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Items: 1 to 50 of 236

1.

Crystal Structures of Cystathionine β-Synthase from Saccharomyces cerevisiae: One Enzymatic Step at a Time.

Tu Y, Kreinbring CA, Hill M, Liu C, Petsko GA, McCune CD, Berkowitz DB, Liu D, Ringe D.

Biochemistry. 2018 Jun 5;57(22):3134-3145. doi: 10.1021/acs.biochem.8b00092. Epub 2018 Apr 13.

PMID:
29630349
2.

Correction to Selective Targeting by a Mechanism-Based Inactivator against Pyridoxal 5'-Phosphate-Dependent Enzymes: Mechanisms of Inactivation and Alternative Turnover.

Mascarenhas R, Le HV, Clevenger KD, Lehrer HJ, Ringe D, Kelleher NL, Silverman RB, Liu D.

Biochemistry. 2017 Oct 31;56(43):5844-5845. doi: 10.1021/acs.biochem.7b00961. Epub 2017 Oct 18. No abstract available.

PMID:
29045130
3.

Selective Targeting by a Mechanism-Based Inactivator against Pyridoxal 5'-Phosphate-Dependent Enzymes: Mechanisms of Inactivation and Alternative Turnover.

Mascarenhas R, Le HV, Clevenger KD, Lehrer HJ, Ringe D, Kelleher NL, Silverman RB, Liu D.

Biochemistry. 2017 Sep 19;56(37):4951-4961. doi: 10.1021/acs.biochem.7b00499. Epub 2017 Sep 6. Erratum in: Biochemistry. 2017 Oct 31;56(43):5844-5845.

4.

The Metal Drives the Chemistry: Dual Functions of Acireductone Dioxygenase.

Deshpande AR, Pochapsky TC, Ringe D.

Chem Rev. 2017 Aug 9;117(15):10474-10501. doi: 10.1021/acs.chemrev.7b00117. Epub 2017 Jul 21. Review.

5.

The EMBO biocatalysis conference "The biochemistry and chemistry of biocatalysis: from understanding to design".

Wierenga RK, Ringe D.

Protein Eng Des Sel. 2017 Apr 24:1. doi: 10.1093/protein/gzx020. [Epub ahead of print] No abstract available.

PMID:
28444392
6.

PLP and GABA trigger GabR-mediated transcription regulation in Bacillus subtilis via external aldimine formation.

Wu R, Sanishvili R, Belitsky BR, Juncosa JI, Le HV, Lehrer HJ, Farley M, Silverman RB, Petsko GA, Ringe D, Liu D.

Proc Natl Acad Sci U S A. 2017 Apr 11;114(15):3891-3896. doi: 10.1073/pnas.1703019114. Epub 2017 Mar 27.

7.

Structure Determination of Mycobacterium tuberculosis Serine Protease Hip1 (Rv2224c).

Naffin-Olivos JL, Daab A, White A, Goldfarb NE, Milne AC, Liu D, Baikovitz J, Dunn BM, Rengarajan J, Petsko GA, Ringe D.

Biochemistry. 2017 May 2;56(17):2304-2314. doi: 10.1021/acs.biochem.6b01066. Epub 2017 Apr 7.

8.

Structure and mechanism of benzaldehyde dehydrogenase from Pseudomonas putida ATCC 12633, a member of the Class 3 aldehyde dehydrogenase superfamily.

Zahniser MPD, Prasad S, Kneen MM, Kreinbring CA, Petsko GA, Ringe D, McLeish MJ.

Protein Eng Des Sel. 2017 Mar 1;30(3):271-278. doi: 10.1093/protein/gzx015.

9.

Dual chemistry catalyzed by human acireductone dioxygenase.

Deshpande AR, Pochapsky TC, Petsko GA, Ringe D.

Protein Eng Des Sel. 2017 Mar 1;30(3):197-204. doi: 10.1093/protein/gzw078.

10.

