Relevant bibliographies by topics / Gramicidin

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  1. Journal articles
  2. Dissertations / Theses
  3. Books
  4. Book chapters
  5. Conference papers
  6. Reports

Academic literature on the topic 'Gramicidin'

Author: Grafiati
Published: 4 June 2021
Last updated: 25 April 2022

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Journal articles on the topic "Gramicidin"

1

Sugár, István, Alexander Bonanno, and Parkson Chong. "Gramicidin Lateral Distribution in Phospholipid Membranes: Fluorescence Phasor Plots and Statistical Mechanical Model." International Journal of Molecular Sciences 19, no. 11 (November 21, 2018): 3690. http://dx.doi.org/10.3390/ijms19113690.

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When using small mole fraction increments to study gramicidins in phospholipid membranes, we found that the phasor dots of intrinsic fluorescence of gramicidin D and gramicidin A in dimyristoyl-sn-glycero-3-phosphocholine (DMPC) unilamellar and multilamellar vesicles exhibit a biphasic change with peptide content at 0.143 gramicidin mole fraction. To understand this phenomenon, we developed a statistical mechanical model of gramicidin/DMPC mixtures. Our model assumes a sludge-like mixture of fluid phase and aggregates of rigid clusters. In the fluid phase, gramicidin monomers are randomly distributed. A rigid cluster is formed by a gramicidin dimer and DMPC molecules that are condensed to the dimer, following particular stoichiometries (critical gramicidin mole fractions, Xcr including 0.143). Rigid clusters form aggregates in which gramicidin dimers are regularly distributed, in some cases, even to superlattices. At Xcr, the size of cluster aggregates and regular distributions reach a local maximum. Before a similar model was developed for cholesterol/DMPC mixtures (Sugar and Chong (2012) J. Am. Chem. Soc. 134, 1164–1171) and here the similarities and differences are discussed between these two models.
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Olczak, A., M. L. Główka, M. Szczesio, J. Bojarska, Z. Wawrzak, and W. L. Duax. "The first crystal structure of a gramicidin complex with sodium: high-resolution study of a nonstoichiometric gramicidin D–NaI complex." Acta Crystallographica Section D Biological Crystallography 66, no. 8 (July 9, 2010): 874–80. http://dx.doi.org/10.1107/s0907444910019876.

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The crystal structure of the nonstoichiometric complex of gramicidin D with NaI has been studied using synchrotron radiation at 100 K. The limiting resolution was 1.25 Å and theRfactor was 16% for 19 883 observed reflections. The general architecture of the antiparallel two-stranded gramicidin dimers in the studied crystal was a right-handed antiparallel double-stranded form that closely resembles the structures of other right-handed species published to date. However, there were several surprising observations. In addition to the significantly different composition of linear gramicidins identified in the crystal structure, including the absence of the gramicidin C form, only two cationic sites were found in each of the two independent dimers (channels), which were partially occupied by sodium, compared with the seven sites found in the RbCl complex of gramicidin. The sum of the partial occupancies of Na+was only 1.26 per two dimers and was confirmed by the similar content of iodine ions (1.21 ions distributed over seven sites), which was easily visible from their anomalous signal. Another surprising observation was the significant asymmetry of the distributions and occupancies of cations in the gramicidin dimers, which was in contrast to those observed in the high-resolution structures of the complexes of heavier alkali metals with gramicidin D, especially that of rubidium.
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Antoinette Killian, J. "Gramicidin and gramicidin-lipid interactions." Biochimica et Biophysica Acta (BBA) - Reviews on Biomembranes 1113, no. 3-4 (December 1992): 391–425. http://dx.doi.org/10.1016/0304-4157(92)90008-x.

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Andersen, O. S., R. E. Koeppe, and B. Roux. "Gramicidin Channels." IEEE Transactions on Nanobioscience 4, no. 1 (March 2005): 10–20. http://dx.doi.org/10.1109/tnb.2004.842470.

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Bali, Doreen, Lionel King, and Sungho Kim. "Syntheses of New Gramicidin A Derivatives." Australian Journal of Chemistry 56, no. 4 (2003): 293. http://dx.doi.org/10.1071/ch02142.

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Gramicidin A was covalently coupled with theophylline, thyroxine, digoxigenin, and biotin. New compounds were synthesized when the four molecules were coupled to ethanolamine on the C-terminus of gramicidin. Peptidic linkers were inserted between gramicidin and the bio-molecules.
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MacLeod, R. J., F. Redican, P. Lembessis, J. R. Hamilton, and M. Field. "Sodium-bicarbonate cotransport in guinea pig ileal crypt cells." American Journal of Physiology-Cell Physiology 270, no. 3 (March 1, 1996): C786—C793. http://dx.doi.org/10.1152/ajpcell.1996.270.3.c786.

