<p>Biological membranes play host to a number of processes essential for cellular function and are the most important biological interface. The structurally complex and highly dynamic nature of the membrane poses significant measurement challenges, requiring an experimental technique capable of accessing very short, nanometer length scales, and fast, micro-pico second time scales.</p> <p>The experimental work presented in this thesis uses a variety of neutron scattering techniques to study the structure and dynamics of biologically relevant model membrane systems. The main body of this work can be sub-divided into two distinct topics: (1) lateral diffusion of lipid molecules in a bilayer; and (2) the measurement of domains in the membrane.</p> <p>Diffusion is the fundamental mechanism for lipids and proteins to move throughout the lipid matrix of a biological membrane. Despite a strong effort to model lipid diffusion, there is still no coherent model which describes the motion of lipid molecules from less than a lipid-lipid distance to macroscopic length scales. The experiments presented on this topic attempt to extend the range over which diffusion is typically measured by neutron scattering, to initiate the development of a more complete lipid diffusion model.</p> <p>Lipid domains and rafts are thought be platforms for many cellular functions; however, their small size and transient nature makes them notoriously difficult to observe. The penultimate chapter of this thesis provides evidence supporting the existence of domains in a model lipid/cholesterol system by probing of the dynamics of the system. The challenge of observing these structures directly was addressed by modifying the traditional neutron triple-axis spectrometry setup to increase its sensitivity to systems with short-range order. This technique was employed to examine the coexistence of fluid and gel domains in a single-component lipid bilayer system, as well as the presence of highly ordered lipid domains in a model membrane containing cholesterol.</p> / Doctor of Philosophy (PhD)

Arrays of fully hydrogel-supported, artificial hair cell (AHC) sensors based on bilayer membrane mechanotransduction are designed and characterized to determine sensitivity to multiple stimuli. The work draws upon key engineering design principles inspired by the characteristics of biological hair cells, primarily the use of slender hair-like structures as flow measurement elements. Many hair cell microelectromechanical (MEMS) devices to sense fluid flow have already been built based on this principle. However, recent developments in lipid bilayer applications, namely physically encapsulated bilayers and hydrogel interface bilayers, have facilitated the development of AHCs made primarily from biomolecular materials. The most current research in this field of "membrane based AHCs," shows promise, yet still lacks the modularity to create large sensor arrays similar to those in nature. This paper presents a novel bilayer based AHC platform, developed for array implementation by applying some of the core design principles of biological hair cells. These principles are translated into key design, fabrication and material considerations toward improved sensor sensitivity and modularity. Single hair cell responses to base excitation and short air pulses are to investigate the dynamic coupling between hair and bilayer membrane transducer. In addition, a spectral analysis of the AHC system under varying voltages and air flow velocities helps to build simple, predictive models for the sensitivity properties of the AHC. And finally, based on these results, we implement a spatial sensing strategy that involves mapping frequency content to stimulus location by "tuning" linear, three-unit arrays of AHCs. Individual AHC sensors characterization results demonstrate peak current outputs in the nanoamp range and measure flow velocities as high as 72 m/s. Characterization of the AHC response to base excitation and air pulses show that membrane current oscillates with the first three bending modes of the hair. Output magnitudes reflect of vibrations near the base of the hair. A 2 degree-of-freedom Rayleigh-Ritz approximation of the system dynamics yields estimates of 19 N/m and 0.0011 Nm/rad for the equivalent linear and torsional stiffness of the hair's hydrogel base, although double modes suggest non-symmetry in the gel's linear stiffness. The sensor output scales linearly with applied voltage (1.79 pA/V), avoiding a higher-order dependence on electrowetting effects. The free vibration amplitude of the sensor also increases in a linear fashion with applied airflow pressure (3.39 pA/m s??). Array sensing tests show that the bilayers' consistent spectral responses allow for an accurate localization of the airflow source. However, temporal variations in bilayer size affect sensitivity properties and make airflow magnitude estimation difficult. The overall successful implementation of the array sensing method validates the sensory capability of the bilayer based AHC. / Master of Science

The research presented in this thesis includes the development of designs, materials, and fabrication processes and the results of characterization experiments for a meso-scale hydrogel-based lipid bilayer array system. Two design concepts are investigated as methods for forming Droplet Interface Bilayer (DIB) arrays. Both concepts use a base of patterned silver with Ag/AgCl electrodes patterned onto a flat polymer substrate. In one technique, photopolymerizable hydrogel is cured through a mask to form an array of individual hydrogels on top of the patterned electrodes. The other technique introduces a second type of polymer substrate that physically supports an array of hydrogels using a set of microchannels. This second substrate is fitted onto the first to contact the hydrogels to the electrodes. The hydrogels are used to support and shape droplets of water containing phospholipids, which self-assemble at the surface of the droplet when submerged in oil. Two opposing substrates can then be pushed together, and a bilayer will form at the point where each pair of monolayers come into contact. The photopatterning technique is used to produce small arrays of hydrogels on top of a simple electrode pattern. Systems utilizing the microchannel substrate are used to create mesoscale hydrogel arrays of up to 3x3 that maintained a low resistance (~50-150 kΩ) connection to the substrate. Up to three bilayers are formed simultaneously and verified through visual observation and by recording the current response behavior. Arrays of varying sizes and dimensions and with different electrode patterns can be produced quickly and inexpensively using basic laboratory techniques. The designs and fabrication processes for both types of arrays are created with an eye toward future development of similar systems at the microscale. / Master of Science

