Loading...
Header Logo
Keywords
Last Name
Institution

JOHN TAINER

TitleProfessor
InstitutionMD Anderson
DepartmentMolecular & Cellular Oncology
vCardDownload vCard

    Collapse ORNG Applications 
    Collapse Verify Publications

    Collapse Bibliographic 
    Collapse selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
    List All   |   Timeline
    1. Zhang H, Chen Z, Ye Y, Ye Z, Cao D, Xiong Y, Srivastava M, Feng X, Tang M, Wang C, Tainer JA, Chen J. SLX4IP acts with SLX4 and XPF-ERCC1 to promote interstrand crosslink repair. Nucleic Acids Res. 2019 Sep 09. PMID: 31495888.
      View in: PubMed
    2. Bacolla A, Tainer JA. DNA damage response mechanisms and structures fundamental to cancer research progress. Prog Biophys Mol Biol. 2019 Aug 27. PMID: 31470026.
      View in: PubMed
    3. Zhou Y, Millott R, Kim HJ, Peng S, Edwards RA, Skene-Arnold T, Hammel M, Lees-Miller SP, Tainer JA, Holmes CFB, Glover JNM. Flexible Tethering of ASPP Proteins Facilitates PP-1c Catalysis. Structure. 2019 Oct 01; 27(10):1485-1496.e4. PMID: 31402222.
      View in: PubMed
    4. Brosey CA, Tainer JA. Evolving SAXS versatility: solution X-ray scattering for macromolecular architecture, functional landscapes, and integrative structural biology. Curr Opin Struct Biol. 2019 Oct; 58:197-213. PMID: 31204190.
      View in: PubMed
    5. Yan C, Dodd T, He Y, Tainer JA, Tsutakawa SE, Ivanov I. Transcription preinitiation complex structure and dynamics provide insight into genetic diseases. Nat Struct Mol Biol. 2019 Jun; 26(6):397-406. PMID: 31110295.
      View in: PubMed
    6. Bacolla A, Ye Z, Ahmed Z, Tainer JA. Cancer mutational burden is shaped by G4 DNA, replication stress and mitochondrial dysfunction. Prog Biophys Mol Biol. 2019 Mar 14. PMID: 30880007.
      View in: PubMed
    7. Appel MJ, Meier KK, Lafrance-Vanasse J, Lim H, Tsai CL, Hedman B, Hodgson KO, Tainer JA, Solomon EI, Bertozzi CR. Formylglycine-generating enzyme binds substrate directly at a mononuclear Cu(I) center to initiate O2 activation. Proc Natl Acad Sci U S A. 2019 03 19; 116(12):5370-5375. PMID: 30824597.
      View in: PubMed
    8. Syed A, Tainer JA. Charge Transport Communication through DNA by Protein Fe-S Clusters: How Far Is Not Too Far? ACS Cent Sci. 2019 Jan 23; 5(1):7-9. PMID: 30693320.
      View in: PubMed
    9. Tang HYH, Shin DS, Hura GL, Yang Y, Hu X, Lightstone FC, McGee MD, Padgett HS, Yannone SM, Tainer JA. Structural Control of Nonnative Ligand Binding in Engineered Mutants of Phosphoenolpyruvate Carboxykinase. Biochemistry. 2018 12 04; 57(48):6688-6700. PMID: 30376300.
      View in: PubMed
    10. Thapar R, Bacolla A, Oyeniran C, Brickner JR, Chinnam NB, Mosammaparast N, Tainer JA. RNA Modifications: Reversal Mechanisms and Cancer. Biochemistry. 2019 02 05; 58(5):312-329. PMID: 30346748.
      View in: PubMed
    11. Guo HF, Tsai CL, Terajima M, Tan X, Banerjee P, Miller MD, Liu X, Yu J, Byemerwa J, Alvarado S, Kaoud TS, Dalby KN, Bota-Rabassedas N, Chen Y, Yamauchi M, Tainer JA, Phillips GN, Kurie JM. Author Correction: Pro-metastatic collagen lysyl hydroxylase dimer assemblies stabilized by Fe2+-binding. Nat Commun. 2018 07 10; 9(1):2719. PMID: 29988035.
      View in: PubMed
    12. Wang JL, Duboc C, Wu Q, Ochi T, Liang S, Tsutakawa SE, Lees-Miller SP, Nadal M, Tainer JA, Blundell TL, Strick TR. Dissection of DNA double-strand-break repair using novel single-molecule forceps. Nat Struct Mol Biol. 2018 06; 25(6):482-487. PMID: 29786079.
      View in: PubMed
    13. Syed A, Tainer JA. The MRE11-RAD50-NBS1 Complex Conducts the Orchestration of Damage Signaling and Outcomes to Stress in DNA Replication and Repair. Annu Rev Biochem. 2018 06 20; 87:263-294. PMID: 29709199.
      View in: PubMed
    14. Moiani D, Ronato DA, Brosey CA, Arvai AS, Syed A, Masson JY, Petricci E, Tainer JA. Targeting Allostery with Avatars to Design Inhibitors Assessed by Cell Activity: Dissecting MRE11 Endo- and Exonuclease Activities. Methods Enzymol. 2018; 601:205-241. PMID: 29523233.
      View in: PubMed
    15. Ogorzalek TL, Hura GL, Belsom A, Burnett KH, Kryshtafovych A, Tainer JA, Rappsilber J, Tsutakawa SE, Fidelis K. Small angle X-ray scattering and cross-linking for data assisted protein structure prediction in CASP 12 with prospects for improved accuracy. Proteins. 2018 03; 86 Suppl 1:202-214. PMID: 29314274.
      View in: PubMed
    16. Guo HF, Tsai CL, Terajima M, Tan X, Banerjee P, Miller MD, Liu X, Yu J, Byemerwa J, Alvarado S, Kaoud TS, Dalby KN, Bota-Rabassedas N, Chen Y, Yamauchi M, Tainer JA, Phillips GN, Kurie JM. Pro-metastatic collagen lysyl hydroxylase dimer assemblies stabilized by Fe2+-binding. Nat Commun. 2018 02 06; 9(1):512. PMID: 29410444.
      View in: PubMed
    17. Tsai CL, Tainer JA. Robust Production, Crystallization, Structure Determination, and Analysis of [Fe-S] Proteins: Uncovering Control of Electron Shuttling and Gating in the Respiratory Metabolism of Molybdopterin Guanine Dinucleotide Enzymes. Methods Enzymol. 2018; 599:157-196. PMID: 29746239.
      View in: PubMed
    18. Hura GL, Tainer JA. Coiled coils unspring protein origami. Nat Biotechnol. 2017 11 09; 35(11):1044-1045. PMID: 29121029.
      View in: PubMed
    19. Trewhella J, Duff AP, Durand D, Gabel F, Guss JM, Hendrickson WA, Hura GL, Jacques DA, Kirby NM, Kwan AH, Pérez J, Pollack L, Ryan TM, Sali A, Schneidman-Duhovny D, Schwede T, Svergun DI, Sugiyama M, Tainer JA, Vachette P, Westbrook J, Whitten AE. 2017 publication guidelines for structural modelling of small-angle scattering data from biomolecules in solution: an update. Acta Crystallogr D Struct Biol. 2017 Sep 01; 73(Pt 9):710-728. PMID: 28876235.
      View in: PubMed
    20. Tsutakawa SE, Thompson MJ, Arvai AS, Neil AJ, Shaw SJ, Algasaier SI, Kim JC, Finger LD, Jardine E, Gotham VJB, Sarker AH, Her MZ, Rashid F, Hamdan SM, Mirkin SM, Grasby JA, Tainer JA. Corrigendum: Phosphate steering by Flap Endonuclease 1 promotes 5'-flap specificity and incision to prevent genome instability. Nat Commun. 2017; 8:16145. PMID: 31305777.
      View in: PubMed
    21. Tainer JA. Uncovering the secrets of protein interactions with the DNA enforcing genomic stability. Prog Biophys Mol Biol. 2017 08; 127:89-92. PMID: 28709479.
      View in: PubMed
    22. Tsutakawa SE, Thompson MJ, Arvai AS, Neil AJ, Shaw SJ, Algasaier SI, Kim JC, Finger LD, Jardine E, Gotham VJB, Sarker AH, Her MZ, Rashid F, Hamdan SM, Mirkin SM, Grasby JA, Tainer JA. Phosphate steering by Flap Endonuclease 1 promotes 5'-flap specificity and incision to prevent genome instability. Nat Commun. 2017 06 27; 8:15855. PMID: 28653660.
      View in: PubMed
    23. 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 Jun 02; 45(10):6238-6251. PMID: 28453785.
      View in: PubMed
    24. Brosey CA, Ahmed Z, Lees-Miller SP, Tainer JA. What Combined Measurements From Structures and Imaging Tell Us About DNA Damage Responses. Methods Enzymol. 2017; 592:417-455. PMID: 28668129.
      View in: PubMed
    25. Gradia SD, Ishida JP, Tsai MS, Jeans C, Tainer JA, Fuss JO. MacroBac: New Technologies for Robust and Efficient Large-Scale Production of Recombinant Multiprotein Complexes. Methods Enzymol. 2017; 592:1-26. PMID: 28668116.
      View in: PubMed
    26. Dutta A, Eckelmann B, Adhikari S, Ahmed KM, Sengupta S, Pandey A, Hegde PM, Tsai MS, Tainer JA, Weinfeld M, Hegde ML, Mitra S. Microhomology-mediated end joining is activated in irradiated human cells due to phosphorylation-dependent formation of the XRCC1 repair complex. Nucleic Acids Res. 2017 03 17; 45(5):2585-2599. PMID: 27994036.
      View in: PubMed
    27. Rashid F, Harris PD, Zaher MS, Sobhy MA, Joudeh LI, Yan C, Piwonski H, Tsutakawa SE, Ivanov I, Tainer JA, Habuchi S, Hamdan SM. Single-molecule FRET unveils induced-fit mechanism for substrate selectivity in flap endonuclease 1. Elife. 2017 02 23; 6. PMID: 28230529.