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Prior studies show that ileal HCO3- secretion is of crypt origin, possibly involving Na+-HCO3- cotransport. To test for the latter, we isolated crypt cells from guinea pig ileum and determined effects of medium HCO3-, Na+, K+, disulfonic stilbenes, and gramicidin on intracellular pH [pHi;2',7'-bis(carboxyethyl)-5(6)-carboxyfluorescein fluorescence], cell volume (electronic sizing), and Na+ efflux from 22Na+ -preloaded cells. Ileal crypt cells alkalinized when placed in sodium gluconate-HCO3- medium containing N-5-methyl-5-isobutyl amiloride (1 microM), bumetanide (10 microM) and 4,4'-diisothiocyanostilbene-2,2'-disulfonic acid (250 microM which blocks Cl-/HCO3- exchange but not Na+ dependent HCO3- uptake). Depolarization with either gramicidin (50 microM) or 50 mM K+ caused a further 4-acetamido-4'-isothiocyanostilbene-2,2'-disulfonic acid (SITS)-inhibitable increase in pHi. Gramicidin also caused SITS-inhibitable cell swelling. Both gramicidin effects were Na+ dependent: at 0 mM Na+, gramicidin acidified and did not alter cell volume; at 25 mM, gramicidin also acidified; at 90 and 140 mM, gramicidin alkalinized and induced cell swelling. HCO3- -dependent SITS-inhibitable Na+ efflux from 22Na+ -preloaded cells was also seen. We conclude that ileal crypt cells engage in electrogenic Na+ -HCO3- symport.
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Cox, J. A., M. Milos, and M. Comte. "High-affinity formation of a 2:1 complex between gramicidin S and calmodulin." Biochemical Journal 246, no. 2 (September 1, 1987): 495–502. http://dx.doi.org/10.1042/bj2460495.

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Two molecules of gramicidin S, a very rigid cyclic decapeptide rich in beta-sheet structure, can bind in a Ca2+-dependent way to a calmodulin molecule in the presence as well as in the absence of 4 M-urea. The flow-microcalorimetric titration of 25 microM-calmodulin with gramicidin S at 25 degrees C is endothermic for 21.3 kJ.mol-1; the enthalpy change is strictly linear up to a ratio of 2, indicating that the affinity constant for binding of the second gramicidin S is at least 10(7) M-1. In 4 M-urea the peptide quantitatively displaces seminalplasmin from calmodulin, as monitored by tryptophan fluorescence. An iterative data treatment of these competition experiments revealed strong positive co-operativity with K1 less than 5 × 10(5) M-1 and K1.K2 = 2.8 × 10(12) M-2. A competition assay with the use of immobilized melittin enabled us to monitor separately the binding of the second gramicidin S molecule: the K2 value is 1.9 × 10(7) M-1. By complementarity, the K1 value is 1.5 × 10(5) M-1. In the absence of urea the seminalplasmin displacement is incomplete: the data analysis shows optimal fitting with K1 less than 2 × 10(4) M-1 and K1.K2 = 3.2 × 10(11) M-2 and reveals that the mixed complex (calmodulin-seminalplasmin-gramicidin S) is quite stable and is even not fully displaced from calmodulin at high concentrations of gramicidin S. The activation of bovine brain phosphodiesterase by calmodulin is not impaired up to 0.2 microM-gramicidin S. According to our model the ternary complex enzyme-calmodulin-gramicidin is relatively important and displays the same activity as the binary complex enzyme-calmodulin. Gramicidin S also displaces melittin from calmodulin synergistically, as monitored by c.d. Our studies with gramicidin S reveal the importance of multipoint attachments in interactions involving calmodulin and confirm the heterotropic co-operativity in the binding of calmodulin antagonists first demonstrated by Johnson [(1983) Biochem. Biophys. Res. Commun. 112, 787-793].
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Drannikov, A. A., I. S. Vatlin, M. Е. Trusova, A. Di Martino, S. V. Krivoshchekov, А. M. Guriev, and M. V. Belousov. "Investigation of Colloidal Structure and Biopharmaceutical Properties of New Antibacterial Composition of Gramicidin S." Drug development & registration 10, no. 4 (November 25, 2021): 129–37. http://dx.doi.org/10.33380/2305-2066-2021-10-4-129-137.

