Speeding up sequence specific assignment of IDPs

Journal of Biomolecular NMR

Volumn 53, Issue 4, 2012, Pages 293-301

  Bermel, Wolfgang ^a   Bertini, Ivano ^b   Felli, Isabella C ^b   Gonnelli, Leonardo ^b   Koźmiński, Wiktor ^c   Piai, Alessandro ^b   Pierattelli, Roberta ^b   Stanek, Jan ^c  

^a BRUKER BIOSPIN GMBH   (Germany)

^b UNIVERSITY OF FLORENCE   (Italy)

^c UNIVERSITY OF WARSAW   (Poland)

Author keywords

13C detection; Backbone assignment; Intrinsically disordered proteins; Multidimensional NMR experiment; Non uniform sampling; Spin system identification

Indexed keywords

ALPHA SYNUCLEIN; PROTON;

AMINO ACID SEQUENCE; ARTICLE; CARBON NUCLEAR MAGNETIC RESONANCE; POLARIZATION; PRIORITY JOURNAL; PROTEIN PROCESSING; PROTON NUCLEAR MAGNETIC RESONANCE;

ALPHA-SYNUCLEIN; CARBON ISOTOPES; HUMANS; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PROTEIN CONFORMATION; PROTEINS;

EID: 84865108267     PISSN: 09252738     EISSN: 15735001     Source Type: Journal    
DOI: 10.1007/s10858-012-9639-0     Document Type: Article

References (58)

