimensional Probability Density Distributions of Interacting Atoms

    Science.gov (United States)

    Jian, Jhih-Wei; Elumalai, Pavadai; Pitti, Thejkiran; Wu, Chih Yuan; Tsai, Keng-Chang; Chang, Jeng-Yih; Peng, Hung-Pin; Yang, An-Suei

    2016-01-01

    Predicting ligand binding sites (LBSs) on protein structures, which are obtained either from experimental or computational methods, is a useful first step in functional annotation or structure-based drug design for the protein structures. In this work, the structure-based machine learning algorithm ISMBLab-LIG was developed to predict LBSs on protein surfaces with input attributes derived from the three-dimensional probability density maps of interacting atoms, which were reconstructed on the query protein surfaces and were relatively insensitive to local conformational variations of the tentative ligand binding sites. The prediction accuracy of the ISMBLab-LIG predictors is comparable to that of the best LBS predictors benchmarked on several well-established testing datasets. More importantly, the ISMBLab-LIG algorithm has substantial tolerance to the prediction uncertainties of computationally derived protein structure models. As such, the method is particularly useful for predicting LBSs not only on experimental protein structures without known LBS templates in the database but also on computationally predicted model protein structures with structural uncertainties in the tentative ligand binding sites. PMID:27513851

  19. 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.

  20. The effect of ligand-ligand interactions on the formation of photoluminescent gold nanoclusters embedded in Au(i)-thiolate supramolecules.

    Science.gov (United States)

    Chang, Hsiang-Yu; Tseng, Yu-Ting; Yuan, Zhiqin; Chou, Hung-Lung; Chen, Ching-Hsiang; Hwang, Bing-Joe; Tsai, Meng-Che; Chang, Huan-Tsung; Huang, Chih-Ching

    2017-05-17

    In this study, we prepared photoluminescent l-cysteine (Cys)-capped gold nanoclusters (Cys-Au NCs) via NaBH4-mediated reduction of aggregated coordination polymers (supramolecules) of -[Cys-Au(i)]n-. The -[Cys-Au(i)]n- supramolecules with interesting chiral properties were formed through simple reactions of chloroauric acid (HAuCl4) with Cys at certain pH values (pH 3-7). The -[Cys-Au(i)]n- polymers could self-assemble into -[Cys-Au(i)]n- supramolecules with irregular morphologies and diameters larger than 500 nm through stacked hydrogen bonding and zwitterionic interactions between Cys ligands and through Au(i)Au(i) aurophilic interactions in solutions with pH values ≤7. The photoluminescent Au NCs (quantum yield = 11.6%) dominated by a Au13 core were embedded in -[Cys-Au(i)]n- supramolecules after NaBH4-mediated reduction. The optical and structural properties of Cys-Au NCs/-[Cys-Au(i)]n- nanocomposites were investigated, revealing that the interaction between Cys ligands plays a critical role in the self-assembly of -[Cys-Au(i)]n- supramolecules and in the formation of photoluminescent Cys-Au NCs embedded in the supramolecules. To further demonstrate that the photoluminescence properties and structures of the nanocomposites are mediated by the intermolecular forces of thiol ligands, other thiol ligands (l-penicillamine, l-homocysteine, 3-mercaptopropionic acid, and l-glutathione) and a ligand-crosslinking agent [bis(sulfosuccinimidyl) suberate; BS3] were used. We concluded that the electrostatic interactions, hydrogen bonding and steric effects dominate the polymer self-assembly into thiol-ligand-Au(i) supramolecules and thus the formation of Au NCs. Our study provides insights into the bottom-up synthesis of photoluminescent Au NCs from thiol-ligand-Au(i) complexes, polymers, and supramolecules. The hybrid Au NCs/-[Cys-Au(i)]n- nanocomposites can potentially be employed as drug carriers and bioimaging agents.

  1. Structure of the Membrane-tethering GRASP Domain Reveals a Unique PDZ Ligand Interaction That Mediates Golgi Biogenesis

    Energy Technology Data Exchange (ETDEWEB)

    Truschel, S.T.; Heroux, A.; Sengupta, D.; Foote, A.; Macbeth, M. R.; Linstedt, A. D.

    2011-06-10

    Biogenesis of the ribbon-like membrane network of the mammalian Golgi requires membrane tethering by the conserved GRASP domain in GRASP65 and GRASP55, yet the tethering mechanism is not fully understood. Here, we report the crystal structure of the GRASP55 GRASP domain, which revealed an unusual arrangement of two tandem PDZ folds that more closely resemble prokaryotic PDZ domains. Biochemical and functional data indicated that the interaction between the ligand-binding pocket of PDZ1 and an internal ligand on PDZ2 mediates the GRASP self-interaction, and structural analyses suggest that this occurs via a unique mode of internal PDZ ligand recognition. Our data uncover the structural basis for ligand specificity and provide insight into the mechanism of GRASP-dependent membrane tethering of analogous Golgi cisternae.

  2. Structure of the Membrane-tethering GRASP Domain Reveals a Unique PDZ Ligand Interaction That Mediates Golgi Biogenesis

    Energy Technology Data Exchange (ETDEWEB)

    S Truschel; D Sengupta; A Foote; A Heroux; M Macbeth; A Linstedt

    2011-12-31

    Biogenesis of the ribbon-like membrane network of the mammalian Golgi requires membrane tethering by the conserved GRASP domain in GRASP65 and GRASP55, yet the tethering mechanism is not fully understood. Here, we report the crystal structure of the GRASP55 GRASP domain, which revealed an unusual arrangement of two tandem PDZ folds that more closely resemble prokaryotic PDZ domains. Biochemical and functional data indicated that the interaction between the ligand-binding pocket of PDZ1 and an internal ligand on PDZ2 mediates the GRASP self-interaction, and structural analyses suggest that this occurs via a unique mode of internal PDZ ligand recognition. Our data uncover the structural basis for ligand specificity and provide insight into the mechanism of GRASP-dependent membrane tethering of analogous Golgi cisternae.

  3. Protein-Ligand Binding Potential of Mean Force Calculations with Hamiltonian Replica Exchange on Alchemical Interaction Grids

    CERN Document Server

    Minh, David D L

    2015-01-01

    A binding potential of mean force (BPMF) is a free energy of noncovalent association in which one binding partner is flexible and the other is rigid. I have developed a method to calculate BPMFs for protein-ligand systems. The method is based on replica exchange sampling from multiple thermodynamic states at different temperatures and protein-ligand interaction strengths. Protein-ligand interactions are represented by interpolating precomputed electrostatic and van der Waals grids. Using a simple estimator for thermodynamic length, thermodynamic states are initialized at approximately equal intervals. The method is demonstrated on the Astex diverse set, a database of 85 protein-ligand complexes relevant to pharmacy or agriculture. Fifteen independent simulations of each complex were started using poses from crystallography, docking, or the lowest-energy pose observed in the other simulations. Benchmark simulations completed within three days on a single processor. Overall, protocols initialized using the ther...

  4. Forging the Basis for Developing Protein-Ligand Interaction Scoring Functions.

    Science.gov (United States)

    Liu, Zhihai; Su, Minyi; Han, Li; Liu, Jie; Yang, Qifan; Li, Yan; Wang, Renxiao

    2017-02-21

    In structure-based drug design, scoring functions are widely used for fast evaluation of protein-ligand interactions. They are often applied in combination with molecular docking and de novo design methods. Since the early 1990s, a whole spectrum of protein-ligand interaction scoring functions have been developed. Regardless of their technical difference, scoring functions all need data sets combining protein-ligand complex structures and binding affinity data for parametrization and validation. However, data sets of this kind used to be rather limited in terms of size and quality. On the other hand, standard metrics for evaluating scoring function used to be ambiguous. Scoring functions are often tested in molecular docking or even virtual screening trials, which do not directly reflect the genuine quality of scoring functions. Collectively, these underlying obstacles have impeded the invention of more advanced scoring functions. In this Account, we describe our long-lasting efforts to overcome these obstacles, which involve two related projects. On the first project, we have created the PDBbind database. It is the first database that systematically annotates the protein-ligand complexes in the Protein Data Bank (PDB) with experimental binding data. This database has been updated annually since its first public release in 2004. The latest release (version 2016) provides binding data for 16 179 biomolecular complexes in PDB. Data sets provided by PDBbind have been applied to many computational and statistical studies on protein-ligand interaction and various subjects. In particular, it has become a major data resource for scoring function development. On the second project, we have established the Comparative Assessment of Scoring Functions (CASF) benchmark for scoring function evaluation. Our key idea is to decouple the "scoring" process from the "sampling" process, so scoring functions can be tested in a relatively pure context to reflect their quality. In our

  5. Interactions between natural organic ligands and trace metals studied by fluorescence lifetime and fluorescence quenching

    Science.gov (United States)

    Nouhi, Ayoub; Hajjoul, Houssam; Redon, Roland; Gagné, Jean-Pierre; Mounier, Stéphane

    2017-04-01

    Improved insight on the interactions between natural organic ligands and trace metals is of paramount importance for better understanding transport and toxicity pathways of metal ions in the environment. Fluorescence spectroscopy allows introspecting ligands-metals interactions. Time-resolved laser fluorescence spectroscopy (TRLFS) measures fluorophore lifetime probing the local molecular environment. Excitation Emission Fluorescence Matrices (EEFMs) and their statistical treatment : parallel factor analysis (PARAFAC) using PROGMEEF Matlab homemade program, can give insight on the number or nature of organic fluorophores involved in the interactions. Quenching of fluorescence by metals can occur following two processes: dynamic and static quenching (Lakowicz, 2013). In the first case, quenching is caused by physical collisions among molecules and in the second case fluorophores can form nonfluorescent complexes with quenchers. It is possible to identify the different mechanisms because each type of quenching corresponds to a different mathematical model (Lakowicz, 2013; Valeur and Berberan-Santos, 2012). In TRLFS, the study of fluorescence decay's laws induced by nanosecond pulsed laser will allow to exactly qualify the type of interaction. The crucial point of the temporal deconvolution will be the evaluation of the best fitting between the different physical models and the decays measured. From the most suitable time decay model, it will be possible to deduce the quenching which modifies the fluorescence. The aim of this study was to characterize interactions between natural organic ligands and trace metals using fluorescence tools to evaluate the fluorescence lifetime of the fluorophore, the occurrence of quenching in presence of metal, discuss its mechanism and estimate conditional stability constants if a complex organic ligand-metal is formed. This study has been done in two steps. First, we have examined the interactions between salicylic acid and copper in

  6. Compact, Polyvalent Mannose Quantum Dots as Sensitive, Ratiometric FRET Probes for Multivalent Protein-Ligand Interactions.

    Science.gov (United States)

    Guo, Yuan; Sakonsinsiri, Chadamas; Nehlmeier, Inga; Fascione, Martin A; Zhang, Haiyan; Wang, Weili; Pöhlmann, Stefan; Turnbull, W Bruce; Zhou, Dejian

    2016-04-04

    A highly efficient cap-exchange approach for preparing compact, dense polyvalent mannose-capped quantum dots (QDs) has been developed. The resulting QDs have been successfully used to probe multivalent interactions of HIV/Ebola receptors DC-SIGN and DC-SIGNR (collectively termed as DC-SIGN/R) using a sensitive, ratiometric Förster resonance energy transfer (FRET) assay. The QD probes specifically bind DC-SIGN, but not its closely related receptor DC-SIGNR, which is further confirmed by its specific blocking of DC-SIGN engagement with the Ebola virus glycoprotein. Tuning the QD surface mannose valency reveals that DC-SIGN binds more efficiently to densely packed mannosides. A FRET-based thermodynamic study reveals that the binding is enthalpy-driven. This work establishes QD FRET as a rapid, sensitive technique for probing structure and thermodynamics of multivalent protein-ligand interactions.

  7. /sup 13/C nuclear magnetic resonance study of the interaction of ligands with arginine residues in dihydrofolate reductase

    Energy Technology Data Exchange (ETDEWEB)

    Cocco, L. (Univ. of Iowa, Iowa City); Blakley, R.L.; Walker, T.E.; London, R.E.

    1977-01-01

    /sup 13/C NMR spectra of Streptococcus faecium dihydrofolate reductase containing (/sup 13/C-guanidino) arginine and ligand complexes with the labeled enzyme are reported. The spectrum of the native enzyme shows 5 well-resolved resonances (the enzyme contains 8 Arg) with a chemical shift range of 1.2 ppM. Addition of ligands to the enzyme produces distinct changes in the enzyme spectrum, and demonstrates that /sup 13/C NMR of labeled protein can be used in studies of protein-ligand interactions. An example of the use of /sup 13/C-depleted material is also presented.

  8. Secondary Interactions Involving Zinc-Bound Ligands: Roles in Structural Stabilization and Macromolecular Interactions

    OpenAIRE

    Namuswe, Frances; Berg, Jeremy M.

    2011-01-01

    A large number of proteins contain bound zinc ions. These zinc ions are frequently coordinated by a combination of histidine and cysteine residues. In addition to atoms that coordinate directly to the zinc ions, these side chains have groups that can donate or accept hydrogen bonds from other groups. These secondary interactions can help stabilize the zinc-binding sites, can contribute to protein folding and stability, and, on occasion, can participate in interactions with other macromolecule...

  9. Modeling multivalent ligand-receptor interactions with steric constraints on configurations of cell surface receptor aggregates

    Energy Technology Data Exchange (ETDEWEB)

    Monine, Michael [Los Alamos National Laboratory; Posner, Richard [TRANSLATION GENOMICS RESAEARCH INSTITUTE; Savage, Paul [BYU; Faeder, James [UNIV OF PITTSBURGH; Hlavacek, William S [UNM

    2008-01-01

    Signal transduction generally involves multivalent protein-protein interactions, which can produce various protein complexes and post-translational modifications. The reaction networks that characterize these interactions tend to be so large as to challenge conventional simulation procedures. To address this challenge, a kinetic Monte Carlo (KMC) method has been developed that can take advantage of a model specification in terms of reaction rules for molecular interactions. A set of rules implicitly defines the reactions that can occur as a result of the interactions represented by the rules. With the rule-based KMC method, explicit generation of the underlying chemical reaction network implied by rules is avoided. Here, we apply and extend this method to characterize the interactions of a trivalent ligand with a bivalent cell-surface receptor. This system is also studied experimentally. We consider the following kinetic models: an equivalent-site model, an extension of this model, which takes into account steric constraints on the configurations of receptor aggregates, and finally, a model that accounts for cyclic receptor aggregates. Simulation results for the equivalent-site model are consistent with an equilibrium continuum model. Using these models, we investigate the effects of steric constraints and the formation of cyclic aggregates on the kinetics and equilibria of small and large aggregate formation and the percolation phase transition that occurs in this system.

  10. Comprehensive Characterization of Minichromosome Maintenance Complex (MCM) Protein Interactions Using Affinity and Proximity Purifications Coupled to Mass Spectrometry.

    Science.gov (United States)

    Dubois, Marie-Line; Bastin, Charlotte; Lévesque, Dominique; Boisvert, François-Michel

    2016-09-02

    The extensive identification of protein-protein interactions under different conditions is an important challenge to understand the cellular functions of proteins. Here we use and compare different approaches including affinity purification and purification by proximity coupled to mass spectrometry to identify protein complexes. We explore the complete interactome of the minichromosome maintenance (MCM) complex by using both approaches for all of the different MCM proteins. Overall, our analysis identified unique and shared interaction partners and proteins enriched for distinct biological processes including DNA replication, DNA repair, and cell cycle regulation. Furthermore, we mapped the changes in protein interactions of the MCM complex in response to DNA damage, identifying a new role for this complex in DNA repair. In summary, we demonstrate the complementarity of these approaches for the characterization of protein interactions within the MCM complex.

  11. The interfacial nature of proximity-induced magnetism and the Dzyaloshinskii-Moriya interaction at the Pt/Co interface.

    Science.gov (United States)

    Rowan-Robinson, R M; Stashkevich, A A; Roussigné, Y; Belmeguenai, M; Chérif, S-M; Thiaville, A; Hase, T P A; Hindmarch, A T; Atkinson, D

    2017-12-04

    The Dzyaloshinskii-Moriya interaction has been shown to stabilise Nèel domain walls in magnetic thin films, allowing high domain wall velocities driven by spin current effects. The interfacial Dzyaloshinskii-Moriya interaction (IDMI) occurs at the interface between ferromagnetic and heavy metal layers with strong spin-orbit coupling, but details of the interaction remain to be understood and the role of proximity induced magnetism (PIM) in the heavy metal is unknown. Here IDMI and PIM are reported in Pt determined as a function of Au and Ir spacer layers in Pt/Co/Au,Ir/Pt. Both interactions are found to be sensitive to sub-nanometre changes in the spacer thickness, correlating over sub-monolayer spacer thicknesses, but not for thicker spacers where IDMI continues to change even after PIM is lost.

  12. Mapping the Conformational Dynamics of E-selectin upon Interaction with its Ligands

    KAUST Repository

    Aleisa, Fajr A

    2013-05-15

    Selectins are key adhesion molecules responsible for initiating a multistep process that leads a cell out of the blood circulation and into a tissue or organ. The adhesion of cells (expressing ligands) to the endothelium (expressing the selectin i.e.,E-selectin) occurs through spatio-temporally regulated interactions that are mediated by multiple intra- and inter-cellular components. The mechanism of cell adhesion is investigated primarily using ensemble-based experiments, which provides indirect information about how individual molecules work in such a complex system. Recent developments in single-molecule (SM) fluorescence detection allow for the visualization of individual molecules with a good spatio-temporal resolution nanometer spatial resolution and millisecond time resolution). Furthermore, advanced SM fluorescence techniques such as Förster Resonance Energy Transfer (FRET) and super-resolution microscopy provide unique opportunities to obtain information about nanometer-scale conformational dynamics of proteins as well as nano-scale architectures of biological samples. Therefore, the state-of-the-art SM techniques are powerful tools for investigating complex biological system such as the mechanism of cell adhesion. In this project, several constructs of fluorescently labeled E-selectin will be used to study the conformational dynamics of E-selectin binding to its ligand(s) using SM-FRET and combination of SM-FRET and force microscopy. These studies will be beneficial to fully understand the mechanistic details of cell adhesion and migration of cells using the established model system of hematopoietic stem cells (HSCs) adhesion to the selectin expressing endothelial cells (such as the E-selectin expressing endothelial cells in the bone marrow).

  13. Frontal affinity chromatography with MS detection of the ligand binding domain of PPARγ receptor: ligand affinity screening and stereoselective ligand-macromolecule interaction.

    Science.gov (United States)

    Calleri, E; Fracchiolla, G; Montanari, R; Pochetti, G; Lavecchia, A; Loiodice, F; Laghezza, A; Piemontese, L; Massolini, G; Temporini, C

    2012-04-06

    In this study we report the development of new chromatographic tools for binding studies based on the gamma isoform ligand binding domain (LBD) of peroxisome proliferator-activated receptor (PPARγ) belonging to the nuclear receptor superfamily of ligand-activated transcription factors. PPARγ subtype plays important roles in the functions of adipocytes, muscles, and macrophages with a direct impact on type 2 diabetes, dyslipidemia, atherosclerosis, and cardiovascular disease. In order to set up a suitable immobilization chemistry, the LBD of PPARγ receptor was first covalently immobilized onto the surface of aminopropyl silica particles to create a PPARγ-Silica column for zonal elution experiments and then onto the surface of open tubular (OT) capillaries to create PPARγ-OT capillaries following different immobilization conditions. The capillaries were used in frontal affinity chromatography coupled to mass spectrometry (FAC-MS) experiments to determine the relative binding affinities of a series of chiral fibrates. The relative affinity orders obtained for these derivatives were consistent with the EC(50) values reported in literature. The optimized PPARγ-OT capillary was validated by determining the K(d) values of two selected compounds. Known the role of stereoselectivity in the binding of chiral fibrates, for the first time a detailed study was carried out by analysing two enantioselective couples on the LBD-PPARγ capillary by FAC and a characteristic two-stairs frontal profile was derived as the result of the two saturation events. All the obtained data indicate that the immobilized form of PPARγ-LBD retained the ability to specifically bind ligands. Copyright © 2011 Elsevier B.V. All rights reserved.

  14. Metal-Ligand Interactions and Salt Bridges as Sacrificial Bonds in Mussel Byssus-Derived Materials.

    Science.gov (United States)

    Byette, Frédéric; Laventure, Audrey; Marcotte, Isabelle; Pellerin, Christian

    2016-10-10

    The byssus that anchors mussels to solid surfaces is a protein-based material combining strength and toughness as well as a self-healing ability. These exceptional mechanical properties are explained in part by the presence of metal ions forming sacrificial bonds with amino acids. In this study, we show that the properties of hydrogel films prepared from a byssus protein hydrolyzate (BPH) can also be improved following the biomimetic formation of sacrificial bonds. Strengthening and toughening of the materials are both observed when treating films with multivalent ions (Ca2+ or Fe3+) or at the BPH isoelectric point (pI) as a result of the formation of metal-ligand bonds and salt bridges, respectively. These treatments also provide a self-healing behavior to the films during recovery time following a deformation. While pI and Ca2+ treatments have a similar but limited pH-dependent effect, the modulus, strength, and toughness of the films increase largely with Fe3+ concentration and reach much higher values. The affinity of Fe3+ with multiple amino acid ligands, as shown by vibrational spectroscopy, and the more covalent nature of this interaction can explain these observations. Thus, a judicious choice of treatments on polyampholyte protein-based materials enables control of their mechanical performance and self-healing behavior through the strategic exploitation of reversible sacrificial bonds.

  15. Dual ligand/receptor interactions activate urothelial defenses against uropathogenic E. coli.

    Science.gov (United States)

    Liu, Yan; Mémet, Sylvie; Saban, Ricardo; Kong, Xiangpeng; Aprikian, Pavel; Sokurenko, Evgeni; Sun, Tung-Tien; Wu, Xue-Ru

    2015-11-09

    During urinary tract infection (UTI), the second most common bacterial infection, dynamic interactions take place between uropathogenic E. coli (UPEC) and host urothelial cells. While significant strides have been made in the identification of the virulence factors of UPEC, our understanding of how the urothelial cells mobilize innate defenses against the invading UPEC remains rudimentary. Here we show that mouse urothelium responds to the adhesion of type 1-fimbriated UPEC by rapidly activating the canonical NF-κB selectively in terminally differentiated, superficial (umbrella) cells. This activation depends on a dual ligand/receptor system, one between FimH adhesin and uroplakin Ia and another between lipopolysaccharide and Toll-like receptor 4. When activated, all the nuclei (up to 11) of a multinucleated umbrella cell are affected, leading to significant amplification of proinflammatory signals. Intermediate and basal cells of the urothelium undergo NF-κB activation only if the umbrella cells are detached or if the UPEC persistently express type 1-fimbriae. Inhibition of NF-κB prevents the urothelium from clearing the intracellular bacterial communities, leading to prolonged bladder colonization by UPEC. Based on these data, we propose a model of dual ligand/receptor system in innate urothelial defenses against UPEC.

  16. Rapid RNA-ligand interaction analysis through high-information content conformational and stability landscapes

    Energy Technology Data Exchange (ETDEWEB)

    Baird, Nathan J. [National Inst. of Health (NIH), Bethesda, MD (United States); Inglese, James [National Inst. of Health (NIH), Bethesda, MD (United States); Ferré-D’Amaré, Adrian R. [National Inst. of Health (NIH), Bethesda, MD (United States)

    2015-12-07

    The structure and biological properties of RNAs are a function of changing cellular conditions, but comprehensive, simultaneous investigation of the effect of multiple interacting environmental variables is not easily achieved. We have developed an efficient, high-throughput method to characterize RNA structure and thermodynamic stability as a function of multiplexed solution conditions using Förster resonance energy transfer (FRET). In a single FRET experiment using conventional quantitative PCR instrumentation, 19,400 conditions of MgCl2, ligand and temperature are analysed to generate detailed empirical conformational and stability landscapes of the cyclic diguanylate (c-di-GMP) riboswitch. This method allows rapid comparison of RNA structure modulation by cognate and non-cognate ligands. Landscape analysis reveals that kanamycin B stabilizes a non-native, idiosyncratic conformation of the riboswitch that inhibits c-di-GMP binding. Our research demonstrates that allosteric control of folding, rather than direct competition with cognate effectors, is a viable approach for pharmacologically targeting riboswitches and other structured RNA molecules.

  17. Recent Progress in Treating Protein–Ligand Interactions with Quantum-Mechanical Methods

    Directory of Open Access Journals (Sweden)

    Nusret Duygu Yilmazer

    2016-05-01

    Full Text Available We review the first successes and failures of a “new wave” of quantum chemistry-based approaches to the treatment of protein/ligand interactions. These approaches share the use of “enhanced”, dispersion (D, and/or hydrogen-bond (H corrected density functional theory (DFT or semi-empirical quantum mechanical (SQM methods, in combination with ensemble weighting techniques of some form to capture entropic effects. Benchmark and model system calculations in comparison to high-level theoretical as well as experimental references have shown that both DFT-D (dispersion-corrected density functional theory and SQM-DH (dispersion and hydrogen bond-corrected semi-empirical quantum mechanical perform much more accurately than older DFT and SQM approaches and also standard docking methods. In addition, DFT-D might soon become and SQM-DH already is fast enough to compute a large number of binding modes of comparably large protein/ligand complexes, thus allowing for a more accurate assessment of entropic effects.

  18. Global structure-activity relationship model for nonmutagenic carcinogens using virtual ligand-protein interactions as model descriptors.

    Science.gov (United States)

    Cunningham, Albert R; Carrasquer, C Alex; Qamar, Shahid; Maguire, Jon M; Cunningham, Suzanne L; Trent, John O

    2012-10-01

    Structure-activity relationship (SAR) models are powerful tools to investigate the mechanisms of action of chemical carcinogens and to predict the potential carcinogenicity of untested compounds. We describe the use of a traditional fragment-based SAR approach along with a new virtual ligand-protein interaction-based approach for modeling of nonmutagenic carcinogens. The ligand-based SAR models used descriptors derived from computationally calculated ligand-binding affinities for learning set agents to 5495 proteins. Two learning sets were developed. One set was from the Carcinogenic Potency Database, where chemicals tested for rat carcinogenesis along with Salmonella mutagenicity data were provided. The second was from Malacarne et al. who developed a learning set of nonalerting compounds based on rodent cancer bioassay data and Ashby's structural alerts. When the rat cancer models were categorized based on mutagenicity, the traditional fragment model outperformed the ligand-based model. However, when the learning sets were composed solely of nonmutagenic or nonalerting carcinogens and noncarcinogens, the fragment model demonstrated a concordance of near 50%, whereas the ligand-based models demonstrated a concordance of 71% for nonmutagenic carcinogens and 74% for nonalerting carcinogens. Overall, these findings suggest that expert system analysis of virtual chemical protein interactions may be useful for developing predictive SAR models for nonmutagenic carcinogens. Moreover, a more practical approach for developing SAR models for carcinogenesis may include fragment-based models for chemicals testing positive for mutagenicity and ligand-based models for chemicals devoid of DNA reactivity.

  19. Protein-ligand interactions investigated by thermal shift assays (TSA) and dual polarization interferometry (DPI).

    Science.gov (United States)

    Grøftehauge, Morten K; Hajizadeh, Nelly R; Swann, Marcus J; Pohl, Ehmke

    2015-01-01

    Over the last decades, a wide range of biophysical techniques investigating protein-ligand interactions have become indispensable tools to complement high-resolution crystal structure determinations. Current approaches in solution range from high-throughput-capable methods such as thermal shift assays (TSA) to highly accurate techniques including microscale thermophoresis (MST) and isothermal titration calorimetry (ITC) that can provide a full thermodynamic description of binding events. Surface-based methods such as surface plasmon resonance (SPR) and dual polarization interferometry (DPI) allow real-time measurements and can provide kinetic parameters as well as binding constants. DPI provides additional spatial information about the binding event. Here, an account is presented of new developments and recent applications of TSA and DPI connected to crystallography.

  20. Exploring GPCR-Ligand Interactions with the Fragment Molecular Orbital (FMO) Method.

    Science.gov (United States)

    Chudyk, Ewa I; Sarrat, Laurie; Aldeghi, Matteo; Fedorov, Dmitri G; Bodkin, Mike J; James, Tim; Southey, Michelle; Robinson, Roger; Morao, Inaki; Heifetz, Alexander

    2018-01-01

    The understanding of binding interactions between any protein and a small molecule plays a key role in the rationalization of affinity and selectivity. It is essential for an efficient structure-based drug design (SBDD) process. FMO enables ab initio approaches to be applied to systems that conventional quantum-mechanical (QM) methods would find challenging. The key advantage of the Fragment Molecular Orbital Method (FMO) is that it can reveal atomistic details about the individual contributions and chemical nature of each residue and water molecule toward ligand binding which would otherwise be difficult to detect without using QM methods. In this chapter, we demonstrate the typical use of FMO to analyze 19 crystal structures of β1 and β2 adrenergic receptors with their corresponding agonists and antagonists.

  1. Characterization of Monobody Scaffold Interactions with Ligand via Force Spectroscopy and Steered Molecular Dynamics

    Science.gov (United States)

    Cheung, Luthur Siu-Lun; Shea, Daniel J.; Nicholes, Nathan; Date, Amol; Ostermeier, Marc; Konstantopoulos, Konstantinos

    2015-02-01

    Monobodies are antibody alternatives derived from fibronectin that are thermodynamically stable, small in size, and can be produced in bacterial systems. Monobodies have been engineered to bind a wide variety of target proteins with high affinity and specificity. Using alanine-scanning mutagenesis simulations, we identified two scaffold residues that are critical to the binding interaction between the monobody YS1 and its ligand, maltose-binding protein (MBP). Steered molecular dynamics (SMD) simulations predicted that the E47A and R33A mutations in the YS1 scaffold substantially destabilize the YS1-MBP interface by reducing the bond rupture force and the lifetime of single hydrogen bonds. SMD simulations further indicated that the R33A mutation weakens the hydrogen binding between all scaffold residues and MBP and not just between R33 and MBP. We validated the simulation data and characterized the effects of mutations on YS1-MBP binding by using single-molecule force spectroscopy and surface plasmon resonance. We propose that interfacial stability resulting from R33 of YS1 stacking with R344 of MBP synergistically stabilizes both its own bond and the interacting scaffold residues of YS1. Our integrated approach improves our understanding of the monobody scaffold interactions with a target, thus providing guidance for the improved engineering of monobodies.

  2. Multiple receptor-ligand interactions direct tissue resident gamma delta T cell activation

    Directory of Open Access Journals (Sweden)

    Deborah A. Witherden

    2014-11-01

    Full Text Available Gamma delta T cells represent a major T cell population in epithelial tissues, such as skin, intestine, and lung, where they function in maintenance of the epithelium and provide a crucial first line defense against environmental and pathogenic insults. Despite their importance, the molecular mechanisms directing their activation and function have remained elusive. Epithelial resident gamma delta T cells function through constant communication with neighboring cells, either via direct cell-to-cell contact or cell-to-matrix interactions. These intimate relationships allow gamma delta T cells to facilitate the maintenance of epithelial homeostasis, tissue repair following injury, inflammation, and protection from malignancy. Recent studies have identified a number of molecules involved in these complex interactions, under both homeostatic conditions, as well as following perturbation of these barrier tissues. These interactions are crucial to the timely production of cytokines, chemokines, growth factors and extracellular matrix proteins for restoration of homeostasis. In this review, we discuss recent advances in understanding the mechanisms directing epithelial-T cell crosstalk and the distinct roles played by individual receptor-ligand pairs of cell surface molecules in this process.

  3. Surface plasmon resonance spectroscopy for characterisation of membrane protein-ligand interactions and its potential for drug discovery.

    Science.gov (United States)

    Patching, Simon G

    2014-01-01

    Surface plasmon resonance (SPR) spectroscopy is a rapidly developing technique for the study of ligand binding interactions with membrane proteins, which are the major molecular targets for validated drugs and for current and foreseeable drug discovery. SPR is label-free and capable of measuring real-time quantitative binding affinities and kinetics for membrane proteins interacting with ligand molecules using relatively small quantities of materials and has potential to be medium-throughput. The conventional SPR technique requires one binding component to be immobilised on a sensor chip whilst the other binding component in solution is flowed over the sensor surface; a binding interaction is detected using an optical method that measures small changes in refractive index at the sensor surface. This review first describes the basic SPR experiment and the challenges that have to be considered for performing SPR experiments that measure membrane protein-ligand binding interactions, most importantly having the membrane protein in a lipid or detergent environment that retains its native structure and activity. It then describes a wide-range of membrane protein systems for which ligand binding interactions have been characterised using SPR, including the major drug targets G protein-coupled receptors, and how challenges have been overcome for achieving this. Finally it describes some recent advances in SPR-based technology and future potential of the technique to screen ligand binding in the discovery of drugs. This article is part of a Special Issue entitled: Structural and biophysical characterisation of membrane protein-ligand binding. Copyright © 2013 Elsevier B.V. All rights reserved.

  4. In situ proximity ligation assays indicate that hemochromatosis proteins Hfe and transferrin receptor 2 (Tfr2) do not interact.

    Science.gov (United States)

    Rishi, Gautam; Crampton, Emily M; Wallace, Daniel F; Subramaniam, V Nathan

    2013-01-01

    The hemochromatosis associated proteins HFE and Transferrin Receptor 2 (TFR2) have been shown to be important for the proper regulation of hepcidin. A number of in vitro studies using transient overexpression systems have suggested that an interaction between HFE and TFR2 is required for the regulation of hepcidin. This model of iron sensing which centers upon the requirement for an interaction between HFE and TFR2 has recently been questioned with in vivo studies in mice from our laboratory and others which suggest that Hfe and Tfr2 can regulate hepcidin independently of each other. To re-examine the postulated interaction between Hfe and Tfr2 we developed a novel expression system in which both proteins are stably co-expressed and used the proximity ligation assay to examine the interactions between Hfe, Tfr1 and Tfr2 at a cellular level. We were able to detect the previously described interaction between Hfe and Tfr1, and heterodimers between Tfr1 and Tfr2; however no interaction between Hfe and Tfr2 was observed in our system. The results from this study indicate that Hfe and Tfr2 do not interact with each other when they are stably expressed at similar levels. Furthermore, these results support in vivo studies which suggest that Hfe and Tfr2 can independently regulate hepcidin.

  5. In situ proximity ligation assays indicate that hemochromatosis proteins Hfe and transferrin receptor 2 (Tfr2 do not interact.

    Directory of Open Access Journals (Sweden)

    Gautam Rishi

    Full Text Available The hemochromatosis associated proteins HFE and Transferrin Receptor 2 (TFR2 have been shown to be important for the proper regulation of hepcidin. A number of in vitro studies using transient overexpression systems have suggested that an interaction between HFE and TFR2 is required for the regulation of hepcidin. This model of iron sensing which centers upon the requirement for an interaction between HFE and TFR2 has recently been questioned with in vivo studies in mice from our laboratory and others which suggest that Hfe and Tfr2 can regulate hepcidin independently of each other. To re-examine the postulated interaction between Hfe and Tfr2 we developed a novel expression system in which both proteins are stably co-expressed and used the proximity ligation assay to examine the interactions between Hfe, Tfr1 and Tfr2 at a cellular level. We were able to detect the previously described interaction between Hfe and Tfr1, and heterodimers between Tfr1 and Tfr2; however no interaction between Hfe and Tfr2 was observed in our system. The results from this study indicate that Hfe and Tfr2 do not interact with each other when they are stably expressed at similar levels. Furthermore, these results support in vivo studies which suggest that Hfe and Tfr2 can independently regulate hepcidin.

  6. ConsDock: A new program for the consensus analysis of protein-ligand interactions.

    Science.gov (United States)

    Paul, Nicodème; Rognan, Didier

    2002-06-01

    Protein-based virtual screening of chemical libraries is a powerful technique for identifying new molecules that may interact with a macromolecular target of interest. Because of docking and scoring limitations, it is more difficult to apply as a lead optimization method because it requires that the docking/scoring tool is able to propose as few solutions as possible and all of them with a very good accuracy for both the protein-bound orientation and the conformation of the ligand. In the present study, we present a consensus docking approach (ConsDock) that takes advantage of three widely used docking tools (Dock, FlexX, and Gold). The consensus analysis of all possible poses generated by several docking tools is performed sequentially in four steps: (i) hierarchical clustering of all poses generated by a docking tool into families represented by a leader; (ii) definition of all consensus pairs from leaders generated by different docking programs; (iii) clustering of consensus pairs into classes, represented by a mean structure; and (iv) ranking the different means starting from the most populated class of consensus pairs. When applied to a test set of 100 protein-ligand complexes from the Protein Data Bank, ConsDock significantly outperforms single docking with respect to the docking accuracy of the top-ranked pose. In 60% of the cases investigated here, ConsDock was able to rank as top solution a pose within 2 A RMSD of the X-ray structure. It can be applied as a postprocessing filter to either single- or multiple-docking programs to prioritize three-dimensional guided lead optimization from the most likely docking solution. Copyright 2002 Wiley-Liss, Inc.

  7. Revealing the sequence and resulting cellular morphology of receptor-ligand interactions during Plasmodium falciparum invasion of erythrocytes.

    Directory of Open Access Journals (Sweden)

    Greta E Weiss

    2015-02-01

    Full Text Available During blood stage Plasmodium falciparum infection, merozoites invade uninfected erythrocytes via a complex, multistep process involving a series of distinct receptor-ligand binding events. Understanding each element in this process increases the potential to block the parasite's life cycle via drugs or vaccines. To investigate specific receptor-ligand interactions, they were systematically blocked using a combination of genetic deletion, enzymatic receptor cleavage and inhibition of binding via antibodies, peptides and small molecules, and the resulting temporal changes in invasion and morphological effects on erythrocytes were filmed using live cell imaging. Analysis of the videos have shown receptor-ligand interactions occur in the following sequence with the following cellular morphologies; 1 an early heparin-blockable interaction which weakly deforms the erythrocyte, 2 EBA and PfRh ligands which strongly deform the erythrocyte, a process dependant on the merozoite's actin-myosin motor, 3 a PfRh5-basigin binding step which results in a pore or opening between parasite and host through which it appears small molecules and possibly invasion components can flow and 4 an AMA1-RON2 interaction that mediates tight junction formation, which acts as an anchor point for internalization. In addition to enhancing general knowledge of apicomplexan biology, this work provides a rational basis to combine sequentially acting merozoite vaccine candidates in a single multi-receptor-blocking vaccine.

  8. Revealing the Sequence and Resulting Cellular Morphology of Receptor-Ligand Interactions during Plasmodium falciparum Invasion of Erythrocytes

    Science.gov (United States)

    Weiss, Greta E.; Gilson, Paul R.; Taechalertpaisarn, Tana; Tham, Wai-Hong; de Jong, Nienke W. M.; Harvey, Katherine L.; Fowkes, Freya J. I.; Barlow, Paul N.; Rayner, Julian C.; Wright, Gavin J.; Cowman, Alan F.; Crabb, Brendan S.

    2015-01-01

    During blood stage Plasmodium falciparum infection, merozoites invade uninfected erythrocytes via a complex, multistep process involving a series of distinct receptor-ligand binding events. Understanding each element in this process increases the potential to block the parasite’s life cycle via drugs or vaccines. To investigate specific receptor-ligand interactions, they were systematically blocked using a combination of genetic deletion, enzymatic receptor cleavage and inhibition of binding via antibodies, peptides and small molecules, and the resulting temporal changes in invasion and morphological effects on erythrocytes were filmed using live cell imaging. Analysis of the videos have shown receptor-ligand interactions occur in the following sequence with the following cellular morphologies; 1) an early heparin-blockable interaction which weakly deforms the erythrocyte, 2) EBA and PfRh ligands which strongly deform the erythrocyte, a process dependant on the merozoite’s actin-myosin motor, 3) a PfRh5-basigin binding step which results in a pore or opening between parasite and host through which it appears small molecules and possibly invasion components can flow and 4) an AMA1–RON2 interaction that mediates tight junction formation, which acts as an anchor point for internalization. In addition to enhancing general knowledge of apicomplexan biology, this work provides a rational basis to combine sequentially acting merozoite vaccine candidates in a single multi-receptor-blocking vaccine. PMID:25723550

  9. A ligand-reversible dimerization system for controlling protein–protein interactions

    OpenAIRE

    Rollins, Carl T.; Rivera, Victor M.; Woolfson, Derek N.; Keenan, Terence; Hatada, Marcos; Adams, Susan E.; Andrade, Lawrence J.; Yaeger, David; van Schravendijk, Marie Rose; Holt, Dennis A.; Gilman, Michael; Clackson, Tim

    2000-01-01

    Chemically induced dimerization provides a general way to gain control over intracellular processes. Typically, FK506-binding protein (FKBP) domains are fused to a signaling domain of interest, allowing crosslinking to be initiated by addition of a bivalent FKBP ligand. In the course of protein engineering studies on human FKBP, we discovered that a single point mutation in the ligand-binding site (Phe-36 → Met) converts the normally monomeric protein into a ligand-reversible dimer. Two-hybri...

  10. C(X)CR in silico: Computer-aided prediction of chemokine receptor-ligand interactions

    NARCIS (Netherlands)

    Roumen, L.; Scholten, D.J.; de Kruijf, P.; de Esch, I.J.P.; Leurs, R.; de Graaf, C.

    2012-01-01

    This review will focus on the construction, refinement, and validation of chemokine receptor models for the purpose of structure-based virtual screening and ligand design. The review will present a comparative analysis of ligand binding pockets in chemokine receptors, including a review of the

  11. The Role of CD40/CD40 Ligand Interactions in Bone Marrow Granulopoiesis

    Directory of Open Access Journals (Sweden)

    Irene Mavroudi

    2011-01-01

    Full Text Available The CD40 ligand (CD40L and CD40 are two molecules belonging to the TNF/TNF receptor superfamily, and their role in adaptive immune system has widely been explored. However, the wide range of expression of these molecules on hematopoietic as well as nonhematopoietic cells has revealed multiple functions of the CD40/CD40L interactions on different cell types and processes such as granulopoiesis. CD40 triggering on stromal cells has been documented to enhance the expression of granulopoiesis growth factors such as granulocyte-colony-stimulating factor (G-CSF and granulocyte/monocyte-colony-stimulating factor (GM-CSF, and upon disruption of the CD40/CD40L-signaling pathway, as in the case of X-linked hyperimmunoglobulin M (IgM syndrome (XHIGM, it can lead to neutropenia. In chronic idiopathic neutropenia (CIN of adults, however, under the influence of an inflammatory microenvironment, CD40L plays a role in granulocytic progenitor cell depletion, providing thus a pathogenetic cause of CIN.

  12. The Role of CD40/CD40 Ligand Interactions in Bone Marrow Granulopoiesis

    Science.gov (United States)

    Mavroudi, Irene; Papadaki, Helen A.

    2011-01-01

    The CD40 ligand (CD40L) and CD40 are two molecules belonging to the TNF/TNF receptor superfamily, and their role in adaptive immune system has widely been explored. However, the wide range of expression of these molecules on hematopoietic as well as nonhematopoietic cells has revealed multiple functions of the CD40/CD40L interactions on different cell types and processes such as granulopoiesis. CD40 triggering on stromal cells has been documented to enhance the expression of granulopoiesis growth factors such as granulocyte-colony-stimulating factor (G-CSF) and granulocyte/monocyte-colony-stimulating factor (GM-CSF), and upon disruption of the CD40/CD40L-signaling pathway, as in the case of X-linked hyperimmunoglobulin M (IgM) syndrome (XHIGM), it can lead to neutropenia. In chronic idiopathic neutropenia (CIN) of adults, however, under the influence of an inflammatory microenvironment, CD40L plays a role in granulocytic progenitor cell depletion, providing thus a pathogenetic cause of CIN. PMID:22125452

  13. One- and three-dimensional silver(I)-5-sulfosalicylate coordination polymers having ligand-supported and unsupported argentophilic interactions

    Energy Technology Data Exchange (ETDEWEB)

    Arıcı, Mürsel [Department of Chemistry, Faculty of Arts and Sciences, Eskişehir Osmangazi University, 26480 Eskişehir (Turkey); Yeşilel, Okan Zafer, E-mail: yesilel@ogu.edu.tr [Department of Chemistry, Faculty of Arts and Sciences, Eskişehir Osmangazi University, 26480 Eskişehir (Turkey); Yeşilöz, Yeşim [Department of Chemistry, Faculty of Arts and Sciences, Eskişehir Osmangazi University, 26480 Eskişehir (Turkey); Şahin, Onur [Scientific and Technological Research Application and Research Center, Sinop University, 57010 Sinop (Turkey)

    2014-12-15

    Four new coordination polymers, namely, (Hemim·[Ag(Hssa)(H{sub 2}O)]){sub n} (1), ([Ag(ina){sub 2} Ag(Hssa)]·CH{sub 3}OH·H{sub 2}O){sub n} (2), ([Ag{sub 2}(Hssa)(dmp){sub 1.5}]·2H{sub 2}O){sub n} (3) and [Ag{sub 2}(Hssa)(daoc)]{sub n} (4) (Hssa: 5-Sulfosalicylate, emim: 2-ethyl-4-methylimidazole, ina: isonicotinamide, dmp: 2,5-dimethylpyrazine and daoc: 1,8-diaminooctane) were synthesized and characterized by IR spectroscopy, elemental analysis, single crystal X-ray diffraction, powder X-ray diffraction (PXRD) and thermal analysis techniques. Complexes 1 and 2 are one-dimensional (1D) coordination polymers while complexes 3 and 4 are three-dimensional (3D) coordination polymers. Complex 3 consists of three dimensional (3D) 3,3,6-c net with 3,3,6T37 topology. Complex 4 exhibits a 2-fold interpenetrating 3D framework with tfc topology. Complexes 1–4 contain ligand-supported (1–3) and unsupported (4) argentophilic Ag⋯Ag interactions. Photoluminescence spectra of the complexes demonstrate that photoluminescent properties may be attributed to intraligand transition of coordinated Hssa ligand. - Graphical abstract: In this study, four new Ag(I)-coordination polymers with 5-sulfosalicylate and some N-donor ligands were synthesized and characterized. Complexes 1 and 2 are one-dimensional (1D) coordination polymers while complexes 3 and 4 are three-dimensional (3D) coordination polymers. Complex 3 consists of three dimensional (3D) 3,3,6-c net with 3,3,6T37 topology. Complex 4 exhibits a 2-fold interpenetrating 3D framework with tfc topology. The complexes 1–4 contain ligand-supported (1–3) and unsupported (4) argentophilic Ag⋯Ag interactions. Photoluminescence spectra of the complexes demonstrated that photoluminescent properties may be attributed to intraligand transition of coordinated Hssa ligand. - Highlights: • Four novel Ag(I)-coordination polymers with 5-sulfosalicylate and N-donor ligands. • Complexes 1–4 contain ligand-supported (1–3) and

  14. An insight into the ligand-receptor interactions involved in the translocation of pathogens across blood-brain barrier.

    Science.gov (United States)

    Bencurova, Elena; Mlynarcik, Patrik; Bhide, Mangesh

    2011-12-01

    Traversal of pathogen across the blood-brain barrier (BBB) is an essential step for central nervous system (CNS) invasion. Pathogen traversal can occur paracellularly, transcellularly, and/or in infected phagocytes (Trojan horse mechanism). To trigger the translocation processes, mainly through paracellular and transcellular ways, interactions between protein molecules of pathogen and BBB are inevitable. Simply, it takes two to tango: both host receptors and pathogen ligands. Underlying molecular basis of BBB translocation of various pathogens has been revealed in the last decade, and a plethora of experimental data on protein-protein interactions has been created. This review compiles these data and should give insights into the ligand-receptor interactions that occur during BBB translocation. Further, it sheds light on cell signaling events triggered in response to ligand-receptor interaction. Understanding of the molecular principles of pathogen-host interactions that are involved in traversal of the BBB should contribute to develop new vaccine and drug strategies to prevent CNS infections. © 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

  15. Molecular stabilization effects of interactions between anti-metatype antibodies and liganded antibody.

    Science.gov (United States)

    Weidner, K M; Denzin, L K; Voss, E W

    1992-05-25

    Anti-metatype antibodies have been described as antibodies which recognize ligand-induced conformational changes in the antibody variable region. Additionally, anti-metatype antibodies, produced by multiple immunizations with liganded high affinity monoclonal anti-fluorescein antibody 4-4-20, enhanced the lifetime of monoclonal antibody 4-4-20-fluorescein complex. To better understand the mechanism of the delayed dissociation rate, deuterium oxide was used to probe the liganded active site. The rate and extent of deuterium oxide-mediated fluorescence enhancement of bound ligand served to monitor the conformational dynamics of the active site in the presence and absence of anti-metatype antibodies. Results showed that anti-metatype antibodies reduced the rate and extent of deuterium oxide-mediated fluorescence enhancement of 4-4-20, a single-chain derivative of 4-4-20 (consisting of the variable domains and a polylinker), and idiotypically related monoclonal anti-fluorescein antibodies suggesting that anti-metatype stabilized the liganded active site. Size exclusion liquid chromatography was utilized to isolate the liganded antibody-anti-metatype complex. Liganded single chain antibody 4-4-20 was mixed with 10-fold molar excess anti-metatype Fab fragments, and a major complex eluted with an apparent M(r) 249,000. The apparent molecular weight of this complex inferred that one liganded single chain antibody was bound by five antimetatype Fab fragments. Spectral analysis confirmed these results and the characteristic delayed rate of ligand dissociation was also observed for the isolated complex. The results suggest that anti-metatype antibodies stabilize the liganded conformation by forming a large, stable, macromolecular complex.

  16. Structural insights, protein-ligand interactions and spectroscopic characterization of isoformononetin

    Science.gov (United States)

    Srivastava, Anubha; Singh, Harshita; Mishra, Rashmi; Dev, Kapil; Tandon, Poonam; Maurya, Rakesh

    2017-04-01

    Isoformononetin, a methoxylated isoflavone present in medicinal plants, has non-estrogenic bone forming effect via differential mitogen-activated protein kinase (MAPK) signaling. Spectroscopic (FT-Raman, FT-IR, UV-vis and NMR spectra) and quantum chemical calculations using density functional theory (DFT) and 6-311++G(d,p) as a large basis set have been employed to study the structural and electronic properties of isoformononetin. A detailed conformational analysis is performed to determine the stability among conformers and the various possibilities of intramolecular hydrogen bonding formation. Molecular docking studies with different protein kinases were performed on isoformononetin and previously studied isoflavonoid, formononetin in order to understand their inhibitory nature and the effect of functional groups on osteogenic or osteoporosis associated proteins. It is found that the oxygen atoms of methoxy, hydroxyl groups attached to phenyl rings R1, R3 and carbonyl group attached to pyran ring R2, play a major role in binding with the protein kinases that is responsible for the osteoporosis; however, no hydrophobic interactions are observed between rings of ligand and protein. The electronic properties such as HOMO and LUMO energies were determined by time-dependent TD-DFT which predict that conformer II is a little bit more stable and chemically low reactive than conformer I of isoformononetin. To estimate the structure-activity relationship, the molecular electrostatic potential (MEP) surface map, and reactivity descriptors are calculated from the optimized geometry of the molecule. From these results, it is also found that isoformononetin is kinetically more stable, less toxic, weak electrophile and chemically less reactive than formononetin. The atoms in molecules and natural bond orbital analysis are applied for the detailed analysis of intra and intermolecular hydrogen bonding interactions.

  17. Study of the interactions between proximal femur 3d bone shape, cartilage health, and biomechanics in patients with hip Osteoarthritis.

    Science.gov (United States)

    Pedoia, Valentina; Samaan, Michael A; Inamdar, Gaurav; Gallo, Matthew C; Souza, Richard B; Majumdar, Sharmila

    2017-07-08

    In this study quantitative MRI and gait analysis were used to investigate the relationships between proximal femur 3D bone shape, cartilage morphology, cartilage biochemical composition, and joint biomechanics in subject with hip Osteoarthritis (OA). Eighty subjects underwent unilateral hip MR-imaging: T1ρ and T2 relaxation times were extracted through voxel based relaxometry and bone shape was assessed with 3D MRI-based statistical shape modeling. In addition, 3D gait analysis was performed in seventy-six of the studied subjects. Associations between shape, cartilage lesion presence, severity, and cartilage T1ρ and T2 were analyzed with linear regression and statistical parametric mapping. An ad hoc analysis was performed to investigate biomechanics and shape associations. Our results showed that subjects with a higher neck shaft angle in the coronal plane (higher mode 1, coxa valga), thicker femoral neck and a less spherical femoral head (higher mode 5, pistol grip) exhibited more severe acetabular and femoral cartilage abnormalities, showing different interactions with demographics factors. Subjects with coxa valga also demonstrated a prolongation of T1ρ and T2. Subjects with pistol grip deformity exhibited reduced hip internal rotation angles and subjects with coxa valga exhibited higher peak hip adduction moment and moment impulse. The results of this study establish a clear relationship between 3D proximal femur shape variations and markers of hip joint degeneration-morphological, compositional, well as insight on the possible interactions with demographics and biomechanics, suggesting that 3D MRI-based bone shape maybe a promising biomarker of early hip joint degeneration. © 2017 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res. © 2017 Orthopaedic Research Society. Published by Wiley Periodicals, Inc.

  18. Interaction of pyrrolobenzodiazepine (PBD ligands with parallel intermolecular G-quadruplex complex using spectroscopy and ESI-MS.

    Directory of Open Access Journals (Sweden)

    Gajjela Raju

    Full Text Available Studies on ligand interaction with quadruplex DNA, and their role in stabilizing the complex at concentration prevailing under physiological condition, has attained high interest. Electrospray ionization mass spectrometry (ESI-MS and spectroscopic studies in solution were used to evaluate the interaction of PBD and TMPyP4 ligands, stoichiometry and selectivity to G-quadruplex DNA. Two synthetic ligands from PBD family, namely pyrene-linked pyrrolo[2,1-c][1,4]benzodiazepine hybrid (PBD1, mixed imine-amide pyrrolobenzodiazepine dimer (PBD2 and 5,10,15,20-tetrakis(N-methyl-4-pyridylporphyrin (TMPyP4 were studied. G-rich single-stranded oligonucleotide d(5'GGGGTTGGGG3' designated as d(T(2G(8, from the telomeric region of Tetrahymena Glaucoma, was considered for the interaction with ligands. ESI-MS and spectroscopic methods viz., circular dichroism (CD, UV-Visible, and fluorescence were employed to investigate the G-quadruplex structures formed by d(T(2G(8 sequence and its interaction with PBD and TMPyP4 ligands. From ESI-MS spectra, it is evident that the majority of quadruplexes exist as d(T(2G(8(2 and d(T(2G(8(4 forms possessing two to ten cations in the centre, thereby stabilizing the complex. CD band of PBD1 and PBD2 showed hypo and hyperchromicity, on interaction with quadruplex DNA, indicating unfolding and stabilization of quadruplex DNA complex, respectively. UV-Visible and fluorescence experiments suggest that PBD1 bind externally where as PBD2 intercalate moderately and bind externally to G-quadruplex DNA. Further, melting experiments using SYBR Green indicate that PBD1 unfolds and PBD2 stabilizes the G-quadruplex complex. ITC experiments using d(T(2G(8 quadruplex with PBD ligands reveal that PBD1 and PBD2 prefer external/loop binding and external/intercalative binding to quadruplex DNA, respectively. From experimental results it is clear that the interaction of PBD2 and TMPyP4 impart higher stability to the quadruplex complex.

  19. Fluorescent Approaches for Understanding Interactions of Ligands with G Protein Coupled Receptors

    Science.gov (United States)

    Sridharan, Rajashri; Zuber, Jeffrey; Connelly, Sara M.; Mathew, Elizabeth; Dumont, Mark E.

    2014-01-01

    G Protein Coupled Receptors (GPCRs) are responsible for a wide variety of signaling responses in diverse cell types. Despite major advances in the determination of structures of this class of receptors, the underlying mechanisms by which binding of different types of ligands specifically elicits particular signaling responses remains unclear. The use of fluorescence spectroscopy can provide important information about the process of ligand binding and ligand dependent conformational changes in receptors, especially kinetic aspects of these processes, that can be difficult to extract from x-ray structures. We present an overview of the extensive array of fluorescent ligands that have been used in studies of GPCRs and describe spectroscopic approaches for assaying binding and probing the environment of receptor-bound ligands with particular attention to examples involving yeast pheromone receptors. In addition, we discuss the use of fluorescence spectroscopy for detecting and characterizing conformational changes in receptors induced by the binding of ligands. Such studies have provided strong evidence for diversity of receptor conformations elicited by different ligands, consistent with the idea that GPCRs are not simple on and off switches. This diversity of states constitutes an underlying mechanistic basis for biased agonism, the observation that different stimuli can produce different responses from a single receptor. It is likely that continued technical advances will allow fluorescence spectroscopy to play an important role in continued probing of structural transitions in GPCRs. PMID:24055822

  20. Interaction between the DRD4 VNTR Polymorphism and Proximal and Distal Environments in Alcohol Dependence during Emerging and Young Adulthood

    Science.gov (United States)

    Park, Aesoon; Sher, Kenneth J.; Todorov, Alexandre A.; Heath, Andrew C.

    2011-01-01

    The manifestation of alcohol dependence at different developmental stages may be associated with different genetic and environmental factors. Taking a developmental approach, the current study characterized interaction between the dopamine receptor 4 variable number tandem repeat (DRD4 VNTR) polymorphism and developmentally specific environmental factors (childhood adversity, college/Greek involvement, and delayed adult role transition) on alcohol dependence during emerging and young adulthood. Prospective data were obtained from a cohort of 234 Caucasian individuals (56% female) followed up at ages 18 through 34. A longitudinal hierarchical factor model was estimated to model a trait-like persistent alcohol dependence factor throughout emerging and young adulthood and two residual state-like alcohol dependence factors limited to emerging adulthood and young adulthood, respectively. To account for those alcohol dependence factors, three two-way interaction effects between the DRD4 VNTR polymorphism and the three developmentally specific environment factors were modeled. Carriers of the DRD4 long allele showed greater susceptibility to environmental effects; they showed more persistent alcohol dependence symptoms as childhood adversity increased and more alcohol dependence symptoms limited to emerging adulthood as college/Greek involvement increased. Alcohol dependence among non-carriers of the long allele, however, did not differ as a function of those environments. Although replication is necessary, these findings highlight the importance of repeated phenotypic assessments across development and modeling both distal and proximal environments and their interaction with genetic susceptibility at specific developmental stages. PMID:21381802

  1. Contributions of Phenylalanine 335 to Ligand Recognition by Human Surfactant Protein D: Ring Interactions with SP-D Ligands

    Energy Technology Data Exchange (ETDEWEB)

    Crouch,E.; McDonald, B.; Smith, K.; Cararella, T.; Seaton, B.; Head, J.

    2006-01-01

    Surfactant Protein D (SP-D) is an innate immune effector that contributes to antimicrobial host defense and immune regulation. Interactions of SP-D with microorganisms and organic antigens involve binding of glycoconjugates to the C-type lectin carbohydrate recognition domain (CRD). A trimeric fusion protein encoding the human neck+CRD (hNCRD) bound to the aromatic glycoside, p-nitrophenyl-alpha-D-maltoside, with nearly a log-fold higher affinity than maltose, the prototypical competitor. Maltotriose, which has the same linkage pattern as the maltoside, bound with intermediate affinity. Site-directed substitution of leucine for phenylalanine 335 (Phe335) decreased affinities for the maltoside and maltotriose without significantly altering the affinity for maltose or glucose, and substitution of tyrosine or tryptophan for leucine restored preferential binding to maltotriose and the maltoside. A mutant with alanine at this position failed to bind to mannan or maltose-substituted solid supports. Crystallographic analysis of the hNCRD complexed with maltotriose or p-nitrophenyl-maltoside showed stacking of the terminal glucose or nitrophenyl ring with the aromatic ring of Phe335. Our studies indicate that Phe335, which is evolutionarily conserved in all known SP-Ds, plays important - if not critical roles - in SP-D function.

  2. Quantitation of species differences in albumin–ligand interactions for bovine, human and rat serum albumins using fluorescence spectroscopy: A test case with some Sudlow's site I ligands

    Energy Technology Data Exchange (ETDEWEB)

    Poór, Miklós [Institute of Laboratory Medicine, University of Pécs, Ifjúság u. 13, Pécs H-7624 (Hungary); Li, Yin; Matisz, Gergely [Department of General and Physical Chemistry, University of Pécs, Pécs H-7624 (Hungary); János Szentágothai Research Center, Pécs H-7624 (Hungary); Kiss, László [Department of General and Physical Chemistry, University of Pécs, Pécs H-7624 (Hungary); Kunsági-Máté, Sándor [Department of General and Physical Chemistry, University of Pécs, Pécs H-7624 (Hungary); János Szentágothai Research Center, Pécs H-7624 (Hungary); Kőszegi, Tamás, E-mail: koszegit@freemail.hu [Institute of Laboratory Medicine, University of Pécs, Ifjúság u. 13, Pécs H-7624 (Hungary)

    2014-01-15

    Albumin, the most abundant plasma protein is an approximately 67 kDa sized water-soluble macromolecule. Since several drugs and xenobiotics circulate in the blood at least partially in albumin-bound form, albumin plays a key role in the pharmacokinetics/toxicokinetics of these chemicals. Most of the drugs and xenobiotics are Sudlow's site I ligands. In numerous studies, bovine serum albumin (BSA) is used for modeling albumin–ligand interactions and the results are extrapolated to human serum albumin (HSA). Furthermore, only limited information is available related to albumin–ligand interactions of different albumin species. Therefore, in our study, we have focused on the quantification of differences between bovine, human and rat serum albumin (RSA) using four Sudlow's site I ligands (luteolin, ochratoxin A, phenylbutazone and warfarin). Interactions were analyzed by fluorescence spectroscopy. Stability constants as well as competing capacities of the ligands were determined, and thermodynamic study was also performed. Our results highlight that there could be major differences between BSA, HSA and RSA in their ligand binding properties. Based on our observations we emphasize that in molecular aspects BSA behaves considerably differently from HSA or from albumins of other species therefore, it is strongly recommended to apply at least some confirmatory measurements when data obtained from other species are attempted to be extrapolated to HSA. -- Highlights: • Albumin–ligand interactions of human, bovine and rat albumins were studied. • Four Sudlow's site I ligands were tested by fluorescence spectroscopy. • Substantial differences were found in stability constants among albumin complexes. • Competing capacity of ligands showed major differences in the studied species. • Data obtained for BSA cannot be directly extrapolated to human albumin.

