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    Tainer, John

    TitleVisiting Faculty Non-UC
    SchoolLawrence Berkeley National Lab
    DepartmentMolecular Biophys & Integ Bio
    Address1 Cyclotron Road
    Berkeley CA 94720
    Phone510/486-4158
    vCardDownload vCard

      Collapse Bibliographic 
      Collapse Publications
      Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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      1. 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 J, 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.
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      2. Tainer J. Uncovering the secrets of protein interactions with the DNA enforcing genomic stability. Prog Biophys Mol Biol. 2017 Aug; 127:89-92. PMID: 28709479.
        View in: PubMed
      3. 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 J. Phosphate steering by Flap Endonuclease 1 promotes 5'-flap specificity and incision to prevent genome instability. Nat Commun. 2017 Jun 27; 8:15855. PMID: 28653660.
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      4. Aceytuno RD, Piett CG, Havali-Shahriari Z, Edwards RA, Rey M, Ye R, Javed F, Fang S, Mani R, Weinfeld M, Hammel M, Tainer J, 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.
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      5. Brosey CA, Ahmed Z, Lees-Miller SP, Tainer J. What Combined Measurements From Structures and Imaging Tell Us About DNA Damage Responses. Methods Enzymol. 2017; 592:417-455. PMID: 28668129.
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      6. Gradia SD, Ishida JP, Tsai MS, Jeans C, Tainer J, Fuss JO. MacroBac: New Technologies for Robust and Efficient Large-Scale Production of Recombinant Multiprotein Complexes. Methods Enzymol. 2017; 592:1-26. PMID: 28668116.
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      7. Rashid F, Harris PD, Zaher MS, Sobhy MA, Joudeh LI, Yan C, Piwonski H, Tsutakawa SE, Ivanov I, Tainer J, Habuchi S, Hamdan SM. Single-molecule FRET unveils induced-fit mechanism for substrate selectivity in flap endonuclease 1. Elife. 2017 Feb 23; 6. PMID: 28230529.
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      8. Wallen JR, Zhang H, Weis C, Cui W, Foster BM, Ho CM, Hammel M, Tainer J, Gross ML, Ellenberger T. Hybrid Methods Reveal Multiple Flexibly Linked DNA Polymerases within the Bacteriophage T7 Replisome. Structure. 2017 Jan 03; 25(1):157-166. PMID: 28052235.
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      9. Dutta A, Eckelmann B, Adhikari S, Ahmed KM, Sengupta S, Pandey A, Hegde PM, Tsai MS, Tainer J, 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. 2016 Dec 19. PMID: 27994036.
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      10. Lai YT, Hura GL, Dyer KN, Tang HY, Tainer J, Yeates TO. Designing and defining dynamic protein cage nanoassemblies in solution. Sci Adv. 2016 Dec; 2(12):e1501855. PMID: 27990489.
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      11. Brosey CA, Ho C, Long WZ, Singh S, Burnett K, Hura GL, Nix JC, Bowman GR, Ellenberger T, Tainer J. Defining NADH-Driven Allostery Regulating Apoptosis-Inducing Factor. Structure. 2016 Dec 06; 24(12):2067-2079. PMID: 27818101.
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      12. Tsai CL, Tainer J. The ATPase Motor Turns for Type IV Pilus Assembly. Structure. 2016 11 01; 24(11):1857-1859. PMID: 27806257.
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      13. Stingele J, Bellelli R, Alte F, Hewitt G, Sarek G, Maslen SL, Tsutakawa SE, Borg A, Kjær S, Tainer J, Skehel JM, Groll M, Boulton SJ. Mechanism and Regulation of DNA-Protein Crosslink Repair by the DNA-Dependent Metalloprotease SPRTN. Mol Cell. 2016 Nov 17; 64(4):688-703. PMID: 27871365.
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      14. Susa AC, Xia Z, Tang HY, Tainer J, Williams ER. Charging of Proteins in Native Mass Spectrometry. J Am Soc Mass Spectrom. 2017 Feb; 28(2):332-340. PMID: 27734326.
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      15. Hammel M, Amlanjyoti D, Reyes FE, Chen JH, Parpana R, Tang HY, Larabell CA, Tainer J, Adhya S. HU multimerization shift controls nucleoid compaction. Sci Adv. 2016 07; 2(7):e1600650. PMID: 27482541; PMCID: PMC4966879.
      16. Lees-Miller SP, Beattie TL, Tainer J. 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.
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      17. Schneidman-Duhovny D, Hammel M, Tainer J, 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; PMCID: PMC4987932.
