Dagmar Ringe
Degrees
Boston University, Ph.D.Barnard College, B.A.
Expertise
Protein crystallography and structural enzymology. Rational drug design.Profile
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Structures of enzymes and enzyme-substrate complexes; structure and function of metallo-enzymes; X-ray crystallography. molecular biology and biophysics of proteins involved in neurological diseases; drug design.
Courses Taught
| BCBP | 222a | Advanced Topics in Enzyme Mechanism |
Awards and Honors
Affilitate Neruoscience Program (2010)
Wyeth/Douglass Lectureship (2007 - 2008)
Von Humboldt Research Prize (2006)
Abram L Sachar Medallion, Brandeis University (2005)
Alexander von Humbolt Forschungspreis (2005)
Fellow, American Association for the Advancement of Science (2005)
McKnight Endowment Fund For Neuroscience Award (2004)
American Chemical Society Student Award (2003)
Editor, Archives in Biochemistry and Biophysics (2003)
Program Director, Molecular Biophysics Program, National Science Foundation (1997)
Markey Associate Professor (1990 - 1994)
First Recipient, Biophysical Society Margaret Oarkley Dayhoff Award for Outstanding Performance in Research (1985)
Scholarship
Ringe, Dagmar, Tu, Y., Kreinbring, C.A., Hill, M., Liu, C.,Petsko, G.A., McCuyne, C., Berkowitz, D., Liu, D.,. "Crystal Structures of Cystathionine beta-Synthase from S, Cerevisiaea: One Enzymatic Step at a Time." Biochemistry 57. (2018): 3134-3145. (forthcoming)
Ringe, Dagmar. "Detection of ligand hot spots on protein surfaces via fragment-based methods: Application toDJ-1 and Glucocerebrocidase.." J. Computer Aided Molecular Design (2009). (forthcoming)
Ringe, Dagmar. "Novel Inhibitors of the di-Zinc metalloprotease from Vibrio proteolyticus based on a Tris Scaffold." Biochemistry (2007). (forthcoming)
Ringe, Dagmar. "Prediction of Interaction Sites from Apo 3D Structures when the Holo Conformation is different." Proteins: Structure, Function and Bioinformatics (2007). (forthcoming)
Ringe, Dagmar. "The missing atom:reliability of the feterminaiton of hydrogen positions in protein strucutres." Acta Cryst A74. (2018): a30.
Deshpande, A.R., Pochapsky, T.C., Petsko, G.A., Ringe, D.,. "Dual chemistry catalyzed by human acireductone dioxyge." Protein Eng Des Sel doi: 10.1093/protein/gzw078 (2017): 1-8 [Epub ahead of print].
Naffin-Olivos, J.L., Daab, A., White, A., Goldfarb, N., Milne, A.C., Liu, D., Dunn, B.M., Rengarajan, J., Petsko, G.A., Ringe, D.. "Structure Determination of Mycobacterium tuberculosis Serine Protease Hip1 (Rv2224c)." Biochemistry 56. (2017): 2247 - 2348.
Ringe, Dagmar, Mascarenhas, R., Le, H.V., Clevenger, K.D., Lehrer, H.J., Kelleher, N.L., Silverman, R.B., Liu, D.. "Selective Targeting by a mechanism-based Inactivator against PLP_Dependent Enzymes: Mexhanisms of Inactivation and Alternative Turnover." Biochemistry 56. (2017): 4951-4961.
Ringe, Dagmar. "The metal drives the chemistry: Dual functions of acireductone dioxygenase." Chem Rev 117. (2017): 10474-10501.
Wu,R., Sanishvilli, R., Belitsky, B.R., Juncosa, J.I., Le, H.V., Lahrer, H.J.S.,Farley, M., Silverman, R.B., Petsko, G.A.,Ringe, D., Liu, D.,. "PLP and GABA trigger GabR-mediated transcription regulation in Bacillus subtilis via external aldimine formation." Proc. Natl. Acad. Sci. USA (2017) EE 27. March 2017 (2017).
Zahniser, M.P.D., Prasad, S., Kneen, M.M., Petsko, G.A., Ringe, D., McLeish, M.J.,. "Structure and mechanism of benzaldehyde dehydrogenase from Pseudomonas putida ATCC 12633, a member of the class 3 aldehyde Dehydrogenase superfamily." Prot Eng Des Sel doi: 10.1093/protein/gzx015. [Epub ahead of print] (2017): 9:1-8.
