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Publications by SCSB Faculty

Last Update: December, 2017

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  • 2007 Publications

    Fuson KL, Montes M, Robert JJ, Sutton RB. Structure of Human Synaptotagmin 1 C2AB in the Absence of Ca(2+) Reveals a Novel Domain Association. Biochemistry. 2007 Nov 13;46(45):13041-8. Oct 23. {PM}

    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. 2007 Sep 8; {PM}

    Jezewska MJ, Bujalowski PJ, Bujalowski W. Interactions of the DNA Polymerase X from African Swine Fever Virus with Gapped DNA Substrates. Quantitative Analysis of Functional Structures of the Formed Complexes. Biochemistry. 2007 Nov 13;46(45):12909-12924. Oct 17. {PM}

    Marcinowicz A, Jezewska MJ, Bujalowski PJ, Bujalowski W. Structure of the Tertiary Complex of the RepA Hexameric Helicase of Plasmid RSF1010 with the ssDNA and Nucleotide Cofactors in Solution. Biochemistry. 2007 Nov 20;46(46):13279-13296. Oct 16.{PM}

    Negi SS, Schein CH, Oezguen N, Power TD, Braun W. InterProSurf: a web server for predicting interacting sites on protein surfaces. Bioinformatics. 2007 Oct 12; {PM}

    Sahu D, Clore GM, Iwahara J. TROSY-based z-exchange spectroscopy: application to the determination of the activation energy for intermolecular protein translocation between specific sites on different DNA molecules. J Am Chem Soc. 2007 Oct 31;129(43):13232-7. Oct 5. {PM}

    Clore GM, Tang C, Iwahara J. Elucidating transient macromolecular interactions using paramagnetic relaxation enhancement. Curr Opin Struct Biol. 2007 Oct;17(5):603-16. Oct 29. {PM}

    Ji Z, Mei FC, Johnson BH, Thompson EB, Cheng X. PKA, not Epac, suppresses hedgehog activity and regulates glucocorticoid sensitivity in acute lymphoblastic leukemia cells. J Biol Chem. 2007 Sep 25; {PM}

    Prado GN, Suetomi K, Shumate D, Maxwell C, Ravindran A, Rajarathnam K, Navarro J. Chemokine signaling specificity: essential role for the N-terminal domain of chemokine receptors, by. Biochemistry. 2007 Oct 16;46(41):11660. Sep 25. No abstract available.

    Zhao Y, Sun L, Muralidhara BK, Kumar S, White MA, Stout CD, Halpert JR. Structural and thermodynamic consequences of 1-(4-chlorophenyl)imidazole binding to cytochrome P450 2B4. Biochemistry. 2007 Oct 16;46(41):11559-67. Sep 22. {PM}

    Auton M, Holthauzen LM, Bolen DW. Anatomy of energetic changes accompanying urea-induced protein denaturation. Proc Natl Acad Sci U S A. 2007 Sep 25;104(39):15317-22. Sep 18. {PM}

    Auton M, Bolen DW. Application of the transfer model to understand how naturally ccurring Osmolytes affect protein stability. Methods Enzymol. 2007;428:397-418.

    Negi SS, Braun W. Statistical analysis of physical-chemical properties and prediction of protein-protein interfaces. J Mol Model. 2007 Nov;13(11):1157-67. Sep 9.{PM}

    Okorokov AL, Waugh A, Hodgkinson J, Murthy A, Hong HK, Leo E, Sherman MB, Stoeber K, Orlova EV, Williams GH. Hexameric ring structure of human MCM10 DNA replication factor. EMBO Rep. 2007 Oct;8(10):925-30. Sep 7. {PM}

    Brock M, Fan F, Mei FC, Li S, Gessner C, Woods VL Jr, Cheng X. Conformational analysis of Epac activation using amide hydrogen/deuterium exchange mass spectrometry. J Biol Chem. 2007 Nov 2;282(44):32256-63. Sep 4. {PM}

