Selected publications (a full list also available)

Catalase-peroxidase (KatG): A potential frontier in tuberculosis drug development

Liu A

Crit. Rev. Biochem. Mol. Biol., 2025, 60, 1-13 (DOI: 10.1080/10409238.2025.2470630)

Structural insights into 2-oxindole-forming monooxygenase MarE: Divergent architecture and substrate positioning versus tryptophan dioxygenases

Shin I, Nguyen RC, Montoya SR, and Liu A*

J. Biol. Chem., 2025, 301, 108241 (1-14) (DOI: 10.1016/j.jbc.2025.108241)

α-Amino-β-carboxymuconate-ε-semialdehyde decarboxylase catalyzes enol/keto tautomerization of oxaloacetate

Yang Y*, Davis I, Altman RA, and Liu A*

J. Biol. Chem., 2024, 300(11), 107878 (1-11) (DOI: 10.1016/j.jbc.2024.107878)

Indole N-linked hydroperoxyl adduct of protein-derived cofactor modulating catalase-peroxidase functions

Li J, Duan R, Traore ES, Davis I, Nguyen RC, Griffith WP, Goodwin DC, Jarzecki AA, and Liu A*

Angew. Chem. Int. Ed., 2024, 63, e202407018 (1-10) (DOI: 10.1002/anie.202407018)

Cobalt(II)-substituted cysteamine dioxygenase oxygenation proceeds through a cobalt(III)-superoxo complex

Li J*, Duan R, and Liu A*

J. Am. Chem. Soc., 2024, 146, 27, 18292-18297 (DOI: 10.1021/jacs.4c01871)
 

In situ structural observation of a substrate- and peroxide-bound high-spin ferric-hydroperoxo intermediate in P450 enzyme CYP121

Nguyen RC, Davis I, Dasgupta M, Wang Y, Simon P, Butryn A, Makita H, Bogacz I, Dornevil K, Aller P, Bhowmick A, Chatterjee R, Kim I-S, Zhou T, Mendez D, Paley, D, Fuller F, Alonso Mori R, Batyuk A,  Sauter N, Brewster A, Orville AM, Yachandra V, Yano J, Kern J,* and Liu A*

J. Am. Chem. Soc., 2023, 46, 25120-25133 (DOI: 10.1021/jacs.3c04991)
 

Charge maintenance during catalysis in non-heme iron oxygenases

Traore ES and Liu A*

ACS Catalysis, 2022, 12(10), 6191-6208 (DOI: 10.1021/acscatal.1c04770)
 

A new regime of heme-dependent aromatic oxygenase superfamily

Shin I, Wang Y, and Liu A*

 Proc. Natl. Acad. Sci. U.S.A., 2021, 118(43), e210656 (1-10) (DOI: 10.1073/pnas.2106561118)  
 

 

 

 

Crystal structure of human cysteamine dioxygenase provides a structural rationale for its function as an oxygen sensor

Wang Y, Shin I, Li J, and Liu A*

J. Biol. Chem., 2021, 297(4), 101176 (1-10) (DOI: 10.1016/j.jbc.2021.101176)
         

         Narrator: Yifan (Amber) Wang

 

Molecular rationale for partitioning between C-H and C-F bond activation in heme-dependent tyrosine hydroxylase

Wang Y, Davis I, Shin I, Xu H, and Liu A*

J. Am. Chem. Soc., 2021, 143(12), 4680-4693 (DOI: 10.1021/jacs.1c00175)    
         

         Narrator: Yifan (Amber) Wang
           MP4, 8'52"

A novel catalytic heme cofactor in SfmD with a single thioether bond and a bis-His ligand set revealed by de novo crystal structural and spectroscopic study

Shin I, Davis I, Nieves-Merced K, Wang Y, McHardy S, and Liu A*

Chemical Science, 2021, 12(11), 3984-3998 (DOI: 10.1039/D0SC06369J)               
         

      

