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Penzel S, Oss A, Org ML, Samoson A, Böckmann A, Ernst M, Meier BH. Spinning faster: protein NMR at MAS frequencies up to 126 kHz. JOURNAL OF BIOMOLECULAR NMR 2019; 73:19-29. [PMID: 30680507 PMCID: PMC6441448 DOI: 10.1007/s10858-018-0219-9] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Accepted: 12/05/2018] [Indexed: 05/05/2023]
Abstract
We report linewidth and proton T1, T1ρ and T2' relaxation data of the model protein ubiquitin acquired at MAS frequencies up to 126 kHz. We find a predominantly linear improvement in linewidths and coherence decay times of protons with increasing spinning frequency in the range from 93 to 126 kHz. We further attempt to gain insight into the different contributions to the linewidth at fast MAS using site-specific analysis of proton relaxation parameters and present bulk relaxation times as a function of the MAS frequency. For microcrystalline fully-protonated ubiquitin, inhomogeneous contributions are only a minor part of the proton linewidth, and at 126 kHz MAS coherent effects are still dominating. We furthermore present site-specific proton relaxation rate constants during a spinlock at 126 kHz MAS, as well as MAS-dependent bulk T1ρ (1HN).
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Affiliation(s)
- Susanne Penzel
- Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland
| | - Andres Oss
- NMR Instituut, Tartu Teaduspark, Tehnomeedikum, Tallinn University of Technology, Akadeemia tee 15a, 19086, Tallinn, Estonia
| | - Mai-Liis Org
- NMR Instituut, Tartu Teaduspark, Tehnomeedikum, Tallinn University of Technology, Akadeemia tee 15a, 19086, Tallinn, Estonia
| | - Ago Samoson
- NMR Instituut, Tartu Teaduspark, Tehnomeedikum, Tallinn University of Technology, Akadeemia tee 15a, 19086, Tallinn, Estonia.
| | - Anja Böckmann
- Institut de Biologie et Chimie des Protéines, UMR 5086 CNRS/Université de Lyon 1, Labex ECOFECT, 7, Passage du Vercors, 69367, Lyon, France.
| | - Matthias Ernst
- Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland.
| | - Beat H Meier
- Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland.
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2
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Zhang R, Ramamoorthy A. Constant-time 2D and 3D through-bond correlation NMR spectroscopy of solids under 60 kHz MAS. J Chem Phys 2016; 144:034202. [PMID: 26801026 PMCID: PMC4723396 DOI: 10.1063/1.4940029] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 01/04/2016] [Indexed: 12/13/2022] Open
Abstract
Establishing connectivity and proximity of nuclei is an important step in elucidating the structure and dynamics of molecules in solids using magic angle spinning (MAS) NMR spectroscopy. Although recent studies have successfully demonstrated the feasibility of proton-detected multidimensional solid-state NMR experiments under ultrafast-MAS frequencies and obtaining high-resolution spectral lines of protons, assignment of proton resonances is a major challenge. In this study, we first re-visit and demonstrate the feasibility of 2D constant-time uniform-sign cross-peak correlation (CTUC-COSY) NMR experiment on rigid solids under ultrafast-MAS conditions, where the sensitivity of the experiment is enhanced by the reduced spin-spin relaxation rate and the use of low radio-frequency power for heteronuclear decoupling during the evolution intervals of the pulse sequence. In addition, we experimentally demonstrate the performance of a proton-detected pulse sequence to obtain a 3D (1)H/(13)C/(1)H chemical shift correlation spectrum by incorporating an additional cross-polarization period in the CTUC-COSY pulse sequence to enable proton chemical shift evolution and proton detection in the incrementable t1 and t3 periods, respectively. In addition to through-space and through-bond (13)C/(1)H and (13)C/(13)C chemical shift correlations, the 3D (1)H/(13)C/(1)H experiment also provides a COSY-type (1)H/(1)H chemical shift correlation spectrum, where only the chemical shifts of those protons, which are bonded to two neighboring carbons, are correlated. By extracting 2D F1/F3 slices ((1)H/(1)H chemical shift correlation spectrum) at different (13)C chemical shift frequencies from the 3D (1)H/(13)C/(1)H spectrum, resonances of proton atoms located close to a specific carbon atom can be identified. Overall, the through-bond and through-space homonuclear/heteronuclear proximities determined from the 3D (1)H/(13)C/(1)H experiment would be useful to study the structure and dynamics of a variety of chemical and biological solids.
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Affiliation(s)
- Rongchun Zhang
- Biophysics and Department of Chemistry, The University of Michigan, Ann Arbor, Michigan 48109-1055, USA
| | - Ayyalusamy Ramamoorthy
- Biophysics and Department of Chemistry, The University of Michigan, Ann Arbor, Michigan 48109-1055, USA
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3
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Hierarchical Structure and Molecular Dynamics of Metal-Organic Framework as Characterized by Solid State NMR. J CHEM-NY 2016. [DOI: 10.1155/2016/6510253] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Metal-organic framework (MOF) stands out as a promising material with great potential in application areas, such as gas separation and catalysis, due to its extraordinary properties. In order to fully characterize the structure of MOFs, especially those without single crystal, Solid State NMR (SSNMR) is an indispensable tool. As a complimentary analytical technique to X-ray diffraction, SSNMR could provide detailed atomic level structure information. Meanwhile, SSNMR can characterize molecular dynamics over a wide dynamics range. In this review, selected applications of SSNMR on various MOFs are summarized and discussed.
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Nishiyama Y, Kobayashi T, Malon M, Singappuli-Arachchige D, Slowing II, Pruski M. Studies of minute quantities of natural abundance molecules using 2D heteronuclear correlation spectroscopy under 100 kHz MAS. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2015; 66-67:56-61. [PMID: 25773137 DOI: 10.1016/j.ssnmr.2015.02.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2015] [Revised: 02/05/2015] [Accepted: 02/07/2015] [Indexed: 06/04/2023]
Abstract
Two-dimensional (1)H{(13)C} heteronuclear correlation solid-state NMR spectra of naturally abundant solid materials are presented, acquired using the 0.75-mm magic angle spinning (MAS) probe at spinning rates up to 100 kHz. In spite of the miniscule sample volume (290 nL), high-quality HSQC-type spectra of bulk samples as well as surface-bound molecules can be obtained within hours of experimental time. The experiments are compared with those carried out at 40 kHz MAS using a 1.6-mm probe, which offered higher overall sensitivity due to a larger rotor volume. The benefits of ultrafast MAS in such experiments include superior resolution in (1)H dimension without resorting to (1)H-(1)H homonuclear RF decoupling, easy optimization, and applicability to mass-limited samples. The HMQC spectra of surface-bound species can be also acquired under 100 kHz MAS, although the dephasing of transverse magnetization has significant effect on the efficiency transfer under MAS alone.