      18. Bacolla A, Tainer J, Vasquez KM, Cooper DN. Translocation and deletion breakpoints in cancer genomes are associated with potential non-B DNA-forming sequences. Nucleic Acids Res. 2016 Jul 08; 44(12):5673-88. PMID: 27084947; PMCID: PMC4937311.
      19. Deshpande RA, Williams GJ, Limbo O, Williams RS, Kuhnlein J, Lee JH, Classen S, Guenther G, Russell P, Tainer J, 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; PMCID: PMC4818762.
      20. Youngblut MD, Tsai CL, Clark IC, Carlson HK, Maglaqui AP, Gau-Pan PS, Redford SA, Wong A, Tainer J, Coates JD. Perchlorate Reductase Is Distinguished by Active Site Aromatic Gate Residues. J Biol Chem. 2016 Apr 22; 291(17):9190-202. PMID: 26940877; PMCID: PMC4861485 [Available on 04/22/17].
      21. Hodge CD, Ismail IH, Edwards RA, Hura GL, Xiao AT, Tainer J, 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; PMCID: PMC4850281 [Available on 04/29/17].
      22. Brunette TJ, Parmeggiani F, Huang PS, Bhabha G, Ekiert DC, Tsutakawa SE, Hura GL, Tainer J, Baker D. Exploring the repeat protein universe through computational protein design. Nature. 2015 Dec 24; 528(7583):580-4. PMID: 26675729; PMCID: PMC4845728.
      23. Chaudhury P, Neiner T, D'Imprima E, Banerjee A, Reindl S, Ghosh A, Arvai AS, Mills DJ, van der Does C, Tainer J, 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; PMCID: PMC5019145.
      24. Shin DS, Tainer J. Molecular biology: DNA repair without flipping out. Nature. 2015 Nov 12; 527(7577):168-9. PMID: 26524524.
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      25. Pratt AJ, DiDonato M, Shin DS, Cabelli DE, Bruns CK, Belzer CA, Gorringe AR, Langford PR, Tabatabai LB, Kroll JS, Tainer J, 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; PMCID: PMC4652047.
      26. He W, Scharadin TM, Saldana M, Gellner C, Hoang-Phou S, Takanishi C, Hura GL, Tainer J, Carraway KL, Henderson PT, Coleman MA. Cell-free expression of functional receptor tyrosine kinases. Sci Rep. 2015 Aug 14; 5:12896. PMID: 26274523; PMCID: PMC4929682.
      27. Tsai CL, Williams GJ, Perry JJ, Tainer J. An AAA+ ATPase Clamshell Targets Transposition. Cell. 2015 Aug 13; 162(4):701-3. PMID: 26276624.
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      28. Kukshal V, Kim IK, Hura GL, Tomkinson AE, Tainer J, 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; PMCID: PMC4538836.
      29. Tsutakawa SE, Tainer J. Bending Forks and Wagging Dogs--It's about the DNA 3' Tail. Mol Cell. 2015 Jun 18; 58(6):972-3. PMID: 26091346.
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      30. Rambo RP, Tainer J. Modeling macromolecular motions by x-ray-scattering-constrained molecular dynamics. Biophys J. 2015 May 19; 108(10):2421-2423. PMID: 25992719; PMCID: PMC4457040.
      31. Banerjee A, Tsai CL, Chaudhury P, Tripp P, Arvai AS, Ishida JP, Tainer J, 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):863-72. PMID: 25865246; PMCID: PMC4425475.
      32. Tainer J. Dynamic structures in DNA damage responses & cancer. Prog Biophys Mol Biol. 2015 Mar; 117(2-3):129-33. PMID: 25934179.
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      33. Fuss JO, Tsai CL, Ishida JP, Tainer J. Emerging critical roles of Fe-S clusters in DNA replication and repair. Biochim Biophys Acta. 2015 Jun; 1853(6):1253-71. PMID: 25655665; PMCID: PMC4576882.
      34. Lafrance-Vanasse J, Williams GJ, Tainer J. 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):182-93. PMID: 25576492; PMCID: PMC4417436.
      35. Tsutakawa SE, Yan C, Xu X, Zhuang Z, Todd Washington M, Tainer J, Ivanov I. 112 Structurally distinct ubiquitin- and SUMO-modified PCNA: implications for their distinct roles in the DNA damage response. J Biomol Struct Dyn. 2015; 33 Suppl 1:70-1. PMID: 26103323.
