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Publications by SCSB Faculty

Last Update: December, 2017

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  • 2008 Publications

    Steinmann, C.; Landsverk, M.L.; Barral, J.M. and Boehning, D.F. Requirement of IP3R for tumor-mediated lymphocyte apoptosis. J. Biol. Chem. 283:13506-13509; 2008.

    Gauglitz, G.G.; Song, J.; Herndon, D.N.; Finnerty, C.C.; Barral, J.M.; Boehning, D.F. and Jeschke, M.G. Characterization of the inflammatory response during acute and post-acute phases following severe burn. Shock 30:503-508; 2008.

    C. Steinmann, M.L. Landsverk, J.M. Barral, D. Boehning; Requirement of IP3R for Tumor-Mediated Lymphocyte Apoptosis. J. Biol. Chem., May 16;283(20):13506-9. Epub Mar 25 (2008). Accelerated Communication

    G.G. Gauglitz, J. Song, D.N. Herndon, C.C. Finnerty, D. Boehning, J.M. Barral, M.G. Jeschke; Characterization of the Inflammatory Response during Acute and Post-Acute Phases Following Severe Burn. Shock. 2008 Apr 3 [Epub ahead of print].

    X. Qin, H. Kwansa, E. Bucci, S. Doré, D. Boehning, D. Shugar, R.C. Koehler; Role of heme oxygenase-2 in pial arteriolar response to acetylcholine in mice with and without transfusion of cell-free hemoglobin polymers. Am J Physiol Regul Integr Comp Physiol. 2008 May 21 [Epub ahead of print]

    P.M. Jordan, L.D. Ojeda, J.R. Thonhoff, J. Gao, D. Boehning, Y. Yu, and P. Wu; Generation of spinal motor neurons from human fetal brain-derived neural stem cells: role of basic fibroblast growth factor. J. Neurosci. Res., 2008 Sep 19. [Epub ahead of print]

    Matthew Auton , D. Wayne Bolen, and Jörg Rösgen "Structural Thermodynamics of Protein Preferential Solvation" Proteins 73, 802–813 (2008).

    Oezguen N, Zhou B, Negi S, Ivanciuc O., Schein CH, Labesse G, and Braun, W. Comprehensive 3D-modeling of allergenic proteins and structural analysis of linear IgE epitopes. Mol Immunol. 45 3740-3747, 2008. PMID: 18621419

    Oezguen N, Kumar S, Hindupur A, Braun W, Muralidhara BK, Halpert JR.. Identification and Analysis of Conserved Sequence Motifs in Cytochrome P450 Family 2: Functional Role of a Motif 187RFDYKD192 in P450 2B4. J Biol Chem.;283(31):21808-16, 2008.

    Leonard VHL, Sinn PL, Hodge G, Miest T, Devaux P, Oezguen N, Braun W, McCray Jr. PB, McChesney MB, and Cattaneo R. Measles virus blind to its epithelial cell receptor remains virulent in rhesus monkeys but cannot cross the airway epithelium and is not shed. Journal of Clinical Investigation J Clin Invest.118(7):2448-2458, 2008.

    Mantha AK, Oezguen N, Bhakat KK, Tadahide I, Braun W, and Mitra S. Unusual Role of a Cysteine Residue in Substrate Binding and Activity of Human AP-Endonuclease. J Mol Biol.;379(1):28-37, 2008.

    Navaratnarajah, C.K., Vongpunsawad, S., Oezguen, N., Stehle, T., Braun, W., Hashiguchi, T., Maenaka, K., Yanagi, Y. and Cattaneo, R. Dynamic interaction of the measles virus hemagglutinin with its receptor SLAM. J. Biol. Chem. 283(17): 11763-11771, 2008.

    Negi SS, Carol AA, Pandya S , Braun W, Anderson LE. Co-localization of glyceraldehyde-3-phosphate dehydrogenase with ferredoxin-NADP reductase in pea leaf chloroplasts. J Struct Biol. 161(1):18-30, 2008.

