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Items: 1 to 50 of 114

1.

Flexibility in the Periplasmic Domain of BamA Is Important for Function.

Warner LR, Gatzeva-Topalova PZ, Doerner PA, Pardi A, Sousa MC.

Structure. 2017 Jan 3;25(1):94-106. doi: 10.1016/j.str.2016.11.013. Epub 2016 Dec 15.

2.

Structure-Based Assignment of Ile, Leu, and Val Methyl Groups in the Active and Inactive Forms of the Mitogen-Activated Protein Kinase Extracellular Signal-Regulated Kinase 2.

Xiao Y, Warner LR, Latham MP, Ahn NG, Pardi A.

Biochemistry. 2015 Jul 21;54(28):4307-19. doi: 10.1021/acs.biochem.5b00506. Epub 2015 Jul 13.

3.

Dynamics of protein kinases: insights from nuclear magnetic resonance.

Xiao Y, Liddle JC, Pardi A, Ahn NG.

Acc Chem Res. 2015 Apr 21;48(4):1106-14. doi: 10.1021/acs.accounts.5b00001. Epub 2015 Mar 24.

4.

Slow inhibition and conformation selective properties of extracellular signal-regulated kinase 1 and 2 inhibitors.

Rudolph J, Xiao Y, Pardi A, Ahn NG.

Biochemistry. 2015 Jan 13;54(1):22-31. doi: 10.1021/bi501101v. Epub 2014 Dec 4.

5.

Phosphorylation releases constraints to domain motion in ERK2.

Xiao Y, Lee T, Latham MP, Warner LR, Tanimoto A, Pardi A, Ahn NG.

Proc Natl Acad Sci U S A. 2014 Feb 18;111(7):2506-11. doi: 10.1073/pnas.1318899111. Epub 2014 Feb 3.

6.

Optimized reverse micelle surfactant system for high-resolution NMR spectroscopy of encapsulated proteins and nucleic acids dissolved in low viscosity fluids.

Dodevski I, Nucci NV, Valentine KG, Sidhu GK, O'Brien ES, Pardi A, Wand AJ.

J Am Chem Soc. 2014 Mar 5;136(9):3465-74. doi: 10.1021/ja410716w. Epub 2014 Feb 19.

7.

Efficient detection of hydrogen bonds in dynamic regions of RNA by sensitivity-optimized NMR pulse sequences.

Dallmann A, Simon B, Duszczyk MM, Kooshapur H, Pardi A, Bermel W, Sattler M.

Angew Chem Int Ed Engl. 2013 Sep 27;52(40):10487-90. doi: 10.1002/anie.201304391. Epub 2013 Aug 14.

8.

Structure of the BamC two-domain protein obtained by Rosetta with a limited NMR data set.

Warner LR, Varga K, Lange OF, Baker SL, Baker D, Sousa MC, Pardi A.

J Mol Biol. 2011 Aug 5;411(1):83-95. doi: 10.1016/j.jmb.2011.05.022. Epub 2011 May 23.

9.

Electrocardiographic profile and muscle glycogen content of rats treated with nandrolone.

Silva CA, Pardi AC, Gonçalves TM, Borin SH.

Arq Bras Cardiol. 2010 Dec;95(6):720-5. Epub 2010 Nov 12. English, Portuguese, Spanish.

10.

Structure and flexibility of the complete periplasmic domain of BamA: the protein insertion machine of the outer membrane.

Gatzeva-Topalova PZ, Warner LR, Pardi A, Sousa MC.

Structure. 2010 Nov 10;18(11):1492-501. doi: 10.1016/j.str.2010.08.012.

11.
12.

Chemical shift anisotropy of imino 15N nuclei in Watson-Crick base pairs from magic angle spinning liquid crystal NMR and nuclear spin relaxation.

Grishaev A, Yao L, Ying J, Pardi A, Bax A.

J Am Chem Soc. 2009 Jul 15;131(27):9490-1. doi: 10.1021/ja903244s.

13.

Longitudinal-relaxation-enhanced NMR experiments for the study of nucleic acids in solution.

Farjon J, Boisbouvier J, Schanda P, Pardi A, Simorre JP, Brutscher B.

J Am Chem Soc. 2009 Jun 24;131(24):8571-7. doi: 10.1021/ja901633y.

14.

NMR chemical exchange as a probe for ligand-binding kinetics in a theophylline-binding RNA aptamer.

Latham MP, Zimmermann GR, Pardi A.

J Am Chem Soc. 2009 Apr 15;131(14):5052-3. doi: 10.1021/ja900695m.