Bassil, F., Fernagut, P.-O., Bezard, E., Hoang, Q.Q., Ringe, D., Petsko, G.A., Meissner, W.G.. "Reducing C-terminal truncation mitigates synucleinopathy and neurodegeneration in a transgenic model of multiple system atrophy." Proc. Natl. Acad. Sci. USA 113. doi/10.1073/pnas. 1609291113 (2016): 9593 – 9598.
Deshpande et al. "Metal-dependent function of a mammalian acireductone dioxygenase." Biochemistry 55. (2016): 1398-1407.
Liu, C.F., Brandt, G.S., Hoang, Q.Q., Naumova, N., Lazarevic, V., Hwang, E.S., Dekker, J, Glimcher, L.H., Ringe. D., Petsko, G.A.. "Crystal structure of the DNA binding domain of the transcription factor T-bet suggests simultaneous recognition of distant genome sites." Proc. Natl. Acad. Sci. USA 113(43). doi/10.1073/pnas.1613914113 (2016): E6572-E6581.
Wang, W., Nguyen, L.T.T, Burlak, C., Chegini, F., Guo, F., Chataway, T., Ju, S., Fisher, O., Miller, D.W., Datta, D., Wu, F., Wu, C-X., Landeru, A., Wells, J.A., Cookson, M.R., Boxer, M.B., Thomas, C.J., Wei, P. G., Ringe, D., Petsko. "Caspase-1 causes truncation and aggregation of the Parkinson’s disease-associated protein α-synuclein." Proc. Natl. Acad. Sci. USA 113. doi/10.1073/pnas.1610099113 (2016): 9587– 9592.
Berman, D.E., Ringe, D., Petsko, G.A., Small, S.A.. "“The Use of Pharmacological Retromer Chaperones in Alzheimer’s Disease and other Endosomal-related Disorders.”." Neurotherapeutics 12. (2015): 12-18. DOI 10.1007/s13311-014-0321-y.
Brodkin, H.R., DeLateur, N.A., Somarowthu, S., Mills, C.L., Novak, W.R., Beuning, P.J., Ringe, D., Ondrechen. M.J.. "“Prediction of Distal Residue Participation in Enzyme Catalysis”." Protein Science in press. (2015).
Auclair JR, Johnson JL, Liu Q, Salisbury JP, Rotunno MS, Petsko GA, Ringe D, Brown RH Jr, Bosco DA, Agar JN.. "Post-translational modification by cysteine protects Cu/Zn-superoxide dismutase from oxidative damage.." Biochemistry 52. (36) (2014): 6137-44.
Jackson, K.L., Dayton, R.D., Orchard, E.A., Ju, S., Ringe, D., Petsko, G.A., Maquat, L.E., Klein, R.L.. "“ Preservation of forelimb function by UPF1 gene therapy in a rat model of TDP-43-induced motor paralysis.”." Gene Therapy 00. (2014): 1-9 (doi:10.1038/gt.2014.101).
Keedy, D.A., van den Bedem, H., Sivak, D.A., Petsko, G.A., Ringe, D., Wilson, M.A., Fraser, J.S.. "Crystal Cryocooling Distorts Conformational Heterogeneity in a Model Michaelis Complex of DHFR." Structure 22. (2014): 899-910.
Mecozzi, V., Berman, D.E., Simoes, S., Vetanovetz, C., Awal, M., Patel, V.M. Schneider, R.T., Petsko, G.A., Ringe, D., Small, S.A.,. "“Pharmacological chaperones can stabilize the retromer complex and traffic the amyloid-precursor protein away from intracellular sites of pathogenic processing“." Nat Chem Biol 10. (2014): 443-449.
Naffin-Olivos, J.L., Georgieva, M., Goldfarb, N., Madan-Lala, R., Dong, L., Bizzell, E., Valinetz, E., Brandt, G.S., Ringe, D., Dunn, B.M., Petsko, G.A., Rengarajan, J.. "Mycobacterium tuberculosis Hip1 modulates macrophage responses through proteolysis of GroEL2”." PLoS Pathogens 10. (2014): e1004132.
