Abstract ACCURATE METHODOLOGY FOR MONITORING BIOMEMBRANE EVENTS By Christine A. Winschel, Ph.D. A Dissertation submitted in partial fulfillment of the requirements for the degree of Doctorate of Philosophy in Chemistry at Virginia Commonwealth University. Virginia Commonwealth University, 2012 Major Director: Dr. Vladimir A. Sidorov ASSOCIATE PROFESSOR, DEPARTMENT OF CHEMISTRY This study describes the synthesis and characterization of a new receptor (cyclen 1) capable of strong selective binding of pyrene-based anionic dyes under near-physiological conditions. This receptor comprises four naphthylthiourea groups tethered to a cyclen core via an ester linkage. The most important finding was the ability of cyclen 1 to bind efficiently to a pH-sensitive pyranine dye, a dye that is commonly used in various biomembrane assays. The high affinity of cyclen 1 to pyranine, its impermeability to the lipid bilayer membrane, fast kinetics of binding, and ability to quench pyranine’s fluorescence were used as a basis for a new membrane leakage assay. This membrane leakage assay is fully compatible with the commonly applied pH-stat transport assay, and therefore it allows for differentiation of ion transport and nonselective leakage mechanisms within a single set of experiments. In the second part of this study a new methodology for the detection of lipid flip was developed. This methodology relies on the quenching of the fluorescence of a newly synthesized cascade-blue-labeled lipid through complex formation with cyclen 1. This receptor-dye complexation also has high affinity for binding at micromolar concentrations and can be reversed by either competitive displacement of the lipid probe or by enzymatic degradation of the receptor leading to the label release and fluorescence dequenching. This new methodology is suitable for the study of lipid flip in both model spherical bilayer membranes and in-vitro experiments, and is less invasive to the model and cell membranes than the commonly utilized 7-nitro-1,2,3-benzoxadiazol-4-yl (NBD)-dithionite methodology. Lastly, new pH-sensitive lipids were synthesized and utilized in the formulation of liposomes suitable for controlled drug release. These liposomes contain various amounts of internal NaCl and undergo internal acidification upon the exogenous addition of an HCl co-transporter in a physiologically relevant NaCl solution. Therefore, acidification ultimately leads to the hydrolysis of the pH-sensitive lipids and subsequent contents release. These liposomes were found to be insensitive to physiological concentrations of human serum albumin and to be non-toxic to cells at concentrations exceeding pharmacological relevance. These results render this new drug release model potentially suitable for in vivo applications.

Les toxines Cry sont des protéines synthétisées sous forme de cristaux par la bactérie bacille de Thuringe pendant la sporulation. Elles sont largement utilisées comme agents de lutte biologique, car elles sont toxiques envers plusieurs espèces d’invertébrées, y compris les nématodes. Les toxines Cry5B sont actives contre certaines espèces de nématodes parasites, y compris Ankylostoma ceylanicum un parasite qui infeste le système gastro-intestinal des humains. Jusqu’au présent, le mode d’action des toxines Cry nématicides reste grandement inconnu, sauf que leurs récepteurs spécifiques sont des glycolipides et qu’elles causent des dommages importants aux cellules intestinales. Dans cette étude, on démontre pour la première fois que la toxine nématicide Cry5Ba, membre de la famille des toxines à trois domaines et produite par la bactérie bacille de Thuringe, forme des pores dans les bicouches lipidiques planes en absence de récepteurs. Les pores formés par cette toxine sont de sélectivité cationique, à pH acide ou alcalin. Les conductances des pores formés sous conditions symétriques de 150 mM de KCl varient entre 17 et 330 pS, à pH 6.0 et 9.0. Les niveaux des conductances les plus fréquemment observés diffèrent les uns des autres par environ 17 à 18 pS, ce qui est compatible avec l’existence d’arrangement d’un nombre différent de pores élémentaires similaires, activés de façon synchronisée, ou avec la présence d’oligomères de tailles variables et de différents diamètres de pores. / Cry toxins are proteins synthetized as crystal inclusions by the Bacillus thuringiensis bacterium upon sporulation. They are used widely as biological control agents, as they exhibit toxicity to a range of invertebrates, including nematodes. The Cry5B toxins are active against a number of parasitic nematode species, such as Ancylostoma ceylanicum a human gastro-intestinal parasite. So far, the mode of action of nematicidal Cry toxins is largely unknown, except for the facts that their specific receptors are glycolipids and that they cause prominent damage to nematode intestinal cells. In this study, we show for the first time that the nematicidal Cry5Ba toxin, a member of the three domain family of toxins produced by the Bacillus thuringiensis forms pores in receptor-free planar lipid bilayers. The pores formed by the toxin were cation selective, both under acid and alkaline pH conditions. Under symmetrical 150 mM KCl conditions, pore activity was characterized by conductances ranging from 17 to 330 pS, at both pH 6.0 and 9.0. The most frequently observed conductance levels differed from each other by approximately 17 to 18 pS consistent with the existence of clusters of different number of elementary, similar, co-operatively gated pores, or with the presence of variable size oligomers with different pore diameters.

