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Dagmar Ringe

This is a preview profile on BiomedExperts - the first literature-based scientific social network. It brings the right researchers together and allows them to collaborate online. Collexis and Dell provide the BiomedExperts network of +1.5 Million pre-calculated profiles free of charge to researchers worldwide.

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X-Ray Crystallography

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Escherichia coli

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Co-Publications
Name
95
Petsko, Gregory
16
Manning, James
8
Holz, Richard
6
Hasson, Miriam
6
Moulin, Aaron
6
Murphy, John
6
van Ophem, PW
6
Wilson, Mark
5
White, Andre
5
Peisach, D
5
Lepore, Bryan
5
Liu, Dali
5
Gerlt, John
5
Jeffery, CJ
5
Bennett, Brian

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Publications

TOP 3
D'Aquino J Alejandro; Denninger Andrew R; Moulin Aaron G; D'Aquino Katharine E; Ringe Dagmar
Decreased sensitivity to changes in the concentration of metal ions as the basis for the hyperactivity of DtxR(E175K).
Brandt Gabriel S; Kneen Malea M; Chakraborty Sumit; Baykal Ahmet T; Nemeria Natalia; Yep Alejandra; Ruby David I; Petsko Gregory A; Kenyon George L; McLeish Michael J; Jordan Frank; Ringe Dagmar
Snapshot of a reaction intermediate: analysis of benzoylformate decarboxylase in complex with a benzoylphosphonate inhibitor.
Novak Walter R P; Moulin Aaron G; Blakeley Matthew P; Schlichting Ilme; Petsko Gregory A; Ringe Dagmar
A preliminary neutron diffraction study of gamma-chymotrypsin.

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All Publications

2009: D'Aquino J Alejandro; Denninger Andrew R; Moulin Aaron G; D'Aquino Katharine E; Ringe Dagmar
Decreased sensitivity to changes in the concentration of metal ions as the basis for the hyperactivity of DtxR(E175K).
Journal of molecular biology 2009;390(1):112-23.
2009: Brandt Gabriel S; Kneen Malea M; Chakraborty Sumit; Baykal Ahmet T; Nemeria Natalia; Yep Alejandra; Ruby David I; Petsko Gregory A; Kenyon George L; McLeish Michael J; Jordan Frank; Ringe Dagmar
Snapshot of a reaction intermediate: analysis of benzoylformate decarboxylase in complex with a benzoylphosphonate inhibitor.
Biochemistry 2009;48(15):3247-57.
2009: Novak Walter R P; Moulin Aaron G; Blakeley Matthew P; Schlichting Ilme; Petsko Gregory A; Ringe Dagmar
A preliminary neutron diffraction study of gamma-chymotrypsin.
Acta crystallographica. Section F, Structural biology and crystallization communications 2009;65(Pt 3):317-20.
2009: Chakraborty Sumit; Nemeria Natalia S; Balakrishnan Anand; Brandt Gabriel S; Kneen Malea M; Yep Alejandra; McLeish Michael J; Kenyon George L; Petsko Gregory A; Ringe Dagmar; Jordan Frank
Detection and time course of formation of major thiamin diphosphate-bound covalent intermediates derived from a chromophoric substrate analogue on benzoylformate decarboxylase.
Biochemistry 2009;48(5):981-94.
2008: Murga Leonel F; Ondrechen Mary Jo; Ringe Dagmar
Prediction of interaction sites from apo 3D structures when the holo conformation is different.
Proteins 2008;72(3):980-92.
2008: Momb Jessica; Wang Canhui; Liu Dali; Thomas Pei W; Petsko Gregory A; Guo Hua; Ringe Dagmar; Fast Walter
Mechanism of the quorum-quenching lactonase (AiiA) from Bacillus thuringiensis. 2. Substrate modeling and active site mutations.
Biochemistry 2008;47(29):7715-25.
2008: Liu Dali; Momb Jessica; Thomas Pei W; Moulin Aaron; Petsko Gregory A; Fast Walter; Ringe Dagmar
Mechanism of the quorum-quenching lactonase (AiiA) from Bacillus thuringiensis. 1. Product-bound structures.
Biochemistry 2008;47(29):7706-14.
2008: Ataie Niloufar J; Hoang Quyen Q; Zahniser Megan P D; Tu Yupeng; Milne Amy; Petsko Gregory A; Ringe Dagmar
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 2008;47(29):7673-83.
2008: Brandt Gabriel S; Nemeria Natalia; Chakraborty Sumit; McLeish Michael J; Yep Alejandra; Kenyon George L; Petsko Gregory A; Jordan Frank; Ringe Dagmar
Probing the active center of benzaldehyde lyase with substitutions and the pseudosubstrate analogue benzoylphosphonic acid methyl ester.
Biochemistry 2008;47(29):7734-43.
2008: Ringe Dagmar; Petsko Gregory A
Biochemistry. How enzymes work.
