Chemistry Commons^™

Co2 Fixation Kinetics Of Halothiobacillus Neapolitanus Mutant Carboxysomes Lacking Carbonic Anhydrase Suggest The Shell Acts As A Diffusional Barrier For Co2, Zhicheng Dou, Sabine Heinhorst, Eric B. Williams, C. Daniel Murin, Jessup M. Shively, Gordon C. Cannon

Faculty Publications

The widely accepted models for the role of carboxysomes in the carbon-concentrating mechanism of autotrophic bacteria predict the carboxysomal carbonic anhydrase to be a crucial component. The enzyme is thought to dehydrate abundant cytosolic bicarbonate and provide ribulose 1.5-bisphosphate carboxylase/oxygenase (RubisCO) sequestered within the carboxysome with sufficiently high concentrations of its substrate, CO₂, to permit its efficient fixation onto ribulose 1,5-bisphosphate. In this study, structure and function of carboxysomes purified from wild type Halothiobacillus neapolitanus and from a high CO₂-requiring mutant that is devoid of carboxysomal carbonic anhydrase were compared. The kinetic constants for the carbon …

Tetra-μ-Aqua-Octaaquabis(μ-4-Chloropyridine-2,6-Dicarboxylato(Bis(4-Chloro-Pyridine-2,6-Dicarboxylato)Tricobalt(Ii)-Disodium(I) Bis[Triaquabis(4-Chloro-Pyridine-2,6-Dicarboxylato)Cobalt(Ii)] Hexahydrate, Lamaryet Moody, Shawna Balof, Shanika Smith, Varma H. Rambaran, Don Vanderveer, Alvin A. Holder

Faculty Publications

The title compound, [Co₃Na₂(C₇₂ClNO₄)₄(H₂O)₁₂][Co(C₇H₂ClNO₄(H₂O)₃]₂·6H₂O, consists of a centrosymmetric dimer of [Co^II(dipicCl)₂]^2- complex dianions [dipicCl is 4-chloro­pyridine-2,6-dicarboxyl­ate] bridged by an [Na₂Co^II(H₂O)₁₂]⁴⁺ tetra­cationic cluster, two independent [Co(dipicCl)(H₂O)₃] complexes, and six water mol­ecules of crystallization. The metals are all six-coordinate with distorted octahedral geometries. The [Co^II(dipicCl)(H₂O)₃] complexes are neutral, with …

Rheology Of Tin Fluorophosphate Glass/Polyamide 12 Hybrids In The Low Concentration Regime, Kevin Urman, Thomas Schweizer, Joshua U. Otaigbe

Faculty Publications

Phosphate glass (Pglass)/polymer hybrids are a unique material class that promises to help fulfill the growing need for new advanced materials. Rheological investigations into Pglass/polyamide 12 hybrids have shown a strong dependence on temperature and composition. Strong negative deviations from the log-additivity rule are also observed for these materials as well as a reduction in the activation energy for viscous flow. Hybrids containing < 2 vol. % Pglass are theologically simple fluids that display temperature independence in plots of storage modulus versus loss modulus. Hybrids containing >= 2 vol. % Pglass are rheologically complex and do not obey the time-temperature superposition principle. Through application of Han plots, we identified a structural change that occurs in hybrids containing >= 2 vol. % Pglass at …

Instrumentation And Metrology For Single Rna Counting In Biological Complexes Or Nanoparticles By A Single-Molecule Dual-View System, Hui Zhang, Dan Shu, Faqing Huang, Peixuan Guo

Faculty Publications

Limited by the spatial resolution of optical microscopy, direct detection or counting of single components in biological complexes or nanoparticles is challenging, especially for RNA, which is conformationally versatile and structurally flexible. We report here the assembly of a customized single-molecule dual-viewing total internal reflection fluorescence imaging system for direct counting of RNA building blocks. The RNA molecules were labeled with a single fluorophore by in vitro transcription in the presence of a fluorescent AMP. Precise calculation of identical or mixed pRNA building blocks of one, two, three, or six copies within the bacteriophage phi29 DNA packaging motor or other …

