D. Fujimori

发表

Assessment of the nucleotide modifications in the high-resolution cryo-electron microscopy structure of the Escherichia coli 50S subunit

J. Fraser, A. Frost, A. Myasnikov, 2020, Nucleic acids research.

A SARS-CoV-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Potential Drug-Repurposing

Trey Ideker, Claudia Hernandez-Armenta, Brian K. Shoichet, 2020, bioRxiv.

Halogenation strategies in natural product biosynthesis.

C. Walsh, C. Neumann, D. Fujimori, 2008, Chemistry & biology.

What's new in enzymatic halogenations.

C. Walsh, D. Fujimori, 2007, Current opinion in chemical biology.

Viral E protein neutralizes BET protein-mediated post-entry antagonism of SARS-CoV-2

M. Ott, K. Holden, Jared Carlson-Stevermer, 2022, Cell reports.

Catching BETs by viruses

M. Ott, T. Kutateladze, S. Byrareddy, 2022, Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms.

Domain cross-talk in regulation of histone modifications: Molecular mechanisms and targeting opportunities.

D. Fujimori, James E. Longbotham, Meng Yao Zhang, 2020, Current opinion in chemical biology.

Viral E protein neutralizes BET protein-mediated post-entry antagonism of SARS-CoV-2

M. Ott, K. Holden, Jared Carlson-Stevermer, 2022, Cell reports.

First-in-Class Allosteric Inhibitors of DNMT3A Disrupt Protein-Protein Interactions and Induce Acute Myeloid Leukemia Cell Differentiation.

N. Reich, M. Goodell, R. Ramabadran, 2022, Journal of medicinal chemistry.

Chromatin Sensing by the Auxiliary Domains of KDM5C Regulates Its Demethylase Activity and Is Disrupted by X-linked Intellectual Disability Mutations

M. Kelly, Fatima S. Ugur, D. Fujimori, 2022, bioRxiv.

Dissecting contributions of catalytic and reader domains in regulation of histone demethylation.

D. Fujimori, N. Petronikolou, James E. Longbotham, 2020, Methods in enzymology.

A SARS-CoV-2 Protein Interaction Map Reveals Targets for Drug-Repurposing

Benjamin J. Polacco, Robyn M. Kaake, Gwendolyn M. Jang, 2020, Nature.

Spectroscopic evidence for a high-spin Br-Fe(IV)-oxo intermediate in the alpha-ketoglutarate-dependent halogenase CytC3 from Streptomyces.

C. Walsh, C. Krebs, J. Bollinger, 2007, Journal of the American Chemical Society.

Covalent intermediate in the catalytic mechanism of the radical S-adenosyl-L-methionine methyl synthase RlmN trapped by mutagenesis.

C. Gross, K. Medzihradszky, R. Nichols, 2012, Journal of the American Chemical Society.

Improved Peak Detection and Deconvolution of Native Electrospray Mass Spectra from Large Protein Complexes

W. Chiu, S. Guan, A. Burlingame, 2015, Journal of The American Society for Mass Spectrometry.

Functional coupling between writers, erasers and readers of histone and DNA methylation.

I. O. Torres, D. Fujimori, 2015, Current opinion in structural biology.

Structural basis for context-specific inhibition of translation by oxazolidinone antibiotics

D. Klepacki, A. Mankin, N. Vázquez-Laslop, 2022, Nature Structural & Molecular Biology.

Structural basis for context-specific inhibition of translation by oxazolidinone antibiotics

A. Mankin, N. Vázquez-Laslop, J. Fraser, 2021, bioRxiv.

The chemistry of peptidyltransferase center-targeted antibiotics: enzymatic resistance and approaches to countering resistance.

Kevin P. McCusker, D. Fujimori, 2012, ACS chemical biology.

Mutations in RNA methylating enzymes in disease.

Danica Galonić Fujimori, Vanja Stojković, Vanja Stojković, 2017, Current opinion in chemical biology.

