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Abstract
Thanks to recent improvements in NMR spectrometer hardware and pulse sequence design, modern 13C NMR has become a useful tool for biomolecular applications. The complete assignment of a protein can be accomplished by using 13C detected multinuclear experiments and it can provide unique information relevant for the study of a variety of different biomolecules including paramagnetic proteins and intrinsically disordered proteins. A wide range of NMR observables can be measured, concurring to the structural and dynamic characterization of a protein in isolation, as part of a larger complex, or even inside a living cell. We present the different properties of 13C with respect to 1H, which provide the rationale for the experiments developed and their application, the technical aspects that need to be faced, and the many experimental variants designed to address different cases. Application areas where these experiments successfully complement proton NMR are also described.
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Affiliation(s)
- Isabella C. Felli
- Department of Chemistry “Ugo
Schiff” and Magnetic Resonance Center, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino (Florence), Italy
| | - Roberta Pierattelli
- Department of Chemistry “Ugo
Schiff” and Magnetic Resonance Center, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino (Florence), Italy
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2
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Schütz S, Sprangers R. Methyl TROSY spectroscopy: A versatile NMR approach to study challenging biological systems. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2020; 116:56-84. [PMID: 32130959 DOI: 10.1016/j.pnmrs.2019.09.004] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 09/09/2019] [Accepted: 09/25/2019] [Indexed: 05/21/2023]
Abstract
A major goal in structural biology is to unravel how molecular machines function in detail. To that end, solution-state NMR spectroscopy is ideally suited as it is able to study biological assemblies in a near natural environment. Based on methyl TROSY methods, it is now possible to record high-quality data on complexes that are far over 100 kDa in molecular weight. In this review, we discuss the theoretical background of methyl TROSY spectroscopy, the information that can be extracted from methyl TROSY spectra and approaches that can be used to assign methyl resonances in large complexes. In addition, we touch upon insights that have been obtained for a number of challenging biological systems, including the 20S proteasome, the RNA exosome, molecular chaperones and G-protein-coupled receptors. We anticipate that methyl TROSY methods will be increasingly important in modern structural biology approaches, where information regarding static structures is complemented with insights into conformational changes and dynamic intermolecular interactions.
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Affiliation(s)
- Stefan Schütz
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany
| | - Remco Sprangers
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany.
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3
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Hoch JC. Beyond Fourier. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2017; 283:117-123. [PMID: 28385517 PMCID: PMC5730986 DOI: 10.1016/j.jmr.2017.03.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 03/23/2017] [Accepted: 03/25/2017] [Indexed: 06/07/2023]
Abstract
Non-Fourier methods of spectrum analysis are gaining traction in NMR spectroscopy, driven by their utility for processing nonuniformly sampled data. These methods afford new opportunities for optimizing experiment time, resolution, and sensitivity of multidimensional NMR experiments, but they also pose significant challenges not encountered with the discrete Fourier transform. A brief history of non-Fourier methods in NMR serves to place different approaches in context. Non-Fourier methods reflect broader trends in the growing importance of computation in NMR, and offer insights for future software development.
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Affiliation(s)
- Jeffrey C Hoch
- Department of Molecular Biology and Biophysics, UConn Health, 263 Farmington Ave., Farmington, CT 06030-3305, USA.