             Inchul Shin
            (MP4, 13'24")

 

      

Diflunisal derivatives as modulators of ACMS decarboxylase targeting the tryptophan-kynurenine pathway

Yang Y, Borel T, de Azambuja F, Johnson D, Sorrentino JP, Udokwu C, Davis I, Liu A*, and Altman RA*

J. Med. Chem., 2021, 64(1), 797-811  (DOI: 10.1021/acs.jmedchem.0c01762)               
         

 

 

Heme binding to HupZ with a C-terminal tag from Group A Streptococcus

Traore ES, Li J, Chiura T, Geng J, Sachla A, Yoshimoto F, Eichenbaum Z, Davis I, Max P*, and Liu A*

Molecules, 2021, 26(3), 549 (1-19)  (DOI: 10.3390/molecules26030549)               
        

      

            Narrator: Ephrahime S. Traore
            (LiveSlides: pending)

 

Formation of monofluorinated radical cofactor in galactose oxidase through copper-mediated C−F bond scission

Li J, Davis I, Griffith WP, and Liu A*

J. Am. Chem. Soc., 2020, 142(44), 18753-18757  (DOI: 10.1021/jacs.0c08992)               
         

      

            Narrator: Jiasong Li
            (MP4, 7'39")

 

Observing 3-hydroxyanthranilate-3,4-dioxygenase in action through a crystalline lens

Wang Y, Liu KF, Yang Y, Davis I, and Liu A*

 Proc. Natl. Acad. Sci. U.S.A., 2020, 117(33) 19720-19730 (PNAS Direct Submission) (DOI: 10.1073/pnas.2005327117)               
         

      

   Narrators: Yifan Wang & Ian Davis

(an accompany enzyme action movie published by PNAS)

Characterization of the non-heme iron center of cysteamine dioxygenase and its interaction with substrates

Wang Y, Davis I, Yang Y, Chen Y, Naik SG, Griffith WP, and Liu A*

 J. Biol. Chem., 2020, 295(33), 11789-11802  (DOI: 10.1074/jbc.RA120.013915)               
         

          Narrator: Yifan Wang

 

 

 

Kinetic and spectroscopic characterization of the catalytic ternary complex of tryptophan 2,3-dioxygenase

Geng J, Weitz AC, Dornevil K, Hendrich MP, and Liu A*

Biochemistry, 2020, 59(30), 2813-2822  (DOI: 10.1021/acs.biochem.0c00179)
 

 

Carbon-fluorine bond cleavage mediated by metalloenzymes

Wang Y and Liu A*

Chem. Soc. Rev., 2020, 49(14), 4906-4925 (DOI: 10.1039/C9CS00740G)               
         

 

 

 

Substrate-assisted hydroxylation and O-demethylation in the peroxidase-like cytochrome P450 enzyme CYP121

Nguyen RC, Yang Y, Wang Y, Davis I, and Liu A*

ACS Catalysis, 2020, 10(2), 1628-1639  (DOI: 10.1021/acscatal.9b04596)               
         

          Narrator: Romie C. Nguyen

 

Crystal structures of L-DOPA dioxygenase from Streptomyces sclerotialus

Wang Y, Shin I, Fu Y, Colabroy KL*, and Liu A*

Biochemistry, 2019, 58(52), 5339-5350  (DOI: 10.1021/acs.biochem.9b00396)               
(invited contribution for a special issue of Current Topics in Mechanistic Enzymology 2019)
         

      

  Narrators: Yifan Wang & Inchul Shin

 

 

 

Quaternary structure of α-amino-β-carboxymuconate-ε-semialdehyde decarboxylase (ACMSD) controls its activity    

Yang Y, Davis I, Matsui T, Rubalcava I, and Liu A*

J. Biol. Chem., 2019, 294(30), 11609-11621  (DOI: 10.1074/jbc.RA119.009035)   (LiveSlide video presentation) featured as a JBC cover story

         

