Beamline Publications

Are you about to publish a paper made possible by the SIBYLS beamline? If so we would greatly appreciate it if you would acknowledge the beamline, support staff, and our funding sources. This is critical in order for us to maintain SIBYLS beamline as a world class facility for SAXS and MX experiments.

This work was conducted at the the Advanced Light Source (ALS), a national user facility operated by Lawrence Berkeley National Laboratory on behalf of the Department of Energy, Office of Basic Energy Sciences, through the Integrated Diffraction Analysis Technologies (IDAT) program, supported by DOE Office of Biological and Environmental Research. Additional support comes from the National Institute of Health project MINOS (R01GM105404).

Additional acknowledgments to add if the manuscript is resulting from the SBDR P01 project.

Efforts to apply SAXS and crystallography to characterize eukaryotic pathways relevant to human cancers are supported in part by National Cancer Institute grant Structural Biology of DNA Repair (SBDR) CA92584.

If you received substantive help from beamline staff please also consider either adding them as a co-author or mentioning them in the acknowledgments.

Publications from the SIBYLS beamline have been tagged with convenient links to their respective PubMed entries link, and when applicable their entry in Faculty of 1000 link.

2013

  1. Hura, GL, Budworth, H, Dyer, KN, Rambo, RP, Hammel, M, McMurray, CT, and Tainer, JA "Comprehensive macromolecular conformations mapped by quantitative SAXS analyses." (2013) Nat. Methods. April 28 link

  2. Rambo, RP, and Tainer, JA "Accurate assessment of mass, models and resolution by small-angle scattering." (2013). Nature 496, 477–481. link

  3. Bianchetti, CM, Harmann, CH, Takasuka, TE, Hura, GL, Dyer, K, and Fox, BG "Fusion of dioxygenase and lignin-binding domains in a novel secreted enzyme from cellulolytic Streptomyces sp. SirexAA-E." (May 2013). J Biol Chem. link

  4. Rambo, RP, and Tainer, JA "Super-Resolution in Solution X-Ray Scattering and Its Applications to Structural Systems Biology." (2013) Annu Rev Biophys. link

  5. Lazareno-Saez, C, Arutyunova, E, Coquelle, N, and Lemieux, MJ "Domain swapping in the cytoplasmic domain of the Escherichia coli rhomboid protease." (12 Apr 2013) J Mol Biol 425, 1127–1142. link

  6. Reindl, S, Ghosh, A, Williams, GJ, Lassak, K, Neiner, T, Henche, A-L, Albers, S-V, and Tainer, JA "Insights into FlaI Functions in Archaeal Motor Assembly and Motility from Structures, Conformations, and Genetics." Mol Cell. 2013 Feb 12. link

  7. Perry, JJP., and Tainer, JA "Developing advanced X-ray scattering methods combined with crystallography and computation." Methods, 2013 link

  8. Brosey, CA, Yan, C, Tsutakawa, SE, Heller, WT, Rambo, RP, Tainer, JA, Ivanov, I, and Chazin, WJ"A new structural framework for integrating replication protein A into DNA processing machinery." (Feb 2013) Nucleic Acids Res 41, 2313–2327. link

  9. Classen, S, Hura, GL, Holton, JM, Rambo, RP, Rodic, I, McGuire, PJ, Dyer, K, Hammel, M, Meigs, G, Frankel, KA, and Tainer, JA "Implementation and performance of SIBYLS: a dual endstation small-angle X-ray scattering and macromolecular crystallography beamline at the Advanced Light Source." (2013). J Appl Crystallogr 46, 1–13. link

  10. Zhang, M, Pascal, JM, and Zhang, J-F "Unstructured to structured transition of an intrinsically disordered protein peptide in coupling Ca²⁺-sensing and SK channel activation." (19 Mar 2013). Proceedings of the National Academy of Sciences 110, 4828–4833. link

  11. Hegde, ML, Tsutakawa, SE, Hegde, PM, Holthauzen, LMF, Li, J, Oezguen, N, Hilser, VJ, Tainer, JA, and Mitra, S "The Disordered C-Terminal Domain of Human DNA Glycosylase NEIL1 Contributes to Its Stability via Intramolecular Interactions." (March 2013). J Mol Biol. link

  12. Tsutakawa, SE, Shin, DS, Mol, CD, Izumi, T, Arvai, AS, Mantha, AK, Szczesny, B, Ivanov, IN, Hosfield, DJ, Maiti, B, Pique, ME, Frankel, KA, Hitomi, K, Cunningham, RP, Mitra, S, Tainer, JA. "Conserved Structural Chemistry for Incision Activity in Structurally Non-homologous Apurinic/Apyirmidince Endonuclease APE1 and Endonuclease IV DNA repair enzymes." (2013). J Biol Chem. link

  13. Wang, W, Maucuer, A, Gupta, A, Manceau, V, Thickman, KR, Bauer, WJ, Kennedy, SD, Wedekind, JE, Green, MR, and Kielkopf, CL "Structure of Phosphorylated SF1 Bound to U2AF(65) in an Essential Splicing Factor Complex." (5 Feb 2013) Structure 21, 197–208. link

2012

  1. Shi K, Kurahashi K, Gao R, Tsutakawa SE, Tainer JA, Pommier Y, Aihara H. "Structural basis for recognition of 5'-phosphotyrosine adducts by Tdp2." Nat Struct Mol Biol. 2012 Dec;19(12):1372-7. link

  2. Schneidman-Duhovny D, Rossi A, Avila-Sakar A, Kim SJ, Velázquez-Muriel J, Strop P, Liang H, Krukenberg KA, Liao M, Kim HM, Sobhanifar S, Dötsch V, Rajpal A, Pons J, Agard DA, Cheng Y, Sali A. "A method for integrative structure determination of protein-protein complexes." Bioinformatics. 2012 Dec 1;28(24):3282-3289. link

  3. Holton, J. M., Nielsen, C. and Frankel, K. A."The point-spread function of fiber-coupled area detectors" Journal of Synchrotron Radiation, 19, 6, (Nov, 2012) link

  4. Lin DH, Malpede BM, Batchelor JD, Tolia NH. "Crystal and solution structures of Plasmodium falciparum erythrocyte-binding antigen 140 reveal determinants of receptor specificity during erythrocyte invasion." J Biol Chem. 2012 Oct 26;287(44):36830-6. link

  5. Larue R, Gupta K, Wuensch C, Shkriabai N, Kessl JJ, Danhart E, Feng L, Taltynov O, Christ F, Van Duyne GD, Debyser Z, Foster MP, Kvaratskhelia M. "Interaction of the HIV-1 intasome with transportin 3 protein (TNPO3 or TRN-SR2)." J Biol Chem. 2012 Oct 5;287(41):34044-58. link

  6. Wang, L., Pulk, A., Wasserman, M.R., Feldman, M.B., Altman, R.B., Doudna Cate, J.H., and Blanchard, S.C. "Allosteric control of the ribosome by small-molecule antibiotics." Nat Struct Mol Biol 19, 957–963. (Sept, 2012) link

  7. Duda, D.M., Olszewski, J.L., Tron, A.E., Hammel, M., Lambert, L.J., Waddell, M.B., Mittag, T., Decaprio, J.A., and Schulman, B.A. "Structure of a Glomulin-RBX1-CUL1 Complex: Inhibition of a RING E3 Ligase through Masking of Its E2-Binding Surface." Molecular Cell 47, 371–382. (Aug, 2012) link

  8. Luebbering, E.K., Mick, J., Singh, R.K., Tanner, J.J., Mehra-Chaudhary, R., and Beamer, L.J. "Conservation of Functionally Important Global Motions in an Enzyme Superfamily across Varying Quaternary Structures." J Mol Biol. (Aug, 2012) link