  3. Preliminary Studies on Capacitive Proximity Sensing for Touchless Interaction with a Human Finger

    Directory of Open Access Journals (Sweden)

    Leonhard HASLINGER

    2016-12-01

    Full Text Available This contribution deals with preliminary studies for touchless interaction based on capacitive sensor technologies. An existing approach in combination with additional capacitance measurements is used for position estimation. For that, a measurement system is utilized which is able to measure capacitances in a range of a few fF to several pF. The main focus is the 3D position estimation of a human finger through measuring the spatial capacitance distributions caused by its movements. A grounded metallic test object is used as an abstract model of a finger. The capacitance modeling is based on a 2D simplification by considering properties of symmetry. This new model, combined with complex data processing algorithms, ensures precise finger gesture recognition in future research.

  4. A Molecular Dynamics Approach to Ligand-Receptor Interaction in the Aspirin-Human Serum Albumin Complex

    OpenAIRE

    Alvarez, H. Ariel; McCarthy, Andrés N.; Grigera, J. Raúl

    2012-01-01

    In this work, we present a study of the interaction between human serum albumin (HSA) and acetylsalicylic acid (ASA, C9H8O4) by molecular dynamics simulations (MD). Starting from an experimentally resolved structure of the complex, we performed the extraction of the ligand by means of the application of an external force. After stabilization of the system, we quantified the force used to remove the ASA from its specific site of binding to HSA and calculated the mechanical nonequilibrium exter...

  5. A photoactivatable nanopatterned substrate for analyzing collective cell migration with precisely tuned cell-extracellular matrix ligand interactions.

    Directory of Open Access Journals (Sweden)

    Yoshihisa Shimizu

    Full Text Available Collective cell migration is involved in many biological and pathological processes. Various factors have been shown to regulate the decision to migrate collectively or individually, but the impact of cell-extracellular matrix (ECM interactions is still debated. Here, we developed a method for analyzing collective cell migration by precisely tuning the interactions between cells and ECM ligands. Gold nanoparticles are arrayed on a glass substrate with a defined nanometer spacing by block copolymer micellar nanolithography (BCML, and photocleavable poly(ethylene glycol (Mw  =  12 kDa, PEG12K and a cyclic RGD peptide, as an ECM ligand, are immobilized on this substrate. The remaining glass regions are passivated with PEG2K-silane to make cells interact with the surface via the nanoperiodically presented cyclic RGD ligands upon the photocleavage of PEG12K. On this nanostructured substrate, HeLa cells are first patterned in photo-illuminated regions, and cell migration is induced by a second photocleavage of the surrounding PEG12K. The HeLa cells gradually lose their cell-cell contacts and become disconnected on the nanopatterned substrate with 10-nm particles and 57-nm spacing, in contrast to their behavior on the homogenous substrate. Interestingly, the relationship between the observed migration collectivity and the cell-ECM ligand interactions is the opposite of that expected based on conventional soft matter models. It is likely that the reduced phosphorylation at tyrosine-861 of focal adhesion kinase (FAK on the nanopatterned surface is responsible for this unique migration behavior. These results demonstrate the usefulness of the presented method in understanding the process of determining collective and non-collective migration features in defined micro- and nano-environments and resolving the crosstalk between cell-cell and cell-ECM adhesions.

  6. Molecular Characterization of the Interactions between Vascular Selectins and Glycoprotein Ligands on Human Hematopoietic Stem/Progenitor Cells

    KAUST Repository

    Abusamra, Dina

    2016-12-01

    The human bone marrow vasculature constitutively expresses both E-selectin and P-selectin where they interact with the cell-surface glycan moiety, sialyl Lewis x, on circulating hematopoietic stem/progenitor cells (HSPCs) to mediate the essential tethering/rolling step. Although several E-selectin glycoprotein ligands (E-selLs) have been identified, the importance of each E-selL on human HSPCs is debatable and requires additional methodologies to advance their specific involvement. The first objective was to fill the knowledge gap in the in vitro characterization of the mechanisms used by selectins to mediate the initial step in the HSPCs homing by developing a real time immunoprecipitation-based assay on a surface plasmon resonance chip. This novel assay bypass the difficulties of purifying ligands, enables the use of natively glycosylated forms of selectin ligands from any model cell of interest and study its binding affinities under flow. We provide the first comprehensive quantitative binding kinetics of two well-documented ligands, CD44 and PSGL-1, with E-selectin. Both ligands bind monomeric E-selectin transiently with fast on- and off-rates while they bind dimeric E-selectin with remarkably slow on- and off-rates with the on-rate, but not the off-rate, is dependent on salt concentration. Thus, suggest a mechanism through which monomeric selectins mediate initial fast-on and -off binding to capture the circulating cells out of shear-flow; subsequently, tight binding by dimeric/oligomeric selectins is enabled to slow rolling significantly. The second objective is to fully identify and characterize E/P-selectin ligand candidates expressed on CD34+ HSPCs which cause enhanced migration after intravenous transplantation compared to their CD34- counterparts. CD34 is widely recognized marker of human HSPCs but its natural ligand and function on these cells remain elusive. Proteomics identified CD34 as an E-selL candidate on human HSPCs, whose binding to E

  7. Facet-Specific Ligand Interactions on Ternary AgSbS 2 Colloidal Quantum Dots

    Energy Technology Data Exchange (ETDEWEB)

    Choi, Hyekyoung [Nano-Convergence Systems Research Division, Korea Institute of Machinery and Materials, Daejeon 34103 Republic of Korea; Kim, Sungwoo [Nano-Convergence Systems Research Division, Korea Institute of Machinery and Materials, Daejeon 34103 Republic of Korea; Luther, Joseph M. [Chemical and Materials Sciences Center, National Renewable Energy Laboratory, Golden CO 80401 USA; Kim, Sang-Wook [Department of Molecular Science and Technology, Ajou University, Suwon 16499 Republic of Korea; Shin, Dongwoon [Nano-Convergence Systems Research Division, Korea Institute of Machinery and Materials, Daejeon 34103 Republic of Korea; Department of Nanomechatronics, Korea University of Science and Technology (UST), Daejeon 34113 Republic of Korea; Beard, Matthew C. [Chemical and Materials Sciences Center, National Renewable Energy Laboratory, Golden CO 80401 USA; Jeong, Sohee [Nano-Convergence Systems Research Division, Korea Institute of Machinery and Materials, Daejeon 34103 Republic of Korea; Department of Nanomechatronics, Korea University of Science and Technology (UST), Daejeon 34113 Republic of Korea

    2017-11-07

    Silver dimetal chalcogenide (Ag-V-VI2) ternary quantum dots (QDs) are emerging lead-free materials for optoelectronic devices due to their NIR band gaps, large absorption coefficients, and superior electronic properties. However, thin film-based devices of the ternary QDs still lag behind due to the lack of understanding of the surface chemistry, compared to that of lead chalcogenide QDs even with the same crystal structure. Herein the surface ligand interactions of AgSbS2 QDs, synthesized with 1-dodecanethiol used as a stabilizer, are studied. For nonpolar (1 0 0) surfaces, it is suggested that the thiolate ligands are associated with the crystal lattices, thus preventing surface oxidation by protecting sulfur after air-exposure, as confirmed through optical and surface chemical analysis. Otherwise, silver rich (1 1 1) surfaces are passivated by thiolate ligands, allowing ligand exchange processes for the conductive films. This in-depth investigation of the surface chemistry of ternary QDs will prompt the performance enhancement of their optoelectronic devices.

  8. Protein O-fucosyltransferase 1 (Pofut1) regulates lymphoid and myeloid homeostasis through modulation of Notch receptor ligand interactions

    Science.gov (United States)

    Yao, David; Huang, Yuanshuai; Huang, Xiaoran; Wang, Weihuan; Yan, Quanjian; Wei, Lebing; Xin, Wei; Gerson, Stanton; Stanley, Pamela; Lowe, John B.

    2011-01-01

    Notch signaling is essential for lymphocyte development and is also implicated in myelopoiesis. Notch receptors are modified by O-fucosylation catalyzed by protein O-fucosyltransferase 1 (Pofut1). Fringe enzymes add N-acetylglucosamine to O-fucose and modify Notch signaling by altering the sensitivity of Notch receptors to Notch ligands. To address physiologic functions in hematopoiesis of Notch modified by O-fucose glycans, we examined mice with inducible inactivation of Pofut1 using Mx-Cre. These mice exhibited a reduction in T lymphopoiesis and in the production of marginal-zone B cells, in addition to myeloid hyperplasia. Restoration of Notch1 signaling rescued T lymphopoiesis and the marrow myeloid hyperplasia. After marrow transfer, both cell-autonomous and environmental cues were found to contribute to lymphoid developmental defects and myeloid hyperplasia in Pofut1-deleted mice. Although Pofut1 deficiency slightly decreased cell surface expression of Notch1 and Notch2, it completely abrogated the binding of Notch receptors with Delta-like Notch ligands and suppressed downstream Notch target activation, indicating that O-fucose glycans are critical for efficient Notch-ligand binding that transduce Notch signals. The combined data support a key role for the O-fucose glycans generated by Pofut1 in Notch regulation of hematopoietic homeostasis through modulation of Notch-ligand interactions. PMID:21464368

  9. Proteochemometric modeling of the bioactivity spectra of HIV-1 protease inhibitors by introducing protein-ligand interaction fingerprint.

    Directory of Open Access Journals (Sweden)

    Qi Huang

    Full Text Available HIV-1 protease is one of the main therapeutic targets in HIV. However, a major problem in treatment of HIV is the rapid emergence of drug-resistant strains. It should be particularly helpful to clinical therapy of AIDS if one method can be used to predict antivirus capability of compounds for different variants. In our study, proteochemometric (PCM models were created to study the bioactivity spectra of 92 chemical compounds with 47 unique HIV-1 protease variants. In contrast to other PCM models, which used Multiplication of Ligands and Proteins Descriptors (MLPD as cross-term, one new cross-term, i.e. Protein-Ligand Interaction Fingerprint (PLIF was introduced in our modeling. With different combinations of ligand descriptors, protein descriptors and cross-terms, nine PCM models were obtained, and six of them achieved good predictive abilities (Q(2(test>0.7. These results showed that the performance of PCM models could be improved when ligand and protein descriptors were complemented by the newly introduced cross-term PLIF. Compared with the conventional cross-term MLPD, the newly introduced PLIF had a better predictive ability. Furthermore, our best model (GD & P & PLIF: Q(2(test = 0.8271 could select out those inhibitors which have a broad antiviral activity. As a conclusion, our study indicates that proteochemometric modeling with PLIF as cross-term is a potential useful way to solve the HIV-1 drug-resistant problem.

  10. Automated identification of protein-ligand interaction features using Inductive Logic Programming: a hexose binding case study

    Directory of Open Access Journals (Sweden)

    A Santos Jose C

    2012-07-01

    Full Text Available Abstract Background There is a need for automated methods to learn general features of the interactions of a ligand class with its diverse set of protein receptors. An appropriate machine learning approach is Inductive Logic Programming (ILP, which automatically generates comprehensible rules in addition to prediction. The development of ILP systems which can learn rules of the complexity required for studies on protein structure remains a challenge. In this work we use a new ILP system, ProGolem, and demonstrate its performance on learning features of hexose-protein interactions. Results The rules induced by ProGolem detect interactions mediated by aromatics and by planar-polar residues, in addition to less common features such as the aromatic sandwich. The rules also reveal a previously unreported dependency for residues cys and leu. They also specify interactions involving aromatic and hydrogen bonding residues. This paper shows that Inductive Logic Programming implemented in ProGolem can derive rules giving structural features of protein/ligand interactions. Several of these rules are consistent with descriptions in the literature. Conclusions In addition to confirming literature results, ProGolem’s model has a 10-fold cross-validated predictive accuracy that is superior, at the 95% confidence level, to another ILP system previously used to study protein/hexose interactions and is comparable with state-of-the-art statistical learners.

  11. Affinity Interaction between Hexamer Peptide Ligand HWRGWV and Immunoglobulin G Studied by Quartz Crystal Microbalance and Surface Plasmon Resonance

    Science.gov (United States)

    Shen, Fei

    Immunoglobulins (Ig), also referred to as antibodies, act as protective agents against pathogens trying to invade an organism. Human immunoglobulin G (hIgG), as the most prominent immunoglobulin presented in serum and other human fluids, has broad applications in fields like immunotherapy and clinical diagnostics. Staphylococcus aureus Protein A and Streptococcus Protein G are the most common affinity ligands for IgG purifaction and detection. However, drawbacks associated with these two protein ligands have motivated searches for alternative affinity ligands. The hexamer peptide ligand HWRGWV identified from a one-bead-one-peptide combinatorial library synthesized on chromatography resins has demonstrated high affinity and specificity to the Fc fragment of hIgG. A chromatography resin with HWRGWV can purify human IgG (hIgG) from complete minimum essential medium (cMEM) with purities and yields as high as 95%, which are comparable to using Protein A as affinity ligand (4). As a short peptide ligand, HWRGWV can be produced at relatively low costs under good manufacturing practices (GMP) conditions, it is highly robust, less immunogenic and allows for milder elution conditions for the bound antibody (3, 5). Although this short peptide ligand has exhibited promising properties for IgG capture and purification, limited information is available on the intrinsic mechanisms of affinity interaction between the peptide ligand and target protein. In this study, the affinity interaction between hIgG and peptide ligand immobilized on solid surfaces was studied by quartz crystal microbalance (QCM) and surface plasmon resonance (SPR). Compared with previous methods employed for the peptide characterization, QCM and SPR can provide direct measurements of equilibrium adsorption isotherms and rates of adsorption, allowing a complete kinetic and thermodynamics analyses of the ligand-target interactions. New methods were developed to modify gold and silica surfaces of QCM and SPR

  12. Comparison of entropic contributions to binding in a "hydrophilic" versus "hydrophobic" ligand-protein interaction.

    Science.gov (United States)

    Syme, Neil R; Dennis, Caitriona; Bronowska, Agnieszka; Paesen, Guido C; Homans, Steve W

    2010-06-30

    In the present study we characterize the thermodynamics of binding of histamine to recombinant histamine-binding protein (rRaHBP2), a member of the lipocalin family isolated from the brown-ear tick Rhipicephalus appendiculatus. The binding pocket of this protein contains a number of charged residues, consistent with histamine binding, and is thus a typical example of a "hydrophilic" binder. In contrast, a second member of the lipocalin family, the recombinant major urinary protein (rMUP), binds small hydrophobic ligands, with a similar overall entropy of binding in comparison with rRaHBP2. Having extensively studied ligand binding thermodynamics for rMUP previously, the data we obtained in the present study for HBP enables a comparison of the driving forces for binding between these classically distinct binding processes in terms of entropic contributions from ligand, protein, and solvent. In the case of rRaHBP2, we find favorable entropic contributions to binding from desolvation of the ligand; however, the overall entropy of binding is unfavorable due to a dominant unfavorable contribution arising from the loss of ligand degrees of freedom, together with the sequestration of solvent water molecules into the binding pocket in the complex. This contrasts with binding in rMUP where desolvation of the protein binding pocket makes a minor contribution to the overall entropy of binding given that the pocket is substantially desolvated prior to binding.

  13. Design of HIV-1 protease inhibitors with pyrrolidinones and oxazolidinones as novel P1'-ligands to enhance backbone-binding interactions with protease: synthesis, biological evaluation, and protein-ligand X-ray studies

    Energy Technology Data Exchange (ETDEWEB)

    Ghosh, Arun K.; Leshchenko-Yashchuk, Sofiya; Anderson, David D.; Baldridge, Abigail; Noetzel, Marcus; Miller, Heather B.; Tie, Yunfeng; Wang, Yuan-Fang; Koh, Yasuhiro; Weber, Irene T.; Mitsuya, Hiroaki; (GSU); (Purdue); (NCI); (Kumamoto University School of Medicine)

    2009-09-02

    Structure-based design, synthesis, and biological evaluation of a series of novel HIV-1 protease inhibitors are described. In an effort to enhance interactions with protease backbone atoms, we have incorporated stereochemically defined methyl-2-pyrrolidinone and methyl oxazolidinone as the P1{prime}-ligands. These ligands are designed to interact with Gly-27{prime} carbonyl and Arg-8 side chain in the S1{prime}-subsite of the HIV protease. We have investigated the potential of these ligands in combination with our previously developed bis-tetrahydrofuran (bis-THF) and cyclopentanyltetrahydrofuran (Cp-THF) as the P2-ligands. Inhibitor 19b with a (R)-aminomethyl-2-pyrrolidinone and a Cp-THF was shown to be the most potent compound. This inhibitor maintained near full potency against multi-PI-resistant clinical HIV-1 variants. A high resolution protein-ligand X-ray crystal structure of 19b-bound HIV-1 protease revealed that the P1{prime}-pyrrolidinone heterocycle and the P2-Cp-ligand are involved in several critical interactions with the backbone atoms in the S1{prime} and S2 subsites of HIV-1 protease.

  14. Ruthenium(II) complexes containing quinone based ligands: Synthesis, characterization, catalytic applications and DNA interaction

    Science.gov (United States)

    Anitha, P.; Manikandan, R.; Endo, A.; Hashimoto, T.; Viswanathamurthi, P.

    2012-12-01

    1,2-Naphthaquinone reacts with amines such as semicarbazide, isonicotinylhydrazide and thiosemicarbazide in high yield procedure with the formation of tridentate ligands HLn (n = 1-3). By reaction of ruthenium(II) starting complexes and quinone based ligands HLn (n = 1-3), a series of ruthenium complexes were synthesized and characterized by elemental and spectroscopic methods (FT-IR, electronic, 1H, 13C, 31P NMR and ESI-MS). The ligands were coordinated to ruthenium through quinone oxygen, imine nitrogen and enolate oxygen/thiolato sulfur. On the basis of spectral studies an octahedral geometry may be assigned for all the complexes. Further, the catalytic oxidation of primary, secondary alcohol and transfer hydrogenation of ketone was carried out. The DNA cleavage efficiency of new complexes has also been tested.

  15. Affinity-mass spectrometry approaches for elucidating structures and interactions of protein-ligand complexes.

    Science.gov (United States)

    Petre, Brînduşa Alina

    2014-01-01

    Affinity-based approaches in combination with mass spectrometry for molecular structure identification in biological complexes such as protein-protein, and protein-carbohydrate complexes have become popular in recent years. Affinity-mass spectrometry involves immobilization of a biomolecule on a chemically activated support, affinity binding of ligand(s), dissociation of the complex, and mass spectrometric analysis of the bound fraction. In this chapter the affinity-mass spectrometric methodologies will be presented for (1) identification of the epitope structures in the Abeta amyloid peptide, (2) identification of oxidative modifications in proteins such as nitration of tyrosine, (3) determination of carbohydrate recognition domains, and as (4) development of a biosensor chip-based mass spectrometric system for concomitant quantification and identification of protein-ligand complexes.

  16. Strongly Luminescent Cyclometalated Gold(III) Complexes Supported by Bidentate Ligands Displaying Intermolecular Interactions and Tunable Emission Energy.

    Science.gov (United States)

    Chan, Kaai Tung; Tong, Glenna So Ming; Wan, Qingyun; Cheng, Gang; Yang, Chen; Che, Chi-Ming

    2017-08-17

    A series of charge-neutral AuIII complexes, which comprise a dicarbanionic C-deprotonated biphenyl ligand and bidentate ancillary ligands ([Au(C^C)(L^X)]; L^X=β-diketonate and relatives (O^O), quinolinolate and relatives (N^O), and diphosphino (P^P) ligands), were prepared. All the complexes are emissive in degassed CH2 Cl2 solutions and in thin-film samples with Φem up to 18 and 35 %, respectively, except for 5 and 6, which bear (N^O)-type ancillary ligands. Variation of the electronic characteristics of the β-diketonate ancillary ligand was demonstrated to be a viable route for tuning the emission color from blue-green (peak λem at ca. 466 nm for 1 and 2; 501 nm for 4 a and 4 b) to orange (peak λem at 585 nm for 3), in contrast to the common observations that the ancillary ligand has a negligible effect on the excited-state energy of the AuIII complexes reported in the literature. DFT/time-dependent (TD) DFT calculations revealed that the energies of the 3 ππ*(C^C) and the 3 ILCT(O^O) excited states (ILCT=intraligand charge transfer) switch in order on going from O^O=acetylacetonate (acac) to aryl-substituted β-diketonate ligands. Solution-processed and vacuum-deposited organic light-emitting diode (OLED) devices of selected complexes were prepared. The vacuum-deposited OLED fabricated with 2 displays a sky-blue emission with a maximum external quantum efficiency (EQE) of 6.71 % and CIE coordinates of (0.22, 0.40). The crystal structures of 7 and 9 reveal short intermolecular AuIII ⋅⋅⋅AuIII contacts, with intermetal distances of 3.408 and 3.453 Å, respectively. DFT/TDDFT calculations were performed on 7 and 9 to account for the noncovalent interactions. Solid samples of 1, 3, and 9 exhibit excimeric emission at room temperature, which is rarely reported in AuIII complexes. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  17. Electrostatic similarities between protein and small molecule ligands facilitate the design of protein-protein interaction inhibitors.

    Directory of Open Access Journals (Sweden)

    Arnout Voet

    Full Text Available One of the underlying principles in drug discovery is that a biologically active compound is complimentary in shape and molecular recognition features to its receptor. This principle infers that molecules binding to the same receptor may share some common features. Here, we have investigated whether the electrostatic similarity can be used for the discovery of small molecule protein-protein interaction inhibitors (SMPPIIs. We have developed a method that can be used to evaluate the similarity of electrostatic potentials between small molecules and known protein ligands. This method was implemented in a software called EleKit. Analyses of all available (at the time of research SMPPII structures indicate that SMPPIIs bear some similarities of electrostatic potential with the ligand proteins of the same receptor. This is especially true for the more polar SMPPIIs. Retrospective analysis of several successful SMPPIIs has shown the applicability of EleKit in the design of new SMPPIIs.

  18. BP-Dock: a flexible docking scheme for exploring protein-ligand interactions based on unbound structures.

    Science.gov (United States)

    Bolia, Ashini; Gerek, Z Nevin; Ozkan, S Banu

    2014-03-24

    Molecular docking serves as an important tool in modeling protein-ligand interactions. However, it is still challenging to incorporate overall receptor flexibility, especially backbone flexibility, in docking due to the large conformational space that needs to be sampled. To overcome this problem, we developed a novel flexible docking approach, BP-Dock (Backbone Perturbation-Dock) that can integrate both backbone and side chain conformational changes induced by ligand binding through a multi-scale approach. In the BP-Dock method, we mimic the nature of binding-induced events as a first-order approximation by perturbing the residues along the protein chain with a small Brownian kick one at a time. The response fluctuation profile of the chain upon these perturbations is computed using the perturbation response scanning method. These response fluctuation profiles are then used to generate binding-induced multiple receptor conformations for ensemble docking. To evaluate the performance of BP-Dock, we applied our approach on a large and diverse data set using unbound structures as receptors. We also compared the BP-Dock results with bound and unbound docking, where overall receptor flexibility was not taken into account. Our results highlight the importance of modeling backbone flexibility in docking for recapitulating the experimental binding affinities, especially when an unbound structure is used. With BP-Dock, we can generate a wide range of binding site conformations realized in nature even in the absence of a ligand that can help us to improve the accuracy of unbound docking. We expect that our fast and efficient flexible docking approach may further aid in our understanding of protein-ligand interactions as well as virtual screening of novel targets for rational drug design.

  19. 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.

  20. Intravesicular and intervesicular interaction by orthogonal multivalent host-guest and metal-ligand complexation

    NARCIS (Netherlands)

    Lim, Choon Woo; Crespo-Biel, Olga; Stuart, Marc C. A.; Reinhoudt, David N.; Huskens, Jurriaan; Ravoo, Bart Jan

    2007-01-01

    Host vesicles composed of amphiphilic beta-cyclodextrin CID1 recognize metal-coordination complexes of the adamantyl-functionalized ethylenediamine ligand L via hydrophobic inclusion in the beta-cyclodextrin cavities at the vesicle surface. In the case of Cu(II) and L, the resulting coordination

  1. Intravesicular and intervesicular interaction by orthogonal multivalent host-guest and metal-ligand complexation

    NARCIS (Netherlands)

    Lim, C.W.; Crespo biel, O.; Stuart, Marc C.A.; Reinhoudt, David; Huskens, Jurriaan; Ravoo, B.J.

    2007-01-01

    Host vesicles composed of amphiphilic beta-cyclodextrin CD1 recognize metal-coordination complexes of the adamantyl-functionalized ethylenediamine ligand L via hydrophobic inclusion in the beta-cyclodextrin cavities at the vesicle surface. In the case of Cu(II) and L, the resulting coordination

  2. Challenges predicting ligand-receptor interactions of promiscuous proteins: the nuclear receptor PXR.

    Directory of Open Access Journals (Sweden)

    Sean Ekins

    2009-12-01

    Full Text Available Transcriptional regulation of some genes involved in xenobiotic detoxification and apoptosis is performed via the human pregnane X receptor (PXR which in turn is activated by structurally diverse agonists including steroid hormones. Activation of PXR has the potential to initiate adverse effects, altering drug pharmacokinetics or perturbing physiological processes. Reliable computational prediction of PXR agonists would be valuable for pharmaceutical and toxicological research. There has been limited success with structure-based modeling approaches to predict human PXR activators. Slightly better success has been achieved with ligand-based modeling methods including quantitative structure-activity relationship (QSAR analysis, pharmacophore modeling and machine learning. In this study, we present a comprehensive analysis focused on prediction of 115 steroids for ligand binding activity towards human PXR. Six crystal structures were used as templates for docking and ligand-based modeling approaches (two-, three-, four- and five-dimensional analyses. The best success at external prediction was achieved with 5D-QSAR. Bayesian models with FCFP_6 descriptors were validated after leaving a large percentage of the dataset out and using an external test set. Docking of ligands to the PXR structure co-crystallized with hyperforin had the best statistics for this method. Sulfated steroids (which are activators were consistently predicted as non-activators while, poorly predicted steroids were docked in a reverse mode compared to 5alpha-androstan-3beta-ol. Modeling of human PXR represents a complex challenge by virtue of the large, flexible ligand-binding cavity. This study emphasizes this aspect, illustrating modest success using the largest quantitative data set to date and multiple modeling approaches.

  3. Testing a family intervention hypothesis: the contribution of mother-infant skin-to-skin contact (kangaroo care) to family interaction, proximity, and touch.

    Science.gov (United States)

    Feldman, Ruth; Weller, Aron; Sirota, Lea; Eidelman, Arthur I

    2003-03-01

    The provision of maternal-infant body contact during a period of maternal separation was examined for its effects on parent-infant and triadic interactions. Participants were 146 three-month-old preterm infants and their parents, half of whom received skin-to-skin contact, or kangaroo care (KC), in the neonatal nursery. Global relational style and micro-patterns of proximity and touch were coded. Following KC, mothers and fathers were more sensitive and less intrusive, infants showed less negative affect, and family style was more cohesive. Among KC families, maternal and paternal affectionate touch of infant and spouse was more frequent, spouses remained in closer proximity, and infant proximity position was conducive to mutual gaze and touch during triadic play. The role of touch as a constituent of the co-regulatory parent-infant and triadic systems and the effects of maternal contact on mothering, co-parenting, and family processes are discussed.

  4. Role of hydrogen bonding in ligand interaction with the N-methyl-D-aspartate receptor ion channel

    Energy Technology Data Exchange (ETDEWEB)

    Leeson, P.D.; Carling, R.W.; James, K.; Smith, J.D.; Moore, K.W.; Wong, E.H.; Baker, R. (Merck Sharp Laboratory, Harlow, Essex (England))

    1990-05-01

    Displacement of (3H)MK-801 (dizocilpine, 1) binding to rat brain membranes has been used to evaluate the affinities of novel dibenzocycloalkenimines related to 1 for the ion channel binding site (also known as the phencyclidine or PCP receptor) on the N-methyl-D-aspartate (NMDA) subtype of excitory amino acid receptor. In common with many other agents having actions in the central nervous system, these compounds contain a hydrophobic aromatic moiety and a basic nitrogen atom. The conformational rigidity of these ligands provides a unique opportunity to evaluate the importance of specific geometrical properties that influence active-site recognition, in particular the role of the nitrogen atom in hydrogen-bonding interactions. The relative affinities (IC50s) of hydrocarbon-substituted analogues of 1 and ring homologated cyclooctenimines illustrate the importance of size-limited hydrophobic binding of both aryl rings and of the quaternary C-5 methyl group. Analysis of the binding of a series of the 10 available structurally rigid dibenzoazabicyclo(x.y.z)alkanes, by using molecular modeling techniques, uncovered a highly significant correlation between affinity and a proposed ligand-active site hydrogen bonding vector (r = 0.950, p less than 0.001). These results are used to generate a pharmacophore of the MK-801 recognition site/PCP receptor, which accounts for the binding of all of the known ligands.

  5. Synthesis of Ni(II) complexes bearing indole-based thiosemicarbazone ligands for interaction with biomolecules and some biological applications.

    Science.gov (United States)

    Haribabu, Jebiti; Jeyalakshmi, Kumaramangalam; Arun, Yuvaraj; Bhuvanesh, Nattamai S P; Perumal, Paramasivan Thirumalai; Karvembu, Ramasamy

    2017-06-01

    A series of new Ni(II) complexes containing indole-based thiosemicarbazone ligands was synthesized and characterized by elemental analyses, and UV-visible, FT-IR, 1H & 13C NMR and mass spectroscopic techniques. The Ni(II) complexes (1-4) bear the general formula [Ni{C10H9N2NHCSNH(R)}2] where R = hydrogen (1), 4-methyl (2), 4-phenyl (3) and 4-cyclohexyl (4). Molecular structure of ligands (L3 and L4) and complexes (2, 3 and 4) was confirmed by single crystal X-ray crystallography. Four coordinated Ni(II) complexes showed square planar geometry. The interaction of the Ni(II) complexes with calf thymus DNA (CT-DNA) has been evaluated by absorption spectroscopic and ethidium bromide (EB) competitive binding studies, which revealed the intercalative interaction of the complexes with CT-DNA. Gel electrophoresis experiments showed the cleavage of DNA by the complexes without any external agent. Further, the interaction of the complexes with bovine serum albumin (BSA) was investigated using UV-visible, fluorescence and synchronous fluorescence spectroscopic methods, which showed that the complexes could bind strongly with BSA. Molecular docking was employed to understand the binding of the Ni(II) complexes with the molecular target B-DNA, human DNA topoisomerase I and BSA. All the Ni(II) complexes possess high antioxidant activity against 2-2-diphenyl-1-picrylhydrazyl (DPPH) radical and antihaemolytic activity. In addition, in vitro cytotoxicity of the Ni(II) complexes against lung cancer (A549), human breast cancer (MCF7) and mouse embryonic fibroblasts (L929) cell lines was investigated. Complex 4 has high cytotoxicity. The mode of cell death effected by complex 4 has been explored using Hoechst 33258 staining. Nickel(II) complexes of thiosemicarbazone ligands were synthesized and their DNA/protein binding, DNA cleavage and cytotoxicity abilities were studied.

  6. Solution characterization of the extracellular region of CD147 and its interaction with its enzyme ligand cyclophilin-A

    Energy Technology Data Exchange (ETDEWEB)

    Schlegel, Jennifer; Redzic, Jasmina S.; Porter, Christopher; Yurchenko, Vyacheslav; Bukrinsky, Michael; Labeikovsky, Wladimir; Armstrong, Geoffrey S.; Zhang, Fengli; Isern, Nancy G.; Degregori, James; Hodges, Robert; Eisenmesser, Elan Z.

    2009-08-21

    The CD147 receptor plays an integral role in numerous diseases by stimulating the expression of several protein families and serving as the receptor for extracellular cyclophilins, however, neither CD147 nor its interactions with its cyclophilin ligands have been well characterized in solution. CD147 is a unique protein in that it can function both at the cell membrane and after being released from cells where it continues to retain activity. Thus, the CD147 receptor functions through at least two mechanisms that include both cyclophilin-independent and cyclophilin-dependent modes of action. In regard to CD147 cyclophilin-independent activity, CD147 homophilic interactions are thought to underlie its activity. In regard to CD147 cyclophilin-dependent activity, cyclophilin/CD147 interactions may represent a novel means of signaling since cyclophilins are also peptidyl-prolyl isomerases.

  7. The role of the CXCL12 – CXCR4 chemokine ligand – receptor interaction in the metastasis of prostate cancer

    OpenAIRE

    Arya, M

    2011-01-01

    The aim was to investigate whether chemokine ligand – receptor interactions are involved in the chemotaxis of prostate cancer to favoured metastatic sites. Initially, chemokine receptor mRNA expression, CXCR and CCR groups, was determined using conventional RT-PCR in cell lines derived from prostate cancer metastases, DU145, LNCaP and PC3, the primary prostate cancer cell line 1542 CPT3X and the normal prostate epithelial/ stromal cell lines 1542 NPTX, Pre 2.8 and S2.13. It ...

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

    Science.gov (United States)

    Panja, Sudipta; Halder, Mintu

    2016-08-01

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

  9. Cation-π interaction regulates ligand-binding affinity and signaling of integrin α4β7

    Science.gov (United States)

    Pan, YouDong; Zhang, Kun; Qi, JunPeng; Yue, Jiao; Springer, Timothy A.; Chen, JianFeng

    2010-01-01

    Integrin α4β7 mediates rolling and firm adhesion of leucocytes, two of the critical steps in leukocyte migration and tissue specific homing. Affinity of α4β7 for ligand is dynamically regulated by three interlinked metal ion-binding sites in β7-subunit I domain. In this study, we found that Phe185 (F185), a highly conserved aromatic residue in β7-subunit, links the specificity-determining loop and the synergistic metal ion-binding site (SyMBS) through cation-π interaction. Mutations of F185 that disrupted the SyMBS cation-F185 interaction led to deficient firm cell adhesion mediated by high affinity α4β7, and only slightly affected rolling adhesion mediated by low affinity α4β7. Disruption of SyMBS cation-F185 interaction induced partial extension of integrin ectodomain and separation of cytoplasmic tails, and impaired α4β7-mediated bidirectional signaling. In addition, loss of SyMBS cation-F185 interaction increased paxillin expression and promoted paxillin-integrin binding, leading to deficient cell spreading. Furthermore, integrin α4β7-mediated cell migration was decreased by the abolishment of SyMBS cation-F185 interaction. Thus, these findings reveal a cation-π interaction playing vital roles in the regulation of integrin affinity, signaling, and biological functions. PMID:21098296

  10. Interactions between a receptor tyrosine phosphatase and a cell surface ligand regulate axon guidance and glial-neuronal communication.

    Science.gov (United States)

    Lee, Hyung-Kook Peter; Cording, Amy; Vielmetter, Jost; Zinn, Kai

    2013-06-05

    We developed a screening method for orphan receptor ligands, in which cell-surface proteins are expressed in Drosophila embryos from GAL4-dependent insertion lines and ligand candidates identified by the presence of ectopic staining with receptor fusion proteins. Stranded at second (Sas) binds to the receptor tyrosine phosphatase Ptp10D in embryos and in vitro. Sas and Ptp10D can interact in trans when expressed in cultured cells. Interactions between Sas and Ptp10D on longitudinal axons are required to prevent them from abnormally crossing the midline. Sas is expressed on both neurons and glia, whereas Ptp10D is restricted to CNS axons. We conducted epistasis experiments by overexpressing Sas in glia and examining how the resulting phenotypes are changed by removal of Ptp10D from neurons. We find that neuronal Ptp10D restrains signaling by overexpressed glial Sas, which would otherwise produce strong glial and axonal phenotypes. Copyright © 2013 Elsevier Inc. All rights reserved.

  11. Enzyme-ligand interactions that drive active site rearrangements in the Helicobacter pylori 5´-methylthioadenosine/S-adenosylhomocysteine nucleosidase

    Energy Technology Data Exchange (ETDEWEB)

    Ronning, Donald R; Iacopelli, Natalie M; Mishra, Vidhi [Toledo

    2012-03-15

    The bacterial enzyme 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase (MTAN) plays a central role in three essential metabolic pathways in bacteria: methionine salvage, purine salvage, and polyamine biosynthesis. Recently, its role in the pathway that leads to the production of autoinducer II, an important component in quorum-sensing, has garnered much interest. Because of this variety of roles, MTAN is an attractive target for developing new classes of inhibitors that influence bacterial virulence and biofilm formation. To gain insight toward the development of new classes of MTAN inhibitors, the interactions between the Helicobacter pylori-encoded MTAN and its substrates and substrate analogs were probed using X-ray crystallography. The structures of MTAN, an MTAN-Formycin A complex, and an adenine bound form were solved by molecular replacement and refined to 1.7, 1.8, and 1.6 Å, respectively. The ribose-binding site in the MTAN and MTAN-adenine cocrystal structures contain a tris[hydroxymethyl]aminomethane molecule that stabilizes the closed form of the enzyme and displaces a nucleophilic water molecule necessary for catalysis. This research gives insight to the interactions between MTAN and bound ligands that promote closing of the enzyme active site and highlights the potential for designing new classes of MTAN inhibitors using a link/grow or ligand assembly development strategy based on the described H. pylori MTAN crystal structures.

  12. A Saccharomyces cerevisiae assay system to investigate ligand/AdipoR1 interactions that lead to cellular signaling.

    Directory of Open Access Journals (Sweden)

    Mustapha Aouida

    Full Text Available Adiponectin is a mammalian hormone that exerts anti-diabetic, anti-cancer and cardioprotective effects through interaction with its major ubiquitously expressed plasma membrane localized receptors, AdipoR1 and AdipoR2. Here, we report a Saccharomyces cerevisiae based method for investigating agonist-AdipoR interactions that is amenable for high-throughput scale-up and can be used to study both AdipoRs separately. Agonist-AdipoR1 interactions are detected using a split firefly luciferase assay based on reconstitution of firefly luciferase (Luc activity due to juxtaposition of its N- and C-terminal fragments, NLuc and CLuc, by ligand induced interaction of the chimeric proteins CLuc-AdipoR1 and APPL1-NLuc (adaptor protein containing pleckstrin homology domain, phosphotyrosine binding domain and leucine zipper motif 1-NLuc in a S. cerevisiae strain lacking the yeast homolog of AdipoRs (Izh2p. The assay monitors the earliest known step in the adiponectin-AdipoR anti-diabetic signaling cascade. We demonstrate that reconstituted Luc activity can be detected in colonies or cells using a CCD camera and quantified in cell suspensions using a microplate reader. AdipoR1-APPL1 interaction occurs in absence of ligand but can be stimulated specifically by agonists such as adiponectin and the tobacco protein osmotin that was shown to have AdipoR-dependent adiponectin-like biological activity in mammalian cells. To further validate this assay, we have modeled the three dimensional structures of receptor-ligand complexes of membrane-embedded AdipoR1 with cyclic peptides derived from osmotin or osmotin-like plant proteins. We demonstrate that the calculated AdipoR1-peptide binding energies correlate with the peptides' ability to behave as AdipoR1 agonists in the split luciferase assay. Further, we demonstrate agonist-AdipoR dependent activation of protein kinase A (PKA signaling and AMP activated protein kinase (AMPK phosphorylation in S. cerevisiae, which are

  13. A Saccharomyces cerevisiae Assay System to Investigate Ligand/AdipoR1 Interactions That Lead to Cellular Signaling

    KAUST Repository

    Aouida, Mustapha

    2013-06-07

    Adiponectin is a mammalian hormone that exerts anti-diabetic, anti-cancer and cardioprotective effects through interaction with its major ubiquitously expressed plasma membrane localized receptors, AdipoR1 and AdipoR2. Here, we report a Saccharomyces cerevisiae based method for investigating agonist-AdipoR interactions that is amenable for high-throughput scale-up and can be used to study both AdipoRs separately. Agonist-AdipoR1 interactions are detected using a split firefly luciferase assay based on reconstitution of firefly luciferase (Luc) activity due to juxtaposition of its N- and C-terminal fragments, NLuc and CLuc, by ligand induced interaction of the chimeric proteins CLuc-AdipoR1 and APPL1-NLuc (adaptor protein containing pleckstrin homology domain, phosphotyrosine binding domain and leucine zipper motif 1-NLuc) in a S. cerevisiae strain lacking the yeast homolog of AdipoRs (Izh2p). The assay monitors the earliest known step in the adiponectin-AdipoR anti-diabetic signaling cascade. We demonstrate that reconstituted Luc activity can be detected in colonies or cells using a CCD camera and quantified in cell suspensions using a microplate reader. AdipoR1-APPL1 interaction occurs in absence of ligand but can be stimulated specifically by agonists such as adiponectin and the tobacco protein osmotin that was shown to have AdipoR-dependent adiponectin-like biological activity in mammalian cells. To further validate this assay, we have modeled the three dimensional structures of receptor-ligand complexes of membrane-embedded AdipoR1 with cyclic peptides derived from osmotin or osmotin-like plant proteins. We demonstrate that the calculated AdipoR1-peptide binding energies correlate with the peptides\\' ability to behave as AdipoR1 agonists in the split luciferase assay. Further, we demonstrate agonist-AdipoR dependent activation of protein kinase A (PKA) signaling and AMP activated protein kinase (AMPK) phosphorylation in S. cerevisiae, which are homologous to

  14. Signal and binding. II. Converting physico-chemical responses to macromolecule-ligand interactions into thermodynamic binding isotherms.

    Science.gov (United States)

    Bujalowski, Wlodzimierz; Jezewska, Maria J; Bujalowski, Paul J

    2017-03-01

    Physico-chemical titration techniques are the most commonly used methods in characterizing molecular interactions. These methods are mainly based on spectroscopic, calorimetric, hydrodynamic, etc., measurements. However, truly quantitative physico-chemical methods are absolutely based on the determination of the relationship between the measured signal and the total average degree of binding in order to obtain meaningful interaction parameters. The relationship between the observed physico-chemical signal of whatever nature and the degree of binding must be determined and not assumed, based on some ad hoc intuitive relationship/model, leading to determination of the true binding isotherm. The quantitative methods reviewed and discussed here allow an experimenter to rigorously determine the degree of binding and the free ligand concentration, i.e., they lead to the construction of the thermodynamic binding isotherm in a model-independent fashion from physico-chemical titration curves. Copyright © 2016. Published by Elsevier B.V.

  15. Amine Landscaping to Maximize Protein-Dye Fluorescence and Ultrastable Protein-Ligand Interaction.

    Science.gov (United States)

    Jacobsen, Michael T; Fairhead, Michael; Fogelstrand, Per; Howarth, Mark

    2017-08-17

    Chemical modification of proteins provides great opportunities to control and visualize living systems. The most common way to modify proteins is reaction of their abundant amines with N-hydroxysuccinimide (NHS) esters. Here we explore the impact of amine number and positioning on protein-conjugate behavior using streptavidin-biotin, a central research tool. Dye-NHS modification of streptavidin severely damaged ligand binding, necessitating development of a new streptavidin-retaining ultrastable binding after labeling. Exploring the ideal level of dye modification, we engineered a panel bearing 1-6 amines per subunit: "amine landscaping." Surprisingly, brightness increased as amine number decreased, revealing extensive quenching following conventional labeling. We ultimately selected Flavidin (fluorophore-friendly streptavidin), combining ultrastable ligand binding with increased brightness after conjugation. Flavidin enhanced fluorescent imaging, allowing more sensitive and specific cell labeling in tissues. Flavidin should have wide application in molecular detection, providing a general insight into how to optimize simultaneously the behavior of the biomolecule and the chemical probe. Copyright © 2017 The Author(s). Published by Elsevier Ltd.. All rights reserved.

  16. Proximal Hypospadias

    Science.gov (United States)

    Kraft, Kate H.; Shukla, Aseem R.; Canning, Douglas A.

    2011-01-01

    Hypospadias results from abnormal development of the penis that leaves the urethral meatus proximal to its normal glanular position. Meatal position may be located anywhere along the penile shaft, but more severe forms of hypospadias may have a urethral meatus located at the scrotum or perineum. The spectrum of abnormalities may also include ventral curvature of the penis, a dorsally redundant prepuce, and atrophic corpus spongiosum. Due to the severity of these abnormalities, proximal hypospadias often requires more extensive reconstruction in order to achieve an anatomically and functionally successful result. We review the spectrum of proximal hypospadias etiology, presentation, correction, and possible associated complications. PMID:21516286

  17. Study of Interaction Platinum Salts (Ii and Palladium (Ii on the Biologically Active Ligand

    Directory of Open Access Journals (Sweden)

    Asmat Nizami Kyzy Azizova

    2014-09-01

    Full Text Available Studied complexing ability of platinum (II and palladium (II with a time of personal gray-oxygen and sulfur-containing ligands donor nitrogens in different taniyah. A combination of functional groups. It is found that the complexation unimportant role nature of the starting metal salts, the pH of the medium, the nature of the solvent and the ratio of reactants. Determine the actual denticity tiodiuksusnoy, tiodipro propionic acid, mercaptoethanol, and bis -- hydroxyethyl sulfide. Discovered that a molecule entering the reaction of cysteamine origin walks splitting S–S communication and the resulting deproto-bined mercamine enter into complexation. In non-aqueous medium splitting S–S communication occurs.

  18. Friendship quality, social preference, proximity prestige, and self-perceived social competence: interactive influences on children's loneliness.

    Science.gov (United States)

    Zhang, Fengjuan; You, Zhiqi; Fan, Cuiying; Gao, Chuang; Cohen, Robert; Hsueh, Yeh; Zhou, Zongkui

    2014-10-01

    The purpose of this study was to test an integrative model in which peer relations at different levels of social complexity (friendship quality, social preference, and proximity prestige) are associated with children's loneliness, with children's self-perceived social competence acting as a mediator of these associations. A middle childhood sample of 509 Chinese children (233 girls and 276 boys; 3rd to 6th grade) completed a battery of sociometric and self-report questionnaires. Bootstrap analysis showed that self-perceived social competence mediated the relations between each peer variable and loneliness. In the integrative model tested with SEM, the mediating effect of self-perceived social competence in the relation between friendship quality and loneliness and between social preference and loneliness remained significant. However, self-perceived social competence no longer mediated the association between proximity prestige and loneliness, when considering the simultaneous influences of the three peer variables (friendship quality, social preference, and proximity prestige). The whole model accounted for 56% of the variance in loneliness. These findings suggest that self-perceived social competence played an important role in children's loneliness, that the quality and the quantity of direct peer relations (friendship quality, social preference, and part of proximity prestige) were associated with loneliness, and that indirect friends had a relatively lower but significant influence on children's loneliness. The results are discussed in terms of their implications for preventing children's loneliness. Copyright © 2014 Society for the Study of School Psychology. Published by Elsevier Ltd. All rights reserved.

  19. The Quantum Nature of Drug-Receptor Interactions: Deuteration Changes Binding Affinities for Histamine Receptor Ligands.

    Directory of Open Access Journals (Sweden)

    Mojca Kržan

    Full Text Available In this article we report a combined experimental and computational study concerning the effects of deuteration on the binding of histamine and two other histaminergic agonists to 3H-tiotidine-labeled histamine H2 receptor in neonatal rat astrocytes. Binding affinities were measured by displacing radiolabeled tiotidine from H2 receptor binding sites present on cultured neonatal rat astrocytes. Quantum-chemical calculations were performed by employing the empirical quantization of nuclear motion within a cluster model of the receptor binding site extracted from the homology model of the entire H2 receptor. Structure of H2 receptor built by homology modelling is attached in the supporting information (S1 Table Experiments clearly demonstrate that deuteration affects the binding by increasing the affinity for histamine and reducing it for 2-methylhistamine, while basically leaving it unchanged for 4-methylhistamine. Ab initio quantum-chemical calculations on the cluster system extracted from the homology H2 model along with the implicit quantization of the acidic N-H and O-H bonds demonstrate that these changes in the binding can be rationalized by the altered strength of the hydrogen bonding upon deuteration known as the Ubbelohde effect. Our computational analysis also reveals a new mechanism of histamine binding, which underlines an important role of Tyr250 residue. The present work is, to our best knowledge, the first study of nuclear quantum effects on ligand receptor binding. The ligand H/D substitution is relevant for therapy in the context of perdeuterated and thus more stable drugs that are expected to enter therapeutic practice in the near future. Moreover, presented approach may contribute towards understanding receptor activation, while a distant goal remains in silico discrimination between agonists and antagonists based on the receptor structure.

  20. One- and three-dimensional silver(I)-5-sulfosalicylate coordination polymers having ligand-supported and unsupported argentophilic interactions

    Science.gov (United States)

    Arıcı, Mürsel; Yeşilel, Okan Zafer; Yeşilöz, Yeşim; Şahin, Onur

    2014-12-01

    Four new coordination polymers, namely, {Hemim·[Ag(Hssa)(H2O)]}n (1), {[Ag(ina)2 Ag(Hssa)]·CH3OH·H2O}n (2), {[Ag2(Hssa)(dmp)1.5]·2H2O}n (3) and [Ag2(Hssa)(daoc)]n (4) (Hssa: 5-Sulfosalicylate, emim: 2-ethyl-4-methylimidazole, ina: isonicotinamide, dmp: 2,5-dimethylpyrazine and daoc: 1,8-diaminooctane) were synthesized and characterized by IR spectroscopy, elemental analysis, single crystal X-ray diffraction, powder X-ray diffraction (PXRD) and thermal analysis techniques. Complexes 1 and 2 are one-dimensional (1D) coordination polymers while complexes 3 and 4 are three-dimensional (3D) coordination polymers. Complex 3 consists of three dimensional (3D) 3,3,6-c net with 3,3,6T37 topology. Complex 4 exhibits a 2-fold interpenetrating 3D framework with tfc topology. Complexes 1-4 contain ligand-supported (1-3) and unsupported (4) argentophilic Ag⋯Ag interactions. Photoluminescence spectra of the complexes demonstrate that photoluminescent properties may be attributed to intraligand transition of coordinated Hssa ligand.

  1. The IUPHAR/BPS Guide to PHARMACOLOGY in 2016: towards curated quantitative interactions between 1300 protein targets and 6000 ligands.

    Science.gov (United States)

    Southan, Christopher; Sharman, Joanna L; Benson, Helen E; Faccenda, Elena; Pawson, Adam J; Alexander, Stephen P H; Buneman, O Peter; Davenport, Anthony P; McGrath, John C; Peters, John A; Spedding, Michael; Catterall, William A; Fabbro, Doriano; Davies, Jamie A

    2016-01-04

    The IUPHAR/BPS Guide to PHARMACOLOGY (GtoPdb, http://www.guidetopharmacology.org) provides expert-curated molecular interactions between successful and potential drugs and their targets in the human genome. Developed by the International Union of Basic and Clinical Pharmacology (IUPHAR) and the British Pharmacological Society (BPS), this resource, and its earlier incarnation as IUPHAR-DB, is described in our 2014 publication. This update incorporates changes over the intervening seven database releases. The unique model of content capture is based on established and new target class subcommittees collaborating with in-house curators. Most information comes from journal articles, but we now also index kinase cross-screening panels. Targets are specified by UniProtKB IDs. Small molecules are defined by PubChem Compound Identifiers (CIDs); ligand capture also includes peptides and clinical antibodies. We have extended the capture of ligands and targets linked via published quantitative binding data (e.g. Ki, IC50 or Kd). The resulting pharmacological relationship network now defines a data-supported druggable genome encompassing 7% of human proteins. The database also provides an expanded substrate for the biennially published compendium, the Concise Guide to PHARMACOLOGY. This article covers content increase, entity analysis, revised curation strategies, new website features and expanded download options. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  2. The IUPHAR/BPS Guide to PHARMACOLOGY in 2016: towards curated quantitative interactions between 1300 protein targets and 6000 ligands

    Science.gov (United States)

    Southan, Christopher; Sharman, Joanna L.; Benson, Helen E.; Faccenda, Elena; Pawson, Adam J.; Alexander, Stephen P. H.; Buneman, O. Peter; Davenport, Anthony P.; McGrath, John C.; Peters, John A.; Spedding, Michael; Catterall, William A.; Fabbro, Doriano; Davies, Jamie A.

    2016-01-01

    The IUPHAR/BPS Guide to PHARMACOLOGY (GtoPdb, http://www.guidetopharmacology.org) provides expert-curated molecular interactions between successful and potential drugs and their targets in the human genome. Developed by the International Union of Basic and Clinical Pharmacology (IUPHAR) and the British Pharmacological Society (BPS), this resource, and its earlier incarnation as IUPHAR-DB, is described in our 2014 publication. This update incorporates changes over the intervening seven database releases. The unique model of content capture is based on established and new target class subcommittees collaborating with in-house curators. Most information comes from journal articles, but we now also index kinase cross-screening panels. Targets are specified by UniProtKB IDs. Small molecules are defined by PubChem Compound Identifiers (CIDs); ligand capture also includes peptides and clinical antibodies. We have extended the capture of ligands and targets linked via published quantitative binding data (e.g. Ki, IC50 or Kd). The resulting pharmacological relationship network now defines a data-supported druggable genome encompassing 7% of human proteins. The database also provides an expanded substrate for the biennially published compendium, the Concise Guide to PHARMACOLOGY. This article covers content increase, entity analysis, revised curation strategies, new website features and expanded download options. PMID:26464438

  3. Effects of protein-protein interactions and ligand binding on the ion permeation in KCNQ1 potassium channel.

    Science.gov (United States)

    Jalily Hasani, Horia; Ganesan, Aravindhan; Ahmed, Marawan; Barakat, Khaled H

    2018-01-01

    The voltage-gated KCNQ1 potassium ion channel interacts with the type I transmembrane protein minK (KCNE1) to generate the slow delayed rectifier (IKs) current in the heart. Mutations in these transmembrane proteins have been linked with several heart-related issues, including long QT syndromes (LQTS), congenital atrial fibrillation, and short QT syndrome. Off-target interactions of several drugs with that of KCNQ1/KCNE1 ion channel complex have been known to cause fatal cardiac irregularities. Thus, KCNQ1/KCNE1 remains an important avenue for drug-design and discovery research. In this work, we present the structural and mechanistic details of potassium ion permeation through an open KCNQ1 structural model using the combined molecular dynamics and steered molecular dynamics simulations. We discuss the processes and key residues involved in the permeation of a potassium ion through the KCNQ1 ion channel, and how the ion permeation is affected by (i) the KCNQ1-KCNE1 interactions and (ii) the binding of chromanol 293B ligand and its derivatives into the complex. The results reveal that interactions between KCNQ1 with KCNE1 causes a pore constriction in the former, which in-turn forms small energetic barriers in the ion-permeation pathway. These findings correlate with the previous experimental reports that interactions of KCNE1 dramatically slows the activation of KCNQ1. Upon ligand-binding onto the complex, the energy-barriers along ion permeation path are more pronounced, as expected, therefore, requiring higher force in our steered-MD simulations. Nevertheless, pulling the ion when a weak blocker is bound to the channel does not necessitate high force in SMD. This indicates that our SMD simulations have been able to discern between strong and week blockers and reveal their influence on potassium ion permeation. The findings presented here will have some implications in understanding the potential off-target interactions of the drugs with the KCNQ1/KCNE1 channel

  4. The interaction between uPAR and vitronectin triggers ligand-independent adhesion signalling by integrins

    Science.gov (United States)

    Ferraris, Gian Maria Sarra; Schulte, Carsten; Buttiglione, Valentina; De Lorenzi, Valentina; Piontini, Andrea; Galluzzi, Massimiliano; Podestà, Alessandro; Madsen, Chris D; Sidenius, Nicolai

    2014-01-01

    The urokinase-type plasminogen activator receptor (uPAR) is a non-integrin vitronectin (VN) cell adhesion receptor linked to the plasma membrane by a glycolipid anchor. Through structure–function analyses of uPAR, VN and integrins, we document that uPAR-mediated cell adhesion to VN triggers a novel type of integrin signalling that is independent of integrin–matrix engagement. The signalling is fully active on VN mutants deficient in integrin binding site and is also efficiently transduced by integrins deficient in ligand binding. Although integrin ligation is dispensable, signalling is crucially dependent upon an active conformation of the integrin and its association with intracellular adaptors such as talin. This non-canonical integrin signalling is not restricted to uPAR as it poses no structural constraints to the receptor mediating cell attachment. In contrast to canonical integrin signalling, where integrins form direct mechanical links between the ECM and the cytoskeleton, the molecular mechanism enabling the crosstalk between non-integrin adhesion receptors and integrins is dependent upon membrane tension. This suggests that for this type of signalling, the membrane represents a critical component of the molecular clutch. PMID:25168639

  5. Interaction of NaCl and behavioral stress on endogenous sodium pump ligands in rats.

    Science.gov (United States)

    Fedorova, O V; Anderson, D E; Lakatta, E G; Bagrov, A Y

    2001-07-01

    Our study investigated the hypothesis that the combination of a high NaCl diet and social isolation stress would increase systolic blood pressure (SBP) and endogenous sodium pump ligands (SPL), ouabainlike compound (OLC), and marinobufagenin (MBG). Excretion of MBG and OLC, SBP, and organ weights were studied in four groups (n = 8) of male Fisher 344 x Norwegian brown rats: controls, socially isolated (Iso), 4% NaCl diet (Salt), and the combination of Salt and Iso (Iso+Salt). In Salt, MBG excretion increased by 78% (P < 0.01), whereas SBP and OLC remained unchanged. In Iso, SBP and MBG did not change, but OLC peaked on day 1. In the Iso+Salt, SBP increased by 9 mmHg, MBG excretion increased (42.0 +/- 7.6 vs. 10.0 +/- 1.5 pmol/24 h, P < 0.01), whereas OLC peaked at day 1 (25.0 +/- 2.5 vs. 10.0 +/- 2.0 pmol/24 h, P < 0.01) and remained elevated. Heart and kidney weights were increased in Salt and Iso+Salt. Aortic weights were increased in Iso and Iso+Salt. Thus a high NaCl intake stimulates MBG excretion, whereas isolation stress stimulates OLC. The combination of Salt and Iso is accompanied by marked stimulation of both SPL.

  6. 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

  7. Ligand-modulated interactions between charged monolayer-protected Au144(SR)60 gold nanoparticles in physiological saline.

    Science.gov (United States)

    Villarreal, Oscar D; Chen, Liao Y; Whetten, Robert L; Yacaman, Miguel J

    2015-02-07

    In order to determine how functionalized gold nanoparticles (AuNPs) interact in a near-physiological environment, we performed all-atom molecular dynamics simulations on the icosahedral Au144 nanoparticles each coated with a homogeneous set of 60 thiolates selected from one of these five (5) types: 11-mercapto-1-undecanesulfonate -SC11H22(SO3(-)), 5-mercapto-1-pentanesulfonate -SC5H10(SO3(-)), 5-mercapto-1-pentaneamine -SC5H10(NH3(+)), 4-mercapto-benzoate -SPh(COO(-)), or 4-mercapto-benzamide -SPh(CONH3(+)). These thiolates were selected to elucidate how the aggregation behavior of AuNPs depends on ligand parameters, including the charge of the terminal group (anionic vs. cationic), and its length and conformational flexibility. For this purpose, each functionalized AuNP was paired with a copy of itself, placed in an aqueous cell, neutralized by 120 Na(+)/Cl(-) counter-ions and salinated with a 150 mM concentration of NaCl, to form five (5) systems of like-charged AuNPs pairs in a saline. We computed the potential of mean force (the reversible work of separation) as a function of the intra-pair distance and, based on which, the aggregation affinities. We found that the AuNPs coated with negatively charged, short ligands have very high affinities. Structurally, a significant number of Na(+) counter-ions reside on a plane between the AuNPs, mediating the interaction. Each such ion forms a "salt bridge" (or "ionic bonds") to both of the AuNPs when they are separated by its diameter plus 0.2-0.3 nm. The positively charged AuNPs have much weaker affinities, as Cl(-) counter-ions form fewer and weaker salt bridges between the AuNPs. In the case of Au144(SC11H22(SO3(-)))60 pair, the flexible ligands fluctuate much more than the other four cases. The large fluctuations disfavor the forming of salt bridges between two AuNPs, but enable hydrophobic contact between the exposed hydrocarbon chains of the two AuNPs, which are subject to an effective attraction at a separation

  8. Molecular Docking Explains Atomic Interaction between Plant-originated Ligands and Oncogenic E7 Protein of High Risk Human Papillomavirus Type 16

    Directory of Open Access Journals (Sweden)

    Satish Kumar

    2014-12-01

    Full Text Available Cervical cancer caused by Human papillomavirus (HPV is one of the leading causes of cancer mortality in women worldwide, particularly in the developing countries. In the last few decades, various compounds from plant origin such as Curcumin, Epigallocatechin gallate (EGCG, Jaceosidin, Resveratrol etc. have been used as anti cancer therapeutic agents. Different studies have shown these plant-originated compounds are able to suppress HPV infection. The E6 and E7 oncoproteins of high-risk HPV play a key role in HPV related cancers. In this study, we explored these ligands from plants origin against E7 oncoprotein of high risk HPV 16, which is known to inactivate tumor suppressor pRb protein. A robust homology model of HPV 16 E7 was built to foresee the interaction mechanism of E7 oncoprotein with these ligands using structure-based drug designing approach. Docking studies demonstrate the interaction of these ligands with pRb binding site of E7 protein by residues Tyr52, Asn53, Val55, Phe57, Cys59, Ser63, Thr64, Thr72, Arg77, Glu80 and Asp81 and help restoration of pRb functioning. This in silico based atomic interaction between these ligands and E7 protein may assist in validating the plant-originated ligands as effective drugs against HPV.

