Abstract
The assignment of resonances in the complex nuclear magnetic resonance (NMR) spectrum of a protein is the first step in any NMR study of protein structure, function or dynamics. This chapter aims to provide a tutorial on protein NMR resonance assignment. Two approaches to the assignment are commonly used: the triple resonance methodology, which uses a suite of three-dimensional (3D) 13C/15N/1H NMR experiments, relies on through-bond 1J and 2J intra- and interresidue spin–spin couplings that are observed in 13C–15N double-labelled proteins; and the sequential assignment methodology, which can be applied to unlabelled or 15N single-labelled proteins, relies on through-bond total correlation spectroscopy (TOCSY) data to identify spin systems and through-space nuclear Overhauser effect (NOE) data to establish connections between neighbouring amino acid residues. This chapter describes both the methodologies for protein NMR resonance assignment. Examples of how sequence specific resonance assignments can be obtained using a suite of 2D and 3D NMR experiments are presented and suggestions on how overlap problems can be overcome are included.
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Akke M, Carr PA, Palmer AG 3rd (1994) Heteronuclear-correlation NMR spectroscopy with simultaneous isotope filtration, quadrature detection, and sensitivity enhancement using z rotations. J Magn Reson Ser B 104:298–302
Arseniev AS, Wider G, Joubert FJ, Wüthrich K (1982) Assignment of the H-1 nuclear magnetic-resonance spectrum of the trypsin inhibitor-e from Dendroaspis-Polylepis-Polylepis two-dimensional nuclear magnetic-resonance at 500 MHz. J Mol Biol 159:323–351
Aue WP, Bartholdi E, Ernst RR (1976) 2-Dimensional spectroscopy—application to nuclear magnetic-resonance. J Chem Phys 64:2229–2246
Bai YW, Milne JS, Mayne L, Englander SW (1993) Primary Structure Effects on Peptide Group Hydrogen-Exchange. Proteins 17:75–86
Bartels C, Guntert 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
Bax A, Ikura M (1991) An efficient 3D NMR technique for correlating the proton and 15N backbone amide resonances with the alpha-carbon of the preceding residue in uniformly 15N/13C enriched proteins. J Biomol NMR 1:99–104
Bax A, Clore GM, Gronenborn AM (1990) H-1-H-1 correlation via isotropic mixing of C-13 magnetization, a new 3-Dimensional approach for assigning H-1 and C-13 spectra of C-13-enriched proteins. J Magn Reson 88:425–431
Bermel W, Bruix M, Felli IC, Kumar MVV, Pierattelli R, Serrano S (2013a) Improving the chemical shift dispersion of multidimensional NMR spectra of intrinsically disordered proteins. J Biomol NMR 55:231–237
Bermel W, Felli IC, Gonnelli L, Kozminski W, Piai A, Pierattelli R, Zawadzka-Kazimierczuk A (2013b) High-dimensionality C-13 direct-detected NMR experiments for the automatic assignment of intrinsically disordered proteins. J Biomol NMR 57:353–361
Bertini I, Jimenez B, Pierattelli R, Wedd AG, Xiao Z (2008a) Protonless C-13 direct detection NMR: Characterization of the 37 kDa trimeric protein CutA1. Proteins Struct Funct Bioinform 70:1196–1205
Bertini I, Luchinat C, Parigi G, Pierattelli R (2008b) Perspectives in paramagnetic NMR of metalloproteins. Dalton Trans 29:3782–3790
Billeter M, Braun W, Wüthrich K (1982) Sequential resonance assignments in protein H-1 nuclear magnetic-resonance spectra—computation of sterically allowed proton proton distances and statistical-analysis of proton–proton distances in single-crystal protein conformations. J Mol Biol 155:321–346
Bodenhausen G, Ruben DJ (1980) Natural abundance nitrogen-15 NMR by enhanced heteronuclear spectroscopy. Chem Phys Lett 69:185–189
Buck M, Boyd J, Redfield C, Mackenzie DA, Jeenes DJ, Archer DB, Dobson CM (1995) Structural determinants of protein dynamics—analysis of N-15 NMR relaxation measurements for main-chain and side-chain nuclei of hen egg-white lysozyme. Biochemistry 34:4041–4055
Cavanagh J, Fairbrother WJ, Palmer AG, Rance M, Skelton NJ (2007) Protein NMR spectroscopy—principles and practice, 2nd edn. Elsevier Academic Press, Burlington
Cheung MS, Maguire ML, Stevens TJ, Broadhurst RW (2010) DANGLE: A Bayesian inferential method for predicting protein backbone dihedral angles and secondary structure. J Magn Reson 202:223–233
Clubb RT, Thanabal V, Wagner G (1992) A constant-time 3-Dimensional triple-resonance pulse scheme to correlate intraresidue H-1(N), N-15, and C-13(′) Chemical-Shifts in N-15-C-13-Labeled Proteins. J Magn Reson 97:213–217
