2006

Holmstrom E, Olovsson W, Abrikosov IA, Niklasson AM, Johansson B, Gorgoi M, Karis O, Svensson S, Schafers F, Braun W, Ohrwall G, Andersson G, Marcellini M, Eberhardt W. Sample preserving deep interface characterization technique. Phys Rev Lett. 2006 Dec 31;97(26):266106. Epub 2006 Dec 29. {PM}
Yu S, Fan F, Flores SC, Mei F, Cheng X. Dissecting the Mechanism of Epac Activation via Hydrogen-Deuterium Exchange FT-IR and Structural Modeling.Biochemistry. 2006 Dec 26;45(51):15318-26. Epub 2006 Dec 5. {PM}
Miller RK, Qadota H, Landsverk ML, Mercer KB, Epstein HF, Benian GM. UNC-98 links an integrin-associated complex to thick filaments in Caenorhabditis elegans muscle. J Cell Biol.2006 Dec 18;175(6):853-9. Epub 2006 Dec 11. {PM}

Aditya Hindupur, Deqian Liu, Yonghong Zhao, Henry D. Bellamy, Mark A. White, and Robert O. Fox, The crystal structure of the E. coli stress protein YciF. Protein Science 2006: Sept 25. {PM}

Yang X, Wang H, Beasley DW, Volk DE, Zhao X, Luxon BA, Lomas LO, Herzog NK, Aronson JF, Barrett AD, Leary JF, Gorenstein DG. Selection of thioaptamers for diagnostics and therapeutics. Ann N Y Acad Sci. 2006 Oct;1082:116-9. {PM}
Volk DE, Lee YC, Li X, Barrett AD, Gorenstein DG. NMR assignment of the Dengue 4 virus envelope protein domain III. J Biomol NMR. 2006 Dec;36 Suppl 5:62. {PM}
Kaiser CM, Chang HC, Agashe VR, Lakshmipathy SK, Etchells SA, Hayer-Hartl M, Hartl FU, Barral JM. Real-time observation of trigger factor function on translating ribosomes. Nature. 2006 Nov 23;444(7118):455-60. {PM}
He J, Sheng T, Stelter AA, Li C, Zhang X, Sinha M, Luxon BA, Xie J. Suppressing Wnt signaling by the hedgehog pathway through sFRP-1. J Biol Chem. 2006 Nov 24;281(47):35598-602. {PM}
Rajagopalan L, Rajarathnam K. Structural basis of chemokine receptor function--a model for binding affinity and ligand selectivity. Biosci Rep. 2006 Oct;26(5):325-39. Review. {PM}
Bowick GC, Fennewald SM, Elsom BL, Aronson JF, Luxon BA, Gorenstein DG, Herzog NK. Differential signaling networks induced by mild and lethal hemorrhagic fever virus infections. J Virol. 2006 Oct;80(20):10248-52. {PM}
Hindupur A, Liu D, Zhao Y, Bellamy HD, White MA, Fox RO. The crystal structure of the E. coli stress protein YciF. Protein Sci. 2006 Nov;15(11):2605-11. {PM}
Street TO, Bolen DW, Rose GD. A molecular mechanism for osmolyte-induced protein stability. Proc Natl Acad Sci U S A. 2006 Sep 19;103(38):13997-4002. Erratum in: Proc Natl Acad Sci U S A. 2006 Nov 7;103(45):17064. {PM}
Miller E, Garcia T, Hultgren S, Oberhauser AF. The mechanical properties of E. coli type 1 pili measured by atomic force microscopy techniques. Biophys J. 2006 Nov 15;91(10):3848-56. {PM}
Montes M, Fuson KL, Sutton RB, Robert JJ. Purification, crystallization and X-ray diffraction analysis of human synaptotagmin 1 C2A-C2B. Acta Crystallograph Sect F Struct Biol Cryst Commun. 2006 Sep 1;62(Pt 9):926-9. {PM}
Deng Y, Chen Y, Reuss L, Altenberg GA. Mutations of connexin 26 at position 75 and dominant deafness: essential role of arginine for the generation of functional gap-junctional channels. Hear Res. 2006 Oct;220(1-2):87-94. {PM}