  9. Dynamic strength of the interaction between lung surfactant protein D (SP-D) and saccharide ligands

    DEFF Research Database (Denmark)

    Thormann, Esben; Dreyer, Jakob K; Simonsen, Adam C

    2007-01-01

    In order to investigate the dynamic strength of the interaction between lung surfactant protein D (SP-D) and different sugars, maltose, mannose, glucose, and galactose, we have used an atomic force microscope to monitor the interaction on a single molecule scale. The experiment is performed...... by measuring the rupture force when the SP-D-sugar bond is subjected to a continuously increasing force. Under these dynamic conditions, SP-D binds strongest to d-mannose and weakest to maltose and d-galactose. These results differ from equilibrium measurements wherein SP-D exhibits preference for maltose...

  10. Macromolecular Competition Titration Method: Accessing Thermodynamics of the Unmodified Macromolecule–Ligand Interactions Through Spectroscopic Titrations of Fluorescent Analogs

    Science.gov (United States)

    Bujalowski, Wlodzimierz; Jezewska, Maria J.

    2011-01-01

    Analysis of thermodynamically rigorous binding isotherms provides fundamental information about the energetics of the ligand–macromolecule interactions and often an invaluable insight about the structure of the formed complexes. The Macromolecular Competition Titration (MCT) method enables one to quantitatively obtain interaction parameters of protein–nucleic acid interactions, which may not be available by other methods, particularly for the unmodified long polymer lattices and specific nucleic acid substrates, if the binding is not accompanied by adequate spectroscopic signal changes. The method can be applied using different fluorescent nucleic acids or fluorophores, although the etheno-derivatives of nucleic acid are especially suitable as they are relatively easy to prepare, have significant blue fluorescence, their excitation band lies far from the protein absorption spectrum, and the modification eliminates the possibility of base pairing with other nucleic acids. The MCT method is not limited to the specific size of the reference nucleic acid. Particularly, a simple analysis of the competition titration experiments is described in which the fluorescent, short fragment of nucleic acid, spanning the exact site-size of the protein–nucleic acid complex, and binding with only a 1:1 stoichiometry to the protein, is used as a reference macromolecule. Although the MCT method is predominantly discussed as applied to studying protein–nucleic acid interactions, it can generally be applied to any ligand–macromolecule system by monitoring the association reaction using the spectroscopic signal originating from the reference macromolecule in the presence of the competing macromolecule, whose interaction parameters with the ligand are to be determined. PMID:21195223

  11. Combination of isothermal titration calorimetry and time-resolved luminescence for high affinity antibody-ligand interaction thermodynamics and kinetics

    Science.gov (United States)

    Aweda, Tolulope A.; Meares, Claude F.

    2011-01-01

    For experiments using synthetic ligands as probes for biological experiments, it is useful to determine the specificity and affinity of the ligands for their receptors. As ligands with higher affinities are developed (KA >108 M−1; KD titration calorimetry measures heat produced or consumed during ligand binding, and also provides the equilibrium binding constant. However, as normally practiced, its range is limited. Displacement titration, where a competing weaker ligand is used to lower the apparent affinity of the stronger ligand, can be used to determine the binding affinity as well as the complete thermodynamic data for ligand-antibody complexes with very high affinity. These equilibrium data have been combined with kinetic measurements to yield the rate constants as well. We describe this methodology, using as an example antibody 2D12.5, which captures yttrium S-2-(4-aminobenzyl)-1, 4, 7, 10-tetraazacyclododecanetetraacetate. PMID:21964396

  12. Structure and ligand interactions of the urokinase receptor (uPAR)

    DEFF Research Database (Denmark)

    Kjaergaard, Magnus; Hansen, Line V.; Jacobsen, Benedikte

    2008-01-01

    The urokinase-type plasminogen activator receptor (uPAR or CD87) is a glycolipid-anchored membrane glycoprotein, which is responsible for focalizing plasminogen activation to the cell surface through its high-affinity binding to the serine protease uPA. This tight interaction (KD less than 1 nM) ...

  13. Ice-proximal Marine Sedimentation in the Ross Sea during LGM: Ice-sheet and Ocean Interactions

    Science.gov (United States)

    Turetta, C.; Aghib, F. S.; Ferretti, P.; Barbante, C.

    2016-12-01

    We present preliminary results from a multi-proxy study of different cores from the Ross Sea, Antarctica. Thirty cores have been sampled at the Antarctic Marine Geology Research Facility (AMRF), Florida State University in order to discriminate different source areas and to reconstruct the depositional setting and related climate implications in a peculiar ice-proximal marine setting. Sediment characterizations, trace elements (TE) and rare earth elements (REEs) compositional analysis and evaluation about their source areas have been performed on sediment cores collected widespread in the Ross Sea area. Analysis of 72 samples from thirty cores was performed to determine total concentration of Li, Be, Mg, Al, K, Ca, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, As, Rb, Sr, Ag, Cd, Cs, Ba, Tl, Pb, Bi, Th, U, Y and REEs. This extensive geochemical characterization of cores from several sites in the Ross Sea, will allow to better define the sedimentary processes, to understand the evolution of the ice-proximal marine setting, to evaluate areas with different geochemical features related to different provenances. In particular REEs allow us to discriminate different source areas and to better define the ocean input in the sediment composition. Moreover, 17 sediment cores from Coulman High area collected along two transects were characterized in order to constrain sediment bulk composition, biogenic vs non-biogenic components and the related depositional setting. Sediments from the two transects show a completely different bulk composition, those from the Northern transect mainly consist of fine-grained sediments containing well-preserved biogenic carbonate remains. Sediments from the Southern cores mainly consist of dark greenish diatomaceous sandy mud containing abundant diatoms in fragments. Sedimentation along the two transects seems to reflect the extent of the ice sheets in an ice-proximal marine setting. REEs compositional analyses have confirmed different source regions, a

  14. Upregulation of Programmed Death-1 and Its Ligand in Cardiac Injury Models: Interaction with GADD153.

    Directory of Open Access Journals (Sweden)

    Babak Baban

    Full Text Available Programmed Death-1 (PD-1 and its ligand, PD-L1, are regulators of immune/ inflammatory mechanisms. We explored the potential involvement of PD-1/PD-L1 pathway in the inflammatory response and tissue damage in cardiac injury models.Ischemic-reperfused and cryoinjured hearts were processed for flow cytometry and immunohistochemical studies for determination of cardiac PD-1 and PD-L1 in the context of assessment of the growth arrest- and DNA damage-inducible protein 153 (GADD153 which regulates both inflammation and cell death. Further, we explored the potential ability of injured cardiac cells to influence proliferation of T lymphocytes.The isolated ischemic-reperfused hearts displayed marked increases in expression of PD-1 and PD-L1 in cardiomyocytes; however, immunofluorescent studies indicate that PD-1 and PD-L1 are not primarily co-expressed on the same cardiomyocytes. Upregulation of PD-1/PD-L1 was associated with a marked increases in GADD153 and interleukin (IL-17 but a mild increase in IL-10 and b disruption of mitochondrial membrane potential (ψm as well as apoptotic and necrotic cell death. Importantly, while isotype matching treatment did not affect the aforementioned changes, treatment with the PD-L1 blocking antibody reversed those effects in association with marked cardioprotection. Further, ischemic-reperfused cardiac cells reduced proliferation of T lymphocytes, an effect partially reversed by PD-L1 antibody. Subsequent studies using the cryoinjury model of myocardial infarction revealed significant increases in PD-1, PD-L1, GADD153 and IL-17 positive cells in association with significant apoptosis/necrosis.The data suggest that upregulation of PD-1/PD-L1 pathway in cardiac injury models mediates tissue damage likely through a paracrine mechanism. Importantly, inhibition of T cell proliferation by ischemic-reperfused cardiac cells is consistent with the negative immunoregulatory role of PD-1/PD-L1 pathway, likely reflecting an

  15. Site-Specific Ligand Interactions Favor the Tetragonal Distortion of PbS Nanocrystal Superlattices.

    Science.gov (United States)

    Novák, Jiřı́; Banerjee, Rupak; Kornowski, Andreas; Jankowski, Maciej; André, Alexander; Weller, Horst; Schreiber, Frank; Scheele, Marcus

    2016-08-31

    We analyze the structure and morphology of mesocrystalline, body-centered tetragonal (bct) superlattices of PbS nanocrystals functionalized with oleic acid. On the basis of combined scattering and real space imaging, we derive a three-dimensional (3D) model of the superlattice and show that the bct structure benefits from a balanced combination of {100}PbS-{100}PbS and {111}PbS-{111}PbS interactions between neighboring layers of nanocrystals, which uniquely stabilizes this structure. These interactions are enabled by the coaxial alignment of the atomic lattices of PbS with the superlattice. In addition, we find that this preferential orientation is already weakly present within isolated monolayers. By adding excess oleic acid to the nanocrystal solution, tetragonal distortion is suppressed, and we observe assembly into a bilayered hexagonal lattice reminiscent of a honeycomb with grain sizes of several micrometers.

  16. Probing the structure of Leishmania donovani chagasi DHFR-TS: comparative protein modeling and protein-ligand interaction studies.

    Science.gov (United States)

    Maganti, Lakshmi; Manoharan, Prabu; Ghoshal, Nanda

    2010-09-01

    Dihydrofolate reductase (DHFR) has been used successfully as a drug target in the area of anti-bacterial, anti-cancer and anti-malarial therapy. It also acts as a drug target for Leishmaniasis. Inhibition of DHFR leads to cell death through lack of thymine (nucleotide metabolism). Although the crystal structures of Leishmania major and Trypanosoma cruzi DHFR-thymidylate synthase (TS) have been resolved, to date there is no three-dimensional (3D)-structural information on DHFR-TS of Leishmania donovani chagasi, which causes visceral leishmaniasis. Our aim in this study was to model the 3D structure of L. donovani chagasi DHFR-TS, and to investigate the structural requirements for its inhibition. In this paper we describe a highly refined homology model of L. donovani chagasi DHFR-TS based on available crystallographic structures by using the Homology module of Insight II. Structural refinement and minimization of the generated L. donovani chagasi DHFR-TS model employed the Discover 3 module of Insight II and molecular dynamic simulations. The model was further validated through use of the PROCHECK, Verify_3D, PROSA, PSQS and ERRAT programs, which confirm that the model is reliable. Superimposition of the model structure with the templates L. major A chain, L. major B chain And T. cruzi A chain showed root mean square deviations of 0.69 A, 0.71 A and 1.11 A, respectively. Docking analysis of the L. donovani chagasi DHFR-TS model with methotrexate enabled us to identify specific residues, viz. Val156, Val30, Lys95, Lys75 and Arg97, within the L. donovani chagasi DHFR-TS binding pocket, that play an important role in ligand or substrate binding. Docking studies clearly indicated that these five residues are important determinants for binding as they have strong hydrogen bonding interactions with the ligand.

  17. Positive Modulatory Interactions of NMDA Receptor GluN1/2B Ligand Binding Domains Attenuate Antagonists Activity

    Directory of Open Access Journals (Sweden)

    Douglas Bledsoe

    2017-05-01

    Full Text Available N-methyl D-aspartate receptors (NMDAR play crucial role in normal brain function and pathogenesis of neurodegenerative and psychiatric disorders. Functional tetra-heteromeric NMDAR contains two obligatory GluN1 subunits and two identical or different non-GluN1 subunits that include six different gene products; four GluN2 (A–D and two GluN3 (A–B subunits. The heterogeneity of subunit combination facilities the distinct function of NMDARs. All GluN subunits contain an extracellular N-terminal Domain (NTD and ligand binding domain (LBD, transmembrane domain (TMD and an intracellular C-terminal domain (CTD. Interaction between the GluN1 and co-assembling GluN2/3 subunits through the LBD has been proven crucial for defining receptor deactivation mechanisms that are unique for each combination of NMDAR. Modulating the LBD interactions has great therapeutic potential. In the present work, by amino acid point mutations and electrophysiology techniques, we have studied the role of LBD interactions in determining the effect of well-characterized pharmacological agents including agonists, competitive antagonists, and allosteric modulators. The results reveal that agonists (glycine and glutamate potency was altered based on mutant amino acid sidechain chemistry and/or mutation site. Most antagonists inhibited mutant receptors with higher potency; interestingly, clinically used NMDAR channel blocker memantine was about three-fold more potent on mutated receptors (N521A, N521D, and K531A than wild type receptors. These results provide novel insights on the clinical pharmacology of memantine, which is used for the treatment of mild to moderate Alzheimer's disease. In addition, these findings demonstrate the central role of LBD interactions that can be exploited to develop novel NMDAR based therapeutics.

  18. Role of platelet CD40 ligand for endothelial cell-monocyte interaction in the presence of flow

    Science.gov (United States)

    Wagner, Andreas H.; Schwarz, Manuel; König, Gerd; Hecker, Markus

    2014-11-01

    CD40 ligand (CD154)-induced ultra-large von Willebrand factor (vWF) multimer-mediated endothelial cell-platelet-monocyte interaction may play an important role in adaptive and maladaptive vascular remodeling processes. Here we analyzed the impact of and conditions favouring the deposition of these multimers on the endothelial cell (EC) surface by way of CD40-CD154 co-stimulation in settings mimicking different forms of blood flow. Upon exposure to low oscillatory shear stress and sCD154, a release of vWF multimers comparable to histamine stimulation was monitored on the EC surface in a string-like fashion. Moreover, ex vivo perfused carotid arteries of wild type mice at low laminar shear stress rates showed a luminal release of vWF as ultra-large vWF multimers (ULVWF) upon stimulation with sCD154 which was absent in blood vessels of CD40 knockout mice. The observed CD40- and flow-dependent vWF release from intact endothelial cells and subsequent vWF multimer formation may facilitate adhesion and subsequent activation of circulating platelets at atherosclerotic predilection sites, which are characterized by disturbed flow patterns. This in turn may amplify endothelial cell-monocyte interaction, thus possibly initiating or promoting early atherosclerotic lesion formation.

  19. 5f state interaction with inner coordination sphere ligands: einsteinium 3+ ion fluorescence in aqueous and organic phases

    Energy Technology Data Exchange (ETDEWEB)

    Beitz, J.V.; Wester, D.W.; Williams, C.W.

    1983-01-01

    The interaction between 5f electron states of einsteinium 3+ ion and coordinated ligands in solution has been probed using laser-induced fluorescence. Aquo einsteinium 3+ ion was observed to fluoresce from its first excited J = 5 state in a broad-band peaking at 9260 wavenumbers. The observed fluorescence lifetimes were 1.05 microseconds and 2.78 microseconds in H/sub 2/O and D/sub 2/O (99+ % D atom), respectively. The non-radiative decay rates derived from the lifetime data are compared with previously reported data for Cm, Sm, Eu, Tb, and Dy aquo 3+ ions. The 5f actinide states exhibit substantially greater non-radiative decay rates than do lanthanide 4f states of similar energy gap. This provides evidence that actinide 5f electrons interact more strongly with their inner coordination sphere than do lanthanide ion 4f electrons. The fluorescence lifetime of einsteinium 3+ ion complexed with 1 formal di(2-ethylhexyl)orthophosphoric acid in h-heptane was 2.34 microseconds. 3 figures, 1 table.

  20. Control of stripelike and hexagonal self-assembly of gold nanoparticles by the tuning of interactions between triphenylene ligands.

    Science.gov (United States)

    Shen, Zhongrong; Yamada, Mami; Miyake, Mikio

    2007-11-21

    We describe the self-assembly of gold nanoparticles (Au NPs) protected with newly synthesized discotic liquid crystalline molecules of hexaalkoxy-substituted triphenylene (TP) in mixed toluene/methanol solvent. The stripelike (i.e., 2D consisting of linear 1D in stripe) self-assembly is realized successfully by the aid of pi-pi stacking of TP ligand on Au NPs. The smaller Au NPs with TP (AuTP) or the longer alkyl chain between TP and the gold core provide more free spaces among TP moieties. These spaces allow easy insertion of TP on adjacent AuTPs to lead an interparticle pi-pi interaction to form the stripelike arrangement. The solvent hydrophilicity can also serve as a controlled index to tune arrangement among stripelike, hexagonal close packed (hcp), or disorder. We have changed the solvent hydrophilicity by changing the ratio of methanol to toluene, which affects the balance of solution of AuTP (in toluene) and deposition (in methanol). The larger space between TPs and appropriate solvent hydrophilicity realize stripelike self-assembly caused by a strong pi-pi interaction between TPs, which was characterized by TEM, as well as fluorescence, dynamic light scattering, and 1H NMR spectra.

  1. Synthesis, DNA/HSA Interaction Spectroscopic Studies and In Vitro Cytotoxicity of a New Mixed Ligand Cu(II) Complex.

    Science.gov (United States)

    Gan, Qian; Fu, Xiabing; Chen, Weijiang; Xiong, Yahong; Fu, Yinlian; Chen, Shi; Le, Xueyi

    2016-05-01

    A new mixed ligand copper(II)-dipeptide complex with 2-(2'-pyridyl)benzothiazole (pbt), [Cu(Gly-L-leu)(pbt)(H2O)]·ClO4 (Gly-L-leu = Glycyl-L-leucine anion) was synthesized and characterized by various physico-chemical means. The DNA binding and cleavage properties of the complex investigated by viscosity, agarose gel electrophoresis and multi-spectroscopic techniques (UV, circular dichroism (CD) and fluorescence) showed that the complex was bound to CT-DNA through intercalation mode with moderate binding constant (K b = 3.132 × 10(4) M(-1)), and cleaved pBR322 DNA efficiently (~ 5 μM) in the presence of Vc, probably via an oxidative mechanism induced by •OH. Additionally, the interaction of the complex with human serum albumin (HSA) was explored by UV-visible, CD, fluorescence, synchronous fluorescence and 3D fluorescence spectroscopy. The complex exhibits desired affinity to HSA through hydrophobic interaction. Moreover, the cytotoxicity of the complex against three human carcinoma cell lines (HeLa, HepG2 and A549) was evaluated by MTT assay, which showed that the complex had effective cytotoxicity and higher inhibition toward A549 cell lines with IC50 of 38.0 ± 3.2 μM.

  2. Ni(II Complexes with Schiff Base Ligands: Preparation, Characterization, DNA/Protein Interaction and Cytotoxicity Studies

    Directory of Open Access Journals (Sweden)

    Hui Yu

    2017-10-01

    Full Text Available In this study, two Ni(II complexes, namely [Ni(HL12(OAc2] (1 and [Ni(L22] (2 (where HL1 and HL2 are (E-1-((1-(2-hydroxyethyl-1H-pyrazol-5-yliminomethyl-naphthalen-2-ol and (E-ethyl-5-((2-hydroxynaphthalen-1-ylmethyleneamino-1-methyl-1H-pyrazole-4-carboxylate, respectively, were synthesized and characterized by X-ray crystallography, Electrospray Ionization Mass Spectrometry (ESI-MS, elemental analysis, and IR. Their uptake in biological macromolecules and cancer cells were preliminarily investigated through electronic absorption (UV-Vis, circular dichroism (CD and fluorescence quenching measurements. Bovine serum albumin (BSA interaction experiments were investigated by spectroscopy which showed that the complexes and ligands could quench the intrinsic fluorescence of BSA through an obvious static quenching process. The spectroscopic studies indicated that these complexes could bind to DNA via groove, non-covalent, and electrostatic interactions. Furthermore, in vitro methyl thiazolyl tetrazolium (MTT assays and Annexin V/PI flow cytometry experiments were performed to assess the antitumor capacity of the complexes against eight cell lines. The results show that both of the complexes possess reasonable cytotoxicities.

  3. Square pyramidal copper(II) complexes with forth generation fluoroquinolone and neutral bidentate ligand: structure, antibacterial, SOD mimic and DNA-interaction studies.

    Science.gov (United States)

    Patel, Mohan N; Parmar, Pradhuman A; Gandhi, Deepen S

    2010-02-01

    Coordination of neutral bidentate ligand to copper ion in combination with gatifloxacin have been focused in this article. The effect of complexation reflects antibacterial activity, DNA interaction and SOD mimic activity of individual greatly. The geometry at the central metal ion provides a site for binding of superoxide anion responsible for better SOD mimic behaviour. Copyright (c) 2009 Elsevier Ltd. All rights reserved.

  4. Interactions of algal ligands, metal complexation and availability, and cell responses of the diatom Ditylum brightwellii with a gradual increase in copper

    NARCIS (Netherlands)

    Rijstenbil, J.W.; Gerringa, L.J.A.

    2002-01-01

    A continuous culture experiment was conducted to study interactions between copper-binding ligands released by light- limited Ditylum brightwellii, and toxic effects of Cu. on this diatom. Over 6 months, the Cu concentration in the medium has been increased in seven steps (3-173 nM). At each Cu.

  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. Alignment of SWNTs by protein-ligand interaction of functionalized magnetic particles under low magnetic fields.

    Science.gov (United States)

    Park, Tae Jung; Park, Jong Pil; Lee, Seok Jae; Jung, Dae-Hwan; Ko, Young Koan; Jung, Hee-Tae; Lee, Sang Yup

    2011-05-01

    Carbon nanotubes (CNTs) have attracted considerable attention for applications using their superior mechanical, thermal and electrical properties. A simple method to controllably align single-walled CNTs (SWNTs) by using magnetic particles embedded with superparamagnetic iron oxide as an accelerator under the magnetic field was developed. The functionalization of SWNTs using biotin, interacted with streptavidin-coupled magnetic particles (micro-to-nano in diameter), and layer-by-layer assembly were performed for the alignment of a particular direction onto the clean silicon and the gold substrate at very low magnetic forces (0.02-0.89 T) at room temperature. The successful alignment of the SWNTs with multi-layer film was observed by scanning electron microscopy (SEM) and transmission electron microscopy (TEM). By changing the orientation and location of the substrates, crossed-networks of SWNTs-magnetic particle complex could easily be fabricated. We suggest that this approach, which consists of a combination of biological interaction among streptavidin-biotin and magnetite particles, should be useful for lateral orientation of individual SWNTs with controllable direction.

  7. Role of Carboxylate ligands in the Synthesis of AuNPs: Size Control, Molecular Interaction and Catalytic Activity

    KAUST Repository

    Aljohani, Hind Abdullah

    2016-05-22

    low temperature. The structure of the citrate layer on the AuNP surface may be a key factor in gaining a more detailed understanding of nanoparticle formation and stabilization. This can be affecting the catalytic activity. These thoughts invited us to systematically examine the role of sodium citrate as a stabilizer of gold nanoparticles, which is the main theme of this thesis. This research is focused on three main objectives, controlling the size of the gold nanoparticles based on citrate (and other carboxylate ligands Trisodium citrate dihydrate, Isocitric Acid, Citric acid, Trimesic acid, Succinic Acid, Phthalic acid, Disodium glutarate, Tartaric Acid, Sodium acetate, Acetic Acid and Formic Acid by varying the concentration of Gold/sodium citrate, investigating the interaction of the citrate layer on the AuNP surface, and testing the activity of the Au/TiO2 catalysts for the oxidation of carbon monoxide. This thesis will be divided into five chapters. In Chapter 1, a general literature study on the various applications and methods of synthesis of Au nanoparticles is described. Then we present the main synthetic pathways of Au nanoparticles we selected. A part of the bibliographic study was given to the use of Au nanoparticles in catalysis. In Chapter 2, we give a brief description of the different experimental procedures and characterization techniques utilized over the course of the present work. The study of the size control and the interaction between gold nanoparticles and the stabilizer (carboxylate groups) was achieved by using various characterization techniques such as UV-visible spectroscopy, Transmission Electron Microscopy (TEM), X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS), Nuclear Magnetic resonance spectroscopy (NMR) and Fourier transform infrared spectroscopy (FTIR). In Chapter 3, we discuss the synthesis and size control of Au nanoparticles by following the growth of these nanoparticles by UV-Visible spectroscopy and TEM. We

  8. Understanding the Selectivity Mechanism of the Human Asialoglycoprotein Receptor (ASGP-R) toward Gal- and Man- type Ligands for Predicting Interactions with Exogenous Sugars

    OpenAIRE

    Emo Chiellini; Federica Chiellini; Anna Maria Bianucci; Laura Murgia; Ilaria Massarelli

    2007-01-01

    A practical approach for addressing the computer simulation of protein-carbohydrate interactions is described here. An articulated computational protocol was set up and validated by checking its ability to predict experimental data, available in the literature, and concerning the selectivity shown by the Carbohydrate Recognition Domain (CRD) of the human asialoglycoprotein receptor (ASGP-R) toward Gal-type ligands. Some required features responsible for the interactions were identified. Subse...

  9. High pressure as a tool for investigating protein-ligand interactions

    Energy Technology Data Exchange (ETDEWEB)

    Marchal, S [INSERM U128, IFR 122, 1919 route de Mende, F-34293 Montpellier Cedex 5 (France); Lange, R [INSERM U128, IFR 122, 1919 route de Mende, F-34293 Montpellier Cedex 5 (France); Tortora, P [Dipartimento di Biotecnologie e Bioscienze, Universita di Milano-Bicocca, Piazza della Scienza 2, I-20126 Milan (Italy); Balny, C [INSERM U128, IFR 122, 1919 route de Mende, F-34293 Montpellier Cedex 5 (France)

    2004-04-14

    In recent years, the application of pressure on biological systems has gained increasing interest. Pressure-induced destabilization of electrostatic and hydrophobic interactions is currently exploited to study conformational protein stability and macromolecular assemblies of proteins. Due to links between severe human pathologies and ordered protein oligomerization into aggregates, which have become apparent, a better knowledge of the molecular and structural determinants that ensure the packing efficiency and stability of such complexes has taken on special importance. Here, we report the effect of pressure on the property of human ataxin-3 of aggregation. The results indicate the importance of its polyglutamine chain length in the stability and the tendency of the protein to form spheroids. Partial unfolding of the protein leading to solvent exposure of hydrophobic domains appears to be a prerequisite in the aggregation process of ataxin-3.

  10. 1,3-dialkoxycalix[4]arenecrowns-6 in 1,3-alternate conformation: Cesium-selective ligands that exploit cation-arene interactions

    Energy Technology Data Exchange (ETDEWEB)

    Ungaro, R. (Dipt. di Chimica Organica e Industriale, Univ. degli Studi di Parma (Italy)); Casnati, A. (Dipt. di Chimica Organica e Industriale, Univ. degli Studi di Parma (Italy)); Ugozzoli, F. (Dipt. di Chimica Generale ed Inorganica, Analitica, Chimica Fisica e Centro di Studio per la Strutturistica Diffrattometrica del CNR, Univ. degli Studi di Parma (Italy)); Pochini, A. (Dipt. di Chimica Organica e Industriale, Univ. degli Studi di Parma (Italy)); Dozol, J.F. (SEP/SETED, CEA, Centre d' Etudes de Cadarache (France)); Hill, C. (SEP/SETED, CEA, Centre d' Etudes de Cadarache (France)); Rouquette, H. (SEP/SETED, CEA, Centre d' Etudes de Cadarache (France))

    1994-08-02

    The complexation properties of these ligands are the result of the simultaneous operation of several effects: the size of the crown ether ring, the polarity of the calix conformation, and the strength of the cation/[pi]-electron interactions. The easy removal of cesium cation from the complexes by stripping and the consequent possibility of recycling the ligands, as well as their high lipophilicity, which allows their use in supported liquid membranes, make these new cesium-selective ionophores highly attractive for treatment of radioactive waste. (orig.)

  11. Screening for antiviral inhibitors of the HIV integrase-LEDGF/p75 interaction using the AlphaScreen luminescent proximity assay.

    Science.gov (United States)

    Hou, Yan; McGuinness, Debra E; Prongay, Andrew J; Feld, Boris; Ingravallo, Paul; Ogert, Robert A; Lunn, Charles A; Howe, John A

    2008-06-01

    Small-molecule inhibitors of HIV integrase (HIV IN) have emerged as a promising new class of antivirals for the treatment of HIV/AIDS. The compounds currently approved or in clinical development specifically target HIV DNA integration and were identified using strand-transfer assays targeting the HIV IN/viral DNA complex. The authors have developed a second biochemical assay for identification of HIV integrase inhibitors, targeting the interaction between HIV IN and the cellular cofactor LEDGF/p75. They developed a luminescent proximity assay (AlphaScreen) designed to measure the association of the 80-amino-acid integrase binding domain of LEDGF/p75 with the 163-amino-acid catalytic core domain of HIV IN. This assay proved to be quite robust (with a Z' factor of 0.84 in screening libraries arrayed as orthogonal mixtures) and successfully identified several compounds specific for this protein-protein interaction.

  12. Synthesis, characterization, DNA/protein interaction and cytotoxicity studies of Cu(II) and Co(II) complexes derived from dipyridyl triazole ligands

    Science.gov (United States)

    Zhang, Wei; Yao, Di; Wei, Yi; Tang, Jie; Bian, He-Dong; Huang, Fu-Ping; Liang, Hong

    2016-06-01

    Four different transition metal complexes containing dipyridyl triazole ligands, namely [Cu(abpt)2Cl2]·2H2O (1), [Cu(abpt)2(ClO4)2] (2), [Co2(abpt)2(H2O)2Cl2]·Cl2·4H2O (3) and [Co2(Hbpt)2(CH3OH)2(NO3)2] (4) have been designed, synthesized and further structurally characterized by X-ray crystallography, ESI-MS, elemental analysis, IR and Raman spectroscopy. In these complexes, the both ligands act as bidentate ligands with N, N donors. DNA binding interactions with calf thymus DNA (ct-DNA) of the ligand and its complexes 1 ~ 4 were investigated via electronic absorption, fluorescence quenching, circular dichroism and viscosity measurements as well as confocal Laser Raman spectroscopy. The results show these complexes are able to bind to DNA via the non-covalent mode i.e. intercalation and groove binding or electrostatic interactions. The interactions with bovine serum albumin (BSA) were also studied using UV-Vis and fluorescence spectroscopic methods which indicated that fluorescence quenching of BSA by these compounds was the presence of both static and dynamic quenching. Moreover, the in vitro cytotoxic effects of the complexes against four cell lines SK-OV-3, HL-7702, BEL7404 and NCI-H460 showed the necessity of the coordination action on the biological properties on the respective complex and that all four complexes exhibited substantial cytotoxic activity.

  13. Isothermal titration calorimetry: experimental design, data analysis, and probing macromolecule/ligand binding and kinetic interactions.

    Science.gov (United States)

    Freyer, Matthew W; Lewis, Edwin A

    2008-01-01

    Isothermal titration calorimetry (ITC) is now routinely used to directly characterize the thermodynamics of biopolymer binding interactions and the kinetics of enzyme-catalyzed reactions. This is the result of improvements in ITC instrumentation and data analysis software. Modern ITC instruments make it possible to measure heat effects as small as 0.1 microcal (0.4 microJ), allowing the determination of binding constants, K's, as large as 10(8) - 10(9)M(-1). Modern ITC instruments make it possible to measure heat rates as small as 0.1 microcal/sec, allowing for the precise determination of reaction rates in the range of 10(-12) mol/sec. Values for K(m) and k(cat), in the ranges of 10(-2) - 10(3) microM and 0.05 - 500 sec(-1), respectively, can be determined by ITC. This chapter reviews the planning of an optimal ITC experiment for either a binding or kinetic study, guides the reader through simulated sample experiments, and reviews analysis of the data and the interpretation of the results.

  14. Short Intramolecular N–H⋯C(carbonyl Interactions in Mixed-Ligand Molybdenum Hexacarbonyl Derivatives

    Directory of Open Access Journals (Sweden)

    Matthew G. Budge

    2011-06-01

    Full Text Available The syntheses and single-crystal structures of Mo(CO3(phen(dipy (1, Mo(CO3(biquin(dipy (2 and Mo(CO3(dpme(dipy (3, (phen = 1,10-phenanthroline, C12H8N2; dipy = 2,2'-dipyridylamine, C10H9N3; biquin = 2,2'-biquinoline, C18H12N2; dpme = 2,2'-dipyridylmethane, C11H10N2 are described. In each case, distorted fac-MoC3N3 octahedral coordination geometries arise for the metal atoms. Short intramolecular N–H…C interactions from the dipy N–H group to a carbonyl carbon atom occur in each structure. Crystal data: 1 (C25H17MoN5O3, Mr = 531.38, monoclinic, P21/n (No. 14, Z = 4, a = 11.0965 (5 Å, b = 13.0586 (6 Å, c = 16.6138 (8 Å, b = 108.324 (1°, V = 2285.31 (18 Å3, R(F = 0.035, wR(F2 = 0.070. 2 (C31H21MoN5O3, Mr = 607.47, monoclinic, P21/n (No. 14, Z = 4, a = 11.4788 (6 Å, b = 19.073 (1 Å, c = 11.9881 (6 Å, b = 95.179 (1°, V = 2613.9 (2 Å3, R(F = 0.030, wR(F2 = 0.076. 3 (C24H19MoN5O3, Mr = 521.38, monoclinic, P21/n (No. 14, Z = 4, a = 8.4222 (3 Å, b = 21.5966 (9 Å, c = 12.5011 (5 Å, b = 94.065 (1°, V = 2268.12 (15 Å3, R(F = 0.025, wR(F2 = 0.065.

  15. Design of HIV-1 Protease Inhibitors with Amino-bis-tetrahydrofuran Derivatives as P2-Ligands to Enhance Backbone-Binding Interactions: Synthesis, Biological Evaluation, and Protein-Ligand X-ray Studies.

    Science.gov (United States)

    Ghosh, Arun K; Martyr, Cuthbert D; Osswald, Heather L; Sheri, Venkat Reddy; Kassekert, Luke A; Chen, Shujing; Agniswamy, Johnson; Wang, Yuan-Fang; Hayashi, Hironori; Aoki, Manabu; Weber, Irene T; Mitsuya, Hiroaki

    2015-09-10

    Structure-based design, synthesis, and biological evaluation of a series of very potent HIV-1 protease inhibitors are described. In an effort to improve backbone ligand-binding site interactions, we have incorporated basic-amines at the C4 position of the bis-tetrahydrofuran (bis-THF) ring. We speculated that these substituents would make hydrogen bonding interactions in the flap region of HIV-1 protease. Synthesis of these inhibitors was performed diastereoselectively. A number of inhibitors displayed very potent enzyme inhibitory and antiviral activity. Inhibitors 25f, 25i, and 25j were evaluated against a number of highly-PI-resistant HIV-1 strains, and they exhibited improved antiviral activity over darunavir. Two high resolution X-ray structures of 25f- and 25g-bound HIV-1 protease revealed unique hydrogen bonding interactions with the backbone carbonyl group of Gly48 as well as with the backbone NH of Gly48 in the flap region of the enzyme active site. These ligand-binding site interactions are possibly responsible for their potent activity.

  16. A Molecular Dynamics Approach to Ligand-Receptor Interaction in the Aspirin-Human Serum Albumin Complex

    Directory of Open Access Journals (Sweden)

    H. Ariel Alvarez

    2012-01-01

    Full Text Available In this work, we present a study of the interaction between human serum albumin (HSA and acetylsalicylic acid (ASA, C9H8O4 by molecular dynamics simulations (MD. Starting from an experimentally resolved structure of the complex, we performed the extraction of the ligand by means of the application of an external force. After stabilization of the system, we quantified the force used to remove the ASA from its specific site of binding to HSA and calculated the mechanical nonequilibrium external work done during this process. We obtain a reasonable value for the upper boundary of the Gibbs free energy difference (an equilibrium thermodynamic potential between the complexed and noncomplexed states. To achieve this goal, we used the finite sampling estimator of the average work, calculated from the Jarzynski Equality. To evaluate the effect of the solvent, we calculated the so-called “viscous work,” that is, the work done to move the aspirin in the same trajectory through the solvent in absence of the protein, so as to assess the relevance of its contribution to the total work. The results are in good agreement with the available experimental data for the albumin affinity constant for aspirin, obtained through quenching fluorescence methods.

  17. Novel Interactive Data Visualization: Exploration of the ESCAPE Trial (Endovascular Treatment for Small Core and Anterior Circulation Proximal Occlusion With Emphasis on Minimizing CT to Recanalization Times) Data.

    Science.gov (United States)

    Brigdan, Matthew; Hill, Michael D; Jagdev, Abhijeet; Kamal, Noreen

    2018-01-01

    The ESCAPE (Endovascular Treatment for Small Core and Anterior Circulation Proximal Occlusion With Emphasis on Minimizing CT to Recanalization Times) randomized clinical trial collected a large diverse data set. However, it is difficult to fully understand the effects of the study on certain patient groups and disease progression. We developed and evaluated an interactive visualization of the ESCAPE trial data. We iteratively designed an interactive visualization using Python's Bokeh software library. The design was evaluated through a user study, which quantitatively evaluated its efficiency and accuracy against traditional modified Rankin Scalegraphic. Qualitative feedback was also evaluated. The novel interactive visualization of the ESCAPE data are publicly available at http://escapevisualization.herokuapp.com/. There was no difference in the efficiency and accuracy when comparing the use of the novel with the traditional visualization. However, users preferred the novel visualization because it allowed for greater exploration. Some insights obtained through exploration of the ESCAPE data are presented. Novel interactive visualizations can be applied to acute stroke trial data to allow for greater exploration of the results. URL: http://www.clinicaltrials.gov. Unique identifier: NCT01778335. © 2017 American Heart Association, Inc.

  18. Using UHF proximity loggers to quantify male-female interactions: a scoping study of estrous activity in cattle.

    Science.gov (United States)

    O'Neill, C J; Bishop-Hurley, G J; Williams, P J; Reid, D J; Swain, D L

    2014-12-10

    Reproductive efficiency is an important determinant of profitable cattle breeding systems and the success of assisted reproductive techniques (ART) in wildlife conservation programs. Methods of estrous detection used in intensive beef and dairy cattle systems lack accuracy and remain the single biggest issue for improvement of reproductive rates and such methods are not practical for either large-scale extensive beef cattle enterprises or free-living mammalian species. Recent developments in UHF (ultra high frequency) proximity logger telemetry devices have been used to provide a continuous pair-wise measure of associations between individual animals for both livestock and wildlife. The objective of this study was to explore the potential of using UHF telemetry to identify the reproductive cycle phenotype in terms of intensity and duration of estrus. The study was conducted using Belmont Red (interbred Africander Brahman Hereford-Shorthorn) cattle grazing irrigated pasture on Belmont Research Station, northeastern Australia. The cow-bull associations from three groups of cows each with one bull were recorded over a 7-week breeding season and the stage of estrus was identified using ultrasonography. Telemetry data from bull and cows, collected over 4 8-day logger deployments, were log transformed and analyzed by ANOVA. Both the number and duration of bull-cow affiliations were significantly (P<0.001) greater in estrous cows compared to anestrus cows. These results support the development of the UHF technology as a hands-off and noninvasive means of gathering socio-sexual information on both wildlife and livestock for reproductive management. Crown Copyright © 2014. Published by Elsevier B.V. All rights reserved.

  19. Molecular interactions of agonist and inverse agonist ligands at serotonin 5-HT2C G protein-coupled receptors: computational ligand docking and molecular dynamics studies validated by experimental mutagenesis results

    Science.gov (United States)

    Córdova-Sintjago, Tania C.; Liu, Yue; Booth, Raymond G.

    2015-02-01

    To understand molecular determinants for ligand activation of the serotonin 5-HT2C G protein-coupled receptor (GPCR), a drug target for obesity and neuropsychiatric disorders, a 5-HT2C homology model was built according to an adrenergic β2 GPCR (β2AR) structure and validated using a 5-HT2B GPCR crystal structure. The models were equilibrated in a simulated phosphatidyl choline membrane for ligand docking and molecular dynamics studies. Ligands included (2S, 4R)-(-)-trans-4-(3'-bromo- and trifluoro-phenyl)-N,N-dimethyl-1,2,3,4-tetrahydronaphthalene-2-amine (3'-Br-PAT and 3'-CF3-PAT), a 5-HT2C agonist and inverse agonist, respectively. Distinct interactions of 3'-Br-PAT and 3'-CF3-PAT at the wild-type (WT) 5-HT2C receptor model were observed and experimental 5-HT2C receptor mutagenesis studies were undertaken to validate the modelling results. For example, the inverse agonist 3'-CF3-PAT docked deeper in the WT 5-HT2C binding pocket and altered the orientation of transmembrane helices (TM) 6 in comparison to the agonist 3'-Br-PAT, suggesting that changes in TM orientation that result from ligand binding impact function. For both PATs, mutation of 5-HT2C residues S3.36, T3.37, and F5.47 to alanine resulted in significantly decreased affinity, as predicted from modelling results. It was concluded that upon PAT binding, 5-HT2C residues T3.37 and F5.47 in TMs 3 and 5, respectively, engage in inter-helical interactions with TMs 4 and 6, respectively. The movement of TMs 5 and 6 upon agonist and inverse agonist ligand binding observed in the 5-HT2C receptor modelling studies was similar to movements reported for the activation and deactivation of the β2AR, suggesting common mechanisms among aminergic neurotransmitter GPCRs.

  20. Correlative Förster Resonance Electron Transfer-Proximity Ligation Assay (FRET-PLA) Technique for Studying Interactions Involving Membrane Proteins.

    Science.gov (United States)

    Ivanusic, Daniel; Denner, Joachim; Bannert, Norbert

    2016-08-01

    This unit provides a guide and detailed protocol for studying membrane protein-protein interactions (PPI) using the acceptor-sensitized Förster resonance electron transfer (FRET) method in combination with the proximity ligation assay (PLA). The protocol in this unit is focused on the preparation of FRET-PLA samples and the detection of correlative FRET/PLA signals as well as on the analysis of FRET-PLA data and interpretation of correlative results when using cyan fluorescent protein (CFP) as a FRET donor and yellow fluorescent protein (YFP) as a FRET acceptor. The correlative application of FRET and PLA combines two powerful tools for monitoring PPI, yielding results that are more reliable than with either technique alone. © 2016 by John Wiley & Sons, Inc. Copyright © 2016 John Wiley & Sons, Inc.

  1. Inorganic Phosphate Modulates the Expression of the NaPi-2a Transporter in the trans-Golgi Network and the Interaction with PIST in the Proximal Tubule

    Directory of Open Access Journals (Sweden)

    Miguel A. Lanaspa

    2013-01-01

    Full Text Available Inorganic phosphate (Pi homeostasis is maintained by the tight regulation of renal Pi excretion versus reabsorption rates that are in turn modulated by adjusting the number of Pi transporters (mainly NaPi-2a in the proximal tubules. In response to some hormones and a high dietary Pi content, NaPi-2a is endocytosed and degraded in the lysosomes; however, we show here that some NaPi-2a molecules are targeted to the trans-Golgi network (TGN during the endocytosis. In the TGN, NaPi-2a interacts with PIST (PDZ-domain protein interacting specifically with TC10, a TGN-resident PDZ-domain-containing protein. The extension of the interaction is proportional to the expression of NaPi-2a in the TGN, and, consistent with that, it is increased with a high Pi diet. When overexpressed in opossum kidney (OK cells, PIST retains NaPi-2a in the TGN and inhibits Na-dependent Pi transport. Overexpression of PIST also prevents the adaptation of OK cells to a low Pi culture medium. Our data supports the view that NaPi-2a is subjected to retrograde trafficking from the plasma membrane to the TGN using one of the machineries involved in endosomal transport and explains the reported expression of NaPi-2a in the TGN.

  2. Rapid and accurate assessment of GPCR-ligand interactions Using the fragment molecular orbital-based density-functional tight-binding method.

    Science.gov (United States)

    Morao, Inaki; Fedorov, Dmitri G; Robinson, Roger; Southey, Michelle; Townsend-Nicholson, Andrea; Bodkin, Mike J; Heifetz, Alexander

    2017-09-05

    The reliable and precise evaluation of receptor-ligand interactions and pair-interaction energy is an essential element of rational drug design. While quantum mechanical (QM) methods have been a promising means by which to achieve this, traditional QM is not applicable for large biological systems due to its high computational cost. Here, the fragment molecular orbital (FMO) method has been used to accelerate QM calculations, and by combining FMO with the density-functional tight-binding (DFTB) method we are able to decrease computational cost 1000 times, achieving results in seconds, instead of hours. We have applied FMO-DFTB to three different GPCR-ligand systems. Our results correlate well with site directed mutagenesis data and findings presented in the published literature, demonstrating that FMO-DFTB is a rapid and accurate means of GPCR-ligand interactions. © 2017 Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc. © 2017 Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.

  3. Synthesis, characterization, DNA interaction and antimicrobial screening of isatin-based polypyridyl mixed-ligand Cu(II and Zn(II complexes

    Directory of Open Access Journals (Sweden)

    NATARAJAN RAMAN

    2010-06-01

    Full Text Available Several mixed ligand Cu(II/Zn(II complexes using 3-(phenyl-imino-1,3-dihydro-2H-indol-2-one (obtained by the condensation of isatin and aniline as the primary ligand and 1,10-phenanthroline (phen/2,2’-bipyridine (bpy as an additional ligand were synthesized and characterized analytically and spectroscopically by elemental analyses, magnetic susceptibility and molar conductance measurements, as well as by UV–Vis, IR, NMR and FAB mass spectroscopy. The interaction of the complexes with calf thymus (CT DNA was studied using absorption spectra, cyclic voltammetric and viscosity measurements. They exhibit absorption hypochromicity, and the specific viscosity increased during the binding of the complexes to calf thymus DNA. The shifts in the oxidation–reduction potential and changes in peak current on addition of DNA were shown by CV measurements. The Cu(II/Zn(II complexes were found to promote cleavage of pUC19 DNA from the supercoiled form I to the open circular form II and linear form III. The complexes show enhanced antifungal and antibacterial activities compared with the free ligand.

  4. Network of nuclear receptor ligands in multiple sclerosis: Common pathways and interactions of sex-steroids, corticosteroids and vitamin D3-derived molecules.

    Science.gov (United States)

    Rolf, Linda; Damoiseaux, Jan; Hupperts, Raymond; Huitinga, Inge; Smolders, Joost

    2016-09-01

    Sex-steroids, corticosteroids and vitamin D3-derived molecules have all been subject to experimental studies and clinical trials in a plethora of autoimmune diseases. These molecules are all derived from cholesterol metabolites and are ligands for nuclear receptors. Ligation of these receptors results in direct regulation of multiple gene transcription involved in general homeostatic and adaptation networks, including the immune system. Indeed, the distinct ligands affect the function of both myeloid and lymphoid cells, eventually resulting in a less pro-inflammatory immune response which is considered beneficial in autoimmune diseases. Next to the immune system, also the central nervous system is prone to regulation by these nuclear receptor ligands. Understanding of the intricate interactions between sex-steroids, corticosteroids and vitamin D3 metabolites, on the one hand, and the immune and central nervous system, on the other hand, may reveal novel approaches to utilize these nuclear receptor ligands to full extent as putative treatments in multiple sclerosis, the prototypic immune-driven disease of the central nervous system. Copyright © 2016 Elsevier B.V. All rights reserved.

  5. Synthesis, characterization, DNA/protein interaction and cytotoxicity studies of Cu(II) and Co(II) complexes derived from dipyridyl triazole ligands.

    Science.gov (United States)

    Zhang, Wei; Yao, Di; Wei, Yi; Tang, Jie; Bian, He-Dong; Huang, Fu-Ping; Liang, Hong

    2016-06-15

    Four different transition metal complexes containing dipyridyl triazole ligands, namely [Cu(abpt)2Cl2]·2H2O (1), [Cu(abpt)2(ClO4)2] (2), [Co2(abpt)2(H2O)2Cl2]·Cl2·4H2O (3) and [Co2(Hbpt)2(CH3OH)2(NO3)2] (4) have been designed, synthesized and further structurally characterized by X-ray crystallography, ESI-MS, elemental analysis, IR and Raman spectroscopy. In these complexes, the both ligands act as bidentate ligands with N, N donors. DNA binding interactions with calf thymus DNA (ct-DNA) of the ligand and its complexes 1~4 were investigated via electronic absorption, fluorescence quenching, circular dichroism and viscosity measurements as well as confocal Laser Raman spectroscopy. The results show these complexes are able to bind to DNA via the non-covalent mode i.e. intercalation and groove binding or electrostatic interactions. The interactions with bovine serum albumin (BSA) were also studied using UV-Vis and fluorescence spectroscopic methods which indicated that fluorescence quenching of BSA by these compounds was the presence of both static and dynamic quenching. Moreover, the in vitro cytotoxic effects of the complexes against four cell lines SK-OV-3, HL-7702, BEL7404 and NCI-H460 showed the necessity of the coordination action on the biological properties on the respective complex and that all four complexes exhibited substantial cytotoxic activity. Copyright © 2016. Published by Elsevier B.V.

  6. Convergent study of Ru-ligand interactions through QTAIM, ELF, NBO molecular descriptors and TDDFT analysis of organometallic dyes

    Science.gov (United States)

    Sánchez-Coronilla, Antonio; Sánchez-Márquez, Jesús; Zorrilla, David; Martín, Elisa I.; de los Santos, Desireé M.; Navas, Javier; Fernández-Lorenzo, Concha; Alcántara, Rodrigo; Martín-Calleja, Joaquín

    2014-08-01

    We report a theoretical study of a series of Ru complexes of interest in dye-sensitised solar cells, in organic light-emitting diodes, and in the war against cancer. Other metal centres, such as Cr, Co, Ni, Rh, Pd, and Pt, have been included for comparison purposes. The metal-ligand trends in organometallic chemistry for those compounds are shown synergistically by using three molecular descriptors: quantum theory of atoms in molecules (QTAIM), electron localisation function (ELF) and second-order perturbation theory analysis of the natural bond orbital (NBO). The metal-ligand bond order is addressed through both delocalisation index (DI) of QTAIM and fluctuation index (λ) of ELF. Correlation between DI and λ for Ru-N bond in those complexes is introduced for the first time. Electron transfer and stability was also assessed by the second-order perturbation theory analysis of the NBO. Electron transfer from the lone pair NBO of the ligands toward the antibonding lone pair NBO of the metal plays a relevant role in stabilising the complexes, providing useful insights into understanding the effect of the 'expanded ligand' principle in supramolecular chemistry. Finally, absorption wavelengths associated to the metal-to-ligand charge transfer transitions and the highest occupied molecular orbital (HOMO)--lowest unoccupied molecular orbital (LUMO) characteristics were studied by time-dependent density functional theory.

  7. Sensitivity and specificity of in situ proximity ligation for protein interaction analysis in a model of steatohepatitis with Mallory-Denk bodies.

    Directory of Open Access Journals (Sweden)

    Bernhard Zatloukal

    Full Text Available The in situ proximity ligation assay (isPLA is an increasingly used technology for in situ detection of protein interactions, post-translational modifications, and spatial relationships of antigens in cells and tissues, in general. In order to test its performance we compared isPLA with immunofluorescence microscopy by analyzing protein interactions in cytoplasmic protein aggregates, so-called Mallory Denk bodies (MDBs. These structures represent protein inclusions in hepatocytes typically found in human steatohepatitis and they can be generated in mice by feeding of 3,5-diethoxy-carbonyl-1,4-dihydrocollidine (DDC. We investigated the colocalization of all three key MDB components, namely keratin 8 (K8, keratin 18 (K18, and p62 (sequestosome 1 by isPLA and immunofluorescence microscopy. Sensitivity and specificity of isPLA was assessed by using Krt8-/- and Krt18-/- mice as biological controls, along with a series of technical controls. isPLA signal visualization is a robust technology with excellent sensitivity and specificity. The biological relevance of signals generated critically depends on the performance of antibodies used, which requires careful testing of antibodies like in immunofluorescence microscopy. There is a clear advantage of isPLA in visualizing protein co-localization, particularly when antigens are present at markedly different concentrations. Furthermore, isPLA is superior to confocal microscopy with respect to spatial resolution of colocalizing antigens. Disadvantages compared to immunofluorescence are increased costs and longer duration of the laboratory protocol.

  8. Molecular mechanism of kNBC1—carbonic anhydrase II interaction in proximal tubule cells

    Science.gov (United States)

    Pushkin, Alexander; Abuladze, Natalia; Gross, Eitan; Newman, Debra; Tatishchev, Sergei; Lee, Ivan; Fedotoff, Olga; Bondar, Galyna; Azimov, Rustam; Ngyuen, Matt; Kurtz, Ira

    2004-01-01

    We have recently shown that carbonic anhydrase II (CAII) binds in vitro to the C-terminus of the electrogenic sodium bicarbonate cotransporter kNBC1 (kNBC1-ct). In the present study we determined the molecular mechanisms for the interaction between the two proteins and whether kNBC1 and CAII form a transport metabolon in vivo wherein bicarbonate is transferred from CAII directly to the cotransporter. Various residues in the C-terminus of kNBC1 were mutated and the effect of these mutations on both the magnitude of CAII binding and the function of kNBC1 expressed in mPCT cells was determined. Two clusters of acidic amino acids, L958DDV and D986NDD in the wild-type kNBC1-ct involved in CAII binding were identified. In both acidic clusters, the first aspartate residue played a more important role in CAII binding than others. A significant correlation between the magnitude of CAII binding and kNBC1-mediated flux was shown. The results indicated that CAII activity enhances flux through the cotransporter when the enzyme is bound to kNBC1. These data are the first direct evidence that a complex of an electrogenic sodium bicarbonate cotransporter with CAII functions as a transport metabolon. PMID:15218065

  9. Molecular modeling of the AhR structure and interactions can shed light on ligand-dependent activation and transformation mechanisms.

    Science.gov (United States)

    Bonati, Laura; Corrada, Dario; Tagliabue, Sara Giani; Motta, Stefano

    2017-02-01

    Molecular modeling has given important contributions to elucidation of the main stages in the AhR signal transduction pathway. Despite the lack of experimentally determined structures of the AhR functional domains, information derived from homologous systems has been exploited for modeling their structure and interactions. Homology models of the AhR PASB domain have provided information on the binding cavity and contributed to elucidate species-specific differences in ligand binding. Molecular Docking simulations of the ligand binding process have given insights into differences in binding of diverse agonists, antagonists, and selective AhR modulators, and their application to virtual screening of large databases of compounds have allowed identification of novel AhR ligands. Recently available structural information on protein-protein and protein-DNA complexes of other bHLH-PAS systems has opened the way for modeling the AhR:ARNT dimer structure and investigating the mechanisms of AhR transformation and DNA binding. Future research directions should include simulation of the protein dynamics to obtain a more reliable description of intermolecular interactions involved in signal transmission.

  10. Evaluation of DNA/Protein interactions and cytotoxic studies of copper(II) complexes incorporated with N, N donor ligands and terpyridine ligand.

    Science.gov (United States)

    Tummalapalli, Kiran; C S, Vasavi; Munusami, Punnagai; Pathak, Madhvesh; M M, Balamurali

    2017-02-01

    A series of four new copper(II) heteroleptic complexes, [Cu(2‴-pytpy) (L)] (NO 3 ) 2 ·2H 2 O (1-4), where 2‴-pytpy=4'-(2'''-Pyridyl)-2, 2':6', 2''-terpyridine, L=bipyridyl (bpy), 1, 10 phenanthroline(phen), dipyridoquinoxaline(dpq) and dipyridophenazine (dppz) were synthesized and characterized by spectroscopic techniques. Further, the molecular structure of the complex (2) was confirmed by single crystal X-ray diffraction technique and the data revealed a penta coordinated, distorted square-pyramidal geometry with triclinic system. The interactions of four complexes with calf thymus DNA and bovine serum albumin (BSA) were investigated by electronic absorption, fluorescence and circular dichroism spectroscopy techniques. Spectral studies substantiated an intercalative binding mode of metal complexes with ct-DNA. Significant binding interactions of the complexes with protein have been further revealed from fluorescence studies. Furthermore, all the four complexes show potential cytotoxicity towards the human liver carcinoma cell line (HepG-2). Copyright © 2016 Elsevier B.V. All rights reserved.

  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. Self-assembling hydrogels crosslinked solely by receptor-ligand interactions: tunability, rationalization of physical properties, and 3D cell culture.

    Science.gov (United States)

    Thompson, Michael S; Tsurkan, Mikhail V; Chwalek, Karolina; Bornhauser, Martin; Schlierf, Michael; Werner, Carsten; Zhang, Yixin

    2015-02-16

    We report a novel, noncovalent hydrogel system crosslinked solely by receptor-ligand interactions between biotin and avidin. The simple hydrogel synthesis and functionalization together with the widespread use of biotinylated ligands in biosciences make this versatile system suitable for many applications. The gels possess a range of tunable physical properties, including stiffness, lifetime, and swelling. The erosion rates, unexpectedly fast compared to the kinetic parameters for biotin-avidin, are explored in terms of stretching tensions on the polymers, a concept well-known on the single-molecule level, but largely unexplored in supramolecular systems. As proof of utility, the gels were functionalized with different peptide sequences to control human mesenchymal stromal cell morphology in 3D culture. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  13. Cyclophilin B interacts with sodium-potassium ATPase and is required for pump activity in proximal tubule cells of the kidney.

    Directory of Open Access Journals (Sweden)

    Guillermo Suñé

    Full Text Available Cyclophilins (Cyps, the intracellular receptors for Cyclosporine A (CsA, are responsible for peptidyl-prolyl cis-trans isomerisation and for chaperoning several membrane proteins. Those functions are inhibited upon CsA binding. Albeit its great benefits as immunosuppressant, the use of CsA has been limited by undesirable nephrotoxic effects, including sodium retention, hypertension, hyperkalemia, interstial fibrosis and progressive renal failure in transplant recipients. In this report, we focused on the identification of novel CypB-interacting proteins to understand the role of CypB in kidney function and, in turn, to gain further insight into the molecular mechanisms of CsA-induced toxicity. By means of yeast two-hybrid screens with human kidney cDNA, we discovered a novel interaction between CypB and the membrane Na/K-ATPase β1 subunit protein (Na/K-β1 that was confirmed by pull-down, co-immunoprecipitation and confocal microscopy, in proximal tubule-derived HK-2 cells. The Na/K-ATPase pump, a key plasma membrane transporter, is responsible for maintenance of electrical Na+ and K+ gradients across the membrane. We showed that CypB silencing produced similar effects on Na/K-ATPase activity than CsA treatment in HK-2 cells. It was also observed an enrichment of both alpha and beta subunits in the ER, what suggested a possible failure on the maturation and routing of the pump from this compartment towards the plasma membrane. These data indicate that CypB through its interaction with Na/K-β1 might regulate maturation and trafficking of the pump through the secretory pathway, offering new insights into the relationship between cyclophilins and the nephrotoxic effects of CsA.

  14. Platinum(II Complexes with Tetradentate Schiff Bases as Ligands: Synthesis, Characterization and Detection of DNA Interaction by Differential Pulse Voltammetry

    Directory of Open Access Journals (Sweden)

    Lijun Li

    2012-01-01

    Full Text Available Five sterically hindered platinum(II complexes with tetradentate schiff bases as ligands, [Pt(L] (L= N,N′-bisalicylidene-1,2-ethylenediamine (L1, N,N′-bisalicylidene-1,2-cyclohexanediamine (L2, N,N′-bis(5-hydroxyl-salicylidene-1,2-cyclohexanediamine (L3, N,N′-bisalicylidene-1,2-diphenyl-ethylenediamine (L4 and N,N′-bis(3-tert-butyl-5-methyl-salicylidene-1,2-diphenylethylenediamine (L5 have been synthesized and characterized by IR spectroscopy and elemental analysis. The sterical hindrance of antitumor drug candidates potentially makes them less susceptible to deactivation by sulphur containing proteins and helping to overcome resistance mechanisms. The interaction of these metal complexes with fish sperm single-stranded DNA (ssDNA was studied electrochemically based on the oxidation signals of guanine and adenine. Differential pulse voltammetry was employed to monitor the DNA interaction in solution by using renewable pencil graphite electrode. The results indicate that ligands with different groups can strongly affect the interaction between [Pt(L] complexes and ssDNA due to sterical hindrances and complex [Pt(L1] has the best interaction with DNA among the five complexes.

  15. Proximal renal tubular acidosis

    Science.gov (United States)

    Renal tubular acidosis - proximal; Type II RTA; RTA - proximal; Renal tubular acidosis type II ... by alkaline substances, mainly bicarbonate. Proximal renal tubular acidosis (Type II RTA) occurs when bicarbonate is not ...

  16. Quantifying protein-ligand interactions by direct electrospray ionization-MS analysis: evidence of nonuniform response factors induced by high molecular weight molecules and complexes.

    Science.gov (United States)

    Lin, Hong; Kitova, Elena N; Klassen, John S

    2013-10-01

    The deleterious effects of high molecular weight (MW) solute (polymers and noncovalent assemblies) on protein-ligand (PL) affinity measurements carried out using the direct electrospray ionization mass spectrometry (ESI-MS) assay are described. The presence of high MW solute, that do not interact with the protein (P) or ligand (L) of interest, is shown to result in a decrease in the abundance (Ab) ratio (R) of ligand-bound to free protein ions (i.e., Ab(PL)/Ab(P)) measured for protein-carbohydrate complexes. This effect, which can reduce the apparent association constant by more than 60%, is found to be more pronounced as the differences in the surface properties of P and PL become more significant. It is proposed that the decrease in R reflects a reduction in the number of available surface sites in the ESI droplets upon introduction of large solute and increased competition between P and the more hydrophilic PL for these sites. That a similar decrease in R is observed upon introduction of surfactants to solution provides qualitative support for this hypothesis.