    Marcinowicz, A., Jezewska, M. J. and Bujalowski, W., Multiple Global Conformational States of the Hexameric RepA Helicase of Plasmid RSF1010 With Different ssDNA-Binding Capabilities Are Induced By Different Numbers of Bound Nucleotides. Analytical Ultracentrifugation and Dynamic Light Scattering Studies, J. Mol. Biol. 375: 386-408, 2008.

    Cheng, X. Silent assassin: Oncogenic Ras directs epigenetic inactivation of target genes. Science Signaling. 1:pe14, 2008.

    Ji, Z., Mei, F. C., Miller, A. L., Thompson, E. B., and Cheng, X. Protein kinase A (PKA) isoform RIIβ mediates the synergistic killing effect of cAMP and glucocorticoid in acute lymphoblastic leukemia cells. J. Biol. Chem. 283:21920-21925, 2008.

    Cheng, X., Ji, Z., Tsalkova, T., and Mei, F. C. Epac and PKA: a tale of two intracellular cAMP receptors. Acta Biochimica et Biophysica Sinica. 40:651-662, 2008.

    Choi KH, McPartland J, Kaganman I, Bowman VD, Rothman-Denes LB, Rossmann MG (2008) Insight into DNA and protein transport in double-stranded DNA viruses: The structure of bacteriophage N4. J. Mol. Biol. 378(3): 726-36

    Exploring the impact of conformational bias on the binding of peptides to the SEM-5 SH3 domain. S.T. Whitten, H.-W. Yang, R.O. Fox, and V.J. Hilser. Protein Science 17, 1200-1211; 2008.

    Overexpression and functional characterization of the extracellular domain of the human alpha1 glycine receptor. Z. Liu, G. Ramanoudjame, R.O. Fox, V. Jayaraman, M. Kurnikova, M. Cascio Biochemistry 47, 9803–9810; 2008. 

    Varatharasa Thiviyanathan, Anoma Somasunderam, David E. Volk, Tapas K. Hazra, Sankar Mitra and David G. Gorenstein, "Base-pairing properties of the oxidized cytosine derivative, 5-Hydroxy uracil," Biochem Biophys Res Commun., 366:752-757 (2008).

    D. E. Volk, K. M. Anderson, S. H. A. Gandham, F. J. May, L. Li, David W. C. Beasley, A. D. T. Barrett and D. G. Gorenstein "NMR Assignments of the Sylvatic Dengue 1 Virus Envelope Protein Domain III." Biomol. NMR Assigments 2:155-157, 2008.

    Jonghoon Kang, Myung Soog Lee, John A. Copland III, Bruce A. Luxon David G. Gorenstein, "Combinatorial selection of a single stranded DNA thioaptamer targeting TGF-beta1 protein," Bioorganic & Medicinal Chemistry Letters, 18, 1835-9 (2008).

    Xianbin Yang, Duane Beasley, Bruce A. Luxon, Johnnie Engelhardt, Mark Shumbera, David G. Gorenstein, Bead-based Approaches to Develop Thioaptamers for Diagnostics and Therapeutics", Phosphorus, Sulfur, and Silica and the Related Elements (Proceedings of ICPU2007),183, 469-472 (2008).

    Gu, J., and Hilser VJ. Predicting the energetics of conformational fluctuations in proteins from sequence: a strategy for profiling the proteome. Structure. 2008; 16:1627-37.

    Wang S, Gu J, Larson SA, Whitten ST, Hilser VJ. Denatured-state energy landscapes of a protein structural database reveal the energetic determinants of a framework model for folding. J Mol Biol 2008; 381:1184-201.

    Whitten ST, Yang HW, Fox RO, Hilser VJ. Exploring the impact of polyproline II (PII) conformational bias on the binding of peptides to the SEM-5 SH3 domain. Protein Sci 2008; 17:1200-11.

    Sayar K, Uğur O, Liu T, Hilser VJ, Onaran O. Exploring allosteric coupling in the alpha-subunit of heterotrimeric G proteins using evolutionary and ensemble-based approaches. BMC Struct Biol 2008; 2:8-23.

