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 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) and a High-End Instrumentation Grant S10OD018483.

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.

2017

  1. Aceytuno RD, Piett CG, Havali-Shahriari Z, Edwards RA, Rey M, Ye R, Javed F, Fang S, Mani R, Weinfeld M, Hammel M, Tainer JA, Schriemer DC, Lees-Miller SP, Glover JNM. "Structural and functional characterization of the PNKP-XRCC4-LigIV DNA repair complex." Nucleic Acids Res. 2017 Apr 27 link

  2. Susa AC, Xia Z, Tang HY, Tainer JA, Williams ER. "Charging of Proteins in Native Mass Spectrometry." J. Am. Soc. Mass Spectrom. 2017 Feb ;28(2)link

  3. Michael AK, Fribourgh JL, Chelliah Y, Sandate CR, Hura GL, Schneidman-Duhovny D, Tripathi SM, Takahashi JS, Partch CL. "Formation of a repressive complex in the mammalian circadian clock is mediated by the secondary pocket of CRY1." Proc. Natl. Acad. Sci. U.S.A. 2017 Feb 14 ;114(7)link

  4. Wallen JR, Zhang H, Weis C, Cui W, Foster BM, Ho CM, Hammel M, Tainer JA, Gross ML, Ellenberger T. "Hybrid Methods Reveal Multiple Flexibly Linked DNA Polymerases within the Bacteriophage T7 Replisome." Structure 2017 Jan 03 ;25(1)link

2016

  1. Wallace BD, Berman Z, Mueller GA, Lin Y, Chang T, Andres SN, Wojtaszek JL, DeRose EF, Appel CD, London RE, Yan S, Williams RS. "APE2 Zf-GRF facilitates 3'-5' resection of DNA damage following oxidative stress." Proc. Natl. Acad. Sci. U.S.A. 2016 Dec 27 link

  2. Arentson BW, Hayes EL, Zhu W, Singh H, Tanner JJ, Becker DF. "Engineering a trifunctional proline utilization A chimaera by fusing a DNA-binding domain to a bifunctional PutA." Biosci. Rep. 2016 Dec ;36(6)link

  3. Liu S, Street TO. "5'-N-ethylcarboxamidoadenosine is not a paralog-specific Hsp90 inhibitor." Protein Sci. 2016 Dec ;25(12)link

  4. Brosey CA, Ho C, Long WZ, Singh S, Burnett K, Hura GL, Nix JC, Bowman GR, Ellenberger T, Tainer JA. "Defining NADH-Driven Allostery Regulating Apoptosis-Inducing Factor." Structure 2016 Nov 02 link

  5. Luo M, Gamage TT, Arentson BW, Schlasner KN, Becker DF, Tanner JJ. "Structures of Proline Utilization A (PutA) Reveal the Fold and Functions of the Aldehyde Dehydrogenase Superfamily Domain of Unknown Function." J. Biol. Chem. 2016 Nov 11 ;291(46)link

  6. Li J, Rodriguez JP, Niu F, Pu M, Wang J, Hung LW, Shao Q, Zhu Y, Ding W, Liu Y, Da Y, Yao Z, Yang J, Zhao Y, Wei GH, Cheng G, Liu ZJ, Ouyang S. "Structural basis for DNA recognition by STAT6." Proc. Natl. Acad. Sci. U.S.A. 2016 Nov 15 ;113(46)link

  7. Hammel M, Yu Y, Radhakrishnan SK, Chokshi C, Tsai MS, Matsumoto Y, Kuzdovich M, Remesh SG, Fang S, Tomkinson AE, Lees-Miller SP, Tainer JA. "An Intrinsically Disordered APLF Links Ku, DNA-PKcs and XRCC4-DNA Ligase IV in an Extended Flexible Non-Homologous End Joining Complex." J. Biol. Chem. 2016 Nov 14 link

  8. Keppel TR, Sarpong K, Murray EM, Monsey J, Zhu J, Bose R. "Biophysical Evidence for Intrinsic Disorder in the C-terminal Tails of the EGFR and HER3 Receptor Tyrosine Kinases." J. Biol. Chem. 2016 Nov 21 link