  17. Two crystal structures of dihydrofolate reductase-thymidylate synthase from Cryptosporidium hominis reveal protein–ligand interactions including a structural basis for observed antifolate resistance

    Energy Technology Data Exchange (ETDEWEB)

    Anderson, Amy C., E-mail: aca@dartmouth.edu [Dartmouth College, Department of Chemistry, Burke Laboratories, Hanover, NH 03755 (United States)

    2005-03-01

    An analysis of the protein–ligand interactions in two crystal structures of DHFR-TS from C. hominis reveals a possible structural basis for observed antifolate resistance in C. hominis DHFR. A comparison with the structure of human DHFR reveals residue substitutions that may be exploited for the design of species-selective inhibitors. Cryptosporidium hominis is a protozoan parasite that causes acute gastrointestinal illness. There are no effective therapies for cryptosporidiosis, highlighting the need for new drug-lead discovery. An analysis of the protein–ligand interactions in two crystal structures of dihydrofolate reductase-thymidylate synthase (DHFR-TS) from C. hominis, determined at 2.8 and 2.87 Å resolution, reveals that the interactions of residues Ile29, Thr58 and Cys113 in the active site of C. hominis DHFR provide a possible structural basis for the observed antifolate resistance. A comparison with the structure of human DHFR reveals active-site differences that may be exploited for the design of species-selective inhibitors.

  18. The Role of Coulomb Interactions for Spin Crossover Behaviors and Crystal Structural Transformation in Novel Anionic Fe(III Complexes from a π-Extended ONO Ligand

    Directory of Open Access Journals (Sweden)

    Suguru Murata

    2016-05-01

    Full Text Available To investigate the π-extension effect on an unusual negative-charged spin crossover (SCO FeIII complex with a weak N2O4 first coordination sphere, we designed and synthesized a series of anionic FeIII complexes from a π-extended naphthalene derivative ligand. Acetonitrile-solvate tetramethylammonium (TMA salt 1 exhibited an SCO conversion, while acetone-solvate TMA salt 2 was in a high-spin state. The crystal structural analysis for 2 revealed that two-leg ladder-like cation-anion arrays derived from π-stacking interactions between π-ligands of the FeIII complex anion and Coulomb interactions were found and the solvated acetone molecules were in one-dimensional channels between the cation-anion arrays. A desolvation-induced single-crystal-to-single-crystal transformation to desolvate compound 2’ may be driven by Coulomb energy gain. Furthermore, the structural comparison between quasi-polymorphic compounds 1 and 2 revealed that the synergy between Coulomb and π-stacking interactions induces a significant distortion of coordination structure of 2.

  19. Functional glass slides for in vitro evaluation of interactions between osteosarcoma TE85 cells and mineral-binding ligands

    Energy Technology Data Exchange (ETDEWEB)

    Song, Jie; Chen, Julia; Klapperich, Catherine M.; Eng, Vincent; Bertozzi, Carolyn R.

    2004-07-20

    Primary amine-functionalized glass slides obtained through a multi-step plasma treatment were conjugated with anionic amino acids that are frequently found as mineral binding elements in acidic extracellular matrix components of natural bone. The modified glass surfaces were characterized by X-ray photoelectron spectroscopy (XPS) and contact angle measurements. Human osteosarcoma TE85 cells were cultured on these functionalized slides and analyses on both protein and gene expression levels were performed to probe the ''biocompatibility'' of the surface ligands. Cell attachment and proliferation on anionic surfaces were either better than or comparable to those of cells cultured on tissue culture polystyrene (TCPS). The modified glass surfaces promoted the expression of osteocalcin, alkaline phosphatase activity and ECM proteins such as fibronectin and vitronectin under differentiation culture conditions. Transcript analysis using gene chip microarrays confirmed that culturing TE85 cells on anionic surfaces did not activate apoptotic pathways. Collectively, these results suggest that the potential mineral-binding anionic ligands examined here do not exert significant adverse effects on the expression of important osteogenic markers of TE85 cells. This work paves the way for the incorporation of these ligands into 3-dimensional artificial bone-like scaffolds.

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

    Science.gov (United States)

    Ricci, Clarisse G; Netz, Paulo A

    2009-08-01

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

  1. Ligand modeling and design

    Energy Technology Data Exchange (ETDEWEB)

    Hay, B.P. [Pacific Northwest National Lab., Richland, WA (United States)

    1997-10-01

    The purpose of this work is to develop and implement a molecular design basis for selecting organic ligands that would be used in the cost-effective removal of specific radionuclides from nuclear waste streams. Organic ligands with metal ion specificity are critical components in the development of solvent extraction and ion exchange processes that are highly selective for targeted radionuclides. The traditional approach to the development of such ligands involves lengthy programs of organic synthesis and testing, which in the absence of reliable methods for screening compounds before synthesis, results in wasted research effort. The author`s approach breaks down and simplifies this costly process with the aid of computer-based molecular modeling techniques. Commercial software for organic molecular modeling is being configured to examine the interactions between organic ligands and metal ions, yielding an inexpensive, commercially or readily available computational tool that can be used to predict the structures and energies of ligand-metal complexes. Users will be able to correlate the large body of existing experimental data on structure, solution binding affinity, and metal ion selectivity to develop structural design criteria. These criteria will provide a basis for selecting ligands that can be implemented in separations technologies through collaboration with other DOE national laboratories and private industry. The initial focus will be to select ether-based ligands that can be applied to the recovery and concentration of the alkali and alkaline earth metal ions including cesium, strontium, and radium.

  2. Knowledge networks in the Dutch aviation industry: The proximity paradox

    NARCIS (Netherlands)

    Broekel, T.; Boschma, R.A.

    2012-01-01

    The importance of geographical proximity for interaction and knowledge sharing has been discussed extensively in recent years. There is increasing consensus that geographical proximity is just one out of many types of proximities that might be relevant. We argue that proximity may be a crucial

  3. Fluorescent Cross-Linked Supramolecular Polymer Constructed by Orthogonal Self-Assembly of Metal-Ligand Coordination and Host-Guest Interaction.

    Science.gov (United States)

    Qian, Xiaomin; Gong, Weitao; Li, Xiaopeng; Fang, Le; Kuang, Xiaojun; Ning, Guiling

    2016-05-10

    A new host molecule consists of four terpyridine groups as the binding sites with zinc(II) ion and a copillar[5]arene incorporated in the center as a spacer to interact with guest molecule was designed and synthesized. Due to the 120 ° angle of the rigid aromatic segment, a cross-linked dimeric hexagonal supramolecular polymer was therefore generated as the result of the orthogonal self-assembly of metal-ligand coordination and host-guest interaction. UV/Vis spectroscopy, (1) H NMR spectroscopy, viscosity and dynamic light-scattering techniques were employed to characterize and understand the cross-linking process with the introduction of zinc(II) ion and guest molecule. More importantly, well-defined morphology of the self-assembled supramolecular structure can be tuned by altering the adding sequence of the two components, that is, the zinc(II) ion and the guest molecule. In addition, introduction of a competitive ligand suggested the dynamic nature of the supramolecular structure. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  4. Ranking docking poses by graph matching of protein-ligand interactions: lessons learned from the D3R Grand Challenge 2

    Science.gov (United States)

    da Silva Figueiredo Celestino Gomes, Priscila; Da Silva, Franck; Bret, Guillaume; Rognan, Didier

    2017-08-01

    A novel docking challenge has been set by the Drug Design Data Resource (D3R) in order to predict the pose and affinity ranking of a set of Farnesoid X receptor (FXR) agonists, prior to the public release of their bound X-ray structures and potencies. In a first phase, 36 agonists were docked to 26 Protein Data Bank (PDB) structures of the FXR receptor, and next rescored using the in-house developed GRIM method. GRIM aligns protein-ligand interaction patterns of docked poses to those of available PDB templates for the target protein, and rescore poses by a graph matching method. In agreement with results obtained during the previous 2015 docking challenge, we clearly show that GRIM rescoring improves the overall quality of top-ranked poses by prioritizing interaction patterns already visited in the PDB. Importantly, this challenge enables us to refine the applicability domain of the method by better defining the conditions of its success. We notably show that rescoring apolar ligands in hydrophobic pockets leads to frequent GRIM failures. In the second phase, 102 FXR agonists were ranked by decreasing affinity according to the Gibbs free energy of the corresponding GRIM-selected poses, computed by the HYDE scoring function. Interestingly, this fast and simple rescoring scheme provided the third most accurate ranking method among 57 contributions. Although the obtained ranking is still unsuitable for hit to lead optimization, the GRIM-HYDE scoring scheme is accurate and fast enough to post-process virtual screening data.

  5. Nifedipine inhibits advanced glycation end products (AGEs) and their receptor (RAGE) interaction-mediated proximal tubular cell injury via peroxisome proliferator-activated receptor-gamma activation

    Energy Technology Data Exchange (ETDEWEB)

    Matsui, Takanori [Department of Pathophysiology and Therapeutics of Diabetic Vascular Complications, Kurume University School of Medicine, Kurume (Japan); Yamagishi, Sho-ichi, E-mail: shoichi@med.kurume-u.ac.jp [Department of Pathophysiology and Therapeutics of Diabetic Vascular Complications, Kurume University School of Medicine, Kurume (Japan); Takeuchi, Masayoshi [Department of Pathophysiological Science, Faculty of Pharmaceutical Science, Hokuriku University, Kanazawa (Japan); Ueda, Seiji; Fukami, Kei; Okuda, Seiya [Department of Medicine, Kurume University School of Medicine, Kurume (Japan)

    2010-07-23

    Research highlights: {yields} Nifedipine inhibited the AGE-induced up-regulation of RAGE mRNA levels in tubular cells, which was prevented by GW9662, an inhibitor of peroxisome proliferator-activated receptor-{gamma}. {yields} GW9662 treatment alone increased RAGE mRNA levels in tubular cells. {yields} Nifedipine inhibited the AGE-induced reactive oxygen species generation, NF-{kappa}B activation and increases in intercellular adhesion molecule-1 and transforming growth factor-{beta} gene expression in tubular cells, all of which were blocked by GW9662. -- Abstract: There is a growing body of evidence that advanced glycation end products (AGEs) and their receptor (RAGE) interaction evokes oxidative stress generation and subsequently elicits inflammatory and fibrogenic reactions, thereby contributing to the development and progression of diabetic nephropathy. We have previously found that nifedipine, a calcium-channel blocker (CCB), inhibits the AGE-induced mesangial cell damage in vitro. However, effects of nifedipine on proximal tubular cell injury remain unknown. We examined here whether and how nifedipine blocked the AGE-induced tubular cell damage. Nifedipine, but not amlodipine, a control CCB, inhibited the AGE-induced up-regulation of RAGE mRNA levels in tubular cells, which was prevented by the simultaneous treatment of GW9662, an inhibitor of peroxisome proliferator-activated receptor-{gamma} (PPAR{gamma}). GW9662 treatment alone was found to increase RAGE mRNA levels in tubular cells. Further, nifedipine inhibited the AGE-induced reactive oxygen species generation, NF-{kappa}B activation and increases in intercellular adhesion molecule-1 and transforming growth factor-beta gene expression in tubular cells, all of which were blocked by GW9662. Our present study provides a unique beneficial aspect of nifedipine on diabetic nephropathy; it could work as an anti-oxidative and anti-inflammatory agent against AGEs in tubular cells by suppressing RAGE expression

  6. Quantifying the Sigma and Pi interactions between U(V) f orbitals and halide, alkyl, alkoxide, amide and ketimide ligands

    Energy Technology Data Exchange (ETDEWEB)

    University of California, Berkeley; Lukens, Wayne W.; Edelstein, Norman M.; Magnani, Nicola; Hayton, Trevor W.; Fortier, Skye; Seaman, Lani A.

    2013-06-20

    f Orbital bonding in actinide and lanthanide complexes is critical to their behavior in a variety of areas from separations to magnetic properties. Octahedral f1 hexahalide complexes have been extensively used to study f orbital bonding due to their simple electronic structure and extensive spectroscopic characterization. The recent expansion of this family to include alkyl, alkoxide, amide, and ketimide ligands presents the opportunity to extend this study to a wider variety of ligands. To better understand f orbital bonding in these complexes, the existing molecular orbital (MO) model was refined to include the effect of covalency on spin orbit coupling in addition to its effect on orbital angular momentum (orbital reduction). The new MO model as well as the existing MO model and the crystal field (CF) model were applied to the octahedral f1 complexes to determine the covalency and strengths of the ? and ? bonds formed by the f orbitals. When covalency is significant, MO models more precisely determined the strengths of the bonds derived from the f orbitals; however, when covalency was small, the CF model was better than either MO model. The covalency determined using the new MO model is in better agreement with both experiment and theory than that predicted by the existing MO model. The results emphasize the role played by the orbital energy in determining the strength and covalency of bonds formed by the f orbitals.

  7. Templated Formation of Discrete RNA and DNA:RNA Hybrid G-Quadruplexes and Their Interactions with Targeting Ligands.

    Science.gov (United States)

    Bonnat, Laureen; Dejeu, Jérôme; Bonnet, Hugues; Génnaro, Béatrice; Jarjayes, Olivier; Thomas, Fabrice; Lavergne, Thomas; Defrancq, Eric

    2016-02-24

    G-rich RNA and DNA oligonucleotides derived from the human telomeric sequence were assembled onto addressable cyclopeptide platforms through oxime ligations and copper-catalyzed azide-alkyne cycloaddition (CuAAc) reactions. The resulting conjugates were able to fold into highly stable RNA and DNA:RNA hybrid G-quadruplex (G4) architectures as demonstrated by UV, circular dichroism (CD), and NMR spectroscopic analysis. Whereas rationally designed parallel RNA and DNA:RNA hybrid G4 topologies could be obtained, we could not force the formation of an antiparallel RNA G4 structure, thus supporting the idea that this topology is strongly disfavored. The binding affinities of four representative G4 ligands toward the discrete RNA and DNA:RNA hybrid G4 topologies were compared to the one obtained with the corresponding DNA G4 structure. Surface plasmon resonance (SPR) binding analysis suggests that the accessibility to G4 recognition elements is different among the three structures and supports the idea that G4 ligands might be shaped to achieve structure selectivity in a biological context. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  8. The non-canonical NOTCH1 ligand Delta-like 1 homolog (DLK1) self interacts in mammals

    DEFF Research Database (Denmark)

    Traustadóttir, Gunnhildur Ásta; Jensen, Charlotte Harken; Garcia Ramirez, Jose Javier

    2017-01-01

    data suggest that DLK1 interacts with itself through EGF domain 4 and 5, which is distinct from the recently described NOTCH1-DLK1 interaction, which occurs between EGF domain 5 and 6. This opens up the possibility that Notch independent mechanisms like the DLK1-DLK1 interaction may modulate the non...

  9. Screening protein-ligand interactions using {sup 1}H NMR techniques for detecting the ligand; Mapeamento das interacoes proteina-ligante atraves de tecnicas de RMN de {sup 1}H utilizando deteccao do ligante

    Energy Technology Data Exchange (ETDEWEB)

    Figueiredo, Isis Martins; Marsaioli, Anita Jocelyne [Universidade Estadual de Campinas (UNICAMP), SP (Brazil). Inst. de Quimica. Dept. de Quimica Organica]. E-mail: anita@iqm.unicamp.br

    2007-07-01

    NMR is a valuable screening tool for the binding of ligands to proteins providing structural information on both protein and ligands and is thus largely applied to drug-discovery. Among the recent NMR techniques to probe weak binding protein-ligand complexes we have critically evaluated the advantages and disadvantages of STD (Saturation Transfer Difference), WaterLOGSY (Water Ligand Observation with Gradient Spectroscopy), NOE pumping and DOSY-NOESY (Diffusion-Ordered NOESY) using a mixture of BSA (bovine serum albumin) plus salicylic acid, caffeine, citric acid, adipic acid and D-glucose. (author)

  10. Identification of Xin-repeat proteins as novel ligands of the SH3 domains of nebulin and nebulette and analysis of their interaction during myofibril formation and remodeling

    Science.gov (United States)

    Eulitz, Stefan; Sauer, Florian; Pelissier, Marie-Cecile; Boisguerin, Prisca; Molt, Sibylle; Schuld, Julia; Orfanos, Zacharias; Kley, Rudolf A.; Volkmer, Rudolf; Wilmanns, Matthias; Kirfel, Gregor; van der Ven, Peter F. M.; Fürst, Dieter O.

    2013-01-01

    The Xin actin-binding repeat–containing proteins Xin and XIRP2 are exclusively expressed in striated muscle cells, where they are believed to play an important role in development. In adult muscle, both proteins are concentrated at attachment sites of myofibrils to the membrane. In contrast, during development they are localized to immature myofibrils together with their binding partner, filamin C, indicating an involvement of both proteins in myofibril assembly. We identify the SH3 domains of nebulin and nebulette as novel ligands of proline-rich regions of Xin and XIRP2. Precise binding motifs are mapped and shown to bind both SH3 domains with micromolar affinity. Cocrystallization of the nebulette SH3 domain with the interacting XIRP2 peptide PPPTLPKPKLPKH reveals selective interactions that conform to class II SH3 domain–binding peptides. Bimolecular fluorescence complementation experiments in cultured muscle cells indicate a temporally restricted interaction of Xin-repeat proteins with nebulin/nebulette during early stages of myofibril development that is lost upon further maturation. In mature myofibrils, this interaction is limited to longitudinally oriented structures associated with myofibril development and remodeling. These data provide new insights into the role of Xin actin-binding repeat–containing proteins (together with their interaction partners) in myofibril assembly and after muscle damage. PMID:23985323

  11. DNA interaction, antimicrobial studies of newly synthesized copper (II) complexes with 2-amino-6-(trifluoromethoxy)benzothiazole Schiff base ligands.

    Science.gov (United States)

    Rambabu, Aveli; Pradeep Kumar, Marri; Tejaswi, Somapangu; Vamsikrishna, Narendrula; Shivaraj

    2016-12-01

    Four novel Schiff base ligands, L 1 (1-((E)-(6-(trifluoromethoxy)benzo[d]thiazol-2-ylimino)methyl)naphthalen-2-ol, C 19 H 11 F 3 N 2 O 2 S), L 2 (3-((E)-(6-(trifluoromethoxy)benzo[d]thiazol-2-ylimino)methyl)benzene-1,2-diol, C 15 H 9 F 3 N 2 O 3 S), L 3 (2-((E)-(6-(trifluoromethoxy)benzo[d]thiazol-2-ylimino)methyl)-5-methoxyphenol, C 16 H 11 F 3 N 2 O 3 S) and L 4 (2-((E)-(6-(trifluoromethoxy)benzo[d]thiazol-2-ylimino)methyl)-4-bromophenol, C 15 H 8 BrF 3 N 2 O 2 S) and their binary copper(II) complexes 1 [Cu(L 1 ) 2 ], 2 [Cu(L 2 ) 2 ], 3 [Cu(L 3 ) 2 ] and 4 [Cu(L 4 ) 2 ] have been synthesized and characterized by elemental analysis, 1 H NMR, 13 C NMR, ESI mass, FT-IR, ESR, UV-Visible, magnetic susceptibility, TGA, SEM and powder XRD studies. Based on spectral and analytical data, a square planar geometry is assigned for all Cu(II) complexes. The ligands and their Cu(II) complexes have been screened for antimicrobial activity against bacterial species E. coli, P. aeruginosa, B. amyloliquefaciens and S. aureus and fungal species S. rolfsii and M. phaseolina and it is observed that all Cu(II) complexes are more potent than corresponding ligands. DNA binding (UV absorption, fluorescence and viscosity titrations) and cleavage (oxidative and photo cleavage) studies of Cu(II) complexes have also been investigated against calf thymus DNA (CT-DNA) and supercoiled pBR322 DNA respectively. From the experimental results, it is found that the complexes bound effectively to CT-DNA through an intercalative mode and also cleaved pBR322 DNA in an efficient manner. The DNA binding and cleavage affinities of newly synthesized Cu(II) complexes are in the order of 2>1>3>4. Copyright © 2016 Elsevier B.V. All rights reserved.

  12. Interaction of the phosphorylated DNA-binding domain in nuclear receptor CAR with its ligand-binding domain regulates CAR activation.

    Science.gov (United States)

    Shizu, Ryota; Min, Jungki; Sobhany, Mack; Pedersen, Lars C; Mutoh, Shingo; Negishi, Masahiko

    2018-01-05

    The nuclear protein constitutive active/androstane receptor (CAR or NR1I3) regulates several liver functions such as drug and energy metabolism and cell growth or death, which are often involved in the development of diseases such as diabetes and hepatocellular carcinoma. CAR undergoes a conversion from inactive homodimers to active heterodimers with retinoid X receptor α (RXRα), and phosphorylation of the DNA-binding domain (DBD) at Thr-38 in CAR regulates this conversion. Here, we uncovered the molecular mechanism by which this phosphorylation regulates the intramolecular interaction between CAR's DBD and ligand-binding domain (LBD), enabling the homodimer-heterodimer conversion. Phosphomimetic substitution of Thr-38 with Asp increased co-immunoprecipitation of the CAR DBD with CAR LBD in Huh-7 cells. Isothermal titration calorimetry assays also revealed that recombinant CAR DBD-T38D, but not nonphosphorylated CAR DBD, bound the CAR LBD peptide. This DBD-LBD interaction masked CAR's dimer interface, preventing CAR homodimer formation. Of note, EGF signaling weakened the interaction of CAR DBD T38D with CAR LBD, converting CAR to the homodimer form. The DBD-T38D-LBD interaction also prevented CAR from forming a heterodimer with RXRα. However, this interaction opened up a CAR surface, allowing interaction with protein phosphatase 2A. Thr-38 dephosphorylation then dissociated the DBD-LBD interaction, allowing CAR heterodimer formation with RXRα. We conclude that the intramolecular interaction of phosphorylated DBD with the LBD enables CAR to adapt a transient monomer configuration that can be converted to either the inactive homodimer or the active heterodimer.

  13. Nuclear magnetic resonance study of interaction of ligands with Streptococcus faecium dihydrofolate reductase labeled with (. gamma. -/sup 13/C)tryptophan

    Energy Technology Data Exchange (ETDEWEB)

    London, R.E. (Los Alamos National Lab., NM); Groff, J.P.; Cocco, L.; Blakley, R.L.

    1982-01-01

    Dihydrofolate reductase from Streptococcus faecium has been labeled with (..gamma..-/sup 13/C)tryptophan. We have determined changes occurring in the chemical shifts and line widths of the four resonances of the /sup 13/C NMR spectrum of the labeled enzyme, due to its interaction with various ligands. These include the coenzyme, NPDPH and related nucleotides, folate and its polyglutamate derivatives, and many inhibitors including methotrexate and trimethoprim. In addition, paramagnetic relaxation effects produced by a bound spin-labeled analogue of 2'-phosphoadenosine-5'-diphosphoribose on the tryptophan C/sup ..gamma../ carbons have been measured. Distances calculated from the relaxation data have been compared with corresponding distances in the crystallographic model of the NADPH-methotrexate ternary complex of Lactobacillus casei reductase. The paramagnetic relaxation data indicate that the two downfield resonances (1 and 2) correspond to tryptophans (W/sub A/ and W/sub B/) that are more remote from the catalytic site, and from the crystallographic model these are seen to be Trp-115 and Trp-160. The upfield resonances (3 and 4) that show broadening due to chemical exchange correspond to closer residues (W/sub C/ and W/sub D/), and these are identified with Trp-6 and Trp-22. However, the relaxation data do not permit specific assignments within the nearer and farther pairs. Although resonance 3, which is split due to chemical exchange, was formerly assigned to Trp-6, data obtained for the enzyme in the presence of various ligands are better interpreted if resonance 3 is assigned to Trp-22, which is located on a loop that joins elements of secondary structure and forms one side of the ligand-binding cavity.

  14. Application of frontal affinity chromatography with mass spectrometry (FAC-MS) for stereospecific ligand-macromolecule interaction, detection and screening.

    Science.gov (United States)

    Slon-Usakiewicz, Jacek J; Redden, Peter

    2009-01-01

    Using frontal affinity chromatography coupled to mass spectrometry (FAC-MS) we have established a general stereoselective detection and screening method of intact racemates which can generate binding affinity information about the individual enantiomers that is also applicable to other ligand isomeric mixtures. FAC-MS has been shown to be a versatile technology utilizing direct binding in screening assays and extending its application toward chiral drug development, especially in the early discovery stages as well as its utility in secondary Structure-activity relationship (SAR) studies allow this platform to make a significant step toward facilitating the demand for pure enantiomeric drugs. Using renin, which is as an important drug target, we show that for detection and screening purposes there is no need to first use timely and costly methods of separating racemates in order to get precise information about the binding affinities of the composite enantiomers.

  15. DNA interaction and cytotoxic activities of square planar platinum(II) complexes with N, S-donor ligands

    Science.gov (United States)

    Patel, Mohan N.; Patel, Chintan R.; Joshi, Hardik N.; Thakor, Khyati P.

    2014-06-01

    The platinum(II) complexes with N, S-donor ligands have been synthesized and characterized by physicochemical methods viz. elemental, electronic, FT-IR, 1H NMR and LC-MS spectra. The binding mode and potency of the complexes with HS DNA (Herring Sperm) have been examined by absorption titration and viscosity measurement studies. The results revealed that complexes bind to HS DNA via covalent mode with the intrinsic binding constant (Kb) in the range 1.37-7.76 × 105 M-1. Decrease in the relative viscosity of HS DNA also supports the covalent mode of binding. The DNA cleavage activity of synthesized complexes has been carried out by gel electrophoresis experiment using supercoiled form of pUC19 DNA; showing the unwinding of the negatively charged supercoiled DNA. Brine shrimp (Artemia Cysts) lethality bioassay technique has been applied for the determination of toxic property of synthesized complexes in terms of μM.

  16. Inhibition of Human Aldehyde Oxidase Activity by Diet-Derived Constituents: Structural Influence, Enzyme-Ligand Interactions, and Clinical Relevance

    OpenAIRE

    Barr, John T.; Jones, Jeffrey P.; Oberlies, Nicholas H.; Paine, Mary F.

    2015-01-01

    The mechanistic understanding of interactions between diet-derived substances and conventional medications in humans is nascent. Most investigations have examined cytochrome P450–mediated interactions. Interactions mediated by other phase I enzymes are understudied. Aldehyde oxidase (AO) is a phase I hydroxylase that is gaining recognition in drug design and development programs. Taken together, a panel of structurally diverse phytoconstituents (n = 24) was screened for inhibitors of the AO-m...

  17. Photoactivated In Vivo Proximity Labeling.

    Science.gov (United States)

    Beck, David B; Bonasio, Roberto

    2017-06-19

    Identification of molecular interactions is paramount to understanding how cells function. Most available technologies rely on co-purification of a protein of interest and its binding partners. Therefore, they are limited in their ability to detect low-affinity interactions and cannot be applied to proteins that localize to difficult-to-solubilize cellular compartments. In vivo proximity labeling (IPL) overcomes these obstacles by covalently tagging proteins and RNAs based on their proximity in vivo to a protein of interest. In IPL, a heterobifunctional probe comprising a photoactivatable moiety and biotin is recruited by a monomeric streptavidin tag fused to a protein of interest. Following UV irradiation, candidate interacting proteins and RNAs are covalently biotinylated with tight spatial and temporal control and subsequently recovered using biotin as an affinity handle. Here, we describe experimental protocols to discover novel protein-protein and protein-RNA interactions using IPL. © 2017 by John Wiley & Sons, Inc. Copyright © 2017 John Wiley & Sons, Inc.

  18. Controlled immobilization of His-tagged proteins for protein-ligand interaction experiments using Ni²⁺-NTA layer on glass surfaces.

    Science.gov (United States)

    Cherkouk, Charaf; Rebohle, Lars; Lenk, Jens; Keller, Adrian; Ou, Xin; Laube, Markus; Neuber, Christin; Haase-Kohn, Cathleen; Skorupa, Wolfgang; Pietzsch, Jens

    2015-01-01

    Gold surfaces functionalized with nickel-nitrilotriacetic acid (Ni²⁺-NTA) as self-assembled monolayers (SAM) to immobilize histidine (His)-tagged biomolecules are broadly reported in the literature. However, the increasing demand of using microfluidic systems and biosensors takes more and more advantage on silicon technology which provides dedicated glass surfaces and substantially allows cost and resource savings. Here we present a novel method for the controlled oriented immobilization of His-tagged proteins on glass surfaces functionalized with a Ni²⁺-NTA layer. Exemplarily, the protein pattern morphology after immobilization on the Ni²⁺-NTA layer of His6-tagged soluble receptor for advanced glycation endproducts (sRAGE) was investigated and compared to non-oriented immobilization of sRAGE on amino SAM by using scanning electron microscopy (SEM). Moreover, we demonstrated interaction of immobilized sRAGE with three structurally different ligands, S100A12, S100A4, and glycated low density lipoproteins (glycLDL), by means of peak-force tapping atomic force microscopy (PF-AFM). We showed a clear discrimination of different protein-ligand orientations by differential height measurements.

  19. Ligand field and intermolecular interactions tuning the magnetic properties of spin-crossover Fe(II) polymer with 4,4‧-bipyridine

    Science.gov (United States)

    Luo, Yang-Hui; Liu, Qing-Ling; Yang, Li-Jing; Ling, Yang; Wang, Wei; Sun, Bai-Wang

    2015-02-01

    A new spin crossover coordination polymer (SCO-CPs) of Fe(II)-4,4‧-bipyridine (4,4‧-bipy) family: {Fe(4,4‧-bipy)2(H2O)2}·(4,4‧-bipy)· 8(H2O)·2(ClO4) (3), which displays half spin transitions between 100 and 300 K, has been synthesized and structurally characterized. Compound 3 featured with two-dimensional (2-D) grids connected by hydrogen bonds and π…π packing between one-dimensional (1-D) chains, the 2-D grids expand to three-dimensional (3-D) architecture supported by a "S-shaped holder" involving lattice 4-4‧-bipy, water molecules and perchlorate anion. We compared 3 with the other two analogous complexes: ({Fe(4,4‧-bipy) (H2O)2 (NCS)2}·4,4‧-bipy, 1 and {Fe(4,4‧-bipy)2(NCS)2}·mSolv, 2) through Hirshfeld surfaces analysis, which revealed that the low ligand field strength (NCS-) and lone-pair…H contacts contribute to the stabilization of HS (high-spin) state of the Fe(II) ion, while the high ligand field strength (4,4‧-bipy) and strong intermolecular contacts (hydrogen bonds and π…π packing interactions) make for the LS (low-spin) state.

  20. Protocols and pitfalls in obtaining fatty acid-binding proteins for biophysical studies of ligand-protein and protein-protein interactions

    Directory of Open Access Journals (Sweden)

    Qian Wang

    2017-07-01

    Full Text Available Adipocyte fatty acid-binding protein (AFABP: FABP4 is a member of the intracellular lipid-binding protein family that is thought to target long-chain fatty acids to nuclear receptors such as peroxisome proliferator-activated receptor gamma (PPARγ, which in turn plays roles in insulin resistance and obesity. A molecular understanding of AFABP function requires robust isolation of the protein in liganded and free forms as well as characterization of its oligomerization state(s under physiological conditions. We report development of a protocol to optimize the production of members of this protein family in pure form, including removal of their bound lipids by mixing with hydrophobically functionalized hydroxypropyl dextran beads and validation by two-dimensional NMR spectroscopy. The formation of self-associated or covalently bonded protein dimers was evaluated critically using gel filtration chromatography, revealing conditions that promote or prevent formation of disulfide-linked homodimers. The resulting scheme provides a solid foundation for future investigations of AFABP interactions with key ligand and protein partners involved in lipid metabolism.

  1. Attachment of streptavidin to β-cyclodextrin molecular printboards via orthogonal host-guest and protein-ligand interactions

    NARCIS (Netherlands)

    Ludden, M.J.W.; Péter, M.; Reinhoudt, David; Huskens, Jurriaan

    2006-01-01

    Streptavidin (SAv) is attached to β-cyclodextrin (β-CD) self-assembled monolayers (SAMs) via orthogonal host-guest and SAv-biotin interactions. The orthogonal linkers consist of a biotin functionality for binding to SAv and adamantyl functionalities for host-guest interactions at β-CD SAMs. SAv

  2. Molecular recognition in a diverse set of protein-ligand interactions studied with molecular dynamics simulations and end-point free energy calculations.

    Science.gov (United States)

    Wang, Bo; Li, Liwei; Hurley, Thomas D; Meroueh, Samy O

    2013-10-28

    End-point free energy calculations using MM-GBSA and MM-PBSA provide a detailed understanding of molecular recognition in protein-ligand interactions. The binding free energy can be used to rank-order protein-ligand structures in virtual screening for compound or target identification. Here, we carry out free energy calculations for a diverse set of 11 proteins bound to 14 small molecules using extensive explicit-solvent MD simulations. The structure of these complexes was previously solved by crystallography and their binding studied with isothermal titration calorimetry (ITC) data enabling direct comparison to the MM-GBSA and MM-PBSA calculations. Four MM-GBSA and three MM-PBSA calculations reproduced the ITC free energy within 1 kcal·mol(-1) highlighting the challenges in reproducing the absolute free energy from end-point free energy calculations. MM-GBSA exhibited better rank-ordering with a Spearman ρ of 0.68 compared to 0.40 for MM-PBSA with dielectric constant (ε = 1). An increase in ε resulted in significantly better rank-ordering for MM-PBSA (ρ = 0.91 for ε = 10), but larger ε significantly reduced the contributions of electrostatics, suggesting that the improvement is due to the nonpolar and entropy components, rather than a better representation of the electrostatics. The SVRKB scoring function applied to MD snapshots resulted in excellent rank-ordering (ρ = 0.81). Calculations of the configurational entropy using normal-mode analysis led to free energies that correlated significantly better to the ITC free energy than the MD-based quasi-harmonic approach, but the computed entropies showed no correlation with the ITC entropy. When the adaptation energy is taken into consideration by running separate simulations for complex, apo, and ligand (MM-PBSAADAPT), there is less agreement with the ITC data for the individual free energies, but remarkably good rank-ordering is observed (ρ = 0.89). Interestingly, filtering MD snapshots by prescoring

  3. Noncovalent interactions of Cu+ with N-donor ligands (pyridine, 4,4-dipyridyl, 2,2-dipyridyl, and 1,10-phenanthroline): collision-induced dissociation and theoretical studies.

    Science.gov (United States)

    Rannulu, N S; Rodgers, M T

    2007-05-10

    Collision-induced dissociation of complexes of Cu+ bound to a variety of N-donor ligands (N-L) with Xe is studied using guided ion beam tandem mass spectrometry. The N-L ligands examined include pyridine, 4,4-dipyridyl, 2,2-dipyridyl, and 1,10-phenanthroline. In all cases, the primary and lowest-energy dissociation channel observed corresponds to the endothermic loss of a single intact N-L ligand. Sequential dissociation of additional N-L ligands is observed at elevated energies for the pyridine and 4,4-dipyridyl complexes containing more than one ligand. Ligand exchange processes to produce Cu+Xe are also observed as minor reaction pathways in several systems. The primary cross section thresholds are interpreted to yield 0 and 298 K bond dissociation energies (BDEs) after accounting for the effects of multiple ion-neutral collisions, the kinetic and internal energy distributions of the reactants, and dissociation lifetimes. Density functional theory calculations at the B3LYP/6-31G* level are performed to obtain model structures, vibrational frequencies, and rotational constants for the neutral N-L ligands and the Cu+(N-L)x complexes. The relative stabilities of the various conformations of these N-L ligands and Cu+(N-L)x complexes as well as theoretical BDEs are determined from single point energy calculations at the B3LYP/6-311+G(2d,2p) level of theory using B3LYP/6-31G* optimized geometries. Excellent agreement between theory and experiment is observed for all complexes containing one or two N-L ligands, while theory systematically underestimates the strength of binding for complexes containing more than two N-L ligands. The ground-state structures of these complexes and the trends in the sequential BDEs are explained in terms of stabilization gained from sd-hybridization and repulsive ligand-ligand interactions. The nature of the binding interactions in the Cu+(N-L)x complexes are examined via natural bond orbital analyses.

  4. Silica- and germania-based dual-ligand sol-gel organic-inorganic hybrid sorbents combining superhydrophobicity and π-π interaction. The role of inorganic substrate in sol-gel capillary microextraction.

    Science.gov (United States)

    Seyyal, Emre; Malik, Abdul

    2017-04-29

    Principles of sol-gel chemistry were utilized to create silica- and germania-based dual-ligand surface-bonded sol-gel coatings providing enhanced performance in capillary microextraction (CME) through a combination of ligand superhydrophobicity and π-π interaction. These organic-inorganic hybrid coatings were prepared using sol-gel precursors with bonded perfluorododecyl (PF-C12) and phenethyl (PhE) ligands. Here, the ability of the PF-C12 ligand to provide enhanced hydrophobic interaction was advantageously combined with π-π interaction capability of the PhE moiety to attain the desired sorbent performance in CME. The effect of the inorganic sorbent component on microextraction performance of was explored by comparing microextraction characteristics of silica- and germania-based sol-gel sorbents. The germania-based dual-ligand sol-gel sorbent demonstrated superior CME performance compared to its silica-based counterpart. Thermogravimetric analysis (TGA) of the created silica- and germania-based dual-ligand sol-gel sorbents suggested higher carbon loading on the germania-based sorbent. This might be indicative of more effective condensation of the organic ligand-bearing sol-gel-active chemical species to the germania-based sol-gel network (than to its silica-based counterpart) evolving in the sol solution. The type and concentration of the organic ligands were varied in the sol-gel sorbents to fine-tune extraction selectivity toward different classes of analytes. Specific extraction (SE) values were used for an objective comparison of the prepared sol-gel CME sorbents. The sorbents with higher content of PF-C12 showed remarkable affinity for aliphatic hydrocarbons. Compared to their single-ligand sol-gel counterparts, the dual-ligand sol-gel coatings demonstrated significantly superior CME performance in the extraction of alkylbenzenes, providing up to ∼65.0% higher SE values. The prepared sol-gel CME coatings provided low ng L-1 limit of detections (LOD) (4

  5. Time efficient detection of protein-ligand interactions with the polarization optimized PO-WaterLOGSY NMR experiment.

    Science.gov (United States)

    Gossert, Alvar D; Henry, Christelle; Blommers, Marcel J J; Jahnke, Wolfgang; Fernández, César

    2009-04-01

    The identification of compounds that bind to a protein of interest is of central importance in contemporary drug research. For screening of compound libraries, NMR techniques are widely used, in particular the Water-Ligand Observed via Gradient SpectroscopY (WaterLOGSY) experiment. Here we present an optimized experiment, the polarization optimized WaterLOGSY (PO-WaterLOGSY). Based on a water flip-back strategy in conjunction with model calculations and numerical simulations, the PO-WaterLOGSY is optimized for water polarization recovery. Compared to a standard setup with the conventional WaterLOGSY, time consuming relaxation delays have been considerably shortened and can even be omitted through this approach. Furthermore, the robustness of the pulse sequence in an industrial setup was increased by the use of hard pulse trains for selective water excitation and water suppression. The PO-WaterLOGSY thus yields increased time efficiency by factor of 3-5 when compared with previously published schemes. These time savings have a substantial impact in drug discovery, since significantly larger compound libraries can be tested in screening campaigns.

  6. Time efficient detection of protein-ligand interactions with the polarization optimized PO-WaterLOGSY NMR experiment

    Energy Technology Data Exchange (ETDEWEB)

    Gossert, Alvar D.; Henry, Christelle; Blommers, Marcel J. J.; Jahnke, Wolfgang; Fernandez, Cesar [Novartis Institutes for Biomedical Research (Switzerland)], E-mail: cesar.fernandez@novartis.com

    2009-04-15

    The identification of compounds that bind to a protein of interest is of central importance in contemporary drug research. For screening of compound libraries, NMR techniques are widely used, in particular the Water-Ligand Observed via Gradient SpectroscopY (WaterLOGSY) experiment. Here we present an optimized experiment, the polarization optimized WaterLOGSY (PO-WaterLOGSY). Based on a water flip-back strategy in conjunction with model calculations and numerical simulations, the PO-WaterLOGSY is optimized for water polarization recovery. Compared to a standard setup with the conventional WaterLOGSY, time consuming relaxation delays have been considerably shortened and can even be omitted through this approach. Furthermore, the robustness of the pulse sequence in an industrial setup was increased by the use of hard pulse trains for selective water excitation and water suppression. The PO-WaterLOGSY thus yields increased time efficiency by factor of 3-5 when compared with previously published schemes. These time savings have a substantial impact in drug discovery, since significantly larger compound libraries can be tested in screening campaigns.

  7. On the accuracy of DFT methods in reproducing ligand substitution energies for transition metal complexes in solution: The role of dispersive interactions

    KAUST Repository

    Jacobsen, Heiko

    2011-12-23

    The performance of a series of density functionals when tested on the prediction of the phosphane substitution energy of transition metal complexes is evaluated. The complexes Fe-BDA and Ru-COD (BDA=benzylideneacetone, COD=cyclooctadiene) serve as reference systems, and calculated values are compared with the experimental values in THF as obtained from calorimetry. Results clearly indicate that functionals specifically developed to include dispersion interactions usually outperform other functionals when BDA or COD substitution is considered. However, when phosphanes of different sizes are compared, functionals including dispersion interactions, at odd with experimental evidence, predict that larger phosphanes bind more strongly than smaller phosphanes, while functionals not including dispersion interaction reproduce the experimental trends with reasonable accuracy. In case of the DFT-D functionals, inclusion of a cut-off distance on the dispersive term resolves this issue, and results in a rather robust behavior whatever ligand substitution reaction is considered. Ne quid nimis: Describing chemical reactions in solution by computational techniques developed for gas-phase scenarios might produce erroneous results (see histogram). Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  8. Mixed-ligand copper(II) phenolate complexes: Synthesis, spectral characterization, phosphate-hydrolysis, antioxidant, DNA interaction and cytotoxic studies

    Science.gov (United States)

    Gurumoorthy, Perumal; Mahendiran, Dharmasivam; Prabhu, Durai; Arulvasu, Chinnasamy; Rahiman, Aziz Kalilur

    2015-01-01

    A series of phenol-based mixed-ligand copper(II) complexes of the type [CuL1-4(diimine)] (1-8), where L1-4 = N1,N2-bis(5-substituted-2-hydroxybenzylidene)-1,2-ethylene/phenylenediimine and diimine = 2,2‧-bipyridyl (bpy) or 1,10-phenanthroline (phen), have been isolated and fully characterized by analytical and spectral techniques. Electronic spectra of complexes suggest Cu(II) cation has a d9 electronic configuration, adopting distorted octahedral geometry with axial elongation, due to Jahn-Teller effect. Electrochemical studies of complexes evidenced one-electron irreversible reduction wave in the cathodic region. The observed rate constant (k) values for the hydrolysis of 4-nitrophenylphosphate (4-NPP) are in the range of 0.25-3.82 × 10-2 min-1. The obtained room temperature magnetic moment values (1.79-1.90 BM) lies within the range observed for octahedral copper(II) complexes. Antioxidant studies revealed that these complexes possess considerable radical scavenging potency against DPPH. The binding studies of complexes with calf thymus DNA (CT-DNA) revealed intercalation with minor-groove binding, and the complex 4 exhibits highest binding activity than the other complexes. The cleavage activity on supercoiled pBR322 DNA revealed the involvement of hydroxyl radical and singlet-oxygen as reactive oxygen species, and complexes encourage binding to minor-groove. Further, the cytotoxicity of complex 4 on human hepatocellular liver carcinoma HepG2 cell line implies the cell death through apoptosis.

  9. 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.

  10. Multiset proximity spaces

    Directory of Open Access Journals (Sweden)

    A. Kandil

    2016-10-01

    Full Text Available A multiset is a collection of objects in which repetition of elements is essential. This paper is an attempt to explore the theoretical aspects of multiset by extending the notions of compact, proximity relation and proximal neighborhood to the multiset context. Examples of new multiset topologies, open multiset cover, compact multiset and many identities involving the concept of multiset have been introduced. Further, an integral examples of multiset proximity relations are obtained. A multiset topology induced by a multiset proximity relation on a multiset M has been presented. Also the concept of multiset δ- neighborhood in the multiset proximity space which furnishes an alternative approach to the study of multiset proximity spaces has been mentioned. Finally, some results on this new approach have been obtained and one of the most important results is: every T4- multiset space is semi-compatible with multiset proximity relation δ on M (Theorem 5.10.

  11. Synthesis and spectroscopic characterization of photo-affinity peptide ligands to study rhodopsin-G protein interaction.

    Science.gov (United States)

    Chen, Yihui; Herrmann, Rolf; Fishkin, Nathan; Henklein, Peter; Nakanishi, Koji; Ernst, Oliver P

    2008-01-01

    G protein-coupled receptors (GPCRs) are involved in the control of virtually all aspects of our behavior and physiology. Activated receptors catalyze nucleotide exchange in heterotrimeric G proteins (composed of alpha.GDP, beta and gamma subunits) on the inner surface of the cell membrane. The GPCR rhodopsin and the G protein transducin (G(t)) are key proteins in the early steps of the visual cascade. The main receptor interaction sites on G(t) are the C-terminal tail of the G(t)alpha-subunit and the farnesylated C-terminal tail of the G(t)gamma-subunit. Synthetic peptides derived from these C-termini specifically bind and stabilize the active rhodopsin conformation (R*). Here we report the synthesis of R*-interacting peptides containing photo-reactive groups with a specific isotope pattern, which can facilitate detection of cross-linked products by mass spectrometry. In a preliminary set of experiments, we characterized such peptides derived from the farnesylated G(t)gamma C-terminus (G(t)gamma(60-71)far) in terms of their capability to bind R*. Here, we describe novel peptides with photo-affinity labels that bind R* with affinities similar to that of the native G(t)gamma(60-71)far peptide. Such peptides will enable an improved experimental strategy to probe rhodopsin-G(t) interaction and to map so far unknown interaction sites between both proteins.

  12. Evidence for two interacting ligand binding sites in human multidrug resistance protein 2 (ATP binding cassette C2)

    NARCIS (Netherlands)

    Zelcer, Noam; Huisman, Maarten T.; Reid, Glen; Wielinga, Peter; Breedveld, Pauline; Kuil, Annemieke; Knipscheer, Puck; Schellens, Jan H. M.; Schinkel, Alfred H.; Borst, Piet

    2003-01-01

    Multidrug resistance protein 2 (MRP2) belongs to the ATP binding cassette family of transporters. Its substrates include organic anions and anticancer drugs. We have used transport assays with vesicles derived from Sf9 insect cells overproducing MRP2 to study the interactions of drugs, organic

  13. Importance of a Conserved Lys/Arg Residue for Ligand/PDZ Domain Interactions as Examined by Protein Semisynthesis

    DEFF Research Database (Denmark)

    Pedersen, Søren W; Moran, Griffin E; Sereikaité, Vita

    2016-01-01

    drug targets for diseases (in the brain in particular), so understanding the molecular details of PDZ domain interactions is of fundamental importance. PDZ domains bind to a protein partner at either a C-terminal peptide or internal peptide motifs. Here, we examined the importance of a conserved Lys...

  14. Interaction of the sigma(2) receptor ligand PB28 with the human nucleosome: computational and experimental probes of interaction with the H2A/H2B dimer.

    Science.gov (United States)

    Abate, Carmen; Elenewski, Justin; Niso, Mauro; Berardi, Francesco; Colabufo, Nicola Antonio; Azzariti, Amalia; Perrone, Roberto; Glennon, Richard A

    2010-02-01

    Sigma-2 (sigma(2)) binding sites are an emerging target for anti-neoplastic agents due to the strong apoptotic effect exhibited by sigma(2) agonists in vitro and the overexpression of these sites in tumor cells. Nonetheless, no sigma(2) receptor protein has been identified. Affinity chromatography using the high-affinity sigma(2) ligand PB28 and human SK-N-SH neuroblastoma cells was previously utilized to identify sigma(2) ligand binding proteins, specifically histones H1, H2A, H2B, and H3.3a. To rationalize this finding, homology modeling and automated docking studies were employed to probe intermolecular interactions between PB28 and human nucleosomal proteins. These studies predicted interaction of PB28 with the H2A/H2B dimer at a series of sites previously found to be implicated in chromatin compaction and nucleosomal assembly. To experimentally verify this prediction, a competitive binding assay was performed on the reconstituted H2A/H2B dimer using [(3)H]PB28 as radioligand, and an IC(50) value of 0.50 nM was determined for PB28 binding. In addition, [(3)H]PB28 was found to accumulate with up to a fivefold excess in nuclear fractions over cytosolic fractions of SK-N-SH and MCF7 cells, indicating that PB28 is capable of entering the nucleus to interact with histone proteins. In conjunction with computational results, these data suggest that PB28 may exert its cytotoxic effect through direct interaction with nuclear material.

  15. Fluorescence and electron paramagnetic resonance studies of norfloxacin and N-donor mixed-ligand ternary copper(II) complexes: Stability and interaction with SDS micelles

    Science.gov (United States)

    Vignoli Muniz, Gabriel S.; Incio, Jimmy Llontop; Alves, Odivaldo C.; Krambrock, Klaus; Teixeira, Letícia R.; Louro, Sonia R. W.

    2018-01-01

    The stability of ternary copper(II) complexes of a heterocyclic ligand, L (L being 2,2‧-bipyridine (bipy) or 1,10-phenanthroline (phen)) and the fluorescent antibacterial agent norfloxacin (NFX) as the second ligand was studied at pH 7.4 and different ionic strengths. Fluorescence quenching upon titration of NFX with the binary complexes allowed to obtain stability constants for NFX binding, Kb, as a function of ionic strength. The Kb values vary by more than two orders of magnitude when buffer concentration varies from 0.5 to 100 mM. It was observed that previously synthesized ternary complexes dissociate in buffer according with the obtained stability constants. This shows that equimolar solutions of NFX and binary complexes are equivalent to solutions of synthesized ternary complexes. The interaction of the ternary copper complexes with anionic SDS (sodium dodecyl sulfate) micelles was studied by fluorescence and electron paramagnetic resonance (EPR). Titration of NFX-loaded SDS micelles with the complexes Cu:L allowed to determine the stability constants inside the micelles. Fluorescence quenching demonstrated that SDS micelles increase the stability constants by factors around 50. EPR spectra gave details of the copper(II) local environment, and demonstrated that the structure of the ternary complexes inside SDS micelles is different from that in buffer. Mononuclear ternary complexes formed inside the micelles, while in buffer most ternary complexes are binuclear. The results show that anionic membrane interfaces increase formation of copper fluoroquinolone complexes, which can influence bioavailability, membrane diffusion, and mechanism of action of the antibiotics.

  16. Homology modeling and ligand interaction of human trafficking protein particle complex subunit 3-like protein and its correlation with Alzheimer’s disease

    Directory of Open Access Journals (Sweden)

    Manoj G

    2011-01-01

    Full Text Available In order to understand the mechanism of molecular interactions at active sites of trafficking protein particle complex (TRAPPC subunit 3-like protein (Accession number Q5T215 homology modeling and docking studies were taken up. We generated a three-dimensional (3D model of target protein based on the Crystal structure of Human BET3 protein (PDB code 1SZ7 using modeller software. Under the process of homology modeling 25 models were generated, and the model having the lowest modeler objective function value was chosen for further assessment. The generated model was assessed and validated using PROCHECK software and found to be reliable.With the generated model, we carried out a flexible docking study using the FlexX docking tool available on the Sybyl Software in order to find better antagonist site for drug binding. We carried out a flexible docking with the Palmatic acid and Donepezil as ligands; these were found to bind at LEU87, LYS84 and THR90 residues on given generated protein in our studies. We therefore concluded that the above mentioned residues were the key residue sites for ligand binding showing strong hydrogen bonding contacts.The target protein is more prevalently seen in the amygdala region of brain which forms one of the key subunit of TRAPP complex. As per functional similarity with BET3, target protein might play key role in trafficking abnormally folded A-beta and tau proteins along endoplasmic reticulum to Golgi apparatus there by leading to formation of senile plaques in various regions of brain, whose accumulation causes Alzheimer’s disease.

  17. Regulation of the Src-PP2A interaction in tumor necrosis factor (TNF)-related apoptosis-inducing ligand (TRAIL)-induced apoptosis.

    Science.gov (United States)

    Xu, Jing; Xu, Zhengfan; Zhou, Jun-Ying; Zhuang, Zhengping; Wang, Enhua; Boerner, Julie; Wu, Gen Sheng

    2013-11-15

    TNF-related apoptosis-inducing ligand (TRAIL) selectively induces apoptosis in transformed and tumor cells but not in normal cells, making it a promising agent for cancer therapy. However, many cancer cells are resistant to TRAIL, and the underlying mechanisms are not fully understood. Here, we show that the regulation of the PP2A and Src interaction plays a critical role in TRAIL resistance. Specifically, we show that TRAIL treatment activates the tyrosine kinase Src, which subsequently phosphorylates caspase-8 at tyrosine 380, leading to the inhibition of caspase-8 activation. We also show that upon TRAIL treatment, Src, caspase-8, and PP2A/C (a catalytic subunit of the PP2A phosphatase) are redistributed into lipid rafts, a microdomain of the plasma membrane enriched with cholesterol, where PP2A dephosphorylates Src at tyrosine 418 and in turn inhibits caspase-8 phosphorylation. Furthermore, we find that TRAIL treatment causes PP2A/C degradation. These data suggest that the balance between Src-mediated caspase-8 phosphorylation and the inactivation of Src-mediated caspase-8 phosphorylation by PP2A determines the outcome of TRAIL treatment in breast cancer cells. Therefore, this work identifies a novel mechanism by which the interaction between PP2A and Src in the context of caspase-8 activation modulates TRAIL sensitivity in cancer cells.

  18. Regulation of the Src-PP2A Interaction in Tumor Necrosis Factor (TNF)-related Apoptosis-inducing Ligand (TRAIL)-induced Apoptosis*

    Science.gov (United States)

    Xu, Jing; Xu, Zhengfan; Zhou, Jun-Ying; Zhuang, Zhengping; Wang, Enhua; Boerner, Julie; Wu, Gen Sheng

    2013-01-01

    TNF-related apoptosis-inducing ligand (TRAIL) selectively induces apoptosis in transformed and tumor cells but not in normal cells, making it a promising agent for cancer therapy. However, many cancer cells are resistant to TRAIL, and the underlying mechanisms are not fully understood. Here, we show that the regulation of the PP2A and Src interaction plays a critical role in TRAIL resistance. Specifically, we show that TRAIL treatment activates the tyrosine kinase Src, which subsequently phosphorylates caspase-8 at tyrosine 380, leading to the inhibition of caspase-8 activation. We also show that upon TRAIL treatment, Src, caspase-8, and PP2A/C (a catalytic subunit of the PP2A phosphatase) are redistributed into lipid rafts, a microdomain of the plasma membrane enriched with cholesterol, where PP2A dephosphorylates Src at tyrosine 418 and in turn inhibits caspase-8 phosphorylation. Furthermore, we find that TRAIL treatment causes PP2A/C degradation. These data suggest that the balance between Src-mediated caspase-8 phosphorylation and the inactivation of Src-mediated caspase-8 phosphorylation by PP2A determines the outcome of TRAIL treatment in breast cancer cells. Therefore, this work identifies a novel mechanism by which the interaction between PP2A and Src in the context of caspase-8 activation modulates TRAIL sensitivity in cancer cells. PMID:24100030

  19. The Netrin-related domain of Sfrp1 interacts with Wnt ligands and antagonizes their activity in the anterior neural plate

    Directory of Open Access Journals (Sweden)

    Esteve Pilar

    2008-08-01

    Full Text Available Abstract Background Secreted frizzled related proteins (SFRPs are multifunctional modulators of Wnt and BMP (Bone Morphogenetic Protein signalling necessary for the development of most organs and the homeostasis of different adult tissues. SFRPs fold in two independent domains: the cysteine rich domain (SfrpCRD related to the extracellular portion of Frizzled (Fz, Wnt receptors and the Netrin module (SfrpNTR defined by homologies with molecules such as Netrin-1, inhibitors of metalloproteinases and complement proteins. Due to its structural relationship with Fz, it is believed that SfrpCRD interferes with Wnt signalling by binding and sequestering the ligand. In contrast, the functional relevance of the SfrpNTR has been barely addressed. Results Here, we combine biochemical studies, mutational analysis and functional assays in cell culture and medaka-fish embryos to show that the Sfrp1NTR mimics the function of the entire molecule, binds to Wnt8 and antagonizes Wnt canonical signalling. This activity requires intact tertiary structure and is shared by the distantly related Netrin-1NTR. In contrast, the Sfrp1CRD cannot mirror the function of the entire molecule in vivo but interacts with Fz receptors and antagonizes Wnt8-mediated β-catenin transcriptional activity. Conclusion On the basis of these results, we propose that SFRP modulation of Wnt signalling may involve multiple and differential interactions among Wnt, Fz and SFRPs.

  20. Allosteric interactions across native adenosine-A3 receptor homodimers: quantification using single-cell ligand-binding kinetics

    OpenAIRE

    May, Lauren T.; Bridge, Lloyd J.; Stoddart, Leigh A.; Briddon, Stephen J.; Hill, Stephen J

    2011-01-01

    A growing awareness indicates that many G-protein-coupled receptors (GPCRs) exist as homodimers, but the extent of the cooperativity across the dimer interface has been largely unexplored. Here, measurement of the dissociation kinetics of a fluorescent agonist (ABA-X-BY630) from the human A1 or A3 adenosine receptors expressed in CHO-K1 cells has provided evidence for highly cooperative interactions between protomers of the A3-receptor dimer in single living cells. In the absence of competiti...

  1. Control of endothelial cell tube formation by Notch ligand intracellular domain interactions with activator protein 1 (AP-1)

    DEFF Research Database (Denmark)

    Forghany, Zary; Robertson, Francesca; Lundby, Alicia

    2017-01-01

    localization. We further show that it is cleaved and interacts with the JUN proto-oncogene, which forms part of the activator protein 1 (AP-1) transcription factor complex. Mechanistically, the DLL4 ICD inhibited JUN binding to DNA and thereby controlled the expression of JUN target genes, including DLL4. Our...... work further demonstrated that JUN strongly stimulates endothelial cell tube formation and that DLL4 constrains this process. These results raise the possibility that Notch/DLL4 signaling is bi-directional and suggest that the DLL4 ICD could represent a point of cross-talk between Notch and receptor...

  2. Proximal Probes Facility

    Data.gov (United States)

    Federal Laboratory Consortium — The Proximal Probes Facility consists of laboratories for microscopy, spectroscopy, and probing of nanostructured materials and their functional properties. At the...

  3. 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.

  4. Synthesis, interactions, molecular structure, biological properties and molecular docking studies on Mn, Co, Zn complexes containing acetylacetone and pyridine ligands with DNA duplex.

    Science.gov (United States)

    Thamilarasan, V; Sengottuvelan, N; Stalin, N; Srinivasan, P; Chakkaravarthi, G

    2016-07-01

    Three metal complexes (1-3) of the type [Mn(acac)2(py)·H2O] (1), [Co(acac)2(py)·H2O] (2) and [Zn(acac)2(py)·H2O] (3), [Where acac=acetylacetone, py=pyridine] were synthesized and characterized by spectral (UV-vis, FT-IR, ESI-mass) analysis. The structure of complex 2 has been determined by single crystal X-ray diffraction studies and the configuration of ligand-coordinated to metal(II) ion was well described as distorted octahedral coordination geometry. The interaction of the complexes with CT-DNA has been explored by absorption, fluorescence, circular dichromism spectroscopy, viscosity measurements and molecular docking studies. The intrinsic binding constant Kb of complexes 1-3 with CT-DNA obtained from UV-vis absorption spectral studies were 2.1×10(4), 2.1×10(5) and 1.98×10(4)M(-1), respectively, which revealed that the complexes could interact with CT-DNA through groove binding. The results indicated that the complexes (1-3) were able to bind to DNA with different binding affinity, in the order: 2>1>3. The interaction of the compounds with bovine serum albumins were also investigated using fluorescence methods and the gel electrophoresis assay demonstrates weak cleavage ability of the pBR322 plasmid DNA in the presence of the metal complexes (1-3) with various activators. Further, the in vitro cytotoxic effect of the complexes were examined on cancerous cell line, with human breast cancer cells MCF-7. Copyright © 2016. Published by Elsevier B.V.

  5. Intramolecular interaction influences binding of the Flax L5 and L6 resistance proteins to their AvrL567 ligands.

    Directory of Open Access Journals (Sweden)

    Michael Ravensdale

    Full Text Available L locus resistance (R proteins are nucleotide binding (NB-ARC leucine-rich repeat (LRR proteins from flax (Linum usitatissimum that provide race-specific resistance to the causal agent of flax rust disease, Melampsora lini. L5 and L6 are two alleles of the L locus that directly recognize variants of the fungal effector AvrL567. In this study, we have investigated the molecular details of this recognition by site-directed mutagenesis of AvrL567 and construction of chimeric L proteins. Single, double and triple mutations of polymorphic residues in a variety of AvrL567 variants showed additive effects on recognition strength, suggesting that multiple contact points are involved in recognition. Domain-swap experiments between L5 and L6 show that specificity differences are determined by their corresponding LRR regions. Most positively selected amino acid sites occur in the N- and C-terminal LRR units, and polymorphisms in the first seven and last four LRR units contribute to recognition specificity of L5 and L6 respectively. This further confirms that multiple, additive contact points occur between AvrL567 variants and either L5 or L6. However, we also observed that recognition of AvrL567 is affected by co-operative polymorphisms between both adjacent and distant domains of the R protein, including the TIR, ARC and LRR domains, implying that these residues are involved in intramolecular interactions to optimize detection of the pathogen and defense signal activation. We suggest a model where Avr ligand interaction directly competes with intramolecular interactions to cause activation of the R protein.