Wang H, Yang X, Bowick GC, Herzog NK, Luxon BA, Lomas LO, Gorenstein DG. Identification of proteins bound to a thioaptamer probe on a proteomics array. Biochem Biophys Res Commun. 2006 Sep 1;347(3):586-93. {PM}
Ilies MA, Seitz WA, Johnson BH, Ezell EL, Miller AL, Thompson EB, Balaban AT. Lipophilic pyrylium salts in the synthesis of efficient pyridinium-based cationic lipids, gemini surfactants, and lipophilic oligomers for gene delivery. J Med Chem. 2006 Jun 29;49(13):3872-87. {PM}
Rajarathnam K, Prado GN, Fernando H, Clark-Lewis I, Navarro J. Probing receptor binding activity of interleukin-8 dimer using a disulfide trap. Biochemistry. 2006 Jun 27;45(25):7882-8. {PM}
Brobey RK, Mei FC, Cheng X, Soong L. Comparative two-dimensional gel electrophoresis maps for promastigotes of Leishmania amazonensis and Leishmania major. Braz J Infect Dis. 2006 Feb;10(1):1-6. {PM}
Geng T, Seitz PK, Thomas ML, Xu B, Soman KV, Kurosky A, Luxon BA, Cunningham KA. Use of surface enhanced laser desorption/ionization-time of flight mass spectrometry (SELDI-TOF MS) to study protein expression in a rat model of cocaine withdrawal. J Neurosci Methods. 2006 Nov 15;158(1):1-12. {PM}
Rajarathnam K. Reply to 'A novel peptide CXCR ligand derived from extracellular matrix degradation during airway inflammation'. Nat Med. 2006 Jun;12(6):603-4
Russo AT, Watowich SJ. Purification, crystallization and X-ray diffraction analysis of the C-terminal protease domain of Venezuelan equine encephalitis virus nsP2. Acta Crystallograph Sect F Struct Biol Cryst Commun.2006 Jun 1;62(Pt6):514-7. {PM}
Lucius AL, Jezewska MJ, Roychowdhury A, Bujalowski W. Kinetic mechanisms of the nucleotide cofactor binding to the strong and weak nucleotide-binding site of the Escherichia coli PriA helicase. 2. Biochemistry. 2006 Jun 13;45(23):7217-36. {PM}
Lucius AL, Jezewska MJ, Bujalowski W. The Escherichia coli PriA helicase has two nucleotide-binding sites differing dramatically in their affinities for nucleotide cofactors. 1. Intrinsic affinities, cooperativities, and base specificity of nucleotide cofactor binding. Biochemistry. 2006 Jun 13;45(23):7202-16. {PM}
Lucius AL, Jezewska MJ, Bujalowski W. Allosteric interactions between the nucleotide-binding sites and the ssDNA-binding site in the PriA helicase-ssDNA complex. 3. Biochemistry. 2006 Jun 13;45(23):7237-55. {PM}
Volk DE, Chavez L, Beasley DW, Barrett AD, Holbrook MR, Gorenstein DG. Structure of the envelope protein domain III of Omsk hemorrhagic fever virus. Virology. 2006 Jul 20;351(1):188-95. {PM}
Singh R, White MA, Ramana KV, Petrash JM, Watowich SJ, Bhatnagar A, Srivastava SK. Structure of a glutathione conjugate bound to the active site of aldose reductase. Proteins. 2006 Jul 1;64(1):101-10. {PM}
Volk DE, Thiviyanathan V, Somasunderam A, Gorenstein DG. Ab initio base-pairing energies of uracil and 5-hydroxyuracil with standard DNA bases at the BSSE-free DFT and MP2 theory levels. Org Biomol Chem. 2006 May 7;4(9):1741-5. {PM}
Hilser VJ, Garcia-Moreno E B, Oas TG, Kapp G, Whitten ST. A statistical thermodynamic model of the protein ensemble. Chem Rev. 2006 May;106(5):1545-58.

