S. Tsutakawa

发表

Conformational Dynamics in the Interaction of SARS-CoV-2 Papain-like Protease with Human Interferon-Stimulated Gene 15 Protein

H. O’Neill, S. Qian, Wellington Leite, 2021, The journal of physical chemistry letters.

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

John A Tainer, Jose M. Duarte, Krzysztof Fidelis, 2019, Proteins.

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

John A Tainer, Kun Yang, Xiaojun Xu, 2015, Structure.

Structural and Biochemical Characterization of Human PR70 in Isolation and in Complex with the Scaffolding Subunit of Protein Phosphatase 2A

P. Nordlund, R. Dovega, S. Tsutakawa, 2014, PloS one.

High-throughput SAXS for the characterization of biomolecules in solution: a practical approach.

John A Tainer, Greg L. Hura, Greg L Hura, 2014, Methods in molecular biology.

Sample preparation methods to analyze DNA-induced structural changes in replication protein A.

W. Chazin, S. Tsutakawa, C. Brosey, 2012, Methods in molecular biology.

The structure of the CRISPR-associated protein Csa3 provides insight into the regulation of the CRISPR/Cas system.

J. Tainer, K. Frankel, M. Young, 2011, Journal of molecular biology.

Structural dynamics and ssDNA binding activity of the three N-terminal domains of the large subunit of Replication Protein A from small angle X-ray scattering

John A. Tainer, Walter J. Chazin, Marie-Eve, 2010 .

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.

Dalyir I. Pretto, John A Tainer, J. Tainer, 2010, Biochemistry.

The BARD1 C-Terminal Domain Structure and Interactions with Polyadenylation Factor CstF-50

J. Tainer, J. Glover, S. Tsutakawa, 2008, Biochemistry.

Uncovering DNA-PKcs ancient phylogeny, unique sequence motifs and insights for human disease

O. Lichtarge, J. Tainer, Panagiotis Katsonis, 2020, Progress in biophysics and molecular biology.

The cutting edges in DNA repair, licensing, and fidelity: DNA and RNA repair nucleases sculpt DNA to measure twice, cut once.

J. Tainer, J. Lafrance-Vanasse, S. Tsutakawa, 2014, DNA repair.

Super resolution for X-ray scattering and biological insights from its applications to dynamic DNA replication and repair complexes

Greg L. Hura, J. Tainer, M. Hammel, 2017 .

Double strand binding–single strand incision mechanism for human flap endonuclease: Implications for the superfamily

J. Tainer, S. Tsutakawa, 2012, Mechanisms of Ageing and Development.

Robust, high-throughput solution structural analyses by small angle X-ray scattering (SAXS)

John A. Tainer, Susan E. Tsutakawa, Greg L. Hura, 2009, Nature Methods.

Structural mimicry in transcription regulation of human RNA polymerase II by the DNA helicase RECQL5

E. Nogales, M. Jinek, Jie Fang, 2013, Nature Structural &Molecular Biology.

Mapping interactions between the RNA chaperone FinO and its RNA targets

J. Tainer, J. Glover, J. Glover, 2011, Nucleic acids research.

Human XPG nuclease structure, assembly, and activities with insights for neurodegeneration and cancer from pathogenic mutations

Daniel J. Rosenberg, J. Tainer, J. Griffith, 2020, Proceedings of the National Academy of Sciences.

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

J. Tainer, S. Mirkin, S. Hamdan, 2017, Nature Communications.

Strengthening of enterococcal biofilms by Esp

Greg L. Hura, V. Nizet, Ashok Kumar, 2022, bioRxiv.

Access to phosphorylation in isocitrate dehydrogenase may occur by domain shifting.

D. Koshland, R. Stroud, J. Finer-Moore, 1997, Biochemistry.

Transcription preinitiation complex structure and dynamics provide insight into genetic diseases

J. Tainer, Chunli Yan, S. Tsutakawa, 2019, Nature Structural & Molecular Biology.

New recognition mode for a TG mismatch: the atomic structure of a very short patch repair endonuclease-DNA complex.

K. Morikawa, S. Tsutakawa, 2000, Cold Spring Harbor symposia on quantitative biology.

The wonders of flap endonucleases: structure, function, mechanism and regulation.

J. Tainer, S. Classen, L. Finger, 2012, Sub-cellular biochemistry.

Identification of unique α4 chain structure and conserved anti-angiogenic activity of α3NC1 type IV collagen in zebrafish

L. Zon, J. Tainer, V. LeBleu, 2022, bioRxiv.

structural in non-homologous apurinic/apyrimidinic endonuclease APE1 and endonuclease IV DNA repair enzymes.

