2006 Publications

Majka J. Niedziela-Majka A., & Burgers P.M. (2006). “The checkpoint clamp activates Mec1 kinase during initiation of the DNA damage checkpoint.” Mol Cell. 2006 Dec 28;24(6):891-901. (Abstract)

Anderson M.A., Ogbay B., Kisselev O.G., Cistola D.P., & Marshall G.R. (2006). “Alternate binding mode of C-terminal phenethylamine analogs of G(t)alpha(340-350) to photoactivated rhodopsin.” Chem Biol Drug Des. 2006 Dec;68(6):295-307. (Abstract)

Nikiforovich G.V., Zhang M., Yang Q., Jagadeesh G., Chen H.C., Hunyady L., Marshall G.R., & Catt K.J. (2006). “Interactions between conserved residues in transmembrane helices 2 and 7 during angiotensin AT1 receptor activation.” Chem Biol Drug Des. 2006 Nov;68(5):239-49. (Abstract)

Canton D.A., Olsten M.E., Niederstrasser H., Cooper J.A., & Litchfield D.W. (2006). “The role of CKIP-1 in cell morphology depends on its interaction with actin-capping protein.” J Biol Chem. 2006 Nov 24;281(47):36347-59. Epub 2006 Sep 20. (Abstract)

Sukumar N., Chen Z.W., Ferrari D., Merli A., Rossi G.L., Bellamy H.D., Chistoserdov A., Davidson V.L., & Mathews F.S. (2006). “Crystal structure of an electron transfer complex between aromatic amine dehydrogenase and azurin from Alcaligenes faecalis.” Biochemistry. 2006 Nov 14;45(45):13500-10. (Abstract)

Pascal J.M. & Ellenberger T. (2006). “RNA ligase does the AMP shuffle.” Nat Struct Mol Biol. 2006 Nov;13(11):950-1. (Abstract)

Crick S.L., Jayaraman M., Frieden C., Wetzel R., & Pappu R.V. (2006). “Fluorescence correlation spectroscopy shows that monomeric polyglutamine molecules form collapsed structures in aqueous solutions.” Proc Natl Acad Sci U S A. 2006 Nov 7;103(45):16764-9. Epub 2006 Oct 30. (Abstract)

Pineda A.O., Chen Z.W., Bah A., Garvey L.C., Mathews F.S., & Di Cera E (2006). “Crystal structure of thrombin in a self-inhibited conformation.” J Biol Chem. 2006 Oct 27;281(43):32922-8. Epub 2006 Sep 5. (Abstract)

Pascal J.M., Tsodikov O.V., Hura G.L., Song W., Cotner E.A., Classen S., Tomkinson A.E., Tainer J.A., & Ellenberger T. (2006). “A flexible interface between DNA ligase and PCNA supports conformational switching and efficient ligation of DNA.” Mol Cell. 2006 Oct 20;24(2):279-91. (Abstract)

Bhattacharya N., Ghosh S., Sept D., & Cooper J.A. (2006). “Binding of myotrophin/V-1 to actin-capping protein: implications for how capping protein binds to the filament barbed end.” J Biol Chem. 2006 Oct 13;281(41):31021-30. Epub 2006 Aug 7. (Abstract)

Wille J.J., Elson E.L., & Okamoto R.J. (2006). “Cellular and matrix mechanics of bioartificial tissues during continuous cyclic stretch.” Ann Biomed Eng. 2006 Nov;34(11):1678-90. Epub 2006 Oct 11. (Abstract)

Hu T., Krezel A.M., Li C., & Coffey R.J. (2006). “Structural studies of human Naked2: a biologically active intrinsically unstructured protein.” Biochem Biophys Res Commun. 2006 Dec 1;350(4):911-5. Epub 2006 Oct 2. (Abstract)

Hynson R.M., Mathews F.S., & Schuman Jorns M. (2006). “Identification of a stable flavin-thiolate adduct in heterotetrameric sarcosine oxidase.” J Mol Biol. 2006 Sep 29;362(4):656-63. Epub 2006 Jul 29. (Abstract)

Moon J.Y., Henzler-Wildman K.A., & Ramamoorthy A. (2006). “Expression and purification of a recombinant LL-37 from Escherichia coli.” Biochim Biophys Acta. 2006 Sep;1758(9):1351-8. Epub 2006 Feb 28. (Abstract)

Majka J., Binz S.K., Wold M.S., & Burgers P.M. (2006). “Replication protein A directs loading of the DNA damage checkpoint clamp to 5′-DNA junctions.” J Biol Chem. 2006 Sep 22;281(38):27855-61. Epub 2006 Jul 24. (Abstract)

Downs M.A., Arimoto R., Marshall G.R., & Kisselev O.G. (2006). “G-protein alpha and beta-gamma subunits interact with conformationally distinct signaling states of rhodopsin.” Vision Res. 2006 Dec;46(27):4442-8. Epub 2006 Sep 20. (Abstract)

