Reliability of exclusively NOESY-based automated resonance assignment and structure determination of proteins

Journal of Biomolecular NMR

Volumn 57, Issue 2, 2013, Pages 193-204

  Schmidt, Elena ^a   Güntert, Peter ^a,b  

^a FRANKFURT INSTITUTE FOR ADVANCED STUDIES   (Germany)

^b TOKYO METROPOLITAN UNIVERSITY   (Japan)

Author keywords

Automated NOESY assignment; Automated resonance assignment; CASD NMR; CYANA; FLYA; Protein structure determination

Indexed keywords

ALGORITHM; ARTICLE; CALCULATION; CARBON NUCLEAR MAGNETIC RESONANCE; CONTROLLED STUDY; NITROGEN NUCLEAR MAGNETIC RESONANCE; NONHUMAN; NUCLEAR OVERHAUSER EFFECT; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN STRUCTURE; PROTON NUCLEAR MAGNETIC RESONANCE; RELIABILITY; STRUCTURAL GENOMICS;

ALGORITHMS; AMINO ACID SEQUENCE; DATABASES, PROTEIN; HUMANS; MOLECULAR SEQUENCE DATA; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PROTEIN STRUCTURE, SECONDARY; PROTEINS; REPRODUCIBILITY OF RESULTS;

EID: 84892937420     PISSN: 09252738     EISSN: 15735001     Source Type: Journal    
DOI: 10.1007/s10858-013-9779-x     Document Type: Article

References (30)

