WorldWideScience

Sample records for acid molecular switches

  1. Monitoring Gene Expression In Vivo with Nucleic Acid Molecular Switches

    David C. Ward; Patricia Bray-Ward

    2005-01-26

    The overall objectives of this project were (1) to develop allosteric ribozymes capable of acting as molecular switches for monitoring the levels of both wild-type and mutant mRNA species in living cells and whole animals and (2) to develop highly efficient reagents to deliver nucleic acid molecular switches into living cells, tissues and animals with the ultimate goal of expression profiling specific mRNAs of diagnostic or prognostic value within tumors in animals. During the past year, we have moved our laboratory to Nevada and in the moving process we have lost electronic and paper copies of prior progress reports concerning the construction and biological properties of the molecular switches. Since there was minimal progress during the last year on molecular switches, we are relying on past project reports to provide a summary of our data on this facet of the grant. Here we are summarizing the work done on the delivery reagents and their application to inducing mutations in living cells, which will include work done during the no cost extension.

  2. Molecular Rotors as Switches

    Kang L. Wang

    2012-08-01

    Full Text Available The use of a functional molecular unit acting as a state variable provides an attractive alternative for the next generations of nanoscale electronics. It may help overcome the limits of conventional MOSFETd due to their potential scalability, low-cost, low variability, and highly integratable characteristics as well as the capability to exploit bottom-up self-assembly processes. This bottom-up construction and the operation of nanoscale machines/devices, in which the molecular motion can be controlled to perform functions, have been studied for their functionalities. Being triggered by external stimuli such as light, electricity or chemical reagents, these devices have shown various functions including those of diodes, rectifiers, memories, resonant tunnel junctions and single settable molecular switches that can be electronically configured for logic gates. Molecule-specific electronic switching has also been reported for several of these device structures, including nanopores containing oligo(phenylene ethynylene monolayers, and planar junctions incorporating rotaxane and catenane monolayers for the construction and operation of complex molecular machines. A specific electrically driven surface mounted molecular rotor is described in detail in this review. The rotor is comprised of a monolayer of redox-active ligated copper compounds sandwiched between a gold electrode and a highly-doped P+ Si. This electrically driven sandwich-type monolayer molecular rotor device showed an on/off ratio of approximately 104, a read window of about 2.5 V, and a retention time of greater than 104 s. The rotation speed of this type of molecular rotor has been reported to be in the picosecond timescale, which provides a potential of high switching speed applications. Current-voltage spectroscopy (I-V revealed a temperature-dependent negative differential resistance (NDR associated with the device. The analysis of the device

  3. Molecular current switch

    Nešpůrek, Stanislav; Sworakowski, J.

    Brno : Faculty of Chemistry, Brno University of Technology, 2002 - (Schauer, F.), s. 89-96 ISBN 80-214-2265-3. [Seminar on Physics and Chemistry of Molecular Systems /7./. Brno (CZ), 13.12.2001] R&D Projects: GA AV ČR IAA1050901; GA ČR GA202/01/0518 Institutional research plan: CEZ:AV0Z4050913 Keywords : current switch * local states * dipolar species Subject RIV: BM - Solid Matter Physics ; Magnetism

  4. A Novel Molecular Switch

    Daber, Robert; Lewis, Mitchell

    2009-01-01

    Transcriptional regulation is a fundamental process for regulating the flux of all metabolic pathways. For the last several decades, the lac operon has served as a valuable model for studying transcription. More recently, the switch that controls the operon has also been successfully adapted to function in mammalian cells. Here we describe how, using directed evolution, we have created a novel switch that recognizes an asymmetric operator sequence. The new switch has a repressor with altered ...

  5. The Smallest Molecular Switch

    Emberly, Eldon G.; Kirczenow, George

    2003-01-01

    Ab-initio total energy calculations reveal benzene-dithiolate (BDT) molecules on a gold surface, contacted by a monoatomic gold STM tip to have two classes of low energy conformations with differing symmetries. Lateral motion of the tip or excitation of the molecule cause it to change from one conformation class to the other and to switch between a strongly and a weakly conducting state. Thus, surprisingly, despite their apparent simplicity these Au/BDT/Au nanowires are shown to be electrical...

  6. Switching in molecular systems

    Nešpůrek, Stanislav; Wang, Geng; Sworakowski, J.

    Lanškroun : IMAPS, Brno University of Technology, 2004 - (Šikula, J.), s. 215-220 ISBN 80-239-2835-X. [European Microelectronics and Packaging Symposium /3./. Prague (CZ), 16.06.2004-18.06.2004] R&D Projects: GA MŠk OC D14.30 Institutional research plan: CEZ:AV0Z4050913 Keywords : poly[3,4-(ethylenedioxy)thiophene] * electrical conductivity * charge carrier transport Subject RIV: BG - Nuclear, Atomic and Molecular Physics, Colliders

  7. An acidic loop and cognate phosphorylation sites define a molecular switch that modulates ubiquitin charging activity in Cdc34-like enzymes.

    Elena Papaleo

    2011-05-01

    Full Text Available E2 ubiquitin-conjugating enzymes are crucial mediators of protein ubiquitination, which strongly influence the ultimate fate of the target substrates. Recently, it has been shown that the activity of several enzymes of the ubiquitination pathway is finely tuned by phosphorylation, an ubiquitous mechanism for cellular regulation, which modulates protein conformation. In this contribution, we provide the first rationale, at the molecular level, of the regulatory mechanism mediated by casein kinase 2 (CK2 phosphorylation of E2 Cdc34-like enzymes. In particular, we identify two co-evolving signature elements in one of the larger families of E2 enzymes: an acidic insertion in β4α2 loop in the proximity of the catalytic cysteine and two conserved key serine residues within the catalytic domain, which are phosphorylated by CK2. Our investigations, using yeast Cdc34 as a model, through 2.5 µs molecular dynamics simulations and biochemical assays, define these two elements as an important phosphorylation-controlled switch that modulates opening and closing of the catalytic cleft. The mechanism relies on electrostatic repulsions between a conserved serine phosphorylated by CK2 and the acidic residues of the β4α2 loop, promoting E2 ubiquitin charging activity. Our investigation identifies a new and unexpected pivotal role for the acidic loop, providing the first evidence that this loop is crucial not only for downstream events related to ubiquitin chain assembly, but is also mandatory for the modulation of an upstream crucial step of the ubiquitin pathway: the ubiquitin charging in the E2 catalytic cleft.

  8. Remotely Controlled Isomer Selective Molecular Switching.

    Schendel, Verena; Borca, Bogdana; Pentegov, Ivan; Michnowicz, Tomasz; Kraft, Ulrike; Klauk, Hagen; Wahl, Peter; Schlickum, Uta; Kern, Klaus

    2016-01-13

    Nonlocal addressing-the "remote control"-of molecular switches promises more efficient processing for information technology, where fast speed of switching is essential. The surface state of the (111) facets of noble metals, a confined two-dimensional electron gas, provides a medium that enables transport of signals over large distances and hence can be used to address an entire ensemble of molecules simultaneously with a single stimulus. In this study we employ this characteristic to trigger a conformational switch in anthradithiophene (ADT) molecules by injection of hot carriers from a scanning tunneling microscope (STM) tip into the surface state of Cu(111). The carriers propagate laterally and trigger the switch in molecules at distances as far as 100 nm from the tip location. The switching process is shown to be long-ranged, fully reversible, and isomer selective, discriminating between cis and trans diastereomers, enabling maximum control. PMID:26619213

  9. MNAzymes, a Versatile New Class of Nucleic Acid Enzymes That Can Function as Biosensors and Molecular Switches

    Mokany, Elisa; Bone, Simon M.; Young, Paul E; Doan, Tram B.; Todd, Alison V.

    2009-01-01

    To increase the versatility and utility of nucleic acid enzymes, we developed multicomponent complexes, known as MNAzymes, which produce amplified “output” signals in response to specific “input” signals. Multiple oligonucleotide partzymes assemble into active MNAzymes only in the presence of an input assembly facilitator such as a target nucleic acid. Once formed, MNAzymes catalytically modify a generic substrate, generating an amplified output signal that heralds the presence of the target ...

  10. Self-consistent theory of molecular switching

    Pistolesi, F; Blanter, Ya. M.; Martin, I.

    2008-01-01

    International audience We study the model of a molecular switch comprised of a molecule with a soft vibrational degree of freedom coupled to metallic leads. In the presence of strong electron-ion interaction, different charge states of the molecule correspond to substantially different ionic configurations, which can lead to very slow switching between energetically close configurations (Franck-Condon blockade). Application of transport voltage, however, can drive the molecule far out of t...

  11. Light-driven molecular current switch

    Nešpůrek, Stanislav; Toman, Petr; Sworakowski, J.; Lipinski, J.

    Seoul: Yonsei University, 2002, s. 279-291. ISBN 89-88706-43-9. [Multilateral Symposium between the Korean Academy of Science and Technology and the Foreign Academies. Seoul (KR), 08.05.2002-10.05.2002] R&D Projects: GA AV ČR IAA1050901 Institutional research plan: CEZ:AV0Z4050913 Keywords : molecular switch * molecular electronics * charge transport Subject RIV: BG - Nuclear, Atomic and Molecular Physics, Colliders

  12. A nanoplasmonic switch based on molecular machines

    Zheng, Yue Bing

    2009-06-01

    We aim to develop a molecular-machine-driven nanoplasmonic switch for its use in future nanophotonic integrated circuits (ICs) that have applications in optical communication, information processing, biological and chemical sensing. Experimental data show that an Au nanodisk array, coated with rotaxane molecular machines, switches its localized surface plasmon resonances (LSPR) reversibly when it is exposed to chemical oxidants and reductants. Conversely, bare Au nanodisks and disks coated with mechanically inert control compounds, do not display the same switching behavior. Along with calculations based on time-dependent density functional theory (TDDFT), these observations suggest that the nanoscale movements within surface-bound "molecular machines" can be used as the active components in plasmonic devices. ©2009 IEEE.

  13. 8-Quinolineboronic acid as a potential phosphorescent molecular switch for the determination of alpha-fetoprotein variant for the prediction of primary hepatocellular carcinoma

    8-Quinolineboronic acid phosphorescent molecular switch (8-QBA-PMS) in the 'off' state emitted weak room temperature phosphorescence (RTP) of 8-QBA on the acetylcellulose membrane (ACM) with the perturbation of Pb2+. When 8-QBA-PMS was used to label concanavalin agglutinin (Con A) to form 8-QBA-PMS-Con A based on the reaction between -OH of 8-QBA-PMS and -COOH of Con A, 8-QBA-PMS turned 'on' automatically due to its structure change, and RTP of the system increased 2.7 times. Besides, -NH2 of 8-QBA-PMS-Con A could carry out affinity adsorption (AA) reaction with the -COOH of alpha-fetoprotein variant (AFP-V) to form the product Con A-AFP-V-Con A-8-QBA-PMS containing -NH-CO- bond, causing the RTP of the system to further increase. Moreover, the amount of AFP-V was linear to the ΔIp of the system in the range of 0.012-2.40 (fg spot-1). Thus, a new affinity sensitive adsorption solid substrate room temperature phosphorimetry using 8-QBA-PMS as labelling reagent (8-QBA-PMS-AASSRTP) for the determination of AFP-V was proposed with the detection limit (LD) of 9 x 10-15 g mL-1. It had been used to determine AFP-V in human serum with the results agreeing with enzyme-link immunoassay (ELISA), showing promise for the prediction of PHC due to the intimate association between AFP-V and primary hepatocellular carcinoma (PHC). The mechanism of the promethod was also discussed.

  14. Light-driven molecular current switch

    Nešpůrek, Stanislav; Toman, Petr; Sworakowski, J.; Lipinski, J.

    2002-01-01

    Roč. 2, č. 4 (2002), s. 299-304. ISSN 1567-1739. [Multilateral Symposium between the Korean Academy of Science and Technology and the Foreign Academies. Seoul, 08.05.2002-10.05.2002] R&D Projects: GA AV ČR IAA1050901 Grant ostatní: GA-(PL) 4T09A 13222 Institutional research plan: CEZ:AV0Z4050913 Keywords : molecular switch * molecular electronics * charge transport Subject RIV: BG - Nuclear, Atomic and Molecular Physics, Colliders Impact factor: 1.117, year: 2002

  15. Active Molecular Plasmonics: Controlling Plasmon Resonances with Molecular Switches

    Zheng, Yue Bing

    2009-02-11

    A gold nanodisk array, coated with bistable, redox-controllable [2]rotaxane molecules, when exposed to chemical oxidants and reductants, undergoes switching of its plasmonic properties reversibly. By contrast, (i) bare gold nanodisks and (ii) disks coated with a redox-active, but mechanically inert, control compound do not display surface-plasmon-based switching. Along with calculations based on time-dependent density functional theory, these experimental observations suggest that the nanoscale movements within surface-bound “molecular machines” can be used as the active components in plasmonic devices.

  16. Molecular machines: stimulation of cation motion in molecular switches

    The theoretical aspects of the mechanism of the motion of cations and ligands in molecular machines referred to as redox switches are presented. The interrelated properties of cations - the energetic, electrochemical, spectral, and magnetic properties; their propensity to form either covalent or ionic bonds; and the relative softness and hardness of cations and ligands - stimulate molecular motion. These properties determine the thermal stability and stability to destruction caused by electrochemical processes and, eventually, the maximal number of transformation cycles. The maximal efficiency of redox switches is attained when the redox reaction involves a cation with a half-filled (d5, f7) or complete (d10, f14) electronic shell. The role of the Jahn-Teller effect is considered: it is responsible for geometry distortion, which stimulates cation motion. The properties of nd- and 4f-block cations are compared from the standpoint of their use for designing redox switches. In switches constructed on the basis of supramolecular compounds containing hard and soft moieties, softer cations (Fe2+, Co2+, Cu+, etc.) prefer to coordinate to soft ligands and harder cations (Fe3+, Co3+, Cu2+, etc.) prefer to coordinate to hard ligands. A cation moves due to the soft-hard change of its coordination sphere in the course of the redox reaction. Design of redox switches based on solid compounds with a cation in mixed oxidation state is shown to be promising. Cations can change their oxidation state with a change in temperature or pressure. The possibility of designing magnetic switches is considered

  17. An acidic loop and cognate phosphorylation sites define a molecular switch that modulates ubiquitin charging activity in Cdc34-like enzymes

    Papaleo, Elena; Ranzani, Valeria; Tripodi, Farida; Vitriolo, Alessandro; Cirulli, Claudia; Fantucci, Piercarlo; Alberghina, Lilia; Vanoni, Marco; De Gioia, Luca; Coccetti, Paola

    2011-01-01

    mechanism for cellular regulation, which modulates protein conformation. In this contribution, we provide the first rationale, at the molecular level, of the regulatory mechanism mediated by casein kinase 2 (CK2) phosphorylation of E2 Cdc34-like enzymes. In particular, we identify two co-evolving signature...... elements in one of the larger families of E2 enzymes: an acidic insertion in β4α2 loop in the proximity of the catalytic cysteine and two conserved key serine residues within the catalytic domain, which are phosphorylated by CK2. Our investigations, using yeast Cdc34 as a model, through 2.5 µs molecular...

  18. Determination of trace alkaline phosphatase by affinity adsorption solid substrate room temperature phosphorimetry based on wheat germ agglutinin labeled with 8-quinolineboronic acid phosphorescent molecular switch and prediction of diseases

    Liu, Jia-Ming; Gao, Hui; Li, Fei-Ming; Shi, Xiu-Mei; Lin, Chang-Qing; Lin, Li-Ping; Wang, Xin-Xing; Li, Zhi-Ming

    2010-09-01

    The 8-quinolineboronic acid phosphorescent molecular switch (abbreviated as PMS-8-QBA. Thereinto, 8-QBA is 8-quinolineboronic acid, and PMS is phosphorescent molecular switch) was found for the first time. PMS-8-QBA, which was in the "off" state, could only emit weak room temperature phosphorescence (RTP) on the acetyl cellulose membrane (ACM). However, PMS-8-QBA turned "on" automatically for its changed structure, causing that the RTP of 8-QBA in the system increased, after PMS-8-QBA-WGA (WGA is wheat germ agglutinin) was formed by reaction between -OH of PMS-8-QBA and -COOH of WGA. More interesting is that the -NH 2 of PMS-8-QBA-WGA could react with the -COOH of alkaline phosphatase (AP) to form the affinity adsorption (AA) product WGA-AP-WGA-8-QBA-PMS (containing -NH-CO- bond), which caused RTP of the system to greatly increase. Thus, affinity adsorption solid substrate room temperature phosphorimetry using PMS-8-QBA as labelling reagent (PMS-8-QBA-AA-SSRTP) for the determination of trace AP was established. The method had many advantages, such as high sensitivity (the detection limit (LD) was 2.5 zg spot -1. For sample volume of 0.40 μl spot -1, corresponding concentration was 6.2 × 10 -18 g ml -1), good selectivity (the allowed concentration of coexisting material was higher, when the relative error was ±5%), high accuracy (applied to detection of AP content in serum samples, the result was coincided with those obtained by enzyme-linked immunoassay), which was suitable for the detection of trace AP content in serum samples and the forecast of human diseases. Meanwhile, the mechanism of PMS-8-QBA-AASSRTP was discussed. The new field of analytical application and clinic diagnosis technique of molecule switch are exploited, based on the phosphorescence characteristic of PMS-8-QBA, the AA reaction between WGA and AP, as well as the relation between AP content and human diseases. The research results promote the development and interpenetrate among molecule

  19. Tunneling Nanoelectromechanical Switches Based on Compressible Molecular Thin Films.

    Niroui, Farnaz; Wang, Annie I; Sletten, Ellen M; Song, Yi; Kong, Jing; Yablonovitch, Eli; Swager, Timothy M; Lang, Jeffrey H; Bulović, Vladimir

    2015-08-25

    Abrupt switching behavior and near-zero leakage current of nanoelectromechanical (NEM) switches are advantageous properties through which NEMs can outperform conventional semiconductor electrical switches. To date, however, typical NEMs structures require high actuation voltages and can prematurely fail through permanent adhesion (defined as stiction) of device components. To overcome these challenges, in the present work we propose a NEM switch, termed a "squitch," which is designed to electromechanically modulate the tunneling current through a nanometer-scale gap defined by an organic molecular film sandwiched between two electrodes. When voltage is applied across the electrodes, the generated electrostatic force compresses the sandwiched molecular layer, thereby reducing the tunneling gap and causing an exponential increase in the current through the device. The presence of the molecular layer avoids direct contact of the electrodes during the switching process. Furthermore, as the layer is compressed, the increasing surface adhesion forces are balanced by the elastic restoring force of the deformed molecules which can promote zero net stiction and recoverable switching. Through numerical analysis, we demonstrate the potential of optimizing squitch design to enable large on-off ratios beyond 6 orders of magnitude with operation in the sub-1 V regime and with nanoseconds switching times. Our preliminary experimental results based on metal-molecule-graphene devices suggest the feasibility of the proposed tunneling switching mechanism. With optimization of device design and material engineering, squitches can give rise to a broad range of low-power electronic applications. PMID:26244821

  20. Arylazopyrazoles as Light-Responsive Molecular Switches in Cyclodextrin-Based Supramolecular Systems.

    Stricker, Lucas; Fritz, Eva-Corinna; Peterlechner, Martin; Doltsinis, Nikos L; Ravoo, Bart Jan

    2016-04-01

    A simple and high yield synthesis of water-soluble arylazopyrazoles (AAPs) featuring superior photophysical properties is reported. The introduction of a carboxylic acid allows the diverse functionalization of AAPs. Based on structural modifications of the switching unit the photophysical properties of the AAPs could be tuned to obtain molecular switches with favorable photostationary states. Furthermore, AAPs form stable and light-responsive host-guest complexes with β-cyclodextrin (β-CD). Our most efficient AAP shows binding affinities comparable to azobenzenes, but more effective switching and higher thermal stability of the Z-isomer. As a proof-of-principle, we investigated two CD-based supramolecular systems, containing either cyclodextrin vesicles (CDVs) or cyclodextrin-functionalized gold nanoparticles (CDAuNPs), which revealed excellent reversible, light-responsive aggregation and dispersion behavior. To conclude, AAPs have great potential to be incorporated as molecular switches in highly demanding and multivalent photoresponsive systems. PMID:26972671

  1. Switching Molecular Orientation of Individual Fullerene at Room Temperature

    Liu, Lacheng; Liu, Shuyi; Chen, Xiu; Li, Chao; Ling, Jie; Liu, Xiaoqing; Cai, Yingxiang; Wang, Li

    2013-01-01

    Reversible molecular switches with molecular orientation as the information carrier have been achieved on individual fullerene molecules adsorbed on Si (111) surface at room temperature. Scanning tunneling microscopy imaging directly demonstrates that the orientation of individual fullerene with an adsorption geometry of 5-6 bond is rotated by integral times as 30 degree after a pulse bias is applied between the STM tip and the molecule. Dependences of the molecular rotation probability on th...

  2. An Acidic Loop and Cognate Phosphorylation Sites Define a Molecular Switch That Modulates Ubiquitin Charging Activity in Cdc34-Like Enzymes

    Papaleo, Elena; Ranzani, Valeria; Tripodi, Farida; Vitriolo, Alessandro; Cirulli, Claudia; Fantucci, Piercarlo; Alberghina, Lilia; Vanoni, Marco; De Gioia, Luca; Coccetti, Paola

    2011-01-01

    E2 ubiquitin-conjugating enzymes are crucial mediators of protein ubiquitination, which strongly influence the ultimate fate of the target substrates. Recently, it has been shown that the activity of several enzymes of the ubiquitination pathway is finely tuned by phosphorylation, an ubiquitous mechanism for cellular regulation, which modulates protein conformation. In this contribution, we provide the first rationale, at the molecular level, of the regulatory mechanism mediated by casein kin...

  3. Single-walled carbon nanotube based molecular switch tunnel junctions.

    Diehl, Michael R; Steuerman, David W; Tseng, Hsian-Rong; Vignon, Scott A; Star, Alexander; Celestre, Paul C; Stoddart, J Fraser; Heath, James R

    2003-12-15

    This article describes two-terminal molecular switch tunnel junctions (MSTJs) which incorporate a semiconducting, single-walled carbon nanotube (SWNT) as the bottom electrode. The nanotube interacts noncovalently with a monolayer of bistable, nondegenerate [2]catenane tetracations, self-organized by their supporting amphiphilic dimyristoylphosphatidyl anions which shield the mechanically switchable tetracations from a two-micrometer wide metallic top electrode. The resulting 0.002 micron 2 area tunnel junction addresses a nanometer wide row of approximately 2000 molecules. Active and remnant current-voltage measurements demonstrated that these devices can be reconfigurably switched and repeatedly cycled between high and low current states under ambient conditions. Control compounds, including a degenerate [2]catenane, were explored in support of the mechanical origin of the switching signature. These SWNT-based MSTJs operate like previously reported silicon-based MSTJs, but differently from similar devices incorporating bottom metal electrodes. The relevance of these results with respect to the choice of electrode materials for molecular electronics devices is discussed. PMID:14714382

  4. Simple technique for sequential Q-switching of molecular lasers.

    Lucht, R. A.; Allario, F.; Jarrett, O., Jr.

    1972-01-01

    A simple technique for sequentially Q-switching molecular lasers is discussed in which an optical scanner is used as an optical folding element in a laser cavity consisting of a stationary diffraction grating and partially reflecting mirror. Sequential Q-switching of a conventional CO2 laser is demonstrated in which over sixty-two transitions between 9.2 and 10.8 microns are observed. Rapid repetition rates (200 Hz) and narrow laser pulses (less than 5 microsec) allow conventional signal processing techniques to be used with this multiwavelength laser source which is a versatile tool for laser propagation studies, absorption spectroscopy, and gain measurements. Results of a preliminary experiment demonstrating the utility of measuring selective absorption of CO2 laser wavelengths by C2H4 are shown.

  5. Light-Triggered Control of Plasmonic Refraction and Group Delay by Photochromic Molecular Switches

    Großmann, Malte; Klick, Alwin; Lemke, Christoph; Falke, Julian; Black, Maximilian; Fiutowski, Jacek; Goszczak, Arkadiusz Jaroslaw; Sobolewska, Elzbieta; Zillohu, Ahnaf Usman; Hedayati, Mehdi Keshavarz; Rubahn, Horst-Günter; Faupel, Franz; Elbahri, Mady; Bauer, Michael

    2015-01-01

    An interface supporting plasmonic switching is prepared from a gold substrate coated with a polymerfilm doped with photochromic molecular switches. A reversible light-induced change in the surface plasmon polariton dispersion curve of the interface is experimentally demonstrated, evidencing...

  6. Charge mobilities in molecular materials reversibly modified by light: towards a molecular switch

    Nešpůrek, Stanislav; Sworakowski, J.; Wang, Geng; Toman, Petr; Bartkowiak, W.; Combellas, C.

    Arcachon : University of Bordeaux, 2004. s. P111. [International Symposium on Photochromism /4./. 12.09.2004-15.09.2004, Arcachon] R&D Projects: GA MŠk OC D14.30 Keywords : molecular switch * charge mobility * photochromism Subject RIV: BM - Solid Matter Physics ; Magnetism

  7. Nonmechanical Conductance Switching in a Molecular Tunnel Junction.

    Baratz, Adva; Baer, Roi

    2012-02-16

    We present a molecular junction composed of a donor (polyacetylene strands) and an acceptor (malononitrile) connected together via a benzene ring and coupled weakly to source and drain electrodes on each side, for which a gate electrode induces intramolecular charge transfer, switching reversibly the character of conductance. Using a new brand of density functional theory, for which orbital energies are similar to the quasiparticle energies, we show that the junction displays a single, gate-tunable differential conductance channel in a wide energy range. The gate field must align parallel to the displacement vector between donors and acceptor to affect their potential difference; for strong enough fields, spontaneous intramolecular electron transfer occurs. This event radically affects conductance, reversing the charge of carriers, enabling a spin-polarized current channel. We discuss the physical principles controlling the operation of the junction and find interplay of quantum interference, charging, Coulomb blockade, and electron-hole binding energy effects. We expect that this switching behavior is a generic property for similar donor-acceptor systems of sufficient stability. PMID:26286054

  8. Symmetry as a new element to control molecular switches.

    Schweighauser, Luca; Häussinger, Daniel; Neuburger, Markus; Wegner, Hermann A

    2014-06-01

    The isomerization properties of an azocarbazole macrocycle in solution were investigated utilizing NMR spectroscopy with in situ irradiation in combination with DFT calculations. It was demonstrated that the position of azo units in a rigid macrocyclic system influences the photoisomerization pathway even if the initial all-E isomer is highly symmetric. Furthermore, the effect of ring strain on lowering the rates of thermal isomerization was demonstrated and a mechanism via an inversion-rotation proposed. The herein presented results and methods give new insights into the general nature of the azobenzene unit. In particular we illustrate the effect of symmetry changes due to macrocyclic arrangement on the photochemical and thermal isomerization properties, which will stimulate future development towards multinary molecular switches. PMID:24691779

  9. Electronic Transport Properties of a Naphthopyran-Based Optical Molecular Switch:an ab initio Study

    XIA Cai-Juan; LIU De-Sheng; ZHANG Ying-Tang

    2011-01-01

    The electronic transport properties of a. Naphthopyran-based molecular optical switch are investigated by using the nonequilibrium Green's Function formalism combined with first-principles density functional theory. The molecule that comprises the switch can convert between its open and closed forms upon photoexcitation. Theoretical results show that the current through the open form is significantly larger than that through the closed form, which is different from other optical switches based on ring-opening reactions of the molecular bridge. The maximum on-off ratio (about 90) can be obtained at 1.4 V. The physical origin of the switching behavior is interpreted based on the spatial distributions of molecular orbitals and the HOMO-LUMO gap. Our result shows that the naphthopyran-based molecule is a good candidate for optical molecular switches and will be useful in the near future.%@@ ronic transport properties of a naphthopyran-based molecular optical switch are investigated by using the nonequilibrium Green's function formalism combined with first-principles density functional theory.The molecule that comprises the switch can convert between its open and closed forms upon photoexcitation.Theoretical results show that the current through the open form is significantly larger than that through the closed form,which is different from other optical switches based on ring-opening reactions of the molecular bridge.The maximum on-off ratio(about 90)can be obtained at 1.4 V.The physical origin of the switching behavior is interpreted based on the spatial distributions of molecular orbitals and the HOMO-LUMO gap.Our result shows that the naphthopyran-based molecule is a good candidate for optical molecular switches and will be useful in the near future.

  10. Molecular Interaction of Pinic Acid with Sulfuric Acid

    Elm, Jonas; Kurten, Theo; Bilde, Merete;

    2014-01-01

    We investigate the molecular interactions between the semivolatile α-pinene oxidation product pinic acid and sulfuric acid using computational methods. The stepwise Gibbs free energies of formation have been calculated utilizing the M06-2X functional, and the stability of the clusters is evaluated...... from the corresponding ΔG values. The first two additions of sulfuric acid to pinic acid are found to be favorable with ΔG values of -9.06 and -10.41 kcal/mol. Addition of a third sulfuric acid molecule is less favorable and leads to a structural rearrangement forming a bridged sulfuric acid-pinic acid...... without the further possibility for attachment of either sulfuric acid or pinic acid. This suggests that pinic acid cannot be a key species in the first steps in nucleation, but the favorable interactions between sulfuric acid and pinic acid imply that pinic acid can contribute to the subsequent growth of...

  11. Switching dynamics in reaction networks induced by molecular discreteness

    To study the fluctuations and dynamics in chemical reaction processes, stochastic differential equations based on the rate equation involving chemical concentrations are often adopted. When the number of molecules is very small, however, the discreteness in the number of molecules cannot be neglected since the number of molecules must be an integer. This discreteness can be important in biochemical reactions, where the total number of molecules is not significantly larger than the number of chemical species. To elucidate the effects of such discreteness, we study autocatalytic reaction systems comprising several chemical species through stochastic particle simulations. The generation of novel states is observed; it is caused by the extinction of some molecular species due to the discreteness in their number. We demonstrate that the reaction dynamics are switched by a single molecule, which leads to the reconstruction of the acting network structure. We also show the strong dependence of the chemical concentrations on the system size, which is caused by transitions to discreteness-induced novel states

  12. A biomimetic molecular switch at work: coupling photoisomerization dynamics to peptide structural rearrangement.

    García-Iriepa, Cristina; Gueye, Moussa; Léonard, Jérémie; Martínez-López, David; Campos, Pedro J; Frutos, Luis Manuel; Sampedro, Diego; Marazzi, Marco

    2016-03-01

    In spite of considerable interest in the design of molecular switches towards photo-controllable (bio)materials, few studies focused on the major influence of the surrounding environment on the switch photoreactivities. We present a combined experimental and computational study of a retinal-like molecular switch linked to a peptide, elucidating the effects on the photoreactivity and on the α-helix secondary structure. Temperature-dependent, femtosecond UV-vis transient absorption spectroscopy and high-level hybrid quantum mechanics/molecular mechanics methods were applied to describe the photoisomerization process and the subsequent peptide rearrangement. It was found that the conformational heterogeneity of the ground state peptide controls the excited state potential energy surface and the thermally activated population decay. Still, a reversible α-helix to α-hairpin conformational change is predicted, paving the way for a fine photocontrol of different secondary structure elements, hence (bio)molecular functions, using retinal-inspired molecular switches. PMID:26876376

  13. STM investigation of imine-based molecular switches on Au(111)

    Mielke, Johannes; Grill, Leonhard [Institut fuer Experimentalphysik, Freie Universitaet Berlin (Germany); Luo, Ying; Haag, Rainer [Institut fuer Chemie und Biochemie - Organische Chemie, Freie Universitaet Berlin (Germany)

    2009-07-01

    In the field of molecular electronics, molecular switches are highly relevant because they can control the conductance. Switches based on azobenzene molecules have attracted large interest in the last years. A very similar molecular switch can be created by replacing the functional azo group by an imine group, which does not considerably alter the electronic structure of the molecule and conserves the capability of undergoing a reversible trans-cis isomerisation. Such processes have already been studied in solution and the gas phase but not on surfaces. In this work, imine molecules with four tert-butyl groups were adsorbed on Au(111) and their adsorption and switching behaviour were studied using a low temperature STM. The molecules were found to form two types of ordered islands and an interesting irreversible switching behaviour was observed when looking at their temperature dependence, because the number of trans isomers was reduced upon heating of the sample.

  14. Magnesium coordination controls the molecular switch function of DNA mismatch repair protein MutS

    J.H.G. Lebbink (Joyce); A. Fish (Alexander); A. Reumer (Annet); G. Natrajan; H.H.K. Winterwerp (Herrie); T.K. Sixma (Titia)

    2010-01-01

    textabstractThe DNA mismatch repair protein MutS acts as a molecular switch. It toggles between ADP and ATP states and is regulated by mismatched DNA. This is analogous to G-protein switches and the regulation of their "on" and "off" states by guanine exchange factors. Although GDP release in monome

  15. A pH-Sensitive Peptide-Containing Lasso Molecular Switch

    Karine Fournel-Marotte; Caroline Clavel; Frédéric Coutrot

    2013-01-01

    The synthesis of a peptide-containing lasso molecular switch by a self-entanglement strategy is described. The interlocked [1] rotaxane molecular machine consists of a benzometaphenylene[25]crown-8 (BMP25C8) macrocycle surrounding a molecular axle. This molecular axle contains a tripeptidic sequence and two molecular stations: a N-benzyltriazolium and a pH-sensitive anilinium station. The tripeptide is located between the macrocycle and the triazolium station, so that its conformation can be ...

  16. Electronic transport properties of a molecular switch with carbon nanotube electrodes: A first-principles study

    Zhao, P., E-mail: ss_zhaop@ujn.edu.c [School of Science, University of Jinan, Jinan 250022 (China); School of Physics, State Key Laboratory of Crystal Materials, Shandong University, Jinan 250100 (China); Wang, P.J.; Zhang, Z. [School of Science, University of Jinan, Jinan 250022 (China); Liu, D.S. [School of Physics, State Key Laboratory of Crystal Materials, Shandong University, Jinan 250100 (China); Department of Physics, Jining University, Qufu 273155 (China)

    2010-01-01

    We have studied the electronic transport properties of a new kind of optical molecular switch with two single-walled carbon nanotube (SWCNT) electrodes using first-principles transport calculations. It is shown that the enol form shows an overall higher conductance than the keto form at low-bias voltage, which is independent of the SWCNTs' chirality. Meantime, it is possible to tune the conductance of the molecular switch by changing the chirality of the SWCNTs.

  17. Laser Field Alignment of Organic Molecules on Semiconductor Surfaces: Toward Ultrafast Molecular Switches

    An ultrafast, nanoscale molecular switch is proposed, based on extension of the concept of nonadiabatic alignment to surface-adsorbed molecules. The switch consists of a conjugated organic molecule adsorbed onto a semiconducting surface and placed near a scanning tunneling microscope tip. A low-frequency, polarized laser field is used to switch the system by orienting the molecule with the field polarization axis, enabling conductance through the junction. Enhancement and spatial localization of the incident field by the metallic tip allow operation at low intensities. The principles of nonadiabatic alignment lead to switch on and off time scales far below rotational time scales

  18. Asymmetric Stochastic Switching Driven by Intrinsic Molecular Noise

    David Frigola; Laura Casanellas; Sancho, José M.; Marta Ibañes

    2012-01-01

    Low-copy-number molecules are involved in many functions in cells. The intrinsic fluctuations of these numbers can enable stochastic switching between multiple steady states, inducing phenotypic variability. Herein we present a theoretical and computational study based on Master Equations and Fokker-Planck and Langevin descriptions of stochastic switching for a genetic circuit of autoactivation. We show that in this circuit the intrinsic fluctuations arising from low-copy numbers, which are i...

  19. Oxidized Fatty Acid Analysis by Charge Switch Derivatization, Selected Reaction Monitoring and Accurate Mass Quantification

    Liu, Xinping; Moon, Sung Ho; Mancuso, David J.; Jenkins, Christopher M.; Guan, Shaoping; Sims, Harold F.; Gross, Richard W.

    2013-01-01

    A highly sensitive, specific and robust method for the analysis of oxidized metabolites of linoleic, acid (LA), arachidonic acid (AA) and docosahexaenoic acid (DHA) was developed using charge-switch derivatization, LC-ESI MS/MS with selected reaction monitoring (SRM) and quantitation by high mass accuracy analysis of product ions thereby minimizing interferences from contaminating ions. Charge-switch derivatization of LA, AA and DHA metabolites with N-(4-aminomethylphenyl)-pyridinium resulted...

  20. Molecular modeling and molecular dynamics simulation of the polarization switching phenomena in the ferroelectric polymers PVDF at the nanoscale

    The molecular modeling and molecular dynamics of polarization switching for the ferroelectric films model of polyvinylidene fluoride (PVDF) are investigated at the nanoscale. We consider a molecular model of PVDF film, consisting of two and four a chains [–CH2–CF2–]n limited by n=6 elementary units. The first-principle approach is applied to the switching and kinetics of these models. Two types of behavior were established for PVDF chains: simultaneous and sequential rotation in high and low electric fields. Kinetics of sequential polarization switching shows a homogeneous critical behavior in the low electric field with a critical point at Landau–Ginzburg–Devonshire (LGD) coercive field E=EC. This type of kinetics demonstrates a kink-like behavior for polarization solitary wave propagation. The simultaneous type of kinetics demonstrates the total domain-like polarization switching, corresponding to exponential behavior of switching time in high electric field as for bulk samples. Corresponding LGD intrinsic coercive field for a two-chain and four-chains model is EC∼2.0 GV/m with revealing size effect. Obtained results show common quantum nature of PVDF chains switching phenomena—the quantum interaction of the PVDF molecular orbitals under applied electric field at the nanoscale level. The results obtained are compared with experimental data

  1. Molecular modeling of nucleic acid structure

    Galindo-Murillo, Rodrigo; Bergonzo, Christina; Cheatham, Thomas E

    2001-01-01

    This unit is the first in a series of four units covering the analysis of nucleic acid structure by molecular modeling. This unit provides an overview of computer simulation of nucleic acids. Topics include the static structure model, computational graphics and energy models, generation of an initial model, and characterization of the overall three-dimensional structure.

  2. Amino acid properties conserved in molecular evolution.

    Witold R Rudnicki

    Full Text Available That amino acid properties are responsible for the way protein molecules evolve is natural and is also reasonably well supported both by the structure of the genetic code and, to a large extent, by the experimental measures of the amino acid similarity. Nevertheless, there remains a significant gap between observed similarity matrices and their reconstructions from amino acid properties. Therefore, we introduce a simple theoretical model of amino acid similarity matrices, which allows splitting the matrix into two parts - one that depends only on mutabilities of amino acids and another that depends on pairwise similarities between them. Then the new synthetic amino acid properties are derived from the pairwise similarities and used to reconstruct similarity matrices covering a wide range of information entropies. Our model allows us to explain up to 94% of the variability in the BLOSUM family of the amino acids similarity matrices in terms of amino acid properties. The new properties derived from amino acid similarity matrices correlate highly with properties known to be important for molecular evolution such as hydrophobicity, size, shape and charge of amino acids. This result closes the gap in our understanding of the influence of amino acids on evolution at the molecular level. The methods were applied to the single family of similarity matrices used often in general sequence homology searches, but it is general and can be used also for more specific matrices. The new synthetic properties can be used in analyzes of protein sequences in various biological applications.

  3. Insight into the molecular switch mechanism of human Rab5a from molecular dynamics simulations

    Rab5a is currently a most interesting target because it is responsible for regulating the early endosome fusion in endocytosis and possibly the budding process. We utilized longtime-scale molecular dynamics simulations to investigate the internal motion of the wild-type Rab5a and its A30P mutant. It was observed that, after binding with GTP, the global flexibility of the two proteins is increasing, while the local flexibility in their sensitive sites (P-loop, switch I and II regions) is decreasing. Also, the mutation of Ala30 to Pro30 can cause notable flexibility variations in the sensitive sites. However, this kind of variations is dramatically reduced after binding with GTP. Such a remarkable feature is mainly caused by the water network rearrangements in the sensitive sites. These findings might be of use for revealing the profound mechanism of the displacements of Rab5a switch regions, as well as the mechanism of the GDP dissociation and GTP association.

  4. X-ray Analyses of the Ribosomal A-Site Molecular Switches

    Kondo, Jiro

    The aminoacyl-tRNA decoding site (A-site) on the small ribosomal subunit is an RNA molecular switch guaranteeing high translation fidelity. Due to the similarity of the secondary structure of the A-site, it has long been believed that the functional characteristics and tertiary structure of the A-site molecular switch are basically conserved in three main cell types, bacteria, mitochondria and eukaryotic cytoplasm. However, these three cell types are noticeably different in their biological properties such as life cycle, genome size, structural component of ribosome and number of tRNA species. In our structural studies, we have shown how a small difference of nucleotide sequences affects the dynamics of the A-site molecular switches underlying the decoding mechanism adapted to their biological properties and environments. The observed structural insights into the decoding process allowed us to understand molecular mechanisms of non-syndromic hearing loss and toxicity mechanism of aminoglycoside antibiotics.

  5. The stochastic behavior of a molecular switching circuit with feedback

    Smith Eric

    2007-05-01

    Full Text Available Abstract Background Using a statistical physics approach, we study the stochastic switching behavior of a model circuit of multisite phosphorylation and dephosphorylation with feedback. The circuit consists of a kinase and phosphatase acting on multiple sites of a substrate that, contingent on its modification state, catalyzes its own phosphorylation and, in a symmetric scenario, dephosphorylation. The symmetric case is viewed as a cartoon of conflicting feedback that could result from antagonistic pathways impinging on the state of a shared component. Results Multisite phosphorylation is sufficient for bistable behavior under feedback even when catalysis is linear in substrate concentration, which is the case we consider. We compute the phase diagram, fluctuation spectrum and large-deviation properties related to switch memory within a statistical mechanics framework. Bistability occurs as either a first-order or second-order non-equilibrium phase transition, depending on the network symmetries and the ratio of phosphatase to kinase numbers. In the second-order case, the circuit never leaves the bistable regime upon increasing the number of substrate molecules at constant kinase to phosphatase ratio. Conclusion The number of substrate molecules is a key parameter controlling both the onset of the bistable regime, fluctuation intensity, and the residence time in a switched state. The relevance of the concept of memory depends on the degree of switch symmetry, as memory presupposes information to be remembered, which is highest for equal residence times in the switched states. Reviewers This article was reviewed by Artem Novozhilov (nominated by Eugene Koonin, Sergei Maslov, and Ned Wingreen.

  6. Proteomic analysis of mitochondria reveals a metabolic switch from fatty acid oxidation to glycolysis in the failing heart

    2009-01-01

    This work characterizes the mitochondrial proteomic profile in the failing heart and elucidates the molecular basis of mitochondria in heart failure. Heart failure was induced in rats by myocardial infarction, and mitochondria were isolated from hearts by differential centrifugation. Using two-dimensional gel electrophoresis and matrix-assisted laser desorption/ionization-time of flight mass spectrometry, a system biology approach was employed to investigate differences in mitochondrial proteins between normal and failing hearts. Mass spectrometry identified 27 proteins differentially expressed that involved in energy metabolism. Among those, the up-regulated proteins included tricarboxylic acid cycle enzymes and pyruvate dehydrogenase complex subunits while the down-regulated proteins were involved in fatty acid oxidation and the OXPHOS complex. These results suggest a substantial metabolic switch from free fatty acid oxidation to glycolysis in heart failure and provide molecular evidence for alterations in the structural and functional parameters of mitochondria that may contribute to cardiac dysfunction during ischemic injury.

  7. Nanoscale switch based on interacting molecular dipoles: Cooperativity can improve the device characteristics

    Mafé, , Salvador; Manzanares, , José A.; Reiss, Howard

    2011-02-01

    We propose a nanoscale switch, giving a nonlinear function with two conductive states separated by a sharp transition region, on the basis of an array of molecular dipoles. We show theoretically that the local interactions between dipoles result in cooperative phenomena that can significantly improve the switching characteristics. We demonstrate the general validity of the concept in the cases of (i) an electrical switch robust to the finite size and variability effects inherent to the nanoscale and (ii) a sensing layer based on the voltage and ligand concentration dependence of the dipole array conductance.

  8. Synthetic molecular machines and polymer/monomer size switches that operate through dynamic and non-dynamic covalent changes.

    Stadler, Adrian-Mihail; Ramírez, Juan

    2012-01-01

    The present chapter is focused on how synthetic molecular machines (e.g. shuttles, switches and molecular motors) and size switches (conversions between polymers and their units, i.e., conversions between relatively large and small molecules) can function through covalent changes. Amongst the interesting examples of devices herein presented are molecular motors and size switches based on dynamic covalent chemistry which is an area of constitutional dynamic chemistry. PMID:22169959

  9. Molecular Epigenetic Switches in Neurodevelopment in Health and Disease

    Dietmar Spengler

    2015-05-01

    Full Text Available Epigenetic mechanisms encode information above and beyond DNA sequence and play a critical role in brain development and the long-lived effects of environmental cues on the pre- and postnatal brain. Switch-like, rather than graded changes, illustrate par excellence how epigenetic events perpetuate altered activity states in the absence of the initial cue. They occur from early neural development to maturation and can give rise to distinct diseases upon deregulation. Many neurodevelopmental genes harbor bivalently marked chromatin domains, states of balanced inhibition, which guide dynamic ‘ON or OFF’ decisions once the balance is tilted in response to developmental or environmental cues. Examples discussed in this review include neuronal differentiation of embryonic stem cells into progenitors and beyond, activation of Kiss1 at puberty onset, and early experience-dependent programming of Avp, a major stress gene. At the genome-scale, genomic imprinting can be epigenetically switched on or off at select genes in a tightly controlled temporospatial manner and provides a versatile mechanism for dosage regulation of genes with important roles in stem cell quiescence or differentiation. Moreover, retrotransposition in neural progenitors provides an intriguing example of an epigenetic-like switch, which is stimulated by bivalently marked neurodevelopmental genes and possibly results in increased genomic flexibility regarding unprecedented challenge. Overall, we propose that epigenetic switches illuminate the catalyzing function of epigenetic mechanisms in guiding dynamic changes in gene expression underpinning robust transitions in cellular and organismal phenotypes as well as in the mediation between dynamically changing environments and the static genetic blueprint.

  10. Light controlled charge carrier mobilities on polymer chains. Towards a molecular switch

    Sworakowski, J.; Nešpůrek, Stanislav; Wang, Geng; Weiter, M.

    Saclay: Atomic Energy Research Centre, Saclay, 2003. s. 131. [European Conference on Molecular Electronics /7./. 10.09.2003-14.09.2003, Avignon] R&D Projects: GA MŠk OC D14.30 Grant ostatní: Polish State Committee for Sci. Res.(PL) T09A 132 22 Institutional research plan: CEZ:AV0Z4050913 Keywords : molecular switch * molecular wire * poly[methyl-(phenyl)silylene] Subject RIV: BM - Solid Matter Physics ; Magnetism

  11. Biodegradation of high molecular weight polylactic acid

    Stloukal, Petr; Koutný, Marek; Sedlařík, Vladimír; Kucharczyk, Pavel

    2012-01-01

    Polylactid acid seems to be an appropriate replacement of conventional non-biodegradable synthetic polymer primarily due to comparable mechanical, thermal and processing properties in its high molecular weight form. Biodegradation of high molecular PLA was studied in compost for various forms differing in their specific surface area. The material proved its good biodegradability under composting conditions and all investigated forms showed to be acceptable for industrial composting. Despite e...

  12. Do nucleic acids moonlight as molecular chaperones?

    Docter, Brianne E.; Horowitz, Scott; Gray, Michael J.; Jakob, Ursula; Bardwell, James C.A.

    2016-01-01

    Organisms use molecular chaperones to combat the unfolding and aggregation of proteins. While protein chaperones have been widely studied, here we demonstrate that DNA and RNA exhibit potent chaperone activity in vitro. Nucleic acids suppress the aggregation of classic chaperone substrates up to 300-fold more effectively than the protein chaperone GroEL. Additionally, RNA cooperates with the DnaK chaperone system to refold purified luciferase. Our findings reveal a possible new role for nucleic acids within the cell: that nucleic acids directly participate in maintaining proteostasis by preventing protein aggregation. PMID:27105849

  13. Molecular circuits, biological switches, and nonlinear dose-response relationships.

    Andersen, Melvin E.; Yang, Raymond S.H.; French, C. Tenley; Chubb, Laura S; Dennison, James E

    2002-01-01

    Signaling motifs (nuclear transcriptional receptors, kinase/phosphatase cascades, G-coupled protein receptors, etc.) have composite dose-response behaviors in relation to concentrations of protein receptors and endogenous signaling molecules. "Molecular circuits" include the biological components and their interactions that comprise the workings of these signaling motifs. Many of these molecular circuits have nonlinear dose-response behaviors for endogenous ligands and for exogenous toxicants...

  14. Molecular transformations in connective tissue hyaluronic acid

    Free radicals, either induced by the action of ionizing radiations or produced by metal ion induced electron transfer reactions in situ, can initiate a marked reduction in the viscoelasticity of the connective tissue matrix. This paper examines the dominant role of hyaluronic acid in controlling this behavior at molecular level. The results indicate that after a dose of 5Gy (500 rads), the average molecular weight of hyaluronic acid in skin would be reduced by a factor of 4, which would lead to a 60-fold reduction in viscosity of the glycosaminoglycan. Shorter chains so produced would further inhibit hyperentanglement and chain-chain interactions which are responsible for the viscoelasticity of the hyaluronic acid-polymer network. The results are relevant to preservation of skin grafts and to the effects of low-dose radiation in vivo

  15. Two-terminal nanoelectromechanical bistable switches based on molybdenum-sulfur-iodine molecular wire bundles

    Andzane, J.; Prikulis, J.; Dvorsek, D.; Mihailovic, D.; Erts, D.

    2010-03-01

    We demonstrate the application of Mo6S3I6 molecular wire bundles for electrically controllable two-terminal on-off switches. We investigate how changes in the contact electrode material and geometry influence the device characteristics, hysteretic switching behavior and device stability. We also determine the device operating parameters, particularly the Young's moduli (40-270 GPa), operating current densities (3.2 × 105-7 × 106 A m - 2) and force constants. Although qualitatively, the properties of Mo6S3I6 nanowires in nanoelectromechanical (NEM) switches are similar to those of carbon nanotubes (CNTs), their lower friction coefficient, higher mechanical stability and higher operation voltages give specific advantages in terms of smaller differences in on-off operating potentials, higher switching speeds and lower energy consumption than CNTs, which are critical for applications in NEM devices.

  16. Two-terminal nanoelectromechanical bistable switches based on molybdenum-sulfur-iodine molecular wire bundles

    We demonstrate the application of Mo6S3I6 molecular wire bundles for electrically controllable two-terminal on-off switches. We investigate how changes in the contact electrode material and geometry influence the device characteristics, hysteretic switching behavior and device stability. We also determine the device operating parameters, particularly the Young's moduli (40-270 GPa), operating current densities (3.2 x 105-7 x 106 A m-2) and force constants. Although qualitatively, the properties of Mo6S3I6 nanowires in nanoelectromechanical (NEM) switches are similar to those of carbon nanotubes (CNTs), their lower friction coefficient, higher mechanical stability and higher operation voltages give specific advantages in terms of smaller differences in on-off operating potentials, higher switching speeds and lower energy consumption than CNTs, which are critical for applications in NEM devices.

  17. Hydrochromic molecular switches for water-jet rewritable paper

    Sheng, Lan; Li, Minjie; Zhu, Shaoyin; Li, Hao; Xi, Guan; Li, Yong-Gang; Wang, Yi; Li, Quanshun; Liang, Shaojun; Zhong, Ke; Zhang, Sean Xiao-An

    2014-01-01

    The days of rewritable paper are coming, printers of the future will use water-jet paper. Although several kinds of rewritable paper have been reported, practical usage of them is rare. Herein, a new rewritable paper for ink-free printing is proposed and demonstrated successfully by using water as the sole trigger to switch hydrochromic dyes on solid media. Water-jet prints with various colours are achieved with a commercial desktop printer based on these hydrochromic rewritable papers. The prints can be erased and rewritten dozens of times with no significant loss in colour quality. This rewritable paper is promising in that it can serve an eco-friendly information display to meet the increasing global needs for environmental protection.

  18. Infrared spectroscopic characterization of [2]rotaxane molecular switch tunnel junction devices.

    DeIonno, Erica; Tseng, Hsian-Rong; Harvey, Desmond D; Stoddart, J Fraser; Heath, James R

    2006-04-20

    Langmuir-Blodgett monolayers of a bistable [2]rotaxane were prepared at packing densities of 118, 73, and 54 A(2)/molecule. The monolayers were both characterized via infrared spectroscopy before and after evaporation of a 2 nm film of titanium and incorporated into molecular switch tunnel junction devices. The study suggests that the evaporation process primarily affects portions of the molecule exposed to the metal atom source. Thus, in tightly packed monolayers (73 and 54 A(2)/molecule), only the portions of the [2]rotaxane that are present at the molecule/air interface are clearly affected, leaving key functionality necessary for switching intact. Monolayers transferred at a lower pressure (118 A(2)/molecule) exhibit nonspecific damage and poor switching behavior following Ti deposition. These results indicate that tightly packed monolayers and sacrificial functionality displayed at the molecule/air interface are important design principles for molecular electronic devices. PMID:16610848

  19. Deciphering mechanism of the 'myristoyl switch' with classical and accelerated molecular dynamics

    Magarkar, Aniket; Kohagen, Miriam; Jungwirth, Pavel

    2015-01-01

    Roč. 44, Suppl 1 (2015), S169. ISSN 0175-7571. [EBSA European Biophysics Congress /10./. 18.07.2015-22.07.2015, Dresden] Institutional support: RVO:61388963 Keywords : molecular dynamics * myristoyl switch * calcium ion binding Subject RIV: CF - Physical ; Theoretical Chemistry

  20. Chemical Talking with Living Systems: Molecular Switches Steer Quorum Sensing in Bacteria.

    Schweighauser, Luca; Wegner, Hermann A

    2015-08-17

    New avenues in bacterial engineering: An azobenzene molecular switch has been incorporated into an autoinducer for quorum sensing (QS) in bacteria. The authors demonstrated that irradiation with different wavelengths of light influences the QS system thereby controlling gene expression as well as the phenotype, as exemplified by pyocyanin production. PMID:26078043

  1. Electrospun Nanofibers from a Tricyanofuran-Based Molecular Switch for Colorimetric Recognition of Ammonia Gas.

    Khattab, Tawfik A; Abdelmoez, Sherif; Klapötke, Thomas M

    2016-03-14

    A chromophore based on tricyanofuran (TCF) with a hydrazone (H) recognition moiety was developed. Its molecular-switching performance is reversible and has differential sensitivity towards aqueous ammonia at comparable concentrations. Nanofibers were fabricated from the TCF-H chromophore by electrospinning. The film fabricated from these nanofibers functions as a solid-state optical chemosensor for probing ammonia vapor. Recognition of ammonia vapor occurs by proton transfer from the hydrazone fragment of the chromophore to the ammonia nitrogen atom and is facilitated by the strongly electron withdrawing TCF fragment. The TCF-H chromophore was added to a solution of poly(acrylic acid), which was electrospun to obtain a nanofibrous sensor device. The morphology of the nanofibrous sensor was determined by SEM, which showed that nanofibers with a diameter range of 200-450 nm formed a nonwoven mat. The resultant nanofibrous sensor showed very good sensitivity in ammonia-vapor detection. Furthermore, very good reversibility and short response time were also observed. PMID:26864701

  2. Thermodynamic principles for the engineering of pH-driven conformational switches and acid insensitive proteins

    Bell-Upp, Peregrine; Robinson, Aaron C.; Whitten, Steven; Wheeler, Erika L.; Lin, Janine; Stites, Wesley E.; García-Moreno E., Bertrand

    2011-01-01

    The general thermodynamic principles behind pH driven conformational transitions of biological macromolecules are well understood. What is less obvious is how they can be used to engineer pH switches in proteins. The acid unfolding of staphylococcal nuclease (SNase) was used to illustrate different factors that can affect pH-driven conformational transitions. Acid unfolding is a structural transition driven by preferential H+ binding to the acid unfolded state (U) over the native (N) state of...

  3. Understanding and Controlling Regime Switching in Molecular Diffusion

    Hallerberg, S.; de Wijn, A. S.

    2013-01-01

    Diffusion can be strongly affected by ballistic flights (long jumps) as well as long-lived sticking trajectories (long sticks). Using statistical inference techniques in the spirit of Granger causality, we investigate the appearance of long jumps and sticks in molecular-dynamics simulations of diffusion in a prototype system, a benzene molecule on a graphite substrate. We find that specific fluctuations in certain, but not all, internal degrees of freedom of the molecule can be linked to eith...

  4. Models of charge transport and transfer in molecular switch tunnel junctions of bistable catenanes and rotaxanes

    The processes by which charge transfer can occur play a foundational role in molecular electronics. Here we consider simplified models of the transfer processes that could be present in bistable molecular switch tunnel junction (MSTJ) devices during one complete cycle of the device from its low- to high- and back to low-conductance state. The bistable molecular switches, which are composed of a monolayer of either switchable catenanes or rotaxanes, exist in either a ground-state co-conformation or a metastable one in which the conduction properties of the two co-conformations, when measured at small biases (+0.1 V), are significantly different irrespective of whether transport is dominated by tunneling or hopping. The voltage-driven generation (±2 V) of molecule-based redox states, which are sufficiently long-lived to allow the relative mechanical movements necessary to switch between the two co-conformations, rely upon unequal charge transfer rates on to and/or off of the molecules. Surface-enhanced Raman spectroscopy has been used to image the ground state of the bistable rotaxane in MSTJ-like devices. Consideration of these models provide new ways of looking at molecular electronic devices that rely, not only on nanoscale charge-transport, but also upon the bustling world of molecular motion in mechanically interlocked bistable molecules

  5. Adsorption and switching properties of a N-benzylideneaniline based molecular switch on a Au(111) surface

    High resolution electron energy loss spectroscopy has been employed to analyze the adsorption geometry and the photoisomerization ability of the molecular switch carboxy-benzylideneaniline (CBA) adsorbed on Au(111). CBA on Au(111) adopts a planar (trans) configuration in the first monolayer (ML) as well as for higher coverages (up to 6 ML), in contrast to the strongly nonplanar geometry of the molecule in solution. Illumination with UV light of CBA in direct contact with the Au(111) surface (≤1 ML) caused no changes in the vibrational structure, whereas at higher coverages (>1 ML) pronounced modifications of vibrational features were observed, which we assign to a trans→cis isomerization. Thermal activation induced the back reaction to trans-CBA. We propose that the photoisomerization is driven by a direct (intramolecular) electronic excitation of the adsorbed CBA molecules in the second ML (and above) analogous to CBA in the liquid phase.

  6. Investigation of a metal-organic interface. Realization and understanding of a molecular switch

    Neucheva, Olga [Forschungszentrum Juelich (DE). Institute of Bio- and Nanosystems (IBN), Functional Nanostructures at Surfaces (IBN-3)

    2010-07-01

    The field of molecular organic electronics is an emerging and very dynamic area. The continued trend to miniaturisation, combined with increasing complexity and cost of production in conventional semiconductor electronics, forces companies to turn their attention to alternatives that promise the next levels of scale at significantly lower cost. After consumer electronic devices based on organic transistors, such as TVs and book readers, have already been presented, molecular electronics is expected to offer the next breakthrough in feature size. Unfortunately, most of the organic/metal interfaces contain intrinsic defects that break the homogeneity of the interface properties. In this thesis, the electronic and structural properties of such defects were examined in order to understand the influence of the inhomogeneities on the quality of the interface layer. However, the main focus of this work was the investigation of the local properties of a single molecule. Taking advantage of the Scanning Tunnelling Microscope's (STM's) ability to act as a local probe, a single molecular switch was realized and studied. Moreover, in close collaboration with theory groups, the underlying mechanism driving the switching process was identified and described. Besides the investigation of the switching process, the ability of the STM to build nanostructures of different shapes from large organic molecules was shown. Knowing the parameters for realization and control of the switching process and for building the molecular corrals, the results of this investigation enable the reconstruction of the studied molecular ensemble and its deployment in electric molecular circuits, constituting a next step towards further miniaturization of electronic devices. (orig.)

  7. Quantum current of a molecular photo-switch between two graphene sheets

    Brivio, G. P.; Motta, C.; Trioni, M. I.; Sebastian, K. L.

    2011-03-01

    Light responsive materials that reversibly change shape under alternate UV and visible irradiation have attracted much interest because they can be used as optical switches, since the isomers show different features in the dimension, HOMO-LUMO gap and transmission spectrum. In view to integrate the photo-switch in the carbon based electronics devices, the conductance of a system constituted by a photochromic molecule between two graphene electrodes is investigated. In this work the conductance of the junction formed by diarylperfluorocyclopentene between two semi-infinite graphene sheets was computed using the non-equilibrium Green's function method combined with density functional theory via the TranSiesta code. The results emphasize the role of the graphene and the molecular electronic states in the switching behaviour of this hybrid system.

  8. The importance of the rotor in hydrazone-based molecular switches

    Xin Su

    2012-06-01

    Full Text Available The pH-activated E/Z isomerization of a series of hydrazone-based systems having different functional groups as part of the rotor (R = COMe, CN, Me, H, was studied. The switching efficiency of these systems was compared to that of a hydrazone-based molecular switch (R = COOEt whose E/Z isomerization is fully reversible. It was found that the nature of the R group is critical for efficient switching to occur; the R group should be a moderate H-bond acceptor in order to (i provide enough driving force for the rotor to move upon protonation, and (ii stabilize the obtained Z configuration, to achieve full conversion.

  9. Single Molecule Switches and Molecular Self-Assembly: Low Temperature STM Investigations and Manipulations

    This dissertation is devoted to single molecule investigations and manipulations of two porphyrin-based molecules, chlorophyll-a and Co-popphyrin. The molecules are absorbed on metallic substrates and studied at low temperatures using a scanning tunneling microscope. The electronic, structural and mechanical properties of the molecules are investigated in detail with atomic level precision. Chlorophyll-a is the key ingredient in photosynthesis processes while Co-porphyrin is a magnetic molecule that represents the recent emerging field of molecular spintronics. Using the scanning tunneling microscope tip and the substrate as electrodes, and the molecules as active ingredients, single molecule switches made of these two molecules are demonstrated. The first switch, a multiple and reversible mechanical switch, is realized by using chlorophyll-a where the energy transfer of a single tunneling electron is used to rotate a C-C bond of the molecule's tail on a Au(111) surface. Here, the det

  10. Ab initio theory for current-induced molecular switching: Melamine on Cu(001)

    Ohto, Tatsuhiko

    2013-05-28

    Melamine on Cu(001) is mechanically unstable under the current of a scanning tunneling microscope tip and can switch among configurations. However, these are not equally accessible, and the switching critical current depends on the bias polarity. In order to explain such rich phenomenology, we have developed a scheme to evaluate the evolution of the reaction paths and activation barriers as a function of bias, which is rooted in the nonequilibrium Green\\'s function method implemented within density functional theory. This, combined with the calculation of the inelastic electron tunneling spectroscopy signal, allows us to identify the vibrational modes promoting the observed molecular conformational changes. Finally, once our ab initio results are used within a resonance model, we are able to explain the details of the switching behavior, such as its dependence on the bias polarity, and the noninteger power relation between the reaction rate constants and both the bias voltage and the electric current. © 2013 American Physical Society.

  11. Understanding and controlling regime switching in molecular diffusion

    Hallerberg, S.; de Wijn, A. S.

    2014-12-01

    Diffusion can be strongly affected by ballistic flights (long jumps) as well as long-lived sticking trajectories (long sticks). Using statistical inference techniques in the spirit of Granger causality, we investigate the appearance of long jumps and sticks in molecular-dynamics simulations of diffusion in a prototype system, a benzene molecule on a graphite substrate. We find that specific fluctuations in certain, but not all, internal degrees of freedom of the molecule can be linked to either long jumps or sticks. Furthermore, by changing the prevalence of these predictors with an outside influence, the diffusion of the molecule can be controlled. The approach presented in this proof of concept study is very generic and can be applied to larger and more complex molecules. Additionally, the predictor variables can be chosen in a general way so as to be accessible in experiments, making the method feasible for control of diffusion in applications. Our results also demonstrate that data-mining techniques can be used to investigate the phase-space structure of high-dimensional nonlinear dynamical systems.

  12. Single molecular switch based on thiol tethered iron(II)clathrochelate on gold

    Molecular electronics has been associated with high density nano-electronic devices. Developments of molecular electronic devices were based on reversible switching of molecules between the two conductive states. In this paper, self-assembled monolayers of dodecanethiol (DDT) and thiol tethered iron(II)clathrochelate (IC) have been prepared on gold film. The electrochemical and electronic properties of IC molecules inserted into the dodecanethiol monolayer (IC-DDT SAM) were investigated using voltammetric, electrochemical impedance spectroscopy (EIS), scanning tunneling microscopy (STM) and cross-wire tunneling measurements. The voltage triggered switching behaviour of IC molecules on mixed SAM was demonstrated. Deposition of polyaniline on the redox sites of IC-DDT SAM using electrochemical polymerization of aniline was performed in order to confirm that this monolayer acts as nano-patterned semiconducting electrode surface.

  13. The Limiting Dynamics of a Bistable Molecular Switch With and Without Noise

    Mackey, Michael C.; Tyran-Kaminska, Marta

    2015-01-01

    We consider the dynamics of a population of organisms containing two mutually inhibitory gene regulatory networks, that can result in a bistable switch-like behaviour. We completely characterize their local and global dynamics in the absence of any noise, and then go on to consider the effects of either noise coming from bursting (transcription or translation), or Gaussian noise in molecular degradation rates when there is a dominant slow variable in the system. We show analytically how the s...

  14. Multitarget Molecular Hybrids of Cinnamic Acids

    Aikaterini Peperidou

    2014-12-01

    Full Text Available In an attempt to synthesize potential new multitarget agents, 11 novel hybrids incorporating cinnamic acids and paracetamol, 4-/7-hydroxycoumarin, benzocaine, p-aminophenol and m-aminophenol were synthesized. Three hybrids—2e, 2a, 2g—and 3b were found to be multifunctional agents. The hybrid 2e derived from the phenoxyphenyl cinnamic acid and m-acetamidophenol showed the highest lipoxygenase (LOX inhibition and analgesic activity (IC50 = 0.34 μΜ and 98.1%, whereas the hybrid 3b of bromobenzyloxycinnamic acid and hymechromone exhibited simultaneously good LOX inhibitory activity (IC50 = 50 μΜ and the highest anti-proteolytic activity (IC50= 5 μΜ. The hybrid 2a of phenyloxyphenyl acid with paracetamol showed a high analgesic activity (91% and appears to be a promising agent for treating peripheral nerve injuries. Hybrid 2g which has an ester and an amide bond presents an interesting combination of anti-LOX and anti-proteolytic activity. The esters were found very potent and especially those derived from paracetamol and m-acetamidophenol. The amides follow. Based on 2D-structure–activity relationships it was observed that both steric and electronic parameters play major roles in the activity of these compounds. Molecular docking studies point to the fact that allosteric interactions might govern the LOX-inhibitor binding.

  15. Research Update: Molecular electronics: The single-molecule switch and transistor

    Kai Sotthewes

    2014-01-01

    Full Text Available In order to design and realize single-molecule devices it is essential to have a good understanding of the properties of an individual molecule. For electronic applications, the most important property of a molecule is its conductance. Here we show how a single octanethiol molecule can be connected to macroscopic leads and how the transport properties of the molecule can be measured. Based on this knowledge we have realized two single-molecule devices: a molecular switch and a molecular transistor. The switch can be opened and closed at will by carefully adjusting the separation between the electrical contacts and the voltage drop across the contacts. This single-molecular switch operates in a broad temperature range from cryogenic temperatures all the way up to room temperature. Via mechanical gating, i.e., compressing or stretching of the octanethiol molecule, by varying the contact's interspace, we are able to systematically adjust the conductance of the electrode-octanethiol-electrode junction. This two-terminal single-molecule transistor is very robust, but the amplification factor is rather limited.

