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    Tsutakawa, Susan

    TitleBiochemist Scientist/Engineer
    SchoolLawrence Berkeley National Lab
    DepartmentMolecular Biophys & Integ Bio
    Address1 Cyclotron Road
    Berkeley CA 94720
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      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. Ogorzalek TL, Hura GL, Belsom A, Burnett KH, Kryshtafovych A, Tainer JA, Rappsilber J, Tsutakawa S, 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 Jan 04. PMID: 29314274.
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      2. Tsutakawa S, 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 Jun 27; 8:15855. PMID: 28653660.
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      3. Leksa NC, Chiu PL, Bou-Assaf GM, Quan C, Liu Z, Goodman AB, Chambers MG, Tsutakawa S, Hammel M, Peters RT, Walz T, Kulman JD. The structural basis for the functional comparability of factor VIII and the long-acting variant recombinant factor VIII Fc fusion protein. J Thromb Haemost. 2017 Jun; 15(6):1167-1179. PMID: 28397397.
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      4. Rashid F, Harris PD, Zaher MS, Sobhy MA, Joudeh LI, Yan C, Piwonski H, Tsutakawa S, Ivanov I, Tainer JA, 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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      5. Stingele J, Bellelli R, Alte F, Hewitt G, Sarek G, Maslen SL, Tsutakawa S, 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 Nov 17; 64(4):688-703. PMID: 27871365.
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      6. Brunette TJ, Parmeggiani F, Huang PS, Bhabha G, Ekiert DC, Tsutakawa S, 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; PMCID: PMC4845728.
      7. Tsutakawa S, 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.
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      8. Tsutakawa S, Yan C, Xu X, Weinacht CP, Freudenthal BD, Yang K, Zhuang Z, Washington MT, Tainer JA, Ivanov I. Structurally Distinct Ubiquitin- and Sumo-Modified PCNA: Implications for Their Distinct Roles in the DNA Damage Response. Structure. 2015 Apr 7; 23(4):724-33. PMID: 25773143.
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      9. Tsutakawa S, Yan C, Xu X, Zhuang Z, Todd Washington M, Tainer JA, 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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      10. Dovega R, Tsutakawa S, Quistgaard EM, Anandapadamanaban M, Löw C, Nordlund P. Structural and biochemical characterization of human PR70 in isolation and in complex with the scaffolding subunit of protein phosphatase 2A. PLoS One. 2014; 9(7):e101846. PMID: 25007185; PMCID: PMC4090178.
      11. Tsutakawa S, 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; PMCID: PMC4051888.
      12. Dyer KN, Hammel M, Rambo RP, Tsutakawa S, 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; PMCID: PMC4057279.
      13. Kassube SA, Jinek M, Fang J, Tsutakawa S, Nogales E. Structural mimicry in transcription regulation of human RNA polymerase II by the DNA helicase RECQL5. Nat Struct Mol Biol. 2013 Jul; 20(7):892-9. PMID: 23748380; PMCID: PMC3702667.
      14. Hegde ML, Tsutakawa S, 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; PMCID: PMC3779128.
      15. Tsutakawa S, 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; PMCID: PMC3605660.
      16. Brosey CA, Yan C, Tsutakawa S, 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; PMCID: PMC3575853.
      17. Shi K, Kurahashi K, Gao R, Tsutakawa S, 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; PMCID: PMC3515695.
      18. Querol-Audí J, Yan C, Xu X, Tsutakawa S, 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; PMCID: PMC3365210.
      19. 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; PMCID: PMC3378889.
      20. Tsutakawa S, 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; PMCID: PMC3345168.
      21. 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; PMCID: PMC3728657.
      22. Brosey CA, Tsutakawa S, Chazin WJ. Sample preparation methods to analyze DNA-induced structural changes in replication protein A. Methods Mol Biol. 2012; 922:101-22. PMID: 22976179; PMCID: PMC3713622.
      23. Grasby JA, Finger LD, Tsutakawa S, 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; PMCID: PMC3341984.
      24. Tsutakawa S, 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; PMCID: PMC3203759.
      25. Tsutakawa S, 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; PMCID: PMC3086263.
      26. 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; PMCID: PMC3105414.
      27. Lintner NG, Frankel KA, Tsutakawa S, 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; PMCID: PMC4507800.
      28. 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; PMCID: PMC2847624.
      29. Hura GL, Menon AL, Hammel M, Rambo RP, Poole FL, Tsutakawa S, 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; PMCID: PMC3094553.
      30. Tsutakawa S, Kobayashi D, Kusama M, Moriya T, Nakahata N. Nicotine enhances skin necrosis and expression of inflammatory mediators in a rat pressure ulcer model. Br J Dermatol. 2009 Nov; 161(5):1020-7. PMID: 19673871.
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      31. Min X, Akella R, He H, Humphreys JM, Tsutakawa S, 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; PMCID: PMC3689539.
      32. Edwards RA, Lee MS, Tsutakawa S, 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; PMCID: PMC2654182.
      33. Tsutakawa S, 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.
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      34. Sarker AH, Tsutakawa S, 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.
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      35. Tsutakawa S, Morikawa K. The structural basis of damaged DNA recognition and endonucleolytic cleavage for very short patch repair endonuclease. Nucleic Acids Res. 2001 Sep 15; 29(18):3775-83. PMID: 11557809; PMCID: PMC55919.
      36. Tsutakawa S, Cooper PK. Transcription-coupled repair of oxidative DNA damage in human cells: mechanisms and consequences. Cold Spring Harb Symp Quant Biol. 2000; 65:201-15. PMID: 12760034.
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      37. Tsutakawa S, Morikawa K. New recognition mode for a TG mismatch: the atomic structure of a very short patch repair endonuclease-DNA complex. Cold Spring Harb Symp Quant Biol. 2000; 65:233-9. PMID: 12760037.
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      38. Tsutakawa S, Jingami H, Morikawa K. Recognition of a TG mismatch: the crystal structure of very short patch repair endonuclease in complex with a DNA duplex. Cell. 1999 Dec 10; 99(6):615-23. PMID: 10612397.
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      39. Tsutakawa S, Muto T, Kawate T, Jingami H, Kunishima N, Ariyoshi M, Kohda D, Nakagawa M, Morikawa K. Crystallographic and functional studies of very short patch repair endonuclease. Mol Cell. 1999 May; 3(5):621-8. PMID: 10360178.
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      40. Finer-Moore J, Tsutakawa S, Cherbavaz DR, LaPorte DC, Koshland DE, Stroud RM. Access to phosphorylation in isocitrate dehydrogenase may occur by domain shifting. Biochemistry. 1997 Nov 11; 36(45):13890-6. PMID: 9374867.
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      41. Tsutakawa S, Medzihradszky KF, Flint AJ, Burlingame AL, Koshland DE. Determination of in vivo phosphorylation sites in protein kinase C. J Biol Chem. 1995 Nov 10; 270(45):26807-12. PMID: 7592921.
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