Dissertations / Theses on the topic 'Crowded lipid membrane biophysics'

G-protein coupled receptors (GPCRs) are transmembrane proteins capable of recognizing an astonishing variety of biological signals, ranging from photons of light to hormones, odorants, and neurotransmitters involved in key biological signaling processes. The aim of this work is to identify how lipid-protein interactions involving the membrane bilayer ultimately affect such vital biological functions. Here the relationship between the bilayer thickness, hydrophobic mismatch, and protein aggregation are investigated by expanding the framework of membrane-receptor interactions in terms of a new flexible surface model. Previously, we have shown how coupling of the elastic stress-strain due to mismatch of the spontaneous curvature and hydrophobic thickness at the lipid/protein interface can govern the conformational transitions of membrane proteins. This approach has now been extended to include coupling of the lateral organization of the GPCR rhodopsin to the curvature and area stress and strain of the proteolipid membrane. Rhodopsin was labeled with site-specific fluorophores, and a FRET technique was employed to probe protein association in different lipid environments. Moreover, UV-visible spectroscopy was used for thermodynamic characterization of the conformational change of rhodopsin. Lastly, the deformation of the lipids with and without rhodopsin was probed in terms of acyl chain order parameters and relaxation rates by solid-state NMR methods, giving insight into the lipid deformation. The results showed that optimal receptor activation occurs in phosphatidylcholine bilayers of 20-carbon acyl chain length, hence one can say that metarhodopsin II is likely to adopt an elongated shape. Lipids promoting aggregation, or below their gel to liquid crystalline transition temperature all favor formation of metarhodopsin I. The data also showed that association and activation of rhodopsin do not always correlate. In terms of the extended flexible surface model, the stress due to hydrophobic mismatch is coupled via the effective number of lipids surrounding the protein due to the lateral organization of the membrane. The measured changes in rhodopsin-rhodopsin interactions and membrane influences on the conformation of the protein after photoisomerization may be crucial to understanding physiological regulation of the rod disk membranes. They are relevant to understanding the complexity of biomembranes involved in many cellular mechanisms, including signal transduction.

Many important biological processes occur near or in membranes. The role of membranes is not merely confined to compartmentalization, they also form the matrix for membrane associated proteins and are of functional importance. Membrane associated proteins on the other hand require specific membrane properties for proper function. The interactions between membranes and proteins are thus of paramount importance and are at the focus of this work. To draw valid conclusions about the nature of such interactions the membrane mimetics required in biophysical methods must faithfully mimic crucial properties of biological membranes. To this end, new types of small isotropic bicelles which mimic plant and bacterial membranes were characterized by their size and lipid dynamics using solution-state NMR. Small isotropic bicelles are specifically well suited for solution-state NMR studies since they maintain a bilayer while being sufficiently small to conduct interpretable experiments at the same time. Monogalactosyl diacylglycerol and digalactosyl diacylglycerol, which are highly abundant in thylakoid membranes, were successfully incorporated into bicelles. Also, it was possible to make bicelles containing a lipid mixture extracted from Escherichia coli cells. A fundamental physical property of lipids in bilayers is their phase behaviour and thus the dynamics that lipids undergo in a membrane. Here, the dynamics of 13C-1H bonds in lipids were studied by nuclear spin relaxation. From such studies it was found that the glycerol backbone of lipids in bicelles is rigid while the flexibility of the acyl chain increases towards its end. Bulky head groups are rigid, while smaller head groups are more dynamic than the glycerol backbone. Acyl chain modifications, like unsaturations or cyclopropane moities, that are typically found in E. coli lipids, locally increase the rigidity of the acyl chain. Membrane interactions of a putative membrane anchor of the glycosyltransferase WaaG, MIR-WaaG, were studied by fluorescence methods, circular dichroism and solution-state NMR. It was found that MIR-WaaG binds to vesicles that mimic the anionic charge of E. coli inner membranes and that α-helical structure is induced upon interaction. The NMR-structure of MIR-WaaG agrees well with the crystal structure and from paramagnetic relaxation enhancement studies it could be concluded that a central part of MIR-WaaG is immersed in the membrane mimetic. Based on these results a model of the membrane interaction of WaaG is proposed where MIR-WaaG anchors WaaG to the cytosolic leaflet of the E. coli inner membrane via electrostatic interactions. These are potentially enhanced by membrane interactions of Tyr residues at the membrane interface and of hydrophobic residues inside the membrane.

Les tubes membranaires sont des structures omniprésentes dans les cellules, et la compréhension de leur dynamique et de leur morphologie est d'une importance cruciale pour la biophysique cellulaire. Cette thèse aborde plusieurs aspects de la dynamique des tubes membranaires dans des situations où ils sont déséquilibrés par divers processus inspirés par des phénomènes biologiques. Nous analysons le gonflement de tubes due à des pompes ioniques entraînant une différence de pression osmotique, ainsi que les instabilités qui en résultent. Ceci est inspiré par la structure d'un organelle appelé le vacuole contractile, et conduit à une nouvelle instabilité avec une longueur d'onde naturelle beaucoup plus longue que celle résultant d'une instabilité de type pearling. La stabilité des tubes membranaires présentant un écoulement de cisaillement à leur surface est également analysée. Nous avons découvert et analysé une nouvelle instabilité hélicoïdale qui conduit à l’amplification des fluctuations du tube. Nous discutons de la pertinence de cette instabilité dans le processus de scission des tubes induite par la dynamine. Enfin, nous considérons la dynamique et les fluctuations d'un tube membranaire sur lequel agissent des forces actives
Membrane tubes are structures ubiquitous in cells, and understanding their dynamics and morphology is of vital importance for cellular biophysics. This thesis will discuss several aspects of the dynamics of membrane tubes in situations where they are driven out of equilibrium by various biologically inspired processes. We analyse the inflation of membrane tubes and their subsequent instability due to ion pumps driving an osmotic pressure difference. This is inspired by the structure of an organelle called the contractile vacuole complex, and leads to a new instability with a much longer natural wavelength than a typical Pearling instability. The stability of membrane tubes with a shear in the membrane flow is analysed and a novel helical instability which acts to amplify the fluctuations is found. We discuss the relevance of this instability in the process of Dynamin mediated tube scission. Finally we consider the dynamics and fluctuations of a membrane tube with active forces acting on it

The complexity of multi cellular organisms demands systems that facilitate communicationbetween cells. The neurons in our brains for instance are specialized in this cell-cellcommunication. The flow of ions, through their different ion channels, across the membrane, isresponsible for almost all of the communication between neurons in the brain by changing theneurons membrane potentials. Voltage-gated ion channels open when a certain thresholdpotential is reached. This change in membrane potential is detected by voltage-sensors in the ionchannels. In this licentiate thesis the Homo sapiens voltage- and calcium-gated BK potassiumchannel (HsapBK) has been studied. The NMR solution structure of the voltage-sensor ofHsapBK was solved to shed light upon the voltage-gating in these channels. Structures of othervoltage-gated potassium channels (Kv) have been determined by other groups, enablingcomparison among different types of Kv channels. Interestingly, the peptide-lipid interactions ofthe voltage-sensor in HsapBK are crucial for its mechanism of action.Uni cellular organisms need to sense their environment too, to be able to move towardsmore favorable areas and from less favorable ones, and to adapt their gene profiles to currentcircumstances. This is accomplished by the two-component system, comprising a sensor proteinand a response regulator. The sensor protein transfers signals across the membrane to thecytoplasm. Many sensor proteins contain a HAMP domain close to the membrane that isinvolved in transmitting the signal. The mechanism of this transfer is not yet revealed. Ourstudies show that HAMP domains can be divided into two groups based on the membraneinteraction of their AS1 segments. Further, these two groups are suggested to work by differentmechanisms; one membrane-dependent and one membrane-independent mechanism.Both the voltage-gating mechanism and the signal transduction carried out by HAMPdomains in the membrane-dependent group, demand peptide-lipid interactions that can be readilymodulated. This modulation enables movement of peptides within membranes or within thelipid-water interface. These conditions make these peptides especially suitable for NMR studies.