J. Tainer, M. Pique, C. Mol, 2013 .

The structural basis for the functional comparability of factor VIII and the long‐acting variant recombinant factor VIII Fc fusion protein

T. Walz, M. Hammel, S. Tsutakawa, 2017, Journal of thrombosis and haemostasis : JTH.

Lawrence Berkeley National Laboratory Recent Work Title The structural basis for the functional comparability of factor VIII and the long-acting variant recombinant factor VIII Fc fusion protein Permalink

M. Hammel, S. Tsutakawa, J. Kulman, 2017 .

Recognition of RNA polymerase II and transcription bubbles by XPG, CSB, and TFIIH: insights for transcription-coupled repair and Cockayne Syndrome.

E. Nogales, J. Tainer, Seth A. Kostek, 2005, Molecular cell.

EXO5-DNA structure and BLM interactions direct DNA resection critical for ATR-dependent replication restart.

P. Russell, J. Tainer, T. Pandita, 2021, Molecular cell.

Structural and Biochemical Characterization of Human PR 70 in Isolation and in Complex with the Scaffolding Subunit of Protein Phosphatase 2 A

P. Nordlund, R. Dovega, S. Tsutakawa, 2018 .

Decoding Cancer Variants of Unknown Significance for Helicase–Nuclease–RPA Complexes Orchestrating DNA Repair During Transcription and Replication

O. Lichtarge, J. Tainer, S. Hamdan, 2021, Frontiers in Molecular Biosciences.

Target highlights in CASP14: Analysis of models by structure providers

K. Fidelis, J. Moult, J. Tainer, 2021, Proteins.

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

J. Tainer, S. Boulton, S. Tsutakawa, 2016, Molecular cell.

Envisioning how the prototypic molecular machine TFIIH functions in transcription initiation and DNA repair.

J. Tainer, S. Hamdan, W. Chazin, 2020, DNA repair.

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

Juri Rappsilber, John A Tainer, Adam Belsom, 2018, Proteins.

The structure of the MAP2K MEK6 reveals an autoinhibitory dimer.

John A Tainer, Radha Akella, Haixia He, 2009, Structure.

Determination of in Vivo Phosphorylation Sites in Protein Kinase C (*)

D. Koshland, A. Burlingame, K. Medzihradszky, 1995, The Journal of Biological Chemistry.

Lawrence Berkeley National Laboratory Recent Work Title Mechanism and Regulation of DNA-Protein Crosslink Repair by the DNA-Dependent Metalloprotease

J. Tainer, S. Boulton, S. Tsutakawa, 2022 .

Exploring the repeat protein universe through computational protein design

David Baker, John A. Tainer, Po-Ssu Huang, 2015, Nature.

Efficient production of oxidized terpenoids via engineering fusion proteins of terpene synthase and cytochrome P450.

J. H. Pereira, P. Adams, A. Mukhopadhyay, 2021, Metabolic engineering.

Human Flap Endonuclease Structures, DNA Double-Base Flipping, and a Unified Understanding of the FEN1 Superfamily

J. Tainer, S. Classen, L. Finger, 2011, Cell.

Recognition of a TG Mismatch The Crystal Structure of Very Short Patch Repair Endonuclease in Complex with a DNA Duplex

K. Morikawa, S. Tsutakawa, H. Jingami, 1999, Cell.

Transcription-coupled repair of oxidative DNA damage in human cells: mechanisms and consequences.

S. Tsutakawa, P. Cooper, 2001, Cold Spring Harbor symposia on quantitative biology.

Flap endonucleases pass 5′-flaps through a flexible arch using a disorder-thread-order mechanism to confer specificity for free 5′-ends

J. Tainer, L. Finger, J. Exell, 2012, Nucleic acids research.

Crystallographic and functional studies of very short patch repair endonuclease.

N. Kunishima, D. Kohda, K. Morikawa, 1999, Molecular cell.

Transient and stabilized complexes of Nsp7, Nsp8, and Nsp12 in SARS-CoV-2 replication

Greg L. Hura, Daniel J. Rosenberg, A. Joachimiak, 2021, Biophysical Journal.

Unpairing and gating: sequence-independent substrate recognition by FEN superfamily nucleases.

J. Tainer, L. Finger, J. Grasby, 2012, Trends in biochemical sciences.

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

T. Blundell, J. Tainer, S. Lees-Miller, 2018, Nature Structural & Molecular Biology.

The structural basis of damaged DNA recognition and endonucleolytic cleavage for very short patch repair endonuclease.