Auclair JR, Johnson JL, Liu Q, Salisbury JP, Rotunno MS, Petsko GA, Ringe D, Brown RH Jr, Bosco DA, Agar JN. "Post-translational modification by cysteine protects Cu/Zn-superoxide dismutase from oxidative damage." Biochemistry 52. (36) (2013): 6137-44.
Edayathumangalam R1, 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." Proc Natl Acad Sci U S A. 110. (44) (2013): 17820-5.
Liu, CF, Liu, D, Momb, J, Thomas, PW, Lajoie, A, Petsko, GA, Fast, W, and Ringe D. "A phenylalanine clamp controls substrate specificity in the quorum-quenching metallo-y-lactonase from Bacillus thuringiensis." Biochemistry 52. (9) (2013): 1603-10.
Sigala PA, Fafarman AT, Schwans JP, Fried SD, Fenn TD, Caaveiro JM, Pybus B, Ringe D, Petsko GA, Boxer SG, Herschlag. "Quantitative dissection of hydrogen bond-mediated proton transfer in the ketosteroid isomerase active site." Proc Natl Acad Sci U S A 110. (28) (2013): E2552-61.
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, Wang R, Ringe D, Fraser P, Westaway D, St George-Hyslop PH, Szabo P, Relkin NR, Buxbaum JD, Glabe C. "Latrepirdine improves cognition and arrests progression of neuropathology in an Alzheimer's mouse model." Mol Psychiatry 18. (8) (2013): 889-97.
Steele JW1, 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, Wang R, Ringe D, Protter AA, Martins RN, Ehrlich ME, Yue Z, Petsko GA, Gandy S.. "Latrepirdine stimulates autophagy and reduces accumulation of α-synuclein in cells and in mouse brain." Mol Psychiatry. 18. (8) (2013): 882-8.
Ringe, Dagmar. "A yeast model for FUS/TLS-dependent cytotoxicity." PloS In Press. (2011).
Ringe, Dagmar. "Active site engineering of benzaldehyde lyase shows that a point mutation can confer both new reactivity and susceptibility to mechanism-based inhibition.." JACS 132. (2010): 438-439.
Ringe, Dagmar. "Chiral discrimination among transferases: inactivation by 4-amino-4,5-dihyrdro-thiophenecarboxylic acid (ADTA).." Biochemistry 49. (2010): 3138-3147.
Ringe, Dagmar. "Evidence for Remote Residue Involvement in catalysis: Are Enzyme Active Sites Built in Multiple Layers?." J. Mol. Biol. (2010).
Ringe, Dagmar. "Mechanism of Inactivation of E.coli aspartate aminotransferase by (S)-4-amino-4,5-dihydro-2-furancarboxylic acid (S-ADFA)." Biochemistry 49. (2010): 10507-15.
Ringe, Dagmar. "Strategies for stabilizing superoxide dismutase (SOD1), the protein that is destabilized in the most common form of familial amyotrophic lateral sclerosis." Proc. Natl. Acad. Sci. Nov 22 [Epub]. (2010).
Ringe, Dagmar. "The polyamine pathway contributes to the pathogenesis of Parkinson's disease.." Proc. Natl. Acad. Sci. 107. (2010): 16970-5.
Ringe, Dagmar. X-ray Crystallography in the Service of Structure-Based Drug Design”. 1 ed. Cambridge University Press, 2010.
Ringe, Dagmar. "A preliminary neutron diffraction study of gamma-chymotrypsin." Acta Crystallogr F F65. (2009): 317-320.
Ringe, Dagmar. "Decreased Sensitivity to Changes in the Concentration of Metal Ions as the Basis for the Hyperactivity of DtxR(E175K)." J. Mol. Biol. 390. (2009): 112-123.
Ringe, Dagmar. "Detection and time-course of formation of major thiamin diphosphate-bound covalent intermediates derived from a chromophoric substrate analogue on benzoylformate decarboxylase.." Biochemistry 48. (2009): 981-994.
Ringe, Dagmar. "Hydrogen Bond Coupling in the Ketosteroid Isomerase Active Site." Biochemistry 48. (2009): 6932-9.
