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Chemistry Faculty Publications

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Articles 841 - 870 of 1129

Full-Text Articles in Chemistry

High-Resolution Structure Of A Beta-Peptide Bundle, Douglas S. Daniels, E. James Petersson, Jade X. Qiu, Alanna S. Schepartz Jan 2007

High-Resolution Structure Of A Beta-Peptide Bundle, Douglas S. Daniels, E. James Petersson, Jade X. Qiu, Alanna S. Schepartz

Chemistry Faculty Publications

We recently reported that β-peptides can form discrete hetero-oligomers in aqueous solution. Here we describe the structure of such an oligomer as determined by X-ray crystallography. The structure of Zwit-1F reveals a homo-octamer of two cupped “hands” composed of both parallel and antiparallel 314-helices. The core of the assembly is composed entirely of solvent-excluded β3-homoleucine residues. The Zwit-1F assembly shares many of the physical characteristics of natural proteins.

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The Visual Image Of Chemistry: Perspectives From The History Of Art And Science, Joachim Schummer, Tami I. Spector Jan 2007

The Visual Image Of Chemistry: Perspectives From The History Of Art And Science, Joachim Schummer, Tami I. Spector

Chemistry Faculty Publications

In this paper we investigate the most important visual stereotypes of chemistry as they occur in current portraits of chemists, depictions of chemical plants, and images of chemical glassware and apparatus. By studying the historical origin and development of these stereotypes within the broader context of the history of art and science, and by applying aesthetic and cultural theories, we explore what these images implicitly communicate about the chemical profession to the public. We conclude that chemists, along with commercial artists, have unknowingly created a visual image of chemistry that frequently conveys negative historical associations, ranging from imposture to kitsch. …

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The Dissociation Energy Of The New Diatomic Molecules Sipb And Gepb, A Ciccioli, G Gigli, Giovanni Meloni, E Testani, National Library Of Medicine Jan 2007

The Dissociation Energy Of The New Diatomic Molecules Sipb And Gepb, A Ciccioli, G Gigli, Giovanni Meloni, E Testani, National Library Of Medicine

Chemistry Faculty Publications

The diatomic molecules SiPb and GePb were for the first time identified by producing high temperature vapors of the constituent pure elements in a "double-oven-like" molecular-effusion assembly. The partial pressures of the atomic, heteronuclear, and homonuclear gaseous species observed in the vapor, namely, Si, Ge, Pb, SiPb, GePb, Pb2, Gen, and Sin (n=2-3), were mass-spectrometrically measured in the overall temperature ranges 1753-1961 K (Ge-Pb) and 1992-2314 K (Si-Pb). The dissociation energies of the new species were determined by second- and third-law analyses of both the direct dissociation reactions and isomolecular exchange reactions involving homonuclear molecules. The selected values of the …

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Jonas Kamlet (1914-1960) Chemist/Entrepreneur, Dean F. Martin, Barbara B. Martin Jan 2007

Jonas Kamlet (1914-1960) Chemist/Entrepreneur, Dean F. Martin, Barbara B. Martin

Chemistry Faculty Publications

Jonas Kamlet, Ph.D., as a chemist, inventor, and a significant entrepreneur who founded Kamlet Laboratories in New York City that became the model of a successful consulting firm. Among his hundreds of patents and inventions were a tablet that could be used to measure glucose in urine, a treated strip that could detect pregnancy, a fodder for ruminants that used newsprint, and biuret (a self-condensation product of urea) that could be used as a non-protein component of fodder. Following his death in an airplane collision on December 16, 1960, his wife and collaborator (and later a resident of Florida) carried …

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Synthesis Of The Giant Dielectric Constant Material Cacu3ti4o12 By Wet-Chemistry Methods, Jianjun Liu, Robert W. Smith, Wai-Ning Mei Jan 2007

Synthesis Of The Giant Dielectric Constant Material Cacu3ti4o12 By Wet-Chemistry Methods, Jianjun Liu, Robert W. Smith, Wai-Ning Mei

Chemistry Faculty Publications

CaCu3Ti4O12 (CCTO) has a giant dielectric constant of up to 105 at room temperature and great potential for technological application. In this work, we report two wet-chemistry methods to synthesize CCTO at relatively low temperatures and short reaction times. The pure-phase sample was obtained at 800 °C for 0.5 h, and the grain size of a pellet sample sintered at 1030 °C has a homogeneous distribution in the range of 0.4–1.5 μm.