      View in: PubMed
    28. Wallen JR, Zhang H, Weis C, Cui W, Foster BM, Ho CMW, Hammel M, Tainer JA, Gross ML, Ellenberger T. Hybrid Methods Reveal Multiple Flexibly Linked DNA Polymerases within the Bacteriophage T7 Replisome. Structure. 2017 01 03; 25(1):157-166. PMID: 28052235.
      View in: PubMed
    29. Tang HYH, Tainer JA, Hura GL. High Resolution Distance Distributions Determined by X-Ray and Neutron Scattering. Adv Exp Med Biol. 2017; 1009:167-181. PMID: 29218559.
      View in: PubMed
    30. Lai YT, Hura GL, Dyer KN, Tang HY, Tainer JA, Yeates TO. Designing and defining dynamic protein cage nanoassemblies in solution. Sci Adv. 2016 12; 2(12):e1501855. PMID: 27990489.
      View in: PubMed
    31. 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 12 30; 291(53):26987-27006. PMID: 27875301.
      View in: PubMed
    32. 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 12 06; 24(12):2067-2079. PMID: 27818101.
      View in: PubMed
    33. Tsai CL, Tainer JA. The ATPase Motor Turns for Type IV Pilus Assembly. Structure. 2016 11 01; 24(11):1857-1859. PMID: 27806257.
      View in: PubMed
    34. Stingele J, Bellelli R, Alte F, Hewitt G, Sarek G, Maslen SL, Tsutakawa SE, Borg A, Kjær S, Tainer JA, Skehel JM, Groll M, Boulton SJ. Mechanism and Regulation of DNA-Protein Crosslink Repair by the DNA-Dependent Metalloprotease SPRTN. Mol Cell. 2016 11 17; 64(4):688-703. PMID: 27871365.
      View in: PubMed
    35. Susa AC, Xia Z, Tang HYH, Tainer JA, Williams ER. Charging of Proteins in Native Mass Spectrometry. J Am Soc Mass Spectrom. 2017 02; 28(2):332-340. PMID: 27734326.
      View in: PubMed
    36. 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 07; 2(7):e1600650. PMID: 27482541.
      View in: PubMed
    37. Lees-Miller SP, Beattie TL, Tainer JA. Noncoding RNA joins Ku and DNA-PKcs for DNA-break resistance in breast cancer. Nat Struct Mol Biol. 2016 06 07; 23(6):509-10. PMID: 27273637.
      View in: PubMed
    38. 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 08; 44(W1):W424-9. PMID: 27151198.
      View in: PubMed
    39. Bacolla A, Tainer JA, Vasquez KM, Cooper DN. Translocation and deletion breakpoints in cancer genomes are associated with potential non-B DNA-forming sequences. Nucleic Acids Res. 2016 07 08; 44(12):5673-88. PMID: 27084947.
      View in: PubMed
    40. Deshpande RA, Williams GJ, Limbo O, Williams RS, Kuhnlein J, Lee JH, Classen S, Guenther G, Russell P, Tainer JA, Paull TT. ATP-driven Rad50 conformations regulate DNA tethering, end resection, and ATM checkpoint signaling. EMBO J. 2016 Apr 01; 35(7):791. PMID: 27037288.
      View in: PubMed
    41. 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. PMID: 26940877.
      View in: PubMed
    42. 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. PMID: 26903517.
      View in: PubMed
    43. 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. PMID: 26675729.
      View in: PubMed
    44. 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. PMID: 26508112.
      View in: PubMed
    45. Shin DS, Tainer JA. Molecular biology: DNA repair without flipping out. Nature. 2015 Nov 12; 527(7577):168-9. PMID: 26524524.
      View in: PubMed
    46. 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; 197(24):3834-47. PMID: 26459556.
      View in: PubMed
    47. He W, Scharadin TM, Saldana M, Gellner C, Hoang-Phou S, Takanishi C, Hura GL, Tainer JA, Carraway KL, Henderson PT, Coleman MA. Cell-free expression of functional receptor tyrosine kinases. Sci Rep. 2015 Aug 14; 5:12896. PMID: 26274523.
      View in: PubMed
    48. Tsai CL, Williams GJ, Perry JJ, Tainer JA. An AAA+ ATPase Clamshell Targets Transposition. Cell. 2015 Aug 13; 162(4):701-3. PMID: 26276624.
      View in: PubMed
    49. 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. PMID: 26130724.
      View in: PubMed
    50. 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. PMID: 26091346.
      View in: PubMed
    51. Rambo RP, Tainer JA. Modeling macromolecular motions by x-ray-scattering-constrained molecular dynamics. Biophys J. 2015 May 19; 108(10):2421-2423. PMID: 25992719.
      View in: PubMed
    52. Banerjee A, Tsai CL, Chaudhury P, Tripp P, Arvai AS, Ishida JP, Tainer JA, Albers SV. FlaF Is a ß-Sandwich Protein that Anchors the Archaellum in the Archaeal Cell Envelope by Binding the S-Layer Protein. Structure. 2015 May 05; 23(5):863-872. PMID: 25865246.
      View in: PubMed
    53. 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 07; 23(4):724-733. PMID: 25773143.
      View in: PubMed
    54. Tainer JA. Dynamic structures in DNA damage responses & cancer. Prog Biophys Mol Biol. 2015 Mar; 117(2-3):129-133. PMID: 25934179.
      View in: PubMed
    55. 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. PMID: 25655665.
      View in: PubMed
    56. 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 Mar; 117(2-3):182-193. PMID: 25576492.
      View in: PubMed
    57. Tsai CL, Burkinshaw BJ, Strynadka NC, Tainer JA. The Salmonella type III secretion system virulence effector forms a new hexameric chaperone assembly for export of effector/chaperone complexes. J Bacteriol. 2015 Feb 15; 197(4):672-5. PMID: 25488302.
      View in: PubMed
    58. 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. PMID: 25411884.
      View in: PubMed
    59. Pratt AJ, Shin DS, Merz GE, Rambo RP, Lancaster WA, Dyer KN, Borbat PP, Poole FL, Adams MW, Freed JH, Crane BR, Tainer JA, Getzoff ED. Aggregation propensities of superoxide dismutase G93 hotspot mutants mirror ALS clinical phenotypes. Proc Natl Acad Sci U S A. 2014 Oct 28; 111(43):E4568-76. PMID: 25316790.
      View in: PubMed
    60. Holton JM, Classen S, Frankel KA, Tainer JA. The R-factor gap in macromolecular crystallography: an untapped potential for insights on accurate structures. FEBS J. 2014 Sep; 281(18):4046-60. PMID: 25040949.
      View in: PubMed
    61. Tsai CL, Shi Y, Tainer JA. How substrate specificity is imposed on a histone demethylase--lessons from KDM2A. Genes Dev. 2014 Aug 15; 28(16):1735-8. PMID: 25128493.
      View in: PubMed
    62. McTernan PM, Chandrayan SK, Wu CH, Vaccaro BJ, Lancaster WA, Yang Q, Fu D, Hura GL, Tainer JA, Adams MW. Intact functional fourteen-subunit respiratory membrane-bound [NiFe]-hydrogenase complex of the hyperthermophilic archaeon Pyrococcus furiosus. J Biol Chem. 2014 Jul 11; 289(28):19364-72. PMID: 24860091.
      View in: PubMed
    63. Mason AC, Rambo RP, Greer B, Pritchett M, Tainer JA, Cortez D, Eichman BF. A structure-specific nucleic acid-binding domain conserved among DNA repair proteins. Proc Natl Acad Sci U S A. 2014 May 27; 111(21):7618-23. PMID: 24821763.
      View in: PubMed
    64. Tsutakawa SE, Lafrance-Vanasse J, Tainer JA. The cutting edges in DNA repair, licensing, and fidelity: DNA and RNA repair nucleases sculpt DNA to measure twice, cut once. DNA Repair (Amst). 2014 Jul; 19:95-107. PMID: 24754999.
      View in: PubMed
    65. Groocock LM, Nie M, Prudden J, Moiani D, Wang T, Cheltsov A, Rambo RP, Arvai AS, Hitomi C, Tainer JA, Luger K, Perry JJ, Lazzerini-Denchi E, Boddy MN. RNF4 interacts with both SUMO and nucleosomes to promote the DNA damage response. EMBO Rep. 2014 May; 15(5):601-8. PMID: 24714598.
      View in: PubMed
    66. Seeger F, Quintyn R, Tanimoto A, Williams GJ, Tainer JA, Wysocki VH, Garcin ED. Interfacial residues promote an optimal alignment of the catalytic center in human soluble guanylate cyclase: heterodimerization is required but not sufficient for activity. Biochemistry. 2014 Apr 08; 53(13):2153-65. PMID: 24669844.
      View in: PubMed
    67. Williams GJ, Hammel M, Radhakrishnan SK, Ramsden D, Lees-Miller SP, Tainer JA. Structural insights into NHEJ: building up an integrated picture of the dynamic DSB repair super complex, one component and interaction at a time. DNA Repair (Amst). 2014 May; 17:110-20. PMID: 24656613.
      View in: PubMed
    68. Shin DS, Pratt AJ, Tainer JA. Archaeal genome guardians give insights into eukaryotic DNA replication and damage response proteins. Archaea. 2014; 2014:206735. PMID: 24701133.
      View in: PubMed
    69. Roset R, Inagaki A, Hohl M, Brenet F, Lafrance-Vanasse J, Lange J, Scandura JM, Tainer JA, Keeney S, Petrini JH. The Rad50 hook domain regulates DNA damage signaling and tumorigenesis. Genes Dev. 2014 Mar 01; 28(5):451-62. PMID: 24532689.
      View in: PubMed
    70. Deshpande RA, Williams GJ, Limbo O, Williams RS, Kuhnlein J, Lee JH, Classen S, Guenther G, Russell P, Tainer JA, Paull TT. ATP-driven Rad50 conformations regulate DNA tethering, end resection, and ATM checkpoint signaling. EMBO J. 2014 Mar 03; 33(5):482-500. PMID: 24493214.
