Department of Chemistry and Chemical Biology
Permanent URI for this community
Browse
Browsing Department of Chemistry and Chemical Biology by Issue Date
Now showing 1 - 10 of 208
Results Per Page
Sort Options
Item Rapid and Accurate Determination of Stern-Volmer Quenching Constants(1999) Goodpaster, John V.; McGuffin, Victoria LIn this work, a novel system has been designed, characterized, and validated for the determination of fluorescence quenching constants. Capillary flow injection methods are used to automate the preparation and mixing of the fluorophore and quencher solutions. Because of the small diameter of the capillary (75-200 mu m), fluorescence measurements can be made without corrections for primary and secondary absorbance effects. The fluorescence spectrometer is equipped with a charge-coupled device (CCD) that has a detection limit of 3.0 X 10-9 M (2.3 ppb) and a linear dynamic range of 10 5 for integration times of 0.01-10 s. This spectrometer has a 300 nm spectral range with 1 nm resolution, allowing the fluorescence quenching constants to be calculated at single wavelengths or over integrated wavelength ranges. This system was validated by comparison to traditional methods for the determination of Stern-Volmer constants for alternant and nonalternant polycyclic aromatic hydrocarbons with nitromethane and triethylamine.Item Direct detection and quantification of microRNAs(Elsevier, 2009-04-01) Hunt, Eric A.; Goulding, Ann M.; Deo, Sapna K.; Department of Chemistry & Chemical Biology, School of ScienceItem Molecular recognition of physiological substrate noradrenaline by the adrenaline-synthesizing enzyme PNMT and factors influencing its methyltransferase activity(Biochemical Society, 2009-08-27) Drinkwater, Nyssa; Gee, Christine L.; Puri, Munish; Criscione, Kevin R.; McLeish, Michael J.; Grunewald, Gary L.; Martin, Jennifer L.; Chemistry and Chemical Biology, School of ScienceSubstrate specificity is critically important for enzyme catalysis. In the adrenaline-synthesizing enzyme PNMT (phenylethanolamine N-methyltransferase), minor changes in substituents can convert substrates into inhibitors. Here we report the crystal structures of six human PNMT complexes, including the first structure of the enzyme in complex with its physiological ligand R-noradrenaline. Determining this structure required rapid soak methods because of the tendency for noradrenaline to oxidize. Comparison of the PNMT-noradrenaline complex with the previously determined PNMT-p-octopamine complex demonstrates that these two substrates form almost equivalent interactions with the enzyme and show that p-octopamine is a valid model substrate for PNMT. The crystal structures illustrate the adaptability of the PNMT substrate binding site in accepting multi-fused ring systems, such as substituted norbornene, as well as noradrenochrome, the oxidation product of noradrenaline. These results explain why only a subset of ligands recognized by PNMT are methylated by the enzyme; bulky substituents dictate the binding orientation of the ligand and can thereby place the acceptor amine too far from the donor methyl group for methylation to occur. We also show how the critical Glu(185) catalytic residue can be replaced by aspartic acid with a loss of only 10-fold in catalytic efficiency. This is because protein backbone movements place the Asp(185) carboxylate almost coincident with the carboxylate of Glu(185). Conversely, replacement of Glu(185) by glutamine reduces catalytic efficiency almost 300-fold, not only because of the loss of charge, but also because the variant residue does not adopt the same conformation as Glu(185)Item Solid-phase synthetic route to multiple derivatives of a fundamental peptide unit(MDPI, 2010-07-20) Scott, William L.; Zhou, Ziniu; Zajdel, Pawel; Pawlowski, Maciej; O'Donnell, Martin J.; Chemistry and Chemical Biology, School of ScienceAmino acids are Nature's combinatorial building blocks. When substituted on both the amino and carboxyl sides they become the basic scaffold present in all peptides and proteins. We report a solid-phase synthetic route to large combinatorial variations of this fundamental scaffold, extending the variety of substituted biomimetic molecules available to successfully implement the Distributed Drug Discovery (D3) project. In a single solid-phase sequence, compatible with basic amine substituents, three-point variation is performed at the amino acid a-carbon and the amino and carboxyl functionalities.Item Characterization of Automotive Paint Clear Coats by