Snell's Law Of Refraction Observed In Thermal Frontal Polymerization, John A. Pojman, Veronika Viner, Burcu Binici, Shanna Lavergne, Melanie Winsper, Dmitry Golovaty, Laura Gross

Faculty Publications

We demonstrate that Snell’s law of refraction can be applied to thermal fronts propagating through a boundary between regions that support distinct frontal velocities. We use the free-radical frontal polymerization of a triacrylate with clay filler that allows for two domains containing two different concentrations of a peroxide initiator to be molded together. Because the polymerization reaction rates depend on the initiator concentration, the propagation speed is different in each domain. We study fronts propagating in two parallel strips in which the incident angle is 90°. Our data fit Snell’s law v_r/v_i = sin θ_r/sin …

Synthesis, Characterization, And Cyclopolymerization Of A Functional Non-Symmetric Divinyl Monomer, Bekir Dizman, Lon J. Mathias

Faculty Publications

A non-symmetric divinyl monomer with terminal carboxylic acid functionality was readily synthesized from the reaction of ethyl α-hydroxymethylacrylate (EHMA) with maleic anhydride. The new monomer (EHMA–MA) was homopolymerized in both bulk and ethyl acetate using AIBN as an initiator to give cyclopolymers. The synthesis of the monomer and cyclopolymers were followed by ¹³C NMR, ¹H NMR, and FTIR. ¹H NMR was also utilized to obtain the degree of cyclization of the polymers, which were found to be 95% or higher in all cases. The molecular weights of the cyclopolymers were around 40–60,000 g/mol as estimated by SEC. …

Structural Analysis Of Csos1a And The Protein Shell Of The Halothiobacillus Neapolitanus Carboxysome, Yingssu Tsai, Michael R. Sawaya, Gordon C. Cannon, Fei Cai, Eric B. Williams, Sabine Heinhorst, Cheryl A. Kerfeld, Todd O. Yeates

Faculty Publications

The carboxysome is a bacterial organelle that functions to enhance the efficiency of CO2 fixation by encapsulating the enzymes ribulose bisphosphate carboxylase/ oxygenase (RuBisCO) and carbonic anhydrase. The outer shell of the carboxysome is reminiscent of a viral capsid, being constructed from many copies of a few small proteins. Here we describe the structure of the shell protein CsoS1A from the chemoautotrophic bacterium Halothiobacillus neapolitanus. The CsoS1A protein forms hexameric units that pack tightly together to form a molecular layer, which is perforated by narrow pores. Sulfate ions, soaked into crystals of CsoS1A, are observed in the pores of the …

Accumulation Of Pathological Tau Species And Memory Loss In A Conditional Model Of Tauopathy, Zdenek Berger, Hanno Roder, Amanda Hanna, Vijayaraghavan Rangachari, Mei Yue, Zbigniew Wszolek, Karen Ashe, Joshua Knight, Dennis Dickson, Cathy Andorfer, Terrone L. Rosenberry, Jada Lewis, Mike Hutton, Christopher Janus

Faculty Publications

Neurofibrillary tangles (NFTs) are a pathological hallmark of Alzheimer's disease and other tauopathies, but recent studies in a conditional mouse model of tauopathy (rTg4510) have suggested that NFT formation can be dissociated from memory loss and neurodegeneration. This suggests that NFTs are not the major neurotoxic tau species, at least during the early stages of pathogenesis. To identify other neurotoxic tau protein species, we performed biochemical analyses on brain tissues from the rTg4510 mouse model and then correlated the levels of these tau proteins with memory loss. We describe the identification and characterization of two forms of tau multimers (140 …

Antibacterial Fluoromicas: A Novel Delivery Medium, Bekir Dizman, Jonathan C. Badger, Mohamed O. Elasri, Lon J. Mathias

