Automated NMR structure determination of stereo-array isotope labeled ubiquitin from minimal sets of spectra using the SAIL-FLYA system

Teppei Ikeya1,2,3, Mitsuhiro Takeda4,3, Hitoshi Yoshida3, Tsutomu Terauchi3, Jun Goo Jee3, Masatsune Kainosho4,3, Peter Güntert1,2,3
1Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt am Main, Frankfurt am Main, Germany
2Frankfurt Institute for Advanced Studies, Goethe University Frankfurt am Main, Frankfurt am Main, Germany
3Graduate School of Science, Tokyo Metropolitan University, Tokyo, Japan
4Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya, Japan

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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 (2009) Automated structure determination from NMR spectra. Eur Biophys J 38:129–143

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

Hooft RWW, Vriend G, Sander C, Abola EE (1996) Errors in protein structures. Nature 381:272

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

Ponder JW, Case DA (2003) Force fields for protein simulations. Adv Protein Chem 66:27–85

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

Schultze P, Feigon J (1997) Chirality errors in nucleic acid structures. Nature 387:668

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

Sippl MJ (1993) Recognition of errors in 3-dimensional structures of proteins. Proteins 17:355–362

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

Wallner B, Elofsson A (2003) Can correct protein models be identified? Protein Sci 12:1073–1086

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