    Whitten ST, García-Moreno BE, Hilser VJ. Ligand effects on the protein ensemble: unifying the descriptions of ligand binding, local conformational fluctuations, and protein stability. Methods Cell Biol 2008; 84:871-891.

    Gu J, Hilser VJ. Predicting the energetics of conformational fluctuations in proteins from sequence: A strategy for profiling the proteome. Structure 2008; 16:1627-1637.

    Sahu D, Debnath P, Takayama Y, Iwahara J (2008) Redox properties of the A-domain of the HMGB1 protein. FEBS Lett 582, 3973-3978.

    Takayama Y, Castaneda CA, Chimenti M, Garcia-Moreno B, Iwahara J (2008) Direct evidence for deprotonation of a lysine side-chain buried in the hydrophobic core of a protein. J Am Chem Soc 130, 6714-6715.

    Takayama Y, Sahu D, Iwahara J (2008) Observing in-phase single-quantum 15N multiplets for NH2/NH3+ groups with two-dimensional heteronuclear correlation spectroscopy. J Magn Reson 194, 313-316.

    Maillard, R., Jordan, M., Beasley, D., Barrett, A. and Lee, J.C. "Long-range communication in the envelop protein domain III and its effect on the resistance of West Nile Virus to antibody- mediated neutralization" J. Biol. Chem. 283, 613-622, 2008. (PMID17986445)

    Jawanda, N., Ebalunode, J., Gribenko, A. V., Briggs, J., Lee, J. C. and Tu, S-C. " A single residue mutation destabilizes Vibrio harveyi flavin reductase FRP dimer" Arch. Biochem. Biophys. 472, 51-57, 2008. (PMID18294448)

    Lida Q. Fuentes, Carlos E. Reyes, José M. Sarmiento, Carolina I. Villanueva, Carlos D. Figueroa, Javier Navarro, Carlos B. González. Vasopressin up-regulates the expression of growth-related immediate-early genes via two distinct EGF receptor transactivation pathways. Cell Signal, 20:1642-1650, 2008

    Oberhauser, AF & Carrion-Vazquez, M. Mechanical biochemistry of proteins one molecule at a time (2008). J Biol Chem. Mar 14;283(11):6617-21.

    Greene, D.N., Garcia T., Sutton, RB, Gernert K. M., Benian, G. M., & Oberhauser AF. Single-molecule force spectroscopy reveals a stepwise unfolding of C. elegans giant protein kinase domains. (2008). Biophys J. Aug;95(3):1360-70. [Figure featured on journal cover]

    Garcia, T., Oberhauser AF and Braun W. Mechanical Stability and Differentially Conserved Physical-chemical Properties of Titin Ig-domains. (2008). Proteins Sep 25;75(3):706-718.

    Adams EL, Rice PJ, Graves B, Ensley HE, Yu H., Brown GD, Gordon S, Monteiro MA, Papp-Szabo E, Lowman DW, Power TD, Wempe MF, Williams DL; Differential High Affinity Interaction of Dectin-1 with Natural or Synthetic Glucans is Dependent upon Primary Structure and is Influenced by Polymer Chain Length and Side Chain Branching. J. Pharmacol. Exp. Ther. 2008;325(1):115-123.

    Parmenter C., S. Stoilova-McPhie and S. Bonn 2008. A Cryo-Transmission Electron Microscopy Study of Asymmetric PMMA Copolymers. Microscopy and Analysis, 22: 11-13.

    Parmenter C. and S. Stoilova-McPhie 2008. Binding of recombinant human coagulation factor VIII to lipid nanotubes. FEBS Letters, 28:1657-60.

    Clokie M.R.J., K. Thalassinos, P. Boulanger, S.E. Slade, S. Stoilova-McPhie, M.C. Cane, J.H. Scrivens and N.H. Mann 2008. A proteomic approach to the identification of the major virion structural proteins of the marine cyanomyovirus S-PM2. Micorbiology 154:1775-82

    Parmenter C.D.J., M.C. Cane, R. Zhang and S. Stoilova-McPhie 2008. Cryo-electron microscopy of coagulation Factor VIII bound to lipid nanotubes. Biochem Biophys Res Comm 366, 288 – 293.