Ringe, Dagmar. "Snapshot of a reaction intermediate: analysis of benzoylformate decarboxylase in complex with a benzoylphosphonate inhibitor.." Biochemistry 47. (2009): 7734-7743.
Ringe, Dagmar. "The effects of pH and iminosugar pharmacological chaperones on lysosomal gycosidase structure and stability.." Biochemistry (2009).
Ringe, Dagmar. "What are pharmacological chaperones and why are they interesting?." J. Biol 8. (2009): 80.
Dagmar Ringe. "Mechanism of the quorum-quenching lactonase (AiiA) from Bacillus thuringiensis. 2. Substrate modeling and active site mutations.." Biochemistry 47. (2008): 7715-7725.
Ringe, Dagmar. ""Probing the Active Center of Benzaldehyde Lyase with Substitutions and the Pseudosubstrate Analog Benzoylphosphonic Acid Methyl Ester"." Biochemistry 47. (2008): 7734-7743.
Ringe, Dagmar. "How Enzymes Work." Science 320. (2008): 1428-1429.
Ringe, Dagmar. "Mechanism of the Quorum-Quenching Lactonase (AiiA) from Bacillus thuringiensis. 1. Substrate Modeling and Active Site Mutations.." Biochemistry 47. (2008): 7706-7714.
Ringe, Dagmar. "Prediction of interaction sites from apo 3D structures when the holo conformation is different.." Proteins: Structure, Function and Bioinformatics 72. (2008): 980-992.
Ringe, Dagmar. "Review of Broken Harmony." Early Music America Magazine Winter 2008: 50-51.
Ringe, Dagmar. "Testing Geometrical Discrimination within an Enzyme Active Site: Constrained Hydrogen Bonding in the Ketosteroid Isomerase Oxyanion Hole.." J. Am. Chem. Soc. 130. (2008): 13696-13708.
Ringe, Dagmar. "Zinc Coordination Geometry and Ligand Binding Affinity: The Structural and Kinetic Analysis of Second-Shell Serine 228 Residue and the Methionine 180 residue of the Aminopeptidase from Vibrio proteolyticus.." Biochemistry 47. (2008): 7673-7683.
Ringe, Dagmar. "Identification of Functional Subclasses in the DJ-1 Superfamily Proteins." PLoS Computational Biology 3 (1). e10.doi:10 (2007): 1371/journal.pcbi.0030010.
Ringe, Dagmar. "Inactivation of E.coli L-aspartate aminotransferase by (S)-4,5-amino-dihydro-2-thiophenecarboxylic acid (SADTA) reveals 'A Tale of Two Mechanisms'." Biochemistry 46. (2007): 10517-27.
Ringe, Dagmar. "Inhibition of Chymotrypsin by a Complex of Othro-Vanadate and Benzohydroxamic Acid." Biochemistry 46. (2007): 5982-5990.
Ringe, Dagmar. "Structure and specificity of a quorum-quenching lactonase (AiiB) from Agrobacterium tumefaciens." Biochemistry 46. (2007): 11789-99.
Ringe, Dagmar. "Structure of acid-beta-glucosidase with pharmacological chaperone provides insight into Gaucher disease.." Nat.Chem.Biol 3. (2007): 101-107.
Ringe, Dagmar. "The Role of N-terminal Helix in the Metal Ion-Induced Activation of the Diphtheria Toxin Repressor DtxR"." Biochemistry 46. (2007): 11761-11770.
Ringe, Dagmar. "X-ray crystallographic characterization of the Co(II)-substituted Tris-bound form of the aminopeptidase from Aeromonas proteolytica." J.Inorg.Biochem. 101. (2007): 1099-1107.
Ringe, Dagmar. "Diversity in Hapten recognition: Structural Study of an Anti-cocaine Antibody M82G2." J. Mol. Biol. (2005).
Ringe, Dagmar. "Effect of a Y265F Mutant on the Transamination Based Cycloserine Inactivation of Alanine Racemase." Biochemistry 44. (2005): 5317-5327.
Ringe, Dagmar, C. Stamper, et al.. "Spectroscopic and X-ray Crystallographic Characterization of Bestatin Bound to the Aminopeptidase from Aeromonas (Vibrio) proteolytica." Biochemistry (2004): 9620-9628.
