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Items: 1 to 50 of 96

1.

Promiscuity of methionine salvage pathway enzymes in Methanocaldococcus jannaschii.

Miller DV, Rauch BJ, Harich K, Xu H, Perona JJ, White RH.

Microbiology. 2018 Jul;164(7):969-981. doi: 10.1099/mic.0.000670. Epub 2018 Jun 7.

PMID:
29877790
2.

Improving target amino acid selectivity in a permissive aminoacyl tRNA synthetase through counter-selection.

Sungwienwong I, Hostetler ZM, Blizzard RJ, Porter JJ, Driggers CM, Mbengi LZ, Villegas JA, Speight LC, Saven JG, Perona JJ, Kohli RM, Mehl RA, Petersson EJ.

Org Biomol Chem. 2017 May 3;15(17):3603-3610. doi: 10.1039/c7ob00582b.

3.

Persulfide Formation Mediates Cysteine and Homocysteine Biosynthesis in Methanosarcina acetivorans.

Rauch BJ, Klimek J, David L, Perona JJ.

Biochemistry. 2017 Feb 28;56(8):1051-1061. doi: 10.1021/acs.biochem.6b00931. Epub 2017 Feb 16.

PMID:
28165724
4.

Efficient Sulfide Assimilation in Methanosarcina acetivorans Is Mediated by the MA1715 Protein.

Rauch BJ, Perona JJ.

J Bacteriol. 2016 Jun 27;198(14):1974-83. doi: 10.1128/JB.00141-16. Print 2016 Jul 15.

5.

Improved Incorporation of Noncanonical Amino Acids by an Engineered tRNA(Tyr) Suppressor.

Rauch BJ, Porter JJ, Mehl RA, Perona JJ.

Biochemistry. 2016 Jan 26;55(3):618-28. doi: 10.1021/acs.biochem.5b01185. Epub 2016 Jan 8.

6.

Homocysteine is biosynthesized from aspartate semialdehyde and hydrogen sulfide in methanogenic archaea.

Allen KD, Miller DV, Rauch BJ, Perona JJ, White RH.

Biochemistry. 2015 May 26;54(20):3129-32. doi: 10.1021/acs.biochem.5b00118. Epub 2015 May 11.

PMID:
25938369
7.

Novel proteins for homocysteine biosynthesis in anaerobic microorganisms.

Rauch BJ, Gustafson A, Perona JJ.

Mol Microbiol. 2014 Dec;94(6):1330-42. doi: 10.1111/mmi.12832. Epub 2014 Nov 6.

8.

Recoding aminoacyl-tRNA synthetases for synthetic biology by rational protein-RNA engineering.

Hadd A, Perona JJ.

ACS Chem Biol. 2014 Dec 19;9(12):2761-6. doi: 10.1021/cb5006596. Epub 2014 Oct 31.

9.

Determinants for tRNA-dependent pretransfer editing in the synthetic site of isoleucyl-tRNA synthetase.

Dulic M, Perona JJ, Gruic-Sovulj I.

Biochemistry. 2014 Oct 7;53(39):6189-98. doi: 10.1021/bi5007699. Epub 2014 Sep 23.

10.

Coevolution of specificity determinants in eukaryotic glutamyl- and glutaminyl-tRNA synthetases.

Hadd A, Perona JJ.

J Mol Biol. 2014 Oct 23;426(21):3619-33. doi: 10.1016/j.jmb.2014.08.006. Epub 2014 Aug 19.

PMID:
25149203
11.

Structural dynamics of a mitochondrial tRNA possessing weak thermodynamic stability.

Bhaskaran H, Taniguchi T, Suzuki T, Suzuki T, Perona JJ.

Biochemistry. 2014 Mar 11;53(9):1456-65. doi: 10.1021/bi401449z. Epub 2014 Feb 26.

12.

Synthetic and editing mechanisms of aminoacyl-tRNA synthetases.

Perona JJ, Gruic-Sovulj I.

Top Curr Chem. 2014;344:1-41. doi: 10.1007/128_2013_456. Review.

PMID:
23852030
13.

Structural and mechanistic basis for enhanced translational efficiency by 2-thiouridine at the tRNA anticodon wobble position.

Rodriguez-Hernandez A, Spears JL, Gaston KW, Limbach PA, Gamper H, Hou YM, Kaiser R, Agris PF, Perona JJ.

J Mol Biol. 2013 Oct 23;425(20):3888-906. doi: 10.1016/j.jmb.2013.05.018. Epub 2013 May 28.

14.

Structural diversity and protein engineering of the aminoacyl-tRNA synthetases.

Perona JJ, Hadd A.

Biochemistry. 2012 Nov 6;51(44):8705-29. doi: 10.1021/bi301180x. Epub 2012 Oct 26. Review.

PMID:
23075299
15.

Kinetic partitioning between synthetic and editing pathways in class I aminoacyl-tRNA synthetases occurs at both pre-transfer and post-transfer hydrolytic steps.

