We have investigated the noncovalent interactions in carbohydrate-aromatic interactions which are pivotal to the recognition of carbohydrates in proteins. We have employed quantum mechanical methods to study carbohydrate-aromatic complexes. Due to the importance of dispersion contribution to the interaction energy, we mainly use density functional theory augmented with an empirical correction for the dispersion interactions (DFT-D). We have validated this method with a limited number of high level ab initio calculations. We have also analysed the vibrational and NMR chemical shift characteristics using the DFT-D method. We have mainly studied the complexes involving β-glucose with 3-methylindole and p-hydroxytoluene, which are analogues of tryptophan and tyrosine, respectively. We find that the contribution for interaction energy mainly comes from CH/π and OH/π interactions. We find that the interaction energy of complexes involving CH/π and OH/π interactions is reflected in the associated blue and red shifts of vibrational spectrum. We also find that the interactions involving 3-methylindole are somewhat greater than those for p-hydroxytoluene. The C-H blueshifts are also in parallel with the predicted NMR proton shift. We have also tested different density functionals including both standard density functionals and newly developed M0x functionals and MP2 method for studying carbohydrate-aromatic complexes. The DFT-D method and M06 functionals of the M0x family are found to perform better, while B3LYP and BLYP functionals perform poorly. We find that the inclusion of a dispersion term to BLYP is found to perform better. The dispersion energy dominates over the interaction energy of carbohydrate-aromatic complexes. From the DFT-D calculations, we found that the complexes would be unstable without the contribution from dispersive energy. We have also studied the importance of noncovalent interactions in functionalization of nanotubes by nucleic acid bases and aromatic amino acids by using semi-empirical methods with dispersion term such asPM3-D and PM3-D*. We find that the both semi-empirical schemes give reasonable interaction energies with respect to DFT-D interaction energies. We have also used PM3-D method to study the adsorption of organic pollutants on graphene sheet and on nanotubes. We found that the semi-empirical schemes, which are faster and cheaper, are suitable to study these larger molecules involving noncovalent interactions and can be used as an alternative to DFT-D method. We have also studied the importance of dispersion interaction and the effect of steric hindrance in aggregation of functionalized anthracenes and pentacenes. We have also employed molecular dynamics simulation methods to study the aggregation of anthracene molecules in toluene solution.

<p>According to the Global Cancer Incidence, Mortality, and Prevention (GLOBOCAN) study for 2018, 2,089,000 women will have been diagnosed with breast cancer worldwide, with 627,000 breast cancer-related mortalities. It is estimated that between 15 – 20 % of breast cancer diagnoses are of the triple-negative subtype. Triple-negative breast cancers (TNBCs) do not express the receptors for estrogen, progesterone, and human epidermal growth factor 2, and hence cannot be treated using hormone receptor-targeted therapy. </p> <p>TNBCs are commonly of the basal-like phenotype, with high expression levels of proteins involved in epithelial-mesenchymal transition, extracellular-matrix (ECM) remodeling, cell cycle progression, survival and drug resistance, invasion, and metastasis. 5-year survival rates are significantly lower for TNBC patients, and the disease is characterized by poorer grade at the time of diagnosis as well as higher 5-year distant relapse rates, with a greater chance of lung and CNS metastases. Current treatments for TNBC take the form of aggressive cytotoxic chemotherapy regimens with multiple adverse side-effects. An important goal of on-going studies is to identify new compounds with significant TNBC-specificity, in order to improve patient survival outcomes while preserving a high quality of life during treatment.