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Items: 1 to 50 of 383

1.

Targeting Allostery with Avatars to Design Inhibitors Assessed by Cell Activity: Dissecting MRE11 Endo- and Exonuclease Activities.

Moiani D, Ronato DA, Brosey CA, Arvai AS, Syed A, Masson JY, Petricci E, Tainer JA.

Methods Enzymol. 2018;601:205-241. doi: 10.1016/bs.mie.2017.11.030. Epub 2018 Feb 22.

PMID:
29523233
2.

Pro-metastatic collagen lysyl hydroxylase dimer assemblies stabilized by Fe2+-binding.

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 Jr., Kurie JM.

Nat Commun. 2018 Feb 6;9(1):512. doi: 10.1038/s41467-018-02859-z.

3.

Small angle X-ray scattering and cross-linking for data assisted protein structure prediction in CASP 12 with prospects for improved accuracy.

Ogorzalek TL, Hura GL, Belsom A, Burnett KH, Kryshtafovych A, Tainer JA, Rappsilber J, Tsutakawa SE, Fidelis K.

Proteins. 2018 Mar;86 Suppl 1:202-214. doi: 10.1002/prot.25452. Epub 2018 Feb 7.

PMID:
29314274
4.

High Resolution Distance Distributions Determined by X-Ray and Neutron Scattering.

Tang HYH, Tainer JA, Hura GL.

Adv Exp Med Biol. 2017;1009:167-181. doi: 10.1007/978-981-10-6038-0_10.

PMID:
29218559
5.

Coiled coils unspring protein origami.

Hura GL, Tainer JA.

Nat Biotechnol. 2017 Nov 9;35(11):1044-1045. doi: 10.1038/nbt.4003. No abstract available.

PMID:
29121029
6.

2017 publication guidelines for structural modelling of small-angle scattering data from biomolecules in solution: an update.

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.

Acta Crystallogr D Struct Biol. 2017 Sep 1;73(Pt 9):710-728. doi: 10.1107/S2059798317011597. Epub 2017 Aug 18.

7.

Uncovering the secrets of protein interactions with the DNA enforcing genomic stability.

Tainer JA.

Prog Biophys Mol Biol. 2017 Aug;127:89-92. doi: 10.1016/j.pbiomolbio.2017.07.002. No abstract available.

PMID:
28709479
8.

What Combined Measurements From Structures and Imaging Tell Us About DNA Damage Responses.

Brosey CA, Ahmed Z, Lees-Miller SP, Tainer JA.

Methods Enzymol. 2017;592:417-455. doi: 10.1016/bs.mie.2017.04.005. Epub 2017 May 29.

9.

MacroBac: New Technologies for Robust and Efficient Large-Scale Production of Recombinant Multiprotein Complexes.

Gradia SD, Ishida JP, Tsai MS, Jeans C, Tainer JA, Fuss JO.

Methods Enzymol. 2017;592:1-26. doi: 10.1016/bs.mie.2017.03.008. Epub 2017 May 15.

PMID:
28668116
10.

Phosphate steering by Flap Endonuclease 1 promotes 5'-flap specificity and incision to prevent genome instability.

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.

Nat Commun. 2017 Jun 27;8:15855. doi: 10.1038/ncomms15855.

11.

Structural and functional characterization of the PNKP-XRCC4-LigIV DNA repair complex.

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.

Nucleic Acids Res. 2017 Jun 2;45(10):6238-6251. doi: 10.1093/nar/gkx275.

12.

Single-molecule FRET unveils induced-fit mechanism for substrate selectivity in flap endonuclease 1.

Rashid F, Harris PD, Zaher MS, Sobhy MA, Joudeh LI, Yan C, Piwonski H, Tsutakawa SE, Ivanov I, Tainer JA, Habuchi S, Hamdan SM.

Elife. 2017 Feb 23;6. pii: e21884. doi: 10.7554/eLife.21884.

13.

Hybrid Methods Reveal Multiple Flexibly Linked DNA Polymerases within the Bacteriophage T7 Replisome.

Wallen JR, Zhang H, Weis C, Cui W, Foster BM, Ho CMW, Hammel M, Tainer JA, Gross ML, Ellenberger T.

Structure. 2017 Jan 3;25(1):157-166. doi: 10.1016/j.str.2016.11.019.

14.