Cvetesic N, Perona JJ, Gruic-Sovulj I.

J Biol Chem. 2012 Jul 20;287(30):25381-94. doi: 10.1074/jbc.M112.372151. Epub 2012 May 30.

16.

Linking energy production and protein synthesis in hydrogenotrophic methanogens.

Oza JP, Sowers KR, Perona JJ.

Biochemistry. 2012 Mar 27;51(12):2378-89. doi: 10.1021/bi300106p. Epub 2012 Mar 13.

17.

Kinetics of tRNA folding monitored by aminoacylation.

Bhaskaran H, Rodriguez-Hernandez A, Perona JJ.

RNA. 2012 Mar;18(3):569-80. doi: 10.1261/rna.030080.111. Epub 2012 Jan 27.

18.

Structural conservation of an ancient tRNA sensor in eukaryotic glutaminyl-tRNA synthetase.

Grant TD, Snell EH, Luft JR, Quartley E, Corretore S, Wolfley JR, Snell ME, Hadd A, Perona JJ, Phizicky EM, Grayhack EJ.

Nucleic Acids Res. 2012 Apr;40(8):3723-31. doi: 10.1093/nar/gkr1223. Epub 2011 Dec 17.

19.

Two-step aminoacylation of tRNA without channeling in Archaea.

Bhaskaran H, Perona JJ.

J Mol Biol. 2011 Aug 26;411(4):854-69. doi: 10.1016/j.jmb.2011.06.039. Epub 2011 Jun 25. Erratum in: J Mol Biol. 2011 Oct 14;413(1):292-3.

20.

Formation of m2G6 in Methanocaldococcus jannaschii tRNA catalyzed by the novel methyltransferase Trm14.

Menezes S, Gaston KW, Krivos KL, Apolinario EE, Reich NO, Sowers KR, Limbach PA, Perona JJ.

Nucleic Acids Res. 2011 Sep 1;39(17):7641-55. doi: 10.1093/nar/gkr475. Epub 2011 Jun 21.

21.

Heat maps for intramolecular communication in an RNP enzyme encoding glutamine.

Rodríguez-Hernández A, Perona JJ.

Structure. 2011 Mar 9;19(3):386-96. doi: 10.1016/j.str.2010.12.017.

22.

The energetic contribution of induced electrostatic asymmetry to DNA bending by a site-specific protein.

Hancock SP, Hiller DA, Perona JJ, Jen-Jacobson L.

J Mol Biol. 2011 Feb 18;406(2):285-312. doi: 10.1016/j.jmb.2010.12.012. Epub 2010 Dec 15.

23.

Crystal structure of a reverse polymerase.

Perona JJ, Oza JP.

Proc Natl Acad Sci U S A. 2010 Nov 23;107(47):20149-50. doi: 10.1073/pnas.1015283107. Epub 2010 Nov 15. No abstract available.

24.

Mechanism of N-methylation by the tRNA m1G37 methyltransferase Trm5.

Christian T, Lahoud G, Liu C, Hoffmann K, Perona JJ, Hou YM.

RNA. 2010 Dec;16(12):2484-92. doi: 10.1261/rna.2376210. Epub 2010 Oct 27.

25.

Synthesis of Glu-tRNA(Gln) by engineered and natural aminoacyl-tRNA synthetases.

Rodríguez-Hernández A, Bhaskaran H, Hadd A, Perona JJ.

Biochemistry. 2010 Aug 10;49(31):6727-36. doi: 10.1021/bi100886z.

26.

Partitioning of tRNA-dependent editing between pre- and post-transfer pathways in class I aminoacyl-tRNA synthetases.

Dulic M, Cvetesic N, Perona JJ, Gruic-Sovulj I.

J Biol Chem. 2010 Jul 30;285(31):23799-809. doi: 10.1074/jbc.M110.133553. Epub 2010 May 24.

27.

Stereochemical mechanisms of tRNA methyltransferases.

Hou YM, Perona JJ.

FEBS Lett. 2010 Jan 21;584(2):278-86. doi: 10.1016/j.febslet.2009.11.075. Review.

28.

Architectural underpinnings of the genetic code for glutamine.

Corigliano EM, Perona JJ.

Biochemistry. 2009 Feb 3;48(4):676-87. doi: 10.1021/bi801552y.

29.

The homotetrameric phosphoseryl-tRNA synthetase from Methanosarcina mazei exhibits half-of-the-sites activity.

Hauenstein SI, Hou YM, Perona JJ.

J Biol Chem. 2008 Aug 8;283(32):21997-2006. doi: 10.1074/jbc.M801838200. Epub 2008 Jun 17.

30.

Redundant synthesis of cysteinyl-tRNACys in Methanosarcina mazei.

Hauenstein SI, Perona JJ.

J Biol Chem. 2008 Aug 8;283(32):22007-17. doi: 10.1074/jbc.M801839200. Epub 2008 Jun 17.

31.

A rationally engineered misacylating aminoacyl-tRNA synthetase.

