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Publications


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Sandoval JE et al. First-in-Class Allosteric Inhibitors of DNMT3A Disrupt Protein-Protein Interactions and Induce Acute Myeloid Leukemia Cell Differentiation. J. Med. Chem. 2022 July 22.
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Chen IP, Longbotham JE et al. Viral E Protein Neutralizes BET Protein-Mediated Post-Entry Antagonism of SARS-CoV-2. Cell Rep. 2022 June 27.
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Zhang MY, Yang H, Ortiz G, Trnka MJ, Petronikolou N, Burlingame AL, DeGrado B, Fujimori DG. Covalent labeling of a chromatin reader domain using proximity- reactive cyclic peptides. Chem. Sci. 2022 May 10.
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Tsai K, Stojković V, Lee DJ, Young ID, Szal T, Vasquez-Laslop N, Mankin AS, Fraser JS, Fujimori DG. Structural basis for context-specific inhibition of translation by oxazolidinone antibiotics.
Nat. Struct. Mol. Biol. 2022 Feb 29.
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Tsai K, Stojković V, Noda-Garcia L, Young ID, Myasnikov AG, Kleinman J, Palla A, Floor SN, Frost A, Fraser JS, Tawfik DS, Fujimori DG. Directed evolution of the rRNA methylating enzyme Cfr reveals molecular basis of antibiotic resistance. eLife 2022 Jan 11.
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Stojković V, Weinberg DE, Fujimori DG. miCLIP-MaPseq Identifies Substrates of Radical SAM RNA-Methylating Enzyme Using Mechanistic Cross-Linking and Mismatch Profiling. Methods Mol. Biol. 2021 Jun 4.
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Longbotham JE, Kelly MJS, Fujimori DG. Recognition of Histone H3 Methylation States by the PHD1 Domain of Histone Demethylase KDM5A. ACS Chem. Biol. 2021 Feb 18.
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Anderson SE, Longbotham JE, O'Kane PT, Ugur FS, Fujimori DG, Mrksich M. Exploring the Ligand Preferences of the PHD1 Domain of Histone Demethylase KDM5A Reveals Tolerance for Modifications of the Q5 Residue of Histone 3. ACS Chem. Biol.  2020 Dec 14.
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Longbotham JE, Zhang ME, Fujimori DG. Domain cross-talk in regulation of histone modifications: Molecular mechanisms and targeting opportunities. Curr Opin Chem Biol​ 2020 Aug 2020;57:105-113
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​Gordon DE. et al. A SARS-CoV-2 protein interaction map reveals targets for drug repurposing. Nature 2020 Apr 30.
PMID: 32353859
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Petronikolou N, ​Longbotham JE, Fujimori DG. Dissecting contributions of catalytic and reader domains in regulation of histone demethylation. Methods Enzymol 2020 Apr, 639:217-236
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​Petronikolou N, 
​Longbotham JE, Fujimori DG. ​Extended Recognition of the Histone H3 Tail by Histone Demethylase KDM5A. Biochemistry 2020 Feb 11;59(5):647-651
PMID: 31985200
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​Stojković V, Myasnikov AG, Young ID, 
Frost A, Fraser JS, Fujimori DG. Assessment of the Nucleotide Modifications in the High-Resolution Cryo-Electron Microscopy Structure of the Escherichia Coli 50S Subunit. Nucleic Acids Res 2020 Mar 18;48(5):2723-2732
PMID: 31989172
Deposited Structure: 6PJ6
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Stojković V, Ulate ME, Hidalgo F, Aguilar E, Monge-Cascante C,Pizarro M, Tsai K, Tzoc E, Camorlinga M, Paredes-Sabja D, Quesada-Gómez C, Fujimori DG, Rodríguez C. cfr(B), cfr(C), and a new cfr-like gene, cfr(E), in Clostridium difficile strains recovered across Latin America. Antimicrob. Agents Chemother 2019 Nov 4, AAC.01074-19
