This work focuses on the effects of formulation and manufacturing as it effects protein structure and physical stability. Using common physical characterization techniques, X-ray photoelectron spectroscopy, and solid-state hydrogen/deuterium exchange with mass spectrometry, correlations are identified between these results and accelerated stability studies.

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Chloride channel family has been shown to play a significant role in physiological homeostasis processes. The function mechanism of these proteins has not yet been clearly understood. Their deficiency or mutation causes serious human illnesses. Our understanding of the chloride channels' transporting mechanisms can lead to better treatment of these illnesses. As mammalian chloride channels are difficult to prepare in laboratory, the experiments are usually done on homologous chloride channels from prokaryotic organisms. The structures of prokaryotic chloride channels have been solved and moreover they are produced with high yields. Most experiments currently use protein crystallography and provide a static picture of the system. This thesis is focused on the study of structural changes of an E. coli chloride channel using hydrogen/deuterium exchange. This method enables us to monitor dynamic conformation changes dependent on pH and exchanged ions. The measurements were done for the protonated (pH 4.5) and deprotonated state (pH 7.5) and/or in the presence of various anions: Cl− , SCN− , I− , F− , TAR. (tartaric anion). The obtained results justified the theories explaining the function of chloride channel as Cl− /H+ antiporter and provided new findings. Subject words biochemistry, protein...

<div><div><div><p>To prolong their long-term stability, protein molecules are commonly dispensed as lyophilized powders to be reconstituted before use. Evaluating the stability of these biomolecules in the solid state is routinely done by using various analytical techniques such as glass transition temperature, residual moisture content and other spectroscopic techniques. However, these techniques often show poor correlation with long term storage stability studies. As a result, time intensive long term storage stability studies are still the golden standard for evaluating protein formulations in the solid state. Over the past few years, our lab has developed solid-state hydrogen deuterium exchange- mass spectrometry (ssHDX-MS) as an analytical tool that probes the backbone of a protein molecule in the solid state. ssHDX-MS gives a snapshot of protein-matrix interactions in the solid state and has a quick turnaround of a few weeks as opposed to a few months for accelerated stability testing. Additionally, various studies in the past have demonstrated that ssHDX-MS can be used for a wide range of biomolecules and shows strong correlation to long term stability studies routinely employed.</p><p>The main aim of this dissertation is to provide an initial understanding of the mechanism behind ssHDX-MS in structured protein formulations. Specifically, this dissertation is an attempt at studying the effects of various experimental variables on the ssHDX-MS of myoglobin formulations as well as demonstrating the utility of this analytical technique. Firstly, the effects of varying temperature and relative humidity on ssHDX-MS of myoglobin formulations is studied with the help of statistical modeling. Secondly, the effects of pressure on ssHDX-MS of myoglobin formulations are evaluated at an intact and peptide digest levels. Finally, ssHDX-MS is used as a characterization tool to evaluate the effects of two different lyophilization methods on the structure and stability of myoglobin formulations. The results of studies described in this dissertation show ssHDX-MS to be sensitive to changes in experimental parameters, namely temperature, relative humidity, pressure, and excipients. Additionally, ssHDX-MS results were in good agreement with other routinely employed analytical and stability testing techniques when used to compare the effects of two lyophilization methods on myoglobin formulations.</p></div></div></div>

<div>Proteins are susceptible to physical and chemical degradation in solution, which can lead to the loss of therapeutic activity and increase the potential for immunogenic responses when administered. Many degradation reactions are mediated by water, and therefore the proteins are often formulated as solids in which degradation rates are slowed significantly. Lyophilization is the most common method for producing solid protein formulations, which removes the water by sublimation and desorption under vacuum from the frozen protein solutions. Lyophilization requires excipients to protect the protein from the inherent stresses involved in the process. Degradation can still occur during lyophilization and storage, and needs to be characterized in order to develop a successful formulation with desired storage stability. The analytical techniques to characterize solid-state proteins are limited, however, and many do not provide site-specific information and lack the ability to predict stability beforehand.</div><div>Recently, solid-state hydrogen-deuterium exchange mass spectrometry (ssHDX-MS) has been developed to characterize proteins in solid powders with peptide level resolution. The technique was found to be sensitive to formulation and process changes. The ssHDX-MS metrics are highly correlated to the long-term storage stability, suggesting that the method can serve as a formulation screening tool. This dissertation aims to evaluate the factors affecting ssHDX kinetics and to develop a mechanistic understanding of the exchange process in solid samples, which in turn will support the solid-state protein development and enable it to be conducted in a more a cost and time-effective way. First, the contribution of peptide-matrix interactions to deuterium incorporation kinetics in the absence of higher-order structure was assessed using lyophilized poly-D, L-alanine peptides. Deuterium incorporation depended on excipient type and D₂O_(g) activity in the solid samples. A reversible pseudo-first-order kinetic model was proposed and validated using the experimental data. Second, the reversibility of the hydrogen-deuterium exchange reaction in the solid-state was evaluated to support the ssHDX mechanistic model further. The reaction was found to be reversible irrespective of initial conditions and independent of the excipient type. Pre-hydration of the peptide samples prior to deuterium labeling did not affect deuterium incorporation in amorphous samples compared to the controls not subjected to pre-hydration. Third, the contribution of peptide secondary structure to deuterium uptake kinetics was quantified using structured PDLA analogs. The deuterium incorporation in structured peptides was less than that of the PDLA peptides suggesting that both peptide structure and peptide-matrix interactions contribute to ssHDX-MS. Finally, a quantitative data analysis method was presented that allows the interpretation of ssHDX-MS data of a protein relative to controls. Altogether, the findings present a comprehensive mechanistic understanding of the ssHDX-MS of proteins that is relevant to the industry.</div>

