Dagmar Ringe - Publications

Affiliations: 
Biochemistry, Chemistry Brandeis University, Waltham, MA, United States 
Area:
relationship of protein three-dimensional structure to chemical function
Website:
http://www.bio.brandeis.edu/faculty01/ringe.html

145 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 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  0.84
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  0.72
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  0.72
2017 Deshpande AR, Pochapsky TC, Ringe D. The Metal Drives the Chemistry: Dual Functions of Acireductone Dioxygenase. Chemical Reviews. PMID 28731690 DOI: 10.1021/acs.chemrev.7b00117  0.4
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  0.84
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  0.84
2017 Zahniser MP, Prasad S, Kneen MM, Kreinbring CA, Petsko GA, Ringe D, McLeish MJ. Structure and mechanism of benzaldehyde dehydrogenase from Pseudomonas putida ATCC 12633, a member of the Class 3 aldehyde dehydrogenase superfamily. Protein Engineering, Design & Selection : Peds. 1-8. PMID 28338942 DOI: 10.1093/protein/gzx015  0.84
2017 Deshpande AR, Pochapsky TC, Petsko GA, Ringe D. Dual chemistry catalyzed by human acireductone dioxygenase. Protein Engineering, Design & Selection : Peds. PMID 28062648 DOI: 10.1093/protein/gzw078  0.84
2016 Liu CF, Brandt GS, Hoang QQ, Naumova N, Lazarevic V, Hwang ES, Dekker J, Glimcher LH, Ringe D, Petsko GA. Crystal structure of the DNA binding domain of the transcription factor T-bet suggests simultaneous recognition of distant genome sites. Proceedings of the National Academy of Sciences of the United States of America. 113: E6572-E6581. PMID 27791029 DOI: 10.1073/pnas.1613914113  0.84
2016 Bassil F, Fernagut PO, Bezard E, Pruvost A, Leste-Lasserre T, Hoang QQ, Ringe D, Petsko GA, Meissner WG. Reducing C-terminal truncation mitigates synucleinopathy and neurodegeneration in a transgenic model of multiple system atrophy. Proceedings of the National Academy of Sciences of the United States of America. PMID 27482103 DOI: 10.1073/pnas.1609291113  0.84
2016 Wang W, Nguyen LT, Burlak C, Chegini F, Guo F, Chataway T, Ju S, Fisher OS, Miller DW, Datta D, Wu F, Wu CX, Landeru A, Wells JA, Cookson MR, ... ... Ringe D, et al. Caspase-1 causes truncation and aggregation of the Parkinson's disease-associated protein α-synuclein. Proceedings of the National Academy of Sciences of the United States of America. PMID 27482083 DOI: 10.1073/pnas.1610099113  1
2016 Deshpande AR, Wagenpfeil K, Pochapsky TC, Petsko GA, Ringe D. Metal-dependent function of a mammalian acireductone dioxygenase. Biochemistry. PMID 26858196 DOI: 10.1021/acs.biochem.5b01319  1
2015 Kim CH, Han BS, Moon J, Kim DJ, Shin J, Rajan S, Nguyen QT, Sohn M, Kim WG, Han M, Jeong I, Kim KS, Lee EH, Tu Y, Naffin-Olivos JL, ... ... Ringe D, et al. Nuclear receptor Nurr1 agonists enhance its dual functions and improve behavioral deficits in an animal model of Parkinson's disease. Proceedings of the National Academy of Sciences of the United States of America. PMID 26124091 DOI: 10.1073/pnas.1509742112  1
2015 Barmada SJ, Ju S, Arjun A, Batarse A, Archbold HC, Peisach D, Li X, Zhang Y, Tank EM, Qiu H, Huang EJ, Ringe D, Petsko GA, Finkbeiner S. Amelioration of toxicity in neuronal models of amyotrophic lateral sclerosis by hUPF1. Proceedings of the National Academy of Sciences of the United States of America. 112: 7821-6. PMID 26056265 DOI: 10.1073/pnas.1509744112  0.84
2015 Brodkin HR, DeLateur NA, Somarowthu S, Mills CL, Novak WR, Beuning PJ, Ringe D, Ondrechen MJ. Prediction of distal residue participation in enzyme catalysis. Protein Science : a Publication of the Protein Society. 24: 762-78. PMID 25627867 DOI: 10.1002/pro.2648  1
2015 Berman DE, Ringe D, Petsko GA, Small SA. The use of pharmacological retromer chaperones in Alzheimer's disease and other endosomal-related disorders. Neurotherapeutics : the Journal of the American Society For Experimental Neurotherapeutics. 12: 12-8. PMID 25472693 DOI: 10.1007/s13311-014-0321-y  1
2015 Jackson KL, Dayton RD, Orchard EA, Ju S, Ringe D, Petsko GA, Maquat LE, Klein RL. Preservation of forelimb function by UPF1 gene therapy in a rat model of TDP-43-induced motor paralysis. Gene Therapy. 22: 20-8. PMID 25354681 DOI: 10.1038/gt.2014.101  1
2015 Barmada SJ, Ju S, Arjun A, Batarse A, Archbold HC, Peisach D, Li X, Zhang Y, Tank EMH, Qiu H, Huang EJ, Ringe D, Petsko GA, Finkbeiner S. Amelioration of toxicity in neuronal models of amyotrophic lateral sclerosis by hUPF1 Proceedings of the National Academy of Sciences of the United States of America. 112: 7821-7826. DOI: 10.1073/pnas.1509744112  1
