The processes localized to biological membranes are of great interest, both from a scientific and pharmaceutical point of view. Understanding aspects such as the detailed mechanism and regulation of these processes requires investigation of the structure and function of the membrane-bound proteins in which they take place. The study of these processes is often complicated by the need to create in vitro systems that mimic the environment in which these proteins are normally found in vivo. This thesis describes some of the methods available for membrane-protein studies in membrane-mimetic systems, as well as our work aimed at developing such systems. Furthermore, results from studies using these systems are described. In the first two studies, described in Papers I &amp; II, we investigated the use of silica particle-supported lipid bilayers, both for membrane-protein studies and as possible drug-delivery vehicles. Successful reconstitution of a multisubunit proton-pump, cytochrome c oxidase is described and characterized. Initial attempts to develop drug-delivery systems with two different targeting peptides are also described in the thesis. The second part of this thesis revolves around our work with membraneprotein dependent pathways. Results from studies of systems where the proton- pump bo3 oxidase and ATP synthase work in concert are described. The results show a surprising lipid-composition dependence for the coupled bo3- ATP-synthase activity (Paper III). Finally, a new system utilizing synaptic vesicle-fusion proteins for coreconstitution of membrane proteins is described, showing successful coreconstitution of a small respiratory chain, delivery of soluble proteins to preformed liposomes and reconstitution of ATP synthase in native membranes (Paper IV). / <p>At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 3: Manuscript. Paper 4: Manuscript.</p>

High–resolution multidimensional proton-detected NMR was used to study the solvent-exposed regions of a seven-helical integral membrane proton pump proteorhodopsin (PR). Fully deuterated PR samples with protons reintroduced to solvent-accessible sites through back exchange were prepared and found to produce NMR spectra with acceptable proton resolution (~0.2 ppm). Novel three-dimensional proton-detected chemical shift correlation spectroscopy was used for the identification and resonance assignment of the solvent–exposed regions of PR. Though most of the observed residues were located at the membrane interface there were notable exceptions, particularly in helix G. This helix contains the Schiff base-forming Lys231 and many conserved polar residues in the extracellular half. Solvent accessibility of helix G supports the hypothesis that high mobility of the F-G loop could transiently expose a hydrophilic cavity in the extracellular half of PR, and implies that such a cavity may be part of the protein’s proton-conduction pathway. / Natural Sciences and Engineering Research Council, Ontario Ministry of Training, Colleges, and Universities, Canadian Foundation for Innovation, Ontario Ministry of Research and Innovation, University of Guelph

Diacylglycerol acyltransferase (DGAT), an integral membrane protein of the endoplasmic reticulum, catalyses the final step in the sn-glycerol-3-phosphate pathway leading to triacylglycerol. Although DGAT has been cloned from a variety of species, including the major oilseed crop of Canada, canola (Brassica napus), little is known about the structure/function of the enzyme. BnDGAT1 is the major isoform of type I DGAT (DGAT-I) in microspore-derived cell suspension cultures of B. napus L. cv Jet Neuf, with the possible existence of a truncated form of BnDGAT1 known as BnDGAT2. In order to gain some insight into the topology of the enzyme, type I DGAT from B. napus was investigated using two approaches: (1) in vitro translation in the presence of microsomes and (2) immunochemical analyses of microsomes isolated from cell suspension cultures, both in combination with proteolytic mapping. Difficulties were encountered with the in vitro translation approach, possibly due to proper incorporation of the polypeptide into microsomal vesicles. Two cytocolic regions were identified in BnDGAT1, and one cytosolic region in putative BnDGAT2, using the immunochemical approach, thus providing some insight into the topology of B. napus DGAT-I. The results here support and nine and eight membrane-spanning topology for BnDGAT1 and BnGAT2, respectively. / xvii, 194 leaves ; 29 cm.

