Transcription factors play crucial regulatory role within the cell and the entire multicellular organism. The important factor is its ability to interact with other regulatory proteins and DNA. Despite the fact that a large part of the interaction network is already documented, detailed information on the structure and dynamics of protein-protein and protein-DNA complexes is still scarce. In this thesis we focused on the possibility of studying conformational changes given by the transcription factor-DNA complex formation using the methods of structural mass spectrometry: hydrogen/deuterium exchange and chemical crosslinking. As a model, we chose a transcription factor FOXO4 which DNA binding domain is structurally well characterized both in free form and in the complex with DNA.

Rain-on-snow events represent one of the basic mechanisms causing floods. Rain falling on the snow cover causes enhanced melting and the resulting runoff often exceeds the runoff caused by rain. During the winter seasons 2018 and 2019, water samples from the stream, snowpack and precipitation were repeatedly taken in the the Ptačí Brook catchment in the Šumava mountains, and the concentrations of 2 H and 18 O were measured in the laboratory. Based on the observed isotope ratios 18 O/16 O and 2 H/1 H in combination with other variables measured in the catchment, the two ROS events from 2019 were reconstructed. The ratio of heavy isotopes increased in the snowpack due to ROS events. Using the end member mixing equation, a hydrograph separation was performed for both investigated events. For the first event, it was not possible to clearly separate groundwater from rainfall, and thus the range of snow in the total runoff was determined by its separation from rainfall and subsequent separation from groundwater. The second event examined was separated directly into three components: rainfall, groundwater and snow. According to the analyses, the total runoff during ROS events in both cases was mostly formed by event water (a combination of rainfall and melt water). The melting water from the snow cover...

<p>Therapeutic peptides have become a clinically and commercially important drug class providing novel treatment options in variety of disease areas. Today, more than 80 peptide drugs are marketed worldwide and hundreds more are in development. However, the development of peptide drugs can be hindered by their tendency to self-associate to form fibrils, an impurity that can affect potency and increase the potential for adverse immune responses in patients. Fibrillation of therapeutic peptides can present significant quality concerns and poses challenges for manufacturing and storage. From a pharmaceutical development perspective, early detection of instabilities can inform the development of mitigation strategies to minimize the risk of product failure and avoid costly delays in clinical development. A fundamental understanding of the mechanisms of fibrillation is critical for the rational design of fibrillation-resistant peptide drugs and formulations.</p> <p>The objective of this dissertation was to develop structurally modified fibrillation-resistant peptides based on a mechanistic understanding of the fibrillation process. The therapeutic peptides studied were human calcitonin (hCT), a glucagon/GLP-1 analog, and human insulin B-chain (INSB). Pulsed hydrogen-deuterium exchange mass spectrometry (HDX-MS) and other biophysical methods were used to provide mechanistic understanding of the intermolecular interactions and structural transitions during peptide fibrillation. Coupled with proteolytic digestion, pulsed HDX-MS of fibrillating peptides enabled identification of the residues involved in the early interactions leading to fibrillation based on their differential deuterium exchange rates. The high-resolution residue level information was used to make site-specific modifications to hCT, with phosphorylation in the central region resulting in complete inhibition of fibrillation for the phospho-Thr-13 hCT analog under the stress conditions employed. Reversible ‘prodrug’ modifications such as phosphorylation can aid the rational design of fibrillation-resistant therapeutic peptides. Furthermore, the effects of structural modifications on peptide fibrillation were evaluated by reducing the Cys1-Cys7 disulfide bond in hCT, and by C-terminal amidation or substitution with a helix-stabilizing residue (α-aminoisobutyric acid, Aib) in the glucagon/GLP-1 analog peptide. Finally, studies of insulin B-chain probed fibrillation mechanisms of this therapeutically important peptide, contributing to our understanding of the mechanisms of insulin fibrillation with the broad goal of developing fibrillation-resistant, rapid-acting, monomeric insulin analogs. Overall, the results demonstrate that small structural changes can have significant effects on peptide fibrillation, that pulsed HDX-MS can be used to probe these effects, and that an understanding of these effects can inform the rational development of fibrillation-resistant peptide drugs. </p>

