Helix-coil-transition in solid polypeptides

Abstract Poly(L-glutamic acid) (PLGA) was synthesized by living anionic ring-opening polymerization of the NCA monomer, which was obtained by reacting diphosgene with an amino acid derivative. The chemical structures and thermal properties were characterized by 1H-NMR, 13C-NMR, TGA and DSC. XRD powder patterns found to be amorphous for all polymers obtained. The molecular weights could be determined under severe limitations due to low solubility and high aggregation tendency. The secondary structure of the PLGA films was analyzed in the solid state by IR spectroscopy; the order was determined mainly by XRD. Uniform bulk films (1-5 µm) were produced by drop-casting of PLGA solutions in TFA on silica. The XRD film analysis indicated the absence of a long range order or an orientation even if a helical microstructure was confirmed by IR spectroscopy. The coil solvent TFA delivered constantly a helical or a β-sheet structure in the solid state depending on the water content of the solvent which was observed for the first time to exhibit a high influence on the crystallization process for PLGA. Temperature dependent in-situ IR measurements were examined to analyze if a helix-coil transition occurs, but there could be no solvent system determined, which resulted in a disordered coil structure in the solid state. General parameters like solvent systems, evaporation conditions, concentration, substrates etc. were analyzed. New crystallizations were obtained on silica prepared by drop-casting of solutions of PLGA in DMF, DMA, TMU, NMP, and pyridine/water mixtures, respectively. PSCBC in DMF, CDCl3/TFA-d, and PSBC in CDCl3/TFA-d exhibited the same crystalline diffraction patterns like PLGA. The long range order in the X-ray diffraction pattern is proven by extremely sharp crystalline signals, which are not changing the shape or the position of the peak by increasing the temperature up to 160°C. The substrate seems to play a decisive role because the crystalline structures were not obtainable on glass. The crystal structure consists probably of two different layered structures based on the intensity ratios of the two series of crystalline signals in the X-ray diffraction patterns. The source of the layered structure remains unclear and needs further studies to investigate the spatial arrangement of the chains in more detail. The secondary structure was still not changing upon heating even if a highly crystalline diffraction pattern occurs. Concluding that even the newly investigated crystallization did not show a helix-coil transition in the solid state by annealing, the phenomenon known in solution has to be claimed as unachievable in the solid state based on the results of this work. A remaining open question represents the observation that the same crystalline pattern can be reproducibly prepared with exhibiting two different ordered secondary structures (helix and β-sheet). After the investigation that the evaporation time cannot be decisive for the crystal growth, the choice of a strong hydrogen bonding interrupting solvent is most probably the key to support and induce the crystallization process.

Ion channels in mixed tethered bilayer lipid membranes

Mixed tethered bilayer lipid membranes (tBLMs) are described based on the self-assembly of a monolayer on template stripped gold, of an archea analogue thiolipid, 2,3-di-o-phytanyl-sn-glycerol-1-tetraethylene glycol-D,L--lipoic acid ester lipid (DPTL), and a newly designed dilution molecule, tetraethylene glycol-D,L--lipoic acid ester (TEGL). The usage of spacer and addition of extra dilution molecules between the substrate and the bilayer is that this architecture provides an ionic reservoir underneath the membrane, avoiding direct contact of the embedded membrane proteins with the gold electrodes and increasing the lateral diffusion of the bilayer, thus allowing for the incorporation of complex channels proteins which are failed in non-diluted systems. The tBLM is completed by fusion of liposomes made from a mixture of 1,2-diphythanolyl-sn-glycero-3-phosphocholine (DPhyPC), cholesterol, and 1,2-diphytanoyl-sn-Glycero-3-phosphate (DPhyPG) in a molar ratio of 6:3:1. Varying the mixing ratio, the optimum mixing ratio was obtained at a dilution factor of DPTL and TEGL at 90%:10%. Only under these conditions, the mixed tBLM showed electrical properties, as shown by EIS, which are comparable to a BLM. With higher dilution factors, a defect-free lipid bilayer was not formed. Formation of bilayers have been characterized by different techniques, such as surface plasmon resonance (SPR), electrochemical impedance spectroscopy (EIS), atomic force microscopy (AFM), and quartz crystal microbalance (QCM). Different proteins such as hemolysin, melittin, gramicidin, M2, Maxi-K, nAChR and bacteriohodopsin are incorporated into these tBLMs as shown by SPR and EIS studies. Ionic conductivity at 0 V vs. Ag|AgCl, 3M KCl were measured by EIS measurements. Our results indicate that these proteins have been successfully incorporated into a very stable tBLM environment in a functionally active form. Therefore, we conclude that the mixed tBLMs have been successfully designed as a general platform for biosensing and screening purposes of membrane proteins.