    Jezewska MJ, Bujalowski PJ, Bujalowski W. Interactions of the DNA polymerase X of African swine fever virus with double-stranded DNA. Functional structure of the complex. J Mol Biol. 2007 Oct 12;373(1):75-95. Jun 27. {PM}

    Gumz ML, Zou H, Kreinest PA, Childs AC, Belmonte LS, LeGrand SN, Wu KJ, Luxon,BA, Sinha M, Parker AS, Sun LZ, Ahlquist DA, Wood CG, Copland JA. Secreted frizzled-related protein 1 loss contributes to tumor phenotype of clear cell renal cell carcinoma. Clin Cancer Res. 2007 Aug 15;13(16):4740-9. {PM}

    Gulotta M, Qiu L, Desamero R, Rösgen J, Bolen DW, Callender R. Effects of cell volume regulating osmolytes on glycerol 3-phosphate binding to triosephosphate isomerase. Biochemistry. 2007 Sep 4;46(35):10055-62. Aug 15. {PM}

    Kokubo H, Rösgen J, Bolen DW, Pettitt BM. Molecular basis of the apparent near ideality of urea solutions. Biophys J. 2007 Nov 15;93(10):3392-407. Aug 10. {PM}

    Iwahara J. [Intermediates in macromolecular binding process as revealed by new NMR methods] Tanpakushitsu Kakusan Koso. 2007 Aug;52(9):952-8. Review. Japanese. No abstract available.

    Kumar R, Serrette JM, Khan SH, Miller AL, Thompson EB. Effects of different osmolytes on the induced folding of the N-terminal activation domain (AF1) of the glucocorticoid receptor. Arch Biochem Biophys. 2007 Sep 15;465(2):452-60. Jun 29. {PM}

    Kobayashi N, Iwahara J, Koshiba S, Tomizawa T, Tochio N, Güntert P, Kigawa T, Yokoyama S. KUJIRA, a package of integrated modules for systematic and interactive analysis of NMR data directed to high-throughput NMR structure studies. J Biomol NMR. 2007 Sep;39(1):31-52. Jul 18. {PM}

    Prado GN, Suetomi K, Shumate D, Maxwell C, Ravindran A, Rajarathnam K, Navarro J. Chemokine signaling specificity: essential role for the N-terminal domain of chemokine receptors. Biochemistry. 2007 Aug 7;46(31):8961-8. Jul 13. Erratum in: Biochemistry. 2007 Oct 16;46(41):11660. {PM}

    Webb MS, Miller AL, Thompson EB. In CEM cells the autosomal deafness gene dfna5 is regulated by glucocorticoids and forskolin.J Steroid Biochem Mol Biol. 2007 Oct;107(1-2):15-21. May 24. {PM}

    Young TW, Rosen DG, Mei FC, Li N, Liu J, Wang XF, Cheng X. Up-regulation of tumor susceptibility gene 101 conveys poor prognosis through suppression of p21 expression in ovarian cancer. Clin Cancer Res. 2007 Jul 1;13(13):3848-54. {PM}

    Miller AL, Webb MS, Thompson EB. Comparison of two structurally diverse glucocorticoid receptor agonists: cortivazol selectively regulates a distinct set of genes separate from dexamethasone in CEM cells. Steroids. 2007 Sep;72(9-10):673-81. May 29. {PM}

    Volk DE, Thiviyanathan V, Somasunderam A, Gorenstein DG. Ab initio base-pairing energies of an oxidized thymine product, 5-formyluracil, with standard DNA bases at the BSSE-free DFT and MP2 theory levels. Org Biomol Chem. 2007 May 21;5(10):1554-8. Apr 17. {PM}

    Cheng X, Young TW, Mei FC. Proteomics analyses of ovarian cancer using genetically defined human ovarian cancer models. Front Biosci. 2007 Sep 1;12:5166-74. {PM}

