Dali Liu - Publications

Loyola University Chicago, Chicago, IL, United States 
Biochemistry, Enzymology, Protein Crystallography

37 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2018 Tashiro S, Caaveiro JMM, Nakakido M, Tanabe A, Nagatoishi S, Tamura Y, Matsuda N, Liu D, Hoang QQ, Tsumoto K. Discovery and optimization of inhibitors of the Parkinson's disease associated protein DJ-1. Acs Chemical Biology. PMID 30063823 DOI: 10.1021/acschembio.8b00701  1
2018 Tu Y, Kreinbring CA, Hill M, Liu C, Petsko GA, McCune CD, Berkowitz DB, Liu D, Ringe D. Crystal Structures of Cystathionine β-Synthase from Saccharomyces cerevisiae: One Enzymatic Step at a Time. Biochemistry. PMID 29630349 DOI: 10.1021/acs.biochem.8b00092  1
2018 Juncosa JI, Takaya K, Le HV, Moschitto MJ, Weerawarna PM, Mascarenhas R, Liu D, Dewey SL, Silverman RB. Design and Mechanism of (S)-3-Amino-4-(difluoromethylenyl)cyclopent-1-ene-1-carboxylic Acid, a Highly Potent γ-Aminobutyric Acid Aminotransferase Inactivator for the Treatment of Addiction. Journal of the American Chemical Society. PMID 29381352 DOI: 10.1021/jacs.7b10965  1
2018 Zhu B, Chen S, Wang H, Yin C, Han C, Peng C, Liu Z, Wan L, Zhang X, Zhang J, Lian CG, Ma P, Xu ZX, Prince S, Wang T, ... ... Liu D, et al. The protective role of DOT1L in UV-induced melanomagenesis. Nature Communications. 9: 259. PMID 29343685 DOI: 10.1038/s41467-017-02687-7  0.16
2017 Mascarenhas R, Le HV, Clevenger KD, Lehrer HJ, Ringe D, Kelleher NL, Silverman RB, Liu D. Correction to Selective Targeting by a Mechanism-Based Inactivator against Pyridoxal 5'-Phosphate-Dependent Enzymes: Mechanisms of Inactivation and Alternative Turnover. Biochemistry. PMID 29045130 DOI: 10.1021/acs.biochem.7b00961  1
2017 Mascarenhas R, Le HV, Clevenger KD, Lehrer HJ, Ringe D, Kelleher NL, Silverman RB, Liu D. Selective Targeting by a Mechanism-based Inactivator against PLP-Dependent Enzymes: Mechanisms of Inactivation and Alternative Turnover. Biochemistry. PMID 28816437 DOI: 10.1021/acs.biochem.7b00499  1
2017 Stein N, Gumataotao N, Hajnas N, Wu R, Lankathilaka KPW, Bornscheuer UT, Liu D, Fiedler AT, Holz RC, Bennett B. Multiple States of Nitrile Hydratase from Rhodococcus equi TG328-2: Structural and Mechanistic Insights from EPR and DFT Studies. Biochemistry. PMID 28520398 DOI: 10.1021/acs.biochem.6b00876  1
2017 Wu R, Sanishvili R, Belitsky BR, Juncosa JI, Le HV, Lehrer HJ, Farley M, Silverman RB, Petsko GA, Ringe D, Liu D. PLP and GABA trigger GabR-mediated transcription regulation in Bacillus subtilis via external aldimine formation. Proceedings of the National Academy of Sciences of the United States of America. PMID 28348215 DOI: 10.1073/pnas.1703019114  1
2017 Naffin-Olivos JL, Daab A, White A, Goldfarb NE, Milne AC, Liu D, Baikovitz J, Dunn BM, Rengarajan J, Petsko GA, Ringe D. Structure Determination of Mycobacterium tuberculosis Serine Protease Hip1 (Rv2224c). Biochemistry. PMID 28346784 DOI: 10.1021/acs.biochem.6b01066  1
2017 Clevenger KD, Mascarenhas R, Catlin D, Wu R, Kelleher NL, Drake EJ, Gulick AM, Liu D, Fast W. Substrate Trapping in the Siderophore Tailoring Enzyme PvdQ. Acs Chemical Biology. PMID 28186406 DOI: 10.1021/acschembio.7b00031  1
2015 Al-Zyoud WA, Hynson RM, Ganuelas LA, Coster AC, Duff AP, Baker MA, Stewart AG, Giannoulatou E, Ho JW, Gaus K, Liu D, Lee LK, Böcking T. Binding of transcription factor GabR to DNA requires recognition of DNA shape at a location distinct from its cognate binding site. Nucleic Acids Research. PMID 26681693 DOI: 10.1093/nar/gkv1466  1
