Susan E. Tsutakawa - Publications

Affiliations: 
Lawrence Berkeley National Laboratory, Berkeley, CA, USA 

64 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2024 Woltz R, Schweibenz B, Tsutakawa SE, Zhao C, Ma L, Shurina B, Hura GL, John R, Vorobiev S, Swapna G, Solotchi M, Tainer JA, Krug RM, Patel SS, Montelione GT. The NS1 protein of influenza B virus binds 5'-triphosphorylated dsRNA to suppress RIG-I activation and the host antiviral response. Biorxiv : the Preprint Server For Biology. PMID 38328244 DOI: 10.1101/2023.09.25.559316  0.432
2023 Yu J, Yan C, Dodd T, Tsai CL, Tainer JA, Tsutakawa SE, Ivanov I. Dynamic conformational switching underlies TFIIH function in transcription and DNA repair and impacts genetic diseases. Nature Communications. 14: 2758. PMID 37179334 DOI: 10.1038/s41467-023-38416-6  0.545
2023 LeBleu VS, Dai J, Tsutakawa S, MacDonald BA, Alge JL, Sund M, Xie L, Sugimoto H, Tainer J, Zon LI, Kalluri R. Identification of unique α4 chain structure and conserved antiangiogenic activity of α3NC1 type IV collagen in zebrafish. Developmental Dynamics : An Official Publication of the American Association of Anatomists. PMID 37002899 DOI: 10.1002/dvdy.590  0.353
2022 Chinnam NB, Syed A, Hura GL, Hammel M, Tainer JA, Tsutakawa SE. Combining small angle X-ray scattering (SAXS) with protein structure predictions to characterize conformations in solution. Methods in Enzymology. 678: 351-376. PMID 36641214 DOI: 10.1016/bs.mie.2022.09.023  0.67
2022 Bralić A, Tehseen M, Sobhy MA, Tsai CL, Alhudhali L, Yi G, Yu J, Yan C, Ivanov I, Tsutakawa SE, Tainer JA, Hamdan SM. A scanning-to-incision switch in TFIIH-XPG induced by DNA damage licenses nucleotide excision repair. Nucleic Acids Research. PMID 36477609 DOI: 10.1093/nar/gkac1095  0.575
2022 Chinnam NB, Syed A, Burnett KH, Hura GL, Tainer JA, Tsutakawa SE. Universally Accessible Structural Data on Macromolecular Conformation, Assembly, and Dynamics by Small Angle X-Ray Scattering for DNA Repair Insights. Methods in Molecular Biology (Clifton, N.J.). 2444: 43-68. PMID 35290631 DOI: 10.1007/978-1-0716-2063-2_4  0.753
2021 Tsutakawa SE, Bacolla A, Katsonis P, Bralić A, Hamdan SM, Lichtarge O, Tainer JA, Tsai CL. Decoding Cancer Variants of Unknown Significance for Helicase-Nuclease-RPA Complexes Orchestrating DNA Repair During Transcription and Replication. Frontiers in Molecular Biosciences. 8: 791792. PMID 34966786 DOI: 10.3389/fmolb.2021.791792  0.491
2021 Moiani D, Link TM, Brosey CA, Katsonis P, Lichtarge O, Kim Y, Joachimiak A, Ma Z, Kim IK, Ahmed Z, Jones DE, Tsutakawa SE, Tainer JA. An efficient chemical screening method for structure-based inhibitors to nucleic acid enzymes targeting the DNA repair-replication interface and SARS CoV-2. Methods in Enzymology. 661: 407-431. PMID 34776222 DOI: 10.1016/bs.mie.2021.09.003  0.46
2021 Alexander LT, Lepore R, Kryshtafovych A, Adamopoulos A, Alahuhta M, Arvin AM, Bomble YJ, Böttcher B, Breyton C, Chiarini V, Chinnam NB, Chiu W, Fidelis K, Grinter R, Gupta GD, ... ... Tsutakawa SE, et al. Target highlights in CASP14: analysis of models by structure providers. Proteins. PMID 34561912 DOI: 10.1002/prot.26247  0.445
2021 Hambarde S, Tsai CL, Pandita RK, Bacolla A, Maitra A, Charaka V, Hunt CR, Kumar R, Limbo O, Le Meur R, Chazin WJ, Tsutakawa SE, Russell P, Schlacher K, Pandita TK, et al. EXO5-DNA structure and BLM interactions direct DNA resection critical for ATR-dependent replication restart. Molecular Cell. PMID 34197737 DOI: 10.1016/j.molcel.2021.05.027  0.61
2021 Tsutakawa SE, Sarker AH. Breaking the Rules: Protein Sculpting in NEIL2 Regulation. Structure (London, England : 1993). 29: 1-2. PMID 33417890 DOI: 10.1016/j.str.2020.12.011  0.361
