Recent advances in solution NMR: fast methods and heteronuclear direct detection.

Today, NMR spectroscopy is the technique of choice to investigate molecular structure, dynamics, and interactions in solution at atomic resolution. A major limitation of NMR spectroscopy for the study of biological macromolecules such as proteins, nucleic acids, and their complexes, has always been its low sensitivity, a consequence of the weak magnetic spin interactions. Therefore many efforts have been invested in the last decade to improve NMR instrumentation in terms of experimental sensitivity. As a result of these efforts, the availability of high-field magnets, cryogenically cooled probes, and probably in the near future hyperpolarization techniques, the intrinsic NMR sensitivity has increased by at least one order of magnitude. Stimulated by new challenges in the life sciences, these technical improvements have triggered the development of new NMR methods for the study of molecular systems of increasing size and complexity. Herein, we focus on two examples of recently developed NMR methodologies. First, advanced multidimensional data acquisition schemes provide a speed increase of several orders of magnitude. Second, NMR methods based on the direct detection of low-gamma nuclei present a new spectroscopic tool, highly complementary to conventional NMR techniques. These new methods provide powerful new NMR tools for the study of short-lived molecules, large and intrinsically unstructured proteins, paramagnetic systems, as well as for the characterization of molecular kinetic processes at atomic resolution. These examples illustrate how NMR is continuously adapting to the new challenges in the life sciences, with the focus shifting from the characterization of single biomolecules to an integrated view of interacting molecular networks observed at varying levels of biological organization.

[1]  P. Tompa,et al.  H-start for exclusively heteronuclear NMR spectroscopy: the case of intrinsically disordered proteins. , 2009, Journal of magnetic resonance.

[2]  S. Glaser,et al.  Relaxation-optimised Hartmann–Hahn transfer using a specifically Tailored MOCCA-XY16 mixing sequence for carbonyl–carbonyl correlation spectroscopy in 13C direct detection NMR experiments , 2009, Journal of biomolecular NMR.

[3]  P. Tompa,et al.  Structural and dynamic characterization of intrinsically disordered human securin by NMR spectroscopy. , 2008, Journal of the American Chemical Society.

[4]  Wolfgang Bermel,et al.  Assignment of protein NMR spectra based on projections, multi-way decomposition and a fast correlation approach , 2008, Journal of biomolecular NMR.

[5]  Sebastian Hiller,et al.  References and Notes Supporting Online Material Materials and Methods Figures S1 to S5 Table S1 References Solution Structure of the Integral Human Membrane Protein Vdac-1 in Detergent Micelles , 2022 .

[6]  Jeffrey W. Peng,et al.  Direct 13C-detection for carbonyl relaxation studies of protein dynamics. , 2008, Journal of magnetic resonance.

[7]  V. Tugarinov,et al.  An NMR experiment for simultaneous TROSY-based detection of amide and methyl groups in large proteins. , 2008, Journal of the American Chemical Society.

[8]  Ray Freeman,et al.  Molecular structure from a single NMR experiment. , 2008, Journal of the American Chemical Society.

[9]  Wolfgang Bermel,et al.  13C Direct‐detection biomolecular NMR , 2008 .

[10]  B. Brutscher,et al.  Hadamard amino-acid-type edited NMR experiment for fast protein resonance assignment. , 2008, Journal of the American Chemical Society.

[11]  Vladislav Yu Orekhov,et al.  Hyperdimensional NMR spectroscopy with nonlinear sampling. , 2008, Journal of the American Chemical Society.

[12]  S. Pochapsky,et al.  Completing the circuit: direct-observe 13C,15N double-quantum spectroscopy permits sequential resonance assignments near a paramagnetic center in acireductone dioxygenase. , 2008, Journal of the American Chemical Society.

[13]  F. Allain,et al.  Improved segmental isotope labeling methods for the NMR study of multidomain or large proteins: application to the RRMs of Npl3p and hnRNP L. , 2008, Journal of molecular biology.

[14]  Teresa Carlomagno,et al.  13C-detection in RNA bases: revealing structure-chemical shift relationships. , 2007, Journal of the American Chemical Society.

[15]  H. Schwalbe,et al.  Time-resolved NMR methods resolving ligand-induced RNA folding at atomic resolution , 2007, Proceedings of the National Academy of Sciences.