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Affiliation(s)
- Y Nishiyama
- JEOL Resonance Inc., 3-1-2 Musashino, Akishima, Tokyo 196-8558, Japan; RIKEN CLST-JEOL Collaboration Center, Yokohama, Kanagawa 230-0045, Japan.
| | - T Kobayashi
- U.S. DOE Ames Laboratory, Ames, IA 50011-3020, USA
| | - M Malon
- JEOL Resonance Inc., 3-1-2 Musashino, Akishima, Tokyo 196-8558, Japan; RIKEN CLST-JEOL Collaboration Center, Yokohama, Kanagawa 230-0045, Japan
| | - D Singappuli-Arachchige
- U.S. DOE Ames Laboratory, Ames, IA 50011-3020, USA; Department of Chemistry, Iowa State University, Ames, IA 50011-3020, USA
| | - I I Slowing
- U.S. DOE Ames Laboratory, Ames, IA 50011-3020, USA; Department of Chemistry, Iowa State University, Ames, IA 50011-3020, USA
| | - M Pruski
- U.S. DOE Ames Laboratory, Ames, IA 50011-3020, USA; Department of Chemistry, Iowa State University, Ames, IA 50011-3020, USA.
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Böckmann A, Ernst M, Meier BH. Spinning proteins, the faster, the better? JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2015; 253:71-9. [PMID: 25797006 DOI: 10.1016/j.jmr.2015.01.012] [Citation(s) in RCA: 106] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Revised: 01/09/2015] [Accepted: 01/18/2015] [Indexed: 05/26/2023]
Abstract
Magic-angle spinning (MAS) is a technique that is a prerequisite for high-resolution solid-state NMR spectroscopy of proteins and other biomolecules. Recently, the 100 kHz limit for the rotation frequency has been broken, arguably making MAS rotors the man-made objects with the highest rotation frequency. This development is expected to have a significant impact on biomolecular NMR as it facilitates proton detection, which allows to partially compensate the loss in overall sensitivity associated with the small sample amounts that fit into MAS rotors with less than 1 mm outer diameter. Under these conditions, the mass-normalized sensitivity of a small rotor becomes much higher than that of larger-volume rotor.
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Affiliation(s)
- Anja Böckmann
- Institut de Biologie et Chimie des Protéines, BMSSI, UMR 5086 CNRS/Université de Lyon 1, 7 passage du Vercors, 69367 Lyon, France.
| | - Matthias Ernst
- Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland.
| | - Beat H Meier
- Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland.
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6
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Althaus SM, Mao K, Stringer JA, Kobayashi T, Pruski M. Indirectly detected heteronuclear correlation solid-state NMR spectroscopy of naturally abundant 15N nuclei. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2014; 57-58:17-21. [PMID: 24287060 DOI: 10.1016/j.ssnmr.2013.11.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Revised: 10/22/2013] [Accepted: 11/01/2013] [Indexed: 06/02/2023]
Abstract
Two-dimensional indirectly detected through-space and through-bond (1)H{(15)N} solid-state NMR experiments utilizing fast magic angle spinning (MAS) and homonuclear multipulse (1)H decoupling are evaluated. Remarkable efficiency of polarization transfer can be achieved at a MAS rate of 40 kHz by both cross-polarization and INEPT, which makes these methods applicable for routine characterizations of natural abundance solids. The first measurement of 2D (1)H{(15)N} HETCOR spectrum of natural abundance surface species is also reported.
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Affiliation(s)
- Stacey M Althaus
- U.S. DOE Ames Laboratory, Ames, IA 50011-3020, USA; Department of Chemistry, Iowa State University, Ames, IA 50011-3020, USA
| | - Kanmi Mao
- U.S. DOE Ames Laboratory, Ames, IA 50011-3020, USA; Department of Chemistry, Iowa State University, Ames, IA 50011-3020, USA
| | - John A Stringer
- Agilent Technologies, 900 South Taft, Loveland, CO 80537, USA
| | - Takeshi Kobayashi
- Department of Chemistry, Iowa State University, Ames, IA 50011-3020, USA
| | - Marek Pruski
- U.S. DOE Ames Laboratory, Ames, IA 50011-3020, USA; Department of Chemistry, Iowa State University, Ames, IA 50011-3020, USA.
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7
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Gutmann T, Grünberg A, Rothermel N, Werner M, Srour M, Abdulhussain S, Tan S, Xu Y, Breitzke H, Buntkowsky G. Solid-state NMR concepts for the investigation of supported transition metal catalysts and nanoparticles. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2013; 55-56:1-11. [PMID: 23972428 DOI: 10.1016/j.ssnmr.2013.06.004] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Revised: 06/20/2013] [Accepted: 06/21/2013] [Indexed: 05/24/2023]
Abstract
In recent years, solid-state NMR spectroscopy has evolved into an important characterization tool for the study of solid catalysts and chemical processes on their surface. This interest is mainly triggered by the need of environmentally benign organic transformations ("green chemistry"), which has resulted in a large number of new catalytically active hybrid materials, which are organized on the meso- and nanoscale. Typical examples of these catalysts are supported homogeneous transition metal catalysts or transition metal nanoparticles (MNPs). Solid-state NMR spectroscopy is able to characterize both the structures of these materials and the chemical processes on the catalytic surface. This article presents recent trends both on the characterization of immobilized homogeneous transition metal catalysts and on the characterization of surface species on transition metal surfaces.
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Affiliation(s)
- Torsten Gutmann
- Institute of Physical Chemistry, Technical University Darmstadt, Petersenstrasse 22, D-64287 Darmstadt, Germany
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8
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Agarwal V, Tuherm T, Reinhold A, Past J, Samoson A, Ernst M, Meier BH. Amplitude-modulated low-power decoupling sequences for fast magic-angle spinning NMR. Chem Phys Lett 2013. [DOI: 10.1016/j.cplett.2013.07.073] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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9
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Li J, van der Wel PCA. Spinning-rate encoded chemical shift correlations from rotational resonance solid-state NMR experiments. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2013; 230:117-24. [PMID: 23475055 PMCID: PMC3635064 DOI: 10.1016/j.jmr.2013.02.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Revised: 01/22/2013] [Accepted: 02/04/2013] [Indexed: 05/23/2023]
Abstract
Structural measurements in magic-angle-spinning (MAS) solid-state NMR rely heavily on (13)C-(13)C distance measurements. Broadbanded recoupling methods are used to generate many cross-peaks, but have complex polarization transfer mechanisms that limit the precision of distance constraints and can suffer from weak intensities for distant peaks due to relaxation, the broad distribution of polarization, as well as dipolar truncation. Frequency-selective methods that feature narrow-banded recoupling can reduce these effects. Indeed, rotational resonance (R(2)) experiments have found application in many different biological systems, where they have afforded improved precision and accuracy. Unfortunately, a highly selective transfer mechanism also leads to few cross-peaks in the resulting spectra, which complicates the extraction of multiple constraints. R(2)-width (R(2)W) measurements that scan a range of MAS rates to probe the R(2) matching conditions of one or more sites can improve precision, and also permit multiple simultaneous distance measurements. However, multidimensional R(2)W can be very time-consuming. Here, we present an approach that facilitates the acquisition of 2D-like spectra based on a series of 1D R(2)W experiments, by taking advantage of the chemical shift information encoded in the MAS rates where matching occurs. This yields a more time-efficient experiment with many of the benefits of more conventional multidimensional R(2)W measurements. The obtained spectra reveal long-distance (13)C-(13)C cross-peaks resulting from R(2)-mediated polarization transfer. This experiment also enables the efficient setup and targeted implementation of traditional R(2) or R(2)W experiments. Analogous applications may extend to other variable-MAS and frequency-selective solid-state NMR experiments.