1. HS Atreya T Szyperski 2005 Rapid NMR data collection Methods Enzymol 394 78 108 10.1016/S0076-6879(05)94004-4 (Pubitemid 40460913)
2. 13C direct detection experiments on the paramagnetic oxidized monomeric copper, zinc superoxide dismutase J Am Chem Soc 125 16423 16429 10.1021/ja037676p (Pubitemid 38020667)
3. 13C direct detection experiments, including extension to the third dimension, to perform the complete assignment of proteins J Magn Reson 178 56 64 2006JMagR.178...56B 10.1016/j.jmr.2005.08.011 (Pubitemid 41774011)
4. W Bermel I Bertini IC Felli Y-M Lee C Luchinat R Pierattelli 2006 Protonless NMR experiments for sequence-specific assignment of backbone nuclei in unfolded proteins J Am Chem Soc 128 3918 3919 10.1021/ja0582206
5. 13C-detected protonless NMR spectroscopy of proteins in solution Progr NMR Spectrosc 48 25 45 10.1016/j.pnmrs.2005.09.002 (Pubitemid 44508624)
6. 13C direct-detection biomolecular NMR Concepts Magn Reson 32A 183 200 10.1002/cmr.a.20109
7. W Bermel I Bertini V Csizmok IC Felli R Pierattelli P Tompa 2009 H-start for exclusively heteronuclear NMR spectroscopy: the case of intrinsically disordered proteins J Magn Reson 198 275 281 2009JMagR.198..275B 10.1016/j.jmr.2009.02.012
8. 13C direct detection NMR experiments J Am Chem Soc 131 15339 15345 10.1021/ja9058525
9. W Bermel I Bertini IC Felli R Peruzzini R Pierattelli 2010 Exclusively heteronuclear NMR experiments to obtain structural and dynamic information on proteins ChemPhysChem 11 689 695 10.1002/cphc.200900772
10. 13C direct-detection biomolecular NMR spectroscopy in living cells Angew Chem Int Ed 50 1 4 10.1002/anie.201006633
11. I Bertini IC Felli L Gonnelli MV Vasantha Kumar R Pierattelli 2011 High-resolution characterization of intrinsic disorder in proteins ChemBioChem 12 2347 2352 10.1002/cbic.201100406
12. J-M Boehlen G Bodenhausen 1993 Experimental aspects of chirp NMR spectroscopy J Magn Reson, Ser A 102 293 301 10.1006/jmra.1993.1107
13. V Csizmok IC Felli P Tompa L Banci I Bertini 2008 Structural and dynamic characterization of intrinsically disordered human securing by NMR J Am Chem Soc 130 16873 16879 10.1021/ja805510b
14. M Deschamps ID Campbell 2006 Cooling overall spin temperature: protein NMR experiments optimized for longitudinal relaxation effects J Magn Reson 178 206 211 2006JMagR.178..206D 10.1016/j.jmr.2005.09.011 (Pubitemid 43107928)
15. AK Dunker JD Lawson CJ Brown RM Williams P Romero JS Oh CM Ratliff KW Hipps J Ausio MS Nissen R Reeves C Kang CR Kissinger RW Bailey MD Griswold W Chiu EC Garner 2001 Intrinsically disordered protein J Mol Graph Model 19 26 59 10.1016/S1093-3263(00)00138-8 (Pubitemid 32411501)
16. HJ Dyson PE Wright 2004 Unfolded proteins and protein folding studied by NMR Chem Rev 104 3607 3622 10.1021/cr030403s
17. HJ Dyson PE Wright 2005 Intrinsically unstructured proteins and their functions Nat Rev Mol Cell Biol 6 197 208 10.1038/nrm1589 (Pubitemid 40314921)
18. D Eliezer 2009 Biophysical characterization of intrinsically disordered proteins Curr Opin Struct Biol 19 23 30 10.1016/j.sbi.2008.12.004
19. L Emsley G Bodenhausen 1992 Optimization of shaped selective pulses for NMR using a quaternion description of their overall propagators J Magn Reson 97 135 148
20. 13C direct detection NMR. In: McGreevy KS, Parigi G (eds) Bertini I, NMR of biomolecules. Wiley-Blackwell, London, pp 433-442
21. Goddard TD, Kneller DG (2000) SPARKY 3. University of Califofnia, San Francisco
22. S Hiller F Fiorito K Wüthrich G Wider 2005 Automated projection spectroscopy (APSY) Proc Natl Acad Sci USA 102 10876 10881 2005PNAS..10210876H 10.1073/pnas.0504818102 (Pubitemid 41105960)
23. ST Hsu CW Bertoncini CM Dobson 2009 Use of protonless NMR spectroscopy to alleviate the loss of information resulting from exchange-broadening J Am Chem Soc 131 7222 7223 10.1021/ja902307q
24. K Hu B Vögeli GM Clore 2007 Spin-state selective carbon-detected HNCO with TROSY optimization in all dimensions and double echo-antiecho sensitivity enhancement in both indirect dimensions J Am Chem Soc 129 5484 5491 10.1021/ja067981l (Pubitemid 46697636)
25. C Huang G Ren H Zhou C Wang 2005 A new method for purification of recombinant human alpha-synuclein in Escherichia coli Protein Expr Purif 42 173 177 10.1016/j.pep.2005.02.014 (Pubitemid 40793408)
26. VA Jaravine AV Zhuravleva P Permi I Ibraghimov VY Orekhov 2008 Hyperdimensional NMR spectroscopy with nonlinear sampling J Am Chem Soc 130 3927 3936 10.1021/ja077282o (Pubitemid 351429859)
27. K Kazimierczuk A Zawadzka W Koźmiński I Zhukov 2006 Random sampling of evolution time space and Fourier transform processing J Biomol NMR 36 157 168 10.1007/s10858-006-9077-y (Pubitemid 44740879)
28. K Kazimierczuk A Zawadzka W Koźmiński I Zhukov 2007 Lineshapes and artifacts in multidimensional Fourier transform of arbitrary sampled NMR data sets J Magn Reson 188 344 356 2007JMagR.188..344K 10.1016/j.jmr.2007.08.005 (Pubitemid 47562815)
29. K Kazimierczuk A Zawadzka W Koźmiński 2008 Optimization of random time domain sampling in multidimensional NMR J Magn Reson 192 123 130 2008JMagR.192..123K 10.1016/j.jmr.2008.02.003 (Pubitemid 351609413)