  16. The limiting dynamics of a bistable molecular switch with and without noise.

    Mackey, Michael C; Tyran-Kamińska, Marta

    2016-08-01

    We consider the dynamics of a population of organisms containing two mutually inhibitory gene regulatory networks, that can result in a bistable switch-like behaviour. We completely characterize their local and global dynamics in the absence of any noise, and then go on to consider the effects of either noise coming from bursting (transcription or translation), or Gaussian noise in molecular degradation rates when there is a dominant slow variable in the system. We show analytically how the steady state distribution in the population can range from a single unimodal distribution through a bimodal distribution and give the explicit analytic form for the invariant stationary density which is globally asymptotically stable. Rather remarkably, the behaviour of the stationary density with respect to the parameters characterizing the molecular behaviour of the bistable switch is qualitatively identical in the presence of noise coming from bursting as well as in the presence of Gaussian noise in the degradation rate. This implies that one cannot distinguish between either the dominant source or nature of noise based on the stationary molecular distribution in a population of cells. We finally show that the switch model with bursting but two dominant slow genes has an asymptotically stable stationary density. PMID:26692266

  17. Age-associated Cognitive Decline: Insights into Molecular Switches and Recovery Avenues

    Konar, Arpita; Singh, Padmanabh; Thakur, Mahendra K.

    2016-01-01

    Age-associated cognitive decline is an inevitable phenomenon that predisposes individuals for neurological and psychiatric disorders eventually affecting the quality of life. Scientists have endeavored to identify the key molecular switches that drive cognitive decline with advancing age. These newly identified molecules are then targeted as recovery of cognitive aging and related disorders. Cognitive decline during aging is multi-factorial and amongst several factors influencing this trajectory, gene expression changes are pivotal. Identifying these genes would elucidate the neurobiological underpinnings as well as offer clues that make certain individuals resilient to withstand the inevitable age-related deteriorations. Our laboratory has focused on this aspect and investigated a wide spectrum of genes involved in crucial brain functions that attribute to senescence induced cognitive deficits. We have recently identified master switches in the epigenome regulating gene expression alteration during brain aging. Interestingly, these factors when manipulated by chemical or genetic strategies successfully reverse the age-related cognitive impairments. In the present article, we review findings from our laboratory and others combined with supporting literary evidences on molecular switches of brain aging and their potential as recovery targets.

  18. Lactobacillus plantarum possesses the capability for wall teichoic acid backbone alditol switching

    Bron Peter A

    2012-09-01

    Full Text Available Abstract Background Specific strains of Lactobacillus plantarum are marketed as health-promoting probiotics. The role and interplay of cell-wall compounds like wall- and lipo-teichoic acids (WTA and LTA in bacterial physiology and probiotic-host interactions remain obscure. L. plantarum WCFS1 harbors the genetic potential to switch WTA backbone alditol, providing an opportunity to study the impact of WTA backbone modifications in an isogenic background. Results Through genome mining and mutagenesis we constructed derivatives that synthesize alternative WTA variants. The mutants were shown to completely lack WTA, or produce WTA and LTA that lack D-Ala substitution, or ribitol-backbone WTA instead of the wild-type glycerol-containing backbone. DNA micro-array experiments established that the tarIJKL gene cluster is required for the biosynthesis of this alternative WTA backbone, and suggest ribose and arabinose are precursors thereof. Increased tarIJKL expression was not observed in any of our previously performed DNA microarray experiments, nor in qRT-PCR analyses of L. plantarum grown on various carbon sources, leaving the natural conditions leading to WTA backbone alditol switching, if any, to be identified. Human embryonic kidney NF-κB reporter cells expressing Toll like receptor (TLR-2/6 were exposed to purified WTAs and/or the TA mutants, indicating that WTA is not directly involved in TLR-2/6 signaling, but attenuates this signaling in a backbone independent manner, likely by affecting the release and exposure of immunomodulatory compounds such as LTA. Moreover, human dendritic cells did not secrete any cytokines when purified WTAs were applied, whereas they secreted drastically decreased levels of the pro-inflammatory cytokines IL-12p70 and TNF-α after stimulation with the WTA mutants as compared to the wild-type. Conclusions The study presented here correlates structural differences in WTA to their functional characteristics, thereby

  19. Proteomic analysis of mitochondria reveals a metabolic switch from fatty acid oxidation to glycolysis in the failing heart

    WANG Jun; WANG TingZhong; LIU Ping; FAN FenLing; GUAN YouFei; MA AiQun; BAI Ling; LI Jing; SUN ChaoFeng; ZHAO Jin; CUI ChangCong; HAN Ke; LIU Yu; ZHUO XiaoZhen

    2009-01-01

    This work characterizes the mitochondrial proteomic profile in the failing heart and elucidates the molecular basis of mitochondria in heart failure.Heart failure was induced in rats by myocardial infarction,and mitochondria were isolated from hearts by differential centrifugation.Using two-dimensional gel electrophoresis and matrix-assisted laser desorption/ionization-time of flight mass spectrometry,a system biology approach was employed to investigate differences in mitochondrial proteins between normal and failing hearts.Mass spectrometry identified 27 proteins differentially expressed that involved in energy metabolism.Among those,the up-regulated proteins included tricarboxylic acid cycle enzymes and pyruvate dehydrogenase complex subunita while the down-regulated proteins were involved in fatty acid oxidation and the OXPHOS complex.These results suggest a substantial metabolic switch from free fatty acid oxidation to glycolysis in heart failure and provide molecular evidence for alterations in the structural and functional parameters of mitochondria that may contribute to cardiac dysfunction during ischemic injury.

  20. Photocontrolled Reversible Luminescent Lanthanide Molecular Switch Based on a Diarylethene-Europium Dyad.

    Cheng, Hong-Bo; Hu, Guo-Fei; Zhang, Zhan-Hui; Gao, Liang; Gao, Xingfa; Wu, Hai-Chen

    2016-08-15

    A new europium complex coordinated between a Eu(III) ion and an unsymmetrical diarylperfluorocyclopentene yields a light-controlled diarylethene-europium dyad, DAE@TpyEu(tta)3, whose photophysical properties can be reversibly switched by optical stimuli. When DAE@TpyEu(tta)3 is exposed to 365 nm UV light, an efficient intramolecular photochromic fluorescence resonance energy transfer (pc-FRET) occurs between the emission of the Eu(3+) donor (D) and the absorption of the diarylethene acceptor (A) in closed-form DAE@TpyEu(tta)3 accompanied by luminescence quenching. However, the pc-FRET process could be effectively inhibited by visible light (λ > 600 nm) irradiation, and the lanthanide emission of DAE@TpyEu(tta)3 is rapidly recovered. Furthermore, this luminescent lanthanide molecular switch could serve as a highly reliable and sensitive "turn on" fluorescent marker in living cells irradiated by red light without any optical interference. PMID:27447742

  1. 'Molecular switch' vectors for hypoxia- and radiation-mediated gene therapy of cancer

    Intratumoral areas of low oxygen concentration are known to be refractive to radiotherapy treatment. However, this physiological condition can be exploited for selective cancer gene therapy. We have developed a series of synthetic promoters selectively responsive to both hypoxia and ionizing radiation (IR). These promoters contain hypoxia regulatory elements (HREs) from the erythropoietin (Epo), the phosphoglycerate kinase1(PGK1) and vascular endothelial growth factor (VEGF) genes, and/or IR-responsive CArG elements from the Early Growth Response 1 (Egr1) gene. The HRE and CArG promoters were able to regulate expression of reporter and suicide genes in human tumor cells, following corresponding stimulation with hypoxia (0.1% O2) or X-irradiation (5Gy) [Greco et al, 2002, Gene Therapy 9:1403]. Furthermore, the chimeric HRE + CArG promoters could be activated by these stimuli independently or even more significantly when given in combination, with the Epo HRE/CArG promoter proving to be the most responsive and robust. In order to amplify and maintain transgene expression even following withdrawal of the triggering stimuli, we have developed a 'molecular switch' system [Scott et al, 2000, Gene Therapy 7:1121]. This 'switch' system has now been engineered as a single vector molecule, containing HRE and CArG promoters. This new series of HRE/CArG switch vectors have been tested in a herpes simplex thymidine kinase (HSVtk)/ganciclovir (GCV) suicide gene assay. Results indicate that a) higher and more selective tumor cell kill is achieved with the switch when compared with the HRE and CArG promoters directly driving HSVtk expression and b) the Epo HRE/CArG switch vectors appear to function as efficiently as the strong constitutive cytomegalovirus (CMV) promoter construct

  2. Transient photocurrent in molecular junctions: singlet switching on and triplet blocking.

    Petrov, E G; Leonov, V O; Snitsarev, V

    2013-05-14

    The kinetic approach adapted to describe charge transmission in molecular junctions, is used for the analysis of the photocurrent under conditions of moderate light intensity of the photochromic molecule. In the framework of the HOMO-LUMO model for the single electron molecular states, the analytic expressions describing the temporary behavior of the transient and steady state sequential (hopping) as well as direct (tunnel) current components have been derived. The conditions at which the current components achieve their maximal values are indicated. It is shown that if the rates of charge transmission in the unbiased molecular diode are much lower than the intramolecular singlet-singlet excitation/de-excitation rate, and the threefold degenerated triplet excited state of the molecule behaves like a trap blocking the charge transmission, a possibility of a large peak-like transient switch-on photocurrent arises. PMID:23676066

  3. Mucosal transmissibility, disease induction and coreceptor switching of R5 SHIVSF162P3N molecular clones in rhesus macaques

    Ren Wuze

    2013-01-01

    Full Text Available Abstract Background Mucosally transmissible and pathogenic CCR5 (R5-tropic simian-human immunodeficiency virus (SHIV molecular clones are useful reagents to identity neutralization escape in HIV-1 vaccine experiments and to study the envelope evolutionary process and mechanistic basis for coreceptor switch during the course of natural infection. Results We observed progression to AIDS in rhesus macaques infected intrarectally with molecular clones of the pathogenic R5 SHIVSF162P3N isolate. Expansion to CXCR4 usage was documented in one diseased macaque that mounted a neutralizing antibody response and in another that failed to do so, with the latter displaying a rapid progressor phenotype. V3 loop envelop glycoprotein gp120 sequence changes that are predictive of a CXCR4 (X4-using phenotype in HIV-1 subtype B primary isolates, specifically basic amino acid substations at positions 11 (S11R, 24 (G24R and 25 (D25K of the loop were detected in the two infected macaques. Functional assays showed that envelopes with V3 S11R or D25K mutation were dual-tropic, infecting CD4+ target cells that expressed either the CCR5 or CXCR4 coreceptor. And, consistent with findings of coreceptor switching in macaques infected with the pathogenic isolate, CXCR4-using variant was first detected in the lymph node of the chronically infected rhesus monkey several weeks prior to its presence in peripheral blood. Moreover, X4 emergence in this macaque coincided with persistent peripheral CD4+ T cell loss and a decline in neutralizing antibody titer that are suggestive of immune deterioration, with macrophages as the major virus-producing cells at the end-stage of disease. Conclusions The data showed that molecular clones derived from the R5 SHIVSF162P3N isolate are mucosally transmissible and induced disease in a manner similar to that observed in HIV-1 infected individuals, providing a relevant and useful animal infection model for in-depth analyses of host selection

  4. Novel tailor-made externally triggerable single-molecular switches for molecular electronics

    Harzmann, Gero

    2015-01-01

    Molecular electronics marks a highly interdisciplinary scientific field, in which physicists, chemists, and biologist jointly investigate electronic phenomena on a molecular level. Herein, the foremost task of the chemist is the design and synthesis of novel, tailor-made model compounds bearing externally addressable or controllable functions, which are predominantly of electronic nature. This present PhD thesis mainly focusses on the synthetic aspects towards innovative metalorga...

  5. A molecular beacon-based DNA switch for reversible pH sensing in vesicles and live cells.

    Narayanaswamy, Nagarjun; Nair, Raji R; Suseela, Y V; Saini, Deepak Kumar; Govindaraju, T

    2016-07-01

    In this Communication, a molecular beacon-based DNA switch (LMB) is developed as an efficient and reversible pH sensing probe. Remarkably, LMB exhibited reversible structural transition between the closed (molecular beacon) and open (A-motif) states very efficiently in synthetic vesicles and live cells without the need for any transfection agents. PMID:27338808

  6. Electron induced conformational changes of imine-based molecular switches on a Au(111) surface

    Lotze, Christian; Pascual, Jose Ignacio [Inst. f. Experimentalphysik, Freie Universitaet Berlin (Germany); Luo, Ying; Haag, Rainer [Inst. f. Organische Chemie, Freie Universitaet Berlin (Germany)

    2010-07-01

    Organic molecules exhibiting controllable reversible transitions between isomeric states on surfaces promise an enormous potential in the field of molecular electronics. The reversible cis-trans isomerization of azobenzene-like molecules is often hindered by a strong interaction of the nitrogen lone-pair electrons of the di-azo bridge (-N=N-) with the substrate. In order to improve the isomerization capabilities, the di-azo bridge is substituted by an imine-group (-N=CH-). Here, we use low-temperature scanning tunneling microscopy to investigate a sub-monolayer of the newly designed imine-based molecular switch NPCI on a Au(111) surface. Its carboxylic termination mediates the formation of hydrogen-bonded dimers, which align in rows along the herringbone reconstruction. We were able to induce reversible conformational changes with the tunneling electrons from the STM tip and determine its efficiency as a function of electron energy.

  7. Ferroelectric molecular field-switch based on double proton transfer process: Static and dynamical simulations

    Rode, Michał F.; Jankowska, Joanna; Sobolewski, Andrzej L.

    2016-04-01

    In this work, we present a reversible ferroelectric molecular switch controlled by an external electric field. The studied (2Z)-1-(6-((Z)-2-hydroxy-2-phenylvinyl)pyridin-3-yl)-2-(pyridin-2(1H)-ylidene)ethanone (DSA) molecule is polarized by two uniaxial intramolecular hydrogen bonds. Two protons can be transferred along hydrogen bonds upon an electric field applied along the main molecular axis. The process results in reversion of the dipole moment of the system. Static ab initio and on-the-fly dynamical simulations of the DSA molecule placed in an external electric field give insight into the mechanism of the double proton transfer (DPT) in the system and allow for estimation of the time scale of this process. The results indicate that with increasing strength of the electric field, the step-wise mechanism of DPT changes into the downhill barrierless process in which the synchronous and asynchronous DPTs compete with each other.

  8. Simultaneous and coordinated rotational switching of all molecular rotors in a network.

    Zhang, Y; Kersell, H; Stefak, R; Echeverria, J; Iancu, V; Perera, U G E; Li, Y; Deshpande, A; Braun, K-F; Joachim, C; Rapenne, G; Hla, S-W

    2016-08-01

    A range of artificial molecular systems has been created that can exhibit controlled linear and rotational motion. In the further development of such systems, a key step is the addition of communication between molecules in a network. Here, we show that a two-dimensional array of dipolar molecular rotors can undergo simultaneous rotational switching when applying an electric field from the tip of a scanning tunnelling microscope. Several hundred rotors made from porphyrin-based double-decker complexes can be simultaneously rotated when in a hexagonal rotor network on a Cu(111) surface by applying biases above 1 V at 80 K. The phenomenon is observed only in a hexagonal rotor network due to the degeneracy of the ground-state dipole rotational energy barrier of the system. Defects are essential to increase electric torque on the rotor network and to stabilize the switched rotor domains. At low biases and low initial rotator angles, slight reorientations of individual rotors can occur, resulting in the rotator arms pointing in different directions. Analysis reveals that the rotator arm directions are not random, but are coordinated to minimize energy via crosstalk among the rotors through dipolar interactions. PMID:27159740

  9. Molecular and Supramolecular Information Processing From Molecular Switches to Unconventional Computing

    Katz, Evgeny

    2012-01-01

    Edited by a renowned and much cited chemist, this book covers the whole span of molecular computers that are based on non-biological systems. The contributions by all the major scientists in the field provide an excellent overview of the latest developments in this rapidly expanding area. A must-have for all researchers working on this very hot topic. Perfectly complements Biomolecular Information Processing, also by Prof. Katz, and available as a two-volume set.

  10. Molecular Simulation of Naphthenic Acid Removal on Acidic Catalyst Ⅱ. Experimental results of catalytic decarboxylation over acidic catalysts

    Fu Xiaoqin; Tian Songbai; Hou Shuandi; Longjun; Wang Xieqing

    2008-01-01

    The energy barriers of thermal decarboxylation reactions of petroleum acids and catalytic decarboxylation reactions of Br(o)nsted acid and Lewis acid were analyzed using molecular simulation technology.Compared with thermal decarboxylation reactions of petroleum acids, the decarboxylation reactions by acid catalysts were easier to occur. The decarboxylaton effect by Lewis acid was better than Br(o)nsted acid. The mechanisms of catalytic decarboxylation over acid catalyst were also verified by experiments on a fixed bed and a fluidized bed, the experimental results showed that the rate of acid removal could reach up to 97% over the acidic catalyst at a temperature above 400℃.

  11. Photoisomerization dynamics of a rhodopsin-based molecule (potential molecular switch) with high quantum yields

    Allen, Roland; Jiang, Chen-Wei; Zhang, Xiu-Xing; Fang, Ai-Ping; Li, Hong-Rong; Xie, Rui-Hua; Li, Fu-Li

    2015-03-01

    It is worthwhile to explore the detailed reaction dynamics of various candidates for molecular switches, in order to understand, e.g., the differences in quantum yields and switching times. Here we report density-functional-based simulations for the rhodopsin-based molecule 4-[4-Methylbenzylidene]-5-p-tolyl-3,4-dihydro-2H-pyrrole (MDP), synthesized by Sampedro et al. We find that the photoisomerization quantum yields are remarkably high: 82% for cis-to-trans, and 68% for trans-to-cis. The lifetimes of the S1 excited state in cis-MDP in our calculations are in the range of 900-1800 fs, with a mean value of 1270 fs, while the range of times required for full cis-to-trans isomerization are 1100-2000 fs, with a mean value of 1530 fs. In trans-MDP, the calculated S1 excited state lifetimes are 860-2140 fs, with a mean value of 1330 fs, and with the full trans-to-cis isomerization completed about 200 fs later. In both cases, the dominant reaction mechanism is rotation around the central C =C bond (connected to the pyrroline ring), and de-excitation occurs at an avoided crossing between the ground state and the lowest singlet state, near the midpoint of the rotational pathway. Research Fund for the Doctoral Program of Higher Education of China; Fundamental Research Funds for the Central Universities; Robert A. Welch Foundation; National Natural Science Foundation of China.

  12. Selective detection of fenaminosulf via a molecularly imprinted fluorescence switch and silver nano-film amplification.

    Li, Shuhuai; Yin, Guihao; Zhang, Qun; Li, Chunli; Luo, Jinhui; Xu, Zhi; Qin, Anli

    2015-09-15

    A novel fluorescence switch sensor was constructed for detecting the fungicide fenaminosulf (FM), based on a dye-doped molecularly imprinted polymer (MIP) and silver nanofilm amplification. The MIP was prepared by electropolymerization of hydroquinone doped with neutral red on the silver nanofilm modified electrode. A fluorescence signal was produced by the neutral red and the fluorescence intensity was diminished by the ion pair that formed via electrostatic forces between FM and the dye. Therefore, elution and adsorption of FM by the MIP acted as a switch to control the fluorescence intensity, which was effectively amplified by the silver nanofilm. The decrease in fluorescence intensity was linear with the FM concentration, establishing a new method for FM detection. Under optimal conditions, good linear correlation was obtained for FM concentrations over the range from 2.0 × 10(-10) to 4.0 × 10(-8)mol/L, with a detection limit of 1.6 × 10(-11)mol/L. This method was utilized to determine residual FM in vegetable samples, and recoveries ranging from 92.0% to 110% were obtained. PMID:25930004

  13. Photoinduced reversible switching of porosity in molecular crystals based on star-shaped azobenzene tetramers

    Baroncini, Massimo; D'Agostino, Simone; Bergamini, Giacomo; Ceroni, Paola; Comotti, Angiolina; Sozzani, Piero; Bassanetti, Irene; Grepioni, Fabrizia; Hernandez, Taylor M.; Silvi, Serena; Venturi, Margherita; Credi, Alberto

    2015-08-01

    The development of solid materials that can be reversibly interconverted by light between forms with different physico-chemical properties is of great interest for separation, catalysis, optoelectronics, holography, mechanical actuation and solar energy conversion. Here, we describe a series of shape-persistent azobenzene tetramers that form porous molecular crystals in their E-configuration, the porosity of which can be tuned by changing the peripheral substituents on the molecule. Efficient E→Z photoisomerization of the azobenzene units takes place in the solid state and converts the crystals into a non-porous amorphous melt phase. Crystallinity and porosity are restored upon Z→E isomerization promoted by visible light irradiation or heating. We demonstrate that the photoisomerization enables reversible on/off switching of optical properties such as birefringence as well as the capture of CO2 from the gas phase. The linear design, structural versatility and synthetic accessibility make this new family of materials potentially interesting for technological applications.

  14. Photodynamic activation as a molecular switch to promote osteoblast cell differentiation via AP-1 activation.

    Kushibiki, Toshihiro; Tu, Yupeng; Abu-Yousif, Adnan O; Hasan, Tayyaba

    2015-01-01

    In photodynamic therapy (PDT), cells are impregnated with a photosensitizing agent that is activated by light irradiation, thereby photochemically generating reactive oxygen species (ROS). The amounts of ROS produced depends on the PDT dose and the nature of the photosensitizer. Although high levels of ROS are cytotoxic, at physiological levels they play a key role as second messengers in cellular signaling pathways, pluripotency, and differentiation of stem cells. To investigate further the use of photochemically triggered manipulation of such pathways, we exposed mouse osteoblast precursor cells and rat primary mesenchymal stromal cells to low-dose PDT. Our results demonstrate that low-dose PDT can promote osteoblast differentiation via the activation of activator protein-1 (AP-1). Although PDT has been used primarily as an anti-cancer therapy, the use of light as a photochemical "molecular switch" to promote differentiation should expand the utility of this method in basic research and clinical applications. PMID:26279470

  15. Synthesis and Characterization of Molecularly Imprinted Polymers for Phenoxyacetic Acids

    Canping Pan

    2008-01-01

    Full Text Available 2-methylphenoxyacetic acid (2-MPA, 2-methyl-4-chlorophenxyacetic acid (MCPA and 4-chlorophenoxyacetic acid (4-CPA were imprinted to investigate the cross-selectivities of molecularly imprinted polymers (MIPs. The result indicates that 2-MPA, which is similar in shape, size and functionality with phenoxyacetic herbicides, are suitable to be used as a suitable template to prepare the MIPs for retaining phenoxyacetic herbicides. To study the ion-pair interactions between template molecules and functional monomer 4-vinylpiridine (4-VP, computational molecular modeling was employed. The data indicate that the cross-selectivities of MIPs for phenoxyacetic acid herbicides depend on the binding energies of complexes.

  16. The molecular physiology of uric acid homeostasis.

    Mandal, Asim K; Mount, David B

    2015-01-01

    Uric acid, generated from the metabolism of purines, has proven and emerging roles in human disease. Serum uric acid is determined by production and the net balance of reabsorption or secretion by the kidney and intestine. A detailed understanding of epithelial absorption and secretion of uric acid has recently emerged, aided in particular by the results of genome-wide association studies of hyperuricemia. Novel genetic and regulatory networks with effects on uric acid homeostasis have also emerged. These developments promise to lead to a new understanding of the various diseases associated with hyperuricemia and to novel, targeted therapies for hyperuricemia. PMID:25422986

  17. Molecular Modeling of Nucleic Acid Structure: Energy and Sampling

    Bergonzo, Christina; Galindo-Murillo, Rodrigo; Cheatham, Thomas E.

    2001-01-01

    An overview of computer simulation techniques as applied to nucleic acid systems is presented. This unit discusses methods used to treat the energy and to sample representative configurations. Emphasis is placed on molecular mechanics and empirical force fields.

  18. Contribution of the metal/SiO2 interface potential to photoinduced switching in molecular single-electron tunneling junctions

    Photoinduced switching of the Coulomb staircase in molecular single-electron tunneling junctions was previously observed. These junctions consisted of evaporated SiO2 insulator (∼5 nm), with tetrakis-3,5-di-t-butylphenyl-porphyrin (H2-TBPP) molecules as Coulomb islands, sandwiched between top and bottom electrodes. The reversible response and the relaxation time of the photoinduced switching suggest that this phenomenon depends on the properties of the metal/SiO2 interface rather than those of the H2-TBPP molecule or SiO2 tunneling layer. We analyzed the photoinduced switching according to the theory of single-electron tunneling taking into account the discrete molecular energy states and the metal/SiO2 interfacial electrostatic phenomena. We conclude that the main contributor to the photoinduced shift was the electrostatic potential formed through the space-charge exchange at the metal/SiO2 interface

  19. Tip-induced domain structures and polarization switching in ferroelectric amino acid glycine

    Bioorganic ferroelectrics and piezoelectrics are becoming increasingly important in view of their intrinsic compatibility with biological environment and biofunctionality combined with strong piezoelectric effect and a switchable polarization at room temperature. Here, we study tip-induced domain structures and polarization switching in the smallest amino acid β-glycine, representing a broad class of non-centrosymmetric amino acids. We show that β-glycine is indeed a room-temperature ferroelectric and polarization can be switched by applying a bias to non-polar cuts via a conducting tip of atomic force microscope (AFM). Dynamics of these in-plane domains is studied as a function of an applied voltage and pulse duration. The domain shape is dictated by polarization screening at the domain boundaries and mediated by growth defects. Thermodynamic theory is applied to explain the domain propagation induced by the AFM tip. Our findings suggest that the properties of β-glycine are controlled by the charged domain walls which in turn can be manipulated by an external bias

  20. Tip-induced domain structures and polarization switching in ferroelectric amino acid glycine

    Seyedhosseini, E., E-mail: Seyedhosseini@ua.pt; Ivanov, M. [CICECO-Aveiro Institute of Materials and Department of Physics, University of Aveiro, 3810-193 Aveiro (Portugal); Bdikin, I. [TEMA and Department of Mechanical Engineering, University of Aveiro, 3810-193 Aveiro (Portugal); Vasileva, D. [Institute of Natural Sciences, Ural Federal University, 620000 Ekaterinburg (Russian Federation); Kudryavtsev, A. [Moscow State Institute of Radioengineering, Electronics and Automation, 119454 Moscow (Russian Federation); Rodriguez, B. J. [Conway Institute of Biomolecular and Biomedical Research and School of Physics, University College Dublin, Dublin (Ireland); Kholkin, A. L. [CICECO-Aveiro Institute of Materials and Department of Physics, University of Aveiro, 3810-193 Aveiro (Portugal); Institute of Natural Sciences, Ural Federal University, 620000 Ekaterinburg (Russian Federation)

    2015-08-21

    Bioorganic ferroelectrics and piezoelectrics are becoming increasingly important in view of their intrinsic compatibility with biological environment and biofunctionality combined with strong piezoelectric effect and a switchable polarization at room temperature. Here, we study tip-induced domain structures and polarization switching in the smallest amino acid β-glycine, representing a broad class of non-centrosymmetric amino acids. We show that β-glycine is indeed a room-temperature ferroelectric and polarization can be switched by applying a bias to non-polar cuts via a conducting tip of atomic force microscope (AFM). Dynamics of these in-plane domains is studied as a function of an applied voltage and pulse duration. The domain shape is dictated by polarization screening at the domain boundaries and mediated by growth defects. Thermodynamic theory is applied to explain the domain propagation induced by the AFM tip. Our findings suggest that the properties of β-glycine are controlled by the charged domain walls which in turn can be manipulated by an external bias.

  1. Mucosal transmissibility, disease induction and coreceptor switching of R5 SHIVSF162P3N molecular clones in rhesus macaques

    Ren Wuze; Mumbauer Alexandra; Zhuang Ke; Harbison Carole; Knight Heather; Westmoreland Susan; Gettie Agegnehu; Blanchard James; Cheng-Mayer Cecilia

    2013-01-01

    Abstract Background Mucosally transmissible and pathogenic CCR5 (R5)-tropic simian-human immunodeficiency virus (SHIV) molecular clones are useful reagents to identity neutralization escape in HIV-1 vaccine experiments and to study the envelope evolutionary process and mechanistic basis for coreceptor switch during the course of natural infection. Results We observed progression to AIDS in rhesus macaques infected intrarectally with molecular clones of the pathogenic R5 SHIVSF162P3N isolate. ...

  2. Controlling the color of cholesteric liquid-crystalline films by photoirradiation of a chiroptical molecular switch used as dopant

    van Delden, RA; Huck, NPM; Feringa, BL; Delden, Richard A. van; Gelder, Marc B. van; Huck, Nina P.M.

    2003-01-01

    Using thin films of a cholesteric mixture of acrylates 2 and 3 doped with the chiroptical molecular switch (M)-trans-1, photo-control of the reflection color between red and green is possible. This doped liquid-crystal (LC) film can be used for photoinduced writing, color reading, and photoinduced l

  3. Accurate Molecular Dimensions from Stearic Acid Monolayers.

    Lane, Charles A.; And Others

    1984-01-01

    Discusses modifications in the fatty acid monolayer experiment to reduce the inaccurate moleculary data students usually obtain. Copies of the experimental procedure used and a Pascal computer program to work up the data are available from the authors. (JN)

  4. Molecular Modeling of Trifluoromethanesulfonic Acid for Solvation Theory

    Paddison, S J; Zawodzinski, T; Reagor, D W; Paddison, Stephen J.; Pratt, Lawrence R.; Zawodzinski, Thomas; Reagor, David W.

    1997-01-01

    Reported here are theoretical calculations on the triflic acid and water, establishing molecular scale information necessary to modeling of the structure, thermodynamics, and ionic transport of Nafion membranes. To characterize side chain flexibility and accessibility of the acid proton, free energies for rotation of both carbon-sulfur and sulfur-oxygen (hydroxyl) bonds are presented. The energetic barrier to rotation of the acid proton away from the sulfonic acid oxygen plane is substantially flattened, with barrier less than one kcal/mol, by electrostatic solvation. The activation free energy for acid-water proton interchange is about 4.7 kcal/mol.

  5. Synthesis and Characterization of Molecularly Imprinted Polymers for Phenoxyacetic Acids

    Canping Pan; Tiechun Chen; Fulin Zong; Tao Song; Huiting Zhang

    2008-01-01

    2-methylphenoxyacetic acid (2-MPA), 2-methyl-4-chlorophenxyacetic acid (MCPA) and 4-chlorophenoxyacetic acid (4-CPA) were imprinted to investigate the cross-selectivities of molecularly imprinted polymers (MIPs). The result indicates that 2-MPA, which is similar in shape, size and functionality with phenoxyacetic herbicides, are suitable to be used as a suitable template to prepare the MIPs for retaining phenoxyacetic herbicides. To study the ion-pair interactions between template molecules a...

  6. The Molecular Switching Mechanism at the Conserved D(E)RY Motif in Class-A GPCRs.

    Sandoval, Angelica; Eichler, Stefanie; Madathil, Sineej; Reeves, Philip J; Fahmy, Karim; Böckmann, Rainer A

    2016-07-12

    The disruption of ionic and H-bond interactions between the cytosolic ends of transmembrane helices TM3 and TM6 of class-A (rhodopsin-like) G protein-coupled receptors (GPCRs) is a hallmark for their activation by chemical or physical stimuli. In the bovine photoreceptor rhodopsin, this is accompanied by proton uptake at Glu(134) in the class-conserved D(E)RY motif. Studies on TM3 model peptides proposed a crucial role of the lipid bilayer in linking protonation to stabilization of an active state-like conformation. However, the molecular details of this linkage could not be resolved and have been addressed in this study by molecular dynamics (MD) simulations on TM3 model peptides in a bilayer of 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC). We show that protonation of the conserved glutamic acid alters the peptide insertion depth in the membrane, its side-chain rotamer preferences, and stabilizes the C-terminal helical structure. These factors contribute to the rise of the side-chain pKa (> 6) and to reduced polarity around the TM3 C terminus as confirmed by fluorescence spectroscopy. Helix stabilization requires the protonated carboxyl group; unexpectedly, this stabilization could not be evoked with an amide in MD simulations. Additionally, time-resolved Fourier transform infrared (FTIR) spectroscopy of TM3 model peptides revealed a different kinetics for lipid ester carbonyl hydration, suggesting that the carboxyl is linked to more extended H-bond clusters than an amide. Remarkably, this was seen as well in DOPC-reconstituted Glu(134)- and Gln(134)-containing bovine opsin mutants and demonstrates that the D(E)RY motif is a hydrated microdomain. The function of the D(E)RY motif as a proton switch is suggested to be based on the reorganization of the H-bond network at the membrane interface. PMID:27410736

  7. A dynamic view of molecular switch behavior at serotonin receptors: implications for functional selectivity.

    Martí-Solano, Maria; Sanz, Ferran; Pastor, Manuel; Selent, Jana

    2014-01-01

    Functional selectivity is a property of G protein-coupled receptors that allows them to preferentially couple to particular signaling partners upon binding of biased agonists. Publication of the X-ray crystal structure of serotonergic 5-HT1B and 5-HT2B receptors in complex with ergotamine, a drug capable of activating G protein coupling and β-arrestin signaling at the 5-HT1B receptor but clearly favoring β-arrestin over G protein coupling at the 5-HT2B subtype, has recently provided structural insight into this phenomenon. In particular, these structures highlight the importance of specific residues, also called micro-switches, for differential receptor activation. In our work, we apply classical molecular dynamics simulations and enhanced sampling approaches to analyze the behavior of these micro-switches and their impact on the stabilization of particular receptor conformational states. Our analysis shows that differences in the conformational freedom of helix 6 between both receptors could explain their different G protein-coupling capacity. In particular, as compared to the 5-HT1B receptor, helix 6 movement in the 5-HT2B receptor can be constrained by two different mechanisms. On the one hand, an anchoring effect of ergotamine, which shows an increased capacity to interact with the extracellular part of helices 5 and 6 and stabilize them, hinders activation of a hydrophobic connector region at the center of the receptor. On the other hand, this connector region in an inactive conformation is further stabilized by unconserved contacts extending to the intracellular part of the 5-HT2B receptor, which hamper opening of the G protein binding site. This work highlights the importance of considering receptor capacity to adopt different conformational states from a dynamic perspective in order to underpin the structural basis of functional selectivity. PMID:25313636

  8. A dynamic view of molecular switch behavior at serotonin receptors: implications for functional selectivity.

    Maria Martí-Solano

    Full Text Available Functional selectivity is a property of G protein-coupled receptors that allows them to preferentially couple to particular signaling partners upon binding of biased agonists. Publication of the X-ray crystal structure of serotonergic 5-HT1B and 5-HT2B receptors in complex with ergotamine, a drug capable of activating G protein coupling and β-arrestin signaling at the 5-HT1B receptor but clearly favoring β-arrestin over G protein coupling at the 5-HT2B subtype, has recently provided structural insight into this phenomenon. In particular, these structures highlight the importance of specific residues, also called micro-switches, for differential receptor activation. In our work, we apply classical molecular dynamics simulations and enhanced sampling approaches to analyze the behavior of these micro-switches and their impact on the stabilization of particular receptor conformational states. Our analysis shows that differences in the conformational freedom of helix 6 between both receptors could explain their different G protein-coupling capacity. In particular, as compared to the 5-HT1B receptor, helix 6 movement in the 5-HT2B receptor can be constrained by two different mechanisms. On the one hand, an anchoring effect of ergotamine, which shows an increased capacity to interact with the extracellular part of helices 5 and 6 and stabilize them, hinders activation of a hydrophobic connector region at the center of the receptor. On the other hand, this connector region in an inactive conformation is further stabilized by unconserved contacts extending to the intracellular part of the 5-HT2B receptor, which hamper opening of the G protein binding site. This work highlights the importance of considering receptor capacity to adopt different conformational states from a dynamic perspective in order to underpin the structural basis of functional selectivity.

  9. An electrostatic/hydrogen bond switch as the basis for the specific interaction of phosphatidic acid with proteins.

    Kooijman, Edgar E; Tieleman, D Peter; Testerink, Christa; Munnik, Teun; Rijkers, Dirk T S; Burger, Koert N J; de Kruijff, Ben

    2007-04-13

    Phosphatidic acid (PA) is a minor but important phospholipid that, through specific interactions with proteins, plays a central role in several key cellular processes. The simple yet unique structure of PA, carrying just a phosphomonoester head group, suggests an important role for interactions with the positively charged essential residues in these proteins. We analyzed by solid-state magic angle spinning 31P NMR and molecular dynamics simulations the interaction of low concentrations of PA in model membranes with positively charged side chains of membrane-interacting peptides. Surprisingly, lysine and arginine residues increase the charge of PA, predominantly by forming hydrogen bonds with the phosphate of PA, thereby stabilizing the protein-lipid interaction. Our results demonstrate that this electrostatic/hydrogen bond switch turns the phosphate of PA into an effective and preferred docking site for lysine and arginine residues. In combination with the special packing properties of PA, PA may well be nature's preferred membrane lipid for interfacial insertion of positively charged membrane protein domains. PMID:17277311

  10. A novel colorimetric triple-helix molecular switch aptasensor for ultrasensitive detection of tetracycline.

    Ramezani, Mohammad; Mohammad Danesh, Noor; Lavaee, Parirokh; Abnous, Khalil; Mohammad Taghdisi, Seyed

    2015-08-15

    Detection methods of antibiotic residues in blood serum and animal derived foods are of great interest. In this study a colorimetric aptasensor was designed for sensitive, selective and fast detection of tetracycline based on triple-helix molecular switch (THMS) and gold nanoparticles (AuNPs). As a biosensor, THMS shows distinct advantages including high stability, sensitivity and preserving the selectivity and affinity of the original aptamer. In the absence of tetracycline, THMS is stable, leading to the aggregation of AuNPs by salt and an obvious color change from red to blue. In the presence of tetracycline, aptamer binds to its target, signal transduction probe (STP) leaves the THMS and adsorbs on the surface of AuNPs. So the well-dispersed AuNPs remain stable against salt-induced aggregation with a red color. The presented aptasensor showed high selectivity toward tetracyclines with a limit of detection as low as 266 pM for tetracycline. The designed aptasensor was successfully applied to detect tetracycline in serum and milk. PMID:25814407

  11. Molecular switch for tuning ions across nanopores by an external electric field

    Active control of ion transport in nanoscale channels is attracting increasing attention. Recently, experimental and theoretical results have verified that depending on the charged surface of nanopores, the solution inside nanopores can contain either negative or positive ions, which does not happen in macroscale channels. However, the control of the surface chemistry of synthetic nanopores is difficult and the design of nanotubes with novel recognition mechanisms that regulate the ionic selectivity of negative and positive charges remains a challenge. We present here a design for an ion-selective nanopore that is controllable by external charges. Our molecular dynamics simulations show that this remarkable selectivity can be switched from predominantly negative to positive ions and that the magnitude of the ionic flux can be varied by changing the distance of the external charges. The results suggest that the hydration structures around ions play a prominent role in the selectivity process, which is tuned by the external charge. These studies may be useful for developing ways to control the behavior, properties and chemical composition of liquids and provide possible technical applications for nanofluidic field effect transistors. (paper)

  12. Temperature control of molecular circuit switch responsible for virulent phenotype expression in uropathogenic Escherichia coli

    Samoilov, Michael

    2010-03-01

    The behavior and fate of biological organisms are to a large extent dictated by their environment, which can be often viewed as a collection of features and constraints governed by physics laws. Since biological systems comprise networks of molecular interactions, one such key physical property is temperature, whose variations directly affect the rates of biochemical reactions involved. For instance, temperature is known to control many gene regulatory circuits responsible for pathogenicity in bacteria. One such example is type 1 fimbriae (T1F) -- the foremost virulence factor in uropathogenic E. coli (UPEC), which accounts for 80-90% of all community-acquired urinary tract infections (UTIs). The expression of T1F is randomly `phase variable', i.e. individual cells switch between virulent/fimbriate and avirulent/afimbriate phenotypes, with rates regulated by temperature. Our computational investigation of this process, which is based on FimB/FimE recombinase-mediated inversion of fimS DNA element, offers new insights into its discrete-stochastic kinetics. In particular, it elucidates the logic of T1F control optimization to the host temperature and contributes further understanding toward the development of novel therapeutic approaches to UPEC-caused UTIs.

  13. Electropolymerized Molecularly Imprinted Polypyrrole Film for Sensing of Clofibric Acid

    Bianca Schweiger

    2015-02-01

    Full Text Available Piezoelectric quartz crystals and analogous gold substrates were electrochemically coated with molecularly imprinted polypyrrole films for pulsed amperometric detection (PAD of clofibric acid, a metabolite of clofibrate. Cyclic voltammetry data obtained during polymerization and deposited weight estimations revealed a decrease of the polymerization rate with increasing clofibric acid concentration. XPS measurements indicated that clofibric acid could be removed after imprinting with an aqueous ethanol solution, which was further optimized by using PAD. Zeta potential and contact angle measurements revealed differences between molecularly imprinted (MIP and non-imprinted polymer (NIP layers. Binding experiments with clofibric acid and other substances showed a pronounced selectivity of the MIP for clofibric acid vs. carbamazepine, but the response of MIP and NIP to 2,4-dichlorophenoxyacetic acid was higher than that for clofibric acid. A smooth surface, revealed by AFM measurements, with roughness of 6–8 nm for imprinted and non-imprinted layers, might be a reason for an excessively low density of specific binding sites for clofibric acid. Furthermore, the decreased polymerization rate in the presence of clofibric acid might not result in well-defined polymer structures, which could be the reason for the lower sensitivity.

  14. Simultaneous determination of amino acids and carbohydrates in culture media of Clostridium thermocellum by valve-switching ion chromatography.

    Fa, Yun; Yang, Haiyan; Ji, Chengshuai; Cui, He; Zhu, Xinshu; Du, Juan; Gao, Jun

    2013-10-10

    An improved method for the simultaneous determination of 20 amino acids and 7 carbohydrates using one-valve switching after injection, ion chromatography, and integrated pulsed amperometric detection is proposed. The resolution of the amino acids and carbohydrates in the cation trap column was investigated. In addition, parameters including flow liquid type, flow rate, concentration, and valve-switch timing were optimized. The method is time-saving, effective, and accurate for the simultaneous separation of amino acids and carbohydrates, with a mean correlation coefficient of >0.99 and repeatability of 0.5-4.6% for eight replicates. The method was successfully applied in the analysis of amino acids and carbohydrates in aseptic media and in extracellular culture media of three phenotypes of Clostridium thermocellum. PMID:24070489

  15. Ultrafast quantum spin-state switching in the Co-octaethylporphyrin molecular magnet with a terahertz pulsed magnetic field

    Farberovich, Oleg V.; Mazalova, Victoria L.

    2016-05-01

    Molecular spin crossover switches are the objects of intense theoretical and experimental studies in recent years. This interest is due to the fact that these systems allow one to control their spin state by applying an external photo-, thermo-, piezo-, or magnetic stimuli. The greatest amount of research is currently devoted to the study of the effect of the photoexcitation on the bi-stable states of spin crossover single molecular magnets (SMMs). The main limitation of photo-induced bi-stable states is their short lifetime. In this paper we present the results of a study of the spin dynamics of the Co-octaethylporphyrin (CoOEP) molecule in the Low Spin (LS) state and the High Spin (HS) state induced by applying the magnetic pulse of 36.8 T. We show that the spin switching in case of the HS state of the CoOEP molecule is characterized by a long lifetime and is dependent on the magnitude and duration of the applied field. Thus, after applying an external stimuli the system in the LS state after the spin switching reverts to its ground state, whereas the system in the HS state remains in the excited state for a long time. We found that the temperature dependency of magnetic susceptibility shows an abrupt thermal spin transition between two spin states at 40 K. Here the proposed theoretical approach opens the way to create modern devices for spintronics with the controllable spin switching process.

  16. Isomerization of Orthogonal Molecular Switches Encapsulated within Micelles Solubilizing Carbon Nanotubes

    Kreft, Stefanie K.; Petersen, Michael Åxman; Nielsen, Mogens Brøndsted;

    2015-01-01

    We study the effects of the proximity of the orthogonal dipole-switching moiety dihydroazulene/vinylheptafulvene (DHA/VHF) to carbon nanotubes (CNTs). The switches are introduced into a micelle surrounding the CNTs, thereby achieving very close proximity between the molecules and the CNTs for the...... first time. The change of the molecules' configuration is not hindered by its encapsulation: We report the reversible switching of molecules inside CNT surrounding micelles. The orthogonality of the switch also allows us for the first time to observe the effect of the molecule on the emission spectra of...

  17. Study on Triplex DNA by Use of Molecular "Light Switch" Complex of Ru(phen)2(dppx)2+

    2003-01-01

    A new method for the study of triplex DNA is established according the fluorescence enhancement of molecular "Light Switch" complex of Ru(phen)2(dppx)2+ when it intercalate into triplex DNA. Because the fluorescence intensity of Ru(phen)2(dppx)2+ bonded to triplex DNA is in the case higher than that bonded to duplex DNA in certain range of DNA concentration, the method is much more sensitive than other methods reported previously.

  18. Identification of the molecular switch that regulates access of 5α-DHT to the androgen receptor.

    Penning, Trevor M.; Bauman, David R.; Jin, Yi; Rizner, Tea Lanisik

    2007-01-01

    Pairs of hydroxysteroid dehydrogenases (HSDs) govern ligand access to steroid receptors in target tissues and act as molecular switches. By acting as reductases or oxidases, HSDs convert potent ligands into their cognate inactive metabolites or vice-versa. This pre-receptor regulation of steroid hormone action may have profound effects on hormonal response. We have identified the HSDs responsible for regulating ligand access to the androgen receptor (AR) in human prostate. Type 3 3α-hydroxyst...

  19. A Redox-Controllable Molecular Switch Based on Weak Recognition of BPX26C6 at a Diphenylurea Station

    Jia-Cheng Chang

    2015-01-01

    Full Text Available The Na+ ion–assisted recognition of urea derivatives by BPX26C6 has allowed the construction of a redox-controllable [2]rotaxane-type molecular switch based on two originally very weakly interacting host/guest systems. Using NOBF4 to oxidize the triarylamine terminus into a corresponding radical cation attracted the macrocyclic component toward its adjacent carbamate station; subsequent addition of Zn powder moved the macrocyclic component back to its urea station.

  20. Preparing and regulating a bi-stable molecular switch by atomic manipulation

    We present a scanning tunneling microscopy (STM) investigation into the influence of the STM tip on the adsorption site switching of polychlorinatedbiphenyl (PCB) molecules on the Si(111)-7 × 7 surface at room temperature. From an initially stable adsorption configuration, atomic manipulation by charge injection from the STM tip prepared a new bi-stable configuration that switched between two bonding arrangements. No switching rate bias dependence was found for + 1.0 to + 2.2 V. Assuming a thermally driven switching process we find that the measured energy barriers to switching are influenced by the exact location of the STM tip by more than 10%. We propose that this energy difference is due the dispersion interaction between the tip and the molecule.

  1. Aptamer contained triple-helix molecular switch for rapid fluorescent sensing of acetamiprid.

    Liu, Xin; Li, Ying; Liang, Jing; Zhu, Wenyue; Xu, Jingyue; Su, Ruifang; Yuan, Lei; Sun, Chunyan

    2016-11-01

    In this study, an aptamer-based fluorescent sensing platform using triple-helix molecular switch (THMS) was developed for the pesticide screening represented by acetamiprid. The THMS was composed of two tailored DNA probes: a label-free central target specific aptamer sequence flanked by two arm segments acting as a recognition probe; a hairpin-shaped structure oligonucleotide serving as a signal transduction probe (STP), labeled with a fluorophore and a quencher at the 3' and 5'-end, respectively. In the absence of acetamiprid, complementary bindings of two arm segments of the aptamers with the loop sequence of STP enforce the formation of THMS with the "open" configuration of STP, and the fluorescence of THMS is on. In the presence of target acetamiprid, the aptamer-target binding results in the formation of a structured aptamer/target complex, which disassembles the THMS and releases the STP. The free STP is folded to a stem loop structure, and the fluorescence is quenched. The quenched fluorescence intensity was proportional to the concentration of acetamiprid in the range from 100 to 1200nM, with the limit of detection (LOD) as low as 9.12nM. In addition, this THMS-based method has been successfully used to test and quantify acetamiprid in Chinese cabbage with satisfactory recoveries, and the results were in full agreement with those from LC-MS. The aptamer-based THMS presents distinct advantages, including high stability, remarkable sensitivity, and preservation of the affinity and specificity of the original aptamer. Most importantly, this strategy is convenient and generalizable by virtue of altering the aptamer sequence without changing the triple-helix structure. So, it is expected that this aptamer-based fluorescent assay could be extensively applied in the field of food safety inspection. PMID:27591592

  2. Molecular phylogeny of beetle associated diplogastrid nematodes suggests host switching rather than nematode-beetle coevolution

    Sommer Ralf J

    2009-08-01

    diplogastrid nematodes and their beetle hosts. Instead, frequent host switching is observed. The molecular phylogeny of the Diplogastridae provides a framework for further examinations of the evolution of these associations, for the study of interactions within the ecosystems, and for investigations of diplogastrid genome evolution.

  3. Incorporation of oxygen into abscisic acid and phaseic acid for molecular oxygen

    Abscisic acid accumulates in detached, wilted leaves of Xanthium strumariu. When these leaves are subsequently rehydrated, phaseic acid, a catabolite of abscisic acid, accumulates. Analysis by gas chromatography-mass spectrometry of phaseic acid isolated from stressed and subsequently rehydrated leaves placed in an atmosphere containing 20% 18O2 and 80% N2 indicates that one atom of 18O is incorporated in the 6'-hydroxymethyl group of phaseic acid. This suggests that the enzyme that converts abscisic acid to phaseic acid is an oxygenase. Analysis by gas chromatography-mass spectrometry of abscisic acid isolated from stressed leaves kept in an atmosphere containing 18O2 indicates that one atom of 18O is presented in the carboxyl group of abscisic acid. Thus, when abscisic acid accumulates in water-streesed leaves, only one of the four oxygens present in the abscisic acid molecule is derived from molecular oxygen. This suggest that either (a) the oxygen present in the 1'-, 4'-, and one of the two oxygens at the 1-position of abscisic acid arise from water, or (b) there exists a stored precursor with oxygen atoms already present in the 1'- and 4'-positions of abscisic acid which is converted to abscisic acid under conditions of water stress. 17 references, 2 figures, 1 tables

  4. Kinetics of molecular transformations in connective tissue hyaluronic acid

    When exposed to ionizing radiations or inflammatory disease, the glycosaminolycan component of connective tissue is preferentially degraded, probably by a free-radical mediate pathway. The resulting changes in molecular structure adversely change the properties of the matrix. Rooster comb hyaluronic acid of high molecular weight was used to investigate the mechanisms of these structural changes at macro and molecular level. Intrinsic viscosity and gel permeation chromatography measurements are suitable for demonstrating that random chain session occurs. Fast kinetic techniques are necessary to identify the mechanisms of single strand breaks. Pulse conductivity and low-angle laser light scattering pulse radiolysis can quantify the rate and yield of strand breaks. Competitive radical scavenging methods have also allowed the quantification of the rate of spontaneous and alkali-catalyzed hydrolysis of a-hydroxy radicals on polysaccharide chains, which control molecular structure changes

  5. Cyclic Zinc(II) Bisporphyrin-Based Molecular Switches: Supramolecular Control of Complexation-Mediated Conformational Switching and Photoinduced Electron Transfer.

    Mondal, Pritam; Rath, Sankar Prasad

    2016-04-11

    A cyclic zinc(II) bisporphyrin with flexible linker was employed as a dynamic molecular switch under the regulation of π-acceptors (tetracyanoquinodimethane, trinitrofluorenone, 9-dicyanomethylenefluorene) and bidentate N-donor ligands (1,4-diazabicyclo[2.2.2]octane, pyrazine, 4,4'-bipyridine). The cyclic bisporphyrin host can efficiently encapsulate the π-acceptor guests through the strong π-π interaction, which can be replaced again by using a bidentate N-donor ligand, which coordinates strongly with the metal centers. The open conformation of the bisporphyrin can be efficiently recovered by removing the bidentate ligands using Cu(+) ion. During the process, two porphyrin rings also reversibly change their relative orientation between perpendicular and parallel. The behavior of the cyclic bisporphyrin was followed by using UV/Vis, (1) H NMR, fluorescence, and electrochemical analyses along with X-ray structure determination of the complexes. Moreover, control of photoinduced electron transfer (PET "ON-OFF") is also achieved by the use of guest exchange. Association constants for the host-guest binding were very high, which further explains the robust nature of such assemblies in solution. The experimental evidence is supported by DFT calculations. Such controllable dynamic features can constitute a new step towards "smart" adaptive molecular devices and the emergence of such systems is of significant interest in supramolecular chemistry. PMID:27062017

  6. Molecular Dynamic Studies on Langmuir Monolayers of Stearic Acid

    KONG Chui-peng; ZHANG Hong-xing; ZHAO Zeng-xia; ZHENG Qing-chuan

    2013-01-01

    Compression isotherm for stearic acid was obtained by means of molecular dynamic simulation and compared to experimentally measured values for the Langmuir monolayers.Compared to the previous simulation,the present simulation has provided a method to reproduce the compression of the monolayer.The result is consistent with other experimental results.By analyzing the alkyl tails,the configuration of stearic acid molecules during the compression process was studied and a uniform monolayer was obtained after compression.Stearic acid molecules were observed to form fine organized monolayer from completely random structure.Hexatic order of the arrangement has been identified for the distribution of stearic acid molecules in the monolayer.At the end of the compression,the stearic acid molecules were tightly packed in the gap of two other molecules.At last,the hydrogen bonds in the system were analyzed.The main hydrogen bonds were from stearic acid-water interaction and their intensities constantly decreased with the decreased of surface area per molecule.The weak hydrogen bond interaction between stearic acid molecules may be the reason of easy collapse.

  7. Solvent extraction of molybdophosphoric acid with high-molecular alkylamines

    Extraction of dodecamolibdophosphoric acid H3PMo12O40 by nitrates of some high molecular amines (di-(2-ethylene-hexyl)-amine, diponylamine, diisoamyloctylamine) dichlorthane solution has been studied. The composition of associates in the organic phase may be presented as (BH3)PMo12O40, where BH+ is the protonized form of the amine. The overall conventional equilibrium constant of complex formation and extraction equals (1.51+-0.35)x1011

  8. A theoretical study of magnetoelectronic and switching properties of molecular magnetic tunnel junctions

    Soti, V.; Ravan, B. Abedi

    2016-01-01

    Electronic transport and switching properties of molecule-based magnetic tunnel junctions are investigated using the first-principles density functional theory and non-equilibrium Green function methods. As a result of being sandwiched between the ferromagnetic electrodes, a spin-polarization is induced in the nonmagnetic organic atoms. Magnitudes of the spin-polarizations in the trans-polyacetylene, cis-polyacetylene, terphenyl and pentacene chains are calculated and it is suggested that among these the pentacene molecules, because of showing a relatively higher magnetization can theoretically be more appropriate for utilization in spintronic devices. Furthermore, electrical switching capabilities of the junctions are studied and the results reveal that the pentacene junction due to having a larger ON/OFF ratio shows a better switching behavior. Finally, magnetoresistive properties are studied and it is shown that applying torsion can be an effective method to enhance and also adjust magnitudes of the magnetoresistances of the junctions.

  9. Single electron bipolar conductance switch driven by the molecular Aharonov-Bohm effect.

    Lee, Joonhee; Tallarida, Nicholas; Rios, Laura; Perdue, Shawn M; Apkarian, Vartkess Ara

    2014-06-24

    We demonstrate a conductance switch controlled by the spin-vibronic density of an odd electron on a single molecule. The junction current is modulated by the spin-flip bistability of the electron. Functional images are provided as wiring diagrams for control of the switch's frequency, amplitude, polarity, and duty-cycle. The principle of operation relies on the quantum mechanical phase associated with the adiabatic circulation of a spin-aligned electron around a conical intersection. The functional images quantify the governing vibronic Hamiltonian. PMID:24824563

  10. Voltage Regulated Uptake and Release of L-Glutamate from a Molecularly Selective Switch for Physiological Applications

    Fuchs, Kathrin; Hauff, Elizabeth von; Parisi, Jürgen; Weiler, Reto

    2009-12-01

    In this paper results are presented on the development of a device demonstrating the uptake and release of L-glutamate in solutions with neutral pH. A device which selectively regulates the concentration of biomolecules, such as the primary neural transmitter L-glutamate, could be useful for many biological and medical applications. In the literature it has been demonstrated that polypyrrole (PPy) is a promising material for the recognition basis of molecularly selective devices [1, 2]. In this study we investigated the feasibility of the PPy based "glutamate switch" for the voltage dependent uptake and release of L-glutamate for physiological applications

  11. First Acetic Acid Survey with CARMA in Hot Molecular Cores

    Shiao, Y -S Jerry; Remijan, Anthony J; Snyder, Lewis E; Friedel, Douglas N

    2010-01-01

    Acetic acid (CH$_3$COOH) has been detected mainly in hot molecular cores where the distribution between oxygen (O) and nitrogen (N) containing molecular species is co-spatial within the telescope beam. Previous work has presumed that similar cores with co-spatial O and N species may be an indicator for detecting acetic acid. However, does this presumption hold as higher spatial resolution observations become available of large O and N-containing molecules? As the number of detected acetic acid sources is still low, more observations are needed to support this postulate. In this paper, we report the first acetic acid survey conducted with the Combined Array for Research in Millimeter-wave Astronomy (CARMA) at 3 mm wavelengths towards G19.61-0.23, G29.96-0.02 and IRAS 16293-2422. We have successfully detected CH$_3$COOH via two transitions toward G19.61-0.23 and tentatively confirmed the detection toward IRAS 16293-2422 A. The determined column density of CH$_3$COOH is 2.0(1.0)$\\times 10^{16}$ cm$^{-2}$ and the...

  12. Memory effect of photoinduced conductivity switching controlled by pulsed voltages in a molecular conductor

    Iimori, Toshifumi; Ohta, Nobuhiro [Research Institute for Electronic Science, Hokkaido University, Sapporo 001-0020 (Japan); Naito, Toshio, E-mail: nohta@es.hokudai.ac.j [Division of Chemistry, Graduate School of Science, Hokkaido University, Sapporo 060-0810 (Japan)

    2009-02-01

    Transient photoresponses of the electrical conductivity in single crystals of an organic conductor alpha-(BEDT-TTF){sub 2}I{sub 3} are studied in the charge-ordered insulating phase. Electrical conductivity switching is observed in the presence of pulsed voltages and synchronous irradiation of nanosecond laser pulse. Current in the photoirradiated crystal as a function of applied voltages shows a bistability in a certain range of voltage. For the initial triggering of the conductivity switching, not only pulsed voltages but also photoirradiation is necessary. A high conductivity state produced by the switching can be repeatedly recovered by applying the pulsed voltages without further photoirradiation even after the current has been reduced to zero. This observation indicates a memory effect of the photoinduced conductivity switching. The appearance of the memory effect depends on the temporal width of the pulsed voltages, which are applied at a rate of approximately 8 Hz. In the measurement using short pulse widths, the memory effect is not observed. This controllability of the memory effect with the pulse width is related to the bistability of the current with respect to the photoirradiation intensity. The shape of the hysteresis loop appearing in the current versus photoirradiation intensity curve can be varied by changing the pulse width.

  13. Molecular Simulation of Naphthenic Acid Removal on Acidic Catalyst (Ⅰ) Mechanism of Catalytic Decarboxylation

    Fu Xiaoqin; Dai Zhenyu; Tian Songbai; Hou Suandi; Wang Xieqing

    2008-01-01

    In this paper, the charge distribution, the chemical bond order and the reactive performance of carboxylic acid model compounds on acidic catalyst were investigated by using molecular simulation technology. The simulation results showed that the bond order of C-O was higher than that of C-C,and C-C bond connected to the carbon atom in the carboxyl radical had the lowest bond order. The charge distributions of model naphthenic acids were similar in characteristics that the negative charges were concentrated on carboxyls. According to the simulation results, the mechanisms of catalytic decarboxylation over acidic solid catalyst were proposed, and a new route was put forward regarding removal of the naphthenic acid from crude oil through catalytic decarboxylation.

  14. Electrochemical control of quantum interference in anthraquinone-based molecular switches

    Markussen, Troels; Schiøtz, Jakob; Thygesen, Kristian Sommer

    2010-01-01

    absent in the hydroquinone molecular bridge. A simple explanation of the interference effect is achieved by transforming the frontier molecular orbitals into localized molecular orbitals thereby obtaining a minimal tight-binding model describing the transport in the relevant energy range in terms of...

  15. Determination of Acid Herbicides Using Modified QuEChERS with Fast Switching ESI(+)/ESI(-) LC-MS/MS.

    Sack, Chris; Vonderbrink, John; Smoker, Michael; Smith, Robert E

    2015-11-01

    A method for the determination of 35 acid herbicides in food matrices was developed, validated, and implemented. It utilizes a modified QuEChERS extraction procedure coupled with quantitation by liquid chromatography tandem mass spectrometry (LC-MS/MS). The acid herbicides analyzed are all organic carboxylic acids, including the older chlorophenoxy acid herbicides such as 2,4-dichlorophenoxyacetic acid (2,4-D), dicamba, 4-chlorophenoxyacetic acid (4-CPA), quinclorac, and many of the newer imidazolinone herbicides such as imazethapyr and imazaquin. In the procedure, 10 mL of water is added to 5 g of sample and then extracted with 1% formic acid in acetonitrile for 1 min. The acetonitrile phase is salted out of the extract by adding sodium chloride and magnesium sulfate, followed by centrifugation. The acetonitrile is diluted 1:1 with water to enable quantitation by LC-MS/MS using fast switching between positive and negative electrospray ionization modes. The average recoveries for all the compounds except aminocyclopyrachlor were 95% with a precision of 8%. The method detection limits for all residues were less than 10 ng/g, and the correlation coefficients for the calibration curves was greater than 0.99 for all but two compounds tested. The method was used successfully for the quantitation of acid herbicides in the FDA's total diet study. The procedure proved to be accurate, precise, linear, sensitive, and rugged. PMID:26473587

  16. Multilayered proteomics reveals molecular switches dictating ligand-dependent EGFR trafficking

    Francavilla, Chiara; Papetti, Moreno; Rigbolt, Kristoffer T G;

    2016-01-01

    , we devised an integrated multilayered proteomics approach (IMPA). We analyzed dynamic changes in the receptor interactome, ubiquitinome, phosphoproteome, and late proteome in response to both ligands in human cells by quantitative MS and identified 67 proteins regulated at multiple levels. We...... identified RAB7 phosphorylation and RCP recruitment to EGFR as switches for EGF and TGF-α outputs, controlling receptor trafficking, signaling duration, proliferation, and migration. By manipulating RCP levels or phosphorylation of RAB7 in EGFR-positive cancer cells, we were able to switch a TGF......-α-mediated response to an EGF-like response or vice versa as EGFR trafficking was rerouted. We propose IMPA as an approach to uncover fine-tuned regulatory mechanisms in cell signaling....

  17. Extrapolative Analysis of Fast-Switching Free Energy Estimates in a Molecular System

    Zuckerman, Daniel M.; Woolf, Thomas B.

    2001-01-01

    We perform an extrapolative analysis of "fast-growth" free-energy-difference (DF) estimates of a computer-modeled, fully-solvated ethanemethanol transformation. The results suggest that extrapolation can greatly reduce the systematic error in DF estimated from a small number of very fast switches. Our extrapolation procedure uses block-averages of finite-data estimates, and appears to be particularly useful for broad, non-Gaussian distributions of data which produce substantial systematic err...

  18. First principle calculations of molecular polarization switching in P(VDF-TrFE) ferroelectric thin Langmuir-Blodgett films

    This paper reports first principle calculations and analysis of the molecular mechanism of the polarization switching in polyvinylidene fluoride and its copolymer with trifluoroethylene (P(VDF-TrFE)) using semi-empirical and ab initio quantum chemical methods based on the HyperChem 7.5 and Gaussian98 programs. The simulations were performed for different copolymer contents in P(VDF-TrFE)-(70:30), (60:40) and pure PVDF. The calculated values of the dipole moment and average polarization of the molecular chains show a clear hysteresis under varying electric field with polarization saturated at ∼0.1-0.14 C m-2. The calculated coercive fields (corresponding to the rotation of molecular chains to opposite orientation) are consistent (within an order of magnitude) with experimental data obtained for thin films (Ec = 5-18 MV cm-1). In the absence of external electric fields, the interactions between several molecular chains lead to the orientation of all dipole moments along one direction parallel to the chain plane. This model corresponds to the PVDF layer on the dielectric surface. For the electric field in the perpendicular direction, all chains are rotated along this direction corresponding to the model of conductive substrate

  19. Molecular phylogeny of the bivalve superfamily Galeommatoidea (Heterodonta, Veneroida reveals dynamic evolution of symbiotic lifestyle and interphylum host switching

    Goto Ryutaro

    2012-09-01

    Full Text Available Abstract Background Galeommatoidea is a superfamily of bivalves that exhibits remarkably diverse lifestyles. Many members of this group live attached to the body surface or inside the burrows of other marine invertebrates, including crustaceans, holothurians, echinoids, cnidarians, sipunculans and echiurans. These symbiotic species exhibit high host specificity, commensal interactions with hosts, and extreme morphological and behavioral adaptations to symbiotic life. Host specialization to various animal groups has likely played an important role in the evolution and diversification of this bivalve group. However, the evolutionary pathway that led to their ecological diversity is not well understood, in part because of their reduced and/or highly modified morphologies that have confounded traditional taxonomy. This study elucidates the taxonomy of the Galeommatoidea and their evolutionary history of symbiotic lifestyle based on a molecular phylogenic analysis of 33 galeommatoidean and five putative galeommatoidean species belonging to 27 genera and three families using two nuclear ribosomal genes (18S and 28S ribosomal DNA and a nuclear (histone H3 and mitochondrial (cytochrome oxidase subunit I protein-coding genes. Results Molecular phylogeny recovered six well-supported major clades within Galeommatoidea. Symbiotic species were found in all major clades, whereas free-living species were grouped into two major clades. Species symbiotic with crustaceans, holothurians, sipunculans, and echiurans were each found in multiple major clades, suggesting that host specialization to these animal groups occurred repeatedly in Galeommatoidea. Conclusions Our results suggest that the evolutionary history of host association in Galeommatoidea has been remarkably dynamic, involving frequent host switches between different animal phyla. Such an unusual pattern of dynamic host switching is considered to have resulted from their commensalistic lifestyle, in

  20. How Ligands Throw the Molecular Switch in an Ion Channel: What >Patch-Clamping can Reveal.

    Tibbs, Gareth R.

    1998-03-01

    Ion channels are integral membrane proteins with two distinctive characteristics: they are gated (opened and closed) by specific signals such as membrane voltage or the direct binding of chemical ligands and, once open, they conduct ions across the cell membrane at very high rates (>10^7 s-1). Although analysis of the atomic structure of membrane proteins presents a daunting challenge, the relatively large currents carried by ion channels enable their active (open) state(s) to be readily distinguished from their inactive (closed) state(s). Coupled with the use of molecular biological techniques, this permits us to 1. Obtain details of kinetically distinguishable states of the channel, 2. Identify and characterize the functional roles of specific domains of the protein, and 3. Explore the thermodynamic contribution of domains or individual bonds to activation. I shall present data that explores such structure-function relationships within the cyclic nucleotide-gated (CNG) channel branch of the voltage-gated (VG) channel superfamily. Like the closely related VG K+ channels, the CNG channels are tetramers with each subunit having six putative transmembrane helices and cytoplasmic N and C termini. By measuring the amplitude of the current flowing through single chimeric channels we have demonstrated that the loop between the fifth and sixth helices is the major determinant of the ion-conducting pore. Guided by homology to cyclic nucleotide-binding (CNB) proteins whose crystal structure is known, it has been established that an 120 amino acid sequence within the C-terminus of each subunit forms a CNB site. By making selective mutations within this pocket and measuring the affinity and ability of bound agonist to activate the channel, it has been possible to establish whether the free energy of specific channel-agonist bonds contributes to activation of the protein or stabilization of ligand in the binding pocket. Finally, we have measured the ability of the channel to

  1. A theoretical investigation on anomalous switching of single-stranded deoxyribonucleic acid (ssDNA) monolayers by water vapor

    Zhao, Xin-Jun; Gao, Zhi-Fu; Jiang, Zhong-Ying

    2015-04-01

    In this paper, we use a molecular theory to study the anomalous switching of ssDNA monolayers. Here, both ssDNA-water and water-water hydrogen bonds and their explicit coupling to the ssDNA conformations are considered. We find that hydrogen bonding becomes a key element in inducing the anomalous switching of ssDNA monolayers. This finding accords well with the experimental observations. Based on our theoretical model, we predict that the anomalous switching induced by water vapor will be applicable to a wide range of hydrogen bonds polymers, and ssDNA-water hydrogen bonds and water-water hydrogen bonds hybridization will lead to the hydrogen-bond network formation of 3D ssDNA monolayers. Project supported by the National Natural Science Foundation of China (Grant Nos. 21264016, 11464047, and 21364016), the National Basic Research Program of China (Grant No. 2012CB821500), and the Natural Science Foundation of Xinjiang Uygur Autonomous Region, China (Grant No. 2013211A053).