</p> <p> For several decades, compounds originally isolated from bioactive natural extracts, such as the taxanes and vinca<i> </i>alkaloids, have been at the forefront of chemotherapy. However, due to their non -specific mechanisms of action, treatment with these compounds eventually leads to significant toxicity to normal cells and tissues. Modern transcriptomics, metabolomics, and proteomics tools have greatly improved our understanding of the mechanisms governing cancer initiation and progression, and revealed the considerable heterogeneity of tumor cells. This has allowed for the identification of potential vulnerabilities in multiple cancers, including TNBCs. By leveraging these new technologies and insights with the tremendous diversity of bioactive compounds from organisms that remain unstudied, new classes of onco-drugs targeting pathways specific to TNBC cells could be identified in the near future.</p> <p>Here, we describe the cytotoxic effects of extracts from <i>Lippia origanoides </i>- a species of medicinal shrub native to Central and South America - on TNBC cells. We report that these extracts induce rapid, sustained, and irreversible apoptosis in TNBC cells <i>in vitro</i>, with significantly reduced cytotoxicity against normal mammary epithelial cells. The <i>L. origanoides </i>extracts LOE and L42 exploited two TNBC-specific characteristics to induce apoptosis in these cells: i) inhibiting the constitutively active survival and inflammatory NF-kB signaling pathway, and ii) significantly dysregulating the expression levels of mitochondrial enzymes required to maintain the TCA cycle and oxidative phosphorylation; metabolic pathways that are required for the maintenance of TNBC cell growth and proliferation.</p> <p>Finally, to lay the foundations for future studies on the abilities of these extracts to prevent tumor initiation and inhibit tumor growth <i>in vivo</i>, we also show that the <i>L. origanoides </i>extract, L42, is non-toxic<i> </i>to immunocompetent C57BL/6 mice, and have developed an <i>in vivo </i>model of human TNBC in athymic <i>nu/nu</i> mice. </p> <p>Collectively, our studies are the first to identify the anti-TNBC-specific properties of bioactive extracts from the <i>Lippia </i>species, and reveal that targeting NF-kB signaling and mitochondrial metabolism are potential avenues to new therapeutics against this subtype of breast cancer. Future work in our lab will focus on identifying the bioactive components (BACs) of the extract mediating its apoptotic effects, and shedding light on their protein binding partners within the cell.</p>

<div>The use of computational approaches to understand kinase substrate preference has been a powerful tool in the search to develop artificial peptide probes to monitor kinase activity, however, most of these efforts focus on a small portion of the human kinome. The use of high throughput techniques to identify known kinase substrates plays an important role in development of sensitive protein kinase activity assays.</div><div>The KINATEST-ID pipeline is an example of a computational tool that uses known kinase substrate sequence information to identify kinase substrate preference. This approach was used to design three artificial substrates for ABL, JAK2 and SRC family kinases. These biosensors were used to design ELISA and lanthanide-based assays to monitor in vitro kinase activity. The KINATEST-ID pipeline relies on a high number of reported kinase substrates to predict artificial substrate sequences, however, not all kinases have the sufficient number of known substrates to make an accurate prediction. </div><div>The adaptation of kinase assay linked with phosphoproteomics technique was used to increase the number of known FLT3 kinase variant substrate sequences. Subsequently, a set of data formatting tools were developed to curate the