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Role Of 2-5a-Dependent Rnase-L In Senescence And Longevity, J. B. Andersen, X. L. Li, C. S. Judge, Aimin Zhou, B. K. Jha, S. Shelby, L. Zhou, Robert H. Silverman, B. A. Hassel Jan 2007

Role Of 2-5a-Dependent Rnase-L In Senescence And Longevity, J. B. Andersen, X. L. Li, C. S. Judge, Aimin Zhou, B. K. Jha, S. Shelby, L. Zhou, Robert H. Silverman, B. A. Hassel

Chemistry Faculty Publications

Senescence is a permanent growth arrest that restricts the lifespan of primary cells in culture, and represents an in vitro model for aging. Senescence functions as a tumor suppressor mechanism that can be induced independent of replicative crisis by diverse stress stimuli. RNase-L mediates antiproliferative activities and functions as a tumor suppressor in prostate cancer, therefore, we examined a role for RNase-L in cellular senescence and aging. Ectopic expression of RNase-L induced a senescent morphology, a decrease in DNA synthesis, an increase in senescence-associated -galactosidase activity, and accelerated replicative senescence. In contrast, senescence was retarded in RNase-L-null fibroblasts compared with …

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Tumour Suppressor Function Of Rnase L In A Mouse Model, Wendy Liu, Shu Ling Liang, Hongli Liu, Robert Silverman, Aimin Zhou Jan 2007

Tumour Suppressor Function Of Rnase L In A Mouse Model, Wendy Liu, Shu Ling Liang, Hongli Liu, Robert Silverman, Aimin Zhou

Chemistry Faculty Publications

RNase L is one of the key enzymes involved in the molecular mechanisms of interferon (IFN) actions. Upon binding with its activator, 5′-phosphorylated, 2′-5′ oligoadenylates (2-5A), RNase L plays an important role in the antiviral and anti-proliferative functions of IFN, and exerts proapoptotic activity independent of IFN. In this study, we have found that RNase L retards proliferation in an IFN-dependent and independent fashion. To directly measure the effect of RNase L on tumour growth in the absence of other IFN-induced proteins, human RNase L cDNA was stably expressed in P-57 cells, an aggressive mouse fibrosarcoma cell line. Three clonal …

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Exploring The Mechanism Of Flexible Biomolecular Recognition With Single Molecule Dynamics, H. Peter Lu, Qiang Lu, Jin Wang Jan 2007

Exploring The Mechanism Of Flexible Biomolecular Recognition With Single Molecule Dynamics, H. Peter Lu, Qiang Lu, Jin Wang

Chemistry Faculty Publications

Combining a single-molecule study of protein binding with a coarse grained molecular dynamics model including solvent (water molecules) effects, we find that biomolecular recognition is determined by flexibilities in addition to structures. Our single-molecule study shows that binding of CBD (a fragment of Wiskott-Aldrich syndrome protein) to Cdc42 involves bound and loosely bound states, which can be quantitatively explained in our model as a result of binding with large conformational changes. Our model identified certain key residues for binding consistent with mutational experiments. Our study reveals the role of flexibility and a new scenario of dimeric binding between the monomers: …

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Structure And Antiferroelectric Properties Of Cesium Niobate, Cs2nb4o11, Robert W. Smith, Chunhua Hu, Jianjun Liu, Wai-Ning Mei, Kuan-Jiuh Lin Jan 2007

Structure And Antiferroelectric Properties Of Cesium Niobate, Cs2nb4o11, Robert W. Smith, Chunhua Hu, Jianjun Liu, Wai-Ning Mei, Kuan-Jiuh Lin