The ability to evade apoptosis is an acquired characteristic associated with many normal and pathophysiological processes. TMEM 85 represents a novel transmembrane domain containing human protein isolated in our previous screen for Bax suppressors, but whose function is currently unknown. Using viability and growth assays, we confirmed that TMEM 85 is anti-apoptotic. Four unique human cDNA sequences containing regions distinct from and of perfect identity to our cDNA were present in the database. Analysis of TMEM 85 suggests that it consists of five exons, alternatively spliced to produce at least four different mRNA's and proteins (TMEM 85v1-v4). RT-PCR analysis using RNA isolated from mice and humane tissues show that all transcripts are expressed. Yeast contain an orthologue of the human TMEM 85v1 protein, YGL213C. Surprisingly, the viability assay indicated that mutants lacking YGL231c do not show a hyper-responsive apoptotic phenotype, however its overexpression shows that it is nevertheless anti-apoptotic. Using a yeast strain expressing chromosomally TAP-tagged YGL231c, we found no up-regulation of the endogenous gene due to stress. The deletion mutant is also known to expresses a synthetically lethal phenotype in the presence of alpha-synuclein. While expression of alpha-synuclein caused significant death in both the wild type and deletion mutants, TMEM 85v2 was unable to exhibit a protective role. These findings demonstrate the complexity of the TMEM 85 gene and its anti-apoptotic function in both yeast and human.

The World Health Organization has identified antimicrobial resistance as one of the top three threats to human health. Gram-negative bacteria such as Escherichia coli are intrinsically more resistant to antimicrobials. There are very few drugs either on the market or in the pharmaceutical pipeline targeting Gram-negative pathogens. Two mechanisms, the protection of the outer membrane and the active efflux by the multidrug transporters, play important roles in conferring multidrug resistance to Gram-negative bacteria. My work focuses on two main directions, each aligning with one of the known multidrug resistance mechanisms. The first direction of my research is in the area of the biogenesis of the bacterial outer membrane. The outer membrane serves as a permeability barrier in Gram-negative bacteria. Antibiotics cross the membrane barrier mainly via diffusion into the lipid bilayer or channels formed by outer membrane proteins. Therefore, bacterial drug resistance is closely correlated with the integrity of the outer membrane, which depends on the correct folding of the outer membrane proteins. The folding of the outer membrane proteins has been studied extensively in dilute buffer solution. However, the cell periplasm, where the folding actually occurs, is a crowded environment. In Chapter 2, effects of the macromolecular crowding on the folding mechanisms of two bacterial outer membrane proteins (OmpA and OmpT) were examined. Our results suggested that the periplasmic domain of OmpA improved the efficiency of the OmpA maturation under the crowding condition, while refolding of OmpT was barely affected by the crowding. The second direction of my research focuses on the major multidrug efflux transporter in Gram-negative bacteria, AcrB. AcrB is an obligate trimer, which exists and functions exclusively in a trimeric state. In Chapter 3, the unfolding of the AcrB trimer was investigated. Our results revealed that sodium dodecyl sulfate induced unfolding of the trimeric AcrB started with a local structural rearrangement. While the refolding of secondary structure in individual monomers could be achieved, the re-association of the trimer might be the limiting factor to obtain folded wild type AcrB. In Chapter 4, the correlation between the AcrB trimer stability and the transporter activity was studied. A non-linear correlation was observed, in which the threshold trimer stability was required to maintain the efflux activity. Finally, in Chapter 5, the stability of another inner membrane protein, AqpZ, was studied. AqpZ was remarkably stable. Several molecular engineering approaches were tested to improve the thermal stability of the protein.

Membrane proteins are essential cellular components, responsible for a wide variety of biological functions. In order to better understand such aspects of cell activity, researchers have pursued detailed structural analysis of this class of proteins. Because of the complexities in isolating and studying membrane proteins in their native environment, detergents are often employed as a membrane mimetic media. This thesis examines several features of transmembrane (TM) protein structure and folding in detergents through which we are able to gain insights into membrane protein folding, as well as explore the suitability of detergents as membrane-mimetic environments. We first compare the helix-helix association of a series of model TM sequences in a native bilayer to the corresponding association in a detergent environment. We find that while various classes of helix-helix interaction motifs are preserved in detergents, alterations in detergent solvation may, in turn, lead to altered association affinity. We further explore this phenomenon through investigation of the consequences of the insertion of a strongly polar residue into a TM segment. In these studies we find a correlation between sequence-dependent alterations in detergent solvation and predicted in vivo folding. We also extend such analyses to a variety of detergents and native TM segments, finding that native secondary structure, as it occurs in the context of a full-length protein, is generally well preserved in a variety of detergents. Finally, we assess the determinants of membrane protein folding using two-transmembrane segment constructs, in the process optimizing expression, production and characterization techniques for a diverse range of transmembrane protein sequences. Overall this thesis finds that, detergents are capable of solubilizing membrane proteins in a form suitable for in-depth structural characterization that may not be feasible in other environments. Thus, as an approximation of a native membrane, detergents are able to preserve certain features of membrane proteins such as helix-helix association and native secondary structure.

