Our lab is interested in the development of novel chemical tools which, in conjunction with biochemistry, molecular and cellular biology techniques, will allow us to interrogate biological processes on a molecular level.

Stojkovic, V, Fujimori DG. Radical SAM-mediated methylation of ribosomal RNA. Methods Enzymol, accepted. 2015. 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 6: 6204. doi: 10.1038/ncomms7204, 2015. 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 160(1-2): 204-218, 2015. Fujimori DG. Radical SAM-mediated Methylation Reactions. Curr Opin Chem Biol 17: 597-604, 2013. (review) 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 20: 494-99, 2013. 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 135: 2879-2882, 2013. Le DD, Fujimori DG. Protein and Nucleic Acid Methylating Enzymes: Mechanisms and Regulation. Curr Opin Chem Biol 16: 507-515, 2012. 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 134: 18074-81, 2012. McCusker KP, Fujimori DG. The Chemistry of Peptidyltransferase Center-Targeted Antibiotics: Enzymatic Resistance Mechanisms and Approaches to Countering Resistance, ACS Chem Biol 7: 64-72, 2012. 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 108: 3930-34, 2011. Fujimori, DG. A Novel Enzymatic Rearrangement, Chem Biol 17: 1269-70, 2010. 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 132: 3953-64, 2010. (Highlighted in C&EN.) Fujimori DG. Hypoxia Sensing Goes Gauche, Nature Chem Biol 5: 202-3, 2009. (news & views) Prior to UCSF 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. Neumann CS, Fujimori DG, Walsh CT. Halogenation Strategies in Natural Products Biosynthesis. Chem Biol 15: 99-109, 2008. (review) 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. Fujimori DG, Walsh CT. What’s New in Enzymatic Halogenations. Curr Opin Chem Biol 11: 553-60, 2007. (review) 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. 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. Krebs C, Fujimori DG, Walsh CT, Bollinger Jr JM. Non-heme Fe(IV)-Oxo Intermediates. Acc Chem Res 40: 484-92, 2007. (review) 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. 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. Galonić DP, Gin DY. Chemical Glycosylation in the Synthesis of Glycoconjugate Antitumor Vaccines. Nature 446: 1000-7, 2007. (review) 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. 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.