Chemistry Faculty Publications

The compound cesium niobate, Cs2Nb4O11, is an antiferroelectric, as demonstrated by double hysteresis loops in the electric-field versus polarization plot. The crystal structure refinement by X-ray diffraction at both 100 and 297 K shows it to have a centrosymmetric structure in point group mmm and orthorhombic space group Pnna, which is consistent with its antiferroelectric behavior. The 100-K data is reported herein. The lattice is comprised of niobium-centered tetrahedra and octahedra connected through shared vertices and edges; cesium atoms occupy channels afforded by the three-dimensional polyhedral network. The critical field for onset of ferroelectric behavior in a single-crystal sample is …

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Interaction Energy Decomposition In Protein–Protein Association: A Quantum Mechanical Study Of Barnase–Barstar Complex, Abdessamad Ababou, Arjan Van Der Vaart, Valentin Gogonea, Kenneth M. Merz Jr. Jan 2007

Interaction Energy Decomposition In Protein–Protein Association: A Quantum Mechanical Study Of Barnase–Barstar Complex, Abdessamad Ababou, Arjan Van Der Vaart, Valentin Gogonea, Kenneth M. Merz Jr.

Chemistry Faculty Publications

Protein–protein interactions are very important in the function of a cell. Computational studies of these interactions have been of interest, but often they have utilized classical modelling techniques. In recent years, quantum mechanical (QM) treatment of entire proteins has emerged as a powerful approach to study biomolecular systems. Herein, we apply a semi-empirical divide and conquer (DC) methodology coupled with a dielectric continuum model for the solvent, to explore the contribution of electrostatics, polarization and charge transfer to the interaction energy between barnase and barstar in their complex form. Molecular dynamic (MD) simulation was performed to account for the dynamic …

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Reactivation Pathway Of The Hydrogenase H-Cluster: Density Functional Theory Study, Stefan Motiu, Daniela Dogaru, Valentin Gogonea Jan 2007

Reactivation Pathway Of The Hydrogenase H-Cluster: Density Functional Theory Study, Stefan Motiu, Daniela Dogaru, Valentin Gogonea

Chemistry Faculty Publications

This work puts forth a reaction pathway for the reactivation of exogenous ligand inhibited H-cluster, the active site of Fe-only hydrogenases. The H-cluster is a dimetal complex, Fe–Fe, with the metal centers bridged by di(thiomethyl)amine. Exogenous ligands, H2O, and OH−, are bound to the distal iron (Fed). Density functional theory (DFT) calculations on the native and ruthenium-modified H-cluster have been performed using the B3LYP functional with 6-31+G** and 6-311+G** basis sets. We have ascertained that there is a thermodynamically favorable pathway for the reactivation of the OH− inhibited H-cluster, which proceeds by an initial protonation of the Fed–OH− complex. The …

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Oxidative Dna Damage In Mild Cognitive Impairment And Late-Stage Alzheimer's Disease, Mark A. Lovell, William R. Markesbery Jan 2007

Oxidative Dna Damage In Mild Cognitive Impairment And Late-Stage Alzheimer's Disease, Mark A. Lovell, William R. Markesbery

Chemistry Faculty Publications

Increasing evidence supports a role for oxidative DNA damage in aging and several neurodegenerative diseases including Alzheimer's disease (AD). Attack of DNA by reactive oxygen species (ROS), particularly hydroxyl radicals, can lead to strand breaks, DNA–DNA and DNA–protein cross-linking, and formation of at least 20 modified bases adducts. In addition, α,β-unsaturated aldehydic by-products of lipid peroxidation including 4-hydroxynonenal and acrolein can interact with DNA bases leading to the formation of bulky exocyclic adducts. Modification of DNA bases by direct interaction with ROS or aldehydes can lead to mutations and altered protein synthesis. Several studies of DNA base adducts in late-stage …