mass spectrometry data to become compatible with a command line version of the KINATEST-ID pipeline modules. This approach was used to design seven pan-FLT3 artificial substrate (FAStides) sequences. The pair of FAStides that were deemed the most sensitive toward FLT3 kinase phosphorylation were assayed in increasing concentrations of clinically relevant tyrosine kinase inhibitors. </div><div>To improve the automation of the mass spectrometry data analysis and formatting for use with the KINATEST-ID pipeline, a streamlined process was developed within a bioinformatic platform, GalaxyP. The data formatting tools used to process the FLT3 mass spectrometry data were converted into compatible versions to execute within the GalaxyP framework. This process was used to design four BTK artificial substrates (BAStide) to monitor kinase activity. Additionally, one of the BAStide sequences was designed in the lanthanide chelating motif to develop an antibody-free activity assay for BTK. </div><div>Lastly, a multicolored time resolved lanthanide assay was designed by labeling SYK artificial substrate and a SRC family artificial substrate to measure the activity of both kinases in the same kinase reaction. This highlighted the functionality of lanthanide-based time resolved assays for potential multiplexing assay development. </div><div><br></div>

<p>  </p> <p>Cyclic dinucleotides (CDNs) such as the bacterial CDNs (cyclic-di-AMP, cyclic-di-GMP and 3’3’cyclic GMP-AMP) and mammalian CDN, 2’3’-cGAMP, are essential immune response second messenger signaling molecules. These CDNs act via Stimulator of interferon genes (STING)-TANK Binding Kinase 1 (TBK1)-Interferon Regulatory Factor 3 (IRF3) pathway. However, data from our lab and others indicate that beyond the classical STING-TBK1-IRF3 pathway, CDNs also regulate other signaling axes related to both inflammatory and non-inflammatory pathways. But, a global view of how these CDNs affect signaling in diverse cells or through non-STING pathways is lacking. There is also paucity of data on CDN modulated kinases and no global assessment of phosphorylation events that follow cyclic GMP AMP synthase (cGAS)-STING axis stimulation in immune cells. Herein, I have used a proteomics approach to determine signaling pathways regulated by bacterial CDNs, c-di-GMP and c-di-AMP in human gingival fibroblasts such as pathways related to nucleotide excision repair (NER) which ordinarily do not channel through STING (Chapter 3). Additionally, with the use of phosphoproteomics and bioinformatics, this project accomplished a system-wide phosphorylation analyses of T cells treated with 2’3’cGAMP and showed that 2’3’cGAMP impact various, yet unreported critical kinases (E.g. LCK, ZAP70, ARG2) and signaling pathways important for T cell function (Chapter 4). Asides known interferon signaling, these differentially phosphorylated kinases were involved in T cell receptor (TCR) signaling, myeloid cell differentiation, cell cycle regulation, and regulation of double strand break repair. </p> <p>Another area of interest addressed by this project is the discovery of novel antibacterial agents against multi-drug resistant (MDR) bacteria. Thus, in Chapters 5 and 6, I show the identification, antibacterial activity and characterization of <strong>HSD1835</strong> and <strong>HSD1919 </strong>as novel SF5 and SCF-containing membrane active compounds, highly potent against preformed MDR biofilms with fast bactericidal activity against persister bacteria. Plus, an exciting addition to the fight against MDR bacteria in Chapter 7, the discovery of <strong>HSD1624</strong> and analogs, which are able to re-sensitize MDR and colistin resistant bacteria such as <em>Pseudomonas aeruginosa</em> from a colistin MIC of 1024 μg/mL to 0.03 μg/mL (64000-fold reduction). Ultimately, these compounds could be translated into anti-biofilm and, anti-MDR bacteria therapeutics, preventing repeated surgeries due to infections, and saving lives. </p>

No description available.