      View in: PubMed
    71. Dyer KN, Hammel M, Rambo RP, Tsutakawa SE, Rodic I, Classen S, Tainer JA, Hura GL. High-throughput SAXS for the characterization of biomolecules in solution: a practical approach. Methods Mol Biol. 2014; 1091:245-58. PMID: 24203338.
      View in: PubMed
    72. 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. Methods Enzymol. 2014; 549:235-63. PMID: 25432752.
      View in: PubMed
    73. Tsai CL, Tainer JA. Probing DNA by 2-OG-dependent dioxygenase. Cell. 2013 Dec 19; 155(7):1448-50. PMID: 24360270.
      View in: PubMed
    74. Shibata A, Moiani D, Arvai AS, Perry J, Harding SM, Genois MM, Maity R, van Rossum-Fikkert S, Kertokalio A, Romoli F, Ismail A, Ismalaj E, Petricci E, Neale MJ, Bristow RG, Masson JY, Wyman C, Jeggo PA, Tainer JA. DNA double-strand break repair pathway choice is directed by distinct MRE11 nuclease activities. Mol Cell. 2014 Jan 09; 53(1):7-18. PMID: 24316220.
      View in: PubMed
    75. Pieper U, Webb BM, Dong GQ, Schneidman-Duhovny D, Fan H, Kim SJ, Khuri N, Spill YG, Weinkam P, Hammel M, Tainer JA, Nilges M, Sali A. ModBase, a database of annotated comparative protein structure models and associated resources. Nucleic Acids Res. 2014 Jan; 42(Database issue):D336-46. PMID: 24271400.
      View in: PubMed
    76. Crown KN, Savytskyy OP, Malik SB, Logsdon J, Williams RS, Tainer JA, Zolan ME. A mutation in the FHA domain of Coprinus cinereus Nbs1 Leads to Spo11-independent meiotic recombination and chromosome segregation. G3 (Bethesda). 2013 Nov 06; 3(11):1927-43. PMID: 24062528.
      View in: PubMed
    77. Zhao W, Saro D, Hammel M, Kwon Y, Xu Y, Rambo RP, Williams GJ, Chi P, Lu L, Pezza RJ, Camerini-Otero RD, Tainer JA, Wang HW, Sung P. Mechanistic insights into the role of Hop2-Mnd1 in meiotic homologous DNA pairing. Nucleic Acids Res. 2014 Jan; 42(2):906-17. PMID: 24150939.
      View in: PubMed
    78. Hura GL, Tsai CL, Claridge SA, Mendillo ML, Smith JM, Williams GJ, Mastroianni AJ, Alivisatos AP, Putnam CD, Kolodner RD, Tainer JA. DNA conformations in mismatch repair probed in solution by X-ray scattering from gold nanocrystals. Proc Natl Acad Sci U S A. 2013 Oct 22; 110(43):17308-13. PMID: 24101514.
      View in: PubMed
    79. Liu X, Hammel M, He Y, Tainer JA, Jeng US, Zhang L, Wang S, Wang X. Structural insights into the interaction of IL-33 with its receptors. Proc Natl Acad Sci U S A. 2013 Sep 10; 110(37):14918-23. PMID: 23980170.
      View in: PubMed
    80. Schneidman-Duhovny D, Hammel M, Tainer JA, Sali A. Accurate SAXS profile computation and its assessment by contrast variation experiments. Biophys J. 2013 Aug 20; 105(4):962-74. PMID: 23972848.
      View in: PubMed
    81. Trewhella J, Hendrickson WA, Kleywegt GJ, Sali A, Sato M, Schwede T, Svergun DI, Tainer JA, Westbrook J, Berman HM. Report of the wwPDB Small-Angle Scattering Task Force: data requirements for biomolecular modeling and the PDB. Structure. 2013 Jun 04; 21(6):875-81. PMID: 23747111.
      View in: PubMed
    82. Hura GL, Budworth H, Dyer KN, Rambo RP, Hammel M, McMurray CT, Tainer JA. Comprehensive macromolecular conformations mapped by quantitative SAXS analyses. Nat Methods. 2013 Jun; 10(6):453-4. PMID: 23624664.
      View in: PubMed
    83. Rambo RP, Tainer JA. Accurate assessment of mass, models and resolution by small-angle scattering. Nature. 2013 Apr 25; 496(7446):477-81. PMID: 23619693.
      View in: PubMed
    84. Hegde ML, Tsutakawa SE, Hegde PM, Holthauzen LM, Li J, Oezguen N, Hilser VJ, Tainer JA, Mitra S. The disordered C-terminal domain of human DNA glycosylase NEIL1 contributes to its stability via intramolecular interactions. J Mol Biol. 2013 Jul 10; 425(13):2359-71. PMID: 23542007.
      View in: PubMed
    85. Rambo RP, Tainer JA. Super-resolution in solution X-ray scattering and its applications to structural systems biology. Annu Rev Biophys. 2013; 42:415-41. PMID: 23495971.
      View in: PubMed
    86. Reindl S, Ghosh A, Williams GJ, Lassak K, Neiner T, Henche AL, Albers SV, Tainer JA. Insights into FlaI functions in archaeal motor assembly and motility from structures, conformations, and genetics. Mol Cell. 2013 Mar 28; 49(6):1069-82. PMID: 23416110.
      View in: PubMed
    87. Mahaney BL, Hammel M, Meek K, Tainer JA, Lees-Miller SP. XRCC4 and XLF form long helical protein filaments suitable for DNA end protection and alignment to facilitate DNA double strand break repair. Biochem Cell Biol. 2013 Feb; 91(1):31-41. PMID: 23442139.
      View in: PubMed
    88. Perry JJ, Tainer JA. Developing advanced X-ray scattering methods combined with crystallography and computation. Methods. 2013 Mar; 59(3):363-71. PMID: 23376408.
      View in: PubMed
    89. 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/apyrimidinic endonuclease APE1 and endonuclease IV DNA repair enzymes. J Biol Chem. 2013 Mar 22; 288(12):8445-55. PMID: 23355472.
      View in: PubMed
    90. Classen S, Hura GL, Holton JM, Rambo RP, Rodic I, McGuire PJ, Dyer K, Hammel M, Meigs G, Frankel KA, Tainer JA. Implementation and performance of SIBYLS: a dual endstation small-angle X-ray scattering and macromolecular crystallography beamline at the Advanced Light Source. J Appl Crystallogr. 2013 Feb 01; 46(Pt 1):1-13. PMID: 23396808.
      View in: PubMed
    91. Brosey CA, Yan C, Tsutakawa SE, Heller WT, Rambo RP, Tainer JA, Ivanov I, Chazin WJ. A new structural framework for integrating replication protein A into DNA processing machinery. Nucleic Acids Res. 2013 Feb 01; 41(4):2313-27. PMID: 23303776.
      View in: PubMed
    92. Dalhus B, Nilsen L, Korvald H, Huffman J, Forstrøm RJ, McMurray CT, Alseth I, Tainer JA, Bjørås M. Sculpting of DNA at abasic sites by DNA glycosylase homolog mag2. Structure. 2013 Jan 08; 21(1):154-166. PMID: 23245849.
      View in: PubMed
    93. Wilkinson OJ, Latypov V, Tubbs JL, Millington CL, Morita R, Blackburn H, Marriott A, McGown G, Thorncroft M, Watson AJ, Connolly BA, Grasby JA, Masui R, Hunter CA, Tainer JA, Margison GP, Williams DM. Alkyltransferase-like protein (Atl1) distinguishes alkylated guanines for DNA repair using cation-p interactions. Proc Natl Acad Sci U S A. 2012 Nov 13; 109(46):18755-60. PMID: 23112169.
      View in: PubMed
    94. 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. PMID: 23104058.
      View in: PubMed
    95. Limbo O, Moiani D, Kertokalio A, Wyman C, Tainer JA, Russell P. Mre11 ATLD17/18 mutation retains Tel1/ATM activity but blocks DNA double-strand break repair. Nucleic Acids Res. 2012 Dec; 40(22):11435-49. PMID: 23080121.
      View in: PubMed
    96. Lee KC, Padget K, Curtis H, Cowell IG, Moiani D, Sondka Z, Morris NJ, Jackson GH, Cockell SJ, Tainer JA, Austin CA. MRE11 facilitates the removal of human topoisomerase II complexes from genomic DNA. Biol Open. 2012 Sep 15; 1(9):863-73. PMID: 23213480.
      View in: PubMed
    97. Omanakuttan A, Nambiar J, Harris RM, Bose C, Pandurangan N, Varghese RK, Kumar GB, Tainer JA, Banerji A, Perry JJ, Nair BG. Anacardic acid inhibits the catalytic activity of matrix metalloproteinase-2 and matrix metalloproteinase-9. Mol Pharmacol. 2012 Oct; 82(4):614-22. PMID: 22745359.
      View in: PubMed
    98. Latypov VF, Tubbs JL, Watson AJ, Marriott AS, McGown G, Thorncroft M, Wilkinson OJ, Senthong P, Butt A, Arvai AS, Millington CL, Povey AC, Williams DM, Santibanez-Koref MF, Tainer JA, Margison GP. Atl1 regulates choice between global genome and transcription-coupled repair of O(6)-alkylguanines. Mol Cell. 2012 Jul 13; 47(1):50-60. PMID: 22658721.
      View in: PubMed
    99. Kim IK, Kiefer JR, Ho CM, Stegeman RA, Classen S, Tainer JA, Ellenberger T. Structure of mammalian poly(ADP-ribose) glycohydrolase reveals a flexible tyrosine clasp as a substrate-binding element. Nat Struct Mol Biol. 2012 May 20; 19(6):653-6. PMID: 22609859.
      View in: PubMed
    100. Querol-Audí J, Yan C, Xu X, Tsutakawa SE, Tsai MS, Tainer JA, Cooper PK, Nogales E, Ivanov I. Repair complexes of FEN1 endonuclease, DNA, and Rad9-Hus1-Rad1 are distinguished from their PCNA counterparts by functionally important stability. Proc Natl Acad Sci U S A. 2012 May 29; 109(22):8528-33. PMID: 22586102.