    Bush CR, Havens JM, Necela BM, Su W, Chen L, Yanagisawa M, Anastasiadis PZ, Guerra R, Luxon BA, Thompson EA. Functional genomic analysis reveals cross-talk between peroxisome proliferator-activated receptor gamma and calcium signaling in human colorectal cancer cells. J Biol Chem. 2007 Aug 10;282(32):23387-401. Jun 12. {PM}

    Braun W, Fung JJ. Can partial auxiliary liver transplantation protect kidney grafts in highly sensitized patients? Nat Clin Pract Nephrol. 2007 Jul;3(7):370-1. May 29. No abstract available.

    Rajagopalan L, Chin CC, Rajarathnam K. Role of intramolecular disulfides in stability and structure of a noncovalent homodimer. Biophys J. 2007 Sep 15;93(6):2129-34. May 18. {PM}

    Hilser VJ, Thompson EB. Intrinsic disorder as a mechanism to optimize allosteric coupling in proteins. Proc Natl Acad Sci U S A. 2007 May 15;104(20):8311-5. May 9. {PM}

    Kang J, Lee MS, Watowich SJ, Gorenstein DG. Combinatorial selection of a RNA thioaptamer that binds to Venezuelan equine encephalitis virus capsid protein. FEBS Lett. 2007 May 29;581(13):2497-502. May 4. {PM}

    Basquiera AL, Fassetta F, Soria N, Barral JM, Ricchi B, García JJ. Accuracy of leukocyte alkaline phosphatase score to predict JAK2 V617F mutation. Haematologica. 2007 May;92(5):704-5. {PM}

    Marcinowicz A, Jezewska MJ, 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. 2007 Jun 27; {PM}:

    Maillard RA, Jordan M, Beasley DW, Barrett AD, Lee JC. Long-range communication in the envelope protein domain III and its effect on the resistance of west nile virus to antibody-mediated neutralization. J Biol Chem. 2007 Nov 6; {PM}

    Kang J, Lee MS, Gorenstein DG. Magnesium ion is an effective inhibitor of the binding of Escherichia coli to heparin. J Microbiol Methods. 2007 Oct 12; {PM}

    Landsverk ML, Li S, Hutagalung AH, Najafov A, Hoppe T, Barral JM, Epstein HF. The UNC-45 chaperone mediates sarcomere assembly through myosin degradation in Caenorhabditis elegans. J Cell Biol. 2007 Apr 23;177(2):205-10. Apr 16. {PM}

    Miller AL, Garza AS, Johnson BH, Thompson EB. Pathway interactions between MAPKs, mTOR, PKA, and the glucocorticoid receptor in lymphoid cells. Cancer Cell Int. 2007 Mar 28;7:3. {PM}

    Liu T, Whitten ST, Hilser VJ. Functional residues serve a dominant role in mediating the cooperativity of the protein ensemble. Proc Natl Acad Sci U S A. 2007 Mar 13;104(11):4347-52. Mar 5. {PM}

    Bao X, Lee SC, Reuss L, Altenberg GA. Change in permeant size selectivity by phosphorylation of connexin 43 gap-junctional hemichannels by PKC. Proc Natl Acad Sci U S A. 2007 Mar 20;104(12):4919-24. Mar 8. {PM}

    Ji Z, Mei FC, Xie J, Cheng X. Oncogenic kras supresses GLI1 degradation and activates hedgehog signaling pathway in pancreatic cancer cells. J Biol Chem. 2007 Mar 12. {PM}

    Lagow RD, Bao H, Cohen EN, Daniels RW, Zuzek A, Williams WH, Macleod GT, Sutton RB, Zhang B. Modification of a Hydrophobic Layer by a Point Mutation in Syntaxin 1A Regulates the Rate of Synaptic Vesicle Fusion. PLoS Biol. 2007 Mar 6;5(4):e72 {PM}

