Biochemistry, Biophysics, and Structural Biology Commons^™

Paper-Based Standard Addition Assays, Cory A. Chaplan, Haydn T. Mitchell, Andres W. Martinez

Chemistry and Biochemistry

Standard addition assays conducted on paper-based microfluidic devices are introduced as an alternative to external standards for calibrating quantitative tests. To demonstrate this technique, a colorimetric, paper-based, standard addition assay was optimized for the determination of glucose concentrations in the range of 0 to 5 mM. Comparable results were obtained from the assay via digital image colorimetry under three different lighting conditions.

Polymeric Monolithic Stationary Phases For Capillary Reversed-Phase Liquid Chromatography Of Small Molecules, Kun Liu

Theses and Dissertations

Highly cross-linked monoliths prepared from single cross-linking monomers were found to increase surface area and stability. Therefore, seven cross-linking monomers, i.e., 1,3-butanediol dimethacrylate (1,3-BDDMA), 1,4-butanediol dimethacrylate (1,4-BDDMA), neopentyl glycol dimethacrylate (NPGDMA), 1,5-pentanediol dimethacrylate (1,5-PDDMA), 1,6-hexanediol dimethacrylate (1,6-HDDMA), 1,10-decanediol dimethacrylate (1,10-DDDMA), and 1,12-dodecanediol dimethacrylate (1,12-DoDDMA), were used to synthesize highly cross-linked monolithic columns in 75-µm i.d. capillaries by one-step UV-initiated polymerization using dodecanol and methanol as porogens for reversed-phase liquid chromatography (RPLC) of small molecules. Selection of porogen type and concentration was investigated in detail. Isocratic elution of alkylbenzenes at a flow rate of 300 nL/min was conducted for all of …

Bsa–Boronic Acid Conjugate As Lectin Mimetics, Satya Nandana Narla, Poornima Pinnamaneni, Huan Nie, Yu Li, Xue-Long Sun

Chemistry Faculty Publications

We report bovine serum albumin (BSA)–boronic acid (BA) conjugates as lectin mimetics and their glyco-capturing capacity. The BSA–BA conjugates were synthesized by amidation of carboxylic acid groups in BSA with aminophenyl boronic acid in the presence of EDC, and were characterized by Alizarin Red S (ARS) assay and SDS–PAGE gel. The BSA–BA conjugates were immobilized onto maleimide-functionalized silica beads and their sugar capturing capacity and specificity were confirmed by ARS displacement assay. Further, surface plasmon resonance (SPR) analysis of the glyco-capturing activity of the BSA–BA conjugates was conducted by immobilizing BSA–BA onto SPR gold chip. Overall, we demonstrated a BSA–BA-based …

Collisional Dynamic Elements Of The Pyrazine - N2o System:Middle And Low J States, La Moyne Tyler Mix

Theses and Dissertations

Unimolecular reactions based on the Lindemann - Hinchelwood mechanism are important to understanding combustion and atmospheric processes. The main feature of this mechanism is the energy transfer probability distribution function, P(E',E). We have chosen to study P(E',E) through gas phase collisional dynamics probed with IR transient absorption spectroscopy. Post-collision absorption line widths for the pyrazine-N2O system are used to calculate lab frame translational temperatures. The translational temperatures reveal that collisions with large rotational energy transfer also transfer large amounts of translational energy. For J states >47 the relationship is linear indicating a constant impact parameter. Line widths for J=47 through …

Effects Of Charge And Substituent On The S∙∙∙N Chalcogen Bond, U. Adhikari, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

Neutral complexes containing a S···N chalcogen bond are compared with similar systems in which a positive charge has been added to the S-containing electron acceptor, using high-level ab initio calculations. The effects on both XS···N and XS+···N bonds are evaluated for a range of different substituents X = CH3, CF3, NH2, NO2, OH, Cl, and F, using NH3 as the common electron donor. The binding energy of XMeS···NH3 varies between 2.3 and 4.3 kcal/mol, with the strongest interaction occurring for X = F. The binding is strengthened by a factor of 2–10 in charged XH2S+···NH3 complexes, reaching a maximum of …

