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Publications by SCSB Faculty

Last Update: 2016

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  • 2009 Publications

    Jeschke, M.G.; Gauglitz, G.G.; Song, J.; Kulp, G.A.; Finnerty, C.C.; Cox, R.; Barral, J.M.; Herndon, D.N. and Boehning, D. Calcium and ER stress mediate hepatic apoptosis after burn injury. J. Cell Mol. Med. 13:1857 (2009).

    Gauglitz, G.G.; Halder, S.; Boehning, D.F.; Kulp, G.A.; Herndon, D.N.; Barral, J.M. and Jeschke, M.G. Post-burn hepatic insulin resistance is associated with ER stress. Shock. 2009. Jun 18 [Epub ahead of print]. PMID: 19543150.

    M.G. Jeschke, G. Gauglitz, J. Song, G.A. Kulp, C.C. Finnerty, R.A. Cox, J.M. Barral, D.N. Herdon, and D. Boehning; Calcium and ER stress mediate hepatic apoptosis after burn injury. Journal of Cellular and Molecular Medicine, 13(8b): 1857-1865 (2009).

    G.G. Gauglitz, S. Halder, D. Boehning, G.A. Kulp, D.N. Herndon, J. M. Barral, M.G. Jeschke. Post-burn hepatic insulin resistance is associated with ER stress. Shock 2009 Jun 18. [Epub ahead of print]

    J. Song, Finnerty C.C., D.N. Herndon, D. Boehning, M.G. Jeschke. Severe burn-induced endoplasmic reticulum stress and hepatic damage in mice. Molecular Medicine 2009 Jul 15. [Epub ahead of print]

    Travis P. Schrank, D. Wayne Bolen, and Vincent J. Hilser "Rational modulation of conformational fluctuations in adenylate kinase reveals a local unfolding mechanism for allostery and functional adaptation of proteins" Proc. Natl. Acad. Sci. 106, 16984-16989 (2009).

    Negi SS and Braun W. Automated Detection of Conformational Epitopes using Phage Display Peptide Sequences. Bioinform. Biol. Insights, 3, 71-81, 2009.

    Ivanciuc O, Garcia TI, Torres M, Schein CH, Braun W. Characteristic Motifs for Families of Allergenic Protein. Mol Immunol. 46(4):559-568, 2009 PMID: 18951633

    Garcia T, Oberhauser A, and Braun W. Mechanical Stability and Differentially Conserved Physical-chemical Properties of Titin Ig-domains, Proteins: Struct. Funct. And Bioinf., 75(3), 706-718, 2009

    Ivanciuc O, Midoro-Horiuti T, Schein CH, Xie L, Hillman, GR, Goldblum RM, Braun W. The property distance index PD predicts peptides that cross-react with IgE antibodies. Molecular Immunology 46(5):873-883, 2009 PMID: 18950868.

    Ivanciuc O, Schein CH, Garcia T, Oezguen N, Negi S, and Braun W. Structural Analysis of Linear and Conformational Epitopes of Allergens. Regulatory Toxicology and Pharmacology, 54(3 Suppl), S11-S19, 2009.

    Andreeva, I. E. Szymanski, M. R., Jezewska, M. J., Galletto, R., and Bujalowski, W., Dynamics of the ssDNA Recognition by the RepA Hexameric Helicase of Plasmid RSF1010. Analyses Using Fluorescence Stopped-Flow Intensity and Anisotropy Methods, J. Mol. Biol. J. Mol. Biol. 388: 751-775, 2009.

    Roychowdhury, A., Szymanski, M. R., Jezewska, M. J., and Bujalowski W., Interactions of the E. coli DnaB - DnaC Protein Complex With Nucleotide Cofactors. 1. Allosteric Conformational Transitions of the Complex, Biochemistry 48: 6712-6729, 2009.

    Roychowdhury, A., Szymanski, M. R., Jezewska, M. J., and Bujalowski W., Mechanism of NTP Hydrolysis by the Escherichia coli Primary Replicative Helicase DnaB Protein. 2. Nucleotide and Nucleic Acid Specificities, Biochemistry 48: 6730-6746, 2009.

    Roychowdhury, A., Szymanski, M. R., Jezewska, M. J., and Bujalowski W., The Escherichia coli DnaB Helicase - DnaC Protein Complex: Allosteric Effects of the Nucleotides on the Nucleic Acid Binding and the Kinetic Mechanism of NTP Hydrolysis. 3., Biochemistry 48: 6747-6763, 2009.

    Andreeva I. E., Roychowdhury A., Szymanski M. R., Jezewska, M. J., and Bujalowski W., Mechanisms of Nucleotide Cofactor Interactions With the RepA Protein of Plasmid RSF1010. Binding Dynamics Studied Using Fluorescence Stopped-Flow Method, Biochemistry, 48:10620-10636 2009.