2020 Lees-Miller JP, Cobban A, Katsonis P, Bacolla A, Tsutakawa SE, Hammel M, Meek K, Anderson DW, Lichtarge O, Tainer JA, Lees-Miller SP. Uncovering DNA-PKcs ancient phylogeny, unique sequence motifs and insights for human disease. Progress in Biophysics and Molecular Biology. PMID 33035590 DOI: 10.1016/j.pbiomolbio.2020.09.010  0.607
2020 Tsutakawa SE, Tsai CL, Yan C, Bralić A, Chazin WJ, Hamdan SM, Schärer OD, Ivanov I, Tainer JA. Envisioning how the prototypic molecular machine TFIIH functions in transcription initiation and DNA repair. Dna Repair. 96: 102972. PMID 33007515 DOI: 10.1016/J.Dnarep.2020.102972  0.648
2020 Tsutakawa SE, Sarker AH, Ng C, Arvai AS, Shin DS, Shih B, Jiang S, Thwin AC, Tsai MS, Willcox A, Her MZ, Trego KS, Raetz AG, Rosenberg D, Bacolla A, et al. Human XPG nuclease structure, assembly, and activities with insights for neurodegeneration and cancer from pathogenic mutations. Proceedings of the National Academy of Sciences of the United States of America. PMID 32522879 DOI: 10.1073/Pnas.1921311117  0.73
2019 Hura GL, Hodge CD, Rosenberg D, Guzenko D, Duarte JM, Monastyrskyy B, Grudinin S, Kryshtafovych A, Tainer JA, Fidelis K, Tsutakawa SE. Small angle X-ray scattering-assisted protein structure prediction in CASP13 and emergence of solution structure differences. Proteins. PMID 31589784 DOI: 10.1002/Prot.25827  0.54
2019 Yan C, Dodd T, He Y, Tainer JA, Tsutakawa SE, Ivanov I. Transcription preinitiation complex structure and dynamics provide insight into genetic diseases. Nature Structural & Molecular Biology. PMID 31110295 DOI: 10.1038/s41594-019-0220-3  0.576
2019 Yan C, Dodd T, He Y, Tainer JA, Tsutakawa SE, Ivanov I. Transcription preinitiation complex structure and dynamics provide insight into genetic diseases. Nature Structural & Molecular Biology. 26: 397-406. DOI: 10.2210/Pdb6O9M/Pdb  0.506
2019 Yan C, Todd T, He Y, Tsutakawa SE, Ivanov I, Tainer JA. Transcription pre-initiation complex with TFIIH reveals transcription-ready repair-regulated helicase machine from combined cryo-EM and crystallography datasets Acta Crystallographica Section a Foundations and Advances. 75: a161-a161. DOI: 10.1107/S0108767319098398  0.325
2018 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. Nature Structural & Molecular Biology. PMID 29786079 DOI: 10.1038/S41594-018-0065-1  0.641
2018 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. PMID 29314274 DOI: 10.1002/Prot.25452  0.524
2018 Ogorzalek TL, Hura GL, Kryshtafovych A, Tainer JA, Fidelis K, Tsutakawa SE. Small Angle X-ray Scattering for Data-Assisted Structure Prediction in CASP12 with Prospects to Improve Accuracy Biophysical Journal. 114: 576a-577a. DOI: 10.1016/J.Bpj.2017.11.3152  0.497
2017 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, et al. Corrigendum: Phosphate steering by Flap Endonuclease 1 promotes 5'-flap specificity and incision to prevent genome instability. Nature Communications. 8: 16145. PMID 31305777 DOI: 10.1038/ncomms16145  0.39
2017 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, et al. Phosphate steering by Flap Endonuclease 1 promotes 5'-flap specificity and incision to prevent genome instability. Nature Communications. 8: 15855. PMID 28653660 DOI: 10.1038/Ncomms15855  0.625
2017 Leksa NC, Chiu PL, Bou-Assaf GM, Quan C, Liu Z, Goodman AB, Chambers MG, Tsutakawa SE, 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. Journal of Thrombosis and Haemostasis : Jth. PMID 28397397 DOI: 10.1111/Jth.13700  0.317
2017 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. 6. PMID 28230529 DOI: 10.7554/Elife.21884  0.656
