The number of allosteric sites and active sites in phosphofructokinase from Bacillus stearothermophilus create an intricate network of communication within the enzyme. With thermodynamic linkage analysis, the overall allosteric communication can be quantified. This value, however, represents an average contribution for all the interactions involved. The recent development of a hybrid strategy has allowed for the quantification of single interactions, both heterotropic and homotropic. Focusing on the heterotropic interactions whose inhibition is entropy-driven, residues and regions within the enzyme can now be identified to further characterize each specific interaction using the hybrid strategy. Among the many components of entropy, the hybrid strategy has now allowed for the strategic placement of a reporter of side chain dynamics to identify conformational differences between the four ligand bound enzyme species of a single heterotropic interaction. In this study, a combination of these approaches was used in the methodology including constructing hybrids to isolate a single heterotropic interaction along with single tryptophan reporter. Site directed mutagenesis combined with the hybrid strategy was also implemented to directly assess the role of a single residue in the communication path of a single interaction. The region surrounding the allosteric site with the nearest active site has been implicated to be significant in transmitting the allosteric signal. In addition two single residues, T158 and D59, within this region have been identified to potentially contribute to the inhibition of this same interaction. An additional residue, G184, located outside this local region has also been identified as possibly having a significant role in the transmission of the inhibitory signal of a unique heterotropic interaction. The implications of this study have led to the initial identification of residues involved in the 22A route of allosteric communication of a single active site and allosteric site. This allosteric communication occurs to allow the enzyme to compensate for the binding of both ligands. With the location of these residues implicated to be involved in the communication of this isolated interaction, this compensation is not contained within a confined region but is however felt throughout the single subunit.

In all kinds of disease models, many proteins involved in protein-protein interactions (PPIs) are mutated and do not function properly. The important role of PPIs in disease makes the design of small molecule inhibition an interesting proposition. This project looks at mouse double minute 2 (MDM2) and mouse double minute X (MDMX) which binds and inhibits the tumour suppressor protein p53. MDM2 and MDMX are therefore attractive therapeutic targets due to their role in tumour progression. The aim is to identify small molecule dual inhibitors that are able to disrupt MDM2 and MDMX from binding to p53. Both N-terminal MDM2 and MDMX were successfully expressed and purified with high purity and decent yield. These proteins were used to develop Fluoresence Polarization (FP) and Capillary Electrophoresis (CE) assays for small molecule inhibitors screening. This work has successfully developed FP and CE assays for detecting weakly interacting fragments. The CE assay is a novel method for detecting weak fragments for protein-protein interactions, which are a challenging target. Two approaches were employed to identify small molecule inhibitors for MDM2- N/p53 interaction. At first, small molecules were identified using in silico screening and these hits were verified using FP and CE assays. Second, analogue exploration was applied to identify fragments from the small molecule inhibitors discovered from the in silico screening. Diphenylamine and oxindole fragments were identified as the most potent. However, diphenylamine fragment was discovered to aggregate MDM2-N and was ranked as a false positive hit. No protein aggregation was found when incubated with the oxindole fragment. Therefore oxindole can provide a good starting point for the design of higher affinity analogues. Studying the interaction of MDMX has only recently been undertaken. MDMX contains a high homology binding site with MDM2. Hence, developing a dual MDM2/MDMX inhibitor has become an attractive target to focus on. FP and CE assays were developed to screen compounds against MDMX-N. In silico screening against MDM2-N and MDMX-N found several hits. One compound was discovered as a dual binder to MDM2-N and MDMX-N with low μM affinity. This novel hit is potentially a good starting point for the design of higher affinity analogues.