  9. Martin EW, Holehouse AS, Grace CR, Hughes A, Pappu RV, Mittag T. "Sequence Determinants of the Conformational Properties of an Intrinsically Disordered Protein Prior to and upon Multisite Phosphorylation." J. Am. Chem. Soc. 2016 Nov 30 ;138(47)link

  10. Araya-Secchi R, Neel BL, Sotomayor M. "An elastic element in the protocadherin-15 tip link of the inner ear." Nat Commun 2016 Nov 18 ;7link

  11. Liu LK, Abdelwahab H, Martin Del Campo JS, Mehra-Chaudhary R, Sobrado P, Tanner JJ. "The Structure of the Antibiotic Deactivating, N-hydroxylating Rifampicin Monooxygenase." J. Biol. Chem. 2016 Oct 07 ;291(41)link

  12. Schulze-Gahmen U, Echeverria I, Stjepanovic G, Bai Y, Lu H, Schneidman-Duhovny D, Doudna JA, Zhou Q, Sali A, Hurley JH. "Insights into HIV-1 proviral transcription from integrative structure and dynamics of the Tat:AFF4:P-TEFb:TAR complex." Elife 2016 Oct 12 ;5link

  13. Johnson PM, Gucinski GC, Garza-Sánchez F, Wong T, Hung LW, Hayes CS, Goulding CW. "Functional Diversity of Cytotoxic tRNase/Immunity Protein Complexes from Burkholderia pseudomallei." J. Biol. Chem. 2016 Sep 9 ;291(37):19387-400 link

  14. Schiffer JM, Malmstrom RD, Parnell J, Ramirez-Sarmiento C, Reyes J, Amaro RE, Komives EA. "Model of the Ankyrin and SOCS Box Protein, ASB9, E3 Ligase Reveals a Mechanism for Dynamic Ubiquitin Transfer." Structure 2016 Aug 2 ;24(8):1248-56 link

  15. Yachnin BJ, Lau PC, Berghuis AM. "The role of conformational flexibility in Baeyer-Villiger monooxygenase catalysis and structure." Biochim. Biophys. Acta 2016 Aug 26 ;1864(12):1641-1648 link

  16. Bhowmick A, Brookes DH, Yost SR, Dyson HJ, Forman-Kay JD, Gunter D, Head-Gordon M, Hura GL, Pande VS, Wemmer DE, Wright PE, Head-Gordon T. "Finding Our Way in the Dark Proteome." J. Am. Chem. Soc. 2016 Aug 10 ;138(31):9730-42 link

  17. Nikolaienko RM, Hammel M, Dubreuil V, Zalmai R, Hall DR, Mehzabeen N, Karuppan SJ, Harroch S, Stella SL, Bouyain S. "Structural Basis for Interactions Between Contactin Family Members and Protein Tyrosine Phosphatase Receptor Type G in Neural Tissues." J. Biol. Chem. 2016 Aug 18 link

  18. Gilmore SF, Blanchette CD, Scharadin TM, Hura GL, Rasley A, Corzett M, Pan CX, Fischer NO, Henderson PT. "Lipid Cross-Linking of Nanolipoprotein Particles Substantially Enhances Serum Stability and Cellular Uptake." ACS Appl Mater Interfaces 2016 Aug 17 ;8(32):20549-57 link

  19. Horvath MP, George EW, Tran QT, Baumgardner K, Zharov G, Lee S, Sharifzadeh H, Shihab S, Mattinson T, Li B, Bernstein PS. "Structure of the lutein-binding domain of human StARD3 at 1.74 Å resolution and model of a complex with lutein." Acta Crystallogr F Struct Biol Commun 2016 Aug 1 ;72(Pt 8):609-18 link

  20. Riccio AA, McCauley M, Langelier MF, Pascal JM. "Tankyrase Sterile α Motif Domain Polymerization Is Required for Its Role in Wnt Signaling." Structure 2016 Aug 3 link

  21. Chu J, Oh Y, Sens A, Ataie N, Dana H, Macklin JJ, Laviv T, Welf ES, Dean KM, Zhang F, Kim BB, Tang CT, Hu M, Baird MA, Davidson MW, Kay MA, Fiolka R, Yasuda R, Kim DS, Ng HL, Lin MZ. "A bright cyan-excitable orange fluorescent protein facilitates dual-emission microscopy and enhances bioluminescence imaging in vivo." Nat. Biotechnol. 2016 Jul ;34(7):760-7 link

