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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 GaoMy 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
5
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 poursuiviesIn 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 GaoAs 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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Schröder, Sabine. "cis-THF- und cis-THP-Aminosäuren als Bausteine für Gramicidin A Hybrid-Ionenkanäle Synthese, Struktur- und Funktionsuntersuchung." Berlin Logos-Verl, 2005. http://deposit.ddb.de/cgi-bin/dokserv?id=2820897&prov=M&dok_var=1&dok_ext=htm.
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Mori, Takaharu, and Yuko Okamoto. "Folding simulations of gramicidin A into theβ-helix conformations: Simulated annealing molecular dynamics study." American Institute of Physics, 2009. http://hdl.handle.net/2237/14159.
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Booth, Victoria Kaye. "Linking of FTIR data to structure : application to cinnamoyl serine proteases and gramicidin D." Thesis, University of Birmingham, 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.288868.
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Kubota, Shintaro. "Single Channel Analysis of Ion Transport across Membranes Containing Gramicidin A and KAT1 Channels." Kyoto University, 2016. http://hdl.handle.net/2433/215593.
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Kyoto University (京都大学)0048
新制・課程博士
博士(農学)
甲第19767号
農博第2163号
新制||農||1040(附属図書館)
学位論文||H28||N4983(農学部図書室)
32803
京都大学大学院農学研究科応用生命科学専攻
(主査)教授 加納 健司, 教授 三芳 秀人, 教授 三上 文三
学位規則第4条第1項該当
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WANG, ZHENG. "HIERARCHICAL APPROACH TO PREDICTING TRANSPORT PROPERTIES OF A GRAMICIDIN ION CHANNEL WITHIN A LIPID BILAYER." University of Cincinnati / OhioLINK, 2003. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1069794237.
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Korfhagen, Scott. "Stabilization of Scaffold-Supported, Photopolymerized Bilayer Lipid Membranes with Gramicidin-D for Novel Fuel Cells." University of Cincinnati / OhioLINK, 2008. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1212085821.
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Pfeifer, Jochen Robert. "Kronenether als Bausteine für selektive Hybridionenkanäle." Berlin Logos-Verl, 2005. http://deposit.ddb.de/cgi-bin/dokserv?id=2762593&prov=M&dok_var=1&dok_ext=htm.
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Vlok, Nicolaas Mare. "Investigation of complexation and antimicrobial activity of gramicidin S in the presence of lipopeptides from Bacillus subtilis." Thesis, Stellenbosch : Stellenbosch University, 2005. http://hdl.handle.net/10019.1/50379.
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Thesis (PhD)--Stellenbosch University, 2005.ENGLISH ABSTRACT: The implication of biologically active peptides from different organisms on one another in complex ecological communities is largely unknown at this stage. The elucidation of the nature of this influence may have practical implications in terms of organism resistance and the conservation of an optimal agricultural environment. This study was aimed to elucidate the effect of antimicrobial peptides from different co-habitational organisms, on each other, both in terms of bioactivity and interaction. The two peptides investigated were gramicidin S, a decapeptide from Bacillus brevis, and surfactin, a heptalipopeptide from Bacillus subtilis. Preliminary studies were also done on iturin A and synthetic analogues of iturin A and iturin C, both octalipopeptides from Bacillus subtilis. Analytical antimicrobial assay systems were used to study the effect of surfactin on the antibiotic action of gramicidin S towards three different target cells namely, a Gram-positive bacterium (Micrococcus luteus), a Gram-negative bacterium, (Escherichia coli) and a fungus (Penicillium corylophilium). The investigation of the antifungal activity was hampered by the insensitivity and subjectivity of the majority of antifungal assays and necessitated the development of two new testing methodologies. The investigation showed that surf actin had an antagonistic effect on the antimicrobial activity of gramicidin S against all three of the target cells. This antagonism is dose-dependent at concentrations lower than required for surfactin to exert biological activity. Electrospray mass spectrometry (ESMS) showed the formation of surfactin-gramicidin S complexes in 1:1 and 2: 1 ratios with enhanced complex formation in an apolar environment. Dissociation experiments indicated that the peptide complexes were slightly less stable than the peptides alone. The presence of NaCI up to 80 mM had little effect on the stability of preformed complexes. Incubating surfactin with NaCI and CaCh before titration with gramicidin S also did not affect complex formation. Furthermore, results from the pre-incubation studies with CaCh indicated that surfactin-gramicidin S complexes might be formed through the displacement of the metal ion. The mechanism of this displacement is unlikely to be direct competition but rather the result of conformational' changes induced by peptide-peptide interaction/interactions. A likely point of interaction the p-tums in the peptide ring. Linear iturin A2 and iturin C analogues were synthesised (8-Beta and 8-Betac) with solid phase peptide synthesis and purified using self-assembly and high performance liquid chromatography. The products of the syntheses wete analysed by ESMS and found to be correct. The products, together with commercially obtained iturin A, were used in biological assays and it was found that iturin A antagonises the antibiotic activity of gramicidin S but the linear analogues had no effect. Complex formation between iturin A and gramicidin S was observed using ESMS but no complexes were detected for the analogues, which reinforces the hypothesis that antagonism is related to the formation of inactive complexes. In general, the formation of peptide-gramicidin S complexes may indicate that a defence mechanism may be present in which toxic peptides of the competitor organism are inactivated by peptides from co-habiting organisms.