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Introduction. Gramicidin S has been conventionally manufactured as buccal tablets. However, in the past decade, the interest in the development of spray formulations has been growing. Those formulations contain excipients that enhance the solubility of the antibiotic in water solutions. However, the real structure of gramicidin S containing sprays remains unrevealed.Aim. Investigation of colloidal structure and biopharmaceutical properties of new gramicidin S antibacterial composition.Materials and methods. The composition sample was obtained using gramicidin S dihydrochloride, propylene glycol, polysorbate-80, ethanol and purified water. Raman spectroscopy has been performed to determine the composition of the phases. Dynamic light scattering analysis was performed to characterize the composition particles. Release of gramicidin S was performed by dialysis method and the concentration was determined by HPLC. The antimicrobial properties were investigated in accordance with the requirements of the XIV edition of the Russian pharmacopoeia.Results and discussion. Dynamic light scattering analysis results show gramicidin S formulation particles having an average size in solution 5–50 nm and ζ-potential (–1.1: +7.9 mV). Based on the obtained data on the composition properties and formulation parameters it was classified as colloidal solution. The kinetic stability evaluation was performed. We compared the solubility in water and release parameters of the active pharmaceutical ingredient in the native state and in the micelles. The enhancement of the antimicrobial activity of the peptide in the colloidal solution was confirmed and ascribed to the synergic effect gramicidin S – surfactant.Conclusion. We reported the colloidal type of the composition, that aggregate gramicidin S at a concentration of 8 mg/mL. We found that gramicidin S inclusion into the colloidal solution led to significant efficiency increase, which reveals the potential to reduce the drug dose and side effects level.
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Carillo, Kathleen D., Chi-Jen Lo, Der-Lii M. Tzou, Yi-Hung Lin, Shang-Ting Fang, Shu-Hsiang Huang, and Yi-Cheng Chen. "The Effect of Calcium and Halide Ions on the Gramicidin A Molecular State and Antimicrobial Activity." International Journal of Molecular Sciences 21, no. 17 (August 27, 2020): 6177. http://dx.doi.org/10.3390/ijms21176177.

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Gramicidin A (gA) forms several convertible conformations in different environments. In this study, we investigated the effect of calcium halides on the molecular state and antimicrobial activity of gramicidin A. The molecular state of gramicidin A is highly affected by the concentration of calcium salt and the type of halide anion. Gramicidin A can exist in two states that can be characterized by circular dichroism (CD), mass, nuclear magnetic resonance (NMR) and fluorescence spectroscopy. In State 1, the main molecular state of gramicidin A is as a dimer, and the addition of calcium salt can convert a mixture of four species into a single species, which is possibly a left-handed parallel double helix. In State 2, the addition of calcium halides drives gramicidin A dissociation and denaturation from a structured dimer into a rapid equilibrium of structured/unstructured monomer. We found that the abilities of dissociation and denaturation were highly dependent on the type of halide anion. The dissociation ability of calcium halides may play a vital role in the antimicrobial activity, as the structured monomeric form had the highest antimicrobial activity. Herein, our study demonstrated that the molecular state was correlated with the antimicrobial activity.
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Poxleitner, M., J. Seitz-Beywl, and K. Heinzinger. "Ion Transport through Gramicidin A. Water Structure and Functionality." Zeitschrift für Naturforschung C 48, no. 7-8 (August 1, 1993): 654–65. http://dx.doi.org/10.1515/znc-1993-7-820.

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Dynamics (MD) simulations were performed on a gramicidin A dimer model representing a transmembrane channel. Different from previous simulations the peptide was in contact with bulk water at both ends of the dimer to guarantee a realistic description of the hydration of the biomolecule. The flexible BJH model for water was employed in the simula­tions and the gramicidin-water, gramicidin-ion and ion-water potentials used are based on molecular orbital calculations. The water structure near the gramicidin was investigated first by a simulation without ions, while for the energy profiles of the ion transport through the channel a potassium or a sodium ion was added. These investigations provide a detailed and conclusive picture on a molecular level of the role of water in the ion transport through a gramicidin A channel and can explain the experimental results on the selectivity between alkali ions, their double or even triple occupancy, the exclusion or permeability of anions depending upon cation concentration and the consequences of differences in the ionic charge. The investi­gation demonstrate that the water molecules around the gramicidin behave as an integral part of the peptide and the functionality is the result of the whole complex biomolecule-water.
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Dissertations / Theses on the topic "Gramicidin"

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Lyons, Michael James. "A deuterium NMR study of gramicidin A’." Thesis, University of British Columbia, 1985. http://hdl.handle.net/2429/24848.