  22. Bale JB, Gonen S, Liu Y, Sheffler W, Ellis D, Thomas C, Cascio D, Yeates TO, Gonen T, King NP, Baker D. "Accurate design of megadalton-scale two-component icosahedral protein complexes." Science 2016 Jul 22 ;353(6297):389-94 link

  23. Hammel M, Amlanjyoti D, Reyes FE, Chen JH, Parpana R, Tang HY, Larabell CA, Tainer JA, Adhya S. "HU multimerization shift controls nucleoid compaction." Sci Adv 2016 Jul ;2(7):e1600650 link

  24. Schneidman-Duhovny D, Hammel M, Tainer JA, Sali A. "FoXS, FoXSDock and MultiFoXS: Single-state and multi-state structural modeling of proteins and their complexes based on SAXS profiles." Nucleic Acids Res. 2016 Jul 8 ;44(W1):W424-9 link

  25. Sivá M, Svoboda M, Veverka V, Trempe JF, Hofmann K, Kožíšek M, Hexnerová R, Sedlák F, Belza J, Brynda J, Šácha P, Hubálek M, Starková J, Flaisigová I, Konvalinka J, Šašková KG. "Human DNA-Damage-Inducible 2 Protein Is Structurally and Functionally Distinct from Its Yeast Ortholog." Sci Rep 2016 ;6:30443 link

  26. Aydin H, Sultana A, Li S, Thavalingam A, Lee JE. "Molecular architecture of the human sperm IZUMO1 and egg JUNO fertilization complex." Nature 2016 Jun 23 ;534(7608):562-5 link

  27. Chen E, Salinas ND, Huang Y, Ntumngia F, Plasencia MD, Gross ML, Adams JH, Tolia NH. "Broadly neutralizing epitopes in the Plasmodium vivax vaccine candidate Duffy Binding Protein." Proc. Natl. Acad. Sci. U.S.A. 2016 May 31 ;113(22):6277-82 link

  28. Boyken SE, Chen Z, Groves B, Langan RA, Oberdorfer G, Ford A, Gilmore JM, Xu C, DiMaio F, Pereira JH, Sankaran B, Seelig G, Zwart PH, Baker D. "De novo design of protein homo-oligomers with modular hydrogen-bond network-mediated specificity." Science 2016 May 6 ;352(6286):680-7 link

  29. Das RK, Huang Y, Phillips AH, Kriwacki RW, Pappu RV. "Cryptic sequence features within the disordered protein p27Kip1 regulate cell cycle signaling." Proc. Natl. Acad. Sci. U.S.A. 2016 May 17 ;113(20):5616-21 link

  30. Youngblut MD, Tsai CL, Clark IC, Carlson HK, Maglaqui AP, Gau-Pan PS, Redford SA, Wong A, Tainer JA, Coates JD. "Perchlorate Reductase Is Distinguished by Active Site Aromatic Gate Residues." J. Biol. Chem. 2016 Apr 22 ;291(17):9190-202 link

  31. Hodge CD, Ismail IH, Edwards RA, Hura GL, Xiao AT, Tainer JA, Hendzel MJ, Glover JN. "RNF8 E3 Ubiquitin Ligase Stimulates Ubc13 E2 Conjugating Activity That Is Essential for DNA Double Strand Break Signaling and BRCA1 Tumor Suppressor Recruitment." J. Biol. Chem. 2016 Apr 29 ;291(18):9396-410 link

  32. Brooun A, Gajiwala KS, Deng YL, Liu W, Bolaños B, Bingham P, He YA, Diehl W, Grable N, Kung PP, Sutton S, Maegley KA, Yu X, Stewart AE. "Polycomb repressive complex 2 structure with inhibitor reveals a mechanism of activation and drug resistance." Nat Commun 2016 ;7:11384 link