Single enzymes of E. coli sourced B-galactosidase were analysed in effort to expand the wealth of knowledge in the area of heterogeneity. Static and dynamic heterogeneity was studied with respect to catalytic rate, electrophoretic mobility, and heat shock protein chaperone systems. Temperature was found to be a contributing factor to the observed range of dynamic heterogeneity, with the range increasing with temperature. The inhibitor dissociation constant was determined to be a heterogeneous property of B-galactosidase. A novel assay was developed in which a single enzyme molecule was subjected to three separate solutions while the enzyme itself remained free in solution. / October 2016

As technology improves, scientists are able to generate high-throughput data faster and cheaper. Consequently, the field of biological sciences is progressively becoming more reliant on data science tools like machine learning methods for analysis and sorting of big data. The Complex Object Parametric Analyzer and Sorter (COPAS) is a large particle flow cytometer that can perform high-throughput fluorescence screens on small animals, like Caenorhabditis elegans. The outputs of the COPAS are extinction coefficient (EXT), Time of Flight (TOF, arbitrary length unit) and fluorescence. However, the COPAS outputs include unwanted objects like bubbles or bacteria and some animals pass the flow cell in a non-straight manner producing abnormal profiles leading to inaccurate developmental staging. In this thesis, I have created an R package, named COPASProfiler, that generates experiment-specific supervised machine learning (ML) classification models which can detect and remove abnormal profiles enabling standardized fluorescence quantification and analysis. I used COPASProfiler to develop a pipeline to automate fluorescence analysis of high-throughput COPAS data sets. Using R shiny, I created a web program with a graphical user interface that allows users to view, annotate, quantify fluorescence, and classify COPAS-generated datasets. The COPASProfiler is available on GitHub and can be installed using one single R command. Lastly, the COPASProfiler comes with multiple tutorials and examples, and was designed to accommodate users with minimal programming experience. COPASProfiler should enable robust high-throughput fluorescence studies of regulatory elements (e.g., enhancers, promoters, and 3’UTRs) and long-term epigenetic silencing in C. elegans.

<p dir="ltr">Fluorescence microscopy, a cornerstone in biological imaging, faces inherent challenges due to photon budget constraints that affect the signal-to-noise ratio (SNR), ultimately limiting imaging performance. This thesis explores theoretical frameworks to address two fundamental issues: the denoising limit of fluorescence microscopy images and the resolution limit in the presence of photon noise. Firstly, we extend the application of the Cramér-Rao Lower Bound (CRLB) to establish a variance lower bound for image denoising algorithms in fluorescence microscopy. By incorporating constraints specific to the imaging system and biological specimens, we provide a benchmark for evaluating the performance of state-of-the-art denoising algorithms. Our analysis reveals that this lower bound is determined by factors such as photon count, readout noise, detection wavelength, effective pixel size, and numerical aperture of the microscope system. Secondly, building upon the pioneering work by Ernest Abbe and leveraging modern fluorescence and nanoscopy advancements, we propose a novel theoretical framework to quantify the resolving power of fluorescence microscopes under finite photon conditions. This model integrates the traditional diffraction limit with photon statistics to determine the practical resolution limit, highlighting the trade-offs between photon noise and resolution enhancement in techniques like confocal microscopy. This dual approach not only refined the theoretical understanding of fluorescence microscopy's capabilities but also assisted in designing and optimizing more effective imaging protocols. Through these investigations, this thesis provided a comprehensive theoretical foundation for improving fluorescence microscopy imaging techniques, paving the way for future innovations in biological imaging.</p>

A growing body of literature suggests Breast Cancer-Associated Protein 1 (BRCA1) is important not only as a cause, but also as a target in the quest for cancer treatment. BRCA1 deficient cells treated with radiation as well as PARP inhibitors and other chemotherapeutics demonstrate a greater sensitivity than cells with wild type BRCA1. Inhibitors of BRCA1 would take advantage of this synthetic lethality and represent a significant advance in cancer treatment as well as an understanding of the biology of DNA repair. Despite significant study of BRCA1 protein and function, it is a large protein (220 KDa) that is still largely uncharacterized, but its N- and C-terminal domains have been described by significant structural data. The BRCT (BRCA1 C-Terminal) Domain is a phosphoprotein binding domain that is commonly mutated or lost in cancers and has a binding cleft seemingly very suitable for drug design. Small molecule screens have been conducted against this domain, but the resulting hits with moderate affinity have not been shown to induce BRCA1 deficient phenotypes. Phosphopeptides have also been studied as potential BRCA1 inhibitors, yet despite some having affinities in the mid-nanomolar range the presence of a phosphate is not without its pharmacologic challenges. We generated an mRNA display library with 1.3 x 10^13 cyclized peptides covalently attached to the mRNA that encoded them. Eight rounds of selection exposing the library to a GST-BRCT fusion resulted in selection of non-phosphorylated peptides that bind to a BRCT domain of BRCA1. The sequences resulting from the selection have common homologies and initial characterization has shown that these peptides may be the first viable non-phosphoserine containing inhibitors of BRCA1.