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Kakita VMR, Hosur RV. Non-Uniform-Sampling Ultrahigh Resolution TOCSY NMR: Analysis of Complex Mixtures at Microgram Levels. Chemphyschem 2016; 17:2304-8. [DOI: 10.1002/cphc.201600255] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Indexed: 12/27/2022]
Affiliation(s)
- Veera M. R. Kakita
- UM-DAE Centre for Excellence in Basic Sciences; Mumbai University Campus, Kalina, Santa Cruz Mumbai 400 098 India
| | - Ramakrishna V. Hosur
- UM-DAE Centre for Excellence in Basic Sciences; Mumbai University Campus, Kalina, Santa Cruz Mumbai 400 098 India
- Department of Chemical Sciences; Tata Institute of Fundamental Research (TIFR); 1-Homi Bhabha Road, Colaba Mumbai 400 005 India
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Mobli M, Hoch JC. Nonuniform sampling and non-Fourier signal processing methods in multidimensional NMR. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2014; 83:21-41. [PMID: 25456315 PMCID: PMC5776146 DOI: 10.1016/j.pnmrs.2014.09.002] [Citation(s) in RCA: 146] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Revised: 09/26/2014] [Accepted: 09/26/2014] [Indexed: 05/03/2023]
Abstract
Beginning with the introduction of Fourier Transform NMR by Ernst and Anderson in 1966, time domain measurement of the impulse response (the free induction decay, FID) consisted of sampling the signal at a series of discrete intervals. For compatibility with the discrete Fourier transform (DFT), the intervals are kept uniform, and the Nyquist theorem dictates the largest value of the interval sufficient to avoid aliasing. With the proposal by Jeener of parametric sampling along an indirect time dimension, extension to multidimensional experiments employed the same sampling techniques used in one dimension, similarly subject to the Nyquist condition and suitable for processing via the discrete Fourier transform. The challenges of obtaining high-resolution spectral estimates from short data records using the DFT were already well understood, however. Despite techniques such as linear prediction extrapolation, the achievable resolution in the indirect dimensions is limited by practical constraints on measuring time. The advent of non-Fourier methods of spectrum analysis capable of processing nonuniformly sampled data has led to an explosion in the development of novel sampling strategies that avoid the limits on resolution and measurement time imposed by uniform sampling. The first part of this review discusses the many approaches to data sampling in multidimensional NMR, the second part highlights commonly used methods for signal processing of such data, and the review concludes with a discussion of other approaches to speeding up data acquisition in NMR.
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Affiliation(s)
- Mehdi Mobli
- Centre for Advanced Imaging, The University of Queensland, St. Lucia 4072, Brisbane, Australia.
| | - Jeffrey C Hoch
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT 06030-3305, USA.
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Kovacs H, Gossert A. Improved NMR experiments with ¹³C-isotropic mixing for assignment of aromatic and aliphatic side chains in labeled proteins. JOURNAL OF BIOMOLECULAR NMR 2014; 58:101-112. [PMID: 24390406 DOI: 10.1007/s10858-013-9808-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Accepted: 12/20/2013] [Indexed: 06/03/2023]
Abstract
Three improved ¹³C-spinlock experiments for side chain assignments of isotope labelled proteins in liquid state are presented. These are based on wide bandwidth spinlock techniques that have become possible with contemporary cryogenic probes. The first application, the H(C(ali)C(aro))H-TOCSY, is an HCCH-TOCSY in which all CHn moieties of a protein are detected in a single experiment, including the aromatic ones. This enables unambiguous assignment of aromatic and aliphatic amino acids in a single, highly sensitive experiment. In the second application, the ¹³C-detected C(all)-TOCSY, magnetization transfer comprises all carbons--aliphatic, aromatic as well as the carbonyl carbons--making the complete carbon assignment possible using one spectrum only. Thirdly, the frequently used HC(CCO)NH experiment was redesigned by replacing the long C-carbonyl refocused INEPT transfer step by direct ¹³C-¹³C-TOCSY magnetization transfer from side chain carbons to the backbone carbonyls. The resulting HC(CCO)NH experiment minimizes relaxation losses because it is shorter and represents a more sensitive alternative particularly for larger proteins. The performance of the experiments is demonstrated on isotope labeled proteins up to the size of 43 kDa.
