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

Journal of Biomolecular NMR

Volumn 43, Issue 2, 2009, Pages 121-129

  Latham, Michael P ^a,b   Pardi, Arthur ^a  

^a UNIVERSITY OF COLORADO   (United States)

^b UNIVERSITY OF TORONTO   (Canada)

Author keywords

Iron responsive element RNA; Partial alignment; Residual dipolar couplings; RNA structure; tRNA

Indexed keywords

ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; CALCULATION; CARBON NUCLEAR MAGNETIC RESONANCE; DYNASSIGN ALGORITHM; INTERMETHOD COMPARISON; MEASUREMENT ERROR; MOLECULAR DYNAMICS; NITROGEN NUCLEAR MAGNETIC RESONANCE; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PRIORITY JOURNAL; PROCESS OPTIMIZATION; PROTEIN ANALYSIS; PROTEIN STRUCTURE; PROTON NUCLEAR MAGNETIC RESONANCE; RELIABILITY; SCORING SYSTEM; STRUCTURE ANALYSIS; CHEMISTRY; ESCHERICHIA COLI; GENETICS; METHODOLOGY; NUCLEAR MAGNETIC RESONANCE;

BACTERIAL RNA; IMINE; IRON REGULATORY FACTOR; NITROGEN; RNA; VALINE TRANSFER RNA;

ESCHERICHIA COLI; IMINES; IRON-REGULATORY PROTEINS; NITROGEN ISOTOPES; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; RNA; RNA, BACTERIAL; RNA, TRANSFER, VAL;

EID: 58149458420     PISSN: 09252738     EISSN: 15735001     Source Type: Journal    
DOI: 10.1007/s10858-008-9293-8     Document Type: Article

References (40)

