Dagmar Ringe

Dagnar RingeHarold and Bernice Davis Professor of Aging and Neurodegenerative Disease

Research Description

Structures of enzymes and enzyme-substrate complexes.

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.

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.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.

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).

"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. (2010) JACS, 2010, 132 (2), pp 438–439.

"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

"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

"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

"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

"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

"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

"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