Automated NMR structure determination of stereo-array isotope labeled ubiquitin from minimal sets of spectra using the SAIL-FLYA system
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Baran MC, Huang YJ, Moseley HNB, Montelione GT (2004) Automated analysis of protein NMR assignments and structures. Chem Rev 104:3541–3555
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
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
Billeter M, Wagner G, Wüthrich K (2008) Solution NMR structure determination of proteins revisited. J Biomol NMR 42:155–158
Bowie JU, Lüthy R, Eisenberg D (1991) A method to identify protein sequences that fold into a known 3-dimensional structure. Science 253:164–170
Brünger AT (1992) Free R value: a novel statistical quantity for assessing the accuracy of crystal structures. Nature 355:472–475
Cornell WD, Cieplak P, Bayly CI, Gould IR, Merz KM, Ferguson DM, Spellmeyer DC, Fox T, Caldwell JW, Kollman PA (1995) A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J Am Chem Soc 117:5179–5197
Cornilescu G, Delaglio F, Bax A (1999) Protein backbone angle restraints from searching a database for chemical shift and sequence homology. J Biomol NMR 13:289–302
Delaglio F, Grzesiek S, Vuister GW, Zhu G, Pfeifer J, Bax A (1995) NMRPipe—a multidimensional spectral processing system based on Unix pipes. J Biomol NMR 6:277–293
Gronwald W, Kalbitzer HR (2004) Automated structure determination of proteins by NMR spectroscopy. Prog Nucl Magn Reson Spectrosc 44:33–96
Güntert P (2003) Automated NMR protein structure calculation. Prog Nucl Magn Reson Spectrosc 43:105–125
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
Herrmann T, Güntert P, Wüthrich K (2002) 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
Hiller S, Fiorito F, Wüthrich K, Wider G (2005) Automated projection spectroscopy (APSY). Proc Natl Acad Sci USA 102:10876–10881
Ikeya T, Terauchi T, Güntert P, Kainosho M (2006) Evaluation of stereo-array isotope labeling (SAIL) patterns for automated structural analysis of proteins with CYANA. Magn Reson Chem 44:S152–S157
Johnson BA (2004) Using NMRView to visualize and analyze the NMR spectra of macromolecules. Meth Mol Biol 278:313–352
Johnson BA, Blevins RA (1994) NMR view—a computer program for the visualization and analysis of NMR data. J Biomol NMR 4:603–614
Kainosho M, Torizawa T, Iwashita Y, Terauchi T, Ono AM, Güntert P (2006) Optimal isotope labelling for NMR protein structure determinations. Nature 440:52–57
Koradi R, Billeter M, Wüthrich K (1996) MOLMOL: a program for display and analysis of macromolecular structures. J Mol Graph 14:51–55
Koradi R, Billeter M, Güntert P (2000) Point-centered domain decomposition for parallel molecular dynamics simulation. Comput Phys Commun 124:139–147
Kraulis PJ (1989) ANSIG: a program for the assignment of protein 1H 2D NMR spectra by interactive computer graphics. J Magn Reson 84:627–633
Kraulis PJ, Domaille PJ, Campbell-Burk SL, Van Aken T, Laue ED (1994) Solution structure and dynamics of Ras p21-GDP determined by heteronuclear three- and four-dimensional NMR spectroscopy. Biochemistry 33:3515–3531
Kupče E, Freeman R (2008) Hyperdimensional NMR spectroscopy. Prog Nucl Magn Reson Spectrosc 52:22–30
Laskowski RA, Rullmann JAC, MacArthur MW, Kaptein R, Thornton JM (1996) AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR. J Biomol NMR 8:477–486