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Identification And Characterization Of A New Tubulin-Binding, Susan L. Mooberry, Kimberly N. Weiderhold, Sivanesan Dakshanamurthy, Ernest Hamel, Edith J. Banner, Anastasia Kharlamova, Jonathan Hempel, John T. Gupton, Milton L. Brown Jan 2007

Identification And Characterization Of A New Tubulin-Binding, Susan L. Mooberry, Kimberly N. Weiderhold, Sivanesan Dakshanamurthy, Ernest Hamel, Edith J. Banner, Anastasia Kharlamova, Jonathan Hempel, John T. Gupton, Milton L. Brown

Chemistry Faculty Publications

We studied the mechanism of action of 3,5-dibromo-4-(3,4-dimethoxyphenyl)-1H-pyrrole-2-carboxylic acid ethyl ester (JG-03-14) and found that it is a potent microtubule depolymerizer. JG-03-14 caused a dose-dependent loss of cellular microtubules, formation of aberrant mitotic spindles, accumulation of cells in the G2/M phase of the cell cycle, and Bcl-2 phosphorylation. These events culminated in the initiation of apoptosis, as evidenced by the caspase 3-dependent cleavage of poly(ADP-ribose) polymerase (PARP). JG-03-14 has antiproliferative activity against a wide range of cancer cell lines, with an average IC50 value of 62 nM, and it is a poor substrate for transport …

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A Control Switch For Prothrombinase: Characterization Of A Hirudin-Like Pentapeptide From The Cooh Terminus Of Factor Va Heavy Chain That Regulates The Rate And Pathway For Prothrombin Activation, Michael A. Bukys, Paul Y. Kim, Michael E. Nesheim, Michael Kalafatis Dec 2006

A Control Switch For Prothrombinase: Characterization Of A Hirudin-Like Pentapeptide From The Cooh Terminus Of Factor Va Heavy Chain That Regulates The Rate And Pathway For Prothrombin Activation, Michael A. Bukys, Paul Y. Kim, Michael E. Nesheim, Michael Kalafatis

Chemistry Faculty Publications

Membrane-bound factor Xa alone catalyzes prothrombin activation following initial cleavage at Arg(271) and prethrombin 2 formation (pre2 pathway). Factor Va directs prothrombin activation by factor Xa through the meizothrombin pathway, characterized by initial cleavage at Arg(320) (meizo pathway). We have shown previously that a pentapeptide encompassing amino acid sequence 695-699 from the COOH terminus of the heavy chain of factor Va (Asp-Tyr-Asp-Tyr-Gln, DYDYQ) inhibits prothrombin activation by prothrombinase in a competitive manner with respect to substrate. To understand the mechanism of inhibition of thrombin formation by DYDYQ, we have studied prothrombin activation by gel electrophoresis. Titration of plasma-derived prothrombin activation …

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Biomass Burning And Anthropogenic Sources Of Co Over New England In The Summer 2004, Carsten Warneke, J. A. De Gouw, A. Stohl, O. R. Cooper, P. D. Goldan, W. C. Kuster, J. S. Holloway, E. J. Williams, B. M. Lerner, S. A. Mckeen, M. Trainer, F. C. Fehsenfeld, E. L. Atlas, Stephen G. Donnelly Ph.D., Verity Stroud, Amy Lueb, S. Kato Dec 2006

Biomass Burning And Anthropogenic Sources Of Co Over New England In The Summer 2004, Carsten Warneke, J. A. De Gouw, A. Stohl, O. R. Cooper, P. D. Goldan, W. C. Kuster, J. S. Holloway, E. J. Williams, B. M. Lerner, S. A. Mckeen, M. Trainer, F. C. Fehsenfeld, E. L. Atlas, Stephen G. Donnelly Ph.D., Verity Stroud, Amy Lueb, S. Kato