2014 Keedy DA, van den Bedem H, Sivak DA, Petsko GA, Ringe D, Wilson MA, Fraser JS. Crystal cryocooling distorts conformational heterogeneity in a model Michaelis complex of DHFR. Structure (London, England : 1993). 22: 899-910. PMID 24882744 DOI: 10.1016/j.str.2014.04.016  1
2014 Naffin-Olivos JL, Georgieva M, Goldfarb N, Madan-Lala R, Dong L, Bizzell E, Valinetz E, Brandt GS, Yu S, Shabashvili DE, Ringe D, Dunn BM, Petsko GA, Rengarajan J. Mycobacterium tuberculosis Hip1 modulates macrophage responses through proteolysis of GroEL2. Plos Pathogens. 10: e1004132. PMID 24830429 DOI: 10.1371/journal.ppat.1004132  1
2014 Mecozzi VJ, Berman DE, Simoes S, Vetanovetz C, Awal MR, Patel VM, Schneider RT, Petsko GA, Ringe D, Small SA. Pharmacological chaperones stabilize retromer to limit APP processing. Nature Chemical Biology. 10: 443-9. PMID 24747528 DOI: 10.1038/nchembio.1508  1
2014 Auclair JR, Salisbury JP, Johnson JL, Petsko GA, Ringe D, Bosco DA, Agar NY, Santagata S, Durham HD, Agar JN. Artifacts to avoid while taking advantage of top-down mass spectrometry based detection of protein S-thiolation. Proteomics. 14: 1152-7. PMID 24634066 DOI: 10.1002/pmic.201300450  1
2014 Kreinbring CA, Remillard SP, Hubbard P, Brodkin HR, Leeper FJ, Hawksley D, Lai EY, Fulton C, Petsko GA, Ringe D. Structure of a eukaryotic thiaminase I. Proceedings of the National Academy of Sciences of the United States of America. 111: 137-42. PMID 24351929 DOI: 10.1073/pnas.1315882110  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 Auclair JR, Johnson JL, Liu Q, Salisbury JP, Rotunno MS, Petsko GA, Ringe D, Brown RH, Bosco DA, Agar JN. Post-translational modification by cysteine protects Cu/Zn-superoxide dismutase from oxidative damage. Biochemistry. 52: 6137-44. PMID 23927036 DOI: 10.1021/bi4006122  1
2013 Auclair JR, Brodkin HR, D'Aquino JA, Petsko GA, Ringe D, Agar JN. Structural consequences of cysteinylation of Cu/Zn-superoxide dismutase Biochemistry. 52: 6145-6150. PMID 23919400 DOI: 10.1021/bi400613h  1
2013 Sigala PA, Fafarman AT, Schwans JP, Fried SD, Fenn TD, Caaveiro JM, Pybus B, Ringe D, Petsko GA, Boxer SG, Herschlag D. Quantitative dissection of hydrogen bond-mediated proton transfer in the ketosteroid isomerase active site. Proceedings of the National Academy of Sciences of the United States of America. 110: E2552-61. PMID 23798390 DOI: 10.1073/pnas.1302191110  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
2013 Benkovic SJ, Theriot J, Ringe D. Open questions - in brief: beyond -omics, missing motor proteins, and getting from molecules to organisms. Bmc Biology. 11: 8. PMID 23369202 DOI: 10.1186/1741-7007-11-8  1
2013 Steele JW, Ju S, Lachenmayer ML, Liken J, Stock A, Kim SH, Delgado LM, Alfaro IE, Bernales S, Verdile G, Bharadwaj P, Gupta V, Barr R, Friss A, Dolios G, ... ... Ringe D, et al. Latrepirdine stimulates autophagy and reduces accumulation of α-synuclein in cells and in mouse brain. Molecular Psychiatry. 18: 882-8. PMID 22869031 DOI: 10.1038/mp.2012.115  1
2013 Steele JW, Lachenmayer ML, Ju S, Stock A, Liken J, Kim SH, Delgado LM, Alfaro IE, Bernales S, Verdile G, Bharadwaj P, Gupta V, Barr R, Friss A, Dolios G, ... ... Ringe D, et al. Latrepirdine improves cognition and arrests progression of neuropathology in an Alzheimer's mouse model. Molecular Psychiatry. 18: 889-97. PMID 22850627 DOI: 10.1038/mp.2012.106  1
2012 Ringe D, Petsko GA. Behind the movement Cell. 150: 1093-1095. PMID 22980970 DOI: 10.1016/j.cell.2012.08.031  1
2012 Bharadwaj PR, Verdile G, Barr RK, Gupta V, Steele JW, Lachenmayer ML, Yue Z, Ehrlich ME, Petsko G, Ju S, Ringe D, Sankovich SE, Caine JM, Macreadie IG, Gandy S, et al. Latrepirdine (dimebon) enhances autophagy and reduces intracellular GFP-Aβ42 levels in yeast. Journal of Alzheimer's Disease : Jad. 32: 949-67. PMID 22903131 DOI: 10.3233/JAD-2012-120178  1
2012 Auclair JR, Somasundaran M, Green KM, Evans JE, Schiffer CA, Ringe D, Petsko GA, Agar JN. Mass spectrometry tools for analysis of intermolecular interactions. Methods in Molecular Biology (Clifton, N.J.). 896: 387-98. PMID 22821539 DOI: 10.1007/978-1-4614-3704-8_26  1
2012 Davies CW, Chaney J, Korbel G, Ringe D, Petsko GA, Ploegh H, Das C. The co-crystal structure of ubiquitin carboxy-terminal hydrolase L1 (UCHL1) with a tripeptide fluoromethyl ketone (Z-VAE(OMe)-FMK). Bioorganic & Medicinal Chemistry Letters. 22: 3900-4. PMID 22617491 DOI: 10.1016/j.bmcl.2012.04.124  1