          Narrator: Yu Yang

 

Biocatalytic carbon−hydrogen and carbon−fluorine bond cleavage through hydroxylation promoted by a histidyl-ligated heme enzyme

Wang Y, Davis I, Shin I, Wherritt DJ, Griffith WP, Dornevil K, Colabroy KL, and Liu A*

ACS Catalysis, 2019, 9(6), 4764-4776  (DOI: 10.1021/acscatal.9b00231) featured as an ACS Editors Choice article
 

      

       

      

   Narrators: Yifan Wang and Ian Davis

  (Short version published by ACS: 8 slides)

  (Full version: 22 slides)

 

 

Probing the Cys-Tyr cofactor biogenesis in cysteine dioxygenase by the genetic incorporation of fluorotyrosine

Li J, Koto, T, Davis I, and Liu A*

Biochemistry, 2019, 58(17), 2218-2227  (DOI: 10.1021/acs.biochem.9b00006) (a highly cited original paper in the journal)
 

Cleavage of a carbon−fluorine bond by an engineered cysteine dioxygenase

Li J, Griffith WP, Davis I, Shin I, Wang J, Li F, Wang Y, Wherritt D, and Liu A*

Nature Chemical Biology, 2018, 14(9), 853-860 (DOI: 10.1038/s41589-018-0085-5)
 

Adapting to oxygen: 3-hydroxyanthranilate 3,4-dioxygenase employs loop dynamics to accommodate two substrates with disparate polarities

Yang Y, Liu F*, and Liu A*

J. Biol. Chem., 2018, 293(27), 293, 10415-10424  (DOI: 10.1074/jbc.RA118.002698) (featured as a JBC cover story)
 

Cofactor biogenesis in cysteamine dioxygenase: C−F bond cleavage with genetically incorporated unnatural tyrosine

Wang Y, Griffith WP, Li J, Koto T, Wherritt D, Fritz E, and Liu A*

Angew. Chem. Int. Ed., 2018, 57(27), 8149-8153 (DOI: 10.1002/anie.201803907)
 

Reassignment of the human aldehyde dehydrogenase ALDH8A1 (ALDH12) to the kynurenine pathway in tryptophan catabolism

Davis I, Yang Y, Wherritt D, and Liu A*

J. Biol. Chem., 2018, 293(25), 9594-9603  (DOI: 10.1074/jbc.RA118.003320)
 

Stepwise O-atom transfer in heme-based tryptophan dioxygenase: Role of substrate ammonium in epoxide ring opening

Shin I, Ambler BR, Wherritt DJ, Griffith WP, Maldonado AC, Altman RA, and Liu A*

J. Am. Chem. Soc., 2018, 140(12), 4372-4379 (DOI: 10.1021/jacs.8b00262)
 

High-frequency/high-field EPR and theoretical studies of tryptophan-based radicals

Davis I, Koto T, Terrell JR, Kozhanov A, Krzystek J, and Liu A*

J. Phys. Chem. A, 2018, 122(12), 3170-3176  (DOI: 10.1021/acs.jpca.7b12434)
 

 

Backbone dehydrogenation in pyrrole-based pincer ligands

Krishnan VM, Davis I, Baker TM, Curran DJ, Arman H, Neidig ML, Liu A, and Tonzetich ZJ*

Inorg. Chem., 2018, 57(15), 9544-9553  (DOI: 10.1021/acs.inorgchem.8b01643)
 

Radical trapping study of the relaxation of bis-Fe(IV) MauG

Davis I, Koto T, and Liu A*

Reactive Oxygen Species, 2018, 5(13), 46-55  (DOI: 10.20455/ros.2018.801)
 

Probing ligand exchange in the P450 enzyme CYP121 from Mycobacterium tuberculosis: Dynamic equilibrium of the distal heme ligand as a function of pH and temperature