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Affiliation(s)
- Jun Li
- Department of Structural Biology, University of Pittsburgh School of Medicine, Biomedical Science Tower 3, 3501 Fifth Ave, Pittsburgh, Pennsylvania 15260, USA
| | - Patrick C. A. van der Wel
- Department of Structural Biology, University of Pittsburgh School of Medicine, Biomedical Science Tower 3, 3501 Fifth Ave, Pittsburgh, Pennsylvania 15260, USA
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10
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Barbet-Massin E, Pell AJ, Knight MJ, Webber AL, Felli IC, Pierattelli R, Emsley L, Lesage A, Pintacuda G. 13C-Detected Through-Bond Correlation Experiments for Protein Resonance Assignment by Ultra-Fast MAS Solid-State NMR. Chemphyschem 2013; 14:3131-7. [DOI: 10.1002/cphc.201201097] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2012] [Revised: 02/02/2013] [Indexed: 11/11/2022]
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11
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Gardiennet C, Schütz AK, Hunkeler A, Kunert B, Terradot L, Böckmann A, Meier BH. Hochaufgelöste Festkörper-NMR-Spektren einer sedimentierten, nichtkristallinen dodekameren Helicase (59 kDa). Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201200779] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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12
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Gardiennet C, Schütz AK, Hunkeler A, Kunert B, Terradot L, Böckmann A, Meier BH. A Sedimented Sample of a 59 kDa Dodecameric Helicase Yields High-Resolution Solid-State NMR Spectra. Angew Chem Int Ed Engl 2012; 51:7855-8. [DOI: 10.1002/anie.201200779] [Citation(s) in RCA: 103] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2012] [Revised: 04/10/2012] [Indexed: 11/10/2022]
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Sun S, Han Y, Paramasivam S, Yan S, Siglin AE, Williams JC, Byeon IJL, Ahn J, Gronenborn AM, Polenova T. Solid-state NMR spectroscopy of protein complexes. Methods Mol Biol 2012; 831:303-31. [PMID: 22167681 PMCID: PMC4890720 DOI: 10.1007/978-1-61779-480-3_17] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Protein-protein interactions are vital for many biological processes. These interactions often result in the formation of protein assemblies that are large in size, insoluble, and difficult to crystallize, and therefore are challenging to study by structure biology techniques, such as single crystal X-ray diffraction and solution NMR spectroscopy. Solid-state NMR (SSNMR) spectroscopy is emerging as a promising technique for studies of such protein assemblies because it is not limited by molecular size, solubility, or lack of long-range order. In the past several years, we have applied magic angle spinning SSNMR-based methods to study several protein complexes. In this chapter, we discuss the general SSNMR methodologies employed for structural and dynamics analyses of protein complexes with specific examples from our work on thioredoxin reassemblies, HIV-1 capsid protein assemblies, and microtubule-associated protein assemblies. We present protocols for sample preparation and characterization, pulse sequences, SSNMR spectra collection, and data analysis.
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Affiliation(s)
- Shangjin Sun
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, USA
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Lalli D, Schanda P, Chowdhury A, Retel J, Hiller M, Higman VA, Handel L, Agarwal V, Reif B, van Rossum B, Akbey U, Oschkinat H. Three-dimensional deuterium-carbon correlation experiments for high-resolution solid-state MAS NMR spectroscopy of large proteins. JOURNAL OF BIOMOLECULAR NMR 2011; 51:477-485. [PMID: 22038621 DOI: 10.1007/s10858-011-9578-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2011] [Accepted: 09/23/2011] [Indexed: 05/31/2023]
Abstract
Well-resolved (2)H-(13)C correlation spectra, reminiscent of (1)H-(13)C correlations, are obtained for perdeuterated ubiquitin and for perdeuterated outer-membrane protein G (OmpG) from E. coli by exploiting the favorable lifetime of (2)H double-quantum (DQ) states. Sufficient signal-to-noise was achieved due to the short deuterium T (1), allowing for high repetition rates and enabling 3D experiments with a (2)H-(13)C transfer step in a reasonable time. Well-resolved 3D (2)H(DQ)-(13)C-(13)C correlations of ubiquitin and OmpG were recorded within 3.5 days each. An essentially complete assignment of (2)H(DQα) shifts and of a substantial fraction of (2)H(DQβ) shifts were obtained for ubiquitin. In the case of OmpG, (2)H(DQα) and (2)H(DQβ) chemical shifts of a considerable number of threonine, serine and leucine residues were assigned. This approach provides the basis for a general heteronuclear 3D MAS NMR assignment concept utilizing pulse sequences with (2)H(DQ)-(13)C transfer steps and evolution of deuterium double-quantum chemical shifts.
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Affiliation(s)
- Daniela Lalli
- Leibniz-Institut für Molekulare Pharmakologie (FMP), Berlin, Germany
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Demers JP, Chevelkov V, Lange A. Progress in correlation spectroscopy at ultra-fast magic-angle spinning: basic building blocks and complex experiments for the study of protein structure and dynamics. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2011; 40:101-113. [PMID: 21880471 DOI: 10.1016/j.ssnmr.2011.07.002] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2011] [Revised: 07/21/2011] [Accepted: 07/22/2011] [Indexed: 05/31/2023]
Abstract
Recent progress in multi-dimensional solid-state NMR correlation spectroscopy at high static magnetic fields and ultra-fast magic-angle spinning is discussed. A focus of the review is on applications to protein resonance assignment and structure determination as well as on the characterization of protein dynamics in the solid state. First, the consequences of ultra-fast spinning on sensitivity and sample heating are considered. Recoupling and decoupling techniques at ultra-fast MAS are then presented, as well as more complex experiments assembled from these basic building blocks. Furthermore, we discuss new avenues in biomolecular solid-state NMR spectroscopy that become feasible in the ultra-fast spinning regime, such as sensitivity enhancement based on paramagnetic doping, and the prospect of direct proton detection.