Derivate des Ionentransporters Valinomycin

In der vorliegenden Arbeit wurden Derivate des Ionentransporters Valinomycin synthetisiert und als Sensorelemente in Modellmembransysteme inkorporiert. Als Modellmembranen wurden festkörpergestützte Lipiddoppelschichten (tBLMs, tethered bilayer lipid membranes) verwendet. rnValinomycin transportiert selektiv Kalium-Ionen durch Membranen, was durch einen Rückgang des Widerstandes über elektrochemische Messmethoden nachgewiesen werden kann. Es ist ein zyklisches Dodecadepsipeptid, das aus zwei verschiedenen Aminosäuren (L- und D-Valin) und  Hydroxysäuren (L Milchsäure und D Hydroxyisovaleriansäure) besteht. In dieser Arbeit wurde ein L Valin durch ein L-Lysin ausgetauscht, um eine freie Aminogruppe zum Anbinden verschiedenster Liganden zu erhalten. rnDie Synthese erfolgte in Lösung über einen linearen Decadepsipeptid-Precursor, hierbei wurde hauptsächlich mit Benzyl- und Boc-Schutzgruppen gearbeitet. An den Precursor wurden dann unterschiedlich modifizierte Lysin-Didepside gebunden und das daraus erhaltene lineare Dodecadepsipeptid zyklisiert.rnInsgesamt wurden sechs verschiedene Derivate synthetisiert, deren Ionentransportfähigkeit mit Hilfe eines angebundenen Liganden blockiert wurde. Diese Blockade kann entweder mechanisch durch Festhalten des Ionencarriers an der Oberfläche der Membran oder chemisch durch Einbringen einer Ladung erfolgen, da geladene Moleküle eine Membran nicht überwinden können. rnAcetyl-Lysin-Valinomycin wurde als Testsystem hergestellt, um zu zeigen, dass die Synthese einen funktionsfähigen Ionencarrier ergeben hatte. Im nächsten Schritt wurde Lysin-Valinomycin mit freier Aminogruppe synthetisiert, um es als pH-Sensor zu nutzen und damit zu überprüfen, ob das chemische Einbringen einer Ladung möglich ist. Es konnte ein pH abhängiger Kalium-Transport nachgewiesen werden, die Blockade der Ionentransportfähigkeit über eine eingebrachte Ladung ist somit möglich. rnAuf dem gleichen Konzept beruht Ferrocen-Valinomycin. Wird der Ferrocen-Ligand oxidiert, liegt eine positive Ladung vor und der Ionencarrier kann die Membran nicht mehr überwinden. Eine Reduktion macht diesen Prozess reversibel. Ferrocen-Valinomycin konnte innerhalb einer tBLM chemisch oxidiert und reduziert werden, dieses System kann somit als chemischer Redox-Sensor eingesetzt werden.rnEine mechanische Blockade liegt dem Biotin- und dem Sulfonamid-Valinomycin zugrunde. Dabei soll die Zugabe von Streptavidin bzw. BCA II (bovine Carboanhydrase) den Ionentransport durch die Membran stoppen. Beide Valinomycin-Derivate zeigten aber keine Ionentransportfähigkeit, eine Inkorporation in tBLMs konnte jedoch über SPR gezeigt werden. rnDie Synthese eines fluoreszenz-markierten (FITC) Valinomycins ergab zwar auch keinen transportfähigen Ionencarrier, aber mit diesem Derivat konnte der Diffusionskoeffizient von Valinomycin in sBLMs mit Hilfe von Fluorescence Recovery after photobleaching (FRAP) bestimmt werden.rn

Synthese und Charakterisierung von zylindrischen Bürsten mit Polypeptidseitenketten