Science (New York, N.Y.) 2008;320(5882):1428-9.
2007: D'Aquino J Alejandro; Lattimer Judith R; Denninger Andrew; D'Aquino Katharine E; Ringe Dagmar
Role of the N-terminal helix in the metal ion-induced activation of the diphtheria toxin repressor DtxR.
Biochemistry 2007;46(42):11761-70.
2007: Liu Dali; Thomas Pei W; Momb Jessica; Hoang Quyen Q; Petsko Gregory A; Ringe Dagmar; Fast Walter
Structure and specificity of a quorum-quenching lactonase (AiiB) from Agrobacterium tumefaciens.
Biochemistry 2007;46(42):11789-99.
2007: Liu Dali; Pozharski Edwin; Lepore Bryan W; Fu Mengmeng; Silverman Richard B; Petsko Gregory A; Ringe Dagmar
Inactivation of Escherichia coli L-aspartate aminotransferase by (S)-4-amino-4,5-dihydro-2-thiophenecarboxylic acid reveals "a tale of two mechanisms".
Biochemistry 2007;46(37):10517-27.
2007: Munih Petra; Moulin Aaron; Stamper Carin C; Bennett Brian; Ringe Dagmar; Petsko Gregory A; Holz Richard C
X-ray crystallographic characterization of the Co(II)-substituted Tris-bound form of the aminopeptidase from Aeromonas proteolytica.
Journal of inorganic biochemistry 2007;101(8):1099-107.
2007: Moulin Aaron; Bell Jason H; Pratt R F; Ringe Dagmar
Inhibition of chymotrypsin by a complex of ortho-vanadate and benzohydroxamic acid: structure of the inert complex and its mechanistic interpretation.
Biochemistry 2007;46(20):5982-90.
2007: Wei Ying; Ringe Dagmar; Wilson Mark A; Ondrechen Mary Jo
Identification of functional subclasses in the DJ-1 superfamily proteins.
PLoS computational biology 2007;3(1):e10.
2006: Ding Xiaochun; Rasmussen Bjarne F; Petsko Gregory A; Ringe Dagmar
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 2006;34(6):410-23.
2006: Chen Dawei; Frey Perry A; Lepore Bryan W; Ringe Dagmar; Ruzicka Frank J
Identification of structural and catalytic classes of highly conserved amino acid residues in lysine 2,3-aminomutase.
Biochemistry 2006;45(42):12647-53.
2006: Desmarais William; Bienvenue David L; Bzymek Krzysztof P; Petsko Gregory A; Ringe Dagmar; Holz Richard C
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 2006;11(4):398-408.
2006: Mattos Carla; Bellamacina Cornelia R; Peisach Ezra; Pereira Antonio; Vitkup Dennis; Petsko Gregory A; Ringe Dagmar
Multiple solvent crystal structures: probing binding sites, plasticity and hydration.
Journal of molecular biology 2006;357(5):1471-82.
2006: Das Chittaranjan; Hoang Quyen Q; Kreinbring Cheryl A; Luchansky Sarah J; Meray Robin K; Ray Soumya S; Lansbury Peter T; Ringe Dagmar; Petsko Gregory A
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 2006;103(12):4675-80.
2005: D'Aquino J Alejandro; Tetenbaum-Novatt Jaclyn; White Andre; Berkovitch Fred; Ringe Dagmar
Mechanism of metal ion activation of the diphtheria toxin repressor DtxR.
Proceedings of the National Academy of Sciences of the United States of America 2005;102(51):18408-13.
2005: Wilson Mark A; Ringe Dagmar; Petsko Gregory A
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 2005;353(3):678-91.
2005: Lepore Bryan W; Ruzicka Frank J; Frey Perry A; Ringe Dagmar
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 2005;102(39):13819-24.
2005: Bzymek Krzysztof P; Moulin Aaron; Swierczek Sabina I; Ringe Dagmar; Petsko Gregory A; Bennett Brian; Holz Richard C
Kinetic, spectroscopic, and X-ray crystallographic characterization of the functional E151H aminopeptidase from Aeromonas proteolytica.
Biochemistry 2005;44(36):12030-40.
2005: Liu Dali; Lepore Bryan W; Petsko Gregory A; Thomas Pei W; Stone Everett M; Fast Walter; Ringe Dagmar
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 2005;102(33):11882-7.
2005: Pozharski Edwin; Moulin Aaron; Hewagama Anura; Shanafelt Armen B; Petsko Gregory A; Ringe Dagmar
Diversity in hapten recognition: structural study of an anti-cocaine antibody M82G2.
Journal of molecular biology 2005;349(3):570-82.
2005: Fenn Timothy D; Holyoak Todd; Stamper Geoffrey F; Ringe Dagmar
Effect of a Y265F mutant on the transamination-based cycloserine inactivation of alanine racemase.
Biochemistry 2005;44(14):5317-27.
