Biochemistry, Biophysics, and Structural Biology Commons^™

The Dissolution Of Cellulose In Ionic Liquids - A Molecular Dynamics Study, Barmak Mostofian

Doctoral Dissertations

The use of ionic liquids for the dissolution of cellulose promises an alternative method for the thermochemical pretreatment of biomass that may be more efficient and environmentally acceptable than conventional techniques in aqueous solution. Understanding how ionic liquids act on cellulose is essential for improving pretreatment conditions and thus detailed knowledge of the interactions between solute and solvent molecules is necessary. Here, results from the first all-atom molecular dynamics simulation of an entire cellulose microfibril in 1-butyl-3-methylimidazolium chloride (BmimCl) are presented and the interactions and orientations of solvent ions with respect to glucose units on the hydrophobic and hydrophilic surfaces …

Pore Selectivity And Gating Of Arabidopsis Nodulin 26 Intrinsic Proteins And Roles In Boric Acid Transport In Reproductive Growth, Tian Li

Doctoral Dissertations

Plant nodulin-26 intrinsic proteins (NIPs) are members of the aquaporin superfamily that serve as multifunctional channels of uncharged metabolites and water. They share the same canonical hourglass fold as the aquaporin family. The aromatic arginine (ar/R) selectivity filter controls transport selectivity based on size, hydrophobicity, and hydrogen bonding with substrates. In Arabidopsis thaliana, NIP II subclass proteins contain a conserved ar/R “pore signature” that is composed of Alanine at the helix 2 position (H2), Valine/Isoleucine at the helix 5 position (H5), and an Alanine (LE1) and an invariant Arginine (LE2) at the two loop E positions. In this study, …

Computer Simulations Of Enzymes, Jianzhuang Yao

Doctoral Dissertations

Enzymes are important catalysts in living systems, and understanding catalytic mechanisms of enzymes is an important task for modern biophysics and biochemistry. Computer simulations have emerged as very useful tools for understanding how enzymes work. In this dissertation, QM/MM MD simulations were applied to study the catalytic mechanisms of several enzymes, including sedolisin, S-adenosyl-L-methionine (AdoMet)-dependent methyltransferases, and salicylic acid binding protein 2. For sedolisin, we focus on the acylation and deacylation reactions catalyzed by the enzymes. We proposed a general acid/base mechanism involving the Glu/Asp residues at the active site. MD and QM/MM free energy simulations on pro-kumamolisin show that …

The Role Of Nag-1 In Tumorigenesis, Kyung-Won Min

Doctoral Dissertations

This dissertation explores the nature of a divergent member of the Transforming Growth Factor-β [beta] superfamily, the non-steroidal anti-inflammatory drugs activated gene (NAG-1), as it relates to its regulation and biological activity in cancer context. Our lab has extensively studied on the molecular mechanism by which phytochemicals and NSAIDs induce apoptosis correlation with NAG-1 expression in human colorectal cancer (CRC) cells. Significant data from in vitro studies suggest that NAG-1 has an anti-tumorigenic activity which elicits apoptosis in a cyclooxygenase (COX)-independent manner in CRC cells. Indeed, NAG-1 transgenic mice developed less aberrant polyp foci (APC) compared to those of control …

Comparative Genomics Of Microbial Chemoreceptor Sequence, Structure, And Function, Aaron Daniel Fleetwood

Doctoral Dissertations

Microbial chemotaxis receptors (chemoreceptors) are complex proteins that sense the external environment and signal for flagella-mediated motility, serving as the GPS of the cell. In order to sense a myriad of physicochemical signals and adapt to diverse environmental niches, sensory regions of chemoreceptors are frenetically duplicated, mutated, or lost. Conversely, the chemoreceptor signaling region is a highly conserved protein domain. Extreme conservation of this domain is necessary because it determines very specific helical secondary, tertiary, and quaternary structures of the protein while simultaneously choreographing a network of interactions with the adaptor protein CheW and the histidine kinase CheA. This dichotomous …