Applications Of Epr With An Emphasis On Tau Fibril Structure, Virginia Meyer

Electronic Theses and Dissertations

Substances containing unpaired electrons have been studied by electron paramagnetic resonance (EPR) for nearly 70 years. With continual development and enhancement of EPR techniques, questions have arisen regarding optimum method selection for a given sample based on its properties. In this work, radiation defects, natural lattice defects, solid organic radicals, radicals in solution, and spin-labeled proteins were analyzed using CW, pulse, and rapid scan EPR to compare methods. Studies of solid BDPA, E' in quartz, N_s⁰ in diamond, and a-Si:H, showed that rapid scan could overcome many obstacles presented by other techniques, cementing rapid scan as an effective …

Investigation Into The Cellular Actions Of Carnosine And C-Peptide, Emma H. Gardner

Theses, Dissertations and Capstones

Carnosine is a dipeptide composed of beta-alanine and histidine found exclusively in long-lived animal tissues. The cellular action of carnosine is still under extensive investigation; however, it has been proposed to have a role as an anti-oxidant and oxygen free radical scavenger, a physiological buffer, a heavy metal chelator, and has been implicated as an anti-aging agent.^2,4 Our lab has been studying the interaction between carnosine and heme by analyzing both the effect carnosine has on the glycation of the heme containing protein cytochrome c and the interaction of carnosine with free hemin. We have observed that the addition …

Competition Between Lone Pair-Π, Halogen Bond, And Hydrogen Bond In Adducts Of Water With Perhalogenated Alkenes C2clnf4-N (N = 0-4), U. Adhikari, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

A thorough search of the potential energy surface is carried out for heterodimers of water with C2ClnF4−n. Three different types of interactions are observed. Structures dominated by a lone pair–π interaction have the highest binding energies, and are stabilized by charge transfer from O lone pairs of H2O to the Csingle bondC π* antibonding orbital of the alkene. Halogen-bonded O⋯Cl complexes are slightly less strongly bound, followed by OH⋯X hydrogen bonds. The replacements of Cl by F atoms have only small effects upon binding energies. Inclusion of vibrational and entropic effects removes the clear energetic superiority of lp–π binding energies. …

A Td-Dft Study Of The Absorption Spectra Of Mono-Nitrated Fluoranthenes [Abstract], Kefa Karimu Onchoke

Faculty Publications

No abstract provided.

Vibrational Spectroscopy: Disease Diagnostics And Beyond, Hugh Byrne, Kamila Ostrowska, Haq Nawaz, Jennifer Dorney, Aidan Meade, Franck Bonnier, Fiona Lyng

Books/Book Chapters

Summary

This chapter outlines some developments in the applications of vibrational spectroscopy for disease diagnostics and demonstrates how the applications of the spectroscopic techniques can be extended to the analysis and evaluation of disease aetiology and the mechanisms of interaction and the cellular and subcellular responses to, for example chemotherapeutic agents and nanoparticles. The primary emphasis is on Raman spectroscopy, although some examples are based on infrared absorption spectroscopy. The studies presented are chosen to illustrate how a range of multivariate analytical techniques can be employed to maximize the potential benefits of the complex spectral information obtained from tissue or …

Complexation Of N So2 Molecules (N=1,2,3) With Formaldehyde And Thioformaldehyde, L. M. Azofra, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

Ab initio and density functional theory calculations are used to examine complexes formed between H2CO and H2CS with 1, 2, and 3 molecules of SO2. The nature of the interactions is probed by a variety of means, including electrostatic potentials, natural bond orbital, atoms in molecules, energy decomposition, and electron density redistribution maps. The dimers are relatively strongly bound, with interaction energies exceeding 5 kcal/mol. The structures are cyclic, containing both a O/S⋯S chalcogen bond and a CH⋯O H-bond. Addition of a second SO2 molecule leads to a variety of heterotrimer structures, most of which resemble the original dimer, where …

Complexes Containing Co2 And So2. Mixed Dimers, Trimers And Tetramers, L. M. Azofra, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