Chemistry Faculty Publications

During the summer of 2004 large wildfires were burning in Alaska and Canada, and part of the emissions were transported toward the northeast United States, where they were measured during the NEAQS-ITCT 2k4 (New England Air Quality Study-Intercontinental Transport and Chemical Transformation) study on board the NOAA WP-3 aircraft and the NOAA research vessel Ronald H. Brown. Using acetonitrile and chloroform as tracers the biomass burning and the anthropogenic fraction of the carbon monoxide (CO) enhancement are determined. As much as 30% of the measured enhancement is attributed to the forest fires in Alaska and Canada transported into the region, …

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Generating New Specific Rna Interaction Interfaces Using C-Loops, Kirill A. Afonin, Neocles B. Leontis Dec 2006

Generating New Specific Rna Interaction Interfaces Using C-Loops, Kirill A. Afonin, Neocles B. Leontis

Chemistry Faculty Publications

New RNA interaction interfaces are reported for designing RNA modules for directional supramolecular self-assembly. The new interfaces are generated from existing ones by inserting C-loops between the interaction motifs that mediate supramolecular assembly. C-Loops are new modular motifs recently identified in crystal structures that increase the helical twist of RNA helices in which they are inserted and thus reduce the distance between pairs of loop or loop-receptor motifs from 11 to 9 base-stacking layers while maintaining correct orientation for binding to cognate interaction interfaces. Binding specificities of C-loop-containing molecules for cognate molecules that also have inserted C-loops were found to …

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Incorporating Electron-Transfer Functionality Into Synthetic Metalloproteins From The Bottom-Up, Jing Hong, Olesya A. Kharenko, Michael Y. Ogawa Dec 2006

Incorporating Electron-Transfer Functionality Into Synthetic Metalloproteins From The Bottom-Up, Jing Hong, Olesya A. Kharenko, Michael Y. Ogawa

Chemistry Faculty Publications

The alpha-helical coiled-coil motif serves as a robust scaffold for incorporating electron-transfer (ET) functionality into synthetic metalloproteins. These structures consist of a supercoiling of two or more R helices that are formed by the self-assembly of individual polypeptide chains whose sequences contain a repeating pattern of hydrophobic and hydrophilic residues. Early work from our group attached abiotic Ru-based redox sites to the most surface-exposed positions of two stranded coiled-coils and used electron-pulse radiolysis to study both intra- and intermolecular ET reactions in these systems. Later work used smaller metallopeptides to investigate the effects of conformational gating within electrostatic peptide-protein complexes. …

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True Blue: Blue-Emitting Aluminum(Iii) Quinolinolate Complexes, Cesar Perez-Bolivar, Victor A. Montes, Pavel Anzenbacher Jr. Nov 2006

True Blue: Blue-Emitting Aluminum(Iii) Quinolinolate Complexes, Cesar Perez-Bolivar, Victor A. Montes, Pavel Anzenbacher Jr.

Chemistry Faculty Publications

Blue-emitting heteroleptic aluminum(III) bis(2-methyl-8-quinolinolate) phenolate complexes were synthesized. A tunable, blue-to-green emission is achieved by attaching electron-withdrawing modulators to the emisssive quinaldinate ligand. The electronic nature of modulator substituents attached to the position of the highest HOMO (highest occupied molecular orbital) density is used to modulate ligand HOMO levels to achieve effective emission tuning to obtain blue-emitting materials. Optical and electrochemical properties of the resulting complexes were investigated and compared to the results of density functional theory (DFT/B3LYP/6-31G*) studies. The resulting materials may find application as organic light-emitting device materials.

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Nano-Chemistry, Erwin P. Enriquez Oct 2006

Nano-Chemistry, Erwin P. Enriquez

Chemistry Faculty Publications

Nanotechnology is a highly interdisciplinary field, with contributions from all fields: physics, chemistry, biology, materials science, engineering, and others. The explosive number of publications in this field makes it nearly impossible to give an extensive review even in chemistry alone. Nonetheless, one may track its emergence and rapid advancement from the point of view of a chemist's. This paper aims to provide a conceptual overview of chemistry for nanotechnology, a brief classification of different approaches and applications, together with some sample cases.

