Accurate relaxation parameters for large proteins

Journal of Magnetic Resonance

Volumn 167, Issue 1, 2004, Pages 107-113

  Gutmanas, Aleksandras ^a   Tu, Luan ^a   Orekhov, Vladislav Yu ^a   Billeter, Martin ^a  

^a UNIVERSITY OF GOTHENBURG   (Sweden)

Author keywords

Dynamics; Maltose binding protein; MUNIN; NMR; Three way decomposition

Indexed keywords

ALGORITHMS; DATA REDUCTION; DECOMPOSITION; GRAPHICAL USER INTERFACES; MAGNETIC RELAXATION; MALTOSE; NUCLEAR MAGNETIC RESONANCE; VECTORS;

MALTOSE BINDING PROTEIN; MUNIN; THREE-WAY DECOMPOSITION;

PROTEINS;

CARRIER PROTEIN; MALTOSE BINDING PROTEIN; MALTOSE-BINDING PROTEIN; NITROGEN;

ALGORITHM; ARTICLE; CHEMICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; EVALUATION; METHODOLOGY; MOTION; NUCLEAR MAGNETIC RESONANCE; QUALITY CONTROL; VALIDATION STUDY;

ALGORITHMS; CARRIER PROTEINS; MODELS, CHEMICAL; MODELS, MOLECULAR; MOTION; NITROGEN ISOTOPES; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; QUALITY CONTROL;

EID: 1242332383     PISSN: 10907807     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmr.2003.12.002     Document Type: Article

References (30)