This research documents the creation and use of an open-loop feed forward control scheme designed to manipulate the DC potential across lipid bilayer membranes in artificial hair cell sensors. Inspired by the human cochlea's non-linear gain phenomenon, whereby the cochlea can increase or decrease the effective gain of the auditory system, this controller is the first step in developing more sophisticated signal processing schemes for use with future bio-inspired artificial hair cell development. This open-loop controller allows for three preset gain mappings to tailor the DC offset in response to an external stimulus. Linear, nonlinear and sigmoidal mappings were created to observe the differences in system response during constant frequency and variable frequency excitation. In constant frequency testing, artificial hair cell sensors were excited at 100 Hz across a range of input intensities to observer current output response during increasing or decreasing excitation levels. Results showed average coherence values above 0.98 for the relationship between current output and fluid velocity, indicating a strong correlation between excitation and measured output. In the bilayer with stereocilia test case, RMS power increased with higher excitation levels but the various control laws did not appear to have any discernible impact on output power. In variable frequency testing, sensors were excited from 0-300 Hz to observe the real time effects of our control law on amplification or attenuation of output current with varying input intensity. Results of the variable frequency excitation could not definitively prove that the varied DC potential had an effect on current output due to excessive capacitive noise, but the controller did provide some encouraging results from its behavior during testing. We observed three distinct DC potential response curves for each mapping, indicating, that with some refinement, we should be able to manipulate output current with user defined gain tunings. / Master of Science

Les canaux ioniques sont des protéines membranaires permettant le transport ionique au travers des membranes biologiques. Du fait de leur omniprésence dans l'organisme, ils représentent une classe de cibles thérapeutiques encore actuellement peu exploitée du fait de limitations expérimentales dans leur étude. La mesure électrique de l'activité des canaux ioniques au sein de bicouches biomimétiques reconstituées in vitro permettrait de répondre à ces limitations. Cependant, il n'existe actuellement pas de système satisfaisant au cahier des charges complet pour de telles analyses : stabilité et pureté de la bicouche, faible niveau de bruit, insertion rapide des canaux ioniques, intégration dans un dispositif fluidique, possibilité de mener une caractérisation optique simultanée. L'objectif de ces travaux de thèse était d'évaluer dans quelle mesure l'utilisation d'un substrat SOI (Silicon On Insulator) comprenant des nanopores pourrait permettre de répondre à tous ces critères. Des nanopores de diamètre compris entre 10 nm et 160 nm ont été réalisés à partir d'un substrat SOI. Une cellule fluidique transparente est utilisée pour l'adressage fluidique. Cette cellule permet d'autre part la double caractérisation électrique et optique. Les propriétés électriques en milieu liquide du dispositif ont été étudiées et permettent de dégager des perspectives d'amélioration. La double caractérisation électrique et optique est démontrée au moyen d'expériences de capture de nanoparticules fluorescentes sur les nanopores. Enfin, des premiers résultats prometteurs d'obtention d'une bicouche lipidique suspendue sont présentés. / Ion channels are membrane proteins responsible for ion transport across biological membranes. Due to their ubiquity, they are promising drug targets but are not yet fully exploited as such due to experimental restrictions in their study. Electrical measurement of ion channels activity within in vitro artificial lipid bilayers would enable to overcome these restrictions. However, there is not yet a system satisfying all the requirements for ion channels studies: stability and purity of the lipid bilayer, low noise level, fast insertion of ion channels, fluidic integration, ability to perform simultaneous optical characterization. The aim of this phD was to assess in which extent the use of an SOI (Silicon On Insulator) substrate bearing nanopores could satisfy all these requirements. 10 nm to 160 nm diameter nanopores were fabricated in an SOI substrate and characterized. A transparent fluidic cell was used for fluidic addressing. This transparent cell allows combined electrical and optical characterization. Electrical properties of the device in aqueous environment were studied, allowing to bring out improvement prospects. The combined electrical and optical characterization was demonstrated with fluorescent nanoparticle trapping experiments on the nanopores. Finally, promising results about the formation of a free-standing lipid bilayer are presented.