Ringe, Dagmar, E.M. Vogan, et al.. "Crystal structure at 1.8 Ångstrom resolution of CDP-D-glucose 4,6-dehydratase from Yersinia pseudotubercylosis." Biochemistry (2004): 3057-3067.
Ringe, Dagmar, J.V. Gray, et al.. "Sleeping Beauty: Quiescence in Saccharomyces cerevisiae." Microbial and Mol. Biol Rev. (2004): 187-206.
Ringe, Dagmar, L.F. Murga, et al.. "Physicochemical Methods for Protein Function Prediction." Israel Journal of Chemistry (2004): 299-308.
Ringe, Dagmar, M.A. Wilson, et al.. "The 1.8 Å Resolution Crystal Structure of YDR533Cp from Saccharomyces cerevisiae; A member of the DJ-1/ThiJ/PfpI superfamily." Proc. Natl. Acad. Sci. (2004): 1531-1536.
Ringe, Dagmar, R. Canet-Aviles, et al.. "The Parkinson's disease protein DJ-1 is neuroprotective due to cysteine-sulfinic acid-driven mitochondrial localization." Proc. Natl. Acad. Sci. (2004): 9103-9108.
Ringe, Dagmar, T. Holyoak, et al.. "The Structural Basis for Differences in Substrate Selectivity in Kex2 and Furin Protein Convertases." Biochemistry (2004): 2412-2421.
Ringe, Dagmar, Y. Wei, K.R. Boino, M.J. Ondrechen. "Protein Structure to Function: Insights from Computation." Cell. & Mol. Life Sci. (2004): 387-392.
Ringe, Dagmar. "Anchoring A Cationic Ligang: The Structure of the Fab Fragment of the Anti-Morphine Antibody 9B1 and its Complex with Morphine." J. Mol. Biol. (2004).
Ringe, Dagmar. "Crystal structure at 1.8 ngstrom resolution of CDP-D-glucose, 4,6-dehydratase from Yersinia pseudotubercylois." Biochemistry (2004).
Ringe, Dagmar. "Physicochemical Methods for Protein Function Prediction." Israel Journal of Chemistry (2004).
Ringe, Dagmar. "Protein Structure to Function: Insights from Compuation." Cell & Mol. Life Sci. (2004).
Ringe, Dagmar. "Sleeping Beauty: Quiescence in Saccharomyces cerevisiae." Microbial and Mol. Biol. Rev (2004).
Ringe, Dagmar. "The 1.8 Resolution Crystal and Structure of YDR533Cp from Saccharomyces cerevisiae; A member of the DJ-1/ThiJ/Pfpl superfamily." Proc. National Academy of Science (2004).
Ringe, Dagmar. "The Parkinson's disease protein DJ-1 is neuroprotective due to cysteine-sulfinic acid-drive mitochondrial localization." Proc. Natil. Acad. Sci. (2004).
Ringe, Dagmar. "The Structural Basis for Difference in Substrate Selectivity in Kex2 and Furin Protein Convertases." Biochemistry (2004).
Ringe, Dagmar. "Xylose Isomerase in Substrate and Inhibitor Michaelis States: Atomic Resolution Studies of a Metal-Mediated Hydride Shift." Bio Chemistry (2004).
Ringe,Dagmar, T. D. Fenn, et al.. "Xylose Isomerase in Substrate and Inhibitor Michaelis States: Atomic Resolution Studies of a Metal-Mediated Hydride Shift." Biochemistry (2004): 6464-6474.
Ringe,Dagmar, E. Pozharski, et al.. "Anchoring A Cationic Ligand: The Structure of the Fab Fragment of the Anti-Morphine Antibody 9B1 and its Complex with Morphine." J. Mol. Biol. (2004): 691-697.
Ringe,Dagmar, G.A. Petsko and Dagmar Ringe. Protein Structure and Function. New Science Press, Ltd, London, 2004.
Ringe,Dagmar. "Spectroscopic and X-ray Crystallograhic Characterization of Bestatin Bound to the Aminopeptidase from Aeromonas (Vibrio,) proteolytica." Biochemistry (2004).
Ringe, Dagmar, ed. L.F. Tietze and T. Eicher. Reactions and Syntheses in the Organic Chemistry Laboratory (trans.). Mill Valley, CA.: University Science Books, 1989.