<p dir="ltr">Adipose tissue is characterized by the dominant presence of adipocytes, specialized cells adept at lipid metabolism. These adipocytes act as critical nodes, coordinating the complex processes of energy storage and mobilization according to the body's metabolic requirements. Within the adipocyte population of mammals, there are three main subtypes: white, beige, and brown adipocytes. White adipocytes are primarily dedicated to the sequestration of energy in the form of triglycerides. Conversely, beige and brown adipocytes are distinguished by their capacity for thermogenesis, the process of dissipating nutritional energy as heat. The contemporary challenge of chronic overnutrition has precipitated a global surge in obesity and cardiometabolic diseases. Addressing this issue necessitates the maintenance of white adipocyte homeostasis and the enhancement of the quantity and function of thermogenic adipocytes, which are imperative for mitigating the global obesity epidemics.</p><p dir="ltr">Mitochondrion, a multifunctional organelle, is integral to a broad spectrum of cellular processes, including anabolic and catabolic metabolism, bioenergetics, and signal transduction, all of which are essential for maintaining cellular functions and homeostasis. The efficacy of mitochondrial operations is intrinsically linked to their membrane dynamics. In this study, transmission electron microscopy and mass spectrometry were employed to investigate the proteins implicated in the cold-induced mitochondrial membrane remodeling in brown adipocytes. Through this approach, a poorly characterized protein, Family with Sequence Similarity 210 Member A (FAM210A), was identified as a mitochondrial inner membrane protein that is induced by cold stimulation. Subsequent loss-of-function experiments were conducted to elucidate the role of FAM210A in adipocytes. Mice with adipose-specific deletion of <i>Fam210a</i> (<i>Fam210a</i>^<em>AKO</em>) exhibited compromised mitochondrial cristae structure and a reduced thermogenic capacity in brown adipose tissue (BAT), resulting in an increased susceptibility to lethal hypothermia during acute cold challenge. Moreover, in mice with inducible ablation of <i>Fam210a</i> in adipocytes (<i>Fam210</i>^{<em>iAKO</em>}), mitochondrial alterations in BAT were negligible at thermoneutral conditions; however, they exhibited defective cold-induced mitochondrial cristae remodeling, culminating in a progressive loss of cristae and diminished mitochondrial density. Mechanistically, it was determined that FAM210A interacts with mitochondrial protease YME1L and modulates its activity toward OMA1 and OPA1 cleavage, thus compromising cold-induced mitochondrial remodeling in BAT.</p><p dir="ltr">Additionally, this research delved into the role of FAM210A in adipocytes in response to dietary stress by feeding mice with high-fat diet (HFD). The study found a consistent correlation between FAM210A expression and OPA1 cleavage in adipocytes under HFD challenge. Mice lacking FAM210A in all adipocytes and subjected to HFD exhibited lipoatrophy in white adipose tissue (WAT) and a downregulation of genes associated with adipogenesis and lipid metabolism. In contrast, mice with a brown adipocyte-specific ablation of <i>Fam210a </i>(<i>Fam210a</i>^<em>UKO</em>) displayed no significant change in WAT mass but had enlarged livers. Crucially, both <i>Fam210a</i>^<em>AKO</em> and <i>Fam210a</i>^<em>UKO</em> mice presented increased WAT inflammation, deteriorated glucose tolerance, and exacerbated insulin resistance. These findings underscore the pivotal role of FAM210A in brown adipose tissue (BAT) in the preservation of WAT homeostasis and the regulation of systemic glucose clearance in diet-induced obesity.</p><p dir="ltr">In summary, these studies characterize the mitochondrial dynamics in brown adipocytes in response to cold stress, identify a new cold-induced mitochondrial protein, FAM210A, and uncover its functions in adipocytes under cold and dietary stresses. These findings highlight the importance of mitochondrial remodeling in the adaptive response of adipocytes to evolving metabolic demands. This work establishes FAM210A as a key regulator of mitochondrial cristae remodeling, shedding light on the mechanisms that govern mitochondrial plasticity in adipocytes.</p>