Crystal structure of the DNA binding domain of the transcription factor T-bet suggests simultaneous recognition of distant genome sites.

Liu CF, Brandt GS, Hoang QQ, Naumova N, Lazarevic V, Hwang ES, Dekker J, Glimcher LH, Ringe D, Petsko GA.

Proc Natl Acad Sci U S A. 2016 Oct 25;113(43):E6572-E6581. Epub 2016 Oct 10.

11.

Reducing C-terminal truncation mitigates synucleinopathy and neurodegeneration in a transgenic model of multiple system atrophy.

Bassil F, Fernagut PO, Bezard E, Pruvost A, Leste-Lasserre T, Hoang QQ, Ringe D, Petsko GA, Meissner WG.

Proc Natl Acad Sci U S A. 2016 Aug 23;113(34):9593-8. doi: 10.1073/pnas.1609291113. Epub 2016 Aug 1.

12.

Caspase-1 causes truncation and aggregation of the Parkinson's disease-associated protein α-synuclein.

Wang W, Nguyen LT, Burlak C, Chegini F, Guo F, Chataway T, Ju S, Fisher OS, Miller DW, Datta D, Wu F, Wu CX, Landeru A, Wells JA, Cookson MR, Boxer MB, Thomas CJ, Gai WP, Ringe D, Petsko GA, Hoang QQ.

Proc Natl Acad Sci U S A. 2016 Aug 23;113(34):9587-92. doi: 10.1073/pnas.1610099113. Epub 2016 Aug 1.

13.

Metal-Dependent Function of a Mammalian Acireductone Dioxygenase.

Deshpande AR, Wagenpfeil K, Pochapsky TC, Petsko GA, Ringe D.

Biochemistry. 2016 Mar 8;55(9):1398-407. doi: 10.1021/acs.biochem.5b01319. Epub 2016 Feb 24.

14.

Nuclear receptor Nurr1 agonists enhance its dual functions and improve behavioral deficits in an animal model of Parkinson's disease.

Kim CH, Han BS, Moon J, Kim DJ, Shin J, Rajan S, Nguyen QT, Sohn M, Kim WG, Han M, Jeong I, Kim KS, Lee EH, Tu Y, Naffin-Olivos JL, Park CH, Ringe D, Yoon HS, Petsko GA, Kim KS.

Proc Natl Acad Sci U S A. 2015 Jul 14;112(28):8756-61. doi: 10.1073/pnas.1509742112. Epub 2015 Jun 29.

15.

Amelioration of toxicity in neuronal models of amyotrophic lateral sclerosis by hUPF1.

Barmada SJ, Ju S, Arjun A, Batarse A, Archbold HC, Peisach D, Li X, Zhang Y, Tank EM, Qiu H, Huang EJ, Ringe D, Petsko GA, Finkbeiner S.

Proc Natl Acad Sci U S A. 2015 Jun 23;112(25):7821-6. doi: 10.1073/pnas.1509744112. Epub 2015 Jun 8.

16.

Prediction of distal residue participation in enzyme catalysis.

Brodkin HR, DeLateur NA, Somarowthu S, Mills CL, Novak WR, Beuning PJ, Ringe D, Ondrechen MJ.

Protein Sci. 2015 May;24(5):762-78. doi: 10.1002/pro.2648. Epub 2015 Apr 2.

17.

The use of pharmacological retromer chaperones in Alzheimer's disease and other endosomal-related disorders.

Berman DE, Ringe D, Petsko GA, Small SA.

Neurotherapeutics. 2015 Jan;12(1):12-8. doi: 10.1007/s13311-014-0321-y. Review.

18.

Preservation of forelimb function by UPF1 gene therapy in a rat model of TDP-43-induced motor paralysis.

Jackson KL, Dayton RD, Orchard EA, Ju S, Ringe D, Petsko GA, Maquat LE, Klein RL.