Guanidinium-Rich Romp Polymers Drive Phase, Charge, And Curvature-Specific Interactions With Phospholipid Membranes, Michael T W Lis

Doctoral Dissertations

Protein transduction domains (PTDs) and their and their synthetic mimics are short sequences capable of unusually high uptake in cells. Several varieties of these molecules, including the arginine-rich Tat peptide from HIV, have been extensively used as vectors for protein, DNA, and siRNA delivery into cells. Despite the wide-ranging utility of PTDs and their mimics, their uptake mechanism is still under considerable debate. How the molecules are able to cross phospholipid membranes, and what structural components are necessary for optimal activity are poorly understood. This thesis explores how PTDMs interact with phospholipid membrane phase, anionic lipid content and negative Gaussian …

Nanoparticle Building Blocks For Functional Structures, Youngdo Jeong

Doctoral Dissertations

A major goal in material science is achieving a desired function using structures fabricated with designed building blocks. Advanced synthetic and self-assembly techniques allow various nanomaterials to become promising building blocks, providing the control of the interaction between building blocks. The unique properties of nanomaterials can be transferred to structured systems. Among nanomaterials, inorganic nanoparticles such as gold nanoparticles (AuNPs), magnetic particles, and quantum dots (QDs) provide useful physical properties stemming from their inorganic core, large surface areas, and oriented surface functionalities. My research has focused on fabricating functional systems using gold nanoparticles (AuNPs), manipulating the interaction between AuNPs, bio-entities, …

Factor Inhibiting Hif's (Fih) Structure Controls O2 Activation And Reactivity, John A. Hangasky Iii

Doctoral Dissertations

Factor Inhibiting HIF (FIH) is a Fe(II)-αKG dependent oxygenase that acts as a cellular oxygen sensor in humans. FIH regulates the transcriptional activity of the hypoxia-inducible factor-1 (HIF-1a or HIF), a transcription factor responsible cellular O₂ homeostasis. Hydroxylation of the target residue HIF-Asn⁸⁰³, found in the C-terminal transactivation domain (CTAD), inactivates HIF-dependent gene expression. Central to FIH’s function is the activation of O₂ after CTAD binding. The mechanistic and structural features of FIH leading to tight coupling between CTAD binding and subsequent O₂-activation and reactivity are key for efficient O₂ sensing. Our mechanistic …

The Estradiol-Induced Transcriptome Of The Female Mouse Anteroventral Periventricular Nucleus: More Than Just A Kiss, Leah K. Aggison

Doctoral Dissertations

Estradiol (E₂) is critical in the reproductive mechanisms of mammals. In female rodents E₂ acts through the neurons of the anteroventral periventricular nucleus (AVPV) to exert neuroendocrine control over ovulation, via synaptic activation of the gonadotropin releasing hormone (GnRH) neurons. The neurocircuitry of the AVPV is complex, receiving input from the suprachiasmatic nucleus and ventral premammillary nucleus and the as well as projecting to organum vasculosum of lamina terminalis and the arcuate. This suggests a broader role for the AVPV as a center of multisignal-integration in regards to ovulation. I used full genome expression microarrays to assess …

Protein Behavior Directed By Heparin Charge And Chain Length, Burcu Baykal Minsky

Doctoral Dissertations

Glycosaminoglycans (GAGs), highly charged biological polyelectrolytes, are of growing importance as biomaterials and pharmaceutical drugs due to their immense range of physiological functions. They bind to many proteins; however, the degree of structural selectivity in GAG-protein interactions is largely unknown .Our studies have focused on the importance of heparin (a model GAG) charge and chain length in protein binding in order to explore its potential applications in biofunctional tissue scaffold materials, as polysaccharide drugs in anticoagulation, and as inhibitory agents in protein aggregation. We used electrospray ionization mass spectrometry, capillary electrophoresis, size exclusion chromatography, dynamic/static light scattering and electrostatic protein …

