The appropriate lipid environment is crucial for the proper function of membrane proteins. There is a tremendous variety of lipid molecules in the membrane and so far it is often unclear which component of the lipid matrix is essential for the function of a respective protein. Lipid molecules and proteins mutually influence each other; parameters such as acyl chain order, membrane thickness, membrane elasticity, permeability, lipid-domain and annulus formation are strongly modulated by proteins. More recent data also indicates that the influence of proteins goes beyond a single annulus of next-neighbor boundary lipids. Therefore, a mesoscopic approach to membrane lipid-protein interactions in terms of elastic membrane deformations has been developed. Solid-state NMR has greatly contributed to the understanding of lipid-protein interactions and the modern view of biological membranes. Methods that detect the influence of proteins on the membrane as well as direct lipid-protein interactions have been developed and are reviewed here. Examples for solid-state NMR studies on the interaction of Ras proteins, the antimicrobial peptide protegrin-1, the G protein-coupled receptor rhodopsin, and the K+ channel KcsA are discussed.

Nuclear magnetic resonance (NMR) spectroscopy was used to determine the structure of transmembrane (TM) segment IX of the Na+/H+ exchanger isoform 1 (NHE1) in dodecylphosphocholine micelles. Studying isolated TM segments in this fashion constitutes a well-established "divide and conquer" approach to the study of membrane proteins, which are often extremely difficult to produce, purify, and reconstitute in full-length polytopic form. A similar approach was combined with NMR spin relaxation experiments to determine the peptide backbone flexibility of NHE1 TM VII. The combined NMR structural and dynamics studies are consistent with an important role for TM segment flexibility in the function of NHE1, a protein involved in apoptosis and myocardial disease. The study of the rhomboid protease system is also described from two perspectives: 1) I attempted to produce several TM constructs of the substrate spitz or a related construct and the production and purification are described in detail; and 2) I present coarse-grained molecular dynamics simulation results for the E. coli rhomboid ecGlpG and a spitz TM construct. Spitz appears to preferentially associate with rhomboid near TMs 1 and 3 rather than the proposed substrate gate at TM 5. The two proteins primarily interact at the termini of helices rather than within the hydrocarbon core of the bilayer. Finally, I present a detailed analysis of coarse-grained molecular dynamics simulations of the fibroblast growth factor receptor 3 TM domain dimerization. Specifically, algorithms are described for analyzing critical features of wild-type and G380R mutant constructs. The G380R mutation is the cause of achondroplasia, the most common form of human dwarfism. The results suggest that the proximity of a residue to the dimer interface may impact the severity of the mutant phenotype. Strikingly, heterodimer and mutant homodimer constructs exhibit a secondary dimer interface which may explain the increased signaling activity previously reported for the G380R mutation--the helices may rotate with the introduction of G380R. The unifying theme of this work is the 'study of membrane proteins' using complementary techniques from structural biology and computational biochemistry.

In this thesis the synthesis and full characterization of a new bulky diphosphine, tetrakis-(2,6-diisopropylphenyl)diphosphine, are described. This compound displays facile oxidation and a thorough investigation of its redox properties has been studied by combining solution electrochemical techniques such as cyclic voltammetry (CV) and rotating disk electrode (RDE) voltammetry, with spectroscopic methods such as electron paramagnetic resonance (EPR) and Simultaneous Electrochemical Electron Paramagnetic Resonance (SEEPR) spectroscopy over a wide temperature range. Density functional theory (DFT) calculations were carried out to aid in structural characterization of the radical cation that is produced and to provide computed hyperfine splitting (HFS) constants for comparison with experimental results. For comparison to this species with bulky aromatic substituents, similar studies were conducted that have identified the previously unreported radical cation of tetrakis-tert-butyldiphosphine with a bulky aliphatic substituent that provides even higher steric pressure than the 2,6-diisopropylphenyl group. DFT calculations are reported, as is full characterization with fluid and frozen-solution EPR spectroscopy. Further CV and EPR (SEEPR) studies are reported that led to the identification of radical cations of tris(2,6-diisopropylphenyl)arsine and bis(2,4,6-triisopropylphenyl)(2,6-diisopropylphenyl)phosphine. DFT calculations are reported, as is full characterization with fluid and frozen-solution EPR spectroscopy. / xix, 172 leaves : ill (some col.) ; 29 cm

Thesis (Ph.D. (Chemistry)) - Rhodes University, 2008.

Thesis (Ph.D.) -- University of Western Sydney, 2008. / A thesis submitted to the University of Western Sydney, College of Health and Science, School of Natural Sciences, in fulfilment of the requirements for the degree of Doctor of Philosophy. Includes bibliographical references.

Thesis (M.Sc.). / Written for the Dept. of Chemistry. Title from title page of PDF (viewed 2009/06/23). Includes bibliographical references.

Thesis (Ph. D.)--Ohio State University, 2006. / Title from first page of PDF file. Includes bibliographical references (p. 355-382).

Thesis (Msc Food Sc (Food Science))--University of Stellenbosch, 2005. / Near infrared (NIR) spectroscopy prediction models were developed for the rapid determination of the peroxide value, free fatty acid content, specific extinction coefficients at 232 and 270 nm, thiobarbituric acid reactive substances value, pigment, total polyphenol, oleic acid, linoleic acid and saturated fatty acid contents ...