      View in: PubMed
    101. Christie JM, Hitomi K, Arvai AS, Hartfield KA, Mettlen M, Pratt AJ, Tainer JA, Getzoff ED. Structural tuning of the fluorescent protein iLOV for improved photostability. J Biol Chem. 2012 Jun 22; 287(26):22295-304. PMID: 22573334.
      View in: PubMed
    102. Roberts VA, Pique ME, Hsu S, Li S, Slupphaug G, Rambo RP, Jamison JW, Liu T, Lee JH, Tainer JA, Ten Eyck LF, Woods VL. Combining H/D exchange mass spectroscopy and computational docking reveals extended DNA-binding surface on uracil-DNA glycosylase. Nucleic Acids Res. 2012 Jul; 40(13):6070-81. PMID: 22492624.
      View in: PubMed
    103. Ruigrok VJ, van Duijn E, Barendregt A, Dyer K, Tainer JA, Stoltenburg R, Strehlitz B, Levisson M, Smidt H, van der Oost J. Kinetic and stoichiometric characterisation of streptavidin-binding aptamers. Chembiochem. 2012 Apr 16; 13(6):829-36. PMID: 22416028.
      View in: PubMed
    104. Yamagata A, Milgotina E, Scanlon K, Craig L, Tainer JA, Donnenberg MS. Structure of an essential type IV pilus biogenesis protein provides insights into pilus and type II secretion systems. J Mol Biol. 2012 May 25; 419(1-2):110-24. PMID: 22387466.
      View in: PubMed
    105. Patel N, Atack JM, Finger LD, Exell JC, Thompson P, Tsutakawa S, Tainer JA, Williams DM, Grasby JA. Flap endonucleases pass 5'-flaps through a flexible arch using a disorder-thread-order mechanism to confer specificity for free 5'-ends. Nucleic Acids Res. 2012 May; 40(10):4507-19. PMID: 22319208.
      View in: PubMed
    106. Sontz PA, Mui TP, Fuss JO, Tainer JA, Barton JK. DNA charge transport as a first step in coordinating the detection of lesions by repair proteins. Proc Natl Acad Sci U S A. 2012 Feb 07; 109(6):1856-61. PMID: 22308447.
      View in: PubMed
    107. Tsutakawa SE, Tainer JA. Double strand binding-single strand incision mechanism for human flap endonuclease: implications for the superfamily. Mech Ageing Dev. 2012 Apr; 133(4):195-202. PMID: 22244820.
      View in: PubMed
    108. Finger LD, Atack JM, Tsutakawa S, Classen S, Tainer J, Grasby J, Shen B. The wonders of flap endonucleases: structure, function, mechanism and regulation. Subcell Biochem. 2012; 62:301-26. PMID: 22918592.
      View in: PubMed
    109. Hitomi K, Arvai AS, Yamamoto J, Hitomi C, Teranishi M, Hirouchi T, Yamamoto K, Iwai S, Tainer JA, Hidema J, Getzoff ED. Eukaryotic class II cyclobutane pyrimidine dimer photolyase structure reveals basis for improved ultraviolet tolerance in plants. J Biol Chem. 2012 Apr 06; 287(15):12060-9. PMID: 22170053.
      View in: PubMed
    110. Yannone SM, Hartung S, Menon AL, Adams MW, Tainer JA. Metals in biology: defining metalloproteomes. Curr Opin Biotechnol. 2012 Feb; 23(1):89-95. PMID: 22138493.
      View in: PubMed
    111. Grasby JA, Finger LD, Tsutakawa SE, Atack JM, Tainer JA. Unpairing and gating: sequence-independent substrate recognition by FEN superfamily nucleases. Trends Biochem Sci. 2012 Feb; 37(2):74-84. PMID: 22118811.
      View in: PubMed
    112. Hartung S, Arvai AS, Wood T, Kolappan S, Shin DS, Craig L, Tainer JA. Ultrahigh resolution and full-length pilin structures with insights for filament assembly, pathogenic functions, and vaccine potential. J Biol Chem. 2011 Dec 23; 286(51):44254-65. PMID: 22027840.
      View in: PubMed
    113. 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 25; 108(43):17672-7. PMID: 22006297.
      View in: PubMed
    114. Mui TP, Fuss JO, Ishida JP, Tainer JA, Barton JK. ATP-stimulated, DNA-mediated redox signaling by XPD, a DNA repair and transcription helicase. J Am Chem Soc. 2011 Oct 19; 133(41):16378-81. PMID: 21939244.
      View in: PubMed
    115. 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. PMID: 21775435.
      View in: PubMed
    116. Tomlinson CG, Syson K, Sengerová B, Atack JM, Sayers JR, Swanson L, Tainer JA, Williams NH, Grasby JA. Neutralizing mutations of carboxylates that bind metal 2 in T5 flap endonuclease result in an enzyme that still requires two metal ions. J Biol Chem. 2011 Sep 02; 286(35):30878-87. PMID: 21734257.
      View in: PubMed
    117. 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 01; 437(1):43-52. PMID: 21506936.
      View in: PubMed
    118. Trego KS, Chernikova SB, Davalos AR, Perry JJ, Finger LD, Ng C, Tsai MS, Yannone SM, Tainer JA, Campisi J, Cooper PK. The DNA repair endonuclease XPG interacts directly and functionally with the WRN helicase defective in Werner syndrome. Cell Cycle. 2011 Jun 15; 10(12):1998-2007. PMID: 21558802.
      View in: PubMed
    119. Tubbs JL, Tainer JA. P53 conformational switching for selectivity may reveal a general solution for specific DNA binding. EMBO J. 2011 Jun 01; 30(11):2099-100. PMID: 21629273.
      View in: PubMed
    120. Fuss JO, Tainer JA. XPB and XPD helicases in TFIIH orchestrate DNA duplex opening and damage verification to coordinate repair with transcription and cell cycle via CAK kinase. DNA Repair (Amst). 2011 Jul 15; 10(7):697-713. PMID: 21571596.
      View in: PubMed
    121. Kazantsev AV, Rambo RP, Karimpour S, Santalucia J, Tainer JA, Pace NR. Solution structure of RNase P RNA. RNA. 2011 Jun; 17(6):1159-71. PMID: 21531920.
      View in: PubMed
    122. Rambo RP, Tainer JA. Characterizing flexible and intrinsically unstructured biological macromolecules by SAS using the Porod-Debye law. Biopolymers. 2011 Aug; 95(8):559-71. PMID: 21509745.
      View in: PubMed
    123. Tsutakawa SE, Classen S, Chapados BR, Arvai AS, Finger LD, Guenther G, Tomlinson CG, Thompson P, Sarker AH, Shen B, Cooper PK, Grasby JA, 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. PMID: 21496641.
      View in: PubMed
    124. Perry JJ, Tainer JA. All stressed out without ATM kinase. Sci Signal. 2011 Apr 05; 4(167):pe18. PMID: 21467296.
      View in: PubMed
    125. 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. PMID: 21444718.
      View in: PubMed
    126. 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. PMID: 21441914.
      View in: PubMed
    127. Heideker J, Prudden J, Perry JJ, Tainer JA, Boddy MN. SUMO-targeted ubiquitin ligase, Rad60, and Nse2 SUMO ligase suppress spontaneous Top1-mediated DNA damage and genome instability. PLoS Genet. 2011 Mar; 7(3):e1001320. PMID: 21408210.
      View in: PubMed
    128. Lancaster WA, Praissman JL, Poole FL, Cvetkovic A, Menon AL, Scott JW, Jenney FE, Thorgersen MP, Kalisiak E, Apon JV, Trauger SA, Siuzdak G, Tainer JA, Adams MW. A computational framework for proteome-wide pursuit and prediction of metalloproteins using ICP-MS and MS/MS data. BMC Bioinformatics. 2011 Feb 28; 12:64. PMID: 21356119.
      View in: PubMed
    129. 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):4450-63. PMID: 21278162.
      View in: PubMed
    130. 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 25; 286(8):6733-41. PMID: 21173145.
      View in: PubMed
    131. 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. PMID: 21093452.
      View in: PubMed
    132. 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. PMID: 21070960.
      View in: PubMed
    133. 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. PMID: 21070942.
      View in: PubMed
    134. Williams GJ, Lees-Miller SP, Tainer JA. Mre11-Rad50-Nbs1 conformations and the control of sensing, signaling, and effector responses at DNA double-strand breaks. DNA Repair (Amst). 2010 Dec 10; 9(12):1299-306. PMID: 21035407.
      View in: PubMed
    135. Dobbs TA, Tainer JA, Lees-Miller SP. A structural model for regulation of NHEJ by DNA-PKcs autophosphorylation. DNA Repair (Amst). 2010 Dec 10; 9(12):1307-14. PMID: 21030321.
      View in: PubMed
    136. Kashiwagi S, Kuraoka I, Fujiwara Y, Hitomi K, Cheng QJ, Fuss JO, Shin DS, Masutani C, Tainer JA, Hanaoka F, Iwai S. Characterization of a Y-Family DNA Polymerase eta from the Eukaryotic Thermophile Alvinella pompejana. J Nucleic Acids. 2010 Sep 20; 2010. PMID: 20936172.
      View in: PubMed
    137. 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 Radiat. 2010 Nov; 17(6):774-81. PMID: 20975223.
      View in: PubMed
    138. 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. PMID: 20518483.
      View in: PubMed
    139. Rosenfeld RJ, Bonaventura J, Szymczyna BR, MacCoss MJ, Arvai AS, Yates JR, Tainer JA, Getzoff ED. Nitric-oxide synthase forms N-NO-pterin and S-NO-cys: implications for activity, allostery, and regulation. J Biol Chem. 2010 Oct 08; 285(41):31581-9. PMID: 20659888.