2011 Wang W, Perovic I, Chittuluru J, Kaganovich A, Nguyen LT, Liao J, Auclair JR, Johnson D, Landeru A, Simorellis AK, Ju S, Cookson MR, Asturias FJ, Agar JN, Webb BN, ... ... Ringe D, et al. A soluble α-synuclein construct forms a dynamic tetramer. Proceedings of the National Academy of Sciences of the United States of America. 108: 17797-802. PMID 22006323 DOI: 10.1073/pnas.1113260108  1
2011 Somarowthu S, Brodkin HR, DAquino JA, Ringe D, Ondrechen MJ, Beuning PJ. A tale of two isomerases: Compact versus extended active sites in ketosteroid isomerase and phosphoglucose isomerase Biochemistry. 50: 9283-9295. PMID 21970785 DOI: 10.1021/bi201089v  1
2011 Bosco DA, LaVoie MJ, Petsko GA, Ringe D. Proteostasis and movement disorders: Parkinson's disease and amyotrophic lateral sclerosis. Cold Spring Harbor Perspectives in Biology. 3: a007500. PMID 21844169 DOI: 10.1101/cshperspect.a007500  1
2011 Lazar LM, Fisher SZ, Moulin AG, Kovalevsky A, Novak WR, Langan P, Petsko GA, Ringe D. Time-of-flight neutron diffraction study of bovine γ-chymotrypsin at the Protein Crystallography Station. Acta Crystallographica. Section F, Structural Biology and Crystallization Communications. 67: 587-90. PMID 21543868 DOI: 10.1107/S1744309111009341  1
2011 Ju S, Tardiff DF, Han H, Divya K, Zhong Q, Maquat LE, Bosco DA, Hayward LJ, Brown RH, Lindquist S, Ringe D, Petsko GA. A yeast model of FUS/TLS-dependent cytotoxicity. Plos Biology. 9: e1001052. PMID 21541368 DOI: 10.1371/journal.pbio.1001052  1
2011 Brodkin HR, Novak WRP, Milne AC, D'Aquino JA, Karabacak NM, Goldberg IG, Agar JN, Payne MS, Petsko GA, Ondrechen MJ, Ringe D. Evidence of the participation of remote residues in the catalytic activity of co-type nitrile hydratase from Pseudomonas putida Biochemistry. 50: 4923-4935. PMID 21473592 DOI: 10.1021/bi101761e  1
2010 Auclair JR, Boggio KJ, Petsko GA, Ringe D, Agar JN. Strategies for stabilizing superoxide dismutase (SOD1), the protein destabilized in the most common form of familial amyotrophic lateral sclerosis Proceedings of the National Academy of Sciences of the United States of America. 107: 21394-21399. PMID 21098299 DOI: 10.1073/pnas.1015463107  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 Lewandowski NM, Ju S, Verbitsky M, Ross B, Geddie ML, Rockenstein E, Adame A, Muhammad A, Vonsattel JP, Ringe D, Cote L, Lindquist S, Masliah E, Petsko GA, Marder K, et al. Polyamine pathway contributes to the pathogenesis of Parkinson disease. Proceedings of the National Academy of Sciences of the United States of America. 107: 16970-5. PMID 20837543 DOI: 10.1073/pnas.1011751107  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
2010 Brandt GS, Kneen MM, Petsko GA, Ringe D, McLeish MJ. Active-site engineering of benzaldehyde lyase shows that a point mutation can confer both new reactivity and susceptibility to mechanism-based inhibition Journal of the American Chemical Society. 132: 438-439. PMID 20030408 DOI: 10.1021/ja907064w  1
2009 Ringe D, Petsko GA. What are pharmacological chaperones and why are they interesting? Journal of Biology. 8. PMID 19833004 DOI: 10.1186/jbiol186  1
2009 Landon MR, Lieberman RL, Hoang QQ, Ju S, Caaveiro JM, Orwig SD, Kozakov D, Brenke R, Chuang GY, Beglov D, Vajda S, Petsko GA, Ringe D. Detection of ligand binding hot spots on protein surfaces via fragment-based methods: application to DJ-1 and glucocerebrosidase. Journal of Computer-Aided Molecular Design. 23: 491-500. PMID 19521672 DOI: 10.1007/s10822-009-9283-2  1
2009 Sigala PA, Caaveiro JM, Ringe D, Petsko GA, Herschlag D. Hydrogen bond coupling in the ketosteroid isomerase active site. Biochemistry. 48: 6932-9. PMID 19469568 DOI: 10.1021/bi900713j  1
2009 D'Aquino JA, Denninger AR, Moulin AG, D'Aquino KE, Ringe D. Decreased sensitivity to changes in the concentration of metal ions as the basis for the hyperactivity of DtxR(E175K). Journal of Molecular Biology. 390: 112-23. PMID 19433095 DOI: 10.1016/j.jmb.2009.05.003  1
2009 Lieberman RL, D'aquino JA, Ringe D, Petsko GA. Effects of pH and iminosugar pharmacological chaperones on lysosomal glycosidase structure and stability. Biochemistry. 48: 4816-27. PMID 19374450 DOI: 10.1021/bi9002265  1
2009 Brandt GS, Kneen MM, Chakraborty S, Baykal AT, Nemeria N, Yep A, Ruby DI, Petsko GA, Kenyon GL, McLeish MJ, Jordan F, Ringe D. Snapshot of a reaction intermediate: analysis of benzoylformate decarboxylase in complex with a benzoylphosphonate inhibitor. Biochemistry. 48: 3247-57. PMID 19320438 DOI: 10.1021/bi801950k  1