2004: Yang Jian; Wang Yi; Woolridge Elisa M; Arora Vandana; Petsko Gregory A; Kozarich John W; Ringe Dagmar
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 2004;43(32):10424-34.
2004: Stamper Carin C; Bienvenue David L; Bennett Brian; Ringe Dagmar; Petsko Gregory A; Holz Richard C
Spectroscopic and X-ray crystallographic characterization of bestatin bound to the aminopeptidase from Aeromonas (Vibrio) proteolytica.
Biochemistry 2004;43(30):9620-8.
2004: Fenn Timothy D; Ringe Dagmar; Petsko Gregory A
Xylose isomerase in substrate and inhibitor michaelis states: atomic resolution studies of a metal-mediated hydride shift.
Biochemistry 2004;43(21):6464-74.
2004: Vogan Erik M; Bellamacina Cornelia; He Xuemei; Liu Hung-wen; Ringe Dagmar; Petsko Gregory A
Crystal structure at 1.8 A resolution of CDP-D-glucose 4,6-dehydratase from Yersinia pseudotuberculosis.
Biochemistry 2004;43(11):3057-67.
2004: Pozharski Edwin; Wilson Mark A; Hewagama Anura; Shanafelt Armen B; Petsko Gregory; Ringe Dagmar
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 2004;337(3):691-7.
2004: Holyoak Todd; Kettner Charles A; Petsko Gregory A; Fuller Robert S; Ringe Dagmar
Structural basis for differences in substrate selectivity in Kex2 and furin protein convertases.
Biochemistry 2004;43(9):2412-21.
2004: Ringe D; Wei Y; Boino K R; Ondrechen M J
Protein structure to function: insights from computation.
Cellular and molecular life sciences : CMLS 2004;61(4):387-92.
2004: Wilson Mark A; St Amour Courtney V; Collins Jennifer L; Ringe Dagmar; Petsko Gregory A
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 2004;101(6):1531-6.
2003: Holyoak Todd; Fenn Timothy D; Wilson Mark A; Moulin Aaron G; Ringe Dagmar; Petsko Gregory A
Malonate: a versatile cryoprotectant and stabilizing solution for salt-grown macromolecular crystals.
Acta crystallographica. Section D, Biological crystallography 2003;59(Pt 12):2356-8.
2003: Ringe Dagmar; Petsko Gregory A
The 'glass transition' in protein dynamics: what it is, why it occurs, and how to exploit it.
Biophysical chemistry 2003;105(2-3):667-80.
2003: Wilson Mark A; Collins Jennifer L; Hod Yaacov; Ringe Dagmar; Petsko Gregory A
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 2003;100(16):9256-61.
2003: D'Aquino J Alejandro; Ringe Dagmar
Determinants of the SRC homology domain 3-like fold.
Journal of bacteriology 2003;185(14):4081-6.
2003: Holyoak Todd; Wilson Mark A; Fenn Timothy D; Kettner Charles A; Petsko Gregory A; Fuller Robert S; Ringe Dagmar
2.4 A resolution crystal structure of the prototypical hormone-processing protease Kex2 in complex with an Ala-Lys-Arg boronic acid inhibitor.
Biochemistry 2003;42(22):6709-18.
2003: Fenn Timothy D; Stamper Geoffrey F; Morollo Anthony A; Ringe Dagmar
A side reaction of alanine racemase: transamination of cycloserine.
Biochemistry 2003;42(19):5775-83.
2003: Beebe Jane A; Arabshahi Abolfazl; Clifton James G; Ringe Dagmar; Petsko Gregory A; Frey Perry A
Galactose mutarotase: pH dependence of enzymatic mutarotation.
Biochemistry 2003;42(15):4414-20.
2002: Desmarais William T; Bienvenue David L; Bzymek Krzysztof P; Holz Richard C; Petsko Gregory A; Ringe Dagmar
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) 2002;10(8):1063-72.
2002: Taoka Shinichi; Lepore Bryan W; Kabil Omer; Ojha Sunil; Ringe Dagmar; Banerjee Ruma
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 2002;41(33):10454-61.
2002: Vitkup Dennis; Ringe Dagmar; Karplus Martin; Petsko Gregory A
Why protein R-factors are so large: a self-consistent analysis.
Proteins 2002;46(4):345-54.
2002: Vogan Erik M; Bellamacina Cornelia R; He Xuemei; Foxman Bruce M; Ringe Dagmar; Liu Hung-Wen; Petsko Gregory A
Purification, crystallization and molecular symmetry of CDP-D-glucose 4,6-dehydratase from Yersinia pseudotuberculosis.
Acta crystallographica. Section D, Biological crystallography 2002;58(Pt 2):370-3.
2002: Bienvenue David L; Mathew Rebecca S; Ringe Dagmar; Holz Richard C
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 2002;7(1-2):129-35.
2001: Mattos C; Ringe D
Proteins in organic solvents.
Current opinion in structural biology 2001;11(6):761-4.