1. Aeschbacher T, Schmidt E, Blatter M, Maris C, Duss O, Allain FH-T, Güntert P, Schubert M (2013) Automated and assisted RNA resonance assignment using NMR chemical shift statistics. Nucleic Acids Res. doi:10.1093/nar/gkt665
2. Altieri AS, Byrd RA (2004) Automation of NMR structure determination of proteins. Curr Opin Struct Biol 14:547-553
3. Baran MC, Huang YJ, Moseley HNB, Montelione GT (2004) Automated analysis of protein NMR assignments and structures. Chem Rev 104:3541-3555
4. Bartels C, Xia TH, Billeter M, Güntert P, Wüthrich K (1995) The program XEASY for computer-supported NMR spectral analysis of biological macromolecules. J Biomol NMR 6:1-10
5. Bartels C, Billeter M, Güntert P, Wüthrich K (1996) Automated sequence-specific NMR assignment of homologous proteins using the program GARANT. J Biomol NMR 7:207-213
6. Bartels C, Güntert P, Billeter M, Wüthrich K (1997) GARANT - a general algorithm for resonance assignment of multidimensional nuclear magnetic resonance spectra. J Comput Chem 18:139-149
7. Bhattacharya A, Tejero R, Montelione GT (2007) Evaluating protein structures determined by structural genomics consortia. Proteins 66:778-795
8. Folmer RHA, Hilbers CW, Konings RNH, Nilges M (1997) Floating stereospecific assignment revisited: application to an 18 kDa protein and comparison with J-coupling data. J Biomol NMR 9:245-258
9. Guerry P, Herrmann T (2011) Advances in automated NMR protein structure determination. Q Rev Biophys 44:257-309
10. Güntert P (1998) Structure calculation of biological macromolecules from NMR data. Q Rev Biophys 31:145-237
11. Güntert P (2009) Automated structure determination from NMR spectra. Eur Biophys J 38:129-143
12. Güntert P, Braun W, Wüthrich K (1991) Efficient computation of three-dimensional protein structures in solution from nuclear magnetic resonance data using the program DIANA and the supporting programs CALIBA, HABAS and GLOMSA. J Mol Biol 217:517-530
13. Güntert P, Mumenthaler C, Wüthrich K (1997) Torsion angle dynamics for NMR structure calculation with the new program DYANA. J Mol Biol 273:283-298
14. Herrmann T, Güntert P, Wüthrich K (2002a) Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA. J Mol Biol 319:209-227
15. Herrmann T, Güntert P, Wüthrich K (2002b) Protein NMR structure determination with automated NOE-identification in the NOESY spectra using the newsoftwareATNOS. J Biomol NMR24:171-189
16. Ikeya T, Jee J-G, Shigemitsu Y, Hamatsu J, Mishima M, Ito Y, Kainosho M, Güntert P (2011) Exclusively NOESY-based automated NMR assignment and structure determination of proteins. J Biomol NMR 50:137-146
17. Jee J, Güntert P (2003) Influence of the completeness of chemical shift assignments on NMR structures obtained with automated NOE assignment. J Struct Funct Genom 4:179-189
18. Kainosho M, Torizawa T, Iwashita Y, Terauchi T, Ono A, Güntert P (2006) Optimal isotope labelling for NMR protein structure determinations. Nature 440:52-57
19. Koga N, Tatsumi-Koga R, Liu GH, Xiao R, Acton TB, Montelione GT, Baker D (2012) Principles for designing ideal protein structures. Nature 491:222-227
20. Liu GH, Shen Y, Atreya HS, Parish D, Shao Y, Sukumaran DK, Xiao R, Yee A, Lemak A, Bhattacharya A, Acton TA, Arrowsmith CH, Montelione GT, Szyperski T (2005) NMR data collection and analysis protocol for high-throughput protein structure determination. Proc Natl Acad Sci USA 102:10487-10492
21. Liu GOH, Huang YJ, Xiao R, Wang DY, Acton TB, Montelione GT (2010) Solution NMR structure of the ARID domain of human AT-rich interactive domain-containing protein 3A: a human cancer protein interaction network target. Protein Struct Funct Bioinfo 78:2170-2175
22. López-Méndez B, Güntert P (2006) Automated protein structure determination from NMR spectra. J Am Chem Soc 128:13112-13122
23. Malmodin D, Papavoine CHM, Billeter M (2003) Fully automated sequence-specific resonance assignments of heteronuclear protein spectra. J Biomol NMR 27:69-79
24. Rosato A, Bagaria A, Baker D, Bardiaux B, Cavalli A, Doreleijers JF, Giachetti A, Guerry P, Güntert P, Herrmann T, Huang YJ, Jonker HRA, Mao B, Malliavin TE, Montelione GT, Nilges M, Raman S, van der Schot G, Vranken WF, Vuister GW, Bonvin AMJJ (2009) CASD-NMR: critical assessment of automated structure determination by NMR. Nat Methods 6:625-626
25. Rosato A, Aramini JM, Arrowsmith C, Bagaria A, Baker D, Cavalli A, Doreleijers JF, Eletsky A, Giachetti A, Guerry P, Gutmanas A, Güntert P, He YF, Herrmann T, Huang YPJ, Jaravine V, Jonker HRA, Kennedy MA, Lange OF, Liu GH, Malliavin TE, Mani R, Mao BC, Montelione GT, Nilges M, Rossi P, van der Schot G, Schwalbe H, Szyperski TA, Vendruscolo M, Vernon R, Vranken WF, de Vries S, Vuister GW, Wu B, Yang YH, Bonvin AMJJ (2012) Blind testing of routine, fully automated determination of protein structures from NMR data. Structure 20: 227-236
26. Schmidt E, Güntert P (2012) A new algorithm for reliable and general NMR resonance assignment. J Am Chem Soc 134:12817-12829
27. Schmidt E, Gath J, Habenstein B, Ravotti F, Székely K, Huber M, Buchner L, Böckmann A, Meier BH, Güntert P (2013) Automated solid-state NMR resonance assignment of protein microcrystals and amyloids. J Biomol NMR 56:243-254
28. Shen Y, Delaglio F, Cornilescu G, Bax A (2009) TALOS+: a hybrid method for predicting protein backbone torsion angles from NMR chemical shifts. J Biomol NMR 44:213-223
29. Ulrich EL, Akutsu H, Doreleijers JF, Harano Y, Ioannidis YE, Lin J, Livny M, Mading S, Maziuk D, Miller Z, Nakatani E, Schulte CF, Tolmie DE, Wenger RK, Yao HY, Markley JL (2008) BioMagResBank. Nucleic Acids Res 36:D402-D408
30. Williamson MP, Craven CJ (2009) Automated protein structure calculation from NMR data. J Biomol NMR 43:131-143