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Affiliation(s)
- Jean-Philippe Demers
- Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
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16
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Hou G, Yan S, Sun S, Han Y, Byeon IJL, Ahn J, Concel J, Samoson A, Gronenborn AM, Polenova T. Spin diffusion driven by R-symmetry sequences: applications to homonuclear correlation spectroscopy in MAS NMR of biological and organic solids. J Am Chem Soc 2011; 133:3943-53. [PMID: 21361320 PMCID: PMC3148607 DOI: 10.1021/ja108650x] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We present a family of homonuclear (13)C-(13)C magic angle spinning spin diffusion experiments, based on R2(n)(v) (n = 1 and 2, v = 1 and 2) symmetry sequences. These experiments are well suited for (13)C-(13)C correlation spectroscopy in biological and organic systems and are especially advantageous at very fast MAS conditions, where conventional PDSD and DARR experiments fail. At very fast MAS frequencies the R2(1)(1), R2(2)(1), and R2(2)(2) sequences result in excellent quality correlation spectra both in model compounds and in proteins. Under these conditions, individual R2(n)(v) display different polarization transfer efficiency dependencies on isotropic chemical shift differences: R2(2)(1) recouples efficiently both small and large chemical shift differences (in proteins these correspond to aliphatic-to-aliphatic and carbonyl-to-aliphatic correlations, respectively), while R2(1)(1) and R2(2)(2) exhibit the maximum recoupling efficiency for the aliphatic-to-aliphatic or carbonyl-to-aliphatic correlations, respectively. At moderate MAS frequencies (10-20 kHz), all R2(n)(v) sequences introduced in this work display similar transfer efficiencies, and their performance is very similar to that of PDSD and DARR. Polarization transfer dynamics and chemical shift dependencies of these R2-driven spin diffusion (RDSD) schemes are experimentally evaluated and investigated by numerical simulations for [U-(13)C,(15)N]-alanine and the [U-(13)C,(15)N] N-formyl-Met-Leu-Phe (MLF) tripeptide. Further applications of this approach are illustrated for several proteins: spherical assemblies of HIV-1 U-(13)C,(15)N CA protein, U-(13)C,(15)N-enriched dynein light chain DLC8, and sparsely (13)C/uniformly (15)N enriched CAP-Gly domain of dynactin. Due to the excellent performance and ease of implementation, the presented R2(n)(v) symmetry sequences are expected to be of wide applicability in studies of proteins and protein assemblies as well as other organic solids by MAS NMR spectroscopy.
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Affiliation(s)
- Guangjin Hou
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
| | - Si Yan
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Shangjin Sun
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Yun Han
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
| | - In-Ja L. Byeon
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
- Department of Structural Biology, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
| | - Jinwoo Ahn
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
- Department of Structural Biology, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
| | - Jason Concel
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
- Department of Structural Biology, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
| | - Ago Samoson
- Tallinn University of Technology, Ehitajate tee 5, 19086, Tallinn, Estonia
- Physics Department, University of Warwick, Coventry, UK
| | - Angela M. Gronenborn
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
- Department of Structural Biology, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
| | - Tatyana Polenova
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
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Huang KY, Siemer AB, McDermott AE. Homonuclear mixing sequences for perdeuterated proteins. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2011; 208:122-7. [PMID: 21094063 PMCID: PMC3021637 DOI: 10.1016/j.jmr.2010.10.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2010] [Revised: 10/18/2010] [Accepted: 10/21/2010] [Indexed: 05/08/2023]
Abstract
We tested the performance of several (13)C homonuclear mixing sequences on perdeuterated microcrystalline ubiquitin. All sequences were applied without (1)H decoupling and at relatively low MAS frequencies. We found that RFDR gave the highest overall transfer efficiency and that DREAM performs surprisingly well under these conditions being twice as efficient in the aliphatic region of the spectrum than the other mixing sequences tested.
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Affiliation(s)
- Kuo-Ying Huang
- Department of Chemistry MC3113, Columbia University, 3000 Broadway, New York, NY 10027, USA
| | - Ansgar B. Siemer
- Department of Chemistry MC3113, Columbia University, 3000 Broadway, New York, NY 10027, USA
| | - Ann E. McDermott
- Department of Chemistry MC3113, Columbia University, 3000 Broadway, New York, NY 10027, USA
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18
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Chan JCC. Solid-state NMR techniques for the structural determination of amyloid fibrils. Top Curr Chem (Cham) 2011; 306:47-88. [PMID: 21630137 DOI: 10.1007/128_2011_154] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
This review discusses the solid-state NMR techniques developed for the study of amyloid fibrils. Literature up to the end of 2010 has been surveyed and the materials are organized according to five categories, viz. homonuclear dipolar recoupling and polarization transfer via J-coupling, heteronuclear dipolar recoupling, correlation spectroscopy, recoupling of chemical shift anisotropy, and tensor correlation. Our emphasis is on the NMR techniques and their practical aspects. The biological implications of the results obtained for amyloid fibrils are only briefly discussed. Our main objective is to showcase the power of NMR in the study of biological unoriented solids.
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Affiliation(s)
- Jerry C C Chan
- Department of Chemistry, National Taiwan University, Taipei, Taiwan.
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19
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Demers JP, Vijayan V, Becker S, Lange A. Tailored low-power cross-polarization under fast magic-angle spinning. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2010; 205:216-23. [PMID: 20570194 DOI: 10.1016/j.jmr.2010.04.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2010] [Accepted: 04/29/2010] [Indexed: 05/10/2023]
Abstract
High static magnetic fields and very fast magic-angle spinning (MAS) promise to improve resolution and sensitivity of solid-state NMR experiments. The fast MAS regime has permitted the development of low-power cross-polarization schemes, such as second-order cross-polarization (SOCP), which prevent heat deposition in the sample. Those schemes are however limited in bandwidth, as weak radio-frequency (RF) fields only cover a small chemical shift range for rare nuclei (e.g. (13)C). Another consideration is that the efficiency of cross-polarization is very sensitive to magnetization decay that occurs during the spin-lock pulse on the abundant nuclei (e.g. (1)H). Having characterized this decay in glutamine at 60 kHz MAS, we propose two complementary strategies to tailor cross-polarization to desired spectral regions at low RF power. In the case of multiple sites with small chemical shift dispersion, a larger bandwidth for SOCP is obtained by slightly increasing the RF power while avoiding recoupling conditions that lead to fast spin-lock decay. In the case of two spectral regions with large chemical shift offset, an extension of the existing low-power schemes, called MOD-CP, is introduced. It consists of a spin-lock on (1)H and an amplitude-modulated spin-lock on the rare nucleus. The range of excited chemical shifts is assessed by experimental excitation profiles and numerical simulation of an I(2)S spin system. All SOCP-based schemes exhibit higher sensitivity than high-power CP schemes, as demonstrated on solid (glutamine) and semi-solid (hydrated, micro-crystalline ubiquitin) samples.
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Affiliation(s)
- Jean-Philippe Demers
- Max Planck Institute for Biophysical Chemistry, Solid-state NMR, Göttingen 37077, Germany
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20
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Broadband magnetization transfer using moderate radio-frequency fields for NMR with very high static fields and spinning speeds. Chem Phys Lett 2010. [DOI: 10.1016/j.cplett.2010.01.072] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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21
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Han Y, Ahn J, Concel J, Byeon IJL, Gronenborn AM, Yang J, Polenova T. Solid-state NMR studies of HIV-1 capsid protein assemblies. J Am Chem Soc 2010; 132:1976-87. [PMID: 20092249 PMCID: PMC2829833 DOI: 10.1021/ja908687k] [Citation(s) in RCA: 106] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In mature HIV-1 virions, the 26.6 kDa CA protein is assembled into a characteristic cone-shaped core (capsid) that encloses the RNA viral genome. The assembled capsid structure is best described by a fullerene cone model that is made up from a hexameric lattice containing a variable number of CA pentamers, thus allowing for closure of tubular or conical structures. In this paper, we present a solid-state NMR analysis of the wild-type HIV-1 CA protein, prepared as conical and spherical assemblies that are stable and are not affected by magic angle spinning of the samples at frequencies between 10 and 25 kHz. Multidimensional homo- and heteronuclear correlation spectra of CA assemblies of uniformly (13)C,(15)N-labeled CA exhibit narrow lines, indicative of the conformational homogeneity of the protein in these assemblies. For the conical assemblies, partial residue-specific resonance assignments were obtained. Analysis of the NMR spectra recorded for the conical and spherical assemblies indicates that the CA protein structure is not significantly different in the different morphologies. The present results demonstrate that the assemblies of CA protein are amenable to detailed structural analysis by solid-state NMR spectroscopy.