  33. Hilario E, Caulkins BG, Huang YM, You W, Chang CE, Mueller LJ, Dunn MF, Fan L. "Visualizing the tunnel in tryptophan synthase with crystallography: Insights into a selective filter for accommodating indole and rejecting water." Biochim. Biophys. Acta 2016 Mar ;1864(3):268-79 link

  34. Melchior JT, Walker RG, Morris J, Jones MK, Segrest JP, Lima DB, Carvalho PC, Gozzo FC, Castleberry M, Thompson TB, Davidson WS. "An Evaluation of the Crystal Structure of C-terminal Truncated Apolipoprotein A-I in Solution Reveals Structural Dynamics Related to Lipid Binding." J. Biol. Chem. 2016 Mar 4 ;291(10):5439-51 link

  35. Militi S, Maywood ES, Sandate CR, Chesham JE, Barnard AR, Parsons MJ, Vibert JL, Joynson GM, Partch CL, Hastings MH, Nolan PM. "Early doors (Edo) mutant mouse reveals the importance of period 2 (PER2) PAS domain structure for circadian pacemaking." Proc. Natl. Acad. Sci. U.S.A. 2016 Mar 8 ;113(10):2756-61 link

  36. Duffy CM, Hilbert BJ, Kelch BA. "A Disease-Causing Variant in PCNA Disrupts a Promiscuous Protein Binding Site." J. Mol. Biol. 2016 Mar 27 ;428(6):1023-40 link

  37. Edeling MA, Diamond MS, Fremont DH. "Structural basis of Flavivirus NS1 assembly and antibody recognition." Proc. Natl. Acad. Sci. U.S.A. 2014 Mar 18 ;111(11):4285-90 link

  38. Chaudhury P, Neiner T, D'Imprima E, Banerjee A, Reindl S, Ghosh A, Arvai AS, Mills DJ, van der Does C, Tainer JA, Vonck J, Albers SV. "The nucleotide-dependent interaction of FlaH and FlaI is essential for assembly and function of the archaellum motor." Mol. Microbiol. 2016 Feb ;99(4):674-85 link

  39. Chen M, Chou WK, Toyomasu T, Cane DE, Christianson DW. "Structure and Function of Fusicoccadiene Synthase, a Hexameric Bifunctional Diterpene Synthase." ACS Chem. Biol. 2016 Apr 15 ;11(4):889-99 link

  40. Woods RD, O'Shea VL, Chu A, Cao S, Richards JL, Horvath MP, David SS. "Structure and stereochemistry of the base excision repair glycosylase MutY reveal a mechanism similar to retaining glycosidases." Nucleic Acids Res. 2016 Jan 29 ;44(2):801-10 link

2015

  1. Brunette TJ, Parmeggiani F, Huang PS, Bhabha G, Ekiert DC, Tsutakawa SE, Hura GL, Tainer JA, Baker D. "Exploring the repeat protein universe through computational protein design." Nature 2015 Dec 24 ;528(7583):580-4 link

  2. Eustermann S, Wu WF, Langelier MF, Yang JC, Easton LE, Riccio AA, Pascal JM, Neuhaus D. "Structural Basis of Detection and Signaling of DNA Single-Strand Breaks by Human PARP-1." Mol. Cell 2015 Dec 3 ;60(5):742-54 link

  3. Dawicki-McKenna JM, Langelier MF, DeNizio JE, Riccio AA, Cao CD, Karch KR, McCauley M, Steffen JD, Black BE, Pascal JM. "PARP-1 Activation Requires Local Unfolding of an Autoinhibitory Domain." Mol. Cell 2015 Dec 3 ;60(5):755-68 link

  4. Fields JB, Hollingsworth SA, Chreifi G, Heyden M, Arce AP, Magaña-Garcia HI, Poulos TL, Tobias DJ. ""Bind and Crawl" Association Mechanism of Leishmania major Peroxidase and Cytochrome c Revealed by Brownian and Molecular Dynamics Simulations." Biochemistry 2015 Dec 15 ;54(49):7272-82 link

  5. Harris GG, Lombardi PM, Pemberton TA, Matsui T, Weiss TM, Cole KE, Köksal M, Murphy FV, Vedula LS, Chou WK, Cane DE, Christianson DW. "Structural Studies of Geosmin Synthase, a Bifunctional Sesquiterpene Synthase with αα Domain Architecture That Catalyzes a Unique Cyclization-Fragmentation Reaction Sequence." Biochemistry 2015 Dec 08 ;54(48)link

