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SAIL – stereo-array isotope labeling

Published online by Cambridge University Press:  07 April 2010

Masatsune Kainosho*
Affiliation:
Graduate School of Science and Technology, Tokyo Metropolitan University, Tokyo, Japan Graduate School of Science, Nagoya University, Nagoya, Japan Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, Frankfurt am Main, Germany
Peter Güntert
Affiliation:
Graduate School of Science and Technology, Tokyo Metropolitan University, Tokyo, Japan Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, Frankfurt am Main, Germany Frankfurt Institute for Advanced Studies, Goethe University, Frankfurt am Main, Germany
*
*Author for correspondence: Prof. M. Kainosho, Center of Priority Areas, Graduate School of Science and Technology, Tokyo Metropolitan University, 1-1 Minami-ohsawa, Hachioji, Tokyo192-0397, Japan. Tel.: 81-42-677-4873; Fax: 81-42-677-4873; Email: kainosho@nmr.chem.metro-u.ac.jp

Abstract

Optimal stereospecific and regiospecific labeling of proteins with stable isotopes enhances the nuclear magnetic resonance (NMR) method for the determination of the three-dimensional protein structures in solution. Stereo-array isotope labeling (SAIL) offers sharpened lines, spectral simplification without loss of information and the ability to rapidly collect and automatically evaluate the structural restraints required to solve a high-quality solution structure for proteins up to twice as large as before. This review gives an overview of stable isotope labeling methods for NMR spectroscopy with proteins and provides an in-depth treatment of the SAIL technology.

Type
Review Article
Copyright
Copyright © Cambridge University Press 2010

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References

Aberhart, D. J. & Russell, D. J. (1984). Steric course of ketopantoate hydroxymethyltransferase in E. coli. Journal of the American Chemical Society 106, 49024906.CrossRefGoogle Scholar
Aghazadeh, B., Zhu, K., Kubiseski, T. J., Liu, G. A., Pawson, T., Zheng, Y. & Rosen, M. K. (1998). Structure and mutagenesis of the Dbl homology domain. Nature Structural Biology 5, 10981107.CrossRefGoogle ScholarPubMed
Akke, M., Carr, P. A. & Palmer, A. G. (1994). Heteronuclear-correlation NMR spectroscopy with simultaneous isotope filtration, quadrature detection, and sensitivity enhancement using z rotations. Journal of Magnetic Resonance Series B 104, 298302.CrossRefGoogle ScholarPubMed
Arata, Y., Kato, K., Takahashi, H. & Shimada, I. (1994). Nuclear magnetic resonance study of antibodies – a multinuclear approach. Methods in Enzymology 239, 440464.CrossRefGoogle ScholarPubMed
Arnesano, F., Banci, L., Bertini, I., Felli, I. C., Luchinat, C. & Thompsett, A. R. (2003). A strategy for the NMR characterization of type II copper(II) proteins: the case of the copper trafficking protein CopC from Pseudomonas syringae. Journal of the American Chemical Society 125, 72007208.CrossRefGoogle ScholarPubMed
Arnold, L. D., Kalantar, T. H. & Vederas, J. C. (1985). Conversion of serine to stereochemically pure β-substituted α-amino acids via β-lactones. Journal of the American Chemical Society 107, 71057109.CrossRefGoogle Scholar
Arnold, L. D., May, R. G. & Vederas, J. C. (1988). Synthesis of optically pure α-amino acids via salts of α-amino-β-propiolactone. Journal of the American Chemical Society 110, 22372241.CrossRefGoogle Scholar
Arrowsmith, C. H. & Wu, Y. S. (1998). NMR of large (>25 kDa) proteins and protein complexes. Progress in Nuclear Magnetic Resonance Spectroscopy 32, 277286.CrossRefGoogle Scholar
Atreya, H. S. & Chary, K. V. R. (2001). Selective ‘unlabeling’ of amino acids in fractionally 13C labeled proteins: an approach for stereospecific NMR assignments of CH3 groups in Val and Leu residues. Journal of Biomolecular NMR 19, 267272.CrossRefGoogle ScholarPubMed
Axelsson, B. S., Otoole, K. J., Spencer, P. A. & Young, D. W. (1991). A versatile synthesis of stereospecifically labelled D-amino acids and related enzyme inhibitors. Journal of the Chemical Society-Chemical Communications 10851086.CrossRefGoogle Scholar
Bartels, C., Billeter, M., Güntert, P. & Wüthrich, K. (1996). Automated sequence-specific NMR assignment of homologous proteins using the program GARANT. Journal of Biomolecular NMR 7, 207213.CrossRefGoogle ScholarPubMed
Bartels, C., Güntert, P., Billeter, M. & Wüthrich, K. (1997). GARANT – a general algorithm for resonance assignment of multidimensional nuclear magnetic resonance spectra. Journal of Computational Chemistry 18, 139149.3.0.CO;2-H>CrossRefGoogle Scholar
Bax, A., Clore, G. M. & Gronenborn, A. M. (1990). 1H-1H correlation via isotropic mixing of 13C magnetization, a new three-dimensional approach for assigning 1H and 13C spectra of 13C-enriched proteins. Journal of Magnetic Resonance 88, 425431.Google Scholar
Bax, A. & Pochapsky, S. S. (1992). Optimized recording of heteronuclear multidimensional NMR spectra using pulsed field gradients. Journal of Magnetic Resonance 99, 638643.Google Scholar
Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., Shindyalov, I. N. & Bourne, P. E. (2000). The Protein Data Bank. Nucleic Acids Research 28, 235242.CrossRefGoogle ScholarPubMed
Bermel, W., Bertini, I., Duma, L., Felli, I. C., Emsley, L., Pierattelli, R. & Vasos, P. R. (2005). Complete assignment of heteronuclear protein resonances by protonless NMR spectroscopy. Angewandte Chemie – International Edition 44, 30893092.CrossRefGoogle ScholarPubMed
Bertini, I., Duma, L., Felli, I. C., Fey, M., Luchinat, C., Pierattelli, R. & Vasos, P. R. (2004). A heteronuclear direct-detection NMR spectroscopy experiment for protein-backbone assignment. Angewandte Chemie – International Edition 43, 22572259.CrossRefGoogle Scholar
Betton, J. M. (2003). Rapid translation system (RTS): a promising alternative for recombinant protein production. Current Protein & Peptide Science 4, 7380.CrossRefGoogle ScholarPubMed
Beyer, J., Lang-Fugmann, S., Mühlbauer, A. & Steglich, W. (1998). A convenient synthesis of 4-hydroxy[1-13C]benzoic acid and related ring-labelled phenolic compounds. Synthesis-Stuttgart 10471051.CrossRefGoogle Scholar
Brenzel, S., Kurpiers, T. & Mootz, H. D. (2006). Engineering artificially split inteins for applications in protein chemistry: biochemical characterization of the split Ssp DnaB intein and comparison to the split Sce VMA intein. Biochemistry 45, 15711578.CrossRefGoogle Scholar
Burk, M. J. (1991). C2-symmetric bis(phospholanes) and their use in highly enantioselective hydrogenation reactions. Journal of the American Chemical Society 113, 85188519.CrossRefGoogle Scholar
