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Publications by SCSB Faculty

Last Update: 2016

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  • 2004 Publications

    Thompson EB, Webb MS, Miller AL, Fofanov Y, Johnson BH. Identification of genes leading to glucocorticoid-induced leukemic cell death. Lipids. 2004 Aug;39(8):821-5. Review.

    Liu D, Zhao Y, Fan X, Sun Y, Fox RO. Escherichia coli stress protein YciF: expression, crystallization and preliminary crystallographic analysis. Acta Crystallogr D Biol Crystallogr. 2004 Dec;60(Pt 12 Pt 2):2389-90.

    Yang X, Gorenstein DG. Progress in thioaptamer development.

    Bigger CB, Guerra B, Brasky KM, Hubbard G, Beard MR, Luxon BA, Lemon SM, Lanford RE. Intrahepatic gene expression during chronic hepatitis C virus infection in chimpanzees. J Virol. 2004 Dec;78(24):13779-92.

    Kumar R, Volk DE, Li J, Lee JC, Gorenstein DG, Thompson EB. TATA box binding protein induces structure in the recombinant glucocorticoid receptor AF1 domain. Proc Natl Acad Sci U S A. 2004 Nov 23;101(47):16425-30.

    Rosgen J, Pettitt BM, Bolen DW. Uncovering the basis for nonideal behavior of biological molecules. Biochemistry. 2004 Nov 16;43(45):14472-84. Review.

    10: Qutub Y, Reviakine I, Maxwell C, Navarro J, Landau EM, Vekilov PG. Crystallization of transmembrane proteins in cubo: mechanisms of crystal growth and defect formation. J Mol Biol. 2004 Nov 5;343(5):1243-54.

    Ferreon AC, Bolen DW. Thermodynamics of denaturant-induced unfolding of a protein that exhibits variable two-state denaturation. Biochemistry. 2004 Oct 26;43(42):13357-69.

    1Rijnbrand R, Thiviyanathan V, Kaluarachchi K, Lemon SM, Gorenstein DG. Mutational and structural analysis of stem-loop IIIC of the hepatitis C virus and GB virus B internal ribosome entry sites. J Mol Biol. 2004 Oct 29;343(4):805-17.

    Ferreon JC, Hamburger JB, Hilser VJ. An experimental strategy to evaluate the thermodynamic stability of highly dynamic binding sites in proteins using hydrogen exchange. J Am Chem Soc. 2004 Oct 13;126(40):12774-5. No abstract available.

    Beckerling A, Braun W, Sommer M. Process of measuring in clinical medicine--implications of different definitions in clinical therapeutic studies. Digestion. 2004;70(3):139-45. Epub 2004 Oct 1. Review.

    Braun W, Calmuschi B, Drexler HJ, Englert U, Heller D, Salzer A. (R,R)-Tricarbonyl[eta6-1-(diphenylphosphino)-2-[1-(diphenylphosphino)ethyl]benz ene] chromium(0), (R,R)-tricarbonyl-1kappa3C-[mu1(eta6):2kappa2P,P'-1-(diphenylphosphino)-2-[1-(di phenylphosphino)ethyl]benzene][2(eta4)-norbornadiene]chromium(0)rhodium(I) tetrafluoroborate methanol 0.75-solvate and (R,R)-tricarbonyl-1kappa3C-[mu-1(eta6):2kappa2P,P'-1-(diphenylphosphino)-2-[1-(d iphenylphosphino)ethyl]benzene][2(eta4)-(Z,Z)-cycloocta-1,5-diene]chromium(0)rho dium(I) tetrafluoroborate methanol 1.5-solvate. Acta Crystallogr C. 2004 Oct;60(Pt 10):m532-6. No abstract available.

    Liu D, Zhao Y, Fan X, Sun Y, Fox RO. Expression, crystallization and preliminary crystallographic analysis of YciE, a stress protein from Escherichia coli. Acta Crystallogr D Biol Crystallogr. 2004 Oct;60(Pt 10):1888-9.

    Jezewska MJ, Galletto R, Bujalowski W. Interactions of the RepA helicase hexamer of plasmid RSF1010 with the ssDNA. Quantitative analysis of stoichiometries, intrinsic affinities, cooperativities, and heterogeneity of the total ssDNA-binding site. J Mol Biol. 2004 Oct 8;343(1):115-36.

    Galletto R, Jezewska MJ, Bujalowski W. Unzipping mechanism of the double-stranded DNA unwinding by a hexameric helicase: the effect of the 3' arm and the stability of the dsDNA on the unwinding activity of the Escherichia coli DnaB helicase. J Mol Biol. 2004 Oct 8;343(1):101-14.

