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:
Wei Y, Ringe D, Wilson MA, Ondrechen MJ. (2007) Identification
of functional subclasses in the DJ-1 superfamily proteins.
PLoS Comput Biol. 2007 Jan 26;3:e10. [abstract]
Lieberman RL, Wustman BA, Huertas P, Powe AC Jr, Pine CW,
Khanna R, Schlossmacher MG, Ringe D, Petsko GA (2007). Structure
of acid beta-glucosidase with pharmacological chaperone
provides insight into Gaucher disease. Nat Chem Biol.
2007 Feb;3(2):101-107. Epub 2006 Dec 24. [abstract]
Ding X, Rasmussen BF, Petsko GA, Ringe D. (2006) 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. Bioorg Chem. 2006 Dec; 34(6):410-23. Epub
2006 Nov 2. [abstract]
Kraut DA, Sigala PA, Pybus B, Liu CW, Ringe D, Petsko GA,
Herschlag D. (2006) Testing electrostatic complementarity
in enzyme catalysis: hydrogen bonding in the ketosteroid
isomerase oxyanion hole. PLoS Biol. 2006 Apr; 4:e99.
Epub 2006 Mar 28. [abstract]
Desmarais W, Bienvenue DL, Bzymek KP, Petsko GA, Ringe
D, Holz RC. (2006) The high-resolution structures of the
neutral and the low pH crystals of aminopeptidase from Aeromonas
proteolytica. J Biol Inorg Chem. 2006 Jun;11(4):398-408.
Epub 2006 Apr 5. [abstract]
Das C, Hoang QQ, Kreinbring CA, Luchansky SJ, Meray RK,
Ray SS, Lansbury PT, Ringe D, Petsko GA. (2006) Structural
basis for conformational plasticity of the Parkinson's disease-associated
ubiquitin hydrolase UCH-L1. 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]
Mattos C, Bellamacina CR, Peisach E, Pereira A, Vitkup
D, Petsko GA, Ringe D. (2006) Multiple solvent crystal structures:
probing binding sites, plasticity and hydration. J Mol
Biol. 2006 Apr 14;357(5):1471-82. Epub 2006 Jan 30.
[abstract]
D'Aquino JA, Tetenbaum-Novatt J, White A, Berkovitch F,
Ringe D. (2005) Mechanism of metal ion activation of the
diphtheria toxin repressor DtxR. Proc Natl Acad Sci U
S A. 2005 Dec 20;102(51):18408-13. Epub 2005 Dec 13.
[abstract]
Lepore BW, Ruzicka FJ, Frey PA, Ringe D. (2005) The x-ray
crystal structure of lysine-2,3-aminomutase from Clostridium
subterminale. Proc Natl Acad Sci U S A. 2005 Sep
27;102(39):13819-24. Epub 2005 Sep 15. [abstract]
Liu D, Lepore BW, Petsko GA, Thomas PW, Stone EM, Fast
W, Ringe D. (2005) Three-dimensional structure of the quorum-quenching
N-acyl homoserine lactone hydrolase from Bacillus thuringiensis.
Proc Natl Acad Sci U S A. 102:11882-7. [abstract]
Gray JV, Petsko GA, Johnston GC, Ringe D, Singer RA, Werner-Washburne
M. (2004) "Sleeping beauty": quiescence in Saccharomyces
cerevisiae. Microbiol Mol Biol Rev. 68:187-206. [abstract]
Canet-Aviles RM, Wilson MA, Miller DW, Ahmad R, McLendon
C, Bandyopadhyay S, Baptista MJ, Ringe D, Petsko GA, Cookson
MR. (2004) The Parkinson's disease protein DJ-1 is neuroprotective
due to cysteine-sulfinic acid-driven mitochondrial localization.
Proc Natl Acad Sci U S A. 101:9103-8. [abstract]
Yang J, Wang Y, Woolridge EM, Arora V, Petsko GA, Kozarich
JW, Ringe D. (2004) 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. [abstract]
Vogan EM, Bellamacina C, He X, Liu HW, Ringe D, Petsko
GA. (2004) Crystal structure at 1.8 A resolution of CDP-D-glucose
4,6-dehydratase from Yersinia pseudotuberculosis. Biochemistry.
43:3057-67. [abstract]
Pozharski E, Wilson MA, Hewagama A, Shanafelt AB, Petsko
G, Ringe D. (2004) Anchoring a cationic ligand: the structure
of the Fab fragment of the anti-morphine antibody 9B1 and
its complex with morphine. J Mol Biol., 337:691-7.