Histone demethylase KDM5A is regulated by its reader domain through a positive-feedback mechanism

Mark J. S. Kelly, Robert J. Fletterick, R. Fletterick, 2015, Nature Communications.

Product Binding Enforces the Genomic Specificity of a Yeast Polycomb Repressive Complex

J. Yates, H. Madhani, B. Strahl, 2015, Cell.

Opposing Chromatin Signals Direct and Regulate the Activity of Lysine Demethylase 4C (KDM4C)*

K. Yamamoto, Lindsey R. Pack, D. Fujimori, 2016, The Journal of Biological Chemistry.

Structure-based discovery of inhibitors of the SARS-CoV-2 Nsp14 N7-methyltransferase

Yurii S. Moroz, J. Irwin, B. Shoichet, 2023, bioRxiv.

High-resolution cryo-electron microscopy structure of the Escherichia coli 50S subunit and validation of nucleotide modifications

J. Fraser, A. Frost, A. Myasnikov, 2019, bioRxiv.

Antibiotic resistance evolved via inactivation of a ribosomal RNA methylating enzyme

Dan S. Tawfik, Vanja Stojković, D. Fujimori, 2016, Nucleic acids research.

Directed evolution of the rRNA methylating enzyme Cfr reveals molecular basis of antibiotic resistance.

Dan S. Tawfik, J. Fraser, S. Floor, 2022, eLife.

Histone H3 binding to the PHD1 domain of histone demethylase KDM5A enables active site remodeling

A. Burlingame, P. Griffin, M. Trnka, 2019, Nature Communications.

miCLIP-MaPseq, a Substrate Identification Approach for Radical SAM RNA Methylating Enzymes.

D. Weinberg, Gabriel Thérizols, Vanja Stojković, 2018, Journal of the American Chemical Society.

cfr(B), cfr(C), and a New cfr-Like Gene, cfr(E), in Clostridium difficile Strains Recovered across Latin America

D. Paredes-Sabja, M. Camorlinga, C. Rodríguez, 2019, Antimicrobial Agents and Chemotherapy.

Reconstitution of nucleosome demethylation and catalytic properties of a Jumonji histone demethylase.

A. Burlingame, M. Trnka, G. Narlikar, 2013, Chemistry & biology.

Structural Analysis of an Open Active Site Conformation of Nonheme Iron Halogenase CytC3

C. Walsh, C. Drennan, Cintyu Wong, 2009, Journal of the American Chemical Society.

RlmN and Cfr are radical SAM enzymes involved in methylation of ribosomal RNA.

J. Wiesner, H. Jomaa, A. Mankin, 2010, Journal of the American Chemical Society.

Cloning and characterization of the biosynthetic gene cluster for kutznerides

Sinisa Hrvatin, M. Marahiel, C. Walsh, 2007, Proceedings of the National Academy of Sciences.

Docking and Linking of Fragments To Discover Jumonji Histone Demethylase Inhibitors.

Elisabet Gregori-Puigjané, Udo Oppermann, Anthony Tumber, 2016, Journal of medicinal chemistry.

Determinants of tRNA Recognition by the Radical SAM Enzyme RlmN

D. G. Fujimori, C. Fitzsimmons, D. Fujimori, 2016, PloS one.

RNA methylation by Radical SAM enzymes RlmN and Cfr proceeds via methylene transfer and hydride shift

F. Yan, D. Fujimori, 2011, Proceedings of the National Academy of Sciences.

A SARS-CoV-2 protein interaction map reveals targets for drug repurposing

Robyn M. Kaake, Gwendolyn M. Jang, Matthew J. O’Meara, 2020, Nature.

Radical SAM-mediated methylation reactions.

D. G. Fujimori, D. Fujimori, 2013, Current opinion in chemical biology.

Protein and nucleic acid methylating enzymes: mechanisms and regulation.