    Galletto R, Jezewska MJ, Bujalowski W. Unzipping mechanism of the double-stranded DNA unwinding by a hexameric helicase: quantitative analysis of the rate of the dsDNA unwinding, processivity and kinetic step-size of the Escherichia coli DnaB helicase using rapid quench-flow method.J Mol Biol. 2004 Oct 8;343(1):83-99.

    Bolen DW. Effects of naturally occurring osmolytes on protein stability and solubility: issues important in protein crystallization. Methods. 2004 Nov;34(3):312-22.

    Galletto R, Jezewska MJ, Bujalowski W. Multistep sequential mechanism of Escherichia coli helicase PriA protein-ssDNA interactions. Kinetics and energetics of the active ssDNA-searching site of the enzyme.

    Galletto R, Maillard R, Jezewska MJ, Bujalowski W. Global conformation of the Escherichia coli replication factor DnaC protein in absence and presence of nucleotide cofactors. Biochemistry. 2004 Aug 31;43(34):10988-1001.

    Thiviyanathan V, Yang Y, Kaluarachchi K, Rijnbrand R, Gorenstein DG, Lemon SM. High-resolution structure of a picornaviral internal cis-acting RNA replication element (cre). Proc Natl Acad Sci U S A. 2004 Aug 24;101(34):12688-93.

    Hays JL, Watowich SJ. Oligomerization-dependent changes in the thermodynamic properties of the TPR-MET receptor tyrosine kinase. Biochemistry. 2004 Aug 17;43(32):10570-8.

    Chen Y, Button B, Altenberg GA, Reuss L. Potentiation of effect of PKA stimulation of Xenopus CFTR by activation of PKC: role of NBD2. Am J Physiol Cell Physiol. 2004 Nov;287(5):C1436-44.

    Hamburger JB, Ferreon JC, Whitten ST, Hilser VJ. Thermodynamic mechanism and consequences of the polyproline II (PII) structural bias in the denatured states of proteins. Biochemistry. 2004 Aug 3;43(30):9790-9.

    Zhang S. Near neighbor approximation in nuclear magnetic resonance. J Chem Phys. 2004 Jan 22;120(4):1886-91.

    Fernando H, Chin C, Rosgen J, Rajarathnam K. Dimer dissociation is essential for interleukin-8 (IL-8) binding to CXCR1 receptor. J Biol Chem. 2004 Aug 27;279(35):36175-8.

    Yu S, Wuu A, Basu R, Holbrook MR, Barrett AD, Lee JC. Solution structure and structural dynamics of envelope protein domain III of mosquito- and tick-borne flaviviruses. Biochemistry. 2004 Jul 20;43(28):9168-76.

    Bassett SE, Fennewald SM, King DJ, Li X, Herzog NK, Shope R, Aronson JF, Luxon BA, Gorenstein DG. Combinatorial selection and edited combinatorial selection of phosphorothioate aptamers targeting human nuclear factor-kappaB RelA/p50 and RelA/RelA. Biochemistry. 2004 Jul 20;43(28):9105-15.

    Dai J, Lin SH, Kemmis C, Chin AJ, Lee JC. Interplay between site-specific mutations and cyclic nucleotides in modulating DNA recognition by Escherichia coli cyclic AMP receptor protein. Biochemistry. 2004 Jul 20;43(28):8901-10.

    Mukherjee M, Dutta K, Pascal SM, Fox RO. Backbone and side chain resonance assignments of domain III of the tick-borne Langat flavivirus envelope protein. J Biomol NMR. 2004 Aug;29(4):535-6. No abstract available.

    Kumar R, Johnson BH, Thompson EB. Overview of the structural basis for transcription regulation by nuclear hormone receptors. Essays Biochem. 2004;40:27-39. Review.

    Ilies MA, Seitz WA, Ghiviriga I, Johnson BH, Miller A, Thompson EB, Balaban AT. Pyridinium cationic lipids in gene delivery: a structure-activity correlation study. J Med Chem. 2004 Jul 15;47(15):3744-54.

    Young TW, Mei FC, Yang G, Thompson-Lanza JA, Liu J, Cheng X. Activation of antioxidant pathways in ras-mediated oncogenic transformation of human surface ovarian epithelial cells revealed by functional proteomics and mass spectrometry. Cancer Res. 2004 Jul 1;64(13):4577-84.

    Chen Y, Altenberg GA, Reuss L. Mechanism of activation of Xenopus CFTR by stimulation of PKC. Am J Physiol Cell Physiol2004 Nov;287(5):C1256-63.