[abstract]
Ringe D, Wei Y, Boino KR, Ondrechen MJ. (2004) Protein
structure to function: insights from computation. Cell
Mol Life Sci. 61: 387-92. [abstract]
Holyoak T, Kettner CA, Petsko GA, Fuller RS, Ringe D. (2004)
Structural basis for differences in substrate selectivity
in Kex2 and furin protein convertases. Biochemistry.
43:2412-21. [abstract]
Wilson MA, St Amour CV, Collins JL, Ringe D, Petsko GA.
(2004) The 1.8-A resolution crystal structure of YDR533Cp
from Saccharomyces cerevisiae: a member of the DJ-1/ThiJ/PfpI
superfamily. Proc Natl Acad Sci U S A. 101:1531-6.
[abstract]
Holyoak T, Fenn TD, Wilson MA, Moulin AG, Ringe D, Petsko
GA. (2003) Malonate: a versatile cryoprotectant and stabilizing
solution for salt-grown macromolecular crystals. Acta
Crystallogr D Biol Crystallogr. 59(Pt 12):2356-8. [abstract]
Ringe D, Petsko GA. (2003) The 'glass transition' in protein
dynamics: what it is, why it occurs, and how to exploit
it. Biophys Chem. 105:667-80. [abstract]
Wilson MA, Collins JL, Hod Y, Ringe D, Petsko GA. (2003)
The 1.1-A resolution crystal structure of DJ-1, the protein
mutated in autosomal recessive early onset Parkinson's disease.
Proc Natl Acad Sci U S A. 100:9256-61. [abstract]
D'Aquino JA, Ringe D. (2003) Determinants of the SRC homology
domain 3-like fold. J Bacteriol. 185:4081-6. [abstract]
Holyoak T, Wilson MA, Fenn TD, Kettner CA, Petsko GA, Fuller
RS, Ringe D. (2003) 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. [abstract]
Fenn TD, Stamper GF, Morollo AA, Ringe D. (2003) A side
reaction of alanine racemase: transamination of cycloserine.
Biochemistry. 42:5775-83. [abstract]
Beebe JA, Arabshahi A, Clifton JG, Ringe D, Petsko GA,
Frey PA. (2003) Galactose mutarotase: pH dependence of enzymatic
mutarotation. Biochemistry. 42:4414-20. [abstract]
Spiering MM, Ringe D, Murphy JR, Marletta MA. (2003) Metal
stoichiometry and functional studies of the diphtheria toxin
repressor. Proc Natl Acad Sci U S A. 100:3808-13.
[abstract]
Kenyon GL, DeMarini DM, Fuchs E, Galas DJ, Kirsch JF, Leyh
TS, Moos WH, Petsko GA, Ringe D, Rubin GM, Sheahan LC; National
Research Council Steering Committee. (2002) Defining the
mandate of proteomics in the post-genomics era: workshop
report. Mol Cell Proteomics. 1:763-80. [abstract]
Desmarais, W., Bienvenue, D.L., Bzymek, K.P., Holz, R.C.,
Petsko, G.A., Ringe, D., (2002) "The 1.20 Å Resolution Crystal
Structure of the Aminopeptidase from Aeromonas proteolytica
Complexed with Tris: A Tale of Buffer Inhibition",
Structure, 10:1063-72.
Taoka S., Lepore, B.W., Kabil, O., Ojha, S., Ringe, D.,
Banerjee, R. (2002), "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 41:10454-10461.
Bienvenue, D.L., Mathew, R.S., Ringe, D. Holz, R.C., (2002)
"The Aminopeptidase from Aeromonas proteolytica can function
as an esterase", J. Biol. Inorg. Chem., 7:129-135.
Vitkup, D., Ringe, D., Karplus, M., Petsko, G.A.(2002)
"Why Protein R-factors are so large: A self-consistent analysis",
Proteins, 46:345-354. [abstract]
Ringe, D.(2002), "Function by Serendipidy", Nature,
415:488-489.
Vogan, E.M., Bellamacina, C.R., He, X., Foxman, B.M., Ringe,
D., Liu, H.W., Petsko, G.A. (2002). "Purification, crystallization
and molecular symmetry of CDP-D glucose, 4, 6-dehydratase
from Yersinia pseudotuberculosis", Acta Cryst. D.
58:370-373. [abstract]
Mattos, C. and Ringe, D. (2001) "Proteins in organic solvents",
Current Opinion in Structural Biology, 11:761-764.
Ondrechen, M.J., Clifton, J. G., Ringe, D. (2001) "THEMATICS:
A Simple Computational Predictor of Enzyme Function from
Structure", Proc. Natl. Acad. Sci., USA, 98:12473-12478.