Connelly GP, Bai YW, Jeng MF, Englander SW (1993) Isotope effects in peptide group hydrogen-exchange. Proteins 17:87–92
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
Driscoll PC, Hill HAO, Redfield C (1987) H-1-NMR sequential assignments and cation-binding studies of spinach plastocyanin. Eur J Biochem 170:279–292
Englander SW, Wand AJ (1987) Main-chain-directed strategy for the assignment of H-1-NMR spectra of proteins. Biochemistry 26:5953–5958
Fesik SW, Eaton HL, Olejniczak ET, Zuiderweg ERP, Mcintosh LP, Dahlquist FW (1990) 2D and 3D NMR-spectroscopy employing C-13-C-13 magnetization transfer by isotropic mixing—spin system-identification in large proteins. J Am Chem Soc 112:886–888
Frenkiel T, Bauer C, Carr MD, Birdsall B, Feeney J (1990) Hmqc-Noesy-Hmqc, a 3-Dimensional NMR experiment which allows detection of nuclear overhauser effects between protons with overlapping signals. J Magn Reson 90:420–425
Grzesiek S, Bax A (1992a) Improved 3D triple-resonance NMR techniques applied to a 31-Kda protein. J Magn Reson 96:432–440
Grzesiek S, Bax A (1992b) An efficient experiment for sequential backbone assignment of medium-sized isotopically enriched proteins. J Magn Reson 99:201–207
Grzesiek S, Bax A (1992c) Correlating backbone amide and side-chain resonances in larger proteins by multiple relayed triple resonance NMR. J Am Chem Soc 114:6291–6293
Grzesiek S, Bax A (1993a) Amino-acid type determination in the sequential assignment procedure of uniformly C-13/N-15-enriched proteins. J Biomol NMR 3:185–204
Grzesiek S, Bax A (1993b) The importance of not saturating H2O in protein NMR—application to sensitivity enhancement and NOE measurements. J Am Chem Soc 115:12593–12594
Grzesiek S, Anglister J, Bax A (1993) Correlation of backbone amide and aliphatic side-chain resonances in C-13/N-15-enriched proteins by isotropic mixing of C-13 magnetization. J Magn Reson Ser B 101:114–119
Herrmann T, Guntert 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
Ikura M, Bax A, Clore GM, Gronenborn AM (1990a) Detection of nuclear overhauser effects between degenerate amide proton resonances by heteronuclear 3-Dimensional nuclear-magnetic-resonance spectroscopy. J Am Chem Soc 112:9020–9022
Ikura M, Kay LE, Bax A (1990b) A novel-approach for sequential assignment of H-1, C-13, and N-15 spectra of larger proteins—heteronuclear triple-resonance 3-Dimensional NMR-spectroscopy—application to calmodulin. Biochemistry 29:4659–4667
Jeener J, Meier BH, Bachmann P, Ernst RR (1979) Investigation of exchange processes by 2-Dimensional NMR-spectroscopy. J Chem Phys 71:4546–4553
Jung YS, Zweckstetter M (2004) Mars—robust automatic backbone assignment of proteins. J Biomol NMR 30:11–23
Kay LE (1995) Pulsed field gradient multi-dimensional NMR methods for the study of protein structure and dynamics in solution. Prog Biophys Mol Bio 63:277–299
Kay LE, Ikura M, Bax A (1990a) Proton–proton correlation via carbon carbon couplings—a 3-Dimensional NMR approach for the assignment of aliphatic resonances in proteins labeled with C-13. J Am Chem Soc 112:888–889
Kay LE, Ikura M, Tschudin R, Bax A (1990b) 3-Dimensional triple-resonance NMR-spectroscopy of isotopically enriched proteins. J Magn Reson 89:496–514
Logan TM, Olejniczak ET, Xu RX, Fesik SW (1993) A general-method for assigning NMR-spectra of denatured proteins using 3d Hc(Co)Nh-Tocsy triple resonance experiments. J Biomol NMR 3:225–231
Lyons BA, Montelione GT (1993) An hccnh triple-resonance experiment using C-13 isotropic mixing for correlating backbone amide and side-chain aliphatic resonances in isotopically enriched proteins. J Magn Reson Ser B 101:206–209
Marion D, Driscoll PC, Kay LE, Wingfield PT, Bax A, Gronenborn AM, Clore GM (1989) Overcoming the overlap problem in the assignment of H-1-NMR spectra of larger proteins by use of 3-dimensional heteronuclear H-1-N-15 hartmann-hahn multiple quantum coherence and nuclear overhauser multiple quantum coherence spectroscopy—application to interleukin-1-Beta. Biochemistry 28:6150–6156
McIntosh LP, Brun E, Kay LE (1997) Stereospecific assignments of the NH2 resonances from the primary amides of asparagine and glutamine side chains in isotopically labeled proteins. J Biomol NMR 9:306–312
Messerle BA, Wider G, Otting G, Weber C, Wüthrich K (1989) Solvent suppression using a spin lock in 2D and 3D NMR-spectroscopy with H2O solutions. J Magn Reson 85:608–613