    Larson SA, Hilser VJ. Analysis of the "thermodynamic information content" of a Homo sapiens structural database reveals hierarchical thermodynamic organization. Protein Sci. 2004 Jul;13(7):1787-801.

    Volk DE, Kallick DA, Holbrook MR, Beasley DW, Barrett AD, Gorenstein DG. 1H, 13C and 15N resonance assignments for domain III of the West Nile virus envelope protein.J Biomol NMR. 2004 Jul;29(3):445-6. No abstract available.

    Lee YC, Volk DE, Thiviyanathan V, Kleerekoper Q, Gribenko AV, Zhang S, Gorenstein DG, Makhatadze GI, Luxon BA. NMR structure of the Apo-S100P protein. J Biomol NMR. 2004 Jul;29(3):399-402. No abstract available.

    Ferreon JC, Hilser VJ. Thermodynamics of binding to SH3 domains: the energetic impact of polyproline II (PII) helix formation. Biochemistry. 2004 Jun 22;43(24):7787-97.

    Volk DE, Beasley DW, Kallick DA, Holbrook MR, Barrett AD, Gorenstein DG. Solution structure and antibody binding studies of the envelope protein domain III from the New York strain of West Nile virus. J Biol Chem. 2004 Sep 10;279(37):38755-61.

    Iftikhar R, Kladney RD, Havlioglu N, Schmitt-Graff A, Gusmirovic I, Solomon H, Luxon BA, Bacon BR, Fimmel CJ. Disease- and cell-specific expression of GP73 in human liver disease. Am J Gastroenterol. 2004 Jun;99(6):1087-95.

    Szaniszlo P, Wang N, Sinha M, Reece LM, Van Hook JW, Luxon BA, Leary JF. Getting the right cells to the array: Gene expression microarray analysis of cell mixtures and sorted cells. Cytometry A. 2004 Jun;59(2):191-202.

    Rajagopalan L, Rajarathnam K. Ligand selectivity and affinity of chemokine receptor CXCR1. Role of N-terminal domain. J Biol Chem. 2004 Jul 16;279(29):30000-8.

    Painter SD, Cummins SF, Nichols AE, Akalal DB, Schein CH, Braun W, Smith JS, Susswein AJ, Levy M, de Boer PA, ter Maat A, Miller MW, Scanlan C, Milberg RM, Sweedler JV, Nagle GT. Structural and functional analysis of Aplysia attractins, a family of water-borne protein pheromones with interspecific attractiveness. Proc Natl Acad Sci U S A. 2004 May 4;101(18):6929-33.

    Scott EE, White MA, He YA, Johnson EF, Stout CD, Halpert JR. Structure of mammalian cytochrome P450 2B4 complexed with 4-(4-chlorophenyl)imidazole at 1.9-A resolution: insight into the range of P450 conformations and the coordination of redox partner binding. J Biol Chem. 2004 Jun 25;279(26):27294-301.

    Yu S, Lee JC. Role of residue 138 in the interdomain hinge region in transmitting allosteric signals for DNA binding in Escherichia coli cAMP receptor protein. Biochemistry. 2004 Apr 27;43(16):4662-9.

    Agashe VR, Guha S, Chang HC, Genevaux P, Hayer-Hartl M, Stemp M, Georgopoulos C, Hartl FU, Barral JM. Function of trigger factor and DnaK in multidomain protein folding: increase in yield at the expense of folding speed. Cell. 2004 Apr 16;117(2):199-209.

    Bufe A, Ziegler-Kirbach E, Stoeckmann E, Heidemann P, Gehlhar K, Holland-Letz T, Braun W. Efficacy of sublingual swallow immunotherapy in children with severe grass pollen allergic symptoms: a double-blind placebo-controlled study. Allergy. 2004 May;59(5):498-504.

    Cummins SF, Nichols AE, Rajarathnam K, Nagle GT. A conserved heptapeptide sequence in the waterborne attractin pheromone stimulates mate attraction in Aplysia. Peptides. 2004 Feb;25(2):185-9.

    Ivanciuc O, Oezguen N, Mathura VS, Schein CH, Xu Y, Braun W. Using property based sequence motifs and 3D modeling to determine structure and functional regions of proteins. Curr Med Chem. 2004 Mar;11(5):583-93. Review.

    Kumar R, Betney R, Li J, Thompson EB, McEwan IJ. Induced alpha-helix structure in AF1 of the androgen receptor upon binding transcription factor TFIIF. Biochemistry. 2004 Mar 23;43(11):3008-13.