Novel Strategies To Modulate Synaptic Communication And Investigate The Role Of Hdac6 In Alzheimer’S Disease, Kathryne A. Medeiros

Doctoral Dissertations

Neuronal communication is mediated by chemical signaling at the synapse. The underlying molecular mechanisms of learning and memory are poorly understood. Very few tools are available to study how memories are formed in the mammalian brain. This dissertation focuses on developing novel strategies to study neural activity. Here we develop and use a chemical-genetic approach to enable target-specific photocontrol of inhibitory synaptic neurotransmission of GABA_A receptor subtypes. The tools developed here selectively photocontrolled GABA_A receptor subtypes. This enabled the investigation of the functional role these receptor subtypes have in inhibitory synaptic neurotransmission. This dissertation also focuses on identifying …

Structural Biology And Pharmacology Of Human Cathepsin A And Neuraminidase 1, Nilima Kolli

Doctoral Dissertations

Human cathepsin A (also known as Protective Protein/Cathepsin A, PPCA; E.C. 3.4.16.5) is a lysosomal serine carboxypeptidase. Cathepsin A is also involved in a complex with two other lysosomal enzymes: lysosomal neuraminidase (NEU1, E.C. 3.2.1.18) and β-galactosidase (GLB1, E.C. 3.2.1.23). Deficiency in cathepsin A and NEU1 result in the lysosomal storage diseases, galactosialidosis and sialidosis respectively. Deficiency in GLB1 results in G_M1 gangliosidosis and Morquio B diseases. Cathepsin A protease activity is spatially regulated by activation of the inactive precursor form to the mature form in the lysosome. Structural studies on the mature form of cathepsin A were performed …

Engineering Probes To Detect Cholesterol Accessibility On Membranes Using Perfringolysin O, Benjamin B. Johnson

Doctoral Dissertations

Cholesterol is an essential component of mammalian cell membranes and it is important to regulate the structure and function of lipid bilayers. Changes in cholesterol levels are involved in many physiological and pathological events such as the formation of arterial plaques, viral entry into cells, sperm capacitation, and receptor organization. Determination of cholesterol trafficking and distribution is essential for understanding how cells regulate cholesterol. A key factor in the regulation of cholesterol is cholesterol accessibility. Through it interactions in the membrane, cholesterol is sequestered below the surface of the membrane. Based on the composition of the membrane, a certain amount …

Ligand-Receptor Interactions For Supramolecular Disassembly With Applications In Screening And Drug Delivery, Diego Amado Torres

Doctoral Dissertations

Proteins have the capacity to bind specific sets of compounds known as ligands, these are small molecules with a recurrent theme in their molecular design that is a characteristic exploited here to (i) identify particular affinities of small molecules for proteins with the aim of using them as ligands, inhibitors, or targeting moieties in more complex systems by means of a methodology that screens small molecules based on protein affinity; (ii) decorate a self-assembling supramolecular system at different positions, making it responsive to a complementary protein with the aim of exploring differences in disassembly and sensitivity of the release of …

Applications And Improvements In The Molecular Modeling Of Protein And Ligand Interactions, Jason Bret Harris

Doctoral Dissertations

Understanding protein and ligand interactions is fundamental to treat disease and avoid toxicity in biological organisms. Molecular modeling is a helpful but imperfect tool used in computer-aided toxicology and drug discovery. In this work, molecular docking and structural informatics have been integrated with other modeling methods and physical experiments to better understand and improve predictions for protein and ligand interactions. Results presented as part of this research include:

1.) an application of single-protein docking for an intermediate state structure, specifically, modeling an intermediate state structure of alpha-1-antitrypsin and using the resulting model to virtually screen for chemical inhibitors that can …

Structure, Function And Regulation Of Two Isoforms Of Glutamine Synthetase From Soybean Root Nodules, Pintu Daulatrao Masalkar