  9. Lyubimov, A.Y., Costa, A., Bleichert, F., Botchan, M.R., and Berger, J.M. "ATP-dependent conformational dynamics underlie the functional asymmetry of the replicative helicase from a minimalist eukaryote." Proceedings of the National Academy of Sciences 109, 11999–12004. (July 24, 2012) link

  10. Hilario, E., Li, Y., Niks, D., and Fan, L. "The structure of a Xanthomonas general stress protein involved in citrus canker reveals its flavin-binding property." Acta Crystallogr D Biol Crystallogr 68, 846–853. link

  11. Bussetta, C., and Choi, K.H. "Dengue Virus Nonstructural Protein 5 Adopts Multiple Conformations in Solution." Biochemistry, 51(30), pp 5921-5931. (July 16, 2012) link

  12. Latypov, V.F., Tubbs, J.L., Watson, A.J., Marriott, A.S., McGown, G., Thorncroft, M., Wilkinson, O.J., Senthong, P., Butt, A., Arvai, A.S., et al. "Atl1 Regulates Choice between Global Genome and Transcription-Coupled Repair of O(6)-Alkylguanines." Molecular Cell, 47, 1-11 (July 13, 2012) link

  13. Zheng, Y., Kim, S.H., Patel, A.B., Narayanaswami, V., Iavarone, A.T., Hura, G.L., and Bielicki, J.K. "The Positional Specificity of EXXK Motifs within an Amphipathic α-Helix Dictates Preferential Lysine Modification by Acrolein: Implications for the Design of High-Density Lipoprotein Mimetic Peptides." Biochemistry, 51 (32), pp 6400–6412 (July 2012) link

  14. Logsdon, N.J., Deshpande, A., Harris, B.D., Rajashankar, K.R., and Walter, M.R. "Structural basis for receptor sharing and activation by interleukin-20 receptor-2 (IL-20R2) binding cytokines." Proceedings of the National Academy of Sciences 109, 12704–12709. (June 2012) link

  15. Jenkins, J.L., Laird, K.M., and Kielkopf, C.L. "A Broad Range of Conformations Contribute to the Solution Ensemble of the Essential Splicing Factor U2AF(65)." Biochemistry, 51 (26), pp 5223-5224 (June 19, 2012) link

  16. Wang W, Wu EY, Hellinga HW, Beese LS. "Structural factors that determine selectivity of a high-fidelity DNA polymerase for deoxy-, dideoxy-, and ribo-nucleotides" J Biol Chem. (May 30, 2012) link

  17. Hammel, M. "Validation of macromolecular flexibility in solution by small-angle X-ray scattering (SAXS)." Eur Biophys J. (May 2012) link

  18. Campbell, S.J., Edwards, R.A., Leung, C.C.Y., Neculai, D., Hodge, C.D., Dhe-Paganon, S., and Glover, J.N.M. "Molecular insights into the function of RING Finger (RNF) containing proteins hRNF8 and hRNF168 in Ubc13/Mms2-dependent ubiquitylation." J Biol Chem. (May 2012) link

  19. Burke, J.R., Hura, G.L., and Rubin, S.M. "Structures of inactive retinoblastoma protein reveal multiple mechanisms for cell cycle control." Genes Dev. (May 2012) link

  20. Kim, I.-K., Kiefer, J.R., Ho, C.M.W., Stegeman, R.A., Classen, S., Tainer, J.A., and Ellenberger, T. "Structure of mammalian poly(ADP-ribose) glycohydrolase reveals a flexible tyrosine clasp as a substrate-binding element." Nat Struct Mol Biol. (May 2012) link

  21. Finger LD, Atack JM, Tsutakawa S, Classen S, Tainer J, Grasby J, Shen B. "The wonders of flap endonucleases: structure, function, mechanism and regulation." Subcellular Biochemistry, 2012, Volume 62, 301-326. link

  22. Ru, H., Zhao, L., Ding, W., Jiao, L., Shaw, N., Liang, W., Zhang, L., Hung, L.-W., Matsugaki, N., Wakatsuki, S., et al. "S-SAD phasing study of death receptor 6 and its solution conformation revealed by SAXS." Acta Crystallogr D Biol Crystallogr 68, 521–530. (May 2012) link

  23. Christie, J.M., Hitomi, K., Arvai, A.S., Hartfield, K.A., Mettlen, M., Pratt, A.J., Tainer, J.A., and Getzoff, E.D. "Structural Tuning of the Fluorescent Protein iLOV for Improved Photostability." J Biol Chem. (May 2012) link

  24. Tsutakawa, S.E., Tainer, J.A. "Double strand binding-single strand incision mechanism for human flap endonuclease: implications for the superfamily." Mech. Ageing Dev. 133, 195–202. (April 2012) link

  25. Pratt, A.J., Rambo, R.P., Lau, P.-W., and MacRae, I.J. "Preparation and characterization of the extracellular domain of human Sid-1." PLoS ONE 7, e33607. (April 2012) link

  26. Ruigrok, V.J.B., van Duijn, E., Barendregt, A., Dyer, K., Tainer, J.A., Stoltenburg, R., Strehlitz, B., Levisson, M., Smidt, H., and van der Oost, J. "Kinetic and stoichiometric characterisation of streptavidin-binding aptamers." Chembiochem 13, 829–836. (April 2012) link

  27. Dhatwalia, R., Singh, H., Oppenheimer, M., Karr, D.B., Nix, J.C., Sobrado, P., and Tanner, J.J. "Crystal structures and small-angle x-ray scattering analysis of UDP-galactopyranose mutase from the pathogenic fungus Aspergillus fumigatus." J Biol Chem 287, 9041–9051. (March 16, 2012) link

  28. Christie, J.M., Arvai, A.S., Baxter, K.J., Heilmann, M., Pratt, A.J., O'Hara, A., Kelly, S.M., Hothorn, M., Smith, B.O., Hitomi, K., Jenkins, G.I., Getzoff, E.D. "Plant UVR8 Photoreceptor Senses UV-B by Tryptophan-Mediated Disruption of Cross-Dimer Salt Bridges." Science, 23 March 2012: Vol. 335 no. 6075 pp. 1492-1496 link

  29. Grasby, J.A., Finger, L.D., Tsutakawa, S.E., Atack, J.M., and Tainer, J.A. "Unpairing and gating: sequence-independent substrate recognition by FEN superfamily nucleases." Trends Biochem Sci 37, 74–84. (Feb 2012) link

  30. Bétous, R., Mason, A. C., Rambo, R. P., Bansbach, C. E., Badu-Nkansah, A., Sirbu, B. M., Eichman, B. F., Cortez, D. "SMARCAL1 catalyzes fork regression and Holliday junction migration to maintain genome stability during DNA replication." Genes Dev, 26(2), 151–162. link

  31. Williams, C. K., Vaithiyalingam, S., Hammel, M., Pipas, J., & Chazin, W. J. "Binding to retinoblastoma pocket domain does not alter the inter-domain flexibility of the J domain of SV40 large T antigen." Archives of biochemistry and biophysics, 518(2), 111–118. link

  32. Zhou, J., Lancaster, L., Trakhanov, S., & Noller, H. F. "Crystal structure of release factor RF3 trapped in the GTP state on a rotated conformation of the ribosome." RNA (New York, NY), 18(2), 230–240. link

  33. Bauer, W.J., Heath, J., Jenkins, J.L., and Kielkopf, C.L. "Three RNA recognition motifs participate in RNA recognition and structural organization by the pro-apoptotic factor TIA-1." J Mol Biol 415, 727–740. (Jan. 2012) link

2011

  1. Grasby JA, Finger LD, Tsutakawa SE, Atack JM, Tainer JA. " Unpairing and gating: sequence-independent substrate recognition by FEN superfamily nucleases. " Trends Biochem Sci. 2011 Nov 23. link