Gene Ther. 2015 Jan;22(1):20-8. doi: 10.1038/gt.2014.101. Epub 2014 Nov 6.

19.

Crystal cryocooling distorts conformational heterogeneity in a model Michaelis complex of DHFR.

Keedy DA, van den Bedem H, Sivak DA, Petsko GA, Ringe D, Wilson MA, Fraser JS.

Structure. 2014 Jun 10;22(6):899-910. doi: 10.1016/j.str.2014.04.016. Epub 2014 May 29.

20.

Mycobacterium tuberculosis Hip1 modulates macrophage responses through proteolysis of GroEL2.

Naffin-Olivos JL, Georgieva M, Goldfarb N, Madan-Lala R, Dong L, Bizzell E, Valinetz E, Brandt GS, Yu S, Shabashvili DE, Ringe D, Dunn BM, Petsko GA, Rengarajan J.

PLoS Pathog. 2014 May 15;10(5):e1004132. doi: 10.1371/journal.ppat.1004132. eCollection 2014 May.

21.

Pharmacological chaperones stabilize retromer to limit APP processing.

Mecozzi VJ, Berman DE, Simoes S, Vetanovetz C, Awal MR, Patel VM, Schneider RT, Petsko GA, Ringe D, Small SA.

Nat Chem Biol. 2014 Jun;10(6):443-9. doi: 10.1038/nchembio.1508. Epub 2014 Apr 20.

22.

Artifacts to avoid while taking advantage of top-down mass spectrometry based detection of protein S-thiolation.

Auclair JR, Salisbury JP, Johnson JL, Petsko GA, Ringe D, Bosco DA, Agar NY, Santagata S, Durham HD, Agar JN.

Proteomics. 2014 May;14(10):1152-7. doi: 10.1002/pmic.201300450. Epub 2014 Apr 17.

23.

Structure of a eukaryotic thiaminase I.

Kreinbring CA, Remillard SP, Hubbard P, Brodkin HR, Leeper FJ, Hawksley D, Lai EY, Fulton C, Petsko GA, Ringe D.

Proc Natl Acad Sci U S A. 2014 Jan 7;111(1):137-42. doi: 10.1073/pnas.1315882110. Epub 2013 Dec 18.

24.

Crystal structure of Bacillus subtilis GabR, an autorepressor and transcriptional activator of gabT.

Edayathumangalam R, 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.

Proc Natl Acad Sci U S A. 2013 Oct 29;110(44):17820-5. doi: 10.1073/pnas.1315887110. Epub 2013 Oct 14.

25.

Post-translational modification by cysteine protects Cu/Zn-superoxide dismutase from oxidative damage.

Auclair JR, Johnson JL, Liu Q, Salisbury JP, Rotunno MS, Petsko GA, Ringe D, Brown RH Jr, Bosco DA, Agar JN.

Biochemistry. 2013 Sep 10;52(36):6137-44. doi: 10.1021/bi4006122. Epub 2013 Aug 26.

26.

Structural consequences of cysteinylation of Cu/Zn-superoxide dismutase.

Auclair JR, Brodkin HR, D'Aquino JA, Petsko GA, Ringe D, Agar JN.

Biochemistry. 2013 Sep 10;52(36):6145-50. doi: 10.1021/bi400613h. Epub 2013 Aug 26.

27.

Quantitative dissection of hydrogen bond-mediated proton transfer in the ketosteroid isomerase active site.

Sigala PA, Fafarman AT, Schwans JP, Fried SD, Fenn TD, Caaveiro JM, Pybus B, Ringe D, Petsko GA, Boxer SG, Herschlag D.

Proc Natl Acad Sci U S A. 2013 Jul 9;110(28):E2552-61. doi: 10.1073/pnas.1302191110. Epub 2013 Jun 24.

28.

A phenylalanine clamp controls substrate specificity in the quorum-quenching metallo-γ-lactonase from Bacillus thuringiensis.