Hadfield, A., Shammas, C., Kryger, G., Ringe, D., Petsko,
G.A., Ouyang, J., Viola, R. E. (2001) "Active Site Analysis
of the Potential Antimicrobial Target Aspartate Semialdehyde
Dehydrongenase", Biochemistry 40:14475-14483.
Amor, J.C., Horton, J., Zhu, X., Wang, Y., Sullards, C.,
Ringe, D., Cheng, X., Kahn, R.A. (2001) "Structures of yeast
ARF2 and ARL1: distinct roless for the N-terminus in the
structure and function of ARF family GTPases", J. Biol
Chem. 276:42477-42484.
Pasternak A, White A, Jeffery CJ, Medina N, Cahoon M, Ringe
D, Hedstrom L. (2001) The energetic cost of induced fit
catalysis: Crystal structures of trypsinogen mutants with
enhanced activity and inhibitor affinity. Protein Sci.
10:1331-42. [abstract]
Stamper C, Bennett B, Edwards T, Holz RC, Ringe D, Petsko
G. (2001) 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.
[abstract]
Chen CS, White A, Love J, Murphy JR, Ringe D. (2000) Methyl
groups of thymine bases are important for nucleic acid recognition
by DtxR. Biochemistry. 39:10397-407. [abstract]
Jeffery, C.J., Bahnson, B.J., Chien, W., Ringe, D., Petsko,
G.A. (2000) Crystal Structure of Rabbit Phosphoglucose Isomerase,
a Glycolytic Enzyme that Moonlights as Neuroleukin, Autocrine
Motility Factor, and Differentiation Mediator, Biochemistry,
39:955-964.
Petsko, G. A. and Ringe, D. (2000) Observation of unstable
species in enzyme-catalyzed transformations using protein
crystallography, Current Opinion in Chemical Biology,
4:89-94. [abstract]
Vitkup, Dennis, Ringe, D., Petsko, G.A., and Karplus,
Martin. (2000) Solvent Mobility and the Protein "Glass"
Transition, Nature Structural Biology, 7:34-38. [abstract]
Schlichting, I., Berendzen, J., Chu, K., Stock, A.M.,
Maves, S.A., Benson, D.E., Sweet, R.M., Ringe, D., Petsko,
G.A., Sligar, S.G. (2000) The Catalytic Pathway of Cytochrome
P450 at Atomic Resolution, Science, 287:1615-1622.
McMillan, F.M., Cahoon, M., White, A., Hedstrom, L., Petsko,
G.A., Ringe, D. (2000) 2.4 Å Crystal Structure of Borrelia
burgdorferi IMP Dehydrogenase: Evidence of a Substrate Induced
Hinged-Lid Motion by Loop 6, Biochemistry, 39:4533-4542.
[abstract]
De Paola CC, Bennett B, Holz RC, Ringe D, Petsko GA. (1999)
1-Butaneboronic acid binding to Aeromonas proteolytica aminopeptidase:
a case of arrested development, Biochemistry, 38:9048-53.
Hadfield A, Kryger G, Ouyang J, Petsko GA, Ringe D, Viola
R. (1999) Structure of aspartate-beta-semialdehyde dehydrogenase
from Escherichia coli, a key enzyme in the aspartate family
of amino acid biosynthesis,. J Mol Biol, 289:991-1002.
Zhang Z, Komives EA, Sugio S, Blacklow SC, Narayana N,
Xuong NH, Stock AM, Petsko GA, Ringe D. (1999) The role
of water in the catalytic efficiency of triosephosphate
isomerase. Biochemistry, 38:4389-97.
Morollo AA, Petsko GA, Ringe D. (1999) Structure of a Michaelis
complex analogue: propionate binds in the substrate carboxylate
site of alanine racemase. Biochemistry, 38:3293-301.
White A, Ding X, vanderSpek JC, Murphy JR, Ringe D. (1998)
Structure of the metal-ion-activated diphtheria toxin repressor/tox
operator complex. Nature 394:502-6.
Hasson MS, Muscate A, McLeish MJ, Polovnikova LS, Gerlt
JA, Kenyon GL, Petsko GA, Ringe D (1998). The crystal structure
of benzoylformate decarboxylase at 1.6 Å resolution:
diversity of catalytic residues in thiamin diphosphate-dependent
enzymes, Biochemistry, 37:9918-30.
Brenner C, Garrison P, Gilmour J, Peisach D, Ringe D, Petsko
GA, Lowenstein JM. (1997) Crystal structures of HINT demonstrate
that histidine triad proteins are GalT-related nucleotide-binding
proteins. Nature Structural Biology, 4:231-8.
View Complete Publication List on PubMed:
Dagmar Ringe
Last update: February 12, 2007. E-mail comments
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