Ultraviolet Absorption Microspectrophotometry with Subsequent Chemometric Analysis(2010-10) Liszewski, Elisa A; Lewis, Simon W; Siegel, Jay A; Goodpaster, John V.Clear coats have been a staple in automobile paints for almost thirty years and are of forensic interest when comparing transferred and native paints. However, the ultraviolet (UV) absorbers in these paint layers are not typically characterized using UV microspectrophotometry, nor are the results studied using multivariate statistical methods. In this study, measurements were carried out by UV microspectrophotometry on 71 samples from American and Australian automobiles, with subsequent chemometric analysis of the absorbance spectra. Sample preparation proved to be vital in obtaining accurate absorbance spectra and a method involving peeling the clear coat layer and not using a mounting medium was preferred. Agglomerative hierarchical clustering indicated three main groups of spectra, corresponding to spectra with one, two, and three maxima. Principal components analysis confirmed this clustering and the factor loadings indicated that a substantial proportion of the variance in the data set originated from specific spectral regions (230–265 nm, 275–285 nm, and 300–370 nm). The three classes were well differentiated using discriminant analysis, where the cross-validation accuracy was 91.6% and the external validation accuracy was 81.1%. However, results showed no correlation between the make, model, and year of the automobiles.Item Solid-Phase Synthesis of Arylpiperazine Derivatives and Implementation of the Distributed Drug Discovery (D3) Project in the Search for CNS Agents(MDPI, 2011-05) Zajdel, Pawel; Król, Joanna; Grychowska, Katarzyna; Pawłowski, Maciej; Subra, Gilles; Nomezine, Gaël; Martinez, Jean; Satala, Grzegorz; Bojarski, Andrzej J.; Zhou, Ziniu; O'Donnell, Martin J.; Scott, William; Chemistry and Chemical Biology, School of ScienceWe have successfully implemented the concept of Distributed Drug Discovery (D3) in the search for CNS agents. Herein, we demonstrate, for the first time, student engagement from different sites around the globe in the development of new biologically active compounds. As an outcome we have synthesized a 24-membered library of arylpiperazine derivatives targeted to 5-HT1A and 5-HT2A receptors. The synthesis was simultaneously performed on BAL-MBHA-PS resin in Poland and the United States, and on BAL-PS-SynPhase Lanterns in France. The D3 project strategy opens the possibility of obtaining potent 5-HT1A/5-HT2A agents in a distributed fashion. While the biological testing is still centralized, this combination of distributed synthesis with screening will enable a D3 network of students world-wide to participate, as part of their education, in the synthesis and testing of this class of biologically active compounds.Item Solid-Phase Synthesis of Arylpiperazine Derivatives and Implementation of the Distributed Drug Discovery (D3) Project in the Search for CNS Agents(MDPI, 2011-05-19) Zajdel, Paweł; Król, Joanna; Grychowska, Katarzyna; Pawłowski, Maciej; Subra, Gilles; Nomezine, Gaël; Martinez, Jean; Satała, Grzegorz; Bojarski, Andrzej J.; Zhou, Ziniu; O’Donnell, Martin J.; Scott, William L.; Chemistry and Chemical Biology, School of ScienceWe have successfully implemented the concept of Distributed Drug Discovery (D3) in the search for CNS agents. Herein, we demonstrate, for the first time, student engagement from different sites around the globe in the development of new biologically active compounds. As an outcome we have synthesized a 24-membered library of arylpiperazine derivatives targeted to 5-HT1A and 5-HT2A receptors. The synthesis was simultaneously performed on BAL-MBHA-PS resin in Poland and the United States, and on BAL-PS-SynPhase Lanterns in France. The D3 project strategy opens the possibility of obtaining potent 5-HT1A/5-HT2A agents in a distributed fashion. While the biological testing is still centralized, this combination of distributed synthesis with screening will enable a D3 network of students world-wide to participate, as part of their education, in the synthesis and testing of this class of biologically active compounds.Item Physisorbed Polymer-Tethered Lipid Bilayer with Lipopolymer Gradient(MDPI, 2012-11) Lin, Yu-Hung; Minner, Daniel E.; Herring, Vincent L.; Naumann, Christoph A.; Chemistry and Chemical Biology, School of SciencePhysisorbed polymer-tethered lipid bilayers consisting of phospholipids and lipopolymers represent an attractive planar model membrane