  2. Design and Synthesis of Chiral Molecular Tweezers Based on Deoxycholic Acid

    2001-01-01

    A series of new chiral molecular tweezers have been designed and synthesized by using deoxycholic acid as spacer and aromatic amines as arms.Instead of using toxic phosgene,the triphosgene was employed in synthesis of the molecular tweezers receptors.These chiral molecular tweezers showed good enantioselectivity for D-amino acid methyl esters.

  3. PRODUCTION OF LOW MOLECULAR WEIGHT CHITOSAN BY HOT DILUTE SULFURIC ACID

    Akram Zamani; Mohammad Taherzadeh

    2010-01-01

    new method was developed for production of low molecular weight chitosan, in which high molecular weight chitosan was treated with dilute sulfuric acid at 120°C. Chitosan was dissolved in the acid solution in a few minutes, and as depolymerized to low molecular weight chitosan by longer times. Low molecular weight chitosan was recovered from the acid by cooling down the solution and increasing the pH to 8-10. A low molecular weight chitosan with Mv (viscosity average molecular weight) of 174×...

  4. Voltage-Induced Switching Dynamics of a Coupled Spin Pair in a Molecular Junction.

    Saygun, T; Bylin, J; Hammar, H; Fransson, J

    2016-04-13

    Molecular spintronics is made possible by the coupling between electronic configuration and magnetic polarization of the molecules. For control and application of the individual molecular states, it is necessary to both read and write their spin states. Conventionally, this is achieved by means of external magnetic fields or ferromagnetic contacts, which may change the intentional spin state and may present additional challenges when downsizing devices. Here, we predict that coupling magnetic molecules together opens up possibilities for all electrical control of both the molecular spin states as well as the current flow through the system. By tuning between the regimes of ferromagnetic and antiferromagnetic exchange interaction, the current can be at least an order of magnitude enhanced or reduced. The effect is susceptible to the tunnel coupling and molecular level alignment that can be used to achieve current rectification. PMID:27010805

  5. Molecular current switch: principles and photoelectronic characterization of the model system

    Vala, M.; Weiter, M.; Nešpůrek, Stanislav

    2005-01-01

    Roč. 15, č. 3 (2005), s. 28. ISSN 1210-7409 Institutional research plan: CEZ:AV0Z40500505 Keywords : molecular electronics * photochromism * charge transport Subject RIV: CD - Macromolecular Chemistry

  6. Deep molecular responses achieved in patients with CML-CP who are switched to nilotinib after long-term imatinib.

    Hughes, Timothy P; Lipton, Jeffrey H; Spector, Nelson; Cervantes, Francisco; Pasquini, Ricardo; Clementino, Nelma Cristina D; Dorlhiac Llacer, Pedro Enrique; Schwarer, Anthony P; Mahon, Francois-Xavier; Rea, Delphine; Branford, Susan; Purkayastha, Das; Collins, LaTonya; Szczudlo, Tomasz; Leber, Brian

    2014-07-31

    Patients in complete cytogenetic response (CCyR) with detectable BCR-ABL1 after ≥2 years on imatinib were randomized to nilotinib (400 mg twice daily, n = 104) or continued imatinib (n = 103) in the Evaluating Nilotinib Efficacy and Safety in clinical Trials-Complete Molecular Response (ENESTcmr) trial. By 1 and 2 years, confirmed undetectable BCR-ABL1 was achieved by 12.5% vs 5.8% (P = .108) and 22.1% vs 8.7% of patients in the nilotinib and imatinib arms, respectively (P = .0087). Among patients without molecular response 4.5 (BCR-ABL1(IS) ≤0.0032%; MR(4.5)) and those without major molecular response at study start, MR(4.5) by 2 years was achieved by 42.9% vs 20.8% and 29.2% vs 3.6% of patients in the nilotinib and imatinib arms, respectively. No patient in the nilotinib arm lost CCyR, vs 3 in the imatinib arm. Adverse events were more common in the nilotinib arm, as expected with the introduction of a new drug vs remaining on a well-tolerated drug. The safety profile of nilotinib was consistent with other reported studies. In summary, switching to nilotinib enabled more patients with chronic myeloid leukemia in chronic phase (CML-CP) to sustain lower levels of disease burden vs remaining on imatinib. This trial was registered at www.clinicaltrials.gov as #NCT00760877. PMID:24948656

  7. Voltage induced switching dynamics of a coupled spin pair in a molecular junction

    Saygun, T.; Bylin, J.; Hammar, H.; J. Fransson

    2016-01-01

    Molecular spintronics is made possible by the coupling between electronic configuration and magnetic po- larization of the molecules. For control and application of the individual molecular states it is necessary to both read and write their spin states. Conventionally, this is achieved by means of external magnetic fields or ferromagnetic contacts, which may change the intentional spin state and may present additional challenges when downsizing devices. Here, we predict that coupling magneti...

  8. A solid-state electrochemiluminescence biosensing switch for detection of DNA hybridization based on ferrocene-labeled molecular beacon

    A solid-state electrochemiluminescence (ECL) biosensing switch incorporating quenching of ECL of ruthenium(II) tris-(bipyridine) (Ru(bpy)32+) by ferrocene (Fc) has been successfully developed for DNA hybridization detection. The important issue for this biosensing system is based on the ferrocene-labeled molecular beacon (Fc-MB), i.e. using the special Fc-MB to react with the target DNA and then change its structure, resulting in an ECL intensity change. Under the optimal conditions, the difference of ECL intensity before and after the hybridization reaction (ΔIECL) was linearly related to the concentration of the complementary sequence in the range of 10 fM-10 pM and the detection limit was down to 1.0 fM.

  9. Current-induced forces: a new mechanism to induce negative differential resistance and current-switching effect in molecular junctions

    Gu, Lei; Fu, Hua-Hua

    2015-12-01

    Current-induced forces can excite molecules, polymers and other low-dimensional materials, which in turn leads to an effective gate voltage through Holstein interaction. Here, by taking a short asymmetric DNA junction as an example, and using the Langevin approach, we find that when suppression of charge transport by the effective gate voltage surpasses the current increase from an elevated voltage bias, the current-voltage (I-V) curves display strong negative differential resistance (NDR) and perfect current-switching characteristics. The asymmetric DNA chain differs in mechanical stability under inverse voltages and the I-V curve is asymmetric about inverse biases, which can be used to understand recent transport experiments on DNA chains, and meanwhile provides a new strategy to realize NDR in molecular junctions and other low-dimensional quantum systems.

  10. Sensitive and selective detection of uracil-DNA glycosylase activity with a new pyridinium luminescent switch-on molecular probe.

    Lu, Yu-Jing; Hu, Dong-Ping; Deng, Qiang; Wang, Zheng-Ya; Huang, Bao-Hua; Fang, Yan-Xiong; Zhang, Kun; Wong, Wing-Leung

    2015-09-01

    Uracil-deoxyribonucleic acid glycosylase (UDG) is known to function as an important base-excision repair enzyme and eliminate uracil from DNA molecules to maintain genomic integrity. A new small organic molecule (DID-VP) with interesting structural properties was synthesized as a G-quadruplex selective ligand and was demonstrated to be a sensitive luminescent switch-on probe in a convenient luminescent assay specifically for UDG detection in fetal bovine serum samples under rapid and simple conditions. This newly developed analytical method is based on the UDG enzymatic activity to unwind a duplex DNA substrate, and comprises a G-quadruplex-forming sequence (ON1) and uracil-containing DNA strand (ON2) to generate a remarkable fluorescence signal through the specific interaction of DID-VP with ON1. This luminescent switch-on assay is able to achieve high sensitivity and specificity for UDG over other enzymes. The application range of the present analytical system is found to be 0.05 to 1.00 U mL(-1) UDG with a very low detection limit of 0.005 U mL(-1). The recovery study of UDG in real samples gave a very good performance with 75.05%-102.7% recovery. In addition, an extended application of the assay in screening of UDG inhibitors is demonstrated. A good dose-dependence of the luminescence response with respect to the concentration of UDG inhibitors in samples was observed. PMID:26185800

  11. Lewis acid enhanced switching of the 1,1-dicyanodihydroazulene/vinylheptafulvene photo/thermoswitch

    Parker, Christian Richard; Tortzen, Christian Gregers; Broman, Søren Lindbæk;

    2011-01-01

    Mild Lewis acids enhance the rate of the thermal conversion of vinylheptafulvene (VHF) to dihydroazulene (DHA). In the absence of light, stronger Lewis acids promote the otherwise photoinduced DHA to VHF conversion....

  12. A novel purification process for dodecanedioic acid by molecular distillation

    Jiang Yu; Xigang Yuan; Aiwu Zeng

    2015-01-01

    A novel purification process is involved to obtain the high purity [N 99%(by mass)] dodecanedioic acid (DC12). It involves a re-crystal ization followed by molecular distil ation from the crude product. The objective of this study is to investigate general conditions, feed rate, distil ing temperature and vacuum, necessary for centrifugal distil-lation of DC12. Under the optimum conditions, distilling temperature 180 °C, pressure 30 Pa and feed flow rate 700 ml·h−1, the purity of DC12 in the residence reached 97.55%with a yield of 53.18%by the analysis of gas chromatography. Multiple-pass distillation made a considerable contribution by improving the purity to 99.22%. Additionally, the effect of pretreatment (re-crystallization) on distillation process was revealed through a series of comparative experiments.

  13. Fast transient current response to switching events in short chains of molecular islands

    Kalvová, Anděla; Špička, Václav; Velický, B.

    2013-01-01

    Roč. 26, č. 4 (2013), s. 773-777. ISSN 1557-1939 R&D Projects: GA ČR GAP204/12/0897 Institutional support: RVO:68378271 Keywords : nonequilibrium * molecular islands * initial correlations * transient currents Subject RIV: BE - Theoretical Physics Impact factor: 0.930, year: 2013

  14. The measurement of the molecular weight of humic acid by ultracentrifugation

    This report is concerned with the application of ultracentrifuge methods to the determination of humic acid molecular weights. The work has been undertaken as part of the Co-Co club intercomparison exercise on humic acid characterisation. Knowledge of the molecular weight distribution of humic acid will be an important parameter in assessing the likely physical and chemical behaviour under the near-field environment. Molecular weights of a sample of purified Aldrich humic acid have been obtained by sedimentation velocity and sedimentation equilibrium studies using an analytical ultracentrifuge. The results have shown the material to be polydisperse with a weight average molecular weight in the region 2700 to 4000. (author)

  15. Amino acid detection using fluoroquinolone–Cu2+ complex as a switch-on fluorescent probe by competitive complexation without derivatization

    In this work, we describe the use of fluoroquinolone–Cu2+ complex as a competitive switch-on fluorescence probe for amino acid determination without derivatization. The fluorescence intensity of this probe, which has been reduced due to effective quenching by Cu2+ ion, increases drastically by an addition of amino acid (glycine, phenylalanine, sarcosine, aspargine, alanine, proline, arginine, aspartic acid, glutamic acid, lysine, leucine and isoleucine). The overall stability constants of Cu2+ ion complexes with amino acids were determined by fluorometric titration of fluoroquinolone-Cu2+ complex with the amino acid solution. Furthermore, the probe shows high calibration sensitivity toward aspartic acid. The fluorescence signal depends linearly on the amino acid concentration within the range of concentration from 1.2×10−7 to 1.1×10−5 mol L−1 for aspartic acid. The detection limit was found 2.7×10−8 mol L−1 with the relative standard deviation (RSD%) about 2.1% (five replicate). -- Highlights: • Amino acids are detected by using fluoroquinolone–Cu2+ complex as fluorescent probe. • Amino acids were detected based on a competitive complexation reaction. • Probe has been able to recognize amino acids through switch-on fluorescence behavior. • Ultra-trace level of aspartic and glutamic acid is determined without derivatization

  16. Amino acid detection using fluoroquinolone–Cu{sup 2+} complex as a switch-on fluorescent probe by competitive complexation without derivatization

    Farokhcheh, Alireza; Alizadeh, Naader, E-mail: alizaden@modares.ac.ir

    2014-01-15

    In this work, we describe the use of fluoroquinolone–Cu{sup 2+} complex as a competitive switch-on fluorescence probe for amino acid determination without derivatization. The fluorescence intensity of this probe, which has been reduced due to effective quenching by Cu{sup 2+} ion, increases drastically by an addition of amino acid (glycine, phenylalanine, sarcosine, aspargine, alanine, proline, arginine, aspartic acid, glutamic acid, lysine, leucine and isoleucine). The overall stability constants of Cu{sup 2+} ion complexes with amino acids were determined by fluorometric titration of fluoroquinolone-Cu{sup 2+} complex with the amino acid solution. Furthermore, the probe shows high calibration sensitivity toward aspartic acid. The fluorescence signal depends linearly on the amino acid concentration within the range of concentration from 1.2×10{sup −7} to 1.1×10{sup −5} mol L{sup −1} for aspartic acid. The detection limit was found 2.7×10{sup −8} mol L{sup −1} with the relative standard deviation (RSD%) about 2.1% (five replicate). -- Highlights: • Amino acids are detected by using fluoroquinolone–Cu{sup 2+} complex as fluorescent probe. • Amino acids were detected based on a competitive complexation reaction. • Probe has been able to recognize amino acids through switch-on fluorescence behavior. • Ultra-trace level of aspartic and glutamic acid is determined without derivatization.

  17. Molecular weight distribution broadening of polypropylene by periodic switching of hydrogen and catalyst additions

    Ali, M. Al-Haj; Stroomer, J.; Betlem, B.; Weickert, G.; Roffel, B.

    2008-01-01

    This study presents a feasibility study of the broadening of the polypropylene molecular weight distribution produced using a multisite Ziegler-Natta catalyst in a continuous liquid-pool polymerization reactor. The broadening is achieved by operating the reactor under periodic forcing of both hydrogen and catalyst feed flows. Model-based dynamic optimization is used to determine the cycle period and peak width for these inputs. Through simulation it is shown that limited widening (similar to ...

  18. Electron induced conformational changes of an imine-based molecular switch on a Au(111) surface

    Lotze, Christian; Henningsen, Nils; Franke, Katharina; Schulze, Gunnar; Pascual, Jose Ignacio [Inst. f. Experimentalphysik, Freie Universitaet Berlin (Germany); Luo, Ying; Haag, Rainer [Inst. f. Organische Chemie, Freie Universitaet Berlin (Germany)

    2009-07-01

    Azobenzene-based molecules exhibit a cis-trans configurational photoisomerisation in solution. Recently, the adsorption properties of azobenzene derivatives have been investigated on different metal surfaces in order to explore the possible changes in the film properties induced by external stimuli. In azobenzene, the diazo-bridge is a key group for the isomerization process. Its interaction with a metal surface is dominated through the N lone-pair electrons, which reduces the efficiency of the conformational change. In order to reduce the molecule-surface interaction, we explore an alternative molecular architecture by substituting the diazo-bridge (-N=N-) of azobenzene by an imine-group (-N=CH-). We have investigated the imine-based compound para-carboxyl-di-benzene-imine (PCI) adsorbed on a Au(111) surface. The carboxylic terminations mediates the formation of strongly bonded molecular dimers, which align in ordered rows preferentially following the fcc regions of the Au(111) herringbone reconstruction. Low temperature scanning tunneling microscopy was used to induce conformational changes between trans and cis state of individual molecules in a molecular monolayer.

  19. Solvent extraction studies on uranium (VI) with high molecular weight carboxylic acids from acetate medium

    Carboxylic acids are cation exchanger type of extractant which extract metal ions from weak acidic solutions by ion exchange mechanism. They are present as dimer (H2A2) in the non polar organic diluents. High molecular weight carboxylic acids such as versatic 10 acid and naphthenic acid are used for the separation of high purity of yttrium from heavy fraction of rare earths. Extraction behavior of rare earths with different types of carboxylic acids is also reported. Literature survey revealed that the extraction behavior of uranium from aqueous solutions with carboxylic acids is scanty. An attempt has been made in the present work to examine the extraction behavior of U(VI) with three different types of high molecular weight carboxylic acids namely cekanoic acid, neoheptanoic acid and versatic 10 acid dissolved in xylene. Extraction of metal ions is very much dependent on pH of the solution

  20. Investigation of molecular interactions in the complex formation of tartaric acid derivatives with di(2-ethylhexyl) phosphoric acid

    2008-01-01

    The molecular interactions in the complex formation of two tartaric acid derivatives with di(2-ethylhexyl) phosphoric acid are investigated. The complex formation with a 1:1 stoichiometry between tartaric acid derivatives and D2EHPA can be obtained through UV-Vis titration, NMR chemical shifts and molecular dynamic simulations. Furthermore, the differences of the two complexes on the binding constants and strength of hydrogen bonds can also be determined. Such research will ideally provide insight into ways of regulating the complex forming properties of tartaric acid derivatives for composing or syn- thesizing new chiral resolving agents.

  1. Investigation of molecular interactions in the complex formation of tartaric acid derivatives with di(2-ethylhexyl) phosphoric acid

    TAN Bin; ZHAI Zheng; LUO GuangSheng; WANG JiaDing

    2008-01-01

    The molecular interactions in the complex formation of two tartaric acid derivatives with di(2-ethylhexyl) phosphoric acid are investigated. The complex formation with a 1:1 stoichiometry between tartaric acid derivatives and D2EHPA can be obtained through UV-Vis titration, NMR chemical shifts and molecular dynamic simulations. Furthermore, the differences of the two complexes on the binding constants and strength of hydrogen bonds can also be determined. Such research will ideally provide insight into ways of regulating the complex forming properties of tartaric acid derivatives for composing or syn-thesizing new chiral resolving agents.

  2. Interplay of Oct4 with Sox2 and Sox17: a molecular switch from stem cell pluripotency to specifying a cardiac fate.

    Stefanovic, Sonia; Abboud, Nesrine; Désilets, Stéphanie; Nu, David; Cowan, Chad; Pucéat, Michel

    2009-01-01

    Oct4 exerts a dose-dependent dual action, as both a gatekeeper for stem cell pluripotency and in driving cells toward specific lineages. Here, we identify the molecular mechanism underlying this dual function. BMP2- or transgene-induced Oct4 up-regulation drives human embryonic and induced pluripotent stem cells to become cardiac progenitors. When embryonic stem cell pluripotency is achieved, Oct4 switches from the Sox2 to the Sox17 promoter. This switch allows the cells to turn off the pluri...

  3. Bistability in a Metabolic Network Underpins the De Novo Evolution of Colony Switching in Pseudomonas fluorescens

    Gallie, Jenna; Libby, Eric; Bertels, Frederic;

    2015-01-01

    central metabolism (carB) generates such a striking phenotype. We show that colony switching is underpinned by ON/OFF expression of capsules consisting of a colanic acid-like polymer. We use molecular genetics, biochemical analyses, and experimental evolution to establish that capsule switching results...

  4. Amino Acid Molecular Units: Building Primary and Secondary Protein Structures

    Aparecido R. Silva

    2008-05-01

    Full Text Available In order to guarantee the learning quality and suitable knowledge  use  about structural biology, it is fundamental to  exist, since the beginning of  students’ formation, the possibility of clear visualization of biomolecule structures. Nevertheless, the didactic books can only bring  schematic  drawings; even more elaborated figures and graphic computation  do not permit the necessary interaction.  The representation of three-dimensional molecular structures with ludic models, built with representative units, have supplied to the students and teachers a successfully experience to  visualize such structures and correlate them to the real molecules.  The design and applicability of the representative units were discussed with researchers and teachers before mould implementation.  In this stage  it  will be presented the  developed  kit  containing the  representative  plastic parts of the main amino acids.  The kit can demonstrate the interaction among the amino acids  functional groups  (represented by colors, shapes,  sizes and  the peptidic bonds between them  facilitating the assembly and visuali zation of the primary and secondary protein structure.  The models were designed for  Ca,  amino,  carboxyl groups  and  hydrogen. The  lateral chains have  well defined models that represent their geometrical shape.  The completed kit set  will be presented in this meeting (patent requested.  In the last phase of the project will be realized  an effective evaluation  of the kit  as a facilitative didactic tool of the teaching/learning process in the Structural Molecular Biology area.

  5. Retinoic acid receptors: from molecular mechanisms to cancer therapy.

    di Masi, Alessandra; Leboffe, Loris; De Marinis, Elisabetta; Pagano, Francesca; Cicconi, Laura; Rochette-Egly, Cécile; Lo-Coco, Francesco; Ascenzi, Paolo; Nervi, Clara

    2015-02-01

    Retinoic acid (RA), the major bioactive metabolite of retinol or vitamin A, induces a spectrum of pleiotropic effects in cell growth and differentiation that are relevant for embryonic development and adult physiology. The RA activity is mediated primarily by members of the retinoic acid receptor (RAR) subfamily, namely RARα, RARβ and RARγ, which belong to the nuclear receptor (NR) superfamily of transcription factors. RARs form heterodimers with members of the retinoid X receptor (RXR) subfamily and act as ligand-regulated transcription factors through binding specific RA response elements (RAREs) located in target genes promoters. RARs also have non-genomic effects and activate kinase signaling pathways, which fine-tune the transcription of the RA target genes. The disruption of RA signaling pathways is thought to underlie the etiology of a number of hematological and non-hematological malignancies, including leukemias, skin cancer, head/neck cancer, lung cancer, breast cancer, ovarian cancer, prostate cancer, renal cell carcinoma, pancreatic cancer, liver cancer, glioblastoma and neuroblastoma. Of note, RA and its derivatives (retinoids) are employed as potential chemotherapeutic or chemopreventive agents because of their differentiation, anti-proliferative, pro-apoptotic, and anti-oxidant effects. In humans, retinoids reverse premalignant epithelial lesions, induce the differentiation of myeloid normal and leukemic cells, and prevent lung, liver, and breast cancer. Here, we provide an overview of the biochemical and molecular mechanisms that regulate the RA and retinoid signaling pathways. Moreover, mechanisms through which deregulation of RA signaling pathways ultimately impact on cancer are examined. Finally, the therapeutic effects of retinoids are reported. PMID:25543955

  6. Study on fluorescence spectra of molecular association of acetic acid-water

    Caiqin Han; Ying Liu; Yang Yang; Xiaowu Ni; Jian Lu; Xiaosen Luo

    2009-01-01

    Fluorescence spectra of acetic acid-water solution excited by ultraviolet (UV) light are studied, and the relationship between fluorescence spectra and molecular association of acetic acid is discussed. The results indicate that when the exciting light wavelength is longer than 246 nm, there are two fluorescence peaks located at 305 and 334 nm, respectively. By measuring the excitation spectra, the optimal wavelengths of the two fluorescence peaks are obtained, which are 258 and 284 nm, respectively. Fluorescence spectra of acetic acid-water solution change with concentrations, which is primarily attributed to changes of molecular association of acetic acid in aqueous solution. Through theoretical analysis, three variations of molecular association have been obtained in acetic acid-water solution, which are the hydrated monomers, the linear dimers, and the water separated dimers. This research can provide references to studies of molecular association of acetic acid-water, especially studies of hydrogen bonds.

  7. Solving nucleic acid structures by molecular replacement: examples from group II intron studies

    Strategies for phasing nucleic acid structures by molecular replacement, using both experimental and de novo designed models, are discussed. Structured RNA molecules are key players in ensuring cellular viability. It is now emerging that, like proteins, the functions of many nucleic acids are dictated by their tertiary folds. At the same time, the number of known crystal structures of nucleic acids is also increasing rapidly. In this context, molecular replacement will become an increasingly useful technique for phasing nucleic acid crystallographic data in the near future. Here, strategies to select, create and refine molecular-replacement search models for nucleic acids are discussed. Using examples taken primarily from research on group II introns, it is shown that nucleic acids are amenable to different and potentially more flexible and sophisticated molecular-replacement searches than proteins. These observations specifically aim to encourage future crystallographic studies on the newly discovered repertoire of noncoding transcripts

  8. Solving nucleic acid structures by molecular replacement: examples from group II intron studies

    Marcia, Marco, E-mail: marco.marcia@yale.edu; Humphris-Narayanan, Elisabeth; Keating, Kevin S.; Somarowthu, Srinivas [Yale University, New Haven, CT 06511 (United States); Rajashankar, Kanagalaghatta [Argonne National Laboratory, Argonne, IL 60439 (United States); Pyle, Anna Marie, E-mail: marco.marcia@yale.edu [Yale University, New Haven, CT 06511 (United States); Yale University, New Haven, CT 06511 (United States); Howard Hughes Medical Institute, Chevy Chase, MD 20815 (United States)

    2013-11-01

    Strategies for phasing nucleic acid structures by molecular replacement, using both experimental and de novo designed models, are discussed. Structured RNA molecules are key players in ensuring cellular viability. It is now emerging that, like proteins, the functions of many nucleic acids are dictated by their tertiary folds. At the same time, the number of known crystal structures of nucleic acids is also increasing rapidly. In this context, molecular replacement will become an increasingly useful technique for phasing nucleic acid crystallographic data in the near future. Here, strategies to select, create and refine molecular-replacement search models for nucleic acids are discussed. Using examples taken primarily from research on group II introns, it is shown that nucleic acids are amenable to different and potentially more flexible and sophisticated molecular-replacement searches than proteins. These observations specifically aim to encourage future crystallographic studies on the newly discovered repertoire of noncoding transcripts.

  9. A Molecular Switch Abrogates Glycoprotein 100 (gp100) T-cell Receptor (TCR) Targeting of a Human Melanoma Antigen*

    Bianchi, Valentina; Bulek, Anna; Fuller, Anna; Lloyd, Angharad; Attaf, Meriem; Rizkallah, Pierre J.; Dolton, Garry; Sewell, Andrew K.; Cole, David K.

    2016-01-01

    Human CD8+ cytotoxic T lymphocytes can mediate tumor regression in melanoma through the specific recognition of HLA-restricted peptides. Because of the relatively weak affinity of most anti-cancer T-cell receptors (TCRs), there is growing emphasis on immunizing melanoma patients with altered peptide ligands in order to induce strong anti-tumor immunity capable of breaking tolerance toward these self-antigens. However, previous studies have shown that these immunogenic designer peptides are not always effective. The melanocyte differentiation protein, glycoprotein 100 (gp100), encodes a naturally processed epitope that is an attractive target for melanoma immunotherapies, in particular peptide-based vaccines. Previous studies have shown that substitutions at peptide residue Glu3 have a broad negative impact on polyclonal T-cell responses. Here, we describe the first atomic structure of a natural cognate TCR in complex with this gp100 epitope and highlight the relatively high affinity of the interaction. Alanine scan mutagenesis performed across the gp100280–288 peptide showed that Glu3 was critically important for TCR binding. Unexpectedly, structural analysis demonstrated that the Glu3 → Ala substitution resulted in a molecular switch that was transmitted to adjacent residues, abrogating TCR binding and T-cell recognition. These findings help to clarify the mechanism of T-cell recognition of gp100 during melanoma responses and could direct the development of altered peptides for vaccination. PMID:26917722

  10. A metal-ion-responsive adhesive material via switching of molecular recognition properties

    Nakamura, Takashi; Takashima, Yoshinori; Hashidzume, Akihito; Yamaguchi, Hiroyasu; Harada, Akira

    2014-08-01

    Common adhesives stick to a wide range of materials immediately after they are applied to the surfaces. To prevent indiscriminate sticking, smart adhesive materials that adhere to a specific target surface only under particular conditions are desired. Here we report a polymer hydrogel modified with both β-cyclodextrin (βCD) and 2,2‧-bipyridyl (bpy) moieties (βCD-bpy gel) as a functional adhesive material responding to metal ions as chemical stimuli. The adhesive property of βCD-bpy gel based on interfacial molecular recognition is expressed by complexation of metal ions to bpy that controlled dissociation of supramolecular cross-linking of βCD-bpy. Moreover, adhesion of βCD-bpy gel exhibits selectivity on the kinds of metal ions, depending on the efficiency of metal-bpy complexes in cross-linking. Transduction of two independent chemical signals (metal ions and host-guest interactions) is achieved in this adhesion system, which leads to the development of highly orthogonal macroscopic joining of multiple objects.

  11. A molecular switch driving inactivation in the cardiac K+ channel HERG.

    David A Köpfer

    Full Text Available K(+ channels control transmembrane action potentials by gating open or closed in response to external stimuli. Inactivation gating, involving a conformational change at the K(+ selectivity filter, has recently been recognized as a major K(+ channel regulatory mechanism. In the K(+ channel hERG, inactivation controls the length of the human cardiac action potential. Mutations impairing hERG inactivation cause life-threatening cardiac arrhythmia, which also occur as undesired side effects of drugs. In this paper, we report atomistic molecular dynamics simulations, complemented by mutational and electrophysiological studies, which suggest that the selectivity filter adopts a collapsed conformation in the inactivated state of hERG. The selectivity filter is gated by an intricate hydrogen bond network around residues S620 and N629. Mutations of this hydrogen bond network are shown to cause inactivation deficiency in electrophysiological measurements. In addition, drug-related conformational changes around the central cavity and pore helix provide a functional mechanism for newly discovered hERG activators.

  12. Characterization of Hydroxyphthioceranoic and Phthioceranoic Acids by Charge-Switch Derivatization and CID Tandem Mass Spectrometry

    Hsu, Fong-Fu

    2016-04-01

    Hydroxyphthioceranoic (HPA) and phthioceranoic (PA) acids are polymethylated long chain fatty acids with and without a hydroxyl group attached to the carbon next to the terminal methyl-branched carbon distal to the carboxylic end of the long-chain fatty acid, respectively. They are the major components of the sulfolipids found in the cell wall of Mycobacterium tuberculosis (M. tuberculosis) strain H37Rv. In this report, I describe CID linear ion-trap MSn mass spectrometric approaches combined with charge-reverse derivatization strategy toward characterization of these complex lipids, which were released from sulfolipids by alkaline hydrolysis and sequentially derivatized to the N-(4-aminomethylphenyl) pyridinium (AMPP) derivatives. This method affords complete characterization of HPA and PA, including the location of the hydroxyl group and the multiple methyl side chains. The study also led to the notion that the hydroxyphthioceranoic acid in sulfolipid consists of two (for hC24) to 12 (for hC52) methyl branches, and among them 2,4,6,8,10,12,14,16-octamethyl-17-hydroxydotriacontanoic acid (hC40) is the most prominent, while phthioceranoic acids are the minor constituents. These results confirm our previous findings that sulfolipid II, a family of homologous 2-stearoyl(palmitoyl)-3,6,6'-tris(hydroxyphthioceranoy1)-trehalose 2'-sulfates is the predominant species, and sulfolipid I, a family of homologous 2-stearoyl(palmitoyl)-3-phthioceranoyl-6,6'-bis(hydroxyphthioceranoy1)-trehalose 2'-sulfates is the minor species in the cell wall of M. tuberculosis.

  13. Postprandial fate of amino acids: adaptation to molecular forms

    Nolles, J.A.

    2006-01-01

    During the postprandial phase dietary proteins are digested to peptides and amino acids and absorbed. Once absorbed the peptides are further hydrolyzed to amino acids and transported to the tissues. These amino acids are largely incorporated into body proteins. Not all amino acids are, however, inco

  14. Postprandial fate of amino acids: adaptation to molecular forms

    Nolles, J.A.

    2006-01-01

    During the postprandial phase dietary proteins are digested to peptides and amino acids and absorbed. Once absorbed the peptides are further hydrolyzed to amino acids and transported to the tissues. These amino acids are largely incorporated into body proteins. Not all amino acids are, however, incorporated into body proteins part of these amino acids are oxidized, and can, thus, no longer be utilized to support protein metabolism in the body. The objective of this thesis was to increase the ...

  15. Towards single molecule switches.

    Zhang, Jia Lin; Zhong, Jian Qiang; Lin, Jia Dan; Hu, Wen Ping; Wu, Kai; Xu, Guo Qin; Wee, Andrew T S; Chen, Wei

    2015-05-21

    The concept of using single molecules as key building blocks for logic gates, diodes and transistors to perform basic functions of digital electronic devices at the molecular scale has been explored over the past decades. However, in addition to mimicking the basic functions of current silicon devices, molecules often possess unique properties that have no parallel in conventional materials and promise new hybrid devices with novel functions that cannot be achieved with equivalent solid-state devices. The most appealing example is the molecular switch. Over the past decade, molecular switches on surfaces have been intensely investigated. A variety of external stimuli such as light, electric field, temperature, tunneling electrons and even chemical stimulus have been used to activate these molecular switches between bistable or even multiple states by manipulating molecular conformations, dipole orientations, spin states, charge states and even chemical bond formation. The switching event can occur either on surfaces or in break junctions. The aim of this review is to highlight recent advances in molecular switches triggered by various external stimuli, as investigated by low-temperature scanning tunneling microscopy (LT-STM) and the break junction technique. We begin by presenting the molecular switches triggered by various external stimuli that do not provide single molecule selectivity, referred to as non-selective switching. Special focus is then given to selective single molecule switching realized using the LT-STM tip on surfaces. Single molecule switches operated by different mechanisms are reviewed and discussed. Finally, molecular switches embedded in self-assembled monolayers (SAMs) and single molecule junctions are addressed. PMID:25757483

  16. Activation of coherent lattice phonon following ultrafast molecular spin-state photo-switching: A molecule-to-lattice energy transfer

    A. Marino

    2016-03-01

    Full Text Available We combine ultrafast optical spectroscopy with femtosecond X-ray absorption to study the photo-switching dynamics of the [Fe(PM-AzA2(NCS2] spin-crossover molecular solid. The light-induced excited spin-state trapping process switches the molecules from low spin to high spin (HS states on the sub-picosecond timescale. The change of the electronic state (<50 fs induces a structural reorganization of the molecule within 160 fs. This transformation is accompanied by coherent molecular vibrations in the HS potential and especially a rapidly damped Fe-ligand breathing mode. The time-resolved studies evidence a delayed activation of coherent optical phonons of the lattice surrounding the photoexcited molecules.

  17. Effect of Molecular Structure on the Performance of Polyacrylic Acid Superplasticizer

    ZHANG Rongguo; GUO Huiling; LEI Jiaheng; ZHANG Anfu; GU Huajun

    2007-01-01

    The effects of structure parameters, such as molecular structure, segment kinds, molecular weight, and organic functional groups, on the performance of polyacrylic acid superplasticizer were discussed. According to the differences of chain sections, functional groups, etc, polyacrylic acid superplasticizer could be divided into A, B, C three parts. Among them, A chain section included sulfonic acid groups, B chain section carboxyl groups, C chain section polyester. Polyacrylic acid superplasticizers with different matching of A, B, C chain sections, different length of C chain section and different molecular weights were synthesized by acrylic acid, polyethylene glycol, sodium methyl allylsulfonate; the relation between the molecular structure and performance was also studied. The expetimental results indicate that the water-reduction ratio increases obviously with the increment of the proportion of sodium methyl allylsulfonate chain section in the molecular; the slump retention increases greatly with the increment of the proportion of acrylic acid chain section; the dispersion of cement particles increases with the increment of the chain length of polyethylene glycol; when the molecular weight is in the range of 5000, the dispersion and slump retentibity increase with the increment of the average molecular weight of polymers.

  18. Role of accelerated segment switch in exons to alter targeting (ASSET in the molecular evolution of snake venom proteins

    Kini R Manjunatha

    2009-06-01

    Full Text Available Abstract Background Snake venom toxins evolve more rapidly than other proteins through accelerated changes in the protein coding regions. Previously we have shown that accelerated segment switch in exons to alter targeting (ASSET might play an important role in its functional evolution of viperid three-finger toxins. In this phenomenon, short sequences in exons are radically changed to unrelated sequences and hence affect the folding and functional properties of the toxins. Results Here we analyzed other snake venom protein families to elucidate the role of ASSET in their functional evolution. ASSET appears to be involved in the functional evolution of three-finger toxins to a greater extent than in several other venom protein families. ASSET leads to replacement of some of the critical amino acid residues that affect the biological function in three-finger toxins as well as change the conformation of the loop that is involved in binding to specific target sites. Conclusion ASSET could lead to novel functions in snake venom proteins. Among snake venom serine proteases, ASSET contributes to changes in three surface segments. One of these segments near the substrate binding region is known to affect substrate specificity, and its exchange may have significant implications for differences in isoform catalytic activity on specific target protein substrates. ASSET therefore plays an important role in functional diversification of snake venom proteins, in addition to accelerated point mutations in the protein coding regions. Accelerated point mutations lead to fine-tuning of target specificity, whereas ASSET leads to large-scale replacement of multiple functionally important residues, resulting in change or gain of functions.

  19. Molecular Genetic Characterization of Terreic Acid Pathway in Aspergillus terreus

    Guo, Chun-Jun; Sun, Wei-wen; Bruno, Kenneth S.; Wang, Clay C.

    2014-09-29

    Terreic acid is a natural product derived from 6-methylsalicylic acid (6-MSA). A compact gene cluster for its biosynthesis was characterized. Isolation of the intermediates and shunt products from the mutant strains, in combined with bioinformatic analyses, allowed us to propose a biosynthetic pathway for terreic acid. Defining the pathway and the genes involved will facilitate the engineering of this molecule with interesting antimicrobial and antitumor bioactivities.

  20. Molecular dynamics of sialic acid analogues and their interaction with influenza hemagglutinin

    Blessia T

    2010-01-01

    Full Text Available Synthetic sialic acid analogues with multiple modifications at different positions(C-1/C-2/C-4/C-8/C-9 are investigated by molecular mechanics and molecular dynamics to determine their conformational preferences and structural stability to interact with their natural receptors. Sialic acids with multiple modifications are soaked in a periodic box of water as solvent. Molecular mechanics and a 2 nanosecond molecular dynamics are done using amber force fields with 30 picosecond equilibrium. Direct and water mediated hydrogen bonds existing in the sialic acid analogues, aiding for their structural stabilization are identified in this study. The accessible conformations of side chain linkages of sialic acid analogues holding multiple substituents are determined from molecular dynamics trajectory at every 1ps interval. Transitions between different minimum energy regions in conformational maps are also noticed in C-1, C-2, C-4, C-8 and C-9 substituents. Docking studies were done to find the binding mode of the sialic acid analogues with Influenza hemagglutinin. This finding provides stereo chemical explanation and conformational preference of sialic acid analogues which may be crucial for the design of sialic acid analogues as inhibitors for different sialic acid specific pathogenic proteins such as influenza toxins and neuraminidases.

  1. Study of the effects of dietary polyunsaturated fatty acids: Molecular mechanisms involved intestinal inflammation

    Knoch, B.; Barnett, M. P. G.; Roy, N. C.; McNabb, W. C.

    2009-07-01

    The use of omics techniques in combination with model systems and molecular tools allows to understand how foods and food components act on metabolic pathways to regulate transcriptional processes. Polyunsaturated fatty acids have distinctive nutritional and metabolic effects because they give rise to lipid mediated products and affect the expression of various genes involved in intestinal inflammation. The present review focuses on the molecular effects of dietary polyunsaturated fatty acids on intestinal inflammation. (Author) 74 refs.

  2. Low-molecular-weight carboxylic acids produced from hydrothermal treatment of organic wastes.

    Quitain, Armando T; Faisal, Muhammad; Kang, Kilyoon; Daimon, Hiroyuki; Fujie, Koichi

    2002-07-22

    This article reports production of low-molecular-weight carboxylic acids from the hydrothermal treatment of representative organic wastes and compounds (i.e. domestic sludge, proteinaceous, cellulosic and plastic wastes) with or without oxidant (H(2)O(2)). Organic acids such as acetic, formic, propionic, succinic and lactic acids were obtained in significant amounts. At 623 K (16.5 MPa), acetic acid of about 26 mg/g dry waste fish entrails was obtained. This increased to 42 mg/g dry waste fish entrails in the presence of H(2)O(2). Experiments on glucose to represent cellulosic wastes were also carried out, getting acetic acid of about 29 mg/g glucose. The study was extended to terephthalic acid and glyceraldehyde, reaction intermediates of hydrothermal treatment of polyethylene terephthalate (PET) plastic wastes and glucose, respectively. In addition, production of lactic acid, one of the interesting low-molecular-weight carboxylic acids, was discussed on the viewpoint of resources recovery. Studies on temperature dependence of formation of organic acids showed thermal stability of acetic acid, whereas, formic acid decomposed readily under hydrothermal conditions. In general, results demonstrated that the presence of oxidants favored formation of organic acids with acetic acid being the major product. PMID:12117467

  3. Molecular Determinants of the Response of Tumor Cells to Boswellic Acids

    Thomas Efferth

    2011-08-01

    Full Text Available Frankincense (Boswellia serrata, B. carterii is used as traditional remedy to treat inflammatory diseases. The molecular effects of the active ingredients, the boswellic acids, on the immune system have previously been studied and verified in several clinical studies. Boswellic acids also inhibit cancer cell growth in vitro and in vivo. The molecular basis of the cytotoxicity of boswellic acids is, however, not fully understood as yet. By mRNA-based microarray, COMPARE, and hierarchical cluster analyses, we identified a panel of genes from diverse functional groups, which were significantly associated with sensitivity or resistance of a- or b-boswellic acids, such as transcription factors, signal transducers, growth regulating genes, genes involved in RNA and protein metabolism and others. This indicates that boswellic acids exert profound cytotoxicity on cancer cells by a multiplicity of molecular mechanisms.

  4. Molecular recognition of α-cyclodextrin (CD) to choral amino acids based on methyl orange as a molecular probe

    Yuexian, Fan; Yu, Yang; Shaomin, Shuang; Chuan, Dong

    2005-03-01

    The molecular recognition interaction of α-CD to chiral amino acids was investigated by using spectrophotometry based on methyl orange as a molecular probe. The molecular recognition ability depended on the inclusion formation constants. The molecular recognition of α-CD to aromatic amino acids was the order: DL-tryptophan > L-tryptophan > L-phenylalanine > L-tyrosine ≈ DL-β-3,4-dihydroxy-phenylalanine; whereas for aliphatic amino acids, the order was: L- iso-leucine > L-leucine ≈ L-methionine ≈ DL-mehtionine > D-leucine. The effect of temperature on the inclusion interaction was examined and the thermodynamic parameters of inclusion process, Δ G, Δ H, Δ S, were determined. The experimental results indicated that the inclusion process was an exothermic and enthalpy-driven process accompanied with a negative or minor positive entropic contribution. The inclusion interaction between α-CD and amino acids satisfied the law of enthalpy-entropy compensation. The compensation temperature was 291 K.

  5. Molecular recognition of alpha-cyclodextrin (CD) to choral amino acids based on methyl orange as a molecular probe.

    Yuexian, Fan; Yu, Yang; Shaomin, Shuang; Chuan, Dong

    2005-03-01

    The molecular recognition interaction of alpha-CD to chiral amino acids was investigated by using spectrophotometry based on methyl orange as a molecular probe. The molecular recognition ability depended on the inclusion formation constants. The molecular recognition of alpha-CD to aromatic amino acids was the order: DL-tryptophan > L-tryptophan > L-phenylalanine > L-tyrosine approximately DL-beta-3,4-dihydroxy-phenylalanine; whereas for aliphatic amino acids, the order was: L-iso-leucine > L-leucine approximately L-methionine approximately DL-mehtionine > D-leucine. The effect of temperature on the inclusion interaction was examined and the thermodynamic parameters of inclusion process, delta G, delta H, delta S, were determined. The experimental results indicated that the inclusion process was an exothermic and enthalpy-driven process accompanied with a negative or minor positive entropic contribution. The inclusion interaction between alpha-CD and amino acids satisfied the law of enthalpy-entropy compensation. The compensation temperature was 291 K. PMID:15683802

  6. Isolation and characterisation of high molecular weight ( sup 3 H)hyaluronic acid

    Chabrecek, P. (Slovak Technical Univ., Bratislava (Czechoslovakia). Inst. of Biotechnology); Soltes, L.; Kallay, Z. (Slovenska Akademia Vied, Bratislava (Czechoslovakia). Ustav Experimentalnej Farmakologie); Fugedi, A. (Slovenska Akademia, Bratislava (Czechoslovakia). Computing Centre)

    1990-10-01

    A high-performance gel permeation chromatographic separation method was developed for the isolation and characterisation of high molecular weight ({sup 3}H)hyaluronic acid. The molecular characteristics of the labelled sample were M{sub w}=3.92 x 10{sup 5} Da, M{sub w}/M{sub n}=1.55. (author).

  7. Isolation and characterisation of high molecular weight [3H]hyaluronic acid

    A high-performance gel permeation chromatographic separation method was developed for the isolation and characterisation of high molecular weight [3H]hyaluronic acid. The molecular characteristics of the labelled sample were Mw=3.92 x 105 Da, Mw/Mn=1.55. (author)

  8. What are humic substances? : a molecular approach to the study of organic matter in acid soils

    Naafs, Derck Ferdinand Werner

    2004-01-01

    Molecular studies on the composition of organic matter in soils are scarce. In this thesis, a molecular approach to the study of organic matter in acid soils is presented, with a focus on andic, i.e. volcanic, soils. Analyses include both chemical extractions as well as pyrolysis-GC/MS and CPMAS 13C

  9. A comparative study on efficacy of high and low fluence Q-switched Nd:YAG laser and glycolic acid peel in melasma

    Hemanta Kumar Kar; Lipy Gupta; Amrita Chauhan

    2012-01-01

    Background: Melasma is acquired symmetric hypermelanosis characterized by light-to-deep brown pigmentation over cheeks, forehead, upper lip, and nose. Treatment of this condition is difficult and associated with high recurrence rates. With the advent of newer therapies, there is interest in the use of glycolic acid peels and Q-switched Nd:YAG laser (QSNYL) in high and low fluence for this disorder. Aims: To compare the therapeutic efficacy of low fluence QSNYL, high fluence QSNYL, and glycoli...

  10. A Comparison of Low-Fluence 1064-nm Q-Switched Nd: YAG Laser with Topical 20% Azelaic Acid Cream and their Combination in Melasma in Indian Patients

    Charu Bansal; Hira Naik; Kar, Hemanta K; Amrita Chauhan

    2012-01-01

    Background: Melasma is an acquired symmetric hypermelanosis characterised by irregular light to gray-brown macules on sun-exposed skin with a predilection for the cheeks, forehead, upper lip, nose and chin. The management of melasma is challenging and requires meticulous use of available therapeutic options. Aims: To compare the therapeutic efficacy of low-fluence Q-switched Nd: YAG laser (QSNYL) with topical 20% azelaic acid cream and their combination in melasma in three study groups of 20 ...

  11. INTERRUPTION OF AMINO ACIDS MOLECULAR ASYMMETRY (D/L- ENANTIOMERS DURING NORMAL AGING AND NEURODEGENERATIVE DISEASES

    A.V. Chervyakov

    2010-05-01

    Full Text Available Some facts about D-amino acids, their diffusion in human’s and animal’s organisms, metabolism, identification methods, involving in ageing and pathogenesis of some neurodegenerative diseases are show in this review. Also there is discussing the role of amino acid molecular asymmetry (D and L enantiomers ratio as a fundamental asymmetry of living matter.

  12. Molecular pharmacology of 4-substituted glutamic acid analogues at ionotropic and metabotropic excitatory amino acid receptors

    Bräuner-Osborne, Hans; Nielsen, B; Stensbøl, T B; Johansen, T N; Skjaerbaek, N; Krogsgaard-Larsen, P

    The pharmacology of (2S,4R)-4-methylglutamic acid, (2S,4S)-4-methylglutamic acid and (S)- and (R)-4-methyleneglutamic acids (obtained in high chemical and enantiomeric purity from racemic 4-methyleneglutamic acid by chiral HPLC using a Crownpak CR(+) column), was examined in binding experiments u...

  13. Phosphorus release from phosphate rock and iron phosphate by low-molecular-weight organic acids

    XU Ren-kou; ZHU Yong-guan; David Chittleborough

    2004-01-01

    Low-molecular-weight(LMW) organic acids widely exist in soils, particularly in the rhizosphere. A series of batch experiments were carried out to investigate the phosphorus release from rock phosphate and iron phosphate by Iow-molecular-weight organic acids.Results showed that citric acid had the highest capacity to solubilize P from both rock and iron phosphate. P solubilization from rock phosphate and iron phosphate resulted in net proton consumption. P release from rock phosphate was positively correlated with the pKa values. P release from iron phosphate was positively correlated with Fe-organic acid stability constants except for aromatic acids, but was not correlated with PKa. Increase in the concentrations of organic acids enhanced P solubilization from both rock and iron phosphate almost linearrly. Addition of phenolic compounds further increased the P release from iron phosphate. Initial solution pH had much more substantial effect on P release from rock phosphate than from iron phosphate.

  14. Molecular targets of omega 3 and conjugated linoleic fatty acids – micromanaging cellular response

    Francesco eVisioli

    2012-02-01

    Full Text Available Essential fatty acids cannot be synthesized de novo by mammals and need to be ingested either with the diet or through the use of supplements/functional foods to ameliorate cardiovascular prognosis. This review focus on the molecular targets of omega 3 fatty acids and CLA, as paradigmatic molecules that can be explored both as nutrients and as pharmacological agents, especially as related to cardioprotection. In addition, we indicate novel molecular targets, namely microRNAs that might contribute to the observed biological activities of such essential fatty acids.

  15. Effect of Low-Molecular-Weight Organic Acids on Cl- Adsorption by Variable Charge Soils

    XU Ren-Kou; ANG Ma-Li; WANG Qiang-Sheng; JI Guo-Liang1

    2004-01-01

    Low-molecular-weight (LMW) organic acids exist widely in soils and have been implicated in many soil processes.The objective of the present paper was to evaluate effect of two LMW organic acids, citric acid and oxalic acid, on Cl- adsorption by three variable charge soils, a latosol, a lateritic red soil and a red soil, using a batch method. The results showed that the presence of citric acid and oxalic acid led to a decrease in Cl- adsorption with larger decreases for citric acid. Among the different soils Gl- adsorption in the lateritic red soil and the red soil was more affected by both the LMW organic acids than that in the latosol.

  16. Synthesis, molecular structure, spectroscopic investigations and computational study of a potential molecular switch of 2-([1,1'-biphenyl]-4-yl)-2-methyl-6-(4-nitrophenyl)-4-phenyl-1,3 diazabicyclo [3.1.0]hex-3-ene

    AYOUB KANAANI; DAVOOD AJLOO; HAMZEH I KIYAN; FRESHTE SHAHERI; MAJID AMIRI

    2016-08-01

    This work presents a combined experimental and theoretical study on a photochromic compound, 2-([1,1'-biphenyl]-4-yl)-2-methyl-6-(4-nitrophenyl)-4-phenyl-1,3 diazabicyclo [3.1.0]hex-3-ene, existing in closed form (‘A’) and open form (‘B’). The spectroscopic properties of the title compound have beeninvestigated by using IR, UV–Vis and ¹H NMR techniques. The molecular geometry and spectroscopic data of the title compound have been calculated by using the density functional method (B3LYP) invoking 6-311G(d,p) basis set. UV-Vis spectra of the two forms were recorded. The excitation energies, oscillator strength, etc., were calculated by time-dependent density functional theory (TD-DFT). Furthermore, molecular electrostatic potential map (MEP), frontier molecular orbital analysis (HOMO–LUMO), total density of state (TDOS) and reactivity descriptors were found and discussed. We applied a first-principles computational approach to study a light-sensitive molecular switch. We find that the conductance of the two isomers varies dramatically, which suggests that this system has potential use as a molecular switch.

  17. Potential origin and formation for molecular components of humic acids in soils

    DiDonato, Nicole; Chen, Hongmei; Waggoner, Derek; Hatcher, Patrick G.

    2016-04-01

    Soil humic acids are the base soluble/acid insoluble organic components of soil organic matter. Most of what we know about humic acids comes from studies of their bulk molecular properties or analysis of individual fractions after extraction from soils. This work attempts to better define humic acids and explain similarities and differences for several soils varying in degrees of humification using advanced molecular level techniques. Our investigation using electrospray ionization coupled to Fourier transform ion cyclotron resonance mass spectrometry (ESI-FTICR-MS) and nuclear magnetic resonance spectroscopy (NMR) has given new insight into the distinctive molecular characteristics of humic acids which suggest a possible pathway for their formation. Humic acids from various ecosystems, climate regions and soil textural classes are distinguished by the presence of three predominant molecular components: lignin-like molecules, carboxyl-containing aliphatic molecules and condensed aromatic molecules that bear similarity to black carbon. Results show that humification may be linked to the relative abundance of these three types of molecules as well as the relative abundance of carboxyl groups in each molecular type. This work also demonstrates evidence for lignin as the primary source of soil organic matter, particularly condensed aromatic molecules often categorized as black carbon and is the first report of the non-pyrogenic source for these compounds in soils. We also suggest that much of the carboxyl-containing aliphatic molecules are sourced from lignin.

  18. In-silico design of computational nucleic acids for molecular information processing.

    Ramlan, Effirul Ikhwan; Zauner, Klaus-Peter

    2013-01-01

    Within recent years nucleic acids have become a focus of interest for prototype implementations of molecular computing concepts. During the same period the importance of ribonucleic acids as components of the regulatory networks within living cells has increasingly been revealed. Molecular computers are attractive due to their ability to function within a biological system; an application area extraneous to the present information technology paradigm. The existence of natural information processing architectures (predominately exemplified by protein) demonstrates that computing based on physical substrates that are radically different from silicon is feasible. Two key principles underlie molecular level information processing in organisms: conformational dynamics of macromolecules and self-assembly of macromolecules. Nucleic acids support both principles, and moreover computational design of these molecules is practicable. This study demonstrates the simplicity with which one can construct a set of nucleic acid computing units using a new computational protocol. With the new protocol, diverse classes of nucleic acids imitating the complete set of boolean logical operators were constructed. These nucleic acid classes display favourable thermodynamic properties and are significantly similar to the approximation of successful candidates implemented in the laboratory. This new protocol would enable the construction of a network of interconnecting nucleic acids (as a circuit) for molecular information processing. PMID:23647621

  19. New structure of three-terminal GaAs p(+)-n(-)-delta(p+)-n(-)-n(+) switching device prepared by molecular beam epitaxy

    Wang, Y. H.; Yarn, K. F.; Chang, C. Y.; Jame, M. S.

    1987-08-01

    A new three-terminal GaAs p(+)-n(-)-delta(p+)-n(-)-n(+), voltage-controlled switching device grown by molecular beam epitaxy is presented. A simple method to contact the third terminal is employed by applying the Au-Zn to the delta(p+) barrier using the B-groove etching technique, in which the delta(p+) barrier height can be directly modulated by the external voltage. The device may be more effective than other voltage-controlled devices due to the direct barrier modulation.

  20. Electronic transport properties of indolyl spirooxazine/merooxazine-based light-driven molecular switch: The effect of amino/nitro substituents

    Zhao, H.; Xu, Y. Q.; Zhao, W. K.; Gao, K.; Liu, D. S.

    2014-03-01

    By applying non-equilibrium Green's function formulation combined with first-principles density functional theory, we explore the electronic transport properties of indolinospironaphthoxazine (SO)/indolinomeronaphthoxazine (MO). The results indicate that the MO allows a far larger current than the SO. The substituent group can cause shifts of the energy levels. Higher ON/OFF current ratio can be obtained if either amino or nitro substituent is placed at the position of naphthalene moiety. Our results suggest that such molecular wires can generally display switching function and the efficiency can be increased by adding certain substituent groups to the molecules.

  1. Molecular physiology of weak organic acid stress in Bacillus subtilis

    Brul, S.; Beilen, van, J.W.A.

    2013-01-01

    The mechanism by which weak organic acid (WOA) preservatives inhibit growth of microorganisms may differ between different WOAs and these differences are not well understood. The aim of this thesis has been to obtain a better understanding of the mode of action of these preservatives by which they inhibit the growth of spore-forming bacteria (more specifically Bacillus subtilis).

  2. Molecularly imprinted polymer for caffeic acid by precipitation polymerization and its application to extraction of caffeic acid and chlorogenic acid from Eucommia ulmodies leaves.

    Miura, Chitose; Matsunaga, Hisami; Haginaka, Jun

    2016-08-01

    Molecularly imprinted polymers (MIPs) for caffeic acid (CA) were prepared using 4-vinylpyridine and methacrylamide (MAM) as functional monomers, divinylbenzene as a crosslinker and acetonitrile-toluene (3:1, v/v) as a porogen by precipitation polymerization. The use of MAM as the co-monomer resulted in the formation of microsphere MIPs and non-imprinted polymers (NIPs) with ca. 3- and 5-μm particle diameters, respectively. Binding experiments and Scatchard analyses revealed that the binding capacity and affinity of the MIP to CA are higher than those of the NIP. The retention and molecular-recognition properties of the prepared MIPs were evaluated using water-acetonitrile and sodium phosphate buffer-acetonitrile as mobile phases in hydrophilic interaction chromatography (HILIC) and reversed-phase chromatography, respectively. In HILIC mode, the MIP showed higher molecular-recognition ability for CA than in reversed-phase mode. In addition to shape recognition, hydrophilic interactions seem to work for the recognition of CA on the MIP in HILIC mode, while hydrogen bonding and hydrophobic interactions seem to work for the recognition of CA in reversed-phase mode. The MIP had a specific molecular-recognition ability for CA in HILIC mode, while other structurally related compounds, such as chlorogenic acid (CGA), gallic acid, protocatechuic acid and vanillic acid, could not be recognized by the MIP. Furthermore, the MIP was successfully applied for extraction of CA and CGA in the leaves of Eucommia ulmodies in HILIC mode. PMID:26776340

  3. Palmitic acid interferes with energy metabolism balance by adversely switching the SIRT1-CD36-fatty acid pathway to the PKC zeta-GLUT4-glucose pathway in cardiomyoblasts.

    Chen, Yeh-Peng; Tsai, Chia-Wen; Shen, Chia-Yao; Day, Cecilia-Hsuan; Yeh, Yu-Lan; Chen, Ray-Jade; Ho, Tsung-Jung; Padma, V Vijaya; Kuo, Wei-Wen; Huang, Chih-Yang

    2016-05-01

    Metabolic regulation is inextricably linked with cardiac function. Fatty acid metabolism is a significant mechanism for creating energy for the heart. However, cardiomyocytes are able to switch the fatty acids or glucose, depending on different situations, such as ischemia or anoxia. Lipotoxicity in obesity causes impairments in energy metabolism and apoptosis in cardiomyocytes. We utilized the treatment of H9c2 cardiomyoblast cells palmitic acid (PA) as a model for hyperlipidemia to investigate the signaling mechanisms involved in these processes. Our results show PA induces time- and dose-dependent lipotoxicity in H9c2 cells. Moreover, PA enhances cluster of differentiation 36 (CD36) and reduces glucose transporter type 4 (GLUT4) pathway protein levels following a short period of treatment, but cells switch from CD36 back to the GLUT4 pathway after during long-term exposure to PA. As sirtuin 1 (SIRT1) and protein kinase Cζ (PKCζ) play important roles in CD36 and GLUT4 translocation, we used the SIRT1 activator resveratrol and si-PKCζ to identify the switches in metabolism. Although PA reduced CD36 and increased GLUT4 metabolic pathway proteins, when we pretreated cells with resveratrol to activate SIRT1 or transfected si-PKCζ, both were able to significantly increase CD36 metabolic pathway proteins and reduce GLUT4 pathway proteins. High-fat diets affect energy metabolism pathways in both normal and aging rats and involve switching the energy source from the CD36 pathway to GLUT4. In conclusion, PA and high-fat diets cause lipotoxicity in vivo and in vitro and adversely switch the energy source from the CD36 pathway to the GLUT4 pathway. PMID:27133433

  4. Dissolution of Aluminum in Variably Charged Soils as Affected by Low-Molecular-Weight Organic Acids

    LI Jiu-Yu; XU Ren-Kou; JI Guo-Liang

    2005-01-01

    Low-molecular-weight (LMW) organic acids exist widely in soils and play an important role in soil processes such as mineral weathering, nutrient mobilization and Al detoxification. In this research, a batch experiment was conducted to examine the effects of LMW organic acids on dissolution of aluminum in two variably charged soils, an Ultisol and an Oxisol. The results showed that the LMW organic acids enhanced the dissolution of Al in the two investigated soils in the following order: citric > oxalic > malonic > malic > tartaric > salicylic > lactic > maleic. This was generally in agreement with the magnitude of the stability constants for the Al-organic complexes. The effects of LMW organic acids on Al dissolution were greater in the Ultisol than in the Oxisol as compared to their controls. Also, the accelerating effects of citric and oxalic acids on dissolution of Al increased with an increase in pH, while the effects of lactic and salicylic acids decreased. Additionally, when the organic acid concentration was less than 0.2 mmol L-1, the dissolution of Al changed little with increase in acid concentration. However, when the organic acid concentration was greater than 0.2 mmol L-1,the dissolution of Al increased with increase in acid concentration. In addition to the acid first dissociation constant and stability constant of Al-organic complexes, the promoting effects of LMW organic acids on dissolution of Al were also related to their sorption-desorption equilibrium in the soils.

  5. Molecularly imprinted polymer microspheres for solid-phase extraction of protocatechuic acid in Rhizoma homalomenae.

    Chen, Fang-Fang; Wang, Guo-Ying; Shi, Yan-Ping

    2011-10-01

    Molecularly imprinted polymers (MIPs) had been prepared by precipitation polymerization method using acrylamide as the functional monomer, ethylene glycol dimethacrylate as the cross-linker, acetonitrile as the porogen solvent and protocatechuic acid (PA), one of phenolic acids, as the template molecule. The MIPs were characterized by scanning electron microscopy and Fourier transform infrared, and their performance relative to non-imprinted polymers was assessed by equilibrium binding experiments. Six structurally similar phenolic acids, including p-hydroxybenzoic acid, gallic acid, salicylic acid, syringic acid, vanillic acid, ferulic acid were selected to assess the selectivity and recognition capability of the MIPs. The MIPs were applied to extract PA from the traditional Chinese medicines as a solid-phase extraction sorbent. The resultant cartridge showed that the MIPs have a good extraction performance and were able to selectively extract almost 82% of PA from the extract of Rhizoma homalomenae. Thus, the proposed molecularly imprinted-solid phase extraction-high performance liquid chromatography method can be successfully used to extract and analyse PA in traditional Chinese medicines. PMID:21809445

  6. A molecular switch between the outer and the inner vestibule of the voltage-gated Na+ channel

    conformational change of the inner vestibule generates the IUS state. In order to explain the involvement of both the outer and the inner vestibule in ultra-slow inactivation, we proposed a model in which the mutation K1237E produces a conformational change of the outer vestibule which is transmitted to the internal vestibule through the DIV- S6 segment. The resulting conformational change of the internal vestibule gives rise to the extremely stable IUS state. If this molecular mechanism holds true, then mutations at the location of interaction between the selectivity filter and the adjacent S6 segment should substantially modulate the ultra-slow inactivated state. A homology model of the voltage-gated Na+ channel, based on the crystal structure of the KcsA channel places the domain IV-S6 segment in close proximity to the domain III P-loop (containing the site 1237 which is essential for the generation of IUS). In order to search for experimental evidence for an interaction site between the domain III P-loop and the internal vestibule we generated serial alanine and cysteine replacements of amino acids of the domain DIV- S6 segment in the background of the mutation K1237E. We find that mutations only at the site 1575 substantially decrease the likelihood of entry into IUS or significantly accelerate recovery from IUS, suggesting that this residue represents an interaction site between the domain III p-loop and the domain IV- S6 segment. For the first time these functional data confirm a molecular model in which the turn of the domain III P-loop is in close relationship with the domain IV- S6 segment at the level of I1575. (author)

  7. Charting molecular composition of phosphatidylcholines by fatty acid scanning and ion trap MS3 fragmentation

    Ekroos, Kim; Ejsing, Christer S.; Bahr, Ute;

    2003-01-01

    preliminary separation of lipid classes or of individual molecular species, enzymatic digestion, or chemical derivatization. The approach was validated by the comparative analysis of the molecular composition of PCs from human red blood cells. In the total lipid extract of Madin-Darby canine kidney II cells......The molecular composition of phosphatidylcholines (PCs) in total lipid extracts was characterized by a combination of multiple precursor ion scanning on a hybrid quadrupole time-of-flight mass spectrometer and MS3 fragmentation on an ion trap mass spectrometer. Precursor ion spectra for 50 acyl...... anion fragments of fatty acids (fatty acid scanning) acquired in parallel increased the specificity and the dynamic range of the detection of PCs and identified the fatty acid moieties in individual PC species. Subsequent analysis of detected PC peaks by MS3 fragmentation on an ion trap mass...

  8. An intrinsic propensity of murine peritoneal B1b cells to switch to IgA in presence of TGF-β and retinoic acid.

    Bishnudeo Roy

    Full Text Available AIMS: In the present study we have investigated the comparative switching propensity of murine peritoneal and splenic B cell subpopulations to IgA in presence of retinoic acid (RA and TGF-β. METHODS AND RESULTS: To study the influence of RA and TGF-β on switching of B cell subpopulations to IgA, peritoneal (B1a, B1b and B2 cells and splenic (B1a, marginal zone, and B2 B cells from normal BALB/c mice were FACS purified, cultured for 4 days in presence of RA and TGF-β and the number of IgA producing cells was determined by ELISPOT assay or FACS analysis. In presence of TGF-β, peritoneal B1b cells switched to IgA more potently than other peritoneal B cell subpopulations. When TGF-β was combined with retinoic acid (RA, switching to IgA was even more pronounced. Under these conditions, "innate" B cells like peritoneal and splenic B1 cells and MZ B cells produced IgA more readily than B2 cells. Additionally, high frequency of nucleotide exchanges indicating somatic hypermutation in VH regions was observed. Besides IgA induction, RA treatment of sorted PEC and splenic B cells led to expression of gut homing molecules - α4β7 and CCR9. Intraperitoneal transfer of RA-treated B1 cells into Rag1(-/- recipients resulted in IgA in serum and gut lavage, most efficiently amongst B1b cell recipients. CONCLUSION: Present study demonstrates the differential and synergistic effect of RA and TGF-β on switching of different B cell subpopulations to IgA and establishes the prominence of peritoneal B1b cells in switching to IgA under the influence of these two factors. Our study extends our knowledge about the existing differences among B cell subpopulations with regards to IgA production and indicates towards their differential contribution to gut associated humoral immunity.

  9. Multiscale Reactive Molecular Dynamics for Absolute pK a Predictions and Amino Acid Deprotonation.

    Nelson, J Gard; Peng, Yuxing; Silverstein, Daniel W; Swanson, Jessica M J

    2014-07-01

    Accurately calculating a weak acid's pK a from simulations remains a challenging task. We report a multiscale theoretical approach to calculate the free energy profile for acid ionization, resulting in accurate absolute pK a values in addition to insights into the underlying mechanism. Importantly, our approach minimizes empiricism by mapping electronic structure data (QM/MM forces) into a reactive molecular dynamics model capable of extensive sampling. Consequently, the bulk property of interest (the absolute pK a) is the natural consequence of the model, not a parameter used to fit it. This approach is applied to create reactive models of aspartic and glutamic acids. We show that these models predict the correct pK a values and provide ample statistics to probe the molecular mechanism of dissociation. This analysis shows changes in the solvation structure and Zundel-dominated transitions between the protonated acid, contact ion pair, and bulk solvated excess proton. PMID:25061442

  10. Molecular pharmacology of homologues of ibotenic acid at cloned metabotropic glutamic acid receptors

    Bräuner-Osborne, Hans; Nielsen, B; Krogsgaard-Larsen, P

    We have studied the effects of the enantiomers of 2-amino-3-(3-hydroxyisoxazol-5-yl)propionic acid (homoibotenic acid, HIBO) and analogues substituted with a methyl, bromo or butyl group in the four position of the ring at cloned metabotropic glutamate (mGlu) receptors expressed in Chinese hamste...