  2. Hartung S, Arvai AS, Wood T, Kolappan S, Shin DS, Craig L, Tainer JA. "Ultra-high resolution and full-length pilin structures with insights for filament assembly, pathogenic functions, and vaccine potential." J Biol Chem. 2011 Oct 24.link

  3. Fortenberry C, Bowman EA, Proffitt W, Dorr B, Combs S, Harp J, Mizoue L, Meiler J. "Exploring symmetry as an avenue to the computational design of large protein domains." J Am Chem Soc 2011 Nov.;133(45):18026–18029.link

  4. Taherbhoy AM, Tait SW, Kaiser SE, Williams AH, Deng A, Nourse A, Hammel M, Kurinov I, Rock CO, Green DR, Schulman BA. "Atg8 transfer from atg7 to atg3: a distinctive e1-e2 architecture and mechanism in the autophagy pathway." Mol Cell 2011 Nov.;44(3):451–461.link

  5. Devarakonda S, Gupta K, Chalmers MJ, Hunt JF, Griffin PR, Van Duyne GD, Spiegelman BM. "Disorder-to-order transition underlies the structural basis for the assembly of a transcriptionally active PGC-1α/ERRγ complex." Proceedings of the National Academy of Sciences 2011 Nov.link

  6. Dueber EC, Schoeffler AJ, Lingel A, Elliott JM, Fedorova AV, Giannetti AM, Zobel K, Maurer B, Varfolomeev E, Wu P, Wallweber HJ, Hymowitz SG, Deshayes K, Vucic D, Fairbrother WJ. "Antagonists induce a conformational change in cIAP1 that promotes autoubiquitination." Science. 2011 Oct 21;334(6054):376-80.link

  7. Wang W, Hellinga HW, Beese LS. "Structural evidence for the rare tautomer hypothesis of spontaneous mutagenesis." Proceedings of the National Academy of Sciences 2011 Oct.;108(43):17644–17648.link

  8. Singh RK, Larson JD, Zhu W, Rambo RP, Hura GL, Becker DF, Tanner JJ. "Small-Angle X-ray Scattering Studies of the Oligomeric State and Quaternary Structure of the Trifunctional Proline Utilization A (PutA) Flavoprotein from Escherichia coli." J Biol Chem 2011 Oct.link

  9. Hast MA, Nichols CB, Armstrong SM, Kelly SM, Hellinga HW, Alspaugh JA, Beese LS. "Structures of Cryptococcus neoformans Protein Farnesyltransferase Reveal Strategies for Developing Inhibitors That Target Fungal Pathogens." J Biol Chem 2011 Oct.;286(40):35149–35162.link

  10. Tsutakawa SE, Van Wynsberghe AW, Freudenthal BD, Weinacht CP, Gakhar L, Washington MT, Zhuang Z, Tainer JA, Ivanov I. "Solution X-ray scattering combined with computational modeling reveals multiple conformations of covalently bound ubiquitin on PCNA." Proc Natl Acad Sci U S A. 2011 Oct 17.linklink

  11. Chao LH, Stratton MM, Lee I-H, Rosenberg OS, Levitz J, Mandell DJ, Kortemme T, Groves JT, Schulman H, Kuriyan J. "A mechanism for tunable autoinhibition in the structure of a human Ca2+/calmodulin- dependent kinase II holoenzyme." Cell 2011 Sep.;146(5):732–745.link

  12. Lang, W. H., Coats, J. E., Majka, J., Hura, G. L., Lin, Y., Rasnik, I., & McMurray, C. T. "Conformational trapping of Mismatch Recognition Complex MSH2/MSH3 on repair-resistant DNA loops." Proceedings of the National Academy of Sciences, 108(42), E837–44.link

  13. Low LY, Yang C, Perego M, Osterman A, Liddington R. "Role of net charge on catalytic domain and influence of cell wall binding domain on bactericidal activity, specificity, and host range of phage lysins." Proceedings of the National Academy of Sciences, 108(42), E837–44.J Biol Chem 2011 Sep.;286(39):34391–34403.link

  14. Mehra-Chaudhary R, Mick J, Tanner JJ, Beamer LJ. "Quaternary structure, conformational variability and global motions of phosphoglucosamine mutase." FEBS J. 2011 Sep.;278(18):3298–3307.link

  15. Hammel M, Rey M, Yu Y, Mani RS, Classen S, Liu M, Pique ME, Fang S, Mahaney BL, Weinfeld M, Schriemer DC, Lees-Miller SP, Tainer JA. "XRCC4 protein interactions with XRCC4-like factor (XLF) create an extended grooved scaffold for DNA ligation and double strand break repair." J Biol Chem. 2011 Sep 16;286(37):32638-50. Epub 2011 Jul 20.link

  16. Wong JJW, Lu J, Edwards RA, Frost LS, Glover JNM. "Structural basis of cooperative DNA recognition by the plasmid conjugation factor, TraM." Nucleic Acids Res 2011 Aug.;39(15):6775–6788.link

  17. Tseng Q, Orans J, Hast MA, Iyer RR, Changela A, Modrich PL, Beese LS. "Purification, crystallization and preliminary X-ray diffraction analysis of the human mismatch repair protein MutSβ." Acta Crystallogr Sect F Struct Biol Cryst Commun 2011 Aug.;67(Pt 8):947–952.link

  18. Batchelor JD, Zahm JA, Tolia NH. "Dimerization of Plasmodium vivax DBP is induced upon receptor binding and drives recognition of DARC." Nat Struct Mol Biol 2011 Aug.;18(8):908–914.link

  19. Rambo RP, Tainer JA. "Characterizing flexible and instrinsically unstructured biological macromolecules by SAS using the porod-debye law." Biopolymers. 2011 Aug;95(8):559-71.link

  20. Ghosh A, Hartung S, van der Does C, Tainer JA, Albers SV. "Archaeal flagellar ATPase motor shows ATP-dependent hexameric assembly and activity stimulation by specific lipid binding." Biochem J. 2011 Jul 1;437(1):43-52.link

  21. Wu EY, Beese LS. "The structure of a high fidelity DNA polymerase bound to a mismatched nucleotide reveals an “ajar” intermediate conformation in the nucleotide selection mechanism." J Biol Chem 2011 Jun.;286(22):19758–19767.link

  22. Gesner EM, Schellenberg MJ, Garside EL, George MM, Macmillan AM. "Recognition and maturation of effector RNAs in a CRISPR interference pathway." Nat Struct Mol Biol 2011 Jun.;18(6):688–692.link

  23. Balog ERM, Burke JR, Hura GL, Rubin SM. "Crystal structure of the unliganded retinoblastoma protein pocket domain." Proteins 2011 Jun.;79(6):2010–2014.link

  24. Kazantsev AV, Rambo RP, Karimpour S, Santalucia J Jr, Tainer JA, Pace NR. "Solution structure of RNase P RNA." RNA. 2011 Jun;17(6):1159-71. Epub 2011 Apr 29.link

  25. Prudden J, Perry JJ, Nie M, Vashisht AA, Arvai AS, Hitomi C, Guenther G, Wohlschlegel JA, Tainer JA, Boddy MN. "DNA repair and global sumoylation are regulated by distinct ubc9 noncovalent complexes." Mol Cell Biol. 2011 Jun;31(11):2299-310. Epub 2011 Mar 28.link

  26. Libeu CP, Poksay KS, John V, Bredesen DE. "Structural and functional alterations in amyloid-β precursor protein induced by amyloid-β peptides." J. Alzheimers Dis. 2011;25(3):547–566.link

  27. Arthur DC, Edwards RA, Tsutakawa S, Tainer JA, Frost LS, Glover JN. "Mapping interactions between the RNA chaperone FinO and its RNA targets." Nucleic Acids Res 2011 May;39(10):4450–4463.link

