A presente tese versa sobre resultados obtidos na aplicação da microscopia eletroquímica de varredura no estudo de sistemas micelares e no estudo de bicamadas lipídicas. Os estudos envolvendo sistemas micelares foram realizados utilizando a SECM no modo substrato-gerador/microeletrodo-coletor. Neste modo de operação, um microeletrodo de platina foi posicionado próximo a um substrato de platina e utilizado para monitorar espécies eletrogeradas nesse substrato. Conhecendo o tempo necessário para a espécie eletrogerada difundir do substrato até o microeletrodo, foi possível aplicar a equação de Einstein-Smoluchowski para determinar o coeficiente de difusão da espécie eletroativa e de micelas de surfactantes. Como as micelas não são eletroativas, o ferroceno eletrogerado no substrato e incorporado nas micelas foi utilizado como sonda para a estimativa do tempo de difusão. Os resultados obtidos para o surfactante brometo de tetradecil trimetil amônio (C14TABr) corroboram dados reportados na literatura, demonstrando a utilidade da metodologia proposta no estudo de sistema micelares. Também foram realizados experimentos envolvendo micelas do surfactante cloreto de 1-alquil-3-metilimidazólio, CxMelmCl (x = 10, 12, 14, 16) e com os resultados obtidos foi possível evidenciar o efeito da cadeia carbônica no coeficiente de difusão das espécies. Os experimentos envolvendo a permeação de substâncias através de bicamadas lipídicas foram realizados em duas etapas. Os primeiros ensaios foram realizados utilizando modelo de membrana semipermeável (papel celofane) com o intuito de verificar a aplicabilidade da SECM no monitoramento de espécies eletroativas que permeiam através da membrana. Na segunda etapa, apresentou-se metodologia para a obtenção de microfuros em folhas de poliestireno utilizados para a formação das bicamadas lipídicas, assim como detalhes sobre a construção da célula de medidas utilizadas nos experimentos de permeação. Foram realizados experimentos envolvendo o uso de bicamadas lipídicas planas obtidas pelo método de Miller preparadas com lecitina de soja. Esses experimentos foram realizados com o intuito de avaliar a estabilidade e para verificar a permeabilidade de algumas substâncias nas bicamadas formadas. Os experimentos de permeação foram realizados posicionando um microeletrodo próximo à membrana, com posterior detecção amperométrica da espécie eletroativa que atravessa a membrana. / This thesis shows results on the use of scanning electrochemical microscopy in the study of micellar systems and lipid bilayers. Studies involving micellar systems were performed by using SECM in the substrate-generator/tip-collector mode. In this operation mode a platinum microelectrode was positioned close to a platinum substrate and used to monitor electrogenerated species on this surface. Taking into account the time for the electrogenerated species to diffuse from the substrate to the microelectrode, the diffusion coefficient of the electroactive species and of the micelles can be calculated by applying the Einstein-Smoluchowski equation. As micelles are not electroactive, ferrocene electrogenerated on the substrate and incorporated into the micelles was used as a probe to estimate the diffusion time. The results obtained for tetradecyl trimethyl ammonium bromide (C14TABr) corroborate those reported in the literature, demonstrating the applicability of the proposed methodology in the study of micellar systems. Experiments with micelles obtained from 1-alkyl-3-methylimidazolium, CxMelmCl (x = 10, 12, 14, 16) chloride surfactants were also performed and results showed the effect of the carbon chain in the diffusion coefficient. Experiments involving the permeation of chemical species through lipid bilayers were carried out in two steps. A membrane model (cellophane) was preliminary used in order to investigate the possibility of using SECM as a tool for monitoring the permeation of electroactive species through the membrane. Then, a methodology for obtaining microholes in polystyrene sheets used to form lipid bilayers was presented, as well as details about the design of an electrochemical cell used in the permeation experiments. Experiments involving the use of planar lipid bilayers obtained by the method of Miller prepared using soybean lecithin were performed. These experiments were carried out in order to evaluate the stability and to check the permeation of some substances through the prepared bilayers. Permeation experiments were performed by placing the microelectrode close to the membrane with subsequent amperometric detection of any electroactive species that cross the membrane