  11. Molecular and Functional Characterisation of a new Mammalian Family of Proton-coupled Amino Acid Transporters

    Foltz, Martin

    2006-01-01

    Proton-coupled amino acid transport (PAT) systems in the apical membrane of epithelial cells of the small intestine and the renal tubule have been demonstrated by use of the human intestinal cell line Caco-2 and renal brush border membrane vesicles. The present thesis summarises the revelation of the molecular entity of the PAT system and provides deeper insights into this new mammalian family of proton/amino acid cotransporters. The identified family comprises four structural similar murine ...

  12. Amino acids and proteins at ZnO-water interfaces in molecular dynamics simulations

    Nawrocki, Grzegorz; Cieplak, Marek

    2014-01-01

    We determine potentials of the mean force for interactions of amino acids with four common surfaces of ZnO in aqueous solutions. The method involves all-atom molecular dynamics simulations combined with the umbrella sampling technique. The profiled nature of the density of water with the strongly adsorbed first layer affects the approach of amino acids to the surface and generates either repulsion or weak binding. The largest binding energy is found for tyrosine interacting with the surface i...

  13. Bile acid derivatives as ligands of the farnesoid x receptor: molecular determinants for bile acid binding and receptor modulation.

    Gioiello, Antimo; Cerra, Bruno; Mostarda, Serena; Guercini, Chiara; Pellicciari, Roberto; Macchiarulo, Antonio

    2014-01-01

    Bile acids are a peculiar class of steroidal compounds that never cease to amaze. From being simple detergents with a primary role in aiding the absorption of fats and fat-soluble vitamins, bile acids are now widely considered as crucial hormones endowed with genomic and non-genomic functions that are mediated by their interaction with several proteins including the nuclear receptor Farnesoid X Receptor (FXR). Taking advantages of the peculiar properties of bile acids in interacting with the FXR receptor, several biliary derivatives have been synthesized and tested as FXR ligands. The availability of these compounds has contributed to characterize the receptor from a structural, patho-physiological and therapeutic standpoint. Among these, obeticholic acid is a first-in-class FXR agonist that is demonstrating hepatoprotective effects upon FXR activation in patients with liver diseases such as primary biliary cirrhosis and nonalcoholic steatohepatitis. This review provides an historical overview of the rationale behind the discovery of obeticholic acid and chemical tools generated to depict the molecular features and bio-pharmacological relevance of the FXR receptor, as well as to summarize structure-activity relationships of bile acid-based FXR ligands so far reported. PMID:25388535

  14. Add-on-Statin Extended Release Nicotinic Acid/Laropiprant but Not the Switch to High-Dose Rosuvastatin Lowers Blood Pressure: An Open-Label Randomized Study

    Anastazia Kei

    2011-01-01

    Full Text Available Introduction. Nicotinic acid (NA and statins have been associated with reductions in blood pressure (BP. Patients and Methods. We recruited 68 normotensive and hypertensive dyslipidemic patients who were treated with a conventional statin dose and had not achieved lipid targets. Patients were randomized to switch to high-dose rosuvastatin (40 mg/day or to add-on current statin treatment with extended release (ER NA/laropiprant (1000/20 mg/day for the first 4 weeks followed by 2000/40 mg/day for the next 8 weeks for 3 months. Results. Switching to rosuvastatin 40 mg/day was not associated with significant BP alterations. In contrast, the addition of ER-NA/laropiprant to current statin treatment resulted in a 7% reduction of systolic BP (from 134±12 to 125±10 mmHg, <.001 versus baseline and =.01 versus rosuvastatin group and a 5% reduction of diastolic BP (from 81±9 to 77±6 mmHg, =.009 versus baseline and =.01 versus rosuvastatin group. These reductions were significant only in the subgroup of hypertensives and were independent of the hypolipidemic effects of ER-NA/laropiprant. Conclusions. Contrary to the switch to high-dose rosuvastatin, the addition of ER-NA/laropiprant to statin treatment was associated with significant reductions in both systolic and diastolic BP.

  15. Structure and dynamics studies of the short strong hydrogen bond in the 3,5-dinitrobenzoic acid-nicotinic acid molecular complex.

    Ford, Samantha J.; McIntyre, Garry J.; Johnson, Mark R.; Evans, Ivana Radosavljevic

    2013-01-01

    The molecular complex between 3,5-dinitrobenzoic acid and nicotinic acid (35DBNA) has been studied by variable temperature single crystal X-ray and neutron diffraction (30 to 300 K) and ab initio molecular dynamics, in order to investigate the dynamics and any proton migration in this system, which exhibits structural similarities with the well-known proton migration material 3,5-dicarboxylic acid. The refined structures clearly indicate a significant degree of proton transfer in ...

  16. Realization of a four-step molecular switch in scanning tunneling microscope manipulation of single chlorophyll-a molecules

    Iancu, Violeta; Hla, Saw-Wai

    2006-01-01

    Single chlorophyll-a molecules, a vital resource for the sustenance of life on Earth, have been investigated by using scanning tunneling microscope manipulation and spectroscopy on a gold substrate at 4.6 K. Chlorophyll-a binds on Au(111) via its porphyrin unit while the phytyl-chain is elevated from the surface by the support of four CH3 groups. By injecting tunneling electrons from the scanning tunneling microscope tip, we are able to bend the phytyl-chain, which enables the switching of fo...

  17. UPGRADING OF BIO-OIL MOLECULAR DISTILLATION FRACTION WITH SOLID ACID CATALYST

    Zuogang Guo

    2011-05-01

    Full Text Available Molecular distillation technology has been adopted to obtain a bio-oil fraction rich in carboxylic acids and ketones. This unique bio-oil fraction was then upgraded with a La-promoted solid acid catalyst. Three washing pretreatments were used to prepare catalysts A, B, and C, with the intention of reducing the amounts of residual sulfuric acid. Model reactions were used to estimate their catalytic activities and the residual amounts of sulfuric acid. Catalyst B, with washing after calcination, displayed higher catalytic activity (80.83% and lower residual amount of sulfuric acid (50 μmol/g. The catalysts were characterized by techniques such as BET, XRD, and SEM to explain the differences in their catalytic activities. The optimum catalyst B was used in the upgrading of the bio-oil molecular distillation fraction. After upgrading, the corrosivity of the bio-oil fraction declined and its storage stability was improved. The carboxylic acid content in the upgraded bio-oil fraction decreased from 18.39% to 2.70%, while the ester content increased from 0.72% to 31.17%. The conversion of corrosive carboxylic acids to neutral esters reduced the corrosivity of the bio-oil fraction. Moreover, the ketones with unsaturated carbon-carbon double bonds (such as 2-cyclopenten-1-one, 3-methyl-2-cyclopenten-1-one, etc. were converted into saturated compounds, which improved the stability of the bio-oil fraction.

  18. Relationship between molecular descriptors and the enthalpies of sublimation of natural amino acids

    Badelin, V. G.; Tyunina, V. V.; Girichev, G. V.; Tyunina, E. Yu.

    2016-07-01

    A multiparameter correlation between the enthalpies of sublimation and molecular descriptors of natural amino acids is proposed, based on generalized experimental and literature data on the heat effects of sublimation. The contributions from Van der Waals interactions, hydrogen bond formation, and electrostatic effects into enthalpy of sublimation has been evaluated using regression coefficients.

  19. Comparison of phenotypic and molecular tests to identify lactic acid bacteria

    Paula Mendonça Moraes; Luana Martins Perin; Abelardo Silva Júnior; Luís Augusto Nero

    2013-01-01

    Twenty-nine lactic acid bacteria (LAB) isolates were submitted for identification using Biolog, API50CHL, 16S rDNA sequencing, and species-specific PCR reactions. The identification results were compared, and it was concluded that a polyphasic approach is necessary for proper LAB identification, being the molecular analyzes the most reliable.

  20. Identification of Low-Molecular-Weight Nucleic Acid-Related Substances Secreted by Streptomyces aureofaciens

    De Carvalho, Alírio; Molinari, Rubens

    1983-01-01

    Streptomyces aureofaciens growth in chemically defined medium is actively associated with the secretion of low-molecular-weight nucleic acid-related substances and is linked to low availability of phosphate. Thirteen pure compounds were isolated, of which seven were identified.

  1. Unbinding of Retinoic Acid from its Receptor Studied by Steered Molecular Dynamics

    Kosztin, D; Schulten, K; Kosztin, Dorina; Izrailev, Sergei; Schulten, Klaus

    1999-01-01

    Retinoic acid receptor (RAR) is a ligand-dependent transcription factor that regulates the expression of genes involved in cell growth, differentiation, and development. Binding of the retinoic acid hormone to RAR is accompanied by conformational changes in the protein which induce transactivation or transrepression of the target genes. In this paper we present a study of the hormone binding/unbinding process in order to clarify the role of some of the amino acid contacts and identify possible pathways of the all-trans retinoic acid binding/unbinding to/from human retinoic acid receptor (hRAR)-g. Three possible pathways were explored using steered molecular dynamics simulations. Unbinding was induced on a time scale of 1 ns by applying external forces to the hormone. The simulations suggest that the hormone may employ one pathway for binding and an alternative "back door" pathway for unbinding.

  2. A Metabolic Switch

    Hjorth, Poul G.

    Our muscles are metabolically flexible, i.e., they are capable of `switching' between two types of oxidation: (1) when fasting, a predominantly lipid oxidation with high rates of fatty acid uptake, and (2) when fed, suppression of lipid oxidation in favour of increased glucose uptake, oxidation and...... storage, in response to insulin. One of the many manifestations of obesity and Type 2 diabetes is an insulin resistance of the skeletal muscles, which suppresses this metabolic switch. This talk describes recent development of a low-dimensional system of ODEs that model the metabolic switch, displaying a...

  3. Photoelectron spectroscopy of self-assembled monolayers of molecular switches on noble metal surfaces; Photoelektronenspektroskopie selbstorganisierter Adsorbatschichten aus molekularen Schaltern auf Edelmetalloberflaechen

    Heinemann, Nils

    2012-09-12

    Self-assembled monolayers (SAMs) of butanethiolate (C4) on single crystalline Au(111) surfaces were prepared by adsorption from solution. The thermally activated desorption behaviour of the C4 molecules from the gold substrate was examined by qualitative thermal desorption measurements (TDM), through this a desorption temperature T{sub Des}=473 K could be determined. With this knowledge, it was possible to produce samples of very good surface quality, by thermal treatment T{sub Sample}molecular switch 3-(4-(4-Hexyl-phenylazo)-phenoxy)-propane-1-thiol (ABT), deposited by self-assembly from solution on Au(111), was examined using laser-based photoelectron spectroscopy. Differences in the molecular dipole moment characteristic for the trans and the cis isomer of ABT were observed via changes in the sample work function, accessible by detection of the threshold energy for photoemission. A quantitative

  4. Effect on molecular weight of poly (L-lactic acid) by irradiation graft with NVP

    Copolymer of poly (L-lactic acid) (PLLA) grafted with N-vinylpyrrolidone(PLLA-g-PVP) was prepared by γ-irradiation in the presence of methanol as a solvent. The effects of acetic acid (HAc) concentration, monomer concentration and dose rate on molecular weight of PLLA-g-PVP were investigated and the structure of PLLA-g-PVP was characterized by 1H-NMR, FT-IR and TGA, respectively. It shows that, the HAc concentration, monomer concentration and dose rate have an effect on the molecular weight of PLLA-g-PVP at the same absorbed dose. The maximum molecular weight of the copolymers can be obtained in optimum condition of HAc concentration 0.05 mol/L, monomer concentration 30% and dose rate 500 Gy/h, respectively. The two weight loss stages of graft copolymers have been observed more distinctly with the increment of graft ratio. (authors)

  5. Strong Hydrogen Bonded Molecular Interactions between Atmospheric Diamines and Sulfuric Acid.

    Elm, Jonas; Jen, Coty N; Kurtén, Theo; Vehkamäki, Hanna

    2016-05-26

    We investigate the molecular interaction between methyl-substituted N,N,N',N'-ethylenediamines, propane-1,3-diamine, butane-1,4-diamine, and sulfuric acid using computational methods. Molecular structure of the diamines and their dimer clusters with sulfuric acid is studied using three density functional theory methods (PW91, M06-2X, and ωB97X-D) with the 6-31++G(d,p) basis set. A high level explicitly correlated CCSD(T)-F12a/VDZ-F12 method is used to obtain accurate binding energies. The reaction Gibbs free energies are evaluated and compared with values for reactions involving ammonia and atmospherically relevant monoamines (methylamine, dimethylamine, and trimethylamine). We find that the complex formation between sulfuric acid and the studied diamines provides similar or more favorable reaction free energies than dimethylamine. Diamines that contain one or more secondary amino groups are found to stabilize sulfuric acid complexes more efficiently. Elongating the carbon backbone from ethylenediamine to propane-1,3-diamine or butane-1,4-diamine further stabilizes the complex formation with sulfuric acid by up to 4.3 kcal/mol. Dimethyl-substituted butane-1,4-diamine yields a staggering formation free energy of -19.1 kcal/mol for the clustering with sulfuric acid, indicating that such diamines could potentially be a key species in the initial step in the formation of new particles. For studying larger clusters consisting of a diamine molecule with up to four sulfuric acid molecules, we benchmark and utilize a domain local pair natural orbital coupled cluster (DLPNO-CCSD(T)) method. We find that a single diamine is capable of efficiently stabilizing sulfuric acid clusters with up to four acid molecules, whereas monoamines such as dimethylamine are capable of stabilizing at most 2-3 sulfuric acid molecules. PMID:27128188

  6. New concepts in molecular imaging: non-invasive MRI spotting of proteolysis using an Overhauser effect switch.

    Philippe Mellet

    Full Text Available BACKGROUND: Proteolysis, involved in many processes in living organisms, is tightly regulated in space and time under physiological conditions. However deregulation can occur with local persistent proteolytic activities, e.g. in inflammation, cystic fibrosis, tumors, or pancreatitis. Furthermore, little is known about the role of many proteases, hence there is a need of new imaging methods to visualize specifically normal or disease-related proteolysis in intact bodies. METHODOLOGY/PRINCIPAL FINDINGS: In this paper, a new concept for non invasive proteolysis imaging is proposed. Overhauser-enhanced Magnetic Resonance Imaging (OMRI at 0.2 Tesla was used to monitor the enzymatic hydrolysis of a nitroxide-labeled protein. In vitro, image intensity switched from 1 to 25 upon proteolysis due to the associated decrease in the motional correlation time of the substrate. The OMRI experimental device used in this study is consistent with protease imaging in mice at 0.2 T without significant heating. Simulations show that this enzymatic-driven OMRI signal switch can be obtained at lower frequencies suitable for larger animals or humans. CONCLUSIONS/SIGNIFICANCE: The method is highly sensitive and makes possible proteolysis imaging in three dimensions with a good spatial resolution. Any protease could be targeted specifically through the use of taylor-made cleavable macromolecules. At short term OMRI of proteolysis may be applied to basic research as well as to evaluate therapeutic treatments in small animal models of experimental diseases.

  7. Study of the molecular mobility of methyl-methacrylate and methacrylic acid copolymers by solid state NMR

    Several methyl-methacrylate/methacrylic acid copolymers were prepared in the presence of concentrated nitric acid. The obtained copolymers were characterized by molecular weigh determination and hydrolization degree. The molecular mobility of these copolymers was studied by solid state nuclear magnetic resonance. Results are presented

  8. Separation of phenolic acids from natural plant extracts using molecularly imprinted anion-exchange polymer confined ionic liquids.

    Bi, Wentao; Tian, Minglei; Row, Kyung Ho

    2012-04-01

    Polymer-confined ionic liquids were used for the separation of phenolic acids from natural plant extract by utilizing an anion-exchange mechanism. They were synthesized using molecular imprinting technique to reduce non-directional ion-ion interactions during anion-exchange and other interactions with interference substances that could decrease selectivity. A suitable sorbent for phenolic acid separation could be identified based on the adsorption behaviors of phenolic acids on different polymer-confined ionic liquids. Thus, the developed ionic liquid-based molecularly imprinted anion-exchange polymer (IMAP) achieved high recovery rates by solid-phase extraction of phenolic acids from Salicornia herbacea L. extract: 90.1% for protocatechuic acid, 95.5% for ferulic acid and 96.6% for caffeic acid. Moreover, the phenolic acids were separable from each other by repeated solid phase extraction cycles. The proposed method could be used to separate other phenolic acids or organic acids from complex samples. PMID:21903215

  9. Supra-molecular Association and Polymorphic Behaviour In Systems Containing Bile Acid Salts

    Camillo La Mesa

    2007-08-01

    Full Text Available A wide number of supra-molecular association modes are observed in mixtures containing water and bile salts, BS, (with, eventually, other components. Molecular or micellar solutions transform into hydrated solids, fibres, lyotropic liquid crystals and/or gels by raising the concentration, the temperature, adding electrolytes, surfactants, lipids and proteins. Amorphous or ordered phases may be formed accordingly. The forces responsible for this very rich polymorphism presumably arise from the unusual combination of electrostatic, hydrophobic and hydrogen-bond contributions to the system stability, with subsequent control of the supra-molecular organisation modes. The stabilising effect due to hydrogen bonds does not occur in almost all surfactants or lipids and is peculiar to bile acids and salts. Some supra-molecular organisation modes, supposed to be related to malfunctions and dis-metabolic diseases in vivo, are briefly reported and discussed.

  10. Synthesis of high molecular weight polylactic acid from aqueous lactic acid co-catalyzed by tin(II)chloride dihydrate and succinic anhydride

    LEI Ziqiang; BAI Yanbin; WANG Shoufeng

    2005-01-01

    Polylactic acid was synthesized from commercial available cheap aqueous lactic acid (85%―90% w/w) using succinic anhydride and SnCl2·2H2O as catalyst in the absence of organic solvents. As a result, polylactic acid with a molecular weight of 60000 was prepared in 10 h. The new procedure is much simple, cheap and outstanding in that the start material is aqueous lactic acid; the catalytic system is environmentally benign.

  11. Preparation and characterization of the high molecular weight [3H]hyaluronic acid

    Two methods of preparation were investigated. In the first, hydrogen atoms in the molecule are replaced by tritium. This isotopic substitution was performed in aqueous solution using Pd/CaCO3 as catalyst. In the second method, the high molecular weight hyaluronic acid was alkylated with [3H]methyl bromide in liquid ammonia at a temperature of -33.5 degC. High-performance gel permeation chromatographic separation was used for the separation and characterization of the high molecular weight [3H]hyaluronic acid. Molecular weight parameters for the labelled biopolymers were: M-barw=128 kDa, M-barw/M-barn=1.88 (first method) and M-barw=268 kDa, M-barw/M-barn=1.55 (second method). The high molecular weight [3H]hyaluronic acid with M-barw=268 kDa was degraded further by specific hyaluronidase. Products of the enzymatic depolymerization were observed to be identical for both the labelled and cold biopolymer. This finding indicates that the described labelling procedure using [3H]methyl bromide does not induce any major structural rearrangements in the molecule. (author) 3 figs., 2 tabs., 13 refs

  12. Macromolecular Crowding Studies of Amino Acids Using NMR Diffusion Measurements and Molecular Dynamics Simulations

    Amninder S Virk

    2015-02-01

    Full Text Available Molecular crowding occurs when the total concentration of macromolecular species in a solution is so high that a considerable proportion of the volume is physically occupied and therefore not accessible to other molecules. This results in significant changes in the solution properties of the molecules in such systems. Macromolecular crowding is ubiquitous in biological systems due to the generally high intracellular protein concentrations. The major hindrance to understanding crowding is the lack of direct comparison of experimental data with theoretical or simulated data. Self-diffusion is sensitive to changes in the molecular weight and shape of the diffusing species, and the available diffusion space (i.e., diffusive obstruction. Consequently, diffusion measurements are a direct means for probing crowded systems including the self-association of molecules. In this work, nuclear magnetic resonance measurements of the self-diffusion of four amino acids (glycine, alanine, valine and phenylalanine up to their solubility limit in water were compared directly with molecular dynamics simulations. The experimental data were then analyzed using various models of aggregation and obstruction. Both experimental and simulated data revealed that the diffusion of both water and the amino acids were sensitive to the amino acid concentration. The direct comparison of the simulated and experimental data afforded greater insights into the aggregation and obstruction properties of each amino acid.

  13. Evaluating the molecular weight and characteristics of humic acids gradations using gel filtration and radioisotope tracer technique

    The measurement for molecular weight of humic acids gradations in the drab soil showed that the humic acid could be separated into three gradations of molecular weight using gel filtration by G-50 and two gradations by G-100, the molecular weights by G-50 were 78180, 48339, 22863 and molecular weights by G-100 were 63343 and 19870 respectively. While fulvic acid had only one gradation by both G-50 and G-100, the molecular weight was 2300 approximately. The measurement for complexation capacity of cadmium (zinc)-humic acids showed that the contents of Cd(Zn)-humic acid had two peak values with the volume of eluent compounded by cadmium (or zinc). The Cd(or Zn)-fulvic acid had only one peak value. The curve between contents of Cd (Zn)-humic acid and the volume of eluent met with the curve between spectrum and the volume of eluent. The experiment conducted by radioisotope tracer technique indicated that the complexation capacity of 65Zn-humic acids changed with different gradations of humic acids, the complexation curve met with the spectrum curve on the whole, i.e. the value of 65Zn-humic acid had two peak values, while the 65Zn-fulvic acid had only one, indicating that the use of radioisotope tracer technique could eliminate the intervention accompanied by other heavy metal ions

  14. Photochemical alkylation of inorganic selenium in the presence of low molecular weight organic acids.

    Guo, Xuming; Sturgeon, Ralph E; Mester, Zoltán; Gardner, Graeme J

    2003-12-15

    Using a flow-through photochemical reactor and a low pressure mercury lamp as a UV source, alkyl selenium species are formed from inorganic selenium(IV) in the presence of low molecular weight organic acids (LMW acids). The volatile alkyl Se species were cryogenically trapped and identified by GC-MS and GC-ICP-MS. In the presence of formic, acetic, propionic and malonic acids, inorganic selenium(IV) is converted by UV irradiation to volatile selenium hydride and carbonyl, dimethylselenide and diethylselenide, respectively. Se(IV) was successfully removed from contaminated agricultural drainage waters (California, U.S.A.) using a batch photoreactor system Se. Photochemical alkylation may thus offer a promising means of converting toxic selenium salts, present in contaminated water, to less toxic dimethylselenide. The LMW acids and photochemical alkylation process may also be key to understanding the source of atmospheric selenium and are likely involved in its mobility in the natural anaerobic environment. PMID:14717175

  15. High-molecular-weight polymers for protein crystallization: poly-γ-glutamic acid-based precipitants

    High-molecular-weight poly-γ-glutamic acid-based polymers have been synthesized, tested and adopted for protein crystallization. Protein crystallization has been revolutionized by the introduction of high-throughput technologies, which have led to a speeding up of the process while simultaneously reducing the amount of protein sample necessary. Nonetheless, the chemistry dimension of protein crystallization has remained relatively undeveloped. Most crystallization screens are based on the same set of precipitants. To address this shortcoming, the development of new protein precipitants based on poly-γ-glutamic acid (PGA) polymers with different molecular-weight ranges is reported here: PGA-LM (low molecular weight) of ∼400 kDa and PGA-HM (high molecular weight) of >1000 kDa. It is also demonstrated that protein precipitants can be expanded further to polymers with much higher molecular weight than those that are currently in use. Furthermore, the modification of PGA-like polymers by covalent attachments of glucosamine substantially improved their solubility without affecting their crystallization properties. Some preliminary PGA-based screens are presented here

  16. High-molecular-weight polymers for protein crystallization: poly-γ-glutamic acid-based precipitants

    Hu, Ting-Chou [Department of Chemistry, University of York, York YO10 5YW (United Kingdom); Korczyńska, Justyna [Department of Chemistry, University of York, York YO10 5YW (United Kingdom); Structural Biology Laboratory, University of York, York YO10 5YW (United Kingdom); Smith, David K. [Department of Chemistry, University of York, York YO10 5YW (United Kingdom); Brzozowski, Andrzej Marek, E-mail: marek@ysbl.york.ac.uk [Department of Chemistry, University of York, York YO10 5YW (United Kingdom); Structural Biology Laboratory, University of York, York YO10 5YW (United Kingdom)

    2008-09-01

    High-molecular-weight poly-γ-glutamic acid-based polymers have been synthesized, tested and adopted for protein crystallization. Protein crystallization has been revolutionized by the introduction of high-throughput technologies, which have led to a speeding up of the process while simultaneously reducing the amount of protein sample necessary. Nonetheless, the chemistry dimension of protein crystallization has remained relatively undeveloped. Most crystallization screens are based on the same set of precipitants. To address this shortcoming, the development of new protein precipitants based on poly-γ-glutamic acid (PGA) polymers with different molecular-weight ranges is reported here: PGA-LM (low molecular weight) of ∼400 kDa and PGA-HM (high molecular weight) of >1000 kDa. It is also demonstrated that protein precipitants can be expanded further to polymers with much higher molecular weight than those that are currently in use. Furthermore, the modification of PGA-like polymers by covalent attachments of glucosamine substantially improved their solubility without affecting their crystallization properties. Some preliminary PGA-based screens are presented here.

  17. Application of molecular techniques for identification and ennumeration of acetic acid bacteria

    González Benito, Angel

    2005-01-01

    Application of molecular techniques for identification and enumeration of acetic acid bacteria:Los principales objetivos de la tesis son el desarrollo de técnicas de biología molecular rápidas y fiables para caracterizar bacterias acéticas.Las bacterias acéticas son las principales responsables del picado de los vinos y de la producción de vinagre. Sin embargo, existe un desconocimiento importante sobre su comportamiento y evolución. Las técnicas de enumeración y de identificación basadas en ...

  18. Molecular-scale imaging of unstained deoxyribonucleic acid fibers by phase transmission electron microscopy

    The molecular structure of deoxyribonucleic acid (DNA) fibers was observed by a phase reconstruction method called three-dimensional Fourier filtering using a 200 kV transmission electron microscope. The characteristic helical structure and the spacing of adjacent base pairs of DNA were partially resolved due to an improved signal-to-noise ratio and resolution enhancement by the phase reconstruction although the molecular structure was damaged by the electron beam irradiation. In the spherical aberration-free phase images, the arrangements of single atom-sized spots forming sinusoidal curves were sometimes observed, which seem to be the contrast originating in the sulfur atoms along the main chains

  19. Femtosecond Laser Spectroscopy of the Rhodopsin Photochromic Reaction: A Concept for Ultrafast Optical Molecular Switch Creation (Ultrafast Reversible Photoreaction of Rhodopsin

    Olga Smitienko

    2014-11-01

    Full Text Available Ultrafast reverse photoreaction of visual pigment rhodopsin in the femtosecond time range at room temperature is demonstrated. Femtosecond two-pump probe experiments with a time resolution of 25 fs have been performed. The first рump pulse at 500 nm initiated cis-trans photoisomerization of rhodopsin chromophore, 11-cis retinal, which resulted in the formation of the primary ground-state photoproduct within a mere 200 fs. The second pump pulse at 620 nm with a varying delay of 200 to 3750 fs relative to the first рump pulse, initiated the reverse phototransition of the primary photoproduct to rhodopsin. The results of this photoconversion have been observed on the differential spectra obtained after the action of two pump pulses at a time delay of 100 ps. It was found that optical density decreased at 560 nm in the spectral region of bathorhodopsin absorption and increased at 480 nm, where rhodopsin absorbs. Rhodopsin photoswitching efficiency shows oscillations as a function of the time delay between two рump pulses. The quantum yield of reverse photoreaction initiated by the second pump pulse falls within the range 15% ± 1%. The molecular mechanism of the ultrafast reversible photoreaction of visual pigment rhodopsin may be used as a concept for the development of an ultrafast optical molecular switch.

  20. Molecular dynamics simulations data of the twenty encoded amino acids in different force fields.

    Vitalini, F; Noé, F; Keller, B G

    2016-06-01

    We present extensive all-atom Molecular Dynamics (MD) simulation data of the twenty encoded amino acids in explicit water, simulated with different force fields. The termini of the amino acids have been capped to ensure that the dynamics of the Φ and ψ torsion angles are analogues to the dynamics within a peptide chain. We use representatives of each of the four major force field families: AMBER ff-99SBILDN [1], AMBER ff-03 [2], OPLS-AA/L [3], CHARMM27 [4] and GROMOS43a1 [5], [6]. Our data represents a library and test bed for method development for MD simulations and for force fields development. Part of the data set has been previously used for comparison of the dynamic properties of force fields (Vitalini et al., 2015) [7] and for the construction of peptide basis functions for the variational approach to molecular kinetics [8]. PMID:27054161

  1. Neutral molecular cluster formation of sulfuric acid dimethylamine observed in real time under atmospheric conditions

    Kürten, Andreas; Jokinen, Tuija; Simon, Mario; Sipilä, Mikko; Sarnela, Nina; Junninen, Heikki; Adamov, Alexey; Almeida, João; Amorim, Antonio; Bianchi, Federico; Breitenlechner, Martin; Dommen, Josef; Donahue, Neil M.; Duplissy, Jonathan; Ehrhart, Sebastian

    2015-01-01

    For atmospheric sulfuric acid (SA) concentrations the presence of dimethylamine (DMA) at mixing ratios of several parts per trillion by volume can explain observed boundary layer new particle formation rates. However, the concentration and molecular composition of the neutral (uncharged) clusters have not been reported so far due to the lack of suitable instrumentation. Here we report on experiments from the Cosmics Leaving Outdoor Droplets chamber at the European Organization for Nuclear Res...

  2. Molecular characterization of lactic acid bacteria recovered from natural fermentation of beet root and carrot Kanji

    Kingston, J. J.; Radhika, M.; Roshini, P. T.; Raksha, M. A.; H.S. Murali; Batra, H. V.

    2010-01-01

    The lactic acid bacteria (LAB) play an important role in the fermentation of vegetables to improve nutritive value, palatability, acceptability, microbial quality and shelf life of the fermented produce. The LAB associated with beetroot and carrot fermentation were identified and characterized using different molecular tools. Amplified ribosomal DNA restriction analysis (ARDRA) provided similar DNA profile for the 16 LAB strains isolated from beetroot and carrot fermentation while repetitive ...

  3. n-3 Polyunsaturated fatty acids exert immunomodulatory effects on lymphocytes by targeting plasma membrane molecular organization

    Shaikh, Saame Raza; Jolly, Christopher A.; Chapkin, Robert S.

    2011-01-01

    Fish oil, enriched in bioactive n-3 polyunsaturated fatty acids (PUFA), has therapeutic value for the treatment of inflammation-associated disorders. The effects of n-3 PUFAs are pleiotropic and complex; hence, an understanding of their cellular targets and molecular mechanisms of action remains incomplete. Here we focus on recent data indicating n-3 PUFAs exert immunosuppressive effects on the function of effector and regulatory CD4+ T cells. In addition, we also present emerging evidence th...

  4. In vitro evaluation of antiviral and virucidal activity of a high molecular weight hyaluronic acid

    Blasi Elisabetta; Ardizzoni Andrea; Neglia Rachele G; Bettua Clotilde; Scuri Monica; Cuoghi Alessandro; Cermelli Claudio; Iannitti Tommaso; Palmieri Beniamino

    2011-01-01

    Abstract Background hyaluronic acid (HA), a non-sulphated glycosaminoglycan, is present in synovial fluid, vitreous humour serum and many connective tissues. Pharmaceutical preparations of HA are used in clinical practice for wound healing, joint pain, kerato-conjunctivitis, asthma, mouth care, oesophageal-reflux, and gastritis. Moreover, it is used as a filler to counteract ageing and facial lipoatrophy. Our study aims at investigating the in vitro antiviral activity of a high molecular weig...

  5. Molecular characterization of lactic acid bacteria isolated from industrially fermented Greek table olives

    Doulgeraki, Agapi; Pramateftaki, Paraskevi; Argyri, Anthoula; Nychas, George John; Tassou, Chrysoula; Panagou, Efstathios

    2012-01-01

    A total of 145 lactic acid bacteria (LAB) isolates have been recovered from fermented table olives and brine and characterized at strain level with molecular tools. Pulsed-Field Gel Electrophoresis (PFGE) of ApaI macrorestriction fragments was applied for strain differentiation. Species differentiation was based either on Denaturing Gradient Gel Electrophoresis (PCR-DGGE) (black olives) or on restriction analysis of the amplified 16S rRNA gene (PCR-ARDRA) (brine and green olives). Species ide...

  6. Ancient low–molecular-weight organic acids in permafrost fuel rapid carbon dioxide production upon thaw

    Drake, Travis W.; Wickland, Kimberly P.; Spencer, Robert G.M.; McKnight, Diane M.; Striegl, Robert G.

    2015-01-01

    To our knowledge, this study is the first to directly link rapid microbial consumption of ancient permafrost-derived dissolved organic carbon (DOC) to CO2 production using a novel bioreactor. Rapid mineralization of the freshly thawed DOC was attributed to microbial decomposition of low–molecular-weight organic acids, which were completely consumed during the experiments. Our results indicate that substantial biodegradation of permafrost DOC occurs immediately after thaw and before downstream...

  7. Molecular assessment of complex microbial communities degrading long chain fatty acids in methanogenic bioreactors

    Sousa, D.Z.; Pereira, M.A.; Smidt, Hauke; Stams, A.J.M.; Alves, M. M.

    2007-01-01

    Microbial diversity of anaerobic sludge after extended contact with long chain fatty acids (LCFA) was studied using molecular approaches. Samples containing high amounts of accumulated LCFA were obtained after continuous loading of two bioreactors with oleate or with palmitate. These sludge samples were then incubated in batch assays to allow degradation of the biomass-associated LCFA. In addition, sludge used as inoculum for the reactors was also characterized. Predominant ...

  8. Molecular dynamics study of solvation effects on acid dissociation in aprotic media

    Laria, Daniel; Kapral, Raymond; Estrin, Dario; Ciccotti, Giovanni

    1996-01-01

    Acid ionization in aprotic media is studied using Molecular Dynamics techniques. In particular, models for HCl ionization in acetonitrile and dimethylsulfoxide are investigated. The proton is treated quantum mechanically using Feynman path integral methods and the remaining molecules are treated classically. Quantum effects are shown to be essential for the proper treatment of the ionization. The potential of mean force is computed as a function of the ion pair separation and the local solven...

  9. Photoinduced switching to metallic states in the two-dimensional organic Mott insulator dimethylphenazine-tetrafluorotetracyanoquinodimethane with anisotropic molecular stacks

    Matsuzaki, Hiroyuki; Ohkura, Masa-aki; Ishige, Yu; Nogami, Yoshio; Okamoto, Hiroshi

    2015-06-01

    A photoinduced phase transition was investigated in an organic charge-transfer (CT) complex M2P -TCNQ F4 , [M2P : 5,10-dihydro-5,10-dimethylphenazine, donor (D) molecule; TCNQ F4 : 2,3,5,6-tetrafluoro-7,7,8,8-tetracyanoquinodimethane, acceptor (A) molecule] by means of femtosecond pump-probe reflection spectroscopy. This is an ionic compound and has a peculiar two-dimensional (2D) molecular arrangement; the same A (or D) molecules arrange along the [100] direction, and A and D molecules alternately arrange along the [111] direction. It results in a strongly anisotropic two-dimensional electronic structure. This compound shows a structural and magnetic phase transition at 122 K below which the two neighboring molecules are dimerized along both the [100] and [111] directions. We demonstrate that two kinds of photoinduced phase transitions occur by irradiation of a femtosecond laser pulse; in the high-temperature lattice-uniform phase, a quasi-one-dimensional (1D) metallic state along the AA(DD) stack is generated, and in the low-temperature lattice-dimerized phase, a quasi-2D metallic state is initially produced and molecular dimerizations are subsequently released. Mixed-stack CT compounds consisting of DA stacks are generally insulators or semiconductors in the ground state. Here, such a dynamical metallization in the DA stack is demonstrated. The release of the dimerizations drives several kinds of coherent oscillations which play an important role in the stabilization of the lattice-dimerized phase. The mechanisms of those photoinduced phase transitions are discussed in terms of the magnitudes of the anisotropic bandwidths and molecular dimerizations along two different directions of the molecular stacks.

  10. Molecular Structures and Dynamics of the Stepwise Activation Mechanism of a Matrix Metalloproteinase Zymogen: Challenging the Cysteine Switch Dogma

    Activation of matrix metalloproteinase zymogen (pro-MMP) is a vital homeostatic process, yet its molecular basis remains unresolved. Using stopped-flow X-ray spectroscopy of the active site zinc ion, we determined the temporal sequence of pro-MMP-9 activation catalyzed by tissue kallikrein protease in milliseconds to several minutes. The identity of three intermediates seen by X-ray spectroscopy was corroborated by molecular dynamics simulations and quantum mechanics/molecular mechanics calculations. The cysteine-zinc interaction that maintains enzyme latency is disrupted via active-site proton transfers that mediate transient metal-protein coordination events and eventual binding of water. Unexpectedly, these events ensue as a direct result of complexation of pro-MMP-9 and kallikrein and occur before proteolysis and eventual dissociation of the pro-peptide from the catalytic site. Here we demonstrate the synergism among long-range protein conformational transitions, local structural rearrangements, and fine atomic events in the process of zymogen activation.

  11. Molecular Structures and Dynamics of the Stepwise Activation Mechanism of a Matrix Metalloproteinase Zymogen: Challenging the Cysteine Switch Dogma

    Rosenblum,G.; Meroueh, S.; Toth, M.; Fisher, J.; Fridman, R.; Mobashery, S.; Sagi, I.

    2007-01-01

    Activation of matrix metalloproteinase zymogen (pro-MMP) is a vital homeostatic process, yet its molecular basis remains unresolved. Using stopped-flow X-ray spectroscopy of the active site zinc ion, we determined the temporal sequence of pro-MMP-9 activation catalyzed by tissue kallikrein protease in milliseconds to several minutes. The identity of three intermediates seen by X-ray spectroscopy was corroborated by molecular dynamics simulations and quantum mechanics/molecular mechanics calculations. The cysteine-zinc interaction that maintains enzyme latency is disrupted via active-site proton transfers that mediate transient metal-protein coordination events and eventual binding of water. Unexpectedly, these events ensue as a direct result of complexation of pro-MMP-9 and kallikrein and occur before proteolysis and eventual dissociation of the pro-peptide from the catalytic site. Here we demonstrate the synergism among long-range protein conformational transitions, local structural rearrangements, and fine atomic events in the process of zymogen activation.

  12. SYNTHESIS AND PROPERTIES OF HIGH MOLECULAR WEIGHT POLY(LACTIC ACID) AND ITS RESULTANT FIBERS

    Wang-xi Zhang; Yan-zhi Wang

    2008-01-01

    Direct melt/solid polycondensation of lactic acid (LA) was carried out to obtain high molecular weight poly(lactic acid) (PLA) by a process using various catalysts in the first-step melt polycondensation, and followed solid polycondensation by using p-toulenesulfonic acid monohydrate (TSA) as the catalyst in the second step. Effects of various catalysts and reaction temperature on the molecular weight and crystallinity of resulting PLA polymers were examined. It was shown that SnCl2·2H2O/TSA, SnCl2·2H2O/succinic anhydride, and SnCl2·2H2O/maleic anhydride binary catalysts should be effective binary catalysts to obtain high molecular weight PLA of more than 1.2 × 105. A conventional melt spinning method was used to spin PLA fibers, which displayed tensile strength of (382.76±1.41) MPa and tensile modulus of (4.36±0.07) GPa.

  13. Potential origin and formation for molecular components of humic acids in soils

    Hatcher, Patrick; DiDonato, Nicole; Waggoner, Derek

    2016-04-01

    Humification is defined as the process by which plant and microbial debris are transformed in to humic substances. Proposed pathways for the formation of humic substances, include the lignin and lignin decomposition theories, the lignin-polyphenol theory as well as the melanoidin pathway. It is generally accepted that a combination of several of these pathways with some modifications may be responsible for producing humic substances. The current study examines humic acids from numerous soil samples to demonstrate their molecular composition. In addition we provide an explanation for the formation of these molecules that introduces a new perspective of the humification process. Our work utilizes advanced analytical techniques such as ESI-FTICR-MS and solid state NMR to more completely characterize humic acids at the molecular level. Methods Humic acids were extracted from soils using 0.5 M NaOH followed by treatment with a Dowex™ ion-exchange resin to remove sodium ions. Solid State 13C NMR spectra were obtained on a Bruker 400 MHz Avance II spectrometer equipped with a 4 mm solid state MAS probe. ESI-FTICR-MS analysis was conducted in the negative ion mode on a Bruker Daltonics 12 Tesla Apex Qe FTICR-MS instrument equipped with an Apollo II ESI source. Results: Soil humic acids from numerous soils were investigated in this study. The molecular formulas calculated from ultrahigh resolution mass spectra of well humified soils fall clearly into two predominant regions consisting of condensed aromatic molecules as well as high H/C, low O/C carboxyl-containing aliphatic molecules (CCAM). In contrast, the spectral data for humic acids from a poorly humified spodosol soil show a less dramatic separation of these regions, with relatively more molecular formula plotting in the lignin-like region and relatively fewer condensed aromatic molecules. From the mass spectral observations made for the humic acids, we can readily discern a relationship based on degree of

  14. A Molecular Switch between the Outer and the Inner Vestibules of the Voltage-gated Na+ Channel*

    Zarrabi, Touran; Cervenka, Rene; Sandtner, Walter; Lukacs, Peter; Koenig, Xaver; Hilber, Karlheinz; Mille, Markus; Lipkind, Gregory M; Fozzard, Harry A.; Todt, Hannes

    2010-01-01

    Voltage-gated ion channels are transmembrane proteins that undergo complex conformational changes during their gating transitions. Both functional and structural data from K+ channels suggest that extracellular and intracellular parts of the pore communicate with each other via a trajectory of interacting amino acids. No crystal structures are available for voltage-gated Na+ channels, but functional data suggest a similar intramolecular communication involving the inner and outer vestibules. ...

  15. Molecular mechanisms of Saccharomyces cerevisiae stress adaptation and programmed cell death in response to acetic acid

    Sergio eGiannattasio

    2013-02-01

    Full Text Available Beyond its classical biotechnological applications such as food and beverage production or as a cell factory, the yeast Saccharomyces cerevisiae is a valuable model organism to study fundamental mechanisms of cell response to stressful environmental changes. Acetic acid is a physiological product of yeast fermentation and it is a well-known food preservative due to its antimicrobial action. Acetic acid has recently been shown to cause yeast cell death and aging. Here we shall focus on the molecular mechanisms of S. cerevisiae stress adaptation and programmed cell death in response to acetic acid. We shall elaborate on the intracellular signaling pathways involved in the cross-talk of pro-survival and pro-death pathways underlying the importance of understanding fundamental aspects of yeast cell homeostasis to improve the performance of a given yeast strain in biotechnological applications.

  16. High and low molecular weight hyaluronic acid differentially regulate human fibrocyte differentiation.

    Anu S Maharjan

    Full Text Available BACKGROUND: Following tissue injury, monocytes can enter the tissue and differentiate into fibroblast-like cells called fibrocytes, but little is known about what regulates this differentiation. Extracellular matrix contains high molecular weight hyaluronic acid (HMWHA; ∼2×10(6 Da. During injury, HMWHA breaks down to low molecular weight hyaluronic acid (LMWHA; ∼0.8-8×10(5 Da. METHODS AND FINDINGS: In this report, we show that HMWHA potentiates the differentiation of human monocytes into fibrocytes, while LMWHA inhibits fibrocyte differentiation. Digestion of HMWHA with hyaluronidase produces small hyaluronic acid fragments, and these fragments inhibit fibrocyte differentiation. Monocytes internalize HMWHA and LMWHA equally well, suggesting that the opposing effects on fibrocyte differentiation are not due to differential internalization of HMWHA or LMWHA. Adding HMWHA to PBMC does not appear to affect the levels of the hyaluronic acid receptor CD44, whereas adding LMWHA decreases CD44 levels. The addition of anti-CD44 antibodies potentiates fibrocyte differentiation, suggesting that CD44 mediates at least some of the effect of hyaluronic acid on fibrocyte differentiation. The fibrocyte differentiation-inhibiting factor serum amyloid P (SAP inhibits HMWHA-induced fibrocyte differentiation and potentiates LMWHA-induced inhibition. Conversely, LMWHA inhibits the ability of HMWHA, interleukin-4 (IL-4, or interleukin-13 (IL-13 to promote fibrocyte differentiation. CONCLUSIONS: We hypothesize that hyaluronic acid signals at least in part through CD44 to regulate fibrocyte differentiation, with a dominance hierarchy of SAP>LMWHA≥HMWHA>IL-4 or IL-13.

  17. A comparison of low-fluence 1064-nm Q-switched Nd: YAG laser with topical 20% azelaic acid cream and their combination in melasma in Indian patients

    Charu Bansal

    2012-01-01

    Full Text Available Background: Melasma is an acquired symmetric hypermelanosis characterised by irregular light to gray-brown macules on sun-exposed skin with a predilection for the cheeks, forehead, upper lip, nose and chin. The management of melasma is challenging and requires meticulous use of available therapeutic options. Aims: To compare the therapeutic efficacy of low-fluence Q-switched Nd: YAG laser (QSNYL with topical 20% azelaic acid cream and their combination in melasma in three study groups of 20 patients each. Materials and Methods: Sixty Indian patients diagnosed as melasma were included. These patients were randomly divided in three groups (group A = 20 patients of melasma treated with low-fluence QSNYL at weekly intervals, group B = 20 patients of melasma treated with twice daily application of 20% azelaic acid cream and group C = 20 patients of melasma treated with combination of both. Study period was of 12 weeks each. Response to treatment was assessed using melasma area and severity index score. Statistical Analysis: The statistical analysis was done using Chi-square test, paired and unpaired student t-test. Results: Significant improvement was recorded in all the three groups. The improvement was statistically highly significant in Group C as compared to group A ( P < 0.001 and group B ( P < 0.001. Conclusions: This study shows the efficacy of low-fluence QSNYL, topical 20% azelaic acid cream and their combination in melasma. The combination of low-fluence QSNYL and topical 20% azelaic acid cream yields better results as compared to low-fluence QSNYL and azelaic acid alone.

  18. Pseudospark switches

    The pseudospark discharge is bound to a geometrical structure which is particularly well suited for switching high currents and voltages at high power levels. This type of discharge offers the potential for improvement in essentially all areas of switching operation: peak current and current density, current rise, stand-off voltage, reverse current capability, cathode life, and forward drop. The first pseudospark switch was built at CERN at 1981. Since then, the basic switching characteristics of pseudospark chambers have been studied in detail. The main feature of a pseudospark switch is the confinement of the discharge plasma to the device axis. The current transition to the hollow electrodes is spread over a rather large surface area. Another essential feature is the easy and precise triggering of the pseudospark switch from the interior of the hollow electrodes, relatively far from the main discharge gap. Nanosecond delay and jitter values can be achieved with trigger energies of less than 0.1 mJ, although cathode heating is not required. Pseudospark gaps may cover a wide range of high-voltage, high-current, and high-pulse-power switching at repetition rates of many kilohertz. This report reviews the basic researh on pseudospark switches which has been going on at CERN. So far, applications have been developed in the range of thyratron-like medium-power switches at typically 20 to 40 kV and 0.5 to 10 kA. High-current pseudospark switches have been built for a high-power 20 kJ pulse generator which is being used for long-term tests of plasma lenses developed for the future CERN Antiproton Collector (ACOL). The high-current switches have operated for several hundred thousand shots, with 20 to 50 ns jitter at 16 kV charging voltage and more than 100 kA peak current amplitude. (orig.)

  19. CIRCUIT SWITCHING VERSUS PACKET SWITCHING

    Sneps-Sneppe, Manfred

    2015-01-01

    Communication specialists around the world are facing the same problem: shifting from circuit switching (CS) to packet switching (CS). Communication service providers are favoring “All-over-IP” technologies hoping to boost their profits by providing multimedia services. The main stakeholder in this field of the paradigm shift is the industry itself: packet switching hardware manufacturers are going to earn billions of dollars and thus pay engineers and journalists many millions for the promot...

  20. Amino acids and proteins at ZnO-water interfaces in molecular dynamics simulations.

    Nawrocki, Grzegorz; Cieplak, Marek

    2013-08-28

    We determine potentials of the mean force for interactions of amino acids with four common surfaces of ZnO in aqueous solutions. The method involves all-atom molecular dynamics simulations combined with the umbrella sampling technique. The profiled nature of the density of water with the strongly adsorbed first layer affects the approach of amino acids to the surface and generates either repulsion or weak binding. The largest binding energy is found for tyrosine interacting with the surface in which the Zn ions are at the top. It is equal to 7 kJ mol(-1) which is comparable to that of the hydrogen bonds in a protein. This makes the adsorption of amino acids onto the ZnO surface much weaker than onto the well studied surface of gold. Under vacuum, binding energies are more than 40 times stronger (for one of the surfaces). The precise manner in which water molecules interact with a given surface influences the binding energies in a way that depends on the surface. Among the four considered surfaces the one with Zn at the top is recognized as binding almost all amino acids with an average binding energy of 2.60 kJ mol(-1). Another (O at the top) is non-binding for most amino acids. For binding situations the average energy is 0.66 kJ mol(-1). The remaining two surfaces bind nearly as many amino acids as they do not and the average binding energies are 1.46 and 1.22 kJ mol(-1). For all of the surfaces the binding energies vary between amino acids significantly: the dispersion in the range of 68-154% of the mean. A small protein is shown to adsorb onto ZnO only intermittently and with only a small deformation. Various adsorption events lead to different patterns in mobilities of amino acids within the protein. PMID:23836065

  1. Protective Effect of Ascorbic Acid on Molecular Behavior Changes of Hemoglobin Induced by Magnetic Field

    Hassan, Nahed S.; Abou Aiad, T. H. M.

    With the use of electricity and industrialization of societies, humans are commonly exposed to static magnetic field induced by electric currents. The putative mechanisms by which Static Magnetic Field (SMF) may affect biological systems is that of increasing free radical life span in organisms. To test this hypothesis, we investigate the effect of ascorbic acid (Vitamin C) treatment on the changes in the molecular behavior of hemoglobin as a result of exposure of the animals to magnetic field in the occupation levels. By measuring the relative permittivity, dielectric loss, relaxation time, conductivity, radius and diffusion coefficient of aqueous solutions of hemoglobin. These measurements were calculated in the frequency range of (100 Hz-100 kHz) to give more information about molecular behavior. Twenty four male albino rats were equally divided into four groups 1, 2, 3 and 4. Animals of group 1, were used as control, animals of group 2, were exposed to (0.2T) magnetic field and that of group 3, 4, were treated with Ascorbic Acid by two doses group 3 (20 mg kg-1 body weight), group 4 (50 mg kg-1 body weight) orally half hour before exposure to magnetic field. The sub chronic exposure expanded (1 h day-1) for 30 consecutive days. The results indicated that exposure of animals to magnetic field resulted in changes in the molecular behavior of hemoglobin molecule while treatment with ascorbic acid afforded comparatively more significant amelioration in these molecular changes, via decreasing the radical pair interaction of magnetic field with biological molecules.

  2. Optical switches and switching methods

    Doty, Michael

    2008-03-04

    A device and method for collecting subject responses, particularly during magnetic imaging experiments and testing using a method such as functional MRI. The device comprises a non-metallic input device which is coupled via fiber optic cables to a computer or other data collection device. One or more optical switches transmit the subject's responses. The input device keeps the subject's fingers comfortably aligned with the switches by partially immobilizing the forearm, wrist, and/or hand of the subject. Also a robust nonmetallic switch, particularly for use with the input device and methods for optical switching.

  3. Discovery of a regioselectivity switch in nitrating P450s guided by molecular dynamics simulations and Markov models

    Dodani, Sheel C.; Kiss, Gert; Cahn, Jackson K. B.; Su, Ye; Pande, Vijay S.; Arnold, Frances H.

    2016-05-01

    The dynamic motions of protein structural elements, particularly flexible loops, are intimately linked with diverse aspects of enzyme catalysis. Engineering of these loop regions can alter protein stability, substrate binding and even dramatically impact enzyme function. When these flexible regions are unresolvable structurally, computational reconstruction in combination with large-scale molecular dynamics simulations can be used to guide the engineering strategy. Here we present a collaborative approach that consists of both experiment and computation and led to the discovery of a single mutation in the F/G loop of the nitrating cytochrome P450 TxtE that simultaneously controls loop dynamics and completely shifts the enzyme's regioselectivity from the C4 to the C5 position of L-tryptophan. Furthermore, we find that this loop mutation is naturally present in a subset of homologous nitrating P450s and confirm that these uncharacterized enzymes exclusively produce 5-nitro-L-tryptophan, a previously unknown biosynthetic intermediate.

  4. Discovery of a regioselectivity switch in nitrating P450s guided by molecular dynamics simulations and Markov models.

    Dodani, Sheel C; Kiss, Gert; Cahn, Jackson K B; Su, Ye; Pande, Vijay S; Arnold, Frances H

    2016-05-01

    The dynamic motions of protein structural elements, particularly flexible loops, are intimately linked with diverse aspects of enzyme catalysis. Engineering of these loop regions can alter protein stability, substrate binding and even dramatically impact enzyme function. When these flexible regions are unresolvable structurally, computational reconstruction in combination with large-scale molecular dynamics simulations can be used to guide the engineering strategy. Here we present a collaborative approach that consists of both experiment and computation and led to the discovery of a single mutation in the F/G loop of the nitrating cytochrome P450 TxtE that simultaneously controls loop dynamics and completely shifts the enzyme's regioselectivity from the C4 to the C5 position of L-tryptophan. Furthermore, we find that this loop mutation is naturally present in a subset of homologous nitrating P450s and confirm that these uncharacterized enzymes exclusively produce 5-nitro-L-tryptophan, a previously unknown biosynthetic intermediate. PMID:27102675

  5. Two distinct ferredoxins from Rhodobacter capsulatus: complete amino acid sequences and molecular evolution.

    Saeki, K; Suetsugu, Y; Yao, Y; Horio, T; Marrs, B L; Matsubara, H

    1990-09-01

    Two distinct ferredoxins were purified from Rhodobacter capsulatus SB1003. Their complete amino acid sequences were determined by a combination of protease digestion, BrCN cleavage and Edman degradation. Ferredoxins I and II were composed of 64 and 111 amino acids, respectively, with molecular weights of 6,728 and 12,549 excluding iron and sulfur atoms. Both contained two Cys clusters in their amino acid sequences. The first cluster of ferredoxin I and the second cluster of ferredoxin II had a sequence, CxxCxxCxxxCP, in common with the ferredoxins found in Clostridia. The second cluster of ferredoxin I had a sequence, CxxCxxxxxxxxCxxxCM, with extra amino acids between the second and third Cys, which has been reported for other photosynthetic bacterial ferredoxins and putative ferredoxins (nif-gene products) from nitrogen-fixing bacteria, and with a unique occurrence of Met. The first cluster of ferredoxin II had a CxxCxxxxCxxxCP sequence, with two additional amino acids between the second and third Cys, a characteristics feature of Azotobacter-[3Fe-4S] [4Fe-4S]-ferredoxin. Ferredoxin II was also similar to Azotobacter-type ferredoxins with an extended carboxyl (C-) terminal sequence compared to the common Clostridium-type. The evolutionary relationship of the two together with a putative one recently found to be encoded in nifENXQ region in this bacterium [Moreno-Vivian et al. (1989) J. Bacteriol. 171, 2591-2598] is discussed. PMID:2277040

  6. Probing the molecular and electronic structure of the lichen metabolite usnic acid: A DFT study

    Graphical abstract: DFT calculations of structural preferences, acidic properties, carbonyl vibrations, 13C NMR chemical shifts, and absorption spectrum account for the unique structural backbone, chemical behaviour, and spectroscopic properties of usnic acid, the cortical pigment and potent reactive of lichens. - Abstract: The molecular structure of usnic acid was investigated by the density functional theory (DFT). Two keto-enol tautomers are nearly isoenergetic and more stable than other tautomers. Noteworthy is the energy difference among the three intramolecular O-H...O hydrogen bonds. The DFT/PCM calculated dissociation constants account for the acidic sequence of the three OH-groups. The electronic structure was also studied by calculating IR/Raman, NMR, and absorption features. A reliable assignment of the 'fingerprint' carbonyl stretching modes was supported by calculations on related molecules. The calculated NMR chemical shifts fit expectation in terms of a fast interconversion between the two most preferred tautomers. A variety of π → π* and n → π* excitations, localized on a single ring or involving a charge-transfer between the two lateral rings of the molecule, gives rise to the broad UV-absorption bands. This property accounts for the efficient protection against damaging solar radiation provided by usnic acid for lichens.

  7. Molecular Cloning and Pharmacological Properties of an Acidic PLA2 from Bothrops pauloensis Snake Venom

    Francis Barbosa Ferreira

    2013-12-01

    Full Text Available In this work, we describe the molecular cloning and pharmacological properties of an acidic phospholipase A2 (PLA2 isolated from Bothrops pauloensis snake venom. This enzyme, denominated BpPLA2-TXI, was purified by four chromatographic steps and represents 2.4% of the total snake venom protein content. BpPLA2-TXI is a monomeric protein with a molecular mass of 13.6 kDa, as demonstrated by Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF analysis and its theoretical isoelectric point was 4.98. BpPLA2-TXI was catalytically active and showed some pharmacological effects such as inhibition of platelet aggregation induced by collagen or ADP and also induced edema and myotoxicity. BpPLA2-TXI displayed low cytotoxicity on TG-180 (CCRF S 180 II and Ovarian Carcinoma (OVCAR-3, whereas no cytotoxicity was found in regard to MEF (Mouse Embryonic Fibroblast and Sarcoma 180 (TIB-66. The N-terminal sequence of forty-eight amino acid residues was determined by Edman degradation. In addition, the complete primary structure of 122 amino acids was deduced by cDNA from the total RNA of the venom gland using specific primers, and it was significantly similar to other acidic D49 PLA2s. The phylogenetic analyses showed that BpPLA2-TXI forms a group with other acidic D49 PLA2s from the gender Bothrops, which are characterized by a catalytic activity associated with anti-platelet effects.

  8. Molecular diversity of lactic acid bacteria from cassava sour starch (Colombia).

    Omar, N B; Ampe, F; Raimbault, M; Guyot, J P; Tailliez, P

    2000-06-01

    Lactic acid bacteria and more particularly lactobacilli and Leuconostoc, are widely found in a wide variety of traditional fermented foods of tropical countries, made with cereals, tubers, meat or fish. These products represent a source of bacterial diversity that cannot be accurately analysed using classical phenotypic and biochemical tests. In the present work, the identification and the molecular diversity of lactic acid bacteria isolated from cassava sour starch fermentation were assessed by using a combination of complementary molecular methods: Randomly Amplified Polymorphic DNA fingerprinting (RAPD), plasmid profiling, hybridization using rRNA phylogenetic probes and partial 16S rDNA sequencing. The results revealed a large diversity of bacterial species (Lb. manihotivorans, Lb. plantarum, Lb. casei, Lb. hilgardii, Lb. buchneri, Lb. fermentum, Ln. mesenteroides and Pediococcus sp.). However, the most frequently isolated species were Lb. plantarum and Lb. manihotivorans. The RAPD analysis revealed a large molecular diversity between Lb. manihotivorans or Lb. plantarum strains. These results, observed on a rather limited number of samples, reveal that significant bacterial diversity is generated in traditional cassava sour starch fermentations. We propose that the presence of the amylolytic Lb. manihotivorans strains could have a role in sour starch processing. PMID:10930082

  9. Aggregation of 12-Hydroxystearic Acid and Its Lithium Salt in Hexane: Molecular Dynamics Simulations.

    Gordon, Ryan; Stober, Spencer T; Abrams, Cameron F

    2016-07-28

    12-Hydroxystearic acid (12HSA) is a well-known organogelator, and its metal salts and derivatives find roles in many important applications. The structures of aggregates of 12-hydroxysteric acid and its salts depend sensitively on cation type, but a fundamental understanding of this phenomenon is lacking. In this study, molecular dynamics simulations were conducted on the microsecond long time scales for (1) 12HSA and (2) its lithium salt, each at 12.5 wt % in explicit hexane solvent. Self-assembly was accelerated by using a modified potential to prohibit alkane chain dihedral gauche states (all-trans-12HSA) and then verified by continuation using standard force-field parameters. In three independent simulation, acceleration using "gauche-less" potentials resulted in self-assembled pseudocrystalline aggregates through formation of polarized five- and six-membered rings between inter-12-hydroxyl groups and head-to-head carboxylic acid dimerization. When subjected to the unmodified dihedral potential, two of the three structures remained stable after 1 μs of MD. Stable structures exhibited a "ring-of-rings" motif, composed of two six-membered acetic acid-dimerized ring bundles with six satellite rings, while the unstable structure did not. In strong contrast, the lithium salt produced a network of fibrils that spanned the volume of the sample. When lithium ions were substituted for carboxylic acid protons in the stable acid structures, they remained intact but lost their chiral nature. Both the acid and lithium structures displayed scattering peaks that agreed with experiment. Taken together, our results suggest that this ring-of-rings structure could be a primary feature of the self-assembly of 12HSA in organic solvents. PMID:27387154

  10. A comparative study on efficacy of high and low fluence Q-switched Nd:YAG laser and glycolic acid peel in melasma

    Hemanta Kumar Kar

    2012-01-01

    Full Text Available Background: Melasma is acquired symmetric hypermelanosis characterized by light-to-deep brown pigmentation over cheeks, forehead, upper lip, and nose. Treatment of this condition is difficult and associated with high recurrence rates. With the advent of newer therapies, there is interest in the use of glycolic acid peels and Q-switched Nd:YAG laser (QSNYL in high and low fluence for this disorder. Aims: To compare the therapeutic efficacy of low fluence QSNYL, high fluence QSNYL, and glycolic acid peel in melasma in three study groups of 25 patients each. Methods: Seventy-five Indian patients diagnosed as melasma were included. These patients were randomly divided in three groups (Group A = 25 patients of melasma treated with low-fluence QSNYL at weekly intervals, Group B = 25 patients of melasma treated with glycolic acid peel at 2 weeks intervals, Group C = 25 patients of melasma treated with high-fluence QSNYL at 2 weeks intervals. Study period and follow-up period was of 12 weeks each. Out of the 75 patients included, 21 patients in Group A, 19 patients in Group B, and 20 patients in Group C completed the study. Response to treatment was assessed using melasma area and severity index score. Results: Significant improvement was recorded in all the three groups. The improvement was statistically highly significant in Group A as compared to Group C (P<0.005, significant in Group A as compared to Group B (P<0.05, and also in Group B when compared to Group C (P<0.05. Low-fluence QSNYL was associated with least side effects. Conclusions: This study shows the efficacy of low-fluence QSNYL and glycolic acid peel in melasma. These could be an effective treatment options compared to conventional methods for the treatment of melasma.

  11. Thermo-responsive behavior of borinic acid polymers: experimental and molecular dynamics studies.

    Wan, Wen-Ming; Zhou, Peng; Cheng, Fei; Sun, Xiao-Li; Lv, Xin-Hu; Li, Kang-Kang; Xu, Hai; Sun, Miao; Jäkle, Frieder

    2015-09-28

    The thermo-responsive properties of borinic acid polymers were investigated by experimental and molecular dynamics simulation studies. The homopolymer poly(styrylphenyl(tri-iso-propylphenyl)borinic acid) (PBA) exhibits an upper critical solution temperature (UCST) in polar organic solvents that is tunable over a wide temperature range by addition of small amounts of H2O. The UCST of a 1 mg mL(-1) PBA solution in DMSO can be adjusted from 20 to 100 °C by varying the H2O content from ∼0-2.5%, in DMF from 0 to 100 °C (∼3-17% H2O content), and in THF from 0 to 60 °C (∼4-19% H2O). The UCST increases almost linearly from the freezing point of the solvent with higher freezing point to the boiling point of the solvent with the lower boiling point. The mechanistic aspects of this process were investigated by molecular dynamics simulations. The latter indicate rapid and strong hydrogen-bond formation between BOH moieties and H2O molecules, which serve as crosslinkers to form an insoluble network. Our results suggest that borinic acid-containing polymers are promising as new "smart" materials, which display thermo-responsive properties that are tunable over a wide temperature range. PMID:26256052

  12. [Rapidly labelled low molecular weight components in nucleic acid preparations from plant cells].

    Richter, G; Grotha, R

    1974-09-01

    After pulse-labelling with [(3)H]nucleosides and [(3)H]orotic acid of freely suspended callus cells of Petroselinum sativum and tissue fragments of the liverwort Riella helicophylla, rapidly labelled low molecular weight components were detected among the total nucleic acids when these were extracted in the presence of Mg(2+) and finally precipitated with alcohol. These highly labelled species could clearly be distinguished from the 5 S- and 4 S-RNA on the basis of their migration in agarose-polyacrylamide gels (2.4%) and their elution from Sephadex G-150 columns. No degradation was obtained with DNase and RNase. By using [(14)C]ATP as a marker it was found that the low molecular components consisted mainly of nucleoside triphosphates. Only small amounts of nucleoside diphosphates were detected, which were obviously formed by degradation of the former. Nucleic acid preparations free of nucleoside phosphates were obtained by using Mg-free extraction buffers containing EDTA. PMID:24458196

  13. Glucosidase II β-subunit, a novel substrate for caspase-3-like activity in rice, plays as a molecular switch between autophagy and programmed cell death.

    Cui, Jing; Chen, Bing; Wang, Hongjuan; Han, Yue; Chen, Xi; Zhang, Wei

    2016-01-01

    Endoplasmic reticulum (ER) stress activates unfolded protein response (UPR) and autophagy. However, prolonged, severe stresses activate programmed cell death (PCD) in both animal and plant cells. Compared to the well-studied UPR pathway, the molecular mechanisms of ER-stress-induced PCD are less understood. Here, we report the identification of Gas2, the glucosidase II β subunit in the ER, as a potential switch between PCD and autophagy in rice. MS analysis identified Gas2, GRP94, and HSP40 protein in a purified caspase-3-like activity from heat stressed rice cell suspensions. The three corresponding genes were down-regulated under DTT-induced ER stress. Gas2 and GRP94 were localized to the ER, while HSP40 localized to the cytoplasm. Compared to wild-type, a Gas2 RNAi cell line was much sensitive to DTT treatment and had high levels of autophagy. Both caspase-3 and heat-stressed cell suspension lysate could cleave Gas2, producing a 14 kDa N-terminal fragment. Conditional expression of corresponding C-terminal fragment resulted in enhanced caspase-3-like activity in the protoplasts under heat stress. We proposed that mild ER stress causes down-regulation of Gas2 and induces autophagy, while severe stress results in Gas2 cleavage by caspase-3-like activity and the cleavage product amplifies this activity, possibly participating in the initiation of PCD. PMID:27538481

  14. Cellular Dichotomy Between Anchorage-Independent Growth Responses to bFGF and TA Reflects Molecular Switch in Commitment to Carcinogenesis

    Waters, Katrina M.; Tan, Ruimin; Opresko, Lee K.; Quesenberry, Ryan D.; Bandyopadhyay, Somnath; Chrisler, William B.; Weber, Thomas J.

    2009-11-01

    We have investigated gene expression patterns underlying reversible and irreversible anchorage-independent growth (AIG) phenotypes to identify more sensitive markers of cell transformation for studies directed at interrogating carcinogenesis responses. In JB6 mouse epidermal cells, basic fibroblast growth factor (bFGF) induces an unusually efficient and reversible AIG response, relative to 12-O-tetradecanoyl phorbol-13-acetate (TPA)-induced AIG which is irreversible. The reversible and irreversible AIG phenotypes are characterized by largely non-overlapping global gene expression profiles. However, a subset of differentially expressed genes were identified as common to reversible and irreversible AIG phenotypes, including genes regulated in a reciprocal fashion. Hepatic leukemia factor (HLF) and D-site albumin promoter-binding protein (DBP) were increased in both bFGF and TPA soft agar colonies and selected for functional validation. Ectopic expression of human HLF and DBP in JB6 cells resulted in a marked increase in TPA- and bFGF-regulated AIG responses. HLF and DBP expression were increased in soft agar colonies arising from JB6 cells exposed to gamma radiation and in a human basal cell carcinoma tumor tissue, relative to paired non-tumor tissue. Subsequent biological network analysis suggests that many of the differentially expressed genes that are common to bFGF- and TPA-dependent AIG are regulated by c-Myc, SP-1 and HNF-4 transcription factors. Collectively, we have identified a potential molecular switch that mediates the transition from reversible to irreversible AIG.