Montelione GT, Lyons BA, Emerson SD, Tashiro M (1992) An efficient triple resonance experiment using C-13 isotropic mixing for determining sequence-specific resonance assignments of isotopically-enriched proteins. J Am Chem Soc 114:10974–10975
Moseley HNB, Monleon D, Montelione GT (2001) Automatic determination of protein backbone resonance assignments from triple resonance nuclear magnetic resonance data. Nucl Magn Reson Biol Macromol Pt B 339:91–108
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. Proc Natl Acad Sci U S A 94:12366–12371
Redfield C, Dobson CM (1988) Sequential H-1-NMR assignments and secondary structure of hen egg-white lysozyme in solution. Biochemistry 27:122–136
Redfield C, Smith LJ, Boyd J, Lawrence GMP, Edwards RG, Smith RAG, Dobson CM (1991) Secondary structure and topology of human interleukin-4 in solution. Biochemistry 30:11029–11033
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. Proc Natl Acad Sci USA 95:13585–13590
Salzmann M, Wider G, Pervushin K, Senn H, Wüthrich K (1999) TROSY-type triple-resonance experiments for sequential NMR assignments of large proteins. J Am Chem Soc 121:844–848
Sattler M, Schleucher J, Griesinger C (1999) Heteronuclear multidimensional NMR experiments for the structure determination of proteins in solution employing pulsed field gradients. Prog Nucl Mag Res Sp 34:93–158
Serrano P, Pedrini B, Mohanty B, Geralt M, Herrmann T, Wüthrich K (2012) The J-UNIO protocol for automated protein structure determination by NMR in solution. J Biomol NMR 53:341–354
Shen Y, Bax A (2013) Protein backbone and sidechain torsion angles predicted from NMR chemical shifts using artificial neural networks. J Biomol NMR 56:227–241
Spera S, Bax A (1991) Empirical correlation between protein backbone conformation and Ca and Cb 13C nuclear magnetic resonance chemical shifts. J Am Chem Soc 113:5490–5492
Vranken WF, Boucher W, Stevens TJ, Fogh RH, Pajon A, Llinas P, Ulrich EL, Markley JL, Ionides J, Laue ED (2005) The CCPN data model for NMR spectroscopy: development of a software pipeline. Proteins Struct Funct Bioinform 59:687–696
Vuister GW, Bax A (1993) Quantitative j correlation—a new approach for measuring homonuclear 3-Bond J(H(N)H(Alpha) coupling-constants in N-15-enriched proteins. J Am Chem Soc 115:7772–7777
Wang AC, Lodi PJ, Qin J, Vuister GW, Gronenborn AM, Clore GM (1994) An efficient triple-resonance experiment for proton-directed sequential backbone assignment of medium-sized proteins. J Magn Reson Ser B 105:196–198
Wider G, Lee KH, Wüthrich K (1982) Sequential resonance assignments in protein H-1 nuclear magnetic-resonance spectra—glucagon bound to perdeuterated dodecylphosphocholine micelles. J Mol Biol 155:367–388
Wishart DS, Sykes BD (1994) The C-13 chemical-shift index—a simple method for the identification of protein secondary structure using C-13 Chemical-shift data. J Biomol NMR 4:171–180
Wishart DS, Bigam CG, Holm A, Hodges RS, Sykes BD (1995) H-1, C-13 and N-15 random coil NMR chemical-shifts of the common amino-acids.1. investigations of nearest-neighbor effects (Vol 5, Pg 67, 1995). J Biomol NMR 5:332–332
Wüthrich K (1986) NMR of proteins and nucleic acids. Wiley-Interscience, New York
Wüthrich K, Wider G, Wagner G, Braun W (1982) Sequential resonance assignments as a basis for determination of spatial protein structures by high-resolution proton nuclear magnetic-resonance. J Mol Biol 155:311–319
Yamazaki T, Forman-Kay JD, Kay LE (1993) 2-dimensional NMR experiments for correlating C-13-Beta and H-1-Delta/Epsilon chemical-shifts of aromatic residues in C-13-labeled proteins via scalar couplings. J Am Chem Soc 115:11054–11055
Yamazaki T, Lee W, Arrowsmith CH, Muhandiram DR, Kay LE (1994) A suite of triple-resonance NMR experiments for the backbone assignment of N-15, C-13, H-2 labeled proteins with high-sensitivity. J Am Chem Soc 116:11655–11666
Yang DW, Kay LE (1999) TROSY triple-resonance four-dimensional NMR spectroscopy of a 46 ns tumbling protein. J Am Chem Soc 121:2571–2575
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Redfield, C. (2015). Assignment of Protein NMR Spectra Using Heteronuclear NMR—A Tutorial. In: Berliner, L. (eds) Protein NMR. Biological Magnetic Resonance, vol 32. Springer, Boston, MA. https://doi.org/10.1007/978-1-4899-7621-5_1
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