Abstract
Isotope labeling by residue type (LBRT) has long been an important tool for resonance assignments at the limit where other approaches, such as triple-resonance experiments or NOESY methods do not succeed in yielding complete assignments. While LBRT has become less important for small proteins it can be the method of last resort for completing assignments of the most challenging protein systems. Here we present an approach where LBRT is achieved by adding protonated 14N amino acids that are 13C labeled at the carbonyl position to a medium for uniform deuteration and 15N labeling. This has three important benefits over conventional 15N LBRT in a deuterated back ground: (1) selective TROSY-HNCO cross peaks can be observed with high sensitivity for amino-acid pairs connected by the labeling, and the amide proton of the residue following the 13C labeled amino acid is very sharp since its alpha position is deuterated, (2) the 13C label at the carbonyl position is less prone to scrambling than the 15N at the α-amino position, and (3) the peaks for the 1-13C labeled amino acids can be identified easily from the large intensity reduction in the 1H-15N TROSY-HSQC spectrum for some residues that do not significantly scramble nitrogens, such as alanine and tyrosine. This approach is cost effective and has been successfully applied to proteins larger than 40 kDa.
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Aramburu J, Yaffe MB, Lopez-Rodriguez C, Cantley LC, Hogan PG, Rao A (1999) Affinity-driven peptide selection of an NFAT inhibitor more selective than cyclosporin A. Science 285:2129–2133
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
Fiaux J, Bertelsen EB, Horwich AL, Wuthrich K (2002) NMR analysis of a 900K GroEL-GroES complex. Nature 418:207–211
Fiaux J, Bertelsen EB, Horwich AL, Wuthrich K (2004) Uniform and residue-specific 15N-labeling of proteins on a highly deuterated background. J Biomol NMR 29:289–297
Goddard TD, Kneller DG (2002) Sparky 3. University of California, San Francisco
Horst R, Bertelsen EB, Fiaux J, Wider G, Horwich AL, Wuthrich K (2005) From the cover: direct NMR observation of a substrate protein bound to the chaperonin GroEL. PNAS 102:12748–12753
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 21:6273–6279
Kato K, Matsunaga C, Igarashi T, Kim H, Odaka A, Shimada I, Arata Y (1991) Complete assignment of the methionyl carbonyl carbon resonances in switch variant anti-dansyl antibodies labeled with [1-13C]methionine. Biochemistry 30:270–278
Keller R (2004) PhD thesis, Diss ETH Nr 15947
Kelly MJ, Krieger C, Ball LJ, Yu Y, Richter G, Schmieder P, Bacher A, Oschkinat H (1999) Application of amino acid type-specific 1H- and 14N-labeling in a 2H-, 15N-labeled background to a 47 kDa homodimer: potential for NMR structure determination of large proteins. J Biomol NMR 14:79–83
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 Lett 442:15–19
Kigawa T, Yabuki T, Matsuda N, Matsuda T, Nakajima R, Tanaka A, Yokoyama S (2004) Preparation of Escherichia coli cell extract for highly productive cell-free protein expression. J Struct Funct Genomics 5:63–68
Koglin A, Klammt C, Trbovic N, Schwarz D, Schneider B, Schafer B, Lohr F, Bernhard F, Dotsch V (2006) Combination of cell-free expression and NMR spectroscopy as a new approach for structural investigation of membrane proteins. Magn Reson Chem 44(Spec No): S17–S23
LeMaster DM (1989) Deuteration in protein proton magnetic resonance. Methods Enzymol 177:23–43
Lohr F, Katsemi V, Hartleib J, Gunther U, Ruterjans H (2003) A strategy to obtain backbone resonance assignments of deuterated proteins in the presence of incomplete amide 2H/1H back-exchange. J Biomol NMR 25:291–311
Malia TJ, Wagner G (2007) NMR structural investigation of the mitochondrial outer membrane protein VDAC and its interaction with antiapoptotic Bcl-x(L). Biochemistry 46:514–525
McIntosh LP, Dahlquist FW (1990) Biosynthetic incorporation of 15N and 13C for assignment and interpretation of nuclear magnetic resonance spectra of proteins. Q Rev Biophys 23:1–38
Metzler WJ, Wittekind M, Goldfarb V, Mueller L, Farmer BT (1996) Incorporation of 1H13C15N-{Ile, Leu, Val} into a perdeuterated, 15N-labeled protein: potential in structure determination of large proteins by NMR. J Am Chem Soc 118:6800–6801
Morita EH, Shimizu M, Ogasawara T, Endo Y, Tanaka R, Kohno T (2004) A novel way of amino acid-specific assignment in (1)H-(15)N HSQC spectra with a wheat germ cell-free protein synthesis system. J Biomol NMR 30:37–45
Ozawa K, Headlam MJ, Schaeffer PM, Henderson BR, Dixon NE, Otting G (2004) Optimization of an Escherichia coli system for cell-free synthesis of selectively N-labelled proteins for rapid analysis by NMR spectroscopy. Eur J Biochem 271:4084–4093
Park S, Takeuchi K, Wagner G (2006) Solution structure of the first SRC homology 3 domain of human Nck2. J Biomol NMR 34:203–208
Roehrl MH, Kang S, Aramburu J, Wagner G, Rao A, Hogan PG (2004) Selective inhibition of calcineurin-NFAT signaling by blocking protein-protein interaction with small organic molecules. Proc Natl Acad Sci USA 101:7554–7559
Sawasaki T, Ogasawara T, Morishita R, Endo Y (2002) A cell-free protein synthesis system for high-throughput proteomics. Proc Natl Acad Sci USA 99:14652–14657
Staunton D, Schlinkert R, Zanetti G, Colebrook SA, Campbell ID (2006) Cell-free expression and selective isotope labelling in protein NMR. Magn Reson Chem 44(Spec No):S2–9
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
Tyler RC, Aceti DJ, Bingman CA, Cornilescu CC, Fox BG, Frederick RO, Jeon WB, Lee MS, Newman CS, Peterson FC et al. (2005) Comparison of cell-based and cell-free protocols for producing target proteins from the Arabidopsis thaliana genome for structural studies. Proteins 59:633–643
Vinarov DA, Lytle BL, Peterson FC, Tyler EM, Volkman BF, Markley JL (2004) Cell-free protein production and labeling protocol for NMR-based structural proteomics. Nat Methods 1:149–153
Yabuki T, Kigawa T, Dohmae N, Takio K, Terada T, Ito Y, Laue ED, Cooper JA, Kainosho M, Yokoyama S (1998) Dual amino acid-selective and site-directed stable-isotope labeling of the human c-Ha-Ras protein by cell-free synthesis. J Biomol NMR 11:295–306
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This work is supported by NIH (grants GM47467 and AI37581). K.T. is supported by the Japan Society for Promotion of Science.
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Takeuchi, K., Ng, E., Malia, T.J. et al. 1-13C amino acid selective labeling in a 2H15N background for NMR studies of large proteins. J Biomol NMR 38, 89–98 (2007). https://doi.org/10.1007/s10858-007-9152-z
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DOI: https://doi.org/10.1007/s10858-007-9152-z