  15. A novel transcription factor-like gene SbSDR1 acts as a molecular switch and confers salt and osmotic endurance to transgenic tobacco.

    Singh, Vijay Kumar; Mishra, Avinash; Haque, Intesaful; Jha, Bhavanath

    2016-01-01

    A salt- and drought-responsive novel gene SbSDR1 is predominantly localised to the nucleus, up-regulated under abiotic stresses and is involved in the regulation of metabolic processes. SbSDR1 showed DNA-binding activity to genomic DNA, microarray analysis revealed the upregulation of host stress-responsive genes and the results suggest that SbSDR1 acts as a transcription factor. Overexpression of SbSDR1 did not affect the growth and yield of transgenic plants in non-stress conditions. Moreover, the overexpression of SbSDR1 stimulates the growth of plants and enhances their physiological status by modulating the physiology and inhibiting the accumulation of reactive oxygen species under salt and osmotic stress. Transgenic plants that overexpressed SbSDR1 had a higher relative water content, membrane integrity and concentration of proline and total soluble sugars, whereas they showed less electrolyte leakage and lipid peroxidation than wild type plants under stress conditions. In field conditions, SbSDR1 plants recovered from stress-induced injuries and could complete their life cycle. This study suggests that SbSDR1 functions as a molecular switch and contributes to salt and osmotic tolerance at different growth stages. Overall, SbSDR1 is a potential candidate to be used for engineering salt and drought tolerance in crops without adverse effects on growth and yield. PMID:27550641

  16. Synthesis and Molecular Structures of (E-non-2-enoic Acid and (E-dec-2-enoic Acid

    Marcel Sonneck

    2015-10-01

    Full Text Available The molecular structures of (E-non-2-enoic acid (C9 and (E-dec-2-enoic acid (C10 are reported. The title compounds were crystallized by slow evaporation of ethanolic solutions at −30 °C. C9 crystallizes in the monoclinic space group P21/c and C10 in the triclinic space group P-1, each with 4 molecules in the unit cell. The unit cell parameters for C9 are: a = 10.6473(4 Å, b = 5.2855(2 Å, c = 17.0313(7 Å; β = 106.0985(10° and V = 920.87(6 Å3. The unit cell parameters for C10 are: a = 4.1405(2 Å, b = 15.2839(6 Å, c = 17.7089(7 Å; α = 68.3291(11°, β = 83.3850(13°, γ = 85.0779(12° and V = 1033.39(8 Å3.

  17. Trimethylamine-N-oxide switches from stabilizing nature: A mechanistic outlook through experimental techniques and molecular dynamics simulation.

    Rani, Anjeeta; Jayaraj, Abhilash; Jayaram, B; Pannuru, Venkatesu

    2016-01-01

    In adaptation biology of the discovery of the intracellular osmolytes, the osmolytes are found to play a central role in cellular homeostasis and stress response. A number of models using these molecules are now poised to address a wide range of problems in biology. Here, a combination of biophysical measurements and molecular dynamics (MD) simulation method is used to examine the effect of trimethylamine-N-oxide (TMAO) on stem bromelain (BM) structure, stability and function. From the analysis of our results, we found that TMAO destabilizes BM hydrophobic pockets and active site as a result of concerted polar and non-polar interactions which is strongly evidenced by MD simulation carried out for 250 ns. This destabilization is enthalpically favourable at higher concentrations of TMAO while entropically unfavourable. However, to the best of our knowledge, the results constitute first detailed unambiguous proof of destabilizing effect of most commonly addressed TMAO on the interactions governing stability of BM and present plausible mechanism of protein unfolding by TMAO. PMID:27025561

  18. Polyunsaturated fatty acids of marine origin stimulate adiponectin relase and induce a metabolic switch in white fat

    Flachs, Pavel; Horáková, Olga; Pecina, Petr; Franssen-van Hal, N.; Rossmeisl, Martin; Keijer, J.; Mohamed-Ali, V.; Houštěk, Josef; Kopecký, Jan

    Ystads Saltsjöbad, 2006. s. 79-79. [NAFA 2006. 14.06.2006-16.06.2006, Ystads Saltsjöbad] R&D Projects: GA MŠk(CZ) 1M0520 Institutional research plan: CEZ:AV0Z50110509 Keywords : polyunsaturated fatty acid Subject RIV: FB - Endocrinology, Diabetology, Metabolism, Nutrition

  19. Diversity of the lactic acid bacterium and yeast microbiota in the switch from firm- to liquid-sourdough fermentation.

    Di Cagno, Raffaella; Pontonio, Erica; Buchin, Solange; De Angelis, Maria; Lattanzi, Anna; Valerio, Francesca; Gobbetti, Marco; Calasso, Maria

    2014-05-01

    Four traditional type I sourdoughs were comparatively propagated (28 days) under firm (dough yield, 160) and liquid (dough yield, 280) conditions to mimic the alternative technology options frequently used for making baked goods. After 28 days of propagation, liquid sourdoughs had the lowest pH and total titratable acidity (TTA), the lowest concentrations of lactic and acetic acids and free amino acids, and the most stable density of presumptive lactic acid bacteria. The cell density of yeasts was the highest in liquid sourdoughs. Liquid sourdoughs showed simplified microbial diversity and harbored a low number of strains, which were persistent. Lactobacillus plantarum dominated firm sourdoughs over time. Leuconostoc lactis and Lactobacillus brevis dominated only some firm sourdoughs, and Lactobacillus sanfranciscensis persisted for some time only in some firm sourdoughs. Leuconostoc citreum persisted in all firm and liquid sourdoughs, and it was the only species detected in liquid sourdoughs at all times; it was flanked by Leuconostoc mesenteroides in some sourdoughs. Saccharomyces cerevisiae, Candida humilis, Saccharomyces servazzii, Saccharomyces bayanus-Kazachstania sp., and Torulaspora delbrueckii were variously identified in firm and liquid sourdoughs. A total of 197 volatile components were identified through purge and trap-/solid-phase microextraction-gas chromatography-mass spectrometry (PT-/SPME-GC-MS). Aldehydes, several alcohols, and some esters were at the highest levels in liquid sourdoughs. Firm sourdoughs mainly contained ethyl acetate, acetic acid, some sulfur compounds, and terpenes. The use of liquid fermentation would change the main microbial and biochemical features of traditional baked goods, which have been manufactured under firm conditions for a long time. PMID:24632249

  20. Molecular Modeling of Ammonium, Calcium, Sulfur, and Sodium Lignosulphonates in Acid and Basic Aqueous Environments

    Salazar Valencia, P. J.; Bolívar Marinez, L. E.; Pérez Merchancano, S. T.

    2015-12-01

    Lignosulphonates (LS), also known as lignin sulfonates or sulfite lignin, are lignins in sulfonated forms, obtained from the "sulfite liquors," a residue of the wood pulp extraction process. Their main utility lies in its wide range of properties, they can be used as additives, dispersants, binders, fluxing, binder agents, etc. in fields ranging from food to fertilizer manufacture and even as agents in the preparation of ion exchange membranes. Since they can be manufactured relatively easy and quickly, and that its molecular size can be manipulated to obtain fragments of very low molecular weight, they are used as transport agents in the food industry, cosmetics, pharmaceutical and drug development, and as molecular elements for the treatment of health problems. In this paper, we study the electronic structural and optical characteristics of LS incorporating ammonium, sulfur, calcium, and sodium ions in acidic and basic aqueous media in order to gain a better understanding of their behavior and the very interesting properties exhibit. The studies were performed using the molecular modeling program HyperChem 5 using the semiempirical method PM3 of the NDO Family (neglect of differential overlap), to calculate the structural properties. We calculated the electronic and optical properties using the semiempirical method ZINDO / CI.

  1. Removal of carbamazepine and clofibric acid from water using double templates-molecularly imprinted polymers.

    Dai, Chao-meng; Zhang, Juan; Zhang, Ya-lei; Zhou, Xue-fei; Duan, Yan-ping; Liu, Shu-guang

    2013-08-01

    A novel double templates-molecularly imprinted polymer (MIP) was prepared by precipitation polymerization using carbamazepine (CBZ) and clofibric acid (CA) as the double templates molecular and 2-vinylpyridine as functional monomer. The equilibrium data of MIP was well described by the Freundlich isotherm model. Two kinetic models were adopted to describe the experimental data, and the pseudo second-order model well-described adsorption of CBZ and CA on the MIP. Adsorption experimental results showed that the MIP had good selectivity and adsorption capacity for CBZ and CA in the presence of competitive compounds compared with non-imprinted polymer, commercial powdered activated carbon, and C18 adsorbents. The feasibility of removing CBZ and CA from water by the MIP was demonstrated using tap water, lake water, and river water. PMID:23436062

  2. Molecular interactions in biomineralized hydroxyapatite amino acid modified nanoclay: In silico design of bone biomaterials

    A simulations driven approach to design of a novel biomaterial nanocomposite system is described in this study. Nanoclays modified with amino acids (OMMT) were used to mineralize hydroxyapatite (HAP), mimicking biomineralization. Representative models of organically modified montmorillonite clay (OMMT) and OMMT-hydroxyapatite (OMMT-HAP) were constructed using molecular dynamics and validated using X-ray Diffraction (XRD), Fourier Transforms Infrared (FTIR) spectroscopy and Transmission Electron Microscopy (TEM). Attractive interactions exist between Ca atoms of HAP and C=O group of aminovaleric acid, indicating chelate formation in OMMT-HAP. Interaction energy maps describe molecular interactions among different constituents and their quantitative contributions in the OMMT and OMMT-HAP systems at both parallel and perpendicular orientations. High attractive and high repulsive interactions were found between PO43− and MMT clay as well as aminovaleric molecules in OMMT-HAP perpendicular and parallel models. Large non-bonded interactions in OMMT-HAP indicate influence of neighboring environment on PO43− in in situ HAPclay. Extensive hydrogen bonds were observed between functional hydrogen atoms of modifier and MMT clay in OMMT-HAP as compared to OMMT. Thus, HAP interacts with clay through the aminovaleric acid. This computational study provides a framework for materials design and selection for biomaterials used in tissue engineering and other areas of regenerative medicine. - Highlights: • Representative models of a hybrid nanoclay-hydroxyapatite biomaterial are built. • Interaction energy maps are constructed using a molecular dynamics. • Quantitative interactions between the three components of the biomaterial are found. • The modeling and experimental approach provides insight into the complex nanomaterial

  3. Molecular interactions in biomineralized hydroxyapatite amino acid modified nanoclay: In silico design of bone biomaterials

    Katti, Dinesh R., E-mail: Dinesh.Katti@ndsu.edu; Sharma, Anurag; Ambre, Avinash H.; Katti, Kalpana S.

    2015-01-01

    A simulations driven approach to design of a novel biomaterial nanocomposite system is described in this study. Nanoclays modified with amino acids (OMMT) were used to mineralize hydroxyapatite (HAP), mimicking biomineralization. Representative models of organically modified montmorillonite clay (OMMT) and OMMT-hydroxyapatite (OMMT-HAP) were constructed using molecular dynamics and validated using X-ray Diffraction (XRD), Fourier Transforms Infrared (FTIR) spectroscopy and Transmission Electron Microscopy (TEM). Attractive interactions exist between Ca atoms of HAP and C=O group of aminovaleric acid, indicating chelate formation in OMMT-HAP. Interaction energy maps describe molecular interactions among different constituents and their quantitative contributions in the OMMT and OMMT-HAP systems at both parallel and perpendicular orientations. High attractive and high repulsive interactions were found between PO{sub 4}{sup 3−} and MMT clay as well as aminovaleric molecules in OMMT-HAP perpendicular and parallel models. Large non-bonded interactions in OMMT-HAP indicate influence of neighboring environment on PO{sub 4}{sup 3−} in in situ HAPclay. Extensive hydrogen bonds were observed between functional hydrogen atoms of modifier and MMT clay in OMMT-HAP as compared to OMMT. Thus, HAP interacts with clay through the aminovaleric acid. This computational study provides a framework for materials design and selection for biomaterials used in tissue engineering and other areas of regenerative medicine. - Highlights: • Representative models of a hybrid nanoclay-hydroxyapatite biomaterial are built. • Interaction energy maps are constructed using a molecular dynamics. • Quantitative interactions between the three components of the biomaterial are found. • The modeling and experimental approach provides insight into the complex nanomaterial.

  4. Molecular Recognition and Structural Influences on Function in Bio-nanosystems of Nucleic Acids and Proteins

    Sethaphong, Latsavongsakda

    This work examines smart material properties of rational self-assembly and molecular recognition found in nano-biosystems. Exploiting the sequence and structural information encoded within nucleic acids and proteins will permit programmed synthesis of nanomaterials and help create molecular machines that may carry out new roles involving chemical catalysis and bioenergy. Responsive to different ionic environments thru self-reorgnization, nucleic acids (NA) are nature's signature smart material; organisms such as viruses and bacteria use features of NAs to react to their environment and orchestrate their lifecycle. Furthermore, nucleic acid systems (both RNA and DNA) are currently exploited as scaffolds; recent applications have been showcased to build bioelectronics and biotemplated nanostructures via directed assembly of multidimensional nanoelectronic devices 1. Since the most stable and rudimentary structure of nucleic acids is the helical duplex, these were modeled in order to examine the influence of the microenvironment, sequence, and cation-dependent perturbations of their canonical forms. Due to their negatively charged phosphate backbone, NA's rely on counterions to overcome the inherent repulsive forces that arise from the assembly of two complementary strands. As a realistic model system, we chose the HIV-TAR helix (PDB ID: 397D) to study specific sequence motifs on cation sequestration. At physiologically relevant concentrations of sodium and potassium ions, we observed sequence based effects where purine stretches were adept in retaining high residency cations. The transitional space between adenine and guanosine nucleotides (ApG step) in a sequence proved the most favorable. This work was the first to directly show these subtle interactions of sequence based cationic sequestration and may be useful for controlling metallization of nucleic acids in conductive nanowires. Extending the study further, we explored the degree to which the structure of NA

  5. Selective oxidation of glycerol to formic acid in highly concentrated aqueous solutions with molecular oxygen using V-substituted phosphomolybdic acids

    Zhang, Jizhe

    2014-01-01

    Formic acid is an important commodity chemical as well as a promising medium for hydrogen storage and hydrogen production. In this paper, we report that formic acid can be produced through selective oxidation of glycerol, a low-cost by-product of biodiesel, by using vanadium-substituted phosphomolybdic acids as catalysts and molecular oxygen as the oxidant. Significantly, this catalytic system allows for high-concentration conversions and thus leads to exceptional efficiency. Specifically, 3.64 g of formic acid was produced from 10 g of glycerol/water (50/50 in weight) solution. © 2014 the Partner Organisations.

  6. Fluorescent properties of low-molecular-weight fractions from chernozem humic acids

    Trubetskoi, O. A.; Demin, D. V.; Trubetskaya, O. E.

    2013-10-01

    The polyacrylamide gel electrophoresis of chernozem humic acids (HAs) followed by ultraviolet detection (λ = 312 nm) has revealed a new highly fluorescent fraction that has the highest electrophoretic mobility and the lowest nominal molecular weight (NMW). The preparative isolation of the fraction has been performed using the multiple microfiltration of the same HA sample in a 7 M carbamide solution on a membrane with a nominal pore size of 5 kDa. Thirty ultrafiltrates with NMW 5 kDa. Fluorescence maximums at and below 490 nm have been noted only in the first four ultrafiltrates. All the ultrafiltrates have been combined into the fraction with NMW extracted soil HAs.

  7. In Vitro Selection of Cancer Cell-Specific Molecular Recognition Elements from Amino Acid Libraries

    Williams, Ryan M.; Sooter, Letha J.

    2015-01-01

    Differential cell systematic evolution of ligands by exponential enrichment (SELEX) is an in vitro selection method for obtaining molecular recognition elements (MREs) that specifically bind to individual cell types with high affinity. MREs are selected from initial large libraries of different nucleic or amino acids. This review outlines the construction of peptide and antibody fragment libraries as well as their different host types. Common methods of selection are also reviewed. Additionally, examples of cancer cell MREs are discussed, as well as their potential applications. PMID:26436100

  8. Crystal structure of the 1:2 molecular complex of tetrafluoroboric acid with triphenylphosphine oxide

    Crystalline molecular complex of tetrafluoroboric acid with triphenylphosphine oxide of Ph3PO·0.5HBF4 (1) is prepared and studied by means of x-ray diffraction method. HBF4 molecule is situated near crystallographic axis 2 and is statistically disordered relatively this axis. All the atoms of the molecule have positions of population density equal 0.5. Boron atom has distorted tetrahedral coordination. B-F(H) bond is significantly more lengthy then other three B-F bonds and is donor-acceptor one. HBF4 molecule is bonded with Ph3PO molecule by strong asymmetrical hydrogen bond with 50 % probability

  9. Molecular hybrids of CdSe semiconductor nanocrystals with terthiophene carboxylic acid or its polymeric analogue

    Hybrid materials consisting of CdSe nanocrystals (CdSe NCs) and 7-(4,4''-dioctyl-2,2':5',2''-terthiophene-3'-yl)heptanoic acid (TTHA) or its high molecular analogue-poly(7-(4,4''-dioctyl-2,2':5',2''-terthiophene-3'-yl)heptanoic acid) (PTTHA) have been prepared from TOPO capped NCs via ligand exchange. Detailed spectroscopic and spectroelectrochemical (UV-vis-NIR, Raman) studies of these hybrids enabled us to determine the alignment of the HOMO and LUMO levels of their components. Since, for NCs of 3.7 nm, the alignment of the energy levels in both hybrids is staggered, the elaborated new materials are of potential use in photovoltaic devices. In the CdSe-PTTHA hybrid material a uniform distribution of the NCs within the polymer matrix is evidenced by TEM images. This is caused by strong interactions between nanocrystals surface and coordinating carboxylic function of the polymer.

  10. Possible molecular targets for therapeutic applications of caffeic acid phenethyl ester in inflammation and cancer

    Ghulam Murtaza

    2015-03-01

    Full Text Available Of the various derivatives of caffeic acid, caffeic acid phenethyl ester (CAPE is a hydrophobic, bioactive polyphenolic ester obtained from propolis extract. The objective in writing this review article was to summarize all published studies on therapeutics of CAPE in inflammation and cancer to extract direction for future research. The possible molecular targets for the action of CAPE, include various transcription factors such as nuclear factor-κB, tissue necrosis factor-α, interleukin-6, cyclooxygenase-2, Nrf2, inducible nitric oxide synthase, nuclear factor of activated T cells, hypoxia-inducible factor-1α, and signal transducers and activators of transcription. Based on the valuable data on its therapeutics in inflammation and cancer, clinical studies of CAPE should also be conducted to explore its toxicities, if any.

  11. Molecular interaction of acetylcholinesterase with carnosic acid derivatives: a neuroinformatics study.

    Merad, M; Soufi, W; Ghalem, S; Boukli, F; Baig, M H; Ahmad, K; Kamal, Mohammad A

    2014-04-01

    Alzheimer's disease is a progressive degenerative disease of the brain marked by gradual and irreversible declines in cognitive functions. Acetylcholinesterase (AChE) plays a biological role in the termination of nerve impulse transmissions at cholinergic synapses by rapid hydrolysis of its substrate, "acetylcholine". The deficit level of acetylcholine leads to deprived nerve impulse transmission. Thus the cholinesterase inhibitors would reverse the deficit in acetylcholine level and consequently may reverse the memory impairments, which is characteristic of the Alzheimer's disease. The molecular interactions between AChE and Carnosic acid, a well known antioxidant substance found in the leaves of the rosemary plant has always been an area of interest. Here in this study we have performed in silico approach to identify carnosic acid derivatives having the potential of being a possible drug candidate against AChE. The best candidates were selected on the basis of the results of different scoring functions. PMID:24059305

  12. Biogenic gold nanoparticles as fotillas to fire berberine hydrochloride using folic acid as molecular road map.

    Pandey, Sunil; Mewada, Ashmi; Thakur, Mukeshchand; Shah, Ritu; Oza, Goldie; Sharon, Madhuri

    2013-10-01

    Use of biologically modified gold nanoparticles (GNPs) as molecular vehicle to ferry potential anti-cancer drug berberine hydrochloride (BHC) using folic acid (FA) as targeting molecule is reported in this work. A tropical fruit peel, Trapa bispinosa is used to fabricate highly monodispersed GNPs, passivated with essential functional groups which were used as linkers to attach FA and BHC via amide linkage. Flocculation Parameter (FP) of biologically synthesized GNPs was calculated under different salt concentrations which were found to be very ideal under a physiological condition. Various statistical models were used to find drug release profile out of which Higuchi was found to be the most ideal. GNP-FA-BHC complexes were found to be active against folic acid expressing HeLa cells. PMID:23910269

  13. Molecular dynamics simulations of the adsorption of amino acids on the hydroxyapatite {100}-water interface

    Zhi-sen ZHANG; Hai-hua PAN; Rui-kang TANG

    2008-01-01

    The understanding of interfaces and interaction of organic molecules and inorganic materials are the important issues in biomineralization. Experimentally, it has been found that amino acids (AA) can regulate the morphology of hydroxyapatite (HAP) crystals significantly. In this study, molecular dynamics simulation is employed to investigate the detailed adsorption behavior of polar, ionic, and hydrophobic AA on the {100} face of HAP at the atomic level. The results indicate that various AA are adsorbed on the HAP crystal surface mainly by amino and carboxylate groups at the specific sites. Multiple inter-action points are found for polar and ionic AA. The adsorbed AA molecules occupy the Ca and P sites of the HAP surfaces which may inhibit and regulate the HAP growth. The adsorbed amino acid layer can also change the interfacial hydration layer and influence the transporta-tion of ions in and out of HAP, which may be another strategy of biological control in biomineralization.

  14. A classical reactive potential for molecular clusters of sulphuric acid and water

    Stinson, Jake L; Ford, Ian J

    2016-01-01

    We present a two-state empirical valence bond (EVB) potential describing interactions between sulphuric acid and water molecules and designed to model proton transfer between them within a classical dynamical framework. The potential has been developed in order to study the properties of molecular clusters of these species, which are thought to be relevant to atmospheric aerosol nucleation. The particle swarm optimisation method has been used to fit the parameters of the EVB model to density functional theory (DFT) calculations. Features of the parametrised model and DFT data are compared and found to be in satisfactory agreement. In particular, it is found that a single sulphuric acid molecule will donate a proton when clustered with four water molecules at 300 K and that this threshold is temperature dependent.

  15. Calculating the bulk properties of decalins and fatty acids in decalin according to data from molecular dynamics simulation

    Eremin, R. A.; Kholmurodov, Kh. T.; Petrenko, V. I.; Avdeev, M. V.

    2013-05-01

    Pure solutions of decalin with different contents of its isomeric forms are studied by molecular dynamics simulation. Limiting solutions of fatty acids with different carbon chain length in decalin are considered. Comparison of the features of structural organization of decalin isomers in the vicinity of saturated (myristic, stearic) and unsaturated (oleic) acids molecules are performed. Limiting partial molar volumes of acids are determined using a radial distribution function of atoms in the solution. In contrast to earlier data for benzene, a considerable difference in the volumes of stearic and oleic acids is obtained that is explained by the more complex structure of decalin, which is sensitive to bending of unsaturated acid.

  16. Stearic acid based oleogels: a study on the molecular, thermal and mechanical properties.

    Sagiri, S S; Singh, Vinay K; Pal, K; Banerjee, I; Basak, Piyali

    2015-03-01

    Stearic acid and its derivatives have been used as gelators in food and pharmaceutical gel formulations. However, the mechanism pertaining to the stearic acid based gelation has not been deciphered yet. Keeping that in mind, we investigated the role of stearic acid on physic-chemical properties of oleogel. For this purpose, two different oil (sesame oil and soy bean oil) formulations/oleogels were prepared. In depth analysis of gel kinetics, gel microstructure, molecular interactions, thermal and mechanical behaviors of the oleogels were done. The properties of the oleogels were dependent on the type of the vegetable oil used and the concentration of the stearic acid. Avrami analysis of DSC thermograms indicated that heterogeneous nucleation was coupled with the one-dimensional growth of gelator fibers as the key phenomenon in the formation of oleogels. Viscoelastic and pseudoplastic nature of the oleogels was analyzed in-depth by fitting the stress relaxation data in modified Peleg's model and rheological studies, respectively. Textural studies have revealed that the coexistence of hydrogen bond dissipation and formation of new bonds is possible under stress conditions in the physical oleogels. PMID:25579972

  17. Use of acrylic acid in the synthesis of molecularly imprinted polymers for the analysis of cyproheptadine

    The synthesis and comparative characterization of molecularly imprinted polymers (MIPs) with cyproheptadine (CYP), using two different monomers, acrylic acid (AA) and methacrylic acid (MAA), are described. Polyacids (PA) [poly(methacrylic acid) (PMAA) and poly(acrylic acid) (PAA)] were obtained by the radical polymerization of MAA and AA, respectively, in dichloromethane as the porogen solvent-imprinted medium. The non-covalent imprinting process was performed via thermal decomposition of an azo-initiator at 60 deg. C, using ethylene glycol dimethacrylate as the cross-linker and 2,2'-azobis(2-methylpropionitrile) as the initiator. The selectivities of MIPs and NIPs particles were evaluated in binding experiments of the four synthesized polymeric materials (MIPaa, MIPmaa, NIPmaa and NIPaa) with CYP. The effects of monomers on: a) the surface morphology, b) the binding capacity and c) the swelling properties of imprinted and non-imprinted polymers were studied and are presented here. Polymer material morphology was assessed with scanning electron microscopy (SEM). This revealed differences in monomer function, depending on which one was employed, as well as differences in function when polymerization occurred in the presence of template or without it. Non-specific retention of the template to NIPs was higher for NIPs-PAA polymers than for NIPs-PMAA materials. In terms of specific binding (ΔQ = QMIP - QNIP), MIPmaa showed the greatest value (53.47%) in comparison with MIPaa (50.07%)

  18. Determination of low molecular weight organic acids in soil, plants, and water by capillary zone electrophoresis.

    Li, Ying-Hui; Huang, Bi-Xia; Shan, Xiao-Quan

    2003-03-01

    Determination of low molecular weight organic acids in soils and plants by capillary zone electrophoresis was accomplished using a phthalate buffer and indirect UV detection mode. The influence of some crucial parameters, such as pH, buffer concentration and surfactant were investigated. A good separation of seven organic acids was achieved within 5 min using an electrolyte containing 15 mmol L(-1) potassium hydrogen phthalate, 0.5 mmol L(-1) myristyltrimethylammonium bromide (MTAB), and 5% methanol (MeOH) (v/v) at pH 5.60, separation voltage -20 kV, and temperature 25 degrees C. The relative standard deviation (n=5) of the method was found to be in range 0.18-0.56% for migration time and 3.2-4.8% for peak area. The limit of detection ranged between 0.5 micro mol L(-1) to 6 micro mol L(-1) at a signal-to-noise ratio of 3. The recovery of standard organic acids added to real samples ranged from 87 to 119%. This method was simple, rapid and reproducible, and could be applied to the simultaneous determination of organic acids in environmental samples. PMID:12664177

  19. Molecular dynamics simulation of ligand dissociation from liver fatty acid binding protein.

    Dong Long

    Full Text Available The mechanisms of how ligands enter and leave the binding cavity of fatty acid binding proteins (FABPs have been a puzzling question over decades. Liver fatty acid binding protein (LFABP is a unique family member which accommodates two molecules of fatty acids in its cavity and exhibits the capability of interacting with a variety of ligands with different chemical structures and properties. Investigating the ligand dissociation processes of LFABP is thus a quite interesting topic, which however is rather difficult for both experimental approaches and ordinary simulation strategies. In the current study, random expulsion molecular dynamics simulation, which accelerates ligand motions for rapid dissociation, was used to explore the potential egress routes of ligands from LFABP. The results showed that the previously hypothesized "portal region" could be readily used for the dissociation of ligands at both the low affinity site and the high affinity site. Besides, one alternative portal was shown to be highly favorable for ligand egress from the high affinity site and be related to the unique structural feature of LFABP. This result lends strong support to the hypothesis from the previous NMR exchange studies, which in turn indicates an important role for this alternative portal. Another less favored potential portal located near the N-terminal end was also identified. Identification of the dissociation pathways will allow further mechanistic understanding of fatty acid uptake and release by computational and/or experimental techniques.

  20. Molecular dynamics simulation of ligand dissociation from liver fatty acid binding protein.

    Long, Dong; Mu, Yuguang; Yang, Daiwen

    2009-01-01

    The mechanisms of how ligands enter and leave the binding cavity of fatty acid binding proteins (FABPs) have been a puzzling question over decades. Liver fatty acid binding protein (LFABP) is a unique family member which accommodates two molecules of fatty acids in its cavity and exhibits the capability of interacting with a variety of ligands with different chemical structures and properties. Investigating the ligand dissociation processes of LFABP is thus a quite interesting topic, which however is rather difficult for both experimental approaches and ordinary simulation strategies. In the current study, random expulsion molecular dynamics simulation, which accelerates ligand motions for rapid dissociation, was used to explore the potential egress routes of ligands from LFABP. The results showed that the previously hypothesized "portal region" could be readily used for the dissociation of ligands at both the low affinity site and the high affinity site. Besides, one alternative portal was shown to be highly favorable for ligand egress from the high affinity site and be related to the unique structural feature of LFABP. This result lends strong support to the hypothesis from the previous NMR exchange studies, which in turn indicates an important role for this alternative portal. Another less favored potential portal located near the N-terminal end was also identified. Identification of the dissociation pathways will allow further mechanistic understanding of fatty acid uptake and release by computational and/or experimental techniques. PMID:19564911

  1. Magnetic switching

    Magnetic switching is a pulse compression technique that uses a saturable inductor (reactor) to pass pulses of energy between two capacitors. A high degree of pulse compression can be achieved in a network when several of these simple, magnetically switched circuits are connected in series. Individual inductors are designed to saturate in cascade as a pulse moves along the network. The technique is particularly useful when a single-pulse network must be very reliable or when a multi-pulse network must operate at a high pulse repetition frequency (PRF). Today, magnetic switches trigger spark gaps, sharpen the risetimes of high energy pulses, power large lasers, and drive high PRF linear induction accelerators. This paper will describe the technique of magnetic pulse compression using simple networks and design equations. A brief review of modern magnetic materials and of their role in magnetic switch design will be presented. 12 refs., 8 figs., 1 tab

  2. Solution structure of hyaluronic acid oligomers by experimental and theoretical NMR, and molecular dynamics simulation.

    Donati, A; Magnani, A; Bonechi, C; Barbucci, R; Rossi, C

    2001-11-01

    The conformational properties of hyaluronic acid (HA) oligomers in aqueous solution were investigated by combining high-resolution NMR experimental results, theoretical simulation of NMR two-dimensional (2D) spectra by Complete Relaxation Matrix Analysis (CORMA), and molecular dynamics calculations. New experimental findings recorded for the tetra- and hexasaccharides enabled the stiffness of the HA and its viscoelastic properties to be interpreted. In particular, rotating frame nuclear Overhauser effect spectroscopy spectra provided new information about the arrangement of the glycosidic linkage. From (13)C NMR relaxation the rotational correlation time (tau(c)) were determined. The tau(c) were employed in the calculation of geometrical constraints, by using the MARDIGRAS algorithm. Restrained simulated annealing and 1 ns of unrestrained molecular dynamic simulations were performed on the hexasaccharide in a box of 1215 water molecules. The beta(1 --> 3) and beta(1 --> 4) glycosidic links were found to be rigid. The lack of rotational degree of freedom is due to direct and/or water-mediated interresidue hydrogen bonding. Both single or tandem water bridges were found between carboxylate group and N-acetil group. The carboxylate group of glucuronic acid is not involved in a direct link with the amide group of N-acetyl glucosamine and this facilitated bonding between the residue and the water molecules. PMID:11598878

  3. Molecularly imprinted poly (methacrylamide-co-methacrylic acid) composite membranes for recognition of curcumin

    Wang Ping; Hu Wenming [College of Pharmaceutical Sciences, Zhejiang University of Technology, Zhejiang Key Laboratory of Pharmaceutical Engineering, Hangzhou 310014 (China); Su Weike [College of Pharmaceutical Sciences, Zhejiang University of Technology, Zhejiang Key Laboratory of Pharmaceutical Engineering, Hangzhou 310014 (China)], E-mail: suweike@zjut.edu.cn

    2008-05-12

    In this study, molecularly imprinted poly (methacrylamide-co-methacrylic acid) composite membranes with different ratio of methacrylamide (MAM) versus methacrylic acid (MAA) were prepared via UV initiated photo-copolymerization on the commercial filter paper. Curcumin was chosen as the template molecule. Infra-red (IR) spectroscopy was used to study the binding mechanism between the imprinted sites and the templates. The morphology of the resultant membranes was visualized by scanning electron microscopy (SEM). Static equilibrium binding and recognition properties of the imprinted composite membranes to curcumin (cur-I) and its analogues demethoxycurcumin (cur-II) or bisdemethoxycurcumin (cur-III) were tested. The results showed that curcumin-imprinted membranes had the best recognition ability to curcumin compared to its analogues. From the results, the biggest selectivity factor of {alpha}{sub cur-I/cur-II} and {alpha}{sub cur-I/cur-III} were 1.50 and 5.94, and they were obtained from the composite membranes in which MAM/MAA were 1:4 and 0:1, respectively. The results of this study implied that the molecularly imprinted composite membranes could be used as separation membranes for curcumin enrichment.

  4. Protocatechuic acid and human disease prevention: biological activities and molecular mechanisms.

    Masella, R; Santangelo, C; D'Archivio, M; Li Volti, G; Giovannini, C; Galvano, F

    2012-01-01

    Epidemiological evidence has shown that a high dietary intake of vegetables and fruit rich in polyphenols is associated with a reduction of cancer incidence and mortality from coronary heart disease. The healthy effects associated with polyphenol consumption have made the study of the mechanisms of action a matter of great importance. In particular, the hydroxybenzoic acid protocatechuic acid (PCA) has been eliciting a growing interest for several reasons. Firstly, PCA is one of the main metabolites of complex polyphenols such as anthocyanins and procyanidins that are normally found at high concentrations in vegetables and fruit, and are absorbed by animals and humans. Since the daily intake of anthocyanins has been estimated to be much higher than that of other polyphenols, the nutritional value of PCA is increasingly recognized. Secondly, a growing body of evidence supports the concept that PCA can exert a variety of biological effects by acting on different molecular targets. It has been shown that PCA possesses antioxidant, anti-inflammatory as well as antihyperglycemic and neuroprotective activities. Furthermore, PCA seems to have chemopreventive potential because it inhibits the in vitro chemical carcinogenesis and exerts pro-apoptotic and anti-proliferative effects in different tissues. This review is aimed at providing an up-dated and comprehensive report on PCA giving a special emphasis on its biological activities and the molecular mechanisms of action most likely responsible for a beneficial role in human disease prevention. PMID:22519395

  5. [The molecular mechanism of interaction of trivalent dimethylarsinous acid (DMA(III)) binding to rat hemoglobin].

    Zhang, Min; Wang, Wen-Wen; Jin, Hui-Fang; Bao, Ling-Ling; Naranmandura, Hua; Qin, Ying-Jie; Li, Chun-Hui

    2014-05-01

    In our previous work, we found that trivalent dimethylarsinous acid (DMA(III)) have high affinity binding to cysteine residue 13 of rat hemoglobin. However, it is still unknown why arsenic intermediate metabolite DMA(III) has high binding affinity for Cysl3 but not for other cysteine residues 93, 140, 111 and 125. In order to better understand the molecular mechanism of DMA(III) with rat hemoglobin, we have done current study. So, SD rats were divided into control and arsenic-treated groups randomly. Arsenic species in lysate of red blood cells were analyzed by HPLC-ICP-MS, and then determined by a hybrid quadrupole TOF MS. In addition, trivalent DMA(III) binds to different cysteine residues in rat hemoglobin alpha and beta chains were also simulated by Molecular Docking. Only Cys13 in alpha chain is able to bind to DMA(III) from the experiment results. Cys13 of alpha chain in rat hemoglobin is a specific binding site for DMA(III), and we found that amino acids compose pockets structure and surround Cys13 (but not other cysteine residues), make DMA(III) much easy to bind cysteine 13. Taken together, the DMA(III) specific binding to Cys13 is related to spatial structure of Cys13. PMID:25151739

  6. Investigation of small molecular weight poly(acrylic acid) adsorption on γ-alumina

    Liu, Lei; Luo, Shi-Zhong [College of Chemical Engineering, Sichuan University, Chengdu, Sichuan 610065 (China); Wang, Bin, E-mail: bin_wang@scu.edu.cn [College of Chemical Engineering, Sichuan University, Chengdu, Sichuan 610065 (China); Guo, ZhanHu [Chemical and Biomolecular Engineering Department, University of Tennessee, Knoxville, TN 37996 (United States)

    2015-08-01

    Highlights: • Small molecular weight poly(acrylic acid) incorporated on γ-alumina. • PAA adsorbed primarily on outer surface of alumina at low pH. • PAA infiltrated inside alumina pore at high pH. • Polymer chain reptation motion during the infiltration. - Abstract: The interactions between poly(acrylic acid) (PAA) and alumina have been widely investigated. In this study, the pattern of small molecular weight PAA (M{sub W} 3000) interaction with γ-alumina has been dissected. The alumina/PAA hybrids were prepared at pH 4.0, 5.5, and 7.0, respectively. Nitrogen absorption–desorption analysis, Fourier transform infrared spectroscopy, X-ray diffraction, X-ray photoelectron spectroscopy, scanning electron microscopy, and elemental analysis were conducted to illustrate the characteristics of the hybrids. At pH 4.0, the coiled PAA conformation yielded polymer adsorption primarily on alumina outer surface. At higher pH values, the more stretched PAA molecules were able to infiltrate inside the alumina pores. The phenomenon is explained by the polymer chain reptation motion model. Coiled polymer chains are not oriented enough to penetrate the oxide pore channels. In contrary, stretched polymer chains are more likely to move along the pore channels.

  7. Investigation of small molecular weight poly(acrylic acid) adsorption on γ-alumina

    Highlights: • Small molecular weight poly(acrylic acid) incorporated on γ-alumina. • PAA adsorbed primarily on outer surface of alumina at low pH. • PAA infiltrated inside alumina pore at high pH. • Polymer chain reptation motion during the infiltration. - Abstract: The interactions between poly(acrylic acid) (PAA) and alumina have been widely investigated. In this study, the pattern of small molecular weight PAA (MW 3000) interaction with γ-alumina has been dissected. The alumina/PAA hybrids were prepared at pH 4.0, 5.5, and 7.0, respectively. Nitrogen absorption–desorption analysis, Fourier transform infrared spectroscopy, X-ray diffraction, X-ray photoelectron spectroscopy, scanning electron microscopy, and elemental analysis were conducted to illustrate the characteristics of the hybrids. At pH 4.0, the coiled PAA conformation yielded polymer adsorption primarily on alumina outer surface. At higher pH values, the more stretched PAA molecules were able to infiltrate inside the alumina pores. The phenomenon is explained by the polymer chain reptation motion model. Coiled polymer chains are not oriented enough to penetrate the oxide pore channels. In contrary, stretched polymer chains are more likely to move along the pore channels

  8. Molecularly imprinted poly (methacrylamide-co-methacrylic acid) composite membranes for recognition of curcumin

    In this study, molecularly imprinted poly (methacrylamide-co-methacrylic acid) composite membranes with different ratio of methacrylamide (MAM) versus methacrylic acid (MAA) were prepared via UV initiated photo-copolymerization on the commercial filter paper. Curcumin was chosen as the template molecule. Infra-red (IR) spectroscopy was used to study the binding mechanism between the imprinted sites and the templates. The morphology of the resultant membranes was visualized by scanning electron microscopy (SEM). Static equilibrium binding and recognition properties of the imprinted composite membranes to curcumin (cur-I) and its analogues demethoxycurcumin (cur-II) or bisdemethoxycurcumin (cur-III) were tested. The results showed that curcumin-imprinted membranes had the best recognition ability to curcumin compared to its analogues. From the results, the biggest selectivity factor of αcur-I/cur-II and αcur-I/cur-III were 1.50 and 5.94, and they were obtained from the composite membranes in which MAM/MAA were 1:4 and 0:1, respectively. The results of this study implied that the molecularly imprinted composite membranes could be used as separation membranes for curcumin enrichment

  9. New Diethyl Ammonium Salt of Thiobarbituric Acid Derivative: Synthesis, Molecular Structure Investigations and Docking Studies

    Assem Barakat

    2015-11-01

    Full Text Available The synthesis of the new diethyl ammonium salt of diethylammonium(E-5-(1,5-bis(4-fluorophenyl-3-oxopent-4-en-1-yl-1,3-diethyl-4,6-dioxo-2-thioxohexaydropyrimidin-5-ide 3 via a regioselective Michael addition of N,N-diethylthiobarbituric acid 1 to dienone 2 is described. In 3, the carboanion of the thiobarbituric moiety is stabilized by the strong intramolecular electron delocalization with the adjacent carbonyl groups and so the reaction proceeds without any cyclization. The molecular structure investigations of 3 were determined by single-crystal X-ray diffraction as well as DFT computations. The theoretically calculated (DFT/B3LYP geometry agrees well with the crystallographic data. The effect of fluorine replacement by chlorine atoms on the molecular structure aspects were investigated using DFT methods. Calculated electronic spectra showed a bathochromic shift of the π-π* transition when fluorine is replaced by chlorine. Charge decomposition analyses were performed to study possible interaction between the different fragments in the studied systems. Molecular docking simulations examining the inhibitory nature of the compound show an anti-diabetic activity with Pa (probability of activity value of 0.229.

  10. Biosynthesis of Polyunsaturated Fatty Acids in Marine Invertebrates: Recent Advances in Molecular Mechanisms

    Monroig, Óscar; Tocher, Douglas R.; Navarro, Juan C.

    2013-01-01

    Virtually all polyunsaturated fatty acids (PUFA) originate from primary producers but can be modified by bioconversions as they pass up the food chain in a process termed trophic upgrading. Therefore, although the main primary producers of PUFA in the marine environment are microalgae, higher trophic levels have metabolic pathways that can produce novel and unique PUFA. However, little is known about the pathways of PUFA biosynthesis and metabolism in the levels between primary producers and fish that are largely filled by invertebrates. It has become increasingly apparent that, in addition to trophic upgrading, de novo synthesis of PUFA is possible in some lower animals. The unequivocal identification of PUFA biosynthetic pathways in many invertebrates is complicated by the presence of other organisms within them. These organisms include bacteria and algae with PUFA biosynthesis pathways, and range from intestinal flora to symbiotic relationships that can involve PUFA translocation to host organisms. This emphasizes the importance of studying biosynthetic pathways at a molecular level, and the continual expansion of genomic resources and advances in molecular analysis is facilitating this. The present paper highlights recent research into the molecular and biochemical mechanisms of PUFA biosynthesis in marine invertebrates, particularly focusing on cephalopod molluscs. PMID:24152561

  11. The Molecular Switch of Telomere Phages: High Binding Specificity of the PY54 Cro Lytic Repressor to a Single Operator Site.

    Hammerl, Jens Andre; Roschanski, Nicole; Lurz, Rudi; Johne, Reimar; Lanka, Erich; Hertwig, Stefan

    2015-06-01

    Temperate bacteriophages possess a molecular switch, which regulates the lytic and lysogenic growth. The genomes of the temperate telomere phages N15, PY54 and ɸKO2 harbor a primary immunity region (immB) comprising genes for the prophage repressor, the lytic repressor and a putative antiterminator. The roles of these products are thought to be similar to those of the lambda proteins CI, Cro and Q, respectively. Moreover, the gene order and the location of several operator sites in the prototype telomere phage N15 and in ɸKO2 are also reminiscent of lambda-like phages. By contrast, in silico analyses revealed the presence of only one operator (O\\(_{\\rm{R}}\\)3) in PY54. The purified PY54 Cro protein was used for EMSA studies demonstrating that it exclusively binds to a 16-bp palindromic site (O\\(_{\\rm{R}}\\)3) upstream of the prophage repressor gene. The O\\(_{\\rm{R}}\\)3 operator sequences of PY54 and ɸKO2/N15 only differ by their peripheral base pairs, which are responsible for Cro specificity. PY54 cI and cro transcription is regulated by highly active promoters initiating the synthesis of a homogenious species of leaderless mRNA. The location of the PY54 Cro binding site and of the identified promoters suggests that the lytic repressor suppresses cI transcription but not its own synthesis. The results indicate an unexpected diversity of the growth regulation mechanisms in lambda-related phages. PMID:26043380

  12. The Molecular Switch of Telomere Phages: High Binding Specificity of the PY54 Cro Lytic Repressor to a Single Operator Site

    Jens Andre Hammerl

    2015-06-01

    Full Text Available Temperate bacteriophages possess a molecular switch, which regulates the lytic and lysogenic growth. The genomes of the temperate telomere phages N15, PY54 and ɸKO2 harbor a primary immunity region (immB comprising genes for the prophage repressor, the lytic repressor and a putative antiterminator. The roles of these products are thought to be similar to those of the lambda proteins CI, Cro and Q, respectively. Moreover, the gene order and the location of several operator sites in the prototype telomere phage N15 and in ɸKO2 are also reminiscent of lambda-like phages. By contrast, in silico analyses revealed the presence of only one operator (O\\(_{\\rm{R}}\\3 in PY54. The purified PY54 Cro protein was used for EMSA studies demonstrating that it exclusively binds to a 16-bp palindromic site (O\\(_{\\rm{R}}\\3 upstream of the prophage repressor gene. The O\\(_{\\rm{R}}\\3 operator sequences of PY54 and ɸKO2/N15 only differ by their peripheral base pairs, which are responsible for Cro specificity. PY54 cI and cro transcription is regulated by highly active promoters initiating the synthesis of a homogenious species of leaderless mRNA. The location of the PY54 Cro binding site and of the identified promoters suggests that the lytic repressor suppresses cI transcription but not its own synthesis. The results indicate an unexpected diversity of the growth regulation mechanisms in lambda-related phages.

  13. The 2014 Nucleic Acids Research Database Issue and an updated NAR online Molecular Biology Database Collection.

    Fernández-Suárez, Xosé M; Rigden, Daniel J; Galperin, Michael Y

    2014-01-01

    The 2014 Nucleic Acids Research Database Issue includes descriptions of 58 new molecular biology databases and recent updates to 123 databases previously featured in NAR or other journals. For convenience, the issue is now divided into eight sections that reflect major subject categories. Among the highlights of this issue are six databases of the transcription factor binding sites in various organisms and updates on such popular databases as CAZy, Database of Genomic Variants (DGV), dbGaP, DrugBank, KEGG, miRBase, Pfam, Reactome, SEED, TCDB and UniProt. There is a strong block of structural databases, which includes, among others, the new RNA Bricks database, updates on PDBe, PDBsum, ArchDB, Gene3D, ModBase, Nucleic Acid Database and the recently revived iPfam database. An update on the NCBI's MMDB describes VAST+, an improved tool for protein structure comparison. Two articles highlight the development of the Structural Classification of Proteins (SCOP) database: one describes SCOPe, which automates assignment of new structures to the existing SCOP hierarchy; the other one describes the first version of SCOP2, with its more flexible approach to classifying protein structures. This issue also includes a collection of articles on bacterial taxonomy and metagenomics, which includes updates on the List of Prokaryotic Names with Standing in Nomenclature (LPSN), Ribosomal Database Project (RDP), the Silva/LTP project and several new metagenomics resources. The NAR online Molecular Biology Database Collection, http://www.oxfordjournals.org/nar/database/c/, has been expanded to 1552 databases. The entire Database Issue is freely available online on the Nucleic Acids Research website (http://nar.oxfordjournals.org/). PMID:24316579

  14. Proton transport in triflic acid hydrates studied via path integral car-parrinello molecular dynamics.

    Hayes, Robin L; Paddison, Stephen J; Tuckerman, Mark E

    2009-12-31

    The mono-, di-, and tetrahydrates of trifluoromethanesulfonic acid, which contain characteristic H(3)O(+), H(5)O(2)(+), and H(9)O(4)(+) structures, provide model systems for understanding proton transport in materials with high perfluorosulfonic acid density such as perfluorosulfonic acid membranes commonly employed in hydrogen fuel cells. Ab initio molecular dynamics simulations indicate that protons in these solids are predisposed to transfer to the water most strongly bound to sulfonate groups via a Grotthuss-type mechanism, but quickly return to the most solvated defect structure either due to the lack of a nearby species to stabilize the new defect or a preference for the proton to be maximally hydrated. Path integral molecular dynamics of the mono- and dihydrate reveal significant quantum effects that facilitate proton transfer to the "presolvated" water or SO(3)(-) in the first solvation shell and increase the Zundel character of all the defects. These trends are quantified in free energy profiles for each bonding environment. Hydrogen bonding criteria for HOH-OH(2) and HOH-O(3)S are extracted from the two-dimensional potential of mean force. The quantum radial distribution function, radius of gyration, and root-mean-square displacement position correlation function show that the protonic charge is distributed over two or more water molecules. Metastable structural defects with one excess proton shared between two sulfonate groups and another Zundel or Eigen type cation defect are found for the mono- and dihydrate but not for the tetrahydrate crystal. Results for the tetrahydrate native crystal exhibit minor differences at 210 and 250 K. IR spectra are calculated for all native and stable defect structures. Graph theory techniques are used to characterize the chain lengths and ring sizes in the hydrogen bond network. Low conductivities when limited water is present may be attributable to trapping of protons between SO(3)(-) groups and the increased

  15. Acid-catalyzed conversion of mono- and poly-sugars into platform chemicals: effects of molecular structure of sugar substrate.

    Hu, Xun; Wu, Liping; Wang, Yi; Song, Yao; Mourant, Daniel; Gunawan, Richard; Gholizadeh, Mortaza; Li, Chun-Zhu

    2013-04-01

    Hydrolysis/pyrolysis of lignocellulosic biomass always produces a mixture of sugars with distinct structures as intermediates or products. This study tried to elucidate the effects of molecular structure of sugars on their acid-catalyzed conversions in ethanol/water. Location of carbonyl group in sugars (fructose versus glucose) and steric configuration of hydroxyl groups (glucose versus galactose) significantly affected yields of levulinic acid/ester (fructose>glucose>galactose). The dehydration of fructose to 5-(hydroxymethyl)furfural produces much less soluble polymer than that from glucose and galactose, which results in high yields of levulinic acid/ester from fructose. Anhydrate sugar such as levoglucosan tends to undergo the undesirable decomposition to form less levulinic acid/ester. Catalytic behaviors of the poly-sugars (sucrose, maltose, raffinose, β-cyclodextrins) were determined much by their basic units. However, their big molecular sizes create the steric hindrance that significantly affects their followed conversion over solid acid catalyst. PMID:23454803

  16. Molecular Analysis of the Polymeric Glutenins with Gliadin-Like Characteristics That Were Produced by Acid Dispersion of Wheat Gluten.

    Murakami, Tetsuya; Nishimura, Takahisa; Kitabatake, Naofumi; Tani, Fumito

    2016-03-01

    We had earlier shown that the dispersion of wheat gluten in acetic acid solution conferred gliadin-like characteristics to the polymeric glutenins. To elucidate the molecular behavior of its polymeric glutenins, the characteristics of gluten powder prepared from dispersions with various types of acid were investigated in this study. Mixograph measurements showed that the acid-treated gluten powders, regardless of the type of acid, had dough properties markedly weakened in both resistance and elasticity properties, as though gliadin was supplemented. The polymeric glutenins extracted with 70% ethanol increased greatly in all acid-treated gluten powders. Size exclusion HPLC and SDS-PAGE indicated that the behavior of polymeric glutenins due to acid treatment was attributed to their subunit composition rich in high molecular weight glutenin subunit (HMW-GS) and not their molecular size. The gluten prepared with the addition of NaCl in acid dispersion had properties similar to those of the control gluten. The results suggest that ionic repulsion induced by acid dispersion made the polymeric glutenins rich in HMW-GS disaggregate, and therefore, act like gliadins. PMID:26865190

  17. Interactions of low molecular weight aromatic acids and amino acids with goethite, kaolinite and bentonite with or without organic matter coating

    Gao, Jiajia; Jansen, Boris; Cerli, Chiara; Kalbitz, Karsten

    2015-04-01

    Interaction of organic matter molecules with the soil's solid phase is a key factor influencing the stabilization of carbon in soils and thus forms a crucial aspect of the global carbon cycle. While subject of much research attention so far, we still have much to learn about such interactions at the molecular level; in particular in the light of competition between different classes of organic molecules and in the presence of previously adsorbed soil organic matter. We studied the interaction of a group of low molecular weight (LMW) aromatic acids (salicylic, syringic, vanillic and ferulic acid) and amino acids (lysine, glutamic, leucine and phenylalanine) on goethite, kaolinite and bentonite with and without previously adsorbed dissolved organic matter (DOM). For this we used batch experiments at pH = 6.0 where some of the organic compounds were positively charged (i.e. lysine) or negatively charged (i.e. glutamic and salicylic acid) while the minerals also displayed positively (i.e. goethite) or negatively charged surfaces (i.e. bentonite). We found much higher sorption of salicylic acid and lysine than other compounds. On the bare minerals we found a great variety of sorption strength, with salicylic acid strongly adsorbed, while syringic, vanillic and ferulic acid showed little or no adsorption. For the amino acids, protonated lysine showed a stronger affinity to negatively charged kaolinite and bentonite than other amino acids. While deprotonated glutamic acid showed the strongest adsorption on goethite. Leucine and phenylalanine showed hardly any adsorption on any of the minerals. When present concurrently, amino acids decreased the sorption of salicylic acid on the three types of mineral, while the presence of LMW aromatic acids increased the sorption of lysine on kaolinite and bentonite and the sorption of glutamic acid on goethite. The presence of previously adsorbed DOM reduced the sorption of salicylic acid and lysine. The results confirm that

  18. Selective extraction of derivates of p-hydroxy-benzoic acid from plant material by using a molecularly imprinted polymer.

    Karasová, Gabriela; Lehotay, Jozef; Sádecká, Jana; Skacáni, Ivan; Lachová, Miroslava

    2005-12-01

    Selective SPE of derivates of p-hydroxybenzoic acid (pHBA) from plant extract of Melissa officinalis is presented using a molecularly imprinted polymer (MIP) made with protocatechuic acid (PA) as template molecule. MIP was prepared with acrylamide as functional monomer, ethylene glycol dimethacrylate as crosslinking monomer and ACN as porogen. MIP was evaluated towards six phenolic acids: PA, gallic acid, pHBA, vanillic acid (VA), gentisic acid (GeA) and syringic acid (SyrA), and then steps of molecularly imprinted SPE (MISPE) procedure were optimized. The best specific binding capacity of MIP was obtained for PA in ACN (34.7 microg/g of MIP). Other tested acids were also bound on MIP if they were dissolved in this solvent. ACN was chosen as solvent for sample application. M. officinalis was extracted into methanol/water (4:1, v/v), the extract was then evaporated to dryness and dissolved in ACN before application on MIP. Water and ACN were used as washing solvents and elution of benzoic acids was performed by means of a mixture methanol/acetic acid (9:1, v/v). pHBA, GA, PA and VA were extracted with recoveries of 56.3-82.1% using this MISPE method. GeA was not determined in plant extract. PMID:16405176

  19. Effect of Molecular Structure on the Relative Hydrogen Peroxide Scavenging Ability of Some α-Keto Carboxylic Acids.

    Lopalco, Antonio; Stella, Valentino J

    2016-09-01

    The α-keto carboxylic acid, pyruvic acid (1) was found to be a very effective peroxide scavenger but is subject to an aldol-like self-condensation/polymerization reaction. The purpose of this study was to evaluate the hydrogen peroxide, H2O2, scavenging ability of 3-methyl-2-oxobutanoic acid (2), 4-methyl-2-oxopentanoic acid (3), and 2-oxo-2-phenylacetic acid (phenylglyoxylic acid, 4) in the pH range 2-9 at 25°C and the effect of molecular structure on the relative reactivity. The reaction with H2O2 was followed by UV spectrophotometry at 220 or 260 nm and high-performance liquid chromatography. Pseudo-first order, buffer-independent decarboxylation kinetics were observed in the presence of molar excess H2O2. The second-order rate constants for 2-4 followed a sigmoidal shape and mechanism similar to pyruvic acid. Pyruvic acid was a superior H2O2 scavenger to 2-4 over the pH range 2-9 but 4 was more reactive than 2 and 3 at pH values above 6. There was a qualitative correlation between the degree of keto-group hydration and reactivity of the acids in the pH range 4-6 while the data above pH 7 suggested that the intrinsic decarboxylation step for 4 was faster than for pyruvic acid. Differences in reactivity to molecular structure were analyzed. PMID:27209460

  20. Molecularly imprinted polymer for chlorogenic acid by modified precipitation polymerization and its application to extraction of chlorogenic acid from Eucommia ulmodies leaves.

    Miura, Chitose; Li, Hui; Matsunaga, Hisami; Haginaka, Jun

    2015-10-10

    Molecularly imprinted polymers (MIPs) for chlorogenic acid (CGA) were prepared by modified precipitation polymerization using methacrylic acid as a functional monomer, divinylbenzene as a crosslinker and methanol or dimethylsulfoxide as a co-solvent. The prepared MIPs were microspheres with a narrow particle size distribution. Binding experiments and Scatchard analyses revealed that two classes of binding sites, high and low affinity sites, were formed on the MIP. The retention and molecular-recognition properties of the prepared MIP were evaluated using a mixture of water and acetonitrile as a mobile phase in hydrophilic interaction chromatography. With an increase of acetonitrile content, the retention factor of CGA was increased on the MIP. In addition to shape recognition, hydrophilic interactions seem to work for the recognition of CGA on the MIP. The MIP had a specific molecular-recognition ability for CGA, while other related compounds, such as caffeic acid, gallic acid, protocatechuic acid and vanillic acid, could not be recognized by the MIP. Furthermore, the MIP for CGA was successfully applied for extraction of CGA in the leaves of Eucommia ulmodies. PMID:26037163

  1. Molecular dynamic simulation of asphaltene co-aggregation with humic acid during oil spill.

    Zhu, Xinzhe; Chen, Daoyi; Wu, Guozhong

    2015-11-01

    Humic acid in water and sediment plays a key role in the fate and transport of the spilled oil, but little is known about its influence on the aggregation of heavy oil asphaltenes which is adverse for remediation. Molecular dynamic simulation was performed to characterize the co-aggregation of asphaltenes (continental model and Violanthrone-79 model) with Leonardite humic acid (LHA) at the toluene-water interface and in bulk water, respectively, to simulate the transport of asphaltenes from oil to water. At the toluene-water interface, a LHA layer tended to form and bind to the water by hydrogen bonding which provided a surface for the accumulation of asphaltenes by parallel or T-shape stacking. After entering the bulk water, asphaltene aggregates stacked in parallel were tightly sequestrated inside the inner cavity of LHA aggregates following surface adsorption and structure deformation. Asphaltene aggregation in water was 2-fold higher than at the toluene-water interface. The presence of LHA increased the intensity of asphaltene aggregation by up to 83% in bulk water while relatively less influence was observed at the toluene-water interface. Overall results suggested that the co-aggregation of asphaltene with humic acid should be incorporated to the current oil spill models for better interpreting the overall environmental risks of oil spill. PMID:26149857

  2. Molecular dynamics simulations capture the misfolding of the bovine prion protein at acidic pH.

    Cheng, Chin Jung; Daggett, Valerie

    2014-01-01

    Bovine spongiform encephalopathy (BSE), or mad cow disease, is a fatal neurodegenerative disease that is transmissible to humans and that is currently incurable. BSE is caused by the prion protein (PrP), which adopts two conformers; PrPC is the native innocuous form, which is α-helix rich; and PrPSc is the β-sheet rich misfolded form, which is infectious and forms neurotoxic species. Acidic pH induces the conversion of PrPC to PrPSc. We have performed molecular dynamics simulations of bovine PrP at various pH regimes. An acidic pH environment induced conformational changes that were not observed in neutral pH simulations. Putative misfolded structures, with nonnative β-strands formed in the flexible N-terminal domain, were found in acidic pH simulations. Two distinct pathways were observed for the formation of nonnative β-strands: at low pH, hydrophobic contacts with M129 nucleated the nonnative β-strand; at mid-pH, polar contacts involving Q168 and D178 facilitated the formation of a hairpin at the flexible N-terminus. These mid- and low pH simulations capture the process of nonnative β-strand formation, thereby improving our understanding of how PrPC misfolds into the β-sheet rich PrPSc and how pH factors into the process. PMID:24970211

  3. Molecular Dynamics Simulations Capture the Misfolding of the Bovine Prion Protein at Acidic pH

    Chin Jung Cheng

    2014-02-01

    Full Text Available Bovine spongiform encephalopathy (BSE, or mad cow disease, is a fatal neurodegenerative disease that is transmissible to humans and that is currently incurable. BSE is caused by the prion protein (PrP, which adopts two conformers; PrPC is the native innocuous form, which is α-helix rich; and PrPSc is the β-sheet rich misfolded form, which is infectious and forms neurotoxic species. Acidic pH induces the conversion of PrPC to PrPSc. We have performed molecular dynamics simulations of bovine PrP at various pH regimes. An acidic pH environment induced conformational changes that were not observed in neutral pH simulations. Putative misfolded structures, with nonnative β-strands formed in the flexible N-terminal domain, were found in acidic pH simulations. Two distinct pathways were observed for the formation of nonnative β-strands: at low pH, hydrophobic contacts with M129 nucleated the nonnative β-strand; at mid-pH, polar contacts involving Q168 and D178 facilitated the formation of a hairpin at the flexible N-terminus. These mid- and low pH simulations capture the process of nonnative β-strand formation, thereby improving our understanding of how PrPC misfolds into the β-sheet rich PrPSc and how pH factors into the process.

  4. Molecular cloning and sequence analysis of cDNA encoding human prostatic acid phosphatase.

    Vihko, P; Virkkunen, P; Henttu, P; Roiko, K; Solin, T; Huhtala, M L

    1988-08-29

    lambda gt11 clones encoding human prostatic acid phosphatase (PAP) (EC 3.1.3.2) were isolated from human prostatic cDNA libraries by immunoscreening with polyclonal antisera. Sequence data obtained from several overlapping clones indicated that the composite cDNAs contained the complete coding region for PAP, which encodes a 354-residue protein with a calculated molecular mass of 41,126 Da. In the 5'-end, the cDNA codes for a signal peptide of 32 amino acids. Direct protein sequencing of the amino-terminus of the mature protein and its proteolytic fragments confirmed the identity of the predicted protein sequence. PAP has no apparent sequence homology to other known proteins. However, both the cDNA clones coding for human placental alkaline phosphatase and PAP have an alu-type repetitive sequence about 900 nucleotides downstream from the coding region in the 3'-untranslated region. Two of our cDNA clones differed from others at the 5'-ends. RNA blot analysis indicated mRNA of 3.3 kb. We are continuing to study whether acid phosphatases form a gene family as do alkaline phosphatases. PMID:2842184

  5. Breast Cancer Genetic and Molecular Subtype Impacts Response to Omega-3 Fatty Acid Ethyl Esters.

    Chen, Ching Hui; Fabian, Carol; Hursting, Stephen; deGraffenried, Linda A

    2016-01-01

    Epidemiological studies have correlated frequent omega-3 (n-3) fatty acid consumption with a lower risk for breast cancer; however, recent prospective studies have been less conclusive. Efforts in the preventive setting have focused on the use of n-3 fatty acids, and the pharmaceutical ethyl esters (EE) of these natural compounds, for high-risk patient populations. Limited understanding of specific mechanisms by which these agents function has hampered identification of the cancer subtype(s) that would gain the greatest therapeutic benefit. In this study, we investigated the in vitro effects of n-3 EEs in four distinct breast cancer subtypes and explored how they affect not only breast cancer cell survival but also modulate the nuclear factor kappa-light-chain enhancer of activated B cells (NF-κB) and peroxisome proliferator-activated receptor gamma signaling pathways. Similar to the high variance in response observed in human studies, we found that the effectiveness of n-3 EEs depends on the molecular characteristics of the MCF-7, CAMA-1, MDA-MB-231, and SKBR3 breast cancer cell lines and is closely associated with the suppression of NF-κB. These data strongly suggest that the use of n-3 fatty acids and their pharmaceutical ether esters in the prevention and therapeutic setting should be guided by specific tumor characteristics. PMID:27367296

  6. Effects of molecular weight and ratio of guluronic acid to mannuronic acid on the antioxidant properties of sodium alginate fractions prepared by radiation-induced degradation

    Sen, Murat, E-mail: msen@hacettepe.edu.t [Hacettepe University, Department of Chemistry, Polymer Chemistry Division, Beytepe, 06800 Ankara (Turkey)

    2011-01-15

    In this study, the effects of the molecular weight and ratio of guluronic acid (G) to mannuronic acid (M), G/M, of some sodium alginate (NaAlg) fractions on their antioxidative properties were investigated. Low-molecular-weight-fractions with various G/M were prepared by gamma radiation-induced degradation of NaAlg. Change in their molecular weight was monitored. Antioxidant properties of the fractions with various molecular weight and G/M were evaluated by determining the scavenging ability of 1,1-diphenyl-2-picrylhydrazyl free radical (DPPH{sup {center_dot}}). 50% inhibition concentrations of the 50 kGy-irradiated NaAlgs having molecular weights of 20.5, 17.7, and 16.0 kDa were found to be 11.0, 18.0, and 24.0 mg/ml, respectively, whereas the fractions of the same molecular weight with a lower G/M exhibited a better DPPH{sup {center_dot}}scavenging activity. The results demonstrated that its molecular weight and G/M were important factors in controlling the antioxidant properties of NaAlg.

  7. Proton transport properties of poly(aspartic acid) with different average molecular weights

    Research highlights: → Seven polymers with different average molecular weights were synthesized. → The proton conductivity depended on the number-average degree of polymerization. → The difference of the proton conductivities was more than one order of magnitude. → The number-average molecular weight contributed to the stability of the polymer. - Abstract: We synthesized seven partially protonated poly(aspartic acids)/sodium polyaspartates (P-Asp) with different average molecular weights to study their proton transport properties. The number-average degree of polymerization (DP) for each P-Asp was 30 (P-Asp30), 115 (P-Asp115), 140 (P-Asp140), 160 (P-Asp160), 185 (P-Asp185), 205 (P-Asp205), and 250 (P-Asp250). The proton conductivity depended on the number-average DP. The maximum and minimum proton conductivities under a relative humidity of 70% and 298 K were 1.7 . 10-3 S cm-1 (P-Asp140) and 4.6 . 10-4 S cm-1 (P-Asp250), respectively. Differential thermogravimetric analysis (TG-DTA) was carried out for each P-Asp. The results were classified into two categories. One exhibited two endothermic peaks between t = (270 and 300) oC, the other exhibited only one peak. The P-Asp group with two endothermic peaks exhibited high proton conductivity. The high proton conductivity is related to the stability of the polymer. The number-average molecular weight also contributed to the stability of the polymer.

  8. Kinetic study of acid depolymerization of chitosan and effects of low molecular weight chitosan on erythrocyte rouleaux formation.

