A procedure to validate and correct the 13C chemical shift calibration of RNA datasets

Journal of Biomolecular NMR

Volumn 52, Issue 2, 2012, Pages 179-190

  Aeschbacher, Thomas ^a   Schubert, Mario ^a   Allain, Frédéric H T ^a  

^a ETH ZURICH   (Switzerland)

Author keywords

13C referencing; A form RNA; C2 endo; Chemical shift; NMR Spectroscopy; RNA; Sugar pucker

Indexed keywords

RNA; CARBON; RIBOSE;

ARTICLE; CALIBRATION; CARBON NUCLEAR MAGNETIC RESONANCE; CONFORMATION; DATA MINING; PRIORITY JOURNAL; REFERENCE VALUE; RNA STRUCTURE; STRUCTURE ANALYSIS; CHEMISTRY; METHODOLOGY; NUCLEAR MAGNETIC RESONANCE; NUCLEIC ACID DATABASE; REPRODUCIBILITY;

CARBON ISOTOPES; DATA MINING; DATABASES, NUCLEIC ACID; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; NUCLEIC ACID CONFORMATION; REPRODUCIBILITY OF RESULTS; RIBOSE; RNA;

EID: 84861559026     PISSN: 09252738     EISSN: 15735001     Source Type: Journal    
DOI: 10.1007/s10858-011-9600-7     Document Type: Article

References (34)