  6. Suslov NB, DasGupta S, Huang H, Fuller JR, Lilley DM, Rice PA, Piccirilli JA. "Crystal structure of the Varkud satellite ribozyme." Nat. Chem. Biol. 2015 Nov ;11(11):840-6 link

  7. Wuerth ME, Cragerud RK, Clint Spiegel P. "Structure of the Human Factor VIII C2 Domain in Complex with the 3E6 Inhibitory Antibody." Sci Rep 2015 ;5:17216 link

  8. Min X, Ungureanu D, Maxwell S, Hammarén H, Thibault S, Hillert EK, Ayres M, Greenfield B, Eksterowicz J, Gabel C, Walker N, Silvennoinen O, Wang Z. "Structural and Functional Characterization of the JH2 Pseudokinase Domain of JAK Family Tyrosine Kinase 2 (TYK2)." J. Biol. Chem. 2015 Nov 6 ;290(45):27261-70 link

  9. Pratt AJ, DiDonato M, Shin DS, Cabelli DE, Bruns CK, Belzer CA, Gorringe AR, Langford PR, Tabatabai LB, Kroll JS, Tainer JA, Getzoff ED. "Structural, Functional, and Immunogenic Insights on Cu,Zn Superoxide Dismutase Pathogenic Virulence Factors from Neisseria meningitidis and Brucella abortus." J. Bacteriol. 2015 Dec 15 ;197(24):3834-47 link

  10. Sauvé V, Lilov A, Seirafi M, Vranas M, Rasool S, Kozlov G, Sprules T, Wang J, Trempe JF, Gehring K. "A Ubl/ubiquitin switch in the activation of Parkin." EMBO J. 2015 Oct 14 ;34(20)link

  11. Musayev FN, Zarate-Perez F, Bardelli M, Bishop C, Saniev EF, Linden RM, Henckaerts E, Escalante CR. "Structural Studies of AAV2 Rep68 Reveal a Partially Structured Linker and Compact Domain Conformation." Biochemistry 2015 Sep 29 ;54(38):5907-19 link

  12. Remesh SG, Santosh V, Escalante CR. "Structural Studies of IRF4 Reveal a Flexible Autoinhibitory Region and a Compact Linker Domain." J. Biol. Chem. 2015 Sep 24 link

  13. Meller S, Di Domizio J, Voo KS, Friedrich HC, Chamilos G, Ganguly D, Conrad C, Gregorio J, Le Roy D, Roger T, Ladbury JE, Homey B, Watowich S, Modlin RL, Kontoyiannis DP, Liu YJ, Arold ST, Gilliet M. "T(H)17 cells promote microbial killing and innate immune sensing of DNA via interleukin 26." Nat. Immunol. 2015 Sep ;16(9):970-9 link

  14. Brehove M, Wang T, North J, Luo Y, Dreher SJ, Shimko JC, Ottesen JJ, Luger K, Poirier MG. "Histone Core Phosphorylation Regulates DNA Accessibility." J. Biol. Chem. 2015 Sep 11 ;290(37):22612-21 link

  15. Luo M, Tanner JJ. "Structural Basis of Substrate Recognition by Aldehyde Dehydrogenase 7A1." Biochemistry 2015 Sep 8 ;54(35):5513-22 link

  16. Tsai CL, Williams GJ, Perry JJ, Tainer JA. "An AAA+ ATPase Clamshell Targets Transposition." Cell 2015 Aug 13 ;162(4):701-3 link

  17. He W, Scharadin TM, Saldana M, Gellner C, Hoang-Phou S, Takanishi C, Hura GL, Tainer JA, Carraway Iii KL, Henderson PT, Coleman MA. "Cell-free expression of functional receptor tyrosine kinases." Sci Rep 2015 ;5:12896 link

  18. Lin L, Gopal S, Sharda A, Passam F, Bowley SR, Stopa J, Xue G, Yuan C, Furie BC, Flaumenhaft R, Huang M, Furie B. "Quercetin-3-rutinoside Inhibits Protein Disulfide Isomerase by Binding to Its b'x Domain." J. Biol. Chem. 2015 Sep 25 ;290(39):23543-52 link

