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High resolution methyl selective 13C-NMR of proteins in solution and solid state

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Abstract

New 13C-detected NMR experiments have been devised for molecules in solution and solid state, which provide chemical shift correlations of methyl groups with high resolution, selectivity and sensitivity. The experiments achieve selective methyl detection by exploiting the one bond J-coupling between the 13C-methyl nucleus and its directly attached 13C spin in a molecule. In proteins such correlations edit the 13C-resonances of different methyl containing residues into distinct spectral regions yielding a high resolution spectrum. This has a range of applications as exemplified for different systems such as large proteins, intrinsically disordered polypeptides and proteins with a paramagnetic centre.

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References

  • Amero C, Schanda P, Durá MA, Ayala I, Marion D, Franzetti B, Brutscher B, J Boisbouvier (2009) Fast two-dimensional NMR spectroscopy of high molecular weight protein assemblies. J Am Chem Soc 131:3448–3449

    Article  Google Scholar 

  • Andronesi OC, Becker S, Seidel K, Heise H, Young HS, Baldus M (2005) Determination of membrane protein structure and dynamics by magic-angle-spinning solid-state NMR spectroscopy. J Am Chem Soc 127:12965–12974

    Article  Google Scholar 

  • Arnesano F (2010) The role of copper ion and the ubiquitin system in neurodegenerative disorders. Ideas in chemistry and molecular sciences. Wiley, New York, pp 1–30

    Google Scholar 

  • Arnesano F, Scintilla S, Calò V, Bonfrate E, Ingrosso C, Losacco M, Pellegrino T, Rizzarelli E, Natile G (2009) Copper-triggered aggregation of Ubiquitin. PLoS One 4:e7052

    Article  ADS  Google Scholar 

  • Atreya HS, Chary KVR (2001) Selective ‘unlabeling’ of amino acids in fractionally C-13 labeled proteins: an approach for stereospecific NMR assignments of CH3 groups in Val and Leu residues. J Biomol NMR 19:267–272

    Article  Google Scholar 

  • Barnwal RP, Atreya HS, Chary KVR (2008) Chemical shift based editing of CH3 groups in fractionally C-13-labelled proteins using GFT (3,2)D CT-HCCH-COSY: stereospecific assignments of CH3 groups of Val and Leu residues. J Biomol NMR 42:149–154

    Article  Google Scholar 

  • Bartels C, Xia TH, Billeter M, Güntert P, Wüthrich K (1995) The program xeasy for computer-supported NMR spectral-analysis of biological macromolecules. J Biomol NMR 6:1–10

    Article  Google Scholar 

  • Bennett AE, Rienstra CM, Auger M, Lakshmi KV, Griffin RG (1995) Heteronuclear decoupling in rotating solids. J Chem Phys 103:6951–6958

    Article  ADS  Google Scholar 

  • Bermel W, Bertini I, Felli IC, Piccioli M, Pierattelli R (2006) C-13-detected protonless NMR spectroscopy of proteins in solution. Prog Nucl Magn Reson Spectrosc 48:25–45

    Article  Google Scholar 

  • Bermel W, Bertini I, Felli IC, Matzapetakis M, Pierattelli R, Theil EC, Turano P (2007) A method for Cα direct-detection in protonless NMR. J Magn Reson 188:301–310

    Article  ADS  Google Scholar 

  • Bermel W, Felli IC, Kummerle R, Pierattelli R (2008) C-13 direct-detection biomolecular NMR. Concepts Magn Reson 32A:183–200

    Article  Google Scholar 

  • Bertini I, Luchinat C, Parigi G (2002) Paramagnetic constraints: an aid for quick solution structure determination of paramagnetic metalloproteins. Concepts Magn Reson 14:259–286

    Article  Google Scholar 

  • Cavanagh J, Fairbrother WJ, Palmer AG, Rance M, Skelton NJ (2007) Protein NMR spectroscopy. Academic Press, San Diego

    Google Scholar 

  • Chandra K, Jaipuria G, Shet D, Atreya HS (2012) Efficient sequential assignments in proteins with reduced dimensionality 3D HN(CA)NH. J Biomol NMR 52:115–126

    Article  Google Scholar 

  • Chen L, Kaiser JM, Polenova T, Yang J, Rienstra CM, Müller LJ (2007a) Backbone assignments in solid-state proteins using J-based 3D Heteronuclear correlation spectroscopy. J Am Chem Soc 129:10650–10651

    Article  Google Scholar 

  • Chen L, Kaiser JM, Lai JF, Polenova T, Yang J, Rienstra CM, Müller LJ (2007b) J-based 2D homonuclear and heteronuclear correlation in solid-state proteins. Magn Reson Chem 45:S84–S92

