Publications at University of Pennsylvania

Bustin, KA, Abbas, A, Abt, MC, Zackular, JP, Matthews, ML*. Characterizing metabolic drivers of Clostridioides difficile infection with activity-based hydrazine probes Front. Pharmacol. 14, 1074619 (2023) [PDF] Wang X, Lin Z, Bustin KA, McKnight NR, Parsons WH, Matthews ML*. Discovery of Potent and Selective Inhibitors against Protein-Derived Electrophilic Cofactors J. Am. Chem. Soc. 144, 5377-5388 (2022) [PDF] Lin Z, Wang X. Bustin KA, Shishikura K, McKnight NR, He L, Suciu RM, Hu K, Han X, Ahmadi M, Olson EJ, Parsons WH, Matthews ML*. Activity-Based Hydrazine Probes for Protein Profiling of Electrophilic Functionality in Therapeutic Targets ACS Cent. Sci. 7 (9), 1524-1534 (2021) [PDF] Dettling SE, Ahmadi M, Lin Z, Matthews ML*. Discovery of electrophiles and profiling of enzyme cofactors Curr. Protoc. Chem. Biol. 12, e86 (2020) [PDF] Lin Z, Wang X, Bustin KA, He L, Suciu RM, Schek N, Ahmadi M, Hu K, Olsen EJ, Parsons WH, Witze ES, Morton PD, Gregus AM, Buczynski MW, Matthews ML. Hydrazines as versatile chemical biology probes and drug-discovery tools for cofactor-dependent enzymes bioRxiv (2020) [PDF] EJ Blaesi, GP Palowitch, K Hu, AJ Kim, HR Rose, RB Alapati, MG Lougee, HJ Kim, KO Tan, AT Taguchi, TN Laremore, RG Griffin*, C Krebs*, ML Matthews*, A Silakov*, JM Bollinger, Jr.*, BD Allen*, AK Boal* (*co-corresponding authors). Metal-free class Ie ribonucleotide reductase from pathogens initiates catalysis with a tyrosine-derived dihydroxyphenylalanine radical PNAS 115 (40), 10022-10027 (2018) [PDF]