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This thesis presents the results of the first application of a novel solid state nuclear magnetic resonance technique (K. P. Pauls et. al., Eur. Biophys. J. 11:1) to a naturally occuring membrane polypeptide. Deuterium NMR was used to study the structure and dynamics of hydrogen-exchanged gramicidin A', an ion channel, in model membranes. The technique exploits recently developed procedures for solvent-signal suppression (P. T. Callaghan et. al., J. Magn. Reson. 56:101), and "depakeing" powder spectra (E. Sternin, M.Sc. Thesis,U.B.C.). The spectra of gramicidin A' in crystalline form, and in the gel phase of the lipid bilayer are similar and indicate little molecular motion on the NMR timescale. In the liquid crystalline phase, however, the spectra suggest rapid uniaxial rotation of the gramicidin about the bilayer director. The frequencies of the liquid crystalline phase spectra were found to be independent of bilayer thickness, temperature, and the presence of sodium chloride, in the ranges investigated. The results are discussed in the context of the conduction properties of the gramicidin ion channel, other spectroscopic studies, and thecretical models of the structure and action of gramicidin.
Science, Faculty of
Physics and Astronomy, Department of
Graduate
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Schracke, Nadine. "Die molekulare Logik der nichtribosomalen Peptidsynthetasen Identifizierung und biochemische Charakterisierung der Biosynthesegene für Gramicidin A /." [S.l. : s.n.], 2005. http://archiv.ub.uni-marburg.de/diss/z2005/0092/.

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McHugh, Rosalind Clare. "Sustainable agriculture by development of Brevibacillus brevis biocontrol methods for grey mould (Botrytis cinerea) of greenhouse crops." Thesis, University of Aberdeen, 2003. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.288359.

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Lettuce and tomato field trials were performed in an unheated polytunnel in Aberdeenshire to investigate the efficacy and mode of activity of Brevibacillus brevis against grey mould disease (Botrytis cinerea).  This was achieved by means of treating plants with whole cultures of B. brevis WT (containing gramicidin S and biosurfactant) and B. brevis E1 (containing biosurfactant only) and also with supernatant and spore fractions of such cultures so that the effects of treatments containing one, both or neither of the potentially active components, gramicidin S (bound to the bacterial spore) and biosurfactant (released into the culture medium) could be assessed.  In winter lettuce, WT and E1 reduced grey mould by up to 79% (p=0.05) with no significant disease (p=0.05) between efficacy of these treatments.  WT reduced disease by 59% in spring lettuce but at low significance (p=0.2) although marketable yields were significantly improved (p=0.05).  The biocontrol treatments WT, E1, SWT and SE1 reduced (p=0.05) grey mould by up to 48% in tomato leaves and 73% of WT treated plants had no stem lesions, significantly more (p=0.05) than lesion-free control plants (17%).  These results suggest that both the biosurfactant and gramicidin S play a role in disease reduction.  The biosurfactant appears to be responsible for disease reduction on aerial plant surfaces with large surface areas whilst Gramicidin S reduces disease in regions of higher humidity, such as the base of lettuce plants and on tomato stems.
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Wang, Fang. "Peptide channel redesign: mutations of gramicidin A at membrane-water interface." Thesis, Boston College, 2012. http://hdl.handle.net/2345/3411.

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Thesis advisor: Jianmin Gao
My graduate research focuses on engineering and characterizing gramicidin A (gA), a natural fifteen-residue transmembrane channel peptide. It consists of D- and L- amino acids at alternate positions. gA is believed to fold into a β-helix in membranes, and two folded monomers at each leaflet of the lipid bilayer dimerize to form a transmembrane channel. gA shares the common features of other known membrane channels: a well defined structure that only allows the passage of specific ions, a gating mechanism, and a high abundance of aromatic residues. This dissertation includes two subprojects: I. Understanding Channel Formation: Aromatic Modifications of Gramicidin A Channel Ion channels are key elements in signaling and molecule transport, and therefore crucial for normal function of cells. Defective ion channels are known to be responsible for a number of diseases. Although hundreds of crystallographic structures of membrane proteins have been deposited into the PDB in the past few decades, our knowledge on this large family of proteins is still limited and mostly descriptive. Study of small peptides in model membranes is a good simplification of the more complex biological systems. In chapter 1, I will introduce my research using gA as a model system to understand the significant role of aromatic residues in membrane channel structure formation. Channel activities of these gA-Ar mutants were evaluated by ion leakage assays. The structure activity relationship of a library of gA mutants was discussed. The alternating chirality of amino acids was proven to be essential for gA channel activity. Several additional interesting observations are discussed. II. Towards Bacterium Specific Ion Channels: Solublized Gramicidin A as Potential Systemic Antibiotics The rapid development of multidrug resistance by pathogenic bacteria poses a serious threat to society and demands new antibiotics with different mechanisms. Often considered as a model transmembrane channel, gA also has proven antibiotic activities. The gA channel facilitates passive diffusion of water and monovalent cations (e.g. H+, Na+, K+) thus killing bacteria by disrupting the ion gradient across the cell membrane. However because of its poor solubility and high toxicity, its medicinal application as an antibiotic has been limited to topical reagents. A detailed understanding of gA allows rational optimization of the gA-WT to potential systemic antibiotics. Bacterial membranes are composed of a large fraction of anionic species, therefore, we hypothesize that strategic incorporation of cationic residues into gA will afford bacterium-specific toxicities. In addition, the charged residues will greatly improve the water solubility of gA. In chapter 2, I will introduce my research on developing soluble and bacterium specific gA as a potential systemic antibiotic. We firstly incorporated D-Lys at the C-terminus to obtain our first generation of gA based antibiotics. The best candidate (D-Leu10,12,14D-Lys gA) shows significantly increased water solubility (~ 1, 000 times) and therapeutic index (˃ 50 times). Modifications on the Lys side chain were then carried out to fine tune the antibiotic activities of these cationic gA. My research has pointed out a possible strategy to convert hydrophobic membrane channel peptides into potential systemic antibiotics. In addition to targeting the negative charges of bacterial membranes with cationic gA mutants, we proposed a novel strategy in which boronic acid is used to chase after the 1,2-diol substructure in the PG headgroup through boronate ester formation. Polyvalent display of boronic acids on a peptide scaffold results in enhanced binding with diols, showing promise of the boronate approach in the development of bacterium specific reagents
Thesis (PhD) — Boston College, 2012
Submitted to: Boston College. Graduate School of Arts and Sciences
Discipline: Chemistry
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Doyle, Declan Anthony. "The structure and dynamics of a gramicidin pore." Thesis, Birkbeck (University of London), 1996. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.338656.