Mixed dimers, trimers and tetramers composed of SO2 and CO2 molecules are examined by ab initio calculations to identify all minimum energy structures. While AIM formalism leads to the idea of a pair of C···O bonds in the most stable heterodimer, bound by some 2 kcal mol(-1), NBO analysis describes the bonding in terms of charge transfer from O lone pairs of SO2 to the CO π* antibonding orbitals. The second minimum on the surface, just slightly less stable, is described by AIM as containing a single O···O chalcogen bond. The NBO picture is that of two transfers in opposite …

Interaction Between Temozolomide And Water: Preferred Binding Sites, O. E. Kasende, A. Matondo, M. Muzomwe, J. T. Muya, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

Computational methods are used to predict the most favorable site of temozolomide towards attack by a water molecule. The energetics of the various complexes are presented as well as their geometries, including perturbations of each subunit caused by the presence of the other. Molecular electrostatic potential and Natural Bond Orbital (NBO) data are used to understand the interactions which conclude the terminal amide group is the preferred attack site where water can act as simultaneous proton donor and acceptor. Other potential proton acceptor N atoms within the aromatic ring structure represent weaker binding sites. Some of the less strongly bound …

Substituent Effects In The Noncovalent Bonding Of So2 To Molecules Containing A Carbonyl Group. The Dominating Role Of The Chalcogen Bond, L. M. Azofra, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

The SO2 molecule is paired with a number of carbonyl-containing molecules, and the properties of the resulting complexes are calculated by high-level ab initio theory. The global minimum of each pair is held together primarily by a S···O chalcogen bond wherein the lone pairs of the carbonyl O transfer charge to the π* antibonding SO orbital, supplemented by smaller contributions from weak CH···O H-bonds. The binding energies vary between 4.2 and 8.6 kcal/mol, competitive with even some of the stronger noncovalent forces such as H-bonds and halogen bonds. The geometrical arrangement places the carbonyl O atom above the plane of …

An Exploration Of The Ozone Dimer Potential Energy Surface, L. M. Azofra, I. Alkorta, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

The (O3)2 dimer potential energy surface is thoroughly explored at the ab initio CCSD(T) computational level. Five minima are characterized with binding energies between 0.35 and 2.24 kcal/mol. The most stable may be characterized as slipped parallel, with the two O3 monomers situated in parallel planes. Partitioning of the interaction energy points to dispersion and exchange as the prime contributors to the stability, with varying contributions from electrostatic energy, which is repulsive in one case. Atoms in Molecules analysis of the wavefunction presents specific O⋯O bonding interactions, whose number is related to the overall stability of each dimer. All internal …

Intrinsic Delocalization During The Decay Of Excitons In Polymeric Solar Cells, Thomas George, W. Chen, D. Jiang, R. Chen, S. Li

Chemistry & Biochemistry Faculty Works

In bulk heterojunction polymer solar cells, external photoexcitation results in localized excitons in the polymer chain. After hot exciton formation and subsequent relaxation, the dipole moment drives the electron to partially transfer to extended orbitals from the original localized ones, leading to self-delocalization. Based on the dynamic fluorescence spectra, the delocalization of excitons is revealed to be an intrinsic property dominated by exciton decay, acting as a bridge for the exciton to diffuse in the polymeric solar cell. The modification of the dipole moment enhances the efficiency of polymer solar cells.

Field Measurements Of Trace Gases Emitted By Prescribed Fires In Southeastern Us Pine Forests Using An Open-Path Ftir System, S. K. Akagi, I. R. Burling, A. Mendoza, T. J. Johnson, M. Cameron, David W. T. Griffith, C. Paton-Walsh, D. R. Weise, J. Reardon, Robert Yokelson

Chemistry and Biochemistry Faculty Publications

We report trace-gas emission factors from three pine-understory prescribed fires in South Carolina, US measured during the fall of 2011. The fires were more intense than many prescribed burns because the fuels included mature pine stands not subjected to prescribed fire in decades that were lit following an extended drought. Emission factors were measured with a fixed open-path Fourier transform infrared (OP-FTIR) system that was deployed on the fire control lines. We compare these emission factors to those measured with a roving, point sampling, land-based FTIR and an airborne FTIR deployed on the same fires. We also compare to emission …