  6. DNA binding, BSA interaction and SOD activity of two new nickel(II) complexes with glutamine Schiff base ligands.

    Science.gov (United States)

    Wei, Qiang; Dong, Jianfang; Zhao, Peiran; Li, Manman; Cheng, Fengling; Kong, Jinming; Li, Lianzhi

    2016-08-01

    Two hexacoordinated octahedral nickel(II) complexes, [Ni(o-van-gln)(phen)(H2O)](1) and [Ni(sal-gln)(phen)(H2O)](2) [o-van-gln=a Schiff base derived from o-vanillin and glutamine, sal-gln=a Schiff base derived from salicylaldehyde and glutamine, phen=1,10-phenanthroline], have been synthesized and characterized by elemental analysis, IR spectra and single crystal X-ray diffraction. X-ray studies showed that nickel atoms of both 1 and 2 exhibit distorted NiN3O3 octahedral geometry. In each crystal, intermolecular hydrogen bonds form a two-dimensional network structure. DNA-binding properties of these two nickel(II) complexes were investigated by using UV-Vis absorption, fluorescence, circular dichroism (CD) spectroscopies and viscosity measurements. Results indicated that the two complexes can bind to calf thymus DNA (CT-DNA) via an intercalative mode, and complex 1 exhibits higher interaction with CT-DNA than complex 2. Furthermore, the interactions between the nickel(II) complexes with bovine serum albumin (BSA) have been studied by spectroscopies. The results indicated that both complexes could quench the intrinsic fluorescence of BSA in a static quenching process. The binding constants (Kb) and the numbers of binding sites (n) obtained are 1.10×10(5)M(-1) and 1.05 for complex 1 and 5.05×10(4)M(-1) and 0.997 for complex 2, respectively. Site-selective competitive binding investigation indicated that the binding sites of both the complexes are located in site I of sub-domains IIA of BSA. Assay of superoxide dismutase (SOD) activity of the nickel(II) complexes revealed that they exhibit significant superoxide scavenging activity with IC50=3.4×10(-5)M for complex 1 and 4.3×10(-5)M for complex 2, respectively. Copyright © 2016 Elsevier B.V. All rights reserved.

  7. DNA interaction, SOD, peroxidase and nuclease activity studies of iron complex having ligand with carboxamido nitrogen donors

    Science.gov (United States)

    Ghosh, Kaushik; Tyagi, Nidhi; Kumar, Hemant; Rathi, Sweety

    2015-07-01

    Complex (Et3HN)[FeIII(bpb)Cl2], 1 {where H2bpb: N,N‧-(1,2-phenylene)bis(pyridine-2-carboxamide)} was synthesized and characterized by reported procedure (Yang et al., 1991). Complex 1 was found to be effective in superoxide scavenging activity and an IC50 value of 4.1 μM was obtained in xanthine-xanthine oxidase nitro blue tetrazolium assay. Peroxidase-like activity of this complex was determined by the oxidation of 2,2‧-azino-bis(3-ethylbenzothiazoline-6-sulphonic acid) (ABTS). DNA interaction studies of complex 1 showed binding of DNA through external or groove binding. Complex 1 exhibited chemical nuclease activity in the presence of hydrogen peroxide and cleaved supercoiled pBR322 DNA to its linear and nicked circular form at physiological pH. Mechanistic studies indicated possible role of hydroxyl radical (radOH) species in DNA cleavage activity via hydroperoxo intermediate: [FeIIIsbnd OOH-]2+ → [FeIVdbnd O]2+ + radOH.

  8. A rapid method for selecting suitable animal species for studying pathogen interactions with plasma protein ligands in vivo.

    Science.gov (United States)

    Naudin, Clément; Schumski, Ariane; Salo-Ahen, Outi M H; Herwald, Heiko; Smeds, Emanuel

    2017-05-01

    Species tropism constitutes a serious problem for developing relevant animal models of infection. Human pathogens can express virulence factors that show specific selectivity to human proteins, while their affinity for orthologs from other species can vary significantly. Suitable animal species must be used to analyse whether virulence factors are potential targets for drug development. We developed an assay that rapidly predicts applicable animal species for studying virulence factors binding plasma proteins. We used two well-characterized Staphylococcus aureus proteins, SSL7 and Efb, to develop an ELISA-based inhibition assay using plasma from different animal species. The interaction between SSL7 and human C5 and the binding of Efb to human fibrinogen and human C3 was studied. Affinity experiments and Western blot analyses were used to validate the assay. Human, monkey and cat plasma interfered with binding of SSL7 to human C5. Binding of Efb to human fibrinogen was blocked in human, monkey, gerbil and pig plasma, while human, monkey, gerbil, rabbit, cat and guinea pig plasma inhibited the binding of Efb to human C3. These results emphasize the importance of choosing correct animal models, and thus, our approach is a rapid and cost-effective method that can be used to prevent unnecessary animal experiments. © 2017 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

  9. Knowledge-based modeling of a legume lectin and docking of the carbohydrate ligand: the Ulex europaeus lectin I and its interaction with fucose.

    Science.gov (United States)

    Gohier, A; Espinosa, J F; Jimenez-Barbero, J; Carrupt, P A; Pérez, S; Imberty, A

    1996-12-01

    Ulex europaeus isolectin I is specific for fucose-containing oligosaccharide such as H type 2 trisaccharide alpha-L-Fuc (1-->2) beta-D-Gal (1-->4) beta-D-GlcNAc. Several legume lectins have been crystallized and modeled, but no structural data are available concerning such fucose-binding lectin. The three-dimensional structure of Ulex europaeus isolectin I has been constructed using seven legume lectins for which high-resolution crystal structures were available. Some conserved water molecules, as well as the structural cations, were taken into account for building the model. In the predicted binding site, the most probable locations of the secondary hydroxyl groups were determined using the GRID method. Several possible orientations could be determined for a fucose residue. All of the four possible conformations compatible with energy calculations display several hydrogen bonds with Asp-87 and Ser-132 and a stacking interaction with Tyr-220 and Phe-136. In two orientations, the O-3 and O-4 hydroxyl groups of fucose are the most buried ones, whereas two other, the O-2 and O-3 hydroxyl groups are at the bottom of the site. Possible docking modes are also studied by analysis of the hydrophobic and hydrophilic surfaces for both the ligand and the protein. The SCORE method allows for a quantitative evaluation of the complementarity of these surfaces, on the basis of molecular lipophilicity calculations. The predictions presented here are compared with known biochemical data.

  10. Growth of ligand-target interaction data in ChEMBL is associated with increasing and activity measurement-dependent compound promiscuity.

    Science.gov (United States)

    Hu, Ye; Bajorath, Jürgen

    2012-10-22

    Compounds with high-confidence target annotations and activity measurements in the original and current release of the ChEMBL database have been compared to better understand how the growth of compound activity data might influence the spectrum of ligand-target interactions and the degree of target promiscuity among active compounds. Compared to the original ChEMBL release, a significant increase in the proportion of target promiscuous compounds was observed in the current version. The presence of these compounds led to large-magnitude changes in compound activity-based target and target family relationships and to a reorganization of major target communities. Surprisingly, however, this strong trend toward increasing target promiscuity was largely caused by growth of compounds with exclusive IC(50) measurements. By contrast, compounds with available equilibrium constants, which were also added in large amounts, did not substantially alter compound-based target relationships and notably contribute to increasing target promiscuity. These findings suggest that apparent compound promiscuity is much dependent on experimental conditions under which activities are determined and that care should be taken when evaluating promiscuity and polypharmacology on the basis of assay-dependent activity measurements.

  11. Data on secondary structures and ligand interactions of G-rich oligonucleotides that defy the classical formula for G4 motifs.

    Science.gov (United States)

    Vlasenok, Maria; Varizhuk, Anna; Kaluzhny, Dmitry; Smirnov, Igor; Pozmogova, Galina

    2017-04-01

    The data provided in this article are related to the research article "The expanding repertoire of G4 DNA structures" [1]. Secondary structures of G-rich oligonucleotides (ONs) that represent "imperfect" G-quadruplex (G4) motifs, i.e., contain truncated or interrupted G-runs, were analyzed by optical methods. Presented data on ON structures include circular dichroism (CD) spectra, thermal difference spectra (TDS) and UV -melting curves of the ONs; and rotational relaxation times (RRT) of ethidium bromide (EtBr) complexes with the ONs. TDS, CD spectra and UV-melting curves can be used to characterize the topologies and thermal stabilities of the ON structures. RRTs are roughly proportional to the hydrodynamic volumes of the complexes and thus can be used to distinguish between inter- and intramolecular ON structures. Presented data on ON interactions with small molecules include fluorescence emission spectra of the G4 sensor thioflavin T (ThT) in complexes with the ONs, and CD-melting curves of the ONs in the presence of G4-stabilizing ligands N-methylmesoporphyrin IX (NMM) and pyridostatin (PDS). These data should be useful for comparative analyses of classical G4s and "defective"G4s, such as quadruplexes with vacancies or bulges.

  12. Quantitative Characterization of E-selectin Interaction with Native CD44 and P-selectin Glycoprotein Ligand-1 (PSGL-1) Using a Real Time Immunoprecipitation-based Binding Assay

    KAUST Repository

    Abu Samra, Dina Bashir Kamil

    2015-06-29

    Selectins (E-, P-, and L-selectins) interact with glycoprotein ligands to mediate the essential tethering/rolling step in cell transport and delivery that captures migrating cells from the circulating flow. In this work, we developed a real time immunoprecipitation assay on a surface plasmon resonance chip that captures native glycoforms of two well known E-selectin ligands (CD44/hematopoietic cell E-/L-selectin ligand and P-selectin glycoprotein ligand-1) from hematopoietic cell extracts. Here we present a comprehensive characterization of their binding to E-selectin. We show that both ligands bind recombinant monomeric E-selectin transiently with fast on- and fast off-rates, whereas they bind dimeric E-selectin with remarkably slow onand off-rates. This binding requires the sialyl Lewis x sugar moiety to be placed on both O- and N-glycans, and its association, but not dissociation, is sensitive to the salt concentration. Our results suggest a mechanism through which monomeric selectins mediate initial fast on and fast off kinetics to help capture cells out of the circulating shear flow; subsequently, tight binding by dimeric/oligomeric selectins is enabled to significantly slow rolling. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

  13. Heteroleptic and Homoleptic Iron(III Spin-Crossover Complexes; Effects of Ligand Substituents and Intermolecular Interactions between Co-Cation/Anion and the Complex

    Directory of Open Access Journals (Sweden)

    Wasinee Phonsri

    2017-08-01

    Full Text Available The structural and magnetic properties of a range of new iron(III bis-tridentate Schiff base complexes are described with emphasis on how intermolecular structural interactions influence spin states and spin crossover (SCO in these d5 materials. Three pairs of complexes were investigated. The first pair are the neutral, heteroleptic complexes [Fe(3-OMe-SalEen(thsa] 1 and [Fe(3-MeOSalEen(3-EtOthsa] 2, where 3-R-HSalEen = (E-2-(((2-(ethylaminoethyliminomethyl-6-R-phenol and 3-R-H2thsa = thiosemicarbazone-3-R-salicylaldimine. They display spin transitions above room temperature. However, 2 shows incomplete and gradual change, while SCO in 1 is complete and more abrupt. Lower cooperativity in 2 is ascribed to the lack of π–π interactions, compared to 1. The second pair, cationic species [Fe(3-EtOSalEen2]NO3 3 and [Fe(3-EtOSalEen2]Cl 4 differ only in the counter-anion. They show partial SCO above room temperature with 3 displaying a sharp transition at 343 K. Weak hydrogen bonds from cation to Cl− probably lead to weaker cooperativity in 4. The last pair, CsH2O[Fe(3-MeO-thsa2] 5 and Cs(H2O2[Fe(5-NO2-thsa2] 6, are anionic homoleptic chelates that have different substituents on the salicylaldiminate rings of thsa2−. The Cs cations bond to O atoms of water and the ligands, in unusual ways thus forming attractive 1D and 3D networks in 5 and 6, respectively, and 5 remains HS (high spin at all temperatures while 6 remains LS (low spin. Comparisons are made to other literature examples of Cs salts of [Fe(5-R-thsa2]− (R = H and Br.

  14. From guest to ligand - A study on the competing interactions of antitumor drug resveratrol with {beta}-cyclodextrin and bovine serum albumin

    Energy Technology Data Exchange (ETDEWEB)

    Li, Xudong [College of Chemistry and Chemical Engineering, Liaocheng University, Liaocheng, Shandong Province 252059 (China); Department of Clinical Laboratory, Liaocheng People' s Hospital, Liaocheng, Shandong Province 252000 (China); Li, Hui [College of Chemistry and Chemical Engineering, Liaocheng University, Liaocheng, Shandong Province 252059 (China); Liu, Min, E-mail: liumin_panpan@163.com [College of Chemistry and Chemical Engineering, Liaocheng University, Liaocheng, Shandong Province 252059 (China); Li, Guangqian; Li, Linwei [College of Chemistry and Chemical Engineering, Liaocheng University, Liaocheng, Shandong Province 252059 (China); Sun, Dezhi, E-mail: sundezhisdz@163.com [College of Chemistry and Chemical Engineering, Liaocheng University, Liaocheng, Shandong Province 252059 (China)

    2011-07-10

    Graphical abstract: Thermodynamic behavior of the interaction between bovine serum albumin and antitumor drug resveratrol delivered by {beta}-cyclodextrin in buffer solutions (pH 7.40) have been investigated by ITC combined with UV, FS and circular dichroism at 298.15 K. The results indicated that the affinity of resveratrol with the host ({beta}-cyclodextrin) was evidently weaker than that of the drug with the both classes of binding sites on the protein molecule. Highlights: {yields} Supramolecular complex of a drug with BSA could form in aqueous medium. {yields} A set of thermodynamic parameters were determined. {yields} Affinity of the drug to {beta}-CD is weaker than that of it to the protein. {yields} The molecular conformation of BSA was (slightly) changed by the drug. - Abstract: Interaction between bovine serum albumin (BSA) and resveratrol (RES) included by {beta}-cyclodextrin ({beta}-CD) in Tris-HCl aqueous buffer solutions (pH 7.4) has been investigated by isothermal titration calorimetry (ITC) combined with ultraviolet, fluorescence and circular dichroism spectra analyses. The results indicate that there are two classes of ligand binding sites. The first class of binding is mainly driven by enthalpy, while the second one is driven by both enthalpy and entropy. The secondary structure of BSA in the aqueous system was slightly changed with addition of the drug. Thermodynamic parameters, i.e., equilibrium constants, standard enthalpy changes and the entropy effects for the binding process of RES with BSA were calculated based on the calorimetric data. In fact, due to the poor solubility of RES in aqueous buffer medium, these parameters could not be determined by the employed experimental method without the existence of the CD.

  15. Synthesis, CMC determination, and intercalative binding interaction with nucleic acid of a surfactant-copper(II) complex with modified phenanthroline ligand (dpq).

    Science.gov (United States)

    Nagaraj, Karuppiah; Ambika, Subramanian; Arunachalam, Sankaralingam

    2015-01-01

    A surfactant-copper(II) complex, [Cu(dpq)2DA](ClO4)2 (dpq = dipyrido[3,2-d:2'-3'-f]quinoxaline; DA-dodecylamine), was synthesized and characterized on the basis of elemental analyses, UV-vis, IR, and EPR spectra. The critical micelle concentration (CMC) value of this surfactant-copper(II) complex in aqueous solution was found out from conductance measurements. Specific conductivity data at different temperature served for the evaluation of the temperature-dependent CMC and the thermodynamics of micellization (ΔG°(m), ΔH°(m) and ΔS°(m)). In addition, the complex has been examined by its ability to bind to nucleic acids (DNA and RNA) in tris-HCl buffer by UV-vis absorption, emission spectroscopy techniques, and viscosity measurements. The complex has been found to bind strongly to nucleic acids with apparent binding constants at DNA and RNA is 4.3 × 10(5), 9.0 × 10(5) M(-1), respectively. UV-vis studies of the interaction of the complex with DNA/RNA have revealed that the complex can bind to both DNA and RNA by the intercalative binding mode via ligand dpq into the base pairs of DNA and RNA which has been verified by viscosity measurements. The presence of long aliphatic chain in the surfactant complex increases this hydrophobic interaction. The binding constants have been calculated. The cytotoxic activity of this complex on human liver carcinoma cancer cells was determined by adopting 3-(4, 5-dimethylthiazol-2-yl)-2, 5- diphenyl tetrazolium bromide assay and specific staining techniques. The antimicrobial and antifungal screening tests of this complex have shown good results.

  16. Performance of scintillation proximity assay (SPA) to measure the level of VEGFR 1 protein

    Energy Technology Data Exchange (ETDEWEB)

    LEE, So-Young; LIM, Jae-Cheong; KIM, Jin-Joo [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of)

    2014-10-15

    Scintillation proximity assay is a one of radioimmunoassay and can be assayed without the washing or filtration procedures normally used to separate bound from free fractions. Due to its simplicity and high-throughput protocol, it is broadly applicable to immunology, receptor binding, monitoring receptor-ligand interactions and enzyme reactions. Briefly, an antibody or receptor is coated on SPA beads. When a radiolabeled antigen or ligand binds to the beads, the SPA beads stimulate to emit short range electrons. The {sup 3}H and {sup 125}I are commonly used for radiolabeling and the produced photons are detectable with a liquid scintillation counter (LSC). A binding affinity of unlabeled ligands can be determined by competitive reaction of the radiolabeled ligands. Bevacizumab is a recombinant humanized monoclonal antibody, and can stop or delay growth of tumors by inhibiting vascular endothelial growth factor (VEGF). Bevacizumab was approved by FDA for metastatic cancer such as colorectal cancers, ovarian cancers, breast cancers and glioblastoma multiform of the brain. Recently, Dan G. duda et al. was reported that the concentration of vascular endothelial growth factor receptor-1 (VEGFR-1) in plasma may potentially be used as a negative selection biomarker. In this study, we describe a method using scintillation proximity assay to detect the amounts of VEGFR-1 protein. This method is successfully used to measure the concentration of VEGFR-1 protein in human cell extracts. In summary, a simple and sensitive assay is developed for measuring the amount of VEGFR 1 protein in cancer cell lysate using SPA beads. The antibody coating on the beads and antigen binding are achieved in one mixing step.

  17. A chimeric prokaryotic-eukaryotic pentameric ligand gated ion channel reveals interactions between the extracellular and transmembrane domains shape neurosteroid modulation.

    Science.gov (United States)

    Ghosh, Borna; Tsao, Tzu-Wei; Czajkowski, Cynthia

    2017-10-01

    Pentameric ligand-gated ion channels (pLGICs) are the targets of several clinical and endogenous allosteric modulators including anesthetics and neurosteroids. Molecular mechanisms underlying allosteric drug modulation are poorly understood. Here, we constructed a chimeric pLGIC by fusing the extracellular domain (ECD) of the proton-activated, cation-selective bacterial channel GLIC to the transmembrane domain (TMD) of the human ρ1 chloride-selective GABAAR, and tested the hypothesis that drug actions are regulated locally in the domain that houses its binding site. The chimeric channels were proton-gated and chloride-selective demonstrating the GLIC ECD was functionally coupled to the GABAρ TMD. Channels were blocked by picrotoxin and inhibited by pentobarbital, etomidate and propofol. The point mutation, ρ TMD W328M, conferred positive modulation and direct gating by pentobarbital. The data suggest that the structural machinery mediating general anesthetic modulation resides in the TMD. Proton-activation and neurosteroid modulation of the GLIC-ρ chimeric channels, however, did not simply mimic their respective actions on GLIC and GABAρ revealing that across domain interactions between the ECD and TMD play important roles in determining their actions. Proton-induced current responses were biphasic suggesting that the chimeric channels contain an additional proton sensor. Neurosteroid modulation of the GLIC-ρ chimeric channels by the stereoisomers, 5α-THDOC and 5β-THDOC, were swapped compared to their actions on GABAρ indicating that positive versus negative neurosteroid modulation is not encoded solely in the TMD nor by neurosteroid isomer structure but is dependent on specific interdomain connections between the ECD and TMD. Our data reveal a new mechanism for shaping neurosteroid modulation. Copyright © 2017 Elsevier Ltd. All rights reserved.

  18. Comparison of apoptosis in wild-type and Fas-resistant cells: chemotherapy-induced apoptosis is not dependent on Fas/Fas ligand interactions.

    Science.gov (United States)

    Eischen, C M; Kottke, T J; Martins, L M; Basi, G S; Tung, J S; Earnshaw, W C; Leibson, P J; Kaufmann, S H

    1997-08-01

    The Fas/Fas ligand (FasL) pathway is widely involved in apoptotic cell death in lymphoid and nonlymphoid cells. It has recently been postulated that many chemotherapeutic agents also induce cell death by activating the Fas/FasL pathway. In the present study we compared apoptotic pathways induced by anti-Fas or chemotherapeutic agents in the Jurkat human T-cell leukemia line. Immunoblotting showed that treatment of wild-type Jurkat cells with anti-Fas or the topoisomerase II-directed agent etoposide resulted in proteolytic cleavage of precursors for the cysteine-dependent aspartate-directed proteases caspase-3 and caspase-7 and degradation of the caspase substrates poly(ADP-ribose) polymerase (PARP) and lamin B1. Likewise, affinity labeling with N-(N(alpha)-benzyloxycarbonylglutamyl-N(epsilon)-biotinyllysyl+ ++)aspartic acid [(2,6-dimethyl-benzoyl)oxy]methyl ketone [Z-EK(bio)D-amok] labeled the same five active caspase species after each treatment, suggesting that the same downstream apoptotic pathways have been activated by anti-Fas and etoposide. Treatment with ZB4, an antibody that inhibits Fas-mediated cell death, failed to block etoposide-induced apoptosis, raising the possibility that etoposide does not initiate apoptosis through Fas/FasL interactions. To further explore the relationship between Fas- and chemotherapy-induced apoptosis, Fas-resistant Jurkat cells were treated with various chemotherapeutic agents. Multiple independently derived Fas-resistant Jurkat lines underwent apoptosis that was indistinguishable from that of the Fas-sensitive parental cells after treatment with etoposide, doxorubicin, topotecan, cisplatin, methotrexate, staurosporine, or gamma-irradiation. These results indicate that antineoplastic treatments induce apoptosis through a Fas-independent pathway even though Fas- and chemotherapy-induced pathways converge on common downstream apoptotic effector molecules.

  19. Ammonia transport in the proximal tubule.

    Science.gov (United States)

    Hamm, L L; Simon, E E

    1990-01-01

    The transport of ammonia in the proximal tubule is a complex interaction of a number of processes. Ammonia transport in the proximal tubule is clearly bidirectional; ammonia is secreted into the early proximal tubule lumen, but later in the proximal tubule, efflux out of the lumen may result in net ammonia reabsorption. Two mechanisms of ammonia transport have clearly been established: NH3 diffusion and NH4+ transport on the Na(+)-H+ exchanger. The relative contribution of these pathways to ammonia transport is still unsettled. Other pathways for ammonia transport, particularly NH4+ efflux out of the lumen, may be important as well. A variety of factors may modulate ammonia transport: plasma, cell and luminal pH, luminal flow rate, luminal potassium, and angiotensin II. Each of these factors also alters ammonia production rates and in most circumstances, ammonia transport appears to follow ammonia production rates.

  20. A Leader Intron of a Soybean Elongation Factor 1A (eEF1A Gene Interacts with Proximal Promoter Elements to Regulate Gene Expression in Synthetic Promoters.

    Directory of Open Access Journals (Sweden)

    Ning Zhang

    Full Text Available Introns, especially the first intron in the 5' untranslated region (5'UTR, can significantly impact gene expression via intron-mediated enhancement (IME. In this study, we demonstrate the leader intron of a soybean elongation factor 1A (eEF1A gene (GmScreamM8 was essential for the high activity of the native promoter. Furthermore, the interaction of the GmScreamM8 leader intron with regulatory element sequences from several soybean eEF1A promoters was studied using synthetic promoters, which consisted of element tetramers upstream of a core promoter used to regulate a green fluorescent protein (gfp reporter gene. Element tetramers, placed upstream of a GmScreamM8 core promoter, showed very high activity using both transient expression in lima bean cotyledons and stable expression in soybean hairy roots, only if the native leader intron was included, suggesting an interaction between intronic sequences and promoter elements. Partial deletions of the leader intron showed that a 222 bp intronic sequence significantly contributed to very high levels of GFP expression. Generation of synthetic intron variants with a monomeric or trimeric repeat of the 222 bp intronic sequence, yielded almost two-fold higher expression compared to the original intron, while partial deletion of the 222 bp intronic repeated sequence significantly decreased gene expression, indicating that this intronic sequence was essential for the intron-element interaction enhancement.

  1. Two novel mixed-ligand complexes containing organosulfonate ligands.

    Science.gov (United States)

    Li, Mingtian; Huang, Jun; Zhou, Xuan; Fang, Hua; Ding, Liyun

    2008-07-01

    The structures reported herein, viz. bis(4-aminonaphthalene-1-sulfonato-kappaO)bis(4,5-diazafluoren-9-one-kappa(2)N,N')copper(II), [Cu(C(10)H(8)NO(3)S)(2)(C(11)H(6)N(2)O)(2)], (I), and poly[[[diaquacadmium(II)]-bis(mu-4-aminonaphthalene-1-sulfonato)-kappa(2)O:N;kappa(2)N:O] dihydrate], {[Cd(C(10)H(8)NO(3)S)(2)(H(2)O)(2)].2H(2)O}(n), (II), are rare examples of sulfonate-containing complexes where the anion does not fulfill a passive charge-balancing role, but takes an active part in coordination as a monodentate and/or bridging ligand. Monomeric complex (I) possesses a crystallographic inversion center at the Cu(II) atom, and the asymmetric unit contains one-half of a Cu atom, one complete 4-aminonaphthalene-1-sulfonate (ans) ligand and one 4,5-diazafluoren-9-one (DAFO) ligand. The Cu(II) atom has an elongated distorted octahedral coordination geometry formed by two O atoms from two monodentate ans ligands and by four N atoms from two DAFO molecules. Complex (II) is polymeric and its crystal structure is built up by one-dimensional chains and solvent water molecules. Here also the cation (a Cd(II) atom) lies on a crystallographic inversion center and adopts a slightly distorted octahedral geometry. Each ans anion serves as a bridging ligand linking two Cd(II) atoms into one-dimensional infinite chains along the [010] direction, with each Cd(II) center coordinated by four ans ligands via O and N atoms and by two aqua ligands. In both structures, there are significant pi-pi stacking interactions between adjacent ligands and hydrogen bonds contribute to the formation of two- and three-dimensional networks.

  2. Why mercury prefers soft ligands

    Energy Technology Data Exchange (ETDEWEB)

    Riccardi, Demian M [ORNL; Guo, Hao-Bo [ORNL; Gu, Baohua [ORNL; Parks, Jerry M [ORNL; Summers, Anne [University of Georgia, Athens, GA; Miller, S [University of California, San Francisco; Liang, Liyuan [ORNL; Smith, Jeremy C [ORNL

    2013-01-01

    Mercury (Hg) is a major global pollutant arising from both natural and anthropogenic sources. Defining the factors that determine the relative affinities of different ligands for the mercuric ion, Hg2+, is critical to understanding its speciation, transformation, and bioaccumulation in the environment. Here, we use quantum chemistry to dissect the relative binding free energies for a series of inorganic anion complexes of Hg2+. Comparison of Hg2+ ligand interactions in the gaseous and aqueous phases shows that differences in interactions with a few, local water molecules led to a clear periodic trend within the chalcogenide and halide groups and resulted in the well-known experimentally observed preference of Hg2+ for soft ligands such as thiols. Our approach establishes a basis for understanding Hg speciation in the biosphere.

  3. Capacitive proximity sensor

    Science.gov (United States)

    Kronberg, James W.

    1994-01-01

    A proximity sensor based on a closed field circuit. The circuit comprises a ring oscillator using a symmetrical array of plates that creates an oscillating displacement current. The displacement current varies as a function of the proximity of objects to the plate array. Preferably the plates are in the form of a group of three pair of symmetric plates having a common center, arranged in a hexagonal pattern with opposing plates linked as a pair. The sensor produces logic level pulses suitable for interfacing with a computer or process controller. The proximity sensor can be incorporated into a load cell, a differential pressure gauge, or a device for measuring the consistency of a characteristic of a material where a variation in the consistency causes the dielectric constant of the material to change.

  4. Neighborhoods and manageable proximity

    Directory of Open Access Journals (Sweden)

    Stavros Stavrides

    2011-08-01

    Full Text Available The theatricality of urban encounters is above all a theatricality of distances which allow for the encounter. The absolute “strangeness” of the crowd (Simmel 1997: 74 expressed, in its purest form, in the absolute proximity of a crowded subway train, does not generally allow for any movements of approach, but only for nervous hostile reactions and submissive hypnotic gestures. Neither forced intersections in the course of pedestrians or vehicles, nor the instantaneous crossing of distances by the technology of live broadcasting and remote control give birth to places of encounter. In the forced proximity of the metropolitan crowd which haunted the city of the 19th and 20th century, as well as in the forced proximity of the tele-presence which haunts the dystopic prospect of the future “omnipolis” (Virilio 1997: 74, the necessary distance, which is the stage of an encounter between different instances of otherness, is dissipated.

  5. Mapping Protein–Protein Interactions of the Resistance-Related Bacterial Zeta Toxin–Epsilon Antitoxin Complex (ε2ζ2 with High Affinity Peptide Ligands Using Fluorescence Polarization

    Directory of Open Access Journals (Sweden)

    María Isabel Fernández-Bachiller

    2016-07-01

    Full Text Available Toxin–antitoxin systems constitute a native survival strategy of pathogenic bacteria and thus are potential targets of antibiotic drugs. Here, we target the Zeta–Epsilon toxin–antitoxin system, which is responsible for the stable maintenance of certain multiresistance plasmids in Gram-positive bacteria. Peptide ligands were designed on the basis of the ε2ζ2 complex. Three α helices of Zeta forming the protein–protein interaction (PPI site were selected and peptides were designed conserving the residues interacting with Epsilon antitoxin while substituting residues binding intramolecularly to other parts of Zeta. Designed peptides were synthesized with an N-terminal fluoresceinyl-carboxy-residue for binding assays and provided active ligands, which were used to define the hot spots of the ε2ζ2 complex. Further shortening and modification of the binding peptides provided ligands with affinities <100 nM, allowing us to determine the most relevant PPIs and implement a robust competition binding assay.

  6. Atrofia muscular proximal familiar

    Directory of Open Access Journals (Sweden)

    José Antonio Levy

    1962-09-01

    Full Text Available Os autores relatam dois casos de atrofia muscular proximal familiar, moléstia caracterizada por déficit motor e atrofias musculares de distribuição proximal, secundárias a lesão de neurônios periféricos. Assim, como em outros casos descritos na literatura, foi feito inicialmente o diagnóstico de distrofia muscular progressiva. O diagnóstico correto foi conseguido com auxílio da eletromiografia e da biopsia muscular.

  7. Effect of food types on competitive interaction between Aedes aegypti (LINNAEUS, 1762 and Ae. albopictus (SKUSE, 1894 (Diptera, Culicidae: a proximate level appraisal

    Directory of Open Access Journals (Sweden)

    Banerjee Sampa

    2017-06-01

    Full Text Available Competitive interactions between coexisting Aedes aegypti and Ae. albopictus have been implied as a crucial factor shaping life history traits and population characteristics. The overlap in resource requirements and similarities in the life history strategies of the two Aedes mosquitoes form a basis for competitive interactions. In the present study, the role of the food quality of the larval habitats in influencing the outcome of competition between Ae. aegypti and Ae. albopictus is evaluated to highlight food quality as a basis for asymmetric competitive outcomes. Instar I larvae of the two mosquitoes were reared using conspecifics or heterospecifics of constant size and equal ratio with four different food types: boiled rice, boiled pulses, a mixture of boiled rice and pulses, and fish food. Competitive interactions were evaluated using age at pupation (AP, pupal weight (PW, dry adult weight (AW and wing length (WL with respect to intra- and interspecific competition for the two sexes of each mosquito species. The results show that Ae. albopictus developed faster but achieved a smaller size compared to Ae. aegypti under interspecific competition conditions, the extent of the difference varying significantly with the food type. Given the variety of food resources available in the small container larval habitats, the results of the study imply that food quality may act differentially with respect to larval development and adult body size, depending on the conspecifics or heterospecifics and on the sex of the species concerned. The dominance of one species over the other may also be a consequence of the resource utilization pattern that varies in the larval habitats.

  8. Quinoxaline-2-carboxamide as a carrier ligand in two new platinum(ii) compounds: Synthesis, crystal structure, cytotoxic activity and DNA interaction

    NARCIS (Netherlands)

    Marques Gallego, P.; Amparo Gamiz-Gonzalez, M.; Fortea-Pérez, F. R.; Lutz, M.; Spek, A.L.; Pevec, A.; Kozlevar, B.; Reedijk, J.

    2010-01-01

    The search for platinum compounds structurally different from cisplatin has led to two new platinum(II) compounds containing quinoxaline-2-carboxamide as a carrier ligand, i.e. cis-[Pt(qnxca)(MeCN)Cl2] (1) and the [Pt(qnxca−H)(dmso)Cl] (2). Both compounds have been synthesized and characterized

  9. [Experimental proximal carpectomy. Biodynamics].

    Science.gov (United States)

    Kuhlmann, J N

    1992-01-01

    Proximal carpectomy was performed in 10 fresh cadavre wrists. Dynamic x-rays were taken and the forces necessary to obtain different movements before and after the operation were measured. Comparison of these parameters clearly defines the advantages and limitations of carpectomy and indicates the reasons.

  10. Proximate Analysis of Coal

    Science.gov (United States)

    Donahue, Craig J.; Rais, Elizabeth A.

    2009-01-01

    This lab experiment illustrates the use of thermogravimetric analysis (TGA) to perform proximate analysis on a series of coal samples of different rank. Peat and coke are also examined. A total of four exercises are described. These are dry exercises as students interpret previously recorded scans. The weight percent moisture, volatile matter,…

  11. Proximal Tibial Bone Graft

    Science.gov (United States)

    ... the Big Toe Ailments of the Smaller Toes Diabetic Foot Treatments Currently selected Injections and other Procedures Treatments ... from which the bone was taken if the foot/ankle surgeries done at the same time allow for it. ... problems after a PTBG include infection, fracture of the proximal tibia and pain related ...

  12. The eivaN: A forward-looking interactive orbital trajectory plotting tool for use with proximity operations (PROX OPS) and other maneuvers: Description and user's manual

    Science.gov (United States)

    Brody, Adam R.

    1988-01-01

    The results of vehicle burns on-orbit are very difficult to anticipate because of nonlinearities in the equations of motion governing orbiting bodies. This confusion was noticed firsthand in prior experimentation. Out of plane motion is relatively simple as it is uncoupled from the other two degrees of freedom. However, in plane thrusts are more complex because the motions resulting from these inputs are coupled. An interactive planning device, eivaN, was developed to plot resulting trajectories, to provide a better comprehension of orbital mechanics effects, and to help the user to develop heuristics for on-orbit mission planning. The eivaN runs with Microsoft Excel on a Macintosh computer. It provides a forward looking display: burn parameters in the three orthogonal axes in addition to time inputted, and the resultant trajectory is then plotted. Position and velocity components for any burn at any user specified time are readily available. A new area of research related to the human factors of real time, on-orbit mission planning was identified and is currently being investigated.

  13. Keldysh proximity action for disordered superconductors

    Indian Academy of Sciences (India)

    Abstract. We review a novel approach to the superconductive proximity effect in dis- ordered normal–superconducting (N–S) structures. The method is based on the multi- charge Keldysh action and is suitable for the treatment of interaction and fluctuation effects. As an application of the formalism, we study the subgap ...

  14. Intra- and Interspecific Interactions as Proximate Determinants of Sexual Dimorphism and Allometric Trajectories in the Bottlenose Dolphin Tursiops truncatus (Cetacea, Odontoceti, Delphinidae).

    Science.gov (United States)

    de Francesco, Maria Carla; Loy, Anna

    2016-01-01

    Feeding adaptation, social behaviour, and interspecific interactions related to sexual dimorphism and allometric growth are particularly challenging to be investigated in the high sexual monomorphic Delphinidae. We used geometric morphometrics to extensively explore sexual dimorphism and ontogenetic allometry of different projections of the skull and the mandible of the bottlenose dolphin Tursiops truncatus. Two-dimensional landmarks were recorded on the dorsal, ventral, lateral, and occipital views of the skull, and on the lateral view of the left and the right mandible of 104 specimens from the Mediterranean and the North Seas, differing environmental condition and degree of interspecific associations. Landmark configurations were transformed, standardized and superimposed through a Generalized Procrustes Analysis. Size and shape differences between adult males and females were respectively evaluated through ANOVA on centroid size, Procrustes ANOVA on Procrustes distances, and MANOVA on Procrustes coordinates. Ontogenetic allometry was investigated by multivariate regression of shape coordinates on centroid size in the largest homogenous sample from the North Sea. Results evidenced sexual dimorphic asymmetric traits only detected in the adults of the North Sea bottlenose dolphins living in monospecific associations, with females bearing a marked incision of the cavity hosting the left tympanic bulla. These differences were related to a more refined echolocalization system that likely enhances the exploitation of local resources by philopatric females. Distinct shape in immature versus mature stages and asymmetric changes in postnatal allometry of dorsal and occipital traits, suggest that differences between males and females are established early during growth. Allometric growth trajectories differed between males and females for the ventral view of the skull. Allometric trajectories differed among projections of skull and mandible, and were related to dietary

  15. Intra- and Interspecific Interactions as Proximate Determinants of Sexual Dimorphism and Allometric Trajectories in the Bottlenose Dolphin Tursiops truncatus (Cetacea, Odontoceti, Delphinidae.

    Directory of Open Access Journals (Sweden)

    Maria Carla de Francesco

    Full Text Available Feeding adaptation, social behaviour, and interspecific interactions related to sexual dimorphism and allometric growth are particularly challenging to be investigated in the high sexual monomorphic Delphinidae. We used geometric morphometrics to extensively explore sexual dimorphism and ontogenetic allometry of different projections of the skull and the mandible of the bottlenose dolphin Tursiops truncatus. Two-dimensional landmarks were recorded on the dorsal, ventral, lateral, and occipital views of the skull, and on the lateral view of the left and the right mandible of 104 specimens from the Mediterranean and the North Seas, differing environmental condition and degree of interspecific associations. Landmark configurations were transformed, standardized and superimposed through a Generalized Procrustes Analysis. Size and shape differences between adult males and females were respectively evaluated through ANOVA on centroid size, Procrustes ANOVA on Procrustes distances, and MANOVA on Procrustes coordinates. Ontogenetic allometry was investigated by multivariate regression of shape coordinates on centroid size in the largest homogenous sample from the North Sea. Results evidenced sexual dimorphic asymmetric traits only detected in the adults of the North Sea bottlenose dolphins living in monospecific associations, with females bearing a marked incision of the cavity hosting the left tympanic bulla. These differences were related to a more refined echolocalization system that likely enhances the exploitation of local resources by philopatric females. Distinct shape in immature versus mature stages and asymmetric changes in postnatal allometry of dorsal and occipital traits, suggest that differences between males and females are established early during growth. Allometric growth trajectories differed between males and females for the ventral view of the skull. Allometric trajectories differed among projections of skull and mandible, and were

  16. Proximal femoral fractures

    DEFF Research Database (Denmark)

    Palm, Henrik; Teixidor, Jordi

    2015-01-01

    -displaced femoral neck fractures and prosthesis for displaced among the elderly; and sliding hip screw for stabile- and intramedullary nails for unstable- and sub-trochanteric fractures) but they are based on a variety of criteria and definitions - and often leave wide space for the individual surgeons' subjective...... guidelines for hip fracture surgery and discuss a method for future pathway/guideline implementation and evaluation. METHODS: By a PubMed search in March 2015 six studies of surgical treatment pathways covering all types of proximal femoral fractures with publication after 1995 were identified. Also we...... searched the homepages of the national heath authorities and national orthopedic societies in West Europe and found 11 national or regional (in case of no national) guidelines including any type of proximal femoral fracture surgery. RESULTS: Pathway consensus is outspread (internal fixation for un...

  17. Experimental and Computational Study of an Unexpected Iron-Catalyzed Carboetherification by Cooperative Metal and Ligand Substrate Interaction and Proton Shuttling

    KAUST Repository

    El-Sepelgy, Osama

    2017-09-26

    An iron-catalyzed cycloisomerization of allenols to deoxygenated pyranose glycals has been developed. Combined experimental and computational studies show that the iron complex exhibits a dual catalytic role in that the non-innocent cyclopentadienone ligand acts as proton shuttle by initial hydrogen abstraction from the alcohol and by facilitating protonation and deprotonation events in the isomerization and demetalation steps. Molecular orbital analysis provides insight into the unexpected and selective formation of the 3,4-dihydro-2H-pyran.

  18. Molecular Engineering of Platinum(II) Terpyridine Complexes with Tetraphenylethylene-Modified Alkynyl Ligands: Supramolecular Assembly via Pt···Pt and/or π-π Stacking Interactions and the Formation of Various Superstructures.

    Science.gov (United States)

    Cheng, Heung-Kiu; Yeung, Margaret Ching-Lam; Yam, Vivian Wing-Wah

    2017-10-18

    A series of platinum(II) terpyridine complexes with tetraphenylethylene-modified alkynyl ligands has been designed and synthesized. The introduction of the tetraphenylethylene motif has led to aggregation-induced emission (AIE) properties, which upon self-assembly led to the formation of metal-metal-to-ligand charge transfer (MMLCT) behavior stabilized by Pt···Pt and/or π-π interactions. Tuning the steric bulk or hydrophilicity through molecular engineering of the platinum(II) complexes has been found to alter their spectroscopic properties and result in interesting superstructures (including nanorods, nanospheres, nanowires, and nanoleaves) in the self-assembly process. The eye-catching color and emission changes upon varying the solvent compositions may have potential applications in chemosensing materials for the detection of microenvironment changes. Furthermore, the importance of the directional Pt···Pt and/or π-π interactions on the construction of distinctive superstructures has also been examined by UV-vis absorption and emission spectroscopy and transmission electron microscopy. This work represents the interplay of both inter- and intramolecular interactions as well as the energies of the two different chromophoric/luminophoric systems that may open up a new route for the development of platinum(II)-AIE hybrids as functional materials.

  19. Proximal humeral fractures

    OpenAIRE

    Mauro, Craig S.

    2011-01-01

    Proximal humeral fractures may present with many different configurations in patients with varying co-morbities and expectations. As a result, the treating physician must understand the fracture pattern, the quality of the bone, other patient-related factors, and the expanding range of reconstructive options to achieve the best functional outcome and to minimize complications. Current treatment options range from non-operative treatment with physical therapy to fracture fixation using percuta...

  20. 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....

  1. Page 1 ASSESSMENT OF BINDING ENERGIES AND LIGAND ...

    African Journals Online (AJOL)

    The successive binding energies of up to six water ligands to ferric ion and the reduction in the gross binding energies by ligand-ligand repulsion are determined by electrostatic interaction. The gross binding energy is found to be both geometry and coordination nuitber dependent: whereas it increases with number of ...

  2. Design of HIV-1 Protease Inhibitors with Amino-bis-tetrahydrofuran Derivatives as P2-Ligands to Enhance Backbone-Binding Interactions. Synthesis, Biological Evaluation, and Protein-Ligand X-ray Studies

    Energy Technology Data Exchange (ETDEWEB)

    Ghosh, Arun K.; Martyr, Cuthbert D.; Osswald, Heather L.; Sheri, Venkat Reddy; Kassekert, Luke A.; Chen, Shujing; Agniswamy, Johnson; Wang, Yuan-Fang; Hayashi, Hironori; Aoki, Manabu; Weber, Irene T.; Mitsuya, Hiroaki (GSU); (Kumamoto); (Purdue)

    2015-10-30

    Structure-based design, synthesis, and biological evaluation of a series of very potent HIV-1 protease inhibitors are described. In an effort to improve backbone ligand–binding site interactions, we have incorporated basic-amines at the C4 position of the bis-tetrahydrofuran (bis-THF) ring. We speculated that these substituents would make hydrogen bonding interactions in the flap region of HIV-1 protease. Synthesis of these inhibitors was performed diastereoselectively. A number of inhibitors displayed very potent enzyme inhibitory and antiviral activity. Inhibitors 25f, 25i, and 25j were evaluated against a number of highly-PI-resistant HIV-1 strains, and they exhibited improved antiviral activity over darunavir. Two high resolution X-ray structures of 25f- and 25g-bound HIV-1 protease revealed unique hydrogen bonding interactions with the backbone carbonyl group of Gly48 as well as with the backbone NH of Gly48 in the flap region of the enzyme active site. These ligand–binding site interactions are possibly responsible for their potent activity.

  3. Extracellular Loop 2 of the Adenosine A1 Receptor Has a Key Role in Orthosteric Ligand Affinity and Agonist Efficacy.

    Science.gov (United States)

    Nguyen, Anh T N; Baltos, Jo-Anne; Thomas, Trayder; Nguyen, Toan D; Muñoz, Laura López; Gregory, Karen J; White, Paul J; Sexton, Patrick M; Christopoulos, Arthur; May, Lauren T

    2016-12-01

    The adenosine A 1 G protein-coupled receptor (A 1 AR) is an important therapeutic target implicated in a wide range of cardiovascular and neuronal disorders. Although it is well established that the A 1 AR orthosteric site is located within the receptor's transmembrane (TM) bundle, prior studies have implicated extracellular loop 2 (ECL2) as having a significant role in contributing to orthosteric ligand affinity and signaling for various G protein-coupled receptors (GPCRs). We thus performed extensive alanine scanning mutagenesis of A 1 AR-ECL2 to explore the role of this domain on A 1 AR orthosteric ligand pharmacology. Using quantitative analytical approaches and molecular modeling, we identified ECL2 residues that interact either directly or indirectly with orthosteric agonists and antagonists. Discrete mutations proximal to a conserved ECL2-TM3 disulfide bond selectively affected orthosteric ligand affinity, whereas a cluster of five residues near the TM4-ECL2 juncture influenced orthosteric agonist efficacy. A combination of ligand docking, molecular dynamics simulations, and mutagenesis results suggested that the orthosteric agonist 5'-N-ethylcarboxamidoadenosine binds transiently to an extracellular vestibule formed by ECL2 and the top of TM5 and TM7, prior to entry into the canonical TM bundle orthosteric site. Collectively, this study highlights a key role for ECL2 in A 1 AR orthosteric ligand binding and receptor activation. Copyright © 2016 by The American Society for Pharmacology and Experimental Therapeutics.

  4. A proximity ligation assay using transiently transfected, epitope-tagged proteins: application for in situ detection of dimerized receptor tyrosine kinases.

    Science.gov (United States)

    Gajadhar, Aaron; Guha, Abhijit

    2010-02-01

    The development of small molecule and antibody inhibitors targeting the interaction of receptor tyrosine kinases (RTKs), such as epidermal growth factor receptor (EGFR), is of high pharmacological and biological interest. Unfortunately, conventional biochemical techniques using cell or tissue lysates and co-immunoprecipitation experiments to investigate EGFR dimerization are not always conclusive. Here we describe a series of technical and biological validation experiments demonstrating the utility of a proximity ligation assay (PLA)-based methodology for in situ visualization and quantification of ligand-dependent EGFR receptor dimerization in intact cells. Using the PLA approach combined with a universally applicable epitope tagging strategy, we detected EGFR dimers in cells transiently co-expressing FLAG-tagged and MYC-tagged human EGFRs. Our data strongly suggest that PLA can be used to detect ligand-dependent EGFR dimerization and this signal is generated in a protein interaction-based manner, rather than solely due to proximity of target proteins. This application represents a generalized RTK expression strategy for protein-interaction analysis in a transient expression system where antibody epitopes are not known or not unique enough to discriminate between interaction partners. This assay also holds promise as a general RTK dimerization screening tool in tissue specimens to identify potential dimerization inhibitors with clinical relevance.

  5. New mixed ligand palladium(II) complexes based on the antiepileptic drug sodium valproate and bioactive nitrogen-donor ligands: synthesis, structural characterization, binding interactions with DNA and BSA, in vitro cytotoxicity studies and DFT calculations.

    Science.gov (United States)

    Tabrizi, Leila; Chiniforoshan, Hossein; Tavakol, Hossein

    2015-04-15

    The complexes [Pd(valp)2(imidazole)2] (1), [Pd(valp)2(pyrazine)2] (2) (valp is sodium valproate) have been synthesized and characterized using IR, (1)H NMR, (13)C{(1)H} NMR and UV-Vis spectrometry. The interaction of complexes with CT-DNA has been investigated using spectroscopic tools and viscosity measurement. In each case, the association constant (Kb) was deduced from the absorption spectral study and the number of binding sites (n) and the binding constant (K) were calculated from relevant fluorescence quenching data. As a result, a non-covalent interaction between the metal complex and DNA was suggested, which could be assigned to an intercalative binding. In addition, the interaction of 1 and 2 was ventured with bovine serum albumin (BSA) with the help of absorption and fluorescence spectroscopy measurements. Through these techniques, the apparent association constant (Kapp) and the binding constant (K) could be calculated for each complex. Evaluation of cytotoxic activity of the complexes against four different cancer cell lines proved that the complexes exhibited cytotoxic specificity and significant cancer cell inhibitory rate. Moreover, density functional theory (DFT) calculations were employed to provide more evidence about the observed data. The majority of trans isomers were supported not only by energies, but also by the similarity of its calculated IR frequencies, UV adsorptions and NMR chemical shifts to the experimental values. Copyright © 2015 Elsevier B.V. All rights reserved.

  6. Constitutive expression of a costimulatory ligand on antigen-presenting cells in the nervous system drives demyelinating disease

    DEFF Research Database (Denmark)

    Zehntner, Simone P; Brisebois, Marcel; Tran, Elise

    2003-01-01

    that transgenic mice constitutively expressing the costimulatory ligand B7.2/CD86 on microglia in the central nervous system (CNS) and on related cells in the proximal peripheral nervous tissue spontaneously develop autoimmune demyelinating disease. Disease-affected nervous tissue in transgenic mice showed...... recipients but not into non-transgenic recipients. These data provide evidence that B7/CD28 interactions within the nervous tissue are critical determinants of disease development. Our findings have important implications for understanding the etiology of nervous system autoimmune diseases such as multiple...

  7. Are Free Ion Activity Models Sufficient Alternatives to Biotic Ligand Models in Evaluating Metal Toxic Impacts in Terrestrial Environments?

    DEFF Research Database (Denmark)

    Owsianiak, Mikolaj; Rosenbaum, Ralph K.; Larsen, Henrik Fred

    Metal partitioning between solid and aqueous phases and speciation in soil pore water control the bioavailability of toxic forms of metals, while protons and base cations can mitigate metal ecotoxicity by competitive interactions with biotic ligands. e employment of BLMs to evaluate toxicity...... toxicity scores show large variability even for soils located in close proximity to each other, selection of FIAMs is also justied in deriving soil quality criteria. It remains to be investigated at what spatial scale the FIAMs are a good alternative to TBLMs in evaluating metal toxic impacts...

  8. Ligand Binding and Substrate Discrimination by UDP-Galactopyranose Mutase

    Energy Technology Data Exchange (ETDEWEB)

    Gruber, Todd D.; Borrok, M. Jack; Westler, William M.; Forest, Katrina T.; Kiessling, Laura L.; (UW)

    2009-07-31

    Galactofuranose (Galf) residues are present in cell wall glycoconjugates of numerous pathogenic microbes. Uridine 5{prime}-diphosphate (UDP) Galf, the biosynthetic precursor of Galf-containing glycoconjugates, is produced from UDP-galactopyranose (UDP-Galp) by the flavoenzyme UDP-galactopyranose mutase (UGM). The gene encoding UGM (glf) is essential for the viability of pathogens, including Mycobacterium tuberculosis, and this finding underscores the need to understand how UGM functions. Considerable effort has been devoted to elucidating the catalytic mechanism of UGM, but progress has been hindered by a lack of structural data for an enzyme-substrate complex. Such data could reveal not only substrate binding interactions but how UGM can act preferentially on two very different substrates, UDP-Galp and UDP-Galf, yet avoid other structurally related UDP sugars present in the cell. Herein, we describe the first structure of a UGM-ligand complex, which provides insight into the catalytic mechanism and molecular basis for substrate selectivity. The structure of UGM from Klebsiella pneumoniae bound to the substrate analog UDP-glucose (UDP-Glc) was solved by X-ray crystallographic methods and refined to 2.5 {angstrom} resolution. The ligand is proximal to the cofactor, a finding that is consistent with a proposed mechanism in which the reduced flavin engages in covalent catalysis. Despite this proximity, the glucose ring of the substrate analog is positioned such that it disfavors covalent catalysis. This orientation is consistent with data indicating that UDP-Glc is not a substrate for UGM. The relative binding orientations of UDP-Galp and UDP-Glc were compared using saturation transfer difference NMR. The results indicate that the uridine moiety occupies a similar location in both ligand complexes, and this relevant binding mode is defined by our structural data. In contrast, the orientations of the glucose and galactose sugar moieties differ. To understand the

  9. NetMHCpan-4.0: Improved Peptide-MHC Class I Interaction Predictions Integrating Eluted Ligand and Peptide Binding Affinity Data

    DEFF Research Database (Denmark)

    Jurtz, Vanessa Isabell; Paul, Sinu; Andreatta, Massimo

    2017-01-01

    Cytotoxic T cells are of central importance in the immune system's response to disease. They recognize defective cells by binding to peptides presented on the cell surface by MHC class I molecules. Peptide binding to MHC molecules is the single most selective step in the Ag-presentation pathway. ...... the information from both data types. Large-scale benchmarking of the method demonstrates an increase in predictive performance compared with state-of-the-art methods when it comes to identification of naturally processed ligands, cancer neoantigens, and T cell epitopes....

  10. Application of oxime-diversification to optimize ligand interactions within a cryptic pocket of the polo-like kinase 1 polo-box domain | Center for Cancer Research

    Science.gov (United States)

    By a process involving initial screening of a set of 87 aldehydes using an oxime ligation-based strategy, we were able to achieve a several-fold affinity enhancement over one of the most potent previously known polo-like kinase 1 (Plk1) polo-box domain (PBD) binding inhibitors. This improved binding may result by accessing a newly identified auxiliary region proximal to a key hydrophobic cryptic pocket on the surface of the protein. Our findings could have general applicability to the design of PBD-binding antagonists. Cover design by Joseph Myer

  11. A stereodynamic phosphoramidite ligand derived from 3,3'-functionalized ortho-biphenol and its rhodium(I) complex.

    Science.gov (United States)

    Storch, Golo; Deberle, Luisa; Menke, Jan-Michael; Rominger, Frank; Trapp, Oliver

    2016-11-01

    Stereodynamic ligands and complexes bearing functional groups to attach chiral or achiral binding sites and auxiliaries are highly attractive due to the interesting opportunities for controlling the stereochemical outcome of enantioselective transformations. In this study we report the preparation of a 3,3'-functionalized biphenol (BIPOL) phosphoramidite ligand (PAm ) bearing 3,5-dichlorobenzoyl (3,5-DCB) amide binding sites for noncovalent interactions. Upon coordination to [Rh(COD)2 ]BF4 this substitution pattern directs one of the 3,5-DCB binding sites in close proximity of the metal center resulting in liberation of both COD ligands and the formation of a [Rh(PAm )2 ]BF4 complex. Coordination of the amide carbonyl unit was found to be reversible, since the complex acted as an active catalyst in the hydrogenation of dehydroamino acid derivatives. X-ray crystallographic investigation revealed that the second 3,5-DCB unit is capable of forming noncovalent π-π interactions connecting both phosphoramidite ligands. © 2016 Wiley Periodicals, Inc.

  12. Convex-PL: a novel knowledge-based potential for protein-ligand interactions deduced from structural databases using convex optimization

    Science.gov (United States)

    Kadukova, Maria; Grudinin, Sergei

    2017-10-01

    We present a novel optimization approach to train a free-shape distance-dependent protein-ligand scoring function called Convex-PL. We do not impose any functional form of the scoring function. Instead, we decompose it into a polynomial basis and deduce the expansion coefficients from the structural knowledge base using a convex formulation of the optimization problem. Also, for the training set we do not generate false poses with molecular docking packages, but use constant RMSD rigid-body deformations of the ligands inside the binding pockets. This allows the obtained scoring function to be generally applicable to scoring of structural ensembles generated with different docking methods. We assess the Convex-PL scoring function using data from D3R Grand Challenge 2 submissions and the docking test of the CASF 2013 study. We demonstrate that our results outperform the other 20 methods previously assessed in CASF 2013. The method is available at http://team.inria.fr/nano-d/software/Convex-PL/.

  13. Convex-PL: a novel knowledge-based potential for protein-ligand interactions deduced from structural databases using convex optimization

    Science.gov (United States)

    Kadukova, Maria; Grudinin, Sergei

    2017-09-01

    We present a novel optimization approach to train a free-shape distance-dependent protein-ligand scoring function called Convex-PL. We do not impose any functional form of the scoring function. Instead, we decompose it into a polynomial basis and deduce the expansion coefficients from the structural knowledge base using a convex formulation of the optimization problem. Also, for the training set we do not generate false poses with molecular docking packages, but use constant RMSD rigid-body deformations of the ligands inside the binding pockets. This allows the obtained scoring function to be generally applicable to scoring of structural ensembles generated with different docking methods. We assess the Convex-PL scoring function using data from D3R Grand Challenge 2 submissions and the docking test of the CASF 2013 study. We demonstrate that our results outperform the other 20 methods previously assessed in CASF 2013. The method is available at http://team.inria.fr/nano-d/software/Convex-PL/.

  14. Residue-Ligand Interaction Energy (ReLIE on a Receptor-Dependent 3D-QSAR Analysis of S- and NH-DABOs as Non-Nucleoside Reverse Transcriptase Inhibitors

    Directory of Open Access Journals (Sweden)

    Monique Araújo de Brito

    2012-06-01

    Full Text Available A series of 74 dihydroalkoxybenzyloxopyrimidines (DABOs, a class of highly potent non-nucleoside reverse transcriptase inhibitors (NNRTIs, was retrieved from the literature and studied by receptor-dependent (RD three-dimensional quantitative structure-activity relationship (3D-QSAR analysis to derive RD-3D-QSAR models. The descriptors in this new method are the steric and electrostatic interaction energies of the protein-ligand complexes (per residue simulated by molecular dynamics, an approach named Residue-Ligand Interaction Energy (ReLIE. This study was performed using a training set of 59 compounds and the MKC-442/RT complex structure as reference. The ReLIE-3D-QSAR models were constructed and evaluated by genetic algorithm (GA and partial least squares (PLS. In the best equations, at least one term is related to one of the amino acid residues of the p51 subunit: Asn136, Asn137, Glu138, and Thr139. This fact implies the importance of interchain interaction (p66-p51 in the equations that best describe the structure-activity relationship for this class of compounds. The best equation shows q2 = 0.660, SEcv = 0.500, r2 = 0.930, and SEE = 0.226. The external predictive ability of this best model was evaluated using a test set of 15 compounds. In order to design more potent DABO analogues as anti-HIV/AIDS agents, substituents capable of interactions with residues like Ile94, Lys101, Tyr181, and Tyr188 should be selected. Also, given the importance of the conserved Asn136, this residue could become an attractive target for the design of novel NNRTIs with improved potency and increased ability to avoid the development of drug-resistant viruses.

  15. Tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) induces death receptor 5 networks that are highly organized.

    Science.gov (United States)

    Valley, Christopher C; Lewis, Andrew K; Mudaliar, Deepti J; Perlmutter, Jason D; Braun, Anthony R; Karim, Christine B; Thomas, David D; Brody, Jonathan R; Sachs, Jonathan N

    2012-06-15

    Recent evidence suggests that TNF-related apoptosis-inducing ligand (TRAIL), a death-inducing cytokine with anti-tumor potential, initiates apoptosis by re-organizing TRAIL receptors into large clusters, although the structure of these clusters and the mechanism by which they assemble are unknown. Here, we demonstrate that TRAIL receptor 2 (DR5) forms receptor dimers in a ligand-dependent manner at endogenous receptor levels, and these receptor dimers exist within high molecular weight networks. Using mutational analysis, FRET, fluorescence microscopy, synthetic biochemistry, and molecular modeling, we find that receptor dimerization relies upon covalent and noncovalent interactions between membrane-proximal residues. Additionally, by using FRET, we show that the oligomeric structure of two functional isoforms of DR5 is indistinguishable. The resulting model of DR5 activation should revise the accepted architecture of the functioning units of DR5 and the structurally homologous TNF receptor superfamily members.

  16. Tumor Necrosis Factor-related Apoptosis-inducing Ligand (TRAIL) Induces Death Receptor 5 Networks That Are Highly Organized*

    Science.gov (United States)

    Valley, Christopher C.; Lewis, Andrew K.; Mudaliar, Deepti J.; Perlmutter, Jason D.; Braun, Anthony R.; Karim, Christine B.; Thomas, David D.; Brody, Jonathan R.; Sachs, Jonathan N.