Postdoctoral, Graduate, and Undergraduate Publications

Pan J, Wenger ES, Matthews ML, Pollock CJ, Bhardwaj M, Kim AJ, Allen BD, Grossman RB, Krebs C, and Bollinger, JM Jr (equal contribution). Evidence for Modulation of Oxygen-Rebound Rate in Control of Outcome by Iron(II)- and 2-Oxoglutarate-Dependent Oxygenases. J. Am. Chem. Soc 141, 15153−15165 (2019) [PDF] Matthews ML*, He L, Olson EJ, Horning BD, Correia BE, Yates JR, III, Dawson PE & Cravatt BF*. Chemoproteomic profiling and discovery of protein electrophiles in human cells Nat. Chem.  9, 234–243 (2017) [PDF] Kornahrens, A, Cognetta, A Brody D, Matthews ML, Cravatt BF & Boger D. Design of benzoxathiazin-3-one 1,1-dioxides as a new class of irreversible serine hydrolase inhibitors: discovery of a uniquely selective PNPLA4 inhibitor J. Am. Chem. Soc.  139, 7052–7061 (2017) [PDF] Martinie RJ, Pollock CJ, Matthews ML, Bollinger JM Jr, Krebs C, Silakov A. Vanadyl as a Stable Structural Mimic of Reactive Ferryl Intermediates in Mononuclear Nonheme-Iron Enzymes. Inorg. Chem.  56, 13382-13389 (2017) [PDF] Horning BD, Suciu RM, Ghadiri D, Ulanovskaya O, Matthews ML, Lum KM, Backus KM, Brown SJ, Rosen H & Cravatt BF . Chemical proteomic profiling of human methyltransferases J. Am. Chem. Soc.  138, 13335–13343 (2016) [PDF]  Srnec M, Wong SD, Matthews ML, Krebs C, Bollinger JM, Jr. & Solomon EI. Electronic structure of the ferryl intermediate in the a-ketoglutarate dependent non-heme iron halogenase SyrB2: Contributions to H-atom abstraction reactivity. J. Am. Chem. Soc.  138, 5110-5122 (2016) [PDF] Rajagopalan S, Wang C, Yu K, Kuzin AP, Richter F, Lew S, Miklos AE, Matthews ML, Seetharaman J, Su M, Hunt JF, Cravatt BF & Baker D . Design of activated serine-containing catalytic triads with atomic-level accuracy Nat. Chem. Biol.  10, 386-391 (2014) [PDF] Matthews ML*, Chang WC, Layne AP, Miles LA, Krebs C & Bollinger JM, Jr* . Direct nitration and azidation of aliphatic carbons by an iron-dependent halogenase Nat. Chem. Biol.  10, 209-215 (2014) [PDF] Wong SD, Srnec M, Matthews ML, Liu LV, Kwak Y, Park K, Bell CB, Alp EE, Zhao JY, Yoda Y, Kitao S, Seto M, Krebs C, Bollinger JM, Jr. & Solomon EI. Elucidation of the Fe(IV)=O intermediate in the catalytic cycle of the halogenase SyrB2 Nature  499, 320-323 (2013) [PDF] Krebs C, Dassama LMK, Matthews ML, Jiang W, Price JC, Korboukh V, Li N & Bollinger JM, Jr . Novel approaches for the accumulation of oxygenated intermediates to multi-millimolar concentrations Coord. Chem. Rev.  257, 234-243 (2013) [PDF] Chang JW, Niphakis MJ, Lum KM, Cognetta AB, Wang C, Matthews ML, Niessen S, Buczynski MW, Parsons LH & Cravatt BF . Highly selective inhibitors of monoacylglycerol lipase bearing a reactive group that is bioisosteric with endocannabinoid substrates Chem. Biol.  19, 579-588 (2012) [PDF] Bollinger JM, Jr. & Matthews ML. Remote enzyme microsurgery Science  327, 1337-1338 (2010) [PDF] Hollenhorst MA, Bumpus SB, Matthews ML, Bollinger JM, Jr. Kelleher NL & Walsh CT . The nonribosomal peptide synthetase enzyme DdaD tethers N(b)-fumaramoyl-L-2,3-diaminopropionate for Fe(II)/a-ketoglutarate-dependent epoxidation by DdaC during dapdiamide antibiotic biosynthesis J. Am. Chem. Soc.  132, 15773-15781 (2010) [PDF] Bollinger JM, Jr., Diao Y, Matthews ML, Xing G & Krebs C. Myo-inositol oxygenase: a radical new pathway for O2 Dalton Trans.  905-914 (2009) [PDF] Matthews ML, Neumann CS, Miles LA, Grove TL, Booker SJ, Krebs C, Walsh CT & Bollinger JM, Jr. Substrate positioning controls the partition between halogenation and hydroxylation in the aliphatic halogenase, SyrB2. Proc. Natl. Acad. Sci. USA  106, 17723-17728 (2009) [PDF] Matthews ML, Krest CM, Barr EW, Vaillancourt FH, Walsh CT, Green MT, Krebs C & Bollinger JM, Jr. Substrate-triggered formation and remarkable stability of the C–H bond-cleaving chloroferryl intermediate in the aliphatic halogenase, SyrB2 Biochemistry 48, 4331-4343 (2009) [PDF] Krebs C, Matthews ML, Jiang W & Bollinger JM, Jr. AurF from Streptomyces thioluteus and a possible new family of manganese/iron oxygenases Biochemistry  46, 10413-10418 (2007) [PDF] Fujimori DG, Barr EW, Matthews ML, Koch GM, Yonce JR, Walsh CT, Bollinger JM, Jr., Krebs C & Riggs-Gelasco PJ. Spectroscopic evidence for a high-spin Br-Fe(IV)-oxo intermediate in the a-ketoglutarate-dependent halogenase CytC3 from Streptomyces J. Am. Chem. Soc.  129, 13408-13409 (2007) [PDF] Matthews ML, Periyannan G, Hajdin C, Sidgel TK, Bennett B & Crowder MW. Probing the reaction mechanism of the D-ala-D-ala dipeptidase, VanX, by using stopped-flow kinetic and rapid-freeze quench EPR studies on the Co(II)-substituted enzyme J. Am. Chem. Soc.  128, 13050-13051 (2006) [PDF] Breece RM, Costello A, Bennett B, Sigdel TK, Matthews ML, Tierney DL & Crowder MW. A five-coordinate metal center in Co(II)-substituted VanX J. Biol. Chem.  280, 11074-11081 (2005) [PDF]

Book Chapters

Bollinger JM Jr., Chang WC, Matthews ML, Martinie RJ, Boal AK & Krebs C. Mechanisms of 2-oxoglutarate-dependent oxygenases: the hydroxylation paradigm and beyond (RSC Metallobiology). Royal Society of Chemistry eds. Hausinger RP, Schofield CJ & Garner CD, ISBN 1849739501 (2015)


Matthews ML. Chemoproteomic profiling of protein electrophilic and oxidative post-translational modifications (2020) Cravatt BF, Zuhl AM, Bachovchin DA, Matthews ML, Fu GC, Mohr JT, Berlin JM. Aza-b-lactam compounds and methods of using (2013)