Burk, M. J., Feaster, J. E., Nugent, W. A. & Harlow, R. L. (1993). Preparation and use of C2-symmetric bis(phospholanes): production of α-amino acid derivatives via highly enantioselective hydrogenation reactions. Journal of the American Chemical Society 115, 1012510138.CrossRefGoogle Scholar
Burk, M. J., Kalberg, C. S. & Pizzano, A. (1998). Rh-DuPHOS-catalyzed enantioselective hydrogenation of enol esters. Application to the synthesis of highly enantioenriched α-hydroxy esters and 1,2-diols. Journal of the American Chemical Society 120, 43454353.CrossRefGoogle Scholar
Burz, D. S., Dutta, K., Cowburn, D. & Shekhtman, A. (2006). Mapping structural interactions using in-cell NMR spectroscopy (STINT-NMR). Nature Methods 3, 9193.CrossRefGoogle ScholarPubMed
Busche, A. E., Aranko, A. S., Talebzadeh-Farooji, M., Bernhard, F., Dötsch, V. & Iwai, H. (2009). Segmental isotopic labeling of a central domain in a multidomain protein by protein trans-splicing using only one robust DnaE intein. Angewandte Chemie (English Edition) 48, 61286131.CrossRefGoogle Scholar
Campbell, I. D., Dobson, C. M., Moore, G. R., Perkins, S. J. & Williams, R. J. (1976). Temperature dependent molecular motion of a tyrosine residue of ferrocytochrome C. FEBS Letters 70, 96100.CrossRefGoogle ScholarPubMed
Cavanagh, J., Fairbrother, W. J., Palmer, A. G. III, Skelton, N. J. & Rance, M. (2006). Protein NMR Spectroscopy. Principles and Practice, 2nd edn.San Diego, CA: Academic Press.Google Scholar
Cavanagh, J., Palmer, A. G., Wright, P. E. & Rance, M. (1991). Sensitivity improvement in proton-detected 2-dimensional heteronuclear relay spectroscopy. Journal of Magnetic Resonance 91, 429436.Google Scholar
Chandonia, J. M. & Brenner, S. E. (2006). The impact of structural genomics: expectations and outcomes. Science 311, 347351.CrossRefGoogle ScholarPubMed
Chattopadhyaya, R., Meador, W. E., Means, A. R. & Quiocho, F. A. (1992). Calmodulin structure refined at 1·7 Å resolution. Journal of Molecular Biology 228, 11771192.CrossRefGoogle ScholarPubMed
Chou, J. J., Li, S. P., Klee, C. B. & Bax, A. (2001). Solution structure of Ca2+-calmodulin reveals flexible hand-like properties of its domains. Nature Structural Biology 8, 990997.CrossRefGoogle Scholar
Chrunyk, B. A., Evans, J., Lillquist, J., Young, P. & Wetzel, R. (1993). Inclusion body formation and protein stability in sequence variants of interleukin-1β. Journal of Biological Chemistry 268, 1805318061.CrossRefGoogle Scholar
Clemens, M. J. & Prujin, G. J. (1999). Protein Synthesis in Eukaryotic Cell-Free Systems. New York: Oxford University Press.CrossRefGoogle Scholar
Cornell, W. D., Cieplak, P., Bayly, C. I., Gould, I. R., Merz, K. M., Ferguson, D. M., Spellmeyer, D. C., Fox, T., Caldwell, J. W. & Kollman, P. A. (1995). A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. Journal of the American Chemical Society 117, 51795197.CrossRefGoogle Scholar
Coughlin, P. E., Anderson, F. E., Oliver, E. J., Brown, J. M., Homans, S. W., Pollak, S. & Lustbader, J. W. (1999). Improved resolution and sensitivity of triple-resonance NMR methods for the structural analysis of proteins by use of a backbone-labeling strategy. Journal of the American Chemical Society 121, 1187111874.CrossRefGoogle Scholar
Cowburn, D., Shekhtman, A., Xu, R., Ottesen, J. J. & Muir, T. W. (2004). Segmental isotopic labeling for structural biological applications of NMR. Methods in Molecular Biology 278, 4756.Google ScholarPubMed
Crespi, H. L., Rosenberg, R. M. & Katz, J. J. (1968). Proton magnetic resonance of proteins fully deuterated except for 1H-leucine side chains. Science 161, 795796.CrossRefGoogle ScholarPubMed
Davanloo, P., Rosenberg, A. H., Dunn, J. J. & Studier, F. W. (1984). Cloning and expression of the gene for bacteriophage T7 RNA polymerase. Proceedings of the National Academy of Sciences USA 81, 20352039.CrossRefGoogle ScholarPubMed
Ding, K. & Gronenborn, A. M. (2004). Sensitivity-enhanced IPAP experiments for measuring one-bond 13C′-13Cα and 13Cα-1Hα residual dipolar couplings in proteins. Journal of Magnetic Resonance 167, 253258.CrossRefGoogle ScholarPubMed
Duan, X. Q., Gimble, F. S. & Quiocho, F. A. (1997). Crystal structure of PI-Scel, a homing endonuclease with protein splicing activity. Cell 89, 555564.CrossRefGoogle ScholarPubMed
Edison, A. S., Abildgaard, F., Westler, W. M., Mooberry, E. S. & Markley, J. L. (1994). Practical introduction to theory and implementation of multinuclear, multidimensional nuclear magnetic resonance experiments. Methods in Enzymology 239, 379.CrossRefGoogle ScholarPubMed
Edwards, K. J., Ollis, D. L. & Dixon, N. E. (1997). Crystal structure of cytoplasmic Escherichia coli peptidyl-prolyl isomerase: Evidence for decreased mobility of loops upon complexation. Journal of Molecular Biology 271, 258265.CrossRefGoogle ScholarPubMed
Erlenmeyer, E. (1893). Über die Condensation der Hippursäure mit Phtalsäureanhydrid und mit Benzaldehyd. Justus Liebigs Annalen der Chemie 275, 120.Google Scholar
Ernst, R. R., Bodenhausen, G. & Wokaun, A. (1987). The Principles of Nuclear Magnetic Resonance in One and Two Dimensions. Oxford: Clarendon Press.Google Scholar
Fernández, C., Hilty, C., Wider, G., Güntert, P. & Wüthrich, K. (2004). NMR structure of the integral membrane protein OmpX. Journal of Molecular Biology 336, 12111221.CrossRefGoogle ScholarPubMed
Fesik, S. W. & Zuiderweg, E. R. P. (1988). Heteronuclear 3-dimensional NMR spectroscopy – a strategy for the simplification of homonuclear two-dimensional NMR spectra. Journal of Magnetic Resonance 78, 588593.Google Scholar
Fiaux, J., Bertelsen, E. B., Horwich, A. L. & Wuthrich, K. (2002). NMR analysis of a 900K GroEL-GroES complex. Nature 418, 207211.CrossRefGoogle ScholarPubMed
Folmer, R. H. A., Hilbers, C. W., Konings, R. N. H. & Hallenga, K. (1995). A 13C double-filtered NOESY with strongly reduced artefacts and improved sensitivity. Journal of Biomolecular NMR 5, 427432.CrossRefGoogle ScholarPubMed
Gani, D. & Young, D. W. (1983). Synthesis of l-serine stereospecifically labelled at C-3 with deuterium. Journal of the Chemical Society – Perkin Transactions 1 23932398.CrossRefGoogle Scholar
Gardner, K. H. & Kay, L. E. (1997). Production and incorporation of 15N, 13C, 2H (1H-δ1 Methyl) isoleucine into proteins for multidimensional NMR studies. Journal of the American Chemical Society 119, 75997600.CrossRefGoogle Scholar
Gardner, K. H. & Kay, L. E. (1998). The use of 2H, 13C, 15N multidimensional NMR to study the structure and dynamics of proteins. Annual Review of Biophysics and Biomolecular Structure 27, 357406.CrossRefGoogle Scholar