Northam M.R., Garg P., Baitin D.M., Burgers P.M., & Shcherbakova P.V. (2006). “A novel function of DNA polymerase zeta regulated by PCNA.” EMBO J. 2006 Sep 20;25(18):4316-25. Epub 2006 Sep 7. (Abstract)

Zhong X., Garg P., Stith C.M., McElhinny S.A., Kissling G.E., Burgers P.M., & Kunkel T.A. (2006). “The fidelity of DNA synthesis by yeast DNA polymerase zeta alone and with accessory proteins.” Nucleic Acids Res. 2006;34(17):4731-42. Epub 2006 Sep 13. (Abstract)

Isenberg J.S., Ridnour L.A., Dimitry J., Frazier W.A., Wink D.A., & Roberts D.D. (2006). “CD47 is necessary for inhibition of nitric oxide-stimulated vascular cell responses by thrombospondin-1.” J Biol Chem. 2006 Sep 8;281(36):26069-80. Epub 2006 Jul 11. (Abstract)

Marquez J.P., Genin G.M., Pryse K.M., & Elson E.L. (2006). “Cellular and matrix contributions to tissue construct stiffness increase with cellular concentration.” Ann Biomed Eng. 2006 Sep;34(9):1475-82. Epub 2006 Jul 28. (Abstract)

Fortune J.M., Stith C.M., Kissling G.E., Burgers P.M., & Kunkel T.A. (2006). “RPA and PCNA suppress formation of large deletion errors by yeast DNA polymerase delta.” Nucleic Acids Res. 2006;34(16):4335-41. Epub 2006 Aug 26. (Abstract)

Macdonald J., Li Z., Su W., & Pike L.J. (2006). “The membrane proximal disulfides of the EGF receptor extracellular domain are required for high affinity binding and signal transduction but do not play a role in the localization of the receptor to lipid rafts.” Biochim Biophys Acta. 2006 Aug;1763(8):870-8. Epub 2006 May 13. (Abstract)

Chen Z.W., Hassan-Abdulah A., Zhao G., Jorns M.S., & Mathews F.S. (2006). “Heterotetrameric sarcosine oxidase: structure of a diflavin metalloenzyme at 1.85 A resolution.” J Mol Biol. 2006 Jul 28;360(5):1000-18. Epub 2006 Jun 15. (Abstract)

King D.A., Hall B.E., Iwamoto M.A., Win K.Z., Chang J.F., & Ellenberger T. (2006). “Domain structure and protein interactions of the silent information regulator Sir3 revealed by screening a nested deletion library of protein fragments.” J Biol Chem. 2006 Jul 21;281(29):20107-19. Epub 2006 May 22. (Abstract)

Tehrani S., Faccio R., Chandrasekar I., Ross F.P., & Cooper J.A. (2006). “Cortactin has an essential and specific role in osteoclast actin assembly.” Mol Biol Cell. 2006 Jul;17(7):2882-95. Epub 2006 Apr 12. (Abstract)

Bruck S., Huber T.B., Ingham R.J., Kim K., Niederstrasser H., Allen P.M., Pawson T., Cooper J.A., & Shaw A.S. (2006). “Identification of a novel inhibitory actin-capping protein binding motif in CD2-associated protein.” J Biol Chem. 2006 Jul 14;281(28):19196-203. Epub 2006 May 16. (Abstract)

Ma J.K., Carrell C.J., Mathews F.S., & Davidson V.L. (2006). “Site-directed mutagenesis of proline 52 to glycine in amicyanin converts a true electron transfer reaction into one that is conformationally gated.” Biochemistry. 2006 Jul 11;45(27):8284-93. (Abstract)

Nikiforovich G.V. & Marshall G.R. (2006). “3D modeling of the activated states of constitutively active mutants of rhodopsin.” Biochem Biophys Res Commun. 2006 Jun 23;345(1):430-7. Epub 2006 Apr 25. (Abstract)

Chen X., Pascal J., Vijayakumar S., Wilson G.M., Ellenberger T., & Tomkinson A.E. (2006). “Human DNA ligases I, III, and IV-purification and new specific assays for these enzymes.” Methods Enzymol. 2006;409:39-52. (Abstract)

Bylund G.O., Majka J., & Burgers P.M. (2006). “Overproduction and purification of RFC-related clamp loaders and PCNA-related clamps from Saccharomyces cerevisiae.” Methods Enzymol. 2006;409:1-11. (Abstract)

Asnes C.F., Marquez J.P., Elson E.L., & Wakatsuki T. (2006). “Reconstitution of the Frank-Starling mechanism in engineered heart tissues.” Biophys J. 2006 Sep 1;91(5):1800-10. Epub 2006 Jun 16. (Abstract)

Anderson M.A., Ogbay B., Arimoto R., Sha W., Kisselev O.G., Cistola D.P., & Marshall G.R. (2006). “Relative strength of cation-pi vs salt-bridge interactions: the Gtalpha(340-350) peptide/rhodopsin system.” J Am Chem Soc. 2006 Jun 14;128(23):7531-41. (Abstract)