PMID: 31685464
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​Longbotham JE, Chio CM, Dharmarajan V, Trnka MJ, Torres I, Goswami D, Ruiz K, Burlingame AL, Griffin PR, Fujimori, DG. Histone H3 binding to the PHD1 domain of histone demethylase KDM5A enables active site remodeling. Nat Commun 2019 Jan 9;10(1):94
PMID: 30626866
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​Stojković V, Chu T, Therizols G, Weinberg DE, Fujimori DG. miCLIP-MaPseq, a Substrate Identification Approach for Radical SAM RNA Methylating Enzymes. J Am Chem Soc 2018 Jun 13; 140(23): 7135-7143
PMID: 
29782154
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Stojković V, Fujimori DG. Mutations in RNA methylating enzymes in disease. Curr Opin Chem Biol 2017 Dec; 41:20-27 (review) 
PMCID: 
PMC5723530
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​Fitzsimmons CM, Fujimori DG. Determinants of tRNA Recognition by the Radical SAM Enzyme RlmN. Plos One 2016 Nov 30;11(11):e0167298
PMCID: 
PMC5130265
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Stojković V, Noda-Garcia L, Tawfik DS, Fujimori DG. Antibiotic resistance evolved via inactivation of a ribosomal RNA methylating enzyme. Nucleic Acids Res 2016 Oct 14;44(18):8897-8907
PMCID: 
PMC5062987
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​Fujimori DG, Conway SJ. Editorial overview: Chemical genetics and epigenetics.Curr Opin Chem Biol 2016 Aug; 33: vi-vii
PMID: 27614207
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​Liu YC, Fujimori DG, Weissman JS. Htm1p-Pdi1p is a folding-sensitive mannosidase that marks N-glycoproteins for ER-associated protein degradation. Proc Natl Acad Sci USA 2016; 113(28):E4015-24
PMCID: 
PMC4948361
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​Pack LR, Yamamoto KR, Fujimori DG. Opposing Chromatin Signals Direct and Regulate the Activity of Lysine Demethylase 4C (KDM4C). J Biol Chem 2016 Mar 18; 291(12): 6060-70
PMCID: 
PMC4813556
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Korczynska M, Le DD, Younger N, Gregori-Puigjané E, Tumber A, Krojer T, Velupillai S, Gileadi C, Nowak RP, Iwasa E, Pollock SB, Ortiz Torres I, Oppermann U, Shoichet BK, Fujimori DG. Docking and Linking of Fragments To Discover Jumonji Histone Demethylase Inhibitors. J Med Chem 2016; 59(4):1 580-98
PMCID: 
PMC5080985
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Lu J, Trnka, MJ, Roh SH, Robinson PJJ, Shiau C, Fujimori DG, Chiu W, Burlingame A, Guan G. Improved peak detection and deconvolution of native electrospray mass apectra from large protein complexes. J Am Soc Mass Spec 2015 Dec 26;26: 2141-51
PMCID: 
PMC5067139
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Ortiz Torres I, Fujimori, DG. Functional coupling between writers, erasers and readers of histone and DNA methylation. Curr Opin Struct Biol 2015 Nov 9;35: 68-75
PMCID: PMC4688207
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​Stojkovi
ć, V, Fujimori DG. Radical SAM-mediated methylation of ribosomal RNA. Methods Enzymol 2015;560: 355-376  
PMCID: PMC4530497 
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​Ortiz Torres I, Kuchenbecker KM, Nnadi CI, Fletterick RJ, Kelly MJ, Fujimori DG. Histone demethylase KDM5A is regulated by its reader domain through a positive-feedback mechanism. Nat Commun 2015 Nov 17;6: 6204 
PMCID: 
PMC5080983
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Dumesic PA, Homer CM, Moresco JJ, Pack LR, Coyle SM, Strahl BD, Fujimori DG, Yates III JR, Madhani HD. Product binding enforces the genomic specificity of a yeast polycomb repressive complex. Cell 2015 Jan 15;160(1-2): 204-218
PMCID: PMC4303595

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Fujimori DG. 