Faculty Publications

Antibacterial fluoromicas were prepared by ion-exchanging fluoromicas with different antibacterial agents including various quaternary ammonium compounds, AgNO₃, and norfloxacin. Antibacterial activities of the ion-exchanged fluoromicas were determined against Staphylococcus aureus and Escherichia coli. Minimum inhibitory concentration (MIC) and zone of inhibition (ZOI) tests were performed to determine both antibacterial effectiveness and mode of action associated with the fluoromicas. All treated fluoromicas showed excellent antibacterial activities against both types of bacteria. The antibacterial activities of treated fluoromicas were found to be either better than or the same as those of neat antibacterial agents. The repeated antibacterial activity tests demonstrated …

Regulation Of A Dna-Compacting Plastid Nucleoid Protein, Steven William Adamson

Dissertations

DCP68, a DNA-compacting nucleoid protein, was further characterized in order to understand how plastid nucleoid proteins affect the structure and function of chloroplast DNA. Previously, DCP68 was identified as ferredoxin: sulfite reductase, an enzyme that participates in reductive sulfur assimilation and inhibits chloroplast DNA replication and transcription in vitro [1, 2]. In this study, the portion of SiR that was found to be present in soluble and plastid nucleoid-enriched fractions indicated that most SiR was stromal in Arabidopsis and soybean plants. Although SiR was detected in Arabidopsis chloroplast nucleoid-enriched fractions, the study of nucleoid dynamics proved to be difficult due …

Introduction: Self-Organization In Nonequilibrium Chemical Systems, Irving R. Epstein, John A. Pojman, Oliver Steinbock

Faculty Publications

The field of self-organization in nonequilibrium chemical systems comprises the study of dynamical phenomena in chemically reacting systems far from equilibrium. Systematic exploration of this area began with investigations of the temporal behavior of the Belousov-Zhabotinsky oscillating reaction, discovered accidentally in the former Soviet Union in the 1950s. The field soon advanced into chemical waves in excitable media and propagating fronts. With the systematic design of oscillating reactions in the 1980s and the discovery of Turing patterns in the 1990s, the scope of these studies expanded dramatically. The articles in this Focus Issue provide an overview of the development and …

Energy Storage In Cold Non-Elastic Deformation Of Glassy Polymers, E.F. Oleinik, S.N. Rudnev, O.B. Salamatina, S.V. Shenogin, M.I. Kotelyanskii, T.V. Paramzina, S.I. Nazarenko

Faculty Publications

Experimental results on work W(epsilon), heat Q(epsilon) and stored energy U(epsilon) of deformation for glassy polymers such as linear PS, PC, PMMA, Polyimid, amorphous PET, thermotropic aromatic polyesters, Vectra T for example, crosslinked epoxy are presented. All the data was obtained by a deformation calorimetry technique. Loading and unloading of samples were performed at room temperature with strain rate epsilon = 10(-2) - 10(-4) sec(-1) under uniaxial compression up to engineering strains of epsilon(def) = 40-50%. During straining all polymers accumulate an excess of the latent energy U( e). Elastic fraction of the energy is released completely at sample unloading …

Investigations Of Poly[(Styrene-Co-P-Methylstyrene)-Risobutylene- R-(Styrene-Co-P-Methylstyrene)] And Poly[(Acrylic Acid)-5-Styrene-Jb-Is0butylene-5-Styrene-Jb-(Acrylic Acid)], James Grabill Kopchick

Dissertations

The pMe study was conducted to understand the morphological and physical property changes that occur as the ratio of pMe to styrene is increased, effectively increasing the aliphatic units. By the introduction of pMe, the interface region becomes more blended/compatible as the pMe migrates to the interface. These pMe groups are theorized in effect to create multiple ‘anchors’ to distribute the loads experienced at the interface more effectively creating a synergistic effect on the final properties of the copolymers. The primary goals of the pentablock study were the characterization of unique membranes as related to …