La plupart des toxines de Bacillus thuringiensis perméabilisent la membrane intestinale des insectes sensibles en formant des pores qui abolissent le potentiel électrique et les gradients ioniques. Plusieurs toxines ont été étudiées avec des vésicules purifiées de la bordure en brosse intestinale des insectes. Malheureusement, la membrane intestinale de beaucoup d’insectes ne forme pas des vésicules suffisamment étanches pour les expériences de perméabilisation. Une nouvelle technique utilisant des liposomes géants et une sonde de perméabilité membranaire a été développée pour caractériser deux nouvelles toxines particulièrement prometteuses pour le biocontrôle d’un des principaux ravageurs du maïs, la chrysomèle des racines du maïs (Diabrotica virgifera virgifera LeConte), Cry6Aa1 et la toxine binaire DS10/DS11. Les deux toxines perméabilisent efficacement les liposomes. La toxine binaire forme des pores qui sont légèrement sélectifs pour les cations, comme la plupart des toxines de B. thuringiensis. Bien que la Cry6Aa1 puisse former des pores sélectifs pour les anions, les résultats suggèrent aussi qu’elle pourrait, contrairement aux autres toxines de cette bactérie, ne former des pores qu’en présence d’une force ionique élevée. La formation des pores par ces deux toxines semble être sensible à la courbure de la membrane cible étant donné qu’elle est beaucoup plus efficace dans des liposomes géants que dans des liposomes de même composition, mais plus petits. Ce travail jette les bases de la mise au point d’une technique qui permettrait l’étude des toxines dans des liposomes géants enrichis avec des protéines et des lipides provenant de la membrane intestinale des insectes cibles. / Most Bacillus thuringiensis toxins permeabilize the intestinal membrane of susceptible insects by forming pores that abolish transmembrane electrical potentials and ionic gradients. Several toxins have been studied using brush border membrane vesicles purified from the insect midgut. Unfortunately, the intestinal membrane from many insects does not form vesicles that are tight enough to be used in permeabilisation experiments. A new technique using giant liposomes and a membrane permeability probe was developed to evaluate the pore-forming ability of two particularly promising toxins for the biocontrol of a major corn pest, the Western corn rootworm (Diabrotica virgifera virgifera LeConte), Cry6Aa1 and the binary toxin DS10/DS11. Both toxins permeabilized the liposomes efficiently. However, analysis of the permeabilisation rates under different experimental conditions indicates that these toxins differ in their biophysical properties. The binary toxin forms pores which are slightly selective for cations, like most B. thuringiensis toxins. On the other hand, although the results suggest that Cry6Aa1 could form anion-selective pores, they could also indicate that, in contrast with other toxins produced by this bacterium, it could form pores only under high ionic strength conditions. Pore formation by both toxins appears to be sensitive to membrane curvature since it is much more efficient in giant liposomes than in liposomes with identical composition, but smaller in size. This study sets the bases for the development of a technique that would allow the toxins to be studied in giant liposomes enriched with proteins and lipids from the intestinal membrane of target insects.

Recent experimental studies indicate that polymeric structures with a well-adjusted balance of amphiphilic parts may translocate through self-assembled phospholipid bilayers and enhance the passive trans-membrane transport of smaller molecules. Using a coarse grained lattice Monte Carlo model with explicit solvent we investigate self-assembled lipid bilayers interacting with a linear polymer chain under variation of the hydrophobicity of the chain. Here, we focus on the relationship between the chain's hydrophobicity and its translocation behavior through the membrane as well as induced membrane perturbations. We show, that there is an adsorption transition of the polymer at the bilayer interface, where effectively the solvent phase and the tail phase of the bilayer are equally repulsive for the polymer. Close to this adsorption threshold of the polymer both the translocation probability of the polymer as well as the permeability of the membrane with respect to solvent are enhanced significantly. The frequency of polymer translocation events can be understood quantitatively assuming a simple diffusion along a one-dimensional free energy profile, which is controlled by the effective lipophilicity of the chain and the tail-packing in the bilayer's core. / Dieser Beitrag ist mit Zustimmung des Rechteinhabers aufgrund einer (DFG-geförderten) Allianz- bzw. Nationallizenz frei zugänglich.