In der vorliegenden Arbeit konnte gezeigt werden, dass durch die grafting-from-Methode verschiedene geschützte Polypeptidbürsten basierend auf L-glutaminsäure, L-asparaginsäure, L-lysin und L-ornithin synthetisch zugänglich sind. Zur Verwirklichung dieser Synthesestrategie wurde mehrstufig ein Makroinitiator auf Basis von N-methacrylamid-1,6-diaminohexan hergestellt, der die ringöffnende Polymerisation von Leuchs´schen Anhydriden zur Entwicklung von geschützten Polypeptidseitenketten initiieren kann. Durch stark saure bzw. alkalische Abspaltbedingungen war es möglich, die Schutzgruppen bei allen geschützten Bürsten bis auf eine Spezies erfolgreich zu entfernen. Weitergehende Untersuchungen an den positiv bzw. negativ geladenen Polyelektrolytbürsten mittels statischer Lichtstreuung und Kapillarelektrophorese zeigten, dass lediglich die Z-geschützten Poly-L-lysinbürsten ohne Kettenabbau entschützt werden konnten. In allen anderen Fällen wurden nach Abspaltung der Schutzgruppen lineare Kettenfragmente detektiert. Durch die Zugabe von NaClO4 oder Methanol zu den wässrigen Lösungen der Poly-L-lysinbürsten konnte mittels CD-Spektroskopie gezeigt werden, dass die Seitenketten von einer ungeordneten Konformation in eine helikale Konformation übergehen. In weiterführenden Experimenten wurde mittels statischer Lichtstreuung, dynamischer Lichtstreuung, SAXS, und AFM-Aufnahmen in Lösung bewiesen, dass die helikale Konformation der Seitenketten eine deutliche Abnahme des Zylinderquerschnitts und des Querschnittträgheitsradius zur Folge hat, die Topologie der Bürste allerdings unverändert bleibt. Weiterhin konnte mittels Kapillarelektrophorese die elektrophoretische Mobilität der Poly-L-lysinbürsten und ihrer linearen Analoga bestimmt werden. Mit diesen Resultaten war es in Kombination mit statischen Lichtstreuexperimenten möglich, die effektive Ladung von linearem und verzweigten Poly-L-lysin nach einer Theorie von Muthukumar zu berechnen. Das Ergebnis dieser Rechnungen bestätigt die Ergebnisse früherer Untersuchungen von Peter Dziezok, der in seiner Dissertation durch Leitfähigkeits und Lichtstreumessungen an linearem PVP und PVP-Bürsten herausfand, dass die effektive Ladung von Polymerbürsten mindestens um einen Faktor 10 kleiner ist als bei den korrespondierenden linearen Analoga.

Sources and pathways of methane formed in oxidative environments

Methane is the most abundant reduced organic compound in the atmosphere. As the strongest known long-lived greenhouse gas after water vapour and carbon dioxide methane perturbs the radiation balance of Earth’s atmosphere. The abiotic formation of methane requires ultraviolet irradiation of organic matter or takes place in locations with high temperature and/or pressure, e.g. during biomass burning or serpentinisation of olivine, under hydrothermal conditions in the oceans deep or below tectonic plates. The biotic methane formation was traditionally thought to be formed only by methanogens under strictly anaerobic conditions, such as in wetland soils, rice paddies and agricultural waste. rnIn this dissertation several chemical pathways are described which lead to the formation of methane under aerobic and ambient conditions. Organic precursor compounds such as ascorbic acid and methionine were shown to release methane in a chemical system including ferrihydrite and hydrogen peroxide in aquatic solution. Moreover, it was shown by using stable carbon isotope labelling experiments that the thio-methyl group of methionine was the carbon precursor for the methane produced. Methionine, a compound that plays an important role in transmethylation processes in plants was also applied to living plants. Stable carbon isotope labelling experiments clearly verified that methionine acts as a precursor compound for the methane from plants. Further experiments in which the electron transport chain was inhibited suggest that the methane generation is located in the mitochondria of the plants. The abiotic formation of methane was shown for several soil samples. Important environmental parameter such as temperature, UV irradiation and moisture were identified to control methane formation. The organic content of the sample as well as water and hydrogen peroxide might also play a major role in the formation of methane from soils. Based on these results a novel scheme was developed that includes both biotic and chemical sources of methane in the pedosphere.rn