    2012-01-01

    Recent evidence suggests that TNF-related apoptosis-inducing ligand (TRAIL), a death-inducing cytokine with anti-tumor potential, initiates apoptosis by re-organizing TRAIL receptors into large clusters, although the structure of these clusters and the mechanism by which they assemble are unknown. Here, we demonstrate that TRAIL receptor 2 (DR5) forms receptor dimers in a ligand-dependent manner at endogenous receptor levels, and these receptor dimers exist within high molecular weight networks. Using mutational analysis, FRET, fluorescence microscopy, synthetic biochemistry, and molecular modeling, we find that receptor dimerization relies upon covalent and noncovalent interactions between membrane-proximal residues. Additionally, by using FRET, we show that the oligomeric structure of two functional isoforms of DR5 is indistinguishable. The resulting model of DR5 activation should revise the accepted architecture of the functioning units of DR5 and the structurally homologous TNF receptor superfamily members. PMID:22496450

  17. PuF, an antimetastatic and developmental signaling protein, interacts with the Alzheimer’s amyloid-β precursor protein via a tissue-specific proximal regulatory element (PRE

    Directory of Open Access Journals (Sweden)

    Lahiri Debomoy K

    2013-01-01

    Full Text Available Abstract Background Alzheimer’s disease (AD is intimately tied to amyloid-β (Aβ peptide. Extraneuronal brain plaques consisting primarily of Aβ aggregates are a hallmark of AD. Intraneuronal Aβ subunits are strongly implicated in disease progression. Protein sequence mutations of the Aβ precursor protein (APP account for a small proportion of AD cases, suggesting that regulation of the associated gene (APP may play a more important role in AD etiology. The APP promoter possesses a novel 30 nucleotide sequence, or “proximal regulatory element” (PRE, at −76/−47, from the +1 transcription start site that confers cell type specificity. This PRE contains sequences that make it vulnerable to epigenetic modification and may present a viable target for drug studies. We examined PRE-nuclear protein interaction by gel electrophoretic mobility shift assay (EMSA and PRE mutant EMSA. This was followed by functional studies of PRE mutant/reporter gene fusion clones. Results EMSA probed with the PRE showed DNA-protein interaction in multiple nuclear extracts and in human brain tissue nuclear extract in a tissue-type specific manner. We identified transcription factors that are likely to bind the PRE, using competition gel shift and gel supershift: Activator protein 2 (AP2, nm23 nucleoside diphosphate kinase/metastatic inhibitory protein (PuF, and specificity protein 1 (SP1. These sites crossed a known single nucleotide polymorphism (SNP. EMSA with PRE mutants and promoter/reporter clone transfection analysis further implicated PuF in cells and extracts. Functional assays of mutant/reporter clone transfections were evaluated by ELISA of reporter protein levels. EMSA and ELISA results correlated by meta-analysis. Conclusions We propose that PuF may regulate the APP gene promoter and that AD risk may be increased by interference with PuF regulation at the PRE. PuF is targeted by calcium/calmodulin-dependent protein kinase II inhibitor 1, which also

  18. Fluorescent GPCR ligands as new tools in pharmacology.

    Science.gov (United States)

    Kuder, Kamil; Kieć-Kononowicz, Katarzyna

    2008-01-01

    The expansion of fluorescent techniques for studying the ligand-receptor interaction resulted in a burst of the novel fluorescent ligands development. The discovery of the ligand, that is of high affinity to the receptor and whose localization could be easily visualized, even on the single cell level, gave the researchers a strong impulse to investigate that field of GPCR ligands. Moreover, paying attention to the "non pharmacological" advantages of these ligands, as well as the techniques to be used, fluorescent ligands are becoming treated more seriously, as the ligands themselves, and as novel, useful tools for studying GPCRs. Herein, we review results described in the literature, starting from the year 2000, in the field of the fluorescent GPCR small, non-peptide ligands according to the affinity to the selected receptors (histamine, adenosine, adrenergic, cannabinoid, muscarinie, neuropeptide Y and serotonine) as well as the fluorophores that have been used to tag the molecules.

  19. New pyrimidine based ligand capped gold and platinum nano particles: Synthesis, characterization, antimicrobial, antioxidant, DNA interaction and in vitro anticancer activities.

    Science.gov (United States)

    Sankarganesh, M; Adwin Jose, P; Dhaveethu Raja, J; Kesavan, M P; Vadivel, M; Rajesh, J; Jeyamurugan, R; Senthil Kumar, R; Karthikeyan, S

    2017-11-01

    In this research work, we have synthesized new pyrimidine based Schiff base ligand, 2-((4,6-dimethoxypyrimidine-2-yl)methyleneenamino)-6-methoxyphenol (DPMM) capped gold (Au) and platinum (Pt) nanoparticles (NPs) by modified Brust-Schiffrin method. The characteristics of DPMM-Au NPs and DPMM-Pt NPs have been examined by UV-Visible, FTIR, SEM, TEM and powder XRD analysis. SEM analysis result shows that surface morphology of the DPMM-Au NPs and DPMM-Pt NPs are in granular and spherical shape, correspondingly. The size of the DPMM-Au NPs and DPMM-Pt NPs are approximately 38.14±4.5 and 58.64±3.0nm respectively, which confirmed by TEM analysis. The DPMM-Au NPs and DPMM-Pt NPs have potent antimicrobial against Escherichia coli, Klebsiella pneumonia, Pseudomonas fluorescens, Shigella sonnei, Staphylococcus aureus and Aspergillus niger, Candida albicans, Candida tropicalis, Mucor indicus, Rhizopus strains. The DPMM-Au NPs and DPMM-Pt NPs have good antioxidant activities than the free ligand (DPMM). The spectroscopic and viscometric measurement confirms the hydrophobic DNA binding abilities of the newly prepared DPMM capped metal NPs. Moreover, the in vitro anticancer activity of DPMM, DPMM-Au NPs and DPMM-Pt NPs against cancer (MCF-7, HeLa & HEp2) and normal (NHDF) cell lines have performed using MTT assay. These results reveals that, DPMM-Au NPs and DPMM-Pt NPs having significant cytotoxic activity against the cancer cell lines and least toxic effect on normal cell line as compared to standard drug cisplatin. Copyright © 2017 Elsevier B.V. All rights reserved.

  20. Some Properties of Fuzzy Soft Proximity Spaces

    Science.gov (United States)

    Demir, İzzettin; Özbakır, Oya Bedre

    2015-01-01

    We study the fuzzy soft proximity spaces in Katsaras's sense. First, we show how a fuzzy soft topology is derived from a fuzzy soft proximity. Also, we define the notion of fuzzy soft δ-neighborhood in the fuzzy soft proximity space which offers an alternative approach to the study of fuzzy soft proximity spaces. Later, we obtain the initial fuzzy soft proximity determined by a family of fuzzy soft proximities. Finally, we investigate relationship between fuzzy soft proximities and proximities. PMID:25793224

  1. Cilastatin attenuates cisplatin-induced proximal tubular cell damage.

    Science.gov (United States)

    Camano, Sonia; Lazaro, Alberto; Moreno-Gordaliza, Estefania; Torres, Ana M; de Lucas, Carmen; Humanes, Blanca; Lazaro, Jose A; Milagros Gomez-Gomez, M; Bosca, Lisardo; Tejedor, Alberto

    2010-08-01

    A major area in cancer therapy is the search for protective strategies against cisplatin-induced nephrotoxicity. We investigated the protective effect of cilastatin on cisplatin-induced injury to renal proximal tubular cells. Cilastatin is a specific inhibitor of renal dehydrodipeptidase I (DHP-I), which prevents hydrolysis of imipenem and its accumulation in the proximal tubule. Primary cultures of proximal cells were treated with cisplatin (1-30 microM) in the presence or absence of cilastatin (200 microg/ml). Apoptosis and mitochondrial injury were assessed by different techniques. Cisplatin uptake and DNA binding were measured by inductively coupled plasma spectrometry. HeLa cells were used to control the effect of cilastatin on the tumoricidal activity of cisplatin. Cisplatin increased cell death, apoptotic-like morphology, caspase activation, and mitochondrial injury in proximal tubular cells in a dose- and time-dependent way. Concomitant treatment with cilastatin reduced cisplatin-induced changes. Cilastatin also reduced the DNA-bound platinum but did not modify cisplatin-dependent up-regulation of death receptors (Fas) or ligands (tumor necrosis factor alpha, Fas ligand). In contrast, cilastatin did not show any effects on cisplatin-treated HeLa cells. Renal DHP-I was virtually absent in HeLa cells. Cilastatin attenuates cisplatin-induced cell death in proximal tubular cells without reducing the cytotoxic activity of cisplatin in tumor cells. Our findings suggest that the affinity of cilastatin for renal dipeptidase makes this effect specific for proximal tubular cells and may be related to a reduction in intracellular drug accumulation. Therefore, cilastatin administration might represent a novel strategy in the prevention of cisplatin-induced acute renal injury.

  2. PROXIMITY MANAGEMENT IN CRISIS CONDITIONS

    Directory of Open Access Journals (Sweden)

    Ion Dorin BUMBENECI

    2010-01-01

    Full Text Available The purpose of this study is to evaluate the level of assimilation for the terms "Proximity Management" and "Proximity Manager", both in the specialized literature and in practice. The study has two parts: the theoretical research of the two terms, and an evaluation of the use of Proximity management in 32 companies in Gorj, Romania. The object of the evaluation resides in 27 companies with less than 50 employees and 5 companies with more than 50 employees.

  3. DNA and HSA interaction of Vanadium (IV), Copper (II), and Zinc (II) complexes derived from an asymmetric bidentate Schiff-base ligand: multi spectroscopic, viscosity measurements, molecular docking, and ONIOM studies.

    Science.gov (United States)

    Dehkhodaei, Monireh; Sahihi, Mehdi; Amiri Rudbari, Hadi; Momenbeik, Fariborz

    2018-03-01

    The interaction of three complexes [Zn(II), Cu(II), and V(IV)] derived from an asymmetric bidentate Schiff-base ligand with DNA and HSA was studied using fluorescence quenching, UV-Vis spectroscopy, viscosity measurements, and computational methods [molecular docking and our Own N-layered Integrated molecular Orbital and molecular Mechanics (ONIOM)]. The obtained results revealed that the DNA and HSA affinities for binding of the synthesized compounds follow as V(IV) > Zn(II) > Cu(II) and Zn(II) > V(IV) > Cu(II), respectively. The distance between these compounds and HSA was obtained based on the Förster's theory of non-radiative energy transfer. Furthermore, computational molecular docking was carried out to investigate the DNA- and HSA-binding pose of the compounds. Molecular docking calculations showed that H-bond, hydrophobic, and π-cation interactions have dominant role in stability of the compound-HSA complexes. ONIOM method was utilized to investigate the HSA binding of the compounds more precisely in which molecular-mechanics method (UFF) and semi-empirical method (PM6) were selected for the low layer and the high layer, respectively. The results show that the structural parameters of the compounds changed along with binding, indicating the strong interaction between the compounds with HSA and DNA. Viscosity measurements as well as computational docking data suggest that all metal complexes interact with DNA, presumably by groove-binding mechanism.

  4. N-hydroxyguanidines as new heme ligands: UV-visible, EPR, and resonance Raman studies of the interaction of various compounds bearing a C=NOH function with microperoxidase-8.

    Science.gov (United States)

    Lefevre-Groboillot, D; Dijols, S; Boucher, J L; Mahy, J P; Ricoux, R; Desbois, A; Zimmermann, J L; Mansuy, D

    2001-08-21

    Interaction between microperoxidase-8 (MP8), a water-soluble hemeprotein model, and a wide range of N-aryl and N-alkyl N'-hydroxyguanidines and related compounds has been investigated using UV-visible, EPR, and resonance Raman spectroscopies. All the N-hydroxyguanidines studied bind to the ferric form of MP8 with formation of stable low-spin iron(III) complexes characterized by absorption maxima at 405, 535, and 560 nm. The complex obtained with N-(4-methoxyphenyl) N'-hydroxyguanidine exhibits EPR g-values at 2.55, 2.26, and 1.86. The resonance Raman (RR) spectrum of this complex is also in agreement with an hexacoordinated low-spin iron(III) structure. The dissociation constants (K(s)) of the MP8 complexes with mono- and disubstituted N-hydroxyguanidines vary between 15 and 160 microM at pH 7.4. Amidoximes also form low-spin iron(III) complexes of MP8, although with much larger dissociation constants. Under the same conditions, ketoximes, aldoximes, methoxyguanidines, and guanidines completely fail to form such complexes with MP8. The K(s) values of the MP8-N-hydroxyguanidine complexes decrease as the pH of the solution is increased, and the affinity of the N-hydroxyguanidines toward MP8 increases with the pK(a) of these ligands. Altogether these results show that compounds involving a -C(NHR)=NOH moiety act as good ligands of MP8-Fe(III) with an affinity that depends on the electron-richness of this moiety. The analysis of the EPR spectrum of the MP8-N-hydroxyguanidine complexes according to Taylor's equations shows a strong axial distortion of the iron, typical of those observed for hexacoordinated heme-Fe(III) complexes with at least one pi donor axial ligand (HO(-), RO(-), or RS(-)). These data strongly suggest that N-hydroxyguanidines bind to MP8 iron via their oxygen atom after deprotonation or weakening of their O-H bond. It thus seems that N-hydroxyguanidines could constitute a new class of strong ligands for hemeproteins and iron(III)-porphyrins.

  5. The Interaction of Sheep Genomic DNA with a Cobalt(II Complex Containing p-Nitrobenzoate and N,N`-Diethylnicotinamide Ligands

    Directory of Open Access Journals (Sweden)

    Hacali Necefoglu

    2007-12-01

    Full Text Available The synthesized cobalt(II complex, CoPNBDENA and the binding of thiscomplex with sheep genomic DNA were investigated by UV–Visible absorption andviscosity techniques. Also the interaction of sheep genomic DNA with the complex wasstudied using the agarose gel electrophoresis method. The results indicated that thecomplex interacted with DNA. The nature of the binding seemed to be mainly anelectrostatic interaction between DNA and the cobalt(II complex. Other binding modessuch as hydrogen bonds may also exist in this system. In this study, after the interaction ofDNA– CoPNBDENA, it was observed that the migration of the DNA band became slow asthe amount of cobalt(II complex was increased. This clearly demonstrates that theCoPNBDENA complex neutralizes the negative charges of DNA.

  6. Bromelain decreases neutrophil interactions with P-selectin, but not E-selectin, in vitro by proteolytic cleavage of P-selectin glycoprotein ligand-1.

    Directory of Open Access Journals (Sweden)

    Jessica M Banks

    Full Text Available Stem bromelain, a cysteine protease isolated from pineapples, is a natural anti-inflammatory treatment, yet its mechanism of action remains unclear. Curious as to whether bromelain might affect selectin-mediated leukocyte rolling, we studied the ability of bromelain-treated human neutrophils to tether to substrates presenting immobilized P-selectin or E-selectin under shear stress. Bromelain treatment attenuated P-selectin-mediated tethering but had no effect on neutrophil recruitment on E-selectin substrates. Flow cytometric analysis of human neutrophils, using two antibodies against distinct epitopes within the P-selectin glycoprotein ligand-1 (PSGL-1 active site, revealed that bromelain cleaves PSGL-1 to remove one of two sites required for P-selectin binding, while leaving the region required for E-selectin binding intact. These findings suggest one molecular mechanism by which bromelain may exert its anti-inflammatory effects is via selective cleavage of PSGL-1 to reduce P-selectin-mediated neutrophil recruitment.

  7. Bromelain decreases neutrophil interactions with P-selectin, but not E-selectin, in vitro by proteolytic cleavage of P-selectin glycoprotein ligand-1.

    Science.gov (United States)

    Banks, Jessica M; Herman, Christine T; Bailey, Ryan C

    2013-01-01

    Stem bromelain, a cysteine protease isolated from pineapples, is a natural anti-inflammatory treatment, yet its mechanism of action remains unclear. Curious as to whether bromelain might affect selectin-mediated leukocyte rolling, we studied the ability of bromelain-treated human neutrophils to tether to substrates presenting immobilized P-selectin or E-selectin under shear stress. Bromelain treatment attenuated P-selectin-mediated tethering but had no effect on neutrophil recruitment on E-selectin substrates. Flow cytometric analysis of human neutrophils, using two antibodies against distinct epitopes within the P-selectin glycoprotein ligand-1 (PSGL-1) active site, revealed that bromelain cleaves PSGL-1 to remove one of two sites required for P-selectin binding, while leaving the region required for E-selectin binding intact. These findings suggest one molecular mechanism by which bromelain may exert its anti-inflammatory effects is via selective cleavage of PSGL-1 to reduce P-selectin-mediated neutrophil recruitment.

  8. Correlation between DNA interactions and cytotoxic activity of four new ternary compounds of copper(II) with N-donor heterocyclic ligands.

    Science.gov (United States)

    Silva, Priscila P; Guerra, Wendell; Dos Santos, Geandson Coelho; Fernandes, Nelson G; Silveira, Josiane N; da Costa Ferreira, Ana M; Bortolotto, Tiago; Terenzi, Hernán; Bortoluzzi, Adailton João; Neves, Ademir; Pereira-Maia, Elene C

    2014-03-01

    Four new ternary complexes of copper(II) were synthesized and characterized: [Cu(hyd)(bpy)(acn)(ClO4)](ClO4)] (1), [Cu(hyd)(phen)(acn)(ClO4)](ClO4)] (2), [Cu(Shyd)(bpy)(acn)(ClO4)](ClO4)] (3) and [Cu(Shyd)(phen)(acn)(ClO4)](ClO4)] (4), in which acn=acetonitrile; hyd=2-furoic acid hydrazide, bpy=2,2-bipyridine; phen=1,10-phenanthroline and Shyd=2-thiophenecarboxylic acid hydrazide. The cytotoxic activity of the complexes in a chronic myelogenous leukemia cell line was investigated. All complexes are able to enter cells and inhibit cellular growth in a concentration-dependent manner, with an activity higher than that of the corresponding free ligands. The substitution of Shyd for hyd increases the activity, while the substitution of bpy for phen renders the complex less active. Therefore, the most potent complex is 4 with an IC50 value of 1.5±0.2μM. The intracellular copper concentration needed to inhibit 50% of cell growth is approximately 7×10(-15)mol/cell. It is worth notifying that a correlation between cytotoxic activity, DNA binding affinity and DNA cleavage was found: 1<3<2<4. © 2013.

  9. Water-soluble and photo-stable silver(I) dicarboxylate complexes containing 1,10-phenanthroline ligands: Antimicrobial and anticancer chemotherapeutic potential, DNA interactions and antioxidant activity.

    Science.gov (United States)

    Thornton, Laura; Dixit, Vidya; Assad, Letícia O N; Ribeiro, Thales P; Queiroz, Daniela D; Kellett, Andrew; Casey, Alan; Colleran, John; Pereira, Marcos D; Rochford, Garret; McCann, Malachy; O'Shea, Denis; Dempsey, Rita; McClean, Siobhán; Kia, Agnieszka Foltyn-Arfa; Walsh, Maureen; Creaven, Bernadette; Howe, Orla; Devereux, Michael

    2016-06-01

    The complexes [Ag2(OOC-(CH2)n-COO)] (n=1-10) (1-10) were synthesised and reacted with 1,10-phenanthroline (phen) to yield derivatives formulating as [Ag2(phen)x(OOC-(CH2)y-COO)]·zH2O (x=2 or 3; y=1-10; z=1-4) (11-20) which are highly water-soluble and photo-stable in aqueous solution. The phen derivatives 11-20 exhibit chemotherapeutic potential against Candida albicans, Escherichia coli, Staphylococcus aureus and Pseudomonas aeruginosa and against cisplatin-sensitive breast (MCF-7) and resistant ovarian (SKOV-3) cancer cell lines. Cyclic voltammetric analysis and DNA binding and intercalation studies indicate that the mechanism of action of 11-20 is significantly different to that of their silver(I) dicarboxylate precursors and they do not induce DNA damage or ROS generation in mammalian cells. The representative complexes 9 and 19 (containing the undecanedioate ligand) were both found to significantly reduce superoxide and hydrogen peroxide induced oxidative stress in the yeast S. cerevisiae. Copyright © 2016 Elsevier Inc. All rights reserved.

  10. DNA interaction, antimicrobial, anticancer activities and molecular docking study of some new VO(II), Cr(III), Mn(II) and Ni(II) mononuclear chelates encompassing quaridentate imine ligand.

    Science.gov (United States)

    Abdel-Rahman, Laila H; Abu-Dief, Ahmed M; Aboelez, Moustafa O; Hassan Abdel-Mawgoud, Azza A

    2017-05-01

    The present study was conducted to synthesis of some new imine Cr(III), VO(II), Mn(II) and Ni(II) complexes derived from the condensation of 2-amino phenol with 2-hydroxynapthaldehyde were synthesized. The prepared HNPN imine ligand was analyzed by its melting point, IR, (1)H NMR and (13)C NMR spectroscopies. The investigated HNPN imine complexes were characterized by elemental analysis, FT IR, UV-vis and thermal analysis (TGA) under nitrogen atmosphere from ambient temperature to 750°C. The experimental results revealed that the investigated complexes contain hydrated water molecules. The molar conductance values of complexes are relatively low, indicating the non-electrolytic nature of these complexes. Magnetic susceptibility measurements show that the investigated complexes are paramagnetic. Moreover, the stability constants of the preparing complexes were determined spectrophotometrically. All the complexes were found to be monomeric 1:1 (M:L) stoichiometry in nature with octahedral geometry for Cr(III), tetrahedral for Mn(II), square planner for Ni(II) and square pyramidal for VO(II). Moreover, the prepared HNPN imine ligand and its complexes were evaluated for antimicrobial effect against some types of bacteria such as Bacillus subtilis (+ve), Escherichia coli(-ve) and Staphylococcus aureus (+ve) and some types of fungi such as Aspergillusniger, Candida glabrata and Trichophyton rubrum. The results of these studies indicate that the metal complexes exhibit a stronger antibacterial and antifungal efficiency compared to their corresponding imine ligand. Moreover, the interaction of the investigated complexes with CT-DNA was checked using spectral studies, viscosity measurements and gel electrophoreses. The absorption titration studies revealed that each of these complexes is an avid binder to calf thymus-DNA. Also, there was appreciable changes in the relative viscosity of DNA, which is consistent with enhanced hydrophobic interaction of the aromatic rings and

  11. 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

  12. Drug design targeting protein-protein interactions (PPIs) using multiple ligand simultaneous docking (MLSD) and drug repositioning: discovery of raloxifene and bazedoxifene as novel inhibitors of IL-6/GP130 interface.

    Science.gov (United States)

    Li, Huameng; Xiao, Hui; Lin, Li; Jou, David; Kumari, Vandana; Lin, Jiayuh; Li, Chenglong

    2014-02-13

    The IL-6/GP130/STAT3 pathway is critical for the progression of multiple types of cancers. We report here the discovery of raloxifene and bazedoxifene as novel inhibitors of IL-6/GP130 protein-protein interactions (PPIs) using multiple ligand simultaneous docking (MLSD) and drug repositioning approaches. Multiple drug scaffolds were simultaneously docked into hot spots of GP130 D1 domain by MLSD to compete with the key interacting residues of IL-6, followed by tethering to generate virtual hit compounds. Similarity searches of virtual hits on drug databases identified raloxifene and bazedoxifene as potential inhibitors of IL-6/GP130 interaction. In cancer cell assays both compounds bind to GP130 and demonstrated selective inhibition of IL-6 induced STAT3 phosphorylation and were significantly more potent than the previously reported natural product inhibitor MDL-A. The identified drugs represent a new class of lead compounds with piperidine, benzothiophene, and indole scaffolds to inhibit IL-6 induced homodimerization of GP130. Besides potential direct usage for clinic trials, the two compounds can also serve as lead compounds for optimization to speed the development of drugs selectively targeting the IL-6/GP130/STAT3 cancer signaling pathway.

  13. Tunable Magnetic Proximity Effects in Graphene Junctions

    Science.gov (United States)

    Lazic, Predrag; Belashchenko, Kirill; Zutic, Igor

    2015-03-01

    The characteristic length of the magnetic proximity effects exceed the thickness of a graphene layer leading to an important, but typically overlooked, modifications of equilibrium and transport properties, as well as the implications for graphene spintronics. Using the first-principles studies that integrate a real space density functional theory (GPAW) with the state-of-the art boundary elements electrostatic code based on the Robin Hood method, we explore tunable electronic structure and magnetic proximity effects in the ferromagnet/insulator/graphene junctions. We show that the inclusion of a finite-size gate electrodes and van der Walls interaction lead to nontrivial effects that could also be important in other two-dimensional materials beyond graphene. Work supported by US ONR, NSF-DMR and Nebraska NSF MRSEC.

  14. Spin manipulation and spin-lattice interaction in magnetic colloidal quantum dots

    Science.gov (United States)

    Moro, Fabrizio; Turyanska, Lyudmila; Granwehr, Josef; Patanè, Amalia

    2014-11-01

    We report on the spin-lattice interaction and coherent manipulation of electron spins in Mn-doped colloidal PbS quantum dots (QDs) by electron spin resonance. We show that the phase memory time,TM , is limited by Mn-Mn dipolar interactions, hyperfine interactions of the protons (1H) on the QD capping ligands with Mn ions in their proximity (Rabi oscillations. Our findings suggest routes to the rational design of magnetic colloidal QDs with phase memory times exceeding the current limits of relevance for the implementation of QDs as qubits in quantum information processing.

  15. Palmitoylation of cysteine 415 of CB1 receptor affects ligand-stimulated internalization and selective interaction with membrane cholesterol and caveolin 1.

    Science.gov (United States)

    Oddi, Sergio; Stepniewski, Tomasz Maciej; Totaro, Antonio; Selent, Jana; Scipioni, Lucia; Dufrusine, Beatrice; Fezza, Filomena; Dainese, Enrico; Maccarrone, Mauro

    2017-05-01

    We previously demonstrated that CB1 receptor is palmitoylated at cysteine 415, and that such a post-translational modification affects its biological activity. To assess the molecular mechanisms responsible for modulation of CB1 receptor function by S-palmitoylation, in this study biochemical and morphological approaches were paralleled with computational analyses. Molecular dynamics simulations suggested that this acyl chain stabilizes helix 8 as well as the interaction of CB1 receptor with membrane cholesterol. In keeping with these in silico data, experimental results showed that the non-palmitoylated CB1 receptor was unable to interact efficaciously with caveolin 1, independently of its activation state. Moreover, in contrast with the wild-type receptor, the lack of S-palmitoylation in the helix 8 made the mutant CB1 receptor completely irresponsive to agonist-induced effects in terms of both lipid raft partitioning and receptor internalization. Overall, our results support the notion that palmitoylation of cysteine 415 modulates the conformational state of helix 8 and influences the interactions of CB1 receptor with cholesterol and caveolin 1, suggesting that the palmitoyl chain may serve as a functional interface for CB1 receptor localization and function. Copyright © 2017 Elsevier B.V. All rights reserved.

  16. Type 2 innate lymphoid cell suppression by regulatory T cells attenuates airway hyperreactivity and requires inducible T-cell costimulator-inducible T-cell costimulator ligand interaction.

    Science.gov (United States)

    Rigas, Diamanda; Lewis, Gavin; Aron, Jennifer L; Wang, Bowen; Banie, Homayon; Sankaranarayanan, Ishwarya; Galle-Treger, Lauriane; Maazi, Hadi; Lo, Richard; Freeman, Gordon J; Sharpe, Arlene H; Soroosh, Pejman; Akbari, Omid

    2017-05-01

    Atopic diseases, including asthma, exacerbate type 2 immune responses and involve a number of immune cell types, including regulatory T (Treg) cells and the emerging type 2 innate lymphoid cells (ILC2s). Although ILC2s are potent producers of type 2 cytokines, the regulation of ILC2 activation and function is not well understood. In the present study, for the first time, we evaluate how Treg cells interact with pulmonary ILC2s and control their function. ILC2s and Treg cells were evaluated by using in vitro suppression assays, cell-contact assays, and gene expression panels. Also, human ILC2s and Treg cells were adoptively transferred into NOD SCID γC-deficient mice, which were given isotype or anti-inducible T-cell costimulator ligand (ICOSL) antibodies and then challenged with IL-33 and assessed for airway hyperreactivity. We show that induced Treg cells, but not natural Treg cells, effectively suppress the production of the ILC2-driven proinflammatory cytokines IL-5 and IL-13 both in vitro and in vivo. Mechanistically, our data reveal the necessity of inducible T-cell costimulator (ICOS)-ICOS ligand cell contact for Treg cell-mediated ILC2 suppression alongside the suppressive cytokines TGF-β and IL-10. Using a translational approach, we then demonstrate that human induced Treg cells suppress syngeneic human ILC2s through ICOSL to control airway inflammation in a humanized ILC2 mouse model. These findings suggest that peripheral expansion of induced Treg cells can serve as a promising therapeutic target against ILC2-dependent asthma. Copyright © 2016 American Academy of Allergy, Asthma & Immunology. Published by Elsevier Inc. All rights reserved.

  17. Bio-affinity of copper(II) complexes with nitrogen and oxygen donor ligands: Synthesis, structural studies and in vitro DNA and HSA interaction of copper(II) complexes.

    Science.gov (United States)

    Jain, Surbhi; Khan, Tanveer A; Patil, Yogesh P; Pagariya, Darshana; Kishore, Nand; Tapryal, Suman; Naik, Anil D; Naik, Sunil G

    2017-09-01

    Reported herein the binding affinity between Human Serum Albumin and the DNA binding and cleavage activity of three copper(II) complexes, [Cu(phen)(o-van)ClO 4 ] (1), [Cu(phen)(gly)]ClO 4 (2) and [Cu(L 1 ) 2 (H 2 O) 2 ] (3) wherein 1 and 2 are synthesized with 1,10-phenanthroline (phen) and co-ligands (o-van: o-vanillin; gly: glycine) and 3 with a ligand 2-hydroxy-3-methoxybenzylidene-4H-1,2,4-triazol-4-amine (H 1 L 1 ). Complex 2 crystallizes in monoclinic (P21/n) space group shows square pyramidal geometry. The complex 3 crystallizes in monoclinic (P21/a) space group. All the three complexes exhibit binding affinity towards the transport protein Human Serum albumin (HSA). Quantitative evaluation of the thermodynamics of interaction and the results obtained from fluorescence spectroscopy suggest that metal coordinated glycynate, o-vanillin and perchlorate groups have a major role to play in the binding process, the latter two being stronger in the binding of complex 1. The coordinated water in complex 3 also plays an important role in the binding, which makes binding of complex 3 with HSA stronger than that of complex 2. Experimental results indicate that the binding affinity of the complexes towards CT-DNA is in the order 1>3>2 implying that complex 1 binds stronger than complex 3 and 2.The DNA cleaving activity of all the three complexes was explored in the presence of reactive oxygen compound, H 2 O 2 . All the three complexes have primarily shown the DNA cleaving activity. Copyright © 2017. Published by Elsevier B.V.

  18. Structure of a dinuclear cadmium complex with 2,2′-bipyridine, monodentate nitrate and 3-carboxy-6-methylpyridine-2-carboxylate ligands: intramolecular carbonyl(lone pair...π(ring and nitrate(π...π(ring interactions

    Directory of Open Access Journals (Sweden)

    Juan Granifo

    2015-08-01

    Full Text Available The centrosymmetric dinuclear complex bis(μ-3-carboxy-6-methylpyridine-2-carboxylato-κ3N,O2:O2;κ3O2:N,O2-bis[(2,2′-bipyridine-κ2N,N′(nitrato-κOcadmium] methanol monosolvate, [Cd2(C8H6NO42(NO32(C10H8N22]·CH3OH, was isolated as colourless crystals from the reaction of Cd(NO32·4H2O, 6-methylpyridine-2,3-dicarboxylic acid (mepydcH2 and 2,2′-bipyridine in methanol. The asymmetric unit consists of a CdII cation bound to a μ-κ3N,O2:O2-mepydcH− anion, an N,N′-bidentate 2,2′-bipyridine group and an O-monodentate nitrate anion, and is completed with a methanol solvent molecule at half-occupancy. The Cd complex unit is linked to its centrosymmetric image through a bridging mepydcH− carboxylate O atom to complete the dinuclear complex molecule. Despite a significant variation in the coordination angles, indicating a considerable departure from octahedral coordination geometry about the CdII atom, the Cd—O and Cd—N distances in this complex are surprisingly similar. The crystal structure consists of O—H...O hydrogen-bonded chains parallel to a, further bound by C—H...O contacts along b to form planar two-dimensional arrays parallel to (001. The juxtaposed planes form interstitial columnar voids that are filled by the methanol solvent molecules. These in turn interact with the complex molecules to further stabilize the structure. A search in the literature showed that complexes with the mepydcH− ligand are rare and complexes reported previously with this ligand do not adopt the μ-κ3 coordination mode found in the title compound.

  19. 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...

  20. Ultrafast heme-ligand recombination in truncated hemoglobin HbO from Mycobacterium tuberculosis: A ligand cage

    Science.gov (United States)

    Jasaitis, Audrius; Ouellet, Hugues; Lambry, Jean-Christophe; Martin, Jean-Louis; Friedman, Joel M.; Guertin, Michel; Vos, Marten H.

    2012-03-01

    Truncated hemoglobin HbO from Mycobacterium tuberculosis displays very slow exchange of diatomic ligands with its environment. Using femtosecond spectroscopy, we show that upon photoexcitation, ligands rebind with unusual speed and efficiency. Only ˜1% O2 can escape from the heme pocket and less than 1% NO. Most remarkably, CO rebinding occurs for 95%, predominantly in 1.2 ns. The general CO rebinding properties are unexpectedly robust against changes in the interactions with close by aromatic residues Trp88 (G8) and Tyr36 (CD1). Molecular dynamics simulations of the CO complex suggest that interactions of the ligand with structural water molecules as well as its rotational freedom play a role in the high reactivity of the ligand and the heme. The slow exchange of ligands between heme and environment may result from a combination of hindered ligand access to the heme pocket by the network of distal aromatic residues, and low escape probability from the pocket.

  1. Fractures of the proximal humerus

    DEFF Research Database (Denmark)

    Brorson, Stig

    2013-01-01

    . The bandages were further supported by splints made of wood or coarse grass. Healing was expected in forty days. Different fracture patterns have been discussed and classified since Ancient Greece. Current classification of proximal humeral fractures mainly relies on the classifications proposed by Charles......, classification of proximal humeral fractures remains a challenge for the conduct, reporting, and interpretation of clinical trials. The evidence for the benefits of surgery in complex fractures of the proximal humerus is weak. In three systematic reviews I studied the outcome after locking plate osteosynthesis......Fractures of the proximal humerus have been diagnosed and managed since the earliest known surgical texts. For more than four millennia the preferred treatment was forceful traction, closed reduction, and immobilization with linen soaked in combinations of oil, honey, alum, wine, or cerate...

  2. Ligand mediated evolution of size dependent magnetism in cobalt nanoclusters.

    Science.gov (United States)

    Hartmann, Michael J; Millstone, Jill E; Häkkinen, Hannu

    2018-02-07

    We use density functional theory to model the impact of a ligand shell on the magnetic properties of CoN (15 ≤ N ≤ 55) nanoclusters. We study three different ligand shells on each nanocluster core size, each known to have different electronic interactions with the surface: pure Cl ligand shells (X-type), pure PH3 ligand shells (L-type), and two component ligand shells with mixtures of Cl and PH3 ligands. The simulations show that the identity, arrangement, and total coverage of the ligand shell controls the distribution of local magnetic moments across the CoN core. On the surface of an unpassivated CoN nanocluster, the Co-Co coordination number (CN) is known to determine the local magnetic moments. Upon the introduction of a ligand, the Co-Co CN remains important, however the nature of the metal-ligand bond changes the extent to which increasing Co-Co CN quenches magnetism. Further, we identify an additional and significant long-range impact on local magnetic moments (LMM) from the PH3 ligand shells. Thus, we establish important design principles of magnetic nanoclusters, where ligand shell chemistry mediates the distribution of LMMs across a CoNLM nanocluster, allowing a route to rational design of specific magnetic properties.

  3. Alkaloids as Inhibitors of Malate Synthase from Paracoccidioides spp.: Receptor-Ligand Interaction-Based Virtual Screening and Molecular Docking Studies, Antifungal Activity, and the Adhesion Process

    Science.gov (United States)

    Costa, Fausto Guimaraes; Neto, Benedito Rodrigues da Silva; Gonçalves, Ricardo Lemes; da Silva, Roosevelt Alves; de Oliveira, Cecília Maria Alves; Kato, Lucília; Freitas, Carla dos Santos; Giannini, Maria José Soares Mendes; da Silva, Julhiany de Fátima; Soares, Célia Maria de Almeida

    2015-01-01

    Paracoccidioides is the agent of paracoccidioidomycosis. Malate synthase plays a crucial role in the pathogenicity and virulence of various fungi, such as those that are human pathogens. Thus, an inhibitor of this enzyme may be used as a powerful antifungal without side effects in patients once these enzymes are absent in humans. Here, we searched for compounds with inhibitory capacity against the malate synthase of Paracoccidioides species (PbMLS). The three-dimensional (3D) structure of PbMLS was determined using the I-TASSER server. Compounds were selected from the ZINC database. Based on the mechanism underlying the interaction of the compounds with PbMLS, it was possible to identify β-carboline moiety as a standard key structure. The compounds with β-carboline moiety that are available in our laboratories were investigated. A total of nine alkaloid compounds were selected. The primary mechanisms of interaction of the alkaloid compounds in the binding pocket of PbMLS were identified and compared with the mechanism of interaction of acetyl coenzyme A (acetyl-CoA). We discovered that the amphipathic nature of the compounds, concomitant with the presence of β-carboline moiety, was crucial for their stability in the binding pocket of PbMLS. In addition, the importance of a critical balance of the polar and nonpolar contacts of the compounds in this region was observed. Four β-carboline alkaloid compounds showed the ability to inhibit recombinant PbMLS (PbMLSr) activity, Paracoccidioides species growth, and adhesion of the fungus and PbMLSr to the extracellular matrix components. The cytotoxicity of the alkaloids was also evaluated. PMID:26124176

  4. The infrastructure of psychological proximity

    DEFF Research Database (Denmark)

    Nickelsen, Niels Christian Mossfeldt

    2015-01-01

    ). The experience of psychological proximity between patient and nurse is provided through confidence, continuity and the practical set-up. This constitutes an important enactment of skillfulness, which may render telemedicine a convincing health service in the future. Methodology: The study draws on a pilot...... (Langstrup & Winthereik 2008). This study contributes by showing the infrastructure of psychological proximity, which is provided by way of device, confidence, continuity and accountability....

  5. Human - Robot Proximity

    DEFF Research Database (Denmark)

    Nickelsen, Niels Christian Mossfeldt

    The media and political/managerial levels focus on the opportunities to re-perform Denmark through digitization. Feeding assistive robotics is a welfare technology, relevant to citizens with low or no function in their arms. Despite national dissemination strategies, it proves difficult to recruit...... the study that took place as multi-sited ethnography at different locations in Denmark and Sweden. Based on desk research, observation of meals and interviews I examine socio-technological imaginaries and their practical implications. Human - robotics interaction demands engagement and understanding...

  6. 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.

  7. Atomic force microscopy study of the effect of HER 2 antibody on EGF mediated ErbB ligand-receptor interaction.

    Science.gov (United States)

    Zhang, Xuejie; Shi, Xiaoli; Xu, Li; Yuan, Jinghe; Fang, Xiaohong

    2013-07-01

    HER2, a member of the epidermal growth factor receptor (ErbB) family, is over-expressed in many cancers. Trastuzumab and Pertuzumab are two monoclonal antibodies targeting different extracellular domains of HER2 for cancer therapy. As Pertuzumab binds to the dimerization arm of HER2, it can block HER2 heterodimerization and in turn ErbB signaling. Whether Trastuzumab has the same function is unclear. In this work, we have applied living-cell single-molecule force spectroscopy (SMFS) by Atomic Force Microscopy (AFM) to investigate the effect of Trastuzumab, as well as Pertuzumab, on HER2-modulated EGF-EGFR interaction. The results demonstrated that EGF bound to EGFR more stably in the cells co-expressing EGFR and HER2, and the binding enhancement in the presence of HER2 was inhibited by either Trastuzumab or Pertuzumab. Trastuzumab is expected to exert a similar inhibition effect on HER2/EGFR dimerization as Pertuzumab, although it does not bind directly to the dimerization arm of HER2. Living-cell single-molecule force spectroscopy (SMFS) combined by Atomic Force Microscopy (AFM) was used by this team of scientists to investigate the effect of two monoclonal antibodies used in cancer therapy, Trastuzumab and Pertuzumab, on HER2-modulated EGF-EGFR interaction, demonstrating the utility of this technique in characterizing the effects of protein-based therapeutics on membrane receptors. Copyright © 2013 Elsevier Inc. All rights reserved.

  8. Group epitope mapping considering relaxation of the ligand (GEM-CRL): Including longitudinal relaxation rates in the analysis of saturation transfer difference (STD) experiments

    Science.gov (United States)

    Kemper, Sebastian; Patel, Mitul K.; Errey, James C.; Davis, Benjamin G.; Jones, Jonathan A.; Claridge, Timothy D. W.

    2010-03-01

    In the application of saturation transfer difference (STD) experiments to the study of protein-ligand interactions, the relaxation of the ligand is one of the major influences on the experimentally observed STD factors, making interpretation of these difficult when attempting to define a group epitope map (GEM). In this paper, we describe a simplification of the relaxation matrix that may be applied under specified experimental conditions, which results in a simplified equation reflecting the directly transferred magnetisation rate from the protein onto the ligand, defined as the summation over the whole protein of the protein-ligand cross-relaxation multiplied by with the fractional saturation of the protein protons. In this, the relaxation of the ligand is accounted for implicitly by inclusion of the experimentally determined longitudinal relaxation rates. The conditions under which this "group epitope mapping considering relaxation of the ligand" (GEM-CRL) can be applied were tested on a theoretical model system, which demonstrated only minor deviations from that predicted by the full relaxation matrix calculations (CORCEMA-ST) [7]. Furthermore, CORCEMA-ST calculations of two protein-saccharide complexes (Jacalin and TreR) with known crystal structures were performed and compared with experimental GEM-CRL data. It could be shown that the GEM-CRL methodology is superior to the classical group epitope mapping approach currently used for defining ligand-protein proximities. GEM-CRL is also useful for the interpretation of CORCEMA-ST results, because the transferred magnetisation rate provides an additional parameter for the comparison between measured and calculated values. The independence of this parameter from the above mentioned factors can thereby enhance the value of CORCEMA-ST calculations.

  9. Ligand modeling and design

    Energy Technology Data Exchange (ETDEWEB)

    Hay, B. [Pacific Northwest Lab., Richland, WA (United States)

    1996-10-01

    The purpose of this work is to develop and implement a molecular design basis for selecting organic ligands that would be used tin applications for the cost-effective removal of specific radionuclides from nuclear waste streams.

  10. Interaction of DNA with Simple and Mixed Ligand Copper(II Complexes of 1,10-Phenanthrolines as Studied by DNA-Fiber EPR Spectroscopy

    Directory of Open Access Journals (Sweden)

    Makoto Chikira

    2015-09-01

    Full Text Available The interaction of simple and ternary Cu(II complexes of 1,10-phenanthrolines with DNA has been studied extensively because of their various interesting and important functions such as DNA cleavage activity, cytotoxicity towards cancer cells, and DNA based asymmetric catalysis. Such functions are closely related to the DNA binding modes of the complexes such as intercalation, groove binding, and electrostatic surface binding. A variety of spectroscopic methods have been used to study the DNA binding mode of the Cu(II complexes. Of all these methods, DNA-fiber electron paramagnetic resonance (EPR spectroscopy affords unique information on the DNA binding structures of the complexes. In this review we summarize the results of our DNA-fiber EPR studies on the DNA binding structure of the complexes and discuss them together with the data accumulated by using other measurements.

  11. Interaction of DNA with Simple and Mixed Ligand Copper(II) Complexes of 1,10-Phenanthrolines as Studied by DNA-Fiber EPR Spectroscopy

    Science.gov (United States)

    Chikira, Makoto; Ng, Chew Hee; Palaniandavar, Mallayan

    2015-01-01

    The interaction of simple and ternary Cu(II) complexes of 1,10-phenanthrolines with DNA has been studied extensively because of their various interesting and important functions such as DNA cleavage activity, cytotoxicity towards cancer cells, and DNA based asymmetric catalysis. Such functions are closely related to the DNA binding modes of the complexes such as intercalation, groove binding, and electrostatic surface binding. A variety of spectroscopic methods have been used to study the DNA binding mode of the Cu(II) complexes. Of all these methods, DNA-fiber electron paramagnetic resonance (EPR) spectroscopy affords unique information on the DNA binding structures of the complexes. In this review we summarize the results of our DNA-fiber EPR studies on the DNA binding structure of the complexes and discuss them together with the data accumulated by using other measurements. PMID:26402668

  12. Ligand Interface Chemistry of Lead Chalcogenide Nanocrystals

    Science.gov (United States)

    Liu, Kun; Bealing, Clive; Hennig, Richard; Hennig Group Team

    2013-03-01

    Lead chalcogenides nanocrystals (NCs) have shown promise in photovoltaic applications. Surface chemistry is one of the most important, yet least understood aspects of NC synthesis and functionalization controlling their properties. For example, an incomplete surface passivation could create trap states that enhance undesired exciton recombination. Clever choices of ligands ensure that neighboring NCs are electronically coupled while maintaining their quantum size effects. These two barriers limiting performance of NC solar cells illustrate the importance of fundamental studies for the interaction between ligands and NC surfaces. We use density functional theory to determine the binding sites and energies of ligands commonly used in NC synthesis and functionalization. Specifically we study amine-, carboxyl-, and thiol-ligands on different PbSe and PbS surfaces. For methylamine ligands we find a similar binding energy on the (100) and (111) facet while carboxylic acid ligands strongly prefer the (111) facet leading to different effective NC shapes. This work was supported in part by Award No. KUS-C1-018-02, made by King Abdullah University of Science and Technology (KAUST) and by the Energy Materials Center at Cornell (EMC2) funded by the U.S. Department of Energy under Award Number DE-SC0001086

  13. Mouse model of proximal tubule endocytic dysfunction.

    Science.gov (United States)

    Weyer, Kathrin; Storm, Tina; Shan, Jingdong; Vainio, Seppo; Kozyraki, Renata; Verroust, Pierre J; Christensen, Erik I; Nielsen, Rikke

    2011-11-01

    Several studies have indicated the central role of the megalin/cubilin multiligand endocytic receptor complex in protein reabsorption in the kidney proximal tubule. However, the poor viability of the existing megalin-deficient mice precludes further studies and comparison of homogeneous groups of mice. Megalin- and/or cubilin-deficient mice were generated using a conditional Cre-loxP system, where the Cre gene is driven by the Wnt4 promoter. Kidney tissues from the mice were analysed for megalin and cubilin expression by quantitative reverse transcription-polymerase chain reaction, western blotting and immunohistochemistry. Renal albumin uptake was visualized by immunohistochemistry. Twenty-four-hour urine samples were collected in metabolic cages and analysed by sodium dodecyl sulphate-polyacrylamide gel electrophoresis and western blotting. Urinary albumin/creatinine ratios were measured by ELISA and the alkaline picrate method. The Meg(lox/lox);Cre(+), Cubn(lox/lox);Cre(+) and Meg(lox/lox), Cubn(lox/lox);Cre(+) mice were all viable, fertile and developed normal kidneys. Megalin and/or cubilin expression, assessed by immunohistology and western blotting, was reduced by >89%. Consistent with this observation, the mice excreted megalin and cubilin ligands such as transferrin and albumin in addition to low-molecular weight proteins. We further show that megalin/cubilin double-deficient mice excrete albumin with an average of 1.45 ± 0.54 mg/day, suggesting a very low albumin concentration in the glomerular ultrafiltrate. We report here the efficient genetic ablation of megalin, cubilin or both, using a Cre transgene driven by the Wnt4 promoter. The viable megalin/cubilin double-deficient mice now allow for detailed large-scale group analysis, and we anticipate that the mice will be of great value as an animal model for proximal tubulopathies with disrupted endocytosis.

  14. Methods for Identifying Ligands that Target Nucleic Acid Molecules and Nucleic Acid Structural Motifs

    Science.gov (United States)

    Disney, Matthew D. (Inventor); Childs-Disney, Jessica L. (Inventor)

    2017-01-01

    Disclosed are methods for identifying a nucleic acid (e.g., RNA, DNA, etc.) motif which interacts with a ligand. The method includes providing a plurality of ligands immobilized on a support, wherein each particular ligand is immobilized at a discrete location on the support; contacting the plurality of immobilized ligands with a nucleic acid motif library under conditions effective for one or more members of the nucleic acid motif library to bind with the immobilized ligands; and identifying members of the nucleic acid motif library that are bound to a particular immobilized ligand. Also disclosed are methods for selecting, from a plurality of candidate ligands, one or more ligands that have increased likelihood of binding to a nucleic acid molecule comprising a particular nucleic acid motif, as well as methods for identifying a nucleic acid which interacts with a ligand.

  15. Membrane partitioning of anionic, ligand-coated nanoparticles is accompanied by ligand snorkeling, local disordering, and cholesterol depletion.

    Directory of Open Access Journals (Sweden)

    Paraskevi Gkeka

    2014-12-01

    Full Text Available Intracellular uptake of nanoparticles (NPs may induce phase transitions, restructuring, stretching, or even complete disruption of the cell membrane. Therefore, NP cytotoxicity assessment requires a thorough understanding of the mechanisms by which these engineered nanostructures interact with the cell membrane. In this study, extensive Coarse-Grained Molecular Dynamics (MD simulations are performed to investigate the partitioning of an anionic, ligand-decorated NP in model membranes containing dipalmitoylphosphatidylcholine (DPPC phospholipids and different concentrations of cholesterol. Spontaneous fusion and translocation of the anionic NP is not observed in any of the 10-µs unbiased MD simulations, indicating that longer timescales may be required for such phenomena to occur. This picture is supported by the free energy analysis, revealing a considerable free energy barrier for NP translocation across the lipid bilayer. 5-µs unbiased MD simulations with the NP inserted in the bilayer core reveal that the hydrophobic and hydrophilic ligands of the NP surface rearrange to form optimal contacts with the lipid bilayer, leading to the so-called snorkeling effect. Inside cholesterol-containing bilayers, the NP induces rearrangement of the structure of the lipid bilayer in its vicinity from the liquid-ordered to the liquid phase spanning a distance almost twice its core radius (8-10 nm. Based on the physical insights obtained in this study, we propose a mechanism of cellular anionic NP partitioning, which requires structural rearrangements of both the NP and the bilayer, and conclude that the translocation of anionic NPs through cholesterol-rich membranes must be accompanied by formation of cholesterol-lean regions in the proximity of NPs.

  16. Receptor-ligand binding assays : Technologies and applications

    NARCIS (Netherlands)

    de Jong, LAA; Uges, DRA; Franke, JP; Bischoff, R; A.A. de Jong, Lutea; Piet Franke, Rainer

    2005-01-01

    Receptor-ligand interactions play a crucial role in biological systems and their measurement forms an important part of modem pharmaceutical development. Numerous assay formats are available that can be used to screen and quantify receptor ligands. In this review, we give an overview over both

  17. Monofunctional chorismate mutase from Bacillus subtilis: Kinetic and sup 13 C NMR studies on the interactions of the enzyme with its ligands

    Energy Technology Data Exchange (ETDEWEB)

    Gray, J.V.; Eren, D.; Knowles, J.R. (Harvard Univ., Cambridge, MA (USA))

    1990-09-18

    The interaction of the monofuctional chorismate mutase from Bacillus subtilis with chorismate and prephenate has been studied kinetically and by NMR spectroscopy with {sup 13}C specifically labeled substrates. Prephenate dominates the population of enzyme-bound species, and the off rate constant obtained from line-broadening experiments is close to the value of k{sub cat} for chorismate determined kinetically. The calculated on rate constant for prephenate is similar to the value of k{sub cat}/K{sub m} for chorismate. The kinetic parameters of the Bacillus mutase are remarkably insensitive to pH over a wide range and display no solvent isotope effect. These results suggest that the enzyme-catalyzed reaction may be encounter controlled (slowed from the diffusion limit by some feature of the enzyme's active site) and the k{sub cat} for chorismate is determined by the product off rate. There is now no evidence to suggest that the skeletal rearrangement on the enzyme surface occurs by a pathway other than a pericyclic process.

  18. DNA binding, DNA cleavage and BSA interaction of a mixed-ligand copper(II) complex with taurine Schiff base and 1,10-phenanthroline.

    Science.gov (United States)

    Li, Lianzhi; Guo, Qiong; Dong, Jianfang; Xu, Tao; Li, Jinghong

    2013-08-05

    The DNA-binding properties and DNA-cleavage activities of a Cu(II) complex, [Cu(sal-tau(phen)]·1.5H2O (sal-tau=a Schiff base derived from salicylaldehyde and taurine, phen=1,10-phenanthroline), have been investigated by using UV-Vis absorption, fluorescence, circular dichroism (CD) spectra and agarose gel electrophoresis. Results indicated that this Cu(II) complex can bind to calf thymus DNA (CT-DNA) via an intercalative mode and shows efficient cleavage activity in the absence and presence of reducer. Its intrinsic binding constant Kb (1.66×10(4)M(-1)) was calculated by absorption spectra and its linear Stern-Volmer quenching constant K(sq) (3.05) was obtained from florescence spectroscopy, as well as the cleaving reaction rate constant k1 (2.0×10(-4)s(-1)) was acquired from agarose gel electrophoresis. Meanwhile, the interactions of the complex with BSA have also been studied by spectroscopy. Results showed that the complex could quench the intrinsic fluorescence of bovine serum albumin (BSA) remarkably through a static quenching process, and induce a conformational change with the loss of helical stability of protein. Copyright © 2013 Elsevier B.V. All rights reserved.

  19. Design of Multichannel Osmium-Based Metalloreceptor for Anions and Cations by Taking Profit from Metal-Ligand Interaction and Construction of Molecular Keypad Lock and Memory Device.

    Science.gov (United States)

    Karmakar, Srikanta; Mardanya, Sourav; Pal, Poulami; Baitalik, Sujoy

    2015-12-21

    A polypyridylimidazole-based bifunctional Os(II) complex of the type [(bpy)2Os(tpy-Hbzim-dipy)](ClO4)2 (1), where tpy-Hbzim-dipy = 4'-[4-(4,5-dipyridin-2-yl-1H-imidazol-2-yl)-phenyl]-2,2';6',2″-terpyridine and bpy = 2,2'-bipyridine, has been synthesized and structurally characterized for the construction of multifunctional logic devices. After coordination of an [Os(bpy)2](2+) unit to one of the two bidentate chelating sites, the complex offers a terpyridine motif for binding with cationic guests and an imidazole moiety for interacting with selective anionic species. Consequently, the anion- and cation-binding aspects of the metallorecptor were examined in solution and in the solid state by different spectroscopic and electrochemical methods. The complex behaves as a bifunctional sensor for F(-), AcO(-), CN(-), Fe(2+), and Cu(2+) ions in acetonitrile, whereas it is a highly selective chromogenic chemosensor for only CN(-) and Fe(2+) ions in water. Based on various output signals with a particular set of anionic and cationic inputs, the complex mimics the functions of two-input INHIBIT, OR, NOR, and XNOR logic gates, as well as three-input NOR logic behavior. More importantly, the complicated functions of a keypad lock and memory device were also nicely demonstrated by the complex. Finally, density functional theory (DFT) and time-dependent density functional theory (TD-DFT) calculations also provide a rationale for properly understanding and interpreting the experimentally observed results.

  20. Ligands of Therapeutic Utility for the Liver X Receptors

    Directory of Open Access Journals (Sweden)

    Rajesh Komati

    2017-01-01

    Full Text Available Liver X receptors (LXRs have been increasingly recognized as a potential therapeutic target to treat pathological conditions ranging from vascular and metabolic diseases, neurological degeneration, to cancers that are driven by lipid metabolism. Amidst intensifying efforts to discover ligands that act through LXRs to achieve the sought-after pharmacological outcomes, several lead compounds are already being tested in clinical trials for a variety of disease interventions. While more potent and selective LXR ligands continue to emerge from screening of small molecule libraries, rational design, and empirical medicinal chemistry approaches, challenges remain in minimizing undesirable effects of LXR activation on lipid metabolism. This review provides a summary of known endogenous, naturally occurring, and synthetic ligands. The review also offers considerations from a molecular modeling perspective with which to design more specific LXRβ ligands based on the interaction energies of ligands and the important amino acid residues in the LXRβ ligand binding domain.

  1. New binary copper(II) complexes containing intercalating ligands: DNA interactions, an unusual static quenching mechanism of BSA and cytotoxic activities.

    Science.gov (United States)

    İnci, Duygu; Aydın, Rahmiye; Vatan, Özgür; Zorlu, Yunus; Çinkılıç, Nilüfer

    2017-11-24

    New binary copper(II) complexes - [Cu(4-mphen)2(NO3)]NO3·H2O (1), [Cu(5-mphen)2 (NO3)]NO3·H2O (2), the known complex [Cu(dmphen)2(NO3)]NO3 (3) and [Cu(tmphen)2 (NO3)]NO3·H2O (4) - (4-mphen: 4-methyl-1,10-phenanthroline, 5-mphen: 5-methyl-1,10-phenanthroline, dmphen: 4,7-dimethyl-1,10-phenanthroline, tmphen: 3,4,7,8-tetramethyl-1,10-phenanthroline), have been synthesized and characterized by CHN analysis, ESI-MS, FTIR and single-crystal X-ray diffraction techniques. Interaction of these complexes with calf thymus DNA (CT-DNA) has been investigated by absorption spectral titration, ethidium bromide (EB) and Hoechst 33,258 displacement assay and thermal denaturation measurement. These complexes cleaved pUC19 plasmid DNA in the absence and presence of an external agent. Notably, in the presence of H2O2 as an activator, the cleavage abilities of these complexes are obviously enhanced at low concentration. Addition of hydroxyl radical scavengers like DMSO shows significant inhibition of the DNA cleavage activity of these complexes. BSA quenching mechanism was investigated with regard to the type of quenching, binding constant, number of binding locations and the thermodynamic parameters. The experimental results suggested that the probable quenching mechanism was an unusual static process and hydrophobic forces play a dominant role. The CT-DNA and BSA binding efficiencies of these complexes follow the order: 4 > 3 > 1 > 2. Furthermore, in vitro cytotoxicities of these complexes on tumor cells lines (Caco-2, MCF-7 and A549) and healthy cell line (BEAS-2B) showed that these complexes exhibited anticancer activity with low IC50 values. The effect of hydrophobicity of the methyl-substituted phenanthrolines on DNA and protein binding activities of these complexes is discussed.

  2. Cubesat Proximity Operations Demonstration (CPOD)

    Science.gov (United States)

    Villa, Marco; Martinez, Andres; Petro, Andrew

    2015-01-01

    The CubeSat Proximity Operations Demonstration (CPOD) project will demonstrate rendezvous, proximity operations and docking (RPOD) using two 3-unit (3U) CubeSats. Each CubeSat is a satellite with the dimensions 4 inches x 4 inches x 13 inches (10 centimeters x 10 centimeters x 33 centimeters) and weighing approximately 11 pounds (5 kilograms). This flight demonstration will validate and characterize many new miniature low-power proximity operations technologies applicable to future missions. This mission will advance the state of the art in nanosatellite attitude determination,navigation and control systems, in addition to demonstrating relative navigation capabilities.The two CPOD satellites are scheduled to be launched together to low-Earth orbit no earlier than Dec. 1, 2015.

  3. A polymorphic CD40 ligand (CD154) molecule mediates CD40‐dependent signalling but interferes with the ability of soluble CD40 to functionally block CD154 : CD40 interactions

    Science.gov (United States)

    Barnhart, B; Ford, G S; Bhushan, A; Song, C; Covey, L R

    2000-01-01

    We report the characterization of a naturally occurring polymorphism in CD40 ligand (CD40L, CD154) expressed by activated T cells from a young female patient. This polymorphism encodes a nonconservative Gly → Arg substitution in amino acid 219 in the extracellular, CD40 binding domain of the molecule. Studies carried out with 293 epithelial cells ectopically expressing the polymorphic protein (CD154/G219R) revealed reduced levels of binding to different anti‐CD154 monoclonal antibodies (mAb) and CD40‐immunoglobulin (CD40‐Ig). However, recognition of the polymorphic and wild‐type CD154 molecules by a polyclonal antiserum was comparable, suggesting that the polymorphism affects the ability of the protein to interact with CD40 but does not significantly alter its surface expression. To determine if reduced cross‐linking of CD40 mediated decreased functional effects, three CD40‐dependent properties were measured. We found that pathways leading to the induction of surface CD23, CD80, and Iγ transcription were activated in response to CD154/G219R signalling. However, the decrease in affinity for CD40 by the mutated CD154 affected the ability of CD40‐Ig to efficiently interfere with the binding and effectively block induced CD80 expression. In contrast, we found that the 5c8 mAb, which recognized the polymorphic molecule to a similar extent as wild‐type CD154, effectively blocked the interaction between CD154/G219R and CD40 as measured by CD80 expression. These findings suggest that naturally occurring polymorphisms in the CD154 molecule may affect the ability of CD40‐mediated functions to be blocked by soluble CD40 or anti‐CD154 mAb in the therapeutic treatment of disease and graft rejection. PMID:10651941

  4. A web server for analysis, comparison and prediction of protein ligand binding sites.

    Science.gov (United States)

    Singh, Harinder; Srivastava, Hemant Kumar; Raghava, Gajendra P S

    2016-03-25

    One of the major challenges in the field of system biology is to understand the interaction between a wide range of proteins and ligands. In the past, methods have been developed for predicting binding sites in a protein for a limited number of ligands. In order to address this problem, we developed a web server named 'LPIcom' to facilitate users in understanding protein-ligand interaction. Analysis, comparison and prediction modules are available in the "LPIcom' server to predict protein-ligand interacting residues for 824 ligands. Each ligand must have at least 30 protein binding sites in PDB. Analysis module of the server can identify residues preferred in interaction and binding motif for a given ligand; for example residues glycine, lysine and arginine are preferred in ATP binding sites. Comparison module of the server allows comparing protein-binding sites of multiple ligands to understand the similarity between ligands based on their binding site. This module indicates that ATP, ADP and GTP ligands are in the same cluster and thus their binding sites or interacting residues exhibit a high level of similarity. Propensity-based prediction module has been developed for predicting ligand-interacting residues in a protein for more than 800 ligands. In addition, a number of web-based tools have been integrated to facilitate users in creating web logo and two-sample between ligand interacting and non-interacting residues. In summary, this manuscript presents a web-server for analysis of ligand interacting residue. This server is available for public use from URL http://crdd.osdd.net/raghava/lpicom .