Gardner, K. H., Zhang, X. C., Gehring, K. & Kay, L. E. (1998). Solution NMR studies of a 42 kDa Escherichia coli maltose binding protein β-cyclodextrin complex: chemical shift assignments and analysis. Journal of the American Chemical Society 120, 1173811748.CrossRefGoogle Scholar
Garrett, D. S., Seok, Y. J., Liao, D. I., Peterkofsky, A., Gronenborn, A. M. & Clore, G. M. (1997). Solution structure of the 30 kDa N-terminal domain of enzyme I of the Escherichia coli phosphoenolpyruvate:sugar phosphotransferase system by multidimensional NMR. Biochemistry 36, 25172530.CrossRefGoogle ScholarPubMed
Goff, S. A. & Goldberg, A. L. (1987). An increased content of protease La, the lon gene product, increases protein degradation and blocks growth in Escherichia coli. Journal of Biological Chemistry 262, 45084515.CrossRefGoogle ScholarPubMed
Goto, N. K., Gardner, K. H., Mueller, G. A., Willis, R. C. & Kay, L. E. (1999). A robust and cost-effective method for the production of Val, Leu, Ile (δ1) methyl-protonated 15N-, 13C-, 2H-labeled proteins. Journal of Biomolecular NMR 13, 369374.CrossRefGoogle ScholarPubMed
Goto, N. K. & Kay, L. E. (2000). New developments in isotope labeling strategies for protein solution NMR spectroscopy. Current Opinion in Structural Biology 10, 585592.CrossRefGoogle ScholarPubMed
Griesinger, C., Sørensen, O. W. & Ernst, R. R. (1987a). Novel 3-dimensional NMR techniques for studies of peptides and biological macromolecules. Journal of the American Chemical Society 109, 72277228.CrossRefGoogle Scholar
Griesinger, C., Sørensen, O. W. & Ernst, R. R. (1987b). A practical approach to 3-dimensional NMR spectroscopy. Journal of Magnetic Resonance 73, 574579.Google Scholar
Gronwald, W. & Kalbitzer, H. R. (2004). Automated structure determination of proteins by NMR spectroscopy. Progress in Nuclear Magnetic Resonance Spectroscopy 44, 3396.CrossRefGoogle Scholar
Grzesiek, S., Anglister, J., Ren, H. & Bax, A. (1993). 13C line narrowing by 2H decoupling in 2H/13C/15N-enriched proteins. Application to triple-resonance 4D J-connectivity of sequential amides. Journal of the American Chemical Society 115, 43694370.CrossRefGoogle Scholar
Grzesiek, S. & Bax, A. (1992a). Correlating backbone amide and side-chain resonances in larger proteins by multiple relayed triple resonance NMR. Journal of the American Chemical Society 114, 62916293.CrossRefGoogle Scholar
Grzesiek, S. & Bax, A. (1992b). An efficient experiment for sequential backbone assignment of medium-sized isotopically enriched proteins. Journal of Magnetic Resonance 99, 201207.Google Scholar
Grzesiek, S., Cordier, F., Jaravine, V. & Barfield, M. (2004). Insights into biomolecular hydrogen bonds from hydrogen bond scalar couplings. Progress in Nuclear Magnetic Resonance Spectroscopy 45, 275300.CrossRefGoogle Scholar
Güntert, P. (2003). Automated NMR protein structure calculation. Progress in Nuclear Magnetic Resonance Spectroscopy 43, 105125.CrossRefGoogle Scholar
Güntert, P. (2009). Automated structure determination from NMR spectra. European Biophysics Journal 38, 129143.CrossRefGoogle ScholarPubMed
Güntert, P., Berndt, K. D. & Wüthrich, K. (1993). The program ASNO for computer-supported collection of NOE upper distance constraints as input for protein structure determination. Journal of Biomolecular NMR 3, 601606.CrossRefGoogle Scholar
Güntert, P., Braun, W., Billeter, M. & Wüthrich, K. (1989). Automated stereospecific 1H NMR assignments and their impact on the precision of protein structure determinations in solution. Journal of the American Chemical Society 111, 39974004.CrossRefGoogle Scholar
Güntert, P., Braun, W. & Wüthrich, K. (1991a). Efficient computation of three-dimensional protein structures in solution from nuclear magnetic resonance data using the program DIANA and the supporting programs CALIBA, HABAS and GLOMSA. Journal of Molecular Biology 217, 517530.CrossRefGoogle ScholarPubMed
Güntert, P., Mumenthaler, C. & Wüthrich, K. (1997). Torsion angle dynamics for NMR structure calculation with the new program DYANA. Journal of Molecular Biology 273, 283298.CrossRefGoogle ScholarPubMed
Güntert, P., Qian, Y. Q., Otting, G., Müller, M., Gehring, W. & Wüthrich, K. (1991b). Structure determination of the Antp(C39S) homeodomain from nuclear magnetic resonance data in solution using a novel strategy for the structure calculation with the programs DIANA, CALIBA, HABAS and GLOMSA. Journal of Molecular Biology 217, 531540.CrossRefGoogle Scholar
Güntert, P. & Wüthrich, K. (1991). Improved efficiency of protein structure calculations from NMR data using the program DIANA with redundant dihedral angle constraints. Journal of Biomolecular NMR 1, 447456.CrossRefGoogle ScholarPubMed
Guignard, L., Ozawa, K., Pursglove, S. E., Otting, G. & Dixon, N. E. (2002). NMR analysis of in vitro-synthesized proteins without purification: a high-throughput approach. FEBS Letters 524, 159162.CrossRefGoogle ScholarPubMed
Henrich, B., Lubitz, W. & Plapp, R. (1982). Lysis of Escherichia coli by induction of cloned phi X174 genes. Molecular and General Genetics 185, 493497.CrossRefGoogle ScholarPubMed
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. Journal of Molecular Biology 319, 209227.CrossRefGoogle ScholarPubMed
Hirata, R., Nakano, A., Kawasaki, H., Suzuki, K. & Anraku, Y. (1990). Molecular structure of a gene, VMA1, encoding the catalytic subunit of H+-translocating adenosine triphosphatase from vacuolar membranes of Saccharomyces cerevisiae. Journal of Biological Chemistry 265, 67266733.CrossRefGoogle ScholarPubMed
Huang, Y. P. J., Moseley, H. N. B., Baran, M. C., Arrowsmith, C., Powers, R., Tejero, R., Szyperski, T. & Montelione, G. T. (2005). An integrated platform for automated analysis of protein NMR structures. Methods in Enzymology 394, 111141.CrossRefGoogle ScholarPubMed
Ikeya, T., Takeda, M., Yoshida, H., Terauchi, T., Jee, J., Kainosho, M. & Güntert, P. (2009). Automated NMR structure determination of stereo-array isotope labeled ubiquitin from minimal sets of spectra using the SAIL-FLYA system. Journal of Biomolecular NMR 44, 261272.CrossRefGoogle ScholarPubMed
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. Magnetic Resonance in Chemistry 44, S152S157.CrossRefGoogle ScholarPubMed
Ikura, M. & Bax, A. (1992). Isotope-filtered 2D NMR of a protein-peptide complex: study of a skeletal muscle myosin light chain kinase fragment bound to calmodulin. Journal of the American Chemical Society 114, 24332440.CrossRefGoogle Scholar
Ikura, M., Kay, L. E. & Bax, A. (1990). A novel approach for sequential assignment of 1H, 13C, and 15N spectra of larger proteins: heteronuclear triple-resonance three-dimensional NMR spectroscopy. Application to calmodulin. Biochemistry 29, 46594667.CrossRefGoogle ScholarPubMed