In the north of Sweden lots of the soil is naturally contaminated by acid sulfate. When soil gets in contact with oxygen an oxidation process begins which releases elements that may be harmful to the surroundings. When the Botniabanan was built, soil had to be transported from the railroad area to deposit sites. This study was made to investigate the suspicions a landowner had regarding if his estate had been contaminated sulphide soil soil during the building of the Botniabanan. To do that four pits were dug in the area where the soil had been deposited. Then the soil was analyzed to see the content of sulfate, iron, organic matters and water. When the results was compared to other studies it showed that the content of sulfate and organic matters was to low to classify the soil as an acid sulfate soil.

Imaging of cellular samples has for several hundred years been a way for scientists to investigate biological systems. With the discovery of immunofluorescence labeling in the 1940’s and later genetic fluorescent protein labeling in the 1980’s the most important part in imaging, contrast and specificity, was drastically improved. Eversince, we have seen a increased use of fluorescence imaging in biological research, and the application and tools are constantly being developed further. Specific ion imaging has long been a way to discern signaling events in cell systems. Through use of fluorescent ion reporters, ionic concentrations can be measured inliving cells as result of applied stimuli. Using Ca2+ imaging we have demonstrated that there is a inverse influence by plasma membrane voltage gated calcium channels on angiotensin II type 1 receptor (a protein involved in blood pressure regulation). This has direct implications in treatment of hypertension (high blood pressure),one of the most common serious diseases in the western civilization today with approximately one billion afflicted adults world wide in 2016. Extending from this more lower resolution live cell bioimaging I have moved into super resolution imaging. This thesis includes works on the interpretation of super resolution imaging data of the neuronal Na+, K+ - ATPase α3, a receptor responsible for maintaining cell homeostasis during brain activity. The imaging data is correlated with electrophysiological measurements and computer models to point towards possible artefacts in super resolution imaging that needs to be taken into account when interpreting imaging data. Moreover, I proceeded to develop a software for single-molecule localization microscopy analysis aimed for the wider research community and employ this software to identify expression artifacts in transiently transfected cell systems. In the concluding work super-resultion imaging was used to map out the early steps of the intrinsic apoptotic signaling cascade in space and time. Using superresoultion imaging, I mapped out in intact cells at which time points and at which locations the various proteins involved in apoptotic regulation are activated and interact. / Avbildning av biologiska prover har i flera hundra år varit ett sätt för forskare att undersöka biologiska system. Med utvecklingen av immunofluoresens inmärkn-ing och fluoresens-mikroskopi förbättrades de viktigaste aspekterna av mikroskopi,kontrast och specificitet. Sedan 1941 har vi sett kontinuerligt mer mångsidigt och frekvent användning av fluorosense-mikroskopi i biologisk forskning. Jon-mikroskopi har länge varit en metod att studera signalering i cell-system. Genom användning av fluorosenta jon-sensorer går det att mäta variationer avjon koncentrationer i levande celler som resultat av yttre påverkan. Genom att använda Ca2+ mikroskopi har jag visat att det finns en omvänd koppling mellan kalcium-kanaler i plasma-membran och angiotensin II typ 1 receptorn (ett proteininvolverat i blodtrycksreglering). Detta har direkta implikationer för behandlingav högt blodtryck, en av de mer vanliga sjukdomarna i västvärlden idag med överen miljard drabbade patienter i världen 2016. Efter detta projekt vidgades mitt fokus till att inkludera superupplösnings-mikroskopi. Denna avhandling inkluderar ett arbete fokuserat på tolkningen av superupplösnings-mikroskopi data från neuronal Na+, K+ - ATPase α3, en jon-pump som återställer cellernas jonbalans i samband med cell signalering. Mikroskopi-datan korreleras mot elektrofysiologi experiment och modeller för att illustrera möjliga artefakter i superupplösnings-mikroskopi som måste tas i beaktande i samband med tolkning av data. Jag fortsatte med att utveckla mjukvara för analys av data från singel-molekyl-lokalisations-mikroskopi där fokuset för mjukvaran framförallt varit på användarvänligheten. Detta då jag hoppas att den kommer vara användbar för ett bredare forskingsfält. Mjukvaran användes även i ett separat projekt för att identifiera överuttrycks-artefakter i transfekterade celler. I det avslutande arbetet använder jag superupplösnings-mikroskopi för att karakterisera de tidiga stegen i mitokondriell apoptos. Jag identifierar när och var i cellen de olika proteinerna involverade i apoptos signaleringen är aktiverade och interagerar. / <p>QC 20171003</p>