Membrane fusion is essential for survival in eukaryotic cells. Many physiological processes such as endocytosis and exocytosis are mediated by membrane fusion, which is driven by highly specialized and conserved family of proteins. Neuronal soluble Nethylmaleimide- sensitive factor attachment protein receptors (SNAREs) mediate vesicle fusion with the plasma membrane during neurotransmitter release; however, the mechanism for SNARE-mediated membrane fusion remains to be established. In the current work, we aimed at investigating this mechanism using atomic force microscope (AFM) spectroscopy. We established an AFM lipid bilayer system, which proved effective in detecting fusion of bilayers and measuring compression forces required to generate fusion. It also revealed that SNARE-mediated membrane fusion proceeds through an intermediate hemifused state. Using this system, we revealed the energy landscape for membrane fusion using a dynamic force approach. We carried out compression force measurements at different compression rates and a significant reduction in the force was observed when SNAREs were present in the bilayers. The results also indicated that a single energy barrier governed membrane fusion in our experimental system. The energy barrier is characterized by its width and height, which determine the slope of the activation potential. With SNAREs in the opposing (trans) bilayers, the width of the barrier increased > 2 fold, which is interpreted as an increase in the compressibility of the membranes and subsequently a greater ease in their deformation and fusion under compression. Moreover, specific perturbations to the SNARE interaction interfered with the observed facilitation of membrane fusion, which indicated the involvement of SNAREs in the observed fusion facilitation and increase in the fusion rate. Furthermore, dissociation kinetics analysis of the SNARE interaction revealed a strong binding force during trans SNARE-complex formation, and a correlation between the strength of the SNARE interaction and the degree of fusion facilitation was established. In conclusion, the present findings provide support for a mechanism for SNAREmediated membrane fusion, where trans-interaction between SNAREs provides close apposition of the membranes and reduces fusion energy requirements by locally destabilizing the bilayers, in which the SNAREs are anchored, through pulling on or tilting of their transmembrane segments.

Planar supported, polymerized phospholipid bilayers (PPBs) composed of 1,2-bis[10-(2’,4’-hexadienoyloxy)decanoyl]-sn-glycero-3-phosphocholine (bis-SorbPC or BSPC) were generated by a redox polymerization method. The PPBs were supported by a silicon substrate. The PPBs were characterized and tested for uniformity and stability under physiological conditions. The PPBs were analyzed in vitro with murine derived cells that are pertinent to the host response. Cellular attachment and phenotypic changes in RAW 264.7 macrophages and NIH 3T3 fibroblasts were investigated on PPBs and compared to bare silicon controls. Fluorescent and SEM images were used to observe cellular attachment and changes in cellular behavior. The PPBs showed much lower cellular adhesion for both cell lines than bare silicon controls. Of the cells that attached to the PPBs, a very low percentage showed the same morphological expressions as seen on the controls. The hypothesis generated from this work is that defects in the PPBs mediated the cellular attachment and morphological changes that were observed. Finally, a layer-by-layer (LbL) deposition of a poly(acrylic acid) (PAA) and poly(N-vinylpyrrolidone) (PNVP) alternating bilayer was attempted as a proof of concept for future modification of this system.

Lipid molecules form thin biological membranes that envelop all living cells, and behave as two-dimensional liquid sheets immersed in bulk water. The interactions of such biomembranes with their environment lay the foundation of a plethora of biological processes rooted in the mesoscopic domain - length scales of 1-1000 nm and time scales of 1-1000 ns. Research in this intermediate regime has for a long time been out of reach for conventional experiments, but breakthroughs in computer simulation methods and scattering experimental techniques have made it possible to directly probe static and dynamic properties of biomembranes on these scales. Biomembranes are soft, with a relatively low energy cost of bending, and are thereby influenced by random, thermal fluctuations of individual molecules. Molecular dynamics simulations show how in-plane (density fluctuations) and out-of-plane (undulations) motions are intertwined in the bilayer in the mesoscopic domain. By novel methods, the fluctuation spectra of lipid bilayers can be calculated withdirect Fourier analysis. The interpretation of the fluctuation spectra reveals a picture where density fluctuations and undulations are most pronounced on different length scales, but coalesce in the mesoscopic regime. This analysis has significant consequences for comparison of simulation data to experiments. These new methods merge the molecular fluctuations on small wavelengths, with continuum fluctuations of the elastic membrane sheet on large wavelengths, allowing electron density profiles (EDP) and area per lipid to be extracted from simulations with high accuracy. Molecular dynamics simulations also provide insight on the small-wavelength dynamics of lipid membranes. Rapidly decaying density fluctuations can be described as propagating sound waves in the framework of linearized hydrodynamics, but there is a slow, dispersive, contribution that needs to be described by a stretched exponential over a broad range of length- and time scales - recent experiments suggest that this behavior can prevail even on micrometer length scales. The origin of this behavior is discussed in the context of fluctuations of the bilayer interface and the molecular structure of the bilayer itself. Connections to recent neutron scattering experiments are highlighted. / QC 20111014 / Modelling of biological membranes

