Our interests are generally in the relationship of protein three-dimensional structure to chemical function. To this end, research is focussed on the modification of the catalytic properties of a number of pharmaceutically or industrially important enzymes. The methods used are a combination of X-ray crystallography, design of transition-state analog inhibitors, and site-directed mutagenesis. The objectives are to learn how to re-engineer these catalysts to perform useful chemical reactions which may not occur efficiently with the naturally occurring enzyme, to dissect the individual steps in a mechanism and characterize them structurally, or to learn how to inhibit an enzyme specifically and selectively.

The proteins being studied currently include enzymes utilizing pyridoxal phosphate as cofactor, a GTP-binding protein, a DNA-binding protein, and several proteases. Different methods are being used to study these systems, including traditional kinetic and structural methods, and low-temperature and time-resolved x-ray structural methods. In addition, a new method for mapping of binding surfaces on proteins is being developed for the design of specific inhibitors.

Pyridoxal is capable of catalyzing several types of transformations. However, any one enzyme utilizing this cofactor does only one of them predominantly. The question therefore arises how the protein controls the chemical outcome of such transformations. We are studying a number of these enzymes structurally in order to begin to answer that question.

The expression of diphtheria toxin in toxigenic Corynebacterium diphtheria is controlled by a transition metal ion activated repressor DtxR. The repressor binds DNA after activation by the metal ion and thereby regulates expression of the toxin. The mechanism of activation is being studied structurally.

Serine proteases are important in cellular development, blood clotting, and a variety of defense mechanisms. Disorders involving these proteases are often linked to the absence or inefficiency of a specific inhibitor to control the activity of the enzyme. The design of such inhibitors requires detailed knowledge of the structure of the enzyme, of the enzyme complexed with inhibitors, and if possible, an understanding of the mechanisms of inhibition.

Selected Publications:

"X-ray Crystallography in the Service of Structure-Based Drug Design" in Drug Design: Structure - and Ligand - Based Approaches. Ringe D., Petsko G.A., Merz K.M., Reynolds C.H., D. Ringe, eds., Cambridge University Press (2009) in press

"Active site engineering of benzaldehyde lyase: a point mutation confers new reactivity." Brandt, G.S., Kneen, M.M., Petsko, G.A., Ringe, D., McLeish, M.J. (2009) JACS, submitted

"Snapshot of a reaction intermediate: analysis of benzoylformate decarboxylase in complex with a benzoylphosphonate inhibitor." Brandt GS, Kneen MM, Chakraborty S, Baykal AT, Nemeria N, Yep A, Ruby DI, Petsko GA, Kenyon GL, McLeish MJ, Jordan F, Ringe D. Biochemistry. 2009 Apr 21;48(15):3247-57. [abstract]

"Detection and time course of formation of major thiamin diphosphate-bound covalent intermediates derived from a chromophoric substrate analogue on benzoylformate decarboxylase." Chakraborty S, Nemeria NS, Balakrishnan A, Brandt GS, Kneen MM, Yep A, McLeish MJ, Kenyon GL, Petsko GA, Ringe D, Jordan F. Biochemistry. 2009 Feb 10;48(5):981-94. [abstract]

"A preliminary neutron diffraction study of gamma-chymotrypsin." Novak WR, Moulin AG, Blakeley MP, Schlichting I, Petsko GA, Ringe D. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2009 Mar 1;65(Pt 3):317-20. [abstract]

"Detection of ligand binding hot spots on protein surfaces via fragment-based methods: application to DJ-1 and glucocerebrosidase." 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. J Comput Aided Mol Des. 2009 Jun 12. [abstract]

"Effects of pH and iminosugar pharmacological chaperones on lysosomal glycosidase structure and stability." Lieberman RL, D'aquino JA, Ringe D, Petsko GA. Biochemistry. 2009 Jun 9;48(22):4816-27. [abstract]

"Decreased sensitivity to changes in the concentration of metal ions as the basis for the hyperactivity of DtxR(E175K)." D'Aquino JA, Denninger AR, Moulin AG, D'Aquino KE, Ringe D. J Mol Biol. 2009 Jul 3;390(1):112-23. [abstract]

"Hydrogen bond coupling in the ketosteroid isomerase active site." Sigala PA, Caaveiro JM, Ringe D, Petsko GA, Herschlag D. Biochemistry. 2009 Jul 28;48(29):6932-9. [abstract]

"Prediction of interaction sites from apo 3D structures when the holo conformation is different." Murga LF, Ondrechen MJ, Ringe D. Proteins: Structure, Function and Bioinformatics, 2008 Aug 15;72(3):980-92. [abstract]