The spatiotemporal organization of membrane proteins is implicated in cellular trafficking, signalling and reception. It was proposed that biological membranes partition into lipid rafts that can promote and control the organization of membrane proteins to localize the mentioned processes. Lipid rafts are thought to be transient (microseconds) and small (nanometers), rendering their detection a challenging task. To circumvent this problem, multi-component artificial membrane systems are deployed to study the segregation of lipids at longer time and length scales. In this thesis, multi-component Droplet Interface Bilayers (DIBs) were imaged using fluorescence and interferometric scattering microscopy. DIBs were used to examine and manipulate microscopic lipid domains and to observe, for the first time, transient nanoscopic lipid domains. The techniques and results described here will have important implications on future research in this field.

This dissertation will focus on my work in biophysics, and my work in mean field games and glucose predictive analysis will not be presented. Several problems relating to the effects of thermodynamic coupling and hydrodynamic coupling within the membrane stack system are discussed. Three theoretical approaches are employed and proposed to study the membrane stack system: a diffuse-interface approach is utilized for numerical simulations; a coarse-grained sharp-interface approach is utilized to provide physical understanding of various kinetics; a hybrid intermediate sharp-interface approach is adopted to study the domain coalescence in the absence of diffusion.

In the first part of the thesis, we discuss the thermodynamic coupling in membrane stack systems. Comprehensive analyses are presented to understand the accelerated coarsening kinetics with respect to single layer and long-range alignment. Numerical simulations are conducted for three systems, namely a diffusion dominated system, an advective interlayer friction dominated system, and an advective membrane viscosity dominated system. Experimental results regarding the advective interlayer friction dominated system are supported by simulations. We investigate the mechanism of the enhanced coarsening kinetics in membrane stack systems and the relationship between the coarsening process and vertical alignment. An intuitive understanding along with analytical explanations are further presented. Moreover, numerical results regarding the critical mixture are also discussed.

We then investigate the interfacial fluctuation behavior within membrane stack systems. The hydrodynamic coupling is found to play a significant role and several physical length scales are found to be crucial. Both a sharp-interface approach and a diffuse-interface approach are employed to numerically simulate decay of interface fluctuations in representative two-membrane systems.

To measure the thermodynamic coupling in experiments, the hydrodynamic force needs to be quantified, especially for the non-circular domains. In the last part of this thesis, the drag coefficient relating domain velocity and force acting on the domain is calculated using perturbation theory within two limits: the first limit refers to a domain much larger than the hydrodynamic screening length; the second limit refers to a domain that is much smaller than the hydrodynamic screening length.

DNA nanotechnology has revolutionised our capability to shape and control three-dimensional structures at sub-nanometre length scales. In this thesis, we use DNA to build synthetic membrane-inserting channels. Porphyrin and cholesterol tags serve as membrane anchors to facilitate insertion into the lipid membrane. With atomic force microscopy, confocal imaging and ionic current recordings we characterise our DNA nanochannels that mimic their natural protein-based counterparts in form and function. We find that they exhibit voltage-dependent conductance states. Amongst other architectures, we create the largest man-made pore in a lipid membrane to date approaching the electrical diameter of the nuclear pore complex. Pushing the boundaries on the other end of the spectrum, we demonstrate the ultimately smallest DNA membrane pore made from a single membrane-spanning DNA duplex. Thereby, we proof that ion conduction across lipid membranes does not always require a physical channel. With experiments and MD simulations we show that ions flow through a toroidal pore emerging at the DNA-lipid interface around the duplex. Our DNA pores spanning two orders of magnitude in conductance and molecular weight showcase the rational design of synthetic channels inspired by the diversity of nature - from ion channels to porins.

Membrane proteins represent an important class of proteins that closely associate or reside within the plasma membrane of the cell. They play a multitude of roles in cell function such as signaling, trafficking, and recently discovered, scaffolding and shaping of the plasma membrane itself. For example, caveolin is a membrane protein that is believed to have the ability to curve the plasma membrane forming invaginations that serve as signaling platforms called caveolae. The curvature of the plasma membrane is believed to be a result of caveolin oligomerization. Caveolin oligomerization was characterized using sedimentation equilibrium analytical ultracentrifugation. Due to the extremely hydrophobic nature of caveolin it was necessary to explore different detergents and lipid systems that support membrane protein structure and function. Not all detergents are conducive to studies of membrane proteins and it is often necessary to determine empirically the best detergent / lipid mimic best suited for biophysical studies. One membrane mimic that has been well-characterized and used successfully to study membrane proteins are bicelles. Bicelles are discoidal phospholipid structures comprised of a long-chain and short-chain phospholipid, typically 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) and 1,2-dihexanoyl- sn-glycero-3-phosphocholine (DHPC), respectively. Bicelles provide a true bilayer environment in which to study membrane protein structure and function. These lipid structures were successfully density matched using the method of sedimentation equilibrium in the analytical ultracentrifuge by adding 71.7% D₂O as a density modifier. We explored the utility of bicelles as a medium for studying membrane protein interactions in the analytical ultracentrifuge (AUC) by investigating the interactions of caveolin-1. The results of this work show that caveolin-1 does not have the capacity to oligomerize in detergent micelles or in a bilayer environment (bicelles). On the other hand, a naturally-occuring breast cancer mutant, P132L, forms a strong dimer in detergent micelles. A close investigation of the mutant reveals that an extension of helix 2 in the intramembrane region of the protein where dimerization was shown to occur may play a key role in the dimerization of the mutant.

An alternative bicelle system was also investigated using pentaethylene glycol monooctyl ether (C₈E₅) instead of DHPC to form the rim of the bicelle. The C₈E₅ / DMPC lipid aggregates were density matched and their properties were characterized using ³¹P-phosphorus NMR to assess the heterogeneity of the lipid / detergent arrangement, which confirms a bicellar-like arrangement. C₈E ₅ has a density similar to water (1.007 g / mL) and was shown to form lipid aggregate structures with DMPC that are less dense and require significantly lower quantity of D₂O to density match in the AUC making them better suited to the study of membrane protein interactions of small peptides.