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- 5 - Abstract Hydrogen/deuterium exchange coupled to mass spectrometry (HX-MS) utilizes the spontaneous exchange of protein backbone amide hydrogens for deuterium atoms from solution to gain information about changes in protein structure. To localize these changes to specific areas of the protein, enzymatic digestion by aspartate proteases is used. The proteases' ability to produce small overlapping peptides and to provide full sequence coverage of the studied protein is essential for pinpointing the protein regions of interest. In this study recombinant proteases nepenthesin I (Nepenthes gracilis) and rhizopuspepsin (Rhizopus chinensis) were prepared and compared to commercially available proteases porcine pepsin A and aspergillopepsin (Aspergillus saitoi). The comparison was performed using various activity assays, where the effects of pH, temperature and denaturing and reducing agents on the activity of the proteases were studied. All four proteases were also immobilized on a polymeric resin POROS and their activity in an online HX-MS digestion setup was tested using myoglobin as a model substrate.

Intracellular transport is provided by two major types of molecular motors kinesins and cytoplasmic dynein. Kinesin-1 is a molecular motor that transports molecules and organelles along microtubule tracks anterogradely. Specific protein-protein interactions are required to activate kinesin-1 as the free kinesin exist in an autoinhibited state. The activation of kinesin-1 induces its conformational change, enables microtubule binding and ATP hydrolysis necessary for the directional cargo transport. HDAC6 is a multifunctional protein composed of several domains. It plays an important role in many microtubule dependent processes as HDAC6 is a major tubulin deacetylase. It has been shown that HDAC6 manipulation (inhibition/genetic ablation) affects transport along microtubules but the exact mechanisms are unknown. The effect can be caused either by deacetylation microtubules or direct interaction with molecular motors. This thesis is focused on characterization of interactions between kinesin-1 and HDAC6 that have not been described so far. To this end, we expressed and purified various constructs of kinesin-1 and HDAC6 and tested their interactions by microscale thermophoresis (MST) and hydrogen deuterium exchange (HDX) to determine affinity and interaction sites, respectively. MST data revealed that...

Ce travail de thèse porte sur développement de méthodes en spectrométrie de masse structurale pour l’analyse de protéines recombinantes et de leurs complexes associés. L’objectif central s’est porté sur des développements méthodologiques en échange hydrogène/deutérium couplé à la spectrométrie de masse (HDX-MS). Les techniques biophysiques de caractérisation structurale à haute résolution comme la cristallographie ou la RMN se heurtent régulièrement à des problèmes de productions de cristaux, de taille de complexes analysables ou encore de quantité de matériel nécessaire importante. Le développement de méthodes spécifiques HDX-MS a permis de réaliser une caractérisation structurale de systèmes protéiques variés, et réfractaires aux approches haute résolution. La combinaison de cette approche à différents outils de MS structurale est aussi illustrée, et montre tout son intérêt pour l’obtention d’informations à résolution augmentée. / This thesis work focuses on development of structural mass spectrometry methods for the analysis of recombinant proteins and their associated complex. The central objective has focused on the development of hydrogen/deuterium exchange coupled to mass spectrometry approaches (HDX-MS). The high resolution biophysical techniques for structural characterization such as crystallography or NMR regularly face problems of crystal productions, size analyzable complex or quantity of material required. The development of specific HDX-MS methods allowed the characterization of various, and refractory protein systems to high resolution approaches. The combination of this approach with complementary structural MS tools is also illustrated, and shows its interest to obtain increased resolution information.