2017 Tainer JA, Tsutakawa SE, Hura GL, Hammel M. Super resolution for X-ray scattering and biological insights from its applications to dynamic DNA replication and repair complexes Acta Crystallographica Section a Foundations and Advances. 73: a314-a314. DOI: 10.1107/S0108767317096921  0.589
2016 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. Molecular Cell. 64: 688-703. PMID 27871365 DOI: 10.1016/J.Molcel.2016.09.031  0.646
2015 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. PMID 26675729 DOI: 10.1038/Nature16162  0.538
2015 Tsutakawa SE, 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. Journal of Biomolecular Structure & Dynamics. 33: 70-1. PMID 26103323 DOI: 10.1080/07391102.2015.1032745  0.661
2015 Tsutakawa SE, Tainer JA. Bending Forks and Wagging Dogs--It's about the DNA 3' Tail. Molecular Cell. 58: 972-3. PMID 26091346 DOI: 10.1016/J.Molcel.2015.06.005  0.601
2015 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 (London, England : 1993). 23: 724-33. PMID 25773143 DOI: 10.1016/J.Str.2015.02.008  0.662
2014 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. 9: e101846. PMID 25007185 DOI: 10.1371/Journal.Pone.0101846  0.371
2014 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. 19: 95-107. PMID 24754999 DOI: 10.1016/J.Dnarep.2014.03.022  0.661
2014 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 in Molecular Biology (Clifton, N.J.). 1091: 245-58. PMID 24203338 DOI: 10.1007/978-1-62703-691-7_18  0.462
2014 Tsutakawa S, Yan C, Xu X, Freudenthal B, Weinacht C, Zhuang Z, Washington T, Ivanov I. Structurally Distinct Complexes of Ubiquitin and Sumo-Modified PCNA Lead to Distinct DNA Damage Response Pathways Biophysical Journal. 106: 691a. DOI: 10.1016/J.Bpj.2013.11.3823  0.488
2014 Tsutakawa S, Arvai A, Sarker A, Querol-Audi J, Finger D, Nogales E, Ivanov I, Cooper P, Grasby J, Tainer J. Defining the Superfamily Conserved Mechanism for Flap Endonucleases FEN1 and XPG Specificity for 5' Flap DNA and DNA Bubbles, Respectively, by Hybrids Methods of Crystallography, SAXS, EM, and Computation Biophysical Journal. 106: 230a. DOI: 10.1016/J.Bpj.2013.11.1343  0.699
2013 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. Nature Structural & Molecular Biology. 20: 892-9. PMID 23748380 DOI: 10.1038/Nsmb.2596  0.462
2013 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. Journal of Molecular Biology. 425: 2359-71. PMID 23542007 DOI: 10.1016/J.Jmb.2013.03.030  0.615
2013 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, et al. Conserved structural chemistry for incision activity in structurally non-homologous apurinic/apyrimidinic endonuclease APE1 and endonuclease IV DNA repair enzymes. The Journal of Biological Chemistry. 288: 8445-55. PMID 23355472 DOI: 10.1074/Jbc.M112.422774  0.754
2013 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 Research. 41: 2313-27. PMID 23303776 DOI: 10.1093/Nar/Gks1332  0.666
2012 Shi K, Kurahashi K, Gao R, Tsutakawa SE, Tainer JA, Pommier Y, Aihara H. Structural basis for recognition of 5′-phosphotyrosine adducts by Tdp2 Nature Structural and Molecular Biology. 19: 1372-1377. PMID 23104058 DOI: 10.1038/Nsmb.2423  0.671
2012 Brosey CA, Tsutakawa SE, Chazin WJ. Sample preparation methods to analyze DNA-induced structural changes in replication protein A. Methods in Molecular Biology (Clifton, N.J.). 922: 101-22. PMID 22976179 DOI: 10.1007/978-1-62703-032-8_6  0.554
2012 Finger LD, Atack JM, Tsutakawa S, Classen S, Tainer J, Grasby J, Shen B. The wonders of flap endonucleases: structure, function, mechanism and regulation. Sub-Cellular Biochemistry. 62: 301-26. PMID 22918592 DOI: 10.1007/978-94-007-4572-8_16  0.683