Lipid bilayers form the basis of the membranes that serve as a barrier between a cell and its physiological environment. Their physical properties make them ideally suited for this role: they are extremely soft with respect to bending but essentially incompressible under lateral tension, and they are quite permeable to water but essentially impermeable to ions which allows the rapid establishment of the osmotic gradients. The function of membrane proteins, which are vital for tasks ranging from signal transduction to energy conversion, depends on their interactions with the lipid environment. Because of the complexity of natural membranes, model systems consisting of simpler lipid mixtures have become indispensable tools in the study of membrane biophysics. The objective of the work reported here is to develop a deeper understanding of the underlying physics of lipid bilayers through nanoscale measurements of the mechanical properties of mixed lipid systems including cholesterol, a key ingredient of cell membranes. Atomic force microscopy (AFM) has been used extensively to measure the topographical and elastic properties of supported lipid bilayers displaying complex phase behaviour and containing mixtures of important PC, PE lipids and cholesterol. Phase transformations have been investigated varying the membrane temperature, and the effects of cholesterol in controlling membrane fluidity, phase, and energetics have been studied. Elastic modulus measurements were correlated with phase behaviour observations. To aid in the nanoscale probing of lipid bilayers, AFM probes with a high aspect ratio and tip radii of $sim$4~nm were fabricated and characterised. These probes were used to investigate the phase boundary in binary and ternary lipid systems, leading to the discovery of a raised region at the boundary which has implications for the localisation of reconstituted proteins as well as the role of natural domains or lipid rafts. The electrical properties of the probes were examined to assess their potential application for combined structural and electrical measurements in liquid. A novel technique was developed to aid in the study of the physical properties of lipid bilayers. Membrane budding was induced above microfabricated substrates through osmotic pressure. Modification of the adhesion energy of the bilayer through biotin-avidin linking was successful in modulating budding behaviour of liquid disordered bilayers. The free energy of the system was modelled to allow quantitative information to be extracted from the data.

Vesicles are a type of biological or biomimetic particle consisting of one or more often spherical bilayers made up of amphipathic molecules, creating a closed system. They can function as an encapsulating device, holding hydrophilic molecules on the inside of the bilayer membrane(s) or hydrophobic molecules in the non-polar interstitial space in the middle of the bilayers. Because of this capacity to carry molecules, vesicles are a premier system for drug delivery and even theranostics in vivo. A peptide-based approach to release of encapsulated molecules has previously been developed but since drug delivery vesicles are in the size range of nanometers, the mechanisms have not been visualized. This project aims to produce giant unilamellar vesicles as a model system used to visualize membrane interactions vital to the understanding and further development of smaller vesicle-based systems for drug delivery. Giant unilamellar vesicles were produced successfully and a preparation protocol was established. Additionally, some membrane interactions were investigated using fluorescence microscopy.

Cellular membranes are important targets for many membrane-active peptides and drug compounds. Here we are interested in deciphering how lipid membranes are perturbed by several membrane-active molecules, including the transmembrane domain of the influenza M2 protein (M2TM), aggregates formed by a synthetic polyglutamine peptide, and three polyphenol compounds (i.e., tamoxifen, genistein, and verapamil). We employ phase-separated ternary lipid model membranes in the form of giant unilamellar vesicles (GUVs) to simulate raft-like structures that have been proposed to govern many important processes in plasma membranes (e.g., intracellular singling and trafficking). Specifically, we use fluorescent microscopy to interrogate how those membrane additives modulate the phase behavior of free-standing GUVs, as well as the miscibility transition temperature (Tm). We find that M2TM increases Tm and causes vesicle budding; polyglutamine aggregates disrupt lipid membranes; and the three polyphenol compounds exert disparate effects on GUV Tm.

Die Zellmembran dient der Zelle nicht nur als äußere Hülle, sondern ist auch an einer Vielzahl von lebenswichtigen Prozessen wie Signaltransduktion oder Zelladhäsion beteiligt. Wasser als integraler Bestandteil von Zellen und der extrazellulären Matrix hat sowohl einen großen Einfluss auf die Struktur von Biomolekülen, als auch selbst besondere Merkmale in eingschränkter Geometrie. Im Rahmen dieser Arbeit wurden zwei Effekte an Modellmembranen untersucht: Erstens der Einfluss des Gegenions an kationischen Lipiden (DODAX, X = F, Cl, Br, I) auf die Eigenschaften des Grenzflächenwassers und zweitens das Vermögen durch Viskositätsänderungen das Wachstum von Nervenzellen anzuregen sowie die einzelnen Stadien der Bildung von neuronalen Netzwerken und deren Optimierung zu charakterisieren. Lipidmultischichten und darin adsorbiertes Grenzflächenwasser wurden mittels Infrarotspektroskopie mit abgeschwächter Totalreflexion untersucht. Nach Charakterisierung von Phasenverhalten und Wasserkapazität der Lipide wurden die Eigenschaften des Wassers durch kontrollierte Hydratisierung bei einem Wassergehalt von einem Wassermolekül pro Lipid verglichen. Durch die geringe Wasserkapazität können in diesem besonderen System direkte Wechselwirkungen zwischen Lipiden und Wasser aus der ersten Hydratationsschale beobachtet werden. Bemerkenswert strukturierte OH-Streckschwingungsbanden in Abhängigkeit des Anions und niedrige IR-Ordnungsparameter zeigen, dass stark geordnete, in ihrer Mobilität eingeschränkte Wassermoleküle an DODAX in verschiedenen Populationen mit unterschiedlich starken Wasserstoffbrückenbindungen existieren und sich vermutlich in kleinen Clustern anordnen. Die zweite Fragestellung hatte zum Ziel, das Wachstum von Nervenzellen auf Membranen zu beleuchten. Auf der Ebene einzelner Zellen wurde untersucht, ob sich in Analogie zu den bisher verwendeten elastischen Substraten, die Viskosität von Membranen als neuartiger physikalischer Stimulus dafür eignet, das mechanosensitive Verhalten von Neuronen zu modulieren. Das Wachstum der Neuronen wurde auf substrat- und polymergestützten Lipiddoppelschichten mittels Phasenkontrastmikroskopie beobachtet. Die Quantifizierung der Neuritenlängen, -auswuchsgeschwindigkeiten und -verzweigungen zeigten kaum signifikante Unterschiede. Diffusionsmessungen (FRAP) ergaben, dass entgegen der Erwartungen, die Substrate sehr ähnliche Fluiditäten aufweisen. Die Betrachtung der zeitlichen Entwicklung des kollektiven Neuronenwachstums, also der Bildung von komplexen Netzwerken, offenbarte robuste „Kleine-Welt“-Eigenschaften und darüber hinaus unterschiedliche Stadien. Diese wurden durch graphentheoretische Analyse beschrieben, um anhand typischer Größen wie dem Clusterkoeffizienten und der kürzesten Pfadlänge zu zeigen, wie sich die Neuronen in einem frühen Stadium vernetzen, im Verlauf eine maximale Komplexität erreichen und letztlich das Netzwerk durch effiziente Umstrukturierung hinsichtlich kurzer Pfadlängen optimiert wird.