The Structure Of Β-Carbonic Anhydrase From The Carboxysomal Shell Reveals A Distinct Subclass With One Active Site For The Price Of Two, Michael R. Sawaya, Gordon C. Cannon, Sabine Heinhorst, Shiho Tanaka, Eric B. Williams, Todd O. Yeates, Cheryl A. Kerfeld

Faculty Publications

CsoSCA (formerly CsoS3) is a bacterial carbonic anhydrase localized in the shell of a cellular microcompartment called the carboxysome, where it converts HCO^-₃ to CO₂ for use in carbon fixation by ribulose-bisphosphate carboxylase/oxygenase (RuBisCO). CsoSCA lacks significant sequence similarity to any of the four known classes of carbonic anhydrase (α, β, γ, or δ), and so it was initially classified as belonging to a new class, ϵ. The crystal structure of CsoSCA from Halothiobacillus neapolitanus reveals that it is actually a representative member of a new subclass of β-carbonic anhydrases, distinguished by a lack of active site …

Novel Cyanine-Amp Conjugates For Efficient 5' Rna Fluorescent Labeling By One-Step Transcription And Replacement Of [γ-32P] Atp In Rna Structural Investigation, Na Li, Changjun Yu, Faqing Huang

Faculty Publications

Two novel fluorescent cyanine-AMP conjugates, F550/570 and F650/670, have been synthesized to serve as transcription initiators under the T7 φ2.5 promoter. Efficient fluorophore labeling of 5′ RNA is achieved in a single transcription step by including F550/570 and F650/670 in the transcription solution. The current work makes fluorescently labeled RNA readily available for broad applications in biochemistry, molecular biology, structural biology and biomedicine. In particular, site-specifically fluorophore-labeled large RNAs prepared by the current method may be used to investigate RNA structure, folding and mechanism by various fluorescence techniques. In addition, F550/570 and F650/670 may replace [γ-³²P]ATP to prepare …

Radical Initiated Polymerization In A Bifunctional Mixture Via Computer Simulation, Keri L. Diamond, Ras B. Pandey, Shelby F. Thames

Faculty Publications

Computer simulations are performed to study the polymerization behavior in a mixture of bifunctional groups such as olefins (A) and acrylates (B) in an effective solvent (a coarse description for vegetable oil derived macromonomers (VOMMs) in solution) on a cubic lattice. A set of interactions between these units and solvent (S) constituents and their relative concentrations (p(A), p(B), and p(S)) are considered. Samples are equilibrated with Metropolis algorithm to model the perceived behavior of VOMMs. The covalent bonding between monomeric units is then implemented via reaction pathways initiated by stochastic motion of free radicals (a very small fraction). The rate …

Binary Frontal Polymerization: Velocity Dependence On Initial Composition, John A. Pojman, Jerry A. Griffith, H. Archie Nichols

Faculty Publications

Frontal polymerization is a mode of polymerization in which a localized zone of reaction propagates through the coupling of thermal diffusion and the Arrhenius dependence of the reaction rate. The dependence of the front propagation velocity on the initial composition has been determined in initially miscible binary systems of a free-radically cured diacrylate and an amine- or cationically cured epoxy resin. A minimum of the velocity as a function of the monomer mole fraction is observed if the two polymerizations occur independently. Excellent agreement with an analytical description was found with the diacrylate and an amine-cured epoxy but not for …

Human Glutaminyl Cyclase And Bacterial Zinc Aminopeptidase Share A Common Fold And Active Site, Rachell E. Booth, Simon C. Lovell, Stephanie A. Misquitta, Robert C. Bateman Jr.

Faculty Publications

Background: Glutaminyl cyclase (QC) forms the pyroglutamyl residue at the amino terminus of numerous secretory peptides and proteins. We previously proposed the mammalian QC has some features in common with zinc aminopeptidases. We now have generated a structural model for human QC based on the aminopeptidase fold (pdb code 1AMP) and mutated the apparent active site residues to assess their role in QC catalysis.