1. Addess KJ, Basilion JP, Klausner RD, Rouault TA, Pardi A (1997) Structure and dynamics of the iron responsive element RNA: Implications for binding of the RNA by iron regulatory binding proteins. J Mol Biol 274:72-83
2. Al-Hashimi HM, Gosser Y, Gorin A, Hu WD, Majumdar A, Patel DJ (2002) Concerted motions in HIV-1 TAR RNA may allow access to bound state conformations: RNA dynamics from NMR residual dipolar couplings. J Mol Biol 315:95-102
3. Bax A, Kontaxis G, Tjandra N (2001) Dipolar couplings in macromolecular structure determination. Methods Enzymol 339:127-174
4. Boisbouvier J, Delaglio F, Bax A (2003) Direct observation of dipolar couplings between distant protons in weekly aligned nucleic acids. Proc Natl Acad Sci USA 100:11333-11338
5. Bondensgaard K, Mollova ET, Pardi A (2002) The global conformation of the hammerhead ribozyme determined using residual dipolar couplings. Biochemistry 41:11532-11542
6. Bothner-By AA, Domaille PJ, Gayathri C (1981) Ultra-high-field NMR spectroscopy-Observation of proton-proton dipolar coupling in paramagnetic bis[Tolyltris(Pyrazolyl)Borato]Cobalt(II). J Am Chem Soc 103:5602-5603
7. Cornilescu G, Marquardt JL, Ottiger M, Bax A (1998) Validation of protein structure from anisotropic carbonyl chemical shifts in a dilute liquid crystalline phase. J Am Chem Soc 120:6836-6837
8. D'Souza V, Dey A, Habib D, Summers MF (2004) NMR structure of the 101-nucleotide core encapsidation signal of the Moloney murine leukemia virus. J Mol Biol 337:427-442
9. Davis JH, Tonelli M, Scott LG, Jaeger L, Williamson JR, Butcher SE (2005) RNA helical packing in solution: NMR structure of a 30 kDa GAAA tetraloop-receptor complex. J Mol Biol 351:371-382
10. Fiala R, Munzarova ML, Sklenar V (2004) Experiments for correlating quaternary carbons in RNA bases. J Biomol NMR 29:477-490
11. Getz M, Sun XY, Casiano-Negroni A, Zhang Q, Al-Hashimi HM (2007) NMR studies of RNA dynamics and structural plasticity using NMR residual dipolar couplings. Biopolymers 86:384-402
12. Hansen MR, Mueller L, Pardi A (1998a) Tunable alignment of macromolecules by filamentous phage yields dipolar coupling interactions. Nat Struct Biol 5:1065-1074
13. 1 H distances in solution by dipolar coupling interactions. J Am Chem Soc 120:11210-11211
14. Hansen MR, Hanson P, Pardi A (2000) Filamentous bacteriophage as a versatile method for aligning RNA, DNA and proteins for measurement of NMR dipolar coupling interactions. Methods Enzymol 317:220-240
15. Kung HC, Wang KY, Goljer I, Bolton PH (1995) Magnetic alignment of duplex and quadruplex DNAs. J Magn Reson B 109:323-325
16. Latham MP, Brown DJ, McCallum SA, Pardi A (2005) NMR methods for studying the structure and dynamics of RNA. ChemBioChem 6:1492-1505
17. Lipsitz RS, Tjandra N (2004) Residual dipolar couplings in NMR structure analysis. Ann Rev Biophys Biomol Struct 33:387-413
18. Lukavsky PJ, Kim I, Otto GA, Puglisi JD (2003) Structure of HCV IRES domain II determined by NMR. Nat Struct Biol 10:1033-1038
19. McCallum SA, Pardi A (2003) Refined solution structure of the iron-responsive element RNA using residual dipolar couplings. J Mol Biol 326:1037-1050
20. Meier S, Haussinger D, Jensen P, Rogowski M, Grzesiek S (2003) High-accuracy residual H-1(N)-C-13 and H-1(N)-H-1(N) dipolar couplings in perdeuterated proteins. J Am Chem Soc 125:44-45
21. Mollova ET, Pardi A (2000) NMR solution structure determination of RNAs. Curr Opin Struct Biol 10:298-302
22. Mollova ET, Hansen MR, Pardi A (2000) Global structure of RNA determined with residual dipolar couplings. J Am Chem Soc 122:11561-11562
23. Pervushin K, Vogeli B, Eletsky A (2002) Longitudinal H-1 relaxation optimization in TROSY NMR spectroscopy. J Am Chem Soc 124:12898-12902
24. Prestegard JH, Bougault CM, Kishore AI (2004) Residual dipolar couplings in structure determination of biomolecules. Chem Rev 104:3519-3540
25. Schanda P, Brutscher B (2005) Very fast two-dimensional NMR spectroscopy for real-time investigation of dynamic events in proteins on the time scale of seconds. J Am Chem Soc 127:8014-8015
26. Schanda P, Kupce E, Brutscher B (2005) SOFAST-HMQC experiments for recording two-dimensional heteronuclear correlation spectra of proteins within a few seconds. J Biomol NMR 33:199-211
27. Schanda P, Lescop E, Falge M, Sounier R, Boisbouvier J, Brutscher B (2007) Sensitivity-optimized experiment for the measurement of residual dipolar couplings between amide protons. J Biomol NMR 38:47-55
28. Scott LG, Tolbert TJ, Williamson JR (2000) Preparation of specifically H-2- and C-13-labeled ribonucleotides. Methods Enzymol 317:18-38
29. Sklenár V, Bax A (1987) Spin-echo water suppression for the generation of pure-phase two-dimensional NMR spectra. J Magn Reson 74:469-479
30. Tian F, Fowler CA, Zartler ER, Jenney FA, Adams MW, Prestegard JH (2000) Direct measurement of H-1-H-1 dipolar couplings in proteins: A complement to traditional NOE measurements. J Biomol NMR 18:23-31
31. Tjandra N, Bax A (1997) Direct measurement of distances and angles in biomolecules by NMR in a dilute liquid crystalline medium. Science 278:1111-1114
32. Tjandra N, Marquardt J, Clore GM (2000a) Direct refinement against proton-proton dipolar couplings in NMR structure determination of macromolecules. J Magn Reson 142:393-396
33. Tjandra N, Tate S, Ono A, Kainosho M, Bax A (2000b) The NMR structure of a DNA dodecamer in an aqueous dilute liquid crystalline phase. J Am Chem Soc 122:6190-6200
34. Tolman JR, Flanagan JM, Kennedy MA, Prestegard JH (1995) Nuclear magnetic dipole interactions in field-oriented proteins-information for structure determination in solution. Proc Natl Acad Sci USA 92:9279-9283
35. Valafar H, Prestegard JH (2004) REDCAT: A residual dipolar coupling analysis tool. J Magn Reson 167:228-241
36. Vermeulen A, Zhou HJ, Pardi A (2000) Determining DNA global structure and DNA bending by application of NMR residual dipolar couplings. J Am Chem Soc 122:9638-9647
37. Vermeulen A, McCallum SA, Pardi A (2005) Comparison of the structure and dynamics of native and unmodified tRNA val. Biochemistry 44:6024-6033
38. 1H dipolar couplings in weakly aligned proteins. J Am Chem Soc 124:9672-9673
39. Wu Z, Delaglio F, Tjandra N, Zhurkin VB, Bax A (2003) Overall structure and sugar dynamics of a DNA dodecamer from homo- and heteronuclear dipolar couplings and 31P chemical shift anisotropy. J Biomol NMR 26:297-315
40. Ying J, Grishaev A, Latham MP, Pardi A, Bax A (2007) Magnetic field induced residual dipolar couplings of imino groups in nucleic acids from measurements at a single magnetic field. J Biomol NMR 39:91-96