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Luk, Kai Yiu. "Statistical modeling and application of gramicidin A ion channel." Thesis, University of British Columbia, 2007. http://hdl.handle.net/2429/31984.

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Ion channels are aqueous pores in the cell membrane for selected ions to flow down their electrochemical gradient. These channels play a prominent role in a variety of biological processes in the human body. Determining the structure and function of ion channels is of fundamental importance in biology. Also, the selective conductivity and specific gating mechanism of ion channels have attracted much interest in the area of artificial molecular detectors. Ion channel based biosensors are developed to detect molecular species of interest in medical diagnostics, environmental monitoring and general bio-hazard detection. This thesis is concerned with statistical techniques used to describe ion channel permeation and to develop ion channel based biosensors. Brownian dynamics is a popular technique to simulate ion channel permeation but is too computationally expensive to run when ionic concentration is high. By fitting binding site statistics of BD simulation to a semi-Markov chain, we obtain a simpler model with conduction properties that are statistically the same as the simulations. This approach enables the use of extrapolation techniques to predict channel conduction when performing the actual simulation is computationally infeasible. Numerical studies on the simulation of gramicidin A channels are presented. In a separate study, we show the use of statistical modeling and detection techniques as part of a sensitive biosensing platform. A nano-scale biosensor is built by incorporating dimeric gramicidin A channels into bilayer membranes of giant unilamellar liposomes. The presence of specific target molecules changes the statistics of the biosensor's conduction. By capturing the change in real time, we devise a maximum likelihood detector to detect the presence of target molecules. The performance of the biosensor is tested with the addition of various target molecules known to inhibit conduction of gramicidin A channels. Experimental results show that the detection performed well even when the conductance change was difficult to visualize. The detection algorithm provides a sensitive detection system for ongoing development of membrane-based biosensors.
Applied Science, Faculty of
Electrical and Computer Engineering, Department of
Graduate
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Wan, Yang. "Synthesis of β,γ-diamino acids and their use to design new analogues of the antimicrobial peptide Gramicidin Septide antimicrobien, la Gramicidine S." Thesis, Université Paris-Saclay (ComUE), 2017. http://www.theses.fr/2017SACLS407/document.