      View in: PubMed
    140. Cvetkovic A, Menon AL, Thorgersen MP, Scott JW, Poole FL, Jenney FE, Lancaster WA, Praissman JL, Shanmukh S, Vaccaro BJ, Trauger SA, Kalisiak E, Apon JV, Siuzdak G, Yannone SM, Tainer JA, Adams MW. Microbial metalloproteomes are largely uncharacterized. Nature. 2010 Aug 05; 466(7307):779-82. PMID: 20639861.
      View in: PubMed
    141. Rahal EA, Henricksen LA, Li Y, Williams RS, Tainer JA, Dixon K. ATM regulates Mre11-dependent DNA end-degradation and microhomology-mediated end joining. Cell Cycle. 2010 Jul 15; 9(14):2866-77. PMID: 20647759.
      View in: PubMed
    142. Tainer JA, McCammon JA, Ivanov I. Recognition of the ring-opened state of proliferating cell nuclear antigen by replication factor C promotes eukaryotic clamp-loading. J Am Chem Soc. 2010 Jun 02; 132(21):7372-8. PMID: 20455582.
      View in: PubMed
    143. Lim MS, Ng D, Zong Z, Arvai AS, Taylor RK, Tainer JA, Craig L. Vibrio cholerae El Tor TcpA crystal structure and mechanism for pilus-mediated microcolony formation. Mol Microbiol. 2010 Aug; 77(3):755-70. PMID: 20545841.
      View in: PubMed
    144. Perry JJ, Asaithamby A, Barnebey A, Kiamanesch F, Chen DJ, Han S, Tainer JA, Yannone SM. Identification of a coiled coil in werner syndrome protein that facilitates multimerization and promotes exonuclease processivity. J Biol Chem. 2010 Aug 13; 285(33):25699-707. PMID: 20516064.
      View in: PubMed
    145. Tubbs JL, Tainer JA. Alkyltransferase-like proteins: molecular switches between DNA repair pathways. Cell Mol Life Sci. 2010 Nov; 67(22):3749-62. PMID: 20502938.
      View in: PubMed
    146. Perry JJ, Cotner-Gohara E, Ellenberger T, Tainer JA. Structural dynamics in DNA damage signaling and repair. Curr Opin Struct Biol. 2010 Jun; 20(3):283-94. PMID: 20439160.
      View in: PubMed
    147. Pretto DI, Tsutakawa S, Brosey CA, Castillo A, Chagot ME, Smith JA, Tainer JA, Chazin WJ. Structural dynamics and single-stranded DNA binding activity of the three N-terminal domains of the large subunit of replication protein A from small angle X-ray scattering. Biochemistry. 2010 Apr 06; 49(13):2880-9. PMID: 20184389.
      View in: PubMed
    148. Tomlinson CG, Atack JM, Chapados B, Tainer JA, Grasby JA. Substrate recognition and catalysis by flap endonucleases and related enzymes. Biochem Soc Trans. 2010 Apr; 38(2):433-7. PMID: 20298197.
      View in: PubMed
    149. Aramini JM, Tubbs JL, Kanugula S, Rossi P, Ertekin A, Maglaqui M, Hamilton K, Ciccosanti CT, Jiang M, Xiao R, Soong TT, Rost B, Acton TB, Everett JK, Pegg AE, Tainer JA, Montelione GT. Structural basis of O6-alkylguanine recognition by a bacterial alkyltransferase-like DNA repair protein. J Biol Chem. 2010 Apr 30; 285(18):13736-41. PMID: 20212037.
      View in: PubMed
    150. Das D, Moiani D, Axelrod HL, Miller MD, McMullan D, Jin KK, Abdubek P, Astakhova T, Burra P, Carlton D, Chiu HJ, Clayton T, Deller MC, Duan L, Ernst D, Feuerhelm J, Grant JC, Grzechnik A, Grzechnik SK, Han GW, Jaroszewski L, Klock HE, Knuth MW, Kozbial P, Krishna SS, Kumar A, Marciano D, Morse AT, Nigoghossian E, Okach L, Paulsen J, Reyes R, Rife CL, Sefcovic N, Tien HJ, Trame CB, van den Bedem H, Weekes D, Xu Q, Hodgson KO, Wooley J, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Tainer JA, Wilson IA. Crystal structure of the first eubacterial Mre11 nuclease reveals novel features that may discriminate substrates during DNA repair. J Mol Biol. 2010 Apr 02; 397(3):647-63. PMID: 20122942.
      View in: PubMed
    151. 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. PMID: 20106957.
      View in: PubMed
    152. 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. PMID: 20097063.
      View in: PubMed
    153. 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 17; 29(6):1136-48. PMID: 20094029.
      View in: PubMed
    154. Perry JJ, Shin DS, Tainer JA. Amyotrophic lateral sclerosis. Adv Exp Med Biol. 2010; 685:9-20. PMID: 20687491.
      View in: PubMed
    155. Fang Q, Kanugula S, Tubbs JL, Tainer JA, Pegg AE. Repair of O4-alkylthymine by O6-alkylguanine-DNA alkyltransferases. J Biol Chem. 2010 Mar 12; 285(11):8185-95. PMID: 20026607.
      View in: PubMed
    156. 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. PMID: 19913481.
      View in: PubMed
    157. 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 08; 285(2):1414-23. PMID: 19893054.
      View in: PubMed
    158. Williams RS, Dodson GE, Limbo O, Yamada Y, Williams JS, Guenther G, Classen S, Glover JN, Iwasaki H, Russell P, Tainer JA. Nbs1 flexibly tethers Ctp1 and Mre11-Rad50 to coordinate DNA double-strand break processing and repair. Cell. 2009 Oct 02; 139(1):87-99. PMID: 19804755.
      View in: PubMed
    159. Hura GL, Menon AL, Hammel M, Rambo RP, Poole FL, Tsutakawa SE, Jenney FE, Classen S, Frankel KA, Hopkins RC, Yang SJ, Scott JW, Dillard BD, Adams MW, Tainer JA. Robust, high-throughput solution structural analyses by small angle X-ray scattering (SAXS). Nat Methods. 2009 Aug; 6(8):606-12. PMID: 19620974.
      View in: PubMed
    160. 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. PMID: 19516334.
      View in: PubMed
    161. Perry JJ, Harris RM, Moiani D, Olson AJ, Tainer JA. p38alpha MAP kinase C-terminal domain binding pocket characterized by crystallographic and computational analyses. J Mol Biol. 2009 Aug 07; 391(1):1-11. PMID: 19501598.
      View in: PubMed
    162. Perry JJ, Hitomi K, Tainer JA. Flexibility promotes fidelity. Structure. 2009 May 13; 17(5):633-4. PMID: 19446518.
      View in: PubMed
    163. Perry JJ, Hearn AS, Cabelli DE, Nick HS, Tainer JA, Silverman DN. Contribution of human manganese superoxide dismutase tyrosine 34 to structure and catalysis. Biochemistry. 2009 Apr 21; 48(15):3417-24. PMID: 19265433.
      View in: PubMed
    164. Prudden J, Perry JJ, Arvai AS, Tainer JA, Boddy MN. Molecular mimicry of SUMO promotes DNA repair. Nat Struct Mol Biol. 2009 May; 16(5):509-16. PMID: 19363481.
      View in: PubMed
    165. Hitomi K, DiTacchio L, Arvai AS, Yamamoto J, Kim ST, Todo T, Tainer JA, Iwai S, Panda S, Getzoff ED. Functional motifs in the (6-4) photolyase crystal structure make a comparative framework for DNA repair photolyases and clock cryptochromes. Proc Natl Acad Sci U S A. 2009 Apr 28; 106(17):6962-7. PMID: 19359474.
      View in: PubMed
    166. 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 14; 17(1):96-104. PMID: 19141286.
      View in: PubMed
    167. 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. PMID: 19136958.
      View in: PubMed
    168. Williams RS, Williams GJ, Tainer JA. A charged performance by gp17 in viral packaging. Cell. 2008 Dec 26; 135(7):1169-71. PMID: 19109888.
      View in: PubMed
    169. 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 06; 385(5):1534-55. PMID: 19063897.
      View in: PubMed
    170. Acharya SN, Many AM, Schroeder AP, Kennedy FM, Savytskyy OP, Grubb JT, Vincent JA, Friedle EA, Celerin M, Maillet DS, Palmerini HJ, Greischar MA, Moncalian G, Williams RS, Tainer JA, Zolan ME. Coprinus cinereus rad50 mutants reveal an essential structural role for Rad50 in axial element and synaptonemal complex formation, homolog pairing and meiotic recombination. Genetics. 2008 Dec; 180(4):1889-907. PMID: 18940790.
      View in: PubMed
    171. Garcin ED, Arvai AS, Rosenfeld RJ, Kroeger MD, Crane BR, Andersson G, Andrews G, Hamley PJ, Mallinder PR, Nicholls DJ, St-Gallay SA, Tinker AC, Gensmantel NP, Mete A, Cheshire DR, Connolly S, Stuehr DJ, Aberg A, Wallace AV, Tainer JA, Getzoff ED. Anchored plasticity opens doors for selective inhibitor design in nitric oxide synthase. Nat Chem Biol. 2008 Nov; 4(11):700-7. PMID: 18849972.
      View in: PubMed
    172. Edwards RA, Lee MS, Tsutakawa SE, Williams RS, Nazeer I, Kleiman FE, Tainer JA, Glover JN. The BARD1 C-terminal domain structure and interactions with polyadenylation factor CstF-50. Biochemistry. 2008 Nov 04; 47(44):11446-56. PMID: 18842000.
      View in: PubMed
    173. 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, Tainer JA. Mre11 dimers coordinate DNA end bridging and nuclease processing in double-strand-break repair. Cell. 2008 Oct 03; 135(1):97-109. PMID: 18854158.
      View in: PubMed
    174. Fang Q, Noronha AM, Murphy SP, Wilds CJ, Tubbs JL, Tainer JA, Chowdhury G, Guengerich FP, Pegg AE. Repair of O6-G-alkyl-O6-G interstrand cross-links by human O6-alkylguanine-DNA alkyltransferase. Biochemistry. 2008 Oct 14; 47(41):10892-903. PMID: 18803403.