This thesis uses surface sensitive tools to characterize the effect of a solid surface on immobilized biomacromolecules. This includes understanding how the surface can change the affinity of these macromolecules to small molecules compared to bulk studies. Two classes of immobilized biomacromolecules, the supported lipid bilayer (SLB) and the Lac repressor protein (LacI), are characterized using microcantilever sensors and quartz crystal microbalance with dissipation (QCM-D). The first part of this thesis reports the use of microcantilever beams, an ultrasensitive sensor for measuring the surface free energy changes on a substrate induced by molecular adsorptions, to probe the interaction between a solid surface and a phospholipid bilayer. This sensing method integrates two well-developed techniques: solid-supported lipid bilayers (SLBs) and the microcantilever (MC) sensors. Studying the adsorption free energy of lipid bilayers on a solid surface allows better characterizing of the formation and stability of SLBs. Microcantilever converts the Gibbs free energy change taking place on its surface into a mechanical deformation. As molecules physisorb or chemisorb onto the surface of the microcantilevers, the microcantilevers bend, either due to induced compressive or tensile stresses, which result from the surface free energy change. By monitoring the deflection values of the microcantilevers, the real-time surface free energy change during the SLB formation can be detected. This thesis has led to the development of a novel biosensor--lipid membrane coated microcantilevers--to detect the adsorption, insertion, aggregation and solubilizing effect of membrane-active substances, such as surfactants and peptides, on the phospholipid membranes. To better characterize the surface free energy, SLBs doped with charged lipids or cholesterol are shown to alter the surface free energy. We can predict this change in surface free energy using a thermodynamic model. Application of this membrane-coated cantilever is put into use for detecting how amphiphilic molecules interact with SLBs, as well as for probing the abrupt conformational change of SLBs during a temperature induced phase-transition. This study systematically demonstrates various usage aspects of microcantilever to characterize the SLBs, and how this technique may advance the biophysical knowledge of the lipid membrane, one of the essential building blocks of life. The second part of this thesis reports the use of both microcantilever sensors and QCM-D to measure the adsorption free energy and mass of a model protein, the Lac repressor (LacI), and compare how a modified T334C mutant that includes a cysteine group to orient the protein on the gold surface through a covalent sulfur bonds retains its binding capabilities over that of wild type LacI. The main challenge of this work is to unravel how the adsorption of biomacromolecules at the solid/liquid interface leads to surface free energy changes and ultimately changes the stress of the underlying solid surface (the cantilever). The uses of microcantilever sensors and QCM to probe the interactions that take place on SLBs and surface-bound proteins have the advantage of being a sensitive, real-time, and label-free technique.

Owing to atomic force microscopy’s (AFM) high-resolution in both imaging and force spectroscopy, it is very successful in probing not only structures, but also nanomechanics of biological samples in solution. In this thesis, the nanomechanical properties of lipid bilayers of biological relevance and proteins of the barnacle adhesive were examined using AFM indentation, AFM-based force mapping, and single-molecule pulling experiments. Through high-resolution AFM-based force mapping, the self-organized structures exhibited in phase-segregated supported lipid bilayers consisting of dioleoylphosphatidylcholine / egg sphingomyelin / cholesterol (DEC) in the absence and presence of ceramide (DEC-Ceramide) were directly correlated with their breakthrough forces, elastic moduli, adhesion, and bilayer thickness. Results were presented as two-dimensional visual maps. The highly stable ceramide-enriched domains in DEC-Ceramide bilayers and the effect of different levels of cholesterol as well as of diblock copolymers, on the nanomechanical stability of the model systems studied were further examined. For the proteins of the barnacle adhesive, scanning electron microscopy (SEM), Fourier transform infrared (FTIR) spectroscopy, and chemical staining with amyloid-selective dyes, in addition to AFM imaging, indentation, and pulling experiments were performed to study the structure and nanomechanics of the polymerized barnacle glue. Nanoscale structures exhibiting rod-shaped, globular, and irregularly shaped morphologies were observed in the bulk barnacle cement by AFM. SEM coupled with energy dispersive x-ray (EDX) makes evident the organic nature of the rod-shaped nanoscale structures while FTIR spectroscopy on the bulk cement gave signatures of β-sheet and random coil conformations. Indentation data yielded higher elastic moduli for the rod-shaped structures as compared to the other structures in the bulk cement. Single molecule AFM force-extension curves on the matrix of the bulk cement often exhibited a periodic sawtooth-like profile, observed in both extend and retract portions of the force curve. Rod-shaped structures stained with amyloid protein-selective dyes (Congo Red and Thioflavin-T) revealed that about 5% of the bulk cement are amyloids.

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.