Computational methods, including homology modelling, in-silico dockings, and molecular dynamics simulations have been used to study the functional dynamics and interactions of K⁺ channels. Molecular models were built of the inwardly rectifying K⁺ channel Kir2.2, the bacterial homolog K⁺ channel KirBac3.1, and the twin pore (K2P) K⁺ channels TREK-1 and TRESK. To investigate the electrostatic energy profile of K⁺ permeating through these homology models, continuum electrostatic calculations were performed. The primary mechanism of KirBac3.1 gating is believed to involve an opening at the helix bundle crossing (HBC). However, simulations of Kir channels have not yet revealed opening at the HBC. Here, in simulations of the new KirBac3.1-S129R X-ray crystal structure, in which the HBC was trapped open by the S129R mutation in the inner pore-lining helix (TM2), the HBC was found to exhibit considerable mobility. In a simulation of the new KirBac3.1-S129R-S205L double mutant structure, if the S129R and the S205L mutations were converted back to the wild-type serine, the HBC would close faster than in the simulations of the KirBac3.1-S129R single mutant structure. The double mutant structure KirBac3.1-S129R-S205L therefore likely represents a higher-energy state than the single mutant KirBac3.1-S129R structure, and these simulations indicate a staged pathway of gating in KirBac channels. Molecular modelling and MD simulations of the Kir2.2 channel structure demonstrated that the HBC would tend to open if the C-linker between the transmembrane and cytoplasmic domain was modelled helical. The electrostatic energy barrier for K⁺ permeation at the helix bundle crossing was found to be sensitive to subtle structural changes in the C-linker. Charge neutralization or charge reversal of the PIP2-binding residue R186 on the C-linker decreased the electrostatic barrier for K⁺ permeation through the HBC, suggesting an electrostatic contribution to the PIP2-dependent gating mechanism. Multi-scale simulations determined the PIP2 binding site in Kir2.2, in good agreement with crystallographic predictions. A TREK-1 homology model was built, based on the TRAAK structure. Two PIP2 binding sites were found in this TREK-1 model, at the C-terminal end, in line with existing functional data, and between transmembrane helices TM2 and TM3. The TM2-TM3 site is in reasonably good agreement with electron density attributed to an acyl tail in a recently deposited TREK-2 structure.

Integral membrane proteins (IMPs) assume critical roles in cell biology and are key targets for drug discovery. Given their involvement in a wide range of diseases, the structural and functional characterization of IMPs are of significant importance. However, this remains notoriously challenging due to the difficulties of stably purifying membrane-bound, hydrophobic proteins. Compounding this, many diseases are caused by IMP mutations that further decrease their stability. One such example is cystic fibrosis (CF), which is caused by misfolding or dysfunction of the epithelial cell chloride channel cystic fibrosis transmembrane conductance regulator (CFTR). Roughly 70% of CF patients world-wide harbor the ΔF508-CFTR mutation, which interrupts CFTR’s folding, maturation, trafficking and function. No existing treatment sufficiently addresses the consequences of ΔF508, and the substantial instability that results from this mutation limits our ability to study ΔF508-CFTR in search of better treatments. To that end, my colleagues at Sanofi generated homology models of full-length wild-type and ΔF508-CFTR +/- second-site suppressor mutations (SSSMs) V510D and R1070W, and performed molecular dynamics (MD) simulations for each model. Using information obtained from this analysis, I tested several hypotheses on the mechanism by which ΔF508 destabilizes full-length CFTR and how SSSMs suppress this effect. Leveraging studies of the purified NBD1 subdomain and of full-length CFTR in a cellular context, I confirmed the prediction of a key salt-bridge interaction between V510D and K564 important to second-site suppression. Furthermore, I identified a novel class of SSSMs that support a key prediction from these analyses: that helical unraveling of TM10, within CFTR’s second transmembrane domain, is an important contributor to ΔF508-induced instability. In addition, I developed a detergent-free CFTR purification method using styrene-maleic acid (SMA) copolymer to extract the channel directly from its cell membrane along with the surrounding lipid content. The resulting particles were stable, monodisperse discs containing a single molecule of highly-purified CFTR. With this material, I optimized grid preparation techniques and carried out cryo-EM structural analysis of WT-hCFTR which resulted in 2D particle class averages which were consistent with an ABC transporter shape characteristic of CFTR, and a preliminary 3D reconstruction. This result establishes a foundation for future characterization of ΔF508-CFTR in its native state. I have also applied this SMA-based purification method to the facilitated glucose transporter GLUT1 (SLC2A1). SLC2A1 mutations contribute to a rare and developmentally debilitating disease called GLUT1-deficiency syndrome. Using SMA, I successfully extracted GLUT1 in its native state. With the application of this method, I was able to purify endogenous GLUT1 from erythrocytes, in complex with several associated proteins as well as the surrounding lipids, in its monomeric, dimeric and tetrameric forms without the use of cross-linking or chimeric mutations. These results point to the potential for studying isolated IMPs without the use of destabilizing detergents and thereby offer a pathway to analysis of wild-type and mutant membrane protein structure, function and pharmacodynamics.

Biological membranes form a protective barrier around cells and cellular compartments. A broad range of biochemical processes occur in or at membranes demonstrating that they are not only of structural but also of functional importance. One important class of membrane proteins are membrane-associated glycosyltransferases. WaaG is a representative of this class of proteins; its function is to catalyze one step in the synthesis of lipopolysaccharides, which are outer membrane lipids found in Gram-negative bacteria. To study protein-membrane complexes by biophysical methods, one must employ membrane mimetics, i.e. simplifications of natural membranes. One type of membrane mimetic often employed in solution-state NMR is small isotropic bicelles, obloid aggregates formed from a lipid bilayer that is dissolved in aqueous solvent by detergent molecules that make up the rim of the bicelle. In this thesis, fast dynamics of lipid atoms in bicelles containing lipid mixtures that faithfully mimic plant and bacterial membranes were investigated by NMR relaxation. Lipids were observed to undergo a broad range of motions; while the glycerol backbone was found to be rigid, dynamics in the acyl chains were much more rapid and unrestricted. Furthermore, by employing paramagnetic relaxation enhancements an ‘atomic ruler’ was developed that allows for measurement of the immersion depths of lipid carbon atoms. WaaG is a membrane-associated protein that adopts a GT-B fold. For proteins of this type, it has been speculated that the N-terminal domain anchors tightly to the membrane via electrostatic interactions, while the anchoring of the C-terminal domain is weaker. Here, this model was tested for WaaG. It was found by a set of circular dichroism, fluorescence, and NMR techniques that an anchoring segment located in the N-terminal domain termed MIR-WaaG binds electrostatically to membranes, and the structure and localization of isolated MIR-WaaG inside micelles was determined. Full-length WaaG was also found to bind membranes electrostatically. It senses the surface charge density of the membrane whilst not discriminating between anionic lipid species. Motion of the C-terminal domain could not be observed under the experimental conditions used here. Lastly, the affinity of WaaG to membranes is lower than expected, indicating that WaaG should not be classified as a monotopic membrane protein but rather as a peripheral one.

At the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 5: Manuscript.