    Gokul V, Kruger HG, Govender T, Fourie L, Power TD. An Ab Initio Mechanistic Understanding of the Regioselective Acetylation of 8,11-dihydroxy-pentacyclo[,6.03,10.05,9]undecane-8,11-lactam. J. Mol. Struct. (Theochem). 2004 Mar;672(1-3):119-125.

    Babu CR, Hilser VJ, Wand AJ. Direct access to the cooperative substructure of proteins and the protein ensemble via cold denaturation. Nat Struct Mol Biol. 2004 Apr;11(4):352-7.

    Ferguson MR, Fan X, Mukherjee M, Luo J, Khan R, Ferreon JC, Hilser VJ, Shope RE, Fox RO. Directed discovery of bivalent peptide ligands to an SH3 domain. Protein Sci.2004 Mar;13(3):626-32.

    Bao X, Reuss L, Altenberg GA. Regulation of purified and reconstituted connexin 43 hemichannels by protein kinase C-mediated phosphorylation of Serine 368. J Biol Chem. 2004 May 7;279(19):20058-66.

    Yu S, Mei FC, Lee JC, Cheng X. Probing cAMP-dependent protein kinase holoenzyme complexes I alpha and II beta by FT-IR and chemical protein footprinting. Biochemistry. 2004 Feb 24;43(7):1908-20.

    Auton M, Bolen DW. Additive transfer free energies of the peptide backbone unit that are independent of the model compound and the choice of concentration scale. Biochemistry. 2004 Feb 10;43(5):1329-42.

    Altenberg GA. Structure of multidrug-resistance proteins of the ATP-binding cassette (ABC) superfamily. Curr Med Chem Anticancer Agents. 2004 Jan;4(1):53-62. Review.

    Kunkel M, Watowich SJ. Biophysical characterization of hepatitis C virus core protein: implications for interactions within the virus and host. FEBS Lett. 2004 Jan 16;557(1-3):174-80.

    Izumi T, Schein CH, Oezguen N, Feng Y, Braun W. Effects of backbone contacts 3' to the abasic site on the cleavage and the product binding by human apurinic/apyrimidinic endonuclease (APE1). Biochemistry. 2004 Jan 27;43(3):684-9.

    Balaban AT, Ghiviriga I, Czerwinski EW, De P, Faust R. Simple synthesis of a weak nucleophilic base (4-ethyl-2,6-diisopropyl-3,5-dimethylpyridine) evidencing a double Janus group effect. J Org Chem. 2004 Jan 23;69(2):536-42.

    Scholle F, Li K, Bodola F, Ikeda M, Luxon BA, Lemon SM. Virus-host cell interactions during hepatitis C virus RNA replication: impact of polyprotein expression on the cellular transcriptome and cell cycle association with viral RNA synthesis. J Virol. 2004 Feb;78(3):1513-24.

    Zhang JZ, Sinha M, Luxon BA, Yu XJ. Survival strategy of obligately intracellular Ehrlichia chaffeensis: novel modulation of immune response and host cell cycles. Infect Immun. 2004 Jan;72(1):498-507.

    Bao X, Chen Y, Reuss L, Altenberg GA. Functional expression in Xenopus oocytes of gap-junctional hemichannels formed by a cysteine-less connexin 43. J Biol Chem. 2004 Mar 12;279(11):9689-92.

    Vongpunsawad S, Oezgun N, Braun W, Cattaneo R. Selectively receptor-blind measles viruses: Identification of residues necessary for SLAM- or CD46-induced fusion and their localization on a new hemagglutinin structural model. J Virol. 2004 Jan;78(1):302-13.

    Weaver SC, Ferro C, Barrera R, Boshell J, Navarro JC. Venezuelan equine encephalitis. Annu Rev Entomol. 2004;49:141-74. Review.

    Bao X, Altenberg GA, Reuss L. Mechanism of regulation of the gap junction protein connexin 43 by protein kinase C-mediated phosphorylation. Am J Physiol Cell Physiol. 2004 Mar;286(3):C647-54.

    Gundala S, Wells LD, Milliano MT, Talkad V, Luxon BA, Neuschwander-Tetri BA. The hepatocellular bile acid transporter Ntcp facilitates uptake of the lethal mushroom toxin alpha-amanitin.Arch Toxicol. 2004 Feb;78(2):68-73.

    Edman K, Royant A, Larsson G, Jacobson F, Taylor T, van der Spoel D, Landau EM, Pebay-Peyroula E, Neutze R. Deformation of helix C in the low temperature L-intermediate of bacteriorhodopsin.J Biol Chem. 2004 Jan 16;279(3):2147-58.