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      36. Williams GJ, SilDas S, Anand A, Schild D, Tainer J. 204 Structural insights into the RAD51 paralog complexes reveal molecular details of disease causing mutations. J Biomol Struct Dyn. 2015; 33 Suppl 1:137. PMID: 26103414.
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      37. Tsai CL, Burkinshaw BJ, Strynadka NC, Tainer J. 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; PMCID: PMC4334186.
      38. Lai YT, Reading E, Hura GL, Tsai KL, Laganowsky A, Asturias FJ, Tainer J, 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; PMCID: PMC4239666.
      39. Pratt AJ, Shin DS, Merz GE, Rambo RP, Lancaster WA, Dyer KN, Borbat PP, Poole FL, Adams MW, Freed JH, Crane BR, Tainer J, 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; PMCID: PMC4217430.
      40. Holton JM, Classen S, Frankel KA, Tainer J. 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; PMCID: PMC4282448.
      41. Tsai CL, Shi Y, Tainer J. How substrate specificity is imposed on a histone demethylase--lessons from KDM2A. Genes Dev. 2014 Aug 15; 28(16):1735-8. PMID: 25128493; PMCID: PMC4197959.
      42. McTernan PM, Chandrayan SK, Wu CH, Vaccaro BJ, Lancaster WA, Yang Q, Fu D, Hura GL, Tainer J, 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; PMCID: PMC4094048.
      43. Mason AC, Rambo RP, Greer B, Pritchett M, Tainer J, 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; PMCID: PMC4040553.
      44. Tsutakawa SE, Lafrance-Vanasse J, Tainer J. 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; PMCID: PMC4051888.
      45. Groocock LM, Nie M, Prudden J, Moiani D, Wang T, Cheltsov A, Rambo RP, Arvai AS, Hitomi C, Tainer J, 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; PMCID: PMC4210088.
      46. Seeger F, Quintyn R, Tanimoto A, Williams GJ, Tainer J, 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; PMCID: PMC3985721.
      47. Williams GJ, Hammel M, Radhakrishnan SK, Ramsden D, Lees-Miller SP, Tainer J. 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; PMCID: PMC4102006.
      48. Shin DS, Pratt AJ, Tainer J. Archaeal genome guardians give insights into eukaryotic DNA replication and damage response proteins. Archaea. 2014; 2014:206735. PMID: 24701133; PMCID: PMC3950489.
      49. Roset R, Inagaki A, Hohl M, Brenet F, Lafrance-Vanasse J, Lange J, Scandura JM, Tainer J, 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; PMCID: PMC3950343.
      50. Deshpande RA, Williams GJ, Limbo O, Williams RS, Kuhnlein J, Lee JH, Classen S, Guenther G, Russell P, Tainer J, 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; PMCID: PMC3989629.
      51. Dyer KN, Hammel M, Rambo RP, Tsutakawa SE, Rodic I, Classen S, Tainer J, Hura GL. High-throughput SAXS for the characterization of biomolecules in solution: a practical approach. Methods Mol Biol. 2014; 1091:245-58. PMID: 24203338; PMCID: PMC4057279.
      52. Reyes FE, Schwartz CR, Tainer J, 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.
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      53. Tsai CL, Tainer J. Probing DNA by 2-OG-dependent dioxygenase. Cell. 2013 Dec 19; 155(7):1448-50. PMID: 24360270; PMCID: PMC3916139.
      54. 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 J. 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; PMCID: PMC3909494.
      55. Pieper U, Webb BM, Dong GQ, Schneidman-Duhovny D, Fan H, Kim SJ, Khuri N, Spill YG, Weinkam P, Hammel M, Tainer J, 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; PMCID: PMC3965011.
      56. Crown KN, Savytskyy OP, Malik SB, Logsdon J, Williams RS, Tainer J, 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; PMCID: PMC3815056.
      57. Zhao W, Saro D, Hammel M, Kwon Y, Xu Y, Rambo RP, Williams GJ, Chi P, Lu L, Pezza RJ, Camerini-Otero RD, Tainer J, 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; PMCID: PMC3902922.
      58. Hura GL, Tsai CL, Claridge SA, Mendillo ML, Smith JM, Williams GJ, Mastroianni AJ, Alivisatos AP, Putnam CD, Kolodner RD, Tainer J. 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; PMCID: PMC3808630.
      59. Liu X, Hammel M, He Y, Tainer J, 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; PMCID: PMC3773798.
      60. Schneidman-Duhovny D, Hammel M, Tainer J, Sali A. Accurate SAXS profile computation and its assessment by contrast variation experiments. Biophys J. 2013 Aug 20; 105(4):962-74. PMID: 23972848; PMCID: PMC3752106.