Une fois ingérées par un insecte sensible, les toxines insecticides du bacille de Thuringe doivent être activées par les protéases intestinales de cet insecte. Leur premier domaine, un ensemble de sept hélices-α amphipathiques, est responsable de leur insertion dans la membrane luminale de certaines cellules de l’intestin médian, ce qui crée des pores peu sélectifs. La toxicité et la capacité à former des pores d’une telle toxine, la Cry9Ca, de ses mutants simples R164A et R164K et d’un fragment de 55 kDa résultant d’un clivage protéolytique au niveau de son résidu 164 ont été étudiées à l’aide d’une combinaison de modélisation par homologie, de bioessais, d’expériences de gonflement osmotique avec des vésicules de membrane en bordure en brosse de larves de sphinx du tabac et de mesures électrophysiologiques sur des intestins isolés. Ni les mutations simples ni le clivage protéolytique n’ont altéré la toxicité de la Cry9Ca. Dans une solution à faible force ionique, toutefois, la formation des pores dépend fortement du pH : une augmentation de celui-ci de 6,5 à 10,5 a entraîné une baisse irrégulière et par étapes successives de la perméabilité membranaire. Les quatre préparations de toxine ont néanmoins dépolarisé la membrane apicale d’intestins médians fraîchement isolés baignant dans une solution contenant 122 mM de KCl à pH 10,5. L’activité de la Cry9Ca, et des mutants R164A et R164K, a été grandement stimulée lorsque les expériences ont été effectuées en présence de suc intestinal, de lipides extraits d’un volume équivalent de suc intestinal ou d’un cocktail d’inhibiteurs de protéases solubles dans l’eau. De plus, le rôle des boucles inter-hélicales du Domaine I lors de l’insertion dans la membrane a été étudié avec des mutants doubles de la Cry9Ca dont les mutations introduisaient, neutralisaient ou renversaient une charge électrique. À l’exception de trois d’entres eux, tous ces mutants ont conservé une toxicité et une capacité à former des pores comparables à celles de la toxine parentale. L’ensemble de ces résultats suggère que le micro-environnement de l’intestin médian contribue à minimiser l’influence des charges de surface portées par les résidus des boucles inter-hélicales du Domaine I sur la capacité des toxines du bacille de Thuringe à former des pores. Il indique aussi que, d’une part, selon le site de clivage et les conditions expérimentales utilisées, des protéolyses supplémentaires de la toxine Cry9Ca activée peuvent soit stimuler, soit nuire à son activité et que, d’autre part, le suc intestinal du sphinx du tabac contient probablement un inhibiteur de protéases qui pourrait jouer un rôle important dans l’activité des toxines du bacille de Thuringe. / Once ingested by susceptible insects, Bacillus thuringiensis insecticidal toxins must be activated by the insect’s intestinal proteases. Their first domain, a bundle of seven amphipathic -helices, is responsible for their insertion into the luminal membrane of midgut cells, thereby creating poorly selective pores. The toxicity and pore-forming ability of one such toxin, Cry9Ca, its single-site mutants, R164A and R164K, and of the 55-kDa fragment resulting from its proteolytic cleavage at residue 164 were investigated using a combination of homology modeling, bioassays, osmotic swelling experiments with Manduca sexta larval midgut brush border membrane vesicles and electrophysiological measurements on isolated midguts. Neither the single mutations nor the proteolytic cleavage altered Cry9Ca toxicity. In low ionic strength solutions however, pore formation was highly dependent on pH: increasing pH from 6.5 to 10.5 resulted in an irregular step-wise decrease in membrane permeabilization. All four toxin preparations nevertheless depolarized the apical membrane of freshly isolated midguts bathing in a solution containing 122 mM KCl at pH 10.5. The activity of Cry9Ca, R164A and R164K was greatly enhanced when the experiments were conducted in the presence of midgut juice, the lipids extracted from an equivalent volume of midgut juice or a cocktail of water-soluble protease inhibitors. Additionally, the role of the interhelical loops of Domain I in membrane insertion was investigated with Cry9Ca double mutants with mutations that either introduced, neutralized or reversed an electrical charge. All but three mutants retained a toxicity and a pore-forming ability that were comparable to those of their parental toxin. Overall, the results suggest that the midgut microenvironment contributes to minimizing the influence of surface charges carried by Domain I interhelical loop residues on B. thuringiensis toxins pore-forming ability. They also indicate that, depending on the cleavage site and on the experimental conditions used, further proteolysis of the activated Cry9Ca toxin can either stimulate or be detrimental to its activity and that M. sexta midgut juice probably contains protease inhibitors that could play a major role in the activity of B. thuringiensis toxins in the insect midgut.