2001: Hadfield A; Shammas C; Kryger G; Ringe D; Petsko G A; Ouyang J; Viola R E
Active site analysis of the potential antimicrobial target aspartate semialdehyde dehydrogenase.
Biochemistry 2001;40(48):14475-83.
2001: Ondrechen M J; Clifton J G; 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 2001;98(22):12473-8.
2001: Pasternak A; White A; Jeffery C J; 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 2001;10(7):1331-42.
2001: Stamper C; Bennett B; Edwards T; Holz R C; 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 2001;40(24):7035-46.
2000: Chen C S; White A; Love J; Murphy J R; Ringe D
Methyl groups of thymine bases are important for nucleic acid recognition by DtxR.
Biochemistry 2000;39(34):10397-407.
2000: McMillan F M; Cahoon M; White A; Hedstrom L; Petsko G A; 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 2000;39(15):4533-42.
2000: Jeffery C J; Gloss L M; Petsko G A; Ringe D
The role of residues outside the active site: structural basis for function of C191 mutants of Escherichia coli aspartate aminotransferase.
Protein engineering 2000;13(2):105-12.
2000: Jeffery C J; Bahnson B J; Chien W; Ringe D; Petsko G A
Crystal structure of rabbit phosphoglucose isomerase, a glycolytic enzyme that moonlights as neuroleukin, autocrine motility factor, and differentiation mediator.
Biochemistry 2000;39(5):955-64.
2000: Vitkup D; Ringe D; Petsko G A; Karplus M
Solvent mobility and the protein 'glass' transition.
Nature structural biology 2000;7(1):34-8.
1999: Peisach E; Wang J; de los Santos T; Reich E; Ringe D
Crystal structure of the proenzyme domain of plasminogen.
Biochemistry 1999;38(34):11180-8.
1999: De Paola C C; Bennett B; Holz R C; Ringe D; Petsko G A
1-Butaneboronic acid binding to Aeromonas proteolytica aminopeptidase: a case of arrested development.
Biochemistry 1999;38(28):9048-53.
1999: Ringe D; Mattos C
Analysis of the binding surfaces of proteins.
Medicinal research reviews 1999;19(4):321-31.
1999: Hadfield A; Kryger G; Ouyang J; Petsko G A; 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 1999;289(4):991-1002.
1999: Zhang Z; Komives E A; Sugio S; Blacklow S C; Narayana N; Xuong N H; Stock A M; Petsko G A; Ringe D
The role of water in the catalytic efficiency of triosephosphate isomerase.
Biochemistry 1999;38(14):4389-97.
1999: Morollo A A; Petsko G A; Ringe D
Structure of a Michaelis complex analogue: propionate binds in the substrate carboxylate site of alanine racemase.
Biochemistry 1999;38(11):3293-301.
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 1999;8(1):253-8.
1999: van Ophem P W; Peisach D; Erickson S D; Soda K; Ringe D; Manning J M
Effects of the E177K mutation in D-amino acid transaminase. Studies on an essential coenzyme anchoring group that contributes to stereochemical fidelity.
Biochemistry 1999;38(4):1323-31.
1998: Hasson M S; Schlichting I; Moulai J; Taylor K; Barrett W; Kenyon G L; Babbitt P C; Gerlt J A; Petsko G A; 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 1998;95(18):10396-401.
1998: Sugio S; Kashima A; Kishimoto K; Peisach D; Petsko G A; 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 1998;11(8):613-9.
1998: Jeffery C J; Barry T; Doonan S; Petsko G A; Ringe D
Crystallization and preliminary X-ray diffraction analysis of aspartate aminotransferase from Saccharomyces cerevisiae.
Acta crystallographica. Section D, Biological crystallography 1998;54(Pt 4):659-61.
1998: White A; Ding X; vanderSpek J C; Murphy J R; Ringe D
Structure of the metal-ion-activated diphtheria toxin repressor/tox operator complex.
Nature 1998;394(6692):502-6.
1998: Stamper G F; Morollo A A; Ringe D;
Reaction of alanine racemase with 1-aminoethylphosphonic acid forms a stable external aldimine.
Biochemistry 1998;37(29):10438-45.
1998: Hasson M S; Muscate A; McLeish M J; Polovnikova L S; Gerlt J A; Kenyon G L; Petsko G A; Ringe D
The crystal structure of benzoylformate decarboxylase at 1.6 A resolution: diversity of catalytic residues in thiamin diphosphate-dependent enzymes.
Biochemistry 1998;37(28):9918-30.
1998: Jeffery C J; Barry T; Doonan S; Petsko G A; Ringe D
Crystal structure of Saccharomyces cerevisiae cytosolic aspartate aminotransferase.
Protein science : a publication of the Protein Society 1998;7(6):1380-7.
1998: Peisach D; Chipman D M; Van Ophem P W; Manning J M; Ringe D
Crystallographic study of steps along the reaction pathway of D-amino acid aminotransferase.