Microhomology-mediated end joining is activated in irradiated human cells due to phosphorylation-dependent formation of the XRCC1 repair complex.

Dutta A, Eckelmann B, Adhikari S, Ahmed KM, Sengupta S, Pandey A, Hegde PM, Tsai MS, Tainer JA, Weinfeld M, Hegde ML, Mitra S.

Nucleic Acids Res. 2017 Mar 17;45(5):2585-2599. doi: 10.1093/nar/gkw1262.

15.

Designing and defining dynamic protein cage nanoassemblies in solution.

Lai YT, Hura GL, Dyer KN, Tang HY, Tainer JA, Yeates TO.

Sci Adv. 2016 Dec 14;2(12):e1501855. eCollection 2016 Dec.

16.

An Intrinsically Disordered APLF Links Ku, DNA-PKcs, and XRCC4-DNA Ligase IV in an Extended Flexible Non-homologous End Joining Complex.

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.

J Biol Chem. 2016 Dec 30;291(53):26987-27006. doi: 10.1074/jbc.M116.751867. Epub 2016 Nov 14.

17.

Mechanism and Regulation of DNA-Protein Crosslink Repair by the DNA-Dependent Metalloprotease SPRTN.

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.

Mol Cell. 2016 Nov 17;64(4):688-703. doi: 10.1016/j.molcel.2016.09.031. Epub 2016 Oct 27.

18.

Defining NADH-Driven Allostery Regulating Apoptosis-Inducing Factor.

Brosey CA, Ho C, Long WZ, Singh S, Burnett K, Hura GL, Nix JC, Bowman GR, Ellenberger T, Tainer JA.

Structure. 2016 Dec 6;24(12):2067-2079. doi: 10.1016/j.str.2016.09.012. Epub 2016 Nov 3.

19.

The ATPase Motor Turns for Type IV Pilus Assembly.

Tsai CL, Tainer JA.

Structure. 2016 Nov 1;24(11):1857-1859. doi: 10.1016/j.str.2016.10.002.

20.

Charging of Proteins in Native Mass Spectrometry.

Susa AC, Xia Z, Tang HYH, Tainer JA, Williams ER.

J Am Soc Mass Spectrom. 2017 Feb;28(2):332-340. doi: 10.1007/s13361-016-1517-7. Epub 2016 Oct 12.

21.

HU multimerization shift controls nucleoid compaction.

Hammel M, Amlanjyoti D, Reyes FE, Chen JH, Parpana R, Tang HY, Larabell CA, Tainer JA, Adhya S.

Sci Adv. 2016 Jul 29;2(7):e1600650. doi: 10.1126/sciadv.1600650. eCollection 2016 Jul.

22.

Noncoding RNA joins Ku and DNA-PKcs for DNA-break resistance in breast cancer.

Lees-Miller SP, Beattie TL, Tainer JA.

Nat Struct Mol Biol. 2016 Jun 7;23(6):509-10. doi: 10.1038/nsmb.3240. No abstract available.

23.

FoXS, FoXSDock and MultiFoXS: Single-state and multi-state structural modeling of proteins and their complexes based on SAXS profiles.

Schneidman-Duhovny D, Hammel M, Tainer JA, Sali A.

Nucleic Acids Res. 2016 Jul 8;44(W1):W424-9. doi: 10.1093/nar/gkw389. Epub 2016 May 5.

24.

Translocation and deletion breakpoints in cancer genomes are associated with potential non-B DNA-forming sequences.

Bacolla A, Tainer JA, Vasquez KM, Cooper DN.

Nucleic Acids Res. 2016 Jul 8;44(12):5673-88. doi: 10.1093/nar/gkw261. Epub 2016 Apr 15.

25.

ATP-driven Rad50 conformations regulate DNA tethering, end resection, and ATM checkpoint signaling.

Deshpande RA, Williams GJ, Limbo O, Williams RS, Kuhnlein J, Lee JH, Classen S, Guenther G, Russell P, Tainer JA, Paull TT.

EMBO J. 2016 Apr 1;35(7):791. doi: 10.15252/embj.201694047. No abstract available.

26.

Perchlorate Reductase Is Distinguished by Active Site Aromatic Gate Residues.

Youngblut MD, Tsai CL, Clark IC, Carlson HK, Maglaqui AP, Gau-Pan PS, Redford SA, Wong A, Tainer JA, Coates JD.