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Dans notre groupe, nous nous intéressons au développement de peptides contenant des acides γ-aminés. Comme d’autres peptides contenant des acides aminés non naturels, ils ont montré leur capacité à posséder des conformations stables et/ou des propriétés biologiques intéressantes. De plus, ces peptides sont généralement résistant à la protéolyse. Dans l’objectif de synthétiser des acides -diaminés sous la forme d’un seul stéréoisomère, nous avons développé une voie de synthèse reposant sur une réaction de Blaise suivie d’une réduction diastéréosélective. En appliquant cette méthode, nous avons synthétisé des acides β,γ-diaminés dérivés de la D-phénylalanine et de l’acide L-glutamique. Le premier a été utilisé pour concevoir des analogues d’un peptide antimicrobien, la gramicidine S. Comparé à la molécule parent, les analogues ont montré une cytotoxicité beaucoup moins importante pour les cellules hôtes tout en conservant une activité antibactérienne intéressante. Cette étude nous a donné de meilleures connaissances pour développer d’autres analogues de la gramicidine S ainsi que d’autres peptides antimicrobiens. Nous avons également effectué de nombreuses optimisations pour synthétiser de façon efficace des acides β,γ-diaminés cycliques à partir de l’acide L-glutamique. Les oligomères incorporant ces acides β,γ-diaminés et des acides α-aminés ont montré un fort potentiel pour l’adoption de conformations stables. Ces études vont être poursuivies
In our group, we are interested in developing peptides containing β,γ-diamino acids . Along with many other peptides containing unnatural amino acids, they have shown the ability to possess stable conformations and/or interesting biological activities. Moreover, those peptides are usually more resistant to proteolysis. In order to synthesize stereopure γ-amino acids, we have developed a synthetic route using Blaise reaction and subsequent diastereoselective reduction as key reactions. Through applying this method, we have synthesized β,γ-diamino acids derived from D-phenylalanine and L-glutamic acid. The former β,γ-diamino acid was used for designing antimicrobial peptide gramicidin S analogues. Compared with mother molecule, the analogues exerted much less host cell cytotoxicity while remaining interesting antibacterial activity. Meanwhile, it gave us more knowledge for further developing analogues of gramicidin S as well as other antimicrobial peptides. We also paid lots of effort to efficiently synthesize cyclic β,γ-diamino acids starting from L-glutamic acid. Interestingly, when oligomers incorporating this β,γ-diamino acids and α-amino acids, they have shown the potential to adopt stable conformations. The following studies will be continuously investigated
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Wu, Xiaoming. "Biomimetic approaches to functional optimization of macrocyclic decapeptide gramicidin S /." View Abstract or Full-Text, 2003. http://library.ust.hk/cgi/db/thesis.pl?CHEM%202003%20WUX.

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Thesis (M. Phil.)--Hong Kong University of Science and Technology, 2003.
Includes bibliographical references (leaves 103-107). Also available in electronic version. Access restricted to campus users.
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Blake, Steven. "Designing nanosensors based on ion channel-forming derivatives of Gramicidin A." Diss., Connect to a 24 p. preview or request complete full text in PDF format. Access restricted to UC campuses, 2008. http://wwwlib.umi.com/cr/ucsd/fullcit?p3320124.

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Thesis (Ph. D.)--University of California, San Diego, 2008.
Title from first page of PDF file (viewed Sept. 11, 2008). Available via ProQuest Digital Dissertations. Vita. Includes bibliographical references (p. 111-121).
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Zerfas, Breanna L. "Creating Novel Antimicrobial Peptides: From Gramicidin A to Screening a Cyclic Peptide Library." Thesis, Boston College, 2017. http://hdl.handle.net/2345/bc-ir:107444.

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Thesis advisor: Jianmin Gao
As the threat of microbial resistance to antibiotics grows, we must turn in new directions to find new drugs effective against resistant infections. Antimicrobial peptides (AMPs) and host-defense peptides (HDPs) are a class of natural products that have been well-studied towards this goal, though very few have found success clinically. However, as there is much known about the behavior of these peptides, work has been done to manipulate their sequences and structures in the search for more drug-like properties. Additionally, novel sequences and structures mimicking those seen in nature have been discovered and characterized. Herein, we demonstrate our ability to finely tune the antimicrobial activity of various peptides, such that they can be provided with more clinically desirable characteristics. Our results show that gramicidin A (gA) can be made to be less toxic via incorporation of unnatural cationic amino acids. This is achieved by synthesizing lysine analogues with diverse hydrophobic groups alkylated to the side-chain amine. Through exploring different groups, we achieved peptide structures with improved selectivity for bacterial over mammalian membranes. Additionally, we were able to achieve novel broad-spectrum gram-negative activity for gA peptides. In efforts to combat bacterial resistance to cationic antimicrobial peptides (CAMPs), we have directed our reported amine-targeting iminoboronate chemistry towards neutralizing Lys-PG in bacterial membranes. Originally incorporating 2-APBA into gA, we found this to hinder the peptide’s activity. However, we were successful in increasing the potency of gA3R, a cationic mutant of gA, towards S. aureus by using a co-treatment of this peptide with a Lys-PG binding structure. Currently, we are exploring this strategy further. Finally, we describe our work towards establishing a novel cyclic peptide library incorporating a 2-APBA warhead for iminoboronate formation with a given target. In this, we have achieved intermolecular reduction of iminoboronates, strengthening the stringency of library screening. Although we were unsuccessful in finding a potent hit for binding of the lipid II stem peptide, screening against human transferrin yielded selective hits. Currently we are investigating these hits to understand their activity and therapeutic potential
Thesis (PhD) — Boston College, 2017
Submitted to: Boston College. Graduate School of Arts and Sciences
Discipline: Chemistry
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Books on the topic "Gramicidin"

1

Szule, Joseph A. The effects of gramicidin on the structure of phospholipid assemblies. St. Catharines, Ont: Brock University, Dept. of Biological Sciences, 2001.

