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Development Of Bacterial Quorum Sensing Inhibitors And Molecular Probes, Hanjing Peng

Chemistry Dissertations

Bacterial quorum sensing is regarded as a novel target for the design of antimicrobials. Based on lead structures identified from HTS, 39 analogues have been synthesized and evaluated in Vibrio haveyi. Potent inhibitors with IC₅₀ values at single-digit micromolar concentrations for AI-2 mediated quorum sensing have been identified. On the second project, post-synthesis modifications of DNA provide easy functionalizations for expanded applications such as aptamer selection. A CBT-modified thymidine analogue (CBT-TTP) has been synthesized and used for enzymatic incorporation into DNA. Post-synthesis modifications through condensation with 1,2-aminothiol for installation of a boronic acid moiety or a fluorophore have …

Biophysical Characterization Of Synthetic Imidazole And Pyrrole Containing Analogues Of Netropsin And Distamycin That Target Specific Dna Sequences For The Treatment Of Various Diseases, Joseph P. Ramos

Chemistry Dissertations

The development of small-molecules which target nucleic acids, more specifically the minor groove of DNA, in a sequence specific manner and control gene expression are currently being investigated as potential therapeutic compounds for the treatment of various diseases, including cancer, as well as viral and bacterial infections. The naturally occurring compounds netropsin and distamycin have been shown to demonstrate antitumor and antibacterial properties. Currently, there are synthetic efforts to create pyrrole and imidazole-containing polyamide derivatives of netropsin and distamycin that show potential as medicinal agents. Synthetic pyrrole and imidazole-containing polyamides are potentially useful for targeting and modulating the expression of …

Development Of Antimicrobial Agent With Novel Mechanisms Of Actions And 1,2,4,5-Tetrazine Click Chemistry And Its Application In Dna Postsynthetic Functionalization, Weixuan Chen

Chemistry Dissertations

SecA ATPase is a critical member of the Sec system, which is important in the translocation of membrane and secreted polypeptides/proteins in bacteria. Small molecule inhibitors can be very useful research tools as well as leads for future antimicrobial agent development. Based on previous virtual screening work, we optimized the structures of two hit compounds and obtained SecA ATPase inhibitors with IC50 in the single digit micromolar range. These represent the first low micromolar inhibitors of bacterial SecA and will be very useful for mechanistic studies. Post synthetic modification is an important and efficient way of DNA functionalization especially in …

Electrochemical Characterizations And Theoretical Simulations Of Transport Behaviors At Nanoscale Geometries And Interfaces, Juan Liu

Chemistry Dissertations

Since single nanopores were firstly proposed as a potential rapid and low-cost tool for DNA sequencing in 1990s (PNAS, 1996, 93, 13770), extensive studies on both biological and synthetic nanopores and nanochannels have been reported. Nanochannel based stochastic sensing at single molecular level has been widely reported through the detection of transient ionic current changes induced by geometry blockage due to analytes translocation. Novel properties, including ion current rectification (ICR), memristive and memcapacitive behaviors were reported. These fundamental properties of nanochannels arise from the nanoscale dimensions and enables applications not only in single molecule sensing, but …

Synthesis And Energetics Of Gold Nanoclusters Tailored By Interfacial Bonding Structure, Tang Zhenghua

Chemistry Dissertations

In addition to the well known quantum confinement effects resulted from size and shape, interfacial bond structure is another factor, affecting the properties of the nanomaterial that is rarely studied. Inspired by the “Au-S-Au” staple motif discovered from the crystal structure of monothiol protected Au102 nanocluster (Science, 2007, 318, 430), dithiol molecules (e. g. 1, 2-dithiol, 1, 4-dithiol, etc.) with molecular structural constraint have been employed to create dithiolate protected clusters or mixed monothiolate and dithiolate protected clusters. The structure and properties of the Au clusters are expected to change due to two effects: The entropy …

Biophysical Characterization Of The Binding Of Homologous Anthraquinone Amides To Dna, Shirlene R. Jackson Beckford

Chemistry Dissertations

The synthesis of four homologous anthraquinones (AQ I-IV) bearing increasing lengths of polyethylene glycol (PEG) side chains and their binding to AT- and GC-rich DNA hairpins are reported. The molecules were designed such that the cationic charge is at a constant position and the ethylene glycol units chosen to allow significant increases in size with minimal changes in hydrophobicity. The mode and affinity of binding were assessed using circular dichroism (CD), nuclear magnetic resonance (NMR), surface plasmon resonance (SPR), and isothermal titration calorimetry (ITC). The binding affinity decreased as the AQ chain length increased along the series with …

Calcium Modulates Mglur1 Folding In Er In The Trafficking Process And Regulates The Drug Activity Upon The Receptor Expressing On The Cell Membrane, Yusheng Jiang

Chemistry Dissertations

Metabotropic glutamate receptor 1α (mGluR1α) exerts important effects on numerous neurological processes. Although mGluR1α is known to respond to extracellular Ca²⁺ ([Ca²⁺]_o) and the crystal structures of the extracellular domains (ECDs) of several mGluRs have been determined, the calcium-binding site(s) and structural determinants of Ca²⁺-modulated signaling in the Glu receptor family remain elusive. Here, we identify a novel Ca²⁺-binding site (Site 1) in the ECD-mGluR1α using a recently developed computational algorithm. This predicted site (D318, E325, D322 and the bound L-Glu) is situated in the hinge region in the ECD-mGluR1α adjacent …