Ikura, M., Spera, S., Barbato, G., Kay, L. E., Krinks, M. & Bax, A. (1991). Secondary structure and side-chain 1H and 13C resonance assignments of calmodulin in solution by heteronuclear multidimensional NMR-spectroscopy. Biochemistry 30, 92169228.CrossRefGoogle ScholarPubMed
Ishima, R., Louis, J. M. & Torchia, D. A. (2001). Optimized labeling of 13CHD2 methyl isotopomers in perdeuterated proteins: potential advantages for 13C relaxation studies of methyl dynamics of larger proteins. Journal of Biomolecular NMR 21, 167171.CrossRefGoogle ScholarPubMed
Iwai, H. & Plückthun, A. (1999). Circular β-lactamase: stability enhancement by cyclizing the backbone. FEBS Letters 459, 166172.CrossRefGoogle ScholarPubMed
Iwai, H., Züger, S., Jin, J. & Tam, P. H. (2006). Highly efficient protein trans-splicing by a naturally split DnaE intein from Nostoc punctiforme. FEBS Letters 580, 18531858.CrossRefGoogle ScholarPubMed
Jardetzky, O. & Roberts, G. C. K. (1981). NMR in Molecular Biology. New York: Academic Press.Google Scholar
Jee, J. & Güntert, P. (2003). Influence of the completeness of chemical shift assignments on NMR structures obtained with automated NOE assignment. Journal of Structural and Functional Genomics 4, 179189.CrossRefGoogle ScholarPubMed
Johnson, B. A. (2004). Using NMRView to visualize and analyze the NMR spectra of macromolecules. Methods in Molecular Biology 278, 313352.Google ScholarPubMed
Kainosho, M. (1997). Isotope labelling of macromolecules for structural determinations. Nature Structural Biology 4, 858861.Google ScholarPubMed
Kainosho, M. & Ajisaka, K. (1975). Conformational analysis of amino acids and peptides using specific isotope substitution. II. Conformation of serine, tyrosine, phenylalanine, aspartic acid, asparagine, and asparatic acid β-methyl ester in various ionization states. Journal of the American Chemical Society 97, 56305631.CrossRefGoogle Scholar
Kainosho, M., Torizawa, T., Iwashita, Y., Terauchi, T., Ono, A. M. & Güntert, P. (2006). Optimal isotope labelling for NMR protein structure determinations. Nature 440, 5257.CrossRefGoogle ScholarPubMed
Kainosho, M. & Tsuji, T. (1982). Assignment of the three methionyl carbonyl carbon resonances in Streptomyces subtilisin inhibitor by a carbon-13 and nitrogen-15 double-labeling technique. A new strategy for structural studies of proteins in solution. Biochemistry 21, 62736279.CrossRefGoogle ScholarPubMed
Kalbitzer, H. R., Leberman, R. & Wittinghofer, A. (1985). 1H-NMR spectroscopy on elongation factor Tu from Escherichia coli – resolution enhancement by perdeuteration. FEBS Letters 180, 4042.CrossRefGoogle Scholar
Kane, P. M., Yamashiro, C. T., Wolczyk, D. F., Neff, N., Goebl, M. & Stevens, T. H. (1990). Protein splicing converts the yeast TFP1 gene product to the 69-kD subunit of the vacuolar H+-adenosine triphosphatase Science 250, 651657.CrossRefGoogle Scholar
Kariya, E., Ohki, S., Hayano, T. & Kainosho, M. (2000). Backbone 1H, 13C, and 15N resonance assignments of an 18·2 kDa protein, E. coli peptidyl-prolyl cis-trans isomerase b (EPPIb). Journal of Biomolecular NMR 18, 7576.CrossRefGoogle ScholarPubMed
Kay, L. E. (2005). NMR studies of protein structure and dynamics. Journal of Magnetic Resonance 173, 193207.CrossRefGoogle ScholarPubMed
Kay, L. E., Ikura, M., Tschudin, R. & Bax, A. (1990). Three-dimensional triple-resonance NMR spectroscopy of isotopically enriched proteins. Journal of Magnetic Resonance 89, 496514.Google Scholar
Kay, L. E., Keifer, P. & Saarinen, T. (1992a). Pure absorption gradient enhanced heteronuclear single quantum correlation spectroscopy with improved sensitivity. Journal of the American Chemical Society 114, 1066310665.CrossRefGoogle Scholar
Kay, L. E., Nicholson, L. K., Delaglio, F., Bax, A. & Torchia, D. A. (1992b). Pulse sequences for removal of the effects of cross correlation between dipolar and chemical-shift anisotropy relaxation mechanism on the measurement of heteronuclear T 1 and T 2 values in proteins. Journal of Magnetic Resonance 97, 359375.Google Scholar
Kendrew, J. C., Bodo, G., Dintzis, H. M., Parrish, R. G., Wyckoff, H. & Phillips, D. C. (1958). A three-dimensional model of the myoglobin molecule obtained by X-ray analysis. Nature 181, 662666.CrossRefGoogle ScholarPubMed
Kigawa, T., Muto, Y. & Yokoyama, S. (1995). Cell-free synthesis and amino acid-selective stable isotope labeling of proteins for NMR analysis. Journal of Biomolecular NMR 6, 129134.CrossRefGoogle ScholarPubMed
Kigawa, T., Yabuki, T., Yoshida, Y., Tsutsui, M., Ito, Y., Shibata, T. & Yokoyama, S. (1999). Cell-free production and stable-isotope labeling of milligram quantities of proteins. FEBS Letters 442, 1519.CrossRefGoogle ScholarPubMed
Kim, D. M., Kigawa, T., Choi, C. Y. & Yokoyama, S. (1996). A highly efficient cell-free protein synthesis system from Escherichia coli. European Journal of Biochemistry 239, 881886.CrossRefGoogle ScholarPubMed
Kim, D. M. & Swartz, J. R. (2000). Prolonging cell-free protein synthesis by selective reagent additions. Biotechnology Progress 16, 385390.CrossRefGoogle ScholarPubMed
Klabunde, T., Sharma, S., Telenti, A., Jacobs, W. R. & Sacchettini, J. C. (1998). Crystal structure of GyrA intein from Mycobacterium xenopi reveals structural basis of protein splicing. Nature Structural Biology 5, 3136.CrossRefGoogle ScholarPubMed
Klammt, C., Löhr, F., Schäfer, B., Haase, W., Dötsch, V., Rüterjans, H., Glaubitz, C. & Bernhard, F. (2004). High level cell-free expression and specific labeling of integral membrane proteins. European Journal of Biochemistry 271, 568580.CrossRefGoogle ScholarPubMed
Kobayashi, M., Yagi, H., Yamazaki, T., Yoshida, M. & Akutsu, H. (2008). Dynamic inter-subunit interactions in thermophilic F-1-ATPase subcomplexes studied by cross-correlated relaxation-enhanced polarization transfer NMR. Journal of Biomolecular NMR 40, 165174.CrossRefGoogle ScholarPubMed
Koradi, R., Billeter, M., Engeli, M., Güntert, P. & Wüthrich, K. (1998). Automated peak picking and peak integration in macromolecular NMR spectra using AUTOPSY. Journal of Magnetic Resonance 135, 288297.CrossRefGoogle ScholarPubMed
Koradi, R., Billeter, M. & Güntert, P. (2000). Point-centered domain decomposition for parallel molecular dynamics simulation. Computer Physics Communications 124, 139147.CrossRefGoogle Scholar
Kramer, G., Kudlicki, W. & Hardesty, B. (1999). Cell-Free Coupled Transcription-Translation Systems from Escherichia coli. New York: Oxford University Press.CrossRefGoogle Scholar
Lang, M., Lang-Fugmann, S. & Steglich, W. (2002). Organic Syntheses 78, 113122.Google Scholar