2009 Novak WR, Moulin AG, Blakeley MP, Schlichting I, Petsko GA, Ringe D. A preliminary neutron diffraction study of gamma-chymotrypsin. Acta Crystallographica. Section F, Structural Biology and Crystallization Communications. 65: 317-20. PMID 19255494 DOI: 10.1107/S1744309109006630  1
2009 Chakraborty S, Nemeria NS, Balakrishnan A, Brandt GS, Kneen MM, Yep A, McLeish MJ, Kenyon GL, Petsko GA, Ringe D, Jordan F. Detection and time course of formation of major thiamin diphosphate-bound covalent intermediates derived from a chromophoric substrate analogue on benzoylformate decarboxylase. Biochemistry. 48: 981-94. PMID 19140682 DOI: 10.1021/bi801810h  1
2008 Sigala PA, Kraut DA, Caaveiro JM, Pybus B, Ruben EA, Ringe D, Petsko GA, Herschlag D. Testing geometrical discrimination within an enzyme active site: constrained hydrogen bonding in the ketosteroid isomerase oxyanion hole. Journal of the American Chemical Society. 130: 13696-708. PMID 18808119 DOI: 10.1021/ja803928m  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
2008 Ataie NJ, Hoang QQ, Zahniser MP, Tu Y, Milne A, Petsko GA, Ringe D. Zinc coordination geometry and ligand binding affinity: the structural and kinetic analysis of the second-shell serine 228 residue and the methionine 180 residue of the aminopeptidase from Vibrio proteolyticus. Biochemistry. 47: 7673-83. PMID 18576673 DOI: 10.1021/bi702188e  1
2008 Brandt GS, Nemeria N, Chakraborty S, McLeish MJ, Yep A, Kenyon GL, Petsko GA, Jordan F, Ringe D. Probing the active center of benzaldehyde lyase with substitutions and the pseudosubstrate analogue benzoylphosphonic acid methyl ester. Biochemistry. 47: 7734-43. PMID 18570438 DOI: 10.1021/bi8004413  1
2008 Ringe D, Petsko GA. Biochemistry. How enzymes work. Science (New York, N.Y.). 320: 1428-9. PMID 18556536 DOI: 10.1126/science.1159747  1
2008 Murga LF, Ondrechen MJ, Ringe D. Prediction of interaction sites from apo 3D structures when the holo conformation is different. Proteins. 72: 980-92. PMID 18300225 DOI: 10.1002/prot.21995  1
2008 White A, Ringe D. Metal-ion activation of transcription Iron Metabolism: Inorganic Biochemistry and Regulatory Mechanisms. 359-371. DOI: 10.1002/9783527613700.ch21  1
2007 D'Aquino JA, Lattimer JR, Denninger A, D'Aquino KE, Ringe D. Role of the N-terminal helix in the metal ion-induced activation of the diphtheria toxin repressor DtxR. Biochemistry. 46: 11761-70. PMID 17902703 DOI: 10.1021/bi7007883  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
2007 Munih P, Moulin A, Stamper CC, Bennett B, Ringe D, Petsko GA, Holz RC. X-ray crystallographic characterization of the Co(II)-substituted Tris-bound form of the aminopeptidase from Aeromonas proteolytica. Journal of Inorganic Biochemistry. 101: 1099-107. PMID 17574677 DOI: 10.1016/j.jinorgbio.2007.03.010  1
2007 Moulin A, Bell JH, Pratt RF, Ringe D. Inhibition of chymotrypsin by a complex of ortho-vanadate and benzohydroxamic acid: structure of the inert complex and its mechanistic interpretation. Biochemistry. 46: 5982-90. PMID 17469803 DOI: 10.1021/bi6025209  1
2007 Wei Y, Ringe D, Wilson MA, Ondrechen MJ. Identification of functional subclasses in the DJ-1 superfamily proteins. Plos Computational Biology. 3: e10. PMID 17257049 DOI: 10.1371/journal.pcbi.0030010  1
2007 Lieberman RL, Wustman BA, Huertas P, Powe AC, Pine CW, Khanna R, Schlossmacher MG, Ringe D, Petsko GA. Structure of acid beta-glucosidase with pharmacological chaperone provides insight into Gaucher disease. Nature Chemical Biology. 3: 101-7. PMID 17187079 DOI: 10.1038/nchembio850  1
2006 Ding X, Rasmussen BF, Petsko GA, Ringe D. Direct crystallographic observation of an acyl-enzyme intermediate in the elastase-catalyzed hydrolysis of a peptidyl ester substrate: Exploiting the "glass transition" in protein dynamics. Bioorganic Chemistry. 34: 410-23. PMID 17083959 DOI: 10.1016/j.bioorg.2006.10.002  1
2006 Chen D, Frey PA, Lepore BW, Ringe D, Ruzicka FJ. Identification of structural and catalytic classes of highly conserved amino acid residues in lysine 2,3-aminomutase. Biochemistry. 45: 12647-53. PMID 17042481 DOI: 10.1021/bi061329l  1
2006 Kraut DA, Sigala PA, Pybus B, Liu CW, Ringe D, Petsko GA, Herschlag D. Testing electrostatic complementarity in enzyme catalysis: hydrogen bonding in the ketosteroid isomerase oxyanion hole. Plos Biology. 4: e99. PMID 16602823 DOI: 10.1371/journal.pbio.0040099  1
2006 Desmarais W, Bienvenue DL, Bzymek KP, Petsko GA, Ringe D, Holz RC. The high-resolution structures of the neutral and the low pH crystals of aminopeptidase from Aeromonas proteolytica. Journal of Biological Inorganic Chemistry : Jbic : a Publication of the Society of Biological Inorganic Chemistry. 11: 398-408. PMID 16596389 DOI: 10.1007/s00775-006-0093-x  1