Fielding AJ, Dornevil K, Ma L, Davis I, and Liu A*

J. Am. Chem. Soc., 2017, 139(48), 17484-17499  (DOI: 10.1021/jacs.7b08911)
 

Cross-linking of dicyclotyrosine by the cytochrome P450 enzyme CYP121 from Mycobacterium tuberculosis proceeds through a catalytic shunt pathway

Dornevil K, Davis I, Fielding AJ, Terrell JR, Ma L, and Liu A*

J. Biol. Chem., 2017, 292(33), 13645-13657  (DOI: 10.1074/jbc.M117.794099)
 

Hypertryptophanemia due to tryptophan 2,3-dioxygenase deficiency

Ferreira F,* Shin I, Sosova I, Dornevil K, Jain Shailly, Dewey D, Liu F, and Liu A*

Mol. Genet. Metab., 2017, 120(4), 317-324  (DOI: 10.1016/j.ymgme.2017.02.009)
 

 

Mutual synergy between catalase and peroxidase activities of the bifunctional enzyme KatG is facilitated by electron-hole hopping within the enzyme

Njuma OJ, Davis I, Ndontsa EN, Krewall JR, Liu A, and Goodwin DC*

J. Biol. Chem., 2017, 292(45), 18408-18421   (DOI: 10.1074/jbc.M117.791202)

Oxygen activation by mononuclear nonheme iron dioxygenases involved in the degradation of aromatics

Wang Y, Li J, and Liu A*

J. Biol. Inorg. Chem., 2017, 22(2), 395-405  (DOI: 10.1007/s00775-017-1436-5)

(invited review article for a special issue of the journal under the theme of 60 Years of Oxygen Activation)
 

A pitcher-and-catcher mechanism drives endogenous substrate isomerization by dehydrogenase in kynurenine metabolism

Yang Y, Davis I, Ha U, Wang Y, Shin I, and Liu A*

J. Biol. Chem., 2016, 291(51), 26252-26261 (DOI: 10.1074/jbc.M116.759712)

(featured as "Papers of the Week and selected, after publication, into a collection of Enzymology virtual issue)
 

Control of carotenoid biosynthesis through a heme-based cis-trans isomerase

Beltran J, Kloss B, Hosler JP, Geng J, Liu A, Modi A, Dawson JH, Sono M, Shumskaya M, Ampomah-Dwamena C, Love JD, and Wurtzel ET*

Nature Chemical Biology, 2015, 11(8), 598-605 (DOI: 10.1038/nchembio.1840)

 

What is the tryptophan kynurenine pathway and why is it important to neurotherapeutics? (Invited Editorial)

Davis I and Liu A*

Expert Review of Neurotherapeutics, 2015, 15(7), 719-721 (DOI: 10.1586/14737175.2015.1049999)
 

An iron reservoir to the catalytic metal: The rubredoxin iron in an extradiol dioxygenase

Liu F, Geng J, Gumpper RH, Barman A, Davis I, Ozarowski A, Hamelberg D, and Liu A*

J. Biol. Chem., 2015, 290(25), 15621-15634 (DOI: 10.1074/jbc.M115.650259)
 

Probing bis-Fe(IV) MauG: Experimental evidence for the long-range charge-resonance model

Geng J, Davis I, and Liu A*

Angew. Chem. Int. Ed., 2015, 54, 3692-3696 (DOI: 10.1002/anie.201410247)
   

Crystallographic and spectroscopic snapshots reveal a dehydrogenase in action

Huo L, Davis I, Liu F, Andi B, Esaki S, Hiroaki I, Li T, Hasegawa Y, Orville AM, and Liu A*

Nature Communication, 2015, 6:5935 (DOI: 10.1038/ncomms6935)
(defining the structure of a kynurenine pathway dehydrogenase and sp³-to-sp² transition intermediates during catalysis)  
   

Human α-amino-β-carboxymuconate-ε-semialdehyde decarboxylase (ACMSD): A structural and mechanistic unveiling