J Biol Chem. 2016 Apr 22;291(17):9190-202. doi: 10.1074/jbc.M116.714618. Epub 2016 Mar 3.

27.

RNF8 E3 Ubiquitin Ligase Stimulates Ubc13 E2 Conjugating Activity That Is Essential for DNA Double Strand Break Signaling and BRCA1 Tumor Suppressor Recruitment.

Hodge CD, Ismail IH, Edwards RA, Hura GL, Xiao AT, Tainer JA, Hendzel MJ, Glover JN.

J Biol Chem. 2016 Apr 29;291(18):9396-410. doi: 10.1074/jbc.M116.715698. Epub 2016 Feb 22.

28.

Exploring the repeat protein universe through computational protein design.

Brunette TJ, Parmeggiani F, Huang PS, Bhabha G, Ekiert DC, Tsutakawa SE, Hura GL, Tainer JA, Baker D.

Nature. 2015 Dec 24;528(7583):580-4. doi: 10.1038/nature16162. Epub 2015 Dec 16.

29.

Molecular biology: DNA repair without flipping out.

Shin DS, Tainer JA.

Nature. 2015 Nov 12;527(7577):168-9. doi: 10.1038/nature15646. Epub 2015 Oct 28. No abstract available.

PMID:
26524524
30.

The nucleotide-dependent interaction of FlaH and FlaI is essential for assembly and function of the archaellum motor.

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.

Mol Microbiol. 2016 Feb;99(4):674-85. doi: 10.1111/mmi.13260. Epub 2015 Nov 17.

31.

Structural, Functional, and Immunogenic Insights on Cu,Zn Superoxide Dismutase Pathogenic Virulence Factors from Neisseria meningitidis and Brucella abortus.

Pratt AJ, DiDonato M, Shin DS, Cabelli DE, Bruns CK, Belzer CA, Gorringe AR, Langford PR, Tabatabai LB, Kroll JS, Tainer JA, Getzoff ED.

J Bacteriol. 2015 Dec;197(24):3834-47. doi: 10.1128/JB.00343-15. Epub 2015 Oct 12.

32.

An AAA+ ATPase Clamshell Targets Transposition.

Tsai CL, Williams GJ, Perry JJ, Tainer JA.

Cell. 2015 Aug 13;162(4):701-3. doi: 10.1016/j.cell.2015.07.050.

33.

Cell-free expression of functional receptor tyrosine kinases.

He W, Scharadin TM, Saldana M, Gellner C, Hoang-Phou S, Takanishi C, Hura GL, Tainer JA, Carraway KL 3rd, Henderson PT, Coleman MA.

Sci Rep. 2015 Aug 14;5:12896. doi: 10.1038/srep12896.

34.

Human DNA ligase III bridges two DNA ends to promote specific intermolecular DNA end joining.

Kukshal V, Kim IK, Hura GL, Tomkinson AE, Tainer JA, Ellenberger T.

Nucleic Acids Res. 2015 Aug 18;43(14):7021-31. doi: 10.1093/nar/gkv652. Epub 2015 Jun 29.

35.

204 Structural insights into the RAD51 paralog complexes reveal molecular details of disease causing mutations.

Williams GJ, SilDas S, Anand A, Schild D, Tainer JA.

J Biomol Struct Dyn. 2015;33 Suppl 1:137. doi: 10.1080/07391102.2015.1033150. No abstract available.

PMID:
26103414
36.

112 Structurally distinct ubiquitin- and SUMO-modified PCNA: implications for their distinct roles in the DNA damage response.

Tsutakawa SE, Yan C, Xu X, Zhuang Z, Todd Washington M, Tainer JA, Ivanov I.

J Biomol Struct Dyn. 2015;33 Suppl 1:70-1. doi: 10.1080/07391102.2015.1032745. No abstract available.

PMID:
26103323
37.

Bending Forks and Wagging Dogs--It's about the DNA 3' Tail.

Tsutakawa SE, Tainer JA.

Mol Cell. 2015 Jun 18;58(6):972-3. doi: 10.1016/j.molcel.2015.06.005.

38.

Modeling macromolecular motions by x-ray-scattering-constrained molecular dynamics.

Rambo RP, Tainer JA.

Biophys J. 2015 May 19;108(10):2421-2423. doi: 10.1016/j.bpj.2015.04.023. No abstract available.

39.

Dynamic structures in DNA damage responses & cancer.

Tainer JA.