  28. Thede GL, Arthur DC, Edwards RA, Buelow DR, Wong JL, Raivio TL, Glover JNM. "Structure of the periplasmic stress response protein CpxP." J. Bacteriol. 2011 May;193(9):2149–2157.link

  29. Coquelle N, Green R, Glover JNM. "Impact of BRCA1 BRCT domain missense substitutions on phosphopeptide recognition." Biochemistry 2011 May;50(21):4579–4589.link

  30. Sampathkumar P, Gheyi T, Miller SA, Bain KT, Dickey M, Bonanno JB, Kim SJ, Phillips J, Pieper U, Fernandez-Martinez J, Franke JD, Martel A, Tsuruta H, Atwell S, Thompson DA, Emtage JS, Wasserman SR, Rout MP, Sali A, Sauder JM, Burley SK. "Structure of the C-terminal domain of Saccharomyces cerevisiae Nup133, a component of the nuclear pore complex." Proteins 2011 May;79(5):1672–1677.link

  31. Biersmith BH, Hammel M, Geisbrecht ER, Bouyain S. "The immunoglobulin-like domains 1 and 2 of the protein tyrosine phosphatase LAR adopt an unusual horseshoe-like conformation." J Mol Biol. 2011 May 13;408(4):616-27. Epub 2011 Mar 21.link

  32. Dunkle JA, Wang L, Feldman MB, Pulk A, Chen VB, Kapral GJ, Noeske J, Richardson JS, Blanchard SC, Cate JHD. "Structures of the bacterial ribosome in classical and hybrid states of tRNA binding." Science 2011 May;332(6032):981–984.link

  33. Fang P, Zhang HM, Shapiro R, Marshall AG, Schimmel P, Yang XL, Guo M. "Structural context for mobilization of a human tRNA synthetase from its cytoplasmic complex." Proceedings of the National Academy of Sciences 2011 May;108(20):8239–8244.link

  34. Dechassa ML, Wyns K, Li M, Hall MA, Wang MD, Luger K. "Structure and Scm3-mediated assembly of budding yeast centromeric nucleosomes." Nature Communications, May 2011;2:313.link

  35. Yang C, van der Woerd MJ, Muthurajan UM, Hansen JC, Luger K. "Biophysical analysis and small-angle X-ray scattering-derived structures of MeCP2-nucleosome complexes." Nucleic Acids Res 2011 May;39(10):4122–4135.link

  36. Lammens K, Bemeleit DJ, Möckel C, Clausing E, Schele A, Hartung S, Schiller CB, Lucas M, Angermüller C, Söding J, Strässer K, Hopfner K-P. "The Mre11:Rad50 structure shows an ATP-dependent molecular clamp in DNA double-strand break repair." Cell 2011 Apr.;145(1):54–66.link

  37. Zheng Y, Patel AB, Narayanaswami V, Hura GL, Hang B, Bielicki JK. "HDL mimetic peptide ATI-5261 forms an oligomeric assembly in solution that dissociates to monomers upon dilution." Biochemistry. 2011 May 17;50(19):4068-76. Epub 2011 Apr 20.link

  38. Lingaraju GM, Davis CA, Setser JW, Samson LD, Drennan CL. "Structural basis for the inhibition of human alkyladenine DNA glycosylase (AAG) by 3,N4-ethenocytosine-containing DNA." J Biol Chem 2011 Apr.;286(15):13205–13213.link

  39. Mehra-Chaudhary R, Mick J, Tanner JJ, Henzl MT, Beamer LJ. "Crystal structure of a bacterial phosphoglucomutase, an enzyme involved in the virulence of multiple human pathogens." Proteins 2011 Apr.;79(4):1215–1229.link

  40. Orans J, McSweeney EA, Iyer RR, Hast MA, Hellinga HW, Modrich P, Beese LS. "Structures of human exonuclease 1 DNA complexes suggest a unified mechanism for nuclease family." Cell. 2011 Apr 15;145(2):212-23.linklink

  41. Tsutakawa SE, Classen S, Chapados BR, Arvai A, Finger DL, Guenther G, Tomlinson CG, Thompson P, Sarker AH, Shen B, Cooper PK, Grasby JA, and Tainer JA. "Human flap endonuclease structures, DNA double-base flipping, and a unified understanding of the FEN1 superfamily." Cell. 2011 Apr 15;145(2):198-211.linklink

  42. Lee CF, Hauenstein AV, Fleming JK, Gasper WC, Engelke V, Sankaran B, Bernstein SI, Huxford T. "X-ray crystal structure of the UCS domain-containing UNC-45 myosin chaperone from Drosophila melanogaster." Structure. 2011 Mar 9;19(3):397-408.link

  43. Williams GJ, Williams RS, Williams JS, Moncalian G, Arvai AS, Limbo O, Guenther G, SilDas S, Hammel M, Russell P, Tainer JA. "ABC ATPase signature helices in Rad50 link nucleotide state to Mre11 interface for DNA repair." Nat Struct Mol Biol. 2011 Apr;18(4):423-31. Epub 2011 Mar 27.link

  44. Chim N, Habel JE, Johnston JM, Krieger I, Miallau L, Sankaranarayanan R, Morse RP, Bruning J, Swanson S, Kim H, Kim C-Y, Li H, Bulloch EM, Payne RJ, Manos-Turvey A, Hung L-W, Baker EN, Lott JS, James MNG, Terwilliger TC, Eisenberg DS, Sacchettini JC, Goulding CW. "The TB structural genomics consortium: a decade of progress." Tuberculosis (Edinb) 2011 Mar.;91(2):155–172.link

  45. Langelier M-F, Planck JL, Roy S, Pascal JM. "Crystal structures of poly(ADP-ribose) polymerase-1 (PARP-1) zinc fingers bound to DNA: structural and functional insights into DNA-dependent PARP-1 activity." J Biol Chem 2011 Mar.;286(12):10690–10701.link

  46. Wellhauser L, Luna-Chavez C, D'Antonio C, Tainer J, Bear CE. "ATP induces conformational changes in the carboxyl-terminal region of ClC-5." J Biol Chem 2011 Feb.;286(8):6733–6741.link

  47. Gupta A, Jenkins JL, Kielkopf CL. "RNA induces conformational changes in the SF1/U2AF65 splicing factor complex." J Mol Biol 2011 Feb.;405(5):1128–1138.link

  48. Lintner NG, Frankel KA, Tsutakawa SE, Alsbury DL, Copié V, Young MJ, Tainer JA, Lawrence CM. "The structure of the CRISPR-associated protein Csa3 provides insight into the regulation of the CRISPR/Cas system." J Mol Biol. 2011 Jan 28;405(4):939-55. Epub 2010 Nov 18.link

2010

  1. Hauk G, McKnight JN, Nodelman IM, Bowman GD. "The chromodomains of the Chd1 chromatin remodeler regulate DNA access to the ATPase motor" Mol Cell. 2010 Sep 10;39(5):711-23.link

  2. McMath, L. M., Habel, J. E., Sankaran, B., Yu, M., Hung, L.-W., & Goulding, C. W. "Crystallization and preliminary X-ray crystallographic analysis of a Mycobacterium tuberculosis ferritin homolog, BfrB." Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 Dec 1;66(Pt 12):1657-61. Epub 2010 Nov 26.link

  3. Hammel M, Yu Y, Fang S, Lees-Miller SP, Tainer JA. "XLF regulates filament architecture of the XRCC4·ligase IV complex." Structure. 2010 Nov 10;18(11):1431-42.link

  4. Classen S, Rodic I, Holton J, Hura GL, Hammel M, Tainer JA. "Software for the high-throughput collection of SAXS data using an enhanced Blu-Ice/DCS control system" J. Synchrotron Rad. (2010). 17, 774-781link

  5. Tonthat NK, Arold ST, Pickering BF, Van Dyke MW, Liang S, Lu Y, Beuria TK, Margolin W, Schumacher MA. "Molecular mechanism by which the nucleoid occlusion factor, SlmA, keeps cytokinesis in check." EMBO J. 2011 Jan 5;30(1):154-64. Epub 2010 Nov 26.link