"Probing the active center of benzaldehyde lyase with substitutions and the pseudosubstrate analogue benzoylphosphonic acid methyl ester." Brandt GS, Nemeria N, Chakraborty S, McLeish MJ, Yep A, Kenyon GL, Petsko GA, Jordan F, Ringe D. Biochemistry. 2008 Jul 22;47(29):7734-43. [abstract]

"Testing geometrical discrimination within an enzyme active site: constrained hydrogen bonding in the ketosteroid isomerase oxyanion hole." Sigala PA, Kraut DA, Caaveiro JM, Pybus B, Ruben EA, Ringe D, Petsko GA, Herschlag D. J Am Chem Soc. 2008 Oct 15;130(41):13696-708. [abstract]

"Mechanism of the quorum-quenching lactonase (AiiA) from Bacillus thuringiensis. 1. Product-bound structures." Liu D, Momb J, Thomas PW, Moulin A, Petsko GA, Fast W, Ringe D. Biochemistry. 2008 Jul 22;47(29):7706-14. [abstract]

"Mechanism of the quorum-quenching lactonase (AiiA) from Bacillus thuringiensis. 2. Substrate modeling and active site mutations." Momb J, Wang C, Liu D, Thomas PW, Petsko GA, Guo H, Ringe D, Fast W. Biochemistry. 2008 Jul 22;47(29):7715-25. [abstract]

"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." Ataie NJ, Hoang QQ, Zahniser MP, Tu Y, Milne A, Petsko GA, Ringe D. Biochemistry. 2008 Jul 22;47(29):7673-83. [abstract]

"How enzymes work." Ringe D, Petsko GA. Science. 2008 Jun 13;320(5882):1428-9.

Review of "Broken Harmony." Ringe, D. Early Music America Magazine, Winter 2008, pp. 50-51.

"Identification of functional subclasses in the DJ-1 superfamily proteins." Wei Y, Ringe D, Wilson MA, Ondrechen MJ. (2007) PLoS Comput Biol. 2007 Jan 26;3:e10. [abstract]

"X-ray crystallographic characterization of the Co(II)-substituted Tris-bound form of the aminopeptidase from Aeromonas proteolytica." Munih P, Moulin A, Stamper CC, Bennett B, Ringe D, Petsko GA, Holz RC. J Inorg Biochem. 2007 Aug;101(8):1099-107. [abstract]

"Inhibition of chymotrypsin by a complex of ortho-vanadate and benzohydroxamic acid: structure of the inert complex and its mechanistic interpretation." Moulin A, Bell JH, Pratt RF, Ringe D. Biochemistry. 2007 May 22;46(20):5982-90. [abstract]

"Role of the N-terminal helix in the metal ion-induced activation of the diphtheria toxin repressor DtxR." D'Aquino JA, Lattimer JR, Denninger A, D'Aquino KE, Ringe D. Biochemistry. 2007 Oct 23;46(42):11761-70. [abstract]

"Inactivation of Escherichia coli L-aspartate aminotransferase by (S)-4-amino-4,5-dihydro-2-thiophenecarboxylic acid reveals 'a tale of two mechanisms'." Liu D, Pozharski E, Lepore BW, Fu M, Silverman RB, Petsko GA, Ringe D. Biochemistry. 2007 Sep 18;46(37):10517-27. [abstract]

"Structure and specificity of a quorum-quenching lactonase (AiiB) from Agrobacterium tumefaciens." Liu D, Thomas PW, Momb J, Hoang QQ, Petsko GA, Ringe D, Fast W. Biochemistry. 2007 Oct 23;46(42):11789-99. [abstract]

"Structure of acid beta-glucosidase with pharmacological chaperone provides insight into Gaucher disease." Lieberman RL, Wustman BA, Huertas P, Powe AC Jr, Pine CW, Khanna R, Schlossmacher MG, Ringe D, Petsko GA (2007). Nat Chem Biol. 2007 Feb;3(2):101-107. [abstract] [http://dx.doi.org/10.1038/nchembio850 (2006)]

"Multiple solvent crystal structures: probing binding sites, plasticity and hydration." Mattos C, Bellamacina CR, Peisach E, Pereira A, Vitkup D, Petsko GA, Ringe D. (2006) J Mol Biol. 2006 Apr 14;357(5):1471-82. [abstract]

"Location of Binding Sites on Proteins by the Multiple Solvent Crystal Structure Method." Ringe, D., Mattos, C.. In Fragment-Based Approaches in Drug Discovery, w. Jahnke, D.A. Erlanson (eds.), Vol. 34, Wiley-VCH, Weinheim, 2006, pp. 67-88.