2006 Das C, Hoang QQ, Kreinbring CA, Luchansky SJ, Meray RK, Ray SS, Lansbury PT, Ringe D, Petsko GA. Structural basis for conformational plasticity of the Parkinson's disease-associated ubiquitin hydrolase UCH-L1. Proceedings of the National Academy of Sciences of the United States of America. 103: 4675-80. PMID 16537382 DOI: 10.1073/pnas.0510403103  1
2006 Mattos C, Bellamacina CR, Peisach E, Pereira A, Vitkup D, Petsko GA, Ringe D. Multiple solvent crystal structures: probing binding sites, plasticity and hydration. Journal of Molecular Biology. 357: 1471-82. PMID 16488429 DOI: 10.1016/j.jmb.2006.01.039  1
2005 D'Aquino JA, Tetenbaum-Novatt J, White A, Berkovitch F, Ringe D. Mechanism of metal ion activation of the diphtheria toxin repressor DtxR. Proceedings of the National Academy of Sciences of the United States of America. 102: 18408-13. PMID 16352732 DOI: 10.1073/pnas.0500908102  1
2005 Wilson MA, Ringe D, Petsko GA. The atomic resolution crystal structure of the YajL (ThiJ) protein from Escherichia coli: a close prokaryotic homologue of the Parkinsonism-associated protein DJ-1. Journal of Molecular Biology. 353: 678-91. PMID 16181642 DOI: 10.1016/j.jmb.2005.08.033  1
2005 Lepore BW, Ruzicka FJ, Frey PA, Ringe D. The x-ray crystal structure of lysine-2,3-aminomutase from Clostridium subterminale. Proceedings of the National Academy of Sciences of the United States of America. 102: 13819-24. PMID 16166264 DOI: 10.1073/pnas.0505726102  1
2005 Bzymek KP, Moulin A, Swierczek SI, Ringe D, Petsko GA, Bennett B, Holz RC. Kinetic, spectroscopic, and X-ray crystallographic characterization of the functional E151H aminopeptidase from Aeromonas proteolytica. Biochemistry. 44: 12030-40. PMID 16142900 DOI: 10.1021/bi0505823  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 Pozharski E, Moulin A, Hewagama A, Shanafelt AB, Petsko GA, Ringe D. Diversity in hapten recognition: structural study of an anti-cocaine antibody M82G2. Journal of Molecular Biology. 349: 570-82. PMID 15885702 DOI: 10.1016/j.jmb.2005.03.080  1
2005 Fenn TD, Holyoak T, Stamper GF, Ringe D. Effect of a Y265F mutant on the transamination-based cycloserine inactivation of alanine racemase. Biochemistry. 44: 5317-27. PMID 15807525 DOI: 10.1021/bi047842l  1
2004 Yang J, Wang Y, Woolridge EM, Arora V, Petsko GA, Kozarich JW, Ringe D. Crystal structure of 3-carboxy-cis,cis-muconate lactonizing enzyme from Pseudomonas putida, a fumarase class II type cycloisomerase: enzyme evolution in parallel pathways. Biochemistry. 43: 10424-34. PMID 15301541 DOI: 10.1021/bi036205c  1
2004 Stamper CC, Bienvenue DL, Bennett B, Ringe D, Petsko GA, Holz RC. Spectroscopic and X-ray crystallographic characterization of bestatin bound to the aminopeptidase from Aeromonas (Vibrio) proteolytica. Biochemistry. 43: 9620-8. PMID 15274616 DOI: 10.1021/bi049126p  1
2004 Gray JV, Petsko GA, Johnston GC, Ringe D, Singer RA, Werner-Washburne M. "Sleeping beauty": quiescence in Saccharomyces cerevisiae. Microbiology and Molecular Biology Reviews : Mmbr. 68: 187-206. PMID 15187181 DOI: 10.1128/MMBR.68.2.187-206.2004  1
2004 Canet-Avilés RM, Wilson MA, Miller DW, Ahmad R, McLendon C, Bandyopadhyay S, Baptista MJ, Ringe D, Petsko GA, Cookson MR. The Parkinson's disease protein DJ-1 is neuroprotective due to cysteine-sulfinic acid-driven mitochondrial localization. Proceedings of the National Academy of Sciences of the United States of America. 101: 9103-8. PMID 15181200 DOI: 10.1073/pnas.0402959101  1
2004 Fenn TD, Ringe D, Petsko GA. Xylose isomerase in substrate and inhibitor michaelis states: atomic resolution studies of a metal-mediated hydride shift. Biochemistry. 43: 6464-74. PMID 15157080 DOI: 10.1021/bi049812o  1
2004 Vogan EM, Bellamacina C, He X, Liu HW, Ringe D, Petsko GA. Crystal structure at 1.8 A resolution of CDP-D-glucose 4,6-dehydratase from Yersinia pseudotuberculosis. Biochemistry. 43: 3057-67. PMID 15023057 DOI: 10.1021/bi035547f  1
2004 Pozharski E, Wilson MA, Hewagama A, Shanafelt AB, Petsko G, Ringe D. Anchoring a cationic ligand: the structure of the Fab fragment of the anti-morphine antibody 9B1 and its complex with morphine. Journal of Molecular Biology. 337: 691-7. PMID 15019787 DOI: 10.1016/j.jmb.2003.12.084  1
2004 Ringe D, Wei Y, Boino KR, Ondrechen MJ. Protein structure to function: insights from computation. Cellular and Molecular Life Sciences : Cmls. 61: 387-92. PMID 14999401 DOI: 10.1007/s00018-003-3291-5  1