    Ji, Z., Mei, F. C., Lory, P. L., Gilbertson, S. R., Chen, Y., and Cheng, X. Chemical genetic screening of KRAS-based synthetic lethal inhibitors for pancreatic cancer. Frontiers in Bioscience. 14:2904-2910, 2009.

    Tsalkova, T., Blumenthal D. R., Mei, F. C., and Cheng, X. Mechanism of Epac activation: Structural and functional analyses of Epac2 hinge mutants with Constitutive and reduced activities. J. Biol. Chem. 284:23644-23651, 2009.

    Choi KH and Rossmann MG (2009) RNA-dependent RNA polymerases from Flaviviridae. Curr. Opin. Struct .Biol. 19(6):746-51

    Szymanski MR, Fiebach AR, Tratschin J-D, Gut M, Ramanujam VMS, Patel P, Ye M, Keerthi Gottipati, Ruggli N, Choi KH. (2009) Zinc-binding in pestivirus Npro is required for interferon regulatory factor 3 (IRF3) interaction and degradation. J. Mol. Biol.

    Ruggli N, Summerfield A. Fiebach AR, Guzylack L, Bauhofer O, Lamm CG, Waltersperger S, Matsuno K, Liu L, Gerber M, Choi KH, Hofmann MA, Sakoda Y, Tratschin JD. (2009) Classical swine fever virus can remain virulent after specific elimination of the interferon regulatory factor 3 degrading function of Npro. J. Virol. 83(2):817-29

    Characterizing the Role of Ensemble Modulation in Mutation Induced Changes in Binding Affinity Manson, A., Whitten, S. T., Ferreon, J. C., Fox, R. O. and Hilser, V. J. J. Am. Chem. Soc. 131, 6785-93; 2009.

    Bowick, G.C, Spratt, H.M, Hogg, A.E, Endsley, J.J, Wiktorowicz, J.E, Kurosky, A., Luxon, B.A., Gorenstein, D.G., Herzog, N.K. Analysis of the differential host cell nuclear proteome induced by attenuated and virulent hemorrhagic arenavirus infection. J Virol. 83:687-700 (2009).

    R. Shylini, Varatharasa Thiviyanathan, D. G. Gorenstein, and I. Frolov, "The 5"UTR-specific mutation in VEEV TC-83 genome has a strong effect on RNA replication and subgenomic RNA synthesis, but not on translation of the encoded proteins", Virology, 2009, 387:211-221.

    David E. Volk, Fiona J. May, Sai H. A. Gandham, Anjenique Anderson, Jana von Lindern, David Beasle, Alan D. T. Barrett and David G. Gorenstein, "Yellow Fever Virus Envelope Protein Domain III", Virology, 394(1), 12-18 (2009).

    R. Shylini, S. Atasheva, Varatharasa Thiviyanathan, D. G. Gorenstein, and I. Frolov, "Structural and functional elements of the promoter encoded by 5"UTR of Venezuelan equine encephalitis virus genome" J. Virology, 83(17):8327-39 (2009).

    Thiviyanathan V, Kulasegaran-Shylini R, Rijnbrand R, Kaluarachchi K, Lemon SM, and Gorenstein DG. "Mutational and Structural Analysis of Stem-loop IIId of the Hepatitis C Virus and GB Virus B Internal Ribosome Entry Sites". (Manuscript in revision, (2009).

    Schrank, T., Bolen, D.W., and V.J. Hilser. Rational Modulation of Conformational Fluctuations in Adenylate Kinase Reveal a Local Unfolding Mechanism for Allostery and Functional Adaptation in Proteins. Proc. Nat. Acad. Sci. USA. 2009; 106:16984-16989.

    Vertrees, J., Wrabl, J.O., and V.J. Hilser (2009) An Energetic Representation of Protein Architecture that is Independent of Primary and Secondary Structure. Biophys. J. 2009; 97:1461-1470.

    Gu, J. and V.J. Hilser. Sequence-based Analysis of Protein Energy Landscapes Reveals Non-uniform Thermal Adaptation within the Proteome. Mol. Biol. Evol. 2009; 26:2217-2227.

    Manson, A., Whitten, S.T., Ferreon, J.C., Fox, R.O. and V.J. Hilser. Characterizing the Role of Ensemble Modulation in Mutation-induced Changes in Binding Affinity J. Am. Chem. Soc. 2009; 131:6785-6793.

    Gu, J. and V.J. Hilser. The Significance and Impacts of Protein Disorder and Conformational Variants. In Structural Bioinformatics, Second Edition. Ed. J. Gu and P.E. Bourne, John Wiley & Sons . 2009.