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Affiliation(s)
- Yun Han
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States
| | - Jinwoo Ahn
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
- Department of Structural Biology, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
| | - Jason Concel
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
- Department of Structural Biology, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
| | - In-Ja L. Byeon
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
- Department of Structural Biology, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
| | - Angela M. Gronenborn
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
- Department of Structural Biology, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
| | - Jun Yang
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States
| | - Tatyana Polenova
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States
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22
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Schanda P, Huber M, Verel R, Ernst M, Meier BH. Direct detection of (3h)J(NC') hydrogen-bond scalar couplings in proteins by solid-state NMR spectroscopy. Angew Chem Int Ed Engl 2010; 48:9322-5. [PMID: 19894242 DOI: 10.1002/anie.200904411] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Paul Schanda
- Physical Chemistry, ETH Zürich, Wolfgang-Pauli-Strasse 10, 8093 Zürich, Switzerland.
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23
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Cavadini S. Indirect detection of nitrogen-14 in solid-state NMR spectroscopy. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2010; 56:46-77. [PMID: 20633348 DOI: 10.1016/j.pnmrs.2009.08.001] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2009] [Accepted: 08/12/2009] [Indexed: 05/29/2023]
Affiliation(s)
- Simone Cavadini
- Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne, Batochime, Lausanne, Switzerland.
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24
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Mao K, Pruski M. Directly and indirectly detected through-bond heteronuclear correlation solid-state NMR spectroscopy under fast MAS. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2009; 201:165-174. [PMID: 19833538 DOI: 10.1016/j.jmr.2009.09.004] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2009] [Accepted: 09/03/2009] [Indexed: 05/28/2023]
Abstract
Two-dimensional through-bond (1)H{(13)C} solid-state NMR experiments utilizing fast magic angle spinning (MAS) and homonuclear multipulse (1)H decoupling are presented. Remarkable efficiency of polarization transfer can be achieved at MAS rates exceeding 40 kHz, which is instrumental in these measurements. Schemes utilizing direct and indirect detection of heteronuclei are compared in terms of resolution and sensitivity. A simple procedure for optimization of (1)H homonuclear decoupling sequences under these conditions is proposed. The capabilities of these techniques were confirmed on two naturally abundant solids, tripeptide N-formyl-L-methionyl-L-leucyl-L-phenylalanine (f-MLF-OH) and brown coal.
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Affiliation(s)
- Kanmi Mao
- Ames Laboratory, Iowa State University, Ames, IA 50011-3020, USA
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25
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Schanda P, Huber M, Verel R, Ernst M, Meier B. Direct Detection of3hJNCâ²Hydrogen-Bond Scalar Couplings in Proteins by Solid-State NMR Spectroscopy. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200904411] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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26
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Weingarth M, Bodenhausen G, Tekely P. Broadband Carbon-13 Correlation Spectra of Microcrystalline Proteins in Very High Magnetic Fields. J Am Chem Soc 2009; 131:13937-9. [DOI: 10.1021/ja9036143] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Markus Weingarth
- Département de Chimie, Ecole Normale Supérieure, 24 rue Lhomond, 75231 Paris cedex 05, France, and Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Geoffrey Bodenhausen
- Département de Chimie, Ecole Normale Supérieure, 24 rue Lhomond, 75231 Paris cedex 05, France, and Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Piotr Tekely
- Département de Chimie, Ecole Normale Supérieure, 24 rue Lhomond, 75231 Paris cedex 05, France, and Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
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27
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Tian Y, Chen L, Niks D, Kaiser JM, Lai J, Rienstra CM, Dunn MF, Mueller LJ. J-Based 3D sidechain correlation in solid-state proteins. Phys Chem Chem Phys 2009; 11:7078-86. [PMID: 19652843 PMCID: PMC2798598 DOI: 10.1039/b911570f] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Scalar-based three-dimensional homonuclear correlation experiments are reported for (13)C sidechain correlation in solid-state proteins. These experiments are based on a sensitive constant-time format, in which homonuclear scalar couplings are utilized for polarization transfer, but decoupled during chemical shift evolution, to yield highly resolved indirect dimensions and band selectivity as desired. The methods therefore yield spectra of high quality that give unique sets of sidechain correlations for small proteins even at 9.4 Tesla (400 MHz (1)H frequency). We demonstrate versions of the pulse sequence that enable correlation from the sidechain to the backbone carbonyl as well as purely sidechain correlation sets; together these two data sets provide the majority of (13)C-(13)C correlations for assignment. The polarization transfer efficiency is approximately 30% over two bonds. In the protein GB1 (56 residues), we find essentially all cross peaks uniquely resolved. We find similar efficiency of transfer (approximately 30%) in the 140 kDa tryptophan synthase (TS), since the relaxation rates of immobilized solid proteins are not sensitive to global molecular tumbling, as long as the correlation time is much longer than the magic-angle spinning rotor period. In 3D data sets of TS at 400 MHz, some peaks are resolved and, in combination with higher field data sets, we anticipate that assignments will be possible; in this vein, we demonstrate 2D (13)C-(13)C spectra of TS at 900 MHz that are well resolved. These results together provide optimism about the prospects for assigning the spectra of such large enzymes in the solid state.
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Affiliation(s)
- Ye Tian
- Department of Chemistry, University of California, Riverside, California 92521
| | - Lingling Chen
- Department of Chemistry, University of California, Riverside, California 92521
| | - Dimitri Niks
- Department of Biochemistry, University of California, Riverside, California 92521
| | - J. Michael Kaiser
- Department of Chemistry, University of California, Riverside, California 92521
| | - Jinfeng Lai
- Department of Chemistry, University of California, Riverside, California 92521
| | - Chad M. Rienstra
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Michael F. Dunn
- Department of Biochemistry, University of California, Riverside, California 92521
| | - Leonard J. Mueller
- Department of Chemistry, University of California, Riverside, California 92521
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28
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Lewandowski JR, De Paëpe G, Eddy MT, Struppe J, Maas W, Griffin RG. Proton assisted recoupling at high spinning frequencies. J Phys Chem B 2009; 113:9062-9. [PMID: 19489532 PMCID: PMC2738631 DOI: 10.1021/jp810280t] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We demonstrate the successful application of (13)C-(13)C proton assisted recoupling (PAR) on [U-(13)C,(15)N] N-f-MLF-OH and [U-(13)C,(15)N] protein GB1 at high magic angle spinning (MAS) frequencies (omega(r)/2pi = 65 kHz). Specifically, by combining PAR mixing with low power heteronuclear decoupling (omega(1H)/2pi approximately 16 kHz) and high spinning frequencies, we obtain high resolution 2D spectra displaying long-range (13)C-(13)C contacts from which distance estimates can be extracted. These experiments therefore demonstrate the possibility of performing high resolution structural studies in the limit of high spinning frequency and low power (1)H decoupling, a regime which optimizes the resolution of protein samples and preserves their integrity.