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2

Chadwick, Derek J., and Gail Cardew, eds. Novartis Foundation Symposium 225 - Gramicidin and Related Ion Channel-Forming Peptides. Chichester, UK: John Wiley & Sons, Ltd., 1999. http://dx.doi.org/10.1002/9780470515716.

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Derek, Chadwick, Cardew Gail, Novartis Foundation, and Symposium on Gramicidin and Related Ion Channel-forming Peptides (1998 : London, England), eds. Gramicidin and related ion channel-forming peptides. Chichester: Wiley, 1999.

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4

Gail, Cardew, Chadwick Derek, Novartis Foundation, and Symposium on Gramicidin and Related Ion Channel-forming Peptides (1998 : London, England), eds. Gramicidin and related ion channel-forming peptides. Chichester: Wiley, 1999.

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5

Symposium, Novartis Foundation. Gramicidin and Related Ion Channel-Forming Peptides - No. 225. John Wiley & Sons, 1999.

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6

Short, Kurt William. Comparison of gramicidin A/lipid co-crystals and gramicidin A/lipid dispersions by Raman scattering. 1985.

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Cardew, Gail, and Derek J. Chadwick. Gramicidin and Related Ion Channel-Forming Peptides. Wiley & Sons, Incorporated, John, 2008.

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Book chapters on the topic "Gramicidin"

1

Saito, Yoshitaka, Shuzo Otani, and Shohei Otani. "Biosynthesis of Gramicidin S." In Advances in Enzymology - and Related Areas of Molecular Biology, 337–80. Hoboken, NJ, USA: John Wiley & Sons, Inc., 2006. http://dx.doi.org/10.1002/9780470122785.ch7.

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Hotchkiss, Rollin D. "Gramicidin, Tyrocidine, and Tyrothricin." In Advances in Enzymology - and Related Areas of Molecular Biology, 153–99. Hoboken, NJ, USA: John Wiley & Sons, Inc., 2006. http://dx.doi.org/10.1002/9780470122495.ch5.

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Wallace, B. A., and K. Ravikumar. "The Gramicidin Pore: Crystal Structure of a Gramicidin/Cesium Chloride Complex." In The Jerusalem Symposia on Quantum Chemistry and Biochemistry, 103–13. Dordrecht: Springer Netherlands, 1988. http://dx.doi.org/10.1007/978-94-009-3075-9_8.

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Koeppe, Roger E., Sigrid E. Schmutzer, and Olaf S. Andersen. "Gramicidin Channels as Cation Nanotubes." In Molecular- and Nano-Tubes, 11–30. Boston, MA: Springer US, 2011. http://dx.doi.org/10.1007/978-1-4419-9443-1_2.

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Vater, Joachim. "Chapter 2. Gramicidin S Synthetase." In Biochemistry of Peptide Antibiotics, edited by Horst Kleinkauf and Hans von Döhren, 33–56. Berlin, Boston: De Gruyter, 1990. http://dx.doi.org/10.1515/9783110886139-003.

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Calmes, Monique, Jacques Daunis, Dominique David, René Lazaro, Driss Benamar, and Frédéric Heitz. "New linear gramicidin A analogue." In Peptides 1992, 587–88. Dordrecht: Springer Netherlands, 1993. http://dx.doi.org/10.1007/978-94-011-1470-7_265.

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Woolley, G. Andrew, and B. A. Wallace. "Membrane Protein Structure: Lessons from Gramicidin." In Membrane Protein Structure, 314–34. New York, NY: Springer New York, 1994. http://dx.doi.org/10.1007/978-1-4614-7515-6_14.

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Wallace, B. A. "Introduction: Gramicidin, a Model Ion Channel." In Novartis Foundation Symposium 225 - Gramicidin and Related Ion Channel-Forming Peptides, 1–3. Chichester, UK: John Wiley & Sons, Ltd., 2007. http://dx.doi.org/10.1002/9780470515716.ch1.

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Duax, W. L., V. Pletnev, B. M. Burkhart, and M. Glowka. "Ion Gating and Selectivity in Gramicidin A." In Peptides: The Wave of the Future, 838–40. Dordrecht: Springer Netherlands, 2001. http://dx.doi.org/10.1007/978-94-010-0464-0_392.

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Woolley, G. A., and B. A. Wallace. "Circular dichroism studies of tryptophan residues in gramicidin." In Peptides, 247–49. Dordrecht: Springer Netherlands, 1992. http://dx.doi.org/10.1007/978-94-011-2264-1_87.