2004 Holyoak T, Kettner CA, Petsko GA, Fuller RS, Ringe D. Structural basis for differences in substrate selectivity in Kex2 and furin protein convertases. Biochemistry. 43: 2412-21. PMID 14992578 DOI: 10.1021/bi035849h  1
2004 Wilson MA, St Amour CV, Collins JL, Ringe D, Petsko GA. The 1.8-A resolution crystal structure of YDR533Cp from Saccharomyces cerevisiae: a member of the DJ-1/ThiJ/PfpI superfamily. Proceedings of the National Academy of Sciences of the United States of America. 101: 1531-6. PMID 14745011 DOI: 10.1073/pnas.0308089100  1
2004 Murga LF, Wei Y, André P, Clifton JG, Ringe D, Ondrechen MJ. Physicochemical methods for prediction of functional information for proteins Israel Journal of Chemistry. 44: 299-308. DOI: 10.1560/Q3YD-PEDL-JRU8-8FVM  1
2003 Holyoak T, Fenn TD, Wilson MA, Moulin AG, Ringe D, Petsko GA. Malonate: a versatile cryoprotectant and stabilizing solution for salt-grown macromolecular crystals. Acta Crystallographica. Section D, Biological Crystallography. 59: 2356-8. PMID 14646118 DOI: 10.1107/S0907444903021784  1
2003 Ringe D, Petsko GA. The 'glass transition' in protein dynamics: what it is, why it occurs, and how to exploit it. Biophysical Chemistry. 105: 667-80. PMID 14499926 DOI: 10.1016/S0301-4622(03)00096-6  1
2003 Wilson MA, Collins JL, Hod Y, Ringe D, Petsko GA. The 1.1-A resolution crystal structure of DJ-1, the protein mutated in autosomal recessive early onset Parkinson's disease. Proceedings of the National Academy of Sciences of the United States of America. 100: 9256-61. PMID 12855764 DOI: 10.1073/pnas.1133288100  1
2003 D'Aquino JA, Ringe D. Determinants of the SRC homology domain 3-like fold. Journal of Bacteriology. 185: 4081-6. PMID 12837782 DOI: 10.1128/JB.185.14.4081-4086.2003  1
2003 Holyoak T, Wilson MA, Fenn TD, Kettner CA, Petsko GA, Fuller RS, Ringe D. 2.4 A resolution crystal structure of the prototypical hormone-processing protease Kex2 in complex with an Ala-Lys-Arg boronic acid inhibitor. Biochemistry. 42: 6709-18. PMID 12779325 DOI: 10.1021/bi034434t  1
2003 Fenn TD, Stamper GF, Morollo AA, Ringe D. A side reaction of alanine racemase: transamination of cycloserine. Biochemistry. 42: 5775-83. PMID 12741835 DOI: 10.1021/bi027022d  1
2003 Beebe JA, Arabshahi A, Clifton JG, Ringe D, Petsko GA, Frey PA. Galactose mutarotase: pH dependence of enzymatic mutarotation. Biochemistry. 42: 4414-20. PMID 12693937 DOI: 10.1021/bi020639a  1
2003 Spiering MM, Ringe D, Murphy JR, Marletta MA. Metal stoichiometry and functional studies of the diphtheria toxin repressor. Proceedings of the National Academy of Sciences of the United States of America. 100: 3808-13. PMID 12655054 DOI: 10.1073/pnas.0737977100  1
2003 Fenn TD, Ringe D, Petsko GA. POVScript+: A program for model and data visualization using persistence of vision ray-tracing Journal of Applied Crystallography. 36: 944-947. DOI: 10.1107/S0021889803006721  1
2002 Kenyon GL, DeMarini DM, Fuchs E, Galas DJ, Kirsch JF, Leyh TS, Moos WH, Petsko GA, Ringe D, Rubin GM, Sheahan LC. Defining the mandate of proteomics in the post-genomics era: workshop report. Molecular & Cellular Proteomics : McP. 1: 763-80. PMID 12438560  1
2002 Desmarais WT, Bienvenue DL, Bzymek KP, Holz RC, Petsko GA, Ringe D. The 1.20 A resolution crystal structure of the aminopeptidase from Aeromonas proteolytica complexed with tris: a tale of buffer inhibition. Structure (London, England : 1993). 10: 1063-72. PMID 12176384 DOI: 10.1016/S0969-2126(02)00810-9  1
2002 Taoka S, Lepore BW, Kabil O, Ojha S, Ringe D, Banerjee R. Human cystathionine beta-synthase is a heme sensor protein. Evidence that the redox sensor is heme and not the vicinal cysteines in the CXXC motif seen in the crystal structure of the truncated enzyme. Biochemistry. 41: 10454-61. PMID 12173932 DOI: 10.1021/bi026052d  1
2002 Bienvenue DL, Mathew RS, Ringe D, Holz RC. The aminopeptidase from Aeromonas proteolytica can function as an esterase. Journal of Biological Inorganic Chemistry : Jbic : a Publication of the Society of Biological Inorganic Chemistry. 7: 129-35. PMID 11862549 DOI: 10.1007/s007750100280  1
2002 Vitkup D, Ringe D, Karplus M, Petsko GA. Why protein R-factors are so large: a self-consistent analysis. Proteins. 46: 345-54. PMID 11835510 DOI: 10.1002/prot.10035  1
2002 Ringe D. Function by serendipity. Nature. 415: 488-9. PMID 11823842 DOI: 10.1038/415488b  1
2002 Vogan EM, Bellamacina CR, He X, Foxman BM, Ringe D, Liu HW, Petsko GA. Purification, crystallization and molecular symmetry of CDP-D-glucose 4,6-dehydratase from Yersinia pseudotuberculosis. Acta Crystallographica. Section D, Biological Crystallography. 58: 370-3. PMID 11807280 DOI: 10.1107/S0907444901021473  1