  6. Gatzeva-Topalova, P.Z., Warner, L.R., Pardi, A., and Sousa, M.C. "Structure and flexibility of the complete periplasmic domain of BamA: the protein insertion machine of the outer membrane." Structure 18, 1492–1501.link

  7. Rambo RP, Williams GJ, Tainer JA. "Achieving fidelity in homologous recombination despite extreme complexity: informed decisions by molecular profiling." Mol Cell. 2010 Nov 12;40(3):347-8.link

  8. Nakel K, Hartung SA, Bonneau F, Eckmann CR, Conti E. "Four KH domains of the C. elegans Bicaudal-C ortholog GLD-3 form a globular structural platform." RNA 2010 Nov.;16(11):2058–2067.link

  9. Schneidman-Duhovny D, Hammel M, Sali A. "Macromolecular docking restrained by a small angle X-ray scattering profile." J Struct Biol. 2010 Oct 11.link

  10. Chen H, Ricklin D, Hammel M, Garcia BL, McWhorter WJ, Sfyroera G, Wu YQ, Tzekou A, Li S, Geisbrecht BV, Woods VL Jr, Lambris JD. "Allosteric inhibition of complement function by a staphylococcal immune evasion protein." Proc Natl Acad Sci U S A. 2010 Oct 12;107(41):17621-6. Epub 2010 Sep 27.link

  11. Arold ST, Leonard PG, Parkinson GN, Ladbury JE. "H-NS forms a superhelical protein scaffold for DNA condensation." Proc Natl Acad Sci U S A. 2010 Sep 7;107(36):15728-32. Epub 2010 Aug 23.link

  12. Cotner-Gohara E, Kim IK, Hammel M, Tainer JA, Tomkinson AE, Ellenberger T. "Human DNA Ligase III Recognizes DNA Ends by Dynamic Switching between Two DNA-Bound States." Biochemistry. 2010 Jul 27;49(29):6165-76.link

  13. Stoddard CD, Montange RK, Hennelly SP, Rambo RP, Sanbonmatsu KY, Batey RT. "Free state conformational sampling of the SAM-I riboswitch aptamer domain." Structure 2010 Jul.;18(7):787–797.link

  14. Dunkle JA, Xiong L, Mankin AS, Cate JH. "Structures of the Escherichia coli ribosome with antibiotics bound near the peptidyl transferase center explain spectra of drug action." Proc Natl Acad Sci U S A. 2010 Oct 5;107(40):17152-7.link

  15. Floor SN, Jones BN, Hernandez GA, Gross JD. "A split active site couples cap recognition by Dcp2 to activation." Nat Struct Mol Biol. 2010 Sep;17(9):1096-101. Epub 2010 Aug 15.link

  16. Clark GNI, Hura GL, Teixeira J, Soper AK, Head-Gordon T. "Small-angle scattering and the structure of ambient liquid water" Proc Natl Acad Sci U S A. 2010 Jul 20.link

  17. Habel, J.E., Bursey, E.H., Rho, B.-S., Kim, C.-Y., Segelke, B.W., Rupp, B., Park, M.S., Terwilliger, T.C., and Hung, L.-W. "Structure of Rv1848 (UreA), the Mycobacterium tuberculosis urease gamma subunit." Acta Crystallogr Sect F Struct Biol Cryst Commun 66, 781–786. (July 2010)link

  18. Hammond JA, Rambo RP, Kieft JS. "Multi-domain packing in the aminoacylatable 3' end of a plant viral RNA." J Mol Biol 2010 Jun.;399(3):450–463.link

  19. Schneidman-Duhovny D, Hammel M, Sali A. "FoXS: a web server for rapid computation and fitting of SAXS profiles." Nucleic Acids Res. 2010 Jul;38(Web Server issue):W540-4. Epub 2010 May 27.link

  20. Williams JS, Williams RS, Dovey CL, Guenther G, Tainer JA, Russell P. "gammaH2A binds Brc1 to maintain genome integrity during S-phase."EMBO J 2010 Mar.;29(6):1136–1148.link

  21. Pretto DI, Tsutakawa S, Brosey CA, Castillo A, Chagot ME, Smith JA, Tainer JA, Chazin WJ. "Structural dynamics and ssDNA binding activity of the three N-terminal domains of the large subunit of Replication Protein A from small angle X-ray scattering." Biochemistry. 2010 Feb 25. [Epub ahead of print]link

  22. Iyer RR, Pluciennik A, Genschel J, Tsai MS, Beese LS, Modrich P. "MutLα and proliferating cell nuclear antigen share binding sites on Mutsβ" J Biol Chem. 2010 Feb 16.link

  23. Srivastava D, Schuermann JP, White TA, Krishnan N, Sanyal N, Hura GL, Tan A, Henzl MT, Becker DF, Tanner JJ. "Crystal structure of the bifunctional proline utilization A flavoenzyme from Bradyrhizobium japonicum." Proc Natl Acad Sci U S A. 2010 Feb 16;107(7):2878-83. Epub 2010 Feb 1.link

  24. Rambo RP, Tainer JA. "Improving small-angle X-ray scattering data for structural analyses of the RNA world." RNA. 2010 Mar;16(3):638-46. Epub 2010 Jan 27.linklink

  25. Rambo RP, Tainer JA. "Bridging the solution divide: comprehensive structural analyses of dynamic RNA, DNA, and protein assemblies by small-angle X-ray scattering." Curr Opin Struct Biol. 2010 Feb;20(1):128-37. Epub 2010 Jan 22.link

  26. Street TO, Krukenberg KA, Rosgen J, Bolen DW, Agard DA. "Osmolyte-induced conformational changes in the Hsp90 molecular chaperone." Protein Sci. 2010 Jan;19(1):57-65.link

  27. Hammel M, Yu Y, Mahaney BL, Cai B, Ye R, Phipps BM, Rambo RP, Hura GL, Pelikan M, So S, Abolfath RM, Chen DJ, Lees-Miller SP, Tainer JA. "Ku and DNA-dependent protein kinase dynamic conformations and assembly regulate DNA binding and the initial non-homologous end joining complex." J Biol Chem. 2010 Jan 8;285(2):1414-23. Epub 2009 Nov 5.link

2009

  1. Nishimura N, Hitomi K, Arvai AS, Rambo RP, Hitomi C, Cutler SR, Schroeder JI, Getzoff ED. "Structural mechanism of abscisic acid binding and signaling by dimeric PYR1" Science. 2009 Dec 4;326(5958):1373-9. Epub 2009 Oct 22.link

  2. Fraser JS, Clarkson MW, Degnan SC, Erion R, Kern D, Alber T. "Hidden alternative structures of proline isomerase essential for catalysis." Nature. 2009 Dec 3;462(7273):669-73.link

  3. Aleshin AE, Gramatikova S, Hura GL, Bobkov A, Strongin AY, Stec B, Tainer JA, Liddington RC, Smith JW. "Crystal and solution structures of a prokaryotic M16B peptidase: an open and shut case." Structure. 2009 Nov 11;17(11):1465-75.link

  4. Hammel M, Yu Y, Mahaney BL, Cai B, Ye R, Phipps BM, Rambo RP, Hura GL, Pelikan M, So S, Abolfath RM, Chen DJ, Lees-Miller SP, Tainer JA. "Ku And Dna-Dependent Protein Kinase (DNA-Pk) Dynamic Conformations And Assembly Regulate Dna Binding And The Initial Nonhomologous End Joining Complex." J Biol Chem. 2009 Nov 5. [Epub ahead of print]link

  5. Street TO, Krukenberg KA, Rosgen J, Bolen DW, Agard DA. "Osmolyte-induced conformational changes in the Hsp90 molecular chaperone." Protein Sci. 2009 Nov 4.link