  5. CD40 Induces Apoptosis in Carcinoma Cells through Activation of Cytotoxic Ligands of the Tumor Necrosis Factor Superfamily

    Science.gov (United States)

    Eliopoulos, Aristides G.; Davies, Clare; Knox, Pauline G.; Gallagher, Neil J.; Afford, Simon C.; Adams, David H.; Young, Lawrence S.

    2000-01-01

    CD40, a tumor necrosis factor (TNF) receptor (TNFR) family member, conveys signals regulating diverse cellular responses, ranging from proliferation and differentiation to growth suppression and cell death. The ability of CD40 to mediate apoptosis in carcinoma cells is intriguing given the fact that the CD40 cytoplasmic C terminus lacks a death domain homology with the cytotoxic members of the TNFR superfamily, such as Fas, TNFR1, and TNF-related apoptosis-inducing ligand (TRAIL) receptors. In this study, we have probed the mechanism by which CD40 transduces death signals. Using a trimeric recombinant soluble CD40 ligand to activate CD40, we have found that this phenomenon critically depends on the membrane proximal domain (amino acids 216 to 239) but not the TNFR-associated factor-interacting PXQXT motif in the CD40 cytoplasmic tail. CD40-mediated cytotoxicity is blocked by caspase inhibitors, such as zVAD-fmk and crmA, and involves activation of caspase 8 and caspase 3. Interestingly, CD40 ligation was found to induce functional Fas ligand, TRAIL (Apo-2L) and TNF in apoptosis-susceptible carcinoma cells and to up-regulate expression of Fas. These findings identify a novel proapoptotic mechanism which is induced by CD40 in carcinoma cells and depends on the endogenous production of cytotoxic cytokines and autocrine or paracrine induction of cell death. PMID:10891490

  6. SHORT COMMUNICATION PROXIMATE COMPOSITION, MINERAL ...

    African Journals Online (AJOL)

    Preferred Customer

    SHORT COMMUNICATION. PROXIMATE COMPOSITION, MINERAL CONTENT AND ANTINUTRITIONAL. FACTORS OF SOME CAPSICUM (Capsicum annum) VARIETIES GROWN IN. ETHIOPIA. Esayas K.1, Shimelis A.2, Ashebir F.3, Negussie R.3, Tilahun B.4 and Gulelat D.4*. 1Hawassa University, Department of Food ...

  7. 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

  8. Computational approaches to modeling receptor flexibility upon ligand binding: Application to interfacially activated enzymes

    DEFF Research Database (Denmark)

    Wade, R.C.; Sobolev, V.; Ortiz, A.R. .

    1998-01-01

    Receptors generally undergo conformational change upon ligand binding. We describe how fairly simple techniques may be used in docking and design studies to account for some of the changes in the conformations of proteins on ligand binding. Simulations of protein-ligand interactions that give a m...

  9. A Protein Data Bank survey reveals shortening of intermolecular hydrogen bonds in ligand-protein complexes when a halogenated ligand is an H-bond donor.

    Directory of Open Access Journals (Sweden)

    Jarosław Poznański

    Full Text Available Halogen bonding in ligand-protein complexes is currently widely exploited, e.g. in drug design or supramolecular chemistry. But little attention has been directed to other effects that may result from replacement of a hydrogen by a strongly electronegative halogen. Analysis of almost 30000 hydrogen bonds between protein and ligand demonstrates that the length of a hydrogen bond depends on the type of donor-acceptor pair. Interestingly, lengths of hydrogen bonds between a protein and a halogenated ligand are visibly shorter than those estimated for the same family of proteins in complexes with non-halogenated ligands. Taking into account the effect of halogenation on hydrogen bonding is thus important when evaluating structural and/or energetic parameters of ligand-protein complexes. All these observations are consistent with the concept that halogenation increases the acidity of the proximal amino/imino/hydroxyl groups and thus makes them better, i.e. stronger, H-bond donors.

  10. A Protein Data Bank Survey Reveals Shortening of Intermolecular Hydrogen Bonds in Ligand-Protein Complexes When a Halogenated Ligand Is an H-Bond Donor

    Science.gov (United States)

    Poznański, Jarosław; Poznańska, Anna; Shugar, David

    2014-01-01

    Halogen bonding in ligand-protein complexes is currently widely exploited, e.g. in drug design or supramolecular chemistry. But little attention has been directed to other effects that may result from replacement of a hydrogen by a strongly electronegative halogen. Analysis of almost 30000 hydrogen bonds between protein and ligand demonstrates that the length of a hydrogen bond depends on the type of donor-acceptor pair. Interestingly, lengths of hydrogen bonds between a protein and a halogenated ligand are visibly shorter than those estimated for the same family of proteins in complexes with non-halogenated ligands. Taking into account the effect of halogenation on hydrogen bonding is thus important when evaluating structural and/or energetic parameters of ligand-protein complexes. All these observations are consistent with the concept that halogenation increases the acidity of the proximal amino/imino/hydroxyl groups and thus makes them better, i.e. stronger, H-bond donors. PMID:24933273

  11. 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

  12. Reflections on the Ecolab and the Zone of Proximal Development

    Science.gov (United States)

    Luckin, Rosemary; du Boulay, Benedict

    2016-01-01

    In 1999 we reported a study that explored the way that Vygotsky's Zone of Proximal Development could be used to inform the design of an Interactive Learning Environment called the Ecolab. Two aspects of this work have subsequently been used for further research. Firstly, there is the interpretation of the ZPD and its associated theory that was…

  13. Metal-ligand cooperation at tethered pi-ligands

    NARCIS (Netherlands)

    Verhoeven, Dide G. A.; Moret, Marc-Etienne

    2016-01-01

    Metal–ligand cooperativity in homogeneous catalysis is emerging as a powerful tool for the design of efficient transition-metal catalysts. This perspective highlights recent advances in the use of neutral π-coordinating ligands, tethered to a transition-metal center by other donor ligands, as

  14. Ligand diffusion in proteins via enhanced sampling in molecular dynamics.

    Science.gov (United States)

    Rydzewski, J; Nowak, W

    2017-12-01

    Computational simulations in biophysics describe the dynamics and functions of biological macromolecules at the atomic level. Among motions particularly important for life are the transport processes in heterogeneous media. The process of ligand diffusion inside proteins is an example of a complex rare event that can be modeled using molecular dynamics simulations. The study of physical interactions between a ligand and its biological target is of paramount importance for the design of novel drugs and enzymes. Unfortunately, the process of ligand diffusion is difficult to study experimentally. The need for identifying the ligand egress pathways and understanding how ligands migrate through protein tunnels has spurred the development of several methodological approaches to this problem. The complex topology of protein channels and the transient nature of the ligand passage pose difficulties in the modeling of the ligand entry/escape pathways by canonical molecular dynamics simulations. In this review, we report a methodology involving a reconstruction of the ligand diffusion reaction coordinates and the free-energy profiles along these reaction coordinates using enhanced sampling of conformational space. We illustrate the above methods on several ligand-protein systems, including cytochromes and G-protein-coupled receptors. The methods are general and may be adopted to other transport processes in living matter. Copyright © 2017 Elsevier B.V. All rights reserved.

  15. Characterization of protein/ligand interactions by {sup 1}H/{sup 3}H exchange: application to the hAsf{sup 1}/ histone H{sup 3} complex; Caracterisation des interactions proteine / ligand par echange {sup 1}H/{sup 3}H: application au complexe entre la proteine hAsf{sup 1} et l'histone H{sup 3}

    Energy Technology Data Exchange (ETDEWEB)

    Mousseau, G

    2007-05-15

    In the first chapter will be exposed the main current methods of identification to high debit of the interactions protein-protein. Then the methods allowing to characterize the surfaces of interaction or to determine the structures of the complexes will be listed by discussing the main advantages and the inconveniences. Our approach of characterization of the zones of interaction protein-protein is a method of 'foot-printing' 1, based on the identification and radicals' quantification formed on the residues of proteins accessible to the water. The second chapter will so discuss the development of this method of radical identification using the atom of tritium as radioactive label. Our approach will finally be validated in the third chapter by applying it to the characterization of amino acids involved in the interaction enter the human protein anti silencing factor 1 (hAsf11-156) and a fragment of the histone H{sup 3}. (N.C.)

  16. Scattering Effects in Proximity Effect Tunneling Spectroscopy.

    Science.gov (United States)

    Gai, Wei

    PETS (Proximity Effect Tunneling Spectroscopy) technique has been applied to Niobium/Yttrium and Niobium/Lutetium bilayers. We have determined electron - phonon interaction parameter lambda_{rm e -ph} is 0.55 for Yttrium and 0.67 for Lutetium. Spin fluctuations parameter lambda_{ rm S} is 0.20 for Yttrium and 0.33 for Lutetium. We found that the large spin fluctuations in Yttrium and Lutetium has responsibility to the absence of superconductivity in them. Our results have given a reasonable explanation of high superconducting transition temperature in them under high pressure. The large reflection coefficient and strong diffuse scattering at Nb/Y and Nb/Lu interface has been discovered and it should have strong influence on the transport properties of metallic superlattices. From the modeling study of elastic scattering in proximity effect tunnel junctions, we have explained why some conventional made high {rm T_{C}} superconducting tunnel junctions give ideal like characteristics in the gap region but variable strength phonon structures in the phonon region.

  17. Empathy: Its ultimate and proximate bases.

    Science.gov (United States)

    Preston, Stephanie D; de Waal, Frans B M

    2002-02-01

    There is disagreement in the literature about the exact nature of the phenomenon of empathy. There are emotional, cognitive, and conditioning views, applying in varying degrees across species. An adequate description of the ultimate and proximate mechanism can integrate these views. Proximately, the perception of an object's state activates the subject's corresponding representations, which in turn activate somatic and autonomic responses. This mechanism supports basic behaviors (e.g., alarm, social facilitation, vicariousness of emotions, mother-infant responsiveness, and the modeling of competitors and predators) that are crucial for the reproductive success of animals living in groups. The Perception-Action Model (PAM), together with an understanding of how representations change with experience, can explain the major empirical effects in the literature (similarity, familiarity, past experience, explicit teaching, and salience). It can also predict a variety of empathy disorders. The interaction between the PAM and prefrontal functioning can also explain different levels of empathy across species and age groups. This view can advance our evolutionary understanding of empathy beyond inclusive fitness and reciprocal altruism and can explain different levels of empathy across individuals, species, stages of development, and situations.

  18. Prox-1 Automated Proximity Operations

    Science.gov (United States)

    2016-01-13

    on demonstrating the functionality required to meet minimum mission success criteria. The minimum mission includes on- orbit spacecraft checkout of...also includes deployment of LightSail-B from the P-POD, and imaging of LightSail-B for 20 minutes as it recedes from Prox-1. small satellite ; proximity...criteria. The minimum mission includes on- orbit spacecraft checkout of all spacecraft subsystems, including flight qualification of the following new

  19. 2D MI-DRAGON: a new predictor for protein-ligands interactions and theoretic-experimental studies of US FDA drug-target network, oxoisoaporphine inhibitors for MAO-A and human parasite proteins.

    Science.gov (United States)

    Prado-Prado, Francisco; García-Mera, Xerardo; Escobar, Manuel; Sobarzo-Sánchez, Eduardo; Yañez, Matilde; Riera-Fernandez, Pablo; González-Díaz, Humberto

    2011-12-01

    There are many pairs of possible Drug-Proteins Interactions that may take place or not (DPIs/nDPIs) between drugs with high affinity/non-affinity for different proteins. This fact makes expensive in terms of time and resources, for instance, the determination of all possible ligands-protein interactions for a single drug. In this sense, we can use Quantitative Structure-Activity Relationships (QSAR) models to carry out rational DPIs prediction. Unfortunately, almost all QSAR models predict activity against only one target. To solve this problem we can develop multi-target QSAR (mt-QSAR) models. In this work, we introduce the technique 2D MI-DRAGON a new predictor for DPIs based on two different well-known software. We use the software MARCH-INSIDE (MI) to calculate 3D structural parameters for targets and the software DRAGON was used to calculated 2D molecular descriptors all drugs showing known DPIs present in the Drug Bank (US FDA benchmark dataset). Both classes of parameters were used as input of different Artificial Neural Network (ANN) algorithms to seek an accurate non-linear mt-QSAR predictor. The best ANN model found is a Multi-Layer Perceptron (MLP) with profile MLP 21:21-31-1:1. This MLP classifies correctly 303 out of 339 DPIs (Sensitivity = 89.38%) and 480 out of 510 nDPIs (Specificity = 94.12%), corresponding to training Accuracy = 92.23%. The validation of the model was carried out by means of external predicting series with Sensitivity = 92.18% (625/678 DPIs; Specificity = 90.12% (730/780 nDPIs) and Accuracy = 91.06%. 2D MI-DRAGON offers a good opportunity for fast-track calculation of all possible DPIs of one drug enabling us to re-construct large drug-target or DPIs Complex Networks (CNs). For instance, we reconstructed the CN of the US FDA benchmark dataset with 855 nodes 519 drugs+336 targets). We predicted CN with similar topology (observed and predicted values of average distance are equal to 6.7 vs. 6.6). These CNs can be used to explore

  20. HDX reveals unique fragment ligands for the vitamin D receptor.

    Science.gov (United States)

    Carson, Matthew W; Zhang, Jun; Chalmers, Michael J; Bocchinfuso, Wayne P; Holifield, Karol D; Masquelin, Thierry; Stites, Ryan E; Stayrook, Keith R; Griffin, Patrick R; Dodge, Jeffery A

    2014-08-01

    Modulation of the vitamin D receptor (VDR) with a ligand has the potential to be useful for the oral treatment of osteoporosis. One component of our lead generation strategy to identify synthetic ligands for VDR included a fragment based drug design approach. Screening of ligands in a VDR fluorescence polarization assay and a RXR/VDR conformation sensing assay resulted in the identification of multiple fragment hits (lean >0.30). These fragment scaffolds were subsequently evaluated for interaction with the VDR ligand binding domain using hydrogen-deuterium exchange (HDX) mass spectrometry. Significant protection of H/D exchange was observed for some fragments in helixes 3, 7, and 8 of the ligand binding domain, regions which are similar to those seen for the natural hormone VD3. The fragments appear to mimic the A-ring of VD3 thereby providing viable starting points for synthetic expansion. Copyright © 2014 Elsevier Ltd. All rights reserved.

  1. PROXIMATE AND ELEMENTAL COMPOSITION OF WHITE GRUBS

    African Journals Online (AJOL)

    DR. AMINU

    PROXIMATE AND ELEMENTAL COMPOSITION OF WHITE GRUBS. 1 Alhassan, A. J. 1M .S. Sule, 1J. ... ABSTRACT. This study determined the proximate and mineral element composition of whole white grubs using standard methods of analysis. Proximate ... days, before pulverized to powder and kept in plastic container.

  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. Proteome-wide covalent ligand discovery in native biological systems.

    Science.gov (United States)

    Backus, Keriann M; Correia, Bruno E; Lum, Kenneth M; Forli, Stefano; Horning, Benjamin D; González-Páez, Gonzalo E; Chatterjee, Sandip; Lanning, Bryan R; Teijaro, John R; Olson, Arthur J; Wolan, Dennis W; Cravatt, Benjamin F

    2016-06-23

    Small molecules are powerful tools for investigating protein function and can serve as leads for new therapeutics. Most human proteins, however, lack small-molecule ligands, and entire protein classes are considered 'undruggable'. Fragment-based ligand discovery can identify small-molecule probes for proteins that have proven difficult to target using high-throughput screening of complex compound libraries. Although reversibly binding ligands are commonly pursued, covalent fragments provide an alternative route to small-molecule probes, including those that can access regions of proteins that are difficult to target through binding affinity alone. Here we report a quantitative analysis of cysteine-reactive small-molecule fragments screened against thousands of proteins in human proteomes and cells. Covalent ligands were identified for >700 cysteines found in both druggable proteins and proteins deficient in chemical probes, including transcription factors, adaptor/scaffolding proteins, and uncharacterized proteins. Among the atypical ligand-protein interactions discovered were compounds that react preferentially with pro- (inactive) caspases. We used these ligands to distinguish extrinsic apoptosis pathways in human cell lines versus primary human T cells, showing that the former is largely mediated by caspase-8 while the latter depends on both caspase-8 and -10. Fragment-based covalent ligand discovery provides a greatly expanded portrait of the ligandable proteome and furnishes compounds that can illuminate protein functions in native biological systems.

  4. Finger Proximal Interphalangeal Joint Dislocation.

    Science.gov (United States)

    Ramponi, Denise; Cerepani, Mary Jo

    2015-01-01

    Finger dislocations are common injuries that are often managed by emergency nurse practitioners. A systematic physical examination following these injuries is imperative to avoid complications. Radiographic views, including the anteroposterior, lateral, and oblique views, are imperative to evaluate these finger dislocations. A dorsal dislocation of the proximal interphalangeal (PIP) joint is the most common finger dislocation type often easily reduced. A volar PIP dislocation can often be difficult to reduce and may result in finger deformity. Finger dislocations should be reduced promptly. Referral to an orthopedic hand specialist is required if the dislocation is unable to be reduced or if the finger joint is unstable following reduction attempts.

  5. Equilibrium properties of proximity effect

    Energy Technology Data Exchange (ETDEWEB)

    Esteve, D.; Pothier, H.; Gueron, S.; Birge, N.O.; Devoret, M.

    1996-12-31

    The proximity effect in diffusive normal-superconducting (NS) nano-structures is described by the Usadel equations for the electron pair correlations. We show that these equations obey a variational principle with a potential which generalizes the Ginzburg-Landau energy functional. We discuss simple examples of NS circuits using this formalism. In order to test the theoretical predictions of the Usadel equations, we have measured the density of states as a function of energy on a long N wire in contact with a S wire at one end, at different distances from the NS interface. (authors). 12 refs.

  6. Norovirus Binding to Ligands Beyond Histo-Blood Group Antigens

    Science.gov (United States)

    Almand, Erin A.; Moore, Matthew D.; Jaykus, Lee-Ann

    2017-01-01

    Histo-blood group antigens (HBGAs) are commonly accepted as the cellular receptors for human norovirus. However, some human noroviruses have been found not to bind any HBGA ligand, suggesting potential additional co-factors. Some ligands have been found to bind noroviruses and have the potential to be additional cellular receptors/attachment factors for human norovirus or inhibitors of the HBGA interaction. The studies identifying these mostly characterize different chemical, human, food, or bacterial components and their effect on norovirus binding and infection, although the mechanism of interaction is unknown in many cases. This review seeks to supplement the already well-covered HBGA-norovirus literature by covering non-HBGA human norovirus ligands and inhibitors to provide investigators with a more comprehensive view of norovirus ligands. PMID:29312233

  7. Fluorescent GPCR ligands as new tools in pharmacology-update, years 2008-early 2014.

    Science.gov (United States)

    Kuder, Kamil J; Kieć-Kononowicz, Katarzyna

    2014-01-01

    The robust of fluorescent techniques to study the ligand-receptor interaction followed by rapidly developing fluorescence imaging techniques resulted in a burst of the novel fluorescent ligands development. Taking into consideration not only ligand's high affinity to the receptor, but also their fluorescent properties to visualize the interaction even in the single cell level, gives the researchers a strong impulse to investigate that field of GPCR ligands. Moreover, paying attention to the "non pharmacological" advantages of these ligands, as well as the techniques to be used, fluorescent ligands become commonly used pharmacological tools to study GPCRs. Herein we report on the results described in the literature since late 2007 in the field of the fluorescent GPCR small, non-peptide ligands according the receptor affinity, fluorophores that has been used to tag the molecules and their fluorescent properties as well as their application in GPCR research.

  8. 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.

  9. INTERACT

    DEFF Research Database (Denmark)

    Jochum, Elizabeth; Borggreen, Gunhild; Murphey, TD

    interaction between a human operator and an artificial actor or agent. We can apply insights from puppetry to develop culturally-aware robots. Here we describe the development of a robotic marionette theatre wherein robotic controllers assume the role of human puppeteers. The system has been built, tested...... including puppetry and dance. However, the aesthetics of these traditions vary across cultures and carry different associative and interpretive meanings. Puppetry offers a useful frame for understanding the relationship between abstract and imitative gestures and behavior, and instantiates the complex...

  10. Identification of VDR Antagonists among Nuclear Receptor Ligands Using Virtual Screening

    Directory of Open Access Journals (Sweden)

    Kelly Teske

    2014-04-01

    Full Text Available Herein, we described the development of two virtual screens to identify new vitamin D receptor (VDR antagonists among nuclear receptor (NR ligands. Therefore, a database of 14330 nuclear receptor ligands and their NR affinities was assembled using the online available “Binding Database.” Two different virtual screens were carried out in conjunction with a reported VDR crystal structure applying a stringent and less stringent pharmacophore model to filter docked NR ligand conformations. The pharmacophore models were based on the spatial orientation of the hydroxyl functionalities of VDR's natural ligands 1,25(OH2D3 and 25(OH2D3. The first virtual screen identified 32 NR ligands with a calculated free energy of VDR binding of more than -6.0 kJ/mol. All but nordihydroguaiaretic acid (NDGA are VDR ligands, which inhibited the interaction between VDR and coactivator peptide SRC2-3 with an IC50 value of 15.8 μM. The second screen identified 162 NR ligands with a calculated free energy of VDR binding of more than -6.0 kJ/mol. More than half of these ligands were developed to bind VDR followed by ERα/β ligands (26%, TRα/β ligands (7%, and LxRα/β ligands (7%. The binding between VDR and ERα ligand H6036 as well as TRα/β ligand triiodothyronine and a homoserine analog thereof was confirmed by fluorescence polarization.

  11. Mechanisms of neutrophil transmigration across renal proximal tubular HK-2 cells

    NARCIS (Netherlands)

    Bijuklic, Klaudija; Sturn, Daniel H; Jennings, Paul; Kountchev, Jordan; Pfaller, Walter; Wiedermann, Christian J; Patsch, Josef R; Joannidis, Michael

    2006-01-01

    BACKGROUND: Adhesion of intratubular leukocytes to proximal tubules in biopsies of patients with rapidly progressive glomerulonephritis and the appearance of leukocytes in the urine in interstitial nephritis suggest interactions between leukocytes and tubular epithelia in renal diseases. The aim of

  12. Proximity ligation in situ assay for monitoring the global DNA methylation in cells

    National Research Council Canada - National Science Library

    Hervouet, Eric; Hulin, Philippe; Vallette, François M; Cartron, Pierre-François

    2011-01-01

    .... We here present the development of the detection of protein-protein interactions via the adaptation of the proximity ligation in situ technology to evaluate the DNA methylation status in cells since...

  13. 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.......g., IC(50) = 300 microM for (2R,4S)-4-methyl-AA (5d)]. The two unsaturated analogs (S)- (7a) and (R)-(E)-Delta(4)-5-methyl-AA (7b) turned out to be a weak AMPA receptor agonist and a weak mixed NMDA/AMPA receptor antagonist, respectively....

  14. AMPA receptor ligands

    DEFF Research Database (Denmark)

    Strømgaard, Kristian; Mellor, Ian

    2004-01-01

    Alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid (AMPA) receptors (AMPAR), subtype of the ionotropic glutamate receptors (IGRs), mediate fast synaptic transmission in the central nervous system (CNS), and are involved in many neurological disorders, as well as being a key player...... polyamines are known to modulate the function of these receptors in vivo. In this study, recent developments in the medicinal chemistry of polyamine-based ligands are given, particularly focusing on the use of solid-phase synthesis (SPS) as a tool for the facile generation of libraries of polyamine toxin...

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

    DEFF Research Database (Denmark)

    Venskutonyte, Raminta; Frydenvang, Karla; Gajhede, Michael

    2011-01-01

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

  16. Anion–π, lone pair–π and π–π interactions in VO(O2)+ complexes with one dipicolinato(2-)-N,O,O ligand and bearing picolinamidium, nicotinamidium or phenanthrolinium as counterions

    Czech Academy of Sciences Publication Activity Database

    Gyepes, Robert; Pacigová, S.; Tatiersky, J.; Sivák, M.

    2013-01-01

    Roč. 1041, JUN 2013 (2013), s. 113-121 ISSN 0022-2860 R&D Projects: GA AV ČR KAN100400701 Institutional support: RVO:61388955 Keywords : Monoperoxidovanadium (V) * Dipicolinato(2-) ligand * Anion–π Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 1.599, year: 2013

  17. Touching the upper limit for ferromagnetic interactions in hetero-bridged dinuclear [Cu2(II)] complexes using a novel N5-dinucleating ligand bearing an endogenous monoatomic amido(R-NH(-))-bridging group.

    Science.gov (United States)

    Colacio, Enrique; Perea-Buceta, Jesús E; Mota, Antonio J; Brechin, Euan K; Prescimone, Alessandro; Hänninen, Mikko; Seppälä, Petri; Sillanpää, Reijo

    2012-01-21

    A novel N(5)-dinucleating ligand 4-amino-3,5-bis(bipyridine-2-yl)-1,2,4-triazole allows the preparation for the first time, and under mild conditions, of single and mixed amido(R-NH(-))-bridged copper(II) complexes, the latter exhibiting very strong ferromagnetic coupling. This journal is © The Royal Society of Chemistry 2012

  18. Complications in proximal humeral fractures.

    Science.gov (United States)

    Calori, Giorgio Maria; Colombo, Massimiliano; Bucci, Miguel Simon; Fadigati, Piero; Colombo, Alessandra Ines Maria; Mazzola, Simone; Cefalo, Vittorio; Mazza, Emilio

    2016-10-01

    Necrosis of the humeral head, infections and non-unions are among the most dangerous and difficult-to-treat complications of proximal humeral fractures. The aim of this work was to analyse in detail non-unions and post-traumatic bone defects and to suggest an algorithm of care. Treatment options are based not only on the radiological frame, but also according to a detailed analysis of the patient, who is classified using a risk factor analysis. This method enables the surgeon to choose the most suitable treatment for the patient, thereby facilitating return of function in the shortest possible time. The treatment of such serious complications requires the surgeon to be knowledgeable about the following possible solutions: increased mechanical stability; biological stimulation; and reconstructive techniques in two steps, with application of biotechnologies and prosthetic substitution. Copyright © 2016 Elsevier Ltd. All rights reserved.

  19. Metal-ligand cooperation at tethered π-ligands.

    Science.gov (United States)

    Verhoeven, Dide G A; Moret, Marc-Etienne

    2016-10-12

    Metal-ligand cooperativity in homogeneous catalysis is emerging as a powerful tool for the design of efficient transition-metal catalysts. This perspective highlights recent advances in the use of neutral π-coordinating ligands, tethered to a transition-metal center by other donor ligands, as cooperative reaction centers. The state-of-the-art organometallic complexes, including π-coordinating ligands originating from C[double bond, length as m-dash]C, C[double bond, length as m-dash]E (E = O, N) and boron containing moieties, are described here, with special attention on their specific reactivity. Geometric and electronic aspects of ligand design and their influence on the coordination mode and reactivity of the π-system are discussed.

  20. Proximity sensor technology for manipulator end effectors

    Science.gov (United States)

    Johnston, A. R.

    1975-01-01

    Optical proximity sensing techniques which could be used to help control the critical grasping phase of a remote manipulation are described. The proximity sensors described use a triangulation geometry to detect a surface located in a pre-determined region. The design of the proximity sensors themselves is discussed, as well as their application to manipulator control with a local control loop, and possibilities for future development are discussed.

  1. Balancing specificity, sensitivity, and speed of ligand discrimination by zero-order ultraspecificity

    Science.gov (United States)

    Kajita, Masashi K.; Aihara, Kazuyuki; Kobayashi, Tetsuya J.

    2017-07-01

    Specific interactions between receptors and their target ligands in the presence of nontarget ligands are crucial for biological processes such as T cell ligand discrimination. To discriminate between the target and nontarget ligands, cells have to increase specificity to the target ligands by amplifying the small differences in affinity among ligands. In addition, sensitivity to the ligand concentration and quick discrimination are also important to detect low amounts of target ligands and facilitate fast cellular decision making after ligand recognition. In this work we propose a mechanism for nonlinear specificity amplification (ultraspecificity) based on zero-order saturating reactions, which was originally proposed to explain nonlinear sensitivity amplification (ultrasensitivity) to the ligand concentration. In contrast to the previously proposed proofreading mechanisms that amplify the specificity by a multistep reaction, our model can produce an optimal balance of specificity, sensitivity, and quick discrimination. Furthermore, we show that a model for insensitivity to a large number of nontarget ligands can be naturally derived from a model with the zero-order ultraspecificity. The zero-order ultraspecificity, therefore, may provide an alternative way to understand ligand discrimination from the viewpoint of nonlinear properties in biochemical reactions.

  2. Proximate composition and antinutrient content of pumpkin ...

    African Journals Online (AJOL)

    Proximate composition and antinutrient content of pumpkin ( Cucurbita pepo ) and sorghum ( Sorghum bicolor ) flour blends fermented with Lactobacillus plantarum , Aspergillus niger and Bacillus subtilis.

  3. Macrocyclic G-quadruplex ligands

    DEFF Research Database (Denmark)

    Nielsen, M C; Ulven, Trond

    2010-01-01

    are macrocyclic structures which have been modeled after the natural product telomestatin or from porphyrin-based ligands discovered in the late 1990s. These two structural classes of G-quadruplex ligands are reviewed here with special attention to selectivity and structure-activity relationships, and with focus...

  4. Ligand- and receptor-based docking with LiBELa

    Science.gov (United States)

    dos Santos Muniz, Heloisa; Nascimento, Alessandro S.

    2015-08-01

    Methodologies on molecular docking are constantly improving. The problem consists on finding an optimal interplay between the computational cost and a satisfactory physical description of ligand-receptor interaction. In pursuit of an advance in current methods we developed a mixed docking approach combining ligand- and receptor-based strategies in a docking engine, where tridimensional descriptors for shape and charge distribution of a reference ligand guide the initial placement of the docking molecule and an interaction energy-based global minimization follows. This hybrid docking was evaluated with soft-core and force field potentials taking into account ligand pose and scoring. Our approach was found to be competitive to a purely receptor-based dock resulting in improved logAUC values when evaluated with DUD and DUD-E. Furthermore, the smoothed potential as evaluated here, was not advantageous when ligand binding poses were compared to experimentally determined conformations. In conclusion we show that a combination of ligand- and receptor-based strategy docking with a force field energy model results in good reproduction of binding poses and enrichment of active molecules against decoys. This strategy is implemented in our tool, LiBELa, available to the scientific community.

  5. Ligand- and receptor-based docking with LiBELa.

    Science.gov (United States)

    dos Santos Muniz, Heloisa; Nascimento, Alessandro S

    2015-08-01

    Methodologies on molecular docking are constantly improving. The problem consists on finding an optimal interplay between the computational cost and a satisfactory physical description of ligand-receptor interaction. In pursuit of an advance in current methods we developed a mixed docking approach combining ligand- and receptor-based strategies in a docking engine, where tridimensional descriptors for shape and charge distribution of a reference ligand guide the initial placement of the docking molecule and an interaction energy-based global minimization follows. This hybrid docking was evaluated with soft-core and force field potentials taking into account ligand pose and scoring. Our approach was found to be competitive to a purely receptor-based dock resulting in improved logAUC values when evaluated with DUD and DUD-E. Furthermore, the smoothed potential as evaluated here, was not advantageous when ligand binding poses were compared to experimentally determined conformations. In conclusion we show that a combination of ligand- and receptor-based strategy docking with a force field energy model results in good reproduction of binding poses and enrichment of active molecules against decoys. This strategy is implemented in our tool, LiBELa, available to the scientific community.

  6. Ligand and structure-based methodologies for the prediction of the activity of G protein-coupled receptor ligands

    Science.gov (United States)

    Costanzi, Stefano; Tikhonova, Irina G.; Harden, T. Kendall; Jacobson, Kenneth A.

    2009-11-01

    Accurate in silico models for the quantitative prediction of the activity of G protein-coupled receptor (GPCR) ligands would greatly facilitate the process of drug discovery and development. Several methodologies have been developed based on the properties of the ligands, the direct study of the receptor-ligand interactions, or a combination of both approaches. Ligand-based three-dimensional quantitative structure-activity relationships (3D-QSAR) techniques, not requiring knowledge of the receptor structure, have been historically the first to be applied to the prediction of the activity of GPCR ligands. They are generally endowed with robustness and good ranking ability; however they are highly dependent on training sets. Structure-based techniques generally do not provide the level of accuracy necessary to yield meaningful rankings when applied to GPCR homology models. However, they are essentially independent from training sets and have a sufficient level of accuracy to allow an effective discrimination between binders and nonbinders, thus qualifying as viable lead discovery tools. The combination of ligand and structure-based methodologies in the form of receptor-based 3D-QSAR and ligand and structure-based consensus models results in robust and accurate quantitative predictions. The contribution of the structure-based component to these combined approaches is expected to become more substantial and effective in the future, as more sophisticated scoring functions are developed and more detailed structural information on GPCRs is gathered.

  7. Ligand and structure-based methodologies for the prediction of the activity of G protein-coupled receptor ligands.

    Science.gov (United States)

    Costanzi, Stefano; Tikhonova, Irina G; Harden, T Kendall; Jacobson, Kenneth A

    2009-11-01

    Accurate in silico models for the quantitative prediction of the activity of G protein-coupled receptor (GPCR) ligands would greatly facilitate the process of drug discovery and development. Several methodologies have been developed based on the properties of the ligands, the direct study of the receptor-ligand interactions, or a combination of both approaches. Ligand-based three-dimensional quantitative structure-activity relationships (3D-QSAR) techniques, not requiring knowledge of the receptor structure, have been historically the first to be applied to the prediction of the activity of GPCR ligands. They are generally endowed with robustness and good ranking ability; however they are highly dependent on training sets. Structure-based techniques generally do not provide the level of accuracy necessary to yield meaningful rankings when applied to GPCR homology models. However, they are essentially independent from training sets and have a sufficient level of accuracy to allow an effective discrimination between binders and nonbinders, thus qualifying as viable lead discovery tools. The combination of ligand and structure-based methodologies in the form of receptor-based 3D-QSAR and ligand and structure-based consensus models results in robust and accurate quantitative predictions. The contribution of the structure-based component to these combined approaches is expected to become more substantial and effective in the future, as more sophisticated scoring functions are developed and more detailed structural information on GPCRs is gathered.

  8. Residual ligand entropy in the binding of p-substituted benzenesulfonamide ligands to bovine carbonic anhydrase II.

    Science.gov (United States)

    Stöckmann, Henning; Bronowska, Agnieszka; Syme, Neil R; Thompson, Gary S; Kalverda, Arnout P; Warriner, Stuart L; Homans, Steve W

    2008-09-17

    In studies on the thermodynamics of ligand-protein interactions, it is often assumed that the configurational and conformational entropy of the ligand is zero in the bound state (i.e., the ligand is rigidly fixed in the binding pocket). However, there is little direct experimental evidence for this assumption, and in the case of binding of p-substituted benzenesulfonamide inhibitors to bovine carbonic anhydrase II (BCA II), the observed thermodynamic binding signature derived from isothermal titration calorimetry experiments leads indirectly to the conclusion that a considerable degree of residual entropy remains in the bound ligand. Specifically, the entropy of binding increases with glycine chain length n, and strong evidence exists that this thermodynamic signature is not driven by solvent reorganization. By use of heteronuclear (15)N NMR relaxation measurements in a series (n = 1-6) of (15)N-glycine-enriched ligands, we find that the observed thermodynamic binding signature cannot be explained by residual ligand dynamics in the bound state, but rather results from the indirect influence of ligand chain length on protein dynamics.

  9. DNA-Based Nanostructures: Changes of Mechanical Properties of DNA upon Ligand Binding

    Science.gov (United States)

    Nechipurenko, Yury; Grokhovsky, Sergey; Gursky, Georgy; Nechipurenko, Dmitry; Polozov, Robert

    The formation of DNA-based nanostructures involves the binding of different kinds of ligands to DNA as well as the interaction of DNA molecules with each other. Complex formation between ligand and DNA can alter physicochemical properties of the DNA molecule. In the present work, the accessibility of DNA-ligand complexes to cleavage by DNase I are considered, and the exact algorithms for analysis of diagrams of DNase I footprinting for ligand-DNA complexes are obtained. Changes of mechanical properties of the DNA upon ligand binding are also demonstrated by the cleavage patterns generated upon ultrasound irradiation of cis-platin-DNA complexes. Propagation of the mechanical perturbations along DNA in the presence of bound ligands is considered in terms of a string model with a heterogeneity corresponding to the position of a bound ligand on DNA. This model can reproduce qualitatively the cleavage patterns obtained upon ultrasound irradiation of cis-platin-DNA complexes.

  10. Functional outcome following proximal humeral interlocking system plating for displaced proximal humeral fractures

    OpenAIRE

    Thyagarajan David; Haridas Samarth; Jones Denise; Dent Colin; Evans Richard; Williams Rhys

    2009-01-01

    Aim: To assess the functional outcome following internal fixation with the PHILOS (proximal humeral interlocking system) for displaced proximal humeral fractures. Patients and Methods: We reviewed 30 consecutive patients treated surgically with the proximal humeral locking plate for a displaced proximal humeral fracture. Functional outcome was determined using the American Shoulder and Elbow Society (ASES) score and Constant Murley score. Results: Average age of the patients was 58 years...

  11. Best Proximity Points for a New Class of Generalized Proximal Mappings

    Directory of Open Access Journals (Sweden)

    Tayyab Kamran

    2017-03-01

    Full Text Available The best proximity points are usually used to find the optimal approximate solution of the operator equation Tx = x, when T has no fixed point. In this paper, we prove some best proximity point theorems for nonself multivalued operators, following the foot steps of Basha and Shahzad [Best proximity point theorems for generalized proximal contractions, Fixed Point Theory Appl., 2012, 2012:42].

  12. Reaction chemistry and ligand exchange at cadmium selenide nanocrystal surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Owen, Jonathan; Park, Jungwon; Trudeau, Paul-Emile; Alivisatos, A. Paul

    2008-12-02

    Chemical modification of nanocrystal surfaces is fundamentally important to their assembly, their implementation in biology and medicine, and greatly impacts their electrical and optical properties. However, it remains a major challenge owing to a lack of analytical tools to directly determine nanoparticle surface structure. Early nuclear magnetic resonance (NMR) and X-ray photoelectron spectroscopy (XPS) studies of CdSe nanocrystals prepared in tri-n-octylphosphine oxide (1) and tri-n-octylphosphine (2), suggested these coordinating solvents are datively bound to the particle surface. However, assigning the broad NMR resonances of surface-bound ligands is complicated by significant concentrations of phosphorus-containing impurities in commercial sources of 1, and XPS provides only limited information about the nature of the phosphorus containing molecules in the sample. More recent reports have shown the surface ligands of CdSe nanocrystals prepared in technical grade 1, and in the presence of alkylphosphonic acids, include phosphonic and phosphinic acids. These studies do not, however, distinguish whether these ligands are bound datively, as neutral, L-type ligands, or by X-type interaction of an anionic phosphonate/phosphinate moiety with a surface Cd{sup 2+} ion. Answering this question would help clarify why ligand exchange with such particles does not proceed generally as expected based on a L-type ligand model. By using reagents with reactive silicon-chalcogen and silicon-chlorine bonds to cleave the ligands from the nanocrystal surface, we show that our CdSe and CdSe/ZnS core-shell nanocrystal surfaces are likely terminated by X-type binding of alkylphosphonate ligands to a layer of Cd{sup 2+}/Zn{sup 2+} ions, rather than by dative interactions. Further, we provide spectroscopic evidence that 1 and 2 are not coordinated to our purified nanocrystals.

  13. Vigostsky's formulations on ZDP - Zone of Proximal Development

    Directory of Open Access Journals (Sweden)

    José Moysés Alves

    2005-06-01

    Full Text Available The zone of proximal development (ZPD is, probably, the most known concept from Vygotsky's theory. And has been much discussed recently. Hoping to contribute for the understanding of this contemporary debate, we focus on recurrent themes in Vygotsky's writings. We read ten texts of his where he constructed the concept of ZPD. We have through the reading summarized his formulations about the following topics: criticism to the traditional diagnostic; explicit definitions of ZPD's concept; redefinition of imitation's concept; ZPD and pretend play; ZPD and the interaction between development and learning; ZPD and the interaction among daily and scientific concepts; practical value and theoretical value of ZPD's concept

  14. Preliminary phytochemical screening, proximate and elemental ...

    African Journals Online (AJOL)

    The seed powder of Moringa oleifera was analysed for its phytochemical, proximate and elemental composition using Folin-Denis spectrophotometric method, gravimetric method and energy dispersing X-ray fluorescence (EDXRF) transmission emission technique respectively. The seed powder had the following proximate ...

  15. Bimalleolar ankle fracture with proximal fibular fracture

    NARCIS (Netherlands)

    Colenbrander, R. J.; Struijs, P. A. A.; Ultee, J. M.

    2005-01-01

    A 56-year-old female patient suffered a bimalleolar ankle fracture with an additional proximal fibular fracture. This is an unusual fracture type, seldom reported in literature. It was operatively treated by open reduction and internal fixation of the lateral malleolar fracture. The proximal fibular

  16. Grouping by Proximity in Haptic Contour Detection

    Science.gov (United States)

    Overvliet, Krista E.; Krampe, Ralf Th.; Wagemans, Johan

    2013-01-01

    We investigated the applicability of the Gestalt principle of perceptual grouping by proximity in the haptic modality. To do so, we investigated the influence of element proximity on haptic contour detection. In the course of four sessions ten participants performed a haptic contour detection task in which they freely explored a haptic random dot display that contained a contour in 50% of the trials. A contour was defined by a higher density of elements (raised dots), relative to the background surface. Proximity of the contour elements as well as the average proximity of background elements was systematically varied. We hypothesized that if proximity of contour elements influences haptic contour detection, detection will be more likely when contour elements are in closer proximity. This should be irrespective of the ratio with the proximity of the background elements. Results showed indeed that the closer the contour elements were, the higher the detection rates. Moreover, this was the case independent of the contour/background ratio. We conclude that the Gestalt law of proximity applies to haptic contour detection. PMID:23762364

  17. Proximate analysis on four edible mushrooms ADEDAYO ...

    African Journals Online (AJOL)

    Michael Horsfall

    Vol. 15 (1) 9 - 11. Full-text Available Online at www.bioline.org.br/ja. Proximate analysis on four edible mushrooms. ADEDAYO, MAJEKODUNMI RACHEL. Nigerian Stored Product Research Institute, P.M.B.3032, Kano. ABSTRACT: Proximate study was conducted on four edible mushrooms commonly found in farmlands in.

  18. Proximate Sources of Collective Teacher Efficacy

    Science.gov (United States)

    Adams, Curt M.; Forsyth, Patrick B.

    2006-01-01

    Purpose: Recent scholarship has augmented Bandura's theory underlying efficacy formation by pointing to more proximate sources of efficacy information involved in forming collective teacher efficacy. These proximate sources of efficacy information theoretically shape a teacher's perception of the teaching context, operationalizing the difficulty…

  19. Phytochemical screening, proximate analysis and anticonvulsant ...

    African Journals Online (AJOL)

    Spigelia anthelmia is used traditionally in Southern Nigeria for the treatment of infant convulsion and epilepsy. This study investigated the phytochemical constituents, proximate analysis and anticonvulsant effect of the methanolic extract of Spigelia anthelmia. Phytochemical evaluation and proximate analysis was carried ...

  20. Semiconductor detectors with proximity signal readout

    Energy Technology Data Exchange (ETDEWEB)

    Asztalos, Stephen J. [XIA, LLC, Hayward, CA (United States)

    2014-01-30

    Semiconductor-based radiation detectors are routinely used for the detection, imaging, and spectroscopy of x-rays, gamma rays, and charged particles for applications in the areas of nuclear and medical physics, astrophysics, environmental remediation, nuclear nonproliferation, and homeland security. Detectors used for imaging and particle tracking are more complex in that they typically must also measure the location of the radiation interaction in addition to the deposited energy. In such detectors, the position measurement is often achieved by dividing or segmenting the electrodes into many strips or pixels and then reading out the signals from all of the electrode segments. Fine electrode segmentation is problematic for many of the standard semiconductor detector technologies. Clearly there is a need for a semiconductor-based radiation detector technology that can achieve fine position resolution while maintaining the excellent energy resolution intrinsic to semiconductor detectors, can be fabricated through simple processes, does not require complex electrical interconnections to the detector, and can reduce the number of required channels of readout electronics. Proximity electrode signal readout (PESR), in which the electrodes are not in physical contact with the detector surface, satisfies this need.

  1. Intramedullary compression device for proximal ulna fracture.

    Science.gov (United States)

    Hong, Choon Chiet; Han, Fucai; Decruz, Joshua; Pannirselvam, Vinodhkumar; Murphy, Diarmuid

    2015-02-01

    Proximal ulna fractures account for 20% of all proximal forearm fractures. Many treatment options are available for such fractures, such as cast immobilisation, plate and screw fixation, tension band wiring and intramedullary screw fixation, depending on the fracture pattern. Due to the subcutaneous nature of the proximal forearm, it is vulnerable to open injuries over the dorsal aspect of the proximal ulna. This may in turn prove challenging, as it is critical to obtain adequate soft tissue coverage to reduce the risk of implant exposure and bony infections. We herein describe a patient with a Gustillo III-B open fracture of the proximal ulna, treated with minimally invasive intramedullary screw fixation using a 6.0-mm cannulated headless titanium compression screw (FusiFIX, Péronnas, France).

  2. Ligand binding by the tandem glycine riboswitch depends on aptamer dimerization but not double ligand occupancy

    Science.gov (United States)

    Ruff, Karen M.

    2014-01-01

    The glycine riboswitch predominantly exists as a tandem structure, with two adjacent, homologous ligand-binding domains (aptamers), followed by a single expression platform. The recent identification of a leader helix, the inclusion of which eliminates cooperativity between the aptamers, has reopened the debate over the purpose of the tandem structure of the glycine riboswitch. An equilibrium dialysis-based assay was combined with binding-site mutations to monitor glycine binding in each ligand-binding site independently to understand the role of each aptamer in glycine binding and riboswitch tertiary interactions. A series of mutations disrupting the dimer interface was used to probe how dimerization impacts ligand binding by the tandem glycine riboswitch. While the wild-type tandem riboswitch binds two glycine equivalents, one for each aptamer, both individual aptamers are capable of binding glycine when the other aptamer is unoccupied. Intriguingly, glycine binding by aptamer-1 is more sensitive to dimerization than glycine binding by aptamer-2 in the context of the tandem riboswitch. However, monomeric aptamer-2 shows dramatically weakened glycine-binding affinity. In addition, dimerization of the two aptamers in trans is dependent on glycine binding in at least one aptamer. We propose a revised model for tandem riboswitch function that is consistent with these results, wherein ligand binding in aptamer-1 is linked to aptamer dimerization and stabilizes the P1 stem of aptamer-2, which controls the expression platform. PMID:25246650

  3. Does the ligand-biopolymer equilibrium binding constant depend on the number of bound ligands?

    Science.gov (United States)

    Beshnova, Daria A; Lantushenko, Anastasia O; Evstigneev, Maxim P

    2010-11-01

    Conventional methods, such as Scatchard or McGhee-von Hippel analyses, used to treat ligand-biopolymer interactions, indirectly make the assumption that the microscopic binding constant is independent of the number of ligands, i, already bound to the biopolymer. Recent results on the aggregation of aromatic molecules (Beshnova et al., J Chem Phys 2009, 130, 165105) indicated that the equilibrium constant of self-association depends intrinsically on the number of molecules in an aggregate due to loss of translational and rotational degrees of freedom on formation of the complex. The influence of these factors on the equilibrium binding constant for ligand-biopolymer complexation was analyzed in this work. It was shown that under the conditions of binding of "small" molecules, these factors can effectively be ignored and, hence, do not provide any hidden systematic error in such widely-used approaches, such as the Scatchard or McGhee-von Hippel methods for analyzing ligand-biopolymer complexation. © 2010 Wiley Periodicals, Inc. Biopolymers 93: 932-935, 2010.

  4. Proximity Utilizing Biotinylation of Nuclear Proteins in vivo

    Directory of Open Access Journals (Sweden)

    Arman Kulyyassov

    2015-06-01

    Full Text Available Introduction. The human genome consists of roughly 30,000 genes coding for over 500,000 different proteins, of which more than 10,000 proteins can be produced by the cell at any given time (the cellular “proteome”. It has been estimated that over 80% of proteins do not operate alone, but in complexes. These protein-protein interactions (PPI are regulated by several mechanisms. For example, post-translational modifications (methylation, acetylation, phosphorylation, or ubiquitination or metal-binding can lead to conformational changes that alter the affinity and kinetic parameters of the interaction. Many PPIs are part of larger cellular networks of interactions or interactomes. Indeed, these interactions are at the core of the entire interactomics system of any living cell, and so, aberrant PPIs are the basis of multiple diseases, such as neurodegenerative diseases and cancer. The objective of this study was to develop a method of monitoring protein-protein interactions and proximity dependence in vivo.Methods. The biotin ligase BirA was fused to the protein of interest, and the Biotin Acceptor Peptide (BAP was fused to an interacting partner to make the detection of its biotinylation possible by western blot or mass spectrometry.Results. Using several experimental systems (BirA.A + BAP.B, we showed that the biotinylation is interaction/proximity dependent. Here, A and B are the next nuclear proteins used in the experiments – 3 paralogues of heterochromatin protein HP1a (CBX5, HP1b (CBX1, HP1g (CBX3, wild type and transcription mutant factor Kap1, translesion DNA polymerase PolH and E3, ubiquitin ligase RAD18, Proliferative Cell Nuclear Antigen (PCNA, ubiquitin Ub, SUMO-2/3, different types and isoforms of histones H2A, H2Az, H3.1, H3.3, CenpA, H2A.BBD, and macroH2A. The variant of this approach is termed PUB-NChIP (Proximity Utilizing Biotinylation with Native Chromatin Immuno-precipitation and is designed to purify and study the protein

  5. The thermodynamic principles of ligand binding in chromatography and biology

    DEFF Research Database (Denmark)

    Mollerup, Jørgen

    2007-01-01

    In chromatography, macromolecules do not adsorb in the traditional sense of the word but bind to ligands that are covalently bonded to the surface of the porous bead. Therefore, the adsorption must be modelled as a process where protein molecules bind to the immobilised ligands. The paper discusses...... but it is also observed in chromatography due to protein-protein interactions. Retention measurements on P-lactoglobulin A demonstrate this. A discussion of salt effects on hydrophobic interactions in precipitation and chromatography of proteins concludes the paper. (c) 2007 Elsevier B.V. All rights reserved....... the general thermodynamic principles of ligand binding. Models of the multi-component adsorption in ion-exchange and hydrophobic chromatography, HIC and RPLC, are developed. The parameters in the models have a well-defined physical significance. The models are compared to the Langmuir model...

  6. Proximal Alternating Direction Method with Relaxed Proximal Parameters for the Least Squares Covariance Adjustment Problem

    Directory of Open Access Journals (Sweden)

    Minghua Xu

    2014-01-01

    Full Text Available We consider the problem of seeking a symmetric positive semidefinite matrix in a closed convex set to approximate a given matrix. This problem may arise in several areas of numerical linear algebra or come from finance industry or statistics and thus has many applications. For solving this class of matrix optimization problems, many methods have been proposed in the literature. The proximal alternating direction method is one of those methods which can be easily applied to solve these matrix optimization problems. Generally, the proximal parameters of the proximal alternating direction method are greater than zero. In this paper, we conclude that the restriction on the proximal parameters can be relaxed for solving this kind of matrix optimization problems. Numerical experiments also show that the proximal alternating direction method with the relaxed proximal parameters is convergent and generally has a better performance than the classical proximal alternating direction method.

  7. Selenolate complexes of CYP101 and the heme-bound hHO-1/H25A proximal cavity mutant.

    Science.gov (United States)

    Jiang, Yongying; Ortiz de Montellano, Paul R

    2008-05-05

    Thiolate and selenolate complexes of CYP101 (P450cam) and the H25A proximal cavity mutant of heme-bound human heme oxygenase-1 (hHO-1) have been examined by UV-vis spectroscopy. Both thiolate and selenolate ligands bound to the heme distal side in CYP101 and gave rise to characteristic hyperporphyrin spectra. Thiolate ligands also bound to the proximal side of the heme in the cavity created by the H25A mutation in hHO-1, giving a Soret absorption similar to that of the H25C hHO-1 mutant. Selenolate ligands also bound to this cavity mutant under anaerobic conditions but reduced the heme iron to the ferrous state, as shown by the formation of a ferrous CO complex. Under aerobic conditions, the selenolate ligand but not the thiolate ligand was rapidly oxidized. These results indicate that selenocysteine-coordinated heme proteins will not be stable species in the absence of a redox potential stabilizing effect.

  8. Correcting ligands, metabolites, and pathways

    NARCIS (Netherlands)

    Ott, M.A.; Vriend, G.

    2006-01-01

    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,

  9. FAS Ligand Triggers Pulmonary Silicosis

    Science.gov (United States)

    Borges, Valéria M.; Falcão, Haroldo; Leite-Júnior, José H.; Alvim, Luciana; Teixeira, Gerlinde P.; Russo, Momtchilo; Nóbrega, Alberto F.; Lopes, Marcela F.; Rocco, Patricia M.; Davidson, Wendy F.; Linden, Rafael; Yagita, Hideo; Zin, Walter A.; DosReis, George A.

    2001-01-01

    We investigated the role of Fas ligand in murine silicosis. Wild-type mice instilled with silica developed severe pulmonary inflammation, with local production of tumor necrosis factor (TNF)-α, and interstitial neutrophil and macrophage infiltration in the lungs. Strikingly, Fas ligand–deficient generalized lymphoproliferative disease mutant (gld) mice did not develop silicosis. The gld mice had markedly reduced neutrophil extravasation into bronchoalveolar space, and did not show increased TNF-α production, nor pulmonary inflammation. Bone marrow chimeras and local adoptive transfer demonstrated that wild-type, but not Fas ligand–deficient lung macrophages recruit neutrophils and initiate silicosis. Silica induced Fas ligand expression in lung macrophages in vitro and in vivo, and promoted Fas ligand–dependent macrophage apoptosis. Administration of neutralizing anti-Fas ligand antibody in vivo blocked induction of silicosis. Thus, Fas ligand plays a central role in induction of pulmonary silicosis. PMID:11457890

  10. Structural and biophysical characterisation of G protein-coupled receptor ligand binding using resonance energy transfer and fluorescent labelling techniques.

    Science.gov (United States)

    Ward, Richard J; Milligan, Graeme

    2014-01-01

    The interaction between ligands and the G protein-coupled receptors (GPCRs) to which they bind has long been the focus of intensive investigation. The signalling cascades triggered by receptor activation, due in most cases to ligand binding, are of great physiological and medical importance; indeed, GPCRs are targeted by in excess of 30% of small molecule therapeutic medicines. Attempts to identify further pharmacologically useful GPCR ligands, for receptors with known and unknown endogenous ligands, continue apace. In earlier days direct assessment of such interactions was restricted largely to the use of ligands incorporating radioactive isotope labels as this allowed detection of the ligand and monitoring its interaction with the GPCR. This use of such markers has continued with the development of ligands labelled with fluorophores and their application to the study of receptor-ligand interactions using both light microscopy and resonance energy transfer techniques, including homogenous time-resolved fluorescence resonance energy transfer. Details of ligand-receptor interactions via X-ray crystallography are advancing rapidly as methods suitable for routine production of substantial amounts and stabilised forms of GPCRs have been developed and there is hope that this may become as routine as the co-crystallisation of serine/threonine kinases with ligands, an approach that has facilitated widespread use of rapid structure-based ligand design. Conformational changes involved in the activation of GPCRs, widely predicted by biochemical and biophysical means, have inspired the development of intramolecular FRET-based sensor forms of GPCRs designed to investigate the events following ligand binding and resulting in a signal propagation across the cell membrane. Finally, a number of techniques are emerging in which ligand-GPCR binding can be studied in ways that, whilst indirect, are able to monitor its results in an unbiased and integrated manner. This article is part

  11. The Life Saving Effects of Hospital Proximity

    DEFF Research Database (Denmark)

    Bertoli, Paola; Grembi, Veronica

    We assess the lifesaving effect of hospital proximity using data on fatality rates of road-traffic accidents. While most of the literature on this topic is based on changes in distance to the nearest hospital triggered by hospital closures and use OLS estimates, our identification comes from......) increases the fatality rate by 13.84% on the sample average. This is equal to a 0.92 additional death per every 100 accidents. We show that OLS estimates provide a downward biased measure of the real effect of hospital proximity because they do not fully solve spatial sorting problems. Proximity matters...

  12. U(SMes*)n, (n = 3, 4) and Ln(SMes*)3 (Ln = La, Ce, Pr, Nd): lanthanide(III)/actinide(III) differentiation in agostic interactions and an unprecedented eta3 ligation mode of the arylthiolate ligand, from X-ray diffraction and DFT analysis.

    Science.gov (United States)

    Roger, Mathieu; Barros, Noémi; Arliguie, Thérèse; Thuéry, Pierre; Maron, Laurent; Ephritikhine, Michel

    2006-07-12

    Reaction of U(NEt(2))(4) with HS-2,4,6-(t)Bu(3)C(6)H(2) (HSMes) gave U(SMes)(3)(NEt(2))(py) (1), whereas similar treatment of U[N(SiMe(3))SiMe(2)CH(2)][N(SiMe(3))(2)](2) afforded U(SMes)[N(SiMe(3))(2)](3) (2) and U(SMes)(3)[N(SiMe(3))(2)]. The first neutral homoleptic uranium(IV) thiolate to have been crystallographically characterized, U(SMes)(4) (4), was isolated from the reaction of U(BH(4))(4) and KSMes. The first homoleptic thiolate complex of uranium(III), U(SMes)(3) (5), was synthesized by protonolysis of U[N(SiMe(3))(2)](3) with HSMes in cyclohexane. The crystal structure of 5 exhibits the novel eta(3) ligation mode for the arylthiolate ligand. Comparison of the crystal structure of 5 with those of the isomorphous lanthanide congeners Ln(SMes)(3) (Ln = La, Ce, Pr, and Nd) indicates that the U-S, U-C(ipso)(), and U-C(ortho)() bond lengths are shorter than the corresponding ones in the 4f-element analogues, when taking into account the variation in the ionic radii of the metals. The distance between the uranium and the carbon atoms involved in the U...H-C epsilon agostic interaction of each thiolate ligand is shorter, by approximately 0.05 A, than that expected from a purely ionic bonding model. The lanthanide(III)/actinide(III) differentiation was analyzed by density functional theory (DFT). The nature of the M-S bond is shown to be ionic strongly polarized at the sulfur for M = U and iono-covalent (i.e. strongly ionic with low orbital interaction), for M = Ln. The strength of the U...H-C epsilon agostic interaction is proposed to be controlled by the maximization of the interaction between U(+) and S(-) under steric constraints. The eta(3) ligation mode of the arylthiolate ligand is also obtained from DFT.

  13. Searching for avidity by chemical ligation of combinatorially self-assembled DNA-encoded ligand libraries.

    Science.gov (United States)

    Matysiak, Stefan; Hellmuth, Klaus; El-Sagheer, Afaf H; Shivalingam, Arun; Ariyurek, Yavuz; de Jong, Marco; Hollestelle, Martine J; Out, Ruud; Brown, Tom

    2017-12-19

    DNA encoded ligands are self-assembled into bivalent complexes and chemically ligated to link their identities. To demonstrate their potential as a combinatorial screening platform for avidity interactions, the optimal bivalent aptamer design (examplar ligands) for human alpha-thrombin is determined in a single round of selection and the DNA scaffold replaced with minimal impact on the final design.

  14. Functionalization of Cadmium Selenide Quantum Dots with Poly(ethylene glycol): Ligand Exchange, Surface Coverage, and Dispersion Stability.

    Science.gov (United States)

    Wenger, Whitney Nowak; Bates, Frank S; Aydil, Eray S

    2017-08-22

    Semiconductor quantum dots synthesized using rapid mixing of precursors by injection into a hot solution of solvents and surfactants have surface ligands that sterically stabilize the dispersions in nonpolar solvents. Often, these ligands are exchanged to disperse the quantum dots in polar solvents, but quantitative studies of quantum dot surfaces before and after ligand exchange are scarce. We studied exchanging trioctylphosphine (TOP) and trioctylphosphine oxide (TOPO) ligands on as-synthesized CdSe quantum dots dispersed in hexane with a 2000 g/mol thiolated poly(ethylene glycol) (PEG) polymer. Using infrared spectroscopy we quantify the absolute surface concentration of TOP/TOPO and PEG ligands per unit area before and after ligand exchange. While 50-85% of the TOP/TOPO ligands are removed upon ligand exchange, only a few are replaced with PEG. Surprisingly, the remaining TOP/TOPO ligands outnumber the PEG ligands, but these few PEG ligands are sufficient to disperse the quantum dots in polar solvents such as chloroform, tetrahydrofuran, and water. Moreover, as-synthesized quantum dots once easily dispersed in hexane are no longer dispersible in nonpolar solvents after ligand exchange. A subtle coverage-dependent balance between attractive PEG-solvent interactions and repulsive TOP/TOPO-solvent interactions determines the dispersion stability.