AFRIKAANSE OPSOMMING: Die invloed wat biologiese aktiewe verbindings van verskillende mikro-organismes in komplekse ekologiese omgewings op mekaar het, is onbekend. Die ontrafeling van die rol mag verskeie vrae ten opsigte van weerstandbiedenheid en ontwrigting van ekologiese landbou-omgewings beantwoord. Die doel van hierdie studie was om die invloed wat antimikrobiese peptiede, afkomstig van verskillende ko-habiterende organismes, op mekaar het te ondersoek- beide in terme van biologiese aktiwiteit en interaksie. Die twee peptiede wat ondersoek is, was gramisidien S, 'n dekapeptied geproduseer deur Bacillus brevis en surfaktien, 'n heptalipopeptied, geproduseer deur Bacillus subtilis. Voorlopige ondersoeke is ook uitgevoer op iturin A, en sintetiese iturin A en iturin C analoë, beide oktalipopeptiede van B. subtilis. Analitiese antimikrobiese toetsstelsels is gebruik om die effek van surfaktien op die biologiese aktiwiteit van gramisidien S te bepaal. Drie teikenselle is gebruik nl. 'n Grampositiewe bakterium (Micrococcus luteus), 'n Gram-negatiewe bakterium (Escherichia coli) en 'n fungus (Penicillium corylophilium) Die gebrek aan sensitiwiteit van bestaande antifungiese toetsstelsels het die ontwikkelling van twee nuwe toetstelsels genoodsaak. Die ondersoek het aangetoon dat surfaktien 'n antagonistiese effek op gramisidien S se antimikrobiese werking teen al drie teikenselle het. Die antagonisme is waarneembaar by surfaktien konsentrasies veel laer as wat nodig is vir biologiese aktiwiteit. Elektrosproeimassaspektrometrie (ESMS) van surfaktien en gramisidien S mengsels het aangedui dat komplekse in 'n 1:1 en 2: 1 stoichiometrie voorkom. Die vorming van peptiedkomplekse word ook deur 'n nie-polêre omgewing bevorder. Die stabiliteit van die peptiedkomplekse is ook geëvalueer met dissosiasie eksperimente en daar is gevind dat die komplekse minder stabiel is as die peptiede alleen - dit is 'n aanduiding van kompleksdissosiasie. Die teenwoordigheid van NaCI tot en met 80 mM het 'n minimale invloed op die stabiliteit van voorafgevormde peptiedkomplekse gehad. Inkubasie van surfaktien met NaCl en CaCh voor titrasie met gramisidien S, het ook nie die vorming van peptiedkomplekse beïnvloed nie en die studies het aangetoon dat die komplekse moontlik gevorm word deur die verplasing van die alkaliemetaalioon. Dit is onwaarskynlik dat die meganisme van ioon-verplasing direkte kompetisie is, maar eerder as gevolg van interaksie in een van die p-draaie. Liniêre iturin A2 en liniêre iturin Canaloë (8-Beta en 8-Betac) is gesintetiseer met behulp van soliede fase peptiedsintese en gesuiwer deur middel van "self-assembly" en "high performance liquid chromatography (HPLC)". Volgens die ESMS analise is die korrekte produkte verkry. Die analoë en kommersieel beskikbare iturin A is aan biologiese toetsing onderwerp en daar is gevind dat iturin A, maar nie die analoë nie, die antibiotiese effek van gramisidien S ophef. Die vorming van iturin en gramisidien S komplekse, wat met ESMS waargeneem is, versterk die teorie dat opheffing van aktiwiteit verband hou met die vorming van inaktiewe komplekse. Verder, die analoë het nie komplekse met gramisidien S gevorm me. Dit blyk vanuit hierdie studies dat die vorming van peptied komplekse moontlik deel kan uitmaak van 'n tipe verdedigingsmeganisme waar toksiese peptiede van kompeterende organismes, deur peptiede van ko-habiterende organismes, geïnaktiveer word.
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Wesolowski, Ryszard Leszek [Verfasser], and Robert [Akademischer Betreuer] Bähring. "Einbau und Funktion künstlicher Gramicidin-A-Hybrid-Kanäle in CHO-Zellen / Ryszard Leszek Wesolowski. Betreuer: Robert Bähring." Hamburg : Staats- und Universitätsbibliothek Hamburg, 2013. http://d-nb.info/1033403369/34.
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van, Rensburg Wilma. "Characterization of natural antimicrobial peptides adsorbed to different matrices." Thesis, Stellenbosch : Stellenbosch University, 2015. http://hdl.handle.net/10019.1/97929.
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Thesis (MSc)--Stellenbosch University, 2015.ENGLISH ABSTRACT: Biofouling is the attachment and biofilm formation that leads to negative repercussions such as persistent post-harvest infections, infections obtained from medical implants and continual surface contamination of food processing plants. Much of the problem lies with the resistance that develops against conventional treatments due to the formation of mature biofilms. Thus the focus has shifted from the removal of biofilms to the prevention of initial attachment of organisms. This entails the use of antimicrobial surfaces that either have an inherent antimicrobial activity, e.g. certain metals, or surfaces that are modified by the attachment of antimicrobial agents. The attachment of antimicrobial agents can either be through covalent bonding or adsorption, depending on the intended use of the surface as well as the mode of action of the antimicrobial agent. Antimicrobial peptides (AMPs) are ubiquitous in nature, tend to have a broad spectrum of activity, are very stable and have been shown to maintain activity when covalently bound to solid surfaces. Tyrocidines (Trcs), antimicrobial peptides produced by Bacillus aneurinolyticus, are cyclodecapeptides with a broad spectrum of activity against Grampositive bacteria, fungi, yeasts and the human malaria parasite, Plasmodium falciparum. The aim of this study was to determine the antimicrobial activity of surfaces treated with a tyrocidine extract, under which conditions the activity remained stable and to look into possible applications of these peptide-treated surfaces. The study focussed on different solid surfaces namely mixed cellulose, polyvinylidene fluoride, polycarbonate, cellulose acetate, cellulose (paper)(CL) and high density cellulose packing material (HDC), as a pilot study to assess the antimicrobial activity of Trc and gramicidin S (GS) treated solid surfaces. Peptide desorption and subsequent analysis by mass spectrometry was used to confirm the presence and integrity of the Trcs adsorbed. Scanning electron microscopy was utilised to show that the adsorbed peptides did not affect the structural integrity of the treated filters. However, it was shown that the adsorbed peptides changed the hydrophobic/hydrophilic character by means of a wettability assay. A cell viability assay and erythrocyte assay were developed from existing methodologies to determine the biological activity of the AMP-functionalised polymeric material. Seven of the AMP treated solid surfaces showed antimicrobial activity when challenged with >105 Micrococcus luteus cells/cm2. Although the polycarbonate filter lost antimicrobial activity at the high cell concentrations, it was shown to have potent antimicrobial activity at lower cell concentrations. Complete inhibition of M. luteus growth was observed for both the gramicidin S and tyrocidine extract treated high density cellulose and cellulose filters. Stability tests showed that the tyrocidines remained adsorbed to cellulose filters and biologically active when exposed multiple water washes, water washes at different temperatures (25°C - 100°C) and pH changes (pH 1-12). The antimicrobial activity was only affected after exposure to the water wash of pH 13 which is possible due to susceptibility of the CL filters to high pH solvents. A preliminary study on the effect of Trcs treated CL filters on the sterilization, germination and effect on tomato seedlings was conducted. It was found that Trcs had no effect on the germination and did not fully sterilise the seeds or environment against fungi. However, it was observed that 5 μg/mL Trcs treated filters promoted root length opposed to the toxic effect seen with filters treated with higher Trc concentrations. It is hypothesised that Trcs prefer to bind to hydrophilic surfaces exposing the hydrophobic residues and the cationic residue of the peptide to interact with the bacterial membrane to elicit its antimicrobial response. The exposed residues contain some of the hydrophobic residues and the cationic Orn9/Lys9, which are crucial to the antimicrobial activity of the peptides. Hydrophobic interaction is particularly important for the haemolytic activity which is currently the only viable method of detection of the adsorbed Trcs. Trcs also have a preference for adsorption onto cellulose and cellulose analogues which points to possible application in protective food wrapping and wood surface protection. Trcs maintains its antimicrobial activity regardless of adsorption to solid surfaces. It can therefore be concluded that Trcs treated solid surfaces hold great potential in preventing the initial bacterial colonization and subsequent biofilm formation. Antimicrobial peptide enriched solid surfaces can thus be developed and tailored to a specific application such as filters, catheters and packaging materials.