Liu CF, Liu D, Momb J, Thomas PW, Lajoie A, Petsko GA, Fast W, Ringe D.

Biochemistry. 2013 Mar 5;52(9):1603-10. doi: 10.1021/bi400050j. Epub 2013 Feb 20.

29.

Open questions - in brief: beyond -omics, missing motor proteins, and getting from molecules to organisms.

Benkovic SJ, Theriot J, Ringe D.

BMC Biol. 2013 Jan 31;11:8. doi: 10.1186/1741-7007-11-8. No abstract available.

30.

Behind the movement.

Ringe D, Petsko GA.

Cell. 2012 Sep 14;150(6):1093-5. doi: 10.1016/j.cell.2012.08.031.

31.

Latrepirdine (dimebon) enhances autophagy and reduces intracellular GFP-Aβ42 levels in yeast.

Bharadwaj PR, Verdile G, Barr RK, Gupta V, Steele JW, Lachenmayer ML, Yue Z, Ehrlich ME, Petsko G, Ju S, Ringe D, Sankovich SE, Caine JM, Macreadie IG, Gandy S, Martins RN.

J Alzheimers Dis. 2012;32(4):949-67. doi: 10.3233/JAD-2012-120178.

32.

Latrepirdine stimulates autophagy and reduces accumulation of α-synuclein in cells and in mouse brain.

Steele JW, 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.

Mol Psychiatry. 2013 Aug;18(8):882-8. doi: 10.1038/mp.2012.115. Epub 2012 Aug 7.

33.

Latrepirdine improves cognition and arrests progression of neuropathology in an Alzheimer's mouse model.

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 CG, Protter AA, Martins RN, Ehrlich ME, Petsko GA, Yue Z, Gandy S.

Mol Psychiatry. 2013 Aug;18(8):889-97. doi: 10.1038/mp.2012.106. Epub 2012 Jul 31.

34.

Mass spectrometry tools for analysis of intermolecular interactions.

Auclair JR, Somasundaran M, Green KM, Evans JE, Schiffer CA, Ringe D, Petsko GA, Agar JN.

Methods Mol Biol. 2012;896:387-98. doi: 10.1007/978-1-4614-3704-8_26.

35.

The co-crystal structure of ubiquitin carboxy-terminal hydrolase L1 (UCHL1) with a tripeptide fluoromethyl ketone (Z-VAE(OMe)-FMK).

Davies CW, Chaney J, Korbel G, Ringe D, Petsko GA, Ploegh H, Das C.

Bioorg Med Chem Lett. 2012 Jun 15;22(12):3900-4. doi: 10.1016/j.bmcl.2012.04.124. Epub 2012 May 4.

36.

A soluble α-synuclein construct forms a dynamic tetramer.

Wang W, Perovic I, Chittuluru J, Kaganovich A, Nguyen LT, Liao J, Auclair JR, Johnson D, Landeru A, Simorellis AK, Ju S, Cookson MR, Asturias FJ, Agar JN, Webb BN, Kang C, Ringe D, Petsko GA, Pochapsky TC, Hoang QQ.

Proc Natl Acad Sci U S A. 2011 Oct 25;108(43):17797-802. doi: 10.1073/pnas.1113260108. Epub 2011 Oct 17.

37.

A tale of two isomerases: compact versus extended active sites in ketosteroid isomerase and phosphoglucose isomerase.

Somarowthu S, Brodkin HR, D'Aquino JA, Ringe D, Ondrechen MJ, Beuning PJ.

Biochemistry. 2011 Nov 1;50(43):9283-95. doi: 10.1021/bi201089v. Epub 2011 Oct 4.

PMID:
21970785
38.

Proteostasis and movement disorders: Parkinson's disease and amyotrophic lateral sclerosis.

Bosco DA, LaVoie MJ, Petsko GA, Ringe D.

Cold Spring Harb Perspect Biol. 2011 Oct 1;3(10):a007500. doi: 10.1101/cshperspect.a007500. Review.