    Stoilova-McPhie S., C.D.J. Parmenter, K. Segers, B.O. Villoutreix, G.A.F. Nicolaes 2008. Defining the structure of membrane-bound human blood coagulation Factor Va. J Thromb and Haemost 6, 76 - 82.

    Thompson, E.B. Stepping stones in the path of glucocorticoid-driven apoptosis of lymphoid cells. Acta Biochim. Biophys Sin. (Shanghai) Jul;40(7):595-600. 2008.

    Sheth, J.Hays, L. Elferink and S. J. Watowich, "Biochemical Basis for the Functional Switch That Regulates Hepatocyte Growth Factor Receptor Tyrosine Kinase Activation," Biochemistry,47, 4028-4038, 2008.

    O. A. Kolokoltsova, A. M. Domina, A. A. Kolokoltsov, R. A. Davey, S. C. Weaver and S. J. Watowich, "Alphavirus Production is Inhibited in Neurofibromin 1-Deficient Cells through Activated RAS Signaling," Virology, 377, 133-142, 2008.

    A. N. Freiberg*, M. B. Sherman*, M. C. Morais, M. R. Holbrook, and S. J. Watowich, "Three-Dimensional Organization of Rift Valley Fever Virus Revealed by Cryoelectron Tomography," J. Virology, 82, 10341-10348, 2008.

    S. M. Tomlinson and S. J. Watowich, "Substrate Inhibition Kinetic Model for West Nile Virus NS2B-NS3 Protease," Biochemistry,47, 11763-11770, 2008.

    Ji, Z., Mei, F.C., Miller, A.L., Thompson, E.B. Cheng, X. Protein kinase A (PKA) isoforms RIIbeta mediates the synergistic killing effect of cAMP and glucocorticoid in acute lymphoblastic leukemia cells. J. Biol. Chem. Aug. 8;283(32):21920-5. 2008 Epub 2009 Jun 10.

    Garza, AS., Miller, A.L., Johnson, B.H., Thompson, E.B. Converting cell lines representing hematological malignancies from glucocorticoid-resistant to glucocorticoid-sensitive: Signaling pathway interactions. Leuk. Res. May, 2009 33(5):717-27. 2008 Nov. 12. [Epub ahead of print].

    Smith DR, Adams AP, Kenney JL, Wang E, Weaver SC. Venezuelan equine encephalitis virus in the mosquito vector Aedes taeniorhynchus: infection initiated by a small number of susceptible epithelial cells and a population bottleneck. Virology 372 (1): 176-86, 2008. PMCID: PMC2291444.

    Arrigo NC, Watts DM, Frolov I, Weaver SC. Experimental Infection of Aedes sollicitans and Aedes taeniorhynchus with Two Chimeric Sindbis/Eastern Equine Encephalitis Virus Vaccine Candidates. Am J Trop Med Hyg 78 (1): 93-7, 2008. PMCID: PMC2215343.

    Vasilakis N, Tesh RB, Weaver SC. Sylvatic dengue virus type 2 activity in humans, Nigeria, 1966. Emerg Infect Dis 14 (3): 502-4, 2008. PMCID: PMC2570833.

    Moncayo AC, Lanzaro G, Kang W, Orozco A, Ulloa A, Arredondo-Jimenez J, Weaver SC. Vector competence of eastern and western forms of Psorophora columbiae (Diptera: Culicidae) mosquitoes for enzootic and epizootic Venezuelan equine encephalitis virus. Am J Trop Med Hyg 78 (3): 413-21, 2008. PMCID: not yet available.

    Volkova E, Frolova E, Darwin JR, Forrester NL, Weaver SC, Frolov I. IRES-dependent replication of Venezuelan equine encephalitis virus makes it highly attenuated and incapable of replicating in mosquito cells. Virology 377 (1): 160-9, 2008. PMCID: PMC2483425.

    Kolokoltsova OA, Domina AM, Kolokoltsov AA, Davey RA, Weaver SC, Watowich SJ. Alphavirus production is inhibited in neurofibromin 1-deficient cells through activated RAS signalling. Virology 377 (1): 133-42, 2008. PMCID: not yet available.