    Article  Google Scholar 

  • Choy WY, Kay LE (2003) Model selection for the interpretation of protein side chain methyl dynamics. J Biomol NMR 25:325–333

    Article  Google Scholar 

  • Clore GM, Iwahara J (2009) Theory, practice, and applications of paramagnetic relaxation enhancement for the characterization of transient low-population states of biological macromolecules and their complexes. Chem Rev 109:4108–4139

    Article  Google Scholar 

  • 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

    Article  Google Scholar 

  • Elena B, Lesage A, Steuernagel S, Bockmann A, Emsley L (2005) Proton to carbon-13 INEPT in solid-state NMR spectroscopy. J Am Chem Soc 127:17296–17302

    Article  Google Scholar 

  • Gagne SM, Tsuda S, Spyracopoulos L, Kay LE, Sykes BD (1998) Backbone and methyl dynamics of the regulatory domain of troponin C: anisotropic rotational diffusion and contribution of conformational entropy to calcium affinity. J Mol Biol 278:667–686

    Article  Google Scholar 

  • Gardner KH, Konrat R, Rosen MK, Kay LE (1996) An (H)C(CO)NH-TOCSY pulse scheme for sequential assignment of protonated methyl groups in otherwise deuterated N-15, C-13-labeled proteins. J Biomol NMR 8:351–356

    Article  Google Scholar 

  • Gardner KH, Rosen MK, Kay LE (1997) Global folds of highly deuterated, methyl-protonated proteins by multidimensional NMR. Biochemistry 36:1389–1401

    Article  Google Scholar 

  • Gross JD, Gelev VM, Wagner G (2003) A sensitive and robust method for obtaining intermolecular NOEs between side chains in large protein complexes. J Biomol NMR 25:235–242

    Article  Google Scholar 

  • Iwahara J, Tang C, Clore GM (2007) Practical aspects of (1)H transverse paramagnetic relaxation enhancement measurements on macromolecules. J Magn Reson 184:185–195

    Article  ADS  Google Scholar 

  • Jaipuria G, Thakur A, D’Silva P, Atreya HS (2010) High-resolution methyl edited GFT NMR experiments for protein resonance assignments and structure determination. J Biomol NMR 48:137–145

    Article  Google Scholar 

  • Jordan JB, Kovacs H, Wang Y, Mobli M, Luo R, Anklin C, Hoch JC, Kriwacki RW (2006) Three-dimensional 13C-detected CH3-TOCSY using selectively protonated proteins: facile methyl resonance assignment and protein structure determination. J Am Chem Soc 128:9119–9128

    Article  Google Scholar 

  • Kovacs H, Moskau D, Spraul M (2005) Cryogenically cooled probes—a leap in NMR technology. Prog Nucl Magn Reson Spectrosc 46:131–155

    Article  Google Scholar 

  • Metz G, Wu XL, Smith SO (1994) Ramped-amplitude cross polarization in magic-angle-spinning NMR. J Magn Reson, Series A 110:219–227

    Article  Google Scholar 

  • Metzler WJ, Wittekind M, Goldfarb V, Mueller L, Farmer BT (1996) Incorporation of H-1/C-13/N-15-{Ile, Leu, Val} into a perdeuterated, N-15-labeled protein: potential in structure determination of large proteins by NMR. J Am Chem Soc 118:6800–6801

    Article  Google Scholar 

  • Milardi D, Arnesano F, Grasso G, Magrì A, Tabbì G, Scintilla S, Natile G, Rizzarelli E (2007) Ubiquitin stability and the Lys 63-linked polyubiquitination site are compromised on copper binding. Angew Chem Int Ed 46:7993–7995

    Article  Google Scholar 

  • Nicholson LK, Kay LE, Baldisseri DM, Arango J, Young PE, Bax A, Torchia DA (1992) Dynamics of methyl-groups in proteins as studied by proton-detected C-13 NMR-spectroscopy—application to the leucine residues of staphylococcal nuclease. Biochemistry 31:5253–5263

    Article  Google Scholar 

  • Ottiger M, Delaglio F, Bax A (1998) Measurement of J and dipolar couplings from simplified two-dimensional NMR spectra. J Magn Reson 131:373–378

    Article  ADS  Google Scholar 

  • Rosen MK, Gardner KH, Willis RC, Parris WE, Pawson T, Kay LE (1996) Selective methyl group protonation of perdeuterated proteins. J Mol Biol 263:627–636

    Article  Google Scholar 

  • Swain M, Slomiany MG, Rosenzweig SA, Atreya HS (2010) High-yield bacterial expression and structural characterization of recombinant human insulin-like growth factor binding protein-2. Arch Biochem Biophys 501:195–200