Aerosol Single Scattering Albedo Dependence On Biomass Combustion Efficiency: Laboratory And Field Studies, Shang Liu, Allison C. Aiken, Caleb Arata, Manvendra K. Dubey, C. Stockwell, Robert Yokelson, Elizabeth A. Stone, Thilina Jayarathne, Allen L. Robinson, Paul J. Demott, Sonia M. Kreidenweis

Chemistry and Biochemistry Faculty Publications

Single scattering albedo (ω) of fresh biomass burning (BB) aerosols produced from 92 controlled laboratory combustion experiments of 20 different woods and grasses was analyzed to determine the factors that control the variability in ω. Results show that ω varies strongly with fire-integrated modified combustion efficiency (MCE_FI)—higher MCE_FI results in lower ω values and greater spectral dependence of ω. A parameterization of ω as a function of MCE_FI for fresh BB aerosols is derived from the laboratory data and is evaluated by field observations from two wildfires. The parameterization suggests that MCE_FI explains 60% of …

Assembly And Function Of Macromolecular Complexes For Accurate Trna Aminoacylation In Helicobacter Pylori, Gayathri Niroshani Silva

Wayne State University Dissertations

ABSTRACT

ASSEMBLY AND FUNCTION OF MACROMOLECULAR COMPLEXES FOR ACCURATE TRNA AMINOACYLATION IN HELICOBACTER PYLORI

by

GAYATHRI SILVA

January 2014

Advisor: Dr. Tamara L. Hendrickson

Major: Chemistry (Biochemistry)

Degree: Doctor of Philosophy

Abstract

The aminoacylation of tRNA is a critical step in maintaining the accuracy of the genetic code. Many microorganisms are missing one or more aminoacyl tRNA synthetases (aaRSs) and rely on indirect pathways to produce certain aa–tRNAs. In Helicobacter pylori (H. pylori), the genes encoding both asparaginyl tRNA synthetase (AsnRS) and glutaminyl tRNA synthetase (GlnRS) are missing and the organism consequently relies on the indirect pathway for …

Structural And Functional Characterization Of Proteins Of Unknown Function (Hp0495, Hp0100 And Hp1259) In Helicobacter Pylori, Shirin Fatma

Wayne State University Dissertations

H. pylori is missing the glutaminyl- and asparaginyl-tRNA synthetases (GlnRS and AsnRS, respectively). Consequently, H. pylori uses an indirect aminoacylation pathway to generate Gln-tRNAGln and Asn-tRNAAsn. Within this process, Asn-tRNAAsn is produced by misacylation of tRNAAsn with aspartate by a non-discriminating aspartyl-tRNA synthetase (ND-AspRS). Next, the heterotrimeric, glutamine-dependent amidotransferase (called AdT or GatCAB) converts the misacylated Asp-tRNAAsn into Asn-tRNAAsn. A parallel pathway exists for the synthesis of Gln-tRNAGln, wherein misacylation of tRNAGln with glutamate is catalyzed by a tRNAGln-specific glutamyl-tRNA synthetase (GluRS2) to generate Glu-tRNAGln; this misacylated intermediate is converted to Gln-tRNAGln by the same AdT. This dependence on misacylated …

Investigation Into The Binding Interactions Of Klenow Fragment To Dna Modified With Carcinogens Af And Aaf Using Surface Plasmon Resonance, Ashley M. Floyd

Wayne State University Dissertations

The two major forms of DNA adducts from the carcinogen N-acetoxyacetyl-2-aminofluorene, N-(deoxygunanonsin-8-yl)-2-acetylaminofluorene (dG-C8-AAF) and N-(deoxyguanosin-8-yl)-2-aminofluorene (dG-C8-AF), are both known to impede replication, though in different ways. AAF is a strong block to replication leading to frameshift mutations, while the AF adduct is more easily bypassed, causing base substitutions. Surface plasmon resonance (SPR) was used to study the binding of exonuclease deficient E. coli polymerase I, Klenow fragment (KF), to DNA modified with AF or AAF at two locations: as a templating base or in the last formed base pair. KF binding to the modified DNA bases was also monitored to …