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Affiliation(s)
- Helena Kovacs
- Bruker BioSpin AG, Industriestrasse 26, 8117, Fällanden, Switzerland,
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Jaipuria G, Lobo NP, Shet D, Atreya HS. High resolution methyl selective ¹³C-NMR of proteins in solution and solid state. JOURNAL OF BIOMOLECULAR NMR 2012; 54:33-42. [PMID: 22782234 DOI: 10.1007/s10858-012-9647-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Accepted: 06/19/2012] [Indexed: 05/23/2023]
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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Affiliation(s)
- Garima Jaipuria
- NMR Research Centre, Indian Institute of Science, Bangalore 560012, India
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Kazimierczuk K, Stanek J, Zawadzka-Kazimierczuk A, Koźmiński W. Random sampling in multidimensional NMR spectroscopy. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2010; 57:420-34. [PMID: 20920758 DOI: 10.1016/j.pnmrs.2010.07.002] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2010] [Accepted: 07/27/2010] [Indexed: 05/16/2023]
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Richter C, Kovacs H, Buck J, Wacker A, Fürtig B, Bermel W, Schwalbe H. 13C-direct detected NMR experiments for the sequential J-based resonance assignment of RNA oligonucleotides. JOURNAL OF BIOMOLECULAR NMR 2010; 47:259-69. [PMID: 20544375 PMCID: PMC2900595 DOI: 10.1007/s10858-010-9429-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2010] [Accepted: 05/24/2010] [Indexed: 05/08/2023]
Abstract
We present here a set of (13)C-direct detected NMR experiments to facilitate the resonance assignment of RNA oligonucleotides. Three experiments have been developed: (1) the (H)CC-TOCSY-experiment utilizing a virtual decoupling scheme to assign the intraresidual ribose (13)C-spins, (2) the (H)CPC-experiment that correlates each phosphorus with the C4' nuclei of adjacent nucleotides via J(C,P) couplings and (3) the (H)CPC-CCH-TOCSY-experiment that correlates the phosphorus nuclei with the respective C1',H1' ribose signals. The experiments were applied to two RNA hairpin structures. The current set of (13)C-direct detected experiments allows direct and unambiguous assignment of the majority of the hetero nuclei and the identification of the individual ribose moieties following their sequential assignment. Thus, (13)C-direct detected NMR methods constitute useful complements to the conventional (1)H-detected approach for the resonance assignment of oligonucleotides that is often hindered by the limited chemical shift dispersion. The developed methods can also be applied to large deuterated RNAs.
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Affiliation(s)
- Christian Richter
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438 Frankfurt/M, Germany
| | - Helena Kovacs
- Bruker BioSpin AG, Industriestrasse 26, 8117 Fällanden, Switzerland
| | - Janina Buck
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438 Frankfurt/M, Germany
| | - Anna Wacker
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438 Frankfurt/M, Germany
| | - Boris Fürtig
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438 Frankfurt/M, Germany
- Present Address: Max F. Perutz Laboratories, Dr. Bohr-Gasse 9, 1030 Vienna, Austria
| | - Wolfgang Bermel
- Bruker BioSpin GmbH, Silberstreifen, 76287 Rheinstetten, Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438 Frankfurt/M, Germany
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Bermel W, Bertini I, Felli IC, Peruzzini R, Pierattelli R. Exclusively Heteronuclear NMR Experiments to Obtain Structural and Dynamic Information on Proteins. Chemphyschem 2010; 11:689-95. [DOI: 10.1002/cphc.200900772] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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11
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Kirschstein A, Herbst C, Riedel K, Carella M, Leppert J, Ohlenschläger O, Görlach M, Ramachandran R. Broadband homonuclear TOCSY with amplitude and phase-modulated RF mixing schemes. JOURNAL OF BIOMOLECULAR NMR 2008; 40:227-237. [PMID: 18317934 DOI: 10.1007/s10858-008-9225-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2007] [Accepted: 01/25/2008] [Indexed: 05/26/2023]
Abstract
We have explored the design of broadband scalar coupling mediated (13)C-(13)C and cross-relaxation suppressed (1)H-(1)H TOCSY sequences employing phase/amplitude modulated inversion pulses. Considering a variety of supercycles, pulsewidths and a RF field strength of 10 kHz, the Fourier coefficients defining the amplitude and phase modulation profiles of the 180 degrees pulses were optimised numerically so as to obtain efficient magnetisation transfer within the desired range of resonance offsets. The coherence transfer characteristics of the mixing schemes were assessed via numerical simulations and experimental measurements and were compared with commonly used sequences based on rectangular RF pulses. The efficacies of the clean (1)H-(1)H TOCSY sequences were also examined via numerical simulations for application to weakly oriented systems and sequences with efficient, broadband and clean dipolar transfer characteristics were identified. In general, the amplitude and phase modulated TOCSY sequences presented here have moderately better performance characteristics than the sequences currently employed in biomolecular NMR spectroscopy.