Results: The structural model proposed here for human QC, deposited in the protein databank as 1MOI, is supported by a variety of fold prediction programs, by the circular dichroism spectrum, and by the presence …

Superior 5' Homogeneity Of Rna From Atp-Initiated Transcription Under The T7 Φ2.5 Promoter, Tricia M. Coleman, Guocan Wang, Faqing Huang

Faculty Publications

Transcription from the commonly used GTP- initiating T7 class III promoter phi6.5 frequently produces heterogeneous RNA at both 3' and 5' ends. We demonstrate here that RNA transcripts from the T7 class II promoter phi2.5 have superior 5' homogeneity over those from the phi6.5 promoter, with comparable total RNA yields. The overall homogeneity of RNA transcripts is improved to different degrees depending on RNA sequences, although transcription under phi2.5 does not affect the 3' heterogeneity of RNA. In combination with 3' RNA trimming by DNAzymes or ribozymes, this ATP- initiated transcription system based on the T7 phi2.5 promoter can provide …

Synthesis Of Adenosine Derivatives As Transcription Initiators And Preparation Of 5 ' Fluorescein- And Biotin-Labeled Rna Through One-Step In Vitro Transcription, Faqing Huang, Guocan Wang, Tricia Coleman, Na Li

Faculty Publications

Expanding our previous finding of an adenosine-initiated transcription system, we now demonstrate that either the 5' site or the N6 site of adenosine nucleotides can be modified extensively without abolishing their ability to initiate transcription under the T7 phi2.5 promoter. Two series of amino derivatives of adenosine nucleotides were synthesized. Fluorescein and biotin groups were coupled to AMP derivatives through linkers of different sizes and hydrophobicities. Both fluorescein- and biotin-conjugated (at either the 5' or N6 site) adenosine nucleotides can act as efficient transcription initiators, producing fluorescein- and biotin-labeled RNA at the specific 5' end by a one-step transcription procedure, …

Markov Chains And Dynamic Geometry Of Polygons, Jiu Ding, L. Richard Hitt, Xin-Min Zhang

Faculty Publications

In this paper we construct sequences of polygons from a given n-sided cyclic polygon by iterated procedures and study the limiting behaviors of these sequences in terms of non-negative matrices and Markov chains. (C) 2003 Elsevier Science Inc. All rights reserved.

Efficient Incorporation Of Coa, Nad And Fad Into Rna By In Vitro Transcription, Faqing Huang

Faculty Publications

Protein enzymes frequently recruit small molecule coenzymes to perform a variety of biochemical reactions. While the catalytic activities of RNA have been expanding rapidly, a similar strategy for RNA to utilize coenzymes and to increase its functional capabilities has yet to be demonstrated. A general in vitro transcription procedure has been developed to efficiently prepare RNA with coenzymes CoA, NAD and FAD covalently attached to the 5' end. These adenosine-containing coenzymes initiate transcription under the T7 class II promoter by T7 RNA polymerase. In addition to the three coenzymes, other adenosine-containing molecules may be incorporated into the first nucleotide position …

Crystal Structure Of Boc-Trp(Cho)-Dphe-Ile-Dphe-Leu-Och3, C48h59n6o10, Vijayaraghavan Rangachari, J. Makker, P. Kumar, S. Dey, Tej P. Singh

Faculty Publications

No abstract provided.