2001 Mattos C, Ringe D. Proteins in organic solvents. Current Opinion in Structural Biology. 11: 761-4. PMID 11751059 DOI: 10.1016/S0959-440X(01)00278-0  1
2001 Hadfield A, Shammas C, Kryger G, Ringe D, Petsko GA, Ouyang J, Viola RE. Active site analysis of the potential antimicrobial target aspartate semialdehyde dehydrogenase. Biochemistry. 40: 14475-83. PMID 11724560 DOI: 10.1021/bi015713o  1
2001 Ondrechen MJ, Clifton JG, Ringe D. THEMATICS: a simple computational predictor of enzyme function from structure. Proceedings of the National Academy of Sciences of the United States of America. 98: 12473-8. PMID 11606719 DOI: 10.1073/pnas.211436698  0.88
2001 Amor JC, Horton JR, Zhu X, Wang Y, Sullards C, Ringe D, Cheng X, Kahn RA. Structures of yeast ARF2 and ARL1: distinct roles for the N terminus in the structure and function of ARF family GTPases. The Journal of Biological Chemistry. 276: 42477-84. PMID 11535602 DOI: 10.1074/jbc.M106660200  1
2001 Pasternak A, White A, Jeffery CJ, Medina N, Cahoon M, Ringe D, Hedstrom L. The energetic cost of induced fit catalysis: Crystal structures of trypsinogen mutants with enhanced activity and inhibitor affinity. Protein Science : a Publication of the Protein Society. 10: 1331-42. PMID 11420435 DOI: 10.1110/ps.44101  1
2001 Stamper C, Bennett B, Edwards T, Holz RC, Ringe D, Petsko G. Inhibition of the aminopeptidase from Aeromonas proteolytica by L-leucinephosphonic acid. Spectroscopic and crystallographic characterization of the transition state of peptide hydrolysis. Biochemistry. 40: 7035-46. PMID 11401547  1
2000 Chen CS, White A, Love J, Murphy JR, Ringe D. Methyl groups of thymine bases are important for nucleic acid recognition by DtxR. Biochemistry. 39: 10397-407. PMID 10956029  0.52
2000 McMillan FM, Cahoon M, White A, Hedstrom L, Petsko GA, Ringe D. Crystal structure at 2.4 A resolution of Borrelia burgdorferi inosine 5'-monophosphate dehydrogenase: evidence of a substrate-induced hinged-lid motion by loop 6. Biochemistry. 39: 4533-42. PMID 10758003 DOI: 10.1021/bi992645l  1
2000 Jeffery CJ, Gloss LM, Petsko GA, Ringe D. The role of residues outside the active site: structural basis for function of C191 mutants of Escherichia coli aspartate aminotransferase. Protein Engineering. 13: 105-12. PMID 10708649  1
2000 Schlichting I, Berendzen J, Chu K, Stock AM, Maves SA, Benson DE, Sweet RM, Ringe D, Petsko GA, Sligar SG. The catalytic pathway of cytochrome p450cam at atomic resolution. Science (New York, N.Y.). 287: 1615-22. PMID 10698731 DOI: 10.1126/science.287.5458.1615  1
2000 Petsko GA, Ringe D. Observation of unstable species in enzyme-catalyzed transformations using protein crystallography. Current Opinion in Chemical Biology. 4: 89-94. PMID 10679381  1
2000 Jeffery CJ, Bahnson BJ, Chien W, Ringe D, Petsko GA. Crystal structure of rabbit phosphoglucose isomerase, a glycolytic enzyme that moonlights as neuroleukin, autocrine motility factor, and differentiation mediator. Biochemistry. 39: 955-64. PMID 10653639 DOI: 10.1021/bi991604m  1
2000 Vitkup D, Ringe D, Petsko GA, Karplus M. Solvent mobility and the protein 'glass' transition. Nature Structural Biology. 7: 34-8. PMID 10625424 DOI: 10.1038/71231  1
1999 Peisach E, Wang J, de los Santos T, Reich E, Ringe D. Crystal structure of the proenzyme domain of plasminogen. Biochemistry. 38: 11180-8. PMID 10460175 DOI: 10.1021/bi991130r  0.48
1999 De Paola CC, Bennett B, Holz RC, Ringe D, Petsko GA. 1-Butaneboronic acid binding to Aeromonas proteolytica aminopeptidase: a case of arrested development. Biochemistry. 38: 9048-53. PMID 10413478 DOI: 10.1021/bi9900572  1
1999 Ringe D, Mattos C. Analysis of the binding surfaces of proteins. Medicinal Research Reviews. 19: 321-31. PMID 10398928 DOI: 10.1002/(SICI)1098-1128(199907)19:4<321::AID-MED5>3.0.CO;2-F  1
1999 Hadfield A, Kryger G, Ouyang J, Petsko GA, Ringe D, Viola R. Structure of aspartate-beta-semialdehyde dehydrogenase from Escherichia coli, a key enzyme in the aspartate family of amino acid biosynthesis. Journal of Molecular Biology. 289: 991-1002. PMID 10369777 DOI: 10.1006/jmbi.1999.2828  1
1999 Ringe D, Petsko GA. Quantum enzymology. Tunnel vision. Nature. 399: 417-8. PMID 10365952 DOI: 10.1038/20819  1
1999 Stamper GF, Morollo AA, Ringe D. Reaction of alanine racemase with 1-aminoethylphosphonic acid forms a stable external aldimine Biochemistry. 38: 6714. PMID 10350491 DOI: 10.1021/bi995075y  0.96