Membrane proteins are essential cellular components, responsible for a wide variety of biological functions. In order to better understand such aspects of cell activity, researchers have pursued detailed structural analysis of this class of proteins. Because of the complexities in isolating and studying membrane proteins in their native environment, detergents are often employed as a membrane mimetic media. This thesis examines several features of transmembrane (TM) protein structure and folding in detergents through which we are able to gain insights into membrane protein folding, as well as explore the suitability of detergents as membrane-mimetic environments. We first compare the helix-helix association of a series of model TM sequences in a native bilayer to the corresponding association in a detergent environment. We find that while various classes of helix-helix interaction motifs are preserved in detergents, alterations in detergent solvation may, in turn, lead to altered association affinity. We further explore this phenomenon through investigation of the consequences of the insertion of a strongly polar residue into a TM segment. In these studies we find a correlation between sequence-dependent alterations in detergent solvation and predicted in vivo folding. We also extend such analyses to a variety of detergents and native TM segments, finding that native secondary structure, as it occurs in the context of a full-length protein, is generally well preserved in a variety of detergents. Finally, we assess the determinants of membrane protein folding using two-transmembrane segment constructs, in the process optimizing expression, production and characterization techniques for a diverse range of transmembrane protein sequences. Overall this thesis finds that, detergents are capable of solubilizing membrane proteins in a form suitable for in-depth structural characterization that may not be feasible in other environments. Thus, as an approximation of a native membrane, detergents are able to preserve certain features of membrane proteins such as helix-helix association and native secondary structure.

The topology and dynamics of biomolecules are intricately linked with their biological function. The focus of this thesis is the NMR-based measurement of topology and dynamics in biomolecular systems, and methods of measuring immersion depth and orientation of membrane-associated molecules. In detergent micelles and lipid bilayers, the local concentrations of hydrophobic and hydrophilic molecules are a function of their bilayer immersion depth. For paramagnetic molecular oxygen or metal cations, the magnitudes of the associated paramagnetic isotropic contact shifts and relaxation rate enhancements (PREs) are therefore depth-dependent. NMR measurements of these effects reveal the immersion depth of bilayer- or detergent-associated molecules. This work first explores transbilayer oxygen solubility and thermodynamics, as measured from contact shifts and PREs of the constituent lipid molecules in the presence of 30 bar oxygen. Contact shifts revealed the transmembrane O2 solubility profile spans a factor of seven across the bilayer, while PREs indicated that oxygen partitioning into bilayers and dodecylphosphocholine (DPC) micelles is entropically driven. Next, this work describes how paramagnetic effects from molecular oxygen and Ni(II) cations may be employed to study the immersion depth and topology of drug and protein molecules in DPC micelles. In one study, the positioning of the amphipathic drug imipramine in micelles was determined from O2- and Ni(II)-induced contact shifts. A second study, relying solely on O2-induced PREs, determined the tilt angles and micelle immersion depths of the two alpha helices in a monomeric mutant of the membrane protein phospholamban. A third study utilized 19F NMR to explore the importance of juxtamembraneous tryptophans on the topology of the membrane protein synaptobrevin, via O2-induced contact shifts and solvent-induced isotope shifts of a juxtamembraneous 19F-phenylalanine. Comparison of synaptobrevin constructs with zero, one, and two juxtamembraneous tryptophans revealed that while one tryptophan is sufficient to ‘anchor’ the protein in micelle, the addition of a second tryptophan dampens local dynamics. These solution state NMR studies demonstrate how paramagnetic effects from dissolved oxygen, complemented with measurements of local water exposure, provide detailed, accurate descriptions of membrane immersion depth and topology. These techniques are readily extended to the study of a wide range of biomolecules.