AFRIKAANSE OPSOMMING: Biovervuiling is die aanhegting en vorming van biofilms met negatiewe gevolge soos aanhoudende na-oes infeksies, infeksies op mediese inplantings en voortdurende oppervlak besoedeling van voedselverwerkings fabrieke. Die probleem lê grotendeels by die weerstand wat ontwikkel word teen konvensionele behandelings as gevolg van die vorming van volwasse biofilms. Die fokus het gevolglik verskuif vanaf die verwydering van biofilms na die voorkoming van aanvanklike aanhegting van organismes aan oppervlaktes. Dit behels die gebruik van antimikrobiese oppervlaktes wat of 'n inherente antimikrobiese aktiwiteit het, bv. sekere metale óf oppervlaktes wat aangepas is deur die aanhegting van antimikrobiese middels. Die aanhegting van antimikrobiese agente kan of deur kovalente binding óf adsorpsie plaasvind, afhangende van die beoogde gebruik van die oppervlak, sowel as die metode van werking van die antimikrobiese agent. Antimikrobiese peptiede (AMPe) is alomteenwoordig in die natuur, is geneig om 'n breë spektrum van aktiwiteit te hê, is baie stabiel en het getoon dat aktiwiteit in stand gehou word wanneer dit kovalent gebind word op soliede oppervlaktes. Tirosidiene (Trcs), antimikrobiese peptiede wat deur Bacillus aneurinolyticus geproduseer word, is siklodekapeptiede met 'n breë spektrum van aktiwiteit teen Gram-positiewe bakterieë, swamme, giste en die menslike malaria parasiet Plasmodium falciparum. Die doel van hierdie studie was om die antimikrobiese aktiwiteit te bepaal van oppervlaktes wat met 'n tirosidien ekstrak behandel is, te bepaal onder watter omstandighede die aktiwiteit stabiel bly en om te soek na moontlike toepassings van hierdie peptied-behandelde oppervlaktes. Die studie het gefokus op verskillende soliede oppervlaktes naamlik gemengde sellulose, polyvinylidene fluoried, polikarbonaat, sellulose asetaat, sellulose (papier)(CL) en 'n hoë digtheid sellulose verpakkings materiaal (HDC), as 'n loodsstudie om die antimikrobiese aktiwiteit van die Trcs en gramisidien S (GS) behandelde soliede oppervlaktes te ondersoek. Peptied-desorpsie en daaropvolgende ontleding deur massaspektroskopie is gebruik om die teenwoordigheid en integriteit van die geadsorbeerde Trcs te bevestig. Skandering elektronmikroskopie is gebruik om aan te toon dat die geadsorbeerde peptiede geen invloed op die strukturele integriteit van die behandelde filters het nie. Daar is egter getoon dat die geadsorbeerde peptiede die hidrofobiese / hidrofiliese karakter verander. „n Lewensvatbaarheid selgebaseerde toets en eritrosiet toets is ontwikkel uit bestaande metodes om die biologiese aktiwiteit van die AMP-gefunktionaliseerde polimeriese materiaal te bepaal. Sewe van die AMP behandel soliede oppervlaktes het antimikrobiese aktiwiteit getoon wanneer dit met > 105 Micrococcus luteus selle/cm2 gedaag is. Hoewel die polikarbonaat filter antimikrobiese aktiwiteit met hoë sel konsentrasies verloor het, is dit getoon dat dit wel uitgeproke antimikrobiese aktiwiteit het teen laer konsentrasies selle. Volledige inhibisie van M. luteus groei is waargeneem vir beide die hoë digtheid sellulose en sellulose filters wat met GS en tirosidien ekstrak behandel is. Stabiliteit toetse het getoon dat die tirosidiene geadsorbeer en biologies aktief op sellulose filters bly nadat dit blootgestel is aan verskeie water was-stappe, waterwasse by verskillende temperature (25 °C -100 °C) en pH veranderinge (pH 1-12). Die antimikrobiese aktiwiteit was net beïnvloed ná blootstelling aan die water met 'n pH 13, wat moontlik is te danke aan die vatbaarheid van die CL filters by hoë pH oplosmiddels is. 'n Voorlopige studie is gedoen om die uitwerking van Trcs behandelde CL filters op die sterilisasie, ontkieming en tamatiesaailinge te bepaal. Daar is gevind dat Trcs geen effek op die ontkieming het nie, maar dat dit nie volledig die sade en omgewing steriliseer vir fungiese groei nie. Daar is egter waargeneem dat 5 μg/mL Trcs behandelde filters wortel lengte van die saailinge bevorder teenoor die giftige uitwerking soos waargeneem vir die filters wat met hoër konsentrasies Trcs behandel is. Dit word gepostuleer dat Trcs verkies om aan hidrofiliese oppervlaktes te bind wat die van die hidrofobiese aminosure en die kationiese residu van die peptied blootstel om aan die bakteriële membraan te bind om gevolglik antimikrobiese reaksie te ontlok. Die blootgestelde deel bevat sommige van die hidrofobiese residue en positiewe Orn9/Lys9 wat noodsaaklik vir die antimikrobiese aktiwiteit van die peptiede. Die hidrofobiese interaksies is veral belangrik vir die hemolitiese aktiwiteit wat tans die enigste bruikbare metode van opsporing van die geadsorbeerde Trcs is. Trcs het ook 'n tendens vir adsorpsie op sellulose en sellulose analoë wat dui op die moontlike toepassing in beskermende voedselverpakking en die beskerming van houtoppervlaktes. Trcs handhaaf hul antimikrobiese aktiwiteit, ongeag van adsorpsie aan soliede oppervlaktes. Dit kan dus afgelei word dat Trcs-behandelde soliede oppervlaktes die potensiaal het om die aanvanklike kolonisasie van bakterië te voorkom en die daaropvolgende biofilm vorming. Antimikrobiese peptied verrykde soliede oppervlaktes kan dus ontwikkel en aangepas word vir gebruik in spesifieke toepassing soos in filters, kateters en verpakkingsmateriaal.