      View in: PubMed
    175. Syson K, Tomlinson C, Chapados BR, Sayers JR, Tainer JA, Williams NH, Grasby JA. Three metal ions participate in the reaction catalyzed by T5 flap endonuclease. J Biol Chem. 2008 Oct 17; 283(42):28741-6. PMID: 18697748.
      View in: PubMed
    176. Pebernard S, Perry JJ, Tainer JA, Boddy MN. Nse1 RING-like domain supports functions of the Smc5-Smc6 holocomplex in genome stability. Mol Biol Cell. 2008 Oct; 19(10):4099-109. PMID: 18667531.
      View in: PubMed
    177. Fan L, Fuss JO, Cheng QJ, Arvai AS, Hammel M, Roberts VA, Cooper PK, Tainer JA. XPD helicase structures and activities: insights into the cancer and aging phenotypes from XPD mutations. Cell. 2008 May 30; 133(5):789-800. PMID: 18510924.
      View in: PubMed
    178. 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. PMID: 18589439.
      View in: PubMed
    179. Garcin ED, Hosfield DJ, Desai SA, Haas BJ, Björas M, Cunningham RP, Tainer JA. DNA apurinic-apyrimidinic site binding and excision by endonuclease IV. Nat Struct Mol Biol. 2008 May; 15(5):515-22. PMID: 18408731.
      View in: PubMed
    180. Perry JJ, Tainer JA, Boddy MN. A SIM-ultaneous role for SUMO and ubiquitin. Trends Biochem Sci. 2008 May; 33(5):201-8. PMID: 18403209.
      View in: PubMed
    181. Prudden J, Pebernard S, Raffa G, Slavin DA, Perry JJ, Tainer JA, McGowan CH, Boddy MN. SUMO-targeted ubiquitin ligases in genome stability. EMBO J. 2007 Sep 19; 26(18):4089-101. PMID: 17762865.
      View in: PubMed
    182. Roberts BR, Tainer JA, Getzoff ED, Malencik DA, Anderson SR, Bomben VC, Meyers KR, Karplus PA, Beckman JS. Structural characterization of zinc-deficient human superoxide dismutase and implications for ALS. J Mol Biol. 2007 Nov 02; 373(4):877-90. PMID: 17888947.
      View in: PubMed
    183. Putnam CD, Hammel M, Hura GL, Tainer JA. X-ray 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. PMID: 18078545.
      View in: PubMed
    184. 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. PMID: 17713585.
      View in: PubMed
    185. Tubbs JL, Pegg AE, Tainer JA. DNA binding, nucleotide flipping, and the helix-turn-helix motif in base repair by O6-alkylguanine-DNA alkyltransferase and its implications for cancer chemotherapy. DNA Repair (Amst). 2007 Aug 01; 6(8):1100-15. PMID: 17485252.
      View in: PubMed
    186. Williams R, Sengerová B, Osborne S, Syson K, Ault S, Kilgour A, Chapados BR, Tainer JA, Sayers JR, Grasby JA. Comparison of the catalytic parameters and reaction specificities of a phage and an archaeal flap endonuclease. J Mol Biol. 2007 Aug 03; 371(1):34-48. PMID: 17559871.
      View in: PubMed
    187. Williams RS, Tainer JA. Learning our ABCs: Rad50 directs MRN repair functions via adenylate kinase activity from the conserved ATP binding cassette. Mol Cell. 2007 Mar 23; 25(6):789-91. PMID: 17386254.
      View in: PubMed
    188. Barondeau DP, Kassmann CJ, Tainer JA, Getzoff ED. The case of the missing ring: radical cleavage of a carbon-carbon bond and implications for GFP chromophore biosynthesis. J Am Chem Soc. 2007 Mar 21; 129(11):3118-26. PMID: 17326633.
      View in: PubMed
    189. Vijayakumar S, Chapados BR, Schmidt KH, Kolodner RD, Tainer JA, Tomkinson AE. The C-terminal domain of yeast PCNA is required for physical and functional interactions with Cdc9 DNA ligase. Nucleic Acids Res. 2007; 35(5):1624-37. PMID: 17308348.
      View in: PubMed
    190. Yamagata A, Tainer JA. Hexameric structures of the archaeal secretion ATPase GspE and implications for a universal secretion mechanism. EMBO J. 2007 Feb 07; 26(3):878-90. PMID: 17255937.
      View in: PubMed
    191. Ivanov I, Tainer JA, McCammon JA. Unraveling the three-metal-ion catalytic mechanism of the DNA repair enzyme endonuclease IV. Proc Natl Acad Sci U S A. 2007 Jan 30; 104(5):1465-70. PMID: 17242363.
      View in: PubMed
    192. Hitomi K, Iwai S, Tainer JA. The intricate structural chemistry of base excision repair machinery: implications for DNA damage recognition, removal, and repair. DNA Repair (Amst). 2007 Apr 01; 6(4):410-28. PMID: 17208522.
      View in: PubMed
    193. 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. PMID: 17182256.
      View in: PubMed
    194. Ivanov I, Chapados BR, McCammon JA, Tainer JA. Proliferating cell nuclear antigen loaded onto double-stranded DNA: dynamics, minor groove interactions and functional implications. Nucleic Acids Res. 2006; 34(20):6023-33. PMID: 17071716.
      View in: PubMed
    195. Pascal JM, Tsodikov OV, Hura GL, Song W, Cotner EA, Classen S, Tomkinson AE, Tainer JA, Ellenberger T. A flexible interface between DNA ligase and PCNA supports conformational switching and efficient ligation of DNA. Mol Cell. 2006 Oct 20; 24(2):279-91. PMID: 17052461.
      View in: PubMed
    196. Craig L, Volkmann N, Arvai AS, Pique ME, Yeager M, Egelman EH, Tainer JA. Type IV pilus structure by cryo-electron microscopy and crystallography: implications for pilus assembly and functions. Mol Cell. 2006 Sep 01; 23(5):651-62. PMID: 16949362.
      View in: PubMed
    197. Sundheim O, Vågbø CB, Bjørås M, Sousa MM, Talstad V, Aas PA, Drabløs F, Krokan HE, Tainer JA, Slupphaug G. Human ABH3 structure and key residues for oxidative demethylation to reverse DNA/RNA damage. EMBO J. 2006 Jul 26; 25(14):3389-97. PMID: 16858410.
      View in: PubMed
    198. Perry JJ, Yannone SM, Holden LG, Hitomi C, Asaithamby A, Han S, Cooper PK, Chen DJ, Tainer JA. WRN exonuclease structure and molecular mechanism imply an editing role in DNA end processing. Nat Struct Mol Biol. 2006 May; 13(5):414-22. PMID: 16622405.
      View in: PubMed
    199. Barondeau DP, Kassmann CJ, Tainer JA, Getzoff ED. Understanding GFP posttranslational chemistry: structures of designed variants that achieve backbone fragmentation, hydrolysis, and decarboxylation. J Am Chem Soc. 2006 Apr 12; 128(14):4685-93. PMID: 16594705.
      View in: PubMed
    200. 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. Mol Cell. 2006 Apr 07; 22(1):27-37. PMID: 16600867.
      View in: PubMed
    201. Doi Y, Katafuchi A, Fujiwara Y, Hitomi K, Tainer JA, Ide H, Iwai S. Synthesis and characterization of oligonucleotides containing 2'-fluorinated thymidine glycol as inhibitors of the endonuclease III reaction. Nucleic Acids Res. 2006; 34(5):1540-51. PMID: 16547199.
      View in: PubMed
    202. 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. 2006 May 19; 358(5):1229-43. PMID: 16574152.
      View in: PubMed
    203. Barondeau DP, Tainer JA, Getzoff ED. Structural evidence for an enolate intermediate in GFP fluorophore biosynthesis. J Am Chem Soc. 2006 Mar 15; 128(10):3166-8. PMID: 16522096.
      View in: PubMed
    204. Wood TI, Barondeau DP, Hitomi C, Kassmann CJ, Tainer JA, Getzoff ED. Defining the role of arginine 96 in green fluorescent protein fluorophore biosynthesis. Biochemistry. 2005 Dec 13; 44(49):16211-20. PMID: 16331981.
      View in: PubMed
    205. Ayala P, Wilbur JS, Wetzler LM, Tainer JA, Snyder A, So M. The pilus and porin of Neisseria gonorrhoeae cooperatively induce Ca(2+) transients in infected epithelial cells. Cell Microbiol. 2005 Dec; 7(12):1736-48. PMID: 16309460.
      View in: PubMed
    206. Sarker AH, Tsutakawa SE, Kostek S, Ng C, Shin DS, Peris M, Campeau E, Tainer JA, Nogales E, Cooper PK. Recognition of RNA polymerase II and transcription bubbles by XPG, CSB, and TFIIH: insights for transcription-coupled repair and Cockayne Syndrome. Mol Cell. 2005 Oct 28; 20(2):187-98. PMID: 16246722.
      View in: PubMed
    207. Putnam CD, Tainer JA. Protein mimicry of DNA and pathway regulation. DNA Repair (Amst). 2005 Dec 08; 4(12):1410-20. PMID: 16226493.
      View in: PubMed
    208. Williams RS, Tainer JA. A nanomachine for making ends meet: MRN is a flexing scaffold for the repair of DNA double-strand breaks. Mol Cell. 2005 Sep 16; 19(6):724-6. PMID: 16168369.
      View in: PubMed
    209. Simeoni F, Arvai A, Bello P, Gondeau C, Hopfner KP, Neyroz P, Heitz F, Tainer J, Divita G. Biochemical characterization and crystal structure of a Dim1 family associated protein: Dim2. Biochemistry. 2005 Sep 13; 44(36):11997-2008. PMID: 16142897.
      View in: PubMed
    210. Ayala I, Perry JJ, Szczepanski J, Tainer JA, Vala MT, Nick HS, Silverman DN. Hydrogen bonding in human manganese superoxide dismutase containing 3-fluorotyrosine. Biophys J. 2005 Dec; 89(6):4171-9. PMID: 16150974.