Radical SAM-mediated methylation reactions. Curr Opin Chem Biol 2013 Aug; 17: 597-604 (review) 
PMCID: PMC3799849    
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​Shiau C, Trnka MJ, Bozicevic A, Ortiz Torres I, Al-Sady B, Burlingame AL, Narlikar GJ, Fujimori DG. Reconstitution of nucleosome demethylation and catalytic properties of a jumonji histone demethylase. Chem Biol 2013 Apr 18;20: 494-99
PMCID: PMC3704229    
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​Le DD, Cortesi AT, Myers SA, Burlingame AL, Fujimori DG. Site-specific and regiospecific installation of methylarginine analogues into recombinant histones and insights into effector protein binding. J Am Chem Soc 2013 Feb 27;135: 2879-2882
PMCID: PMC4260808

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​Le DD, Fujimori DG. Protein and nucleic acid methylating enzymes: mechanisms and regulation. Curr Opin Chem Biol 2012 Dec;16: 507-515
PMCID: PMC3545634 
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​McCusker KP, Medzihradszky KF, Shiver AL, Nichols RJ, Yan F, Maltby DA, Gross CA, Fujimori DG. Covalent intermediate in the catalytic mechanism of the radical S-adenosyl-l-methionine methyl synthase RlmN trapped by mutagenesis. J Am Chem Soc 2012 Oct 31;134: 18074-81 
PMCID: PMC3499099    
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​McCusker KP, Fujimori DG. The chemistry of peptidyltransferase center-targeted antibiotics: enzymatic resistance mechanisms and approaches to countering resistance, ACS Chem Biol 2012 Jan 20;7: 64-72
PMCID: PMC3499096    
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​Yan, F, Fujimori, DG. RNA methylation by radical SAM enzymes RlmN and Cfr proceeds via methylene transfer and hydride shift,  Proc Natl Acad Sci USA 2011 Mar 8;108: 3930-34 
PMCID: PMC3054002  
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​Fujimori, DG. A novel enzymatic rearrangement, Chem Biol 2010 Dec 22;17: 1269-70 
PMID: 21168760 
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​Yan F, LaMarre JM, Röhrich R, Wiesner J, Jomaa H, Mankin AS, Fujimori DG. RlmN and Cfr are radical SAM enzymes involved in methylation of ribosomal RNA. J Am Chem Soc 2010 Mar 24;132: 3953-64
PMCID: PMC2859901     
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​Fujimori DG. Hypoxia sensing goes gauche, Nature Chem Biol 2009 Apr;5: 202-3 (news & views)
PMID: 19295524    
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Prior to UCSF (2000-2009)
Wong C, Fujimori DG, Walsh CT, Drennan CL. Structural analysis of an open site conformation of nonheme iron halogenase CytC3.    J Am Chem Soc 131: 4872-9, 2009
PMCID: PMC2663892 
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Neumann CS, Fujimori DG, Walsh CT. Halogenation strategies in natural products biosynthesis. Chem Biol 15: 99-109, 2008 (review)
PMID: 18291314  
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Neidig ML, Brown CD, Light K, Fujimori DG, Nolan EM, Price JC, Barr EW, Bollinger JM Jr, Krebs C, Walsh CT, Solomon EI. CD and MCD of CytC3 and taurine dioxygenase: role of facial triad in α-KG-dependent dioxygenases. J Am Chem Soc 129: 14224-31, 2007
PMCID: PMC2525739 
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Fujimori DG, Walsh CT. What’s new in enzymatic halogenations. Curr Opin Chem Biol 11: 553-60, 2007 (review)
PMCID: PMC2151916  
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Fujimori DG, Barr EW, Matthews ML, Koch GM, Yonce JR, Walsh CT, Bollinger Jr JM, Krebs C, Riggs-Gelasco PJ. Spectroscopic evidence for a high-spin Br-Fe(IV)-oxo intermediate in the α-ketoglutarate-dependent halogenase CytC3 from streptomyces. J Am Chem Soc 129: 13408-9, 2007
PMID: 17939667 