K. Morikawa, S. Tsutakawa, Kosuke Morikawa, 2001, Nucleic acids research.

Lawrence Berkeley National Laboratory Recent Work Title

K. Morikawa, S. Tsutakawa, 2001 .

A new structural framework for integrating replication protein A into DNA processing machinery

J. Tainer, W. Chazin, R. Rambo, 2013, Nucleic acids research.

A scanning-to-incision switch in TFIIH-XPG induced by DNA damage licenses nucleotide excision repair

J. Tainer, S. Hamdan, Chunli Yan, 2022, Nucleic acids research.

Solution X-ray scattering combined with computational modeling reveals multiple conformations of covalently bound ubiquitin on PCNA

Adam W Van Wynsberghe, J. Tainer, Zhihao Zhuang, 2011, Proceedings of the National Academy of Sciences.

Structure of the human apo TFIIH

J. Tainer, Chunli Yan, S. Tsutakawa, 2019 .

Structural basis for recognition of 5′-phosphotyrosine adducts by TDP2

Y. Pommier, J. Tainer, K. Shi, 2009, Nature Structural &Molecular Biology.

The disordered C-terminal domain of human DNA glycosylase NEIL1 contributes to its stability via intramolecular interactions.

N. Oezguen, J. Tainer, V. Hilser, 2013, Journal of molecular biology.

Repair complexes of FEN1 endonuclease, DNA, and Rad9-Hus1-Rad1 are distinguished from their PCNA counterparts by functionally important stability

E. Nogales, J. Tainer, Xiaojun Xu, 2012, Proceedings of the National Academy of Sciences.

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

J. Tainer, Xiaojun Xu, Zhihao Zhuang, 2015, Journal of biomolecular structure & dynamics.

An efficient chemical screening method for structure-based inhibitors to nucleic acid enzymes targeting the DNA repair-replication interface and SARS CoV-2

O. Lichtarge, J. Tainer, A. Joachimiak, 2021, Methods in Enzymology.

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

J. Tainer, S. Hamdan, Chunli Yan, 2017, eLife.

Conserved Structural Chemistry for Incision Activity in Structurally Non-homologous Apurinic/Apyrimidinic Endonuclease APE1 and Endonuclease IV DNA Repair Enzymes*

J. Tainer, M. Pique, K. Frankel, 2013, The Journal of Biological Chemistry.

Identification of unique α4 chain structure and conserved anti-angiogenic activity of α3NC1 type IV collagen in zebrafish

L. Zon, J. Tainer, R. Kalluri, 2023, bioRxiv.

Dynamic conformational switching underlies TFIIH function in transcription and DNA repair and impacts genetic diseases

J. Tainer, Chunli Yan, S. Tsutakawa, 2023, Nature communications.

Transcription preinitiation complex structure and dynamics provide insight into genetic diseases

J. Tainer, Chunli Yan, S. Tsutakawa, 2019, Nature Structural & Molecular Biology.

The role of XPB/Ssl2 dsDNA translocation processivity in transcription-start-site scanning.

D. Taatjes, S. Hahn, S. Tsutakawa, 2021, Journal of molecular biology.

The role of XPB/Ssl2 dsDNA translocation processivity in transcription-start-site scanning

D. Taatjes, S. Hahn, S. Tsutakawa, 2020, bioRxiv.

Transient and stabilized complexes of Nsp7, Nsp8, and Nsp12 in SARS-CoV-2 replication

Greg L. Hura, Daniel J. Rosenberg, A. Joachimiak, 2021, Biophysical Journal.

Supplementary Fig. 1

B. Novák, Y. Pommier, J. Tainer, 2021 .

Structural basis for recognition of 5 ′-phosphotyrosine adducts by TDP 2

Yves, J. Tainer, K. Shi, 2013 .

Structural analysis of flexible proteins in solution by small angle X-ray scattering combined with crystallography.

John A Tainer, Greg L. Hura, Greg L Hura, 2006, Journal of structural biology.

The BARD1 C-Terminal Domain Structure and Interactions with Polyadenylation Factor CstF-50

J. Tainer, J. Glover, S. Tsutakawa, 2009, Biochemistry.

The NS1 protein of influenza B virus binds 5’-triphosphorylated dsRNA to suppress RIG-I activation and the antiviral innate immune response

G. Montelione, J. Tainer, S. Vorobiev, 2023 .

The NS1 protein of influenza B virus binds 5’-triphosphorylated dsRNA to suppress RIG-I activation and the host antiviral response

G. Montelione, J. Tainer, S. Vorobiev, 2024, bioRxiv.

Conserved Structural Chemistry for Incision Activity in Structurally Non-homologous Apurinic/Apyrimidinic Endonuclease APE1 and Endonuclease IV DNA Repair Enzymes*

J. Tainer, M. Pique, K. Frankel, 2013, The Journal of Biological Chemistry.

ASCC1 structures and bioinformatics reveal a novel helix-clasp-helix RNA-binding motif linked to a two-histidine phosphodiesterase

Daniel J. Rosenberg, J. Tainer, Panagiotis Katsonis, 2024, Journal of Biological Chemistry.