Chemical shift prediction for denatured proteins

Journal of Biomolecular NMR

Volumn 55, Issue 2, 2013, Pages 201-209

  Prestegard, James H ^a   Sahu, Sarata C ^a   Nkari, Wendy K ^a   Morris, Laura C ^a   Live, David ^a   Gruta, Christian ^a  

^a NONE

Author keywords

Denatured proteins; Disordered proteins; NMR; Resonance assignments; Sparse labeling

Indexed keywords

AMINO ACID; DENATURED PROTEIN; PENTAPEPTIDE; PROTEIN; UNCLASSIFIED DRUG;

ARTICLE; NUCLEAR MAGNETIC RESONANCE; PARAMETERS; PREDICTION; PRIORITY JOURNAL; PROTEIN DENATURATION; PROTEIN STRUCTURE;

ALANINE; HYDROGEN-ION CONCENTRATION; MODELS, MOLECULAR; NITROGEN ISOTOPES; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PROGRAMMING LANGUAGES; PROTEIN DENATURATION; PROTEINS; UBIQUITIN; UREA;

EID: 84879549760     PISSN: 09252738     EISSN: 15735001     Source Type: Journal    
DOI: 10.1007/s10858-012-9702-x     Document Type: Article

References (26)

1. Bennion BJ, Daggett V (2003) The molecular basis for the chemical denaturation of proteins by urea. Proc Natl Acad Sci USA 100:5142-5147
2. Camilloni C, De Simone A, Vranken WF, Vendruscolo M (2012) Determination of secondary structure populations in disordered states of proteins using nuclear magnetic resonance chemical shifts. Biochemistry 51:2224-2231
3. De Simone A, Cavalli A, Hsu STD, Vranken W, Vendruscolo M (2009) Accurate random coil chemical shifts from an analysis of loop regions in native states of proteins. J Am Chem Soc 131:16332
4. Dutta A, Saxena K, Schwalbe H, Klein-Seetharaman J (2012) Isotope labeling in mammalian cells. In: Shekhtman A, Burz DS (eds) Protein NMR techniques. Methods in molecular biology, vol 831, 3 edn. Humana Press, Totowa, NJ, pp 55-69
5. Dyson HJ, Wright PE (2005) Intrinsically unstructured proteins and their functions. Nat Rev Mol Cell Biol 6:197-208
6. 15N labeled proteins. J Biomol NMR 38:213-219
7. Gossert AD, Hinniger A, Gutmann S, Jahnke W, Strauss A, Fernandez C (2011) A simple protocol for amino acid type selective isotope labeling in insect cells with improved yields and high reproducibility. J Biomol NMR 51:449-456
8. Kemmink J, Creighton TE (1993) Local conformations of peptides representing the entire sequence of bovine pancreatic trypsin-inhibitor and their roles in folding. J Mol Biol 234:861-878
9. Kjaergaard M, Poulsen FM (2011) Sequence correction of random coil chemical shifts: correlation between neighbor correction factors and changes in the Ramachandran distribution. J Biomol NMR 50:157-165
10. Lange OF, Rossi P, Sgourakis NG, Song YF, Lee HW, Aramini JM, Ertekin A, Xiao R, Acton TB, Montelione GT, Baker D (2012) Determination of solution structures of proteins up to 40 kDa using CS-Rosetta with sparse NMR data from deuterated samples. Proc Natl Acad Sci USA 109:10873-10878
11. Li WF, Qin M, Tie ZX, Wang W (2011) Effects of solvents on the intrinsic propensity of peptide backbone conformations. Phys Rev E 84:041933
12. Marsh JA, Singh VK, Jia Z, Forman-Kay JD (2006) Sensitivity of secondary structure propensities to sequence differences between alpha- and gamma-synuclein: implications for fibrillation. Protein Sci 15:2795-2804
13. Nkari WK, Prestegard JH (2009) NMR resonance assignments of sparsely labeled proteins: amide proton exchange correlations in native and denatured states. J Am Chem Soc 131:5344-5349
14. Peti W, Smith LJ, Redfield C, Schwalbe H (2001) Chemical shifts in denatured proteins: resonance assignments for denatured ubiquitin and comparisons with other denatured proteins. J Biomol NMR 19:153-165
15. Raman S, Lange OF, Rossi P, Tyka M, Wang X, Aramini J, Liu GH, Ramelot TA, Eletsky A, Szyperski T, Kennedy MA, Prestegard J, Montelione GT, Baker D (2010) NMR structure determination for larger proteins using backbone-only data. Science 327:1014-1018
16. Rezaei-Ghaleh N, Blackledge M, Zweckstetter M (2012) Intrinsically disordered proteins: from sequence and conformational properties toward drug discovery. ChemBioChem 13:930-950
17. Schwarzinger S, Kroon GJ, Foss TR, Chung J, Wright PE, Dyson HJ (2001) Sequence-dependent correction of random coil NMR chemical shifts. J Am Chem Soc 123:2970-2978
18. 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
19. Shi ZS, Chen K, Liu ZG, Kallenbach NR (2006) Conformation of the backbone in unfolded proteins. Chem Rev 106:1877-1897
20. 15N background for NMR studies of large proteins. J Biomol NMR 38:89-98
21. Tamiola K, Acar B, Mulder FA (2010) Sequence-specific random coil chemical shifts of intrinsically disordered proteins. J Am Chem Soc 132:18000-18003
22. Ting D, Wang GL, Shapovalov M, Mitra R, Jordan MI, Dunbrack RL (2010) Neighbor-dependent Ramachandran probability distributions of amino acids developed from a hierarchical dirichlet process model. PLoS Comput Biol 6:e1000763
23. Wang Y, Jardetzky O (2002a) Investigation of the neighboring residue effects on protein chemical shifts. J Am Chem Soc 124:14075-14084
24. Wang Y, Jardetzky O (2002b) Probability-based protein secondary structure identification using combined NMR chemical-shift data. Protein Sci 11:852-861
25. 15N random coil NMR chemical shifts of the common amino acids. I. Investigations of nearest-neighbor effects. J Biomol NMR 5:67-81
26. Wishart DS, Bigam CG, Yao J, Abildgaard F, Dyson HJ, Oldfield E, Markley JL, Sykes BD (1995b) H-1, C-13 AND N-15 chemical-shift referencing in biomolecular NMR. J Biomol NMR 6:135-140