The stable isotope ratio of non-exchangeable hydrogen (δ2Hn) emerged as a promising new tool for source attribution in aquatic ecology, which can better discriminate between the organic matter sources. However, determining the absolute isotopic values is problematic due to the functional groups with hydrogen (H) that can easily exchange with the ambient water. This can lead to significant uncertainties in the absolute isotopic values, which eventually translates into errors in source attribution. However, controlled H exchange experiments with dual water equilibrations can alleviate this problem. However, current methods report significant variation in the absolute values, likely originating in partial H exchange, uncertainty in fractionation factors between exchangeable H and ambient water, and residual moisture. Here I used two methods for H exchange based on steam and liquid water using novel equipment for sample preparation called the Isobox. I evaluated the exchangeable H fraction in materials commonly analysed in ecology. Furthermore, I have investigated how these methods and associated analytical uncertainties can influence the mathematical mixing models used to resolve the source attribution using known sample mixtures made with soils and algae. The results show that 1) H exchange experiments using liquid water equilibration provide a higher exchangeable H fraction than the steam-based method, which was approximately three times higher. 2) The two-source mixing model proved to effectively determine the source attribution with known soil and algae mixtures, as evidenced by both water and steam equilibration. However, prior exposure to isotopically divergent waters can lead to source attribution errors, particularly with steam-based methods that provide low exchangeable H fractions. 3) When labile H is fully exchanged, source attribution does not depend on absolute δ2Hn determination, and simple one-water equilibration is sufficient. 4) Additional uncertainties in source attribution could originate from fractionation factors and δ2H measurement variability. The findings of this study conclude that the variations in fractionation factors did not significantly alter the mixing model as the error was below 5%. 5) Based on these experiments, I recommend keeping the analytical uncertainty of δ2H below ±5‰, which amounts to about a 6% error factor in source attribution. Finally, these experiments and analyses show how the methods can generate reliable data, depending on the research questions and whether absolute or relative isotopic values are required. This study provides different analytical pathways.

<p>Antibody-drug conjugates (ADCs) combine the cytotoxicity of traditional chemotherapy with the site-specificity of antibodies by conjugating payloads to antibodies with immunoaffinity. However, the conjugation alters the physicochemical properties of antibodies, increasing the risks of various types of degradation. The effects of common risk factors such as pH, temperature, and light on the stability of ADCs differ from their effects on monoclonal antibodies (mAb) due to these altered physicochemical properties. </p> <p>To date, ADC researchers have developed linkers with improved <i>in vivo</i> stability, and begun to understand the deconjugation mechanisms <i>in vivo</i>. In contrast, the <i>in vitro</i> stability of ADCs has not gained comparable attention. All nine of the U.S. FDA approved ADCs are lyophilized to minimize the potential for degradation. However, there are few studies on the solid-state stability of ADCs. To evaluate lyophilized solids, pharmaceutical development relies heavily on accelerated stability studies, which take months to determine the best formulation. Characterization methods that are often used orthogonally with accelerated studies include Fourier-transform infrared spectroscopy (FT-IR), Raman spectroscopy, near-infrared spectroscopy (NIR), differential scanning calorimetry (DSC), and x-ray powder diffraction (XRPD). Results from these methods are often poorly correlated with stability, however. Thus, stability evaluation of solid-state ADC products, and other recombinant protein drugs, is often a bottleneck in their development.</p> <p>To provide knowledge on how to improve the <i>in vitro</i> stability of lyophilized ADC formulations, the solid-state stability of ADC formulations with varying risk factors was studied in this dissertation project. The first study investigated interactions between an ADC and excipients in terms of solid-state stability enhancement. The second study investigated the process-driven instability of ADCs during lyophilization using various concentrations of ADCs. The first two studies incorporate a new method called solid-state hydrogen/deuterium exchange coupled with mass spectrometry (ssHDX-MS) as an analytical predictor of solid-state stability. The last study investigated the effects of pH on the stability of labile hydrazones, as a model for common linker chemistry used in ADCs. </p>

Although computational structure prediction has had great successes in recent years, it regularly fails to predict the interactions of large protein complexes with residue-level accuracy, or even the correct orientation of the protein partners. The performance of computational docking can be notably enhanced by incorporating experimental data from structural biology techniques. A rapid method to probe protein-protein interactions is hydrogen-deuterium exchange mass spectrometry (HDX-MS). HDX-MS has been increasingly used for epitope-mapping of antibodies (Abs) to their respective antigens (Ags) in the past few years. In this paper, we review the current state of HDX-MS in studying protein interactions, specifically Ab-Ag interactions, and how it has been used to inform computational structure prediction calculations. Particularly, we address the limitations of HDX-MS in epitope mapping and techniques and protocols applied to overcome these barriers. Furthermore, we explore computational methods that leverage HDX-MS to aid structure prediction, including the computational simulation of HDX-MS data and the combination of HDX-MS and protein docking. We point out challenges in interpreting and incorporating HDX-MS data into Ab-Ag complex docking and highlight the opportunities they provide to build towards a more optimized hybrid method, allowing for more reliable, high throughput epitope identification.