Lee, W., Revington, M. J., Arrowsmith, C. & Kay, L. E. (1994). A pulsed field gradient isotope-filtered 3D 13C HMQC-NOESY experiment for extracting intermolecular NOE contacts in molecular complexes. FEBS Letters 350, 8790.CrossRefGoogle ScholarPubMed
LeMaster, D. M., LaIuppa, J. C. & Kushlan, D. M. (1994). Differential deuterium isotope shifts and one bond 1H-13C scalar couplings in the conformational analysis of protein glycine residues. Journal of Biomolecular NMR 4, 863870.CrossRefGoogle ScholarPubMed
LeMaster, D. M. & Richards, F. M. (1988). NMR sequential assignment of Escherichia coli thioredoxin utilizing random fractional deuteriation. Biochemistry 27, 142150.CrossRefGoogle ScholarPubMed
Li, G. G., Patel, D. & Hruby, V. J. (1993). An efficient procedure for the demethylation of aryl-methyl ethers in optically pure unusual amino acids. Tetrahedron Letters 34, 53935396.CrossRefGoogle Scholar
Lian, L. Y. & Middleton, D. A. (2001). Labelling approaches for protein structural studies by solution-state and solid-state NMR. Progress in Nuclear Magnetic Resonance Spectroscopy 39, 171190.CrossRefGoogle Scholar
López-Méndez, B. & Güntert, P. (2006). Automated protein structure determination from NMR spectra. Journal of the American Chemical Society 128, 1311213122.CrossRefGoogle ScholarPubMed
Luginbühl, P., Güntert, P., Billeter, M. & Wüthrich, K. (1996). The new program OPAL for molecular dynamics simulations and energy refinements of biological macromolecules. Journal of Biomolecular NMR 8, 136146.CrossRefGoogle ScholarPubMed
Machonkin, T. E., Westler, W. M. & Markley, J. L. (2002). 13C{13C} 2D NMR: a novel strategy for the study of paramagnetic proteins with slow electronic relaxation rates. Journal of the American Chemical Society 124, 32043205.CrossRefGoogle Scholar
Madin, K., Sawasaki, T., Ogasawara, T. & Endo, Y. (2000). A highly efficient and robust cell-free protein synthesis system prepared from wheat embryos: plants apparently contain a suicide system directed at ribosomes. Proceedings of the National Academy of Sciences USA 97, 559564.CrossRefGoogle ScholarPubMed
Malmodin, D., Papavoine, C. H. M. & Billeter, M. (2003). Fully automated sequence-specific resonance assignments of heteronuclear protein spectra. Journal of Biomolecular NMR 27, 6979.CrossRefGoogle ScholarPubMed
Marion, D., Kay, L. E., Sparks, S. W., Torchia, D. A. & Bax, A. (1989). Three-dimensional heteronuclear NMR of 15N labeled proteins. Journal of the American Chemical Society 111, 15151517.CrossRefGoogle Scholar
Markley, J. L., Putter, I. & Jardetzky, O. (1968). High-resolution nuclear magnetic resonance spectra of selectively deuterated staphylococcal nuclease. Science 161, 12491251.CrossRefGoogle ScholarPubMed
Matsuo, H., Kupce, E., Li, H. J. & Wagner, G. (1996a). Increased sensitivity in HNCA and HN(CO)CA experiments by selective Cβ decoupling. Journal of Magnetic Resonance Series B 113, 9196.CrossRefGoogle Scholar
Matsuo, H., Kupce, E. & Wagner, G. (1996b). Resolution and sensitivity gain in HCCH-TOCSY experiments by homonuclear Cβ decoupling. Journal of Magnetic Resonance Series B 113, 190194.CrossRefGoogle Scholar
Maurizi, M. R. (1987). Degradation in vitro of bacteriophage lambda N protein by Lon protease from Escherichia coli. Journal of Biological Chemistry 262, 26962703.CrossRefGoogle ScholarPubMed
McIntosh, L. P. & Dahlquist, F. W. (1990). Biosynthetic incorporation of N-15 and C-13 for assignment and interpretation of nuclear magnetic resonance spectra of proteins. Quarterly Reviews of Biophysics 23, 138.CrossRefGoogle Scholar
Medek, A., Olejniczak, E. T., Meadows, R. P. & Fesik, S. W. (2000). An approach for high-throughput structure determination of proteins by NMR spectroscopy. Journal of Biomolecular NMR 18, 229238.CrossRefGoogle ScholarPubMed
Melacini, G. (2000). Separation of intra- and intermolecular NOEs through simultaneous editing and J-compensated filtering: a 4D quadrature-free constant-time J-resolved approach. Journal of the American Chemical Society 122, 97359738.CrossRefGoogle Scholar
Metzler, W. J., Wittekind, M., Goldfarb, V., Mueller, L. & Farmer, B. T. II (1996). Incorporation of 1H/13C/15N-{Ile, Leu, Val} into a perdeuterated, 15N-labeled protein: potential in structure determination of large proteins by NMR. Journal of the American Chemical Society 118, 68006801.CrossRefGoogle Scholar
Montelione, G. T., Zheng, D. Y., Huang, Y. P. J., Gunsalus, K. C. & Szyperski, T. (2000). Protein NMR spectroscopy in structural genomics. Nature Structural Biology 7, 982985.CrossRefGoogle ScholarPubMed
Mueller, G. A., Choy, W. Y., Yang, D., Forman-Kay, J. D., Venters, R. A. & Kay, L. E. (2000). Global folds of proteins with low densities of NOEs using residual dipolar couplings: application to the 370-residue maltodextrin-binding protein. Journal of Molecular Biology 300, 197212.CrossRefGoogle Scholar
Muona, M., Aranko, A. S. & Iwai, H. (2008). Segmental isotopic labelling of a multidomain protein by protein ligation by protein prans-splicing. ChemBioChem: A European Journal of Chemical Biology 9, 29582961.CrossRefGoogle Scholar
Murray, A. III & Williams, D. L. (1958). Organic Syntheses with Isotopes. Part II: Organic Compounds Labeled with Isotopes of the Halogens, Hydrogen, Nitrogen, Oxygen, Phosphorus and Sulfur. New York: Interscience.Google Scholar
Neri, D., Szyperski, T., Otting, G., Senn, H. & Wüthrich, K. (1989). Sterospecific nuclear magnetic resonance assignments of the methyl groups of valine and leucine in the DNA-binding domain of the 434 repressor by biosynthetically directed fractional 13C labeling. Biochemistry 28, 75107516.CrossRefGoogle Scholar
Nilges, M. (1995). Calculation of protein structures with ambiguous distance restraints – Automated assignment of ambiguous NOE crosspeaks and disulfide connectivities. Journal of Molecular Biology 245, 645660.CrossRefGoogle Scholar
Nishiyama, K., Oba, M., Ueno, R., Morita, A., Nakamura, Y. & Kainosho, M. (1994). Synthesis of phenylalanines regiospecifically labelled with deuterium in the aromatic ring. Journal of Labelled Compounds & Radiopharmaceuticals 34, 831837.CrossRefGoogle Scholar
O'Donoghue, S. I. & Nilges, M. (1999). Calculation of symmetric oligomer structures from NMR data. In Structure Computation and Dynamics in Protein NMR, vol. 17(eds. Krishna, N. R. & Berliner, L. J.), pp. 131161. New York: Kluwer Academic/Plenum Publishers.Google Scholar
Oba, M., Iwasaki, A., Hitokawa, H., Ikegame, T., Banba, H., Ura, K., Takamura, T. & Nishiyama, K. (2006). Preparation of l-serine and l-cystine stereospecifically labeled with deuterium at the β-position. Tetrahedron-Asymmetry 17, 18901894.CrossRefGoogle Scholar
