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Replication-Based Rearrangements Are a Common Mechanism for SNCA Duplication in Parkinson's Disease.

Seo SH, Bacolla A, Yoo D, Koo YJ, Cho SI, Kim MJ, Seong MW, Kim HJ, Kim JM, Tainer JA, Park SS, Kim JY, Jeon B.

Mov Disord. 2020 Feb 10. doi: 10.1002/mds.27998. [Epub ahead of print]


The structure of the periplasmic FlaG-FlaF complex and its essential role for archaellar swimming motility.

Tsai CL, Tripp P, Sivabalasarma S, Zhang C, Rodriguez-Franco M, Wipfler RL, Chaudhury P, Banerjee A, Beeby M, Whitaker RJ, Tainer JA, Albers SV.

Nat Microbiol. 2020 Jan;5(1):216-225. doi: 10.1038/s41564-019-0622-3. Epub 2019 Dec 16.


Selective small molecule PARG inhibitor causes replication fork stalling and cancer cell death.

Houl JH, Ye Z, Brosey CA, Balapiti-Modarage LPF, Namjoshi S, Bacolla A, Laverty D, Walker BL, Pourfarjam Y, Warden LS, Babu Chinnam N, Moiani D, Stegeman RA, Chen MK, Hung MC, Nagel ZD, Ellenberger T, Kim IK, Jones DE, Ahmed Z, Tainer JA.

Nat Commun. 2019 Dec 11;10(1):5654. doi: 10.1038/s41467-019-13508-4.


Small angle X-ray scattering-assisted protein structure prediction in CASP13 and emergence of solution structure differences.

Hura GL, Hodge CD, Rosenberg D, Guzenko D, Duarte JM, Monastyrskyy B, Grudinin S, Kryshtafovych A, Tainer JA, Fidelis K, Tsutakawa SE.

Proteins. 2019 Dec;87(12):1298-1314. doi: 10.1002/prot.25827. Epub 2019 Oct 16.


SLX4IP acts with SLX4 and XPF-ERCC1 to promote interstrand crosslink repair.

Zhang H, Chen Z, Ye Y, Ye Z, Cao D, Xiong Y, Srivastava M, Feng X, Tang M, Wang C, Tainer JA, Chen J.

Nucleic Acids Res. 2019 Nov 4;47(19):10181-10201. doi: 10.1093/nar/gkz769.


DNA damage response mechanisms and structures fundamental to cancer research progress.

Bacolla A, Tainer JA.

Prog Biophys Mol Biol. 2019 Oct;147:1-3. doi: 10.1016/j.pbiomolbio.2019.08.011. Epub 2019 Aug 27. No abstract available.


Flexible Tethering of ASPP Proteins Facilitates PP-1c Catalysis.

Zhou Y, Millott R, Kim HJ, Peng S, Edwards RA, Skene-Arnold T, Hammel M, Lees-Miller SP, Tainer JA, Holmes CFB, Glover JNM.

Structure. 2019 Oct 1;27(10):1485-1496.e4. doi: 10.1016/j.str.2019.07.012. Epub 2019 Aug 8.


Evolving SAXS versatility: solution X-ray scattering for macromolecular architecture, functional landscapes, and integrative structural biology.

Brosey CA, Tainer JA.

Curr Opin Struct Biol. 2019 Oct;58:197-213. doi: 10.1016/ Epub 2019 Jun 13. Review.


Transcription preinitiation complex structure and dynamics provide insight into genetic diseases.

Yan C, Dodd T, He Y, Tainer JA, Tsutakawa SE, Ivanov I.

Nat Struct Mol Biol. 2019 Jun;26(6):397-406. doi: 10.1038/s41594-019-0220-3. Epub 2019 May 20.


Cancer mutational burden is shaped by G4 DNA, replication stress and mitochondrial dysfunction.

Bacolla A, Ye Z, Ahmed Z, Tainer JA.

Prog Biophys Mol Biol. 2019 Oct;147:47-61. doi: 10.1016/j.pbiomolbio.2019.03.004. Epub 2019 Mar 14.


Formylglycine-generating enzyme binds substrate directly at a mononuclear Cu(I) center to initiate O2 activation.

Appel MJ, Meier KK, Lafrance-Vanasse J, Lim H, Tsai CL, Hedman B, Hodgson KO, Tainer JA, Solomon EI, Bertozzi CR.

Proc Natl Acad Sci U S A. 2019 Mar 19;116(12):5370-5375. doi: 10.1073/pnas.1818274116. Epub 2019 Mar 1.


Charge Transport Communication through DNA by Protein Fe-S Clusters: How Far Is Not Too Far?

Syed A, Tainer JA.

ACS Cent Sci. 2019 Jan 23;5(1):7-9. doi: 10.1021/acscentsci.8b00909. Epub 2019 Jan 11. No abstract available.


Structural Control of Nonnative Ligand Binding in Engineered Mutants of Phosphoenolpyruvate Carboxykinase.

Tang HYH, Shin DS, Hura GL, Yang Y, Hu X, Lightstone FC, McGee MD, Padgett HS, Yannone SM, Tainer JA.

Biochemistry. 2018 Dec 4;57(48):6688-6700. doi: 10.1021/acs.biochem.8b00963. Epub 2018 Nov 15.


RNA Modifications: Reversal Mechanisms and Cancer.

Thapar R, Bacolla A, Oyeniran C, Brickner JR, Chinnam NB, Mosammaparast N, Tainer JA.

Biochemistry. 2019 Feb 5;58(5):312-329. doi: 10.1021/acs.biochem.8b00949. Epub 2018 Nov 7.


Author Correction: 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 Jul 10;9(1):2719. doi: 10.1038/s41467-018-05295-1.


Dissection of DNA double-strand-break repair using novel single-molecule forceps.

Wang JL, Duboc C, Wu Q, Ochi T, Liang S, Tsutakawa SE, Lees-Miller SP, Nadal M, Tainer JA, Blundell TL, Strick TR.

Nat Struct Mol Biol. 2018 Jun;25(6):482-487. doi: 10.1038/s41594-018-0065-1. Epub 2018 May 21.


The MRE11-RAD50-NBS1 Complex Conducts the Orchestration of Damage Signaling and Outcomes to Stress in DNA Replication and Repair.

Syed A, Tainer JA.

Annu Rev Biochem. 2018 Jun 20;87:263-294. doi: 10.1146/annurev-biochem-062917-012415. Epub 2018 Apr 25. Review.


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.


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. Erratum in: Nat Commun. 2018 Jul 10;9(1):2719.


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.


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. Review.


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.


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.


Corrigendum: 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 Aug 7;8:16145. doi: 10.1038/ncomms16145. eCollection 2017.


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.


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. Review.


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.


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. Erratum in: Nat Commun. 2017 Aug 07;8:16145.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.

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