Carrell C.J., Bush L.A., Mathews F.S., & Di Cera, E. (2006). “High resolution crystal structures of free thrombin in the presence of K(+) reveal the molecular basis of monovalent cation selectivity and an inactive slow form.” Biophys Chem. 2006 Jun 1;121(3):177-84. Epub 2006 Feb 17. (Abstract)

Våbenø J., Nikiforovich G.V., & Marshall G.R. (2006). “Insight into the binding mode for cyclopentapeptide antagonists of the CXCR4 receptor.” Chem Biol Drug Des. 2006 May;67(5):346-54. (Abstract)

Li H. & Frieden C. (2006). “Fluorine-19 NMR studies on the acid state of the intestinal fatty acid binding protein.” Biochemistry. 2006 May 23;45(20):6272-8. (Abstract)

Ye Y., Liu M., Kao J.L., & Marshall G.R. (2006). “Novel trihydroxamate-containing peptides: design, synthesis, and metal coordination.” Biopolymers. 2006;84(5):472-89. (Abstract)

Hagnerud S., Manna P.P., Cella M., Stenberg A., Frazier W.A., Colonna M., & Oldenborg P.A. (2006). “Deficit of CD47 results in a defect of marginal zone dendritic cells, blunted immune response to particulate antigen and impairment of skin dendritic cell migration.” J Immunol. 2006 May 15;176(10):5772-8. (Abstract)

Chattopadhyay K. & Frieden C. (2006). “Steady-state and time-resolved fluorescence studies of the intestinal fatty acid binding protein.” Proteins. 2006 May 1;63(2):327-35. (Abstract)

Ackers G.K. & Holt J.M. (2006). “Asymmetric cooperativity in a symmetric tetramer: human hemoglobin.” J Biol Chem. 2006 Apr 28;281(17):11441-3. Epub 2006 Jan 19. (Abstract)

Pike L.J. (2006). “Rafts defined: a report on the Keystone Symposium on Lipid Rafts and Cell Function.” J Lipid Res. 2006 Jul;47(7):1597-8. Epub 2006 Apr 27. (Abstract)

Remond M.C., Fee J.A., Elson E.L., & Taber L.A. (2006). “Myosin-based contraction is not necessary for cardiac c-looping in the chick embryo.” Anat Embryol (Berl). 2006 Oct;211(5):443-54. Epub 2006 Apr 25. (Abstract)

Saffarian S., Qian H., Collier I., Elson E., & Goldberg G. (2006). “Powering a burnt bridges Brownian ratchet: a model for an extracellular motor driven by proteolysis of collagen.” Phys Rev E Stat Nonlin Soft Matter Phys. 2006 Apr;73(4 Pt 1):041909. Epub 2006 Apr 10. (Abstract)

Che Y. & Marshall G.R. (2006). “Impact of cis-proline analogs on peptide conformation.” Biopolymers. 2006 Apr 5;81(5):392-406. (Abstract)

Våbenø J., Nikiforovich G.V., & Marshall G.R. (2006). “A minimalistic 3D pharmacophore model for cyclopentapeptide CXCR4 antagonists.” Biopolymers. 2006;84(5):459-71. (Abstract)

Kim K., Galletta B.J., Schmidt K.O., Chang F.S., Blumer K.J., & Cooper J.A. (2006). “Actin-based motility during endocytosis in budding yeast.” Mol Biol Cell. 2006 Mar;17(3):1354-63. Epub 2006 Jan 4. (Abstract)

Che Y., Brooks B.R., & Marshall G.R. (2006). “Development of small molecules designed to modulate protein-protein interactions.” J Comput Aided Mol Des. 2006 Feb;20(2):109-30. Epub 2006 Apr 19. (Abstract)

Zhuang Z., Yoder B.L., Burgers P.M., & Benkovic S.J. (2006). “The structure of a ring-opened proliferating cell nuclear antigen-replication factor C complex revealed by fluorescence energy transfer.” Proc Natl Acad Sci U S A. 2006 Feb 21;103(8):2546-51. Epub 2006 Feb 13. (Abstract)

Radman-Livaja M., Biswas T., Ellenberger T., Landy A., & Aihara, H. (2006). “DNA arms do the legwork to ensure the directionality of lambda site-specific recombination.” Curr Opin Struct Biol. 2006 Feb;16(1):42-50. Epub 2005 Dec 20. (Abstract)

Tomkinson A.E., Vijayakumar S., Pascal J.M., & Ellenberger, T. (2006). “DNA ligases: structure, reaction mechanism, and function.” Chem Rev. 2006 Feb;106(2):687-99. (Abstract)

Kim T.W., Brieba L.G., Ellenberger T., & Kool, E.T. (2006). “Functional evidence for a small and rigid active site in a high fidelity DNA polymerase: probing T7 DNA polymerase with variably sized base pairs.” J Biol Chem. 2006 Jan 27;281(4):2289-95. Epub 2005 Nov 27. (Abstract)