  19. Behera RK, Torres R, Tosha T, Bradley JM, Goulding CW, Theil EC. "Fe(2+) substrate transport through ferritin protein cage ion channels influences enzyme activity and biomineralization." J. Biol. Inorg. Chem. 2015 Sep ;20(6)link

  20. Schumacher MA, Tonthat NK, Lee J, Rodriguez-Castañeda FA, Chinnam NB, Kalliomaa-Sanford AK, Ng IW, Barge MT, Shaw PL, Barillà D. "Structures of archaeal DNA segregation machinery reveal bacterial and eukaryotic linkages." Science 2015 Sep 04 ;349(6252)link

  21. Fan H, Hahm J, Diggs S, Perry JJ, Blaha G. "Structural and Functional Analysis of BipA, a Regulator of Virulence in Enteropathogenic Escherichia coli." J. Biol. Chem. 2015 Aug 21 ;290(34):20856-64 link

  22. Gupta K, Martin R, Sharp R, Sarachan KL, Ninan NS, Van Duyne GD. "Oligomeric Properties of Survival Motor Neuron·Gemin2 Complexes." J. Biol. Chem. 2015 Aug 14 ;290(33):20185-99 link

  23. Zhang ZM, Liu S, Lin K, Luo Y, Perry JJ, Wang Y, Song J. "Crystal Structure of Human DNA Methyltransferase 1." J. Mol. Biol. 2015 Jul 31 ;427(15):2520-31 link

  24. Tan TC, Kracher D, Gandini R, Sygmund C, Kittl R, Haltrich D, Hällberg BM, Ludwig R, Divne C. "Structural basis for cellobiose dehydrogenase action during oxidative cellulose degradation." Nat Commun 2015 ;6:7542 link

  25. Hilbert BJ, Hayes JA, Stone NP, Duffy CM, Sankaran B, Kelch BA. "Structure and mechanism of the ATPase that powers viral genome packaging." Proc. Natl. Acad. Sci. U.S.A. 2015 Jul 21 ;112(29):E3792-9 link

  26. Hodge CD, Edwards RA, Markin CJ, McDonald D, Pulvino M, Huen MS, Zhao J, Spyracopoulos L, Hendzel MJ, Glover JN. "Covalent Inhibition of Ubc13 Affects Ubiquitin Signaling and Reveals Active Site Elements Important for Targeting." ACS Chem. Biol. 2015 Jul 17 ;10(7):1718-28 link

  27. Kukshal V, Kim IK, Hura GL, Tomkinson AE, Tainer JA, Ellenberger T. "Human DNA ligase III bridges two DNA ends to promote specific intermolecular DNA end joining." Nucleic Acids Res. 2015 Aug 18 ;43(14):7021-31 link

  28. Tsutakawa SE, Tainer JA. "Bending Forks and Wagging Dogs--It's about the DNA 3' Tail." Mol. Cell 2015 Jun 18 ;58(6):972-3 link

  29. Ihms EC, Foster MP. "MESMER: minimal ensemble solutions to multiple experimental restraints." Bioinformatics 2015 Jun 15 ;31(12):1951-8 link

  30. Wasserman MR, Pulk A, Zhou Z, Altman RB, Zinder JC, Green KD, Garneau-Tsodikova S, Doudna Cate JH, Blanchard SC. "Chemically related 4,5-linked aminoglycoside antibiotics drive subunit rotation in opposite directions." Nat Commun 2015 ;6:7896 link

  31. Chen X, Kim IK, Honaker Y, Paudyal SC, Koh WK, Sparks M, Li S, Piwnica-Worms H, Ellenberger T, You Z. "14-3-3 proteins restrain the Exo1 nuclease to prevent overresection." J. Biol. Chem. 2015 May 8 ;290(19):12300-12 link

  32. Banerjee A, Tsai CL, Chaudhury P, Tripp P, Arvai AS, Ishida JP, Tainer JA, Albers SV. "FlaF Is a β-Sandwich Protein that Anchors the Archaellum in the Archaeal Cell Envelope by Binding the S-Layer Protein." Structure 2015 May 5 ;23(5):863-72 link