{PM}
Andrew T. Russo, Mark A. White, and Stanley J. Watowich, The Crystal Structure of the Venezuelan Equine Encephalitis Alphavirus nsP2 Protease. Structure 2006 14: 1449-1458. {PM}
Ferguson MR, Rojo DR, Somasunderam A, Thiviyanathan V, Ridley BD, Yang X, Gorenstein DG. Delivery of double-stranded DNA thioaptamers into HIV-1 infected cells for antiviral activity. Biochem Biophys Res Commun. 2006 Jun 9;344(3):792-7.
Negi SS, Kolokoltsov AA, Schein CH, Davey RA, Braun W. Determining functionally important amino acid residues of the E1 protein of Venezuelan equine encephalitis virus. J Mol Model. 2006 Sep;12(6):921-9. {PM}
Zhang, S Quantitative measurement of molecular diffusion coefficients by NMR spectroscopy. J Am Chem Soc. 2006 Apr 19;128(15):4974-5. No abstract available.
Portuondo-Campa E, Schenkl S, Dolder M, Chergui M, Landau EM, Haacke S. Absorption spectroscopy of three-dimensional bacteriorhodopsin crystals at cryogenic temperatures: effects of altered hydration. Acta Crystallogr D Biol Crystallogr. 2006 Apr;62(Pt 4):368-74. Epub 2006 Mar 18. PMID: 16552137 {PM}
Schein CH, Oezguen N, Volk DE, Garimella R, Paul A, Braun W. Related Articles,Links NMR structure of the viral peptide linked to the genome (VPg) of poliovirus. Peptides. 2006 Jul;27(7):1676-84. Epub 2006 Mar 15. PMID: 16540201 {PM}
Bullard B, Garcia T, Benes V, Leake MC, Linke WA, Oberhauser AF. The molecular elasticity of the insect flight muscle proteins projectin and kettin.Proc Natl Acad Sci U S A. 2006 Mar 21;103(12):4451-6. {PM}
Luxon BA. Autoimmune hepatitis: diagnosis, treatment, and prognosis. Curr Gastroenterol Rep. 2006 Feb;8(1):83-8. Review. {PM}
Copik AJ, Webb MS, Miller AL, Wang Y, Kumar R, Thompson EB. Activation function 1 of glucocorticoid receptor binds TATA-binding protein in vitro and in vivo. Mol Endocrinol. 2006 Jun;20(6):1218-30. {PM}
Poggio ED, Hila S, Stephany B, Fatica R, Krishnamurthi V, del Bosque C, Goldfarb D, Herts B, Dennis VW, Heeger PS, Braun W. Donor kidney volume and outcomes following live donor kidney transplantation. Am J Transplant. 2006 Mar;6(3):616-24. {PM}
Bujalowski W. Thermodynamic and kinetic methods of analyses of protein-nucleic acid interactions. From simpler to more complex systems. Chem Rev. 2006 Feb;106(2):556-606. Review. No abstract available.

Wu P, Bolen DW. Osmolyte-induced protein folding free energy changes. Proteins. 2006 May 1;63(2):290-6. {PM}

 