<p dir="ltr">Obesity is a worldwide epidemic that is partially linked to changing lifestyles within the modern world, including increased access to calorically dense foods and decreased energy output due to more sedentary jobs. Obesity can lead to many different health complications, such as cardiovascular diseases or Type 2 Diabetes (T2D). Obesity-induced T2D is caused by dysfunction of the insulin-producing beta cells of the pancreas. However, mechanisms that promote obesity and the mechanisms by which obesity leads to beta cell dysfunction are not fully known.</p><p dir="ltr">Spinophilin is a filamentous (F)-actin binding, protein scaffolding, and protein phosphatase 1 (PP1)-targeting protein that can regulate protein. Spinophilin has multiple actions. Spinophilin can bundle filamentous actin to modulate the cellular cytoskeleton. Spinophilin also mediates substrate phosphorylation by targeting and modulating PP1 activity. In addition, spinophilin interacts with multiple proteins, including certain G-protein coupled receptors and can scaffold them with F-actin and/or PP1. Previous studies established that spinophilin KO mice have decreased fat mass, increased lean mass, and improved glucose tolerance. Yet, how spinophilin modulates the above metabolic parameters is unclear. We found that spinophilin is expressed in hypothalamic tissue and appears to also be expressed in the feeding center of the hypothalamus, as well as in other glucose-sensing cells known as tanycytes that neighbor the arcuate nucleus and the third ventricle. We found that loss of spinophilin limited weight gain observed in both a leptin receptor db/db mouse line (Leprdb/db<i>)</i> and mice fed a high-fat diet. Moreover, we found that the decreased fat mass seen in global spinophilin KO mice, at least in the Leprdb/db mice, was not due to major differences in feeding behaviors, consistent with what was observed by other groups using high-fat diet-fed mice. </p><p dir="ltr">As spinophilin was not associated with alterations in feeding, we posited that its ability to modulate glucose homeostasis may be linked to non-neuronal actions of the protein. Previous studies have found that spinophilin may regulate adipose tissue function and <i>in vitro</i> pancreatic beta cell function; however, its role in the pancreas and beta cells <i>in vivo</i> is not well characterized. We found that spinophilin is expressed in mouse pancreas. Using proteomics-based approaches we identified multiple putative spinophilin interacting proteins isolated from intact pancreas, including: PP1, the spinophilin homolog neurabin, and myosin-9. KEGG pathway analysis of proteomic proteins identified multiple pathways regulating ER stress, such as the unfolded protein response, and cytoskeletal arrangement. We observed decreased associations of spinophilin with PP1 and neurabin and increased association with myosin-9 in obese, Leprdb/db mice as early as 6 weeks, as well as significant decreases in body weight when spinophilin was knocked out in Leprdb/db mice. Moreover, we confirmed a robust and specific increased interaction of spinophilin with myosin-9, and other cytoskeletal proteins. Additionally, we found specific spinophilin interactions with ribosomal proteins, and exocrine and digestion proteins in high-fat diet-fed mice. Using our recently generated pancreatic beta cell-specific spinophilin KO mice, we found that loss of spinophilin in mice on a high-fat diet significantly reduces weight gain and improves whole- body glucose tolerance, and loss of spinophilin specifically within the beta cells also improves whole-body glucose tolerance, with no effect on body weight, further suggesting cell type-specific and independent roles for spinophilin on body weight and glucose homeostasis.</p>

Interaction preferences in protein - DNA complexes Dávid Jakubec Abstract Interactions of proteins with DNA lie at the basis of many fundamental bio- logical processes. Despite ongoing efforts, the rules governing the recognition of specific nucleic acid sequences have still not been universally elucidated. In this work, I attempt to explore the recognition process by splitting the intricate network of contacts at the protein - DNA interface into contribu- tions of individual amino acid - nucleotide pairs. These pairs are extracted from existing high-resolution structures of protein - DNA complexes and in- vestigated by bioinformatics and computational-chemistry based methods. Criteria of specificity based on the coupling of observed geometrical prefer- ences and the respective interaction energies are introduced. The application of these criteria is used to expand the library of amino acid - nucleotide pairs potentially significant for direct sequence recognition. Electrostatic poten- tial maps are calculated for individual nucleotides as well as for selected complexes to investigate the physical basis of the observed specificity. 1