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(E,E)-1,3-Bis[9,10-Dihydro-9-Nitro-10-(Trinitro­Meth­Yl)-9-Anthr­Yl]Propane, Mustafa Arslan, Erol Asker, John Masnovi, Ronald J. Baker Sep 2006

(E,E)-1,3-Bis[9,10-Dihydro-9-Nitro-10-(Trinitro­Meth­Yl)-9-Anthr­Yl]Propane, Mustafa Arslan, Erol Asker, John Masnovi, Ronald J. Baker

Chemistry Faculty Publications

The title compound, C33H24N8O16, was obtained as a product of the photoreaction between 1,3-di-9-anthrylpropane and tetra­nitro­methane. The mol­ecule occupies a special position on a twofold axis. The trinitro­methyl and nitro substituents on the 9,10-dihydro­acridine system are E oriented.

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A 2:1 Complex Of 1,3-Bis­(9h-Carbazol-9-Yl)Propane And Tetra­Chloro-P-Benzoquinone (P-Chloranil), Mustafa Arslan, Randolph B. Krafcik, John Masnovi, Ronald J. Baker Sep 2006

A 2:1 Complex Of 1,3-Bis­(9h-Carbazol-9-Yl)Propane And Tetra­Chloro-P-Benzoquinone (P-Chloranil), Mustafa Arslan, Randolph B. Krafcik, John Masnovi, Ronald J. Baker

Chemistry Faculty Publications

In the title electron donor–acceptor complex, C27H22N2·0.5C6Cl4O2, the p-chloranil mol­ecule lies on a crystallographic inversion center, which is located at the center of the benzene ring. In the crystal structure, one p-chloranil mol­ecule lies above and below the central rings of each donor group of two neighboring 1,3-bis­(9H-carbazol-9-yl)propane mol­ecules, with a ring-centroid separation of 3.444 (1) Å. The angle between the planes of the stacking rings of the carbazole and p-chloranil mol­ecules is 3.4 (2)°.

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Molecular-Wire Behavior Of Oled Materials: Exciton Dynamics In Multichromophoric Alq3-Oligofluorene-Pt(Ii)Porphyrin Triads, Victor A. Montes, Cesar Perez-Bolıvar, Neeraj Agarwal, Joseph Shinar, Pavel Anzenbacher Jr. Sep 2006

Molecular-Wire Behavior Of Oled Materials: Exciton Dynamics In Multichromophoric Alq3-Oligofluorene-Pt(Ii)Porphyrin Triads, Victor A. Montes, Cesar Perez-Bolıvar, Neeraj Agarwal, Joseph Shinar, Pavel Anzenbacher Jr.

Chemistry Faculty Publications

Donor-bridge-acceptor triads consisting of the Alq3 complex, oligofluorene bridge, and PtII tetraphenylporphyrin (PtTPP) were synthesized. The triads were designed to study the energy level/distance-dependence in energy transfer both in a solution and in solid state. The materials show effective singlet transfer from the Alq3-fluorene fluorophore to the porphyrin, while the triplet energy transfer, owing to the shorter delocalization of triplet excitons, appears to take place via a triplet energy cascade. Using femtosecond transient spectroscopy, the rate of the singlet−singlet energy transfer was determined. The exponential dependence of the donor−acceptor distance and the respective energy transfer rates of 7.1 …

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Synthesis, Structure, Anion Binding, And Sensing By Calix[4]Pyrrole Isomers, Ryuhei Nishiyabu, Manuel A. Palacios, Wim Dehaen, Pavel Anzenbacher Jr. Sep 2006

Synthesis, Structure, Anion Binding, And Sensing By Calix[4]Pyrrole Isomers, Ryuhei Nishiyabu, Manuel A. Palacios, Wim Dehaen, Pavel Anzenbacher Jr.