An aqueous droplet in a solution of lipids in oil acquires a lipid monolayer coat, and two such droplets adhere to form a bilayer at their interface. Networks of droplets have been constructed in this way that function as light sensors, batteries and electrical circuits by using membrane proteins incorporated into the bilayers. However, the droplets have been confined to a bulk oil phase, which precludes direct communication with physiological environments. Further, the networks typically have been assembled manually, which limits their scale and complexity. This thesis addresses these limitations, and thereby enables prospective medical and technological applications for droplet networks. In the first part of the work, defined droplet networks are encapsulated within mm-scale drops of oil in water to form structures called multisomes. The encapsulated droplets adhere to one another and to the surface of the oil drop to form interface bilayers that allow them to communicate with each other and with the surrounding aqueous environment through membrane pores. The contents of the droplets can be released by changing the pH or temperature of the surrounding solution. Multisomes have potential applications in synthetic biology and medicine. In the second part of the work, a three-dimensional printing technique is developed that allows the construction of complex networks of tens of thousands of heterologous droplets ~50 µm in diameter. The droplets form a self-supporting material in bulk oil or water analogous to biological tissue. The mechanical properties of the material are calculated to be similar to those of soft tissues. Membrane proteins can be printed in specific droplets, for example to establish a conductive pathway through an otherwise insulating network. Further, the networks can be programmed by osmolarity gradients to fold into designed shapes. Printed droplet networks can serve as platforms for soft devices, and might be interfaced with living tissues for medical applications.

Droplet Interface Bilayers (DIBs) have a number of attributes that distinguish them from conventional artificial lipid bilayers. In particular, the ability to manipulate bilayers mechanically is explored in this thesis. Directed bilayer area changes are used to make precise measurements of the specific capacitance of DIBs and to control the two dimensional concentration of a membrane protein reconstituted in the bilayer. Chapter 1 provides a general introduction to the role of the lipid membrane en- vironment in the function of biological membranes and their integral proteins. An overview of model lipid bilayer systems is given. Chapter 2 introduces work carried out in this laboratory previously and illustrates the experimental setup of DIBs. Some important bilayer biophysical concepts are covered to provide the theoretical background to experiments in this and in later chapters. Results from the characterisation of DIBs are reported, and an account of the development of methods to manipulate the bilayer by mechanical means is given. Chapter 3 describes experiments that apply bilayer area manipulation in DIBs to achieve precise measurement of specific capacitance in a range of lipid systems. Chapter 4 reports results from experiments investigating the response of bilayer specific capacitance to an applied potential. Chapter 5 covers the background and experimental setup for total internal fluo- rescence microscopy experiments in DIBs and describes the expression, purification and characterisation of the bacterial β-barrel membrane protein pore α-Hemolysin. Chapter 6 describes experiments that apply the mechanical manipulation of bilayer area in DIBs to the corralling and control of the surface density of α-Hemolysin.

The very fundamental properties of biological membranes can be understood by studying their formation. This sets a good foundation for research related to how the membranes interact with organic molecules and ions; something of great value in the quest of explaining transport phenomena through cell membranes. It is furthermore of growing interest within the pharmacological research and contributes to the apprehension of life at the molecular level. In this thesis Molecular Dynamics has been used to simulate how evenly distributed phospholipids solvated in water leads to the formation of monolayers. An automation program has been written in Python for performing these simulations and is to be used as the foundation for performing simulations in further studies. The program was used to simulate model systems of high- and low concentrations of DPPC lipids. The DPPC lipid, like most other lipids, consist of a hydrophilic "head" part and two lipophilic "tails", which is the main cause of the lipids interacting in such a manner that forms membranes. The low concentration system was simulated for a total of 3 ns with all lipids having reached the surface at 1.5 ns, and the all lipids in the high concentration system had risen at 41 ns with a total simulation time of 43 ns.
De mest grundläggande egenskaperna hos cellmembran kan förstås genom att studera hur dessa bildas. Detta skapar en bra grund för forskning relaterad till hur membranen interagerar med organiska molekyler och joner; något av stort värde i bemödandet att förklara transportfenomen genom cellmembran. Dessutom är det av växande intresse inom den farmakologiska forskningen och bidrar till kunskapen om liv på den molekylära nivån. I denna avhandling har Molekylär Dynamik använts för att simulera hur jämnt fördelade fosfolipider lösta i vatten leder till bildandet av monoskiktade membran. Ett automatiseringsprogram har skrivits i Python för att utföra dessa simuleringar och ska komma att användas som grund för genomförandet av simuleringar i vidare studier. Programmet användes för att simulera modellsystem med höga och låga koncentrationer av DPPC lipider. DPPC lipiden, liksom de flesta andra lipider, består av en hydrofil ''huvud'' -del och två lipofila ''svansar'', vilket är den huvudsakliga orsaken till att lipiderna interagerar på ett sådant sätt som driver bildandet av ett membran. Lågkoncentrationssystemet simulerades i totalt 3 ns, varav 1,5 ns behövdes för att alla lipider skulle nå vattenytan. Alla lipider i högkoncentrationssystemet hade kommit upp till ytan efter 41 ns och för detta system utfördes simuleringen under en total tid på 43 ns.

Alpha-hemolysin is a pore-forming toxin secreted by pathogenic Staphylococcus aureus. Its spontaneous oligomerization and assembly into a trans-bilayer beta-barrel pore is a model for the assembly of many other pore-forming toxins. It is studied here in vitro as a means to probe general membrane protein oligomerization and lipid bilayer insertion. This thesis details the results of experiments to develop and implement a novel in vitro lipid bilayer system, Droplet-on-Hydrogel Bilayers (DHBs) for the single-molecule imaging of alpha-hemolysin assembly. Chapter 2 describes the development of DHBs and their electrical characterization. Experiments show the detection of membrane channels in SDS-PAGE gels post-electrophoresis and DHBs use as a platform for nanopore stochastic sensing. Chapter 3 describes the engineering and characterization of fluorescently-labelled monomeric alpha-hemolysin for use in protein assembly imaging experiments described in Chapter 6. Chapter 4 describes the characterization of DHB lipid fluidity and suitability for single-molecule studies of membrane protein diffusion. In addition, a novel single-particle tracking algorithm is described. Chapter 5 describes experiments demonstrating simultaneous electrical and fluorescence measurements of alpha-hemolysin pores embedded within DHBs. The first multiple-pore stochastic sensing in a single-lipid bilayer is also described. Chapter 6 describes experiments studying the assembly of alpha-hemolysin monomers in DHBs. Results show that alpha-hemolysin assembles rapidly into its oligomeric state, with no detection of long-lived intermediate states.

The electrostatic properties of lipid bilayer membranes play a significant role in many biological processes. Atomic force microscopy (AFM) is highly sensitive to membrane surface potential in electrolyte solutions. With fully characterized probe tips, AFM can perform quantitative electrostatic analysis of lipid membranes. Electrostatic interactions between Silicon nitride probes and supported zwitterionic dioleoylphosphatidylcholine (DOPC) bilayer with a variable fraction of anionic dioleoylphosphatidylserine (DOPS) were measured by AFM. Classical Gouy-Chapman theory was used to model the membrane electrostatics. The nonlinear Poisson-Boltzmann equation was numerically solved with finite element method to provide the potential distribution around the AFM tips. Theoretical tip-sample electrostatic interactions were calculated with the surface integral of both Maxwell and osmotic stress tensors on tip surface. The measured forces were interpreted with theoretical forces and the resulting surface charge densities of the membrane surfaces were in quantitative agreement with the Gouy-Chapman-Stern model of membrane charge regulation. It was demonstrated that the AFM can quantitatively detect membrane surface potential at a separation of several screening lengths, and that the AFM probe only perturbs the membrane surface potential by <2%. One important application of this technique is to estimate the dipole density of lipid membrane. Electrostatic analysis of DOPC lipid bilayers with the AFM reveals a repulsive force between the negatively charged probe tips and the zwitterionic lipid bilayers. This unexpected interaction has been analyzed quantitatively to reveal that the repulsion is due to a weak external field created by the internai membrane dipole moment. The analysis yields a dipole moment of 1.5 Debye per lipid with a dipole potential of +275 mV for supported DOPC membranes. This new ability to quantitatively measure the membrane dipole density in a noninvasive manner will be useful in identifying the biological effects of the dipole potential. Finally, heterogeneous model membranes were studied with fluid electric force microscopy (FEFM). Electrostatic mapping was demonstrated with 50 nm resolution. The capabilities of quantitative electrostatic measurement and lateral charge density mapping make AFM a unique and powerful probe of membrane electrostatics.