Bullock TL, Rodríguez-Hernández A, Corigliano EM, Perona JJ.

Proc Natl Acad Sci U S A. 2008 May 27;105(21):7428-33. doi: 10.1073/pnas.0711812105. Epub 2008 May 13.

32.

Methods for kinetic and thermodynamic analysis of aminoacyl-tRNA synthetases.

Francklyn CS, First EA, Perona JJ, Hou YM.

Methods. 2008 Feb;44(2):100-18. doi: 10.1016/j.ymeth.2007.09.007.

33.

Indirect readout of tRNA for aminoacylation.

Perona JJ, Hou YM.

Biochemistry. 2007 Sep 18;46(37):10419-32. Epub 2007 Aug 24. Review.

PMID:
17718520
34.

Kinetic quality control of anticodon recognition by a eukaryotic aminoacyl-tRNA synthetase.

Liu C, Gamper H, Shtivelband S, Hauenstein S, Perona JJ, Hou YM.

J Mol Biol. 2007 Apr 6;367(4):1063-78. Epub 2007 Jan 24.

35.

Structure of the Escherichia coli leucine-responsive regulatory protein Lrp reveals a novel octameric assembly.

de los Rios S, Perona JJ.

J Mol Biol. 2007 Mar 9;366(5):1589-602. Epub 2006 Dec 19.

36.
37.

Engineered extrahelical base destabilization enhances sequence discrimination of DNA methyltransferase M.HhaI.

Youngblood B, Shieh FK, De Los Rios S, Perona JJ, Reich NO.

J Mol Biol. 2006 Sep 15;362(2):334-46. Epub 2006 Jul 21.

PMID:
16919299
38.

Distinct kinetic mechanisms of the two classes of Aminoacyl-tRNA synthetases.

Zhang CM, Perona JJ, Ryu K, Francklyn C, Hou YM.

J Mol Biol. 2006 Aug 11;361(2):300-11. Epub 2006 Jun 27.

PMID:
16843487
39.

Active-site assembly in glutaminyl-tRNA synthetase by tRNA-mediated induced fit.

Uter NT, Perona JJ.

Biochemistry. 2006 Jun 6;45(22):6858-65.

40.

Exploring writhe in supercoiled minicircle DNA.

Fogg JM, Kolmakova N, Rees I, Magonov S, Hansma H, Perona JJ, Zechiedrich EL.

J Phys Condens Matter. 2006 Apr 12;18(14):S145-S159.

41.

Non-cognate enzyme-DNA complex: structural and kinetic analysis of EcoRV endonuclease bound to the EcoRI recognition site GAATTC.

Hiller DA, Rodriguez AM, Perona JJ.

J Mol Biol. 2005 Nov 18;354(1):121-36. Epub 2005 Oct 3.

PMID:
16236314
42.

Two-step pathway to aminoacylated tRNA.

Perona JJ.

Structure. 2005 Oct;13(10):1397-8.

43.

Amino acid-dependent transfer RNA affinity in a class I aminoacyl-tRNA synthetase.

Uter NT, Gruic-Sovulj I, Perona JJ.

J Biol Chem. 2005 Jun 24;280(25):23966-77. Epub 2005 Apr 20.

44.

tRNA-dependent aminoacyl-adenylate hydrolysis by a nonediting class I aminoacyl-tRNA synthetase.

Gruic-Sovulj I, Uter N, Bullock T, Perona JJ.

J Biol Chem. 2005 Jun 24;280(25):23978-86. Epub 2005 Apr 20.

45.

Shape-selective RNA recognition by cysteinyl-tRNA synthetase.

Hauenstein S, Zhang CM, Hou YM, Perona JJ.

Nat Struct Mol Biol. 2004 Nov;11(11):1134-41. Epub 2004 Oct 17.

PMID:
15489861
46.

Long-range intramolecular signaling in a tRNA synthetase complex revealed by pre-steady-state kinetics.

Uter NT, Perona JJ.

Proc Natl Acad Sci U S A. 2004 Oct 5;101(40):14396-401. Epub 2004 Sep 27.

47.

DNA cleavage by EcoRV endonuclease: two metal ions in three metal ion binding sites.

Horton NC, Perona JJ.

Biochemistry. 2004 Jun 8;43(22):6841-57.

PMID:
15170321
48.

Simultaneous DNA binding and bending by EcoRV endonuclease observed by real-time fluorescence.

Hiller DA, Fogg JM, Martin AM, Beechem JM, Reich NO, Perona JJ.

Biochemistry. 2003 Dec 16;42(49):14375-85.

PMID:
14661948
49.

Amino acid discrimination by a highly differentiated metal center of an aminoacyl-tRNA synthetase.

Zhang CM, Perona JJ, Hou YM.

Biochemistry. 2003 Sep 23;42(37):10931-7.

PMID:
12974627
50.

tRNA-dependent active site assembly in a class I aminoacyl-tRNA synthetase.

Sherlin LD, Perona JJ.

Structure. 2003 May;11(5):591-603.

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