A probabilistic approach for validating protein NMR chemical shift assignments

Journal of Biomolecular NMR

Volumn 47, Issue 2, 2010, Pages 85-99

  Wang, Bowei ^a   Wang, Yunjun ^b   Wishart, David S ^c  

^a Shanghai American School   (China)

^b Mesolight LLC   (United States)

^c UNIVERSITY OF ALBERTA   (Canada)

Author keywords

BioMagResBank (BMRB); Chemical shift assignment; Chemical shift assignment validation; NMR; Protein chemical shift

Indexed keywords

ARTICLE; CLINICAL PROTOCOL; COMPARATIVE STUDY; METHODOLOGY; PRIORITY JOURNAL; PROTEIN SECONDARY STRUCTURE; PROTON NUCLEAR MAGNETIC RESONANCE; VALIDATION STUDY; WASTE;

AMINO ACID SEQUENCE; MODELS, STATISTICAL; MOLECULAR SEQUENCE DATA; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PROTEINS; REPRODUCIBILITY OF RESULTS; SOFTWARE; USER-COMPUTER INTERFACE;

EID: 77954688894     PISSN: 09252738     EISSN: 15735001     Source Type: Journal    
DOI: 10.1007/s10858-010-9407-y     Document Type: Article

References (22)

1. de Dios AC, Pearson JG, Oldfield E (1993) Secondary and tertiary structural effects on protein NMR chemical shifts: an ab initio approach. Science 260:1491-1496
2. Ginzinger SW, Gerick F, Coles M, Heun V (2007) CheckShift: automatic correction of inconsistent chemical shift referencing. J Biomol NMR 39:223-227
3. Gronenborn AM, Clore GM (1994) Identification of N-terminal helix capping boxes by means of 13C chemical shifts. J Biomol NMR 4:455-458
4. Kohlhoff KJ, Robustelli P, Cavalli A, Salvatella X, Vendruscolo M (2009) Fast and accurate predictions of protein NMR chemical shifts from interatomic distances. J Am Chem Soc 131:13894-13895
5. Metzler WJ, Constantine KL, Friedrichs MS, Bell AJ, Ernst EG, Lavoie TB, Mueller L (1993) Characterization of the threedimensional solution structure of human profiling: 1H, 13C and 15 N NMR assignments and global folding pattern. Biochemistry 32:13818-13829
6. Moseley HN, Sahota G, Montelione GT (2004) Assigment validation software suite for the evaluation and presentatio of protein resonance assignment data. J Biomol NMR 28:341-355
7. Neal S, Nip AM, Zhang H, Wishart DS (2003) Rapid and accurate calculation of protein 1H, 13C and 15 N chemical shifts. J Biomol NMR 26:215-240
8. Seavey BR, Farr EA, Westler WM, Markley JL (1991) A relational database for sequence-specific protein NMR data. J Biomol NMR 1:217-236
9. Shen Y, Lange O, Delaglio F, Rossi P, Aramini JM, Liu G, Eletsky A, Wu Y, Sugnarapu KK, Ignatchenko A, Arrowsmith CH, Syperski 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
10. Spera S, Bax A (1991) Empirical correlation between protein backbone conformatio and Ca and Cb 13C nuclear magnetic resonance chemical shifts. J Am Chem Soc 113:5490-5492
11. 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 H, Markley JL (2008) BioMagResBank. Nucleic Acids Res 36:D402-D408
12. Wang Y, Jardetzky O (2002a) Investigation of the neighboring residue effects on protein chemical shifts. J Am Chem Soc 124:14075-14084
13. Wang Y, Jardetzky O (2002b) Probability-based protein secondary structure identification using combined NMR chemical-shift data. Protein Sci 11:852-861
14. Wang Y, Jardetzky O (2004) Predicting 15 N chemical shifts in proteins using the preceding residue-specific individual shielding surfaces from phi, psi i-1 and chi 1 torsion angles. J Biomol NMR 28:327-340
15. Wang L, Markley JL (2009) Empirical correlation between protein backbone 15 N and 13C secondary chemical shifts and its application to nitrogen chemical shift re-referencing. J Biomol NMR 44:95-99
16. 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
17. Wishart DS, Nip AM (1998) Protein chemical shift analysis: a practical guide. Biochem Cell Biol 76:153-163
18. Wishart DS, Sykes BD (1994) The 13C chemical-shift index: a simple method for the identification of protein secondary structure using 13C chemical-shift data. J Biomol NMR 4:171-180
19. Wishart DS, Sykes BD, Richards FM (1991) Relationship between nuclear magnetic resonance chemical shift and protein secondary structure. J Mol Biol 222:311-333
20. 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
21. Xu XP, Case DA (2001) Automated prediction of 15 N, 13Callpha, 13Cbeta and 13C' chemical shifts in proteins using a density functional database. J Biomol NMR 21:321-333
22. Zhang H, Neal S, Wishart DS (2003) RefDB: a database of uniformly referenced protein chemical shifts. J Biomol NMR 25:173-195