Hydrophobic matching, in which transmembrane proteins cause the surrounding lipid bilayer to adjust its thickness to match the hydrophobic surface of the protein, is a commonly accepted idea in biophysics, but one that until now has not been experimentally tested. One important consequence is that protein interactions will be mediated by the energy cost of deforming the membrane from its protein free state. With X-ray scattering techniques we tested these ideas with the peptide gramicidin embedded in DLPC and DMPC bilayers. Gramicidin pushes the different membranes to a common thickness as expected from hydrophobic matching. Concurrently, gramicidin-gramicidin nearest neighbor distance decreases with increasing mismatch, which confirms that the strain in the lipid bilayer gives rise to an attractive potential between the proteins. We have taken a continuum theory approach to the analysis of the experimental results. This approach treats the energetics of membrane-protein interactions as a function of the material properties of the membrane such as bending rigidity and compressibility. Using numerical methods and a novel simulation technique, we have successfully demonstrated the theoretical relationship between membrane thickness change and protein correlation. By quantitatively reproducing our experimental results, we have shown that the theory of membrane deformation is sufficient to explain the phenomena of hydrophobic matching. We also include a study on the peptide melittin as an example of the type of protein-lipid system we want to understand better. We answer the question of the orientation of the peptide when making membrane pores.

Phosphatidylcholine multilayers containing $\sim$24% water by total sample weight and gramicidin/lipid molar ratios, were aligned by a mechanical stressing and low temperature annealing ($$80$\mu$ thick x 40mm$\sp2$ area) monodomain defect-free multilayers containing as many as 10$\sp{17}$ uniformly oriented gramicidin channels to be prepared. The alignment of the lipid multilayers was monitored by observing conoscopic interference patterns and orthoscopic images. The smectic defects which appeared during the alignment process were identified and dissolved. The incorporation of gramicidin in the multilayers in the form of the transmembrane channels was proven by its circular dichroism spectra (CD). The well defined CD spectrum of uniformly oriented gramicidin channels was obtained. With proof that gramicidin is in the transmembrane conducting state, it is hoped that these oriented samples will permit spectroscopic studies of the ion channel in its conducting state and diffraction studies of the channel-channel organization in the membrane. (Abstract shortened with permission of author.)

The motivation of this work was to produce novel analytical techniques capable of probing the physical properties of the cell surface. Many researchers have used supported lipid bilayers (SLBs) as models to study the structure and function of the cell membrane. The complexity of these models is consistently increasing in order to better understand the myriad of physiologically relevant processes regulated by this surface. In order to aid researchers in studying such phenomenon, the following contributions were made. To manipulate components within the cell membrane, an electrophoretic flow cell was designed which can be used as a probe to study the effect of electrical fields on charged membrane components and for the separation of these components. This devise allows for the strict control of pH and ionic strength as species are observed in real-time using fluorescence microscopy. Additionally, advancements have been made to the production of patterned heterogeneous SLBs for use in separations and to probe the interactions of membrane components. The methodology to couple SLB separations and matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS) imaging was devised. This technology allows for the label-free mapping of the SLB surface post electrophoresis in order to observe naturally occurring species unperturbed by the addition of extrinsic tags. The final contribution, and perhaps the greatest, is the development of a procedure to create highly mobile SLBs from native membranes. These surfaces have vast potential in that they are no longer simple models of the cell surface, they are in fact the actual cell surface made planar. This advancement will be of great use to biophysicists and biochemists interested in using surface specific analytical methods to better understand physiological processes. These highly mobile native membrane surfaces have been coupled with the SLB electrophoresis technology to separate discrete bands of lipids and proteins, a proof of principle that will hopefully be further developed into a standard method for membrane proteomic studies. Collectively the tools and methodologies described herein show great potential in allowing researchers to further add to mankind’s understanding of the cellular membrane.

The response of the bilayer structure and dynamics to different types of inclusions is investigated using X-ray scattering techniques and the evidence is used to deduce details of their interaction with the membrane. In the case of the antimicrobial peptide RTD-1 we identify, combining the outcome of oriented CD spectroscopy and X-ray diffraction experiments, two different bound states of the peptide that differ in the orientation with respect to the membrane. One of which is shown by lamellar X-rays diffraction to considerably thin the membrane, while the other does not affect the membrane thickness. From this we identify the thinning state to be a surface state in which the peptide is embedded in the headgroup region of the bilayer. Furthermore we investigate the effect of small membrane-spanning helical peptides of different lengths on the bilayer using lamellar diffraction. Contrary to our expectations we did not measure any significant change in membrane thickness upon inclusion of these helices, which leads us review our idea of hydrophobic matching in the case of small single transmembrane peptides. In addition we used inelastic X-ray scattering at high energy resolution to investigate the collective chain dynamics of the membrane and how it is affected by inclusions in the membrane. We measure the inelastic X-ray scattering of DMPC bilayers with and without cholesterol. An analysis of these spectra within a generalized hydrodynamic theory yields the dispersion relation and damping of the high frequency sound modes. We show that this dispersion relation systematically changes with the amount of cholesterol in the sample. Comparing this finding with the situation in the pure lipid above and below the main phase transition we show that under the influence of the cholesterol the dynamics of the lipid becomes more gel-like, a fact that might have important implications for the transport of small molecules across the bilayer.

There is a general lack of atomic resolution data of mobile regions of membrane proteins embedded in lipid bilayers. As an inherently complex system, few techniques can capture information about the mobile portions of an otherwise immobilized protein. The nature of crystallography and solid-state NMR relies on structural rigidity. Solution-state NMR relies on overall mobility of a protein for resolution. In the middle regime, there are few solutions to study these systems. The inward-rectifying, pH-gated potassium channel KcsA from Streptomyces lividans makes an excellent model for the development of methods to study mobile regions of membrane proteins. Of its 160 residues, more than a third are in extracellular do- mains and are not typically captured by solid-state NMR or crystallographic techniques. These pages present evidence that KcsA’s C-terminus is highly mobile and becomes increasingly dynamic when the protein is at low pH and high K+ concen- tration, where the channel is known to be active. By applying proton-detected, high-resolution magic angle spinning NMR (HR-MAS) to fractionally deuterated KcsA, previously unattainable correlations are collected and new resonance assignments are made, demonstrating the utility of the technique. The lipid environment is well known to regulate the function of KcsA in particular and membrane proteins in general. It is generally assumed that reconstituting KcsA into a synthetic phospholipid membranes provides the protein a well-defined environment. Data is presented here which shows that KcsA co-purifies with phosphoglycerol lipids from the E. coli membrane and that these molecules are 13C enriched in the course of isotopically labeling KcsA. Further, significant hydrolysis of both co- purifying and synthetic lipids occurs under ordinary experimental conditions. These findings demand that routine analysis of samples must include verification of the chemical integrity of lipids. Finally, the feasibility of applying dynamic nuclear polarization-enhanced NMR (DNP) to KcsA is investigated as a means of elucidating information about its termini. Although KcsA is known to enhance poorly by DNP, data presented here show that this is not an intrinsic property of the protein but rather an effect of the matrix in which KcsA is investigated. The use of a 15N-enriched free amino acid dissolved into buffers used for DNP is shown to be a powerful diagnostic internal standard.