2012 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. Proceedings of the National Academy of Sciences of the United States of America. 109: 8528-33. PMID 22586102 DOI: 10.1073/Pnas.1121116109  0.658
2012 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 Research. 40: 4507-19. PMID 22319208 DOI: 10.1093/Nar/Gks051  0.618
2012 Tsutakawa SE, Tainer JA. Double strand binding-single strand incision mechanism for human flap endonuclease: implications for the superfamily. Mechanisms of Ageing and Development. 133: 195-202. PMID 22244820 DOI: 10.1016/J.Mad.2011.11.009  0.674
2012 Grasby JA, Finger LD, Tsutakawa SE, Atack JM, Tainer JA. Unpairing and gating: sequence-independent substrate recognition by FEN superfamily nucleases. Trends in Biochemical Sciences. 37: 74-84. PMID 22118811 DOI: 10.1016/J.Tibs.2011.10.003  0.642
2012 Kulman J, Tsutakawa S, Bou-Assaf G, Berkowitz S, Light DR, Mezo A, Wang D, Whitlow M, Culyba L, Tainer J, Peters R. Structural Comparability Between Recombinant FVIII-Fc and Its Isolated FVIII and Fc Constituents Blood. 120: 1135-1135. DOI: 10.1182/Blood.V120.21.1135.1135  0.528
2011 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. Proceedings of the National Academy of Sciences of the United States of America. 108: 17672-7. PMID 22006297 DOI: 10.1073/Pnas.1110480108  0.739
2011 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. 145: 198-211. PMID 21496641 DOI: 10.1016/J.Cell.2011.03.004  0.805
2011 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 Research. 39: 4450-63. PMID 21278162 DOI: 10.1093/Nar/Gkr025  0.515
2011 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. Journal of Molecular Biology. 405: 939-55. PMID 21093452 DOI: 10.1016/J.Jmb.2010.11.019  0.586
2010 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. 49: 2880-9. PMID 20184389 DOI: 10.1021/Bi9019934  0.632
2009 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). Nature Methods. 6: 606-12. PMID 19620974 DOI: 10.1038/Nmeth.1353  0.547
2009 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 (London, England : 1993). 17: 96-104. PMID 19141286 DOI: 10.1016/J.Str.2008.11.007  0.55
2009 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), 47, 44 (11446-11456)) Biochemistry. 48: 4008. DOI: 10.1021/Bi900462X  0.487
2008 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. 47: 11446-56. PMID 18842000 DOI: 10.1021/Bi801115G  0.627
2007 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. Journal of Structural Biology. 158: 214-23. PMID 17182256 DOI: 10.1016/J.Jsb.2006.09.008  0.598
2005 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. Molecular Cell. 20: 187-98. PMID 16246722 DOI: 10.1016/J.Molcel.2005.09.022  0.687
2003 Tsutakawa SE, Morikawa K. New recognition mode for a TG mismatch: the atomic structure of a very short patch repair endonuclease-DNA complex. Cold Spring Harbor Symposia On Quantitative Biology. 65: 233-9. PMID 12760037 DOI: 10.1101/Sqb.2000.65.233  0.454
2001 Tsutakawa SE, Morikawa K. The structural basis of damaged DNA recognition and endonucleolytic cleavage for very short patch repair endonuclease. Nucleic Acids Research. 29: 3775-83. PMID 11557809 DOI: 10.1093/Nar/29.18.3775  0.546
2000 Tsutakawa SE, Cooper PK. Transcription-coupled repair of oxidative dna damage in human cells: Mechanisms and consequences Cold Spring Harbor Symposia On Quantitative Biology. 65: 201-215. PMID 12760034 DOI: 10.1101/Sqb.2000.65.201  0.419
2000 Tsutakawa SE, 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. 99: 615-23. PMID 10612397 DOI: 10.1016/S0092-8674(00)81550-0  0.555
1999 Tsutakawa SE, 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. Molecular Cell. 3: 621-8. PMID 10360178 DOI: 10.1016/S1097-2765(00)80355-X  0.499
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