39.

Time-of-flight neutron diffraction study of bovine γ-chymotrypsin at the Protein Crystallography Station.

Lazar LM, Fisher SZ, Moulin AG, Kovalevsky A, Novak WR, Langan P, Petsko GA, Ringe D.

Acta Crystallogr Sect F Struct Biol Cryst Commun. 2011 May 1;67(Pt 5):587-90. doi: 10.1107/S1744309111009341. Epub 2011 Apr 27.

40.

A yeast model of FUS/TLS-dependent cytotoxicity.

Ju S, Tardiff DF, Han H, Divya K, Zhong Q, Maquat LE, Bosco DA, Hayward LJ, Brown RH Jr, Lindquist S, Ringe D, Petsko GA.

PLoS Biol. 2011 Apr;9(4):e1001052. doi: 10.1371/journal.pbio.1001052. Epub 2011 Apr 26.

41.

Evidence of the participation of remote residues in the catalytic activity of Co-type nitrile hydratase from Pseudomonas putida.

Brodkin HR, Novak WR, Milne AC, D'Aquino JA, Karabacak NM, Goldberg IG, Agar JN, Payne MS, Petsko GA, Ondrechen MJ, Ringe D.

Biochemistry. 2011 Jun 7;50(22):4923-35. doi: 10.1021/bi101761e. Epub 2011 May 12.

42.

Strategies for stabilizing superoxide dismutase (SOD1), the protein destabilized in the most common form of familial amyotrophic lateral sclerosis.

Auclair JR, Boggio KJ, Petsko GA, Ringe D, Agar JN.

Proc Natl Acad Sci U S A. 2010 Dec 14;107(50):21394-9. doi: 10.1073/pnas.1015463107. Epub 2010 Nov 22.

43.

Mechanism of inactivation of Escherichia coli aspartate aminotransferase by (S)-4-amino-4,5-dihydro-2-furancarboxylic acid .

Liu D, Pozharski E, Fu M, Silverman RB, Ringe D.

Biochemistry. 2010 Dec 14;49(49):10507-15. doi: 10.1021/bi101325z. Epub 2010 Nov 15.

44.

Polyamine pathway contributes to the pathogenesis of Parkinson disease.

Lewandowski NM, Ju S, Verbitsky M, Ross B, Geddie ML, Rockenstein E, Adame A, Muhammad A, Vonsattel JP, Ringe D, Cote L, Lindquist S, Masliah E, Petsko GA, Marder K, Clark LN, Small SA.

Proc Natl Acad Sci U S A. 2010 Sep 28;107(39):16970-5. doi: 10.1073/pnas.1011751107. Epub 2010 Sep 13.

45.

Chiral discrimination among aminotransferases: inactivation by 4-amino-4,5-dihydrothiophenecarboxylic acid.

Lepore BW, Liu D, Peng Y, Fu M, Yasuda C, Manning JM, Silverman RB, Ringe D.

Biochemistry. 2010 Apr 13;49(14):3138-47. doi: 10.1021/bi902052x.

PMID:
20192272
46.

Active-site engineering of benzaldehyde lyase shows that a point mutation can confer both new reactivity and susceptibility to mechanism-based inhibition.

Brandt GS, Kneen MM, Petsko GA, Ringe D, McLeish MJ.

J Am Chem Soc. 2010 Jan 20;132(2):438-9. doi: 10.1021/ja907064w.

PMID:
20030408
47.

What are pharmacological chaperones and why are they interesting?

Ringe D, Petsko GA.

J Biol. 2009 Oct 13;8(9):80. doi: 10.1186/jbiol186. No abstract available.

48.

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 Aug;23(8):491-500. doi: 10.1007/s10822-009-9283-2. Epub 2009 Jun 12.

49.

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. doi: 10.1021/bi900713j.

50.

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. doi: 10.1016/j.jmb.2009.05.003. Epub 2009 May 8.

PMID:
19433095

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