      61. Trewhella J, Hendrickson WA, Kleywegt GJ, Sali A, Sato M, Schwede T, Svergun DI, Tainer J, 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.
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      62. Hura GL, Budworth H, Dyer KN, Rambo RP, Hammel M, McMurray CT, Tainer J. Comprehensive macromolecular conformations mapped by quantitative SAXS analyses. Nat Methods. 2013 Jun; 10(6):453-4. PMID: 23624664; PMCID: PMC3728378.
      63. Rambo RP, Tainer J. Accurate assessment of mass, models and resolution by small-angle scattering. Nature. 2013 Apr 25; 496(7446):477-81. PMID: 23619693; PMCID: PMC3714217.
      64. Hegde ML, Tsutakawa SE, Hegde PM, Holthauzen LM, Li J, Oezguen N, Hilser VJ, Tainer J, 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; PMCID: PMC3779128.
      65. Rambo RP, Tainer J. Super-resolution in solution X-ray scattering and its applications to structural systems biology. Annu Rev Biophys. 2013; 42:415-41. PMID: 23495971.
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      66. Reindl S, Ghosh A, Williams GJ, Lassak K, Neiner T, Henche AL, Albers SV, Tainer J. 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; PMCID: PMC3615136.
      67. Mahaney BL, Hammel M, Meek K, Tainer J, 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; PMCID: PMC3725335.
      68. Perry JJ, Tainer J. Developing advanced X-ray scattering methods combined with crystallography and computation. Methods. 2013 Mar; 59(3):363-71. PMID: 23376408; PMCID: PMC3684416.
      69. 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 J. 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; PMCID: PMC3605660.
      70. Classen S, Hura GL, Holton JM, Rambo RP, Rodic I, McGuire PJ, Dyer K, Hammel M, Meigs G, Frankel KA, Tainer J. 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.
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      71. Brosey CA, Yan C, Tsutakawa SE, Heller WT, Rambo RP, Tainer J, 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; PMCID: PMC3575853.
      72. Dalhus B, Nilsen L, Korvald H, Huffman J, Forstrøm RJ, McMurray CT, Alseth I, Tainer J, Bjørås M. Sculpting of DNA at abasic sites by DNA glycosylase homolog mag2. Structure. 2013 Jan 08; 21(1):154-166. PMID: 23245849; PMCID: PMC3545110.
      73. 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 J, 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; PMCID: PMC3503161.
      74. Shi K, Kurahashi K, Gao R, Tsutakawa SE, Tainer J, 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; PMCID: PMC3515695.
      75. Limbo O, Moiani D, Kertokalio A, Wyman C, Tainer J, 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; PMCID: PMC3526295.
      76. Lee KC, Padget K, Curtis H, Cowell IG, Moiani D, Sondka Z, Morris NJ, Jackson GH, Cockell SJ, Tainer J, 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; PMCID: PMC3507232.
      77. Omanakuttan A, Nambiar J, Harris RM, Bose C, Pandurangan N, Varghese RK, Kumar GB, Tainer J, 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; PMCID: PMC3463216.
      78. 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 J, 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; PMCID: PMC3398191.
      79. Kim IK, Kiefer JR, Ho CM, Stegeman RA, Classen S, Tainer J, 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; PMCID: PMC3381899.
      80. Querol-Audí J, Yan C, Xu X, Tsutakawa SE, Tsai MS, Tainer J, 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; PMCID: PMC3365210.
      81. Christie JM, Hitomi K, Arvai AS, Hartfield KA, Mettlen M, Pratt AJ, Tainer J, Getzoff ED. Structural tuning of the fluorescent protein iLOV for improved photostability. J Biol Chem. 2012 Jun 22; 287(26):22295-304. PMID: 22573334; PMCID: PMC3381190.
      82. Roberts VA, Pique ME, Hsu S, Li S, Slupphaug G, Rambo RP, Jamison JW, Liu T, Lee JH, Tainer J, 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; PMCID: PMC3401472.
      83. Ruigrok VJ, van Duijn E, Barendregt A, Dyer K, Tainer J, 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.
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      84. Yamagata A, Milgotina E, Scanlon K, Craig L, Tainer J, 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; PMCID: PMC3338861.
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      378. Turner SR, Tainer J. Non-chemokinetic neutrophil attractants derived from arachidonic acid. Cell Biol Int Rep. 1983 Oct; 7(10):843-8. PMID: 6416688.
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