    Vertrees, J., Wrabl, J.O., and V.J. Hilser. Energetic Profiling of Proteins. Meth. in Enzym., 2009; 455:299-327.

    Hilser, V.J. and S.T. Whitten (2009) Energy Flow and Allostery in an Ensemble. In Proteins: Energy, Heat and Signal Flow Eds. David M. Leitner and John E. Straub. CRC Press, Taylor & Francis Group.

    Clore, GM, Iwahara, J (2009) Theory, practice and applications of paramagnetic relaxation enhancement for the characterization of low-population states of biological macromolecules and their complexes. Chem Rev 109, 4108-4139.

    Matsui, K., Gromowski , G. D., Li, L., Schuh, A. J., Lee, J. C. and Barrett, A. D. T. "Characterization of Dengue Complex-specific Epitopes on Dengue 3 Virus Envelope Protein Domain III" Virology, 384, 16-20, 2009.

    Herman, P. and Lee, J. C. "Functional Energetic Landscape in the Allosteric Regulation of Muscle Pyruvate Kinase. I. Calorimetric Study" Biochemistry, 48, 9448-9455, 2009. (PMID: 19719244)

    Herman, P. and Lee, J. C. "Functional Energetic Landscape in the Allosteric Regulation of Muscle Pyruvate Kinase. II. Fluorescence Study" Biochemistry, 48, 9456-9465, 2009. (PMID: 19719323)

    Herman, P. and Lee, J. C. "Functional Energetic Landscape in the Allosteric Regulation of Muscle Pyruvate Kinase. III. Mechanism" Biochemistry, 48, 9466-9470, 2009. ( PMID: 19719322)

    J. Sarmiento, K.E. Kypreos, G.N. Prado, K. Suetomi, C. Stanzel, C. Maxwell, D. Shumate, M.R. Tandang-Silvas, K. Rajarathnam, J. Navarro adenovirus mediated expression "in vivo" of the chemokine receptor CXCR1. J. Struct Funct Genomics 10:17-23, 2009.

    Karina J. Vargas, Jose M. Sarmiento, Pamela Ehrenfeld, Carolina C. Anazco, Carolina I. Villanueva, Pamela L. Carmona, Javier Navarro, Werner Muller-Esterl, Carlos B. Gonzalez. Postnatal Expression of V2 Vasopressin Receptor Splice Variants in the Rat Cerebellum. Differentiation 77:377-85, 2009.

    Fuson, K., Ma, L., Sutton, RB & Oberhauser AF. The C2 domains of human Synaptotagmin 1 have distinct mechanical properties (2009). Biophys J. Feb;96(3):1083-90.

    Xiong G., Qadota, H., Mercer, KB, McGaha,LA., Oberhauser, AF and Benian, GM. A LIM-9 (FHL) / SCPL-1 (SCP) Complex Interacts with the C-terminal Protein Kinase Regions of UNC-89 (Obscurin) in C. elegans Muscle. (2009). Journal of Molecular Biology Mar 6;386(4):976-88.

    Ma L, Xu M, Forman JR, Clarke J. & Oberhauser A.F. (2009). Naturally occurring mutations alter the stability of polycystin-1 PKD domains. J Biol Chem. 284(47):32942-9. PMID: 19759016

    Ravindran, A., Joseph, P. R., and Rajarathnam, K. Structural Basis for Differential Binding of the Interleukin-8 Monomer and Dimer to the CXCR1 N-Domain: Role of Coupled Interactions and Dynamics. Biochemistry 48:8795-805 (2009).

    Nasser, M.W., Raghuwanshi, S.K., Grant, D.J., Jala, V.R., Rajarathnam, K., and Richardson, R.M. Differential activation and regulation of CXCR1 and CXCR2 by CXCL8 monomer and dimer. J Immunol. 183:3425-32 (2009).

    Sarmiento, J., Kypreos, K. E., Prado, G. N., Suetomi, K., Stanzel, C., Maxwell, C., Shumate, D., Tandang-Silvas, M. R., Rajarathnam, K., and Navarro, J. Adenovirus mediated expression "in vivo" of the chemokine receptor CXCR1. J Struct Funct Genomics 1:17-23; 2009.

    R. V. Campbell, Y. Yang, T. Wang, A. Rachamallu, Y. Li, S. J. Watowich, S. A. Weinman, "Effects of Hepatitis C Core Protein on Mitochondrial Electron Transport and Production of Reactive Oxygen Species," Methods in Enzymology 456, 1-18, 2009.

    S. M. Tomlinson, R. D. Malmstrom, A. Russo, N. Mueller, Y.-P. Pang, and S. J. Watowich, "Structure-Based Discovery of Dengue Virus Protease Inhibitors," Antivir. Res. 2009.