Prog Biophys Mol Biol. 2015 Mar;117(2-3):129-33. doi: 10.1016/j.pbiomolbio.2015.04.003. No abstract available.

40.

FlaF Is a β-Sandwich Protein that Anchors the Archaellum in the Archaeal Cell Envelope by Binding the S-Layer Protein.

Banerjee A, Tsai CL, Chaudhury P, Tripp P, Arvai AS, Ishida JP, Tainer JA, Albers SV.

Structure. 2015 May 5;23(5):863-872. doi: 10.1016/j.str.2015.03.001. Epub 2015 Apr 9.

41.

Structurally distinct ubiquitin- and sumo-modified PCNA: implications for their distinct roles in the DNA damage response.

Tsutakawa SE, Yan C, Xu X, Weinacht CP, Freudenthal BD, Yang K, Zhuang Z, Washington MT, Tainer JA, Ivanov I.

Structure. 2015 Apr 7;23(4):724-733. doi: 10.1016/j.str.2015.02.008. Epub 2015 Mar 12.

42.

Emerging critical roles of Fe-S clusters in DNA replication and repair.

Fuss JO, Tsai CL, Ishida JP, Tainer JA.

Biochim Biophys Acta. 2015 Jun;1853(6):1253-71. doi: 10.1016/j.bbamcr.2015.01.018. Epub 2015 Feb 2. Review.

43.

Envisioning the dynamics and flexibility of Mre11-Rad50-Nbs1 complex to decipher its roles in DNA replication and repair.

Lafrance-Vanasse J, Williams GJ, Tainer JA.

Prog Biophys Mol Biol. 2015 Mar;117(2-3):182-93. doi: 10.1016/j.pbiomolbio.2014.12.004. Epub 2015 Jan 7. Review.

44.

The Salmonella type III secretion system virulence effector forms a new hexameric chaperone assembly for export of effector/chaperone complexes.

Tsai CL, Burkinshaw BJ, Strynadka NC, Tainer JA.

J Bacteriol. 2015 Feb 15;197(4):672-5. doi: 10.1128/JB.02524-14. Epub 2014 Dec 8.

45.

Methods for using new conceptual tools and parameters to assess RNA structure by small-angle X-ray scattering.

Reyes FE, Schwartz CR, Tainer JA, Rambo RP.

Methods Enzymol. 2014;549:235-63. doi: 10.1016/B978-0-12-801122-5.00011-8.

PMID:
25432752
46.

Structure of a designed protein cage that self-assembles into a highly porous cube.

Lai YT, Reading E, Hura GL, Tsai KL, Laganowsky A, Asturias FJ, Tainer JA, Robinson CV, Yeates TO.

Nat Chem. 2014 Dec;6(12):1065-71. doi: 10.1038/nchem.2107. Epub 2014 Nov 10.

47.

Aggregation propensities of superoxide dismutase G93 hotspot mutants mirror ALS clinical phenotypes.

Pratt AJ, Shin DS, Merz GE, Rambo RP, Lancaster WA, Dyer KN, Borbat PP, Poole FL 2nd, Adams MW, Freed JH, Crane BR, Tainer JA, Getzoff ED.

Proc Natl Acad Sci U S A. 2014 Oct 28;111(43):E4568-76. doi: 10.1073/pnas.1308531111. Epub 2014 Oct 14.

48.

How substrate specificity is imposed on a histone demethylase--lessons from KDM2A.

Tsai CL, Shi Y, Tainer JA.

Genes Dev. 2014 Aug 15;28(16):1735-8. doi: 10.1101/gad.249755.114.

49.

The R-factor gap in macromolecular crystallography: an untapped potential for insights on accurate structures.

Holton JM, Classen S, Frankel KA, Tainer JA.

FEBS J. 2014 Sep;281(18):4046-60. doi: 10.1111/febs.12922. Epub 2014 Sep 17.

50.

Intact functional fourteen-subunit respiratory membrane-bound [NiFe]-hydrogenase complex of the hyperthermophilic archaeon Pyrococcus furiosus.

McTernan PM, Chandrayan SK, Wu CH, Vaccaro BJ, Lancaster WA, Yang Q, Fu D, Hura GL, Tainer JA, Adams MW.

J Biol Chem. 2014 Jul 11;289(28):19364-72. doi: 10.1074/jbc.M114.567255. Epub 2014 May 23.

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