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Affiliation(s)
- Józef R. Lewandowski
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Gaël De Paëpe
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Matthew T. Eddy
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Jochem Struppe
- Bruker BioSpin Corporation, Billerica, Massachusetts 01821
| | - Werner Maas
- Bruker BioSpin Corporation, Billerica, Massachusetts 01821
| | - Robert G. Griffin
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
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29
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Sun S, Siglin A, Williams JC, Polenova T. Solid-State and Solution NMR Studies of the CAP-Gly Domain of Mammalian Dynactin and Its Interaction with Microtubules. J Am Chem Soc 2009; 131:10113-26. [PMID: 19580321 DOI: 10.1021/ja902003u] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Shangjin Sun
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, and Department of Molecular Medicine, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, California 91010
| | - Amanda Siglin
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, and Department of Molecular Medicine, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, California 91010
| | - John C. Williams
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, and Department of Molecular Medicine, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, California 91010
| | - Tatyana Polenova
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, and Department of Molecular Medicine, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, California 91010
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30
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31
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Herbst C, Herbst J, Kirschstein A, Leppert J, Ohlenschläger O, Görlach M, Ramachandran R. Design of high-power, broadband 180 degrees pulses and mixing sequences for fast MAS solid state chemical shift correlation NMR spectroscopy. JOURNAL OF BIOMOLECULAR NMR 2009; 43:51-61. [PMID: 19018477 DOI: 10.1007/s10858-008-9292-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2008] [Accepted: 10/28/2008] [Indexed: 05/27/2023]
Abstract
An approach for the design of high-power, broadband 180 degrees pulses and mixing sequences for generating dipolar and scalar coupling mediated (13)C-(13)C chemical shift correlation spectra of isotopically labelled biological systems at fast magic-angle spinning frequencies without (1)H decoupling during mixing is presented. Considering RF field strengths in the range of 100-120 kHz, as typically available in MAS probes employed at high spinning speeds, and limited B (1) field inhomogeneities, the Fourier coefficients defining the phase modulation profile of the RF pulses were optimised numerically to obtain broadband inversion and refocussing pulses and mixing sequences. Experimental measurements were carried out to assess the performance characteristics of the mixing sequences reported here.
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Affiliation(s)
- Christian Herbst
- Leibniz Institute for Age Research, Fritz Lipmann Institute, Jena, Germany
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32
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33
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Bayro MJ, Ramachandran R, Caporini MA, Eddy MT, Griffin RG. Radio frequency-driven recoupling at high magic-angle spinning frequencies: homonuclear recoupling sans heteronuclear decoupling. J Chem Phys 2008; 128:052321. [PMID: 18266438 DOI: 10.1063/1.2834736] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We describe solid-state NMR homonuclear recoupling experiments at high magic-angle spinning (MAS) frequencies using the radio frequency-driven recoupling (RFDR) scheme. The effect of heteronuclear decoupling interference during RFDR recoupling at high spinning frequencies is investigated experimentally and via numerical simulations, resulting in the identification of optimal decoupling conditions. The effects of MAS frequency, RF field amplitude, bandwidth, and chemical shift offsets are examined. Most significantly, it is shown that broadband homonuclear correlation spectra can be efficiently obtained using RFDR without decoupling during the mixing period in fully protonated samples, thus considerably reducing the rf power requirements for acquisition of (13)C-(13)C correlation spectra. The utility of RFDR sans decoupling is demonstrated with broadband correlation spectra of a peptide and a model protein at high MAS frequencies and high magnetic field.
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Affiliation(s)
- Marvin J Bayro
- Francis Bitter Magnet Laboratory and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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34
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Gardiennet C, Loquet A, Etzkorn M, Heise H, Baldus M, Böckmann A. Structural constraints for the Crh protein from solid-state NMR experiments. JOURNAL OF BIOMOLECULAR NMR 2008; 40:239-50. [PMID: 18320329 PMCID: PMC2579321 DOI: 10.1007/s10858-008-9229-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2007] [Accepted: 02/06/2008] [Indexed: 05/11/2023]
Abstract
We demonstrate that short, medium and long-range constraints can be extracted from proton mediated, rare-spin detected correlation solid-state NMR experiments for the microcrystalline 10.4 x 2 kDa dimeric model protein Crh. Magnetization build-up curves from cross signals in NHHC and CHHC spectra deliver detailed information on side chain conformers and secondary structure for interactions between spin pairs. A large number of medium and long-range correlations can be observed in the spectra, and an analysis of the resolved signals reveals that the constraints cover the entire sequence, also including inter-monomer contacts between the two molecules forming the domain-swapped Crh dimer. Dynamic behavior is shown to have an impact on cross signals intensities, as indicated for mobile residues or regions by contacts predicted from the crystal structure, but absent in the spectra. Our work validates strategies involving proton distance measurements for large and complex proteins as the Crh dimer, and confirms the magnetization transfer properties previously described for small molecules in solid protein samples.
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Affiliation(s)
- Carole Gardiennet
- Institut de Biologie et Chimie des Protéines, UMR 5086 C.N.R.S./Université de Lyon, 7, passage du Vercors, 69367 Lyon Cedex 07, France
| | - Antoine Loquet
- Institut de Biologie et Chimie des Protéines, UMR 5086 C.N.R.S./Université de Lyon, 7, passage du Vercors, 69367 Lyon Cedex 07, France
| | - Manuel Etzkorn
- Max-Planck-Institute for Biophysical Chemistry, Solid-state NMR, Am Fassberg 11, 37077 Gottingen, Germany
| | - Henrike Heise
- Max-Planck-Institute for Biophysical Chemistry, Solid-state NMR, Am Fassberg 11, 37077 Gottingen, Germany
| | - Marc Baldus
- Max-Planck-Institute for Biophysical Chemistry, Solid-state NMR, Am Fassberg 11, 37077 Gottingen, Germany
| | - Anja Böckmann
- Institut de Biologie et Chimie des Protéines, UMR 5086 C.N.R.S./Université de Lyon, 7, passage du Vercors, 69367 Lyon Cedex 07, France
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35
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Yang J, Paramasivam S, Marulanda D, Cataldi M, Tasayco ML, Polenova T. Magic angle spinning NMR spectroscopy of thioredoxin reassemblies. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2007; 45 Suppl 1:S73-S83. [PMID: 18157811 DOI: 10.1002/mrc.2092] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Differentially isotopically enriched 1-73((13)C,(15)N)/74-108((15)N) and 1-73((15)N)/74-108((13)C,(15)N) Escherichia coli thioredoxin reassemblies prepared by fragment complementation were investigated by high-resolution magic angle spinning solid-state NMR spectroscopy. Nearly complete resonance assignments, secondary and tertiary structure analysis are reported for 1-73((13)C,(15)N)/74-108((15)N) reassembled thioredoxin. Temperature dependence of the dipolar-assisted rotational resonance (DARR) spectra reveals the residues undergoing intermediate timescale motions at temperatures below - 15 degrees C. Analysis of the DARR intensity buildups as a function of mixing time in these reassemblies indicates that at long mixing times medium- and long-range cross-peaks do not experience dipolar truncation, suggesting that isotopic dilution is not required for gaining nontrivial distance restraints for structure calculations.