Biochemistry 1998;37(14):4958-67.
1998: van Ophem P W; Erickson S D; Martinez del Pozo A; Haller I; Chait B T; Yoshimura T; Soda K; Ringe D; Petsko G; Manning J M
Substrate inhibition of D-amino acid transaminase and protection by salts and by reduced nicotinamide adenine dinucleotide: isolation and initial characterization of a pyridoxo intermediate related to inactivation.
Biochemistry 1998;37(9):2879-88.
1997: Harrison D H; Bohren K M; Petsko G A; Ringe D; Gabbay K H
The alrestatin double-decker: binding of two inhibitor molecules to human aldose reductase reveals a new specificity determinant.
Biochemistry 1997;36(51):16134-40.
1997: Wallon G; Lovett S T; Magyar C; Svingor A; Szilagyi A; Zàvodszky P; Ringe D; Petsko G A
Sequence and homology model of 3-isopropylmalate dehydrogenase from the psychrotrophic bacterium Vibrio sp. I5 suggest reasons for thermal instability.
Protein engineering 1997;10(6):665-72.
1997: Hasson M S; Schlichting I; McGowen M M; Woolridge E M; Kozarich J W; Petsko G A; Ringe D
Characterization of two crystal forms of 3-carboxy-cis,cis-muconate lactonizing enzyme from Pseudomonas putida.
Acta crystallographica. Section D, Biological crystallography 1997;53(Pt 3):352-3.
1997: Brenner C; Garrison P; Gilmour J; Peisach D; Ringe D; Petsko G A; Lowenstein J M
Crystal structures of HINT demonstrate that histidine triad proteins are GalT-related nucleotide-binding proteins.
Nature structural biology 1997;4(3):231-8.
1997: Wallon G; Kryger G; Lovett S T; Oshima T; Ringe D; Petsko G A
Crystal structures of Escherichia coli and Salmonella typhimurium 3-isopropylmalate dehydrogenase and comparison with their thermophilic counterpart from Thermus thermophilus.
Journal of molecular biology 1997;266(5):1016-31.
1997: Shaw J P; Petsko G A; Ringe D
Determination of the structure of alanine racemase from Bacillus stearothermophilus at 1.9-A resolution.
Biochemistry 1997;36(6):1329-42.
1996: Babbitt P C; Hasson M S; Wedekind J E; Palmer D R; Barrett W C; Reed G H; Rayment I; Ringe D; Kenyon G L; Gerlt J A
The enolase superfamily: a general strategy for enzyme-catalyzed abstraction of the alpha-protons of carboxylic acids.
Biochemistry 1996;35(51):16489-501.
1996: Jones W M; van Ophem P W; Pospischil M A; Ringe D; Petsko G; Soda K; Manning J M
The ubiquitous cofactor NADH protects against substrate-induced inhibition of a pyridoxal enzyme.
Protein science : a publication of the Protein Society 1996;5(12):2545-51.
1996: Komives E A; Lougheed J C; Zhang Z; Sugio S; Narayana N; Xuong N H; Petsko G A; Ringe D
The structural basis for pseudoreversion of the H95N lesion by the secondary S96P mutation in triosephosphate isomerase.
Biochemistry 1996;35(48):15474-84.
1996: Mattos C; Ringe D
Locating and characterizing binding sites on proteins.
Nature biotechnology 1996;14(5):595-9.
1996: Ding X; Zeng H; Schiering N; Ringe D; Murphy J R
Identification of the primary metal ion-activation sites of the diphtheria tox repressor by X-ray crystallography and site-directed mutational analysis.
Nature structural biology 1996;3(4):382-7.
1996: Martinez del Pozo A; van Ophem P W; Ringe D; Petsko G; Soda K; Manning J M
Interaction of pyridoxal 5'-phosphate with tryptophan-139 at the subunit interface of dimeric D-amino acid transaminase.
Biochemistry 1996;35(7):2112-6.
1995: Ringe D
What makes a binding site a binding site?
Current opinion in structural biology 1995;5(6):825-9.
1995: Van Ophem P W; Pospischil M A; Ringe D; Peisach D; Petsko G; Soda K; Manning J M
Catalytic ability and stability of two recombinant mutants of D-amino acid transaminase involved in coenzyme binding.
Protein science : a publication of the Protein Society 1995;4(12):2578-86.
1995: Kryger G; Wallon G; Lovett S T; Ringe D; Petsko G A
Revision of the amino-acid sequence of 3-isopropylmalate dehydrogenase from Salmonella typhimurium by means of X-ray crystallography.
Gene 1995;164(1):85-7.
1995: Komives E A; Lougheed J C; Liu K; Sugio S; Zhang Z; Petsko G A; Ringe D
The structural basis for pseudoreversion of the E165D lesion by the secondary S96P mutation in triosephosphate isomerase depends on the positions of active site water molecules.
Biochemistry 1995;34(41):13612-21.