  6. Thomsen ND, Berger JM. "Running in reverse: the structural basis for translocation polarity in hexameric helicases." Cell. 2009 Oct 30;139(3):523-34.link

  7. Zhuang M, Calabrese MF, Liu J, Waddell MB, Nourse A, Hammel M, Miller DJ, Walden H, Duda DM, Seyedin SN, Hoggard T, Harper JW, White KP, Schulman BA. "Structures of SPOP-substrate complexes: insights into molecular architectures of BTB-Cul3 ubiquitin ligases." Mol Cell. 2009 Oct 9;36(1):39-50.link

  8. Jain R, Hammel M, Johnson RE, Prakash L, Prakash S, Aggarwal AK. "Structural Insights into Yeast DNA Polymerase delta by Small Angle X-ray Scattering (SAXS)." J Mol Biol. 2009 Oct 7.link

  9. Krukenberg KA, Böttcher UM, Southworth DR, Agard DA. "Grp94, the endoplasmic reticulum Hsp90, has a similar solution conformation to cytosolic Hsp90 in the absence of nucleotide." Protein Sci. 2009 Sep;18(9):1815-27.link

  10. Greenstein AE, Hammel M, Cavazos A, Alber T. "Interdomain communication in the Mycobacterium tuberculosis environmental phosphatase Rv1364c." J Biol Chem. 2009 Aug 20.link

  11. Williams RS, Dodson GE, Limbo O, Yamada Y, Williams JS, Guenther G, Classen S, Glover MJN, Iwasaki H, Russell P, Tainer JA. "Nbs1 Flexibly Tethers Ctp1 and Mre11-Rad50 to Coordinate DNA Double-Strand Break Processing and Repair" Cell, Volume 139, Issue 1, 87-99, 2 October 2009link link

  12. Zhang W, Dunkle JA, Cate JH. "Structures of the ribosome in intermediate states of ratcheting." Science. 2009 Aug 21;325(5943):1014-7link

  13. Ricklin, D., Tzekou, A., Garcia, B.L., Hammel, M., McWhorter, W.J., Sfyroera, G., Wu, Y.-Q., Holers, V.M., Herbert, A.P., Barlow, P.N., et al. "A molecular insight into complement evasion by the staphylococcal complement inhibitor protein family." J. Immunol. 183, 2565–2574. August 2009link

  14. Bernstein NK, Hammel M, Mani RS, Weinfeld M, Pelikan M, Tainer JA, Glover JN. "Mechanism of DNA substrate recognition by the mammalian DNA repair enzyme, Polynucleotide Kinase." Nucleic Acids Res. 2009 Aug 11. [epub].link

  15. Datta AB, Hura GL, Wolberger C. "The structure and conformation of Lys63-linked tetraubiquitin." J Mol Biol. 2009 Oct 9;392(5):1117-24. Epub 2009 Aug 4.link

  16. Hura GL, Menon AL, Hammel M, Rambo RP, Poole II FL, Tsutakawa SE, Jenney Jr FE, Classen S, Frankel KA, Hopkins RC, Yang S, Scott JW, Dillard BD, Adams MWW, & Tainer JA. "Robust, high-throughput solution structural analyses by small angle X-ray scattering (SAXS)" Nature Methods. 2009 Aug;6(8):606-12.linklink

  17. Krukenberg KA, Southworth DR, Street TO, Agard DA. "pH-dependent conformational changes in bacterial Hsp90 reveal a Grp94-like conformation at pH 6 that is highly active in suppression of citrate synthase aggregation." J Mol Biol. 2009 Jul 10;390(2):278-91. Epub 2009 May 7.link

  18. Pelikan M, Hura GL, Hammel M. "Structure and flexibility within proteins as identified through small angle X-ray scattering." Gen Physiol Biophys. 2009 Jun;28(2):174-89link out

  19. Tubbs JL, Latypov V, Kanugula S, Butt A, Melikishvili M, Kraehenbuehl R, Fleck O, Marriott A, Watson AJ, Verbeek B, McGown G, Thorncroft M, Santibanez-Koref MF, Millington C, Arvai AS, Kroeger MD, Peterson LA, Williams DM, Fried MG, Margison GP, Pegg AE, Tainer JA. "Flipping of alkylated DNA damage bridges base and nucleotide excision repair." Nature. 2009 Jun 11;459(7248):808-13.linklink

  20. Yin Q, Lin SC, Lamothe B, Lu M, Lo YC, Hura G, Zheng L, Rich RL, Campos AD, Myszka DG, Lenardo MJ, Darnay BG, Wu H. "E2 interaction and dimerization in the crystal structure of TRAF6." Nature structural & molecular biology 2009 May 24.link

  21. Ahn K, Johnson DS, Mileni M, Beidler D, Long JZ, McKinney MK, Weerapana E, Sadagopan N, Liimatta M, Smith SE, Lazerwith S, Stiff C, Kamtekar S, Bhattacharya K, Zhang Y, Swaney S, Van Becelaere K, Stevens RC, Cravatt BF. "Discovery and characterization of a highly selective FAAH inhibitor that reduces inflammatory pain." Chem Biol. 2009 Apr 24;16(4):411-20. link

  22. Kozlov G, Määttänen P, Schrag JD, Hura GL, Gabrielli L, Cygler M, Thomas DY, Gehring K. "Structure of the Noncatalytic Domains and Global Fold of the Protein Disulfide Isomerase ERp72." Structure. 2009 May 13;17(5):651-9. link

  23. Owen R.L., Holton J.M., Schulze-Briese C. and Garman E.F. "Determination of X-ray flux using silicon pin diodes." Journal of Synchrotron Radiation 2009;16(2):143-151link

  24. Holton J.M. "A beginner's guide to radiation damage" Journal of Synchrotron Radiation 2009;16(2):133-142link

  25. Hammond JA, Rambo RP, Filbin ME, Kieft JS. "Comparison and functional implications of the 3D architectures of viral tRNA-like structures." RNA. 2009 Feb;15(2):294-307 link

  26. Dalhus B, Arvai AS, Rosnes I, Olsen ØE, Backe PH, Alseth I, Gao H, Cao W, Tainer JA, Bjørås M. "Structures of endonuclease V with DNA reveal initiation of deaminated adenine repair." Nat Struct Mol Biol. 2009 Feb;16(2):138-43.link

  27. Shin DS, DiDonato M, Barondeau DP, Hura GL, Hitomi C, Berglund JA, Getzoff ED, Cary SC, Tainer JA. "Superoxide dismutase from the eukaryotic thermophile Alvinella pompejana: structures, stability, mechanism, and insights into amyotrophic lateral sclerosis." J Mol Biol. 2009 Feb 6;385(5):1534-55. link

  28. Min X, Akella R, He H, Humphreys JM, Tsutakawa SE, Lee SJ, Tainer JA, Cobb MH, Goldsmith EJ. "The Structure of the MAP2K MEK6 Reveals an Autoinhibitory Dimer." Structure. 2009 Jan;17(1):96-104. link

2008

  1. Jenkins JL, Shen H, Green MR, Kielkopf CL. "Solution Conformation and Thermodynamic Characteristics of RNA Binding by the Splicing Factor U2AF65." J Biol Chem. 2008 Nov 28;283(48):33641-9

  2. Edwards RA, Lee MS, Tsutakawa SE, Williams RS, Tainer JA, Glover JN. "The BARD1 C-terminal domain structure and interactions with polyadenylation factor CstF-50." Biochemistry. 2008 Nov 4;47(44):11446-56. Epub 2008 Oct 9.