Oba, M., Kobayashi, M., Oikawa, F., Nishiyama, K. & Kainosho, M. (2001). Synthesis of 13C/D doubly labeled L-leucines: probes for conformational analysis of the leucine side-chain. Journal of Organic Chemistry 66, 59195922.CrossRefGoogle Scholar
Oba, M., Terauchi, T., Miyakawa, A., Kamo, H. & Nishiyama, K. (1998). Stereoselective deuterium-labelling of diastereotopic methyl and methylene protons of L-leucine. Tetrahedron Letters 39, 15951598.CrossRefGoogle Scholar
Oba, M., Terauchi, T., Miyakawa, A. & Nishiyama, K. (1999). Asymmetric synthesis of L-proline regio- and stereoselectively labelled wiith deuterium. Tetrahedron-Asymmetry 10, 937945.CrossRefGoogle Scholar
Ogura, K., Terasawa, H. & Inagaki, F. (1996). An improved double-tuned and isotope-filtered pulse scheme based on a pulsed field gradient and a wide-band inversion shaped pulse. Journal of Biomolecular NMR 8, 492498.CrossRefGoogle Scholar
Ohki, S. Y., Eto, M., Kariya, E., Hayano, T., Hayashi, Y., Yazawa, M., Brautigan, D. & Kainosho, M. (2001). Solution NMR structure of the myosin phosphatase inhibitor protein CPI-17 shows phosphorylation-induced conformational changes responsible for activation. Journal of Molecular Biology 314, 839849.CrossRefGoogle ScholarPubMed
Ohki, S. Y. & Kainosho, M. (2008). Stable isotope labeling methods for protein NMR spectroscopy. Progress in Nuclear Magnetic Resonance Spectroscopy 53, 208226.CrossRefGoogle Scholar
Ojima, I., Kato, K., Nakahashi, K., Fuchikami, T. & Fujita, M. (1989). New and effective routes to fluoro analogues of aliphatic and aromatic amino acids. Journal of Organic Chemistry 54, 45114522.CrossRefGoogle Scholar
Okuma, K., Ono, A. M., Tsuchiya, S., Oba, M., Nishiyama, K., Kainosho, M. & Terauchi, T. (2009). Assymetric synthesis of (2S,3R)- and (2S,3S)-[2-13C;3-2H] glutamic acid. Tetrahedron Letters 50, 14821484.CrossRefGoogle Scholar
Olejniczak, E. T., Xu, R. X. & Fesik, S. W. (1992). A 4D-HCCH-TOCSY experiment for assigning the side-chain 1H-resonance and 13C-resonance of proteins. Journal of Biomolecular NMR 2, 655659.CrossRefGoogle Scholar
Ollerenshaw, J. E., Tugarinov, V., Skrynnikov, N. R. & Kay, L. E. (2005). Comparison of 13CH3, 13CH2D, and 13CHD2 methyl labeling strategies in proteins. Journal of Biomolecular NMR 33, 2541.CrossRefGoogle ScholarPubMed
Oschkinat, H., Cieslar, C., Holak, T. A., Clore, G. M. & Gronenborn, A. M. (1989). Practical and theoretical aspects of 3-dimensional homonuclear Hartmann-Hahn-nuclear Overhauser enhancement spectroscopy of proteins. Journal of Magnetic Resonance 83, 450472.Google Scholar
Ostler, G., Soteriou, A., Moody, C. M., Khan, J. A., Birdsall, B., Carr, M. D., Young, D. W. & Feeney, J. (1993). Stereospecific assignments of the leucine methyl resonances in the 1H NMR spectrum of Lactobacillus casei dihydrofolate reductase. FEBS Letters 318, 177180.CrossRefGoogle ScholarPubMed
Otomo, T., Ito, N., Kyogoku, Y. & Yamazaki, T. (1999a). NMR observation of selected segments in a larger protein: central-segment isotope labeling through intein-mediated ligation. Biochemistry 38, 1604016044.CrossRefGoogle Scholar
Otomo, T., Teruya, K., Uegaki, K., Yamazaki, T. & Kyogoku, Y. (1999b). Improved segmental isotope labeling of proteins and application to a larger protein. Journal of Biomolecular NMR 14, 105114.CrossRefGoogle ScholarPubMed
Otting, G. & Wüthrich, K. (1990). Heteronuclear filters in two-dimensional [1H,1H]-NMR spectroscopy: combined use with isotope labelling for studies of macromolecular conformation and intermolecular interactions. Quarterly Reviews of Biophysics 23, 3996.CrossRefGoogle ScholarPubMed
Palmer, A. G., Cavanagh, J., Byrd, R. A. & Rance, M. (1992). Sensitivity improvement in 3-dimensional heteronuclear correlation NMR spectroscopy. Journal of Magnetic Resonance 96, 416424.Google Scholar
Palmer, A. G., Cavanagh, J., Wright, P. E. & Rance, M. (1991a). Sensitivity improvement in proton-detected 2-dimensional heteronuclear correlation NMR spectroscopy. Journal of Magnetic Resonance 93, 151170.Google Scholar
Palmer, A. G., Cavanagh, J., Wright, P. E. & Rance, M. (1991b). Sensitivity improvement in proton-detected two-dimensional heteronuclear correlation NMR spectroscopy. Journal of Magnetic Resonance 93, 151170.Google Scholar
Pervushin, K. & Eletsky, A. (2003). A new strategy for backbone resonance assignment in large proteins using a MQ-HACACO experiment. Journal of Biomolecular NMR 25, 147152.CrossRefGoogle ScholarPubMed
Pervushin, K., Riek, R., Wider, G. & Wüthrich, K. (1997). Attenuated T 2 relaxation by mutual cancellation of dipole-dipole coupling and chemical shift anisotropy indicates an avenue to NMR structures of very large biological macromolecules in solution. Proceedings of the National Academy of Sciences USA 94, 1236612371.CrossRefGoogle ScholarPubMed
Pervushin, K., Riek, R., Wider, G. & Wüthrich, K. (1998). Transverse relaxation-optimized spectroscopy (TROSY) for NMR studies of aromatic spin systems in 13C-labeled proteins. Journal of the American Chemical Society 120, 63946400.CrossRefGoogle Scholar
Pratt, J. M. (1984). Transcription and Translation: A Practical Approach. New York: IRL Press.Google Scholar
Prestegard, J. H., Bougault, C. M. & Kishore, A. I. (2004). Residual dipolar couplings in structure determination of biomolecules. Chemical Reviews 104, 35193540.CrossRefGoogle ScholarPubMed
Rajesh, S., Nietlispach, D., Nakayama, H., Takio, K., Laue, E. D., Shibata, T. & Ito, Y. (2003). A novel method for the biosynthesis of deuterated proteins with selective protonation at the aromatic rings of Phe, Tyr and Trp. Journal of Biomolecular NMR 27, 8186.CrossRefGoogle ScholarPubMed
Ramer, S. E., Moore, R. N. & Vederas, J. C. (1986). Mechanism of formation of serine β-lactones by Mitsunobu cyclization: synthesis and use of l-serine stereospecifically labelled with deuteriun at C-3. Canadian Journal of Chemistry 64, 706713.CrossRefGoogle Scholar
Riegel, E. & Zwilgmeyer, F. (1943). Organic Syntheses II, 126.Google Scholar
Riek, R., Wider, G., Pervushin, K. & Wüthrich, K. (1999). Polarization transfer by cross-correlated relaxation in solution NMR with very large molecules. Proceedings of the National Academy of Sciences USA 96, 49184923.CrossRefGoogle ScholarPubMed
Romanelli, A., Shekhtman, A., Cowburn, D. & Muir, T. W. (2004). Semisynthesis of a segmental isotopically labeled protein splicing precursor: NMR evidence for an unusual peptide bond at the N-extein-intein junction. Proceedings of the National Academy of Sciences USA 101, 63976402.CrossRefGoogle Scholar