Highly fluorescent conjugated polymers (CPs) are an important class of biomaterials used for various biological applications including labelling, sensing, and delivery of biological substances. Synthetic versatility and tunable emission make CPs a superior class of biomaterials. Understanding the structure-function relationship of CPs plays a vital role in designing high performing biomaterials. The cationic CPs are self-assembled to conjugated polymer nanoparticles (CPNs) in an aqueous environment due to their amphiphilicity. The physical and biophysical properties of CPNs are highly dependent on the chemical functionality and backbone structure of CPs. Modulation of the surface property and backbone structure of CPNs play an important role for efficient internalization of CPNs into cells. The goal of this dissertation is to understand the structure function relationship of CPNs in an aqueous environment and the change in their photo physical properties upon the self-assembly of CPNs with different backbone structure upon complexation with biologically significant polysaccharides and cell membrane. This work presents the self-assembly of a set of four cationic CPs with different connectivity and backbone structure upon complexation with a linear polyanion hyaluronic acid (HA). The study of photo physical properties changes upon the complexation with series of Glycosaminoglycans (GAGs) provides more insight about how the self-assembly behavior of cationic CPs changes upon the exposure to negatively charged polysaccharides. The understanding of the self-assembly of CPNs with negatively charged biologically important macromolecules under in vitro conditions can give us an idea of photophysical property changes of CPNs during the treatment of CPNs in the cellular environment. The study of the interaction of CPNs with cell membranes using scanning ion conductance microscopy (SICM)-based topography, potential mapping, and confocal microscopy imaging is presented. CPNs are able to induce transient pore like feature formation on the cell membrane during the cellular internalization process. A comparative study of cellular labelling and delivery of siRNA of five CPNs with guanidine motif is presented. The subcellular localization and delivery of siRNA were dependent on the side chain hydrophilicity. The CPNs fabricated with hydrophilic aminoethoxyethanol possesses excellent cellular imaging with higher siRNA delivery.

Une fois ingérées par un insecte sensible, les toxines insecticides du bacille de Thuringe doivent être activées par les protéases intestinales de cet insecte. Leur premier domaine, un ensemble de sept hélices-α amphipathiques, est responsable de leur insertion dans la membrane luminale de certaines cellules de l’intestin médian, ce qui crée des pores peu sélectifs. La toxicité et la capacité à former des pores d’une telle toxine, la Cry9Ca, de ses mutants simples R164A et R164K et d’un fragment de 55 kDa résultant d’un clivage protéolytique au niveau de son résidu 164 ont été étudiées à l’aide d’une combinaison de modélisation par homologie, de bioessais, d’expériences de gonflement osmotique avec des vésicules de membrane en bordure en brosse de larves de sphinx du tabac et de mesures électrophysiologiques sur des intestins isolés. Ni les mutations simples ni le clivage protéolytique n’ont altéré la toxicité de la Cry9Ca. Dans une solution à faible force ionique, toutefois, la formation des pores dépend fortement du pH : une augmentation de celui-ci de 6,5 à 10,5 a entraîné une baisse irrégulière et par étapes successives de la perméabilité membranaire. Les quatre préparations de toxine ont néanmoins dépolarisé la membrane apicale d’intestins médians fraîchement isolés baignant dans une solution contenant 122 mM de KCl à pH 10,5. L’activité de la Cry9Ca, et des mutants R164A et R164K, a été grandement stimulée lorsque les expériences ont été effectuées en présence de suc intestinal, de lipides extraits d’un volume équivalent de suc intestinal ou d’un cocktail d’inhibiteurs de protéases solubles dans l’eau. De plus, le rôle des boucles inter-hélicales du Domaine I lors de l’insertion dans la membrane a été étudié avec des mutants doubles de la Cry9Ca dont les mutations introduisaient, neutralisaient ou renversaient une charge électrique. À l’exception de trois d’entres eux, tous ces mutants ont conservé une toxicité et une capacité à former des pores comparables à celles de la toxine parentale. L’ensemble de ces résultats suggère que le micro-environnement de l’intestin médian contribue à minimiser l’influence des charges de surface portées par les résidus des boucles inter-hélicales du Domaine I sur la capacité des toxines du bacille de Thuringe à former des pores. Il indique aussi que, d’une part, selon le site de clivage et les conditions expérimentales utilisées, des protéolyses supplémentaires de la toxine Cry9Ca activée peuvent soit stimuler, soit nuire à son activité et que, d’autre part, le suc intestinal du sphinx du tabac contient probablement un inhibiteur de protéases qui pourrait jouer un rôle important dans l’activité des toxines du bacille de Thuringe. / Once ingested by susceptible insects, Bacillus thuringiensis insecticidal toxins must be activated by the insect’s intestinal proteases. Their first domain, a bundle