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Fujimori DG, Hrvatin S, Neumann CS, Strieker M, Marahiel MA, Walsh CT. Cloning and characterization of the biosynthetic gene cluster for kutznerides. Proc Natl Acad Sci USA 104: 16498-503, 2007
PMCID: PMC2034236 
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Krebs C, Fujimori DG, Walsh CT, Bollinger Jr JM. Non-heme Fe(IV)-oxo intermediates. Acc Chem Res 40: 484-92, 2007 (review)
PMID: 17542550 
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Galonić DP, Barr EW, Walsh CT, Bollinger Jr JM, Krebs C. Two Interconverting Fe(IV) intermediates in aliphatic chlorination by the halogenase CytC3. Nature Chem Biol 3: 113-6, 2007
PMID: 17220900 
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Kelly WL, Boyne II MT, Yeh E, Vosburg DA, Galonić DP, Kelleher NL, Walsh CT. Characterization of the aminocarboxycyclopropane-forming enzyme CmaC. Biochemistry 46: 359-68, 2007
PMID: 17209546 
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Galonić DP, Gin DY. Chemical glycosylation in the synthesis of glycoconjugate antitumor vaccines. Nature 446: 1000-7, 2007 
PMCID: PMC2631661 
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Ueki M, Galonić DP, Vaillancourt FH, Garneau-Tsodikova S, Yeh E, Vosburg DA, Schroeder FC, Osada H, Walsh CT. Enzymatic generation of the antimetabolite γ,γ-dichloroaminobutyrate by NRPS and mononuclear iron halogenase action in a streptomycete. Chem Biol 13: 1183-91, 2006
PMID: 17114000 
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Galonić DP, Vaillancourt FH, Walsh CT. Halogenation of unactivated carbon centers in natural product biosynthesis: Trichlorination of leucine during barbamide biosynthesis. J Am Chem Soc 128: 3900-1, 2006
PMID: 16551084 
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Ide ND, Galonić DP, van der Donk WA, Gin DY. Conjugation of selenols with aziridine-2-carboxylic acid-containing peptides. Synlett 13: 2011-4, 2005
PMID: 15469231
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Galonić DP, Ide ND, van der Donk WA, Gin DY. Aziridine-2-Carboxylic Acid Containing Peptides. Application to Solution- and Solid-Phase Convergent Site-Selective Peptide Modification. J Am Chem Soc 127: 7359-69, 2005
PMID: 15898784 
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Galonić DP, van der Donk WA, Gin DY. Convergent Site-Selective Ligation with Aziridine-2-Carboxylic Acid Containing Peptides. J Am Chem Soc 126: 12712-2, 2004
PMID: 15469231    
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Galonić DP, van der Donk WA, Gin DY. Oligosaccharide-Peptide Ligation of Glycosyl Thiolates with Dehydropeptides. Synthesis of S-Linked Mucin Glycopeptide Conjugates. Chem Eur J 9: 5997-6006, 2003
PMID: 14679512 
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Gieselman MD, Zhu Y, Zhou H, Galonić D, van der Donk WA. Selenocysteine Derivatives for Chemoselective Ligations. Chem Bio Chem 3: 709-16, 2002 (review)
PMID: 12203969 
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Lalić G, Galonić D, Matović R, Saičic RN. Model Study of Epothilone Synthesis: An Alternative Synthetic Approach to the C1-C7 fragment. J Serb Chem Soc 67: 221-7, 2002
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Lalić G, Petrovski Z, Galonić D, Matović R, Saičić RN. Alkylation of Carbonyl Compounds in the TiCl4-promoted Reaction of Trimethylsilyl Enol Ethers with Epoxides. Tetrahedron 57: 583-91, 2001
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Lalić G, Petrovski Z, Galonić D, Matović R, Saičić RN. Alkylation of Carbonyl Compounds in the TiCl4-promoted Reaction of Trimethylsilyl Enol Ethers with Ethylene Oxide. Tetrahedron Lett 41: 763-6, 2000
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