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LADHA, PARAG. "POLYMERIC MEMBRANE SUPPORTED BILAYER LIPID MEMBRANES RECONSTITUTED WITH BIOLOGICAL TRANSPORT PROTEINS." University of Cincinnati / OhioLINK, 2006. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1145901880.
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Fidzinski, Pawel. "Elektrophysiologische Charakterisierung künstlicher Ionenkanäle in lebenden Zellen." Doctoral thesis, Humboldt-Universität zu Berlin, Medizinische Fakultät - Universitätsklinikum Charité, 2006. http://dx.doi.org/10.18452/15472.
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Durch Ausübung physiologischer Grundfunktionen spielen Ionenkanäle eine entscheidende Rolle für die reguläre Funktion von Zellen. Zum besseren Verständnis ihrer Struktur und Funktion sind Untersuchungen natürlicher und künstlicher Ionenkanäle wichtige Werkzeuge. Großes analytisches und therapeutisches Potential ist in der Untersuchung künstlicher Kanäle in lebenden Zellen vorhanden, was bisher wenig Beachtung fand. In der vorliegenden Arbeit wurde die Wirkung der künstlichen Ionenkanäle THF-gram, THF-gram-TBDPS sowie linked-gram-TBDPS auf elektrophysiologische Eigenschaften boviner Trabekelwerkszellen des Auges anhand von Patch-Clamp-Untersuchungen im Whole-Cell-Modus analysiert. Die Untersuchung brachte folgende Erkenntnisse: 1. Die Inkorporation aller drei Verbindungen war erfolgreich, was sich durch Anstieg der Stromdichte und Verschiebung des Umkehrpotentials zeigte. 2. Einbau von THF-gram und THF-gram-TBDPS war mit dem Überleben der Zellen vereinbar, während linked-gram-TBDPS aufgrund einer sehr potenten Antwort bereits bei sehr geringen Konzentrationen zum raschen Zelltod führte. 3. Eine Asymmetrie der Stromantwort zugunsten stärkerer Auswärtsströme wurde bei THF-gram und in schwächerer Ausprägung bei THF-gram-TBDPS festgestellt. Linked-gram-TBDPS zeigte keine derartige Asymmetrie. 4. Unter Verwendung von Cs+ als Ladungsträger war der beobachtete Anstieg der Stromdichte bei allen drei Verbindungen eindeutig stärker als unter physiologischen Bedingungen (Na+/K+). 5. Die dargestellten Erkenntnisse sind ein erster Schritt zur therapeutischen Anwendung von künstlichen Ionenkanälen. Eine Weiterentwicklung in Richtung höherer Selektivität und besserer Kontrolle ist jedoch genauso erforderlich wie die Klärung der klinischen Umsetzbarkeit.Ion channels play a pivotal role for regular cell function. To better understand their structure and function, investigation of both natural and artificial ion channels is being performed to date. Investigation of artificial channels in living cells hides a big potential, however, little attention has been paid to this field so far. In this work, the effect of the artificial ion channels THF-gram, THF-gram-TBDPS and linked-gram-TBDPS on electrophysiological properties of bovine trabecular meshwork cells was investigated with the patch-clamp-technique. Following results were obtained: 1. Incorporation of all three compounds was successful, which was proven by increase of current density and cell depolarisation. 2. The cells survived after incorporation of THF-gram and THF-gram-TBDPS but not after linked-gram-TBDPS, which resulted in cell death at very low concentrations. 3. Larger outward currents were observed with THF-gram and, at a lower extent, with THF-gram-TBDPS. Linked-gram-TBDPS did not show such an asymmetry. 4. With Cs+ as charge carrier all three compunds showed a stronger increase of current density than under physiological conditions (Na+/K+). 5. The decribed results are a first step towards therapeutic application of artificial ion channels, however, further development towards higher selectivity and better control is as necessary as clarification of clinical feasibility.
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Berardo, Lydie. "Réalisation d'une membrane solide bio-inspirée constituée d'un film polymere nanoporeux et de gramicidine-A : caracterisation de ses propriétés de transport ionique." Thesis, Montpellier 2, 2012. http://www.theses.fr/2012MON20143/document.
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Ces travaux de thèse s'inscrivent dans le cadre d'un vaste projet qui vise à construire des membranes hybrides constituée d'un support solide nanoporeux et de protéines canal-ionique biologiques. Nous nous intéressons ici à un film polymère nanoporeux en polycarbonate et à la Gramicidine-A. La membrane ainsi réalisée est étudiée par des mesures expérimentales. Ce travail peut être divisé en deux parties. Dans la première, nous rapportons l'étude du confinement de la protéine canal ionique, au sein des nanopores du film « track-etched » en polycarbonate. Après imprégnation de gA, la membrane est étudiée par Spectroscopie de Fluorescence Confocale. Les premiers résultats expérimentaux particulièrement encourageants montrent que la gA est localisée dans les nanopores et non pas à la surface de la membrane. Dans la deuxième, les propriétés de transport ionique de la membrane hybride sont caractérisées par le biais de deux grandeurs : d'une part les coefficients de diffusion mesurés à partir d'une cellule et d'autre part les conductivités via la Spectroscopie d'Impédance Complexe (S.I.C). Les électrolytes aqueux étudiées sont : XCl(2) où X=Na, K, Mg et Ca à des concentrations comprises entre 5.10-3 à 1M. Une étude statistique approfondie des données obtenues par la méthode de la variance permet de déterminer les effets relatifs des différentes variables : nature et concentration du sel, présence de la Gramicidine A et traitement à l'éthanol de la membrane. Cette analyse révèle clairement que la présence de Gramicidine A au sein des nanopores de 15nm modifie de façon positive le transport ionique. Il est, par contre, difficile de conclure sur la nature sélective du transport ionique en présence de cette protéine. Ce travail de thèse ouvre un champ de recherche très prometteur dans le domaine de la nanofiltrationThis project of thesis is to build of a bio-inspired hybrid membrane made of a thin nanoporous polymer film in which a biological ionic channel is confined. Thus, this work may be divided in two parts. First, we report the confinement of the biological ionic channel, i.e. Gramicidin A, inside the nanopore of nanoporous thin film, i.e. a track etched polycarbonate film (Whatman NucleoporeTM). After impregnation with Gramicidine-A, the membrane is studied by means of confocal fluorescence spectroscopy. The results show the ionic channel is well located into the nanopores and not at the surface of the membrane. Secondly, ionic transport properties are measured by means of two experiments: on the one hand, ionic diffusion coefficients are measured using a cell and on the other hand, ionic dc conductivity is measured via Complex Impedance Spectroscopy (SIC). Various aqueous electrolytes (XCl(2) where X=Na,K, Mg et Ca) at different concentrations ranging from 5.10-3 à 1M are carried out. A statistical analysis of the data so-obtained allows to determine the relative effects of the different parameters: the nature and concentration of the electrolytes, the presence of Gramicidine A and the membrane pre-treatment with ethanol treatment. It is thus clearly pointed out that the presence of Gramicidine A inside the 15nm nanopores improves ion permeability. However, it is difficult to conclude about ionic selectivity of the hybrid membrane. Nevertheless, this work which is the first attempt ever to build such a bio-inspired system opens an extremely promising field of research in the domain of nanofiltration
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Wang, Liping. "Regulation of GABA(A) receptor function by hypoxia in rat primary cortical neurons." University of Toledo Health Science Campus / OhioLINK, 2009. http://rave.ohiolink.edu/etdc/view?acc_num=mco1251386977.