One of the most important aspects for all life on this planet is the act to keep their biological processes in a state where they do not reach equilibrium. One part in the upholding of this imbalanced state is the barrier between the cells and their surroundings, created by the cell membrane. Additionally, terrestrial animal life often requires a barrier that protects the organism's body from external hazards and water loss. As an alternative to experiments, the investigation of the processes occurring at these barriers can be performed by using molecular dynamics simulations. Through this method we can obtain an atomistic description of the dynamics associated with events that are not accessible to experimental setups.  In this thesis the first paper presents an improved particle-mesh Ewald method for the calculation of long-range Lennard-Jones interactions in molecular dynamics simulations, which solves the historical performance problem of the method. The second paper demonstrate an improved implementation, with a higher accuracy, that only incurs a performance loss of roughly 15% compared to conventional simulations using the Gromacs simulation package. Furthermore, the third paper presents a study of cholesterol's effect on the permeation of six different solutes across a variety of lipid bilayers. A laterally inhomogeneous permeability in cholesterol-containing membranes is proposed as an explanation for the large differences between experimental permeabilities and calculated partition coefficients in simulations. The fourth paper contains a coarse-grained simulation study of a proposed structural transformation in ceramide bilayer structures, during the formation of the stratum corneum. The simulations show that glycosylceramides are able to stabilize a three-dimensionally folded bilayer structure, while simulations with ceramides collapse into a lamellar bilayer structure. / <p>QC 20160308</p>

Many biological processes, pathogens, and pharmaceuticals act upon, cellular membranes. Accordingly, cell membrane mimics are attractive targets for biosensing, with research, pathology, and pharmacology applications. Lipid bilayers represent a versatile sensor functionalization platform providing antifouling properties, and many receptor integration options, uniquely including transmembrane proteins. Bilayer-coated sensors enable the kinetic characterization of membrane/analyte interactions. Addressed theoretically and experimentally is the self-assembly of model membranes on plasmonic sensors. Two categories of plasmonic sensors are studied in two parts. Part I aims to deposit raft-forming bilayers on planar nanoaperture arrays suitable for multiplexing and device integration. By vesicle fusion, planar bilayers are self-assembled on thiol-acid modified flame-annealed gold without the need for specific lipid head-group requirements. Identification of coexisting lipid phases is accomplished by AFM imaging and force spectroscopy mapping. These methods are successfully extended to metallic, plasmon-active nanohole arrays, nanoslit arrays and annular aperture arrays, with coexisting phases observed among the holes. Vis-NIR transmission spectra of the arrays are measured before and after deposition, indicating bilayer detection. Finally, the extraction of membrane proteins from cell cultures and incorporation into model supported bilayers is demonstrated. These natural membrane proteins potentially act as lipid-bound surface receptors. Part II aims to encapsulate in model lipid bilayers, metallic nanoparticles, which are used as probes in surface enhanced Raman spectroscopy. Three strategies of encapsulating particles, and incorporating Raman-active dyes are demonstrated, each using a different dye: malachite green, rhodamine-PE, and Tryptophan. Dye incorporation is verified by SERS and the bilayer is visualized and measured by TEM, with support from DLS and UV-Vis spectroscopy. In both parts, lipid-coated sensors are successfully fabricated and characterized. These results represent important and novel solutions to the functionalization of plasmonic surfaces with biologically relevant cell membrane mimics.

A signifficant obstacle facing the healthcare industry is the phenomenon of multidrug resistance (MDR) in which a cell acquires simultaneous resistance to many unrelated drugs that it has never been exposed to. At the molecular level, MDR can be characterised by a reduction of intracellular drug levels due to their active efflux by multidrug transporters such as P-glycoprotein (Pgp). Pgp is able to efflux a phenomenally wide variety of chemically unrelated drugs and causal relationships have been established between its expression and the acquisition of MDR to numerous anticancer and central nervous system (CNS) drugs. There has thus been much effort to understand the molecular biology of Pgp and how it functions. However, many aspects of its functioning remain unclear. From a drug discovery viewpoint, we have yet to fully understand what features make some drugs susceptible to Pgp-mediated efflux (substrates) and what makes others able to inhibit Pgp function (inhibitors). From a mechanistic viewpoint, it is still uncertain what the exact nature of Pgp's binding site is, the role of ATP binding and hydrolysis in transport and how both of these interplay with ligand binding. The work presented in this thesis attempts to answer these questions from two perspectives. Firstly the mouse Pgp crystal structure [PDB 3G60] was used as a unique starting point for molecular dynamics (MD) simulations to characterise the dynamics and conformational exibility of Pgp, properties believed to be integral to its function. The simulations revealed Pgp to be a highly dynamic molecule at both its transmembrane (TM) and nucleotide binding domains (NBDs). The latter exhibited a conformational asymmetry that supports the Constant Contact model of ATPase activity. In the presence of the Pgp substrate, daunorubicin, the NBDs exhibited tighter asymmetric dimerisation leading to increased affinity for ATP. In contrast, the presence of the Pgp inhibitor, QZ59-RRR led to NBD conformational changes that reduced their affinity for ATP. Thus providing an appealing mechanism for how QZ59-RRR inhibits Pgp ATPase activity. MD simulation was also used to provide atomic-detail interpretations of multiple binding stoichiometries of drug and lipid molecules observed by collaborator-led mass spectrometry experiments. This also provided opportunity to validate the Pgp simulations against novel experimental data. The second strand of the thesis explored the membrane permeation dynamics of CNS therapeutics in order to identify differences in protonation states, conformations, orientations and membrane localisation that might distinguish those that are Pgp substrates and from those that are not. These properties were studied using complementary MD simulation and nuclear magnetic resonance (NMR) techniques. The simulations revealed a novel set of criteria that in uence the likelihoodof a drug to 'flip-flop' across a membrane, a behaviour that may make drugs more susceptible to Pgp efflux. These observations were broadly consistent with the NMR experiments. However, the NMR data also highlighted limitations in the simulation approaches used in this thesis and emphasised the need to also consider the kinetics of permeation in addition to its thermodynamics.