    Tsao, Ching Ting; Chang, Chih Hao; Lin, Yu Yung; Wu, Ming Fung; Han, Jin Lin; Hsieh, Kuo Huang

    2011-01-01

    In this study, the depolymerization of chitosan was carried out in an acetic acid aqueous solution and was followed by viscometry for molecular weight determination. It was found that the depolymerization rate increased with elevated temperatures and with high acid concentrations. Based on FTIR analysis, the chitosan was depolymerized randomly along the backbone; no other structural change was observed during the acid depolymerization process. Revealed in the TGA study, the degradation temperature and char yield of LMWCs (low molecular weight chitosan) were molecular weight dependent. The blood compatibility of LMWCs was also investigated: rouleaux formation was observed when erythrocyte contacted with LMWCs, which showed that LMWCs are able to interfere with the negatively charged cell membrane through its polycationic properties. Furthermore, as regards a kinetics investigation, the values of M(n) (number-average molecular weight) were obtained from an experimentally determined relationship. The kinetics study showed that the complex salt, formed by amine on chitosan and acetic acid, acted as catalyst. Finally, the activation energy for the hydrolysis of the glycosidic linkage on chitosan was calculated to be 40kJ/mol; the mechanism of acid depolymerization is proposed. In summary, LMWCs could be easily and numerously generated with acid depolymerization for further biological applications. PMID:21075360

  9. Advanced CPMAS-13C NMR techniques for molecular characterization of size-separated fractions from a soil humic acid.

    Conte, Pellegrino; Spaccini, Riccardo; Piccolo, Alessandro

    2006-09-01

    A humic acid extracted from a volcanic soil was subjected to preparative high-performance size-exclusion chromatography (HPSEC) to reduce its molecular complexity and eleven different size fractions were obtained. Cross-polarization magic-angle spinning 13C NMR (CPMAS 13C NMR) analysis performed with variable contact-time (VCT) pulse sequences showed that the largest molecular-size fractions contained aromatic, alkyl, and carbohydrate-like components. The carbohydrate-like content and the alkyl chain length seemed to decrease with decreasing molecular size. Progressive reduction of aromatic carbon atoms was also observed with decreasing molecular size of the separated fractions. Mathematical treatment of the results from VCT experiments enabled cross polarization (T (CH)) and proton spin-lattice relaxation (T(1rho)(H)) times to be related to structural differences among the size fractions. The conformational distribution indicated that the eleven size fractions could be allocated to two main groups. The first group, with larger nominal molecular sizes, was characterized by molecular domains with slower local molecular motion. The second group of size fractions, with smaller nominal molecular sizes, was characterized by a larger number of molecular domains with faster local molecular motion. The T (CH) and (T(1rho)(H)) values suggested that either condensed or strongly associated aromatic systems were predominant in the size fractions with the largest apparent molecular dimensions. PMID:16896626

  10. Use of acrylic acid in the synthesis of molecularly imprinted polymers for the analysis of cyproheptadine

    Feas, Xesus [Analytical Chemistry, Nutrition and Bromatology, Campus Lugo, University of Santiago de Compostela. E-27002, Lugo, Galiza (Spain); Fente, Cristina A. [Analytical Chemistry, Nutrition and Bromatology, Campus Lugo, University of Santiago de Compostela. E-27002, Lugo, Galiza (Spain)], E-mail: cfente@lugo.usc.es; Hosseini, S. Vali [Analytical Chemistry, Nutrition and Bromatology, Campus Lugo, University of Santiago de Compostela. E-27002, Lugo, Galiza (Spain); Seijas, Julio A. [Organic Chemistry, Campus Lugo, University of Santiago de Compostela. Aptdo 280, E-27080, Lugo (Spain); Vazquez, Beatriz I.; Franco, Carlos M.; Cepeda, Alberto [Analytical Chemistry, Nutrition and Bromatology, Campus Lugo, University of Santiago de Compostela. E-27002, Lugo, Galiza (Spain)

    2009-03-01

    The synthesis and comparative characterization of molecularly imprinted polymers (MIP{sub s}) with cyproheptadine (CYP), using two different monomers, acrylic acid (AA) and methacrylic acid (MAA), are described. Polyacids (PA) [poly(methacrylic acid) (PMAA) and poly(acrylic acid) (PAA)] were obtained by the radical polymerization of MAA and AA, respectively, in dichloromethane as the porogen solvent-imprinted medium. The non-covalent imprinting process was performed via thermal decomposition of an azo-initiator at 60 deg. C, using ethylene glycol dimethacrylate as the cross-linker and 2,2'-azobis(2-methylpropionitrile) as the initiator. The selectivities of MIP{sub s} and NIP{sub s} particles were evaluated in binding experiments of the four synthesized polymeric materials (MIP{sub aa}, MIP{sub maa}, NIP{sub maa} and NIP{sub aa}) with CYP. The effects of monomers on: a) the surface morphology, b) the binding capacity and c) the swelling properties of imprinted and non-imprinted polymers were studied and are presented here. Polymer material morphology was assessed with scanning electron microscopy (SEM). This revealed differences in monomer function, depending on which one was employed, as well as differences in function when polymerization occurred in the presence of template or without it. Non-specific retention of the template to NIP{sub s} was higher for NIP{sub s}-PAA polymers than for NIP{sub s}-PMAA materials. In terms of specific binding ({delta}Q = Q{sub MIP} - Q{sub NIP}), MIP{sub maa} showed the greatest value (53.47%) in comparison with MIP{sub aa} (50.07%)

  11. Ferrous iron oxidation by molecular oxygen under acidic conditions: The effect of citrate, EDTA and fulvic acid

    Jones, Adele M.; Griffin, Philippa J.; Waite, T. David

    2015-07-01

    In this study, the rates of Fe(II) oxidation by molecular oxygen in the presence of citrate, ethylenediaminetetraacetic acid (EDTA) and Suwannee River fulvic acid (SRFA) were determined over the pH range 4.0-5.5 and, for all of the ligands investigated, found to be substantially faster than oxidation rates in the absence of any ligand. EDTA was found to be particularly effective in enhancing the rate of Fe(II) oxidation when sufficient EDTA was available to complex all Fe(II) present in solution, with a kinetic model of the process found to adequately describe all results obtained. When Fe(II) was only partially complexed by EDTA, reactions with reactive oxygen species (ROS) and heterogeneous Fe(II) oxidation were found to contribute significantly to the removal rate of iron from solution at different stages of oxidation. This was possible due to the rapid rate at which EDTA enhanced Fe(II) oxidation and formed ROS and Fe(III). The rapid rate of Fe(III) generation facilitated the formation of free ferric ion activities in excess of those required for ferric oxyhydroxide precipitation following Fe(III)-EDTA dissociation. In comparison, the rate of Fe(II) oxidation was slower in the presence of citrate, and therefore the concentrations of free Fe(III) able to form in the initial stages of Fe(II) oxidation were much lower than those formed in the presence of EDTA, despite the resultant Fe(III)-citrate complex being less stable than that of Fe(III)-EDTA. The slower rate of citrate enhanced oxidation also resulted in slower rates of ROS generation, and, as such, oxidation of the remaining inorganic Fe(II) species by ROS was negligible. Overall, this study demonstrates that organic ligands may substantially enhance the rate of Fe(II) oxidation. Even under circumstances where the ligand is not present at sufficient concentrations to complex all of the Fe(II) in solution, ensuing oxidative processes may sustain an enhanced rate of Fe(II) oxidation relative to that of

  12. Emergent Molecular Recognition through Self-Assembly: Unexpected Selectivity for Hyaluronic Acid among Glycosaminoglycans.

    Noguchi, Takao; Roy, Bappaditya; Yoshihara, Daisuke; Sakamoto, Junji; Yamamoto, Tatsuhiro; Shinkai, Seiji

    2016-05-01

    Oligophenylenevinylene (OPV)-based fluorescent (FL) chemosensors exhibiting linear FL responses toward polyanions were designed. Their application to FL sensing of glycosaminoglycans (heparin: HEP, chondroitin 4-sulfate: ChS, and hyaluronic acid: HA) revealed that the charge density encoded as the unit structure directs the mode of OPV self-assembly: H-type aggregate for HEP with 16-times FL increase and J-type aggregate for HA with 93-times FL increase, thus unexpectedly achieving the preferential selectivity for HA in contrast to the conventional HEP selective systems. We have found that the integral magnitude of three factors consisting of binding mechanism, self-assembly, and FL response can amplify the structural information on the target input into the characteristic FL output. This emergent property has been used for a novel molecular recognition system that realizes unconventional FL sensing of HA, potentially applicable to the clinical diagnosis of cancer-related diseases. PMID:27060601

  13. Improvement in Aqueous Solubility of Retinoic Acid Receptor (RAR) Agonists by Bending the Molecular Structure.

    Hiramatsu, Michiaki; Ichikawa, Yuki; Tomoshige, Shusuke; Makishima, Makoto; Muranaka, Atsuya; Uchiyama, Masanobu; Yamaguchi, Takao; Hashimoto, Yuichi; Ishikawa, Minoru

    2016-08-01

    Aqueous solubility is a key requirement for many functional molecules, e. g., drug candidates. Decrease of the partition coefficient (log P) by chemical modification, i.e., introduction of hydrophilic group(s) into molecules, is a classical strategy for improving aqueous solubility. We have been investigating alternative strategies for improving the aqueous solubility of pharmaceutical compounds by disrupting intermolecular interactions. Here, we show that introducing a bend into the molecular structure of retinoic acid receptor (RAR) agonists by changing the substitution pattern from para to meta or ortho dramatically enhances aqueous solubility by up to 890-fold. We found that meta analogs exhibit similar hydrophobicity to the parent para compound, and have lower melting points, supporting the idea that the increase of aqueous solubility was due to decreased intermolecular interactions in the solid state as a result of the structural changes. PMID:27378357

  14. Comparative Molecular Mechanics and Quantum Mechanics Study of Microhydration of Nucleic Acid Bases

    Lino, J; Deriabina, A; Velasco, M; Poltev, V

    2013-01-01

    DNA is the most important biological molecule, and its hydration contributes essentially to the structure and functions of the double helix. We analyze the microhydration of the individual bases of nucleic acids and their methyl derivatives using methods of molecular mechanics (MM) with the Poltev-Malenkov (PM), AMBER and OPLS force fields, as well as ab initio Quantum Mechanics (QM) calculations at MP2/6-31G(d,p) level of theory. A comparison is made between the calculated interaction energies and the experimental enthalpies of microhydration of bases, obtained from mass spectrometry at low temperatures. Each local water-base interaction energy minimum obtained with MM corresponds to the minimum obtained with QM. General qualitative agreement was observed in the geometrical characteristics of the local minima obtained via the two groups of methods. MM minima correspond to slightly more coplanar structures than those obtained via QM methods, and the absolute MM energy values overestimate corresponding values ...

  15. Molecular dynamics study of solvation effects on acid dissociation in aprotic media

    Laria, D; Estrin, D A; Ciccotti, G; Laria, Daniel; Kapral, Raymond; Estrin, Dario; Ciccotti, Giovanni

    1996-01-01

    Acid ionization in aprotic media is studied using Molecular Dynamics techniques. In particular, models for HCl ionization in acetonitrile and dimethylsulfoxide are investigated. The proton is treated quantum mechanically using Feynman path integral methods and the remaining molecules are treated classically. Quantum effects are shown to be essential for the proper treatment of the ionization. The potential of mean force is computed as a function of the ion pair separation and the local solvent structure is examined. The computed dissociation constants in both solvents differ by several orders of magnitude which are in reasonable agreement with experimental results. Solvent separated ion pairs are found to exist in dimethylsulfoxide but not in acetonitrile. Dissociation mechanisms in small clusters are also investigated. Solvent separated ion pairs persist even in aggregates composed of rather few molecules, for instance, as few as thirty molecules. For smaller clusters or for large ion pair separations cluste...

  16. Targeting Amino Acid Metabolism for Molecular Imaging of Inflammation Early After Myocardial Infarction.

    Thackeray, James T; Bankstahl, Jens P; Wang, Yong; Wollert, Kai C; Bengel, Frank M

    2016-01-01

    Acute tissue inflammation after myocardial infarction influences healing and remodeling and has been identified as a target for novel therapies. Molecular imaging holds promise for guidance of such therapies. The amino acid (11)C-methionine is a clinically approved agent which is thought to accumulate in macrophages, but not in healthy myocytes. We assessed the suitability of positron emission tomography (PET) with (11)C-methionine for imaging post-MI inflammation, from cell to mouse to man. Uptake assays demonstrated 7-fold higher (11)C-methionine uptake by polarized pro-inflammatory M1 macrophages over anti-inflammatory M2 subtypes (ptranslation of novel image-guided, inflammation-targeted regenerative therapies. PMID:27570549

  17. Photoresponsive surface molecularly imprinted polymer on ZnO nanorods for uric acid detection in physiological fluids.

    Tang, Qian; Li, Zai-Yong; Wei, Yu-Bo; Yang, Xia; Liu, Lan-Tao; Gong, Cheng-Bin; Ma, Xue-Bing; Lam, Michael Hon-Wah; Chow, Cheuk-Fai

    2016-09-01

    A photoresponsive surface molecularly imprinted polymer for uric acid in physiological fluids was fabricated through a facile and effective method using bio-safe and biocompatible ZnO nanorods as a support. The strategy was carried out by introducing double bonds on the surface of the ZnO nanorods with 3-methacryloxypropyltrimethoxysilane. The surface molecularly imprinted polymer on ZnO nanorods was then prepared by surface polymerization using uric acid as template, water-soluble 5-[(4-(methacryloyloxy)phenyl)diazenyl]isophthalic acid as functional monomer, and triethanolamine trimethacryl ester as cross-linker. The surface molecularly imprinted polymer on ZnO nanorods showed good photoresponsive properties, high recognition ability, and fast binding kinetics toward uric acid, with a dissociation constant of 3.22×10(-5)M in aqueous NaH2PO4 buffer at pH=7.0 and a maximal adsorption capacity of 1.45μmolg(-1). Upon alternate irradiation at 365 and 440nm, the surface molecularly imprinted polymer on ZnO nanorods can quantitatively uptake and release uric acid. PMID:27207036

  18. Structural analysis and investigation of molecular properties of Cefpodoxime acid, a third generation antibiotic

    Suganthi, S.; Balu, P.; Sathyanarayanamoorthi, V.; Kannappan, V.; Kamil, M. G. Mohamed; Kumar, R.

    2016-03-01

    Extensive quantum mechanical studies are carried out on Cefpodoxime acid (CA), a new generation drug by Hartree-Fock (HF) and B3LYP methods to understand the structural and spectral characteristics of the molecule. The most stable geometry of the molecule was optimized and the bond parameters were reported. The spectroscopic properties of this pharmaceutically important compound were investigated by FT-IR, FT-Raman, UV and 1H NMR techniques. The scaled vibrational frequencies of CA in the ground state are calculated by HF and B3LYP methods with 6-311++G (d, p) basis set and compared with the observed FT-IR and FT-Raman spectra. The vibrational spectral analysis indicates the presence of two intra molecular hydrogen bonds in the molecule which is supported by theoretical study. 1H NMR chemical shifts (δ) were calculated for the CA molecule and compared with the experimental values. The theoretical electronic absorption spectral data in water and ethanol solvents were computed by TD-DFT method. UV-Vis absorption spectra of CA are recorded in these two solvents and compared with theoretical spectra. The spectral data and natural bond orbital (NBO) analysis confirm the occurrence of intra molecular interactions in CA. The electronic distribution, in conjunction with electrophilicity index of CA was used to establish the active site and type of interaction between CA and beta lactamases. Mulliken population analysis on atomic charges is also carried out and thermodynamic properties of the title compound are calculated.

  19. Isolation and Molecular Screening of Glucansucrase Gene Harboring-Lactic Acid Bacteria

    Ajitya Kurnia Hermawati

    2010-04-01

    Full Text Available Exopolysaccharides (EPS have been possessed to be used in pharmaceutical, cosmetic and food industries. Lactic acid bacteria (LAB produce a wide variety of exopolysaccharides and have been well reported carrying sucrase genes glucansucrase/ glucosyltransferase (gtf and fructansucrase/fructosyltransferases (ftf, enzymes that are able to produce EPS. In this study, the isolation and screening of EPS producing-LAB (EPS-LAB were carried out on modified de Mann-Rogosa-Sharpe (MRS agar medium supplemented with 10% of sucrose on LAB isolated from various unique sugar containing-foods and -beverages originated from local sources. Besides obtaining EPS-LAB, this study aimed to screen for gtf gene as well as to molecular identify strains by using PCR technique. Degenerate primer pairs DegFor and DegRev which targeted the conserved region of gtf genes catalytic domain were used, whereas LABfw and LABrv were used to molecular identify strains using 16S rRNA gene. An approximately 660 base pairs (bp amplicons which targeted gtf gene were obtained from 13 out of 16 srains chosen. Moreover, from PCR of 16S rRNA gene identification on gtf positive strains result, all strains were molecular identified as LAB after DNA sequencing analysis of 700 bp amplicons by using blastn. A rare EPS-producing LAB were obtain from both foods and beverages i.e. Weissella. Results revealed that strains obtained in this study are potential sources for exploring novel sucrase gene/s and obtain unique EPS polymer product/s.

  20. Effect of Phosphatidic Acid on Biomembrane: Experimental and Molecular Dynamics Simulations Study.

    Kwolek, Urszula; Kulig, Waldemar; Wydro, Paweł; Nowakowska, Maria; Róg, Tomasz; Kepczynski, Mariusz

    2015-08-01

    We consider the impact of phosphatidic acid (namely, 1,2-dioleoyl-sn-glycero-3-phosphate, DOPA) on the properties of a zwitterionic (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, DPPC) bilayer used as a model system for protein-free cell membranes. For this purpose, experimental measurements were performed using differential scanning calorimetry and the Langmuir monolayer technique at physiological pH. Moreover, atomistic-scale molecular dynamics (MD) simulations were performed to gain information on the mixed bilayer's molecular organization. The results of the monolayer studies clearly showed that the DPPC/DOPA mixtures are nonideal and the interactions between lipid species change from attractive, at low contents of DOPA, to repulsive, at higher contents of that component. In accordance with these results, the MD simulations demonstrated that both monoanionic and dianionic forms of DOPA have an ordering and condensing effect on the mixed bilayer at low concentrations. For the DOPA monoanions, this is the result of both (i) strong electrostatic interactions between the negatively charged oxygen of DOPA and the positively charged choline groups of DPPC and (ii) conformational changes of the lipid acyl chains, leading to their tight packing according to the so-called "umbrella model", in which large headgroups of DPPC shield the hydrophobic part of DOPA (the conical shape lipid) from contact with water. In the case of the DOPA dianions, cation-mediated clustering was observed. Our results provide a detailed molecular-level description of the lipid organization inside the mixed zwitterionic/PA membranes, which is fully supported by the experimental data. PMID:26167676

  1. Isolation, enumeration, molecular identification and probiotic potential evaluation of lactic acid bacteria isolated from sheep milk

    L.B. Acurcio

    2014-06-01

    Full Text Available Lactic acid bacteria species were molecularly identified in milk from Lacaune, Santa Inês and crossbred sheep breeds and their in vitro probiotic potential was evaluated. The species identified were Enterococcus faecium (56.25%, E. durans (31.25% and E. casseliflavus (12.5%. No other lactic acid bacteria species, such as lactobacilli, was identified. Most of the isolated enterococci were resistant to gastric pH (2.0 and to 0.3% oxgall. All tested enterococci were resistant to ceftazidime, oxacillin and streptomycin and sensible to clindamycin, erythromycin and penicillin. The resistance to ciprofloxacin, gentamicin, tetracycline and vancomycin varied among tested species. All tested enterococci strongly inhibited (P<0.05 Escherichia coli and Listeria monocytogenes, moderately inhibited E. faecalis and Staphylococcus aureus and did not inhibit Pseudomonas aeruginosa, Salmonella enterica var. Typhimurium and also one E. durans sample isolated from sheep milk. Four samples of E. faecium, one of E. durans and one of E. casseliflavus presented the best probiotic potential.

  2. A classical reactive potential for molecular clusters of sulphuric acid and water

    Stinson, Jake L.; Kathmann, Shawn M.; Ford, Ian J.

    2016-01-17

    We present a two state empirical valence bond (EVB) potential describing interactions between sulphuric acid and water molecules and designed to model proton transfer between them within a classical dynamical framework. The potential has been developed in order to study the properties of molecular clusters of these species, which are thought to be relevant to atmospheric aerosol nucleation. The particle swarm optimisation method has been used to fit the parameters of the EVB model to density functional theory (DFT) calculations. Features of the parametrised model and DFT data are compared and found to be in satisfactory agreement. In particular, it is found that a single sulphuric acid molecule will donate a proton when clustered with four water molecules at 300 K and that this threshold is temperature dependent. SMK was supported in part by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences; JLS and IJF were supported by the IMPACT scheme at University College London (UCL). We acknowledge the UCL Legion High Performance Computing Facility, and associated support services together with the resources of the National Energy Research Scientific Computing Center (NERSC), which is supported by the U.S. Department of Energy under Contract No. DE-AC02- 05CH11231. JLS thanks Dr. Gregory Schenter, Dr. Theo Kurtén and Prof. Hanna Vehkamäki for important guidance and discussions.

  3. Preparation of molecularly imprinted cross-linked chitosan/glutaraldehyde resin for enantioselective separation of L-glutamic acid.

    Monier, M; El-Sokkary, A M A

    2010-08-01

    In the present study, separation of L-glutamic acid from dilute aqueous solution by solid-phase extraction based on molecular imprinting technique using cross-linked chitosan/glutaraldehyde resin was investigated. L-Glutamic acid imprinted cross-linked chitosan (LGIC) was prepared by cross-linking of chitosan by glutaraldehyde cross-linker, in the presence of L-glutamic acid. Non-imprinted cross-linked chitosan (NIC) as control was also prepared by the same procedure in the absence of template molecules. The morphological structures of both LGIC and NIC were examined by scanning electron microscope (SEM). LGIC particles were applied to determine the optimum operational condition for l-glutamic acid separation from dilute aqueous solution. In adsorption step, optimum pH and retention time were 5.5 and 100 min, while corresponding values in extraction step were 2.5 and 60 min, respectively. The adsorption isotherms indicated that the maximum adsorption capacities of L- and D-glutamic acid on LGIC were 42+/-0.8 and 26+/-1.2mg/g, respectively, while in case of NIC, both L- and D-glutamic acid present the same maximum adsorption capacity 7+/-0.6 mg/g, which confirm that the molecular imprinting technique creates an enantioselectivity of LGIC toward L-glutamic acid. In addition, chiral resolution of l-, d-glutamic acid racemic mixture was carried out using column of LGIC. PMID:20441776

  4. Temporal and spatial variations of low-molecular-weight organic acids in Dianchi Lake, China

    Min Xiao; Fengchang Wu; Runyu Zhang; Liying Wang; Xinqing Li; Rongsheng Huang

    2011-01-01

    Low-molecular-weight organic acids (LMWOAs) in eutrophic lake water of Dianchi,Southwestern China Plateau were investigated diurnally and vertically using ion chromatography.Two profiles (P1 and P2) were studied due to the difference of hydrochemical features.Lactic,formic,pyruvic and oxalic acid were detected as major components at P1 and P2 which were on average 7.98 and 6.53 μmol/L,respectively,corresponding to their proportions of 2.68% and 2.48% relative to DOC.Pyruvic acid was regarded as the uppermost species at PI and P2,reaching up to 3.82 and 3.35 μmol/L and accounting for 47.9% and 51.3%,respectively,in individual TOA.Although humus were of biogenetic production at both sites,the significant negative correlation between diurnal variations of TOAs,fluorescence intensity (FI) of protein-like components and humic-like components at P1 indicated LMWOAs were greatly originated from bacterioplankton excretion and degradation.However,correlations between diurnal variations of humic-like FI and physicochemical parameters demonstrated algal origination of LMWOAs at P2.Although content of humus was high,TOA at P2 was 1.45 μmol/L lower than that at P1,due to the co-influence of more intense photo-oxidation and aggregation at P2.Therefore,TOAs exhibited quite opposite diurnal variation trends of increasing-decreasing and decreasing-increasing at P1 and P2,respectively.Except for impact of solar radiation,bacterial decomposition and assimilation rendered shifts of maximal LMWOAs along water colunm at P1.Covering with massive algae,UV rays penetrated shallower depth that LMWOAs assembled in surface layer water before 18:00 at P2 and represented decreasing profiles.

  5. Large second-order optical nonlinearity in a ferroelectric molecular crystal of croconic acid with strong intermolecular hydrogen bonds

    Sawada, R.; Uemura, H.; Sotome, M.; Yada, H.; Kida, N.; Iwano, K.; Shimoi, Y.; Horiuchi, S.; Okamoto, H.

    2013-04-01

    Linear and nonlinear optical responses in a molecular crystal, croconic acid, showing electronic-type ferroelectricity were studied by reflection and second harmonic generation spectroscopy. The second-order nonlinear susceptibility χ(2) was very large, exceeding 10-6 esu in the near-infrared region. The enhancement of χ(2) was attributed to the large dipole moment of the lowest π-π* transition and the large difference between the molecular dipole moments for the ground state and the photoexcited state. We deduced the molecular orbitals (MOs) and dipole moments responsible for the large χ(2) by comparing the experimental optical parameters and MO calculation results based upon density functional theory.

  6. The allosteric switching mechanism in bacteriophage MS2

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

    2016-07-01

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

  7. Effects of cross-linking molecular weights in a hyaluronic acid-poly(ethylene oxide) hydrogel network on its properties

    Noh, Insup [Department of Chemical Engineering, Seoul National University of Technology, 172 Gongnung-dong, Nowon-gu, Seoul 139-743 (Korea, Republic of); Kim, Gun-Woo [Department of Chemical Engineering, Seoul National University of Technology, 172 Gongnung-dong, Nowon-gu, Seoul 139-743 (Korea, Republic of); Choi, Yoon-Jeong [Department of Chemical Engineering, Seoul National University of Technology, 172 Gongnung-dong, Nowon-gu, Seoul 139-743 (Korea, Republic of); Kim, Mi-Sook [Department of Chemical Engineering, Seoul National University of Technology, 172 Gongnung-dong, Nowon-gu, Seoul 139-743 (Korea, Republic of); Park, Yongdoo [Korea Artificial Organ Center, Korea University, Seoul 136-705 (Korea, Republic of); Lee, Kyu-Back [Korea Artificial Organ Center, Korea University, Seoul 136-705 (Korea, Republic of); Kim, In-Sook [Dental Research Institute, Seoul National University, Seoul 110-749 (Korea, Republic of); Hwang, Soon-Jung [Dental Research Institute, Seoul National University, Seoul 110-749 (Korea, Republic of); Tae, Giyoong [Department of Materials Science and Engineering, Gwangju Institute of Science and Technology, Gwangju 500-712 (Korea, Republic of)

    2006-09-15

    We examined the effects of cross-linking molecular weights on the properties of a hyaluronic acid (HA)-poly(ethylene oxide) (PEO) hydrogel. Swelling behaviors, mechanical strength and rheological behaviors of the HA-PEO hydrogel were evaluated by employing different cross-linking molecular weights (100 kDa and 1.63 mDa) of the HAs in the hydrogel networks. The low molecular weight of HA was obtained in advance by treating high molecular weight HA with a hydrogen chloride solution. Methacrylation of HA was obtained by grafting aminopropylmethacrylate to its caroboxylic acid functional groups. While reduction of the HA molecular weights was confirmed by gel permeation chromatography, the degree of methacrylate grafting to the HA was measured by {sup 1}H-nuclear magnetic resonance. Synthesis of the HA-PEO hydrogel was successfully achieved via the Michael-type addition reaction between the methacrylate arm groups in the HA and the six thiol groups in PEO. The hydrogel formation was not dependent upon the HA molecular weights and its gelation behaviors were markedly different. Compared to the properties of the high molecular weight HA-based PEO one, the low molecular weight HA-based hydrogel induced quicker hydrogelation, as observed from the behaviors of the elastic and viscous modulus. Furthermore, the low molecular weight HA-based hydrogel demonstrated stronger mechanical properties as measured with a texture analyzer, lower water absorption as measured with a microbalance and smaller pore sizes on its surface and cross section as observed with scanning electron microscopy. The information about the effects of the cross-linking molecular weights of the gel network on the properties of the HA-based PEO hydrogel may lead to better design of hydrogels, especially in tissue engineering applications.

  8. Effects of cross-linking molecular weights in a hyaluronic acid-poly(ethylene oxide) hydrogel network on its properties

    We examined the effects of cross-linking molecular weights on the properties of a hyaluronic acid (HA)-poly(ethylene oxide) (PEO) hydrogel. Swelling behaviors, mechanical strength and rheological behaviors of the HA-PEO hydrogel were evaluated by employing different cross-linking molecular weights (100 kDa and 1.63 mDa) of the HAs in the hydrogel networks. The low molecular weight of HA was obtained in advance by treating high molecular weight HA with a hydrogen chloride solution. Methacrylation of HA was obtained by grafting aminopropylmethacrylate to its caroboxylic acid functional groups. While reduction of the HA molecular weights was confirmed by gel permeation chromatography, the degree of methacrylate grafting to the HA was measured by 1H-nuclear magnetic resonance. Synthesis of the HA-PEO hydrogel was successfully achieved via the Michael-type addition reaction between the methacrylate arm groups in the HA and the six thiol groups in PEO. The hydrogel formation was not dependent upon the HA molecular weights and its gelation behaviors were markedly different. Compared to the properties of the high molecular weight HA-based PEO one, the low molecular weight HA-based hydrogel induced quicker hydrogelation, as observed from the behaviors of the elastic and viscous modulus. Furthermore, the low molecular weight HA-based hydrogel demonstrated stronger mechanical properties as measured with a texture analyzer, lower water absorption as measured with a microbalance and smaller pore sizes on its surface and cross section as observed with scanning electron microscopy. The information about the effects of the cross-linking molecular weights of the gel network on the properties of the HA-based PEO hydrogel may lead to better design of hydrogels, especially in tissue engineering applications

  9. An equation to estimate the difference between theoretically predicted and SDS PAGE-displayed molecular weights for an acidic peptide

    Yihong Guan; Qinfang Zhu; Delai Huang; Shuyi Zhao; Li Jan Lo; Jinrong Peng

    2015-01-01

    The molecular weight (MW) of a protein can be predicted based on its amino acids (AA) composition. However, in many cases a non-chemically modified protein shows an SDS PAGE-displayed MW larger than its predicted size. Some reports linked this fact to high content of acidic AA in the protein. However, the exact relationship between the acidic AA composition and the SDS PAGE-displayed MW is not established. Zebrafish nucleolar protein Def is composed of 753 AA and shows an SDS PAGE-displayed M...

  10. Interactions of aqueous amino acids and proteins with the (110) surface of ZnS in molecular dynamics simulations

    Nawrocki, Grzegorz; Cieplak, Marek

    2014-01-01

    The growing usage of nanoparticles of zinc sulfide as quantum dots and biosensors calls for a theoretical assessment of interactions of ZnS with biomolecules. We employ the molecular-dynamics-based umbrella sampling method to determine potentials of mean force for 20 single amino acids near the ZnS (110) surface in aqueous solutions. We find that five amino acids do not bind at all and the binding energy of the remaining amino acids does not exceed 4.3 kJ/mol. Such energies are comparable to ...

  11. Bistability in a metabolic network underpins the de novo evolution of colony switching in Pseudomonas fluorescens.

    Jenna Gallie

    2015-03-01

    Full Text Available Phenotype switching is commonly observed in nature. This prevalence has allowed the elucidation of a number of underlying molecular mechanisms. However, little is known about how phenotypic switches arise and function in their early evolutionary stages. The first opportunity to provide empirical insight was delivered by an experiment in which populations of the bacterium Pseudomonas fluorescens SBW25 evolved, de novo, the ability to switch between two colony phenotypes. Here we unravel the molecular mechanism behind colony switching, revealing how a single nucleotide change in a gene enmeshed in central metabolism (carB generates such a striking phenotype. We show that colony switching is underpinned by ON/OFF expression of capsules consisting of a colanic acid-like polymer. We use molecular genetics, biochemical analyses, and experimental evolution to establish that capsule switching results from perturbation of the pyrimidine biosynthetic pathway. Of central importance is a bifurcation point at which uracil triphosphate is partitioned towards either nucleotide metabolism or polymer production. This bifurcation marks a cell-fate decision point whereby cells with relatively high pyrimidine levels favour nucleotide metabolism (capsule OFF, while cells with lower pyrimidine levels divert resources towards polymer biosynthesis (capsule ON. This decision point is present and functional in the wild-type strain. Finally, we present a simple mathematical model demonstrating that the molecular components of the decision point are capable of producing switching. Despite its simple mutational cause, the connection between genotype and phenotype is complex and multidimensional, offering a rare glimpse of how noise in regulatory networks can provide opportunity for evolution.

  12. Use of molecular nuclear methods in communicable diseases: From nucleic acid hybridization to proteomics

    In spite of decades of intensive research on communicable diseases, infection agents still remain a major cause of morbidity and mortality in humans. These rates have driven a major resurgence in biological research efforts for the identification of new targets for vaccine development, drugs and diagnostics assays products. Molecular nuclear techniques focused in nucleic acid hybridization and DNA amplification and more recently proteomic approaches are employed to address questions related to communicable diseases. In nucleic acid hybridization, denatured DNA or RNA is immobilized on an inert support, so that bound sequences are available for hybridization with an added nucleic acid radioactive probe to facilitate analysis. After extensive washing, hybrids are detected by autoradiography or phosphoimager analyzer. Polymerase chain reaction (PCR), is a very sensitive method for nucleic acid amplification used when the targets are scarce in the cells or in clinical material. Differently, the challenge of proteome analysis lies with the task of achieving a combination of high-throughput screening while maintaining high sensitivity for the detection of low copy number proteins. Many different detection technologies have been developed to improve visualization of proteins in protein analysis and radiolabelling is one of the strategies for protein detection. For metabolic experiments, proteins must be labelled with an appropriate radioactive isotope in vivo prior to isolation by electrophoretic analysis. Additionally, protein phosphorylation, an important post-translational modification, is analyzed by using 32P for in vivo labelling of phosphorylated proteins and further identification by mass spectrometry. The major problems which limit proteomic studies deal with the comparative analysis of 2DE gel images. In conventional methodology, the protein samples to be compared are separated independently on different gels. Using a 2DE image analysis software spots are

  13. Molecular analysis of benthic biofilms from acidic coal mine drainage, Pennsylvania, USA

    Mills, D. B.; Jones, D. S.; Burgos, W. D.; Macalady, J. L.

    2010-12-01

    Acid mine drainage (AMD) is a common environmental problem in Pennsylvania that results from the oxidation of sulfide minerals exposed at abandoned coal mines. In these systems, acidophilic microorganisms catalyze the oxidation of ferrous (Fe2+) to ferric iron (Fe3+), which precipitates as iron-hydroxide minerals. To develop and improve low-pH bioremediation strategies, characterization of the microbiology of AMD systems is essential. An acidic (pH 2-4) AMD spring known as ‘Lower Red Eyes’ in Gallitzan State Forest, PA, is fed by anoxic groundwater with ferrous iron concentrations above 550 mg/L. More than half of the total iron is removed after the springwater flows downstream over 80 m of stagnant pools and iron-oxide terraces. We used fluorescence in situ hybridization (FISH) and 16S rDNA cloning to characterize the microbial communities from orange sediments and green benthic biofilms. 16S rDNA sequences were extracted from a green biofilm found in a pH 3.5 pool 10 m downstream of the emergence. Based on chloroplast 16S rDNA sequences and morphological characteristics, we found that Euglena mutabilis was the dominant eukaryotic organism from this location. Euglena mutabilis is a photosynthetic protozoan common in acidic and heavy metal affected environments, and likely contributes to the precipitation of iron oxides through the production of molecular oxygen. Bacterial 16S rDNA sequences were cloned from iron-oxide sediments with orange cauliflower morphology 27 m downstream from the spring emergence. More than 60% of bacterial sequences retrieved from the orange sediment sample are related to the iron-oxidizing Betaproteobacterium Ferrovum myxofaciens. Other bacterial sequences include relatives of iron-oxidizing genera in the Gammaproteobacteria, Betaproteobacteria, and Actinobacteria. FISH analyses show that Betaproteobacteria-dominated communities are associated with Euglena in multiple upstream locations where pH is above 3.0. Using light microscopy

  14. Interfacial Molecular Organization at Aqueous Solution Surfaces of Atmospherically Relevant Dimethyl Sulfoxide and Methanesulfonic Acid Using Sum Frequency Spectroscopy and Molecular Dynamics Simulation

    Chen, X.; Minofar, Babak; Jungwirth, Pavel; Allen, H. C.

    2010-01-01

    Roč. 114, č. 47 (2010), s. 15546-15553. ISSN 1520-6106 R&D Projects: GA MŠk LC512 Grant ostatní: NSF(US) CHE0749807; NSF(US) CHE0909227 Institutional research plan: CEZ:AV0Z40550506; CEZ:AV0Z60870520 Keywords : dimethyl sulfoxide * methanesulfonic acid * molecular dynamics Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 3.603, year: 2010

  15. The gene controlling marijuana psychoactivity: molecular cloning and heterologous expression of Delta1-tetrahydrocannabinolic acid synthase from Cannabis sativa L.

    Sirikantaramas, Supaart; Morimoto, Satoshi; Shoyama, Yoshinari; Ishikawa, Yu; Wada, Yoshiko; Shoyama, Yukihiro; Taura, Futoshi

    2004-09-17

    Delta(1)-tetrahydrocannabinolic acid (THCA) synthase is the enzyme that catalyzes oxidative cyclization of cannabigerolic acid into THCA, the precursor of Delta(1)-tetrahydrocannabinol. We cloned a novel cDNA (GenBank trade mark accession number AB057805) encoding THCA synthase by reverse transcription and polymerase chain reactions from rapidly expanding leaves of Cannabis sativa. This gene consists of a 1635-nucleotide open reading frame, encoding a 545-amino acid polypeptide of which the first 28 amino acid residues constitute the signal peptide. The predicted molecular weight of the 517-amino acid mature polypeptide is 58,597 Da. Interestingly, the deduced amino acid sequence exhibited high homology to berberine bridge enzyme from Eschscholtzia californica, which is involved in alkaloid biosynthesis. The liquid culture of transgenic tobacco hairy roots harboring the cDNA produced THCA upon feeding of cannabigerolic acid, demonstrating unequivocally that this gene encodes an active THCA synthase. Overexpression of the recombinant THCA synthase was achieved using a baculovirus-insect expression system. The purified recombinant enzyme contained covalently attached FAD cofactor at a molar ratio of FAD to protein of 1:1. The mutant enzyme constructed by changing His-114 of the wild-type enzyme to Ala-114 exhibited neither absorption characteristics of flavoproteins nor THCA synthase activity. Thus, we concluded that the FAD binding residue is His-114 and that the THCA synthase reaction is FAD-dependent. This is the first report on molecular characterization of an enzyme specific to cannabinoid biosynthesis. PMID:15190053

  16. Influence of Low Molecular Weight Organic Acids on Transport of Cadmium and Copper Ions across Model Phospholipid Membranes

    Parisová, Martina; Navrátil, Tomáš; Šestáková, Ivana; Jaklová Dytrtová, Jana; Mareček, Vladimír

    2013-01-01

    Roč. 8, č. 1 (2013), s. 27-44. ISSN 1452-3981 R&D Projects: GA AV ČR IAA400400806 Institutional support: RVO:61388963 ; RVO:61388955 Keywords : cadmium * copper * low molecular weight organic acid Subject RIV: CG - Electrochemistry Impact factor: 1.956, year: 2013

  17. Acetic and Acrylic Acid Molecular Imprinted Model Silicone Hydrogel Materials for Ciprofloxacin-HCl Delivery

    Lyndon Jones

    2012-01-01

    Full Text Available Contact lenses, as an alternative drug delivery vehicle for the eye compared to eye drops, are desirable due to potential advantages in dosing regimen, bioavailability and patient tolerance/compliance. The challenge has been to engineer and develop these materials to sustain drug delivery to the eye for a long period of time. In this study, model silicone hydrogel materials were created using a molecular imprinting strategy to deliver the antibiotic ciprofloxacin. Acetic and acrylic acid were used as the functional monomers, to interact with the ciprofloxacin template to efficiently create recognition cavities within the final polymerized material. Synthesized materials were loaded with 9.06 mM, 0.10 mM and 0.025 mM solutions of ciprofloxacin, and the release of ciprofloxacin into an artificial tear solution was monitored over time. The materials were shown to release for periods varying from 3 to 14 days, dependent on the loading solution, functional monomer concentration and functional monomer:template ratio, with materials with greater monomer:template ratio (8:1 and 16:1 imprinted tending to release for longer periods of time. Materials with a lower monomer:template ratio (4:1 imprinted tended to release comparatively greater amounts of ciprofloxacin into solution, but the release was somewhat shorter. The total amount of drug released from the imprinted materials was sufficient to reach levels relevant to inhibit the growth of common ocular isolates of bacteria. This work is one of the first to demonstrate the feasibility of molecular imprinting in model silicone hydrogel-type materials.

  18. Molecular dynamics in conducting polyaniline protonated by camphor sulfonic acid as seen by quasielastic neutron scattering

    Using incoherent quasielastic neutron scattering techniques, the molecular motions were investigated in fully hydrogenated and partially deuterated polyaniline protonated by camphor sulfonic acid (CSA) conducting samples. The obtained results show that on the 10-9-10-12 s time scale the polymer chains do not exhibit any diffusive motions: the whole observed quasielastic scattering has accordingly to be attributed to motions of CSA ions. From our measurements two molecular movements could be differentiated. A rapid one has been attributed to the three-site rotation of methyl groups present on camphor moieties of CSA and a slower one that has been modeled as a rigid body motion of the whole CSA molecule. Due to the disordered character of the system, the methyl rotors appeared to be dynamically nonequivalent. Their dynamics was then described in terms of a log gaussian distribution of correlation times. This description allowed a good fitting of experimental data and gave an activation energy of 12.5 kJ mol-1. However, two different regimes in temperature could be distinguished. At high temperatures (T>280 K) the width of the distribution is nearly zero and thus, the methyl rotors are dynamically equivalent while it turned larger and larger when temperature is decreased below 250 K revealing that the rotors are more and more sensitive to their local environment. In the conducting samples the slowest motion clearly exists in the 280-330 K temperature range and is blocked at temperatures inferior to 250 K. This transition occurs in the temperature range in which the metal-insulator transition also happens

  19. Immunoregulatory Effects Triggered by Lactic Acid Bacteria Exopolysaccharides: New Insights into Molecular Interactions with Host Cells

    Jonathan Laiño

    2016-08-01

    Full Text Available Researchers have demonstrated that lactic acid bacteria (LAB with immunomodulatory capabilities (immunobiotics exert their beneficial effects through several molecules, including cell wall, peptidoglycan, and exopolysaccharides (EPS, that are able to interact with specific host cell receptors. EPS from LAB show a wide heterogeneity in its composition, meaning that biological properties depend on the strain and. therefore, only a part of the mechanism of action has been elucidated for these molecules. In this review, we summarize the current knowledge of the health-promoting actions of EPS from LAB with special focus on their immunoregulatory actions. In addition, we describe our studies using porcine intestinal epithelial cells (PIE cells as a model to evaluate the molecular interactions of EPS from two immunobiotic LAB strains and the host cells. Our studies showed that EPS from immunobiotic LAB have anti-inflammatory capacities in PIE cells since they are able to reduce the production of inflammatory cytokines in cells challenged with the Toll-like receptor (TLR-4-agonist lipopolysaccharide. The effects of EPS were dependent on TLR2, TLR4, and negative regulators of TLR signaling. We also reported that the radioprotective 105 (RP105/MD1 complex, a member of the TLR family, is partially involved in the immunoregulatory effects of the EPS from LAB. Our work described, for the first time, that LAB and their EPS reduce inflammation in intestinal epithelial cells in a RP105/MD1-dependent manner. A continuing challenge for the future is to reveal more effector-receptor relationships in immunobiotic-host interactions that contribute to the beneficial effects of these bacteria on mucosal immune homeostasis. A detailed molecular understanding should lead to a more rational use of immunobiotics in general, and their EPS in particular, as efficient prevention and therapies for specific immune-related disorders in humans and animals.

  20. Preparation of molecularly imprinted polymers based on magnetic nanoparticles for the selective extraction of protocatechuic acid from plant extracts.

    Xie, Xiaoyu; Wei, Fen; Chen, Liang; Wang, Sicen

    2015-03-01

    In this study, highly selective core-shell molecularly imprinted polymers on the surface of magnetic nanoparticles were prepared using protocatechuic acid as the template molecule. The resulting magnetic molecularly imprinted polymers were characterized by transmission electron microscopy, Fourier transform infrared spectroscopy, X-ray diffraction, and vibrating sample magnetometry. The binding performances of the prepared materials were evaluated by static and selective adsorption. The binding isotherms were obtained for protocatechuic acid and fitted by the Langmuir isotherm model and Freundlich isotherm model. Furthermore, the resulting materials were used as the solid-phase extraction materials coupled to high-performance liquid chromatography for the selective extraction and detection of protocatechuic acid from the extracts of Homalomena occulta and Cynomorium songaricum with the recoveries in the range 86.3-102.2%. PMID:25641806

  1. Ion complex membranes of acrylonitrile copolymers having methacrylic acid and amphiphilic quaternized ammonium groups for uracil molecular imprinting

    Copolymers having methacrylic acid and amphiphilic quaternized ammonium groups were used for preparation of molecular imprinting membrane of uracil (URA) template. The imprinted polymeric membranes were prepared by phase inversion molecular imprinting by using poly(acrylonitrile-co-methylacrylic acid) [P(AN-co-MAA)] and poly(acrylonitrile-co-vinylbenzyl-stearyldimethylamine chloride) [P(AN-co-SMA)]. Evidence confirmed that both copolymers were mixed to form ion complex by electrostatic interaction between the methacrylic acid and the quaternized ammonium groups. The electrostatic networks of the resultant membranes made the membrane dense and useful for molecule recognition of the template. The imprinted membranes made of different mole ratio of their copolymer segments were examined in binding of URA and other analog molecules

  2. Inhibitors of the Cdc34 acidic loop: A computational investigation integrating molecular dynamics, virtual screening and docking approaches

    Alberto Arrigoni

    2014-01-01

    Here, we carried out a computational study based on molecular dynamics, virtual screening and docking to identify potential inhibitory compounds of Cdc34, modulating the acidic loop conformation. The molecules identified in this study have been designed to act as molecular hinges that can bind the acidic loop in its closed conformation, thus inhibiting the Cdc34-mediated ubiquitination cascade at the ubiquitin-charging step. In particular, we proposed a pharmacophore model featuring two amino groups in the central part of the model and two lateral aromatic chains, which respectively establish electrostatic interactions with the acidic loop (Asp 108 and Glu 109 and a hydrogen bond with Ser 139, which is one of the key residues for Cdc34 activity.

  3. A novel cyanide-selective colorimetric and fluorescent chemosensor: First molecular security keypad lock based on phosphotungstic acid and CN− inputs

    Highlights: • Our probe is commercially available with good photo stability and high quantum yield. • Both color and fluorescence change with long emission wavelength in aqueous media. • Characteristics of an ON–OFF–ON fluorescence switch. • The simple receptor for CN- detection with low detection limit (≪WHO). • Mimic the function of a security keypad lock on sequential addition of PTA and CN−. -- Abstract: Rhodamine B (RhB) an available dye has been developed as novel and efficient colorimetric and fluorometric chemosensor for cyanide ions in an absolutely aqueous media. The UV–vis absorption and fluorescent emission titrations experiments have been employed to study the sensing process. RhB could act as an efficient “ON–OFF” fluorescent response for phosphotungstic acid (H3PW12O40 or PTA) based on an ion associate process. Also (RhB+)3·PTA3− could operate as an “OFF–ON” fluorescent sensor for cyanide anions based on a ligand substitution process. It has been identified as highly sensitive probe for CN− which responds at 0.3 and 0.04 μmol L−1 concentration levels by absorption and fluorescent method respectively. Depending upon the sequence of addition of PTA and CN− ions into the solution, RhB could be as a molecular security keypad lock with PTA and CN− inputs. The ionic inputs to new fluorophore have been mimicked as a superimposed electronic molecular keypad lock. The results were compared successfully (>96%) with the data of a spectrophotometry approved method (EPA 9014-1) for cyanide ions

  4. Molecular evidence for an involvement of organic anion transporters (OATs) in aristolochic acid nephropathy

    Aristolochic acid (AA), present in Aristolochia species, is the major causative agent in the development of severe renal failure and urothelial cancers in patients with AA nephropathy. It may also be a cause of Balkan endemic nephropathy. Epithelial cells of the proximal tubule are the primary cellular target of AA. To study whether organic anion transporters (OATs) expressed in proximal tubule cells are involved in uptake of AA, we used human epithelial kidney (HEK293) cells stably expressing human (h) OAT1, OAT3 or OAT4. AA potently inhibited the uptake of characteristic substrates, p-aminohippurate for hOAT1 and estrone sulfate for hOAT3 and hOAT4. Aristolochic acid I (AAI), the more cytotoxic and genotoxic AA congener, exhibited high affinity for hOAT1 (Ki = 0.6 μM) as well as hOAT3 (Ki = 0.5 μM), and lower affinity for hOAT4 (Ki = 20.6 μM). Subsequently, AAI-DNA adduct formation (investigated by 32P-postlabelling) was used as a measure of AAI uptake. Significantly higher levels of adducts occurred in hOAT-expressing cells than in control cells: this effect was abolished in the presence of the OAT inhibitor probenecid. In Xenopus laevis oocytes hOAT-mediated efflux of p-aminohippurate was trans-stimulated by extracellular AA, providing further molecular evidence for AA translocation by hOATs. Our study indicates that OATs can mediate the uptake of AA into proximal tubule cells and thereby participate in kidney cell damage by this toxin.

  5. Molecular evidence for an involvement of organic anion transporters (OATs) in aristolochic acid nephropathy.

    Bakhiya, Nadiya; Arlt, Volker M; Bahn, Andrew; Burckhardt, Gerhard; Phillips, David H; Glatt, Hansruedi

    2009-10-01

    Aristolochic acid (AA), present in Aristolochia species, is the major causative agent in the development of severe renal failure and urothelial cancers in patients with AA nephropathy. It may also be a cause of Balkan endemic nephropathy. Epithelial cells of the proximal tubule are the primary cellular target of AA. To study whether organic anion transporters (OATs) expressed in proximal tubule cells are involved in uptake of AA, we used human epithelial kidney (HEK293) cells stably expressing human (h) OAT1, OAT3 or OAT4. AA potently inhibited the uptake of characteristic substrates, p-aminohippurate for hOAT1 and estrone sulfate for hOAT3 and hOAT4. Aristolochic acid I (AAI), the more cytotoxic and genotoxic AA congener, exhibited high affinity for hOAT1 (K(i)=0.6 microM) as well as hOAT3 (K(i)=0.5 microM), and lower affinity for hOAT4 (K(i)=20.6 microM). Subsequently, AAI-DNA adduct formation (investigated by (32)P-postlabelling) was used as a measure of AAI uptake. Significantly higher levels of adducts occurred in hOAT-expressing cells than in control cells: this effect was abolished in the presence of the OAT inhibitor probenecid. In Xenopus laevis oocytes hOAT-mediated efflux of p-aminohippurate was trans-stimulated by extracellular AA, providing further molecular evidence for AA translocation by hOATs. Our study indicates that OATs can mediate the uptake of AA into proximal tubule cells and thereby participate in kidney cell damage by this toxin. PMID:19643159

  6. Molecular dynamics simulations of deoxyribonucleic acids and repair enzyme T4 endonuclease V

    This report describes the results of molecular dynamics (MD) simulation of deoxyribonucleic acids (DNA) and specific repair enzyme T4 endonuclease V. Namely research described here is focused on the examination of specific recognition process, in which this repair enzyme recognizes the damaged site on the DNA molecule-thymine dimer (TD). TD is frequent DNA damage induced by UV radiation in sun light and unless properly repaired it may be mutagenic or lethal for cell, and is also considered among the major causes of skin cancer. T4 endonuclease V is a DNA specific repair enzyme from bacteriophage T4 that catalyzes the first reaction step of TD repair pathway. MD simulations of three molecules - native DNA dodecamer (12 base pairs), DNA of the same sequence of nucleotides as native one but with TD, and repair enzyme T4 endonuclease V - were performed for 1 ns individually for each molecule. Simulations were analyzed to determine the role of electrostatic interaction in the recognition process. It is found that electrostatic energies calculated for amino acids of the enzyme have positive values of around +15 kcal/mol. The electrostatic energy of TD site has negative value of approximately -9 kcal/mol, different from the nearly neutral value of the respective thymines site of the native DNA. The electrostatic interaction of TD site with surrounding water environment differs from the electrostatic interaction of other nucleotides. Differences found between TD site and respective thymines site of native DNA indicate that the electrostatic energy is an important factor contributing to proper recognition of TD site during scanning process in which enzyme scans the DNA. In addition to the electrostatic energy, the important factor in recognition process might be structural complementarity of enzyme and bent DNA with TD. There is significant kink formed around TD site, that is not observed in native DNA. (author)

  7. Molecular Simulation of Oxygen Sorption and Diffusion in the Poly (lactic acid)

    SUN Delin; ZHOU Jian

    2013-01-01

    Grand canonical Monte Carlo and molecular dynamics simulation methods are used to simulate oxygen sorption and diffusion in amorphous poly(lactic acid) (PLA).The simulated solubility coefficient of oxygen is close to experimental data obtained from the quartz crystal microbalance but much higher than those from the time-lag method.This discrepancy is explained by using the dual-mode sorption model.It is found that oxygen sorption in PLA is predominantly Langmuir type controlled,i.e.,through the process of filling holes.The time-lag method only takes into account oxygen molecules that participate the diffusion process whereas a large proportion of oxygen molecules trapped in the void have little chance to execute hopping due to the glassy nature of PLA at room temperature.The simulated diffusion coefficient of oxygen is reasonably close to the data obtained from the time-lag method.The solubility coefficient of oxygen decreases linearly with increasing relative humidity while its diffusion coefficient firstly decreases and then increases as a function of relative humidity.

  8. Molecularly imprinted photo-sensitive polyglutamic acid nanoparticles for electrochemical sensing of hemoglobin

    A voltammetric sensor for hemoglobin (Hb) was prepared from molecularly imprinted polymer nanoparticles (MINPs) via electrophoretic deposition. A photo-sensitive copolymer composed of poly-γ-glutamic grafted with the fluorophore 7-amino-4-methylcoumarin was converted into nanoparticles that were imprinted with Hb. The resultant MINPs were then placed on a glassy carbon electrode (GCE) via electrophoretic deposition. Subsequent photo-crosslinking locks the recognition sites. The template was removed by extraction with a mixture of acetic acid and methanol at a ratio of 1:9 (v:v) to obtain a voltammetric sensor for Hb. The current response of the sensor at a working voltage of −260 mV is linearly related to the concentration of Hb in the range from 5 to 100 μg mL−1, and recoveries range from 98.7 to 102.3 %. Compared to the respective non-imprinted nanoparticles, the sensor displays high recognition capability and affinity for Hb. (author)

  9. High-capacity magnetic hollow porous molecularly imprinted polymers for specific extraction of protocatechuic acid.

    Li, Hui; Hu, Xin; Zhang, Yuping; Shi, Shuyun; Jiang, Xinyu; Chen, Xiaoqin

    2015-07-24

    Magnetic hollow porous molecularly imprinted polymers (HPMIPs) with high binding capacity, fast mass transfer, and easy magnetic separation have been fabricated for the first time. In this method, HPMIPs was firstly synthesized using protocatechuic acid (PCA) as template, 4-vinylpyridine (4-VP) as functional monomer, glycidilmethacrylate (GMA) as co-monomer, and MCM-48 as sacrificial support. After that, epoxide ring of GMA was opened for chemisorbing Fe3O4 nanoparticles to prepare magnetic HPMIPs. The results of characterization indicated that magnetic HPMIPs exhibited large surface area (548m(2)/g) with hollow porous structure and magnetic sensitivity (magnetic saturation at 2.9emu/g). The following adsorption characteristics investigation exhibited surprisingly higher adsorption capacity (37.7mg/g), and faster kinetic binding (25min) than any previously reported PCA imprinted MIPs by traditional or surface imprinting technology. The equilibrium data fitted well to Langmuir equation and the adsorption process could be described by pseudo-second order model. The selective recognition experiments also demonstrated the high selectivity of magnetic HPMIPs towards PCA over analogues. The results of the real sample analysis confirmed the superiority of the proposed magnetic HPMIPs for selective and efficient enrichment of trace PCA from complex matrices. PMID:26044378

  10. Molecularly imprinted polyaniline-polyvinyl sulphonic acid composite based sensor for para-nitrophenol detection

    Graphical abstract: -- Highlights: •Biomimetic para-nitrophenol (PNP) imprinted sensor is used to detect PNP. •The PVSA doped polyaniline shows high conductivity. •The sensor shows excellent sensitivity, 18 times reusability and higher stability. •PANI-PVSA composite shows increased stability of the sensor. -- Abstract: We report results of the studies relating to the fabrication and characterization of a conducting polymer based molecularly imprinted para-nitrophenol (PNP) sensor. A water pollutant, para-nitrophenol is electrochemically imprinted with polyvinyl sulphonic acid (PVSA) doped polyaniline onto indium tin oxide (ITO) glass substrate. This PNP imprinted electrode (PNPI-PANI-PVSA/ITO) prepared via chronopotentiometric polymerization and over-oxidation is characterized by Fourier transform infra-red spectroscopy (FT-IR), UV–visible (UV–vis) spectroscopy, contact angle (CA), scanning electron microscopy (SEM), cyclic voltammetry (CV) and differential pulse voltammetry (DPV) studies. The response studies of PNPI-PANI-PVSA/ITO electrode carried out using DPV reveal a lower detection limit of 1 × 10−3 mM, improved sensitivity as 1.5 × 10−3 A mM−1 and stability of 45 days. The PNPI-PANI-PVSA/ITO electrode shows good precision with relative standard deviation of 2.1% and good reproducibility with standard deviation of 3.78%

  11. Molecularly imprinted polymer for 2, 4-dichlorophenoxyacetic acid prepared by a sol-gel method

    Yanli Sun

    2014-07-01

    Based on a sol-gel procedure, a molecularly imprinted polymer (MIP) for 2, 4-dichlorophenoxyacetic acid (2, 4-D) was synthesized, using phenyltrimethoxysilane (PTMOS), aminopropyltriethoxysilane (APTES) as monomers and tetraethoxysilane (TEOS) as cross-linking agent. In addition to the amount of the template, some factors in the sol-gel process: TEOS/APTES/PTMOS molar ratio, H2O/Si molar ratio, CH3CH2OH/Si molar ratio, etc. were investigated in detail. Results show that the optimum conditions for the preparation of the MIPs were 20:1.5:1 (TEOS: APTES: PTMOS), ca. 4 (H2O/Si), ca. 4 (CH3CH2OH/Si), respectively. Effects of various parameters involved in the adsorption process of 2, 4-D on MIP such as incubation time, pH, etc. were also evaluated. It is found that the adsorption attained equilibrium within 3 h, the optimum pH for adsorption was about 7 and the adsorption obeyed Langmuir model. Test results also demonstrated that the present MIP for 2, 4-D had large adsorption capacity (the maximum adsorption concluded from Langmuir model reached 243.3 mg/g) and good selectivity.

  12. In situ injection of phenylboronic acid based low molecular weight gels for efficient chemotherapy.

    Gao, Wenxia; Liang, Yan; Peng, Xinyu; Hu, Yalong; Zhang, Longgui; Wu, Huayue; He, Bin

    2016-10-01

    Injectable low molecular weight gels (LMWGs) based on the derivatives of phenylboronic acid were prepared and used as substrates for efficient in situ chemotherapy. The gelators as well as LMWGs were characterized by (1)H NMR, UV-vis, FTIR, MS and SEM. Anticancer drug doxorubicin hydrochloride (DOX) was encapsulated in the gels. The rheological properties and rapid recovery capability of both blank and drug-loaded gels were tested. The LMWGs were non-toxic to both 3T3 fibroblasts and 4T1 breast cancer cells. The gels were formed rapidly after injected in vivo. The in vivo anticancer activities of DOX-loaded LMWGs were investigated in breast cancer bearing mice. The intratumoral injection of DOX loaded LMWGs with dose of 30 mg/kg revealed that the gels could coat around the tumor tissues to release DOX sustainingly and maintain effective DOX concentration for chemotherapy. The systemic toxicity of DOX was reduced significantly with the in situ administration of LMWGs formulations. The injectable LMWGs exhibited excellent therapeutic efficacy and low side effects in local chemotherapy. PMID:27497056

  13. Ancient low-molecular-weight organic acids in permafrost fuel rapid carbon dioxide production upon thaw.

    Drake, Travis W; Wickland, Kimberly P; Spencer, Robert G M; McKnight, Diane M; Striegl, Robert G

    2015-11-10

    Northern permafrost soils store a vast reservoir of carbon, nearly twice that of the present atmosphere. Current and projected climate warming threatens widespread thaw of these frozen, organic carbon (OC)-rich soils. Upon thaw, mobilized permafrost OC in dissolved and particulate forms can enter streams and rivers, which are important processors of OC and conduits for carbon dioxide (CO2) to the atmosphere. Here, we demonstrate that ancient dissolved organic carbon (DOC) leached from 35,800 y B.P. permafrost soils is rapidly mineralized to CO2. During 200-h experiments in a novel high-temporal-resolution bioreactor, DOC concentration decreased by an average of 53%, fueling a more than sevenfold increase in dissolved inorganic carbon (DIC) concentration. Eighty-seven percent of the DOC loss to microbial uptake was derived from the low-molecular-weight (LMW) organic acids acetate and butyrate. To our knowledge, our study is the first to directly quantify high CO2 production rates from permafrost-derived LMW DOC mineralization. The observed DOC loss rates are among the highest reported for permafrost carbon and demonstrate the potential importance of LMW DOC in driving the rapid metabolism of Pleistocene-age permafrost carbon upon thaw and the outgassing of CO2 to the atmosphere by soils and nearby inland waters. PMID:26504243

  14. Properties and catalytic activity of magnetic and acidic ionic liquids: experimental and molecular simulation.

    Zhou, Cunshan; Yu, Xiaojie; Ma, Haile; Huang, Xingyi; Zhang, Henan; Jin, Jian

    2014-05-25

    The exploitation of dual functional magnetic and acidic ionic liquids (MAILs) for hydrolysis of cellulose to platform chemicals can solve some practical challenges through easy separation of products and efficient catalyst recyclability. In this work, seven Cnmim/FeCl4 MAILs were synthesized and investigated with combined experimental and molecular dynamics. The MAILs contained FeCl4(-) anions and exhibited a typical hard magnetic materials behavior with rather strong magnetic susceptibilities. These MAILs were stable up to 250-310°C, the decomposition was started up at 250/310-480-810°C in two steps with the formation of the undecomposed residue. The Gibbs energy for the reaction of glucose/xylose conversion to 5-hydroxymethylfurfural by metal chlorides in the CnmimCl ionic liquid was studied using the density functional theory calculations and the results that C3mim/WCl3 may be the most hopeful catalyst. The MAILs have the potential to open up promising new catalytic systems because of their easy product separation and efficient catalyst recyclability. PMID:24708984

  15. Spectroscopic studies on the molecular interaction between salicylic acid and riboflavin (B2) in micellar solution

    The interaction between salicylic acid (SA) and riboflavin (RF) was studied by Fluorescence Resonance Energy Transfer (FRET) in micellar solution. The riboflavin strongly quenches the intrinsic fluorescence of SA by radiative energy transfer. The extent of energy transfer in sodium dodecyl sulphate (SDS) micellar solution of different concentration is quantified from the energy transfer efficiency data. It is seen that the energy transfer is more efficient in the micellar solution. The critical energy transfer distance (R0) was determined from which the mean distance between SA and RF molecules was calculated. The quenching was found to fit into Stern-Volmer relation. The results on variation of Stern-Volmer constant (Ksv) with quencher concentration obtained at different temperatures suggested the formation of complex between SA and RF. The association constant of complex formation was estimated and found to decrease with temperature. The values of thermodynamic parameters ΔH, ΔG and ΔS at different temperatures were estimated and the results indicated that the molecular interaction between SA and RF is electrostatic in nature.

  16. Deep Eutectic Solvents Modified Molecular Imprinted Polymers for Optimized Purification of Chlorogenic Acid from Honeysuckle.

    Li, Guizhen; Wang, Wei; Wang, Qian; Zhu, Tao

    2016-02-01

    Deep eutectic solvents (DES) were synthesized with choline chloride (ChCl), and DES modified molecular imprinted polymers (DES-MIPs), DES modified non-imprinted polymers (DES-NIPs, without template), MIPs and NIPs were prepared in an identical procedure. Fourier transform infrared spectrometer (FT-IR) and field emission scanning electron microscopy (FE-SEM) were used to characterize the obtained polymers. Rebinding experiment and solid-phase extraction (SPE) were used to prove the high selectivity adsorption properties of the polymers. Box-Behnken design (BBD) with three factors was used to optimize the extraction condition of chlorogenic acid (CA) from honeysuckles. The optimum extraction conditions were found to be ultrasonic time optimized (20 min), the volume fraction of ethanol (60%) and ratio of liquid to material (15 mL g(-1)). Under these conditions, the mean extraction yield of CA was 12.57 mg g(-1), which was in good agreement with the predicted BBD model value. Purification of hawthorn extract was achieved by SPE process, and SPE recoveries of CA were 72.56, 64.79, 69.34 and 60.08% by DES-MIPs, DES-NIPs, MIPs and NIPs, respectively. The results showed DES-MIPs had potential for promising functional adsorption material for the purification of bioactive compounds. PMID:26347506

  17. Influences of Bronsted Acidic Sites in H[Al] ZSM-5 on Polarization and Electronegativity of Ethene Studied by Molecular Dynamics

    FAN,Jian-Fen(樊建芬); XIAO,He-Ming(肖鹤鸣); van de GRAAF,B; WANG,Qiu-Xia(王秋霞); NJO,S.L; XIA,Qi-Ying(夏其英)

    2002-01-01

    Molecular dynamics simulation has been performed for studying the polarization and electronegativity of ethene molecules near Bronsted acidic sites in H[Al]ZSM-5. The result shows that the molecules are polarized most at the edges of intersections and least at the segments of channels. On the contrary, the highest global molecular electronegativity is fotund at the centers of channel segments. Al substitution slightly increases the molecular dipole moment, but hardly affects the molecular electronegativity. Bronsted acidic proton decreases the dipole moment of guest molecule, but increases the molecular electronegativity.

  18. Molecular Electronics

    Heath, James R.

    2009-01-01

    Molecular electronics describes the field in which molecules are utilized as the active (switching, sensing, etc.) or passive (current rectifiers, surface passivants) elements in electronic devices. This review focuses on experimental aspects of molecular electronics that researchers have elucidated over the past decade or so and that relate to the fabrication of molecular electronic devices in which the molecular components are readily distinguished within the electronic properties of the de...

  19. Stereocomplexation of low molecular weight poly(L-lactic acid) and high molecular weight poly(D-lactic acid), radiation crosslinking PLLA/PDLA stereocomplexes and their characterization

    Quynh, Tran Minh; Mai, Hoang Hoa; Lan, Pham Ngoc

    2013-02-01

    Poly(L-lactic acid)s (PLLAx) were synthesized from L-lactic acid by polycondensation. Different stereocomplexes were also obtained with equimolar mixtures of synthesized PLLAx and a commercial PDLA. The stereocomplexes were crosslinked with triallyl isocyanurate (TAIC) by gamma irradiation. Crosslinking density increased with radiation doses, the heavier the crosslinking network, the lower its swelling degree. The crosslinking structures were introduced in the stereocomplexes inhibiting the mobility for crystallization of PLLA molecules. Thermal and mechanical properties of PLA stereocomplexes were remarkably enhanced by radiation induced crosslinking. PLA stereocomplex does not seem to be degraded by PLLA degrading microorganisms existing in compost at room temperature, but the synthesized PLLA was significantly degraded.

  20. Complex Formation of Selected Radionuclides with Ligands Commonly Found in Ground Water: Low Molecular Organic Acids

    Jensen, Bror Skytte; Jensen, H.

    1985-01-01

    A general approach to the analysis of potentiometric data on complex formation between cations and polybasic amphoteric acids is described. The method is used for the characterisation of complex formation between Cs+, Sr2+, Co2+, La 3+, and Eu3+ with a α-hydroxy acids, tartaric acid and citric acid......, and with the α-amino acids, aspartic acid and L-cysteine. The cations have been chosen as typical components of reactor waste, and the acids because they are often found as products of microbial activity in pits or wherever organic material decays...