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Affiliation(s)
- Jun Yang
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
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36
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Chen L, Kaiser JM, Lai J, Polenova T, Yang J, Rienstra CM, Mueller LJ. J-based 2D homonuclear and heteronuclear correlation in solid-state proteins. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2007; 45 Suppl 1:S84-S92. [PMID: 18157839 DOI: 10.1002/mrc.2107] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Scalar-based two-dimensional heteronuclear experiments are reported for NCO and NCA chemical shift correlation in the solid state. In conjunction with homonuclear CACO correlation, these experiments form a useful set for tracing connectivities and assigning backbone resonances in solid-state proteins. The applicability of this approach is demonstrated on two proteins, the β 1 immunoglobulin binding domain of protein G at 9.4 T and reassembled thioredoxin at 14.1 T, using different decoupling conditions and MAS frequencies. These constant-time J-based correlation experiments exhibit increased resolution in the indirect dimension owing to homonuclear and heteronuclear decoupling, and because the indirect evolution and transfer periods are combined into a single constant time interval, this increased resolution is not obtained at the cost of sensitivity. These experiments are also shown to be compatible with in-phase anti-phase (IPAP) selection, giving increased resolution in the directly detected dimension.
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Affiliation(s)
- Lingling Chen
- Department of Chemistry, University of California, Riverside, California 92521, USA
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37
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Böckmann A. High-resolution solid-state MAS NMR of proteins-Crh as an example. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2007; 45 Suppl 1:S24-S31. [PMID: 18081212 DOI: 10.1002/mrc.2106] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2007] [Revised: 09/04/2007] [Accepted: 09/12/2007] [Indexed: 05/25/2023]
Abstract
Solid-state NMR spectroscopy provides unique possibilities for the structural investigation of insoluble molecules at the atomic level. Recent efforts aim at solving the complete structures of biological macromolecules using high-resolution magic angle spinning NMR. Structurally homogenous samples of [(13)C,(15)N]-labeled proteins have to be used in this type of studies. Microcrystalline model proteins present valuable tools for the developments of methods towards this goal. This review discusses recent progress in the field, using the Crh protein as an illustrative example. We discuss strategies for resonance assignments and for the determination of structure and dynamics, as well as techniques for the detection of protein interaction partners and folding mechanisms by solid-state NMR methods.
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Affiliation(s)
- Anja Böckmann
- IFR 128 BioSciences Lyon-Gerland, IBCP UMR 5086 CNRS/Université de Lyon Claude Bernard, 7 passage du Vercors, 69367 Lyon, France.
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Wylie BJ, Sperling LJ, Rienstra CM. Isotropic chemical shifts in magic-angle spinning NMR spectra of proteins. Phys Chem Chem Phys 2007; 10:405-13. [PMID: 18174982 DOI: 10.1039/b710736f] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Here we examine the effect of magic-angle spinning (MAS) rate upon lineshape and observed peak position for backbone carbonyl (C') peaks in NMR spectra of uniformly-(13)C,15N-labeled (U-(13)C,15N) solid proteins. 2D N-C' spectra of U-(13)C,15N microcrystalline protein GB1 were acquired at six MAS rates, and the site-resolved C' lineshapes were analyzed by numerical simulations and comparison to spectra from a sparsely labeled sample (derived from 1,3-(13)C-glycerol). Spectra of the U-(13)C,15N sample demonstrate large variations in the signal-to-noise ratio and peak positions, which are absent in spectra of the sparsely labeled sample, in which most 13C' sites do not possess a directly bonded 13CA. These effects therefore are a consequence of rotational resonance, which is a well-known phenomenon. Yet the magnitude of this effect pertaining to chemical shift assignment has not previously been examined. To quantify these effects in high-resolution protein spectra, we performed exact numerical two- and four-spin simulations of the C' lineshapes, which reproduced the experimentally observed features. Observed peak positions differ from the isotropic shift by up to 1.0 ppm, even for MAS rates relatively far (a few ppm) from rotational resonance. Although under these circumstances the correct isotropic chemical shift values may be determined through simulation, systematic errors are minimized when the MAS rate is equivalent to approximately 85 ppm for 13C. This moderate MAS condition simplifies spectral assignment and enables data sets from different labeling patterns and spinning rates to be used most efficiently for structure determination.
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Affiliation(s)
- Benjamin J Wylie
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA
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Chen L, Olsen RA, Elliott DW, Boettcher JM, Zhou DH, Rienstra CM, Mueller LJ. Constant-time through-bond 13C correlation spectroscopy for assigning protein resonances with solid-state NMR spectroscopy. J Am Chem Soc 2007; 128:9992-3. [PMID: 16881610 DOI: 10.1021/ja062347t] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Even as available magnetic fields for NMR continue to increase, resolution remains one of the most critical limitations in assigning and solving structures of larger biomolecules. Here we present a novel constant-time through-bond correlation spectroscopy for solids that offers superior resolution for 13C chemical shift assignments in proteins. In this experiment, the indirect evolution and transfer periods are combined into a single constant time interval, offering increased resolution while not sacrificing sensitivity. In GB1, this allows us to resolve peaks that are otherwise unresolved and to make assignments in the absence of multibond transfers.
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Affiliation(s)
- Lingling Chen
- Department of Chemistry, University of California, Riverside, California 92521, USA
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Mou Y, Chao JCH, Chan JCC. Efficient spin-spin scalar coupling mediated C-13 homonuclear polarization transfer in biological solids without proton decoupling. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2006; 29:278-82. [PMID: 16289520 DOI: 10.1016/j.ssnmr.2005.10.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2005] [Revised: 10/05/2005] [Indexed: 05/05/2023]
Abstract
We demonstrate that an efficient C' <--> C alpha polarization transfer based on J-coupling can be realized under fast magic-angle spinning (MAS) condition without 1H decoupling. Experimental results are presented for model crystalline compounds as well as a non-crystalline 17-residue polypeptide MB(i + 4)EK. Measurements on MB(i + 4)EK demonstrate that 53% of the initial C' polarization was transferred to the cross peaks at 7.05 T under 25 kHz MAS spinning.