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Affiliation(s)
- Anika Kirschstein
- Research Group Biomolecular NMR spectroscopy, Leibniz Institute for Age Research, Fritz Lipmann Institute, 07745, Jena, Germany
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Isaacson RL, Simpson PJ, Liu M, Cota E, Zhang X, Freemont P, Matthews S. A new labeling method for methyl transverse relaxation-optimized spectroscopy NMR spectra of alanine residues. J Am Chem Soc 2007; 129:15428-9. [PMID: 18041839 DOI: 10.1021/ja0761784] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Rivka L Isaacson
- Division of Molecular Biosciences, Faculty of Natural Sciences, Imperial College London, South Kensington, London, UK
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13
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Mobli M, Maciejewski MW, Gryk MR, Hoch JC. Automatic maximum entropy spectral reconstruction in NMR. JOURNAL OF BIOMOLECULAR NMR 2007; 39:133-9. [PMID: 17701276 DOI: 10.1007/s10858-007-9180-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2007] [Revised: 07/09/2007] [Accepted: 07/11/2007] [Indexed: 05/16/2023]
Abstract
Developments in superconducting magnets, cryogenic probes, isotope labeling strategies, and sophisticated pulse sequences together have enabled the application, in principle, of high-resolution NMR spectroscopy to biomolecular systems approaching 1 megadalton. In practice, however, conventional approaches to NMR that utilize the fast Fourier transform, which require data collected at uniform time intervals, result in prohibitively lengthy data collection times in order to achieve the full resolution afforded by high field magnets. A variety of approaches that involve nonuniform sampling have been proposed, each utilizing a non-Fourier method of spectrum analysis. A very general non-Fourier method that is capable of utilizing data collected using any of the proposed nonuniform sampling strategies is maximum entropy reconstruction. A limiting factor in the adoption of maximum entropy reconstruction in NMR has been the need to specify non-intuitive parameters. Here we describe a fully automated system for maximum entropy reconstruction that requires no user-specified parameters. A web-accessible script generator provides the user interface to the system.
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Affiliation(s)
- Mehdi Mobli
- Department of Molecular, Microbial, and Structural Biology, University of Connecticut Health Center, 263 Farmington Ave., Farmington, CT 06030-3305, USA
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Fischer M, Kloiber K, Häusler J, Ledolter K, Konrat R, Schmid W. Synthesis of a 13C-methyl-group-labeled methionine precursor as a useful tool for simplifying protein structural analysis by NMR spectroscopy. Chembiochem 2007; 8:610-2. [PMID: 17328009 DOI: 10.1002/cbic.200600551] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Michael Fischer
- Institute of Organic Chemistry, Department of Biomolecular Structural Chemistry, University of Vienna, Währinger Strasse 38, 1090 Vienna, Austria
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Hu K, Vögeli B, Clore GM. 13C-detected HN(CA)C and HMCMC experiments using a single methyl-reprotonated sample for unambiguous methyl resonance assignment. JOURNAL OF BIOMOLECULAR NMR 2006; 36:259-66. [PMID: 17036159 DOI: 10.1007/s10858-006-9090-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 09/14/2006] [Indexed: 05/12/2023]
Abstract
Methyl groups provide an important source of structural and dynamic information in NMR studies of proteins and their complexes. For this purpose sequence-specific assignments of methyl 1H and 13C resonances are required. In this paper we propose the use of 13C-detected 3D HN(CA)C and HMCMC experiments for assignment of methyl 1H and 13C resonances using a single selectively methyl protonated, perdeuterated and 13C/15N-labeled sample. The high resolution afforded in the 13C directly-detected dimension allows one to rapidly and unambiguously establish correlations between backbone HN strips from the 3D HN(CA)C spectrum and methyl group HmCm strips from the HMCMC spectrum by aligning all possible side-chain carbon chemical shifts and their multiplet splitting patterns. The applicability of these experiments for the assignment of methyl 1H and 13C resonances is demonstrated using the 18.6 kDa B domain of the Escherichia coli mannose transporter (IIBMannose).
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Affiliation(s)
- Kaifeng Hu
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA
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