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Brumback, Audrey Christine. "Thermodynamic regulation of NKCC1-mediated chloride transport underlies plasticity of GABAA signaling /." Connect to full text via ProQuest. Limited to UCD Anschutz Medical Campus, 2006.
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Thesis (Ph.D. in Neuroscience) -- University of Colorado at Denver and Health Sciences Center, 2006.Typescript. Includes bibliographical references (leaves 86-96). Free to UCDHSC affiliates. Online version available via ProQuest Digital Dissertations;
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Song, Hyun Deok. "Computer Simulation Studies of Ion Channels at High Temperatures." University of Cincinnati / OhioLINK, 2012. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1328890332.
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Stephens, Brian Dominic. "BIOCOMPOSITE PROTON EXCHANGE MEMBRANES*." University of Cincinnati / OhioLINK, 2006. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1147968573.
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Etchebest, Catherine. "Etudes théoriques d'un canal ionique transmembranaire la gramicidine A /." Grenoble 2 : ANRT, 1987. http://catalogue.bnf.fr/ark:/12148/cb37604920f.
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Etchebest, Catherine. "Etudes theoriques d'un canal ionique transmembranaire : la gramicidine a." Paris 6, 1987. http://www.theses.fr/1987PA066049.
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Ranjalahy, Rasoloarijao Laurent. "Synthèse de nouveaux effecteurs membranaires analogues de la gramicidine A." Grenoble 2 : ANRT, 1987. http://catalogue.bnf.fr/ark:/12148/cb37609178r.
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Solano, Ana Gabriela Reis. "Desenvolvimento de métodos microbiológicos para doseamento de gramicidina matéria-prima." Universidade Federal de Minas Gerais, 2008. http://hdl.handle.net/1843/EMCO-7SMHYX.
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Gramicidin is a linear N-formylated pentadecapeptide-ethanolamide complex and active against Gram-positive organisms. It was first isolated from Bacillus brevis. The turbidimetric method is described in the United States Pharmacopoeia and British Pharmacopoeia to analyze gramicidin. Moreover, the results obtained in this assay were no satisfactory. The diffusion method is no described to analyze gramicidin. The present study reports the development and validation of the microbiological assays, applying the cylinder-plate and tube-assay, for the quantitation of gramicidin in raw material. The cylinder-plate method was developed using nutrient agar and a strain of Kocuria rhizophila ATCC 9341 as the test organism. The 3x3 and 5x1 experimental designs were applied. The validation of the method demonstrated that the method was precise (intra-assay: R.S.D. 0.81 3x3; 1.90 5x1; inter-assay: R.S.D. 1.35 3x3; 2.64 5x1), accurate (the 95% tolerance interval obtained was totally included within the acceptance limits) and selective. The calibration curve was linear from 5.00 to 25.3 g/ml. The detection, lower and upper quantification limit were 2.00; 5.00 and 25.3 g/ml, respectively. The F-test indicated that there is no significant difference between the two designs applied in the diffusion assay. The turbidimetric method was developed using GCLT broth (formulated in the laboratory) and Enterococcus hirae ATCC 10541 as the test organism. Also the 3x3 and 5x1 experimental designs were applied. The calibration curve was linear from 0.08 to 0.88 g/ml. The results obtained in this assay were precise (intra-assay: R.S.D. 0.18 3x3; 2.32 5x1; inter-assay: R.S.D. 0.69 3x3; 2.47 5x1) and accurate (the 95% tolerance interval obtained was totally included within the acceptance limits). The detection, lower and upper quantitation limit were 0.06; 0.08 and 0.88 g/ml, respectively. When turbidimetric assay was used, the 3x3 design was more precise than 5x1. The F-test indicated that there is no significant difference between the precision of two methods (p>0,05).A gramicidina é um pentadecapeptídeo linear antimicrobiano produzido pelo Bacilus brevis e ativo contra bactérias Gram positivo. O método microbiológico turbidimétrico é preconizado para o doseamento de gramicidina (USP 31 e BP 2007). Contudo, não se conseguiu reproduzir a metodologia farmacopéica em laboratório. Além disso, o método por difusão em ágar, uma outra alternativa para o doseamento, não é descrito para este antibiótico. Em vista do exposto, os objetivos deste trabalho foram desenvolver e validar os métodos microbiológicos, por difusão em ágar e turbidimétrico, para o doseamento da gramicidina. O método em placas foi desenvolvido empregando o ágar nutriente e Kocuria rhizophila ATCC 9341 como microrganismo teste. Foram utilizados dois delineamentos: retas paralelas 3x3 e 5x1. A validação do método demonstrou ser linear a relação entre o diâmetro dos halos de inibição e o logaritmo da concentração numa faixa de 5 a 25,3 g/ml. Os resultados obtidos por ambos os delineamentos foram precisos (desvio padrão relativo, DPR, para precisão intra-dia: 0,81 3x3; 1,90 5x1; DPR inter-dias: 1,35 3x3; 2,64 5x1), exatos (intervalo de tolerância a 95% dentro dos limites permitidos) e com veracidade adequada (erros sistemáticos não significativos). Além disso, o método foi seletivo com limites de detecção e quantificação inferior e superior iguais a 2,00; 5,00 e 25,3 g/ml, respectivamente. Não foi observada diferença entre a precisão dos delineamentos empregados no método de difusão em ágar (p>0,05). O método turbidimétrico utilizando caldo GCLT (formulação desenvolvida no laboratório) e Enterococcus hirae ATCC 10541 foi validado. Também foram empregados os delineamentos 3x3 e 5x1. A curva analítica demonstrou ser linear a relação entre a porcentagem de inibição do crescimento microbiano e a concentração de gramicidina no intervalo de 0,08 a 0,88 g/ml. Os resultados obtidos por ambos os delineamentos também foram precisos (DPR intra-dia: 0,18 3x3; 2,32 5x1; DPR inter-dias: 0,69 3x3; 2,47 5x1), exatos e com veracidade adequada. Os limites de detecção, de quantificação inferior e superior foram iguais a 0,06; 0,08 e 0,88 g/ml, respectivamente. Quando o delineamento 3x3 foi utilizado para o método turbidimétrico, resultados mais precisos foram obtidos. Foi verificada a inexistência de diferença significativa entre as precisões dos dois métodos quando o delineamento 3x3 foi empregado e nem quando o 5x1 foi utilizado.