    Kang, J, Lee MS, Gorenstein DG. Characterization of heparin-living bacteria interactions by chemiluminescence electrophoretic mobility shift assay. Anal Biochem. 2007 Apr 15;363(2):312-4. Feb 2. {PM}

    Zhang S. Pivotal Steps Towards Quantification of Molecular Diffusion Coefficients by NMR. Chemphyschem. 2007 Apr 2;8(5):635-642. {PM}

    Rosgen J, Pettitt BM, Bolen DW. An analysis of the molecular origin of osmolyte-dependent protein stability. Protein Sci. 2007 Apr;16(4):733-43. Feb 27. {PM}

    Fennewald SM, Scott EP, Zhang L, Yang X, Aronson JF, Gorenstein DG, Luxon BA, Shope RE, Beasley DW, Barrett AD, Herzog NK. Thioaptamer decoy targeting of AP-1 proteins influences cytokine expression and the outcome of arenavirus infections. J Gen Virol. 2007 Mar;88(Pt 3):981-90. {PM}

    Lakshmipathy SK, Tomic S, Kaiser CM, Chang HC, Genevaux P, Georgopoulos C, Barral JM, Johnson AE, Hartl FU, Etchells SA. Identification of nascent chain interaction sites on trigger factor. J Biol Chem. 2007 Feb 12. {PM}

    Schein CH, Ivanciuc O, Braun W. Bioinformatics Approaches to Classifying Allergens and Predicting Cross-Reactivity. Immunol Allergy Clin North Am. 2007 Feb;27(1):1-27. {PM}

    Thiviyanathan V, Somasunderam AD, Gorenstein DG. Combinatorial selection and delivery of thioaptamers. Biochem Soc Trans. 2007 Feb;35(Pt 1):50-2. {PM}

    Holthauzen LM, Bolen DW. Mixed osmolytes: the degree to which one osmolyte affects the protein stabilizing ability of another. Protein Sci. 2007 Feb;16(2):293-8. Epub 2006 Dec 22. {PM}

    Fernando H, Nagle GT, Rajarathnam K. Thermodynamic characterization of interleukin-8 monomer binding to CXCR1 receptor N-terminal domain. FEBS J. 2007 Jan;274(1):241-51. {PM}

    Nasser MW, Raghuwanshi SK, Malloy KM, Gangavarapu P, Shim JY, Rajarathnam K, Richardson RM. CXCR1 and CXCR2 activation and regulation. Role of aspartate 199 of the second extracellular loop of CXCR2 in CXCL8-mediated rapid receptor internalization. J Biol Chem. 2007 Mar 2;282(9):6906-15. Jan 4.{PM}

    Bowick GC, Fennewald SM, Scott EP, Zhang L, Elsom BL, Aronson JF, Spratt HM, Luxon BA, Gorenstein DG, Herzog NK. Identification of differentially activated cell-signaling networks associated with pichinde virus pathogenesis by using systems kinomics. J Virol. 2007 Feb;81(4):1923-33. Dec 6.

    Young TW, Mei FC, Rosen DG, Yang G, Li N, Liu J, Cheng X. Up-regulation of tumor susceptibility gene 101 protein in ovarian carcinomas revealed by proteomics analyses. Mol Cell Proteomics. 2007 Feb;6(2):294-304. {PM}

    Li J, O'Connor KL, Cheng X, Mei FC, Uchida T, Townsend CM Jr, Evers BM. Cyclic adenosine 5'-monophosphate-stimulated neurotensin secretion is mediated through Rap1 downstream of both Epac and protein kinase A signaling pathways. Mol Endocrinol. 2007 Jan;21(1):159-71. {PM}

    Ferreon AC, Ferreon JC, Bolen DW, Rosgen J. Protein phase diagrams II: nonideal behavior of biochemical reactions in the presence of osmolytes. Biophys J. 2007 Jan 1;92(1):245-56. {PM}