      View in: PubMed
    211. Huffman JL, Sundheim O, Tainer JA. DNA base damage recognition and removal: new twists and grooves. Mutat Res. 2005 Sep 04; 577(1-2):55-76. PMID: 15941573.
      View in: PubMed
    212. Tubbs JL, Tainer JA, Getzoff ED. Crystallographic structures of Discosoma red fluorescent protein with immature and mature chromophores: linking peptide bond trans-cis isomerization and acylimine formation in chromophore maturation. Biochemistry. 2005 Jul 26; 44(29):9833-40. PMID: 16026155.
      View in: PubMed
    213. Crowther LJ, Yamagata A, Craig L, Tainer JA, Donnenberg MS. The ATPase activity of BfpD is greatly enhanced by zinc and allosteric interactions with other Bfp proteins. J Biol Chem. 2005 Jul 01; 280(26):24839-48. PMID: 15866879.
      View in: PubMed
    214. Barondeau DP, Kassmann CJ, Tainer JA, Getzoff ED. Understanding GFP chromophore biosynthesis: controlling backbone cyclization and modifying post-translational chemistry. Biochemistry. 2005 Feb 15; 44(6):1960-70. PMID: 15697221.
      View in: PubMed
    215. Doi Y, Hitomi K, Tainer JA, Iwai S. Synthesis of oligonucleotides containing 2'-fluorinated thymidine glycol as mechanism-based inhibitors of endonuclease III. Nucleic Acids Symp Ser (Oxf). 2005; (49):195-6. PMID: 17150700.
      View in: PubMed
    216. Manuel RC, Hitomi K, Arvai AS, House PG, Kurtz AJ, Dodson ML, McCullough AK, Tainer JA, Lloyd RS. Reaction intermediates in the catalytic mechanism of Escherichia coli MutY DNA glycosylase. J Biol Chem. 2004 Nov 05; 279(45):46930-9. PMID: 15326180.
      View in: PubMed
    217. Shin DS, Chahwan C, Huffman JL, Tainer JA. Structure and function of the double-strand break repair machinery. DNA Repair (Amst). 2004 Aug-Sep; 3(8-9):863-73. PMID: 15279771.
      View in: PubMed
    218. Barondeau DP, Kassmann CJ, Bruns CK, Tainer JA, Getzoff ED. Nickel superoxide dismutase structure and mechanism. Biochemistry. 2004 Jun 29; 43(25):8038-47. PMID: 15209499.
      View in: PubMed
    219. Daniels DS, Woo TT, Luu KX, Noll DM, Clarke ND, Pegg AE, Tainer JA. DNA binding and nucleotide flipping by the human DNA repair protein AGT. Nat Struct Mol Biol. 2004 Aug; 11(8):714-20. PMID: 15221026.
      View in: PubMed
    220. Garcin ED, Bruns CM, Lloyd SJ, Hosfield DJ, Tiso M, Gachhui R, Stuehr DJ, Tainer JA, Getzoff ED. Structural basis for isozyme-specific regulation of electron transfer in nitric-oxide synthase. J Biol Chem. 2004 Sep 03; 279(36):37918-27. PMID: 15208315.
      View in: PubMed
    221. de Jager M, Trujillo KM, Sung P, Hopfner KP, Carney JP, Tainer JA, Connelly JC, Leach DR, Kanaar R, Wyman C. Differential arrangements of conserved building blocks among homologs of the Rad50/Mre11 DNA repair protein complex. J Mol Biol. 2004 Jun 11; 339(4):937-49. PMID: 15165861.
      View in: PubMed
    222. Greenleaf WB, Perry JJ, Hearn AS, Cabelli DE, Lepock JR, Stroupe ME, Tainer JA, Nick HS, Silverman DN. Role of hydrogen bonding in the active site of human manganese superoxide dismutase. Biochemistry. 2004 Jun 08; 43(22):7038-45. PMID: 15170341.
      View in: PubMed
    223. Connolly S, Aberg A, Arvai A, Beaton HG, Cheshire DR, Cook AR, Cooper S, Cox D, Hamley P, Mallinder P, Millichip I, Nicholls DJ, Rosenfeld RJ, St-Gallay SA, Tainer J, Tinker AC, Wallace AV. 2-aminopyridines as highly selective inducible nitric oxide synthase inhibitors. Differential binding modes dependent on nitrogen substitution. J Med Chem. 2004 Jun 03; 47(12):3320-3. PMID: 15163211.
      View in: PubMed
    224. Craig L, Pique ME, Tainer JA. Type IV pilus structure and bacterial pathogenicity. Nat Rev Microbiol. 2004 May; 2(5):363-78. PMID: 15100690.
      View in: PubMed
    225. Arthur LM, Gustausson K, Hopfner KP, Carson CT, Stracker TH, Karcher A, Felton D, Weitzman MD, Tainer J, Carney JP. Structural and functional analysis of Mre11-3. Nucleic Acids Res. 2004; 32(6):1886-93. PMID: 15047855.
      View in: PubMed
    226. Qiu J, Liu R, Chapados BR, Sherman M, Tainer JA, Shen B. Interaction interface of human flap endonuclease-1 with its DNA substrates. J Biol Chem. 2004 Jun 04; 279(23):24394-402. PMID: 15037610.
      View in: PubMed
    227. Moncalian G, Lengsfeld B, Bhaskara V, Hopfner KP, Karcher A, Alden E, Tainer JA, Paull TT. The rad50 signature motif: essential to ATP binding and biological function. J Mol Biol. 2004 Jan 23; 335(4):937-51. PMID: 14698290.
      View in: PubMed
    228. Chapados BR, Hosfield DJ, Han S, Qiu J, Yelent B, Shen B, Tainer JA. Structural basis for FEN-1 substrate specificity and PCNA-mediated activation in DNA replication and repair. Cell. 2004 Jan 09; 116(1):39-50. PMID: 14718165.
      View in: PubMed
    229. Hearn AS, Fan L, Lepock JR, Luba JP, Greenleaf WB, Cabelli DE, Tainer JA, Nick HS, Silverman DN. Amino acid substitution at the dimeric interface of human manganese superoxide dismutase. J Biol Chem. 2004 Feb 13; 279(7):5861-6. PMID: 14638684.
      View in: PubMed
    230. Barondeau DP, Putnam CD, Kassmann CJ, Tainer JA, Getzoff ED. Mechanism and energetics of green fluorescent protein chromophore synthesis revealed by trapped intermediate structures. Proc Natl Acad Sci U S A. 2003 Oct 14; 100(21):12111-6. PMID: 14523232.
      View in: PubMed
    231. DiDonato M, Craig L, Huff ME, Thayer MM, Cardoso RM, Kassmann CJ, Lo TP, Bruns CK, Powers ET, Kelly JW, Getzoff ED, Tainer JA. ALS mutants of human superoxide dismutase form fibrous aggregates via framework destabilization. J Mol Biol. 2003 Sep 19; 332(3):601-15. PMID: 12963370.
      View in: PubMed
    232. Shin DS, Pellegrini L, Daniels DS, Yelent B, Craig L, Bates D, Yu DS, Shivji MK, Hitomi C, Arvai AS, Volkmann N, Tsuruta H, Blundell TL, Venkitaraman AR, Tainer JA. Full-length archaeal Rad51 structure and mutants: mechanisms for RAD51 assembly and control by BRCA2. EMBO J. 2003 Sep 01; 22(17):4566-76. PMID: 12941707.
      View in: PubMed
    233. Huffman JL, Li H, White RH, Tainer JA. Structural basis for recognition and catalysis by the bifunctional dCTP deaminase and dUTPase from Methanococcus jannaschii. J Mol Biol. 2003 Aug 22; 331(4):885-96. PMID: 12909016.
      View in: PubMed
    234. McMurray CT, Tainer JA. Cancer, cadmium and genome integrity. Nat Genet. 2003 Jul; 34(3):239-41. PMID: 12833042.
      View in: PubMed
    235. Wang M, Howell JM, Libbey JE, Tainer JA, Fujinami RS. Manganese superoxide dismutase induction during measles virus infection. J Med Virol. 2003 Jul; 70(3):470-4. PMID: 12767013.
      View in: PubMed
    236. Craig L, Taylor RK, Pique ME, Adair BD, Arvai AS, Singh M, Lloyd SJ, Shin DS, Getzoff ED, Yeager M, Forest KT, Tainer JA. Type IV pilin structure and assembly: X-ray and EM analyses of Vibrio cholerae toxin-coregulated pilus and Pseudomonas aeruginosa PAK pilin. Mol Cell. 2003 May; 11(5):1139-50. PMID: 12769840.
      View in: PubMed
    237. Cardoso RM, Daniels DS, Bruns CM, Tainer JA. Characterization of the electrophile binding site and substrate binding mode of the 26-kDa glutathione S-transferase from Schistosoma japonicum. Proteins. 2003 Apr 01; 51(1):137-46. PMID: 12596270.
      View in: PubMed
    238. Hopfner KP, Tainer JA. Rad50/SMC proteins and ABC transporters: unifying concepts from high-resolution structures. Curr Opin Struct Biol. 2003 Apr; 13(2):249-55. PMID: 12727520.
      View in: PubMed
    239. Hearn AS, Stroupe ME, Cabelli DE, Ramilo CA, Luba JP, Tainer JA, Nick HS, Silverman DN. Catalytic and structural effects of amino acid substitution at histidine 30 in human manganese superoxide dismutase: insertion of valine C gamma into the substrate access channel. Biochemistry. 2003 Mar 18; 42(10):2781-9. PMID: 12627943.
      View in: PubMed
    240. Aoyagi M, Arvai AS, Tainer JA, Getzoff ED. Structural basis for endothelial nitric oxide synthase binding to calmodulin. EMBO J. 2003 Feb 17; 22(4):766-75. PMID: 12574113.