<p>A significant development in mass spectrometry instrumentation and software in the past decade has led to its application in solving complex biological problems. One of the emerging areas is Chemical Proteomics that involves design and use of chemical reagents to probe protein functions in ‘a live cell’ environment. Another aspect of Chemical Proteomics is the identification of target proteins of a drug or small molecule. This is assisted by photoreactive groups, which on exposure to UV light, covalently link the target proteins that can be purified by affinity-based enrichment followed by mass-spectrometric identification. This phenomenon of Photoaffinity labeling (PAL) has been widely used in a broad range of applications. Herein, we have designed chemical tools to study Zika endocytosis and phosphoproteomics.</p> <p>Zika virus has attracted the interest of researchers globally, following its outbreak in 2016. While a significant development has been made in understanding the structure and pathogenesis, the actual mechanism of Zika entry into host cells is largely unknown. We designed a chemical probe to tag the live virus, leading to the identification of the virus receptors and other host factors involved in viral entry. We further validated neural cell adhesion molecule (NCAM1) as a host protein involved in early phase entry of Zika virus into Vero cells.</p> <p>The second aspect is the development of the DIGE (Difference Gel Electrophoresis) technology for phosphoproteomics. Phosphoproteins are known to be involved in various signaling pathways and implicated in multiple diseased states. We designed chemical reagents composed of titanium (IV) ion, diazirine and a fluorophore, to covalently label the phosphoproteins. Cyanine3 and cyanine5 fluorophores were employed to reveal the difference in phosphorylation between samples for the comparative proteomics. Thus far, we have successfully demonstrated the labeling of standard phosphoproteins in both simple and complex protein mixtures, and the future efforts are towards applying the technology to identify phosphoproteins in a cell lysate.</p>

Work reported in this thesis mainly comprises of the assignments and analysis of the rotational spectra and structures of three weakly bound complexes: C2H4•••H2S, C6H5CCH•••H2O and C6H5CCH•••H2S. All the data have been collected using a home built Pulsed Nozzle Fourier Transform Microwave Spectrometer. Apart from this, the thesis also deals with a criterion of classifying a weakly bound complex to a ‘hydrogen-bonded’ one. First chapter of the thesis gives a brief intermolecular interactions and molecular clusters of π system. It also briefly touches on the structural determination by rotational spectroscopy and the basic information one can gain from the rotational spectrum. Second chapter of the thesis gives a brief introduction to the experimental and theoretical methodology. It also gives a description of the software used in the FTMW spectrometer which was rebuilt using Labview 7.1. Third chapter of the thesis deals with the rotational spectra and structure of eight isotopologoues of C2H4•••H2S complex. The lines are split into four components for the parent isotopologue due to the presence of large amplitude motion. The smaller splitting is 0.14 MHz and the higher splitting is 1.67 MHz in (B+C)/2 for the parent isotopologue. Spectral splitting pattern of the isotopologues confirmed that smaller splitting is due to the rotation of ethylene about its C-C bond axis along with the contraction of S-H bond whereas the larger motion arises due to the interchange of equivalent hydrogens of H2S in the complex. A detailed spectral analysis and ab initio calculation for this system have been described in chapter III. The fourth chapter of the thesis describes the rotational spectroscopic studies of five isotopologues of C6H5CCH•••H2O complex. Rotational spectra unequivocally confirm the structure of the complex to be a one where H2O is donating one of its hydrogen to the acetylenic π cloud forming a O-H••• π bond whereas the ring ortho C-H bond forms C-H•••O bond with the water oxygen. For theparent isotopomer the lines are split into two components due to the rotation of H2O about its C2 symmetric axis. The fifth chapter of thesis describes the rotational spectroscopic and ab initio studies of five isotopologues of C6H5CCH•••H2S complex. Rotational spectra indicate the structure to be the one where H2S is sitting on the top of the phenyl ring and shifted towards the acetylenic group. The sixth chapter of the thesis describes a criterion for calling a complex to be hydrogen bonded based on the dynamic structure rather than the static structure of the complex. The question asked is if the anisotropy of the interaction is strong enough to hold the ‘hydrogen bond’ when one takes dynamics into account. The proposed criterion is that the zero point energy of the motion which takes the hydrogen away from the acceptor should be much less than the barrier height of the respective motion supporting at least one bound level below the barrier. Ab initio calculations have been done on four model systems Ar2•••H2O, Ar2•••H2S, C2H4••• H2O and C2H4••• H2S to emphasize this criterion.