2015 Mascarenhas R, Thomas PW, Wu CX, Nocek BP, Hoang QQ, Liu D, Fast W. Structural and Biochemical Characterization of AidC, a Quorum-Quenching Lactonase With Atypical Selectivity. Biochemistry. PMID 26115006 DOI: 10.1021/acs.biochem.5b00499  1
2015 Lee H, Le HV, Wu R, Doud E, Sanishvili R, Kellie JF, Compton PD, Pachaiyappan B, Liu D, Kelleher NL, Silverman RB. Mechanism of Inactivation of GABA Aminotransferase by (E)- and (Z)-(1S,3S)-3-Amino-4-fluoromethylenyl-1-cyclopentanoic Acid. Acs Chemical Biology. PMID 26110556 DOI: 10.1021/acschembio.5b00212  1
2015 Martinez S, Wu R, Krzywda K, Opalka V, Chan H, Liu D, Holz RC. Analyzing the catalytic role of active site residues in the Fe-type nitrile hydratase from Comamonas testosteroni Ni1. Journal of Biological Inorganic Chemistry : Jbic : a Publication of the Society of Biological Inorganic Chemistry. 20: 885-94. PMID 26077812 DOI: 10.1007/s00775-015-1273-3  1
2015 Wu R, Asención Diez MD, Figueroa CM, Machtey M, Iglesias AA, Ballicora MA, Liu D. The Crystal Structure of Nitrosomonas europaea Sucrose Synthase Reveals Critical Conformational Changes and Insights into Sucrose Metabolism in Prokaryotes. Journal of Bacteriology. 197: 2734-46. PMID 26013491 DOI: 10.1128/JB.00110-15  1
2015 Le HV, Hawker DD, Wu R, Doud E, Widom J, Sanishvili R, Liu D, Kelleher NL, Silverman RB. Design and mechanism of tetrahydrothiophene-based γ-aminobutyric acid aminotransferase inactivators. Journal of the American Chemical Society. 137: 4525-33. PMID 25781189 DOI: 10.1021/jacs.5b01155  1
2015 Lee H, Doud EH, Wu R, Sanishvili R, Juncosa JI, Liu D, Kelleher NL, Silverman RB. Mechanism of inactivation of γ-aminobutyric acid aminotransferase by (1S,3S)-3-amino-4-difluoromethylene-1-cyclopentanoic acid (CPP-115). Journal of the American Chemical Society. 137: 2628-40. PMID 25616005 DOI: 10.1021/ja512299n  1
2014 Clevenger KD, Wu R, Liu D, Fast W. n-Alkylboronic acid inhibitors reveal determinants of ligand specificity in the quorum-quenching and siderophore biosynthetic enzyme PvdQ. Biochemistry. 53: 6679-86. PMID 25290020 DOI: 10.1021/bi501086s  1
2014 Liao J, Wu CX, Burlak C, Zhang S, Sahm H, Wang M, Zhang ZY, Vogel KW, Federici M, Riddle SM, Nichols RJ, Liu D, Cookson MR, Stone TA, Hoang QQ. Parkinson disease-associated mutation R1441H in LRRK2 prolongs the "active state" of its GTPase domain. Proceedings of the National Academy of Sciences of the United States of America. 111: 4055-60. PMID 24591621 DOI: 10.1073/pnas.1323285111  1
2014 Martinez S, Wu R, Sanishvili R, Liu D, Holz R. The active site sulfenic acid ligand in nitrile hydratases can function as a nucleophile. Journal of the American Chemical Society. 136: 1186-9. PMID 24383915 DOI: 10.1021/ja410462j  1
2013 McGregor WC, Gillner DM, Swierczek SI, Liu D, Holz RC. Identification of a Histidine Metal Ligand in the argE-Encoded N-Acetyl-L-Ornithine Deacetylase from Escherichia coli. Springerplus. 2: 482. PMID 25674394 DOI: 10.1186/2193-1801-2-482  1
2013 Edayathumangalam R, Wu R, Garcia R, Wang Y, Wang W, Kreinbring CA, Bach A, Liao J, Stone TA, Terwilliger TC, Hoang QQ, Belitsky BR, Petsko GA, Ringe D, Liu D. Crystal structure of Bacillus subtilis GabR, an autorepressor and transcriptional activator of gabT. Proceedings of the National Academy of Sciences of the United States of America. 110: 17820-5. PMID 24127574 DOI: 10.1073/pnas.1315887110  1
2013 Clevenger KD, Wu R, Er JA, Liu D, Fast W. Rational design of a transition state analogue with picomolar affinity for Pseudomonas aeruginosa PvdQ, a siderophore biosynthetic enzyme. Acs Chemical Biology. 8: 2192-200. PMID 23883096 DOI: 10.1021/cb400345h  1