  1. Nanoelectromechanical contact switches

    Loh, Owen Y.; Espinosa, Horacio D.

    2012-05-01

    Nanoelectromechanical (NEM) switches are similar to conventional semiconductor switches in that they can be used as relays, transistors, logic devices and sensors. However, the operating principles of NEM switches and semiconductor switches are fundamentally different. These differences give NEM switches an advantage over semiconductor switches in some applications -- for example, NEM switches perform much better in extreme environments -- but semiconductor switches benefit from a much superior manufacturing infrastructure. Here we review the potential of NEM-switch technologies to complement or selectively replace conventional complementary metal-oxide semiconductor technology, and identify the challenges involved in the large-scale manufacture of a representative set of NEM-based devices.

  2. Selective Removal of Perfluorooctanoic Acid Using Molecularly Imprinted Polymer-Modified TiO2 Nanotube Arrays

    Yunbo Wu; Yi Li; Aijun Tian; Kai Mao; Jian Liu

    2016-01-01

    Perfluorinated chemicals have attracted worldwide concern owing to their wide occurrence and resistance to most conventional treatment processes. In this work, a novel photocatalyst was fabricated by modifying TiO2 nanotube arrays with molecularly imprinted polymers. The molecularly imprinted polymer-modified TiO2 nanotubes (MIP-TiO2 NTs) were characterized and tested for the selective removal of perfluorooctanoic acid (PFOA) from water. The amount of PFOA adsorbed by the MIP-TiO2 NTs was as ...

  3. Estimation of minimum electron dose necessary to resolve molecular structure of deoxyribonucleic acid by phase transmission electron microscopy

    The minimum electron dose that is necessary to resolve the molecular structure of deoxyribonucleic acid (DNA) was estimated based on experimental measurements of information limits and simulated DNA images, considering conditions of a low electron dose. From these results, a dose of ∼400 e/A2 was found to be necessary to achieve observation of DNA on a molecular scale under the present experimental setup. A DNA molecule was observed by a phase reconstruction method using through-focus images under the limited electron dose. In the reconstructed images, the helical structure and the intervals of the base pairs of DNA were partially resolved

  4. Lipoteichoic acid is an important microbe-associated molecular pattern of Lactobacillus rhamnosus GG

    Claes Ingmar JJ

    2012-12-01

    Full Text Available Abstract Background Probiotic bacteria are increasingly used as immunomodulatory agents. Yet detailed molecular knowledge on the immunomodulatory molecules of these bacteria is lagging behind. Lipoteichoic acid (LTA is considered a major microbe-associated molecular pattern (MAMP of Gram-positive bacteria. However, many details and quantitative data on its immune signalling capacity are still unknown, especially in beneficial bacteria. Recently, we have demonstrated that a dltD mutant of the model probiotic Lactobacillus rhamnosus GG (LGG, having modified LTA molecules, has an enhanced probiotic efficacy in a DSS-induced colitis model as compared to wild-type. Results In this study, the importance of D-alanylated and acylated LTA for the pro-inflammatory activity of LGG was studied in vitro. Purified native LTA of LGG wild-type exhibited a concentration-dependent activation of NF-κB signalling in HEK293T cells after interaction with TLR2/6, but not with TLR2 alone. Chemical deacylation of LTA interfered with the TLR2/6 interaction, while a moderate effect was observed with chemical dealanylation. Similarly, the dltD mutant of LGG exhibited a significantly reduced capacity to activate TLR2/6-dependent NF-κB signalling in a HEK293T reporter cell line compared to wild-type. In addition, the dltD mutant of LGG showed a reduced induction of mRNA of the chemokine IL-8 in the Caco-2 epithelial cell line compared to wild-type. Experiments with highly purified LTA of LGG confirmed that LTA is a crucial factor for IL-8 mRNA induction in Caco-2 epithelial cells. Chemical dealanylation and deacylation reduced IL-8 mRNA expression. Conclusions Taken together, our results indicate that LTA of LGG is a crucial MAMP with pro-inflammatory activities such as IL-8 induction in intestinal epithelial cells and NF-κB induction in HEK293T cells via TLR2/6 interaction. The lipid chains of LGG LTA are needed for these activities, while also the D-alanine substituents

  5. Molecular mechanism of acid-catalyzed hydrolysis of peptide bonds using a model compound.

    Pan, Bin; Ricci, Margaret S; Trout, Bernhardt L

    2010-04-01

    The stability of peptide bonds is a critical aspect of biological chemistry and therapeutic protein applications. Recent studies found elevated nonenzymatic hydrolysis in the hinge region of antibody molecules, but no mechanism was identified. As a first step in providing a mechanistic interpretation, this computational study examines the rate-determining step of the hydrolytic reaction of a peptide bond under acidic pH by a path sampling technique using a model compound N-MAA. Most previous computational studies did not include explicit water molecules, whose effects are significant in solution chemistry, nor did they provide a dynamic picture for the reaction process in aqueous conditions. Because no single trajectory can be used to describe the reaction dynamics due to fluctuations at finite temperatures, a variant version of the transition path sampling technique, the aimless shooting algorithm, was used to sample dynamic trajectories and to generate an ensemble of transition trajectories according to their statistical weights in the trajectory space. Each trajectory was computed as the time evolution of the molecular system using the Car-Parrinello molecular dynamics technique. The likelihood maximization procedure and its modification were used in extracting dynamically relevant degrees of freedom in the system, and approximations of the reaction coordinate were compared. Its low log-likelihood score and poor p(B) histogram indicate that the C-O distance previously assumed as the reaction coordinate for the rate-determining step is inadequate in describing the dynamics of the reaction. More than one order parameter in a candidate set including millions of geometric quantities was required to produce a convergent reaction coordinate model; its involvement of many degrees of freedom suggests that this hydrolytic reaction step is very complex. In addition to affecting atoms directly involved in bond-making and -breaking processes, the water network also has

  6. Molecular Imprinting Fibrous Membranes of Poly(acrylonitrile-co-acrylic acid) Prepared by Electrospinning

    2006-01-01

    @@ Introduction Over the past few decades, molecular imprinting has been described as a technology for preparing "molecular doors" which can be matched to "template keys". It has been found to be a simple and effective approach to introduce specific recognition sites into synthetic polymers, namely, to create molecular imprinting polymers[1-4]. Remarkable features such as stability,ease of preparation and low cost, have made molecular imprinting polymers particularly attractive in chemical sensors, catalysis, drug delivery, and dedicated separations.

  7. Stable carbon isotopic compositions of low-molecular-weight dicarboxylic acids, oxocarboxylic acids, α-dicarbonyls, and fatty acids: Implications for atmospheric processing of organic aerosols

    Zhang, Yan-Lin; Kawamura, Kimitaka; Cao, Fang; Lee, Meehye

    2016-04-01

    Stable carbon isotopic compositions (δ13C) were measured for 23 individual organic species including 9 dicarboxylic acids, 7 oxocarboxylic acids, 1 tricarboxylic acid, 2 α-dicarbonyls, and 4 fatty acids in the aerosols from Gosan background site in East Asia. δ13C values of particle phase glyoxal and methylglyoxal are significantly larger than those previously reported for isoprene and other precursors. The values are consistently less negative in oxalic acid (C2, average -14.1‰), glyoxylic acid (-13.8‰), pyruvic acid (-19.4‰), glyoxal (-13.5‰), and methylglyoxal (-18.6‰) compared to other organic species (e.g., palmitic acid, -26.3‰), which can be explained by the kinetic isotope effects during atmospheric oxidation of pre-aged precursors (e.g., isoprene) and the subsequent gas-particle partitioning after the evaporation of clouds or wet aerosols. The δ13C values of C2 is positively correlated with C2 to organic carbon ratio, indicating that photochemical production of C2 is more pronounced than its degradation during long-range atmospheric transport. The isotopic results also suggest that aqueous phase oxidation of glyoxal and methylglyoxal is a major formation process of oxalic acid via the intermediates such as glyoxylic acid and pyruvic acid. This study provides evidence that organic aerosols are intensively photochemically aged in the western North Pacific rim.

  8. An equation to estimate the difference between theoretically predicted and SDS PAGE-displayed molecular weights for an acidic peptide.

    Guan, Yihong; Zhu, Qinfang; Huang, Delai; Zhao, Shuyi; Jan Lo, Li; Peng, Jinrong

    2015-01-01

    The molecular weight (MW) of a protein can be predicted based on its amino acids (AA) composition. However, in many cases a non-chemically modified protein shows an SDS PAGE-displayed MW larger than its predicted size. Some reports linked this fact to high content of acidic AA in the protein. However, the exact relationship between the acidic AA composition and the SDS PAGE-displayed MW is not established. Zebrafish nucleolar protein Def is composed of 753 AA and shows an SDS PAGE-displayed MW approximately 13 kDa larger than its predicted MW. The first 188 AA in Def is defined by a glutamate-rich region containing ~35.6% of acidic AA. In this report, we analyzed the relationship between the SDS PAGE-displayed MW of thirteen peptides derived from Def and the AA composition in each peptide. We found that the difference between the predicted and SDS PAGE-displayed MW showed a linear correlation with the percentage of acidic AA that fits the equation y = 276.5x - 31.33 (x represents the percentage of acidic AA, 11.4% ≤ x ≤ 51.1%; y represents the average ΔMW per AA). We demonstrated that this equation could be applied to predict the SDS PAGE-displayed MW for thirteen different natural acidic proteins. PMID:26311515

  9. Different low-molecular-mass organic acids specifically control leaching of arsenic and lead from contaminated soil

    Ash, Christopher; Tejnecký, Václav; Borůvka, Luboš; Drábek, Ondřej

    2016-04-01

    Low-molecular-mass organic acids (LMMOA) are of key importance for mobilisation and fate of metals in soil, by functioning as ligands that increase the amount of dissolved metal in solution or by dissociation of metal binding minerals. Column leaching experiments were performed on soil polluted with As and Pb, in order to determine the specificity of LMMOA related release for individual elements, at varying organic acid concentrations. Acetic, citric and oxalic acids were applied in 12 h leaching experiments over a concentration range (0.5-25 mM) to soil samples that represent organic and mineral horizons. The leaching of As followed the order: oxalic > citric > acetic acid in both soils. Arsenic leaching was attributed primarily to ligand-enhanced dissolution of mineral oxides followed by As released into solution, as shown by significant correlation between oxalic and citric acids and content of Al and Fe in leaching solutions. Results suggest that subsurface mineral soil layers are more vulnerable to As toxicity. Leaching of Pb from both soils followed the order: citric > oxalic > acetic acid. Mineral soil samples were shown to be more susceptible to leaching of Pb than samples characterised by a high content of organic matter. The leaching efficiency of citric acid was attributed to formation of stable complexes with Pb ions, which other acids are not capable of. Results obtained in the study are evidence that the extent of As and Pb leaching in contaminated surface and subsurface soil depends significantly on the types of carboxylic acid involved. The implications of the type of acid and the specific element that can be mobilised become increasingly significant where LMMOA concentrations are highest, such as in rhizosphere soil.

  10. High molecular weight hyaluronic acid limits astrocyte activation and scar formation after spinal cord injury

    Khaing, Zin Z.; Milman, Brian D.; Vanscoy, Jennifer E.; Seidlits, Stephanie K.; Grill, Raymond J.; Schmidt, Christine E.

    2011-08-01

    A major hurdle for regeneration after spinal cord injury (SCI) is the ability of axons to penetrate and grow through the scar tissue. After SCI, inflammatory cells, astrocytes and meningeal cells all play a role in developing the glial scar. In addition, degradation of native high molecular weight (MW) hyaluronic acid (HA), a component of the extracellular matrix, has been shown to induce activation and proliferation of astrocytes. However, it is not known if the degradation of native HA actually enhances glial scar formation. We hypothesize that the presence of high MW HA (HA with limited degradation) after SCI will decrease glial scarring. Here, we demonstrate that high MW HA decreases cell proliferation and reduces chondroitin sulfate proteoglycan (CSPG) production in cultured neonatal and adult astrocytes. In addition, stiffness-matched high MW HA hydrogels crosslinked to resist degradation were implanted in a rat model of spinal dorsal hemisection injury. The numbers of immune cells (macrophages and microglia) detected at the lesion site in animals with HA hydrogel implants were significantly reduced at acute time points (one, three and ten days post-injury). Lesioned animals with HA implants also exhibited significantly lower CSPG expression at ten days post-injury. At nine weeks post-injury, animals with HA hydrogel implants exhibited a significantly decreased astrocytic response, but did not have significantly altered CSPG expression. Combined, these data suggest that high MW HA, when stabilized against degradation, mitigates astrocyte activation in vitro and in vivo. The presence of HA implants was also associated with a significant decrease in CSPG deposition at ten days after SCI. Therefore, HA-based hydrogel systems hold great potential for minimizing undesired scarring as part of future repair strategies after SCI.

  11. Perfluorooctanoic acid (PFOA) affects distinct molecular signalling pathways in human primary hepatocytes

    Perfluorooctanoic acid (PFOA) was shown to damage the liver of rodents and to impair embryonic development. At the molecular level, the hepatotoxic effects were attributed to the PFOA-mediated activation of peroxisome proliferator-activated receptor alpha (PPARα). In general, PPARα-dependent effects are less pronounced in humans than in rodents, and the hazard potential of PFOA for humans is controversially discussed. To analyse the effects of PFOA in human hepatocytes, a microarray analysis was conducted to screen for PFOA-mediated alterations in the transcriptome of human primary hepatocytes. A subsequent network analysis revealed that PFOA had an impact on several signalling pathways in addition to the well-known activation of PPARα. The microarray data confirmed earlier findings that PFOA: (i) affects the estrogen receptor ERα, (ii) activates the peroxisome proliferator-activated receptor gamma (PPARγ), and (iii) inhibits the function of the hepatocyte nuclear factor 4α (HNF4α) which is an essential factor for liver development and embryogenesis. Finally, as a novel finding, PFOA was shown to stimulate gene expression of the proto-oncogenes c-Jun and c-Fos. This was confirmed by using the HepG2 cell line as a model for human hepatocytes. PFOA stimulated cellular proliferation and the metabolic activity of the cells, and upregulated the expression of various cyclins which have a central function in the regulation of cell cycle control. Functional studies, however, indicated that PFOA had no impact on c-Jun and c-Fos phosphorylation and on AP-1-dependent gene transcription, thus demonstrating that PFOA-induced proliferation occurs largely independent of c-Jun and c-Fos

  12. Born Oppenheimer Molecular Dynamics calculation of the νO-H IR spectra for acetic acid cyclic dimers

    Both ab initio molecular dynamics simulations based on the Born-Oppenheimer approach calculations and a quantum theoretical model are used in order to study the IR spectrum of the acetic acid dimer in the gas phase. The theoretical model is taking into account the strong anharmonic coupling, Davydov coupling, multiple Fermi resonances between the first harmonics of some bending modes and the first excited state of the symmetric combination of the two vO-H modes and the quantum direct and indirect relaxation. The IR spectra obtained from DFT-based molecular dynamics is compared with our theoretical lineshape and with experiment. Note that in a previous work we have shown that our approach reproduces satisfactorily the main futures of the IR experimental lineshapes of the acetic acid dimer [Mohamed el Amine Benmalti, Paul Blaise, H. T. Flakus, Olivier Henri-Rousseau, Chem Phys, 320(2006) 267-274.

  13. Electrospun Scaffolds from Low Molecular Weight Poly(ester amides Based on Glycolic Acid, Adipic Acid and Odd or Even Diamines

    Sara Keiko Murase

    2015-05-01

    Full Text Available Electrospinning of regular poly(ester amides (PEAs constituted by glycolic acid, adipic acid and diamines with five and six carbon atoms has been carried out. Selected PEAs were constituted by natural origin products and could be easily prepared by a polycondensation method that avoids tedious protection and deprotection steps usually required for obtaining polymers with a regular sequence. Nevertheless, the synthesis had some limitations that mainly concerned the final low/moderate molecular weight that could be attained. Therefore, it was considered interesting to evaluate if electrospun scaffolds could still be prepared taking also advantage of the capability of PEAs to establish intermolecular hydrogen bonds. Results indicated that the crucial factor was the control of polymer concentration in the electrospun solution, being necessary that this concentration was higher than 40% (w/v. The PEA with the lowest molecular weight (Mw close to 8000 g/mol was the most appropriate to obtain electrospun samples with a circular cross-section since higher molecular sized polymers show solvent retention problems derived from the high viscosity of the electrospun solution that rendered ribbon-like morphologies after the impact of fibers into the collector. The studied PEAs were semicrystalline and biodegradable, as demonstrated by calorimetric and degradation studies. Furthermore, the new scaffolds were able to encapsulate drugs with anti-inflammatory and bacteriostatic activities like ketoprofen. The corresponding release and bactericide activity was evaluated in different media and against different bacteria. Finally, biocompatibility was demonstrated using both fibroblast and epithelial cell lines.

  14. PM-IRRAS Determination of Molecular Orientation of Phosphonic Acid Self-Assembled Monolayers on Indium Zinc Oxide.

    Sang, Lingzi; Mudalige, Anoma; Sigdel, Ajaya K; Giordano, Anthony J; Marder, Seth R; Berry, Joseph J; Pemberton, Jeanne E

    2015-05-26

    Self-assembled monolayers (SAMs) of phosphonic acids (PAs) on transparent conductive oxide (TCO) surfaces can facilitate improvement in TCO/organic semiconductor interface properties. When ordered PA SAMs are formed on oxide substrates, interface dipole and electronic structure are affected by the functional group properties, orientation, and binding modes of the modifiers. Choosing octylphosphonic acid (OPA), F13-octylphosphonic acid (F13OPA), pentafluorophenyl phosphonic acid (F5PPA), benzyl phosphonic acid (BnPA), and pentafluorobenzyl phosphonic acid (F5BnPA) as a representative group of modifiers, we report polarization modulation-infrared reflection-absorption spectroscopy (PM-IRRAS) of binding and molecular orientation on indium-doped zinc oxide (IZO) substrates. Considerable variability in molecular orientation and binding type is observed with changes in PA functional group. OPA exhibits partially disordered alkyl chains but on average the chain axis is tilted ∼57° from the surface normal. F13OPA tilts 26° with mostly tridentate binding. The F5PPA ring is tilted 23° from the surface normal with a mixture of bidentate and tridentate binding; the BnPA ring tilts 31° from normal with a mixture of bidentate and tridentate binding, and the F5BnPA ring tilts 58° from normal with a majority of bidentate with some tridenate binding. These trends are consistent with what has been observed previously for the effects of fluorination on orientation of phosphonic acid modifiers. These results from PM-IRRAS are correlated with recent results on similar systems from near-edge X-ray absorption fine structure (NEXAFS) and density functional theory (DFT) calculations. Overall, these results indicate that both surface binding geometry and intermolecular interactions play important roles in dictating the orientation of PA modifiers on TCO surfaces. This work also establishes PM-IRRAS as a routine method for SAM orientation determination on complex oxide substrates

  15. Multistate Switches: Ruthenium Alkynyl-Dihydroazulene/Vinylheptafulvene Conjugates.

    Vlasceanu, Alexandru; Andersen, Cecilie L; Parker, Christian R; Hammerich, Ole; Morsing, Thorbjørn J; Jevric, Martyn; Lindbaek Broman, Søren; Kadziola, Anders; Nielsen, Mogens Brøndsted

    2016-05-23

    Multimode molecular switches incorporating distinct and independently addressable functional components have potential applications as advanced switches and logic gates for molecular electronics and memory storage devices. Herein, we describe the synthesis and characterization of four switches based on the dihydroazulene/vinylheptafulvene (DHA/VHF) photo/thermoswitch pair functionalized with the ruthenium-based Cp*(dppe)Ru ([Ru*]) metal complex (dppe=1,2-bis(diphenylphosphino)ethane; Cp*=pentamethylcyclopentadienyl). The [Ru*]-DHA conjugates can potentially exist in six different states accessible by alternation between DHA/VHF, Ru(II) /Ru(III) , and alkynyl/vinylidene, which can be individually stimulated by using light/heat, oxidation/reduction, and acid/base. Access to the full range of states was found to be strongly dependent on the electronic communication between the metal center and the organic photoswitch in these [Ru*]-DHA conjugates. Detailed electrochemical, spectroscopic (UV/Vis, IR, NMR), and X-ray crystallographic studies indeed reveal significant electronic interactions between the two moieties. When in direct conjugation, the ruthenium metal center was found to quench the photochemical ring-opening of DHA, which in one case could be restored by protonation or oxidation, allowing conversion to the VHF state. PMID:27114110

  16. Stereocomplexation of low molecular weight poly(L-lactic acid) and high molecular weight poly(D-lactic acid), radiation crosslinking PLLA/PDLA stereocomplexes and their characterization

    Poly(L-lactic acid)s (PLLAx) were synthesized from L-lactic acid by polycondensation. Different stereocomplexes were also obtained with equimolar mixtures of synthesized PLLAx and a commercial PDLA. The stereocomplexes were crosslinked with triallyl isocyanurate (TAIC) by gamma irradiation. Crosslinking density increased with radiation doses, the heavier the crosslinking network, the lower its swelling degree. The crosslinking structures were introduced in the stereocomplexes inhibiting the mobility for crystallization of PLLA molecules. Thermal and mechanical properties of PLA stereocomplexes were remarkably enhanced by radiation induced crosslinking. PLA stereocomplex does not seem to be degraded by PLLA degrading microorganisms existing in compost at room temperature, but the synthesized PLLA was significantly degraded. - Highlights: ► Complete PLA stereocomplex was obtained from synthesized PLLA and a commercial PDLA. ► Melting temperature of stereocomplex were much improved by gamma irradiation. ► Crosslinking network inhibited the mobility of polymeric chains for crystallization. ► Biodegradability of PLLA was reduced by stereocomplexation and crosslinking.

  17. Volatile and nonvolatile selective switching of a photo-assisted initialized atomic switch

    A photo-assisted atomic switch, which has a photoconductive molecular layer in a gap of about 20 nm between an Ag2S electrode and a Pt electrode, is set to a conventional gap-type atomic switch operation mode by light irradiation with the application of a small bias that precipitates Ag atoms from an Ag2S electrode. After this initialization, the switch operates only with application of a bias. In this study, we also found that after the set-operation a photo-assisted initialized atomic switch shows different switching modes depending on the bias range, i.e., volatile switching when the applied bias is smaller than the threshold bias, and nonvolatile switching when the applied bias is larger than the threshold bias. These characteristics can be useful in reconfiguring a circuit such as in neural computing systems. (paper)

  18. Real-Time Nucleic Acid Sequence-Based Amplification Using Molecular Beacons for Detection of Enterovirus RNA in Clinical Specimens

    Landry, Marie L.; Garner, Robin; Ferguson, David

    2005-01-01

    Real-time nucleic acid sequence-based amplification (NASBA) using molecular beacon technology (NASBA-beacon) was compared to standard NASBA with postamplification hybridization using electrochemiluminescently labeled probes (NASBA-ECL) for detection of enteroviruses (EV) in 133 cerebrospinal fluid and 27 stool samples. NASBA-ECL and NASBA-beacon were similar in sensitivity, detecting 55 (100%) and 52 (94.5%) EV-positive samples, respectively. There were no false positives. Both NASBA assays w...

  19. Exciton interaction in molecular beacons: a sensitive sensor for short range modifications of the nucleic acid structure

    Bernacchi, Serena; Mély, Yves

    2001-01-01

    Molecular beacons are hairpin-shaped, single-stranded oligonucleotides constituting sensitive fluorescent DNA probes widely used to report the presence of specific nucleic acids. In its closed form the stem of the hairpin holds the fluorophore covalently attached to one end, close to the quencher, which is covalently attached to the other end. Here we report that in the closed form the fluorophore and the quencher form a ground state intramolecular heterodimer whos...

  20. The Effect of Phenazine-1-Carboxylic Acid on the Morphological, Physiological, and Molecular Characteristics of Phellinus noxius

    Huazhi Huang; Longhua Sun; Keke Bi; Guohua Zhong; Meiying Hu

    2016-01-01

    In this study, the effect of phenazine-1-carboxylic acid (PCA) on morphological, physiological, and molecular characteristics of Phellinus noxius has been investigated, and the potential antifungal mechanism of PCA against P. noxius was also explored. The results revealed that PCA showed in vitro antifungal potential against P. noxius and completely inhibited P. noxius hyphae at concentrations >40 μg/mL. PCA inhibited both mycelial growth and the loss of mycelial biomass in vitro in a dose...

  1. Hybrid molecularly imprinted poly(methacrylic acid-TRIM)-silica chemically modified with (3-glycidyloxypropyl)trimethoxysilane for the extraction of folic acid in aqueous medium.

    de Oliveira, Fernanda Midori; Segatelli, Mariana Gava; Tarley, César Ricardo Teixeira

    2016-02-01

    In the present study a hybrid molecularly imprinted poly(methacrylic acid-trimethylolpropane trimethacrylate)-silica (MIP) was synthesized and modified with (3-glycidyloxypropyl)trimethoxysilane (GPTMS) with posterior opening of epoxy ring to provide hydrophilic properties of material in the extraction of folic acid from aqueous medium. The chemical and structural aggregates of hybrid material were characterized by means of Fourier Transform Infrared (FT-IR), Transmission Electron Microscopy (TEM), Scanning Electron Microscopy (SEM), Thermogravimetric analysis (TGA) and textural data. Selectivity data of MIP were compared to non-imprinted polymer (NIP) through competitive sorption studies in the presence of caffeine, paracetamol or 4-aminobenzamide yielding relative selectivity coefficients (k′) higher than one unit, thus confirming the selective character of MIP even in the presence of structurally smaller compounds than the folic acid. The lower hydrophobic sorption by bovine serum albumin (BSA) in the MIP as compared to unmodified MIP proves the hydrophilicity of polymer surface by using GPTMS with opening ring. Under acid medium(pH 1.5) the sorption of folic acid onto MIP from batch experiments was higher than the one achieved for NIP. Equilibrium sorption of folic acid was reached at 120 min for MIP, NIP and MIP without GPTMS and kinetic sorption data were well described by pseudo-second-order, Elovich and intraparticle diffusion models. Thus, these results indicate the existence of different binding energy sites in the polymers and a complex mechanism consisting of both surface sorption and intraparticle transport of folic acid within the pores of polymers. PMID:26652418

  2. Metabolic engineering of Bacillus subtilis for the efficient biosynthesis of uniform hyaluronic acid with controlled molecular weights.

    Jia, Yuning; Zhu, Jing; Chen, Xiaofei; Tang, Dongyang; Su, Ding; Yao, Wenbing; Gao, Xiangdong

    2013-03-01

    Bacillus subtilis was engineered into an efficient hyaluronic acid (HA) producer by introducing two inducible artificial operons carrying HA synthase gene from Pasteurella multocida and precursor genes encoding enzymes involved in synthesis of the sugar precursors. A two-stage induction strategy was established for metabolic engineering of recombinant B. subtilis to efficiently produce uniform HA with controlled molecular weights. Strain TPG223 produced larger HA molecules (yield=6.8 g/L; molecular weight=4.5 MDa) than strain PG6181 (yield=2.4 g/L; molecular weight=13 KDa), indicating that the enzymes involved in the synthesis of UDP-glucuronic acid are essential for HA biosynthesis. Strain TPG223 was able to synthesize HA molecules ranging in molecular weight from 8 KDa to 5.4 MDa indicating that size control is achievable in vivo through appropriate tools. The work reported here not only advanced mechanisms research of size control in vivo, but also could be an attractive alternative for commercial preparation of uniform size-defined HA. PMID:23433979

  3. Crude palm oil from interspecific hybrid Elaeis oleifera×Elaeis guineensis: fatty acid regiodistribution and molecular species of glycerides.

    Mozzon, Massimo; Pacetti, Deborah; Lucci, Paolo; Balzano, Michele; Frega, Natale Giuseppe

    2013-11-01

    The composition and structure of triacylglycerols (TAGs) and partial glycerides of crude palm oil obtained from interspecific hybrid Elaeis oleifera×Elaeis guineensis, grown in Colombia, were fully characterised and compared to data obtained by analysing crude African palm oil. Hybridisation appears to substantially modify the biosynthesis of fatty acids (FAs) rather than their assembly in TAGs. In fact, total FAs analysis showed significant differences between these two types of oil, with hybrid palm oil having a higher percentage of oleic acid (54.6 ± 1.0 vs 41.4 ± 0.3), together with a lower saturated fatty acid content (33.5 ± 0.5 vs 47.3 ± 0.1), while the percentage of essential fatty acid, linoleic acid, does not undergo significant changes. Furthermore, 34 TAG types were identified, with no qualitative differences between African and E. guineensis×E. oleifera hybrid palm oil samples. Short and medium chain FAs (8:0, 10:0, 12:0, 14:0) were utilised, together, to build a restricted number of TAG molecular species. Oil samples from the E. guineensis×E. oleifera hybrid showed higher contents of monosaturated TAGs (47.5-51.0% vs 36.7-37.1%) and triunsaturated TAGs (15.5-15.6% vs 5.2-5.4%). The sn-2 position of TAGs in hybrid palm oil was shown to be predominantly esterified with oleic acid (64.7-66.0 mol% vs 55.1-58.2 mol% in African palm oil) with only 10-15% of total palmitic acid and 6-20% of stearic acid acylated in the secondary position. The total amount of diacylglycerols (DAGs) was in agreement with the values of free acidity; DAG types found were in agreement with the representativeness of different TAG species. PMID:23768354

  4. Preparation and application of molecularly imprinted polymer for isolation of chicoric acid from Chicorium intybus L. medicinal plant.

    Saad, Engy M; Madbouly, Adel; Ayoub, Nahla; El Nashar, Rasha Mohamed

    2015-06-01

    Molecularly imprinted polymer (MIP) was synthesized and applied for the extraction of chicoric acid from Chicory herb (Chicorium intybus L.). A computational study was developed to find a suitable template to functional monomer molar ratio for MIP preparations. The molar ratio was chosen based on the comparison of the binding energy of the complexes between the template and functional monomers. Based on the computational results, eight different polymers were prepared using chicoric acid as the template. The MIPs were synthesized in a non-covalent approach via thermal free-radical polymerization, using two different polymerization methods, bulk and suspension. Batch rebinding experiments were performed to evaluate the binding properties of the imprinted polymers. The best results were obtained with a MIP prepared using bulk polymerization with 4-vinylpyridine (4-VP) as the functional monomer and ethylene glycol dimethacrylate (EGDMA) as the crosslinker with a molar ratio of 1:4:20. The best MIP showed selective binding ability toward chicoric acid in the presence of the template's structural analogues, caffeic acid, caftaric acid and chlorogenic acid. PMID:26002213

  5. Preparation and application of zirconium sulfate supported on SAPO-34 molecular sieve as solid acid catalyst for esterification

    Graphical abstract: - Highlights: • SAPO-34 supported zirconium sulfate solid acid catalyst was prepared. • Esterification of acetic acid with ethanol can be catalyzed by ZS/SAPO-34. • The hydration of ZS is vital to the acidic property and catalytic performance. • The ZS/SAPO-34 catalyst treated at 200 °C shows good reusability. - Abstract: Zirconium sulfate (ZS) was supported on SAPO-34 molecular sieve by using an incipient wetness impregnation method with zirconium sulfate as the precursor. The as-prepared catalysts were used as solid acid catalyst for esterification reaction of acetic acid with ethanol. The influence of calcination temperature on the acidic property, catalytic activity, and reusability of ZS/SAPO-34 catalysts were mainly investigated. FT-IR, SEM, EDS and TG analysis have been carried out to demonstrate the characteristics of ZS/SAPO-34 catalysts. It was found that the 30 wt%ZS/SAPO-34 catalysts display the property of superacid irrespective of calcination temperature. The ZS/SAPO-34 catalyst treated at 200 °C can enhance the interaction between the supported ZS and SAPO-34 and keep the catalyst remaining substantially active after several reaction cycles. However, further increasing calcination temperature will cause the transfer of ZS from hydrate to anhydrous phase, and thus the decrease of activity

  6. Structure of eight molecular salts assembled from noncovalent bonding between carboxylic acids, imidazole, and benzimidazole

    Jin, Shouwen; Zhang, Huan; Liu, Hui; Wen, Xianhong; Li, Minghui; Wang, Daqi

    2015-09-01

    Eight organic salts of imidazole/benzimidazole have been prepared with carboxylic acids as 2-methyl-2-phenoxypropanoic acid, α-ketoglutaric acid, 5-nitrosalicylic acid, isophthalic acid, 4-nitro-phthalic acid, and 3,5-dinitrosalicylic acid. The eight crystalline forms reported are proton-transfer compounds of which the crystals and compounds were characterized by X-ray diffraction analysis, IR, mp, and elemental analysis. These structures adopted hetero supramolecular synthons, with the most common R22(7) motif observed at salts 2, 3, 5, 6 and 8. Analysis of the crystal packing of 1-8 suggests that there are extensive strong Nsbnd H⋯O, and Osbnd H⋯O hydrogen bonds (charge assisted or neutral) between acid and imidazolyl components in all of the salts. Except the classical hydrogen bonding interactions, the secondary propagating interactions also play important roles in structure extension. This variety, coupled with the varying geometries and number of acidic groups of the acids utilized, has led to the creation of eight supramolecular arrays with 1D-3D structure. The role of weak and strong noncovalent interactions in the crystal packing is analyzed. The results presented herein indicate that the strength and directionality of the Nsbnd H⋯O, and Osbnd H⋯O hydrogen bonds between acids and imidazole/benzimidazole are sufficient to bring about the formation of organic salts.

  7. Silylated melamine and cyanuric acid as precursors for imprinted and hybrid silica materials with molecular recognition properties.

    Arrachart, Guilhem; Carcel, Carole; Trens, Philippe; Moreau, Jöel J E; Wong Chi Man, Michel

    2009-06-15

    Two monotrialkoxysilylated compounds that consist of complementary fragments of melamine (M) and cyanuric acid (CA) have been synthesised. The molecular recognition properties of the M and CA fragments through complementary hydrogen bonds (DAD and ADA; D=donor, A=acceptor) are the key factor used to direct the formation of hybrid silica materials by using a sol-gel process. These materials were synthesised following two methods: First, an organo-bridged silsesquioxane was obtained by the hydrolysis of the two complementary monotrialkoxysilylated melamine and cyanuric acid derivatives, with fluoride ions as a catalyst. The hydrogen-bonding interactions between the two organic fragments are responsible for the formation of the bridging unit. The transcription of the assembly into the hybrid material was characterised and evidenced by solid-state NMR (29Si, 13C) and FTIR spectroscopic experiments. Second, the molecular recognition was exploited to synthesise an imprinted hybrid silica. This material was prepared by co-condensation of tetraethyl orthosilicate (TEOS) with the monosilylated cyanuric acid derivative (CA) templated by nonsilylated melamine. The melamine template was completely removed by treating the solid material with hydrochloric acid. The reintroduction of the template was performed by treating the resulting material with an aqueous suspension of melamine. These steps were monitored and analysed by several techniques, such as solid-state NMR (29Si, 13C) and FTIR spectroscopic analysis and nitrogen adsorption-desorption isotherms. PMID:19440996

  8. Quantum dots increased fat storage in intestine of Caenorhabditis elegans by influencing molecular basis for fatty acid metabolism.

    Wu, Qiuli; Zhi, Lingtong; Qu, Yangyang; Wang, Dayong

    2016-07-01

    Caenorhabditis elegans is a useful model animal for fat storage study. In nematodes, CdTe quantum dots (QDs) induced an increase in fat storage in intestine that is partially due to prolonged defecation cycle length, and not attributed to altered feeding or cadmium ion released from CdTe QDs. Moreover, CdTe QDs altered the molecular basis of both synthesis and degradation of fatty acid; however, CdTe QDs did not influence that of degradation of phospholipids. CdTe QDs increased expression of fasn-1 and pod-2 genes encoding enzymes required for fatty acid synthesis, and decreased expression of acs-2 and ech-1 genes encoding enzymes required for fatty acid β-oxidation. The altered molecular basis of fatty acid synthesis or degradation by CdTe QDs acted in intestine to regulate fat storage. Our study highlights the potential of CdTe QDs in influencing lipid metabolism in certain organs or tissues in animals. PMID:26956412

  9. A Prevention of Pre-eclampsia with the Use of Acetylsalicylic Acid and Low-molecular Weight Heparin - Molecular Mechanisms.

    Darmochwal-Kolarz, Dorota; Kolarz, Bogdan; Korzeniewski, Michal; Kimber-Trojnar, Zaneta; Patro-Malysza, Jolanta; Mierzynski, Radzisław; Przegalinska-Kałamucka, Monika; Oleszczuk, Jan

    2016-01-01

    Pre-eclampsia appears to be the main cause for the maternal and fetal morbidity and mortality. Pregnant women with pre-eclampsia are more likely to be threatened with conditions which potentially may be lethal, such as: disseminated intravascular coagulation, cerebral hemorrhage, liver and renal failure. Pregnancy complicated with pre-eclampsia is also associated with a greater risk for iatrogenic prematurity, intrauterine growth retardation, premature abruption of placenta, and even intrauterine fetal death. In the majority of cases the reasons for arterial hypertension among pregnant women remain obscure. For the past decades, there were many abortive attempts in the use of some microelements, vitamins or specific diets, such as polyunsaturated fatty acids, for the prophylaxis of pre-eclampsia. Recently, it has been shown that a prevention of pre-eclampsia with the use of a lowmolecular- weight heparins (LMWHs) and acetylsalicylic acid (ASA) could considerably reduce the frequency of preeclampsia. In this review, we present the studies concerning the applications of LMWHs and aspirin in the prophylaxis of pre-eclampsia and some important data about the mechanisms of anti-inflammatory actions of LMWHs and ASA. PMID:26927215

  10. The nucleic acid revolution continues – will forensic biology become forensic molecular biology?

    Gunn, Peter; Walsh, Simon; Roux, Claude

    2014-01-01

    Molecular biology has evolved far beyond that which could have been predicted at the time DNA identity testing was established. Indeed we should now perhaps be referring to “forensic molecular biology.” Aside from DNA’s established role in identifying the “who” in crime investigations, other developments in medical and developmental molecular biology are now ripe for application to forensic challenges. The impact of DNA methylation and other post-fertilization DNA modifications, plus the emer...

  11. Production and detection of neutral molecular beams : from single amino acids to biomolecular complexes

    This thesis presents a laser desorption source for neutral organic molecules and clusters as well as the first exploration of a superconducting single photon detector for the detection of massive neutral particles. Whereas the source can produce beams of biomolecules for various gas-phase applications, the detector can be used to overcome the current post- ionization detection mass limit of neutral molecules. The aim of our work is to produce and detect neutral molecular gas-phase beams, ranging from small amino acids overlarge polypeptides to massive complexes. The purpose of creating these beams is to use them for quantum optics experiments, like near field matter wave interference and its applications in metrology. Standard effusive sources usually lack the ability to cool the evaporated organic molecules fast enough to prevent fragmentation. In contrast to that, the presented laser desorption source cools the initially evaporated molecules by embedding them into a supersonic seed gas beam. The mixing of the seed gas and the desorbed molecules is implemented both in free expansion as well as inside a closed mixing channel. The desorbed neutral molecules are detected by photo-ionization using UV (266 nm) and FUV (157 nm) light followed by time-of-flight mass spectrometry. For the amino acid tryptophan (204amu) and for the antibiotic polypeptide gramicidin (1884amu) the ion yields for both photo-ionization wavelengths are examined and the ionization cross sections for the UV wavelength are measured. In case of tryptophan the ionization yield is comparable for both wavelengths, whereas gramicidin is detected fifteen times more efficiently under VUV ionization than for UV ionization at equal intensity. Desorption of heavier molecules than gramicidin never resulted in a detectable ion yield, which confirms the known inefficiency for the post-ionization of isolated large organic molecules [1-3]. The desorption source is also used for the formation of large neutral

  12. Interacting quantum fragments-rooted preorganized-interacting fragments attributed relative molecular stability of the Be(II) complexes of nitrilotriacetic acid and nitrilotri-3-propionic acid.

    Cukrowski, Ignacy; Mangondo, Paidamwoyo

    2016-06-01

    A method designed to investigate, on a fundamental level, the origin of relative stability of molecular systems using Be(II) complexes with nitrilotriacetic acid (NTA) and nitrilotri-3-propionic acid (NTPA) is described. It makes use of the primary and molecular fragment energy terms as defined in the IQA/F (Interacting Quantum Atoms/Fragments) framework. An extensive classical-type investigation, focused on single descriptors (bond length, density at critical point, the size of metal ion or coordination ring, interaction energy between Be(II) and a donor atom, etc.) showed that it is not possible to explain the experimental trend. The proposed methodology is fundamentally different in that it accounts for the total energy contributions coming from all atoms of selected molecular fragments, and monitors changes in defined energy terms (e.g., fragment deformation, inter- and intra-fragment interaction) on complex formation. By decomposing combined energy terms we identified the origin of relative stability of Be(II) (NTA) and Be(II) (NTPA) complexes. We found that the sum of coordination bonds' strength, as measured by interaction energies between Be(II) ion and donor atoms, favours Be(II) (NTA) but the binding energy of Be(II) ion to the entire ligand correlates well with experimental trend. Surprisingly, the origin of Be(II) (NTPA) being more stable is due to less severe repulsive interactions with the backbone of NTPA (C and H-atoms). This general purpose protocol can be employed not only to investigate the origin of relative stability of any molecular system (e.g., metal complexes) but, in principle, can be used as a predictive tool for, e.g., explaining reaction mechanism. © 2016 Wiley Periodicals, Inc. PMID:26993356

  13. Molecular Structure, NMR, HOMO, LUMO, and Vibrational Analysis of O-Anisic Acid and Anisic Acid Based on DFT Calculations

    R. Mathammal

    2013-01-01

    Full Text Available This work deals with the vibrational spectroscopy of O-Anisic acid (OAA and Anisic acid (AA. The fundamental vibrational frequencies and intensity of vibrational bands were evaluated using density functional theory (DFT with standard B3LYP/6-31G** method and basis set combinations. The vibrational spectra were interpreted, with the aid of normal coordinate analysis based on a scaled quantum mechanical force field. The infrared and Raman spectra were also predicted from the calculated intensities. The effects of carbonyl and methyl substitutions on the structure and vibrational frequencies have been investigated. Comparison of simulated spectra with the experimental spectra provides important information about the ability of the computational method to describe the vibrational modes. The 13C and 1H NMR chemical shifts of the DFA and CA molecules were calculated using the gauge-invariant-atomic orbital (GIAO method in DMSO solution using IEF-PCM model and compared with experimental data.

  14. Synthesis, binding affinity at glutamic acid receptors, neuroprotective effects, and molecular modeling investigation of novel dihydroisoxazole amino acids

    Conti, Paola; De Amici, Marco; Grazioso, Giovanni;

    2005-01-01

    The four stereoisomers of 5-(2-amino-2-carboxyethyl)-4,5-dihydroisoxazole-3-carboxylic acid(+)-4, (-)-4, (+)-5, and (-)-5 were prepared by stereoselective synthesis of two pairs of enantiomers, which were subsequently resolved by enzymatic procedures. These four stereoisomers and the four...... stereoisomers of the bicyclic analogue 5-amino-4,5,6,6a-tetrahydro-3aH-cyclopenta[d]isoxazole-3,5-dicarboxylic acid (+)-2, (-)-2, (+)-3, and (-)-3 were tested at ionotropic and metabotropic glutamate receptor subtypes. The most potent NMDA receptor antagonists [(+)-2, (-)-4, and (+)-5] showed a significant...... derivatives showed high antagonist potency with preference for the NR2A and NR2B subtypes, with derivative (-)-4 behaving as the most potent antagonist. The biological data are discussed on the basis of homology models reported in the literature for NMDA receptors and mGluRs....

  15. Nitro-Fatty Acids in Plant Signaling: Nitro-Linolenic Acid Induces the Molecular Chaperone Network in Arabidopsis.

    Mata-Pérez, Capilla; Sánchez-Calvo, Beatriz; Padilla, María N; Begara-Morales, Juan C; Luque, Francisco; Melguizo, Manuel; Jiménez-Ruiz, Jaime; Fierro-Risco, Jesús; Peñas-Sanjuán, Antonio; Valderrama, Raquel; Corpas, Francisco J; Barroso, Juan B

    2016-02-01

    Nitro-fatty acids (NO2-FAs) are the product of the reaction between reactive nitrogen species derived of nitric oxide (NO) and unsaturated fatty acids. In animal systems, NO2-FAs are considered novel signaling mediators of cell function based on a proven antiinflammatory response. Nevertheless, the interaction of NO with fatty acids in plant systems has scarcely been studied. Here, we examine the endogenous occurrence of nitro-linolenic acid (NO2-Ln) in Arabidopsis and the modulation of NO2-Ln levels throughout this plant's development by mass spectrometry. The observed levels of this NO2-FA at picomolar concentrations suggested its role as a signaling effector of cell function. In fact, a transcriptomic analysis by RNA-seq technology established a clear signaling role for this molecule, demonstrating that NO2-Ln was involved in plant defense response against different abiotic-stress conditions, mainly by inducing heat shock proteins and supporting a conserved mechanism of action in both animal and plant defense processes. Bioinformatics analysis revealed that NO2-Ln was also involved in the response to oxidative stress conditions, mainly depicted by H2O2, reactive oxygen species, and oxygen-containing compound responses, with a high induction of ascorbate peroxidase expression. Closely related to these results, NO2-Ln levels significantly rose under several abiotic-stress conditions such as wounding or exposure to salinity, cadmium, and low temperature, thus validating the outcomes found by RNA-seq technology. Jointly, to our knowledge, these are the first results showing the endogenous presence of NO2-Ln in Arabidopsis (Arabidopsis thaliana) and supporting the strong signaling role of these molecules in the defense mechanism against different abiotic-stress situations. PMID:26628746

  16. Switched on!

    2008-01-01

    Like a star arriving on stage, impatiently followed by each member of CERN personnel and by millions of eyes around the world, the first beam of protons has circulated in the LHC. After years in the making and months of increasing anticipation, today the work of hundreds of people has borne fruit. WELL DONE to all! Successfully steered around the 27 kilometres of the world’s most powerful particle accelerator at 10:28 this morning, this first beam of protons circulating in the ring marks a key moment in the transition from over two decades of preparation to a new era of scientific discovery. "It’s a fantastic moment," said the LHC project leader Lyn Evans, "we can now look forward to a new era of understanding about the origins and evolution of the universe". Starting up a major new particle accelerator takes much more than flipping a switch. Thousands of individual elements have to work in harmony, timings have to be synchronize...

  17. In vitro evaluation of antiviral and virucidal activity of a high molecular weight hyaluronic acid

    Blasi Elisabetta

    2011-03-01

    Full Text Available Abstract Background hyaluronic acid (HA, a non-sulphated glycosaminoglycan, is present in synovial fluid, vitreous humour serum and many connective tissues. Pharmaceutical preparations of HA are used in clinical practice for wound healing, joint pain, kerato-conjunctivitis, asthma, mouth care, oesophageal-reflux, and gastritis. Moreover, it is used as a filler to counteract ageing and facial lipoatrophy. Our study aims at investigating the in vitro antiviral activity of a high molecular weight HA. Methods the MTT test was used to rule out the potential toxic effects of HA on the different cell lines used in the antiviral assays. The antiviral activity of HA against Coxsackievirus B5, Herpes Simplex Virus-1, Mumps Virus, Adenovirus-5, Influenza Virus A/H1N1, Human Herpesvirus-6, Porcine Parvovirus, Porcine Reproductive and Respiratory Syndrome Virus was assessed by virus yield assays. Results the most effective inhibition was observed against Coxsackievirus B5, with 3Log reduction of the virus yield at 4 mg/ml, and a reduction of 3.5Log and 2Log, at 2 mg/ml and 1 mg/ml, respectively: the selectivity index was 16. Mumps virus was highly inhibited too showing a reduction of 1.7Log at 1 mg/ml and 1Log at 4 mg/ml and 2 mg/ml (selectivity index = 12. The selectivity index for Influenza Virus was 12 with the highest inhibition (1Log observed at 4 mg/ml. Herpes Simplex Virus-1 and Porcine Parvovirus were mildly inhibited, whereas no antiviral activity was observed with respect to Adenovirus-5, Human Herpesvirus-6, Porcine Reproductive and Respiratory Syndrome Virus. No HA virucidal activity was ever observed against any of the viruses tested. Kinetic experiments showed that both Coxsackievirus B5 and Herpes simplex virus-1 replication were consistently inhibited, not influenced by the time of HA addition, during the virus replication cycle. Conclusions the spectrum of the antiviral activity exhibited by HA against both RNA and DNA viruses, known to have

  18. Proton play in the formation of low molecular weight chitosan (LWCS) by hydrolyzing chitosan with a carbon based solid acid.

    Krishnan, R Akhil; Deshmukh, Pranjal; Agarwal, Siddharth; Purohit, Poorvi; Dhoble, Deepa; Waske, Prashant; Khandekar, Dileep; Jain, Ratnesh; Dandekar, Prajakta

    2016-10-20

    Low molecular weight chitosan (LWCS) constitute a special class of value added chemicals that are primarily obtained from crustacean shells, which are the main water pollutants from crabs and shrimp processing centers. Unlike chitin and chitosan, LWCS possess improved solubility in water and aqueous solutions, making them widely applicable in numerous fields ranging from drug delivery to waste water treatment. Among the methods employed for their production, chemical breakdown by strong liquid acids has yielded good success. However, this method is met with severe concerns arising from the harsh nature of liquid acids, which may corrode the reactors for commercial synthesis, and their limited reusability. The physical methods like ultrasound and microwave are energy intensive in nature, while the enzymatic methods are expensive and offers limited scope for reuse. We have attempted to overcome these problems by employing carbon based solid acid (CSA) for hydrolyzing chitosan to LWCS. CSA can be easily produced using activated carbon, a cost-effective and easily available raw material. Reactions were carried out between chitosan and CSA in a hydrothermal glass reactor and the products, separated by cold centrifugation, were purified and dried. The dried products were characterized for their molecular weight and solubility. Results indicated more than ten-fold decrease in the molecular weight of chitosan and the product exhibited water solubility. The CSA could be used upto four times, without regeneration, to give a consistent quality product. The aqueous solution of resulting LWCS exhibited a pH of 6.03±0.11, as against the acidic pH range of solutions of commercially available LWCS, indicating its suitability for biomedical applications. Our investigation facilitates a 'green approach' that may be employed for commercial production of value added chemicals from waste products of marine industry. PMID:27474584

  19. Molecular cloning and characterization of a novel tomato xylosyltransferase specific for gentisic acid

    Tárraga, Susana; Lisón, Purificación; López-Gresa, María Pilar; Torres, Cristina; Rodrigo, Ismael; Bellés, José María; Conejero, Vicente

    2010-01-01

    The importance of salicylic acid (SA) in the signal transduction pathway of plant disease resistance has been well documented in many incompatible plant–pathogen interactions, but less is known about signalling in compatible interactions. In this type of interaction, tomato plants have been found to accumulate high levels of 2,5-dihydroxybenzoic acid (gentisic acid, GA), a metabolic derivative of SA. Exogenous GA treatments induce in tomato plants a set of PR proteins that differ from those i...

  20. Molecular mechanism of recombinant liver fatty acid binding protein's antioxidant activity

    Yan, Jing; Gong, Yuewen; She, Yi-Min; Wang, Guqi; Roberts, Michael S; Burczynski, Frank J.

    2009-01-01

    Hepatocytes expressing liver fatty acid binding protein (L-FABP) are known to be more resistant to oxidative stress than those devoid of this protein. The mechanism for the observed antioxidant activity is not known. We examined the antioxidant mechanism of a recombinant rat L-FABP in the presence of a hydrophilic (AAPH) or lipophilic (AMVN) free radical generator. Recombinant L-FABP amino acid sequence and its amino acid oxidative products following oxidation were identified by MALDI quadrup...

  1. Effects of low-molecular-weight organic acids on phosphorus sorption characteristics in some calcareous soils

    MORADI, Neda; SADAGHIANI, Mir Hassan RASOULI; SEPEHR, Ebrahim

    2012-01-01

    Understanding the role of organic acids in phosphorus sorption in soils is very important for economic and environmentally friendly management of soil P. Thus, calcareous surface soils (0-30 cm) from West Azerbaijan Province, Iran, were sampled to study the effect of different organic acids on P sorption. Soil samples (2.5 g) were equilibrated with 25 mL of 0.01 M CaCl2 solution containing 0-20 mg P L-1 and 5 mmol L-1 of different organic acids (citric, oxalic, and malic acid). The sorption d...

  2. The influence of poly(acrylic) acid number average molecular weight and concentration in solution on the compressive fracture strength and modulus of a glass-ionomer restorative.

    Dowling, Adam H

    2011-06-01

    The aim was to investigate the influence of number average molecular weight and concentration of the poly(acrylic) acid (PAA) liquid constituent of a GI restorative on the compressive fracture strength (σ) and modulus (E).

  3. Thiomers: Influence of molecular mass and thiol group content of poly(acrylic acid) on efflux pump inhibition.

    Grabovac, Vjera; Laffleur, Flavia; Bernkop-Schnürch, Andreas

    2015-09-30

    The aim of the present study was to investigate the influence of molecular mass and thiol group content of poly(acrylic acid)-cysteine conjugates on the permeation of sulforhodamine 101 and penicillin G. acting as substrates for multidrug resistance-associated protein 2 efflux pump. Poly(acrylic acids) of 2 kDa, 100 kDa, 250 kDa, 450 kDa and 3000 kDa were conjugated with cysteine. The thiol group content of all these polymers was in the range from 343.3 ± 48.4 μmol/g to 450.3 ± 76.1 μmol/g. Transport studies were performed on rat small intestine mounted in Ussing-type chambers. Since 250 kDa poly(acrylic acid) showed the highest permeation enhancing effect, additionally thiolated 250 kDa polyacrylates displaying 157.2 μmol/g, 223.0 ± 18.1 and 355.9 μmol/g thiol groups were synthesized in order to investigate the influence of thiol group content on the permeation enhancement. The permeation of sulforhodamine was 3.93- and 3.85-fold improved using 250 kDa poly(acrylic acid)-cysteine conjugate exhibiting 355.9 ± 39.5 μmol/g and 223.0 ± 18.1 μmol/g thiol groups. Using the same conjugates the permeation of penicillin G was 1.70- and 1.59-fold improved, respectively. The study demonstrates that thiolated poly(acrylic acid) inhibits Mrp2 mediated transport and that the extent of inhibition depends on the molecular mass and degree of thiolation of the polymer. PMID:26238816

  4. Experimental Raman and IR spectral and theoretical studies of vibrational spectrum and molecular structure of Pantothenic acid (vitamin B5)

    Srivastava, Mayuri; Singh, N. P.; Yadav, R. A.

    2014-08-01

    Vibrational spectrum of Pantothenic acid has been investigated using experimental IR and Raman spectroscopies and density functional theory methods available with the Gaussian 09 software. Vibrational assignments of the observed IR and Raman bands have been proposed in light of the results obtained from computations. In order to assign the observed IR and Raman frequencies the potential energy distributions (PEDs) have also been computed using GAR2PED software. Optimized geometrical parameters suggest that the overall symmetry of the molecule is C1. The molecule is found to possess eight conformations. Conformational analysis was carried out to obtain the most stable configuration of the molecule. In the present paper the vibrational features of the lowest energy conformer C-I have been studied. The two methyl groups have slightly distorted symmetries from C3V. The acidic Osbnd H bond is found to be the smallest one. To investigate molecular stability and bond strength we have used natural bond orbital analysis (NBO). Charge transfer occurs in the molecule have been shown by the calculated highest occupied molecular orbital-lowest unoccupied molecular orbital (HOMO-LUMO) energies. The mapping of electron density iso-surface with electrostatic potential (ESP), has been carried out to get the information about the size, shape, charge density distribution and site of chemical reactivity of the molecule.

  5. Photochromic switching of spiropyran in polymer matrices

    Janus, K.; Wierzchowiec, P.; Sworakowski, J.; Nešpůrek, Stanislav

    Poznan : Institute of Molecular Physics Polish Academy of Sciences, 2004. s. 40. [Conference on New Concepts and Materials for Molecular Electronics and Nanotechnology. 11.09.2004-15.09.2004, Puszczykovwo near Poznan] R&D Projects: GA ČR GA202/01/0518 Keywords : photochromism * switching * spiropyran Subject RIV: BM - Solid Matter Physics ; Magnetism

  6. Phragmites australis response to Cu in terms of low molecular weight organic acids (LMWOAs) exudation: Influence of the physiological cycle

    Rocha, A. Cristina S.; Almeida, C. Marisa R.; Basto, M. Clara P.; Vasconcelos, M. Teresa S. D.

    2014-06-01

    Plant roots have the ability to produce and secrete substances, such as aliphatic low molecular weight organic acids (ALMWOAs), into the rhizosphere for several purposes, including in response to metal contamination. Despite this, little is yet known about the exudation of such substances from marsh plants roots in response to metal exposure. This work aimed at assessing the influence of the physiological cycle of marsh plants on the exudation of ALMWOAs in response to Cu contamination. In vitro experiments were carried out with Phragmites australis specimens, collected in different seasons. Plant roots were exposed to freshwater contaminated with two different Cu concentrations (67 μg/L and 6.9 mg/L), being the ALMWOAs released by the roots measured. Significant differences (both qualitative and quantitative) were observed during the Phragmites australis life cycle. At growing stage, Cu stimulated the exudation of oxalic and formic acids but no significant stimulation was observed for citric acid. At developing stage, exposure to Cu caused inhibition of oxalic acid exudation whereas citric acid liberation was stimulated but only in the media spiked with the lowest Cu concentration tested. At the decaying stage, no significant variation on oxalic acid was observed, whereas the citric and formic acids release increased as a consequence of the plant exposure to Cu. The physiological cycle of Phragmites australis, and probably also of other marsh plants, is therefore an important feature conditioning plants response to Cu contamination, in terms of ALMWOAs exudation. Hence this aspect should be considered when conducting studies on rhizodeposition involving marsh plants exposed to metals and in the event of using marsh plants for phytoremediation purposes in contaminated estuarine areas.

  7. Molecularly imprinted poly(N-vinyl imidazole) based polymers grafted onto nonwoven fabrics for recognition/removal of phloretic acid

    A solution of N-vinyl imidazole (VIm), ethylene glycol dimethylacrylate (EGDMA), and phloretic acid (p-hydroxyphenylpropionic acid, HPPA) as functional monomer, crosslinker and template, respectively, were used to graft molecularly imprinted polymer (MIP) onto polyethylene/polypropylene (PE/PP) nonwoven fabric via gamma radiation at room temperature. Control grafted films were also synthesized using the same procedure in the absence of HPPA. Binding performance of the MIP grafts was investigated for different template molecule concentrations and contact time. An imprinting factor for the sample prepared at 5 kGy dose was determined as 2.41 for 50 ppm HPPA solution for 3-h incubation. MIP graft layers were investigated by positron annihilation lifetime spectroscopy (PALS) as well as SEM. - Highlights: • Molecularly imprinted matrices (MIP) of phloretic acid were prepared by radiation polymerization of N-vinyl imidazole. • Polymerization and crosslinking were achieved as a thin grafted layer on the surface of PE/PP nonwoven fabric. • Binding performance of MIP graft layers were found to show an imprinting factor of 2.41 for this template. • Grafted layers were characterized by SEM and PALS techniques. • Binding isotherms were found to follow double Langmuir isotherms

  8. Supra-molecular Association and Polymorphic Behaviour In Systems Containing Bile Acid Salts

    Camillo La Mesa; Patrizia Andreozzi; Marco Calabresi

    2007-01-01

    A wide number of supra-molecular association modes are observed in mixtures containing water and bile salts, BS, (with, eventually, other components). Molecular or micellar solutions transform into hydrated solids, fibres, lyotropic liquid crystals and/or gels by raising the concentration, the temperature, adding electrolytes, surfactants, lipids and proteins. Amorphous or ordered phases may be formed accordingly. The forces responsible for this very rich polymorphism presumably arise from th...

  9. pfaB products determine the molecular species produced in bacterial polyunsaturated fatty acid biosynthesis

    Orikasa, Yoshitake; TANAKA, Mika; Sugihara, Shinji; Hori, Ryuji; Nishida, Takanori; Ueno, Akio; Morita, Naoki; Yano, Yutaka; Yamamoto, Kouhei; SHIBAHARA, Akira; Hayashi, Hidenori; Yamada, Yohko; Yamada, Akiko; Yu, Reiko; Watanabe, Kazuo

    2009-01-01

    When pDHA4, a vector carrying all five pfaA-pfaE genes responsible for docosahexaenoic acid (DHA; 22:6) biosynthesis in Moritella marina MP-1, was coexpressed in Escherichia coli with the individual pfaA-pfaD genes for eicosapentaenoic acid (EPA; 20:5) biosynthesis from Shewanella pneumatophori SCRC-2738, both polyunsaturated fatty acids were synthesized only in the recombinant carrying pfaB for EPA synthesis. Escherichia coli coexpressing a deleted construct comprising pfaA, pfaC, pfaD and p...

  10. Membrane Disruption by Antimicrobial Fatty Acids Releases Low-Molecular-Weight Proteins from Staphylococcus aureus

    Parsons, Joshua B; Yao, Jiangwei; Frank, Matthew W.; Jackson, Pamela; Rock, Charles O

    2012-01-01

    The skin represents an important barrier for pathogens and is known to produce fatty acids that are toxic toward Gram-positive bacteria. A screen of fatty acids as growth inhibitors of Staphylococcus aureus revealed structure-specific antibacterial activity. Fatty acids like oleate (18:1Δ9) were nontoxic, whereas palmitoleate (16:1Δ9) was a potent growth inhibitor. Cells treated with 16:1Δ9 exhibited rapid membrane depolarization, the disruption of all major branches of macromolecular synthes...

  11. Acid hydrolysis and molecular density of phytoglycogen and liver glycogen helps understand the bonding in glycogen α (composite particles.

    Prudence O Powell

    Full Text Available Phytoglycogen (from certain mutant plants and animal glycogen are highly branched glucose polymers with similarities in structural features and molecular size range. Both appear to form composite α particles from smaller β particles. The molecular size distribution of liver glycogen is bimodal, with distinct α and β components, while that of phytoglycogen is monomodal. This study aims to enhance our understanding of the nature of the link between liver-glycogen β particles resulting in the formation of large α particles. It examines the time evolution of the size distribution of these molecules during acid hydrolysis, and the size dependence of the molecular density of both glucans. The monomodal distribution of phytoglycogen decreases uniformly in time with hydrolysis, while with glycogen, the large particles degrade significantly more quickly. The size dependence of the molecular density shows qualitatively different shapes for these two types of molecules. The data, combined with a quantitative model for the evolution of the distribution during degradation, suggest that the bonding between β into α particles is different between phytoglycogen and liver glycogen, with the formation of a glycosidic linkage for phytoglycogen and a covalent or strong non-covalent linkage, most probably involving a protein, for glycogen as most likely. This finding is of importance for diabetes, where α-particle structure is impaired.

  12. Surface grafted chitosan gels. Part I. Molecular insight into the formation of chitosan and poly(acrylic acid) multilayers

    Liu, Chao; Thormann, Esben; Claesson, Per M.;

    2014-01-01

    Composite polyelectrolyte multilayers of chitosan and low molecular weight poly(acrylic acid) (PAA) have been assembled by sequential adsorption as a first step toward building a surface anchored chitosan gel. Silane chemistry was used to graft the first chitosan layer to prevent film detachment...... and decomposition. The assembly process is characterized by nonlinear growth behavior, with different adsorption kinetics for chitosan and PAA. In situ analysis of the multilayer by means of surface sensitive total internal reflection Raman (TIRR) spectroscopy, combined with target factor analysis of...... steps. The higher molecular weight chitosan shows a similar behavior, although to a much lower extent. Our data demonstrate that the charged monomeric units of chitosan are mainly compensated by carboxylate ions from PAA. Furthermore, the morphology and mechanical properties of the multilayers were...

  13. Peptide nucleic acid: a new artificial biomacromolecular with great potential applications in molecular biology and biomedicine

    WANG Jin-ke; LU Zu-hong; HE Nong-yue

    2001-01-01

    @@ Peptide nucleic acid (PNA) is a DNA mimic that was originally developed by Peter E Nielsen in 1991 as a reagent for sequence-specific recognition of double stranded (ds) DNA by a conventional triple helix type principle.

  14. Tetrazolyl isoxazole amino acids as ionotropic glutamate receptor antagonists: synthesis, modelling and molecular pharmacology

    Frølund, Bente; Greenwood, Jeremy R; Holm, Mai Marie;

    2005-01-01

    and 1b were pharmacologically characterized in receptor binding assays, and electrophysiologically on homomeric AMPA receptors (GluR1-4), homomeric (GluR5 and GluR6) and heteromeric (GluR6/KA2) kainic acid receptors, using two-electrode voltage-clamped Xenopus laevis oocytes expressing these receptors...... kainic acid receptor subtypes (GluR5 and GluR6/KA2), showing sevenfold preference for GluR6/KA2 (Kb=19 microM). Unlike the iGluR antagonist (S)-2-amino-3-[5-tert-butyl-3-(phosphonomethoxy)-4-isoxazolyl]propionic acid [(S)-ATPO], the corresponding tetrazolyl analogue, 1b, lacks kainic acid receptor...

  15. Molecular Characterization of Intrinsic and Acquired antibiotic resistance in lactic Acid bacteria and Bifidobacteria

    Ammor, M.S.; Flórez, A.B.; Hoek, van A.H.A.M.; Reyes-Gavilan, de los C.G.; Aarts, H.J.M.; Margolles, A.; Mayo, B.

    2008-01-01

    The minimum inhibitory concentrations (MICs) of 6 different antibiotics (chloramphenicol, clindamycin, erythromycin, streptomycin, tetracycline and vancomycin) were determined for 143 strains of lactic acid bacteria and bifidobacteria using the Etest. Different MICs were found for different species

  16. Molecular characteristics of humic acids isolated from vermicomposts and their relationship to bioactivity.

    Martinez-Balmori, Dariellys; Spaccini, Riccardo; Aguiar, Natália Oliveira; Novotny, Etelvino Henrique; Olivares, Fábio Lopes; Canellas, Luciano Pasqualoto

    2014-11-26

    Vermitechnology is an effective composting method, which transforms biomass into nutrient-rich organic fertilizer. Mature vermicompost is a renewable organic product containing humic substances with high biological activity. The aim of this study was to assess the chemical characteristics and the bioactivity of humic acids isolated from different vermicomposts produced with either cattle manure, sugar cane bagasse, sunflower cake from seed oil extraction, or filter cake from a sugar cane factory. More than 200 different molecules were found, and it was possible to identify chemical markers on humic acids according to the nature of the organic source. The large hydrophobic character of humic extracts and the preservation of altered lignin derivatives confer to humic acids the ability to induce lateral root emergence in maize seedlings. Humic acid-like substances extracted from plant biomass residues represent an additional valuable product of vermicomposting that can be used as a plant growth promoter. PMID:25379603

  17. Phenotypic, genetic and molecular characterization of a maize low phytic acid mutant (lpa241)

    Pilu, R.; Panzeri, D.; Gavazzi, G.;

    2003-01-01

    Phytic acid, myo-inositol 1,2,3,4,5,6-hexakisphosphate, is the major storage compound of phosphorous (P) in plants, predominantly accumulating in seeds (up to 4-5% of dry weight) and pollen. In cereals, phytic acid is deposited in embryo and aleurone grain tissues as a mixed 'phytate' salt of...... potassium and magnesium, although phytates contain other mineral cations such as iron and zinc. During germination, phytates are broken down by the action of phytases, releasing their P, minerals and myo-inositol which become available to the growing seedling. Phytic acid represents an anti......-nutritional factor for animals, and isolation of maize low phytic acid (lpa) mutants provides a novel approach to study its biochemical pathway and to tackle the nutritional problems associated with it. Following chemical mutagenesis of pollen, we have isolated a viable recessive mutant named lpa 241 showing about...