    Aguilar PV, Leung LW, Wang E, Weaver SC, Basler CF. A five-amino-acid deletion of the eastern equine encephalitis virus capsid protein attenuates replication in mammalian systems but not in mosquito cells. J Virol 82 (14): 6972-83, 2008. PMCID: PMC2446984.

    Ortiz DI, Kang W, Weaver SC. Susceptibility of Ae. aegypti (Diptera: Culicidae) to infection with epidemic (subtype IC) and enzootic (subtypes ID, IIIC, IIID) Venezuelan equine encephalitis complex alphaviruses. J Med Entomol 45 (6): 1117-25, 2008. PMCID: not yet available.

    Ferro C, Olano V, Ahumada M, Weaver SC. Mosquitos (Diptera: Culicidae) en el caserío Chingalé, Santander, donde se registró un caso humano de encefalitis equina venezolana. Biomédica (Colombia) 28: 234-244, 2008. PMCID: not available.

    Volkova E, Frolova E, Darwin JR, Forrester NL, Weaver SC, Frolov I. IRES-dependent replication of Venezuelan equine encephalitis virus makes it highly attenuated and incapable of replicating in mosquito cells. Virology 377 (1): 160-9, 2008. PMCID: PMC2483425.

    Vasilakis N, Fokam EB, Hanson CT, Weinberg E, Sall AA, Whitehead SS, Hanley KA, Weaver SC. Genetic and phenotypic characterization of sylvatic dengue virus type 2 strains. Virology 377 (2): 296-307, 2008. PMCID: not yet available.

    Vasilakis N, Durbin AP, da Rosa AP, Munoz-Jordan JL, Tesh RB, Weaver SC. Antigenic relationships between sylvatic and endemic dengue viruses. Am J Trop Med Hyg 79 (1): 128-32, 2008. PMCID: not yet available.

    Coffey LL, Vasilakis N, Brault AC, Powers AM, Tripet F, Weaver SC. Arbovirus evolution in vivo is constrained by host alternation. Proc Natl Acad Sci USA 105 (19): 6970-5, 2008. PMCID: PMC2383930.

    Aguilar PV, Adams AP, Wang E, Kang W, Carrara AS, Anishchenko M, Frolov I, Weaver SC. Structural and nonstructural protein genome regions of eastern equine encephalitis virus are determinants of interferon sensitivity and murine virulence. J Virol 82 (10): 4920-30, 2008. PMCID: PMC2346730.

    Wang E, Volkova E, Adams AP, Forrester N, Xiao SY, Frolov I, Weaver SC. Chimeric alphavirus vaccine candidates for chikungunya. Vaccine 26 (39): 5030-5039, 2008. PMCID: PMC2571998.

    Forrester NL, Kenney JL, Deardorff E, Wang E, Weaver SC. Western Equine Encephalitis submergence: lack of evidence for a decline in virus virulence. Virology 380 (2): 170-2, 2008. PMCID: PMC2574696.

    Poluri A, Ainsworth R, Weaver SC, Sutton RE. Functional pseudotyping of human immunodeficiency virus type 1 vectors by Western equine encephalitis virus envelope glycoprotein. J Virol 82 (24): 12580-4, 2008. PMCID: PMC2593314.

    McBride MP, Sims MA, Cooper RW, Nyaoke AC, Cullion C, Kiupel M, Frasca S, Jr., Forrester N, Weaver SC, Weber ES. Eastern equine encephalitis in a captive harbor seal (Phoca vitulina). J Zoo Wildl Med 39 (4): 631-7, 2008. PMCID: not yet available.

    Adams AP, Aronson JF, Tardif SD, Patterson JL, Brasky KM, Geiger R, de la Garza M, Carrion R, Jr., Weaver SC. Common marmosets (Callithrix jacchus) as a nonhuman primate model to assess the virulence of eastern equine encephalitis virus strains. J Virol 82 (18): 9035-42, 2008. PMCID: PMC2546911.