Rosen, M. K., Gardner, K. H., Willis, R. C., Parris, W. E., Pawson, T. & Kay, L. E. (1996). Selective methyl group protonation of perdeuterated proteins. Journal of Molecular Biology 263, 627636.CrossRefGoogle ScholarPubMed
Salzmann, M., Pervushin, K., Wider, G., Senn, H. & Wüthrich, K. (1998). TROSY in triple-resonance experiments: new perspectives for sequential NMR assignment of large proteins. Proceedings of the National Academy of Sciences of the United States of America 95, 1358513590.CrossRefGoogle ScholarPubMed
Santoro, J. & King, G. C. (1992). A constant-time 2D overbodenhausen experiment for inverse correlation of isotopically enriched species. Journal of Magnetic Resonance 97, 202207.Google Scholar
Seeholzer, S. H., Cohn, M., Putkey, J. A., Means, A. R. & Crespi, H. L. (1986). NMR studies of a complex of deuterated calmodulin with melittin. Proceedings of the National Academy of Sciences USA 83, 36343638.CrossRefGoogle ScholarPubMed
Shan, X., Gardner, K. H., Muhandiram, D. R., Rao, N. S., Arrowsmith, C. H. & Kay, L. E. (1996). Assignment of 15N, 13Cα, 13Cβ, and HN resonances in an 15N, 13C, 2H labeled 64 kDa trp repressor-operator complex using triple-resonance NMR spectroscopy and 2H-decoupling. Journal of the American Chemical Society 118, 65706579.CrossRefGoogle Scholar
Sharff, A. J., Rodseth, L. E. & Quiocho, F. A. (1993). Refined 1·8-Å structure reveals the mode of binding of β-cyclodextrin to the maltodextrin binding protein. Biochemistry 32, 1055310559.CrossRefGoogle Scholar
Shi, J., Pelton, J. G., Cho, H. S. & Wemmer, D. E. (2004). Protein signal assignments using specific labeling and cell-free synthesis. Journal of Biomolecular NMR 28, 235247.CrossRefGoogle ScholarPubMed
Shimizu, Y., Inoue, A., Tomari, Y., Suzuki, T., Yokogawa, T., Nishikawa, K. & Ueda, T. (2001). Cell-free translation reconstituted with purified components. Nature Biotechnology 19, 751755.CrossRefGoogle ScholarPubMed
Shuker, S. B., Hajduk, P. J., Meadows, R. P. & Fesik, S. W. (1996). Discovering high-affinity ligands for proteins: SAR by NMR. Science 274, 15311534.CrossRefGoogle ScholarPubMed
Skrisovska, L. & Allain, F. H. T. (2008). Improved segmental isotope labeling methods for the NMR study of multidomain or large proteins: application to the RRMs of Npl3p and hnRNP L. Journal of Molecular Biology 375, 151164.CrossRefGoogle ScholarPubMed
Smith, B. O., Ito, Y., Raine, A., Teichmann, S., BenTovim, L., Nietlispach, D., Broadhurst, R. W., Terada, T., Kelly, M., Oschkinat, H., Shibata, T., Yokoyama, S. & Laue, E. D. (1996). An approach to global fold determination using limited NMR data from larger proteins selectively protonated at specific residue types. Journal of Biomolecular NMR 8, 360368.CrossRefGoogle ScholarPubMed
Spirin, A. S., Baranov, V. I., Ryabova, L. A., Ovodov, S. Y. & Alakhov, Y. B. (1988). A continuous cell-free translation system capable of producing polypeptides in high yield. Science 242, 11621164.CrossRefGoogle ScholarPubMed
Sprangers, R. & Kay, L. E. (2007). Quantitative dynamics and binding studies of the 20S proteasome by NMR. Nature 445, 618622.CrossRefGoogle ScholarPubMed
Staunton, D., Owen, J. & Campbell, I. D. (2003). NMR and structural genomics. Accounts of Chemical Research 36, 207214.CrossRefGoogle ScholarPubMed
Takahashi, H., Nakanishi, T., Kami, K., Arata, Y. & Shimada, I. (2000). A novel NMR method for determining the interfaces of large protein-protein complexes. Nature Structural Biology 7, 220223.Google ScholarPubMed
Takeda, M., Chang, C. K., Ikeya, T., Güntert, P., Chang, Y. H., Hsu, Y. L., Huang, T. H. & Kainosho, M. (2008a). Solution structure of the C-terminal dimerization domain of SARS coronavirus nucleocapsid protein determined by the SAIL-NMR method. Implications for RNA packaging as revealed by nucleic acid interactions. Journal of Molecular Biology 380, 608622.CrossRefGoogle Scholar
Takeda, M., Ikeya, T., Güntert, P. & Kainosho, M. (2007). Automated structure determination of proteins with the SAIL-FLYA NMR method. Nature Protocols 2, 28962902.CrossRefGoogle ScholarPubMed
Takeda, M., Ono, A. M., Terauchi, T. & Kainosho, M. (2009). Application of SAIL phenylalanine and tyrosine with alternative isotope-labeling patterns for protein structure determination. Journal of Biomolecular NMR 44, 261265.Google Scholar
Takeda, M., Sugimori, N., Torizawa, T., Terauchi, T., Ono, A. M., Yagi, H., Yamaguchi, Y., Kato, K., Ikeya, T., Jee, J., Güntert, P., Aceti, D. J., Markley, J. L. & Kainosho, M. (2008b). Structure of the putative 32 kDa myrosinase-binding protein from Arabidopsis (At3g16450.1) determined by SAIL-NMR. FEBS Journal 275, 58735884.CrossRefGoogle ScholarPubMed
Tate, S., Ushioda, T., Utsunomiya-Tate, N., Shibuya, K., Ohyama, Y., Nakano, Y., Kaji, H., Inagaki, F., Samejima, T. & Kainosho, M. (1995). Solution structure of a human cystatin A variant, cystatin A2–98 M65L, by NMR spectroscopy. A possible role of the interactions between the N- and C-termini to maintain the inhibitory active form of cystatin A. Biochemistry 34, 1463714648.CrossRefGoogle Scholar
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. Organic Letters 10, 27852787.CrossRefGoogle ScholarPubMed
Torchia, D. A., Sparks, S. W. & Bax, A. (1988). Delineation of α-helical domains in deuteriated Staphylococcal nuclease by 2D NOE NMR spectroscopy. Journal of the American Chemical Society 110, 23202321.CrossRefGoogle Scholar
Torizawa, T., Ono, A. M., Terauchi, T. & Kainosho, M. (2005). NMR assignment methods for the aromatic ring resonances of phenylalanine and tyrosine residues in proteins. Journal of the American Chemical Society 127, 1262012626.CrossRefGoogle ScholarPubMed
Torizawa, T., Shimizu, M., Taoka, M., Miyano, H. & Kainosho, M. (2004). Efficient production of isotopically labeled proteins by cell-free synthesis: a practical protocol. Journal of Biomolecular NMR 30, 311325.CrossRefGoogle ScholarPubMed
Trbovic, N., Klammt, C., Koglin, A., Löhr, F., Bernhard, F. & Dötsch, V. (2005). Efficient strategy for the rapid backbone assignment of membrane proteins. Journal of the American Chemical Society 127, 1350413505.CrossRefGoogle ScholarPubMed
Tugarinov, V., Choy, W. Y., Orekhov, V. Y. & Kay, L. E. (2005). Solution NMR-derived global fold of a monomeric 82-kDa enzyme. Proceedings of the National Academy of Sciences USA 102, 622627.CrossRefGoogle ScholarPubMed
Ulrich, E. L., Akutsu, H., Doreleijers, J. F., Harano, Y., Ioannidis, Y. E., Lin, J., Livny, M., Mading, S., Maziuk, D., Miller, Z., Nakatani, E., Schulte, C. F., Tolmie, D. E., Wenger, R. K., Yao, H. Y. & Markley, J. L. (2008). BioMagResBank. Nucleic Acids Research 36, D402D408.CrossRefGoogle ScholarPubMed