  15. SMRT recruitment by PPARgamma is mediated by specific residues located in its carboxy-terminal interacting domain.

    Science.gov (United States)

    Sutanto, Maria M; Symons, Melissa S; Cohen, Ronald N

    2006-10-19

    The silencing mediator of retinoid and thyroid hormone receptors (SMRT) has been shown to play an important role in adipogenesis and PPARgamma transcriptional activity. SMRT contains two interacting domains that mediate interactions with nuclear receptors. Interestingly, SMRT is recruited to PPARgamma via its C-terminal interacting domain, and mutation of the proximal interacting domain does not interfere with recruitment via PPARgamma. To understand how the distal interacting domain mediates recruitment by PPARgamma, we have now mutated residues in this domain to the corresponding amino acids found in the proximal domain. We show that specific residues in this distal domain are vital for interactions with PPARgamma, but not for a related receptor, RARalpha. Furthermore, naturally-occuring SMRT isoforms that differ in interacting domain sequences have different effects on PPARgamma as opposed to RARalpha recruitment. These data suggest that PPARgamma and RARalpha interact with SMRT via distinct mechanisms. These differences will be important as ligands are designed that lead to specific patterns of nuclear receptor recruitment of corepressors.

  16. New Oxime Ligand with Potential for Proton-Coupled Electron-Transfer Reactions

    DEFF Research Database (Denmark)

    Deville, Claire; Sundberg, Jonas; McKenzie, Christine Joy

    .2 Metal complex of ligands possessing both H-donor and H-acceptor sites in the second coordination sphere should be interesting candidates for proton transfer reactions induced by photooxidation of the metal ion. We have prepared new oxime-containing ligands which coordinate to metal ions...... such that a pyridine group is sterically restricted so it does not coordinate. Instead it can act as proximal base for accepting the oxime proton. [1] M. H. V. Huynh, T. J. Meyer, Chem. Rev. 2007, 107, 5004-5064. [2] T. Irebo, O. Johansson, L. Hammarström, J. Am. Chem. Soc., 2008, 130, 9194-9195....

  17. Double Insertion of Coordinated Phosphanylalkyne Ligands into a Pt-C(6)F(5) Bond.

    Science.gov (United States)

    Charmant; Forniés; Gómez; Lalinde; Moreno; Orpen; Solano

    1999-10-18

    Enhanced reactivity is shown by uncoordinated C identical withC bonds in the proximity of a metal in phosphanylacetylene complexes. cis-[Pt(C(6)F(5))(2)(thf)(2)] reacts with [M(C(6)F(5))(2)(PPh(2)C identical withCPh)(2)] (M=Pt, Pd) to form binuclear complexes containing the novel 2,3-bis(diphenylphosphanyl)-1,3-butadien-1-yl bridging ligand. Substitution of the solvent ligands with, for example, PPh(2)H (see picture) provides species that could be characterized by X-ray crystallography.

  18. GluR2 ligand-binding core complexes

    DEFF Research Database (Denmark)

    Kasper, C; Lunn, M-L; Liljefors, T

    2002-01-01

    X-ray structures of the GluR2 ligand-binding core in complex with (S)-Des-Me-AMPA and in the presence and absence of zinc ions have been determined. (S)-Des-Me-AMPA, which is devoid of a substituent in the 5-position of the isoxazolol ring, only has limited interactions with the partly hydrophobic...

  19. NMR-based screening of membrane protein ligands

    NARCIS (Netherlands)

    Yanamala, Naveena; Dutta, Arpana; Beck, Barbara; Van Fleet, Bart; Hay, Kelly; Yazbak, Ahmad; Ishima, Rieko; Doemling, Alexander; Klein-Seetharaman, Judith

    2010-01-01

    Membrane proteins pose problems for the application of NMR-based ligand-screening methods because of the need to maintain the proteins in a membrane mimetic environment such as detergent micelles: they add to the molecular weight of the protein, increase the viscosity of the solution, interact with

  20. A motion planning approach to flexible ligand binding.

    Science.gov (United States)

    Singh, A P; Latombe, J C; Brutlag, D L

    1999-01-01

    Most computational models of protein-ligand interactions consider only the energetics of the final bound state of the complex and do not examine the dynamics of the ligand as it enters the binding site. We have developed a novel technique for studying the dynamics of protein-ligand interactions based on motion planning algorithms from the field of robotics. Our algorithm uses electrostatic and van der Waals potentials to compute the most energetically favorable path between any given initial and goal ligand configurations. We use probabilistic motion planning to sample the distribution of possible paths to a given goal configuration and compute an energy-based "difficulty weight" for each path. By statistically averaging this weight over several randomly generated starting configurations, we compute the relative difficulty of entering and leaving a given binding configuration. This approach yields details of the energy contours around the binding site and can be used to characterize and predict good binding sites. Results from tests with three protein-ligand complexes indicate that our algorithm is able to detect energy barriers around the true binding site that distinguish this site from other predicted low-energy binding sites.

  1. Free-energy relationships in ion channels activated by voltage and ligand

    Science.gov (United States)

    Chowdhury, Sandipan

    2013-01-01

    Many ion channels are modulated by multiple stimuli, which allow them to integrate a variety of cellular signals and precisely respond to physiological needs. Understanding how these different signaling pathways interact has been a challenge in part because of the complexity of underlying models. In this study, we analyzed the energetic relationships in polymodal ion channels using linkage principles. We first show that in proteins dually modulated by voltage and ligand, the net free-energy change can be obtained by measuring the charge-voltage (Q-V) relationship in zero ligand condition and the ligand binding curve at highly depolarizing membrane voltages. Next, we show that the voltage-dependent changes in ligand occupancy of the protein can be directly obtained by measuring the Q-V curves at multiple ligand concentrations. When a single reference ligand binding curve is available, this relationship allows us to reconstruct ligand binding curves at different voltages. More significantly, we establish that the shift of the Q-V curve between zero and saturating ligand concentration is a direct estimate of the interaction energy between the ligand- and voltage-dependent pathway. These free-energy relationships were tested by numerical simulations of a detailed gating model of the BK channel. Furthermore, as a proof of principle, we estimate the interaction energy between the ligand binding and voltage-dependent pathways for HCN2 channels whose ligand binding curves at various voltages are available. These emerging principles will be useful for high-throughput mutagenesis studies aimed at identifying interaction pathways between various regulatory domains in a polymodal ion channel. PMID:23250866

  2. Proximity and Collaboration in European Nanotechnology

    NARCIS (Netherlands)

    Cunningham, S.W.; Werker, C.

    2011-01-01

    Collaborations are particularly important for the development and deployment of technology. We analyze the influence of organizational, technological and geographical proximity on European nanotechnology collaborations with the help of a publication dataset and additional geographical information.

  3. Promoting proximal formative assessment with relational discourse

    Science.gov (United States)

    Scherr, Rachel E.; Close, Hunter G.; McKagan, Sarah B.

    2012-02-01

    The practice of proximal formative assessment - the continual, responsive attention to students' developing understanding as it is expressed in real time - depends on students' sharing their ideas with instructors and on teachers' attending to them. Rogerian psychology presents an account of the conditions under which proximal formative assessment may be promoted or inhibited: (1) Normal classroom conditions, characterized by evaluation and attention to learning targets, may present threats to students' sense of their own competence and value, causing them to conceal their ideas and reducing the potential for proximal formative assessment. (2) In contrast, discourse patterns characterized by positive anticipation and attention to learner ideas increase the potential for proximal formative assessment and promote self-directed learning. We present an analysis methodology based on these principles and demonstrate its utility for understanding episodes of university physics instruction.

  4. Proximate composition and cholesterol concentrations of ...

    African Journals Online (AJOL)

    STORAGESEVER

    2009-05-18

    DWB) for raw and fried samples, respectively, but decreased to 295.20 ... Key words: Rhynchophorus phoenicis, Oryctes monoceros, proximate composition, cholesterol, heat treatment. INTRODUCTION. Insects have played ...

  5. COMPARATIVE ANALYSIS OF PROXIMATE COMPOSITIONS OF ...

    African Journals Online (AJOL)

    Babatunde Emmanuel

    2011-10-06

    Oct 6, 2011 ... Fish allows for protein improved nutrition in that it has a high biological value in terms of high ... marine algae upon which the fish feed [11]. ... Proximate composition of catfish Clarias gariepinus and Tarpon atlanticus were.

  6. Analysis of leukocyte membrane protein interactions using protein microarrays

    Directory of Open Access Journals (Sweden)

    Foster-Cuevas Mildred

    2005-03-01

    Full Text Available Abstract Background Protein microarrays represent an emerging class of proteomic tools to investigate multiple protein-protein interactions in parallel. A sufficient proportion of immobilized proteins must maintain an active conformation and an orientation that allows for the sensitive and specific detection of antibody and ligand binding. In order to establish protein array technology for the characterization of the weak interactions between leukocyte membrane proteins, we selected the human leukocyte membrane protein CD200 (OX2 and its cell surface receptor (hCD200R as a model system. As antibody-antigen reactions are generally of higher affinity than receptor-ligand binding, we first analyzed the reactivity of monoclonal antibodies (mAb to normal and mutant forms of immobilized CD200R. Results Fluorescently labelled mAb DX147, DX136 and OX108 were specifically reactive with immobilized recombinant hCD200R extracellular region, over a range of 0.1–40 μg ml-1 corresponding to a limit of sensitivity of 0.01–0.05 femtomol per spot. Orientating hCD200R using capture antibodies, showed that DX147 reacts with an epitope spatially distinct from the more closely related DX136 and OX108 epitopes. A panel of soluble recombinant proteins with mutations in hCD200R domain 1 produced by transiently transfected cells, was arrayed directly without purification and screened for binding to the three mAb. Several showed decreased binding to the blocking mAb DX136 and OX108, suggesting close proximity of these epitopes to the CD200 binding site. Binding of hCD200 to directly immobilized rat, mouse, and hCD200R was achieved with multimeric ligands, in the form of biotinylated-hCD200 coupled to FITC-labelled avidin coated beads. Conclusion We have achieved sensitive, specific and reproducible detection of immobilized CD200R with different antibodies and mapped antigenic epitopes for two mAb in the vicinity of the ligand binding site using protein microarrays

  7. Phytochemical screening, proximate analysis and acute toxicity ...

    African Journals Online (AJOL)

    Phytochemical screening, proximate analysis and acute toxicity studies were carried out on the leaf extract of Cola lepidota, in accordance with established standard procedures. The proximate analysis reveals a moisture content of 27.43 ± 3.11 % w/w, total ash value 9.32 ± 0.27 % w/w, acid insoluble ash 3.12 ± 1.05 % w/w ...

  8. Proximate, Mineral and Phytochemical Composition of Dioscorea ...

    African Journals Online (AJOL)

    ADOWIE PERE

    ABSTRACT: Proximate, mineral and phytochemical composition of Dioscorea dumetorum tubers was investigated using standard procedures. Proximate analysis included in g% dry weight: crude protein (6.44 ± 0.32), crude fat (0.75 ± 0.04), crude fibre (15.00 ± 0.56), total ash. (3.45 ± 0.20) and a moisture content of 70.04 ...

  9. Painful Spastic Hip Dislocation: Proximal Femoral Resection

    OpenAIRE

    Albiñana, Javier; Gonzalez-Moran, Gaspar

    2002-01-01

    The dislocated hip in a non-ambulatory child with spastic paresis tends to be a painful interference to sleep, sitting upright, and perineal care. Proximal femoral resection-interposition arthroplasty is one method of treatment for this condition. We reviewed eight hips, two bilateral cases, with a mean follow-up of 30 months. Clinical improvement was observed in all except one case, with respect to pain relief and sitting tolerance. Some proximal migration was observed in three cases, despit...

  10. Proximity sensor system development. CRADA final report

    Energy Technology Data Exchange (ETDEWEB)

    Haley, D.C. [Oak Ridge National Lab., TN (United States); Pigoski, T.M. [Merrit Systems, Inc. (United States)

    1998-01-01

    Lockheed Martin Energy Research Corporation (LMERC) and Merritt Systems, Inc. (MSI) entered into a Cooperative Research and Development Agreement (CRADA) for the development and demonstration of a compact, modular proximity sensing system suitable for application to a wide class of manipulator systems operated in support of environmental restoration and waste management activities. In teleoperated modes, proximity sensing provides the manipulator operator continuous information regarding the proximity of the manipulator to objects in the workspace. In teleoperated and robotic modes, proximity sensing provides added safety through the implementation of active whole arm collision avoidance capabilities. Oak Ridge National Laboratory (ORNL), managed by LMERC for the United States Department of Energy (DOE), has developed an application specific integrated circuit (ASIC) design for the electronics required to support a modular whole arm proximity sensing system based on the use of capacitive sensors developed at Sandia National Laboratories. The use of ASIC technology greatly reduces the size of the electronics required to support the selected sensor types allowing deployment of many small sensor nodes over a large area of the manipulator surface to provide maximum sensor coverage. The ASIC design also provides a communication interface to support sensor commands from and sensor data transmission to a distributed processing system which allows modular implementation and operation of the sensor system. MSI is a commercial small business specializing in proximity sensing systems based upon infrared and acoustic sensors.

  11. Transformations through Proximity Flying: A Phenomenological Investigation

    Science.gov (United States)

    Holmbom, Maria; Brymer, Eric; Schweitzer, Robert D.

    2017-01-01

    Participation in extreme sports has been linked to personal transformations in everyday life. Descriptions of lived experience resulting from transformative experiences are limited. Proximity flying, a relatively new discipline involving BASE jumping with a wingsuit where participants fly close to solid structures, is arguably one of the most extreme of extreme sports. The aim of this paper, part of a larger phenomenological study on the lived experience of proximity flying, is to explicate the ways in which participating in proximity flying influences the everyday lives of participants. Interpretative phenomenological analysis was used to explicate the lived experience of six proximity pilots. An analysis of interview transcripts revealed three significant themes describing the lived experience of participants. First, experiences of change were described as positive and skills developed through proximity flying were transferable into everyday life. Second, transformative experiences were considered fundamental to participants’ perspectives on life. Third, experience of transformation influenced their sense of personal identity and facilitated flourishing in other aspects of everyday life. Participants were clear that their experiences in proximity flying facilitated a profound process of transformation which manifest as changes in everyday capabilities and behaviors, values and sense of identity. PMID:29104552

  12. Proximate influences on female dispersal in white-tailed deer

    Science.gov (United States)

    Lutz, Clayton L.; Diefenbach, Duane R.; Rosenberry, Christopher S.

    2016-01-01

    Ultimate causes of animal dispersal have been hypothesized to benefit the dispersing individual because dispersal reduces competition for local resources, potential for inbreeding, and competition for breeding partners. However, proximate cues influence important features of dispersal behavior, including when dispersal occurs, how long it lasts, and direction, straightness, and distance of the dispersal path. Therefore, proximate cues that affect dispersal influence ecological processes (e.g., population dynamics, disease transmission, gene flow). We captured and radio-marked 277 juvenile female white-tailed deer (Odocoileus virginianus), of which 27 dispersed, to evaluate dispersal behavior and to determine proximate cues that may influence dispersal behavior. Female dispersal largely occurred at 1 year of age and coincided with the fawning season. Dispersal paths varied but generally were non-linear and prolonged. Physical landscape features (i.e., roadways, rivers, residential areas) influenced dispersal path direction and where dispersal terminated. Additionally, forays outside of the natal range that did not result in dispersal occurred among 52% of global positioning system (GPS)-collared deer (n = 25) during the dispersal period. Our results suggest intra-specific social interactions and physical landscape features influence dispersal behavior in female deer. Female dispersal behavior, particularly the lack of directionality, the semi-permeable nature of physical barriers, and the frequency of forays outside of the natal range, should be considered in regard to population management and controlling the spread of disease.

  13. PRIM: Proximity imaging of green fluorescent protein-tagged polypeptides

    Science.gov (United States)

    De Angelis, Dino A.; Miesenböck, Gero; Zemelman, Boris V.; Rothman, James E.

    1998-01-01

    We report a serendipitous discovery that extends the impressive catalog of reporter functions performed by green fluorescent protein (GFP) or its derivatives. When two GFP molecules are brought into proximity, changes in the relative intensities of green fluorescence emitted upon excitation at 395 vs. 475 nm result. These spectral changes provide a sensitive ratiometric index of the extent of self-association that can be exploited to quantitatively image homo-oligomerization or clustering processes of GFP-tagged proteins in vivo. The method, which we term proximity imaging (PRIM), complements fluorescence resonance energy transfer between a blue fluorescent protein donor and a GFP acceptor, a powerful method for imaging proximity relationships between different proteins. However, unlike fluorescence resonance energy transfer (which is a spectral interaction), PRIM depends on direct contact between two GFP modules, which can lead to structural perturbations and concomitant spectral changes within a module. Moreover, the precise spatial arrangement of the GFP molecules within a given dimer determines the magnitude and direction of the spectral change. We have used PRIM to detect FK1012-induced dimerization of GFP fused to FK506-binding protein and clustering of glycosylphosphatidylinositol-anchored GFP at cell surfaces. PMID:9770483

  14. Molecular interaction fingerprint approaches for GPCR drug discovery

    NARCIS (Netherlands)

    Vass, M.; Kooistra, A.J.; Ritschel, T.; Leurs, R.; Esch, I.J. de; Graaf, C. de

    2016-01-01

    Protein-ligand interaction fingerprints (IFPs) are binary 1D representations of the 3D structure of protein-ligand complexes encoding the presence or absence of specific interactions between the binding pocket amino acids and the ligand. Various implementations of IFPs have been developed and

  15. Isothermal Titration Calorimetry: Assisted Crystallization of RNA-Ligand Complexes.

    Science.gov (United States)

    Da Veiga, Cyrielle; Mezher, Joelle; Dumas, Philippe; Ennifar, Eric

    2016-01-01

    The success rate of nucleic acids/ligands co-crystallization can be significantly improved by performing preliminary biophysical analyses. Among suitable biophysical approaches, isothermal titration calorimetry (ITC) is certainly a method of choice. ITC can be used in a wide range of experimental conditions to monitor in real time the formation of the RNA- or DNA-ligand complex, with the advantage of providing in addition the complete binding profile of the interaction. Following the ITC experiment, the complex is ready to be concentrated for crystallization trials. This chapter describes a detailed experimental protocol for using ITC as a tool for monitoring RNA/small molecule binding, followed by co-crystallization.

  16. Tear lipocalins bind a broad array of lipid ligands.

    Science.gov (United States)

    Glasgow, B J; Abduragimov, A R; Farahbakhsh, Z T; Faull, K F; Hubbell, W L

    1995-05-01

    To identify the native ligands of tear lipocalins, tear proteins were separated by size exclusion chromatography and the lipid content in the major protein fractions identified. Lipids extracted from native tears and purified tear lipocalins comigrated with fatty acids, fatty alcohols, phospholipids, glycolipids, and cholesterol on thin layer chromatograms. Abundant stearic and palmitic acids as well as cholesterol, and lesser amounts of lauric acid were specifically identified in extracts of purified lipocalins by gas chromatography-mass spectroscopy. A preliminary study of the ligand-protein interaction was carried out using nitroxide spin-labeled lipids.

  17. Treatment of three- and four-part proximal humeral fractures with locking proximal humerus plate.

    Science.gov (United States)

    Sun, Jing-Cheng; Li, Yu-Lin; Ning, Guang-Zhi; Wu, Qiang; Feng, Shi-Qing

    2013-08-01

    The purpose of this study was to evaluate the effectiveness and complications of the locking proximal humerus plate to treat proximal humerus fractures. A retrospective clinical trial. Department of Orthopaedics, Tianjin Medical University General Hospital. Sixty-eight consecutive patients with three- or four-part fractures of the proximal humerus were treated with locking proximal humerus plates. The deltopectoral anterolateral acromial approach was used to the proximal humerus; open reduction and locking proximal humerus plate were applied. Constant Score was used to measure the shoulder functional recovery, and Visual Analog Scale (VAS) was used to measure subjective evaluation of pain. The radiology was observed. After average 26.7 months, the average Constant Score was 72.6 ± 13.2 points and the average VAS was 1.2 ± 0.8 points. All the complications such as screw perforation into the glenohumeral joint, screws loosening, soft tissue infections, avascular necrosis and delayed union occurred in eight cases (11.8 %). The effectiveness of the locking proximal humerus plate was similar to other published literatures on treating fractures of the proximal humerus; however, a lower complications rate in short follow-up time was observed in this study. It may potentially provide a favorable option for treating three- or four-part fractures of the proximal humerus. Dealing with each particular fracture pattern, surgeons should have a decision of appropriate way to internal fixation.

  18. Proximity to sports facilities and sports participation for adolescents in Germany.

    Directory of Open Access Journals (Sweden)

    Anne K Reimers

    Full Text Available To assess the relationship between proximity to specific sports facilities and participation in the corresponding sports activities for adolescents in Germany.A sample of 1,768 adolescents aged 11-17 years old and living in 161 German communities was examined. Distances to the nearest sports facilities were calculated as an indicator of proximity to sports facilities using Geographic Information Systems (GIS. Participation in specific leisure-time sports activities in sports clubs was assessed using a self-report questionnaire and individual-level socio-demographic variables were derived from a parent questionnaire. Community-level socio-demographics as covariates were selected from the INKAR database, in particular from indicators and maps on land development. Logistic regression analyses were conducted to examine associations between proximity to the nearest sports facilities and participation in the corresponding sports activities.The logistic regression analyses showed that girls residing longer distances from the nearest gym were less likely to engage in indoor sports activities; a significant interaction between distances to gyms and level of urbanization was identified. Decomposition of the interaction term showed that for adolescent girls living in rural areas participation in indoor sports activities was positively associated with gym proximity. Proximity to tennis courts and indoor pools was not associated with participation in tennis or water sports, respectively.Improved proximity to gyms is likely to be more important for female adolescents living in rural areas.

  19. Proximity to Sports Facilities and Sports Participation for Adolescents in Germany

    Science.gov (United States)

    Reimers, Anne K.; Wagner, Matthias; Alvanides, Seraphim; Steinmayr, Andreas; Reiner, Miriam; Schmidt, Steffen; Woll, Alexander

    2014-01-01

    Objectives To assess the relationship between proximity to specific sports facilities and participation in the corresponding sports activities for adolescents in Germany. Methods A sample of 1,768 adolescents aged 11–17 years old and living in 161 German communities was examined. Distances to the nearest sports facilities were calculated as an indicator of proximity to sports facilities using Geographic Information Systems (GIS). Participation in specific leisure-time sports activities in sports clubs was assessed using a self-report questionnaire and individual-level socio-demographic variables were derived from a parent questionnaire. Community-level socio-demographics as covariates were selected from the INKAR database, in particular from indicators and maps on land development. Logistic regression analyses were conducted to examine associations between proximity to the nearest sports facilities and participation in the corresponding sports activities. Results The logisitic regression analyses showed that girls residing longer distances from the nearest gym were less likely to engage in indoor sports activities; a significant interaction between distances to gyms and level of urbanization was identified. Decomposition of the interaction term showed that for adolescent girls living in rural areas participation in indoor sports activities was positively associated with gym proximity. Proximity to tennis courts and indoor pools was not associated with participation in tennis or water sports, respectively. Conclusions Improved proximity to gyms is likely to be more important for female adolescents living in rural areas. PMID:24675689

  20. Model investigations of vanadium-protein interactions: novel vanadium(III) and oxovanadium(IV) compounds with the diamidate ligand 1,2-bis(2-pyridinecarboxamide)benzene (H2bpb).

    Science.gov (United States)

    Vlahos, A T; Tolis, E I; Raptopoulou, C P; Tsohos, A; Sigalas, M P; Terzis, A; Kabanos, T A

    2000-07-10

    Novel vanadium(III) and oxovanadium(IV) compounds with the diamidate ligand 1,2-bis(2-pyridinecarboxamide)benzene (H2bpb) were synthesized and structurally characterized. H2bpb is capable of binding to vanadium in either its anionic (dianionic-monoanionic) or its neutral form, resulting in complexes of various geometries and stoichiometries. The dianionic form (bpb2-), in NHEt3(trans-[VCl2(bpb)]) (1) and [VO(bpb)(H2O)]05dmso036CH3OH013H2O (6x05dmsox036CH3OHx013H2O), acts as a planar tetradentate bis[N-amidate-N-pyridine] equatorial ligand. The monoanionic form (Hbpb-) behaves as an (Npy,Oam) or (Npy,Nam) chelator in [V(Hbpb)3]2CHCl3 (22CHCl3) as well as a mu 2-bridging-eta 4-(Npy,Oam-Npy,Nam) in [VOCl(Hbpb)](2)x2CH3NO2 (3x2CH3NO2), while the neutral H2bpb behaves as a mu 2-bridging-eta 4-bis(Npy,Oam) in [VOCl(H2bpb)](2)x104CH3OHx123thfx074H2O (4x104CH3OH123thf074H2O). Compound 4x104CH3OHx123thfx074H2O crystallizes in the triclinic system P1, with (at 25 degrees C) a = 9140(2) A, b = 11058(2) A, c = 14175(2) A, alpha = 99013(5) degrees, beta = 104728(7) degrees, gamma = 102992(7) degrees, V = 13149(4) A3, Z = 1, while compound 605dmso036CH3OH013H2O crystallizes in the monoclinic space group P2(1)/n with (at 25 degrees C) a = 11054(5) A, b = 11407(5) A, c = 16964(7) A, beta = 932(1) degrees, V = 2136(2) A3, Z = 4. Variable temperature magnetic susceptibility studies of the dimeric compounds 3x2CH3NO2 and 4x104CH3OH show g values for the V(IV) centers that are slightly smaller than 20 (as expected for d1 ions) and indicate small antiferromagnetic coupling between the two vanadium(IV) centers. Ab initio calculations were also carried out, providing results concerning the effect of the relative strength and the deformation energy involved in the eta 2-(Npy,Nam) and eta 2-(Npy,Oam) bonding modes in the ligation of Hbpb- to vanadium.

  1. New insight into the central benzodiazepine receptor-ligand interactions: design, synthesis, biological evaluation, and molecular modeling of 3-substituted 6-phenyl-4H-imidazo[1,5-a][1,4]benzodiazepines and related compounds.

    Science.gov (United States)

    Anzini, Maurizio; Valenti, Salvatore; Braile, Carlo; Cappelli, Andrea; Vomero, Salvatore; Alcaro, Stefano; Ortuso, Francesco; Marinelli, Luciana; Limongelli, Vittorio; Novellino, Ettore; Betti, Laura; Giannaccini, Gino; Lucacchini, Antonio; Daniele, Simona; Martini, Claudia; Ghelardini, Carla; Di Cesare Mannelli, Lorenzo; Giorgi, Gianluca; Mascia, Maria Paola; Biggio, Giovanni

    2011-08-25

    3-Substituted 6-phenyl-4H-imidazo[1,5-a][1,4]benzodiazepines and related compounds were synthesized as central benzodiazepine receptor (CBR) ligands. Most of the compounds showed high affinity for bovine and human CBR, their K(i) values spanning from the low nanomolar to the submicromolar range. In particular, imidazoester 5f was able to promote a massive flow of (36)Cl(-) in rat cerebrocortical synaptoneurosomes overlapping its efficacy profile with that of a typical full agonist. Compound 5f was then examined in mice for its pharmacological effects where it proved to be a safe anxiolytic agent devoid of the unpleasant myorelaxant and amnesic effects of the classical 1,4-benzodiazepines. Moreover, the selectivity of some selected compounds has been assessed in recombinant α(1)β(2)γ(2)L, α(2)β(1)γ(2)L, and α(5)β(2)γ(2)L human GABA(A) receptors. Finally, some compounds were submitted to molecular docking calculations along with molecular dynamics simulations in the Cromer's GABA(A) homology model. © 2011 American Chemical Society

  2. Ligand screening by saturation-transfer difference (STD) NMR spectroscopy.

    Energy Technology Data Exchange (ETDEWEB)

    Krishnan, V V

    2005-04-26

    NMR based methods to screen for high-affinity ligands have become an indispensable tool for designing rationalized drugs, as these offer a combination of good experimental design of the screening process and data interpretation methods, which together provide unprecedented information on the complex nature of protein-ligand interactions. These methods rely on measuring direct changes in the spectral parameters, that are often simpler than the complex experimental procedures used to study structure and dynamics of proteins. The goal of this review article is to provide the basic details of NMR based ligand-screening methods, with particular focus on the saturation transfer difference (STD) experiment. In addition, we provide an overview of other NMR experimental methods and a practical guide on how to go about designing and implementing them.

  3. Locking plate fixation for proximal humerus fractures.

    LENUS (Irish Health Repository)

    Burke, Neil G

    2012-02-01

    Locking plates are increasingly used to surgically treat proximal humerus fractures. Knowledge of the bone quality of the proximal humerus is important. Studies have shown the medial and dorsal aspects of the proximal humeral head to have the highest bone strength, and this should be exploited by fixation techniques, particularly in elderly patients with osteoporosis. The goals of surgery for proximal humeral fractures should involve minimal soft tissue dissection and achieve anatomic reduction of the head complex with sufficient stability to allow for early shoulder mobilization. This article reviews various treatment options, in particular locking plate fixation. Locking plate fixation is associated with a high complication rate, such as avascular necrosis (7.9%), screw cutout (11.6%), and revision surgery (13.7%). These complications are frequently due to the varus deformation of the humeral head. Strategic screw placement in the humeral head would minimize the possibility of loss of fracture reduction and potential hardware complications. Locking plate fixation is a good surgical option for the management of proximal humerus fractures. Complications can be avoided by using better bone stock and by careful screw placement in the humeral head.

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

    Energy Technology Data Exchange (ETDEWEB)

    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

    2003-11-14

    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{sub 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{sub 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{sub 6}-tagged protein molecules to AFM tips via noncovalent NTA-Ni{sup 2+}-His{sub 6} bridges. The new crosslinker was applied to link a recombinant His{sub 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 {beta}1 was studied in detail by SMRFM, using the new crosslinker to link His{sub 6}-tagged Ran to the measuring tip [Nat. Struct. Biol. (2003), 10, 553-557].

  5. Tetrapyrroles as Endogenous TSPO Ligands in Eukaryotes and Prokaryotes: Comparisons with Synthetic Ligands

    Directory of Open Access Journals (Sweden)

    Leo Veenman

    2016-06-01

    Full Text Available The 18 kDa translocator protein (TSPO is highly 0conserved in eukaryotes and prokaryotes. Since its discovery in 1977, numerous studies established the TSPO’s importance for life essential functions. For these studies, synthetic TSPO ligands typically are applied. Tetrapyrroles present endogenous ligands for the TSPO. Tetrapyrroles are also evolutionarily conserved and regulate multiple functions. TSPO and tetrapyrroles regulate each other. In animals TSPO-tetrapyrrole interactions range from effects on embryonic development to metabolism, programmed cell death, response to stress, injury and disease, and even to life span extension. In animals TSPOs are primarily located in mitochondria. In plants TSPOs are also present in plastids, the nuclear fraction, the endoplasmic reticulum, and Golgi stacks. This may contribute to translocation of tetrapyrrole intermediates across organelles’ membranes. As in animals, plant TSPO binds heme and protoporphyrin IX. TSPO-tetrapyrrole interactions in plants appear to relate to development as well as stress conditions, including salt tolerance, abscisic acid-induced stress, reactive oxygen species homeostasis, and finally cell death regulation. In bacteria, TSPO is important for switching from aerobic to anaerobic metabolism, including the regulation of photosynthesis. As in mitochondria, in bacteria TSPO is located in the outer membrane. TSPO-tetrapyrrole interactions may be part of the establishment of the bacterial-eukaryote relationships, i.e., mitochondrial-eukaryote and plastid-plant endosymbiotic relationships.

  6. Crystal Structure of the Ligand Binding Suppressor Domain of Type 1 Inositol 1,4,5-Trisphosphate Receptor

    Energy Technology Data Exchange (ETDEWEB)

    Bosanac, Ivan; Yamazaki, Haruka; Matsu-ura, Toru; Michikawa, Takayuki; Mikoshiba, Katsuhiko; Ikura, Mitsuhiko (U. of Texas-SMED)

    2010-11-10

    Binding of inositol 1,4,5-trisphosphate (IP{sub 3}) to the amino-terminal region of IP{sub 3} receptor promotes Ca{sup 2+} release from the endoplasmic reticulum. Within the amino terminus, the first 220 residues directly preceding the IP{sub 3} binding core domain play a key role in IP{sub 3} binding suppression and regulatory protein interaction. Here we present a crystal structure of the suppressor domain of the mouse type 1 IP{sub 3} receptor at 1.8 {angstrom}. Displaying a shape akin to a hammer, the suppressor region contains a Head subdomain forming the {beta}-trefoil fold and an Arm subdomain possessing a helix-turn-helix structure. The conserved region on the Head subdomain appeared to interact with the IP{sub 3} binding core domain and is in close proximity to the previously proposed binding sites of Homer, RACK1, calmodulin, and CaBP1. The present study sheds light onto the mechanism underlying the receptor's sensitivity to the ligand and its communication with cellular signaling proteins.

  7. Cloud computing for protein-ligand binding site comparison.

    Science.gov (United States)

    Hung, Che-Lun; Hua, Guan-Jie

    2013-01-01

    The proteome-wide analysis of protein-ligand binding sites and their interactions with ligands is important in structure-based drug design and in understanding ligand cross reactivity and toxicity. The well-known and commonly used software, SMAP, has been designed for 3D ligand binding site comparison and similarity searching of a structural proteome. SMAP can also predict drug side effects and reassign existing drugs to new indications. However, the computing scale of SMAP is limited. We have developed a high availability, high performance system that expands the comparison scale of SMAP. This cloud computing service, called Cloud-PLBS, combines the SMAP and Hadoop frameworks and is deployed on a virtual cloud computing platform. To handle the vast amount of experimental data on protein-ligand binding site pairs, Cloud-PLBS exploits the MapReduce paradigm as a management and parallelizing tool. Cloud-PLBS provides a web portal and scalability through which biologists can address a wide range of computer-intensive questions in biology and drug discovery.

  8. Cloud Computing for Protein-Ligand Binding Site Comparison

    Directory of Open Access Journals (Sweden)

    Che-Lun Hung

    2013-01-01

    Full Text Available The proteome-wide analysis of protein-ligand binding sites and their interactions with ligands is important in structure-based drug design and in understanding ligand cross reactivity and toxicity. The well-known and commonly used software, SMAP, has been designed for 3D ligand binding site comparison and similarity searching of a structural proteome. SMAP can also predict drug side effects and reassign existing drugs to new indications. However, the computing scale of SMAP is limited. We have developed a high availability, high performance system that expands the comparison scale of SMAP. This cloud computing service, called Cloud-PLBS, combines the SMAP and Hadoop frameworks and is deployed on a virtual cloud computing platform. To handle the vast amount of experimental data on protein-ligand binding site pairs, Cloud-PLBS exploits the MapReduce paradigm as a management and parallelizing tool. Cloud-PLBS provides a web portal and scalability through which biologists can address a wide range of computer-intensive questions in biology and drug discovery.

  9. Cloud Computing for Protein-Ligand Binding Site Comparison

    Science.gov (United States)

    2013-01-01

    The proteome-wide analysis of protein-ligand binding sites and their interactions with ligands is important in structure-based drug design and in understanding ligand cross reactivity and toxicity. The well-known and commonly used software, SMAP, has been designed for 3D ligand binding site comparison and similarity searching of a structural proteome. SMAP can also predict drug side effects and reassign existing drugs to new indications. However, the computing scale of SMAP is limited. We have developed a high availability, high performance system that expands the comparison scale of SMAP. This cloud computing service, called Cloud-PLBS, combines the SMAP and Hadoop frameworks and is deployed on a virtual cloud computing platform. To handle the vast amount of experimental data on protein-ligand binding site pairs, Cloud-PLBS exploits the MapReduce paradigm as a management and parallelizing tool. Cloud-PLBS provides a web portal and scalability through which biologists can address a wide range of computer-intensive questions in biology and drug discovery. PMID:23762824

  10. Industrial Computed Tomography using Proximal Algorithm

    KAUST Repository

    Zang, Guangming

    2016-04-14

    In this thesis, we present ProxiSART, a flexible proximal framework for robust 3D cone beam tomographic reconstruction based on the Simultaneous Algebraic Reconstruction Technique (SART). We derive the proximal operator for the SART algorithm and use it for minimizing the data term in a proximal algorithm. We show the flexibility of the framework by plugging in different powerful regularizers, and show its robustness in achieving better reconstruction results in the presence of noise and using fewer projections. We compare our framework to state-of-the-art methods and existing popular software tomography reconstruction packages, on both synthetic and real datasets, and show superior reconstruction quality, especially from noisy data and a small number of projections.

  11. Correlation between social proximity and mobility similarity.

    Science.gov (United States)

    Fan, Chao; Liu, Yiding; Huang, Junming; Rong, Zhihai; Zhou, Tao

    2017-09-20

    Human behaviors exhibit ubiquitous correlations in many aspects, such as individual and collective levels, temporal and spatial dimensions, content, social and geographical layers. With rich Internet data of online behaviors becoming available, it attracts academic interests to explore human mobility similarity from the perspective of social network proximity. Existent analysis shows a strong correlation between online social proximity and offline mobility similarity, namely, mobile records between friends are significantly more similar than between strangers, and those between friends with common neighbors are even more similar. We argue the importance of the number and diversity of common friends, with a counter intuitive finding that the number of common friends has no positive impact on mobility similarity while the diversity plays a key role, disagreeing with previous studies. Our analysis provides a novel view for better understanding the coupling between human online and offline behaviors, and will help model and predict human behaviors based on social proximity.

  12. [Disorders of sex development and proximal hypospadias].

    Science.gov (United States)

    Oswald, J

    2016-01-01

    Children with ambiguous genitalia due to different chromosome or gonadal sex are a particular challenge concerning the diagnostic and therapeutic implications. Proximal hypospadias patients with normal gonadal development should be distinguished from children with DSD (disorders of sex development) to guarantee normal gender identity and the best possible surgical therapy. This paper focuses on the terminology, embryology, and pathophysiology of the different manifestations of DSD. The state of knowledge about this disease pattern with particular emphasis on proximal hypospadias based on national and international scientific discussions is presented. The different clinical pictures as well as therapeutic options of DSD with a special focus on recent literature and giving particular attention to patients with proximal hypospadias are presented. Because of the complexity of patients suffering from disorders of sex development an interdisciplinary DSD healthcare team including a paediatric endocrinologist as well as paediatric urologist should be provided. These specialists enable an accurate diagnosis in severe hypospadias patients without reference to DSD diseases patterns.

  13. Infiltrating/sealing proximal caries lesions

    DEFF Research Database (Denmark)

    Martignon, S; Ekstrand, K R; Gomez, J

    2012-01-01

    This randomized split-mouth controlled clinical trial aimed at assessing the therapeutic effects of infiltration vs. sealing for controlling caries progression on proximal surfaces. Out of 90 adult students/patients assessed at university clinics and agreeing to participate, 39, each with 3...... differences in lesion progression between infiltration and placebo (P = 0.0012) and between sealing and placebo (P = 0.0269). The study showed that infiltration and sealing are significantly better than placebo treatment for controlling caries progression on proximal lesions. No significant difference...... proximal lesions identified radiographically around the enamel-dentin junction to the outer third of the dentin, were included. Lesions were randomly allocated for treatment to test-A (Infiltration: ICON-pre-product; DMG), test-B (Sealing: Prime-Bond-NT; Dentsply), or control-C (Placebo). Primary outcome...

  14. Singular Value Decomposition and Ligand Binding Analysis

    Directory of Open Access Journals (Sweden)

    André Luiz Galo

    2013-01-01

    Full Text Available Singular values decomposition (SVD is one of the most important computations in linear algebra because of its vast application for data analysis. It is particularly useful for resolving problems involving least-squares minimization, the determination of matrix rank, and the solution of certain problems involving Euclidean norms. Such problems arise in the spectral analysis of ligand binding to macromolecule. Here, we present a spectral data analysis method using SVD (SVD analysis and nonlinear fitting to determine the binding characteristics of intercalating drugs to DNA. This methodology reduces noise and identifies distinct spectral species similar to traditional principal component analysis as well as fitting nonlinear binding parameters. We applied SVD analysis to investigate the interaction of actinomycin D and daunomycin with native DNA. This methodology does not require prior knowledge of ligand molar extinction coefficients (free and bound, which potentially limits binding analysis. Data are acquired simply by reconstructing the experimental data and by adjusting the product of deconvoluted matrices and the matrix of model coefficients determined by the Scatchard and McGee and von Hippel equation.

  15. THERMODYNAMIC ASSESSMENT OF ANIONIC LIGANDS ...

    African Journals Online (AJOL)

    DJFLEX

    2010-06-30

    Jun 30, 2010 ... ion. This brings about repulsion between the adsorbent and positively charged ion and consequently a reduction in the amount of heavy metal adsorbed at lower pH. (Lee, 1999). The effectiveness of the anionic ligands in the removal of heavy metal ions from aqueous solution seems to be low for the EDTA.

  16. Major Histocompatibility Complex Class I Molecules Modulate Activation Threshold and Early Signaling of T Cell Antigen Receptor–γ/δ Stimulated by Nonpeptidic Ligands

    Science.gov (United States)

    Carena, Ilaria; Shamshiev, Abdijapar; Donda, Alena; Colonna, Marco; Libero, Gennaro De

    1997-01-01

    Killer cell inhibitory receptors and CD94-NKG2-A/B heterodimers are major histocompatibility complex class I–specific inhibitory receptors expressed by natural killer cells, T cell antigen receptor (TCR)-γ/δ cells, and a subset of TCR-α/β cells. We studied the functional interaction between TCR-γ/δ and CD94, this inhibitory receptor being expressed on the majority of γ/δ T cells. When engaged by human histocompatibility leukocyte antigen class I molecules, CD94 downmodulates activation of human TCR-γ/δ by phosphorylated ligands. CD94-mediated inhibition is more effective at low than at high doses of TCR ligand, which may focus T cell responses towards antigen-presenting cells presenting high amounts of antigen. CD94 engagement has major effects on TCR signaling cascade. It facilitates recruitment of SHP-1 phosphatase to TCR–CD3 complex and affects phosphorylation of Lck and ZAP-70 kinase, but not of CD3 ζ chain upon TCR triggering. These events may cause abortion of proximal TCR-mediated signaling and set a higher TCR activation threshold. PMID:9362537

  17. The developmental spectrum of proximal radioulnar synostosis

    Energy Technology Data Exchange (ETDEWEB)

    Elliott, Alison M. [University of Manitoba, Winnipeg Regional Health Association Program of Genetics and Metabolism, Winnipeg, MB (Canada); University of Manitoba, Department of Paediatrics and Child Health, Winnipeg, MB (Canada); University of Manitoba, Department of Biochemistry and Medical Genetics, Winnipeg, MB (Canada); University of Manitoba, WRHA Program of Genetics and Metabolism, Departments of Paediatrics and Child Health, Biochemistry and Medical Genetics, Winnipeg, MB (Canada); Kibria, Lisa [University of Manitoba, Department of School of Medical Rehabilitation, Winnipeg, MB (Canada); Reed, Martin H. [University of Manitoba, Department of Paediatrics and Child Health, Winnipeg, MB (Canada); University of Manitoba, Department of Biochemistry and Medical Genetics, Winnipeg, MB (Canada); University of Manitoba, Department of Diagnostic Imaging, Winnipeg, MB (Canada)

    2010-01-15

    Proximal radioulnar synostosis is a rare upper limb malformation. The elbow is first identifiable at 35 days (after conception), at which stage the cartilaginous anlagen of the humerus, radius and ulna are continuous. Subsequently, longitudinal segmentation produces separation of the distal radius and ulna. However, temporarily, the proximal ends are united and continue to share a common perichondrium. We investigated the hypothesis that posterior congenital dislocation of the radial head and proximal radioulnar fusion are different clinical manifestations of the same primary developmental abnormality. Records were searched for ''proximal radioulnar fusion/posterior radial head dislocation'' in patients followed at the local Children's Hospital and Rehabilitation Centre for Children. Relevant radiographic, demographic and clinical data were recorded. Ethics approval was obtained through the University Research Ethics Board. In total, 28 patients met the inclusion criteria. The majority of patients (16) had bilateral involvement; eight with posterior dislocation of the radial head only; five had posterior radial head dislocation with radioulnar fusion and two had radioulnar fusion without dislocation. One patient had bilateral proximal radioulnar fusion and posterior dislocation of the left radial head. Nine patients had only left-sided involvement, and three had only right-sided involvement.The degree of proximal fusion varied, with some patients showing 'complete' proximal fusion and others showing fusion that occurred slightly distal to the radial head: 'partially separated.' Associated disorders in our cohort included Poland syndrome (two patients), Cornelia de Lange syndrome, chromosome anomalies (including tetrasomy X) and Cenani Lenz syndactyly. The suggestion of a developmental relationship between posterior dislocation of the radial head and proximal radioulnar fusion is supported by the fact that both anomalies

  18. Ligand-specific homology modeling of human cannabinoid (CB1) receptor.

    Science.gov (United States)

    Ai, Rizi; Chang, Chia-en A

    2012-09-01

    Cannabinoid (CB1) receptor is a therapeutic drug target, and its structure and conformational changes after ligand binding are of great interest. To study the protein conformations in ligand bound state and assist in drug discovery, CB1 receptor homology models are needed for computer-based ligand screening. The known CB1 ligands are highly diverse structurally, so CB1 receptor may undergo considerable conformational changes to accept different ligands, which is challenging for molecular docking methods. To account for the flexibility of CB1 receptor, we constructed four CB1 receptor models based on four structurally distinct ligands, HU-210, ACEA, WIN55212-2 and SR141716A, using the newest X-ray crystal structures of human β₂ adrenergic receptor and adenosine A(2A) receptor as templates. The conformations of these four CB1-ligand complexes were optimized by molecular dynamics (MD) simulations. The models revealed interactions between CB1 receptor and known binders suggested by experiments and could successfully discriminate known ligands and non-binders in our docking assays. MD simulations were used to study the most flexible ligand, ACEA, in its free and bound states to investigate structural mobility achieved by the rearrangement of the fatty acid chain. Our models may capture important conformational changes of CB1 receptor to help improve accuracy in future CB1 drug screening. Copyright © 2012 Elsevier Inc. All rights reserved.

  19. Size and ligand effects on the electrochemical and spectroelectrochemical responses of CdSe nanocrystals.

    Science.gov (United States)

    Querner, Claudia; Reiss, Peter; Sadki, Said; Zagorska, Malgorzata; Pron, Adam

    2005-09-07

    The electrochemical properties of CdSe quantum dots with electrochemically inactive surface ligands (TOPO) have been investigated in comparison with the analogous nanocrystals containing electrochemically active oligoaniline ligands. The TOPO-capped nanocrystals have been studied in a wide size range (from 3 to 6.5 nm) with the goal to amplify the influence of the quantum confinement effect on the electrochemical response. The determined HOMO and LUMO levels have been found in good agreement with the ones obtained from photoluminescence studies and those predicted theoretically. Ligand exchange with aniline tetramer significantly influences the voltammetric peaks associated with the HOMO oxidation and the LUMO reduction of the quantum dots, which are shifted to higher and lower potentials, respectively. These shifts are interpreted in terms of the positive ligand charging which precedes the oxidation of the nanocrystals and the insulating nature of the ligand in the case of the nanocrystal reduction. The ligand-nanocrystal interactions have also been studied by UV-Vis-NIR and Raman spectroelectrochemistry in comparison with a specially prepared model compound which, apart from the anchoring function is identical to the grafted oligoaniline ligand. Both spectroelectrochemical techniques clearly indicate the same nature of the oxidation/reduction pathway for both the model compound and the grafted ligand. The influence of the grafting is manifested by a shift in the onset of the ligand oxidation as compared to the case of the "free" model compound. Since both components (ligands and nanocrystals) mutually influence their electrochemical and spectroelectrochemical properties, the newly developed system can be considered as a true molecular hybrid. Such hybrids are of interest because the potential zone of the ligand electroactivity is well separated from that of the nanocrystals and, as a result, the organic part can be electrochemically switched between the

  20. Ligand-controlled interaction of histone acetyltransferase binding to ORC-1 (HBO1) with the N-terminal transactivating domain of progesterone receptor induces steroid receptor coactivator 1-dependent coactivation of transcription

    NARCIS (Netherlands)

    M. Georgiakaki (Maria); L.J. Blok (Leen); R. Milgrom (Roni); M. Lombès (Marc); A. Guiochon-Mantel (Anne); H. Loosfelt (Hugues); N. Chabbert-Buffet (Nathalie); B. Dasen (Boris); G. Meduri (Geri); S. Wenk (Sandra); L. Rajhi (Leila); L. Amazit (Larbi); A. Chauchereau (Anne); C.W. Burger (Curt)

    2006-01-01

    textabstractModulators of cofactor recruitment by nuclear receptors are expected to play an important role in the coordination of hormone-induced transactivation processes. To identify such factors interacting with the N-terminal domain (NTD) of the progesterone receptor (PR), we used this domain as

  1. Structural basis for alcohol modulation of a pentameric ligand-gated ion channel

    Science.gov (United States)

    Howard, Rebecca J.; Murail, Samuel; Ondricek, Kathryn E.; Corringer, Pierre-Jean; Lindahl, Erik; Trudell, James R.; Harris, R. Adron

    2011-01-01

    Despite its long history of use and abuse in human culture, the molecular basis for alcohol action in the brain is poorly understood. The recent determination of the atomic-scale structure of GLIC, a prokaryotic member of the pentameric ligand-gated ion channel (pLGIC) family, provides a unique opportunity to characterize the structural basis for modulation of these channels, many of which are alcohol targets in brain. We observed that GLIC recapitulates bimodal modulation by n-alcohols, similar to some eukaryotic pLGICs: methanol and ethanol weakly potentiated proton-activated currents in GLIC, whereas n-alcohols larger than ethanol inhibited them. Mapping of residues important to alcohol modulation of ionotropic receptors for glycine, γ-aminobutyric acid, and acetylcholine onto GLIC revealed their proximity to transmembrane cavities that may accommodate one or more alcohol molecules. Site-directed mutations in the pore-lining M2 helix allowed the identification of four residues that influence alcohol potentiation, with the direction of their effects reflecting α-helical structure. At one of the potentiation-enhancing residues, decreased side chain volume converted GLIC into a highly ethanol-sensitive channel, comparable to its eukaryotic relatives. Covalent labeling of M2 positions with an alcohol analog, a methanethiosulfonate reagent, further implicated residues at the extracellular end of the helix in alcohol binding. Molecular dynamics simulations elucidated the structural consequences of a potentiation-enhancing mutation and suggested a structural mechanism for alcohol potentiation via interaction with a transmembrane cavity previously termed the “linking tunnel.” These results provide a unique structural model for independent potentiating and inhibitory interactions of n-alcohols with a pLGIC family member. PMID:21730162

  2. Structural basis for alcohol modulation of a pentameric ligand-gated ion channel.

    Science.gov (United States)

    Howard, Rebecca J; Murail, Samuel; Ondricek, Kathryn E; Corringer, Pierre-Jean; Lindahl, Erik; Trudell, James R; Harris, R Adron

    2011-07-19

    Despite its long history of use and abuse in human culture, the molecular basis for alcohol action in the brain is poorly understood. The recent determination of the atomic-scale structure of GLIC, a prokaryotic member of the pentameric ligand-gated ion channel (pLGIC) family, provides a unique opportunity to characterize the structural basis for modulation of these channels, many of which are alcohol targets in brain. We observed that GLIC recapitulates bimodal modulation by n-alcohols, similar to some eukaryotic pLGICs: methanol and ethanol weakly potentiated proton-activated currents in GLIC, whereas n-alcohols larger than ethanol inhibited them. Mapping of residues important to alcohol modulation of ionotropic receptors for glycine, γ-aminobutyric acid, and acetylcholine onto GLIC revealed their proximity to transmembrane cavities that may accommodate one or more alcohol molecules. Site-directed mutations in the pore-lining M2 helix allowed the identification of four residues that influence alcohol potentiation, with the direction of their effects reflecting α-helical structure. At one of the potentiation-enhancing residues, decreased side chain volume converted GLIC into a highly ethanol-sensitive channel, comparable to its eukaryotic relatives. Covalent labeling of M2 positions with an alcohol analog, a methanethiosulfonate reagent, further implicated residues at the extracellular end of the helix in alcohol binding. Molecular dynamics simulations elucidated the structural consequences of a potentiation-enhancing mutation and suggested a structural mechanism for alcohol potentiation via interaction with a transmembrane cavity previously termed the "linking tunnel." These results provide a unique structural model for independent potentiating and inhibitory interactions of n-alcohols with a pLGIC family member.

  3. Synthesis and characterization of two manganese(II) complexes containing di(4-pyridyl)sulfide (4-DPS) ligand: The effects of the counter ion and of the weak non-covalent interactions in the crystal structures of [Mn(4-DPS) 4(H 2O) 2](ClO 4) 2·H 2O and {[Mn(4-DPS) 2(NCS) 2] ·2H 2O} n

    Science.gov (United States)

    Marinho, Maria Vanda; Yoshida, Maria Irene; Krambrock, Klaus; De Oliveira, Luiz Fernando C.; Diniz, Renata; Machado, Flávia C.

    2009-04-01

    From the reaction between the metallic precursor Mn(ClO 4) 2·6H 2O and the flexible ligand di(4-pyridyl)sulfide (4-DPS) a mononuclear complex [Mn(4-DPS) 4(H 2O) 2](ClO 4) 2·H 2O ( 1) was obtained, while the reaction of MnCl 2·4H 2O with 4-DPS and KSCN afforded a neutral 1-D coordination polymer namely {[Mn(4-DPS) 2(NCS) 2] ·2H 2O} n ( 2). Compounds ( 1) and ( 2) were characterized by means of elemental analysis, thermal analysis (TG/DTA), vibrational (IR and Raman) and electron paramagnetic resonance (EPR) spectroscopies. Additionally, single-crystal X-ray diffraction analysis shows that in ( 1) the 4-DPS ligand acts in the monodentate coordination mode while in ( 2) it exhibits bridging coordination mode. The crystal structure of both compounds shows that each Mn 2+ adopts a distorted octahedral geometry in which the equatorial planes contain four nitrogen atoms from different 4-DPS ligands. In ( 1), the axial positions are occupied by two oxygen atoms from two water molecules and in ( 2) by two other nitrogen atoms from two isothiocyanate groups. The supramolecular array observed in ( 1) was achieved through hydrogen-bonding and π-π interactions and in ( 2) the 1-D doubled stranded polymeric chain is extended by metal-ligand interaction. EPR spectra for both compounds are consistent with the X-ray structures containing isolated Mn 2+ ions in distorted octahedral arrangements with very weak anti-ferromagnetic coupling.

  4. -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.

  5. preliminary phytochemical screening, proximate and elemental

    African Journals Online (AJOL)

    DR. AMINU

    ABSTRACT. The seed powder of Moringa oleifera was analysed for its phytochemical, proximate and elemental composition using Folin-Denis spectrophotometric method, gravimetric method and energy dispersing X-ray fluorescence (EDXRF) transmission emission technique respectively. The seed powder had the ...

  6. Proximate, mineral composition, antioxidant activity, and total ...

    African Journals Online (AJOL)

    Four varieties of the red pepper fruits (Capsicum species) were evaluated for chemical composition, antioxidant activity and total phenolic contents using standard analytical technique, ferric-ion reducing antioxidant potential (FRAP) assay and Folin-Colcalteau method respectively. The proximate composition values ...

  7. 9__43 - 50__Tijjani_Proximate

    African Journals Online (AJOL)

    User

    Sena et al., 1998). In Nigeria, the plant is commonly consumed by the Hausa speaking communities as a spice and a sauce (Ibrahim et al., 2012). However, during preparation the leaves and stem are not carefully separated before processing of food. Thus, the present study was aimed at evaluating the proximate, minerals ...

  8. Phytochemistry and proximate composition of ginger ( Zingiber ...

    African Journals Online (AJOL)

    ... a little crude fibre content of 0.92 %. The results indicated that ginger rhizome is an excellent natural remedy for a wide range of ailments. Keywords: Zingiber officinale, spice, rhizome, phytochemistry, proximate analysis, Zingiberaceae, zingerone, methanolic extraction. Journal of Pharmaceutical and Allied Sciences, Vol.

  9. DEPRESSIONARY EFFECT OF PROXIMITY OF RESIDENTIAL ...

    African Journals Online (AJOL)

    Osondu

    2012-10-24

    Oct 24, 2012 ... opinions are analyzed and it revealed that the site has major impacts on the residents perceived quality of life, security and ... Key words: Landfill, Property value, Health and safety, Residential property, Solous. Introduction. The location ... Proximity to landfills and hazardous waste sites can severely affect ...

  10. Renal fibrosis: Primacy of the proximal tubule.

    Science.gov (United States)

    Gewin, Leslie S

    2018-02-06

    Tubulointerstitial fibrosis (TIF) is the hallmark of chronic kidney disease and best predictor of renal survival. Many different cell types contribute to TIF progression including tubular epithelial cells, myofibroblasts, endothelia, and inflammatory cells. Previously, most of the attention has centered on myofibroblasts given their central importance in extracellular matrix production. However, emerging data focuses on how the response of the proximal tubule, a specialized epithelial segment vulnerable to injury, plays a central role in TIF progression. Several proximal tubular responses such as de-differentiation, cell cycle changes, autophagy, and metabolic changes may be adaptive initially, but can lead to maladaptive responses that promote TIF both through autocrine and paracrine effects. This review discusses the current paradigm of TIF progression and the increasingly important role of the proximal tubule in promoting TIF both in tubulointerstitial and glomerular injuries. A better understanding and appreciation of the role of the proximal tubule in TIF has important implications for therapeutic strategies to halt chronic kidney disease progression. Copyright © 2017 International Society of Matrix Biology. Published by Elsevier B.V. All rights reserved.

  11. 182 179 Comparative Study on the Proximate

    African Journals Online (AJOL)

    2008-12-02

    Dec 2, 2008 ... Key words: Annona squamosa, Fruits, Proximate, Minerals, nutrient density. INTRODUCTION. Sugar apple (Annona squamosa) also called. “Gwanda masar” in Hausa belong to the family. Annonacae. The most widely grown of all the species are A. muricata, A. cherimola, A reticulata, A. senegalensis and ...

  12. Phytochemical Screening, Proximate and Mineral Composition of ...

    African Journals Online (AJOL)

    Leaves of sweet potato (Ipomoea batatas) grown in Tepi area was studied for their class of phytochemicals, mineral and proximate composition using standard analytical methods. The phytochemical screening revealed the presence of alkaloids, flavonoid, terpenoids, saponins, quinones, phenol, tannins, amino acid and ...

  13. Phytochemical screening, proximate and elemental analysis of ...

    African Journals Online (AJOL)

    Citrus sinensis was screened for its phytochemical composition and was evaluated for the proximate and elemental analysis. The phytochemical analysis indicated the presence of reducing sugar, saponins, cardiac glycosides, tannins and flavonoids. The elemental analysis indicated the presence of the following mineral ...

  14. Phytochemical Screening and Proximate Analysis of Newbouldia ...

    African Journals Online (AJOL)

    The study was conducted to assess the phytochemical and proximate composition of Newboudia laevis leaves and Allium sativum bulb extracts. The leaves and bulbs extracts were analyzed for their chemical composition and antinutritional factors (ANFs) which include moisture, crude protein, crude fat, crude fiber, total ash ...

  15. Disability occurrence and proximity to death

    NARCIS (Netherlands)

    Klijs, Bart; Mackenbach, Johan P.; Kunst, Anton E.

    2010-01-01

    Purpose. This paper aims to assess whether disability occurrence is related more strongly to proximity to death than to age. Method. Self reported disability and vital status were available from six annual waves and a subsequent 12-year mortality follow-up of the Dutch GLOBE longitudinal study.

  16. [Four family members with proximal myotonic myopathy

    NARCIS (Netherlands)

    Tieleman, A.A.; Velden, M.P. van der; Visser, M.C.; Wokke, J.H.J.; Scheffer, H.; Engelen, B.G.M. van

    2004-01-01

    A 41-year-old woman had a 15-year history of pain in her thighs and arms, which also became weaker, and a decrease in visual acuity. Her 35-year-old brother, their 38-year-old sister and their 64-year-old mother also had myalgia, myotonia and proximal muscle weakness, and the women also had

  17. Phytochemical screening, proximate and elemental analysis of ...

    African Journals Online (AJOL)

    ... was about 0.01 in concentration. Proximate analysis also shows that it has a high nutritional value such as carbohydrate, fibre, Ash, fat and protein. These results recommended the consumption of these peels of desired physiochemical properties as sources of food fibres or low-calorie bulk ingredients in food applications ...

  18. Proximate composition and consumer acceptability of African ...

    African Journals Online (AJOL)

    The aim of the study was to assess the organoleptic differences of Clarias gariepinus smoked with two different energy sources, Anogeissus leiocarpus and Tamarindus indica with the help of a hedonic scale and to determine possible proximate composition difference between the smoked products. Smoking of the fishes ...

  19. Controllable proximity effect in superconducting hybrid devices

    NARCIS (Netherlands)

    Bakurskiy, S.V.

    2015-01-01

    This thesis is devoted to the study of controllable proximity effects in superconductors, both in terms of fundamental aspects and applications. As a part of this thesis theoretical description was suggested for a number of structures with superconducting electrodes and multiple interlayers. These

  20. Proximate, chemical compositions and sulphur concentrations on ...

    African Journals Online (AJOL)

    0, 10, 20, 50, 100, 150, 200, 250 and 300 ppm) on the nutritional value and the proximate composition of six selected mango cultivars (Tommy Atkins, Peach, Saber, Sunshine, Keitt and Vhavenda) grown in South Africa. The study shows that ...