Seasonality Of Dissolved Rare Earth Elements In The Lower Mississippi River, Alan M. Shiller

Faculty Publications

[1] Dissolved rare earth element (REE) concentrations were determined in a 27-month time series of the lower Mississippi River. Overall, the results agree with limited previous investigations; that is, the river shows enrichment of heavy REEs relative to light REEs and also has a significant Ce anomaly. However, the previous investigations relied on only single samples from the river. This seasonal investigation reveals significant temporal variations in the river's REE chemistry. In particular, large ( approximately fivefold) variations in light REE concentrations are observed. The light REEs follow a seasonality similar to particle-reactive trace elements. Also, the Ce anomaly shows …

The Effect Of Reactor Geometry On Frontal Polymerization Spin Modes, John A. Pojman, Jonathan Masere, Enrico Petretto, Mauro Rustici, Do-Sung Huh, Min Suk Kim, Vladimir Volpert

Faculty Publications

Using reactors of different sizes and geometries the dynamics of the frontal polymerization of 1,6-hexanediol diacrylate (HDDA) and pentaerythritol tetraacrylate (PETAC), with ammonium persulfate as the initiator were studied. For this system, the frontal polymerization exhibits complex behavior that depends on the ratio of the monomers. For a particular range of monomers concentration, the polymerization front becomes nonplanar, and spin modes appear. By varying the reactor diameter, we experimentally confirmed the expected shift of the system to a greater number of "hot spots" for larger diameters. For square test tubes a "zig-zag" mode was observed for the first time in …

Design Of Peptides With, Α,Β-Dehydro-Residues: A Dipeptide With A Branched Β-Carbon Dehydro-Residue At The (I+1) Position, Methyl N-(Benzyloxycarbonyl)-Α,Β-Didehydrovalyl-L-Tryptophanate, Vijayaraghavan Rangachari, Pravindra Kumar, Sharmistha Dey, Tej P. Singh

Faculty Publications

The structure of the title peptide, C₂₅H₂₇N₃O₅, has been determined and its conformation analysed. Values of the standard peptide torsion angles are φ(1) = -44.2 (3)°, ψ(1) = 135.9 (2)°, φ(2) = -141.6 (2)° and ψ(T/2) = 168.0 (2)°. The crystal structure is stabilized by an intermolecular hydrogen bond, with an N···O distance of 2.919 (3)Å, which is formed between screw-axis-related NH and CO groups of dehydrovaline residues.

Thermolysis Of Semicarbazones To The Corresponding Azines Through Reactive N-Substituted Isocyanate Intermediates, Shailesh N. Shah, N.K. Chudgar

Faculty Publications

Thermolysis of semicarbazones (I) to azines (II) occurs through reactive N-substituted isocyanate intermediates (Ia) which can be converted in situ to carbamates and N-substituted ureas.

Effect Of Interfacial Tension On Propagating Polymerization Fronts, R. Texier-Picard, John A. Pojman, Vitaly Volpert

Faculty Publications

This paper is devoted to the investigation of polymerization fronts converting a liquid monomer into a liquid polymer. We assume that the monomer and the polymer are immiscible and study the influence of the interfacial tension on the front stability. The mathematical model consists of the reaction-diffusion equations coupled with the Navier-Stokes equations through the convection terms. The jump conditions at the interface take into account the interfacial tension. Simple physical arguments show that the same temperature distribution could not lead to Marangoni instability for a nonreacting system. We fulfill a linear stability analysis and show that interaction of the …

Trimethyl(Trifluorovinyl)Silane, Roxana M. Trifu, George L. Gould

Faculty Publications

No abstract provided.

Pretransitional Behavior Above The Nematic-Isotropic Phase Transition Of An Auxetic Trimer Liquid Crystal, Daeseung Kang, Milind P. Mahajan, Shiyong Zhang, Rolfe G. Petschek, Charles Rosenblatt, Chaobin He, Puwei Lu, A.C. Griffin

Faculty Publications

Static Light scattering and electric field-induced Kerr measurements were performed above the nematic-isotropic phase transition of a terminal-lateral-lateral-terminal negative Poisson ratio trimer. Far both measurements the inverse susceptibility was observed to be nearly linear with temperature, a result inconsistent with our previously reported Kerr data [Phys. Rev. E 58, 2041 (1998)]. [S1063-651X(99)11010-9].