[16]  Ivano Bertini,et al.  A method for Cα direct-detection in protonless NMR , 2007 .

[17]  Bernhard Brutscher,et al.  Hyperdimensional protein NMR spectroscopy in peptide-sequence space. , 2007, Journal of the American Chemical Society.

[18]  Vladimír Sklenář,et al.  13C-detected NMR experiments for measuring chemical shifts and coupling constants in nucleic acid bases , 2007, Journal of biomolecular NMR.

[19]  G. Wider,et al.  Sequence-specific resonance assignment of soluble nonglobular proteins by 7D APSY-NMR spectroscopy. , 2007, Journal of the American Chemical Society.

[20]  Harald Schwalbe,et al.  Time-resolved NMR studies of RNA folding. , 2007, Biopolymers.

[21]  Paul Schanda,et al.  Protein folding and unfolding studied at atomic resolution by fast two-dimensional NMR spectroscopy , 2007, Proceedings of the National Academy of Sciences.

[22]  Ivano Bertini,et al.  13C–13C NOESY spectra of a 480 kDa protein: solution NMR of ferritin , 2007, Journal of biomolecular NMR.

[23]  K. H. Mok,et al.  A pre-existing hydrophobic collapse in the unfolded state of an ultrafast folding protein , 2007, Nature.

[24]  D. Jeannerat Computer optimized spectral aliasing in the indirect dimension of (1)H-(13)C heteronuclear 2D NMR experiments. A new algorithm and examples of applications to small molecules. , 2007, Journal of magnetic resonance.

[25]  Ray Freeman,et al.  Two‐dimensional spectroscopy with parallel acquisition of 1HX and 19FX correlations , 2007, Magnetic resonance in chemistry : MRC.

[26]  G Marius Clore,et al.  Spin-state selective carbon-detected HNCO with TROSY optimization in all dimensions and double echo-antiecho sensitivity enhancement in both indirect dimensions. , 2007, Journal of the American Chemical Society.

[27]  Christoph Göbl,et al.  Mapping the orientation of helices in micelle-bound peptides by paramagnetic relaxation waves. , 2007, Journal of the American Chemical Society.

[28]  P. Schanda,et al.  Automated spectral compression for fast multidimensional NMR and increased time resolution in real-time NMR spectroscopy. , 2007, Journal of the American Chemical Society.

[29]  J. Forman-Kay,et al.  Atomic-level characterization of disordered protein ensembles. , 2007, Current opinion in structural biology.

[30]  P. Schanda,et al.  UltraSOFAST HMQC NMR and the repetitive acquisition of 2D protein spectra at Hz rates. , 2007, Journal of the American Chemical Society.

[31]  P. Schanda,et al.  HET‐SOFAST NMR for fast detection of structural compactness and heterogeneity along polypeptide chains , 2006, Magnetic resonance in chemistry : MRC.

[32]  Francesco Fiorito,et al.  Automated Resonance Assignment of Proteins: 6 DAPSY-NMR , 2006, Journal of biomolecular NMR.

[33]  Krzysztof Kazimierczuk,et al.  Two-dimensional Fourier transform of arbitrarily sampled NMR data sets. , 2006, Journal of magnetic resonance.

[34]  Ivano Bertini,et al.  13C-detected protonless NMR spectroscopy of proteins in solution , 2006 .

[35]  Ivano Bertini,et al.  Protonless NMR experiments for sequence-specific assignment of backbone nuclei in unfolded proteins. , 2006, Journal of the American Chemical Society.

[36]  M. Piccioli,et al.  Assignment Strategy for Fast Relaxing Signals: Complete Aminoacid Identification in Thulium Substituted Calbindin D9K , 2006, Journal of biomolecular NMR.

[37]  M. Delepierre,et al.  Direct-detected 13C NMR to investigate the iron(III) hemophore HasA. , 2006, Journal of the American Chemical Society.

[38]  G. Wagner,et al.  Unambiguous Assignment of NMR Protein Backbone Signals with a Time-shared Triple-resonance Experiment , 2005, Journal of biomolecular NMR.

[39]  Martin Billeter,et al.  Multiway decomposition of NMR spectra with coupled evolution periods. , 2005, Journal of the American Chemical Society.