Owing to atomic force microscopy’s (AFM) high-resolution in both imaging and force spectroscopy, it is very successful in probing not only structures, but also nanomechanics of biological samples in solution. In this thesis, the nanomechanical properties of lipid bilayers of biological relevance and proteins of the barnacle adhesive were examined using AFM indentation, AFM-based force mapping, and single-molecule pulling experiments. Through high-resolution AFM-based force mapping, the self-organized structures exhibited in phase-segregated supported lipid bilayers consisting of dioleoylphosphatidylcholine / egg sphingomyelin / cholesterol (DEC) in the absence and presence of ceramide (DEC-Ceramide) were directly correlated with their breakthrough forces, elastic moduli, adhesion, and bilayer thickness. Results were presented as two-dimensional visual maps. The highly stable ceramide-enriched domains in DEC-Ceramide bilayers and the effect of different levels of cholesterol as well as of diblock copolymers, on the nanomechanical stability of the model systems studied were further examined. For the proteins of the barnacle adhesive, scanning electron microscopy (SEM), Fourier transform infrared (FTIR) spectroscopy, and chemical staining with amyloid-selective dyes, in addition to AFM imaging, indentation, and pulling experiments were performed to study the structure and nanomechanics of the polymerized barnacle glue. Nanoscale structures exhibiting rod-shaped, globular, and irregularly shaped morphologies were observed in the bulk barnacle cement by AFM. SEM coupled with energy dispersive x-ray (EDX) makes evident the organic nature of the rod-shaped nanoscale structures while FTIR spectroscopy on the bulk cement gave signatures of β-sheet and random coil conformations. Indentation data yielded higher elastic moduli for the rod-shaped structures as compared to the other structures in the bulk cement. Single molecule AFM force-extension curves on the matrix of the bulk cement often exhibited a periodic sawtooth-like profile, observed in both extend and retract portions of the force curve. Rod-shaped structures stained with amyloid protein-selective dyes (Congo Red and Thioflavin-T) revealed that about 5% of the bulk cement are amyloids.

We apply a molecular dynamics (MD) simulation technique to complex molecules at interfaces. Partitioning of dendritic surfactants into clay gallery and Ab protein behavior near hydrated lipids are chosen for the purpose. Using a full atomistic model of dendritic surfactants, the confinement force profiles featuring oscillatory fashion at moderate layer separation of 10 to 25 Å were observed. Integration of the confinement forces led to free energy profiles, which, in turn, were used to determine the final morphology of the nanocomposite. From the free energy profiles, smaller and linear surfactants (G1 and G2L) are expected to intercalate into the clay comfortably, while larger surfactants (G2 and G3) are expected to form frustrated intercalated structures due to the location and depth of the free energy minima. This would agree with the previous observations. As primary steps to understand the Ab protein behavior under biological conditions, simulations of bulk water and hydrated lipids were performed and the results were compared with the literature. Hydrated lipids were simulated using a full atomistic model of lipids (dipalmitoylphosphatidylcholine) and water with a cvff force-field and it was found that structural properties such as the molecular head group area and membrane thickness were accurately produced with MD simulation. Systems of the protein Ab(1-42) in bulk water were simulated and some secondary structural change, with loss of part of the a-helical structure, occurred during the 1 ns of simulation time at 323K. The fragment Ab(31-42) with b-sheet conformation was also simulated in bulk water, and the extended b-sheet structure became a bent structure. Simulations of Ab(1- 42) or Ab(31-42) near lipid bilayers have been performed to investigate the structural property changes under biological conditions. The different nature of structural change was observed from the simulations of the protein or fragment in water and near lipid bilayers due to the different solvent environment. The protein has close contacts with the membrane surface. It was impossible to observe the conformational change to b-sheet and protein entrance into the lipid bilayer within 1 ns simulations.

Planar supported, polymerized phospholipid bilayers (PPBs) composed of 1,2-bis[10-(2’,4’-hexadienoyloxy)decanoyl]-sn-glycero-3-phosphocholine (bis-SorbPC or BSPC) were generated by a redox polymerization method. The PPBs were supported by a silicon substrate. The PPBs were characterized and tested for uniformity and stability under physiological conditions. The PPBs were analyzed in vitro with murine derived cells that are pertinent to the host response. Cellular attachment and phenotypic changes in RAW 264.7 macrophages and NIH 3T3 fibroblasts were investigated on PPBs and compared to bare silicon controls. Fluorescent and SEM images were used to observe cellular attachment and changes in cellular behavior. The PPBs showed much lower cellular adhesion for both cell lines than bare silicon controls. Of the cells that attached to the PPBs, a very low percentage showed the same morphological expressions as seen on the controls. The hypothesis generated from this work is that defects in the PPBs mediated the cellular attachment and morphological changes that were observed. Finally, a layer-by-layer (LbL) deposition of a poly(acrylic acid) (PAA) and poly(N-vinylpyrrolidone) (PNVP) alternating bilayer was attempted as a proof of concept for future modification of this system.