  33. Pascal JM, Ellenberger T. "The rise and fall of poly(ADP-ribose): An enzymatic perspective." DNA Repair (Amst.) 2015 Aug ;32:10-6 link

  34. Rambo RP, Tainer JA. "Modeling macromolecular motions by x-ray-scattering-constrained molecular dynamics." Biophys. J. 2015 May 19 ;108(10):2421-3 link

  35. Tang W, Li H, Doud EH, Chen Y, Choing S, Plaza C, Kelleher NL, Poulos TL, Silverman RB. "Mechanism of Inactivation of Neuronal Nitric Oxide Synthase by (S)-2-Amino-5-(2-(methylthio)acetimidamido)pentanoic Acid." J. Am. Chem. Soc. 2015 May 13 ;137(18):5980-9 link

  36. Köfinger J, Ragusa MJ, Lee IH, Hummer G, Hurley JH. "Solution structure of the Atg1 complex: implications for the architecture of the phagophore assembly site." Structure 2015 May 5 ;23(5):809-18 link

  37. Topolska-Woś AM, Shell SM, Kilańczyk E, Szczepanowski RH, Chazin WJ, Filipek A. "Dimerization and phosphatase activity of calcyclin-binding protein/Siah-1 interacting protein: the influence of oxidative stress." FASEB J. 2015 May ;29(5)link

  38. Tsutakawa SE, Yan C, Xu X, Weinacht CP, Freudenthal BD, Yang K, Zhuang Z, Washington MT, Tainer JA, Ivanov I. "Structurally distinct ubiquitin- and sumo-modified PCNA: implications for their distinct roles in the DNA damage response." Structure 2015 Apr 7 ;23(4):724-33 link

  39. Tainer JA. "Dynamic structures in DNA damage responses & cancer." Prog. Biophys. Mol. Biol. 2015 Mar ;117(2-3):129-33 link

  40. McMillan BJ, Schnute B, Ohlenhard N, Zimmerman B, Miles L, Beglova N, Klein T, Blacklow SC. "A tail of two sites: a bipartite mechanism for recognition of notch ligands by mind bomb E3 ligases." Mol. Cell 2015 Mar 5 ;57(5):912-24 link

  41. Walker RG, Angerman EB, Kattamuri C, Lee YS, Lee SJ, Thompson TB. "Alternative binding modes identified for growth and differentiation factor-associated serum protein (GASP) family antagonism of myostatin." J. Biol. Chem. 2015 Mar 20 ;290(12):7506-16 link

  42. Cai F, Dou Z, Bernstein SL, Leverenz R, Williams EB, Heinhorst S, Shively J, Cannon GC, Kerfeld CA. "Advances in Understanding Carboxysome Assembly in Prochlorococcus and Synechococcus Implicate CsoS2 as a Critical Component." Life (Basel) 2015 Mar 27 ;5(2)link

  43. Andres SN, Appel CD, Westmoreland JW, Williams JS, Nguyen Y, Robertson PD, Resnick MA, Williams RS. "Tetrameric Ctp1 coordinates DNA binding and DNA bridging in DNA double-strand-break repair." Nat. Struct. Mol. Biol. 2015 Feb ;22(2):158-66 link

  44. Schumacher MA, Chinnam NB, Cuthbert B, Tonthat NK, Whitfill T. "Structures of regulatory machinery reveal novel molecular mechanisms controlling B. subtilis nitrogen homeostasis." Genes Dev. 2015 Feb 15 ;29(4):451-64 link

  45. Hashiguchi T, Fusco ML, Bornholdt ZA, Lee JE, Flyak AI, Matsuoka R, Kohda D, Yanagi Y, Hammel M, Crowe JE, Saphire EO. "Structural basis for marburg virus neutralization by a cross-reactive human antibody." Cell 2015 Feb 26 ;160(5):904-12 link

  46. Fuss JO, Tsai CL, Ishida JP, Tainer JA. "Emerging critical roles of Fe-S clusters in DNA replication and repair." Biochim. Biophys. Acta 2015 Jun ;1853(6):1253-71 link