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Affiliation(s)
- Yun Mou
- Department of Chemistry, National Taiwan University, No. 1, Section 4, Roosevelt Road, Taipei, Taiwan
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41
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De Paëpe G, Bayro MJ, Lewandowski J, Griffin RG. Broadband homonuclear correlation spectroscopy at high magnetic fields and MAS frequencies. J Am Chem Soc 2006; 128:1776-7. [PMID: 16464061 DOI: 10.1021/ja0550430] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We present a new homonuclear recoupling sequence, CMAR, that allows observation of 2D 13C-13C correlation spectra at high magnetic fields and MAS frequencies (10-30 kHz). The main advantages of the sequence are that it provides efficient, broadband dipolar recoupling and concurrently decouples the 1H spins from the 13C's. Thus, no additional 1H decoupling is required during the mixing period, thereby significantly reducing the radio frequency power requirements for the experiment. Thus, CMAR significantly extends the range of applicability of the usual homonuclear recoupling techniques and should be of major interest for structure determinations of biomolecules at high magnetic fields.
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Affiliation(s)
- Gaël De Paëpe
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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Siemer AB, Ritter C, Steinmetz MO, Ernst M, Riek R, Meier BH. 13C, 15N resonance assignment of parts of the HET-s prion protein in its amyloid form. JOURNAL OF BIOMOLECULAR NMR 2006; 34:75-87. [PMID: 16518695 DOI: 10.1007/s10858-005-5582-7] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2005] [Accepted: 11/18/2005] [Indexed: 05/07/2023]
Abstract
The partial 15N and 13C solid-state NMR resonance assignment of the HET-s prion protein fragment 218-289 in its amyloid form is presented. It is based on experiments measured at MAS frequencies in the range of 20-40 kHz using exclusively adiabatic polarization-transfer schemes. The resonance assignment within each residue is based on two-dimensional 13C-13C correlation spectra utilizing the DREAM mixing scheme. The sequential linking of the assigned residues used a set of two- and three-dimensional 15N-13C correlation experiments. Almost all cross peaks visible in the spectra are assigned, but only resonances from 43 of the 78 amino-acid residues could be detected. The missing residues are thought to be highly disordered and/or highly dynamic giving rise to broad resonance lines that escaped detection in the experiments applied. The line widths of the observed resonances are narrow and comparable to line widths observed in micro-crystalline samples. The 43 assigned residues are located in two fragments of about 20 residues.
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Affiliation(s)
- Ansgar B Siemer
- Physical Chemistry, ETH Zurich, CH-8093, Zurich, Switzerland
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44
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45
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Ernst M, Samoson A, Meier BH. Decoupling and recoupling using continuous-wave irradiation in magic-angle-spinning solid-state NMR: A unified description using bimodal Floquet theory. J Chem Phys 2005; 123:64102. [PMID: 16122295 DOI: 10.1063/1.1944291] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The application of two or more different time-dependent coherent perturbations with, in general, incommensurable frequencies occurs quite commonly in NMR experiments. Here we develop a unified description of the entire class of experiments using bimodal Floquet theory and van Vleck-Primas perturbation theory. This treatment leads to a time-independent effective Hamiltonian in Hilbert space and can be looked at as a generalization of average Hamiltonian theory to several incommensurate time dependencies. As a prototype experiment we treat the application of continuous-wave (cw) radio-frequency irradiation in combination with magic-angle sample spinning. Practically relevant examples of this type of experiments are heteronuclear spin decoupling and recoupling experiments using cw irradiation, e.g., rotary-resonance recoupling. Perturbations up to the third order must be taken into account to explain all experimentally observed resonance conditions.
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Affiliation(s)
- Matthias Ernst
- Physical Chemistry, Eidgenössische Technische Hochschule (ETH) Zurich, CH-8093 Zürich, Switzerland.
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Antonijevic S, Bodenhausen G. High-Resolution NMR Spectroscopy in Solids by Truly Magic-Angle Spinning. Angew Chem Int Ed Engl 2005; 44:2935-8. [PMID: 15818628 DOI: 10.1002/anie.200463049] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Sasa Antonijevic
- Laboratoire de Résonance Magnétique Biomoléculaire (LRMB), Institut des Sciences et Ingénierie Chimiques (ISIC), Ecole Polytechnique Fédérale de Lausanne (EPFL), BCH, 1015 Lausanne, Switzerland
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47
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Antonijevic S, Bodenhausen G. High-Resolution NMR Spectroscopy in Solids by Truly Magic-Angle Spinning. Angew Chem Int Ed Engl 2005. [DOI: 10.1002/ange.200463049] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Bechinger B, Aisenbrey C, Bertani P. The alignment, structure and dynamics of membrane-associated polypeptides by solid-state NMR spectroscopy. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2005; 1666:190-204. [PMID: 15519315 DOI: 10.1016/j.bbamem.2004.08.008] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2004] [Accepted: 08/06/2004] [Indexed: 10/26/2022]
Abstract
Solid-state NMR spectroscopy is being developed at a fast pace for the structural investigation of immobilized and non-crystalline biomolecules. These include proteins and peptides associated with phospholipid bilayers. In contrast to solution NMR spectroscopy, where complete or almost complete averaging leads to isotropic values, the anisotropic character of nuclear interactions is apparent in solid-state NMR spectra. In static samples the orientation dependence of chemical shift, dipolar or quadrupolar interactions, therefore, provides angular constraints when the polypeptides have been reconstituted into oriented membranes. Furthermore, solid-state NMR spectroscopy of aligned samples offers distinct advantages in allowing access to dynamic processes such as topological equilibria or rotational diffusion in membrane environments. Alternatively, magic angle sample spinning (MAS) results in highly resolved NMR spectra, provided that the sample is sufficiently homogenous. MAS spinning solid-state NMR spectra allow to measure distances and dihedral angles with high accuracy. The technique has recently been developed to selectively establish through-space and through-bond correlations between nuclei, similar to the approaches well-established in solution-NMR spectroscopy.
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Affiliation(s)
- Burkhard Bechinger
- Faculté de chimie, Institut le Bel, 4, rue Blaise Pascal, 67000 Strasbourg, France.
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Affiliation(s)
- Stanley J Opella
- Department of Chemistry and Biochemistry, University of California-San Diego, La Jolla, CA 92093, USA
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50
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Mueller LJ, Elliott DW, Leskowitz GM, Struppe J, Olsen RA, Kim KC, Reed CA. Uniform-sign cross-peak double-quantum-filtered correlation spectroscopy. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2004; 168:327-335. [PMID: 15140444 DOI: 10.1016/j.jmr.2004.03.017] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2003] [Revised: 03/18/2004] [Indexed: 05/24/2023]
Abstract
We detail the uniform-sign cross-peak double-quantum-filtered correlation spectroscopy (UC2QF COSY) experiment, a new through-bond correlation method for disordered solids. This experiment is a refocused version of the popular double-quantum-filtered correlation spectroscopy experiment in liquids. Its key feature is that it provides in-phase and doubly absorptive line shapes, which renders it robust for chemical shift correlation in solids. Both theory and experiment point to distinct advantages of this protocol, which are illustrated by several experiments under challenging conditions, including fast magic-angle spinning (30kHz), anisotropic molecular motion, and (13)C correlation spectroscopy at the natural abundance isotope level.
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Affiliation(s)
- Leonard J Mueller
- Department of Chemistry, University of California, Riverside, CA 92521, USA.
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