"Identification of Structural and Catalytic Classes of Highly Conserved Amino Acid Residues in Lysine 2,3-Aminomutase." Chen, D., Frey, P.A., Lepore, B.W., Ringe, D., Ruzicka, F.J. Biochemistry, 45, 12647-12653 (2006).

"Mechanism of Metal Ion Activation of the Diphtheria Toxin Repressor DtxR" in "From Physics to Biology." D'Aquino, A., Ringe, D., J. Clemente-Gallardo et al., eds., AIP Conference Proceedings, vol 851, 2006.

"Crystallographic observation of an acyl-enzyme intermediate in the elastase-catalyzed hydrolysis of a peptidyl ester substrate: Exploiting the 'glass transition' in protein dynamics." Ding X, Rasmussen BF, Petsko GA, Ringe D. (2006) Bioorg Chem. 2006 Dec; 34(6):410-23. [abstract]

"Testing the Contribution of Electrostatic Complementarity to Enzymatic Catalysis: Hydrogen Bonding in the Oxyanion Hole of Ketosteroid Isomerase." Kraut DA, Sigala PA, Pybus B, Liu CW, Ringe D, Petsko GA, Herschlag D. (2006) PLoS Biol. 2006 Apr; 4:e99. [abstract]

"The high-resolution structures of the neutraland the low pH crystals of the aminopeptidase from Aeromonas proteolytica." Desmarais W, Bienvenue DL, Bzymek KP, Petsko GA, Ringe D, Holz RC. (2006) J Biol Inorg Chem. 2006 Jun;11(4):398-408. Epub 2006 Apr 5. [abstract]

"Structural basis for conformational plasticity of the Parkinson's disease-associated ubiquitin hydrolase UCH-L1." Das C, Hoang QQ, Kreinbring CA, Luchansky SJ, Meray RK, Ray SS, Lansbury PT, Ringe D, Petsko GA. (2006) Proc Natl Acad Sci U S A. 2006 Mar 21;103(12):4675-80. Epub 2006 Mar 13. Erratum in: Proc Natl Acad Sci U S A. 2006 Apr 25;103(17):6776. [abstract]

'Mechanism of metal ion activation of the diphtheria toxin repressor DtxR." D'Aquino JA, Tetenbaum-Novatt J, White A, Berkovitch F, Ringe D. (2005) Proc Natl Acad Sci U S A. 2005 Dec 20;102(51):18408-13. [abstract]

"Kinetic, Spectroscopic and X-ray crystallographic characterization of the functional E151H aminopeptiase from Aeromonas proteolytica," Bzymek, F.P., Moulin, A., Swierczek, S.I., Ringe, D., Petsko, G.A., Bennett, B., Holz, R.C., Biochemistry, 44, 12030-12040 (2005).

"The atomic resolution crystal structure of the YajL (ThiJ) protein from E. coli: A close prokaryotic homologue of the Parkinson's disease-associated protein DJ-1." Wilson, M.A., Ringe, D., Petsko, G.A. J. Mol. Biol. 353, 678-91 (2005).

"The x-ray crystal structure of lysine-2,3-aminomutase from Clostridium subterminale." Lepore BW, Ruzicka FJ, Frey PA, Ringe D. (2005) Proc Natl Acad Sci U S A. 2005 Sep 27;102(39):13819-24. [abstract]

"Three-dimensional structure of the quorum-quenching N-acyl homoserine lactone hydrolase from Bacillus thuringiensis." Liu D, Lepore BW, Petsko GA, Thomas PW, Stone EM, Fast W, Ringe D. (2005) Proc Natl Acad Sci U S A. 102:11882-7. [abstract]

"Diversity in Hapten Recognition: Structural Study of an Anti-cocaine Antibody M82G2." Pozharski, E., Moulin, A., Hewagama, A., Shanafelt, A.R., Petsko, G.A., Ringe, D., J. Mol. Biol. 349, 570-582 (2005).

"Effect of a Y265F Mutant on the Transamination Based Cycloserine Inactivation of Alanine Racemase." Fenn, T.D., Holyoak, T., Stamper, G.F., Ringe, D., Biochemistry 44, 5317-5327 (2005).

"Xylose Isomerase in Substrate and Inhibitor Michaelis States: Atomic Resolution Studies of a Metal-Mediated Hydride Shift." Fenn, T.D., Ringe, D. and Petsko, G.A.Biochemistry 43, 6464-6474 (2004).

 

View Complete Publication List on PubMed: Dagmar Ringe

 

Last update: November 19, 2009