[40]  I. Bertini,et al.  NMR Spectroscopy of Paramagnetic Metalloproteins , 2005, Chembiochem : a European journal of chemical biology.

[41]  V. Orekhov,et al.  Optimization of resolution and sensitivity of 4D NOESY using Multi-dimensional Decomposition , 2005, Journal of biomolecular NMR.

[42]  Dominique Marion,et al.  Fast acquisition of NMR spectra using Fourier transform of non-equispaced data , 2005, Journal of biomolecular NMR.

[43]  Konstantin Pervushin,et al.  Side-chain H and C resonance assignment in protonated/partially deuterated proteins using an improved 3D(13)C-detected HCC-TOCSY. , 2005, Journal of magnetic resonance.

[44]  Manfred Spraul,et al.  Cryogenically cooled probes—a leap in NMR technology , 2005 .

[45]  Paul Schanda,et al.  Very fast two-dimensional NMR spectroscopy for real-time investigation of dynamic events in proteins on the time scale of seconds. , 2005, Journal of the American Chemical Society.

[46]  Ivano Bertini,et al.  Complete assignment of heteronuclear protein resonances by protonless NMR spectroscopy. , 2005, Angewandte Chemie.

[47]  I. Bertini,et al.  13C direct detected experiments: optimization for paramagnetic signals. , 2005, Journal of magnetic resonance.

[48]  Beat Vögeli,et al.  Detection of C′,Cα correlations in proteins using a new time- and sensitivity-optimal experiment , 2005, Journal of biomolecular NMR.

[49]  Vladislav Yu Orekhov,et al.  High-resolution four-dimensional 1H-13C NOE spectroscopy using methyl-TROSY, sparse data acquisition, and multidimensional decomposition. , 2005, Journal of the American Chemical Society.

[50]  Ivano Bertini,et al.  A selective experiment for the sequential protein backbone assignment from 3D heteronuclear spectra. , 2005, Journal of magnetic resonance.

[51]  I. Bertini,et al.  13C-13C NOESY: A constructive use of 13C-13C spin-diffusion , 2004 .

[52]  Ivano Bertini,et al.  Direct carbon detection in paramagnetic metalloproteins to further exploit pseudocontact shift restraints. , 2004, Journal of the American Chemical Society.

[53]  J. Simorre,et al.  Amino acid-type edited NMR experiments for methyl-methyl distance measurement in 13C-labeled proteins. , 2004, Journal of the American Chemical Society.

[54]  A. J. Shaka,et al.  Ultra-high resolution 3D NMR spectra from limited-size data sets. , 2004, Journal of magnetic resonance.

[55]  H. Dyson,et al.  Unfolded proteins and protein folding studied by NMR. , 2004, Chemical reviews.

[56]  Rafael Brüschweiler,et al.  Theory of covariance nuclear magnetic resonance spectroscopy. , 2004, The Journal of chemical physics.

[57]  Ray Freeman,et al.  Projection-reconstruction technique for speeding up multidimensional NMR spectroscopy. , 2004, Journal of the American Chemical Society.

[58]  I. Bertini,et al.  A Heteronuclear Direct‐Detection NMR Spectroscopy Experiment for Protein‐Backbone Assignment , 2004 .

[59]  G. Wider,et al.  Membrane Protein–Lipid Interactions in Mixed Micelles Studied by NMR Spectroscopy with the Use of Paramagnetic Reagents , 2004, Chembiochem : a European journal of chemical biology.

[60]  J. Prestegard,et al.  Quantitation of rapid proton-deuteron amide exchange using hadamard spectroscopy , 2004, Journal of biomolecular NMR.

[61]  R. Brüschweiler,et al.  Covariance nuclear magnetic resonance spectroscopy. , 2004, The Journal of chemical physics.

[62]  Ivano Bertini,et al.  13C-13C NOESY: an attractive alternative for studying large macromolecules. , 2004, Journal of the American Chemical Society.

[63]  Brian E Coggins,et al.  Generalized reconstruction of n-D NMR spectra from multiple projections: application to the 5-D HACACONH spectrum of protein G B1 domain. , 2004, Journal of the American Chemical Society.

[64]  Ivano Bertini,et al.  13C direct detection experiments on the paramagnetic oxidized monomeric copper, zinc superoxide dismutase. , 2003, Journal of the American Chemical Society.