1995: Schiering N; Tao X; Zeng H; Murphy J R; Petsko G A; Ringe D
Structures of the apo- and the metal ion-activated forms of the diphtheria tox repressor from Corynebacterium diphtheriae.
Proceedings of the National Academy of Sciences of the United States of America 1995;92(21):9843-50.
1995: Sugio S; Petsko G A; Manning J M; Soda K; Ringe D
Crystal structure of a D-amino acid aminotransferase: how the protein controls stereoselectivity.
Biochemistry 1995;34(30):9661-9.
1995: Peisach E; Casebier D; Gallion S L; Furth P; Petsko G A; Hogan J C; Ringe D
Interaction of a peptidomimetic aminimide inhibitor with elastase.
Science (New York, N.Y.) 1995;269(5220):66-9.
1995: Ding X; Rasmussen B F; Demuth H U; Ringe D; Steinmetz A C
Nature of the inactivation of elastase by N-peptidyl-O-aroyl hydroxylamine as a function of pH.
Biochemistry 1995;34(23):7749-56.
1995: Ringe D
Structure-aided drug design: crystallography and computational approaches.
Journal of nuclear medicine : official publication, Society of Nuclear Medicine 1995;36(6 Suppl):28S-30S.
1995: Hasson M S; Muscate A; Henehan G T; Guidinger P F; Petsko G A; Ringe D; Kenyon G L
Purification and crystallization of benzoylformate decarboxylase.
Protein science : a publication of the Protein Society 1995;4(5):955-9.
1995: Allen K N; Lavie A; Petsko G A; Ringe D
Design, synthesis, and characterization of a potent xylose isomerase inhibitor, D-threonohydroxamic acid, and high-resolution X-ray crystallographic structure of the enzyme-inhibitor complex.
Biochemistry 1995;34(11):3742-9.
1995: Mattos C; Giammona D A; Petsko G A; Ringe D
Structural analysis of the active site of porcine pancreatic elastase based on the X-ray crystal structures of complexes with trifluoroacetyl-dipeptide-anilide inhibitors.
Biochemistry 1995;34(10):3193-203.
1995: Babbitt P C; Mrachko G T; Hasson M S; Huisman G W; Kolter R; Ringe D; Petsko G A; Kenyon G L; Gerlt J A
A functionally diverse enzyme superfamily that abstracts the alpha protons of carboxylic acids.
Science (New York, N.Y.) 1995;267(5201):1159-61.
1994: Amor J C; Harrison D H; Kahn R A; Ringe D
Structure of the human ADP-ribosylation factor 1 complexed with GDP.
Nature 1994;372(6507):704-8.
1994: Bohren K M; Wermuth B; Harrison D; Ringe D; Petsko G A; Gabbay K H
Expression, crystallization and preliminary crystallographic analysis of human carbonyl reductase.
Journal of molecular biology 1994;244(5):659-64.
1994: Schiering N; Tao X; Murphy J R; Petsko G A; Ringe D
Crystallization and preliminary X-ray studies of the diphtheria Tox repressor from Corynebacterium diphtheriae.
Journal of molecular biology 1994;244(5):654-6.
1994: Kreutter K; Steinmetz A C; Liang T C; Prorok M; Abeles R H; Ringe D
Three-dimensional structure of chymotrypsin inactivated with (2S)-N-acetyl-L-alanyl-L-phenylalanyl alpha-chloroethane: implications for the mechanism of inactivation of serine proteases by chloroketones.
Biochemistry 1994;33(46):13792-800.
1994: Tao X; Schiering N; Zeng H Y; Ringe D; Murphy J R
Iron, DtxR, and the regulation of diphtheria toxin expression.
Molecular microbiology 1994;14(2):191-7.
1994: Steinmetz A C; Demuth H U; Ringe D
Inactivation of subtilisin Carlsberg by N-((tert-butoxycarbonyl)alanylprolylphenylalanyl)-O-benzoylhydroxyl- amine: formation of a covalent enzyme-inhibitor linkage in the form of a carbamate derivative.
Biochemistry 1994;33(34):10535-44.
1994: Ding X; Rasmussen B F; Petsko G A; Ringe D
Direct structural observation of an acyl-enzyme intermediate in the hydrolysis of an ester substrate by elastase.
Biochemistry 1994;33(31):9285-93.
1994: Lavie A; Allen K N; Petsko G A; Ringe D
X-ray crystallographic structures of D-xylose isomerase-substrate complexes position the substrate and provide evidence for metal movement during catalysis.
Biochemistry 1994;33(18):5469-80.
1994: Jones W M; Ringe D; Soda K; Manning J M
Determination of free D-amino acids with a bacterial transaminase: their depletion leads to inhibition of bacterial growth.
Analytical biochemistry 1994;218(1):204-9.
1994: Zhang Z; Sugio S; Komives E A; Liu K D; Knowles J R; Petsko G A; Ringe D
Crystal structure of recombinant chicken triosephosphate isomerase-phosphoglycolohydroxamate complex at 1.8-A resolution.