Muralidhara BK, Negi S, Chin CC, Braun W, Halpert JR. Conformational flexibility of mammalian cytochrome P450 2B4 in binding imidazole inhibitors with different ring chemistry and side chains. Solution thermodynamics and molecular modeling. J Biol Chem. 2006 Mar 24;281(12):8051-61. {PM}
Fitch CA, Whitten ST, Hilser VJ, Garcia-Moreno E B. Molecular mechanisms of pH-driven conformational transitions of proteins: insights from continuum electrostatics calculations of acid unfolding. Proteins. 2006 Apr 1;63(1):113-26. {PM}
Mei FC, Young TW, Liu J, Cheng X. RAS-mediated epigenetic inactivation of OPCML in oncogenic transformation of human ovarian surface epithelial cells. FASEB J. 2006 Mar;20(3):497-9. {PM}
Zhao Y, White MA, Muralidhara BK, Sun L, Halpert JR, Stout CD. Structure of microsomal cytochrome P450 2B4 complexed with the antifungal drug bifonazole: insight into P450 conformational plasticity and membrane interaction. J Biol Chem. 2006 Mar 3;281(9):5973-81. {PM}
Kang J, Lee MS, Gorenstein DG. Chemiluminescence-based electrophoretic mobility shift assay of heparin-protein interactions. Anal Biochem. 2006 Feb 1;349(1):156-8. No abstract available.
Jezewska MJ, Marcinowicz A, Lucius AL, Bujalowski W. DNA polymerase X from African swine fever virus: quantitative analysis of the enzyme-ssDNA interactions and the functional structure of the complex.J Mol Biol. 2006 Feb 10;356(1):121-41. {PM}
Liu T, Whitten ST, Hilser VJ. Ensemble-based signatures of energy propagation in proteins: a new view of an old phenomenon. Proteins. 2006 Mar 15;62(3):728-38. {PM}
Lipniacki T, Paszek P, Brasier AR, Luxon BA, Kimmel M. Stochastic regulation in early immune response. Biophys J. 2006 Feb 1;90(3):725-42. {PM}
Kang J, Lee MS, Watowich SJ, Gorenstein DG. Chemiluminescence-based electrophoretic mobility shift assay of RNA-protein interactions: application to binding of viral capsid proteins to RNA.J Virol Methods. 2006 Feb;131(2):155-9. {PM}
Midoro-Horiuti T, Schein CH, Mathura V, Braun W, Czerwinski EW, Togawa A, Kondo Y, Oka T, Watanabe M, Goldblum RM. Structural basis for epitope sharing between group 1 allergens of cedar pollen. Mol Immunol. 2006 Feb;43(6):509-18. {PM}
Fitch CA, Whitten ST, Hilser VJ, Garcia-Moreno E B. Molecular mechanisms of pH-driven conformational transitions of proteins: insights from continuum electrostatics calculations of acid unfolding. Proteins. 2006 Apr 1;63(1):113-26. {PM}

Liu T, Whitten ST, Hilser VJ. Ensemble-based signatures of energy propagation in proteins: a new view of an old phenomenon. Proteins. 2006 Mar 15;62(3):728-38.

Wu P, Bolen DW. Osmolyte-induced protein folding free energy changes. Proteins. 2006 May 1;63(2):290-6.


Auton M, Ferreon AC, Bolen DW. Metrics that differentiate the origins of osmolyte effects on protein stability: a test of the surface tension proposal. J Mol Biol. 2006 Sep 1;361(5):983-92. Epub 2006 Aug 4.
Montes M, Fuson KL, Sutton RB, Robert JJ. Purification, crystallization and X-ray diffraction analysis of human synaptotagmin 1 C2A-C2B. Acta Cryst. F 62, Page 926-9, Aug 2006. {PM}

Singh R, White MA, Ramana KV, Petrash JM, Watowich SJ, Bhatnagar A, Srivastava SK., Structure of a glutathione conjugate bound to the active site of aldose reductase. Proteins: Structure, Function, and Bioinformatics 2006, July 1, 64(1), 101-110 {PM}

Mukherjee M, Dutta K, White MA, Cowburn D, Fox RO., NMR solution structure and backbone dynamics of domain III of the E protein of tick-borne Langat flavivirus suggests a potential site for molecular recognition. Protein Science 2006, June 15(6), 1342-55. {PM}
Russo AT, Watowich SJ, Purification, crystallization and X-ray diffraction analysis of the C-terminal protease domain of Venezuelan equine encephalitis virus nsP2. Acta Cryst. F 62(6), Page 514-7, June 2006. {PM}
Whitten ST, Kurtz AJ, Pometun MS, Wand AJ, Hilser VJ. Revealing the nature of the native state ensemble through cold denaturation. Biochemistry. 2006 Aug 29;45(34):10163-74. {PM}
Midoro-Horiuti T, Schein CH, Mathura V, Braun W, Czerwinski EW, Togawa A, Kondo Y, Oka T, Watanabe M, Goldblum RM. Structural basis for epitope sharing between group 1 allergens of cedar pollen. Mol Immunol. 2006 Feb;43(6):509-18. {PM}
Zhao Y, White MA, Muralidhara BK, Sun L, Halpert JR, Stout CD., Structure of microsomal cytochrome P450 2B4 complexed with the antifungal drug bifonazole: Insight into P450 conformational plasticity and membrane interaction. J Biol Chem. 2006, March 3, 281(9), 5973-81; {PM}