[65]  R. Freeman,et al.  Projection-reconstruction of three-dimensional NMR spectra. , 2003, Journal of the American Chemical Society.

[66]  Vladislav Yu Orekhov,et al.  Optimizing resolution in multidimensional NMR by three-way decomposition , 2003, Journal of biomolecular NMR.

[67]  B. Brutscher,et al.  Resolution enhancement in multidimensional solid-state NMR spectroscopy of proteins using spin-state selection. , 2003, Journal of the American Chemical Society.

[68]  Lyndon Emsley,et al.  Spin-state selection in solid-state NMR. , 2003, Journal of magnetic resonance.

[69]  R. Freeman,et al.  Hadamard NMR Spectroscopy , 2003 .

[70]  Lucio Frydman,et al.  Single-scan NMR spectroscopy at arbitrary dimensions. , 2003, Journal of the American Chemical Society.

[71]  L. Kay,et al.  Cross-correlated relaxation enhanced 1H[bond]13C NMR spectroscopy of methyl groups in very high molecular weight proteins and protein complexes. , 2003, Journal of the American Chemical Society.

[72]  R. Freeman,et al.  Two-dimensional Hadamard spectroscopy. , 2003, Journal of magnetic resonance.

[73]  Alexander Eletsky,et al.  A novel strategy for the assignment of side-chain resonances in completely deuterated large proteins using 13C spectroscopy , 2003, Journal of biomolecular NMR.

[74]  Ivano Bertini,et al.  A strategy for the NMR characterization of type II copper(II) proteins: the case of the copper trafficking protein CopC from Pseudomonas Syringae. , 2003, Journal of the American Chemical Society.

[75]  David S Wishart,et al.  RefDB: A database of uniformly referenced protein chemical shifts , 2003, Journal of biomolecular NMR.

[76]  Robert G Griffin,et al.  Multiple-quantum magic-angle spinning spectroscopy using nonlinear sampling. , 2003, Journal of magnetic resonance.

[77]  Volker Dötsch,et al.  Elimination of 13Calpha splitting in protein NMR spectra by deconvolution with maximum entropy reconstruction. , 2003, Journal of the American Chemical Society.

[78]  Alexander Eletsky,et al.  A new strategy for backbone resonance assignment in large proteins using a MQ-HACACO experiment , 2003, Journal of biomolecular NMR.

[79]  T. Szyperski,et al.  GFT NMR, a new approach to rapidly obtain precise high-dimensional NMR spectral information. , 2003, Journal of the American Chemical Society.

[80]  Lucio Frydman,et al.  The acquisition of multidimensional NMR spectra within a single scan , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[81]  Beat Vögeli,et al.  Longitudinal (1)H relaxation optimization in TROSY NMR spectroscopy. , 2002, Journal of the American Chemical Society.

[82]  Milka Kostic,et al.  Rapid recycle (13)C',(15)N and (13)C,(13)C' heteronuclear and homonuclear multiple quantum coherence detection for resonance assignments in paramagnetic proteins: example of Ni(2+)-containing acireductone dioxygenase. , 2002, Journal of the American Chemical Society.

[83]  John L Markley,et al.  (13)C[(13)C] 2D NMR: a novel strategy for the study of paramagnetic proteins with slow electronic relaxation rates. , 2002, Journal of the American Chemical Society.

[84]  G. Otting,et al.  Identification of protein surfaces by NMR measurements with a pramagnetic Gd(III) chelate. , 2002, Journal of the American Chemical Society.

[85]  P E Wright,et al.  Sequence-dependent correction of random coil NMR chemical shifts. , 2001, Journal of the American Chemical Society.

[86]  A. J. Shaka,et al.  The Multidimensional Filter Diagonalization Method: II. Application to 2D Projections of 2D, 3D, and 4D NMR Experiments , 2000 .

[87]  Christian Griesinger,et al.  Heteronuclear multidimensional NMR experiments for the structure determination of proteins in solution employing pulsed field gradients , 1999 .

[88]  C. Dobson,et al.  Real-Time NMR Studies of Protein Folding , 1998 .

[89]  J. Weigelt,et al.  Spin-state selection filters for the measurement of heteronuclear one-bond coupling constants , 1998, Journal of biomolecular NMR.