    S. M. Tomlinson*, R. D. Malmstrom*, and S. J. Watowich, "New Approaches to Structure-Based Discovery of Dengue Protease Inhibitors," Infectious Disorders-Drug Targets, 2009.

    M. B. Sherman*, A. N. Freiberg*, M. R. Holbrook, and S. J. Watowich, "Single-particle cryo-electron microscopy of Rift Valley fever virus," Virology, 387, 11-15, 2009.

    Espinosa BJ, Weaver SC, Paessler S, Brining D, Salazar M, Kochel T. Susceptibility of the Aotus nancymaae owl monkey to eastern equine encephalitis. Vaccine 27 (11): 1729-34, 2009. PMCID: not yet available.

    Presley SJ, Willig MR, Castro-Arellani I, Weaver SC. Effects of habitat conversion on temporal activity patterns of phyllostomid bats in lowland Amazonian rainforest. J Mammal. 90 (1): 210-221, 2009. PMCID: not yet available.

    Alonso-Padilla J, Loza-Rubio E, Escribano-Romero E, Cordoba L, Cuevas S, Mejia F, Calderon R, Milian F, Travassos DARA, Weaver SC, Estrada-Franco JG, Saiz JC. The continuous spread of West Nile virus (WNV): seroprevalence in asymptomatic horses. Epidemiol Infect: 1-6, 2009. PMCID: not yet available.

    Atasheva S, Wang E, Adams AP, Plante KS, Ni S, Taylor K, Miller ME, Frolov I, Weaver SC. Chimeric alphavirus vaccine candidates protect mice from intranasal challenge with western equine encephalitis virus. Vaccine 27 (32): 4309-19, 2009. PMCID: not yet available.

    Kim DY, Guzman H, Bueno R, Jr., Dennett JA, Auguste AJ, Carrington CV, Popov VL, Weaver SC, Beasley DW, Tesh RB. Characterization of Culex Flavivirus (Flaviviridae) strains isolated from mosquitoes in the United States and Trinidad. Virology 386 (1): 154-9, 2009. PMCID: not yet available.

    Deardorff ER, Forrester NL, Travassos-da-Rosa AP, Estrada-Franco JG, Navarro-Lopez R, Tesh RB, Weaver SC. Experimental infection of potential reservoir hosts with Venezuelan equine encephalitis virus, Mexico. Emerg Infect Dis 15 (4): 519-25, 2009. PMCID: PMC2671456.

    Quiroz E, Aguilar PV, Cisneros J, Tesh RB, Weaver SC. Venezuelan equine encephalitis in panama: fatal endemic disease and genetic diversity of etiologic viral strains. PLoS Negl Trop Dis 3 (6): e472, 2009. PMCID: PMC2697379.

    Auguste AJ, Volk SM, Arrigo NC, Martinez R, Ramkissoon V, Adams AP, Thompson NN, Adesiyun AA, Chadee DD, Foster JE, Travassos Da Rosa AP, Tesh RB, Weaver SC, Carrington CV. Isolation and phylogenetic analysis of Mucambo virus (Venezuelan equine encephalitis complex subtype IIIA) in Trinidad. Virology 392 (1): 123-30, 2009. PMCID: not yet available.

    Tsetsarkin KA, McGee CE, Volk SM, Vanlandingham DL, Weaver SC, Higgs S. Epistatic roles of E2 glycoprotein mutations in adaption of chikungunya virus to Aedes albopictus and Ae. aegypti mosquitoes. PLoS One 4 (8): e6835, 2009. PMCID: PMC2729410

    Sahu GK, Paar D, Frost SD, Smith MM, Weaver S, Cloyd MW. Low-level plasma HIVs in patients on prolonged suppressive highly active antiretroviral therapy are produced mostly by cells other than CD4 T-cells. J Med Virol 81 (1): 9-15, 2009. PMCID: not yet available.

    Aguilar PV, Adams AP, Suarez V, Beingolea L, Vargas J, Manock S, Freire J, Espinoza WR, Felices V, Diaz A, Liang X, Roca Y, Weaver SC, Kochel TJ. Genetic Characterization of Venezuelan Equine Encephalitis Virus from Bolivia, Ecuador and Peru: Identification of a New Subtype ID Lineage. PLoS Negl Trop Dis 3 (9): e514, 2009. PMCID: 2734058.

    Vasilakis N, Deardorff ER, Kenney JL, Rossi SL, Hanley KA, Weaver SC. Mosquitoes put the brake on arbovirus evolution: experimental evolution reveals slower mutation accumulation in mosquito than vertebrate cells. PLoS Pathog 5 (6): e1000467, 2009. PMCID: PMC2685980