30. K Kazimierczuk A Zawadzka W Koźmiński 2009 Narrow peaks and high dimensionalities: exploiting the advantages of random sampling J Magn Reson 197 219 228 2009JMagR.197..219K 10.1016/j.jmr.2009.01.003
31. K Kazimierczuk J Stanek A Zawadzka-Kazimierczuk W Koźmiński 2010 Random sampling in multidimensional NMR spectroscopy Prog NMR Spectrosc 57 420 434 10.1016/j.pnmrs.2010.07.002
32. K Kazimierczuk M Misiak J Stanek A Zawadzka-Kazimierczuk W Koźmiński 2012 Generalized Fourier transform for non-uniform sampled data Top Curr Chem 316 79 124 10.1007/128-2011-186
33. Keller RLJ (2004) The computer aided resonance assignment tutorial. Cantina Verag, Goldau
34. M Kjaergaard FM Poulsen 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 10.1007/s10858-011-9508-2
35. M Kjaergaard S Brander FM Poulsen 2011 Random coil chemical shift for intrinsically disordered proteins: effects of temperature and pH J Biomol NMR 49 139 149 10.1007/s10858-011-9472-x
36. K Knoblich S Whittaker C Ludwig P Michiels T Jiang B Schafflhausen U Günther 2009 Backbone assignment of the N-terminal polyomavirus large T antigen Biomol NMR Assign 3 119 123 10.1007/s12104-009-9155-7
37. E Lescop P Schanda B Brutscher 2007 A set of BEST triple resonance experiments for time-optimized protein resonance assignment J Magn Reson 187 163 169 2007JMagR.187..163L 10.1016/j.jmr.2007.04.002 (Pubitemid 46898871)
38. D Malmodin M Billeter 2005 Multiway decomposition of NMR Spectra with coupled evolution periods J Am Chem Soc 127 13486 13487 10.1021/ja0545822 (Pubitemid 41401187)
39. T Mittag J Forman-Kay 2007 Atomic-level characterization of disordered protein ensembles Curr Opin Struct Biol 17 3 14 10.1016/j.sbi.2007.01.009 (Pubitemid 46240819)
40. RL Narayanan HN Duerr S Bilbow J Biernat E Mendelkow M Zweckstetter 2010 Automatic assignment of the intrinsically disordered protein Tau with 441-residues J Am Chem Soc 132 11906 11907 10.1021/ja105657f
41. 13C-detected experiments for backbone assignment of unstructured proteins with a very low signal dispersion J Biomol NMR 50 1 11 10.1007/s10858-011-9496-2
42. 1H chemical shift determination into 13C-direct detected spectroscopy of intrinsically disordered proteins in solution J Magn Reson 200 354 358 2009JMagR.200..354O 10.1016/j.jmr.2009.07.014
43. 13C-detection for carbonyl relaxation studies of protein dynamics J Magn Reson 193 226 232 2008JMagR.193..226P 10.1016/j.jmr.2008.05.003
44. Y Pérez M Gairi M Pons P Bernadò 2009 Structural characterization of the natively unfolded N-terminal domain of human c-Src kinase: insights into the role of phosphorylation of the unique domain J Mol Biol 391 136 148 10.1016/j.jmb.2009.06.018
45. 1H relaxation optimization in TROSY NMR spectroscopy J Am Chem Soc 124 12898 12902 10.1021/ja027149q (Pubitemid 35216013)
46. P Schanda B Brutscher 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 10.1021/ja051306e (Pubitemid 40799646)
47. P Schanda H Van Melckebeke B Brutscher 2006 Speeding up three-dimensional protein NMR experiments to a few minutes J Am Chem Soc 128 9042 9043 10.1021/ja062025p (Pubitemid 44078980)
48. Z Serber C Richter D Moskau J-M Boehlen T Gerfin D Marek M Haeberli L Baselgia F Laukien AS Stern JC Hoch V Dötsch 2000 New carbon-detected protein NMR experiments using cryoprobes J Am Chem Soc 122 3554 3555 10.1021/ja991371m (Pubitemid 30211144)
49. AJ Shaka J Keeler R Freeman 1983 Evaluation of a new broadband decoupling sequence: WALTZ-16 J Magn Reson 53 313 340
50. AJ Shaka PB Barker R Freeman 1985 Computer-optimized decoupling scheme for wideband applications and low-level operation J Magn Reson 64 547 552
51. 13C direct detection NMR methods J Biomol NMR 30 175 179 10.1023/B:JNMR.0000048855.35771.11
52. J Stanek R Augustyniak W Koźmiński 2012 Suppression of sampling artefacts in high-resolution four-dimensional NMR spectra using signal separation algorithm J Magn Reson 214 91 102 2012JMagR.214...91S 10.1016/j.jmr.2011.10.009
53. P Tompa 2002 Intrinsically unstructured proteins Trends Biochem Sci 27 527 533 10.1016/S0968-0004(02)02169-2 (Pubitemid 35279598)
54. Tompa P (2009) Structure and function of intrinsically disordered proteins. Taylor and Francis Group, Boca Raton
55. VN Uversky JR Gillespie AL Fink 2000 Why are "natively unfolded" proteins unstructured under physiologic conditions? Proteins Struct Funct Genet 41 415 427 10.1002/1097-0134(20001115)41:3<415::AID- PROT130>3.0.CO;2-7
56. PE Wright HJ Dyson 1999 Intrinsically unstructured proteins: re-assessing the protein structure-function paradigm J Mol Biol 293 321 331 10.1006/jmbi.1999.3110 (Pubitemid 29516173)
57. A Zawadzka-Kazimierczuk W Koźmiński H Š anderová L Krásny 2012 High dimensional and high resolution pulse sequences for backbone resonance assignment of intrinsically disordered proteins J Biomol NMR 52 329 337 10.1007/s10858-012-9613-x
58. H Zhang S Neal DS Wishart 2003 RefDB: a database of uniformly referenced protein chemical shifts J Biomol NMR 25 173 195 10.1023/A:1022836027055 (Pubitemid 36410583)