  3. Williams RS, Moncalian G, Williams JS, Yamada Y, Limbo O, Shin DS, Groocock LM, Cahill D, Hitomi C, Guenther G, Moiani D, Carney JP, Russell P, and Tainer JA. "Mre11 Dimers Coordinate DNA End Bridging and Nuclease Processing in Double-Strand-Break Repair" Cell 2008 Oct 03;135: p 97-109

  4. Duda DM, Borg LA, Scott DC, Hunt HW, Hammel M, Schulman BA. "Structural insights into NEDD8 activation of cullin-RING ligases: conformational control of conjugation." Cell 2008 Sep 19;134(6):995-1006

  5. Bowman GR, Comolli LR, Zhu J, Eckart M, Koenig M, Downing KH, Moerner WE, Earnest T, Shapiro L. "A polymeric protein anchors the chromosomal origin/ParB complex at a bacterial cell pole." Cell. 2008 Sep 19;134(6):945-55.

  6. Iyer RR, Pohlhaus TJ, Chen S, Hura GL, Dzantiev L, Beese LS, Modrich P. "The MutSα-proliferating cell nuclear antigen interaction in human DNA mismatch repair." J Biol Chem (2008) vol. 283 (19) pp. 13310-9

  7. Garst AD, Héroux A, Rambo RP, Batey RT. "Crystal structure of the lysine riboswitch regulatory mRNA element." J Biol Chem. 2008 Aug 15;283(33):22347-51. Epub 2008 Jul 1.

  8. Borovinskaya MA, Shoji S, Fredrick K, Cate JH. "Structural basis for hygromycin B inhibition of protein biosynthesis." RNA. 2008 Aug;14(8):1590-9

  9. Chrencik JE, Brooun A, Zhang H, Mathews II, Hura GL, Foster SA, Perry JJ, Streiff M, Ramage P, Widmer H, Bokoch GM, Tainer JA, Weckbecker G, Kuhn P. "Structural basis of guanine nucleotide exchange mediated by the T-cell essential Vav1." J Mol Biol. 2008 Jul 25;380(5):828-43.

  10. Lee JE, Fusco ML, Hessell AJ, Oswald WB, Burton DR, Saphire EO. "Structure of the Ebola virus glycoprotein bound to an antibody from a human survivor." Nature. 2008 Jul 10;454(7201):177-82.

  11. Cunningham CN, Krukenberg KA, Agard DA. "Intra- and intermonomer interactions are required to synergistically facilitate ATP hydrolysis in Hsp90." J Biol Chem. 2008 Jul 25;283(30):21170-8.

  12. Laurberg M, Asahara H, Korostelev A, Zhu J, Trakhanov S, Noller HF. "Structural basis for translation termination on the 70S ribosome." Nature. 2008 Aug 14;454(7206):852-7.

  13. Krukenberg KA, Förster F, Rice LM, Sali A, Agard DA. "Multiple conformations of E. coli Hsp90 in solution: insights into the conformational dynamics of Hsp90." Structure. 2008 May;16(5):755-65.

  14. Witte G, Hartung S, Büttner K, Hopfner KP. "Structural biochemistry of a bacterial checkpoint protein reveals diadenylate cyclase activity regulated by DNA recombination intermediates." Mol Cell. 2008 Apr 25;30(2):167-78.

  15. Rice LM, Montabana EA, Agard DA. "The lattice as allosteric effector: structural studies of alphabeta- and gamma-tubulin clarify the role of GTP in microtubule assembly." Proc Natl Acad Sci U S A. 2008 Apr 8;105(14):5378-83.

  16. Pai RD, Zhang W, Schuwirth BS, Hirokawa G, Kaji H, Kaji A, Cate JH. "Structural Insights into ribosome recycling factor interactions with the 70S ribosome." J Mol Biol. 2008 Mar 7;376(5):1334-47.

  17. Li Fan, Jill O Fuss, Quen J Cheng, Andrew S Arvai, Michal Hammel, Victoria A Roberts, Priscilla K Cooper, John A Tainer. "XPD helicase structures and activities: insights into the cancer and aging phenotypes from XPD mutations." Cell (2008) vol. 133 (5) pp. 789-800

  18. Roll-Mecak A, Vale RD. "Structural basis of microtubule severing by the hereditary spastic paraplegia protein spastin." Nature. 2008 Jan 17;451(7176):363-7.

  19. Costantino DA, Pfingsten JS, Rambo RP, Kieft JS. "tRNA-mRNA mimicry drives translation initiation from a viral IRES." Nat Struct Mol Biol. 2008 Jan;15(1):57-64.

  20. Fan L, Williams RS, Shin DS, Chapados B, and Tainer JA (2008) in Thermophiles: Biology and Technology at High Temperatures (F. Robb, G. Antranikian, D. Grogan, , A. Driessen editors), Chapter 15: Master keys to DNA Replication, Repair, and Recombination from the Structural Biology of Enzymes from Thermophiles pp. 239- 264.

2007

  1. Putnam CD, Hammel M, Hura GL, Tainer JA "Solution scattering (SAXS) combined with crystallography and computation: defining accurate macromolecular structures, conformations and assemblies in solution" Q Rev Biophys. 2007 Aug;40(3):191-285.

  2. Zhang X, Pickin KA, Bose R, Jura N, Cole PA, Kuriyan J. "Inhibition of the EGF receptor by binding of MIG6 to an activating kinase domain interface." Nature. 450(7170):741-4 November 29, 2007

  3. Korostelev A, Trakhanov S, Asahara H, Laurberg M, Lancaster L, Noller HF. "Interactions and dynamics of the Shine Dalgarno helix in the 70S ribosome." Proc Natl Acad Sci U S A. 2007 Oct 23;104(43):16840-3.

  4. Williams RS, Williams JS, Tainer JA. "Mre11-Rad50-Nbs1 is a keystone complex connecting DNA repair machinery, double-strand break signaling, and the chromatin template." Biochem Cell Biol. 2007 Aug;85(4):509-20

  5. Yin J, Niu C, Cherney MM, Zhang J, Huitema C, Eltis LD, Vederas JC, James MN. "A mechanistic view of enzyme inhibition and peptide hydrolysis in the active site of the SARS-CoV 3C-like peptidase." J Mol Biol. 2007 Aug 24;371(4):1060-74.

  6. Borovinskaya MA, Shoji S, Holton JM, Fredrick K, Cate JH. "A steric block in translation caused by the antibiotic spectinomycin." ACS Chem Biol. 2007 Aug 17;2(8):545-52.

  7. Borovinskaya MA, Pai RD, Zhang W, Schuwirth BS, Holton JM, Hirokawa G, Kaji H, Kaji A, Cate JH. "Structural basis for aminoglycoside inhibition of bacterial ribosome recycling."Nat Struct Mol Biol. 2007 Aug;14(8):727-32.

  8. Corbett KD, Benedetti P, Berger JM. "Holoenzyme assembly and ATP-mediated conformational dynamics of topoisomerase VI." Nat Struct Mol Biol. 2007 Jul;14(7):611-9.

  9. Mendillo ML, Putnam CD, Kolodner RD. "Escherichia coli MutS tetramerization domain structure reveals that stable dimers but not tetramers are essential for DNA mismatch repair in vivo." J Biol Chem. 2007 Jun 1;282(22):16345-54.

  10. Berk V, Cate JH. "Insights into protein biosynthesis from structures of bacterial ribosomes." Curr Opin Struct Biol. 2007 Jun;17(3):302-9.

  11. Aleshin AE, Shiryaev SA, Strongin AY, Liddington RC. "Structural evidence for regulation and specificity of flaviviral proteases and evolution of the Flaviviridae fold." Protein Sci. 2007 May;16(5):795-806.

  12. Peters-Libeu CA, Newhouse Y, Hall SC, Witkowska HE, Weisgraber KH. "Apolipoprotein E*dipalmitoylphosphatidylcholine particles are ellipsoidal in solution." J Lipid Res. 2007 May;48(5):1035-44.