Pseudomonas aeruginosa is a metabolically versatile environmental bacterium that grows in extremely diverse habitats—from sea water to jet fuel—and is able to infect a large variety of organisms. It is a significant cause of human disease and is one of the most frequent healthcare-associated infections. P. aeruginosa uses a sophisticated gene regulatory network to adapt its growth strategy to these diverse environmental niches and the fluctuating conditions it encounters therein. The las and rhl “quorum sensing” (QS) intercellular communication systems play integral roles in this regulatory network and control the expression of factors important to the bacterium’s ecological fitness, including many secreted factors involved in nutrient acquisition, microbial competition, and virulence. These QS systems use diffusible acyl-homoserine lactone (AHL) signalling molecules to infer environmental parameters, including bacterial population density, and to coordinate behaviour across bacterial communities. This dissertation describes an investigation into the relationship between QS and small molecule primary metabolism, using metabolomic methods based on nuclear magnetic resonance spectroscopy and mass spectrometry. Analysis of extracellular metabolic profiles (the bacteria’s “metabolic footprint”) established that QS can modulate the uptake and excretion of primary metabolites and that this effect was strongest during the transition from exponential to stationary phase cell growth. Analysis of the cellular metabolome and proteome demonstrated that QS affected most major branches of primary metabolism, notably central carbon metabolism, amino acid metabolism and fatty acid metabolism. These data indicate that QS repressed acetogenesis and the oxidative C02-evolving portion of the TCA cycle, while inducing the glyoxylate bypass and arginine fermentation. QS also induced changes to fatty acid pools associated with lower membrane fluidity and higher chemical stability. Elevated levels of stress-associated polyamines were detected in QS mutants, which may be a consequence of a lack of QS-dependent adaptations. These findings suggest that wild-type QS directs metabolic adaptations to stationary phase stressors, including oxidative stress. Previous work, including several transcriptomic studies, has suggested that QS can play a role in primary metabolism. However, there has been no previous study of the global impact of AHL QS on the metabolome of P. aeruginosa. Research presented here demonstrates that QS induces a global readjustment in the primary metabolism and provides insight into QS- dependent metabolic changes during stationary-phase adaptation.

Abstract The rare-earth elements (REEs) and bismuth, being classified as the ‘most critical raw materials’ (European Raw Materials Initiatives, 2017), have a high economic importance to the EU combined with a high relative supply risk. REEs are highly important for the evolving technologies such as clean-energy applications, high-technology components, rechargeable batteries, permanent magnets, electric and hybrid vehicles, and phosphors monitors. This scientific research work aims at building a fundamental knowledge base concerning the electronic/molecular structure and properties of rare-earth element (REE) and bismuth complexes with dithiocarbamate (DTC) and 1,10-phenanthroline (PHEN) by employing state-of-the-art experimental techniques such as nuclear magnetic resonance (NMR) spectroscopy and X-ray diffraction (XRD) techniques together with ab initio quantum mechanical computational methods. This combination of methods has played a vital role in analysing the direct and significant effect of the heavy metal ions on the structural and magnetic resonance properties of the complexes, thereby, providing a framework of structure elucidation. This is of special importance for REEs, which are known to exhibit similar chemical and physical properties. The objectives of the work involve i) a systematic investigation of series of REE(III) as well as bismuth(III) complexes to get a profound understanding of the structure-properties relationship and ii) to find an appropriate theoretical modelling and NMR calculation methods, especially, for heavy metal systems in molecular and/or solid-state. This information can later be used in surface interaction studies of REE/bismuth minerals with DTC as well as in design and development of novel ligands for extraction/separation of metal ions. The REE(III) and bismuth(III) complexes with DTC and PHEN ligands have all provided a unique NMR fingerprint of the metal centre both in liquid and solid phase. The solid-state ¹³C and ¹⁵N NMR spectra of the diamagnetic REE(III) and bismuth(III) complexes were in accord with their structural data obtained by single crystal XRD. The density functional theory (DFT) methods were used to get complementary and refined structural and NMR parameters information for all diamagnetic complexes in the solid-state. The relativistic contributions due to scalar and spin-orbit correlations for the calculated ¹H/¹³C/¹⁵N chemical shifts of REE complexes were analysed using two-component zeroth-order regular approximation (ZORA)/DFT while the ‘crystal-lattice’ effects on the NMR parameters were calculated by combining DFT calculations on molecular and periodic solid-state models. The paramagnetic REE complexes display huge differences in their ¹H and ¹³C NMR spectral patterns. The experimental paramagnetic NMR (pNMR) chemical shifts, as well as the sizable difference of the ¹H and ¹³C NMR shifts for these isoelectronic complexes, are well reproduced by the advanced calculations using ab initio/DFT approach. The accuracy of this approach is very promising for further applications to demanding pNMR problems involving paramagnetic f-block elements. The results presented in this thesis demonstrate that a multidisciplinary approach of combined experimental NMR and XRD techniques along with computational modelling and property calculations is highly efficient in studying molecular complexes and solids containing heavy metal systems, such as rare-earths and bismuth.