15.

The cavity-chaperone Skp protects its substrate from aggregation but allows independent folding of substrate domains.

Walton TA, Sandoval CM, Fowler CA, Pardi A, Sousa MC.

Proc Natl Acad Sci U S A. 2009 Feb 10;106(6):1772-7. doi: 10.1073/pnas.0809275106. Epub 2009 Jan 30.

16.

Measurement of imino 1H-1H residual dipolar couplings in RNA.

Latham MP, Pardi A.

J Biomol NMR. 2009 Feb;43(2):121-9. doi: 10.1007/s10858-008-9293-8. Epub 2008 Dec 9.

17.

Solution structure of tRNAVal from refinement of homology model against residual dipolar coupling and SAXS data.

Grishaev A, Ying J, Canny MD, Pardi A, Bax A.

J Biomol NMR. 2008 Oct;42(2):99-109. doi: 10.1007/s10858-008-9267-x. Epub 2008 Sep 12.

18.

Metal ion specificities for folding and cleavage activity in the Schistosoma hammerhead ribozyme.

Boots JL, Canny MD, Azimi E, Pardi A.

RNA. 2008 Oct;14(10):2212-22. doi: 10.1261/rna.1010808. Epub 2008 Aug 28.

19.

High-resolution pyrimidine- and ribose-specific 4D HCCH-COSY spectra of RNA using the filter diagonalization method.

Douglas JT, Latham MP, Armstrong GS, Bendiak B, Pardi A.

J Biomol NMR. 2008 Aug;41(4):209-19. doi: 10.1007/s10858-008-9253-3. Epub 2008 Jul 15.

20.

Imino proton exchange rates imply an induced-fit binding mechanism for the VEGF165-targeting aptamer, Macugen.

Lee JH, Jucker F, Pardi A.

FEBS Lett. 2008 Jun 11;582(13):1835-9. doi: 10.1016/j.febslet.2008.05.003. Epub 2008 May 15.

21.

Comparison of alignment tensors generated for native tRNA(Val) using magnetic fields and liquid crystalline media.

Latham MP, Hanson P, Brown DJ, Pardi A.

J Biomol NMR. 2008 Feb;40(2):83-94. Epub 2007 Nov 17.

22.

Magnetic field induced residual dipolar couplings of imino groups in nucleic acids from measurements at a single magnetic field.

Ying J, Grishaev A, Latham MP, Pardi A, Bax A.

J Biomol NMR. 2007 Oct;39(2):91-6. Epub 2007 Aug 7.

PMID:
17680332
23.

Influence of hydrostatic pressure and cosolutes on RNA tertiary structure.

Downey CD, Crisman RL, Randolph TW, Pardi A.

J Am Chem Soc. 2007 Aug 1;129(30):9290-1. Epub 2007 Jul 7. No abstract available.

PMID:
17616193
24.
25.

Efficient ligation of the Schistosoma hammerhead ribozyme.

Canny MD, Jucker FM, Pardi A.

Biochemistry. 2007 Mar 27;46(12):3826-34. Epub 2007 Feb 24.

26.
27.

Metal ion dependence, thermodynamics, and kinetics for intramolecular docking of a GAAA tetraloop and receptor connected by a flexible linker.

Downey CD, Fiore JL, Stoddard CD, Hodak JH, Nesbitt DJ, Pardi A.

Biochemistry. 2006 Mar 21;45(11):3664-73.

28.

Capturing the moment: innovative approaches to daily alcohol assessment.

Neal DJ, Fromme K, Boca FK, Parks KA, King LP, Pardi AM, Collins RL, Muraven M, Vetter C, Corbin WR.

Alcohol Clin Exp Res. 2006 Feb;30(2):282-91.

PMID:
16441277
29.

A therapeutic aptamer inhibits angiogenesis by specifically targeting the heparin binding domain of VEGF165.

Lee JH, Canny MD, De Erkenez A, Krilleke D, Ng YS, Shima DT, Pardi A, Jucker F.

Proc Natl Acad Sci U S A. 2005 Dec 27;102(52):18902-7. Epub 2005 Dec 15.

30.

Resolution-enhanced base-type-edited HCN experiment for RNA.

Van Melckebeke H, Pardi A, Boisbouvier J, Simorre JP, Brutscher B.

J Biomol NMR. 2005 Aug;32(4):263-71.

PMID:
16211480
31.

NMR methods for studying the structure and dynamics of RNA.