  47. Cheguru P, Majumder A, Yadav R, Gopalakrishna KN, Gakhar L, Artemyev NO. "The solution structure of the transducin-α-uncoordinated 119 protein complex suggests occlusion of the Gβ₁γ₁-binding sites." FEBS J. 2015 Feb ;282(3)link

  48. White MR, Khan MM, Deredge D, Ross CR, Quintyn R, Zucconi BE, Wysocki VH, Wintrode PL, Wilson GM, Garcin ED. "A dimer interface mutation in glyceraldehyde-3-phosphate dehydrogenase regulates its binding to AU-rich RNA." J. Biol. Chem. 2015 Jan 16 ;290(3):1770-85 link

  49. Lafrance-Vanasse J, Williams GJ, Tainer JA. "Envisioning the dynamics and flexibility of Mre11-Rad50-Nbs1 complex to decipher its roles in DNA replication and repair." Prog. Biophys. Mol. Biol. 2015 Jan 7 link

2014

  1. Muia J, Zhu J, Gupta G, Haberichter SL, Friedman KD, Feys HB, Deforche L, Vanhoorelbeke K, Westfield LA, Roth R, Tolia NH, Heuser JE, Sadler JE. "Allosteric activation of ADAMTS13 by von Willebrand factor." Proc. Natl. Acad. Sci. U.S.A. 2014 Dec 30 ;111(52)link

  2. Partridge JR, Lavery LA, Elnatan D, Naber N, Cooke R, Agard DA. "A novel N-terminal extension in mitochondrial TRAP1 serves as a thermal regulator of chaperone activity." Elife 2014 ;3link

  3. Reyes FE, Schwartz CR, Tainer JA, Rambo RP. "Methods for using new conceptual tools and parameters to assess RNA structure by small-angle X-ray scattering." Meth. Enzymol. 2014 ;549:235-63 link

  4. Lai YT, Reading E, Hura GL, Tsai KL, Laganowsky A, Asturias FJ, Tainer JA, Robinson CV, Yeates TO. "Structure of a designed protein cage that self-assembles into a highly porous cube." Nat Chem 2014 Dec ;6(12):1065-71 link

  5. Kim SJ, Fernandez-Martinez J, Sampathkumar P, Martel A, Matsui T, Tsuruta H, Weiss TM, Shi Y, Markina-Inarrairaegui A, Bonanno JB, Sauder JM, Burley SK, Chait BT, Almo SC, Rout MP, Sali A. "Integrative structure-function mapping of the nucleoporin Nup133 suggests a conserved mechanism for membrane anchoring of the nuclear pore complex." Mol. Cell Proteomics 2014 Nov ;13(11):2911-26 link

  6. Peng Y, Lu J, Wong JJ, Edwards RA, Frost LS, Mark Glover JN. "Mechanistic basis of plasmid-specific DNA binding of the F plasmid regulatory protein, TraM." J. Mol. Biol. 2014 Nov 11 ;426(22):3783-95 link

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2013

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2012

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  24. 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

  25. 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

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  27. 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

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2011

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  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. 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

  9. 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

  10. 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

  11. 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

  12. 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

  13. 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

  14. 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

  15. 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

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  17. 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

  18. 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

  19. 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

  20. 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

  21. 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

  22. 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

  23. 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

  24. 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

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

  26. 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

  27. 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

  28. 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

  29. 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

  30. 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

  31. 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

  32. 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

  33. 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

  34. 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

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  37. 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

  38. 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

  39. 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

  40. 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

  41. 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

  42. 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

  43. 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. 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

  8. 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

  9. 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

  10. 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

  11. 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

  12. 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

  13. 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

  14. 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

  15. 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

  16. 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

  17. 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

  18. 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

  19. 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

  20. 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

  21. 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

  22. 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

  23. 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

  24. 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

  25. 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

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  6. 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

  7. 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

  8. 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

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

  10. 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

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  12. 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

  13. 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

  14. 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

  15. 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

  16. 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

  17. 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

  18. 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

  19. 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

  20. 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

  21. 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

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

  23. 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

  24. 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

  25. 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

  26. 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

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  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. 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.

  15. 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

  16. 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.

  17. 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. 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

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

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

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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.