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Conference papers on the topic "Gramicidin"

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Krishnamurthy, Vikram, Kai Yiu Luk, Bruce Cornell, and Don Martin. "Real-Time Molecular Detectors using Gramicidin Ion Channel Nano-Biosensors." In 2007 IEEE International Conference on Acoustics, Speech and Signal Processing - ICASSP '07. IEEE, 2007. http://dx.doi.org/10.1109/icassp.2007.366701.

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Macrae, Michael X., Steven Blake, Thomas Mayer, Michael Mayer, and Jerry Yang. "Reactive derivatives of gramicidin enable light- and ion-modulated ion channels." In SPIE NanoScience + Engineering, edited by Manijeh Razeghi and Hooman Mohseni. SPIE, 2009. http://dx.doi.org/10.1117/12.827686.

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Antolini, R., P. Bernardi, L. Cescatti, L. Cristoforetti, G. D'Inzeo, G. Menestrina, P. Minciacchi, S. Pisa, and R. Pontalti. "Microwave-Induced Conductance Increases in Lipid Bilayer Membranes Modified with Gramicidin-A." In 20th European Microwave Conference, 1990. IEEE, 1990. http://dx.doi.org/10.1109/euma.1990.336310.

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Monfared, S. M., V. Krishnamurthy, and B. Cornell. "Mathematical modeling of a tethered bilayer sensor containing gramicidin a ion channels." In 2009 Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE, 2009. http://dx.doi.org/10.1109/iembs.2009.5333898.

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Saito, Hiroaki, Megumi Nishimura, Hiroyuki Takagi, Takeshi Miyakawa, Kazutomo Kawaguchi, and Hidemi Nagao. "Molecular dynamics study of electrostatic potential along lipid bilayer with gramicidin A." In 4TH INTERNATIONAL SYMPOSIUM ON SLOW DYNAMICS IN COMPLEX SYSTEMS: Keep Going Tohoku. American Institute of Physics, 2013. http://dx.doi.org/10.1063/1.4794649.

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Shao, C., M. Colombini, and D. L. DeVoe. "Planar Phospholipid Membrane Formation in Open Well Thermoplastic Chips." In ASME 2009 International Mechanical Engineering Congress and Exposition. ASMEDC, 2009. http://dx.doi.org/10.1115/imece2009-11432.

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Abstract:
A key requirement for the effective study of interactions between analytes and ion channels is the ability to dynamically vary analyte type and concentration to a membrane-bound ion channel within a planar phospholipid membrane (PPM). Here an open well microfluidic PPM apparatus supporting dynamic perfusion is presented. The plastic chip supports the manual formation of bilayer membranes that are resistant to pressure disturbances during perfusion with stability on the order of several hours. Using a chamber volume of 20 μL and a flow rate of 0.5 μL/min, the system enables rapid perfusion without breaking the membrane. The perfusion capability is demonstrated through gramicidin ion channel measurements.
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Saito, Hiroaki, Masashi Iwayama, Kazutomo Kawaguchi, Taku Mizukami, Takeshi Miyakawa, Masako Takasu, and Hidemi Nagao. "Molecular Dynamics Study of Gramicidin A in Lipid Bilayer: Electrostatic Map and Ion Conduction." In Proceedings of the 12th Asia Pacific Physics Conference (APPC12). Journal of the Physical Society of Japan, 2014. http://dx.doi.org/10.7566/jpscp.1.012053.

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Esquembre, Rocío, José Antonio Poveda, Ricardo Mallavia, and C. Reyes Mateo. "Immobilization and characterization of the transmembrane ion channel peptide gramicidin in a sol-gel matrix." In Microtechnologies for the New Millennium, edited by Paolo Arena, Ángel Rodríguez-Vázquez, and Gustavo Liñán-Cembrano. SPIE, 2007. http://dx.doi.org/10.1117/12.721676.

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DiCecco, John, Michael Segala, Oleg Andreev, Yana Reshetnyak, and Ying Sun. "The effect of Gramicidin on the membrane potential of neurons in the CNS of L. stagnalis." In 2007 IEEE 33rd Annual Northeast Bioengineering Conference. IEEE, 2007. http://dx.doi.org/10.1109/nebc.2007.4413319.

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David, Justin M., and Ayyappan K. Rajasekaran. "Abstract 3451: Gramicidin-based nanopores induce cellular energy depletion and cell death in renal cell carcinoma." In Proceedings: AACR 104th Annual Meeting 2013; Apr 6-10, 2013; Washington, DC. American Association for Cancer Research, 2013. http://dx.doi.org/10.1158/1538-7445.am2013-3451.

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Reports on the topic "Gramicidin"

1

Woolley, G. A., and B. A. Wallace. Circular Dichroism Studies of Tryptophan Residues in Gramicidin. Fort Belvoir, VA: Defense Technical Information Center, January 1992. http://dx.doi.org/10.21236/adp008376.

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