Biochemistry 1994;33(10):2830-7.
1994: Bohren K M; Grimshaw C E; Lai C J; Harrison D H; Ringe D; Petsko G A; Gabbay K H
Tyrosine-48 is the proton donor and histidine-110 directs substrate stereochemical selectivity in the reduction reaction of human aldose reductase: enzyme kinetics and crystal structure of the Y48H mutant enzyme.
Biochemistry 1994;33(8):2021-32.
1994: Harrison D H; Bohren K M; Ringe D; Petsko G A; Gabbay K H
An anion binding site in human aldose reductase: mechanistic implications for the binding of citrate, cacodylate, and glucose 6-phosphate.
Biochemistry 1994;33(8):2011-20.
1994: Almo S C; Smith D L; Danishefsky A T; Ringe D
The structural basis for the altered substrate specificity of the R292D active site mutant of aspartate aminotransferase from E. coli.
Protein engineering 1994;7(3):405-12.
1994: Allen K N; Lavie A; Farber G K; Glasfeld A; Petsko G A; Ringe D
Isotopic exchange plus substrate and inhibition kinetics of D-xylose isomerase do not support a proton-transfer mechanism.
Biochemistry 1994;33(6):1481-7.
1994: Allen K N; Lavie A; Glasfeld A; Tanada T N; Gerrity D P; Carlson S C; Farber G K; Petsko G A; Ringe D
Role of the divalent metal ion in sugar binding, ring opening, and isomerization by D-xylose isomerase: replacement of a catalytic metal by an amino acid.
Biochemistry 1994;33(6):1488-94.
1994: Fitzpatrick P A; Ringe D; Klibanov A M
X-ray crystal structure of cross-linked subtilisin Carlsberg in water vs. acetonitrile.
Biochemical and biophysical research communications 1994;198(2):675-81.
1994: Mattos C; Rasmussen B; Ding X; Petsko G A; Ringe D
Analogous inhibitors of elastase do not always bind analogously.
Nature structural biology 1994;1(1):55-8.
1993: Stock A M; Martinez-Hackert E; Rasmussen B F; West A H; Stock J B; Ringe D; Petsko G A
Structure of the Mg(2+)-bound form of CheY and mechanism of phosphoryl transfer in bacterial chemotaxis.
Biochemistry 1993;32(49):13375-80.
1993: Petsko G A; Kenyon G L; Gerlt J A; Ringe D; Kozarich J W
On the origin of enzymatic species.
Trends in biochemical sciences 1993;18(10):372-6.
1993: Fitzpatrick P A; Steinmetz A C; Ringe D; Klibanov A M
Enzyme crystal structure in a neat organic solvent.
Proceedings of the National Academy of Sciences of the United States of America 1993;90(18):8653-7.
1993: Bhatia M B; Martinez del Pozo A; Ringe D; Yoshimura T; Soda K; Manning J M
Role reversal for substrates and inhibitors. Slow inactivation of D-amino acid transaminase by its normal substrates and protection by inhibitors.
The Journal of biological chemistry 1993;268(24):17687-94.
1993: Wolfson A J; Kanaoka M; Lau F; Ringe D; Young P; Lee J; Blumenthal J
Modularity of protein function: chimeric interleukin 1 beta s containing specific protease inhibitor loops retain function of both molecules.
Biochemistry 1993;32(20):5327-31.
1993: Bhatia M B; Futaki S; Ueno H; Manning J M; Ringe D; Yoshimura T; Soda K
Kinetic and stereochemical comparison of wild-type and active-site K145Q mutant enzyme of bacterial D-amino acid transaminase.
The Journal of biological chemistry 1993;268(10):6932-8.
1993: Ringe D
Fleeting opportunities.
Proceedings of the National Academy of Sciences of the United States of America 1993;90(6):2103-4.
1992: Yoshimura T; Bhatia M B; Manning J M; Ringe D; Soda K
Partial reactions of bacterial D-amino acid transaminase with asparagine substituted for the lysine that binds coenzyme pyridoxal 5'-phosphate.
Biochemistry 1992;31(47):11748-54.
1992: Martinez del Pozo A; Yoshimura T; Bhatia M B; Futaki S; Manning J M; Ringe D; Soda K
Inactivation of dimeric D-amino acid transaminase by a normal substrate through formation of an unproductive coenzyme adduct in one subunit.
Biochemistry 1992;31(26):6018-23.
1992: Gallion S; Ringe D
Molecular modeling studies in the complex between cyclophilin and cyclosporin A.
Protein engineering 1992;5(5):391-7.
1992: Rasmussen B F; Stock A M; Ringe D; Petsko G A
Crystalline ribonuclease A loses function below the dynamical transition at 220 K.
Nature 1992;357(6377):423-4.