Viswanatha, V. & Hruby, V. J. (1980). Conversion of l-tyrosine to l-phenylalanine. Preparation of l-[3′,5′-13C2]phenylalanine. Journal of Organic Chemistry 45, 20102012.CrossRefGoogle Scholar
Vitali, F., Henning, A., Oberstrass, F. C., Hargous, Y., Auweter, S. D., Erat, M. & Allain, F. H. T. (2006). Structure of the two most C-terminal RNA recognition motifs of PTB using segmental isotope labeling. EMBO Journal 25, 150162.CrossRefGoogle ScholarPubMed
Vuister, G. W., Kim, S. J., Wu, C. & Bax, A. (1994). 2D and 3D NMR study of phenylalanine residues in proteins by reverse isotopic labeling. Journal of the American Chemical Society 116, 92069210.CrossRefGoogle Scholar
Wagner, G., DeMarco, A. & Wüthrich, K. (1976). Dynamics of the aromatic amino acid residues in the globular conformation of the basic pancreatic trypsin inhibitor (BPTI). I. 1H NMR studies. Biophysics of Structure and Mechanism 2, 139158.CrossRefGoogle Scholar
Wang, H., Janowick, D. A., Schkeryantz, J. M., Liu, X. H. & Fesik, S. W. (1999). A method for assigning phenylalanines in proteins. Journal of the American Chemical Society 121, 16111612.CrossRefGoogle Scholar
Williams, N. K., Liepinsh, E., Watt, S. J., Prosselkov, P., Matthews, J. M., Attard, P., Beck, J. L., Dixon, N. E. & Otting, G. (2005). Stabilization of native protein fold by intein-mediated covalent cyclization. Journal of Molecular Biology 346, 10951108.CrossRefGoogle ScholarPubMed
Williams, N. K., Prosselkov, P., Liepinsh, E., Line, I., Sharipo, A., Littler, D. R., Curmi, P. M. G., Otting, G. & Dixon, N. E. (2002). In vivo protein cyclization promoted by a circularly permuted Synechocystis sp PCC6803 DnaB mini-intein. Journal of Biological Chemistry 277, 77907798.CrossRefGoogle ScholarPubMed
Williams, R. M. (1989). Synthesis of Optically Active α-Amino Acids. Chapter 2: Homologation of the β-carbon, in Organic Chemistry Series, Ed. Baldwin, J. E.Pergamon Press: Oxford 7, 134166.Google Scholar
Wittekind, M. & Mueller, L. (1993). HNCACB, a high-sensitivity 3D NMR experiment to correlate amide-proton and nitrogen resonances with the alpha-carbon and beta-carbon resonances in proteins. Journal of Magnetic Resonance Series B 101, 201205.CrossRefGoogle Scholar
Wu, P. S. C., Ozawa, K., Lim, S. P., Vasudevan, S. G., Dixon, N. E. & Otting, G. (2007). Cell-free transcription/translation from PCR-amplified DNA for high-throughput NMR studies. Angewandte Chemie-International Edition 46, 33563358.CrossRefGoogle ScholarPubMed
Wüthrich, K. (1986). NMR of Proteins and Nucleic Acids. New York: Wiley.CrossRefGoogle Scholar
Wüthrich, K. (1998). The second decade – into the third millennium. Nature Structural Biology 5, 492495.CrossRefGoogle Scholar
Xu, R., Ayers, B., Cowburn, D. & Muir, T. W. (1999). Chemical ligation of folded recombinant proteins: segmental isotopic labeling of domains for NMR studies. Proceedings of the National Academy of Sciences USA 96, 388393.CrossRefGoogle ScholarPubMed
Yagi, H., Tsujimoto, T., Yamazaki, T., Yoshida, M. & Akutsu, H. (2004). Conformational change of H+-ATPase β monomer revealed on segmental isotope labeling NMR spectroscopy. Journal of the American Chemical Society 126, 1663216638.CrossRefGoogle ScholarPubMed
Yamazaki, T., Forman-Kay, J. D. & Kay, L. E. (1993). Two-dimensional NMR experiments for correlating 13Cβ and 1Hδ/ε chemical shifts of aromatic residues in 13C-labeled proteins via scalar couplings. Journal of the American Chemical Society 115, 1105411055.CrossRefGoogle Scholar
Yamazaki, T., Lee, W., Arrowsmith, C. H., Muhandiram, D. R. & Kay, L. E. (1994). A suite of triple-resonance NMR experiments for the backbone assignment of 15N, 13C, 2H labeled proteins with high-sensitivity. Journal of the American Chemical Society 116, 1165511666.CrossRefGoogle Scholar
Yamazaki, T., Otomo, T., Oda, N., Kyogoku, Y., Uegaki, K., Ito, N., Ishino, Y. & Nakamura, H. (1998). Segmental isotope labeling for protein NMR using peptide splicing. Journal of the American Chemical Society 120, 55915592.CrossRefGoogle Scholar
Yamazaki, T., Tochio, H., Furui, J., Aimoto, S. & Kyogoku, Y. (1997). Assignment of backbone resonances for larger proteins using the 13C-1H coherence of a 1Hα-, 2H, 13C, and 15N-labeled sample. Journal of the American Chemical Society 119, 872880.CrossRefGoogle Scholar
Yee, A., Chang, X. Q., Pineda-Lucena, A., Wu, B., Semesi, A., Le, B., Ramelot, T., Lee, G. M., Bhattacharyya, S., Gutierrez, P., Denisov, A., Lee, C. H., Cort, J. R., Kozlov, G., Liao, J., Finak, G., Chen, L., Wishart, D., Lee, W., McIntosh, L. P., Gehring, K., Kennedy, M. A., Edwards, A. M. & Arrowsmith, C. H. (2002). An NMR approach to structural proteomics. Proceedings of the National Academy of Sciences USA 99, 18251830.CrossRefGoogle ScholarPubMed
Yee, A., Pardee, K., Christendat, D., Savchenko, A., Edwards, A. M. & Arrowsmith, C. H. (2003). Structural proteomics: toward high-throughput structural biology as a tool in functional genomics. Accounts of Chemical Research 36, 183189.CrossRefGoogle ScholarPubMed
Yokoyama, S., Hirota, H., Kigawa, T., Yabuki, T., Shirouzu, M., Terada, T., Ito, Y., Matsuo, Y., Kuroda, Y., Nishimura, Y., Kyogoku, Y., Miki, K., Masui, R. & Kuramitsu, S. (2000). Structural genomics projects in Japan. Nature Structural Biology 7, 943945.CrossRefGoogle ScholarPubMed
Yoshida, H., Furuya, N., Lin, Y. J., Güntert, P., Komano, T. & Kainosho, M. (2008). Structural basis of the role of the NikA ribbon-helix-helix domain in initiating bacterial conjugation. Journal of Molecular Biology 384, 690701.CrossRefGoogle ScholarPubMed
Zangger, K., Oberer, M., Keller, W. & Sterk, H. (2003). X-filtering for a range of coupling constants: application to the detection of intermolecular NOEs. Journal of Magnetic Resonance 160, 97106.CrossRefGoogle Scholar
Zhao, W. T., Zhang, Y. H., Cui, C. X., Li, Q. Q. & Wang, J. J. (2008). An efficient on-column expressed protein ligation strategy: application to segmental triple labeling of human apolipoprotein E3. Protein Science 17, 736747.CrossRefGoogle ScholarPubMed
Zubay, G. (1973). In vitro synthesis of protein in microbial systems. Annual Review of Genetics 7, 267287.CrossRefGoogle ScholarPubMed
Züger, S. & Iwai, H. (2005). Intein-based biosynthetic incorporation of unlabeled protein tags into isotopically labeled proteins for NMR studies. Nature Biotechnology 23, 736740.CrossRefGoogle ScholarPubMed
Zwahlen, C., Legault, P., Vincent, S. J. F., Greenblatt, J., Konrat, R. & Kay, L. E. (1997). Methods for measurement of intermolecular NOEs by multinuclear NMR spectroscopy: application to a bacteriophage λ N-peptide/boxB RNA complex. Journal of the American Chemical Society 119, 67116721.CrossRefGoogle Scholar