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Chavas, Joël. "Effets de l'activation des récepteurs GABAA sur l'activité électrique des interneurones de la couche moléculaire du cervelet de rat." Paris 6, 2003. http://www.theses.fr/2003PA066418.
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Janosi, Lorant. "Multiscale modeling of biomolecular systems." Diss., Columbia, Mo. : University of Missouri-Columbia, 2007. http://hdl.handle.net/10355/4801.
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Thesis (Ph. D.)--University of Missouri-Columbia, 2007.The entire dissertation/thesis text is included in the research.pdf file; the official abstract appears in the short.pdf file (which also appears in the research.pdf); a non-technical general description, or public abstract, appears in the public.pdf file. Title from title screen of research.pdf file (viewed on February 14, 2008) Vita. Includes bibliographical references.
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Daumas, Pascal. "Gramicidines linéaires contribution à l'étude de la relation "structure chimique-activité ionagogue /." Grenoble 2 : ANRT, 1988. http://catalogue.bnf.fr/ark:/12148/cb376129414.
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Lavoie, Hugo. "Propriétés structurales de protéines membranaires à l'interface air-eau : une étude par spectroscopie PM-IRRAS et rayons X." Thèse, Université du Québec à Trois-Rivières, 2002. http://depot-e.uqtr.ca/6654/1/000693512.pdf.
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Benayad, Ahmed. "Interactions lipides-peptides en monocouches : application à l'étude de la gramicidine A (GA) et de ses analogues." Montpellier 2, 1992. http://www.theses.fr/1992MON20117.
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L'etude comparative des conductances du canal ionique de la ga et de ses analogues synthetiques a revele que la conductance depend fortement de la constitution chimique du peptide. L'etude de ces analogues en monocouche a l'interface eau-air en presence ou en absence du lipide a montre qu'ils adoptent plusieurs etats conformationnels. Ce travail a fait ressortir plusieurs principaux points qui doivent etre pris en compte lors de l'etude au niveau moleculaire: l'identification des conformations des differents analogues par les techniques conventionnelles ne correspondent pas necessairement a celles impliquees dans la forme active du canal. L'etude et l'analyse des resultats de la monocouche necessitent la connaissance de l'etat conformationnel du peptide qui peut etre identifie au moyen de la spectroscopie infra-rouge effectuees sur des films preleves
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SILVA, Márcia Pereira da. "Investigação da correlação de longo alcance na cinética de canais iônicos formados pela gramicidina A em membranas artificiais." Universidade Federal Rural de Pernambuco, 2018. http://www.tede2.ufrpe.br:8080/tede2/handle/tede2/7227.
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Ion channels are integral proteins present in cell membranes, being fundamental components in a wide variety of physiological processes, e.g. propagation of the nervous impulse, muscular contraction, control of the cardiac excitability and cellular secretion. The ion channels shift between different states of conductance, sometimes allowing, sometimes interrupting the flow of ions between the cellular compartments. The mechanism of opening and closing ion channels has been modeled as a random process, however, some studies have shown that these transitions in some channels have memory, that is, long-term correlation. Gramicidin A (gA) is a pentadecapeptide produced by Bacillus brevis with the ability to form simple ion channels when inserted into lipid membranes. The structural simplicity, the ability to form channels and the ease of molecular manipulation of gA have made gramicidin a good model for studies of ion channels. There is a large amount of reports about gA channels, however, we did not find studies using mathematical methods of nonlinear dynamics in the analysis of the existence of memory in these channels. In this context we used the Detrended Fluctuation Analysis (DFA) and the Approximate Entropy (ApEn) in the investigation of the existence of memory and complexity in the kinetic process of the gA channels, respectively. The single-channel currents were recorded in real time through a microcomputer coupled to an A / D converter and a patch-clamp amplifier. All experiments were performed under the following experimental conditions: diphytanoyl phosphatidylcholine planar lipid bilayers in 1 M NaCl solution not buffered, initial pH of 6.3 ± 0.2; the transmembrane potential of 200 mV and a temperature of 25 ° C. The conductance of the gA channel was 15.5 ± 0.05 pS. The time constants, , for the gA channel for the open and closed state were 𝑓== 3.1866 ± 0.1752 s and 𝑎= 12.0743 ± 0.8658 s, respectivel. According to the number of events and percentage deletion of time series regions, different behaviors in kinetics of gA channels were observed: antipersistent correlation (𝛼𝐷𝐹𝐴 = 0.4 and 0.44), persistent correlation (𝛼𝐷𝐹𝐴 = 0.63) and presence of random behavior (𝛼𝐷𝐹𝐴 = 0.53 ± 0.2). However, it has been observed in most of the analyzed series that the kinetics of these channels tend to exhibit a random behavior. The results of the ApEn analyzes showed that the series that have random behavior presented greater complexity when compared to the series that have memory. The results obtained allow us to conclude that the kinetic process of the gA channel has high complexity and absence of memory, divergent behavior from those found in many structurally complex ion channels, such as some sodium and potassium channels, which have a deterministic behavior.