Strongly Bound Noncovalent (So3)N:H2co Complexes (N = 1, 2), L. M. Azofra, I. Alkorta, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

The potential energy surfaces (PES) for the SO3:H2CO and (SO3)2:H2CO complexes were thoroughly examined at the MP2/aug-cc-pVDZ computational level. Heterodimers and trimers are held together primarily by SO chalcogen bonds, supplemented by weaker CHO and/or OC bonds. The nature of the interactions is probed by a variety of means, including electrostatic potentials, AIM, NBO, energy decomposition, and electron density redistribution maps. The most stable dimer is strongly bound, with an interaction energy exceeding 10 kcal mol(-1). Trimers adopt the geometry of the most stable dimer, with an added SO3 molecule situated so as to interact with both of the original …

Basic Features Of A Cell Electroporation Model: Illustrative Behavior For Two Very Different Pulses, Reuben S. Son, Kyle C. Smith, Thiruvallur R. Gowrishankar, P. Thomas Vernier, James C. Weaver

Bioelectrics Publications

Science increasingly involves complex modeling. Here we describe a model for cell electroporation in which membrane properties are dynamically modified by poration. Spatial scales range from cell membrane thickness (5 nm) to a typical mammalian cell radius (10 μm), and can be used with idealized and experimental pulse waveforms. The model consists of traditional passive components and additional active components representing nonequilibrium processes. Model responses include measurable quantities: transmembrane voltage, membrane electrical conductance, and solute transport rates and amounts for the representative "long" and "short" pulses. The long pulse-1.5 kV/cm, 100 μs-evolves two pore subpopulations with a valley at ~5 …

An Unexpected Particle Oscillation For Electrophoresis In Viscoelastic Fluids Through A Microchannel Constriction, Xinyu Lu, Saurin Patel, Meng Zhang, Sang Woo Joo, Shizhi Qian, Amod Ogale, Xiangchun Xuan

Mechanical & Aerospace Engineering Faculty Publications

Electrophoresis plays an important role in many applications, which, however, has so far been extensively studied in Newtonian fluids only. This work presents the first experimental investigation of particle electrophoresis in viscoelastic polyethylene oxide (PEO) solutions through a microchannel constriction under pure DC electric fields. An oscillatory particle motion is observed in the constriction region, which is distinctly different from the particle behavior in a polymer-free Newtonian fluid. This stream-wise particle oscillation continues until a sufficient number of particles form a chain to pass through the constriction completely. It is speculated that such an unexpected particle oscillating phenomenon is a …

Hiv-1 Rna Dimerization At Single Molecule Level, Hansini R. Mundigala

Wayne State University Dissertations

The Dimerization Initiation Sequence (DIS) is a conserved hairpin-loop motif on the 5' UTR of the HIV-1 genome. It plays an important role in genome dimerization through formation of a "kissing complex" intermediate between two homologous DIS sequences. This bimolecular kissing complex ultimately leads to the formation of an extended RNA duplex. Understanding the kinetics of this interaction is key to exploiting DIS as a possible drug target against HIV. We wish to report a novel study that makes an important contribution to understanding the dimerization mechanism of HIV-1 RNA in vitro. Our work has employed single-molecule fluorescence resonance energy …

Effects Of Statin Drugs And Tocotrienol Rich Fraction Supplementation In Chronic Hemodialysis Patients And Metabolomic Profile, Eno Latifi

Wayne State University Theses

Chronic kidney disease (CKD) is known as a heterogeneous disorder which currently is on the rise and lately has been classified as a public health issues in the United State and worldwide. CKD is an irreversible and progressive disease which can lead to kidney failure, and this is depicted by the advanced stage of the disorder when it reaches the point, that is classified as end stage of renal disease (ESRD) (Stage 5 of CKD) (eGRF <15 mL/min/ 1.73 m2 working capacity), where both organs are in a total or permanent kidney failure. End-Stage renal disease patients, on hemodialysis have been associated to experience an accelerated form of atherosclerosis, which is induced by inflammation, impairment of antioxidant system and elevated oxidative stress. Since the problem effecting ESRD patients is multifactorial, the objective of this investigation is to explore and look at the effects of supplementing with vitamin E-tocotrienol rich fraction (TRF), a micronutrient which has anti-inflammatory, antioxidant, and lipid lower capabilities into tackling these comorbid conditions experienced by this population. Therefore the aims of this investigation will be to explore changes in lipid profiles, inflammatory markers, and oxidative status, as well as look at any changes in metabolomic profiles. It was hypothesized that by supplementing with TRF a vitamin E, for 16 weeks in ESRD patients undergoing hemodialysis, it may help reverse and/or improve, oxidative status, inflammatory markers, increase antioxidants status and improve lipid profiles.