of seven amphipathic -helices, is responsible for their insertion into the luminal membrane of midgut cells, thereby creating poorly selective pores. The toxicity and pore-forming ability of one such toxin, Cry9Ca, its single-site mutants, R164A and R164K, and of the 55-kDa fragment resulting from its proteolytic cleavage at residue 164 were investigated using a combination of homology modeling, bioassays, osmotic swelling experiments with Manduca sexta larval midgut brush border membrane vesicles and electrophysiological measurements on isolated midguts. Neither the single mutations nor the proteolytic cleavage altered Cry9Ca toxicity. In low ionic strength solutions however, pore formation was highly dependent on pH: increasing pH from 6.5 to 10.5 resulted in an irregular step-wise decrease in membrane permeabilization. All four toxin preparations nevertheless depolarized the apical membrane of freshly isolated midguts bathing in a solution containing 122 mM KCl at pH 10.5. The activity of Cry9Ca, R164A and R164K was greatly enhanced when the experiments were conducted in the presence of midgut juice, the lipids extracted from an equivalent volume of midgut juice or a cocktail of water-soluble protease inhibitors. Additionally, the role of the interhelical loops of Domain I in membrane insertion was investigated with Cry9Ca double mutants with mutations that either introduced, neutralized or reversed an electrical charge. All but three mutants retained a toxicity and a pore-forming ability that were comparable to those of their parental toxin. Overall, the results suggest that the midgut microenvironment contributes to minimizing the influence of surface charges carried by Domain I interhelical loop residues on B. thuringiensis toxins pore-forming ability. They also indicate that, depending on the cleavage site and on the experimental conditions used, further proteolysis of the activated Cry9Ca toxin can either stimulate or be detrimental to its activity and that M. sexta midgut juice probably contains protease inhibitors that could play a major role in the activity of B. thuringiensis toxins in the insect midgut.

In the first part of the thesis, the molecular structure and electronic properties of phospholipids at the single molecule level and also for a monolayer structure are investigated via ab initio calculations under different degrees of hydration. The focus of the study is on phosphatidylcholines, in particular dipalmitoylphosphatidylcholine (DPPC), which are the most abundant phospholipids in biological membranes. Upon hydration, the phospholipid shape into a sickle-like structure. The hydration dramatically alters the surface potential, dipole and quadrupole moments of the lipids, and probably guides the interactions of the lipids with other molecules and the communication between cells. The vibrational spectrum of DPPC and DPPC-water complexes are completely assigned and it is shown that water hydrating the lipid head groups enables efficient energy transfer across membrane leaflets on sub-picosecond time scales. Moreover, the vibrational modes and lifetimes of pure and hydrated DPPC lipids, at human body temperature, are estimated by performing ab initio molecular dynamics simulations. The vibrational modes of the water molecules close to the head group of DPPC are active in the frequency range between 0.5 - 55 THz, with a peak at 2.80 THz in the energy spectrum. The computed lifetimes for the high-frequency modes agree well with recent data measured at room temperature, where high-order phonon scattering is not negligible. The structure and auto-ionization of water at the water-phospholipid interface are investigated by ab initio molecular dynamics and ab initio Monte Carlo simulations using local density approximation and generalized gradient approximation for the exchange-correlation energy functional. Depending on the lipid head group, strongly enhanced ionization is observed, leading to dissociation of several water molecules into H+ and OH- per lipid. The results can shed light on the phenomena of the high proton conductivity along membranes that has been reported experimentally. In the second part of the thesis, Monte Carlo simulations of the lipid bilayer, on the basis of a coarse grained model, are performed to gain insight into the mechanical properties of planar lipid bilayers. By using a rescaling method, the Poisson's ratio is calculated for different phases. Additional information on the bending rigidity, determined from height fluctuations on the basis of the Helfrich Hamiltonian, allows for calculation of the Young's modulus for each phase. In addition, the free energy barrier for lipid flip-flop process in the fluid and gel phases are estimated. The main rate-limiting step to complete a flip-flop process is related to a free energy barrier that has to be crossed in order to reach the center of the bilayer. The free energy cost for performing a lipid flip-flop in the gel phase is found to be five times greater than in the fluid phase, demonstrating the rarity of such events in the gel phase. Moreover, an energy barrier is estimated for formation of transient water pores that often precedes lipid translocation events and accounts for the rate-limiting step of these pore-associated lipid translocation processes.