Gram-negative bacteria possess an asymmetric outer membrane in which the inner leaflet is composed primarily of phospholipids while the outer leaflet contains both phospholipids and lipopolysaccharide (LPS). LPS forms a structural barrier that protects Gram-negative bacteria from antibiotics and other environmental stressors. The lipid A anchor of LPS is a glucosamine-based saccharolipid that is further modified with core and O-antigen sugars. In addition to serving a structural role as the hydrophobic anchor of LPS, lipid A is recognized by the innate immune system in animal cells and macrophages. The enzymes of Lipid A biosynthesis are conserved in Gram-negative bacteria; in most species, a single copy of each bio-synthetic gene is present. The exception is lpxH, which is an essential gene encoding a membrane-associated UDP-2,3-diacylglucosamine hydrolase, which catalyzed the attack of water upon the alpha-phosphate of its substrate and the leaving of UMP, resulting in the formation of lipid X. Many Gram-negatives lack an lpxH orthologue, yet these species must possess an activity analogous to that of LpxH. We used bioinformatics approaches to identify a candidate gene, designated lpxI, encoding this activity in the model organism Caulobacter crescentus. We then demonstrated that lpxI can rescue Escherichia coli deficient in lpxH. Moreover, we have shown that LpxI possesses robust and specific UDP-2,3-diacylglucosamine hydrolase activity in vitro. We have developed high-yield purification schema for Caulobacter crescentus LpxI (CcLpxI) heterologously expressed in E. coli. We crystallized CcLpxI and determined its 2.6 Å x-ray crystal structure in complex with lipid X. CcLpxI, which has no known homologues, consists of two novel domains connected by a linker. Moreover, we have identified a point mutant of CcLpxI which co-purifies with its substrate in a 0.85:1 molar ratio. We have solved the x-ray crystal structure of this mutant to 3.0 Å; preliminary comparison with the product-complexed model reveals striking differences. The findings described herein set the stage for further mechanistic and structural characterization of this novel enzyme.

In this work, we also isolate and characterize LpxB, an essential lipid A biosynthetic gene which is conserved among all Gram-negative bacteria. We purify E. coli and Hemophilus influeznea LpxB to near-homogeneity on a 10 mg scale, and we determine that E. coli LpxB activity is dependent upon the bulk surface concentration of its substrates in a mixed micellar assay system, suggesting that catalysis occurs at the lipid interface. E. coli LpxB partitions with membranes, but this interaction is partially abolished in high-salt conditions, suggesting that a significant component of LpxB's membrane association is ionic in nature. E. coli LpxB (Mr ~ 43 kDa) is a peripheral membrane protein, and we demonstrate that it co-purifies with phospholipids. We estimate, by autoradiography and mass-spectrometry, molar ratios of phospholipids to purified enzyme of 1.6-3.5:1. Transmission electron microscopy reveals the accumulation of intra-cellular membranes when LpxB is massively over-expressed. Alanine-scanning mutagenesis of selected conserved LpxB residues identified two, D89A and R201A, for which no residual catalytic activity is detected. Our data support the hypothesis that LpxB performs catalysis at the cytoplasmic surface of the inner membrane, and provide a rational starting-point for structural studies. This work contributes to knowledge of the small but growing set of structurally and mechanistically characterized enzymes which perform chemistry upon lipids.

Dissertation

Die Zellmembran dient der Zelle nicht nur als äußere Hülle, sondern ist auch an einer Vielzahl von lebenswichtigen Prozessen wie Signaltransduktion oder Zelladhäsion beteiligt. Wasser als integraler Bestandteil von Zellen und der extrazellulären Matrix hat sowohl einen großen Einfluss auf die Struktur von Biomolekülen, als auch selbst besondere Merkmale in eingschränkter Geometrie. Im Rahmen dieser Arbeit wurden zwei Effekte an Modellmembranen untersucht: Erstens der Einfluss des Gegenions an kationischen Lipiden (DODAX, X = F, Cl, Br, I) auf die Eigenschaften des Grenzflächenwassers und zweitens das Vermögen durch Viskositätsänderungen das Wachstum von Nervenzellen anzuregen sowie die einzelnen Stadien der Bildung von neuronalen Netzwerken und deren Optimierung zu charakterisieren. Lipidmultischichten und darin adsorbiertes Grenzflächenwasser wurden mittels Infrarotspektroskopie mit abgeschwächter Totalreflexion untersucht. Nach Charakterisierung von Phasenverhalten und Wasserkapazität der Lipide wurden die Eigenschaften des Wassers durch kontrollierte Hydratisierung bei einem Wassergehalt von einem Wassermolekül pro Lipid verglichen. Durch die geringe Wasserkapazität können in diesem besonderen System direkte Wechselwirkungen zwischen Lipiden und Wasser aus der ersten Hydratationsschale beobachtet werden. Bemerkenswert strukturierte OH-Streckschwingungsbanden in Abhängigkeit des Anions und niedrige IR-Ordnungsparameter zeigen, dass stark geordnete, in ihrer Mobilität eingeschränkte Wassermoleküle an DODAX in verschiedenen Populationen mit unterschiedlich starken Wasserstoffbrückenbindungen existieren und sich vermutlich in kleinen Clustern anordnen. Die zweite Fragestellung hatte zum Ziel, das Wachstum von Nervenzellen auf Membranen zu beleuchten. Auf der Ebene einzelner Zellen wurde untersucht, ob sich in Analogie zu den bisher verwendeten elastischen Substraten, die Viskosität von Membranen als neuartiger physikalischer Stimulus dafür eignet, das mechanosensitive Verhalten von Neuronen zu modulieren. Das Wachstum der Neuronen wurde auf substrat- und polymergestützten Lipiddoppelschichten mittels Phasenkontrastmikroskopie beobachtet. Die Quantifizierung der Neuritenlängen, -auswuchsgeschwindigkeiten und -verzweigungen zeigten kaum signifikante Unterschiede. Diffusionsmessungen (FRAP) ergaben, dass entgegen der Erwartungen, die Substrate sehr ähnliche Fluiditäten aufweisen. Die Betrachtung der zeitlichen Entwicklung des kollektiven Neuronenwachstums, also der Bildung von komplexen Netzwerken, offenbarte robuste „Kleine-Welt“-Eigenschaften und darüber hinaus unterschiedliche Stadien. Diese wurden durch graphentheoretische Analyse beschrieben, um anhand typischer Größen wie dem Clusterkoeffizienten und der kürzesten Pfadlänge zu zeigen, wie sich die Neuronen in einem frühen Stadium vernetzen, im Verlauf eine maximale Komplexität erreichen und letztlich das Netzwerk durch effiziente Umstrukturierung hinsichtlich kurzer Pfadlängen optimiert wird.