Linge JP, O’Donoghue SI, Nilges M (2001) Automated assignment of ambiguous nuclear overhauser effects with ARIA. Methods Enzymol 339:71–90
López-Méndez B, Güntert P (2006) Automated protein structure determination from NMR spectra. J Am Chem Soc 128:13112–13122
Luan T, Jaravine V, Yee A, Arrowsmith CH, Orekhov VY (2005) Optimization of resolution and sensitivity of 4D NOESY using multi-dimensional decomposition. J Biomol NMR 33:1–14
Luginbühl P, Güntert P, Billeter M, Wüthrich K (1996) The new program OPAL for molecular dynamics simulations and energy refinements of biological macromolecules. J Biomol NMR 8:136–146
Lüthy R, Bowie JU, Eisenberg D (1992) Assessment of protein models with 3-dimensional profiles. Nature 356:83–85
Malmodin D, Billeter M (2005) High-throughput analysis of protein NMR spectra. Prog Nucl Magn Reson Spectrosc 46:109–129
Malmodin D, Papavoine CHM, Billeter M (2003) Fully automated sequence-specific resonance assignments of heteronuclear protein spectra. J Biomol NMR 27:69–79
Morris AL, Macarthur MW, Hutchinson EG, Thornton JM (1992) Stereochemical quality of protein structure coordinates. Proteins 12:345–364
Nabuurs SB, Spronk CAEM, Vuister GW, Vriend G (2006) Traditional biomolecular structure determination by NMR spectroscopy allows for major errors. PLoS Comput Biol 2:71–79
Pfändler P, Bodenhausen G, Meier BU, Ernst RR (1985) Toward automated assignment of nuclear magnetic resonance spectra—pattern recognition in two-dimensional correlation spectra. Anal Chem 57:2510–2516
Sakakibara D, Sasaki A, Ikeya T, Hamatsu J, Hanashima T, Mishima M, Yoshimasu M, Hayashi N, Mikawa T, Wälchli M, Smith BO, Shirakawa M, Güntert P, Ito Y (2009) Protein structure determination in living cells by in-cell NMR spectroscopy. Nature 458:102–105
Scott A, López-Méndez B, Güntert P (2006) Fully automated structure determinations of the Fes SH2 domain using different sets of NMR spectra. Magn Reson Chem 44:S83–S88
Spronk C, Nabuurs SB, Krieger E, Vriend G, Vuister GW (2004) Validation of protein structures derived by NMR spectroscopy. Prog Nucl Magn Reson Spectrosc 45:315–337
Szyperski T, Atreya HS (2006) Principles and applications of GFT projection NMR spectroscopy. Magn Reson Chem 44:S51–S60
Takeda M, Ikeya T, Güntert P, Kainosho M (2007) Automated structure determination of proteins with the SAIL-FLYA NMR method. Nat Protoc 2:2896–2902
Takeda M, Sugimori N, Torizawa T, Terauchi T, Ono AM, Yagi H, Yamaguchi Y, Kato K, Ikeya T, Jee J, Güntert P, Aceti DJ, Markley JL, Kainosho M (2008) Structure of the putative 32 kDa myrosinase-binding protein from Arabidopsis (At3g16450.1) determined by SAIL-NMR. FEBS J 275:5873–5884
Terauchi T, Kobayashi K, Okuma K, Oba M, Nishiyama K, Kainosho M (2008) Stereoselective synthesis of triply isotope-labeled Ser, Cys, and Ala: amino acids for stereoarray isotope labeling technology. Org Lett 10:2785–2787
Torizawa T, Shimizu M, Taoka M, Miyano H, Kainosho M (2004) Efficient production of isotopically labeled proteins by cell-free synthesis: a practical protocol. J Biomol NMR 30:311–325
Torizawa T, Ono AM, Terauchi T, Kainosho M (2005) NMR assignment methods for the aromatic ring resonances of phenylalanine and tyrosine residues in proteins. J Am Chem Soc 127:12620–12626
Williamson MP, Craven CJ (2009) Automated protein structure calculation from NMR data. J Biomol NMR 43:131–143
Wüthrich K (1986) NMR of proteins and nucleic acids. Wiley, New York