Huo L, Liu F, Hiroaki I, Li T, Hasegawa Y, and Liu A*

Proteins, 2015, 83(1), 178-187  (DOI: 10.1002/prot.24722)
   

Bis-Fe(IV): Nature's sniper for long-range oxidation

Geng J, Davis I, Liu F, and Liu A*

J. Biol. Inorg. Chem., 2014, 19(7), 1057-1067  (Invited Article)   (DOI: 10.1007/s00775-014-1123-8)

 

 

Amidohydrolase Superfamily

Liu A* and Huo L

Encyclopedia of Life Sciences, 2014, 1-11  (DOI: 10.1002/9780470015902.a0020546.pub2)

Power of two: Arginine 51 and arginine 239* from a neighboring subunit are essential for catalysis in α-amino-β-carboxymuconate-ε-semialdehyde decarboxylase

Huo L, Davis I, Chen L, and Liu A*

J. Biol. Chem., 2013, 288(43), 30862-30871 (DOI: 10.1074/jbc.M113.496869)

Pirin is an iron-dependent redox regulator of NF-κB

Liu F, Rehmani I, Esaki S, Fu R, Chen L, Serroano V, and Liu A*

  Proc. Natl. Acad. Sci. U.S.A., 2013, 110(24), 9722-9727 (PNAS Direct Submission) (DOI: 10.1073/pnas.1221743110)

(** Faculty of 1000 recommended article )

Tryptophan-mediated charge-resonance stabilization in the bis-Fe(IV) redox state of MauG

Geng J, Dornevil K, Davidson VL, and Liu A*

  Proc. Natl. Acad. Sci. U.S.A., 2013, 110(24), 9639-9644 (PNAS Direct Submission) (DOI: 10.1073/pnas.1301544110)

 

Diradical intermediate within the context of tryptophan tryptophylquinone biosynthesis

Yukl ET, Liu F, Krzystek J, Shin S, Jensen LMR, Davidson VL, Wilmot CM,* and Liu A*

  Proc. Natl. Acad. Sci. U. S. A., 2013, 110(12), 4569-4573 (PNAS Direct Submission) (DOI: 10.1073/pnas.1215011110)

 
 * Faculty of 1000 recommended article

An unexpected copper catalyzed 'reduction' of an arylazide to amine through the formation of a nitrene intermediate

Peng H, Dornevil K, Draganov A, Chen W, Dai C, Nelson WH, Liu A,* and Wang B*

Tetrahedron, 2013, 69, 5079-5085 (dedicated to the memory of Professor William H. Nelson) (DOI: 10.1016/j.tet.2013.04.091)    

Chemical rescue of the distal histidine mutants of tryptophan 2,3-dioxygenase

Geng J, Dornevil K, and Liu A*

J. Am. Chem. Soc., 2012, 134, 12209-12218 (DOI: 10.1021/ja304164b) 

Evidence for a dual role of an active site histidine in α -amino-β - carboxymuconate- ε - semialdehyde decarboxylase

Huo L, Fielding AJ, Chen Y, Li T, Iwaki H, Hosler JP, Chen L, Hasegawa Y, Que Jr, L, and Liu A*

Biochemistry, 2012, 51(29), 5811-5821 (DOI: doi.org/10.1021/bi300635b)   

The role of calcium in metalloenzyme: Effects of calcium removal on the axial ligation geometry and magnetic properties of the catalytic diheme center in MauG

Chen Y, Naik SG, Krzystek J, Shin S, Nelson WH, Xue S, Yang JJ, Davidson VL, and Liu A*

Biochemistry, 2012, 51, 1586-1597  (DOI: 10.1021/bi201575f)   

The reactivation mechanism of tryptophan 2,3-dioxygenase by hydrogen peroxide

Fu R, Gupta R, Geng J, Dornevil K, Wang S, Hendrich MP, and Liu A*

J. Biol. Chem., 2011, 286(30), 26541-26554  (DOI: 10.1074/jbc.M111.253237)

 