1. Butcher SE, Dieckmann T, Feigon J (1997) Solution structure of the conserved 16 S-like ribosomal RNA UGAA tetraloop. J Mol Biol 268:348-358 (Pubitemid 27208059)
2. Cavalli A, Salvatella X, Dobson CM, Vendruscolo M (2007) Protein structure determination from NMR chemical shifts. Proc Natl Acad Sci USA 104:9615-9620 (Pubitemid 47175315)
3. Cornilescu G, Delaglio F, Bax A (1999) Protein backbone angle restraints from searching a database for chemical shift and sequence homology. J Biomol NMR 13:289-302 (Pubitemid 29143535)
4. Duarte CM, Pyle AM (1998) Stepping through an RNA structure: a novel approach to conformational analysis. J Mol Biol 284:1465-1478 (Pubitemid 28566081)
5. Ebrahimi M, Rossi P, Rogers C, Harbison GS (2001) Dependence of 13C NMR chemical shifts on conformations of rna nucleosides and nucleotides. J Magn Reson 150:1-9
6. Fares C, Amata I, Carlomagno T (2007) 13C-detection in RNA bases: revealing structure-chemical shift relationships. J Am Chem Soc 129:15814-15823
7. Findeisen M, Brand T, Berger S (2007) A 1H-NMR thermometer suitable for cryoprobes. Magn Reson Chem 45:175-178
8. Ginzinger SW, Gerick F, Coles M, Heun V (2007) CheckShift: automatic correction of inconsistent chemical shift referencing. J Biomol NMR 39:223-227 (Pubitemid 47617506)
9. Goddard TD, Kneller DG (1999) SPARKY 3. University of California, San Francisco
10. Grzesiek S, Bax A (1993) Amino acid type determination in the sequential assignment procedure of uniformly 13C/15 N-enriched proteins. J Biomol NMR 3:185-204
11. Jucker FM, Pardi A (1995) Solution structure of the CUUG hairpin loop: a novel RNA tetraloop motif. Biochemistry 34:14416-14427
12. Lam SL, Chi LM (2010) Use of chemical shifts for structural studies of nucleic acids. Prog Nucl Magn Reson Spectrosc 56:289-310
13. Markley JL, Bax A, Arata Y, Hilbers CW, Kaptein R, Sykes BD, Wright PE, Wuthrich K (1998) Recommendations for the presentation of NMR structures of proteins and nucleic acids. IUPAC-IUBMB-IUPAB Inter-Union Task Group on the standardization of data bases of protein and nucleic acid structures determined by NMR spectroscopy. J Biomol NMR 12:1-23 (Pubitemid 128512831)
14. Meyer SL (1975) Data analysis for scientists and engineers. Wiley, New York
15. Morcombe CR, Zilm KW (2003) Chemical shift referencing in MAS solid state NMR. J Magn Reson 162:479-486
16. Mulder FA, Filatov M (2010) NMR chemical shift data and ab initio shielding calculations: emerging tools for protein structure determination. Chem Soc Rev 39:578-590
17. Oberstrass FC, Lee A, Stefl R, Janis M, Chanfreau G, Allain FH (2006) Shape-specific recognition in the structure of the Vts1p SAM domain with RNA. Nat Struct Mol Biol 13:160-167 (Pubitemid 43214720)
18. Ohlenschlager O, Haumann S, Ramachandran R, Gorlach M (2008) Conformational signatures of 13C chemical shifts in RNA ribose. J Biomol NMR 42:139-142
19. SantaLucia J Jr, Turner DH (1993) Structure of (rGGCGAGCC)2 in solution from NMR and restrained molecular dynamics. Biochemistry 32:12612-12623 (Pubitemid 24005857)
20. Schubert M, Labudde D, Oschkinat H, Schmieder P (2002) A software tool for the prediction of Xaa-Pro peptide bond conformations in proteins based on 13C chemical shift statistics. J Biomol NMR 24:149-154 (Pubitemid 35414678)
21. Schubert M, Lapouge K, Duss O, Oberstrass FC, Jelesarov I, Haas D, Allain FH (2007) Molecular basis of messenger RNA recognition by the specific bacterial repressing clamp RsmA/CsrA. Nat Struct Mol Biol 14:807-813 (Pubitemid 47373832)
22. Seavey BR, Farr EA, Westler W, Markley JL (1991) A relational database for sequence-specific protein NMR data. J Biomol NMR 1:217-236
23. Shen Y, Lange O, Delaglio F, Rossi P, Aramini JM, Liu G, Eletsky A, Wu Y, Singarapu KK, Lemak A, Ignatchenko A, Arrowsmith CH, Szyperski T, Montelione GT, Baker D, Bax A (2008) Consistent blind protein structure generation from NMR chemical shift data. Proc Natl Acad Sci USA 105:4685-4690 (Pubitemid 351753807)
24. Sich C, Ohlenschlager O, Ramachandran R, Gorlach M, Brown LR (1997) Structure of an RNA hairpin loop with a 5'-CGUUUCG-3' loop motif by heteronuclear NMR spectroscopy and distance geometry. Biochemistry 36:13989-14002 (Pubitemid 27509833)
25. Smith JS, Nikonowicz EP (1998) NMR structure and dynamics of an RNA motif common to the spliceosome branch-point helix and the RNA-binding site for phage GA coat protein. Biochemistry 37:13486-13498 (Pubitemid 28455522)
26. Szewczak AA, Moore PB (1995) The sarcin/ricin loop, a modular RNA. J Mol Biol 247:81-98
27. Varani G, Tinoco I (1991) Carbon assignments and heteronuclear coupling-constants for an Rna oligonucleotide from natural abundance C-13-H-1 correlated experiments. J Am Chem Soc 113:9349-9354
28. Varani G, Aboulela F, Allain FHT (1996) NMR investigation of RNA structure. Prog Nucl Magn Reson Spectrosc 29:51-127 (Pubitemid 126381972)
29. Wang Y, Wishart DS (2005) A simple method to adjust inconsistently referenced 13C and 15 N chemical shift assignments of proteins. J Biomol NMR 31:143-148 (Pubitemid 40425221)
30. Wishart DS, Case DA (2001) Use of chemical shifts in macromo-lecular structure determination. Methods Enzymol 338:3-34 (Pubitemid 32666573)
31. Wishart DS, Sykes BD, Richards FM (1992) The chemical shift index: a fast and simple method for the assignment of protein secondary structure through NMR spectroscopy. Biochemistry 31:1647-1651
32. Wishart DS, Bigam CG, Yao J, Abildgaard F, Dyson HJ, Oldfield E, Markley JL, Sykes BD (1995) 1H, 13C and 15 N chemical shift referencing in biomolecular NMR. J Biomol NMR 6:135-140
33. Wishart DS, Arndt D, Berjanskii M, Tang P, Zhou J, Lin G (2008) CS23D: a web server for rapid protein structure generation using NMR chemical shifts and sequence data. Nucleic Acids Res 36:W496-W502
34. Zhang H, Neal S, Wishart DS (2003) RefDB: a database of uniformly referenced protein chemical shifts. J Biomol NMR 25:173-195 (Pubitemid 36410583)