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Indiana University-Purdue University Indianapolis (IUPUI) / Cellular membranes contain a staggering diversity of lipids. The lipids are heterogeneously distr ibuted to create regions, or domains, whose physical properties differ from the bulk membrane and play an essential role in modulating the function of resident proteins. Many basic questions pertaining to the formation of these lateral assemblies remain. T his research employs model membranes of well - defined composition to focus on the potential role of polyunsaturated fatty acids (PUFAs) and their interaction with cholesterol (chol) in restructuring the membrane environment. Omega - 3 (n - 3) PUFAs are the main bioactive components of fish oil, whose consumption alleviates a variety of health problems by a molecular mechanism that is unclear. We hypothesize that the incorporation of PUFAs into membrane lipids and the effect they have on molecular organization may be, in part, responsible. Chol is a major constituent in the plasma membrane of mammals. It determines the arrangement and collective properties of neighboring lipids, driving the formation of domains via differential affinity for different lipids . T he m olecular organization of 1 -[ 2 H 31 ]palmitoyl -2- eicosapentaenoylphosphatidylcholine (PEPC - d 31 ) and 1 -[ 2 H 31 ]palmitoyl -2- docosahexaenoylphosphatidylcholine (PDPC -d 31 ) in membran es with sphingomyelin (SM) and chol (1:1:1 mol) was compared by solid - state 2 H NMR spectroscopy. Eicosapentaenoic (EPA) and docosahexaenoic (DHA) acids are the two major n - 3 PUFAs found in fish oil, while PEPC -d 31 and PDPC -d 31 are phospholipids containing the respective PUFAs at the sn - 2 position and a perdeuterated palmitic acid a t the sn - 1 position . Analysis of s pectra recorded as a function of temperature indicate s that in both cases, formation of PUFA - rich (less ordered) and SM - rich (more ordered) domains occurred. A surprisingly substantial proportion of PUFA was found to infil trate the more ordered domain. There was almost twice as much DHA (65%) as EPA (30%) . The implication is that n - 3 PUFA s can incorporate into lipid rafts, which are domains enriched in SM and chol in the plasma membrane, and potentially disrupt the activity of signaling proteins that reside therein. DHA, furthermore, may be the more potent component of fish oil. PUFA - chol interactions were also examined through affinity measurements. A novel method utilizing electron paramagnetic resonance (EPR) was develope d, to monitor the partitioning of a spin - labeled analog of chol , 3β - doxyl - 5α - cholestane (chlstn), between large unilamellar vesicles (LUVs) and met hyl - β - cyclodextrin (mβCD). The EPR spectra for chlstn in the two environments are distinguishable due to the substantial differences in tumbling rates , allowing the population distribution ratio to be determined by spectral simulation. Advantages of this approach include speed of implementation and a vo idance of potential artifact s associated with physical separation of LUV and mβCD . Additionally, in a check of the method, t he relative partition coefficients between lipids measured for the spin label analog agree with values obtained for chol by isothermal titration calorimetry (ITC). Results from LUV with different composition confirmed a hierarchy of decreased sterol affinity for phospholipids with increasing acyl chain unsaturation , PDPC possessing half the affinity of the corresponding monounsaturated phospholipid. Taken together, the results of these studies on model membranes demonstrate the potential for PUFA - driven alteration of the architecture of biomembranes, a mechanism through which human health may be impacted.

Deuteration is the replacement of a hydrogen atom by deuterium atom in a molecule. The replacement begins at the most acidic hydrogen in the molecule. In ATP, the deshielded hydrogen is C8-H which is the first replaced during deuteration. During ATP deuteration some of the ATP is hydrolysed to ADP concurrently. Using kinetic analysis, it was confirmed that the ATP hydrolysis that occurs is 1st order in ATP concentration, while the hydrogen replacement is 2nd order. The ATP and its C8 deuterated analogue were tested against three enzymes shikimate kinase (SK), acetate kinase (AK) and glutamine synthetase (GS) to determine if a kinetic isotope effect (KIE) exists in these systems. With AK and GS, the KIED increased as the KIEH decreased, while with SK the KIED decreased as the KIEH increased as the concentration of the ATP or deuterated analogue increased. Deuteration of imidazole and purine compounds reduced the specific activity of AK or SK at low concentrations in an enzyme-catalysed reaction. From a library of imidazole-containing compounds that inhibited SK, three compounds were selected and their IC50 values were determined on the SK-catalysed reaction. These compounds show a differential potency and efficiency between their protonated and deuterated analogues when compared in a 1:1 mixture. Synthesized purines incorporating three different substituents at N-9 were tested against AK or SK for their ability to lower the specific activity of the enzymes used / Physics / M. Sc. (Physics)

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