Kinetic Mechanism And Inhibitory Study Of Protein Arginine Methyltransferase 1, You Feng

Chemistry Dissertations

Protein arginine methyltransferase 1 (PRMT1) is a key posttranslational modification enzyme that catalyzes the methylation of specific arginine residues in histone and nonhistone protein substrates, regulating diverse cellular processes such as transcriptional initiation, RNA splicing, DNA repair, and signal transduction. Recently the essential roles of PRMT1 in cancer and cardiovascular complications have intrigued much attention. Developing effective PRMT inhibitors therefore is of significant therapeutic value. The research on PRMT inhibitor development however is greatly hindered by poor understanding of the biochemical basis of protein arginine methylation and lack of effective assays for PRMT1 inhibitor screening.

Herein, we report our effort …

Characterization Of The Heme Uptake Pathway Proteins From Streptococcus Pyogenes And Corynebacterium Diphtheriae, Neval Akbas

Chemistry Dissertations

In Streptococcus pyogenes, the protein SiaA (HtsA) is part of a heme uptake pathway system and involved in heme transfer from Shp to the ABC transporter. SiaA mutants, in which alanine replaces the axial histidine (H229) and methionine (M79) ligands, as well as a lysine (K61) and cysteine (C58) located near the heme propionates, are reported. Studies on a mutant of a cysteine expected to be at a distance from the propionates (C47A) are also reported. The coordination state and spin state of the selected mutants were determined via Resonance Raman studies. The pK_a values of mutants …

Modulation And Recognition Of Nucleic Acid Structures, Alexander M. Spring

Chemistry Dissertations

The fidelity of an organism’s genome is central to biology. DNA, however, is constantly being damaged and modified by a variety of sources. As a result of these changes, repair enzymes, polymerases, and other interrogating biomolecules must be able to recognize, repair, and adapt to a multitude of different structures and dynamics presented. Manipulation of natural systems via the development and introduction of novel bases and DNA structures only adds to this complexity. In addition, specific RNA sequences are becoming more prevalent therapeutic and diagnostic targets. These include retroviruses and other viruses that maintain their genome with RNA. Unlike DNA, …

Dissecting Key Determinants For Calcium And Calmodulin Regulation Of Gap Junction And Viral Protein, Yanyi Chen

Chemistry Dissertations

Calcium and calmodulin are implicated in mediating the Ca²⁺-dependent regulation of gap junctions that are essential for the intercellular transmission of molecules such as nutrients, metabolites, metal ions and signal messengers (< 1000 Da) through its specialized cell membrane channels and communication to extracellular environment. To understand the key determinants for calcium and calmodulin regulation of gap junction, in this study, we identified a calmodulin binding domain in the second half of the intracellular loop of Cxonnexin50 (the major gap junction protein found in an eye lens) using peptide fragments that encompass predicted CaM binding sites and various biophysical methods. Our study provides the first direct evidence that CaM binds to a specific region of the ubiquitous gap junction protein Cx50 in a Ca²⁺-dependent manner. Furthermore, two novel CaM binding regions in cytosolic loop and C-termini of Connexin43 (the most ubiquitous connexin) have been shown to interact with CaM with different binding modes in the presence of Ca²⁺ using high resolution NMR. Our results also elucidate the molecular determinants of regulation of gap junction by multiple CaM targeting regions and provide insight into the molecular basis of …

Rational Design And Application Of Genetically Encoded Fluorescent Reporters In Cellular Physiology, Shen Tang

Chemistry Dissertations

Fluorescent protein based genetically encoded fluorescent reporters play an improtant role in understanding the cellular physiology by directly monitoring real-time cellular signaling pathways with fluorescent microscope.

Quantitative analysis of Ca²⁺ fluctuations in the endoplasmic/sarcoplasmic reticulum (ER/SR) is essential to defining the mechanisms of Ca²⁺-dependent signaling under physiological and pathological conditions. Here, we developed a novel class of genetically encoded indicators by designing a Ca²⁺ binding site in the enhanced green fluorescent protein (EGFP). One of them, CatchER (Calcium sensor for detecting high concentration in the ER), exhibits unprecedented Ca²⁺ release kinetics with an off-rate estimated …

Structure And Function Studies Of Selenium Substituted Nucleic Acids, Wen Zhang

Chemistry Dissertations

Nucleic acids are responsible for the storage of genetic information and directly participate in gene replication, transcription and expression, and thereby the control of nucleic acids leads to the regulation of genetic information flow and gene expression. Meanwhile, many non-coding RNAs are in-volved in signal transduction directly. Moreover, nucleic acid-based therapeutic strategies have been lead to drug candidates and are effective tools in drug discovery and disease study at the molecular level as well as the genetic level. Consequently, the 3D crystal structure study and related functional research on natural and unnatural nucleic acids have become very popular area, expanding …