Os canais iônicos são proteínas integrais presentes nas membranas celulares, sendo componentes fundamentais em uma grande variedade de processos fisiológicos como propagação do impulso nervoso, contração muscular, controle da excitabilidade cardíaca e secreção celular. Os canais iônicos transitam entre diferentes estados de condutância, ora permitindo, ora interrompendo o fluxo de íons entre os compartimentos celulares. O mecanismo de abertura e fechamento dos canais iônicos tem sido modelado como um processo aleatório, no entanto, alguns trabalhos têm demostrado que essas transições em alguns canais apresentam memória, ou seja, correlação de longo alcance. A gramicidina A (gA) é um pentadecapeptídeo produzido pelo Bacillus brevis com a capacidade de formar canais iônicos simples quando inseridas em membranas lipídicas. A simplicidade estrutural, a capacidade de formar canais e a facilidade de manipulação molecular de gA tornaram a gramicidina um bom modelo para estudos dos canais iônicos. Sabe-se da grande quantidade de relatos sobre os canais de gramicidina, porém, não foi encontrado estudos com o emprego de métodos matemáticos de dinâmica não-linear na análise da existência de memória nesses canais. Nesse contexto empregamos a análise de flutuação destendenciada (DFA) e a entropia aproximada (ApEn) na investigação da existência de memória e complexidade no processo cinético dos canais de gA, respectivamente. As correntes iônicas unitárias foram registradas em tempo real através de um microcomputador acoplado a um conversor A/D e um amplificador de patch-clamp. Todos os experimentos foram realizados nas seguintes condições experimentais: bicamadas lipídicas planas de diftanoil-fosfatidilcolina, solução de NaCl 1 M não tamponada, pH de 6,3±0,2; potencial transmembrana de 200 mV e temperatura de 25°C. O valor da condutância do canal de gA foi de 15,5 ± 0.05 pS. As constantes de tempo para o canal de gA para o estado aberto e no estado fechado foram 𝑎= 3,1866 ± 0,1752 s e 𝑓=12,0743 ± 0,8658 s, respectivamente. Em função do número de eventos e do percentual de deleção de regiões das séries temporais observou-se diferentes comportamentos na cinética dos canais de gA: correlação antipersistente (𝛼𝐷𝐹𝐴=0,4 e 0,44), correlação persistente (𝛼𝐷𝐹𝐴=0,63) e presença de comportamento aleatório (𝛼𝐷𝐹𝐴=0,53±0,2). No entanto, foi observado na maioria das séries analisadas que a cinética desses canais tende a apresentar um comportamento aleatório. Os resultados das análises da ApEn mostraram que as séries que possuem comportamento aleatório apresentaram maior complexidade quando comparados as séries que apresentam memória. Os resultados obtidos permitem concluir que o processo cinético do canal de gA possui de elevada complexidade e ausência de memória, comportamento divergente daqueles encontrados em muitos canais iônicos estruturalmente complexos, como alguns canais de sódio e potássio, que possuem um comportamento determinístico.
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Benamar, Driss. "Activités et fonctions ionagogues d'analogues synthétiques de la gramicidine A : effets de modifications portant sur la partie C-terminale." Montpellier 2, 1992. http://www.theses.fr/1992MON20093.
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Notre travail a apporte une contribution a la comprehension du mecanisme de transport ionique a travers le canal de la gramicidine a. Les resultats de tous les analogues etudies ont fait ressortir plusieurs points: 1) la conductance du canal ne depend pas de la taille des chaines laterales aromatiques; 2) le moment dipolaire lie aux chaines laterales aromatiques est une condition necessaire mais non suffisante pour obtenir des canaux de conductance elevee; 3) l'hydrophobicite des chaines laterales est un facteur important pouvant induire des modifications de leurs orientations, ce qui a pour consequence une modification des hauteurs relatives des barrieres energetiques; 4) l'extremite ethanolamine ne joue aucun role dans le transfert ionique. Ces resultats permettent de classer les differents analogues en deux classes: d'une part les gramicidines dont la conductance est elevee et independante du potentiel et d'autre part les analogues dont la conductance est faible et fortement dependante du potentiel
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Demange, Valérie. "Caractérisation structurale et fonctionnelle de monocouches amphiphile-peptide à l'interface air/eau et à l'interface solide/liquide." Compiègne, 1998. http://www.theses.fr/1998COMP1130.
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Des monocouches passivantes d'octadécanethiol (OM) ont pu être construites sur des électrodes planes d'or par la technique de Langmuir-Blodgett. Ces films forment une barrière importante, tant aux espèces rédox qu'aux ions présents en solution. Nous avons recherché leurs caractéristiques microscopiques par microscopie à force atomique (AFM). Nous avons ensuite étudié les propriétés d'un peptide, la gramicidine à la surface de l'eau puis à la surface de l'électrode. Avant réalisation d'une monocouche mixte OM-peptide, cette étude était indispensable pour savoir si la taille et la conformation du peptide étaient compatibles avec la monocouche de thiol. L'AFM a alors été utilisé non seulement comme moyen d'observation mais aussi comme moyen de dissection des couches à l'échelle moléculaire. A faible pression de surface, le film construit est constitué de monomères dont l'axe serait probablement perpendiculaire à la surface. A forte pression, le film est constitué de dimères, plus précisément de deux hélices accolées par leur N-terminal dont l'axe est perpendiculaire à la surface. Le comportement des couches mixtes se révèle à la surface de l'eau comme étant celui d'un mélange idéal à condition que les composés soient déposés séparément sur l'eau. Puis à la surface de l'électrode, lors des expériences de voltamétrie cyclique, le régime de diffusion en présence du peptide ne traduit qu'un très faible degré de défauts. Les mesures de capacitances ont mis en évidence la modification de la constante diélectrique de la couche avec le pourcentage de gramicidine. L'AFM réalisé a démontré que le mélange était miscible pour des pourcentages de peptide adéquats.
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Bélanger, Anne. "Étude de l'orientation magnétique de membranes lipidiques modèles en présence de gramicidine A et d'ions paramagnétiques par résonance magnétique nucléaire du phosphore-31 et du deutérium." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1998. http://www.collectionscanada.ca/obj/s4/f2/dsk2/ftp01/MQ38012.pdf.
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Kurylowicz, Martin. "Principal Component Analysis of Gramicidin." Thesis, 2010. http://hdl.handle.net/1807/24790.