  18. Experimental and Molecular Dynamics Simulations for Investigating the Effect of Fatty Acid and Its Derivatives on Low Sulfur Diesel Lubricity

    Luo Hui; Fan Weiyu; Li Yang; Zhao Pinhui; Nan Guozhi

    2013-01-01

    In this work, fatty acid and its derivatives were adopted as lubricity additives for low sulfur diesel. Tribological evaluation obtained from the High-Frequency Reciprocating Rig (HFRR) apparatus showed that the lubricating performance of the additives increased in the following order:stearic acid>glycol monopalmitate>stearyl alcohol>ethyl palmitate>cetyl ethyl ether. The adsorption behavior of the additives on Fe (110) surface and Fe2O3 (001) surface was investigated by mo-lecular dynamics (MD) simulations to verify their lubricity performance. The results suggested that adsorption energies of the additives on Fe (110) surface are determined by the van der Waals forces, while adsorptions on Fe2O3 (001) surface are signiifcantly attributed to the electrostatic attractive forces. Higher values of adsorption energy of the additives on Fe2O3 (001) surface indicate that the additive has more efifcient lubricity enhancing properties.

  19. A new multi-addressable molecular switch based on a photochromic diarylethene with a 6-aryl[1,2-c]quinazoline unit

    Jia, Hongjing; Pu, Shouzhi; Fan, Congbin; Liu, Gang

    2015-03-01

    A novel diarylethene with a 6-aryl[1,2-c]quinazoline unit has been synthesized via a nucleophilic reaction. Its photochromism and fluorescence exhibited multi-addressable behaviors by the stimulation of both light irradiation and acid/base. Addition of trifluoroacetic acid to the solution of the diarylethene resulted in notable absorption spectral change, and the protonated form also possessed excellent photochromic properties. Meanwhile, its emission intensity was enhanced remarkably and the emission peak redshifted with a notable color change from dark blue to bright green. The changes could be recovered to the initial state by neutralizing with triethylamine. Consequently, a logic circuit was constructed with the diarylethene by using the fluorescence intensity at 482 nm as output and acid/base as inputs.

  20. Ongoing Immunoglobulin Class Switch DNA Recombination in Lupus B Cells: Analysis of Switch Regulatory Regions

    Liu, Shiquan; Cerutti, Andrea; Casali, Paolo; CROW, MARY K.

    2004-01-01

    Inflammation and tissue damage in systemic lupus erythematosus (SLE) are mediated by class-switched autoantibodies reactive with nucleic acids, nucleic acid-binding proteins, phospholipids and other self-antigens. While some healthy individuals produce IgM antibodies with specificities similar to those of lupus patients, immunoglobulin class switching to mature downstream isotypes appears to be required for the generation of pathogenic autoantibodies. To characterize the cellular and molecula...

  1. Molecular assembly of amino acid interlinked, topologically symmetric, π-complementary donor-acceptor-donor triads.

    Avinash, M B; Sandeepa, K V; Govindaraju, T

    2013-01-01

    Amino acid interlinked pyrene and naphthalenediimide (NDI) based novel donor-acceptor-donor (D-A-D) triads are designed to exploit their topological symmetry and complementary π-character for facile charge-transfer complexation. Consequently, free-floating high-aspect-ratio supercoiled nanofibres and hierarchical helical bundles of triads are realized by modulating the chemical functionality of interlinking amino acids. PMID:23946856

  2. Molecular assembly of amino acid interlinked, topologically symmetric, π-complementary donor–acceptor–donor triads

    Avinash, M B; Sandeepa, K V

    2013-01-01

    Summary Amino acid interlinked pyrene and naphthalenediimide (NDI) based novel donor–acceptor–donor (D-A-D) triads are designed to exploit their topological symmetry and complementary π-character for facile charge-transfer complexation. Consequently, free-floating high-aspect-ratio supercoiled nanofibres and hierarchical helical bundles of triads are realized by modulating the chemical functionality of interlinking amino acids. PMID:23946856

  3. Molecular assembly of amino acid interlinked, topologically symmetric, π-complementary donor–acceptor–donor triads

    M. B. Avinash

    2013-08-01

    Full Text Available Amino acid interlinked pyrene and naphthalenediimide (NDI based novel donor–acceptor–donor (D-A-D triads are designed to exploit their topological symmetry and complementary π-character for facile charge-transfer complexation. Consequently, free-floating high-aspect-ratio supercoiled nanofibres and hierarchical helical bundles of triads are realized by modulating the chemical functionality of interlinking amino acids.

  4. Local piezoresponse and polarization switching in nucleobase thymine microcrystals

    Bdikin, Igor; Heredia, Alejandro; Neumayer, Sabine M.; Bystrov, Vladimir S.; Gracio, José; Rodriguez, Brian J.; Kholkin, Andrei L.

    2015-08-01

    Thymine (2-oxy-4-oxy-5 methyl pyrimidine) is one of the four nucleobases of deoxyribonucleic acid (DNA). In the DNA molecule, thymine binds to adenine via two hydrogen bonds, thus stabilizing the nucleic acid structure and is involved in pairing and replication. Here, we show that synthetic thymine microcrystals grown from the solution exhibit local piezoelectricity and apparent ferroelectricity, as evidenced by nanoscale electromechanical measurements via Piezoresponse Force Microscopy. Our experimental results demonstrate significant electromechanical activity and polarization switchability of thymine, thus opening a pathway for piezoelectric and ferroelectric-based applications of thymine and, perhaps, of other DNA nucleobase materials. The results are supported by molecular modeling of polarization switching under an external electric field.

  5. Factors affecting the interactions between beta-lactoglobulin and fatty acids as revealed in molecular dynamics simulations.

    Yi, Changhong; Wambo, Thierry O

    2015-09-21

    Beta-lactoglobulin (BLG), a bovine dairy protein, is a promiscuously interacting protein that can bind multiple hydrophobic ligands. Fatty acids (FAs), common hydrophobic molecules bound to BLG, are important sources of fuel for life because they yield large quantities of ATP when metabolized. The binding affinity increases with the length of the ligands, indicating the importance of the van der Waals (vdW) interactions between the hydrocarbon tail and the hydrophobic calyx of BLG. An exception to this rule is caprylic acid (OCA) which is two-carbon shorter but has a stronger binding affinity than capric acid. Theoretical calculations in the current literature are not accurate enough to shed light on the underlying physics of this exception. The computed affinity values are greater for longer fatty acids without respect for the caprylic exception and those values are generally several orders of magnitude away from the experimental data. In this work, we used hybrid steered molecular dynamics to accurately compute the binding free energies between BLG and the five saturated FAs of 8 to 16 carbon atoms. The computed binding free energies agree well with experimental data not only in rank but also in absolute values. We gained insights into the exceptional behavior of caprylic acid in the computed values of entropy and electrostatic interactions. We found that the electrostatic interaction between the carboxyl group of caprylic acid and the two amino groups of K60/69 in BLG is much stronger than the vdW force between the OCA's hydrophobic tail and the BLG calyx. This pulls OCA to the top of the beta barrel where it is easier to fluctuate, giving rise to greater entropy of OCA at the binding site. PMID:26272099

  6. Molecularly imprinted polymer-matrix nanocomposite for enantioselective electrochemical sensing of D- and L-aspartic acid

    A new molecularly imprinted polymer-matrix (titanium dioxide nanoparticle/multiwalled carbon nanotubes) nanocomposite was developed for the modification of pencil graphite electrode as an enantioselective sensing probe for aspartic acid isomers, prevalent at ultra trace level in aqueous and real samples. The nanocomposite having many shape complementary cavities was synthesized adopting surface initiated-activators regenerated by electron transfer for atom transfer radical polymerization. The proposed sensor has high stability, nanocomposite uniformity, good reproducibility, and enhanced electrocatalytic activity to respond oxidative peak current of L-aspartic acid quantitatively by differential pulse anodic stripping voltammetry, without any cross-reactivity in real samples. Under the optimized operating conditions, the L-aspartic acid imprinted modified electrode showed a wide linear response for L-aspartic acid within the concentration range 9.98–532.72 ng mL−1, with the minimum detection limit of 1.73–1.79 ng mL−1 (S/N = 3) in aqueous and real samples. Almost similar stringent limit (1.79 ng mL−1) was obtained with cerebrospinal fluid which is typical for the primitive diagnosis of neurological disorders, caused by an acute depletion of L-aspartic acid biomarker, in clinical settings. Highlights: • We have adopted surface initiated-activators regenerated by electron transfer for atom transfer radical polymerization. This approach takes advantage of the nanostructured ultrathin imprinted film. • Successful enantioselective sensing and ultratrace analysis of D- and L-aspartic acid. • Stringent detection limit without any non-specific false-positive contribution

  7. Probing thermal stability of the β-lactoglobulin-oleic acid complex by fluorescence spectroscopy and molecular modeling

    Simion (Ciuciu), Ana-Maria; Aprodu, Iuliana; Dumitrașcu, Loredana; Bahrim, Gabriela Elena; Alexe, Petru; Stănciuc, Nicoleta

    2015-09-01

    Bovine β-lactoglobulin is able to interact with different bioactive compounds, thus being an important candidate in the development of delivery systems with improved functionality. The heat induced changes in the β-lactoglobulin-oleic acid complex were examined by means of fluorescence spectroscopy and molecular modeling techniques. Fluorescence spectroscopy results indicated a rigid protein structure in the temperature range 25-70 °C, whereas at temperatures over 75 °C, the rearrangements of the polypeptide chains led to higher exposure of hydrophobic residues. The most significant increase of the accessible surface area with temperature increase was identified in case of Tyr99 and Tyr102. The phase diagram method indicated an all or none transition between two conformations. Due to conformational changes, no contact between Ile56 or Lys60 and the fatty acid could be identified at 85 °C, but new non-bonding interaction were established with Ile12 and Val15. The results obtained in this study provide important details about thermal induced changes in the conformation of β-lactoglobulin-oleic acid complex. Significant conformational changes were registered above 75 °C, suggesting the possibility of obtaining highly functional complexes between whey proteins and natural unsaturated fatty acids.

  8. Molecular cloning and expression in Escherichia coli of an active fused Zea mays L. D-amino acid oxidase.

    Gholizadeh, A; Kohnehrouz, B B

    2009-02-01

    D-Amino acid oxidase (DAAO) is an FAD-dependent enzyme that metabolizes D-amino acids in microbes and animals. However, such ability has not been identified in plants so far. We predicted a complete DAAO coding sequence consisting of 1158 bp and encoding a protein of 386 amino acids. We cloned this sequence from the leaf cDNA population of maize plants that could utilize D-alanine as a nitrogen source and grow normally on media containing D-Ala at the concentrations of 100 and 1000 ppm. For more understanding of DAAO ability in maize plant, we produced a recombinant plasmid by the insertion of isolated cDNA into the pMALc2X Escherichia coli expression vector, downstream of the maltose-binding protein coding sequence. The pMALc2X-DAAO vector was used to transform the TB1 strain of E. coli cells. Under normal growth conditions, fused DAAO (with molecular weight of about 78 kDa) was expressed up to 5 mg/liter of bacterial cells. The expressed product was purified by affinity chromatography and subjected to in vitro DAAO activity assay in the presence of five different D-amino acids. Fused DAAO could oxidize D-alanine and D-aspartate, but not D-leucine, D-isoleucine, and D-serine. The cDNA sequence reported in this paper has been submitted to EMBL databases under accession number AM407717. PMID:19267668

  9. Production of nanocrystalline cellulose from an empty fruit bunches using sulfuric acid hydrolysis: Effect of reaction time on the molecular characteristics

    Al-Dulaimi, Ahmed A.; R, Rohaizu; D, Wanrosli W.

    2015-06-01

    Nanocrystalline cellulose (NCC) was isolated from OPEFB pulp via sulfuric acid hydrolysis. The influence of reaction time to the molecular weight and surface charge of the NCC was investigated. Characterization of the product was carried out using zeta potential measurement and gel permeation chromatography test. Zeta potential measurement showed that the surface negative charge significantly increases with increasing reaction time. Gel permeation chromatography test indicates that molecular weight of NCC change variably with increasing of hydrolysis time. (Keywords: Nanocrystalline cellulose; acid hydrolysis; sulfate content; molecular weight)

  10. Molecular interactions between nucleic acids and antitumor substances by Raman and NMR spectroscopy.

    Bertoluzza, A; Fagnano, C; Tosi, R; Tugnoli, V; Morelli, M A; Barbarella, G

    1986-01-01

    1-Methyladenosine (1-MeAdo) and protonated 1-Methyladenosine (1-MeAdo.H+) were chosen as a model to study the molecular interactions between the carcinogen dimethylsulphate (DMS) and the base adenine, and the interactions between the antitumoral electrophilic cis-diamminedichlorophatinum (II) (cis-Pt) and the methylation product of the base, respectively. Raman and multinuclear NMR studies show the molecular perturbations caused by the carcinogen on the base and those of the antitumoral substance on the reaction product base-carcinogen. PMID:3813493

  11. Improved Inhibition of Telomerase by Short Twisted Intercalating Nucleic Acids under Molecular Crowding Conditions

    Agarwal, Tani; Pradhan, Devranjan; Géci, Imrich;

    2012-01-01

    Human telomeric DNA has the ability to fold into a 4-stranded G-quadruplex structure. Several G-quadruplex ligands are known to stabilize the structure and thereby inhibit telomerase activity. Such ligands have demonstrated efficient telomerase inhibition in dilute conditions, but under molecular......-based telomerase repeat amplification assay (TRAP) assay as well as nondenaturing polyacrylamide gel electrophoresis-based TRAP, we demonstrate remarkable enhancement in their anti-telomerase activity even under molecular crowding conditions. This is the first time in which a G-quadruplex stabilizing agent has...

  12. A mezoscopic model of nucleic acids. Part 1. Lagrangian and quaternion molecular dynamics.

    Rudnicki, W R; Bakalarski, G; Lesyng, B

    2000-06-01

    This study presents a model for mezoscopic molecular dynamics simulations with objects of different scale and properties e.e. atoms, pseudoatoms, rigid and pseudo-elastic bodies, described by the external coordinates and internal degrees of freedom. The Lagrangian approach is used to derive equations of motion and a quaternion representation is used for the description of the dynamics of rigid and pseudo-elastic molecular elements. Stability of the LQMD algorithm was tested for a 10-base pair deoxynucleotide. The total energy, momentum and angular momentum are conserved for time-steps up to 20 fs. PMID:10949175

  13. Bio molecular Tri conjugates Formed between Gold, Protamine, and Nucleic Acid: Comparative Characterization on the Nano scale

    DNA and RNA micro- and nanoparticles are increasingly being used for gene and si RNA drug delivery and a variety of other applications in bio nano technology. On the nano scale, these entities represent unique challenges from a physicochemical characterization perspective. Here, nucleic acid conjugates with protamine and gold nanoparticles (GNP) were characterized comparatively in the nano range of concentration by UV/Vis Nano Drop spectroscopy, fluorimetry, and gel electrophoresis. Given the intense interest in splice-site switching oligomers (SSOs), we utilized a human tumor cell culture system (HeLa pLuc-705), in which SSO-directed splicing repair up regulates luciferase expression, in order to investigate bioactivity of the bio nano conjugates. Process parameters important for bioactivity were investigated, and the bimolecular nano conjugates were confirmed by shifts in the dynamic laser light scatter (DLLS), UV/Vis spectrum, gel electrophoresis, or sedimentation pattern. The data presented herein may be useful in the future development of pharmaceutical and biotechnology formulations, processes, and analyses concerning protein, DNA, or RNA bio nano conjugates.

  14. Molecular Basis of Prodrug Activation by Human Valacyclovirase, an [alpha]-Amino Acid Ester Hydrolase

    Lai, Longsheng; Xu, Zhaohui; Zhou, Jiahai; Lee, Kyung-Dall; Amidon, Gordon L. (Michigan)

    2008-07-08

    Chemical modification to improve biopharmaceutical properties, especially oral absorption and bioavailability, is a common strategy employed by pharmaceutical chemists. The approach often employs a simple structural modification and utilizes ubiquitous endogenous esterases as activation enzymes, although such enzymes are often unidentified. This report describes the crystal structure and specificity of a novel activating enzyme for valacyclovir and valganciclovir. Our structural insights show that human valacyclovirase has a unique binding mode and specificity for amino acid esters. Biochemical data demonstrate that the enzyme hydrolyzes esters of {alpha}-amino acids exclusively and displays a broad specificity spectrum for the aminoacyl moiety similar to tricorn-interacting aminopeptidase F1. Crystal structures of the enzyme, two mechanistic mutants, and a complex with a product analogue, when combined with biochemical analysis, reveal the key determinants for substrate recognition; that is, a flexible and mostly hydrophobic acyl pocket, a localized negative electrostatic potential, a large open leaving group-accommodating groove, and a pivotal acidic residue, Asp-123, after the nucleophile Ser-122. This is the first time that a residue immediately after the nucleophile has been found to have its side chain directed into the substrate binding pocket and play an essential role in substrate discrimination in serine hydrolases. These results as well as a phylogenetic analysis establish that the enzyme functions as a specific {alpha}-amino acid ester hydrolase. Valacyclovirase is a valuable target for amino acid ester prodrug-based oral drug delivery enhancement strategies.

  15. Molecular Properties of Guar Gum and Pectin Modify Cecal Bile Acids, Microbiota, and Plasma Lipopolysaccharide-Binding Protein in Rats.

    Ghaffarzadegan, Tannaz; Marungruang, Nittaya; Fåk, Frida; Nyman, Margareta

    2016-01-01

    Bile acids (BAs) act as signaling molecules in various physiological processes, and are related to colonic microbiota composition as well as to different types of dietary fat and fiber. This study investigated whether guar gum and pectin-two fibers with distinct functional characteristics-affect BA profiles, microbiota composition, and gut metabolites in rats. Low- (LM) or high-methoxylated (HM) pectin, and low-, medium-, or high-molecular-weight (MW) guar gum were administered to rats that were fed either low- or high-fat diets. Cecal BAs, short-chain fatty acids (SCFA) and microbiota composition, and plasma lipopolysaccharide-binding protein (LBP) levels were analyzed, by using novel methodologies based on gas chromatography (BAs and SCFAs) and 16S rRNA gene sequencing on the Illumina MiSeq platform. Strong correlations were observed between cecal BA and SCFA levels, microbiota composition, and portal plasma LBP levels in rats on a high-fat diet. Notably, guar gum consumption with medium-MW increased the cecal amounts of cholic-, chenodeoxycholic-, and ursodeoxycholic acids as well as α-, β-, and ω-muricholic acids to a greater extent than other types of guar gum or the fiber-free control diet. In contrast, the amounts of cecal deoxycholic- and hyodeoxycholic acid were reduced with all types of guar gum independent of chain length. Differences in BA composition between pectin groups were less obvious, but cecal levels of α- and ω-muricholic acids were higher in rats fed LM as compared to HM pectin or the control diet. The inflammatory marker LBP was downregulated in rats fed medium-MW guar gum and HM pectin; these two fibers decreased the cecal abundance of Oscillospira and an unclassified genus in Ruminococcaceae, and increased that of an unclassified family in RF32. These results indicate that the molecular properties of guar gum and pectin are important for their ability to modulate cecal BA formation, gut microbiota composition, and high-fat diet induced

  16. Molecular Properties of Guar Gum and Pectin Modify Cecal Bile Acids, Microbiota, and Plasma Lipopolysaccharide-Binding Protein in Rats.

    Tannaz Ghaffarzadegan

    Full Text Available Bile acids (BAs act as signaling molecules in various physiological processes, and are related to colonic microbiota composition as well as to different types of dietary fat and fiber. This study investigated whether guar gum and pectin-two fibers with distinct functional characteristics-affect BA profiles, microbiota composition, and gut metabolites in rats. Low- (LM or high-methoxylated (HM pectin, and low-, medium-, or high-molecular-weight (MW guar gum were administered to rats that were fed either low- or high-fat diets. Cecal BAs, short-chain fatty acids (SCFA and microbiota composition, and plasma lipopolysaccharide-binding protein (LBP levels were analyzed, by using novel methodologies based on gas chromatography (BAs and SCFAs and 16S rRNA gene sequencing on the Illumina MiSeq platform. Strong correlations were observed between cecal BA and SCFA levels, microbiota composition, and portal plasma LBP levels in rats on a high-fat diet. Notably, guar gum consumption with medium-MW increased the cecal amounts of cholic-, chenodeoxycholic-, and ursodeoxycholic acids as well as α-, β-, and ω-muricholic acids to a greater extent than other types of guar gum or the fiber-free control diet. In contrast, the amounts of cecal deoxycholic- and hyodeoxycholic acid were reduced with all types of guar gum independent of chain length. Differences in BA composition between pectin groups were less obvious, but cecal levels of α- and ω-muricholic acids were higher in rats fed LM as compared to HM pectin or the control diet. The inflammatory marker LBP was downregulated in rats fed medium-MW guar gum and HM pectin; these two fibers decreased the cecal abundance of Oscillospira and an unclassified genus in Ruminococcaceae, and increased that of an unclassified family in RF32. These results indicate that the molecular properties of guar gum and pectin are important for their ability to modulate cecal BA formation, gut microbiota composition, and high

  17. Adenylyl cyclase-5 in the dorsal striatum function as a molecular switch for the generation of behavioral preferences for cue-directed food choices

    Kim, Hannah; Kim, Tae-Kyung; KIM, Ji-Eun; Park, Jin-Young; Lee, Yunjin; Kang, Minkyung; Kim, Kyoung-Shim; Han, Pyung-Lim

    2014-01-01

    Background Behavioral choices in habits and innate behaviors occur automatically in the absence of conscious selection. These behaviors are not easily modified by learning. Similar types of behaviors also occur in various mental illnesses including drug addiction, obsessive-compulsive disorder, schizophrenia, and autism. However, underlying mechanisms are not clearly understood. In the present study, we investigated the molecular mechanisms regulating unconditioned preferred behaviors in food...

  18. Crystal and molecular structure of adduct of 6-benzylaminopurine and 5-sulfosalicylic acid

    The crystal structure of adduct of 6-benzylaminopurine and 5-sulfosalicylic acid C19H25N5O10S 1 is studied using single-crystal diffraction (R = 0.0482 for 2852 reflections with I > 2σ(I)). The asymmetric unit of 1 contains one 6-benzylaminopurine molecule and one 5-sulfosalicylic acid molecule, as well as four lattice water molecules. Hydrogen bonds, formed by 6-benzylaminopurine and 5-sulfosalicylic acid, link the two molecules into one-dimensional chain (omitting four water molecules), further joined to two-dimensional layer network. Short ring-interactions with intra-chain π-π stacking are observed. The data of IR spectroscopy confirm the formation of the two-dimensional supramolecular layer structure. At last, a 3D supramolecular network constructs via hydrogen bonds.

  19. Exciton interaction in molecular beacons: a sensitive sensor for short range modifications of the nucleic acid structure.

    Bernacchi, S; Mély, Y

    2001-07-01

    Molecular beacons are hairpin-shaped, single-stranded oligonucleotides constituting sensitive fluorescent DNA probes widely used to report the presence of specific nucleic acids. In its closed form the stem of the hairpin holds the fluorophore covalently attached to one end, close to the quencher, which is covalently attached to the other end. Here we report that in the closed form the fluorophore and the quencher form a ground state intramolecular heterodimer whose spectral properties can be described by exciton theory. Formation of the heterodimers was found to be poorly sensitive to the stem sequence, the respective positions of the dyes and the nature of the nucleic acid (DNA or RNA). The heterodimer allows strong coupling between the transition dipoles of the two chromophores, leading to dramatic changes in the absorption spectrum that are not compatible with a Förster-type fluorescence resonance energy transfer (FRET) mechanism. The excitonic heterodimer and its associated absorption spectrum are extremely sensitive to the orientation of and distance between the dyes. Accordingly, the application of molecular beacons can be extended to monitoring short range modifications of the stem structure. Moreover, the excitonic interaction was also found to operate for doubly end-labeled duplexes. PMID:11433038

  20. Preparation of ellagic acid molecularly imprinted polymeric microspheres based on distillation-precipitation polymerization for the efficient purification of a crude extract.

    Zhang, Hua; Zhao, Shangge; Zhang, Lu; Han, Bo; Yao, Xincheng; Chen, Wen; Hu, Yanli

    2016-08-01

    Molecularly imprinted polymeric microspheres with a high recognition ability toward the template molecule, ellagic acid, were synthesized based on distillation-precipitation polymerization. The as-obtained polymers were characterized by scanning electron microscopy, infrared spectroscopy, and thermogravimetric analysis. Static, dynamic, and selective binding tests were adopted to study the binding properties and the molecular recognition ability of the prepared polymers for ellagic acid. The results indicated that the maximum static adsorption capacity of the prepared polymers toward ellagic acid was 37.07 mg/g and the adsorption equilibrium time was about 100 min when the concentration of ellagic acid was 40 mg/mL. Molecularly imprinted polymeric microspheres were also highly selective toward ellagic acid compared with its analogue quercetin. It was found that the content of ellagic acid in the pomegranate peel extract was enhanced from 23 to 86% after such molecularly imprinted solid-phase extraction process. This work provides an efficient way for effective separation and enrichment of ellagic acid from complex matrix, which is especially valuable in industrial production. PMID:27311588

  1. Visualization of Early Events in Acetic Acid Denaturation of HIV-1 Protease: A Molecular Dynamics Study

    Borkar, Aditi Narendra; Rout, Manoj Kumar; Hosur, Ramakrishna V.

    2011-01-01

    Protein denaturation plays a crucial role in cellular processes. In this study, denaturation of HIV-1 Protease (PR) was investigated by all-atom MD simulations in explicit solvent. The PR dimer and monomer were simulated separately in 9 M acetic acid (9 M AcOH) solution and water to study the denaturation process of PR in acetic acid environment. Direct visualization of the denaturation dynamics that is readily available from such simulations has been presented. Our simulations in 9 M AcOH re...

  2. An alternating copolymer of maleimide and atropic acid with narrow molecular weight distribution prepared by radical mechanism

    万德成; 黄兆华; 黄骏廉

    1999-01-01

    Three basic conditions for preparation of alternating copolymer with narrow molecular weight distribution were derived from the element kinetic equations of binary radical copolymerization. Using maleimide (MI) and atropie acid (ATA) as model monomer pairs and dioxane as the solvent the alternating copolymer with molecular weight distribution in the range of 1.09--1.20 was prepared successfully by charger transfer complex (CTC) mechanism in the presence of benzoyl peroxide at 85℃. The monomer reactivity ratioes r1(MI)=0.05±0.01 and r2(ATA)=0.03±0.02 were measured. The alternating eopolymerization was carried out through formation of a contact-type CTG and then alternating addition of MI and ATA monomers. The molecular weight of the copolymers is nearly independent of the feed ratio in a large range and the polymerization rate dropped with an increase in ATA in feed ratio.

  3. Separation of rare earths by means of acid organophosphorous compounds. Structure-activity study by molecular simulation

    The increasing number of industrial applications of rare earths has resulted in an increased demand in purified rare earths whereas their separation is difficult due to their high chemical similarity. The search for a better separation leads to the search for more selective extraction agents. Organophosphorous compounds appear to be the most selective. As the search for new extraction agents resulting in high lanthanide extraction efficiency or in a better selectivity between rare earths has been mainly empiric, this research thesis aims at developing a molecular simulation method which allows the number of molecules to be synthesized and tested to be reduced. After having briefly recalled general knowledge on liquid-liquid extraction and on rare earths, and described calculation methods (quantum methods, methods based on molecular mechanics, conformational analysis, methods of charge calculation), the author proposes a critical review of literature related to rare earth liquid-liquid extraction by organophosphorous acids with respect to the used extraction agent. The molecular modelling issue is then addressed by describing ways to apply it to extraction problems, faced problems, brought solutions and obtained results

  4. Chemical modification of chitosan film via surface grafting of citric acid molecular to promote the biomineralization

    Liu, Yang; Shen, Xin; Zhou, Huan; Wang, Yingjun; Deng, Linhong

    2016-05-01

    We develop a novel chitosan-citric acid film (abbreviated as CS-CA) suitable for biomedical applications in this study. In this CS-CA film, the citric acid, which is a harmless organic acid has been extensively investigated as a modifying agent on carbohydrate polymers, was cross-linked by 1-Ethyl-3-(3-dimethyl aminopropyl) carbodiimide (EDC) and N-hydroxysuccinimide (NHS) onto the surface of chitosan (CS) film. Fourier transform infrared spectroscopy (FTIR) and X-ray photoelectron spectroscopy (XPS) confirms the graft copolymerization of the modified chitosan film (CS-CA). Surface wettability, moisturizing performance, the capacity of mineralization in vitro and biocompatibility of the films were characterized. After modification, this CS-CA film has good hydrophilicity. It is very evident that the citric acid grafting treatment significantly promotes the biomineralization of the chitosan based substrates. Cell experiments show that the MC3T3-E1 osteoblasts can adhere and proliferate well on the surface of CS-CA film. This CS-CA film, which can be prepared in large quantities and at low cost, should have potential application in bone tissue engineering.

  5. Molecular mechanisms and cell signaling of 20-hydroxyeicosatetraenoic acid in vascular pathophysiology.

    Fan, Fan; Ge, Ying; Lv, Wenshan; Elliott, Matthew R; Muroya, Yoshikazu; Hirata, Takashi; Booz, George W; Roman, Richard J

    2016-01-01

    Cytochrome P450s enzymes catalyze the metabolism of arachidonic acid to epoxyeicosatrienoic acids (EETs), dihydroxyeicosatetraenoic acid and hydroxyeicosatetraeonic acid (HETEs). 20-HETE is a vasoconstrictor that depolarizes vascular smooth muscle cells by blocking K+ channels. EETs serve as endothelial derived hyperpolarizing factors. Inhibition of the formation of 20-HETE impairs the myogenic response and autoregulation of renal and cerebral blood flow. Changes in the formation of EETs and 20-HETE have been reported in hypertension and drugs that target these pathways alter blood pressure in animal models. Sequence variants in CYP4A11 and CYP4F2 that produce 20-HETE, UDP-glucuronosyl transferase involved in the biotransformation of 20-HETE and soluble epoxide hydrolase that inactivates EETs are associated with hypertension in human studies. 20-HETE contributes to the regulation of vascular hypertrophy, restenosis, angiogenesis and inflammation. It also promotes endothelial dysfunction and contributes to cerebral vasospasm and ischemia-reperfusion injury in the brain, kidney and heart. This review will focus on the role of 20-HETE in vascular dysfunction, inflammation, ischemic and hemorrhagic stroke and cardiac and renal ischemia reperfusion injury. PMID:27100515

  6. Diversity, vitality and activities of intestinal lactic acid bacteria and bifidobacteria assessed by molecular approaches

    Vaughan, E.E.; Heilig, G.H.J.; Ben-Amor, K.; Vos, de W.M.

    2005-01-01

    While lactic acid bacteria and bifidobacteria have been scientifically important for over a century, many of these are marketed today as probiotics and have become a valuable and rapidly expanding sector of the food market that is leading functional foods in many countries. The human gastro-intestin

  7. Visualization of early events in acetic acid denaturation of HIV-1 protease: a molecular dynamics study.

    Aditi Narendra Borkar

    Full Text Available Protein denaturation plays a crucial role in cellular processes. In this study, denaturation of HIV-1 Protease (PR was investigated by all-atom MD simulations in explicit solvent. The PR dimer and monomer were simulated separately in 9 M acetic acid (9 M AcOH solution and water to study the denaturation process of PR in acetic acid environment. Direct visualization of the denaturation dynamics that is readily available from such simulations has been presented. Our simulations in 9 M AcOH reveal that the PR denaturation begins by separation of dimer into intact monomers and it is only after this separation that the monomer units start denaturing. The denaturation of the monomers is flagged off by the loss of crucial interactions between the α-helix at C-terminal and surrounding β-strands. This causes the structure to transit from the equilibrium dynamics to random non-equilibrating dynamics. Residence time calculations indicate that denaturation occurs via direct interaction of the acetic acid molecules with certain regions of the protein in 9 M AcOH. All these observations have helped to decipher a picture of the early events in acetic acid denaturation of PR and have illustrated that the α-helix and the β-sheet at the C-terminus of a native and functional PR dimer should maintain both the stability and the function of the enzyme and thus present newer targets for blocking PR function.

  8. Molecular Cloning and Biochemical Characterization of Indole-3-acetic Acid Methyltransferase from Poplar (Populus trichocarpa)

    Indole-3-acetic acid (IAA) is the most active endogenous auxin involved in various physiological processes in higher plants. Concentrations of IAA in plant tissues are regulated at multiple levels including de novo biosynthesis, degradation, and conjugation/deconjugation. In this paper, we report id...

  9. Molecular basis for amino acid sensing by family C G-protein-coupled receptors

    Wellendorph, Petrine; Bräuner-Osborne, Hans

    2009-01-01

    -alpha;-amino acid receptor G-protein-coupled receptor family C, group 6, subtype A (GPRC6A) and seven orphan receptors. Aside from the orphan receptors, the family C GPCRs are dimeric receptors characterized by a large extracellular Venus flytrap domain which bind the endogenous agonists. Except from the GABA(B1...

  10. Molecular Marker Development and Linkage Analysis in Three Low Phytic Acid Barley (Hordeum vulgare) Mutant Lines

    Phytate is the primary form of phosphorus found in mature cereal grain. This form of phosphorus is not available to monogastric animals due to a lack of the enzyme phytase in their digestive tract. Several barley low phytic acid (lpa) mutants have been identified that contain substantial decreases...

  11. Molecular and biochemical characterization of the jasmonic acid methyltransferase gene from black cottonwood (Populus trichocarpa)

    Zhao, Nan [ORNL; Yao, Jianzhuang [University of Tennessee, Knoxville (UTK); Chaiprasongsuk, Minta [University of Tennessee, Knoxville (UTK); Li, Guanglin [University of Tennessee, Knoxville (UTK); Guan, Ju [University of Tennessee, Knoxville (UTK); Tschaplinski, Timothy J [ORNL; Guo, Hong [University of Tennessee, Knoxville (UTK); Chen, Feng [University of Tennessee, Knoxville (UTK)

    2013-01-01

    Methyl jasmonate is a metabolite known to be produced by many plants and has roles in diverse biological processes. It is biosynthesized by the action of S-adenosyl-L-methionine:jasmonic acid carboxyl methyltransferase (JMT), which belongs to the SABATH family of methyltransferases. Herein is reported the isolation and biochemical characterization of a JMT gene from black cottonwood (Populus trichocarpa). The genome of P. trichocarpa contains 28 SABATH genes (PtSABATH1 to PtSABATH28). Recombinant PtSABATH3 expressed in Escherichia coli showed the highest level of activity with jasmonic acid (JA) among carboxylic acids tested. It was therefore renamed PtJMT1. PtJMT1 also displayed activity with benzoic acid (BA), with which the activity was about 22% of that with JA. PtSABATH2 and PtSABATH4 were most similar to PtJMT1 among all PtSABATHs. However, neither of them had activity with JA. The apparent Km values of PtJMT1 using JA and BA as substrate were 175 lM and 341 lM, respectively. Mutation of Ser-153 and Asn-361, two residues in the active site of PtJMT1, to Tyr and Ser respectively, led to higher specific activity with BA than with JA. Homology-based structural modeling indicated that substrate alignment, in which Asn-361 is involved, plays a role in determining the substrate specificity of PtJMT1. In the leaves of young seedlings of black cottonwood, the expression of PtJMT1 was induced by plant defense signal molecules methyl jasmonate and salicylic acid and a fungal elicitor alamethicin, suggesting that PtJMT1 may have a role in plant defense against biotic stresses. Phylogenetic analysis suggests that PtJMT1 shares a common ancestor with the Arabidopsis JMT, and functional divergence of these two apparent JMT orthologs has occurred since the split of poplar and Arabidopsis lineages.

  12. Nanopore Analysis of Nucleic Acids: Single-Molecule Studies of Molecular Dynamics, Structure, and Base Sequence

    Olasagasti, Felix; Deamer, David W.

    Nucleic acids are linear polynucleotides in which each base is covalently linked to a pentose sugar and a phosphate group carrying a negative charge. If a pore having roughly the crosssectional diameter of a single-stranded nucleic acid is embedded in a thin membrane and a voltage of 100 mV or more is applied, individual nucleic acids in solution can be captured by the electrical field in the pore and translocated through by single-molecule electrophoresis. The dimensions of the pore cannot accommodate anything larger than a single strand, so each base in the molecule passes through the pore in strict linear sequence. The nucleic acid strand occupies a large fraction of the pore's volume during translocation and therefore produces a transient blockade of the ionic current created by the applied voltage. If it could be demonstrated that each nucleotide in the polymer produced a characteristic modulation of the ionic current during its passage through the nanopore, the sequence of current modulations would reflect the sequence of bases in the polymer. According to this basic concept, nanopores are analogous to a Coulter counter that detects nanoscopic molecules rather than microscopic [1,2]. However, the advantage of nanopores is that individual macromolecules can be characterized because different chemical and physical properties affect their passage through the pore. Because macromolecules can be captured in the pore as well as translocated, the nanopore can be used to detect individual functional complexes that form between a nucleic acid and an enzyme. No other technique has this capability.

  13. Heat Switches for ADRs

    DiPirro, M. J.; Shirron, P. J.

    2014-01-01

    Heat switches are key elements in the cyclic operation of Adiabatic Demagnetization Refrigerators (ADRs). Several of the types of heat switches that have been used for ADRs are described in this paper. Key elements in selection and design of these switches include not only ON/OFF switching ratio, but also method of actuation, size, weight, and structural soundness. Some of the trade-off are detailed in this paper.

  14. Controller Architectures for Switching

    Niemann, Hans Henrik; Poulsen, Niels Kjølstad

    2009-01-01

    This paper investigate different controller architectures in connection with controller switching. The controller switching is derived by using the Youla-Jabr-Bongiorno-Kucera (YJBK) parameterization. A number of different architectures for the implementation of the YJBK parameterization are...... described and applied in connection with controller switching. An architecture that does not include inversion of the coprime factors is introduced. This architecture will make controller switching particular simple....

  15. Switching mode power supplies

    Beard, David W.

    1980-01-01

    The subject of switching mode power supplies was examined. A comparison between linear regulators and switching mode power supplies was made to show the options available for the various types of convertors. Two switching mode power supplies were constructed and tested. The operating efficiency of both systems was found to be more than eighty percent over the specified input voltage and load current conditions. The switching mode power supply circuits required additional ...

  16. MOSFET as a Switch

    Dhaval Agrawal

    2014-01-01

    s as a switch. Also it shows the different problems and some remedy to solve those problems with equations and simulatis as a switch. Also it shows the different problems and some remedy to solve those problems with equations and simulatis as a switch. Also it shows the different problems and some remedy to solve those problems with equations and simulatis as a switch. Also it shows the different problems and some remedy to solve those problems with equations and simulatis as ...

  17. Investigating the significance of zero-point motion in small molecular clusters of sulphuric acid and water

    The nucleation of particles from trace gases in the atmosphere is an important source of cloud condensation nuclei, and these are vital for the formation of clouds in view of the high supersaturations required for homogeneous water droplet nucleation. The methods of quantum chemistry have increasingly been employed to model nucleation due to their high accuracy and efficiency in calculating configurational energies; and nucleation rates can be obtained from the associated free energies of particle formation. However, even in such advanced approaches, it is typically assumed that the nuclei have a classical nature, which is questionable for some systems. The importance of zero-point motion (also known as quantum nuclear dynamics) in modelling small clusters of sulphuric acid and water is tested here using the path integral molecular dynamics method at the density functional level of theory. The general effect of zero-point motion is to distort the mean structure slightly, and to promote the extent of proton transfer with respect to classical behaviour. In a particular configuration of one sulphuric acid molecule with three waters, the range of positions explored by a proton between a sulphuric acid and a water molecule at 300 K (a broad range in contrast to the confinement suggested by geometry optimisation at 0 K) is clearly affected by the inclusion of zero point motion, and similar effects are observed for other configurations

  18. Novel binding patterns between ganoderic acids and neuraminidase: Insights from docking, molecular dynamics and MM/PBSA studies.

    Yang, Zhiwei; Wu, Fei; Yuan, Xiaohui; Zhang, Lei; Zhang, Shengli

    2016-04-01

    Recently, ganoderic acids (GAs) give rise to the attractive candidates of novel neuraminidase (NA) inhibitors. However, there is still no evident conclusion about their binding patterns. To this end, docking, molecular dynamics and MM/PBSA methods were combined to study the binding profiles of GAs with the N1 protein and familiar H274Y and N294S mutations (A/Vietnam/1203/04 stain). It was found that the binding affinities of ganoderic acid DM and Z (ΔGbind, -16.83 and -10.99 kcal mol(-1)) are comparable to that of current commercial drug oseltamivir (-23.62 kcal mol(-1)). Electrostatic interaction is the main driving force, and should be one important factor to evaluate the binding quality and rational design of NA inhibitors. The 150-loop residues Asp151 and Arg152 played an important role in the binding processes. Further analysis revealed that ganoderic acid DM is a potential source of anti-influenza ingredient, with novel binding pattern and advantage over oseltamivir. It had steric hindrance on the 150 cavity of N1 protein, and exerted activities across the H274Y and N294S mutations. This work also pointed out how to effectively design dual-site NA inhibitors and reinforce their affinities. These findings should prove valuable for the in-depth understanding of interactions between NA and GAs, and warrant the experimental aspects to design novel anti-influenza drugs. PMID:26905206

  19. Stability of Chloropyromorphite in Ryegrass Rhizosphere as Affected by Root-Secreted Low Molecular Weight Organic Acids

    Wei, Wei; Wang, Yu; Wang, Zheng; Han, Ruiming; Li, Shiyin; Wei, Zhenggui; Zhang, Yong

    2016-01-01

    Understanding the stability of chloropyromorphite (CPY) is of considerable benefit for improving risk assessment and remediation strategies in contaminated water and soil. The stability of CPY in the rhizosphere of phosphorus-deficient ryegrass was evaluated to elucidate the role of root-secreted low molecular weight organic acids (LMWOAs) on the dissolution of CPY. Results showed that CPY treatments significantly reduced the ryegrass biomass and rhizosphere pH. The presence of calcium nitrate extractable lead (Pb) and phosphorus (P) suggested that CPY in the rhizosphere could be bioavailable, because P and Pb uptake by ryegrass potentially provided a significant concentration gradient that would promote CPY dissolution. Pb accumulation and translocation in ryegrass was found to be significantly higher in P-sufficient conditions than in P-deficient conditions. CPY treatments significantly enhanced root exudation of LMWOAs irrigated with P-nutrient solution or P-free nutrient solution. Oxalic acid was the dominant species in root-secreted LMWOAs of ryegrass under P-free nutrient solution treatments, suggesting that root-secreted oxalic acid may be the driving force of root-induced dissolution of CPY. Hence, our work, provides clarifying hints on the role of LMWOAs in controlling the stability of CPY in the rhizosphere. PMID:27494023

  20. Molecularly imprinted polymers combination with deep eutectic solvents for solid-phase extraction of caffeic acid from hawthorn.

    Li, Guizhen; Tang, Weiyang; Cao, Weimin; Wang, Qian; Zhu, Tao

    2015-08-01

    Molecularly imprinted polymers (MIPs) with caffeic acid as template and non-imprinted polymers (NIPs) materials were prepared in the same procedure. Field emission scanning electron microscopy (FE-SEM) and adsorption capacity test were used to evaluate characteristic of the new materials. MIPs, NIPs and C18 were used for rapid purification of caffeic acid from hawthorn with solid-phase extraction ( SPE) , and extract yields of caffeic acid with the proposed materials were 3.46 µg/g, 1.01 µg/g and 1.17 µg/g, respectively. To optimize the MIPs-SPE procedures, different kinds of elution solutions were studied. Deep eutectic solvents (DESs) were prepared by choline chloride (ChCl)-glycerol (1/2, n/n) and choline chloride-urea (1/ 2, n/n). Methanol was mixed with the two kinds of DESs (glycerol-based DESs, urea-based DESs) in different ratios (0.5:1, 1:1, 2:1, 3:1, 4:1, 5:1, v/v), and they were used to investigated as elution solutions in the above MIPs-SPE procedures. The results showed that MIPs were potential SPE materials, and methanol/ glycerol-based DESs (3 :1, v/v) had the best elution capability with the recovery of 82.32%. PMID:26749853

  1. A computational study of the molecular recognition of nucleic acid bases by poly(vinyldiaminotriazine)

    Czernek, Jiří

    2010-01-01

    Roč. 295, č. 1 (2010), s. 125-130. ISSN 1022-1360. [Prague Meetings on Macromolecules /73./ New Frontiers in Macromolecular Science: From Macromolecular Concepts of Living Matter to Polymers for Better Quality of Life . Prague, 05.07.2009-09.07.2009] Institutional research plan: CEZ:AV0Z40500505 Keywords : molecular modeling * nucleobases * poly(vinyldiaminotriazine) Subject RIV: CD - Macromolecular Chemistry

  2. Molecular recognition of isomeric protonated amino acid esters monitored by ESI-mass spectrometry

    Andrea Liesenfeld

    2014-04-01

    Full Text Available Two new 9,9’-spirobifluorene-derived crown ethers were prepared and used to recognise constitutionally isomeric amino acid derivatives. The performance of the receptors was evaluated by ESI-mass spectrometry using the isomer labelled guest method (ILGM. This method revealed the preferred binding of L-norleucine and L-leucine compared to L-isoleucine for both receptors. Furthermore, non-covalent isotope effects demonstrate the relevance of dispersive interactions for the overall binding event. These effects also provide hints for the relative spatial orientation of the guest molecules within the host–guest complex, and thereby prove the importance of the spirobifluorene moiety for the observed binding of the protonated amino acid esters.

  3. Molecular recognition of isomeric protonated amino acid esters monitored by ESI-mass spectrometry.

    Liesenfeld, Andrea; Lützen, Arne

    2014-01-01

    Two new 9,9'-spirobifluorene-derived crown ethers were prepared and used to recognise constitutionally isomeric amino acid derivatives. The performance of the receptors was evaluated by ESI-mass spectrometry using the isomer labelled guest method (ILGM). This method revealed the preferred binding of L-norleucine and L-leucine compared to L-isoleucine for both receptors. Furthermore, non-covalent isotope effects demonstrate the relevance of dispersive interactions for the overall binding event. These effects also provide hints for the relative spatial orientation of the guest molecules within the host-guest complex, and thereby prove the importance of the spirobifluorene moiety for the observed binding of the protonated amino acid esters. PMID:24778737

  4. Molecular understanding of atmospheric particle formation from sulfuric acid and large oxidized organic molecules

    Schobesberger, Siegfried; Bianchi, Federico; Lönn, Gustaf; Ehn, Mikael; Lehtipalo, Katrianne; Dommen, Josef; Ehrhart, Sebastian; Ortega, Ismael K; Franchin, Alessandro; Nieminen, Tuomo; Riccobono, Francesco; Hutterli, Manuel; Duplissy, Jonathan; Almeida, João; Amorim, Antonio; Breitenlechner, Martin; Downard, Andrew J; Dunne, Eimear M; Flagan, Richard C; Kajos, Maija; Keskinen, Helmi; Kirkby, Jasper; Kupc, Agnieszka; Kürten, Andreas; Kurtén, Theo; Laaksonen, Ari; Mathot, Serge; Onnela, Antti; Praplan, Arnaud P; Rondo, Linda; Santos, Filipe D; Schallhart, Simon; Schnitzhofer, Ralf; Sipilä, Mikko; Tomé, António; Tsagkogeorgas, Georgios; Vehkamäki, Hanna; Wimmer, Daniela; Baltensperger, Urs; Carslaw, Kenneth S; Curtius, Joachim; Hansel, Armin; Petäjä, Tuukka; Kulmala, Markku; Donahue, Neil M; Worsnop, Douglas R

    2013-01-01

    Atmospheric aerosols formed by nucleation of vapors affect radiative forcing and therefore climate. However, the underlying mechanisms of nucleation remain unclear, particularly the involvement of organic compounds. Here, we present high-resolution mass spectra of ion clusters observed during new particle formation experiments performed at the Cosmics Leaving Outdoor Droplets chamber at the European Organization for Nuclear Research. The experiments involved sulfuric acid vapor and different stabilizing species, including ammonia and dimethylamine, as well as oxidation products of pinanediol, a surrogate for organic vapors formed from monoterpenes. A striking resemblance is revealed between the mass spectra from the chamber experiments with oxidized organics and ambient data obtained during new particle formation events at the Hyytiälä boreal forest research station. We observe that large oxidized organic compounds, arising from the oxidation of monoterpenes, cluster directly with single sulfuric acid molec...

  5. Molecular recognition of isomeric protonated amino acid esters monitored by ESI-mass spectrometry

    Andrea Liesenfeld; Arne Lützen

    2014-01-01

    Two new 9,9’-spirobifluorene-derived crown ethers were prepared and used to recognise constitutionally isomeric amino acid derivatives. The performance of the receptors was evaluated by ESI-mass spectrometry using the isomer labelled guest method (ILGM). This method revealed the preferred binding of L-norleucine and L-leucine compared to L-isoleucine for both receptors. Furthermore, non-covalent isotope effects demonstrate the relevance of dispersive interactions for the overall binding event...

  6. The Molecular Mechanism of Leptin Secretion and Expression Induced by Aristolochic Acid in Kidney Fibroblast

    Lin, Tsung-Chieh; Lee, Tien-Chiang; Hsu, Shih-Lan; Yang, Chung-Shi

    2011-01-01

    Background Leptin is a peptide hormone playing pivotal role in regulating food intake and energy expenditure. Growing evidence has suggested the pro-inflammatory and fibrogenic properties of leptin. In addition, patients with renal fibrosis have higher level of plasma leptin, which was due to the increased leptin production. Aristolochic acid (AA) is a botanical toxin characterized to associate with the development of renal fibrosis including tubulointerstitial fibrosis. However, whether lept...

  7. Synthesis of acrylic acid derivatives from carbon dioxide and ethylene mediated by molecular nickel complexes

    Lee, Sin Ying Tina

    2013-01-01

    This work aimed at the synthesis of acrylic acid derivatives from ethylene and CO2 and well as the investigation of β-hydride elimination reaction of nickelalactones with methyl iodide and methyl triflate to form methyl acrylate. The oxidative coupling reaction of ethylene and CO2 on nickel center was ligand selective, and gave low yields of nickelalactone product at mild synthetic conditions. Key intermediates identified and characterized in the β-H elimination reaction provided rich insight...

  8. Molecular cloning and ontogenesis expression of fatty acid transport protein-1 in yellow-feathered broilers

    Yuzhen Song; Jiaying Feng; Lihua Zhou; Gang Shu; Xiaotong Zhu; Ping Gao; Yongliang Zhang; Qingyan Jiang

    2008-01-01

    Fatty acid transport protein-1 (FATP-1) is one of the important transporter proteins involved in fatty acid transmembrane transport and fat deposition. To study the relationship between FATP-1 mRNA expression and fat deposition, chicken (Gallus gallus) FATP-1 sequence was first cloned by rapid amplification of cDNA ends (RACE). Tissue samples of chest muscle, leg muscle, subcutaneous fat, and abdominal fat were collected from six male and six female broilers each, at 22 days, 29 days, and 42 days, respectively. The tissue specificity and ontogenesis expression pattern of the FATP-1 mRNA of yellow-feathered broilers was studied by real-time reverse transcription polymerase chain reaction (RT-PCR), and the fat deposition laws in different tissues were also compared. A 2,488 bp cDNA sequence of chicken FATP-1 was cloned by RACE (GenBank accession no. DQ352834), including 547 bp 3' end untranslated region (URT) and 1,941 bp open reading frame (ORF). Chicken FATP-1 encoded 646 amino acid residues, which shared 83.9% and 83.0% identity with those of human and rat, respectively. The results of quantitative PCR demonstrated a constant FATP-1 mRNA expression level in the chest muscle and subcutaneous fat of both male and female broilers at three stages, whereas the expression level of the FATP-1 mRNA in the leg muscle at 42 days was significantly higher than that at 22 days or 29 days. In the abdominal fat of male broilers, the gene expression significantly increased with age, whereas the female broilers showed a dramatic downregulation of FATP-1 expression in abdominal fat at 42 days. This suggested a typical tissue-and gender-specific expression pattern of chicken FATP-1, mediating the specific process of fatty acid transport or utilization in muscle and adipose tissues.

  9. The 2016 database issue of Nucleic Acids Research and an updated molecular biology database collection

    Rigden, Daniel J.; Fernández-Suárez, Xosé M.; Galperin, Michael Y.

    2015-01-01

    The 2016 Database Issue of Nucleic Acids Research starts with overviews of the resources provided by three major bioinformatics centers, the U.S. National Center for Biotechnology Information (NCBI), the European Bioinformatics Institute (EMBL-EBI) and Swiss Institute for Bioinformatics (SIB). Also included are descriptions of 62 new databases and updates on 95 databases that have been previously featured in NAR plus 17 previously described elsewhere. A number of papers in this issue deal wit...

  10. Study of molecular complexation of glycyrrhizic acid with chloramphenicol by electrospray ionization mass spectrometry

    Vetrova, Elena V.; Lekar, Anna V.; Filonova, Olga V.; Borisenko, Sergey N.; Maksimenko, Elena V.; Borisenko, Nikolay I.

    2015-01-01

    Context: Glycyrrhizic acid (GA) is a triterpene glycoside representing the main active component of licorice root extract obtained from plants of the Glycyrrhiza glabra L. and widely used as a complex-forming agent for the synthesis of new transport forms of the well-known drugs. Aims: For the first time, the complexation of GA with chloramphenicol antibiotic (ChlA) was investigated by electrospray ionization mass spectrometry (ESI MS). Subjects and Methods: ESI MS was utilized in order to de...

  11. Molecular evidence for an involvement of organic anion transporters (OATs) in aristolochic acid nephropathy.

    Bakhiya, Nadiya; Arlt, Volker M.; Bahn, Andrew; Burckhardt, Gerhard; Phillips, David H.; Glatt, Hansruedi

    2009-01-01

    Aristolochic acid (AA), present in Aristolochia species, is the major causative agent in the development of severe renal failure and urothelial cancers in patients with AA nephropathy. It may also be a cause of Balkan endemic nephropathy. Epithelial cells of the proximal tubule are the primary cellular target of AA. To study whether organic anion transporters (OATs) expressed in proximal tubule cells are involved in uptake of AA, we used human epithelial kidney (HEK293) cells stably expressin...

  12. Integration of molecular technology and radiation to find gene with low phytic acid content

    Using the mutant population of the short-term high-yielding rice varieties as OM6162 by dried radiation with dose of 10, 20, 30, 40, 50 krad. M1 generation was planted and obtained separately for each individual. M1 individuals were planted under row in M2 generation. M3 seeds were obtained separately by individuals from M2 which were used for analyzing phytic acid content. Subsequently, these seeds were tagged by Indel (SNP) to find the plants having low phytic acid. Recorded result expression of high phosphorous levels in grain contributing to evaluate the fluctuant ability of low phytic acid content on surveyed population. Considering by overall number of analyzed seeds (808 seeds) HIP (High Inorganic Phosphorous) of OM6162 population after radiation shown, the fluctuation of content of phosphorous levels. Most number of seeds did not expressed high phosphorous content. Of which the radio of seed of level 1 reached the highest (55.84%), level 2 of 44.18%, level 3 of 1.36%, and ratio of level 4 as 0.62%. Although the ability of mutation of seed of level 3 and level 4 were low but there were very significant in initial step in selecting lines with low phytic acid content. Evaluated lines had high phosphorous content were tagged and continuously selected in order to generate pure lines in next generations. From above result we found that, there were difference in some agronomic traits of many lines of mutagenized population compared with the original when statistical analysis or otherwise in surveyed population appeared individuals expressing mutant traits. (author)

  13. Textural and structural properties and surface acidity characterization of mesoporous silica-zirconia molecular sieves

    Rodríguez-Castellón, E.; Jiménez-López, A.; Maireles-Torres, P.; Jones, D. J.; Rozière, J.; Trombetta, M.; Busca, G.; Lenarda, M.; Storaro, L.

    2003-11-01

    Homogeneous mesoporous zirconium-containing MCM-41 type silica were prepared by supramolecular templating and their textural and structural properties were studied using powder X-ray diffraction, N 2 porosimetry, atomic force microscopy, EXAFS, XPS, and UV-VIS-NIR diffuse reflectance spectroscopy. Their acid properties were also studied by using IR spectroscopy and by the use of catalytic tests such as the decomposition of isopropanol and the isomerization of 1-butene. The materials prepared show a good degree of crystallinity with a regular ordering of the pores into a hexagonal arrangement and high thermal stability. The specific surface area of the prepared materials decreases as the zirconium content rises. Zirconium atoms are in coordination 7 to 8 and located at the surface of the pores such that a high proportion of the oxygen atoms bonded to zirconium corresponds to surface non-condensed oxygen atoms. Both facts are responsible for the acid properties of the solids that show weak Brønsted and medium strong Lewis acidity.

  14. Molecular understanding of atmospheric particle formation from sulfuric acid and large oxidized organic molecules

    Schobesberger, Siegfried; Junninen, Heikki; Bianchi, Federico; Lönn, Gustaf; Ehn, Mikael; Lehtipalo, Katrianne; Dommen, Josef; Ehrhart, Sebastian; Ortega, Ismael K.; Franchin, Alessandro; Nieminen, Tuomo; Riccobono, Francesco; Hutterli, Manuel; Duplissy, Jonathan; Almeida, João; Amorim, Antonio; Breitenlechner, Martin; Downard, Andrew J.; Dunne, Eimear M.; Flagan, Richard C.; Kajos, Maija; Keskinen, Helmi; Kirkby, Jasper; Kupc, Agnieszka; Kürten, Andreas; Kurtén, Theo; Laaksonen, Ari; Mathot, Serge; Onnela, Antti; Praplan, Arnaud P.; Rondo, Linda; Santos, Filipe D.; Schallhart, Simon; Schnitzhofer, Ralf; Sipilä, Mikko; Tomé, António; Tsagkogeorgas, Georgios; Vehkamäki, Hanna; Wimmer, Daniela; Baltensperger, Urs; Carslaw, Kenneth S.; Curtius, Joachim; Hansel, Armin; Petäjä, Tuukka; Kulmala, Markku; Donahue, Neil M.; Worsnop, Douglas R.

    2013-01-01

    Atmospheric aerosols formed by nucleation of vapors affect radiative forcing and therefore climate. However, the underlying mechanisms of nucleation remain unclear, particularly the involvement of organic compounds. Here, we present high-resolution mass spectra of ion clusters observed during new particle formation experiments performed at the Cosmics Leaving Outdoor Droplets chamber at the European Organization for Nuclear Research. The experiments involved sulfuric acid vapor and different stabilizing species, including ammonia and dimethylamine, as well as oxidation products of pinanediol, a surrogate for organic vapors formed from monoterpenes. A striking resemblance is revealed between the mass spectra from the chamber experiments with oxidized organics and ambient data obtained during new particle formation events at the Hyytiälä boreal forest research station. We observe that large oxidized organic compounds, arising from the oxidation of monoterpenes, cluster directly with single sulfuric acid molecules and then form growing clusters of one to three sulfuric acid molecules plus one to four oxidized organics. Most of these organic compounds retain 10 carbon atoms, and some of them are remarkably highly oxidized (oxygen-to-carbon ratios up to 1.2). The average degree of oxygenation of the organic compounds decreases while the clusters are growing. Our measurements therefore connect oxidized organics directly, and in detail, with the very first steps of new particle formation and their growth between 1 and 2 nm in a controlled environment. Thus, they confirm that oxidized organics are involved in both the formation and growth of particles under ambient conditions. PMID:24101502

  15. Surface Structure and Chemical Switching of Thioctic Acid Adsorbed on Au(111) as Observed Using Near-Edge X-ray Absorption Fine Structure

    Meulenberg, R W; van Buuren, T; Vance, A L; Terminello, L J; Willey, T M; Bostedt, C; Fadley, C S

    2004-01-06

    Thioctic acid (alpha-lipoic acid) is a molecule with a large disulfide-containing base, a short alkyl-chain with four CH{sub 2} units, and a carboxyl termination. Self-assembled monolayer (SAM) films of thioctic acid adsorbed on Au(111) have been investigated with near-edge x-ray absorption fine structure (NEXAFS) spectroscopy and x-ray photoelectron spectroscopy (XPS) to determine film quality, bonding and morphology. Using standard preparation protocols for SAMs, that is, dissolving thioctic acid in ethanol and exposing gold to the solution, results in poor films. These films are highly disordered, contain a mixture of carboxyl and carboxylate terminations, have more than monolayer coverage, and exhibit unbound disulfide. Conversely, forming films by dissolving 1 mmol thioctic acid into 5% acetic acid in ethanol (as previously reported with carboxyl-terminated alkyl-thiols) forms ordered monolayers with small amounts of unbound sulfur. NEXAFS indicates tilted over endgroups with the carboxyl group normal on average 38{sup o} from the surface normal. Slight dichroism in other features indicates alkyl chains statistically more upright than prostrate on the surface. Reflection-absorption Fourier transform infrared (RA-FTIR) spectra indicate hydrogen bonding between neighboring molecules. In such well-formed monolayers, a stark reorientation occurs upon deprotonation of the endgroup by rinsing in a KOH solution. The carboxylate plane normal is now about 66{sup o} from sample normal, a much more upright orientation. Data indicate this reorientation may also cause a more upright orientation to the alkyl portion of the molecules.

  16. Interactions of aqueous amino acids and proteins with the (110) surface of ZnS in molecular dynamics simulations

    Nawrocki, Grzegorz; Cieplak, Marek [Institute of Physics, Polish Academy of Sciences, Al. Lotników 32/46, 02-668 Warsaw (Poland)

    2014-03-07

    The growing usage of nanoparticles of zinc sulfide as quantum dots and biosensors calls for a theoretical assessment of interactions of ZnS with biomolecules. We employ the molecular-dynamics-based umbrella sampling method to determine potentials of mean force for 20 single amino acids near the ZnS (110) surface in aqueous solutions. We find that five amino acids do not bind at all and the binding energy of the remaining amino acids does not exceed 4.3 kJ/mol. Such energies are comparable to those found for ZnO (and to hydrogen bonds in proteins) but the nature of the specificity is different. Cysteine can bind with ZnS in a covalent way, e.g., by forming the disulfide bond with S in the solid. If this effect is included within a model incorporating the Morse potential, then the potential well becomes much deeper—the binding energy is close to 98 kJ/mol. We then consider tryptophan cage, a protein of 20 residues, and characterize its events of adsorption to ZnS. We demonstrate the relevance of interactions between the amino acids in the selection of optimal adsorbed conformations and recognize the key role of cysteine in generation of lasting adsorption. We show that ZnS is more hydrophobic than ZnO and that the density profile of water is quite different than that forming near ZnO—it has only a minor articulation into layers. Furthermore, the first layer of water is disordered and mobile.

  17. Interactions of aqueous amino acids and proteins with the (110) surface of ZnS in molecular dynamics simulations

    Nawrocki, Grzegorz; Cieplak, Marek

    2014-03-01

    The growing usage of nanoparticles of zinc sulfide as quantum dots and biosensors calls for a theoretical assessment of interactions of ZnS with biomolecules. We employ the molecular-dynamics-based umbrella sampling method to determine potentials of mean force for 20 single amino acids near the ZnS (110) surface in aqueous solutions. We find that five amino acids do not bind at all and the binding energy of the remaining amino acids does not exceed 4.3 kJ/mol. Such energies are comparable to those found for ZnO (and to hydrogen bonds in proteins) but the nature of the specificity is different. Cysteine can bind with ZnS in a covalent way, e.g., by forming the disulfide bond with S in the solid. If this effect is included within a model incorporating the Morse potential, then the potential well becomes much deeper—the binding energy is close to 98 kJ/mol. We then consider tryptophan cage, a protein of 20 residues, and characterize its events of adsorption to ZnS. We demonstrate the relevance of interactions between the amino acids in the selection of optimal adsorbed conformations and recognize the key role of cysteine in generation of lasting adsorption. We show that ZnS is more hydrophobic than ZnO and that the density profile of water is quite different than that forming near ZnO—it has only a minor articulation into layers. Furthermore, the first layer of water is disordered and mobile.

  18. Molecular assays for the detection of prostate tumor derived nucleic acids in peripheral blood

    Kinnunen Martin

    2010-07-01

    Full Text Available Abstract Background Prostate cancer is the second leading cause of cancer mortality in American men. Although serum PSA testing is widely used for early detection, more specific prognostic tests are needed to guide treatment decisions. Recently, the enumeration of circulating prostate epithelial cells has been shown to correlate with disease recurrence and metastasis following definitive treatment. The purpose of our study was to investigate an immunomagnetic fractionation procedure to enrich circulating prostate tumor cells (CTCs from peripheral blood specimens, and to apply amplified molecular assays for the detection of prostate-specific markers (PSA, PCA3 and TMPRSS2:ERG gene fusion mRNAs. Results As few as five prostate cancer cells were detected per 5 mL of whole blood in model system experiments using anti-EpCAM magnetic particles alone or in combination with anti-PSMA magnetic particles. In our experiments, anti-EpCAM magnetic particles alone exhibited equivalent or better analytical performance with patient samples compared to a combination of anti-EpCAM + anti-PSMA magnetic particles. Up to 39% of men with advanced prostate cancer tested positive with one or more of the molecular assays tested, whereas control samples from men with benign prostate hyperplasia gave consistently negative results as expected. Interestingly, for the vast majority of men who tested positive for PSA mRNA following CTC enrichment, their matched plasma samples also tested positive, although CTC enrichment gave higher overall mRNA copy numbers. Conclusion CTCs were successfully enriched and detected in men with advanced prostate cancer using an immunomagnetic enrichment procedure coupled with amplified molecular assays for PSA, PCA3, and TMPRSS2:ERG gene fusion mRNAs. Our results indicate that men who test positive following CTC enrichment also exhibit higher detectable levels of non-cellular, circulating prostate-specific mRNAs.

  19. Insights into regioselective metabolism of mefenamic acid by cytochrome P450 BM3 mutants through crystallography, docking, molecular dynamics, and free energy calculations

    Capoferri, Luigi; Leth, Rasmus; Ter Haar, Ernst; Mohanty, Arun K; Grootenhuis, Peter D J; Vottero, Eduardo; Commandeur, Jan M N; Vermeulen, Nico P E; Jørgensen, Flemming Steen; Olsen, Lars; Geerke, Daan P

    2016-01-01

    active-site mutations such as V87I were reported to invert regioselectivity in NSAID hydroxylation. In this work, we combine crystallography and molecular simulation to study the effect of single mutations on binding and regioselective metabolism of mefenamic acid by M11 mutants. The heme domain of the...... protein mutant M11 was expressed, purified, and crystallized, and its X-ray structure was used as template for modeling. A multistep approach was used that combines molecular docking, molecular dynamics (MD) simulation, and binding free-energy calculations to address protein flexibility. In this way...... mefenamic acid by M11 and its mutants by including protein flexibility and dynamics in free-energy computation. In addition, we could obtain structural insights into the change in regioselectivity of mefenamic acid hydroxylation due to single active-site mutations. Our findings confirm that use of MD and...

  20. Two bisthienylethene-Ir(III) complexes showing acid/base-induced structural transformation and on-off luminescence switching in solution.

    Cao, Deng-Ke; Hu, Jiong-Sheng; Li, Min-Qiang; Gong, Dan-Ping; Li, Xiao-Xiong; Ward, Michael D

    2015-12-28

    Complexes [Ir(dfppy)2(pbdtiH)](PF6)·2CHCl3 (1-H) and [Ir(dfppy)2(pbdti)] (1) were synthesized by the reaction of bisthienylethene pbdtiH and an [Ir(dfppy)2Cl]2 dimer under neutral and basic conditions, respectively. Thus, the {Ir(dfppy)2}(+) unit is coordinated by pbdtiH in 1-H, and by pbdti(-) in 1, which are confirmed by their crystal structures. The structures of 1-H and 1 could be interconverted in solution, upon alternately adding NEt3 and TFA, thus resulting in reversible luminescence switching between the on-state of 1-H and the off-state of 1 at room temperature. In addition, both 1-H and 1 show solid-state luminescence, with a broad emission at 534 nm and 525 nm, respectively. The free pbdtiH ligand shows photochromic behavior in CH2Cl2 solution. However, no photochromism has been observed in 1-H and 1, indicating that the coordination of the pbdtiH/pbdti(-) ligand to the {Ir(dfppy)2}(+) unit could suppress their photochromic behaviors. PMID:26586364