2013 Liu CF, Liu D, Momb J, Thomas PW, Lajoie A, Petsko GA, Fast W, Ringe D. A phenylalanine clamp controls substrate specificity in the quorum-quenching metallo-γ-lactonase from Bacillus thuringiensis Biochemistry. 52: 1603-1610. PMID 23387521 DOI: 10.1021/bi400050j  1
2012 Kuhn ML, Martinez S, Gumataotao N, Bornscheuer U, Liu D, Holz RC. The Fe-type nitrile hydratase from Comamonas testosteroni Ni1 does not require an activator accessory protein for expression in Escherichia coli. Biochemical and Biophysical Research Communications. 424: 365-70. PMID 22713452 DOI: 10.1016/j.bbrc.2012.06.036  1
2011 Thomas PW, Zheng M, Wu S, Guo H, Liu D, Xu D, Fast W. Characterization of purified New Delhi metallo-β-lactamase-1. Biochemistry. 50: 10102-13. PMID 22029287 DOI: 10.1021/bi201449r  1
2010 Liu D, Pozharski E, Fu M, Silverman RB, Ringe D. Mechanism of inactivation of escherichia coli aspartate aminotransferase by (S)-4-amino-4,5-dihydro-2-furancarboxylic acid Biochemistry. 49: 10507-10515. PMID 21033689 DOI: 10.1021/bi101325z  1
2010 Lepore BW, Liu D, Peng Y, Fu M, Yasuda C, Manning JM, Silverman RB, Ringe D. Chiral discrimination among aminotransferases: Inactivation by 4-amino-4,5-dihydrothiophenecarboxylic Acid Biochemistry. 49: 3138-3147. PMID 20192272 DOI: 10.1021/bi902052x  1
2008 Momb J, Wang C, Liu D, Thomas PW, Petsko GA, Guo H, Ringe D, Fast W. Mechanism of the quorum-quenching lactonase (AiiA) from Bacillus thuringiensis. 2. Substrate modeling and active site mutations. Biochemistry. 47: 7715-25. PMID 18627130 DOI: 10.1021/bi8003704  1
2008 Liu D, Momb J, Thomas PW, Moulin A, Petsko GA, Fast W, Ringe D. Mechanism of the quorum-quenching lactonase (AiiA) from Bacillus thuringiensis. 1. Product-bound structures. Biochemistry. 47: 7706-14. PMID 18627129 DOI: 10.1021/bi800368y  1
2007 Liu D, Thomas PW, Momb J, Hoang QQ, Petsko GA, Ringe D, Fast W. Structure and specificity of a quorum-quenching lactonase (AiiB) from Agrobacterium tumefaciens. Biochemistry. 46: 11789-99. PMID 17900178 DOI: 10.1021/bi7012849  1
2007 Liu D, Pozharski E, Lepore BW, Fu M, Silverman RB, Petsko GA, Ringe D. Inactivation of Escherichia coli L-aspartate aminotransferase by (S)-4-amino-4,5-dihydro-2-thiophenecarboxylic acid reveals "a tale of two mechanisms". Biochemistry. 46: 10517-27. PMID 17713924 DOI: 10.1021/bi700663n  1
2005 Liu D, Lepore BW, Petsko GA, Thomas PW, Stone EM, Fast W, Ringe D. Three-dimensional structure of the quorum-quenching N-acyl homoserine lactone hydrolase from Bacillus thuringiensis. Proceedings of the National Academy of Sciences of the United States of America. 102: 11882-7. PMID 16087890 DOI: 10.1073/pnas.0505255102  1
2005 Karsten WE, Liu D, Rao GSJ, Harris BG, Cook PF. A catalytic triad is responsible for acid-base chemistry in the Ascaris suum NAD-malic enzyme Biochemistry. 44: 3626-3635. PMID 15736972 DOI: 10.1021/bi047826o  1
2002 Liu D, Hwang CC, Cook PF. Alternative substrates for malic enzyme: Oxidative decarboxylation of L-aspartate Biochemistry. 41: 12200-12203. PMID 12356322 DOI: 10.1021/bi026322s  1
2000 Liu D, Karsten WE, Cook PF. Lysine 199 is the general acid in the NAD-malic enzyme reaction Biochemistry. 39: 11955-11960. PMID 11009609 DOI: 10.1021/bi000790p  1
1999 Karsten WE, Chooback L, Liu D, Hwang CC, Lynch C, Cook PF. Mapping the active site topography of the NAD-malic enzyme via alanine- scanning site-directed mutagenesis Biochemistry. 38: 10527-10532. PMID 10441149 DOI: 10.1021/bi9906165  1
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