  13. Shell SS, Putnam CD, Kolodner RD. "The N terminus of Saccharomyces cerevisiae Msh6 is an unstructured tether to PCNA."

  14. Tsutakawa SE, Hura GL, Frankel KA, Cooper PK, Tainer JA. "Structural analysis of flexible proteins in solution by small angle X-ray scattering combined with crystallography." J Struct Biol. 2007 May;158(2):214-23.

  15. Santelli, E.,Liddington, R.C.,Mohan, M.A.,Hoch, J.A.,Szurmant, H. "The Crystal Structure of Bacillus subtilis YycI Reveals a Common Fold for Two Members of an Unusual Class of Sensor Histidine Kinase Regulatory Proteins." J Bacteriol. 2007 Apr;189(8):3290-5.

  16. Moncoq K, Trieber CA, Young HS. "The molecular basis for cyclopiazonic acid inhibition of the sarcoplasmic reticulum calcium pump." J Biol Chem. 2007 Mar 30;282(13):9748-57.

  17. Yamagata A, Tainer JA. "Hexameric structures of the archaeal secretion ATPase GspE and implications for a universal secretion mechanism." EMBO J. 2007 Feb 7;26(3):878-90.

  18. Aoyagi M, Zhai D, Jin C, Aleshin AE, Stec B, Reed JC, Liddington RC. "Vaccinia virus N1L protein resembles a B cell lymphoma-2 (Bcl-2) family protein." Protein Sci. 2007 Jan;16(1):118-24.

  19. Holton JM "XANES measurements of the rate of radiation damage to selenomethionine side chains" J. Synchrotron Rad. 14, 51-72 January 2007

2006

  1. Buczek P and Horvath MP, "Structural Reorganization and the Cooperative Binding of Single-stranded Telomere DNA in Sterkiella nova" J. Biol. Chem., Vol. 281, Issue 52, 40124-40134, December 29, 2006

  2. Berk V, Zhang W, Pai RD, Cate JH. "Structural basis for mRNA and tRNA positioning on the ribosome." Proc Natl Acad Sci U S A. 2006 Oct 24;103(43):15830-4.

  3. Pioletti M, Findeisen F, Hura GL, Minor DL, Jr. "Three-dimensional structure of the KChIP1/Kv4.3 T1 complex reveals across-shaped octamer." Nat Struct Mol Biol. EPUB October 22.

  4. Pascal JM, Tsodikov OV, Hura GL, Song W, Cotner EA, Classen S, Tomkinson AE, Tainer JA and Ellenberger T, "A Flexible Interface between DNA Ligase and PCNA Supports Conformational Switching and Efficient Ligation of DNA" Molecular Cell, Volume 24, Issue 2, , 20 October 2006, Pages 279-291.

  5. Schuwirth BS, Day JM, Hau CW, Janssen GR, Dahlberg AE, Cate JH, Vila-Sanjurjo A. "Structural analysis of kasugamycin inhibition of translation." Nat Struct Mol Biol. 2006 Oct;13(10):879-86.

  6. Korostelev A, Trakhanov S, Laurberg M, Noller HF. "Crystal structure of a 70S ribosome-tRNA complex reveals functional interactions and rearrangements." Cell. 2006 Sep 22;126(6):1065-77.

  7. Lamers MH, Georgescu RE Sang-Gyu Lee, O'Donnell M, and Kuriyan J, "Crystal Structure of the Catalytic α Subunit of E. coli Replicative DNA Polymerase III." Cell 126, 881–892, September 8, 2006.

  8. Kozlov G, Maattanen P, Schrag JD, Pollock S, Cygler M, Nagar B, Thomas DY, Gehring K, "Crystal Structure of the bb' Domains of the Protein Disulfide Isomerase ERp57" Structure, Volume 14, Issue 8, , August 2006, Pages 1331-1339.

  9. Hansen CL, Classen S, Berger JM, Quake SR, "A microfluidic device for kinetic optimization of protein crystallization and in situ structure determination." J Am Chem Soc. 128(10):3142-3, March 15, 2006.

  10. Sundheim O, Vagbo CB, Bjoras M, Sousa MM, Talstad V, Aas PA, Drablos F, Krokan HE, Tainer JA, Slupphaug G, " Human ABH3 structure and key residues for oxidative demethylation to reverse DNA/RNA damage." EMBO J. 25:3389-97, 2006.

  11. Fan L, Arvai AS, Cooper PK, Iwai S, Hanaoka F, Tainer JA, "Conserved XPB Core Structure and Motifs for DNA Unwinding: Implications for Pathway Selection of Transcription or Excision Repair." Molecular Cell v22 pp.27-37, 2006.

  12. Fan L, Kim S, Farr CL, Schaefer KT, Randolph KM, Tainer JA, Kaguni LS, "A Novel Processive Mechanism for DNA Synthesis Revealed by Structure, Modeling and Mutagenesis of the Accessory Subunit of Human Mitochondrial DNA Polymerase" J Mol Biol. v358 pp.1229-1243, 2006.

  13. Nagar B, Hantschel O, Seeliger M, Davies JM, Weis WI, Superti-Furga G, Kuriyan J, "Organization of the SH3-SH2 unit in active and inactive forms of the c-Abl tyrosine kinase." Molecular Cell 21(6):787-98, 2006.

  14. Levinson NM, Kuchment O, Shen K, Young MA, Koldobskiy M, Karplus M, Cole PA, Kuriyan J, "A SRC-like inactive conformation in the abl tyrosine kinase domain." PloS Biology v4 pp.753-767, 2006.

2005

  1. Khayat R, Tang L, Young M, Johnson JE, "Structure of an archaeal virus capsid protein reveals an evolutionary relationship to eucaryotic and bacterial viruses." Proc Natl Acad Sci USA. 102(52): 18944–18949, December 27, 2005.

  2. Rosenberg OS, Deindl S, Sung RJ, Nairn AC, Kuriyan J, "Structure of the autoinhibited kinase domain of CaMKII and SAXS analysis of the holoenzyme." Cell 123(5):849-60 December 2, 2005.

  3. Schuwirth BS, Borovinskaya MA, Hau CW, Zhang W, Vila-Sanjurjo A, Holton JM, Cate JH, "Structures of the bacterial ribosome at 3.5 A resolution." Science 310(5749):827-34 Novembr 4, 2005.

  4. Corn JE, Pease PJ, Hura GL, Berger JM, "Crosstalk between primase subunits can act to regulate primer synthesis in trans." Molecular Cell 20(3):391-401, November 11, 2005.

  5. Chao JA, Lee JH, Chapados BR, Debler EW, Schneemann A, Williamson JR, "Dual modes of RNA-silencing suppression by Flock House virus protein B2. " Nat Struct Mol Biol. 12(11):952-7, November 2005.

  6. Olson R, Huey-Tubman KE, Dulac C, Bjorkman PJ, "Structure of a pheromone receptor-associated MHC molecule with an open and empty groove. " PLoS Biology 3(8):e257 August 2005.

2004

  1. Pascal JM, O'Brien PJ, Tomkinson AE, Ellenberger T, "Human DNA ligase I completely encircles and partially unwinds nicked DNA." Nature 432(7016):473-8, November 25, 2004.

  2. Barondeau DP, Kassmann CJ, Bruns CK, Tainer JA, Getzoff ED, "Nickel superoxide dismutase structure and mechanism." Biochemistry 43(25):8038-47, June 29, 2004.

  3. MacDowell AA, Celestre RS, Howells M, McKinney W, Krupnick J, Cambie D, Domning EE, Duarte RM, Kelez N, Plate DW, Cork CW, Earnest TN, Dickert J, Meigs G, Ralston C, Holton JM, Alber T, Berger JM, Agard DA, Padmore HA. "Suite of three protein crystallography beamlines with single superconducting bend magnet as the source." J Synchrotron Radiat. 11:447-55, November 2004.