1999 Pasternak A, Ringe D, Hedstrom L. Comparison of anionic and cationic trypsinogens: the anionic activation domain is more flexible in solution and differs in its mode of BPTI binding in the crystal structure. Protein Science : a Publication of the Protein Society. 8: 253-8. PMID 10210204 DOI: 10.1110/ps.8.1.253  1
1999 Zhang Z, Komives EA, Sugio S, Blacklow SC, Narayana N, Xuong NH, Stock AM, Petsko GA, Ringe D. The role of water in the catalytic efficiency of triosephosphate isomerase. Biochemistry. 38: 4389-97. PMID 10194358 DOI: 10.1021/bi9826759  1
1999 Morollo AA, Petsko GA, Ringe D. Structure of a Michaelis complex analogue: propionate binds in the substrate carboxylate site of alanine racemase. Biochemistry. 38: 3293-301. PMID 10079072 DOI: 10.1021/bi9822729  1
1999 van Ophem PW, Peisach D, Erickson SD, Soda K, Ringe D, Manning JM. Effects of the E177K mutation in D-amino acid transaminase. Studies on an essential coenzyme anchoring group that contributes to stereochemical fidelity. Biochemistry. 38: 1323-31. PMID 9930994 DOI: 10.1021/bi982414z  1
1998 Jeffery CJ, Barry T, Doonan S, Petsko GA, Ringe D. Crystallization and preliminary X-ray diffraction analysis of aspartate aminotransferase from Saccharomyces cerevisiae. Acta Crystallographica. Section D, Biological Crystallography. 54: 659-61. PMID 9761867  1
1998 Sugio S, Kashima A, Kishimoto K, Peisach D, Petsko GA, Ringe D, Yoshimura T, Esaki N. Crystal structures of L201A mutant of D-amino acid aminotransferase at 2.0 A resolution: implication of the structural role of Leu201 in transamination. Protein Engineering. 11: 613-9. PMID 9749913  1
1998 Hasson MS, Schlichting I, Moulai J, Taylor K, Barrett W, Kenyon GL, Babbitt PC, Gerlt JA, Petsko GA, Ringe D. Evolution of an enzyme active site: the structure of a new crystal form of muconate lactonizing enzyme compared with mandelate racemase and enolase. Proceedings of the National Academy of Sciences of the United States of America. 95: 10396-401. PMID 9724714 DOI: 10.1073/pnas.95.18.10396  1
1998 White A, Ding X, vanderSpek JC, Murphy JR, Ringe D. Structure of the metal-ion-activated diphtheria toxin repressor/tox operator complex. Nature. 394: 502-6. PMID 9697776 DOI: 10.1038/28893  0.6
1998 Stamper GF, Morollo AA, Ringe D, Stamper CG. Reaction of alanine racemase with 1-aminoethylphosphonic acid forms a stable external aldimine. Biochemistry. 37: 10438-45. PMID 9671513 DOI: 10.1021/bi980692s  0.96
1998 Hasson MS, Muscate A, McLeish MJ, Polovnikova LS, Gerlt JA, Kenyon GL, Petsko GA, Ringe D. The crystal structure of benzoylformate decarboxylase at 1.6 A resolution: diversity of catalytic residues in thiamin diphosphate-dependent enzymes. Biochemistry. 37: 9918-30. PMID 9665697 DOI: 10.1021/bi973047e  1
1998 Jeffery CJ, Barry T, Doonan S, Petsko GA, Ringe D. Crystal structure of Saccharomyces cerevisiae cytosolic aspartate aminotransferase. Protein Science : a Publication of the Protein Society. 7: 1380-7. PMID 9655342 DOI: 10.1002/pro.5560070614  1
1998 Yamakura F, Rardin RL, Petsko GA, Ringe D, Hiraoka BY, Nakayama K, Fujimura T, Taka H, Murayama K. Inactivation and destruction of conserved Trp159 of Fe-superoxide dismutase from Porphyromonas gingivalis by hydrogen peroxide. European Journal of Biochemistry / Febs. 253: 49-56. PMID 9578460  1
1998 Peisach D, Chipman DM, Van Ophem PW, Manning JM, Ringe D. Crystallographic study of steps along the reaction pathway of D-amino acid aminotransferase. Biochemistry. 37: 4958-67. PMID 9538014 DOI: 10.1021/bi972884d  1
1997 Hasson MS, Schlichting I, McGowen MM, Woolridge EM, Kozarich JW, Petsko GA, Ringe D. Characterization of two crystal forms of 3-carboxy-cis,cis-muconate lactonizing enzyme from Pseudomonas putida. Acta Crystallographica. Section D, Biological Crystallography. 53: 352-3. PMID 15299946 DOI: 10.1107/S0907444996015648  1
1997 Harrison DH, Bohren KM, Petsko GA, Ringe D, Gabbay KH. The alrestatin double-decker: binding of two inhibitor molecules to human aldose reductase reveals a new specificity determinant. Biochemistry. 36: 16134-40. PMID 9405046 DOI: 10.1021/bi9717136  1
1997 Wallon G, Lovett ST, Magyar C, Svingor A, Szilagyi A, Zàvodszky P, Ringe D, Petsko GA. Sequence and homology model of 3-isopropylmalate dehydrogenase from the psychrotrophic bacterium Vibrio sp. I5 suggest reasons for thermal instability. Protein Engineering. 10: 665-72. PMID 9278279  1
1995 Peisach E, Casebier D, Gallion SL, Furth P, Petsko GA, Hogan JC, Ringe D. Interaction of a peptidomimetic aminimide inhibitor with elastase. Science (New York, N.Y.). 269: 66-9. PMID 7604279  1
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