Ácidos graxos livres (FFA) são importantes mediadores do transporte de prótons através de membranas. Porém, pouco se sabe sobre a influência estrutural tanto dos FFA como do ambiente lipídico na translocação de prótons através de membranas. Tanto os efeitos do comprimento da cadeia e número de insaturações dos FFA como a composição da membrana foram analisados por medidas elétricas em bicamadas lipídicas planas. Condutância a prótons (GH+) e condutância de vazamento (Gleak) foram calculadas a partir de medidas de voltagem em circuito aberto e de corrente de curto-circuito obtidas através de um eletrômetro ou um amplificador de patch-clamp (modo de voltage-clamp). Nossos resultados mostram que FFA com cis-insaturações causam um efeito mais pronunciado no transporte de próton quando comparados com FFA saturados ou trans-insaturação. Colesterol e cardiolipina diminuem Gleak de membranas. Cardiolipina também diminui GH+. Esses efeitos indicam uma dupla modulação do transporte de prótons: pelo mecanismo de flip-flop dos FFA e por uma via difusional simples adicional. / Free fatty acids (FFA) are important mediatiors of proton transport across membranes. However, little is known about the structural influence of both FFA and the membrane environment have in proton translocation across phospholipid membranes and by which means this influence is brought about. Both the effects of FFA chain length and insaturation and membrane composition on proton transport have been addressed in this study by electrical measurements in planar lipid bilayers. Proton conductance (GH+) and leak conductance (Gleak) were calculated from open-circuit voltage and short-circuit current measurements obtained using either an electrometer or a patch-clamp amplifier (voltage-clamp mode). We found that cis-unsaturated FFA caused a more pronounced effect on proton transport as compared to saturated or trans-unsaturated FFA. Cholesterol and cardiolipin decreased Gleak. Cardiolipin also decreased GH+. These effects indicate a dual modulation of protein-independent proton transport by FFA through flip-flop and by an additional simple diffusional pathway.

Knowledge about the insertion and stabilization of membrane proteins is a key step towards understanding their function and enabling membrane protein design. Transmembrane helices are normally quite hydrophobic to insert efficiently, but there are many exceptions with unfavorable polar or titratable residues. Since evolutionary conserved these amino acids are likely of paramount functional importance, e.g. the four arginines in the S4 voltage sensor helix of voltage-gated ion channels. This has lead to vivid discussion about their conformation, protonation state and cost of insertion. To address such questions, the main focus of this thesis has been membrane protein solvation in lipid bilayers, evaluated using molecular dynamics simulations methods. A main result is that polar and charged amino acids tend to deform the bilayer by pulling water/head-groups into the hydrophobic core to keep their hydrogen bonds paired, thus demonstrating the adaptiveness of the membrane to allow specific and quite complex solvation. In addition, this retained hydration suggests that the solvation cost is mainly due to entropy, not enthalpy loss. To further quantify solvation properties, free energy profiles were calculated for all amino acids in pure bilayers, with shapes correlating well with experimental in vivo values but with higher magnitudes. Additional profiles were calculated for different protonation states of the titratable amino acids, varying lipid composition and with transmembrane helices present in the bilayer. While the two first both influence solvation properties, the latter seems to be a critical aspect. When the protein fraction in the models resemble biological membranes, the solvation cost drops significantly - even to values compatible with experiment. In conclusion, by using simulation based methods I have been able to provide atomic scale explanations to experimental results, and in particular present a hypothesis for how the solvation of charged groups occurs.