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Computational research making use of molecular dynamics (MD) simulations has begun to expand the paradigm of structural biology to include dynamics as the mediator between structure and function. This work aims to expand the utility of MD simulations by developing Principal Component Analysis (PCA) techniques to extract the biologically relevant information in these increasingly complex data sets. Gramicidin is a simple protein with a very clear functional role and a long history of experimental, theoretical and computational study, making it an ideal candidate for detailed quantitative study and the development of new analysis techniques. First we quantify the convergence of our PCA results to underwrite the scope and validity of three 64 ns simulations of gA and two covalently linked analogs (SS and RR) solvated in a glycerol mono-oleate (GMO) membrane. Next we introduce a number of statistical measures for identifying regions of anharmonicity on the free energy landscape and highlight the utility of PCA in identifying functional modes of motion at both long and short wavelengths. We then introduce a simple ansatz for extracting physically meaningful modes of collective dynamics from the results of PCA, through a weighted superposition of eigenvectors. Applied to the gA, SS and RR backbone, this analysis results in a small number of collective modes which relate structural differences among the three analogs to dynamic properties with functional interpretations. Finally, we apply elements of our analysis to the GMO membrane, yielding two simple modes of motion from a large number of noisy and complex eigenvectors. Our results demonstrate that PCA can be used to isolate covariant motions on a number of different length and time scales, and highlight the need for an adequate structural and dynamical account of many more PCs than have been conventionally examined in the analysis of protein motion.
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Schmitt, Eva Katharina. "Hochohmige porenüberspannende Lipidmembranen: Elektrochemische Untersuchungen zur Aktivität von Gramicidin und Bacteriorhodpsin." Doctoral thesis, 2009. http://hdl.handle.net/11858/00-1735-0000-0006-AD40-9.
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Herasymova, Nataliya. "Gramicidin A and cyclic peptides channel conductances in black lipid membranes." 2010. http://hdl.handle.net/10090/15143.
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Harroun, Thad Alan. "Membrane-mediated peptide-peptide interaction: Gramicidin in-plane distribution by x-ray scattering." Thesis, 1997. http://hdl.handle.net/1911/17093.
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While there has been much speculation on the role the lipid matrix plays in controlling and mediating the inter-molecular dynamics of proteins, there has been little direct evidence for how the lipid bilayer can mediate the supra-molecular organization of these proteins. With the technique of X-ray in-plane scattering, we can directly measure the correlation function of gramicidin channels in the plane of the bilayer. We have studied the simple case of gramicidin incorporated into model Dilauroyl and Dimyristoyl-Phosphocholine (DL-,DMPC) membranes, and have seen how changing the membrane thickness changes peptide-peptide correlation. In the fluid phase, DLPC and DMPC present an elastic medium that can perhaps match the hydrophobic length of the peptide. The resulting membrane deformation energy is expected to cause inter-peptide attraction. Indeed, the scattering data shows that the gramicidin-gramicidin correlation distance is smaller in DMPC than in DLPC. Thus we have obtained direct evidence of membrane mediated peptide-peptide interaction. As the temperature drops and DMPC approaches its main transition temperature, gramicidin exhibits close packing. This may indicate that the channels are being excluded from gel lipid regions and are packing closer together.
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Olah, Glenn Allen. "Thallium ion distribution in the gramicidin ion conducting channel determined by x-ray diffraction." Thesis, 1990. http://hdl.handle.net/1911/16378.
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Gramicidin is the best characterized transmembrane ion channel. An opulence of biochemical and physiological data exists and it is the only channel for which a relatively well-defined structure is known. Thus, it has been proven to be an ideal model for actual physiological channels by providing valuable insight into a channel's structural/functional properties. Although much is known about the gramicidin channel, there is still no solid experimental data on the channel molecular dimensions. Therefore, this thesis supplies a very crucial piece of experimental structural data; namely, the direct location of two symmetric cation binding sites within the channel by x-ray diffraction. The binding sites are located at 9.4 $\pm$ 0.4 A about the midpoint of the channel. A previous $\sp{13}$C NMR study (Urry et al., 1982a,b; Urry, 1983) pinpointed cation binding between Trp-11 and Trp-13, and, based on rigid molecular models, this puts the binding sites at 11.0-11.5 A, which is at least 1.2 A larger than the value reported here. This suggests a considerable plasticity of the gramicidin channel consistent with conclusions drawn from recent molecular dynamic simulations (Roux and Karplus, 1988). Also, the smaller value leads to an elegant qualitative picture in which the flexible ends of the channel can conveniently provide the gating mechanism that transmits cations and blocks anions.
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He, Ke. "X-ray scattering with momentum transfer in the plane of membrane: Application to gramicidin organization." Thesis, 1993. http://hdl.handle.net/1911/13735.
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We demonstrate a technique of measuring x-ray (or neutron) scattering with the momentum transfer parallel to the plane of membrane. This technique allows us to investigate the lateral organization of protein and peptide in the membrane. To resolve the question of whether gramicidin (GA) forms lateral aggregates, samples of GA in dilauroylphosphatidycholine (DLPC) bilayers (molar ratio 1:10) were investigated. Very clear scattering signals of GA were obtained, even for the peptide without a heavy atom attached. The experiment showed that the gramicidin channels did not aggregate and were randomly distributed in the membrane.
The non-conducting state of gramicidin channel was also investigated. We use a synthetic GA analogue in which the formyl group of natural GA is replaced by a BOC group. The in-plane scattering measurements show that the gramicidin channel closes by dissociation into two monomers, each remains embedded and freely diffuses in its own monolayer.
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Schmitt, Eva Katharina [Verfasser]. "Hochohmige porenüberspannende Lipidmembranen : elektrochemische Untersuchungen zur Aktivität von Gramicidin und Bacteriorhodopsin / vorgelegt von Eva Katharina Schmitt." 2009. http://d-nb.info/99557488X/34.
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CAI, WEI-HONG, and 蔡煒鴻. "The effect of EM field on the motion of Na﹢ through the gramicidin a ion channel." Thesis, 1993. http://ndltd.ncl.edu.tw/handle/56555049119180521010.
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Hoyer, Maria-Katharina [Verfasser]. "Iterative NRPS-Systeme : Charakterisierung der Gramicidin-S-Thioesterase und Analyse der Thiocoralin-3-Hydroxychinaldinsäure-Biosynthese / vorgelegt von Maria-Katharina Hoyer." 2009. http://d-nb.info/99346579X/34.
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Schracke, Nadine [Verfasser]. "Die molekulare Logik der nichtribosomalen Peptidsynthetasen : Identifizierung und biochemische Charakterisierung der Biosynthesegene für Gramicidin A / vorgelegt von Nadine Schracke geb. Keßler." 2005. http://d-nb.info/975257455/34.
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