1991: Stoddard B L; Koenigs P; Porter N; Petratos K; Petsko G A; Ringe D
Observation of the light-triggered binding of pyrone to chymotrypsin by Laue x-ray crystallography.
Proceedings of the National Academy of Sciences of the United States of America 1991;88(13):5503-7.
1991: Bash P A; Field M J; Davenport R C; Petsko G A; Ringe D; Karplus M
Computer simulation and analysis of the reaction pathway of triosephosphate isomerase.
Biochemistry 1991;30(24):5826-32.
1991: Davenport R C; Bash P A; Seaton B A; Karplus M; Petsko G A; Ringe D
Structure of the triosephosphate isomerase-phosphoglycolohydroxamate complex: an analogue of the intermediate on the reaction pathway.
Biochemistry 1991;30(24):5821-6.
1991: Danishefsky A T; Onnufer J J; Petsko G A; Ringe D
Activity and structure of the active-site mutants R386Y and R386F of Escherichia coli aspartate aminotransferase.
Biochemistry 1991;30(7):1980-5.
1991: Wolfson A J; Kanaoka M; Lau F T; Ringe D
Insertion of an elastase-binding loop into interleukin-1 beta.
Protein engineering 1991;4(3):313-7.
1990: Futaki S; Ueno H; Martinez del Pozo A; Pospischil M A; Manning J M; Ringe D; Stoddard B; Tanizawa K; Yoshimura T; Soda K
Substitution of glutamine for lysine at the pyridoxal phosphate binding site of bacterial D-amino acid transaminase. Effects of exogenous amines on the slow formation of intermediates.
The Journal of biological chemistry 1990;265(36):22306-12.
1990: Stoddard B L; Ringe D; Petsko G A
The structure of iron superoxide dismutase from Pseudomonas ovalis complexed with the inhibitor azide.
Protein engineering 1990;4(2):113-9.
1990: Stoddard B L; Howell P L; Ringe D; Petsko G A
The 2.1-A resolution structure of iron superoxide dismutase from Pseudomonas ovalis.
Biochemistry 1990;29(38):8885-93.
1990: Stoddard B L; Bruhnke J; Koenigs P; Porter N; Ringe D; Petsko G A
Photolysis and deacylation of inhibited chymotrypsin.
Biochemistry 1990;29(35):8042-51.
1990: Stoddard B L; Bruhnke J; Porter N; Ringe D; Petsko G A
Structure and activity of two photoreversible cinnamates bound to chymotrypsin.
Biochemistry 1990;29(20):4871-9.
1989: Martínez del Pozo A; Merola M; Ueno H; Manning J M; Tanizawa K; Nishimura K; Soda K; Ringe D
Stereospecificity of reactions catalyzed by bacterial D-amino acid transaminase.
The Journal of biological chemistry 1989;264(30):17784-9.
1989: Martinez del Pozo A; Pospischil M A; Ueno H; Manning J M; Tanizawa K; Nishimura K; Soda K; Ringe D; Stoddard B; Petsko G A
Effects of D-serine on bacterial D-amino acid transaminase: accumulation of an intermediate and inactivation of the enzyme.
Biochemistry 1989;28(22):8798-803.
1989: Smith D L; Almo S C; Toney M D; Ringe D
2.8-A-resolution crystal structure of an active-site mutant of aspartate aminotransferase from Escherichia coli.
Biochemistry 1989;28(20):8161-7.
1989: Farber G K; Glasfeld A; Tiraby G; Ringe D; Petsko G A
Crystallographic studies of the mechanism of xylose isomerase.
Biochemistry 1989;28(18):7289-97.
1989: Martínez del Pozo A; Merola M; Ueno H; Manning J M; Tanizawa K; Nishimura K; Asano S; Tanaka H; Soda K; Ringe D
Activity and spectroscopic properties of bacterial D-amino acid transaminase after multiple site-directed mutagenesis of a single tryptophan residue.
Biochemistry 1989;28(2):510-6.
1988: Glasfeld A; Farber G K; Ringe D; Marcel T; Drocourt D; Tiraby G; Petsko G A
Characterization of crystals of xylose isomerase from Streptomyces violaceoniger.
The Journal of biological chemistry 1988;263(29):14612-3.
1987: Farber G K; Petsko G A; Ringe D
The 3.0 A crystal structure of xylose isomerase from Streptomyces olivochromogenes.
Protein engineering 1987;1(6):459-66.
1987: Stoddard B; Howell L; Asano S; Soda K; Tanizawa K; Ringe D; Petsko G A
Preliminary X-ray data for a D-amino acid amino-transferase from a novel thermophilic Bacillus.
Journal of molecular biology 1987;196(2):441-2.
1987: Alber T C; Davenport R C; Giammona D A; Lolis E; Petsko G A; Ringe D
Crystallography and site-directed mutagenesis of yeast triosephosphate isomerase: what can we learn about catalysis from a "simple" enzyme?
Cold Spring Harbor symposia on quantitative biology 1987;52():603-13.

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