[90]  R. Riek,et al.  Transverse Relaxation-Optimized Spectroscopy (TROSY) for NMR Studies of Aromatic Spin Systems in 13C-Labeled Proteins , 1998 .

[91]  A. Bax,et al.  Measurement of J and dipolar couplings from simplified two-dimensional NMR spectra. , 1998, Journal of magnetic resonance.

[92]  H. Senn,et al.  Fast-HMQC using Ernst angle pulses: An efficient tool for screening of ligand binding to target proteins , 1997, Journal of biomolecular NMR.

[93]  R. Riek,et al.  Attenuated T2 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. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[94]  J. Duus,et al.  Spin-State-Selective Excitation. Application for E.COSY-Type Measurement ofJHHCoupling Constants , 1997 .

[95]  O. W. Sørensen,et al.  Spin-state-selective coherence transfer via intermediate states of two-spin coherence in IS spin systems: Application to E.COSY-type measurement of J coupling constants , 1997 .

[96]  B. Brutscher,et al.  Determination of an Initial Set of NOE-Derived Distance Constraints for the Structure Determination of15N/13C-Labeled Proteins , 1995 .

[97]  Christopher M. Dobson,et al.  Following protein folding in real time using NMR spectroscopy , 1995, Nature Structural Biology.

[98]  R. Kaptein,et al.  1H, 13C, and 15N resonance assignments and secondary structure analysis of the HU protein from Bacillus stearothermophilus using two- and three-dimensional double- and triple-resonance heteronuclear magnetic resonance spectroscopy. , 1994, Biochemistry.

[99]  L. Mueller,et al.  Simultaneous acquisition of [13C,15N]- and [15N,15N]-separated 4D gradient-enhanced NOESY spectra in proteins , 1994, Journal of biomolecular NMR.

[100]  G. Otting,et al.  Improved Spectral Resolution in 1H NMR Spectroscopy by Homonuclear Semiselective Shaped Pulse Decoupling during Acquisition , 1994 .

[101]  R. Kaptein,et al.  Time-saving methods for heteronuclear multidimensional NMR of (13C, 15N) doubly labeled proteins , 1994, Journal of biomolecular NMR.

[102]  L. Kay,et al.  Simultaneous Acquisition of 15N- and 13C-Edited NOE Spectra of Proteins Dissolved in H2O , 1994 .

[103]  G. Wider,et al.  Reduced dimensionality in triple-resonance NMR experiments , 1993 .

[104]  B. Farmer Simultaneous [13C,15N]-HMQC, a pseudo-triple-resonance experiment , 1991 .

[105]  B. Oh,et al.  Protein carbon-13 spin systems by a single two-dimensional nuclear magnetic resonance experiment. , 1988, Science.

[106]  Timothy F. Havel,et al.  Solution conformation of proteinase inhibitor IIA from bull seminal plasma by 1H nuclear magnetic resonance and distance geometry. , 1985, Journal of molecular biology.

[107]  R. Griffey,et al.  Correlation of proton and nitrogen-15 chemical shifts by multiple quantum NMR☆ , 1983 .

[108]  R. R. Ernst,et al.  Two‐dimensional spectroscopy. Application to nuclear magnetic resonance , 1976 .

[109]  Ivano Bertini,et al.  Novel 13C direct detection experiments, including extension to the third dimension, to perform the complete assignment of proteins. , 2006, Journal of magnetic resonance.

[110]  C. Walsh,et al.  Determination of all NOes in 1H–13C–Me-ILV-U−2H–15N Proteins with Two Time-Shared Experiments , 2006, Journal of biomolecular NMR.

[111]  E. Zuiderweg,et al.  Use of13C-13C NOE for the assignment of NMR lines of larger labeled proteins at larger magnetic fields , 1996 .

[112]  C. Griesinger,et al.  A simultaneous 15N,1H- and 13C,1H-HSQC with sensitivity enhancement and a heteronuclear gradient echo , 1995, Journal of biomolecular NMR.

[113]  G. Bodenhausen,et al.  Natural abundance nitrogen-15 NMR by enhanced heteronuclear spectroscopy , 1980 .

[114]  R. R. Ernst,et al.  Application of Fourier Transform Spectroscopy to Magnetic Resonance , 1966 .

[115]  E. Purcell,et al.  Resonance Absorption by Nuclear Magnetic Moments in a Solid , 1946 .