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Understanding the mechanisms by which proteins act on membrane surfaces is fundamental if we are to exploit their capabilities or halt the progression of the diseases they are associated with. Arguably, the best way to study these interactions is by using techniques that can obtain molecular-scale information, in real time and under physiologically relevant conditions. Studying supported lipid bilayer systems with high spatial resolution tools, such as atomic force microscopy (AFM), and high temporal resolution techniques, such as polarized total internal reflection fluorescence microscopy (pTIRFM), allows us to meet these requirements [1]. The goal of this project is to use methods that are currently available and further their applications and capabilities to provide insight into the mechanisms by which amyloidogenic and antimicrobial peptides act on membranes.

Understanding the mechanisms by which proteins act on membrane surfaces is fundamental if we are to exploit their capabilities or halt the progression of the diseases they are associated with. Arguably, the best way to study these interactions is by using techniques that can obtain molecular-scale information, in real time and under physiologically relevant conditions. Studying supported lipid bilayer systems with high spatial resolution tools, such as atomic force microscopy (AFM), and high temporal resolution techniques, such as polarized total internal reflection fluorescence microscopy (pTIRFM), allows us to meet these requirements [1]. The goal of this project is to use methods that are currently available and further their applications and capabilities to provide insight into the mechanisms by which amyloidogenic and antimicrobial peptides act on membranes.

Physical forces in the cellular microenvironment play an important role in governing cell function. Forces transmitted through the cell cause distinct deformation of the nucleus, and possibly play a role in force-mediated gene expression. The work presented in this thesis drew upon innovative strategies employing simultaneous atomic force and laser-scanning confocal microscopy, as well as parallel optical stretching experiments, to gain unique insights into the response of eukaryotic cell nuclei to external force. Non-destructive approaches confirmed the existence of a clear anisotropy in nuclear mechanical properties, and showed that the nucleus' mechanical response to extracellular forces is differentially governed by both nuclear and cytoskeletal prestress: nuclear prestress regulates shape and anisotropic deformation, whereas cytoskeletal prestress modulates the magnitude and degree of deformation. Importantly, the anisotropic mechanical response was conserved among diverse differentiated cell types from multiple species, suggesting that nuclear mechanical anisotropy plays an important role in cell function.

The experimental work discussed in this thesis explores the effects of metal modification on the electroanalytical ability of boron doped diamond electrodes. Boron doped diamond (BDD) electrodes have found increased application to electroanalysis in the past two decades, yet relatively little of the literature is focused on metal, nano and microparticle modification of the substrate. In this thesis three metals have been used to modify the BDD electrode; bismuth, antimony and nickel. Bismuth and antimony nanoparticle modified BDD electrodes were directly compared to unmodified BDD and a bulk bismuth electrodes in the determination of trace levels of cadmium and lead using anodic stripping voltammetry. In both instances, the modified electrode allowed for the simultaneous determination of each analyte that was otherwise unattainable at the unmodified BDD electrode. The nickel modified BDD (Ni-BDD) electrode was used in the determination of organic analytes, namely glucose, methanol, ethanol and glycerol. The nickel nano and microparticle electrodes gave the characteristic Ni(OH)₂/NiOOH redox couple in alkali pH, the oxidised form of which (NiOOH) catalysed the oxidation of the organic analytes. The chapter on glucose sensing with the Ni-BDD electrode is preceded by an extensive literature review on the advances of non-enzymatic glucose sensing, and the application of catalytic metals and nanomaterials in this field. Throughout the course of this DPhil, there has been a collaborative project between Asylum Research and myself within the Compton group to develop a commercial electrochemical atomic force microscope (EC-AFM) cell. The aim was to produce an adaptable EC-AFM cell capable of dynamic electrochemical experiments whilst simultaneously or instantaneously acquiring an AFM image of the modified surface, in-situ. This project was successful, and the EC-AFM cell has contributed to a number of chapters in this thesis, and has now been commercialised.

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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.

This work aimed at studying biophysical properties of two membrane proteins, one of potential nanotechnological use, bacteriorhodopsin, and one potential drug target, the NTS1 neurotensin receptor, at the single molecule scale. Bacteriorhodopsin (BR) is the only protein in the purple membrane (PM) of the halophilic organism Halobacterium salinarium. It is a light-driven proton pump converting light into a transmembrane proton gradient through isomerization of its retinal chromophore. Its stability, as well as its photoactivity remaining in dry protein layers, has made BR an attractive material for biomolecular devices. Numerous studies have been published on this topic; however, they have all used BR within the PM, on relatively large (µm-wide) surfaces. Here, conducting-probe atomic force microscopy (C-AFM) analysis was performed after removing most of the membrane lipids. For the first time, it was shown that the molecular conductance of BR can be reversibly photoswitched with predictable wavelength sensitivity. Intimate and robust coupling to gold electrodes was achieved by using a strategically engineered cysteine which, combined with partial delipidation, generated protein trimers homogenously orientated on the surface. Numerous controls using biophysical (SPR, ellipsometry, Kelvin-probe AFM) and chemical (photocurrent, cyclic voltammetry) techniques confirmed the wavelength specificity of the photoswitch, the anchoring role of the mutation and the homogenous orientation of the protein on the gold surface. Neurotensin is a brain and gastrointestinal 13 amino acid peptide acting as a neuromodulator in the central nervous system and as a hormone in the periphery. Its wide range of biological activities is primarily mediated through its binding to the neurotensin type 1 receptor (NTS1). NTS1 expressed in E.coli was purified and inserted into 100 nm brain polar lipid liposomes in a conformation which retained its ligand-binding capabilities. Initial AFM characterisation was performed as a prelude for ligand-receptor interaction studies, including high resolution imaging, force spectroscopy and solid state NMR approaches.

<p>Proteins are specialized molecules that catalyze most of the reactions that can sustain life, and they become functional by folding into a specific 3D structure. Despite their importance, the question, "how do proteins fold?" - first pondered in in the 1930's - is still listed as one of the top unanswered scientific questions as of 2005, according to the journal Science. Answering this question would provide a foundation for understanding protein function and would enable improved drug targeting, efficient biofuel production, and stronger biomaterials. Much of what we currently know about protein folding comes from studies on small, single-domain proteins, which may be quite different from the folding of large, multidomain proteins that predominate the proteomes of all organisms.</p><p>In this thesis I will discuss my work to fill this gap in understanding by studying the unfolding and refolding of large, multidomain proteins using the powerful combination of single-molecule force-spectroscopy experiments and molecular dynamic simulations.</p><p>The three model proteins studied - Luciferase, Protein S, and Streptavidin - lend insight into the inter-domain dependence for unfolding and the subdomain stabilization of binding ligands, and ultimately provide new insight into atomistic details of the intermediate states along the folding pathway.</p> / Dissertation