platform, in which bilayer fluidity and membrane elastic properties can be regulated through lipopolymer molar concentration. Herein we report a method for the fabrication of such a planar model membrane system with a lateral gradient of lipopolymer density. In addition, a procedure is described, which leads to a sharp boundary between regions of low and high lipopolymer molar concentrations. Resulting gradients and sharp boundaries are visualized on the basis of membrane buckling structures at elevated lipopolymer concentrations using epifluorescence microscopy and atomic force microscopy. Furthermore, results from spot photobleaching experiments are presented, which provide insight into the lipid lateral fluidity in these model membrane architectures. The presented experimental data highlight a planar, solid-supported membrane characterized by fascinating length scale-dependent dynamics and elastic properties with remarkable parallels to those observed in cellular membranes.Item Cholesterol-Induced Buckling in Physisorbed Polymer-Tethered Lipid Monolayers(MDPI, 2013-04-06) Hussain, Noor F.; Siegel, Amanda P.; Johnson, Merrell A.; Naumann, Christoph A.; Chemistry and Chemical Biology, School of ScienceThe influence of cholesterol concentration on the formation of buckling structures is studied in a physisorbed polymer-tethered lipid monolayer system using epifluorescence microscopy (EPI) and atomic force microscopy (AFM). The monolayer system, built using the Langmuir-Blodgett (LB) technique, consists of 3 mol % poly(ethylene glycol) (PEG) lipopolymers and various concentrations of the phospholipid, 1-stearoyl-2-oleoyl-sn-glycero-3-phosphocholine (SOPC), and cholesterol (CHOL). In the absence of CHOL, AFM micrographs show only occasional buckling structures, which is caused by the presence of the lipopolymers in the monolayer. In contrast, a gradual increase of CHOL concentration in the range of 0–40 mol % leads to fascinating film stress relaxation phenomena in the form of enhanced membrane buckling. Buckling structures are moderately deficient in CHOL, but do not cause any notable phospholipid-lipopolymer phase separation. Our experiments demonstrate that membrane buckling in physisorbed polymer-tethered membranes can be controlled through CHOL-mediated adjustment of membrane elastic properties. They further show that CHOL may have a notable impact on molecular confinement in the presence of crowding agents, such as lipopolymers. Our results are significant, because they offer an intriguing prospective on the role of CHOL on the material properties in complex membrane architecture.Item Quantitative Analysis of Humectants in Tobacco Products Using Gas Chromatography (GC) with Simultaneous Mass Spectrometry (MSD) and Flame Ionization Detection (FID)(2013-06) Rainey, Christina L; Shifflett, John R; Goodpaster, John V.; Bezabeh, Dawit ZThis paper describes the modification of an existing gas chromatographic (GC) method to incorporate simultaneous mass spectrometric (MSD) and flame ionization detection (FID) into the analysis of tobacco humectants. Glycerol, propylene glycol, and triethylene glycol were analyzed in tobacco labeled as roll-your-own (RYO), cigar, cigarette, moist snuff, and hookah tobacco. Tobacco was extracted in methanol containing 1,3-butanediol (internal standard), filtered, and separated on a 15 m megabore DB-Wax column. Post-column flow was distributed using a microfluidic splitter between the MSD and FID for simultaneous detection. The limits of detection for the FID detector were 0.5 μg/mL (propylene glycol and triethylene glycol) and 0.25 μg/mL (glycerol) with a linear range of 2–2000 μg/mL (propylene glycol and triethylene glycol) and 1–4000 μg/mL (glycerol). The limits of detection for the MSD detector were 2 μg/mL (propylene glycol and triethylene glycol) and 4 μg/mL (glycerol) with a linear range of 20–2000 μg/mL (propylene glycol and triethylene glycol) and 40–4000 μg/mL (glycerol). Significant improvement in the sensitivity of the MSD can be achieved by employing selective ion monitoring (SIM) detection mode. Although a high degree of correlation was observed between the results from FID and MSD analyses, marginal chromatographic resolution between glycerol and triethylene glycol limits the applicability of FID to samples containing low levels of both of these humectants. Utilizing MSD greatly improves the reliability of quantitative results because compensation for inadequate chromatographic resolution can be accomplished with mass selectivity in detection.