Chemistry Faculty Publications

The synthesis, structure, and anion binding properties of chromogenic octamethylcalix[4] pyrroles (OMCPs) and their N-confused octamethylcalix[4] pyrrole isomers (NC-OMCPs) containing an inverted pyrrole ring connected via alpha'- and beta-positions are described. X-ray diffraction analyses proved the structures of two synthesized isomeric pairs of OMCPs and NC-OMCPs. The addition of anions to solutions of chromogenic OMCPs and NC-OMCPs resulted in different colors suggesting different anion-binding behaviors. The chromogenic NC-OMCPs showed significantly stronger anion-induced color changes compared to the corresponding chromogenic OMCP, and the absorption spectroscopy titrations indicated that chromogenic OMCPs and NC-OMCPs also possess different anion binding selectivity. Detailed NMR studies …

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Rnase L: Its Biological Roles And Regulation, Shu Ling Liang, David Quirk, Aimin Zhou Sep 2006

Rnase L: Its Biological Roles And Regulation, Shu Ling Liang, David Quirk, Aimin Zhou

Chemistry Faculty Publications

2'-5'oligoadenylate-dependent ribonuclease L (RNase L) is one of the key enzymes involved in the function of interferons (IFNs), a family of cytokines participating in innate immunity against viruses and other microbial pathogens. Upon binding with its activator, 5'-phosphorylated, 2'-5' linked oligoadenylates (2-5A), RNase L degrades single-stranded viral and cellular RNAs and thus plays an important role in the antiviral and antiproliferative functions of IFNs. In recent years, evidence has revealed that RNase L displays a broad range of biological roles which are summarized in this review.

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Tertiary Structural And Functional Analyses Of A Viroid Rna Motif By Isostericity Matrix And Mutagenesis Reveal Its Essential Role In Replication, Neocles B. Leontis, Xuehua Zhong, Shuiming Qian, Asuka Itaya, Yijun Qi, Kathleen Boris-Lawrie, Biao Ding Sep 2006

Tertiary Structural And Functional Analyses Of A Viroid Rna Motif By Isostericity Matrix And Mutagenesis Reveal Its Essential Role In Replication, Neocles B. Leontis, Xuehua Zhong, Shuiming Qian, Asuka Itaya, Yijun Qi, Kathleen Boris-Lawrie, Biao Ding

Chemistry Faculty Publications

RNA-templated RNA replication is essential for viral or viroid infection, as well as for regulation of cellular gene expression. Specific RNA motifs likely regulate various aspects of this replication. Viroids of the Pospiviroidae family, as represented by the Potato spindle tuber viroid (PSTVd), replicate in the nucleus by utilizing DNA-dependent RNA polymerase II. We investigated the role of the loop E (sarcin/ricin) motif of the PSTVd genomic RNA in replication. A tertiary-structural model of this motif, inferred by comparative sequence analysis and comparison with nuclear magnetic resonance and X-ray crystal structures of loop E motifs in other RNAs, is presented …

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10,10′-Dinitro-10,10′-(Butane-1,4-Di­Yl)Dianthracen-9(10h)-One, Mustafa Arslan, Erol Asker, John Masnovi, Ronald J. Baker Jul 2006

10,10′-Dinitro-10,10′-(Butane-1,4-Di­Yl)Dianthracen-9(10h)-One, Mustafa Arslan, Erol Asker, John Masnovi, Ronald J. Baker

Chemistry Faculty Publications

The title compound, C32H24N2O6, was obtained as the decomposition product of (E,E)-1,4-bis­[9,10-dihydro-9-nitro-10-(trinitro­meth­yl)-9-anthr­yl]butane, which was synthesized via a photochemical reaction of 1,4-bis­(9-anthr­yl)butane with tetra­nitro­methane. The asymmetric unit contains one half-mol­ecule; the complete mol­ecule is generated by a center of inversion. The crystal packing is determined mainly by inter­molecular C—H⋯O inter­actions.