Indiana University-Purdue University Indianapolis (IUPUI)
Plasma membranes are complex supramolecular assemblies comprised of lipids and membrane proteins. Both types of membrane constituents are organized in highly dynamic patches with profound impact on membrane functionality, illustrating the functional importance of plasma membrane fluidity. Exemplary, dynamic processes of membrane protein oligomerization and distribution are of physiological and pathological importance. However, due to the complexity of the plasma membrane, the underlying regulatory mechanisms of membrane protein organization and distribution remain elusive. To address this shortcoming, in this thesis work, different mechanisms of dynamic membrane protein assembly and distribution are examined in a polymer-tethered lipid bilayer system using comple-mentary confocal optical detection techniques, including 2D confocal imaging and single molecule-sensitive confocal fluorescence intensity analysis methods [fluorescence correlation spectroscopy (FCS) autocorrelation analysis and photon counting histogram (PCH) method]. Specifically, this complementary methodology was applied to investigate mechanisms of membrane protein assembly and distribution, which are of significance in the areas of membrane biophysics and cellular mechanics. From the membrane biophysics perspective, the role of lipid heterogeneities in the distribution and function of membrane proteins in the plasma membrane has been a long-standing problem. One of the most well-known membrane heterogeneities are known as lipid rafts, which are domains enriched in sphingolipids and cholesterol (CHOL). A hallmark of lipid rafts is that they are important regulators of membrane protein distribution and function in the plasma membrane. Unfortunately, progress in deciphering the mechanisms of raft-mediated regulation of membrane protein distribution has been sluggish, largely due to the small size and transient nature of raft domains in cellular membranes. To overcome this challenge, the current thesis explored the distribution and oligomerization of membrane proteins in raft-mimicking lipid mixtures, which form stable coexisting CHOL-enriched and CHOL-deficient lipid domains of micron-size, which can easily be visualized using optical microscopy techniques. In particular, model membrane experiments were designed, which provided insight into the role of membrane CHOL level versus binding of native ligands on the oligomerization state and distribution of GPI-anchored urokinase plasminogen activator receptor (uPAR) and the transmembrane protein αvβ3 integrin. Experiments on uPAR showed that receptor oligomerization and raft sequestration are predominantly influenced by the binding of natural ligands, but are largely independent of CHOL level changes. In contrast, through a presumably different mechanism, the sequestration of αvβ3 integrin in raft-mimicking lipid mixtures is dependent on both ligand binding and CHOL content changes without altering protein oligomerization state. In addition, the significance of membrane-embedded ligands as regulators of integrin sequestration in raft-mimicking lipid mixtures was explored. One set of experiments showed that ganglioside GM3 induces dimerization of α5β1 integrins in a CHOL-free lipid bilayer, while addition of CHOL suppresses such a dimerization process. Furthermore, GM3 was found to recruit α5β1 integrin into CHOL-enriched domains, illustrating the potential sig-nificance of GM3 as a membrane-associated ligand of α5β1 integrin. Similarly, uPAR was observed to form complexes with αvβ3 integrin in a CHOL dependent manner, thereby causing the translocation of the complex into CHOL-enriched domains. Moreover, using a newly developed dual color FCS and PCH assay, the composition of uPAR and integrin within complexes was determined for the first time. From the perspective of cell mechanics, the characterization of the dynamic assembly of membrane proteins during formation of cell adhesions represents an important scientific problem. Cell adhesions play an important role as force transducers of cellular contractile forces. They may be formed between cell and extracellular matrix, through integrin-based focal adhesions, as well as between different cells, through cadherin-based adherens junctions (AJs). Importantly, both types of cell adhesions act as sensitive force sensors, which change their size and shape in response to external mechanical signals. Traditionally, the correlation between adhesion linker assembly and external mechanical cues was investigated by employing polymeric substrates of adjustable substrate stiffness containing covalently attached linkers. Such systems are well suited to mimic the mechanosensitive assembly of focal adhesions (FAs), but fail to replicate the rich dynamics of cell-cell linkages, such as treadmilling of adherens junctions, during cellular force sensing. To overcome this limitation, the 2D confocal imaging methodology was applied to investigate the dynamic assembly of N-cadherin-chimera on the surface of a polymer-tethered lipid multi-bilayer in the presence of plated cells. Here, the N-cadherin chimera-functionalized polymer-tethered lipid bilayer acts as a cell surface-mimicking cell substrate, which: (i) allows the adjustment of substrate stiffness by changing the degree of bilayer stacking and (ii) enables the free assembly of N-cadherin chimera linkers into clusters underneath migrating cells, thereby forming highly dynamic cell-substrate linkages with remarkable parallels to adherens junctions. By applying the confocal methodology, the dynamic assembly of dye-labeled N-cadherin chimera into clusters was monitored underneath adhered cells. Moreover, the long-range mobility of N-cadherin chimera clusters was analyzed by tracking the cluster positions over time using a MATLAB-based multiple-particle tracking method. Disruption of the cytoskeleton organization of plated cells confirmed the disassembly of N-cadherin chimera clusters, emphasizing the important role of the cytoskeleton of migrating cells during formation of cadherin-based cell-substrate linkages. Size and dynamics of N-cadherin chimera clusters were also analyzed as a function of substrate stiffness.

The study of biological and model membrane systems currently represents an important area of scientific research. Lipids are involved in the regulation of multiple cellular processes, being fundamental for the mantainance of cell homeostasis. Sphingosine (Sph) belongs to this group of biologically active lipids and is an important signaling molecule. When abnormally accumulated in the lysosomes and late endosomes (LE), Sph is associated to one of the most complex lysosomal storage diseases (LSD), Niemann-Pick type C (NPC). Despite this, little is known about its role in the lysosome, in particular with respect to the biophysical effects of its accumulation. By understanding the interactions of Sph with other lipids and their effect on the physical state of model and cell membranes, new insights into its mode of action may arise. Using complementary established techniques (fluorescence spectroscopy, dynamic (DLS) and electrophoretic (ELS) light scattering), a thorough biophysical characterization of membranes containing Sph was performed. This study revealed that Sph is able to decrease membrane fluidity both in fluid 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) and lipid raft-mimicking (POPC/SM/Chol) membrane models in a concentration dependent way. Sph-induced changes on membrane fluidity are highly dependent on pH and membrane lipid composition. It was observed that Sph has a more dramatic impact on membrane organization and permeability in vesicles with a pH gradient resembling the lysosome - the lysosome mimicking vesicles - LMVs (pH 5.0in/7.4out) - particularly in those with a lipid composition mimicking NPC1 conditions (i.e. higher Chol, SM and Sph content), compared to physiological-like situations. In the biological context, it was shown that cells displaying the NPC phenotype have an altered membrane fluidity when compared with the wild-type (WT) cells and that these changes are complex and cell type dependent. Moreover, it was observed that Sph has the ability to decrease the fluidity of biological membranes in accordance with model membrane data. Overall the results suggest that Sph abnormal accumulation in cells is associated with alterations in membrane biophysical properties, likely affecting different membrane associated cellular processes. These changes could urderly some Sph biological actions. In particular, Sph-induced biophysical alterations might affect the endocytic trafficking and consequently the normal cell function in NPC disease.

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.