京都大学 / 0048 / 新制・課程博士 / 博士(農学) / 甲第20767号 / 農博第2250号 / 新制||農||1054(附属図書館) / 学位論文||H29||N5087(農学部図書室) / 京都大学大学院農学研究科地域環境科学専攻 / (主査)教授 近藤 直, 教授 清水 浩, 教授 飯田 訓久 / 学位規則第4条第1項該当 / Doctor of Agricultural Science / Kyoto University / DGAM

Amyloidogenic neurodegenerative disorders such as Alzheimer's disease (AD) and Parkinson's disease (PD) are an important health issue. However, the underlying molecular mechanisms of the disease-related protein aggregates, that are present in humans, are only understood partially. I have used and developed biophysical methods to study the structural and biological properties of individual aggregates of Amyloid β peptide and α-Synuclein, proteins whose aggregation is associated with the development of Alzheimer's and Parkinson's disease respectively. I expanded the single aggregate visualisation through enhancement (SAVE) technique, which is a method based on the fluorescent dye Thioflavin T (ThT) that reversibly bind to the aggregates and whose fluorescence increases upon binding. I firstly explored the use of other dyes for these experiments and found that a ThT dimer has higher affinity to α-Synuclein aggregates in vitro. I then applied the SAVE method to the cerebral spinal fluid (CSF) of a cohort of AD patients and control CSF and observed no clear difference in aggregate number. However, these experiments provided insights into how antibodies bind the aggregates in human CSF. I could show, that despite altering the Ca2+ influx into both cells and vesicles, the antibody did not measurably affect the aggregate structure. To study the size specific effects of the Amyloid β 42 (Aβ42) peptide in more detail, I used and optimised gradient ultracentrifugation combined with single aggregate imaging to study the structural properties of the isolated aggregates. This aggregation kinetic independent method allowed me to compare the properties of fluorescently labelled and unlabelled Aβ42 and characterize the size dependent properties of aggregates in a single experiment. Since I could measure the relative concentration of different size aggregates it was also possible to compare the properties of single aggregates of different sizes. I then used biological assays to examine the ability of aggregates to permeabilise membranes resulting in the entry of calcium ions, and their ability to induce TNFα production in microglia cells. Both processes are thought to play key roles in the development of AD. I found that small soluble oligomers are most potent at inducing Ca2+ influx, whereas longer protofilaments are the most potent inducers of TNFα production. My results suggest that the mechanism by which aggregates damage cells changes as aggregation proceeds, as longer aggregates with different structures are formed. Protofilaments with a diameter of 1 nm or less have a structure that could make them particularly potent at causing the signalling of toll-like receptors, providing a molecular basis for their ability to induce TNFα production.