      View in: PubMed
    241. Brudler R, Hitomi K, Daiyasu H, Toh H, Kucho K, Ishiura M, Kanehisa M, Roberts VA, Todo T, Tainer JA, Getzoff ED. Identification of a new cryptochrome class. Structure, function, and evolution. Mol Cell. 2003 Jan; 11(1):59-67. PMID: 12535521.
      View in: PubMed
    242. Rosenfeld RJ, Garcin ED, Panda K, Andersson G, Aberg A, Wallace AV, Morris GM, Olson AJ, Stuehr DJ, Tainer JA, Getzoff ED. Conformational changes in nitric oxide synthases induced by chlorzoxazone and nitroindazoles: crystallographic and computational analyses of inhibitor potency. Biochemistry. 2002 Nov 26; 41(47):13915-25. PMID: 12437348.
      View in: PubMed
    243. Cardoso RM, Thayer MM, DiDonato M, Lo TP, Bruns CK, Getzoff ED, Tainer JA. Insights into Lou Gehrig's disease from the structure and instability of the A4V mutant of human Cu,Zn superoxide dismutase. J Mol Biol. 2002 Nov 22; 324(2):247-56. PMID: 12441104.
      View in: PubMed
    244. Abdalla AM, Bruns CM, Tainer JA, Mannervik B, Stenberg G. Design of a monomeric human glutathione transferase GSTP1, a structurally stable but catalytically inactive protein. Protein Eng. 2002 Oct; 15(10):827-34. PMID: 12468717.
      View in: PubMed
    245. Hopfner KP, Craig L, Moncalian G, Zinkel RA, Usui T, Owen BA, Karcher A, Henderson B, Bodmer JL, McMurray CT, Carney JP, Petrini JH, Tainer JA. The Rad50 zinc-hook is a structure joining Mre11 complexes in DNA recombination and repair. Nature. 2002 Aug 01; 418(6897):562-6. PMID: 12152085.
      View in: PubMed
    246. Morris MC, Gondeau C, Tainer JA, Divita G. Kinetic mechanism of activation of the Cdk2/cyclin A complex. Key role of the C-lobe of the Cdk. J Biol Chem. 2002 Jun 28; 277(26):23847-53. PMID: 11959850.
      View in: PubMed
    247. Barondeau DP, Kassmann CJ, Tainer JA, Getzoff ED. Structural chemistry of a green fluorescent protein Zn biosensor. J Am Chem Soc. 2002 Apr 10; 124(14):3522-4. PMID: 11929238.
      View in: PubMed
    248. Han S, Tainer JA. The ARTT motif and a unified structural understanding of substrate recognition in ADP-ribosylating bacterial toxins and eukaryotic ADP-ribosyltransferases. Int J Med Microbiol. 2002 Feb; 291(6-7):523-9. PMID: 11890553.
      View in: PubMed
    249. Hopfner KP, Putnam CD, Tainer JA. DNA double-strand break repair from head to tail. Curr Opin Struct Biol. 2002 Feb; 12(1):115-22. PMID: 11839498.
      View in: PubMed
    250. Mol CD, Arvai AS, Begley TJ, Cunningham RP, Tainer JA. Structure and activity of a thermostable thymine-DNA glycosylase: evidence for base twisting to remove mismatched normal DNA bases. J Mol Biol. 2002 Jan 18; 315(3):373-84. PMID: 11786018.
      View in: PubMed
    251. Castagnetto JM, Hennessy SW, Roberts VA, Getzoff ED, Tainer JA, Pique ME. MDB: the Metalloprotein Database and Browser at The Scripps Research Institute. Nucleic Acids Res. 2002 Jan 01; 30(1):379-82. PMID: 11752342.
      View in: PubMed
    252. Adak S, Bilwes AM, Panda K, Hosfield D, Aulak KS, McDonald JF, Tainer JA, Getzoff ED, Crane BR, Stuehr DJ. Cloning, expression, and characterization of a nitric oxide synthase protein from Deinococcus radiodurans. Proc Natl Acad Sci U S A. 2002 Jan 08; 99(1):107-12. PMID: 11756668.
      View in: PubMed
    253. MRE11 facilitates the removal of human topoisomerase II complexes from genomic DNA. Biology Open. 1:863-873.
    254. Crystallographic structures of metalloenzymes for dna repair. Protein Engineering, Design and Selection. 6:39.
    255. Perchlorate reductase is distinguished by active site aromatic gate residues. Journal of Biological Chemistry. 291:9190-9202.
    256. RNF8 E3 ubiquitin ligase stimulates Ubc13 E2 conjugating activity that is essential for DNA double strand break signaling and BRCA1 tumor suppressor recruitment. Journal of Biological Chemistry. 291:9396-9410.
    257. Inhibition of neutrophil migration by metal ions is a function of ion reduction potential. Federation Proceedings. 43.
    258. Noncoding RNA joins Ku and DNA-PKcs for DNA-break resistance in breast cancer. Nature Structural and Molecular Biology. 23:509-510.
    259. Erratum. Proceedings of the National Academy of Sciences of the United States of America. 89:11106.
    260. Summary of 'superoxide dismutase (SOD) and free radicals in amyotrophic lateral sclerosis and neurodegeneration' conference. Neurology. 45:1779-1780.
    261. Theories about oxygen toxicity [5] (multiple letters). Chemical and Engineering News. 62.
    262. Science, citation, and funding [1]. Science. 251:1408.
    263. MICROBIOLOGY 1975. 202-205.
    264. Modeling macromolecular motions by x-ray-scattering-constrained molecular dynamics. Biophysical Journal. 108:2421-2423.
    265. Kinetic and structural characterization of human manganese superoxide dismutase containing 3-fluorotyrosines. Journal of Molecular Structure. 790:168-173.
    266. The crystal structure of inducible nitric oxide synthase oxygenase domain dimer with L-arginine and tetrahydrobiopterin. Chemtracts. 12:557-564.
    267. Defining NADH-Driven Allostery Regulating Apoptosis-Inducing Factor. Structure. 24:2067-2079.
    268. The nucleotide-dependent interaction of FlaH and FlaI is essential for assembly and function of the archaellum motor. Molecular Microbiology. 99:674-685.
    269. Erratum. EMBO Journal. 22:1234.
    270. Cell-free expression of functional receptor tyrosine kinases. Scientific Reports. 5.
    271. Erratum. EMBO Journal. 35:791.
    272. High-throughput SAXS for the characterization of biomolecules in solution. 245-258.
    273. Erratum. Journal of Biological Chemistry. 284:21100.
    274. Envisioning the dynamics and flexibility of Mre11-Rad50-Nbs1 complex to decipher its roles in DNA replication and repair. Progress in Biophysics and Molecular Biology. 117:182-193.
    275. The crystal structure of inducible nitric oxide synthase oxygenase domain dimer with L-arginine and tetrahydrobiopterin. Chemtracts. 13:859-866.
    276. Colour illustration. Journal of Molecular Graphics. 8:145-152.
    277. Structural, functional, and immunogenic insights on Cu,Zn superoxide dismutase pathogenic virulence factors from Neisseria meningitidis and Brucella abortus. Journal of Bacteriology. 197:3834-3847.
    278. Erratum. Nature Structural and Molecular Biology. 19:364.
    279. Erratum DNA Double-Strand Break Repair Pathway Choice Is Directed by Distinct MRE11 Nuclease Activities. [Molecular Cell 53, 9, (2014) 7-18]. Molecular Cell. 53:361.
    280. Structure and design, prediction and evolution. Current Opinion in Biotechnology. 9:335-337.
    281. The total chemical synthesis of L- and D-superoxide dismutnse. Protein Engineering. 10:23.
    282. Amino acid hydrophobicity in the context of folded proteins. Protein Engineering, Design and Selection. 6:129.
    283. Exploring the repeat protein universe through computational protein design. Nature. 528:580-584.
    284. Translocation and deletion breakpoints in cancer genomes are associated with potential non-B DNA-forming sequences. Nucleic Acids Research. 44:5673-5688.
    285. The BARD1 C-terminal domain structure and interactions with polyadenylation factor CstF-50 (Biochemistry (2008), 47, 44 (11446-11456)). Biochemistry. 48:4008.
    286. Erratum. Nature. 404:525.
    287. Mechanism and Regulation of DNA-Protein Crosslink Repair by the DNA-Dependent Metalloprotease SPRTN. Molecular Cell. 64:688-703.
    288. Hybrid Methods Reveal Multiple Flexibly Linked DNA Polymerases within the Bacteriophage T7 Replisome. Structure. 25:157-166.
    289. An intrinsically disordered APLF links Ku, DNA-PKcs, and XRCC4-DNA ligase IV in an extended flexible non-homologous end joining complex. Journal of Biological Chemistry. 291:26987-27006.
    290. Erratum. Nature Structural and Molecular Biology. 18:1084.
    291. Serum albumin perturbs chemotaxis dose-inhibition profiles for 3 nonsteroidal antiinflammatory drugs. Federation Proceedings. 43.
    292. ELECTROSTATIC FORCES BETWEEN LIGANDS AND MACROMOLECULES. 538.
    293. FlaF is a β-sandwich protein that anchors the archaellum in the archaeal cell envelope by binding the S-layer protein. Structure. 23:863-872.
    294. The ATPase Motor Turns for Type IV Pilus Assembly. Structure. 24:1857-1859.
    295. Dynamic structures in DNA damage responses & cancer. Progress in Biophysics and Molecular Biology. 117:129-133.
    296. Implementation and performance of SIBYLS. Journal of Applied Crystallography. 46:1-13.
    297. Erratum. Journal of Molecular Biology. 334:175.
    298. Mobility and evolutionary variability factors in protein antigenicity. Nature. 317:90.
    299. Charging of Proteins in Native Mass Spectrometry. Journal of the American Society for Mass Spectrometry. 28:332-340.
    TAINER's Networks
    Click the "See All" links for more information and interactive visualizations!
    Concepts Expand Description
    _
    Co-Authors Expand Description
    _
    Similar People Expand Description
    _
    Same Department Expand Description