Rod-shaped plasmonic sensors

Plasmonic nanoparticles exhibit strong light scattering efficiency due to the oscillations of their conductive electrons (plasmon), which are excited by light. For rod-shaped nanoparticles, the resonance position is highly tunable by the aspect ratio (length/width) and the sensitivity to changes in the refractive index in the local environment depends on their diameter, hence, their volume. Therefore, rod-shaped nanoparticles are highly suitable as plasmonic sensors.rnWithin this thesis, I study the formation of gold nanorods and nanorods from a gold-copper alloy using a combination of small-angle X-ray scattering and optical extinction spectroscopy. The latter represents one of the first metal alloy nanoparticle synthesis protocols for producing rod-shaped single crystalline gold-copper (AuxCu(1-x)) alloyed nanoparticles. I find that both length and width independently follow an exponential growth behavior with different time-constants, which intrinsically leads to a switch between positive and negative aspect ratio growth during the course of the synthesis. In a parameter study, I find linear relations for the rate constants as a function of [HAuCl4]/[CTAB] ratio and [HAuCl4]/[seed] ratio. Furthermore, I find a correlation of final aspect ratio and ratio of rate constants for length and width growth rate for different [AgNO3]/[HAuCl4] ratios. I identify ascorbic acid as the yield limiting species in the reaction by the use of spectroscopic monitoring and TEM. Finally, I present the use of plasmonic nanorods that absorb light at 1064nm as contrast agents for photoacoustic imaging (BMBF project Polysound). rnIn the physics part, I present my automated dark-field microscope that is capable of collecting spectra in the range of 450nm to 1750 nm. I show the characteristics of that setup for the spectra acquisition in the UV-VIS range and how I use this information to simulate measurements. I show the major noise sources of the measurements and ways to reduce the noise and how the combination of setup charactersitics and simulations of sensitivity and sensing volume can be used to select appropriate gold rods for single unlabeled protein detection. Using my setup, I show how to estimate the size of gold nano-rods directly from the plasmon linewidth measured from optical single particle spectra. Then, I use this information to reduce the distribution (between particles) of the measured plasmonic sensitivity S by 30% by correcting for the systematic error introduced from the variation in particle size. I investigate the single particle scattering of bowtie structures — structures consisting of two (mostly) equilateral triangles pointing one tip at each other. I simulate the spectra of the structures considering the oblique illumination angle in my setup, which leads to additional plasmon modes in the spectra. The simulations agree well with the measurements form a qualitative point of view.rn

Polymer nanoparticles : their functionalization for biomedical applications and dynamics near an electrode

In this work, a method for the functionalization of biocompatible, poly(lactic acid)-based nanoparticles with charged moieties or fluorescent labels is presented. Therefore, a miniemulsion solvent evaporation procedure is used in which prepolymerized poly(L-lactic acid) is used together with a previously synthesized copolymer of methacrylic acid or a polymerizable dye, respectively, and an oligo(lactic acid) macromonomer. Alternatively, the copolymerization has been carried out in one step with the miniemulsion solvent evaporation. The increased stability in salty solutions of the carboxyl-modified nanoparticles compared to nanoparticles consisting of poly(lactic acid) only has been shown in light scattering experiments. The properties of the nanoparticles that were prepared with the separately synthesized copolymer were almost identical to those in which the copolymerization and particle fabrication were carried out simultaneously. During the characterization of the fluorescently labeled nanoparticles, the focus was on the stable bonding between the fluorescent dye and the rest of the polymer chain to ensure that none of it is released from the particles, even after longer storage time or during lengthy experiments. In a fluorescence correlation spectroscopy experiment, it could be shown that even after two weeks, no dye has been released into the solvent. Besides biomedical research for which the above described, functionalized nanoparticles were optimized, nanoparticles also play a role in coating technology. One possibility to fabricate coatings is the electrophoretic deposition of particles. In this process, the mobility of nanoparticles near electrode interfaces plays a crucial role. In this thesis, the nanoparticle mobility has been investigated with resonance enhanced dynamic light scattering (REDLS). A new setup has been developed in which the evanescent electromagnetic eld of a surface plasmon that propagates along the gold-sample interface has been used as incident beam for the dynamic light scattering experiment. The gold layer that is necessary for the excitation of the plasmon doubles as an electrode. Due to the penetration depth of the surface plasmon into the sample layer that is limited to ca. 200 nm, insights on the voltage- and frequency dependent mobility of the nanoparticles near the electrode could be gained. Additionally, simultaneous measurements at four different scattering angles can be carried out with this setup, therefore the investigation of samples undergoing changes is feasible. The results were discussed in context with the mechanisms of electrophoretic deposition.