Doctoral Dissertations

Glutamine synthetase (GS) is a major ammonia assimilatory enzyme in soybean nodules. The four isoforms of cytosolic glutamine synthetase (GS₁[glutamine synthetase 1]β[beta]1, GS₁β2, GS₁γ[gamma]1 and GS₁γ2) present in soybean nodules are 80% identical with respect to amino acid sequence, and share similar kinetic properties. It is shown all major GS₁ isoforms interact with nodulin 26, a member of the aquaporin family of membrane channels. Nodulin 26 is the major protein component of the symbiosome membrane (SM), where it serves a function as an ammonia and water channel. The site of interaction …

Acceleration And Verification Of Virtual High-Throughput Multiconformer Docking, Sally Rose Ellingson

Doctoral Dissertations

The work in this dissertation explores the use of massive computational power available through modern supercomputers as a virtual laboratory to aid drug discovery. As of November 2013, Tianhe-2, the fastest supercomputer in the world, has a theoretical performance peak of 54,902 TFlop/s or nearly 55 thousand trillion calculations per second. The Titan supercomputer located at Oak Ridge National Laboratory has 560,640 computing cores that can work in parallel to solve scientific problems. In order to harness this computational power to assist in drug discovery, tools are developed to aid in the preparation and analysis of high-throughput virtual docking screens, …

Biophysical Studies Of Axonal Transport, Leslie Cyle Conway

Doctoral Dissertations

Intracellular transport provides a mechanism by which cellular material, such as organelles, vesicles, and protein, can be actively transported throughout the cell. This process relies on the activity of the cytoskeletal filament, microtubules, and their associated motor proteins. These motors are able to walk along microtubule tracks while carrying cellular cargos to enable the fast, regulated transport of these cargos. In cells, these microtubule filaments act as a binding platform for numerous different motor species as well as microtubule-associated proteins (MAPs). In addition, these filaments often form higher order structures, such as microtubule bundles. How motors navigate such complex, crowded …

Honesty And Carotenoids In A Pigmented Female Fish, Alexandria Christine Brown

Doctoral Dissertations

The carotenoid tradeoff hypothesis states that diet-derived carotenoids are tradedoff among competing physiological demands, but this statement is rarely tested in ornamented females. The following dissertation tests the carotenoid tradeoff hypothesis in reverse sexually dimorphic convict cichlids (Amantitlania siquia) using carotenoidsupplemented diet treatments and a field-based study of carotenoid intake. Spectral, microscopic, and chemical analysis determined how females allocated the pigments to tissues and how those decisions affected their ventral patch coloration. The results presented in the current study show that carotenoids enhance offspring growth and survival, lower oxidative stress, and reduce the time to clear a parasite. The two …

Reactive Probes For Manipulating Polyketide Synthases, And Photoreactive Probes For Strained Alkyne Click Chemistry, Jon William Amoroso

Doctoral Dissertations

Polyketides are a broad class of natural products that have received attention from the scientific community because they are a rich mine of bioactive structures. The common thread that binds the class together is the method by which they are synthesized, by large enzymatic complexes called polyketide synthases (PKSs) which display assembly line like organization. A great deal of effort has been put into studying PKSs, but their mechanistic steps are still not perfectly understood. In order to further the study of PKSs and their components, we have developed a series of reactive small molecules that covalently modify specific sites …

Allosteric Regulation Of Dengue Virus Type 2 Protease, Muslum Yildiz

Doctoral Dissertations

Dengue Fever is a global problem with a worldwide effectiveness that put 2.5 Billion people under the risk, infect 50 million people and causes 30000-50000 people death each year. DHF was first recognized in the 1950s during the dengue epidemics in the Philippines and Thailand. By 1970 nine countries had experienced epidemic DHF and now, the number has increased more than fourfold and continues to rise. Today emerging DHF cases are causing increased dengue epidemics in the Americas, and in Asia, where all four dengue viruses are endemic. Vaccine development against Dengue Virus has been impossible to date, due to …