    Article  Google Scholar 

  • Takegoshi K, Nakamura S, Terao T (2001) C-13-H-1 dipolar-assisted rotational resonance in magic-angle spinning NMR. Chem Phys Lett 344:631–637

    Article  ADS  Google Scholar 

  • Takegoshi K, Nakamura S, Terao T (2003) C-13-H-1 dipolar-driven C-13-C-13 recoupling without C-13 rf irradiation in nuclear magnetic resonance of rotating solids. J Chem Phys 118:2325–2341

    Article  ADS  Google Scholar 

  • Thruber KR, Tycko R (2009) Measurement of sample temperature under magic angle spinning from the chemical shift and spin lattice relaxation rate of 79Br in KBr powder. J Magn Reson 196:84–87

    Article  ADS  Google Scholar 

  • Tian Y, Chen LL, Niks D, Kaiser JM, Lai JF, Rienstra CM, Dunn MF, Mueller LJ (2009) J-Based 3D sidechain correlation in solid-state proteins. Phys Chem Chem Phys 11:7078–7086

    Article  Google Scholar 

  • Tugarinov V, Kay LE (2004) An isotope labeling strategy for methyl TROSY spectroscopy. J Biomol NMR 28:165–172

    Article  Google Scholar 

  • Tugarinov V, Hwang PM, Ollerenshaw JE, Kay LE (2003) Cross-correlated relaxation enhanced H-1-C-13 NMR spectroscopy of methyl groups in very high molecular weight proteins and protein complexes. J Am Chem Soc 125:10420–10428

    Article  Google Scholar 

  • Tugarinov V, Hwang PM, Kay LE (2004) Nuclear magnetic resonance spectroscopy of high-molecular-weight proteins. Ann Rev Biochem 73:107–146

    Article  Google Scholar 

  • Tugarinov V, Choy WY, Orekhov VY, Kay LE (2005) Solution NMR-derived global fold of a monomeric 82-kDa enzyme. Proc Natl Acad Sci USA 102:622–627

    Article  ADS  Google Scholar 

  • Werbelow LG, Marshall AG (1973) Internal-rotation and nonexponential methyl nuclear relaxation for macromolecules. J Magn Reson 11:299–313

    Google Scholar 

  • Zech SG, Olejniczak E, Hajduk P, Mack J, McDermott AE (2004) Characterization of protein—ligand interactions by high-resolution solid-state NMR spectroscopy. J Am Chem Soc 126:13948–13953

    Article  Google Scholar 

  • Zheng DY, Huang YPJ, Moseley HNB, Xiao R, Aramini J, Swapna GVT, Montelione GT (2003) Automated protein fold determination using a minimal NMR constraint strategy. Protein Sci 12:1232–1246

    Article  Google Scholar 

  • Zhong L, Bamm VV, Ahmed MAM, Harauz G, Ladizhansky V (2007) Solid-state NMR spectroscopy of 18.5 kDa myelin basic protein reconstituted with lipid vesicles: spectroscopic characterisation and spectral assignments of solvent-exposed protein fragments. Biochim Biophys Acta Biomembranes 1768:3193–3205

    Article  Google Scholar 

  • Zwahlen C, Gardner KH, Sarma SP, Horita DA, Byrd RA, Kay LE (1998) An NMR experiment for measuring methyl–methyl NOEs in C-13-labeled proteins with high resolution. J Am Chem Soc 120:7617–7625

    Article  Google Scholar 

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Acknowledgments

The facilities provided by NMR Research Centre at IISc supported by Department of Science and Technology (DST), India is gratefully acknowledged. HSA acknowledges support from Indo-Australia biotechnology fund awarded by the Department of Biotechnology (DBT). GJ acknowledges fellowship from Council of Scientific and Industrial Research (CSIR). The authors are sincerely thankful to Dr. Peter Güntert for useful discussions on structure calculation of Cu(II)-ubiquitin using CYANA. We thank Dr. John Cort, Pacific Northwest National Laboratory, for providing the Ubiquitin plasmid.

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Authors and Affiliations

  1. NMR Research Centre, Indian Institute of Science, Bangalore, 560012, India

    Garima Jaipuria, Nitin Prakash Lobo, Divya Shet & Hanudatta S. Atreya

  2. Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore, 560012, India

    Garima Jaipuria & Hanudatta S. Atreya

  3. Department of Physics, Indian Institute of Science, Bangalore, 560012, India

    Nitin Prakash Lobo

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  1. Garima Jaipuria
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Correspondence to Hanudatta S. Atreya.

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Jaipuria, G., Lobo, N.P., Shet, D. et al. High resolution methyl selective 13C-NMR of proteins in solution and solid state. J Biomol NMR 54, 33–42 (2012). https://doi.org/10.1007/s10858-012-9647-0

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  • DOI: https://doi.org/10.1007/s10858-012-9647-0

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