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The Structural Integrity Of Anion Binding Exosite I Of Thrombin Is Required And Sufficient For Timely Cleavage And Activation Of Factor V And Factor Viii, Michael A. Bukys, Tivadar Orban, Paul Y. Kim, Daniel O. Beck, Michael E. Nesheim, Michael Kalafatis Jul 2006

The Structural Integrity Of Anion Binding Exosite I Of Thrombin Is Required And Sufficient For Timely Cleavage And Activation Of Factor V And Factor Viii, Michael A. Bukys, Tivadar Orban, Paul Y. Kim, Daniel O. Beck, Michael E. Nesheim, Michael Kalafatis

Chemistry Faculty Publications

Alpha-thrombin has two separate electropositive binding exosites (anion binding exosite I, ABE-I and anion binding exosite II, ABE-II) that are involved in substrate tethering necessary for efficient catalysis. Alpha-thrombin catalyzes the activation of factor V and factor VIII following discrete proteolytic cleavages. Requirement for both anion binding exosites of the enzyme has been suggested for the activation of both procofactors by alpha-thrombin. We have used plasma-derived alpha-thrombin, beta-thrombin (a thrombin molecule that has only ABE-II available), and a recombinant prothrombin molecule rMZ-II (R155A/R284A/R271A) that can only be cleaved at Arg(320) (resulting in an enzymatically active molecule that has only ABE-I …

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Crown Ether-Metal ‘Sandwiches’ As Linking Mechanisms In Assembled Nanoparticle Films, Rebecca R. Pompano, Phillip G. Wortley, Leslie M. Moatz, D. J. Tognarelli, Kevin W. Kittredge, Michael C. Leopold Jul 2006

Crown Ether-Metal ‘Sandwiches’ As Linking Mechanisms In Assembled Nanoparticle Films, Rebecca R. Pompano, Phillip G. Wortley, Leslie M. Moatz, D. J. Tognarelli, Kevin W. Kittredge, Michael C. Leopold

Chemistry Faculty Publications

Crown ether ligands attached to monolayer-protected clusters (MPCs) were assembled as films and the linking mechanism between the crown ether–metal ion–crown ether bridges between nanoparticles was examined. Thicker films exhibited a red shift in the absorbance maximum for the surface plasmon band which was attributed to the increasing aggregation and cross linking within the film. Quantized double layer charging peaks suggest that film growth is selective toward a specific core size or exchange rate, either of which affect the number of potential linking ligands in the periphery of the MPCs. Multi-layer growth of films was only achieved with metal ions …

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Numerical Simulation And Graphical Analysis Of In Vitro Benign Tumor Growth: Application Of Single-Particle State Bosonic Matter Equation With Length Scaling, Pradip K. Biswas, Jiansen Niu, Tobias Frederico, Valentin Gogonea Jul 2006

Numerical Simulation And Graphical Analysis Of In Vitro Benign Tumor Growth: Application Of Single-Particle State Bosonic Matter Equation With Length Scaling, Pradip K. Biswas, Jiansen Niu, Tobias Frederico, Valentin Gogonea

Chemistry Faculty Publications

We describe the application of a non-linear single-particle state bosonic condensate equation to simulate multicellular tumor growth by treating it as a coupling of two classical wave equations with real components. With one component representing the amplitude of the cells in their volume growth phase and the other representing the amplitude of the cells in their proliferation or mitosis phase, the two components of the coupled equation feed each other during the time evolution and are coupled together through diffusion and other linear and non-linear terms. The features of quiescent and necrotic cells, which result from poor nutrient diffusion into …

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(Review) Green Fluorescent Proteins, Marc Zimmer Jun 2006

(Review) Green Fluorescent Proteins, Marc Zimmer

Chemistry Faculty Publications

Reviews the book:Green Fluorescent Protein: Properties, Applications, and Protocols. Second Edition. Methods of Biochemical Analysis, Volume 47. Edited by Martin Chalfie and Steven R Kain.Green Fluorescent Protein: Properties, Applications, and Protocols. Second Edition. Methods of Biochemical Analysis, Volume 47. Edited by Martin Chalfie and Steven R Kain. Hoboken (New Jersey): Wiley-Interscience. $89.95. xv + 443 p + 24 pl; ill.; index. ISBN: 0–471–73682–1. 2006.

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