The study was double-blinded, randomized, parallel, placebo-controlled design trial, of 81 adult patients undergoing chronic hemodialysis at Great Lake Dialysis Clinic, Detroit MI, where …

Design And Study Of The Efflux Function Of The Egfp Fused Mexab-Oprm Membrane Transporter In Pseudomonas Aeruginosa Using Spectroscopy, Feng Ding, Kerry J. Lee, Ardeschir Vahedi-Faridi, Hiroshi Yoneyama, Christopher J. Osgood, Xiao-Hong Nancy Xu

Biological Sciences Faculty Publications

Multidrug membrane transporters (efflux pumps) can selectively extrude a variety of structurally and functionally diverse substrates (e.g., chemotoxics, antibiotics), leading to multidrug resistance (MDR) and ineffective treatment of a wide variety of diseases. In this study, we have designed and constructed a fusion gene (egfp-mexB) of N-terminal mexB with C-terminal egfp, inserted it into a plasmid vector (pMMB67EH), and successfully expressed it in the Δ MexB (MexB deletion) strain of Pseudomonas aeruginosato create a new strain that expresses MexA-(EGFP-MexB)-OprM. We characterized the fusion gene using gel electrophoresis and DNA sequencing, and determined its expression in live …

Monitoring Ligand-Induced Nucleic Acid Conformational Changes Using Ion Mobility Spectrometry-Mass Spectrometry, Bill Kenneth Redick

Legacy Theses & Dissertations (2009 - 2024)

Three-dimensional structures of biopolymers frequently dictate the biological role those molecules play. As such, investigation into structure of nucleic acids can provide important information pertaining to how those nucleic acids work. Many nucleic acid species, especially single-stranded RNA, fold into unique structures that allow them to function properly. Metals, and other cationic species, are often bound to the nucleic acid to make folding into the proper structure more favorable by neutralizing the negative charge on the nucleic acid imparted by the phosphate group. This investigation explores tertiary structure of nucleic acids that have been folded in the presence of ligands …

Modeling The Early, Aging-Related Changes In Human Recombinant Gammas-Crystallin In Vitro, Christiana Oluwaseun Salami

Legacy Theses & Dissertations (2009 - 2024)

Cataract is the leading cause of blindness in the world. Cataractous lenses scatter a significant part of the light entering the eye. Cataract can be of several types: Age-related cataract, secondary cataract, traumatic cataract, congenital cataract, and radiation cataract. Age-related cataract is the most common type of cataract. Several factors contribute to age-onset cataract; among them are the Post-Translational Modifications (PTMs) to the major lens proteins or crystallins, which constitute about 80-90% of the protein content of the lens. Predominant PTMs of the crystallins are oxidation, deamidation, phosphorylation, glycation, and disulfide crosslinking, which tend to increase as the lens ages.

Probing Secondary And Tertiary Rna Folding Using Force And Temperature, William Stephenson

Legacy Theses & Dissertations (2009 - 2024)

RNA folding is the process whereby a single stranded RNA molecule assumes its three-dimensional functional conformation. Along with the protein folding problem, the RNA folding problem remains as one of the great unsolved problems in biophysics. Generally RNA folding occurs in a hierarchical manner whereby the sequence of an RNA (primary structure) determines which regions will form helical segments (secondary structure) before further rearrangement and base pairing of secondary structure motifs (tertiary structure). Due to the intimate connection between structure and function within molecular biology, increased familiarity with the thermodynamic and kinetic factors that govern RNA folding will permit the …