1. Korzhnev D.M., Billeter M., Arseniev A.S., Orekhov V.Y. NMR studies of Brownian tumbling and internal motions in proteins. Prog. Nucl. Magn. Res. Spectrosc. 38:2001;197-266.
2. Akke M. NMR methods for characterizing microsecond to millisecond dynamics in recognition and catalysis. Curr. Opin. Struct. Biol. 12:2002;642-647.
3. Ishima R., Torchia D.A. Estimating the time scale of chemical exchange of proteins from measurements of transverse relaxation rates in solution. J. Biomol. NMR. 14:1999;369-372.
4. Millet O., Loria J.P., Kroenke C.D., Pons M., Palmer A.G. The static magnetic field dependence of chemical exchange linebroadening defines the NMR chemical shift time scale. J. Am. Chem. Soc. 122:2000;2867-2877.
5. Tollinger M., Skrynnikov N.R., Mulder F.A., Forman-Kay J.D., Kay L.E. Slow dynamics in folded and unfolded states of an SH3 domain. J. Am. Chem. Soc. 123:2001;11341-11352.
6. Palmer 3rd A.G., Kroenke C.D., Loria J.P. Nuclear magnetic resonance methods for quantifying microsecond-to-millisecond motions in biological macromolecules. Methods Enzymol. 339:2001;204-238.
7. Yang D., Mok Y.K., Forman-Kay J.D., Farrow N.A., Kay L.E. Contributions to protein entropy and heat capacity from bond vector motions measured by NMR spin relaxation. J. Mol. Biol. 272:1997;790-804.
8. Mulder F.A., Hon B., Mittermaier A., Dahlquist F.W., Kay L.E. Slow internal dynamics in proteins: application of NMR relaxation dispersion spectroscopy to methyl groups in a cavity mutant of T4 lysozyme. J. Am. Chem. Soc. 124:2002;1443-1451.
9. Eisenmesser E.Z., Bosco D.A., Akke M., Kern D. Enzyme dynamics during catalysis. Science. 295:2002;1520-1523.
10. Korzhnev D.M., Karlsson B.G., Orekhov V.Y., Billeter M. NMR detection of multiple transitions to low-populated states in azurin. Protein Sci. 12:2003;56-65.
11. Mulder F.A., Mittermaier A., Hon B., Dahlquist F.W., Kay L.E. Studying excited states of proteins by NMR spectroscopy. Nat. Struct. Biol. 8:2001;932-935.
12. 15N relaxation dispersion NMR spectroscopy: application to Asn and Gln residues in a cavity mutant of T4 lysozyme. J. Am. Chem. Soc. 123:2001;967-975.
13. Skrynnikov N.R., Mulder F.A., Hon B., Dahlquist F.W., Kay L.E. Probing slow time scale dynamics at methyl-containing side chains in proteins by relaxation dispersion NMR measurements: application to methionine residues in a cavity mutant of T4 lysozyme. J. Am. Chem. Soc. 123:2001;4556-4566.
14. Tugarinov V., Kay L.E. Side chain assignments of Ile delta 1 methyl groups in high molecular weight proteins: an application to a 46. ns tumbling molecule J. Am. Chem. Soc. 125:2003;5701-5706.
15. Bro R. PARAFAC. Tutorial and applications. Chemometr. Intell. Lab. 38:1997;149-171.
16. Gardner K.H., Zhang X.C., Gehring K., Kay L.E. Solution NMR studies of a 42. kDa Escherichia coli maltose binding protein beta-cyclodextrin complex: chemical shift assignments and analysis J. Am. Chem. Soc. 120:1998;11738-11748.
17. Orekhov V.Y., Ibraghimov I.V., Billeter M. MUNIN: a new approach to multi-dimensional NMR spectra interpretation. J. Biomol. NMR. 20:2001;49-60.
18. Ibraghimov I.V. Application of the three-way decomposition for matrix compression. Numer. Linear Algebra Appl. 9:2002;551-565.
19. Orekhov V.Y., Ibraghimov I.V., Billeter M. Optimizing resolution in multidimensional NMR by three-way decomposition. J. Biomol. NMR. 27:2003;165-173.
20. Damberg C.S., Orekhov V.Y., Billeter M. Automated analysis of large sets of heteronuclear correlation spectra in NMR-based drug discovery. J. Med. Chem. 45:2002;5649-5654.
21. Gutmanas A., Jarvoll P., Orekhov V.Y., Billeter M. Three-way decomposition of a complete 3D (15)N-NOESY-HSQC. J. Biomol. NMR. 24:2002;191-201.
22. Billeter M., Orekhov V.Y. Sloot P.M.A., Abramson D., Bogdanov A.V., Dongarra J.J., Zomaya A.Y., Gorbachev Y.E. Computational Science - ICCS2003. 2003;15-24 Springer, St. Petersburg.
23. Korzhnev D.M., Ibraghimov I.V., Billeter M., Orekhov V.Y. MUNIN: application of three-way decomposition to the analysis of heteronuclear NMR relaxation data. J. Biomol. NMR. 21:2001;263-268.
24. Delaglio F., Grzesiek S., Vuister G.W., Zhu G., Pfeifer J., Bax A. Nmrpipe - a multidimensional spectral processing system based on unix pipes. J. Biomol. NMR. 6:1995;277-293.
25. Press W.H., Teukolsky S.A., Vetterling W.T., Flannery B.P. Numerical Recipes in C. second ed. 1992;Cambridge University Press, Cambridge.
26. Koehl P. Linear prediction spectral analysis of NMR data. Prog. Nucl. Magn. Res. Spectrosc. 34:1999;257-299.
27. Stern A.S., Li K.B., Hoch J.C. Modern spectrum analysis in multidimensional NMR spectroscopy: comparison of linear-prediction extrapolation and maximum-entropy reconstruction. J. Am. Chem. Soc. 124:2002;1982-1993.
28. Denk W., Baumann R., Wagner G. Quantitative-evaluation of cross-peak intensities by projection of two-dimensional noe spectra on a linear-space spanned by a set of reference resonance lines. J. Magn. Reson. 67:1986;386-390.
29. Koradi R., Billeter M., Engeli M., Güntert P., Wüthrich K. Automated peak picking and peak integration in macromolecular NMR spectra using AUTOPSY. J. Magn. Reson. 135:1998;288-297.
30. Orekhov V.Y., Nolde D.E., Golovanov A.P., Korzhnev D.M., Arseniev A.S. Processing of heteronuclear NMR relaxation data with the new software DASHA. Appl. Magn. Reson. 9:1995;581-588.