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(2022)ThesisThe in-depth characterisation of protein–small molecule complexes is of paramount importance to both drug discovery and fundamental molecular biology. Understanding the structural and thermodynamic properties of such biomolecular assemblies can enable the rational development of new therapeutics, assist in the elucidation of protein function, or provide insights into the molecular mechanisms through which biological activity is regulated. Native mass spectrometry (MS) has emerged as a powerful tool for the investigation of protein–small molecule interactions within heterogenous biomolecular systems. Using native MS, numerous protein–small molecule complexes can be resolved in a single mass spectrum, allowing for the quantitative characterisation of multiple ligand binding events. This is in stark contrast to most established biophysical techniques, which are typically unable to characterise multiple protein–ligand interactions simultaneously. This thesis aims to explore proven applications of native MS in the study of protein–small molecule interactions, and to identify novel methods that facilitate the investigation of complex biochemical systems using such approaches. Chapter 1 provides a comprehensive review of the relevant literature, exploring the critical developments in MS instrumentation and methodologies that have enabled the high-resolution characterisation of protein–ligand complexes. Through a critical analysis of past investigations, the review outlines major challenges facing the field and suggests potential approaches for addressing many of these issues. The second chapter of this thesis outlines a novel native MS-based method for the direct identification of protein–ligand complexes formed from natural extracts containing more than 5,000 potential small-molecule binders. Using this approach, several novel ligands of a key human drug target are identified. Improvements in method efficiency are subsequently made to ensure that the approach could be employed for large-scale pharmaceutical screening campaigns or used for the elucidation of novel interactions between protein complexes and endogenous metabolites. Finally, chapter three aims to identify novel chemical additives that can reduce the charge of protein–ligand complexes in native MS. Charge-reducing agents for positive-mode native MS have been previously shown to facilitate accurate quantitative analysis of protein–small molecule interactions, by increasing the kinetic stability of the gas-phase ions. In this chapter the author explores the properties of several chemical agents that reduce the charge of anionic protein complexes. The effect of these agents on the charge state of various model proteins is characterised to critically evaluate their analytical utility. Furthermore, their effect on the gas-phase stability of a labile protein–ligand complex is also explored. Such agents may prove useful in the quantification of weak interactions that cannot be accurately characterised using standard native MS-based approaches.
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(2022)ThesisWastewater processing conditions in manufacturing environments often involve the three key factors for optimum bacterial growth - water, ideal temperature, and a constant food source. Bacteria are problematic because they can reduce product yield by consuming product and metabolise it into organic acids which lower the process pH, requiring large amounts of chemicals to control. At a casestudy wastewater treatment plant, a site-wide analysis of the impacts of chemical sanitation methods had not been conducted and the efficacy of these chemicals had not been established. To understand the impacts of current sanitation practices, standard microbiological plating techniques combined with HPLC testing to measure lactic acid as a proxy for microbial activity were used. Nitrogensource determination and solids analysis were used extensively to provide a comprehensive picture of the stream properties throughout the plant. I show that current microbial control methods are ineffective for significantly limiting microbial growth in the water treatment plant. The most important factors impacting this are the concentration of nitrogen-sources followed by total organic solids at chemical dosing sites, which react more rapidly with oxidative sanitisers than bacteria do. These findings indicate that chemical sanitisers would be more effective if dosed in locations with minimal concentrations of nitrogen-sources and organic solids. In practice, this is difficult to achieve in an existing plant without significant capital expenditure and so investigation of alternative, nonchemical methods of sanitation in combination with more effective use of chemical methods is recommended.
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(2023)ThesisThe requirement for greener, safer, and non-hazardous components in formulations including inkjet ink is one driving factor for the need to continually improve formulations. From a consumer’s perspective, the other is the demand for better print quality. As such generating knowledge surrounding component interactions and their influence on stability, ink-printhead and ink-media is key to advancing ink formulation for a specified printhead. One of the important formulant components that can be substituted is the primary surfactant. Currently, the Surfynol® series of surfactants are known to work well in ink formulations for use with thermal inkjet printheads. However, there is risk that they become obsolete, or their use is restricted. Several alternative surfactants with similar hydrophilic lipophilic balance values have been chosen to evaluate their suitability as alternatives. The baseline surfactant along with alternative surfactants have been investigated by determining their critical micelle concentration and surface-active properties in water. Their interaction with an acrylic polymer was studied via dynamic surface tension, using methods from literature and then via dynamic light scattering and nuclear magnetic resonance. These techniques confirmed the interaction and formation of larger surfactant-polymer complexes. They may associate through hydrogen bonds from the alcohol group in the surfactant head portion with alcohol groups on the acrylic polymer and hydrophobic interactions of methyl and ethyl groups. The degree of interaction in the bulk was found to decrease with increasing ethoxylation units for surfactants in the same family and were enhanced by cosolvents. Polymer saturation with surfactants was identified to be a slow process. Low solubility surfactants caused swelling or contraction of polymer chains, with visible aggregation precipitates. Soluble surfactants formed worm like micelles to continually increase polymer-surfactant complex size. Of the investigated alternative surfactants, one promising alternative was identified to meet the requirements for which it is intended to replace. The print quality and physical properties of the identified surfactant in black formulation was shown to be promising and comparable to the baseline formulation. Further component optimisation of the alternative surfactant formulation can result in the development of a commercially viable printing ink.