Mutagenesis of tryptophan199 suggests that electron hopping is required for MauG-dependent tryptophan tryptophylquinone biosynthesis

Tarboush NA, Jensen LMR, Yukl ET, Geng J, Liu A, Wilmot CM, and Davidson VL

  Proc. Natl. Acad. Sci. U. S. A., 2011, 108(41), 16956-16961 (PNAS Direct Submission) (DOI: 10.1073/pnas.1109423108)

 

EPR and Mössbauer spectroscopy show inequivalent hemes in tryptophan dioxygenase

Gupta R, Fu R, Liu A, and Hendrich MP*

J. Am. Chem. Soc., 2010, 132(3), 1098-1109 (DOI: 10.1021/ja908851e)

 

Heme iron nitrosyl complex of MauG reveals efficient redox equilibrium between hemes with only one heme exclusively binding exogenous ligands

Fu R, Liu F, Davidson VL, and Liu A*

Biochemistry, 2009, 48(49), 11603-11605  (DOI: 10.1021/bi9017544)

Electron Paramagnetic Resonance (EPR) in Enzymology

Liu A*

Wiley  Encyclopedia of Chemical Biology, 2008, 1, 591-601 (DOI: 10.1002/9780470048672.wecb668)

 

A catalytic di-heme bis-Fe(IV) form of MauG, Alternative to an Fe(IV)=O porphyrin radical

Li X, Fu R, Lee S, Krebs C, Davidson VL,* and Liu A*

Proc. Natl. Acad. Sci. U.S.A., 2008, 105(25), 8597-8600 (PNAS Direct Submission) (DOI: 10.1073/pnas.0801643105) 

 

Kinetic and physical evidence that the di-heme enzyme MauG tightly binds to a biosynthetic precursor of methylamine dehydrogenase with incompletely formed tryptophan tryptophylquinone

Li X, Fu R, Liu A*, and Davidson VL*

Biochemistry, 2008, 47(9), 2908-2912 (DOI: 10.1021/bi702259w)

Amidohydrolase Superfamily

Liu A*, Li T, and Fu R

Encyclopedia of Life Sciences, 2007, 1-8 (DOI: 10.1002/9780470015902.a0020546)

Detection of transient intermediates in the metal-dependent non-oxidative decarboxylation catalyzed by α-amino-β-carboxymuconic-ε-semialdehyde decarboxylase

Li T, Ma J, Hosler JP, Davidson VL, and Liu A*

J. Am. Chem. Soc., 2007, 129(30), 9278-9279 (DOI: 10.1021/ja073648le)

 

Crystallographic analysis of α-amino-β-carboxymuconic-ε-semialdehyde decarboxylase: Insight into the active site and catalytic mechanism of a novel decarboxylation reaction

Martynowski D., Eyobo Y., Li T, Yang K., Liu A,* and Zhang H*

Biochemistry, 2006, 45(35), 10412-10421 (DOI: 10.1021/bi060903q)

 

Transition metal-catalyzed nonoxidative decarboxylation reactions

Liu A* and Zhang H*

Biochemistry, 2006, 45(35), 10407-10411 (a New Concept paper) (DOI: 10.1021/bi061031v)

 

α-Amino-β-carboxymuconic-ε-semialdehyde decarboxylase (ACMSD) is a new member of the amidohydrolase superfamily

Li T, Iwaki H, Fu R, Hasegawa Y, Zhang H, Liu A*
Biochemistry, 2006, 45(21), 6628-6634 (DOI: 10.1021/bi060108c)

   

Kinetic and spectroscopic characterization of ACMSD from Pseudomonas fluorescens reveals a pentacoordinate mononuclear metallocofactor
Li T, Walker AL, Iwaki H, Hasegawa Y, Liu A*

J. Am. Chem. Soc., 2005, 127(35), 12282-12290 (DOI: 10.1021/ja0532234)

  

 

 

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