The pathogen Vibrio cholerae uses cations as a primary currency of virulence and environmental persistence, using gradients of those cations to move, acquire nutrients, and control virulence gene expression. An understanding of the overlapping roles of bioenergetics and chemotaxis in the virulence and environmental survival of V. cholerae issues from a large body of prior work, but the interplay of each component is not yet clearly understood. To this end, the activity of the antiporters Vc-NhaP1, Vc-NhaA, and Vc-NhaB was assayed, as was the sodium transporting respiratory pump NQR, and environmental stimuli were paired with potential motilitylinked sensors. The Vc-NhaP1 antiporter was found to be a K⁺(Na⁺)/H⁺ antiporter essential for V. cholerae growth at low environmental pH. Deletion of the V. cholerae nhaP1 gene caused growth inhibition when external potassium was either limited (100 mM and below) or in excess (400 mM and above). This growth defect was most apparent at mid-logarithmic phase, after 4-6 hours of culturing. Using a pH-sensitive GFP protein, cytosolic pH was shown to be dependent on K⁺ in acidic external conditions in a Vc-NhaP1-dependent manner. When functionally expressed in an antiporterless E. coli strain and assayed in everted membrane vesicles, Vc-NhaP1 operated as an electroneutral alkali cation/proton antiporter, exchanging K⁺ or Na⁺ ions for protons within a broad pH range (7.25 to 9.0). These data establish the putative V. cholerae NhaP1 protein as a functional K⁺(Na⁺)/H⁺ antiporter of the CPA- 1 family that is required for bacterial pH homeostasis and growth in an acidic environment. Further, a model system comprised of a V. cholerae strain lacking both the nqr operon and the ORFs of Vc-nhaA or Vc-nhaB was generated and tested with and without lactate. These strains, along with the single mutants of nqr, Vc-nhaA, and Vc-nhaB, were assessed for aerobic growth as a function of media pH and cation concentration (Na⁺, Li⁺, or K⁺). Loss of Vc-NhaA and, to a lesser extent, Vc-NhaB, was better observed when NQR was absent but lactate was added to facilitate replenishment of the quinone pool. Loss of Vc-NhaA in this background inhibited growth most at basic pH under increasing Na⁺ and Li⁺ conditions, and loss of Vc- NhaB in this background inhibited was most severe in acidic conditions in the presence of 0-100 mM Na⁺ or Li⁺. We also observed the growth inhibition of Vc- NhaA in the absence of NQR and in the presence of lactate and 100-450 mM Li⁺, which has not been previously reported. These growth defects were restored upon expression of the cognate antiporter gene on an inducible expression vector. Lastly, potential chemotaxis stimuli were correlated with cognate methyl-accepting chemotaxis protein (MCP) receptors. The homology of MCP sensory domains among Vibrionaceae demonstrated a subset were unique to V. cholerae. Of these unique MCPs, transposon insertion in VC0098 significantly reduced chemotaxis swarm diameter towards Na⁺ and K⁺. Additionally, the MCP VCA0663 was shown, by transposon mutagenesis and complementation, to direct chemotaxis towards N-acetylglucosamine. Additional observations are described concerning the chemotaxis defects incurred by transposon mutagenesis of MCPs in vitro towards mucin, bile, or L-serine. MCP strains were also tested in vivo for 4 and 24 hours in the infant mouse model of infection. None of the observed chemotaxis defects showed complete loss of chemotaxis by transposon mutagenesis, in line with the hypothesis that the large number of MCPs encoded by V. cholerae result in redundant chemotaxis sensory functions. These findings add to the understanding of how bioenergetics and chemotaxis interact within V. cholerae, a foundation from which the bacterium can be understood and, eventually, controlled. / Graduation date: 2012

Errata is tipped in behind bibliography. / Bibliography: leaves 191-215. / xiv, 216, [29] leaves, [81] leaves of plates : ill. (some col.) ; 30 cm. / Title page, contents and abstract only. The complete thesis in print form is available from the University Library. / Reports the partial cloning and characterisation of the human uroplakin 1B gene which has allowed analysis and characterisation of the gene with regard to its structure, chromosomal localisation and integrity. / Thesis (Ph.D.)--University of Adelaide, Dept. of Surgery, 1999?