D. Le, D. Fujimori, 2012, Current opinion in chemical biology.

Histone H3 binding to the PHD1 domain of histone demethylase KDM5A enables active site remodeling

A. Burlingame, P. Griffin, M. Trnka, 2019, Nature Communications.

Chemical tools targeting readers of lysine methylation

T. Kutateladze, D. Fujimori, G. Ortiz, 2023, Current opinion in chemical biology.

CD and MCD of CytC3 and taurine dioxygenase: role of the facial triad in alpha-KG-dependent oxygenases.

J. C. Price, C. Walsh, Elizabeth M. Nolan, 2007, Journal of the American Chemical Society.

Covalent labeling of a chromatin reader domain using proximity-reactive cyclic peptides

A. Burlingame, W. DeGrado, M. Trnka, 2022, Chemical science.

Site-specific and regiospecific installation of methylarginine analogues into recombinant histones and insights into effector protein binding.

A. Burlingame, D. Le, D. Fujimori, 2013, Journal of the American Chemical Society.

Htm1p–Pdi1p is a folding-sensitive mannosidase that marks N-glycoproteins for ER-associated protein degradation

J. Weissman, Yi-Chang Liu, D. Fujimori, 2016, Proceedings of the National Academy of Sciences.

Non‐Heme Fe(IV)—Oxo Intermediates

C. Walsh, C. Krebs, J. Bollinger, 2007 .

Exploring the Ligand Preferences of the PHD1 Domain of Histone Demethylase KDM5A Reveals Tolerance for Modifications of the Q5 Residue of Histone 3.

M. Mrksich, Fatima S. Ugur, P. O’Kane, 2020, ACS chemical biology.

Extended Recognition of the Histone H3 Tail by Histone Demethylase KDM5A

D. Fujimori, N. Petronikolou, James E. Longbotham, 2019, bioRxiv.

Directed evolution of the rRNA methylating enzyme Cfr reveals molecular basis of antibiotic resistance

Dan S. Tawfik, J. Fraser, S. Floor, 2021, bioRxiv.

cfrB, cfrC, and a potential new cfr-like gene in Clostridium difficile strains recovered across Latin America

D. Paredes-Sabja, M. Camorlinga, C. Rodríguez, 2019, bioRxiv.

miCLIP-MaPseq Identifies Substrates of Radical SAM RNA-Methylating Enzyme Using Mechanistic Cross-Linking and Mismatch Profiling.

D. Weinberg, Vanja Stojković, D. Fujimori, 2021, Methods in molecular biology.

Radical SAM-Mediated Methylation of Ribosomal RNA.

Vanja Stojković, D. Fujimori, 2015, Methods in enzymology.

Chromatin Sensing by the Auxiliary Domains of KDM5C Regulates Its Demethylase Activity and Is Disrupted by X-linked Intellectual Disability Mutations

Danica Galonić Fujimori, M. Kelly, Fatima S. Ugur, 2022, bioRxiv.

miCLIP-MaPseq, a Substrate Identification Approach for Radical SAM RNA Methylating Enzymes.

D. Weinberg, Gabriel Thérizols, Vanja Stojković, 2018, Journal of the American Chemical Society.

Radical SAM-Mediated Methylation of Ribosomal RNA.

Vanja Stojković, D. Fujimori, 2015, Methods in enzymology.

Recent developments in catalysis and inhibition of the Jumonji histone demethylases

D. Fujimori, Letitia Sarah, 2023, Current opinion in structural biology.

Angucyclinones rescue PhLOPSA antibiotic activity by inhibiting Cfr-dependent antibiotic resistance

D. Fujimori, K. Tsai, A. Schaenzer, 2023, mBio.

Structural basis for context-specific inhibition of translation by oxazolidinone antibiotics

D. Klepacki, A. Mankin, N. Vázquez-Laslop, 2022, Nature Structural & Molecular Biology.