Latham MP, Brown DJ, McCallum SA, Pardi A.

Chembiochem. 2005 Sep;6(9):1492-505. Review.

PMID:
16138301
32.

Docking kinetics and equilibrium of a GAAA tetraloop-receptor motif probed by single-molecule FRET.

Hodak JH, Downey CD, Fiore JL, Pardi A, Nesbitt DJ.

Proc Natl Acad Sci U S A. 2005 Jul 26;102(30):10505-10. Epub 2005 Jul 15. Erratum in: Proc Natl Acad Sci U S A. 2005 Sep 13;102(37):13351.

33.

Comparison of the global structure and dynamics of native and unmodified tRNAval.

Vermeulen A, McCallum SA, Pardi A.

Biochemistry. 2005 Apr 26;44(16):6024-33.

PMID:
15835891
34.

Fast cleavage kinetics of a natural hammerhead ribozyme.

Canny MD, Jucker FM, Kellogg E, Khvorova A, Jayasena SD, Pardi A.

J Am Chem Soc. 2004 Sep 8;126(35):10848-9.

PMID:
15339162
35.

Self-rated quality of life in celiac disease.

Ciacci C, D'Agate C, De Rosa A, Franzese C, Errichiello S, Gasperi V, Pardi A, Quagliata D, Visentini S, Greco L.

Dig Dis Sci. 2003 Nov;48(11):2216-20.

PMID:
14705832
36.

Role of a heterogeneous free state in the formation of a specific RNA-theophylline complex.

Jucker FM, Phillips RM, McCallum SA, Pardi A.

Biochemistry. 2003 Mar 11;42(9):2560-7.

PMID:
12614150
37.

Refined solution structure of the iron-responsive element RNA using residual dipolar couplings.

McCallum SA, Pardi A.

J Mol Biol. 2003 Feb 28;326(4):1037-50.

PMID:
12589752
38.

The global conformation of the hammerhead ribozyme determined using residual dipolar couplings.

Bondensgaard K, Mollova ET, Pardi A.

Biochemistry. 2002 Oct 1;41(39):11532-42.

PMID:
12269797
39.
40.

Incorporating residual dipolar couplings into the NMR solution structure determination of nucleic acids.

Zhou H, Vermeulen A, Jucker FM, Pardi A.

Biopolymers. 1999-2000;52(4):168-80. Review.

PMID:
11295749
41.

Active site dynamics in the lead-dependent ribozyme.

Hoogstraten CG, Wank JR, Pardi A.

Biochemistry. 2000 Aug 15;39(32):9951-8.

PMID:
10933815
42.

NMR solution structure determination of RNAs.

Mollova ET, Pardi A.

Curr Opin Struct Biol. 2000 Jun;10(3):298-302.

PMID:
10851189
43.

Molecular interactions and metal binding in the theophylline-binding core of an RNA aptamer.

Zimmermann GR, Wick CL, Shields TP, Jenison RD, Pardi A.

RNA. 2000 May;6(5):659-67.

44.

Filamentous bacteriophage for aligning RNA, DNA, and proteins for measurement of nuclear magnetic resonance dipolar coupling interactions.

Hansen MR, Hanson P, Pardi A.

Methods Enzymol. 2000;317:220-40. Review. No abstract available.

PMID:
10829283
45.

Pf1 filamentous phage as an alignment tool for generating local and global structural information in nucleic acids.

Hansen MR, Hanson P, Pardi A.

J Biomol Struct Dyn. 2000;17 Suppl 1:365-9.

PMID:
22607445
46.
47.

Identification and characterization of a novel high affinity metal-binding site in the hammerhead ribozyme.

Hansen MR, Simorre JP, Hanson P, Mokler V, Bellon L, Beigelman L, Pardi A.

RNA. 1999 Aug;5(8):1099-104.

48.

Tunable alignment of macromolecules by filamentous phage yields dipolar coupling interactions.

Hansen MR, Mueller L, Pardi A.

Nat Struct Biol. 1998 Dec;5(12):1065-74.

PMID:
9846877
49.

NMR solution structure of the lead-dependent ribozyme: evidence for dynamics in RNA catalysis.

Hoogstraten CG, Legault P, Pardi A.

J Mol Biol. 1998 Nov 27;284(2):337-50.

PMID:
9813122
50.

Order, dynamics and metal-binding in the lead-dependent ribozyme.

Legault P, Hoogstraten CG, Metlitzky E, Pardi A.

J Mol Biol. 1998 Nov 27;284(2):325-35.

PMID:
9813121

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