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Liu C, Liu J, Xu X, Xiang S, Wang S. Gd 3+-chelated lipid accelerates solid-state NMR spectroscopy of seven-transmembrane proteins. JOURNAL OF BIOMOLECULAR NMR 2017; 68:203-214. [PMID: 28560567 DOI: 10.1007/s10858-017-0120-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 05/26/2017] [Indexed: 06/07/2023]
Abstract
Solid-state NMR (SSNMR) is an attractive technique for studying large membrane proteins in membrane-mimetic environments. However, SSNMR experiments often suffer from low efficiency, due to the inherent low sensitivity and the long recycle delays needed to recover the magnetization. Here we demonstrate that the incorporation of a small amount of a Gd3+-chelated lipid, Gd3+-DMPE-DTPA, into proteoliposomes greatly shortens the spin-lattice relaxation time (1H-T 1) of lipid-reconstituted membrane proteins and accelerates the data collection. This effect has been evaluated on a 30 kDa, seven-transmembrane protein, Leptosphaeria rhodopsin. With the Gd3+-chelated lipid, we can perform 2D SSNMR experiments 3 times faster than by diamagnetic control. By combining this paramagnetic relaxation-assisted data collection with non-uniform sampling, the 3D experimental times are reduced eightfold with respect to traditional 3D experiments on diamagnetic samples. A comparison between the paramagnetic relaxation enhancement (PRE) effects of Cu2+- and Gd3+-chelated lipids indicates the much higher relaxivity of the latter. Hence, a tenfold lower concentration is needed for Gd3+-chelated lipids to achieve comparable PRE effects to Cu2+-chelated lipids. In addition, Gd3+-chelated lipids neither alter the protein structures nor induce significant line-width broadening of the protein signals. This work is expected to be beneficial for structural and dynamic studies of large membrane proteins by SSNMR.
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Affiliation(s)
- Chang Liu
- College of Chemistry and Molecular Engineering, Peking University, Yiheyuan Rd. 5th, Beijing, China
- Beijing NMR Center, Peking University, Yiheyuan Rd. 5th, Beijing, China
| | - Jing Liu
- College of Chemistry and Molecular Engineering, Peking University, Yiheyuan Rd. 5th, Beijing, China
- Beijing NMR Center, Peking University, Yiheyuan Rd. 5th, Beijing, China
| | - Xiaojun Xu
- College of Chemistry and Molecular Engineering, Peking University, Yiheyuan Rd. 5th, Beijing, China
- Beijing NMR Center, Peking University, Yiheyuan Rd. 5th, Beijing, China
| | - ShengQi Xiang
- Department NMR-Based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Shenlin Wang
- College of Chemistry and Molecular Engineering, Peking University, Yiheyuan Rd. 5th, Beijing, China.
- Beijing NMR Center, Peking University, Yiheyuan Rd. 5th, Beijing, China.
- National Laboratories of Beijing National Laboratory for Molecular Science, Beijing, China.
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2
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Lesot P, Kazimierczuk K, Trébosc J, Amoureux JP, Lafon O. Fast acquisition of multidimensional NMR spectra of solids and mesophases using alternative sampling methods. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2015; 53:927-939. [PMID: 26332109 DOI: 10.1002/mrc.4290] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Revised: 06/09/2015] [Accepted: 06/12/2015] [Indexed: 06/05/2023]
Abstract
Unique information about the atom-level structure and dynamics of solids and mesophases can be obtained by the use of multidimensional nuclear magnetic resonance (NMR) experiments. Nevertheless, the acquisition of these experiments often requires long acquisition times. We review here alternative sampling methods, which have been proposed to circumvent this issue in the case of solids and mesophases. Compared to the spectra of solutions, those of solids and mesophases present some specificities because they usually display lower signal-to-noise ratios, non-Lorentzian line shapes, lower spectral resolutions and wider spectral widths. We highlight herein the advantages and limitations of these alternative sampling methods. A first route to accelerate the acquisition time of multidimensional NMR spectra consists in the use of sparse sampling schemes, such as truncated, radial or random sampling ones. These sparsely sampled datasets are generally processed by reconstruction methods differing from the Discrete Fourier Transform (DFT). A host of non-DFT methods have been applied for solids and mesophases, including the G-matrix Fourier transform, the linear least-square procedures, the covariance transform, the maximum entropy and the compressed sensing. A second class of alternative sampling consists in departing from the Jeener paradigm for multidimensional NMR experiments. These non-Jeener methods include Hadamard spectroscopy as well as spatial or orientational encoding of the evolution frequencies. The increasing number of high field NMR magnets and the development of techniques to enhance NMR sensitivity will contribute to widen the use of these alternative sampling methods for the study of solids and mesophases in the coming years.
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Affiliation(s)
- Philippe Lesot
- RMN en Milieu Orienté, ICMMO, UMR-CNRS 8182, Université de Paris-Sud, Orsay, F-91405, Cedex Orsay, France
| | | | - Julien Trébosc
- Univ. Lille Nord de France, Unité de Catalyse et de Chimie du Solide (UCCS), CNRS UMR 8181, Univ. Lille, 59652, Villeneuve d'Ascq, France
| | - Jean-Paul Amoureux
- Univ. Lille Nord de France, Unité de Catalyse et de Chimie du Solide (UCCS), CNRS UMR 8181, Univ. Lille, 59652, Villeneuve d'Ascq, France
- Physics Department and Shanghai Key Laboratory of Magnetic Resonance, East China Normal University, Shanghai, 200062, China
| | - Olivier Lafon
- Univ. Lille Nord de France, Unité de Catalyse et de Chimie du Solide (UCCS), CNRS UMR 8181, Univ. Lille, 59652, Villeneuve d'Ascq, France
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3
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Xiang S, Chevelkov V, Becker S, Lange A. Towards automatic protein backbone assignment using proton-detected 4D solid-state NMR data. JOURNAL OF BIOMOLECULAR NMR 2014; 60:85-90. [PMID: 25193427 DOI: 10.1007/s10858-014-9859-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Accepted: 08/28/2014] [Indexed: 06/03/2023]
Abstract
We introduce an efficient approach for sequential protein backbone assignment based on two complementary proton-detected 4D solid-state NMR experiments that correlate Hi(N)/Ni with CAi/COi or CAi-1/COi-1. The resulting 4D spectra exhibit excellent sensitivity and resolution and are amenable to (semi-)automatic assignment approaches. This strategy allows to obtain sequential connections with high confidence as problems related to peak overlap and multiple assignment possibilities are avoided. Non-uniform sampling schemes were implemented to allow for the acquisition of 4D spectra within a few days. Rather moderate hardware requirements enable the successful demonstration of the method on deuterated type III secretion needles using a 600 MHz spectrometer at a spinning rate of 25 kHz.
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Affiliation(s)
- ShengQi Xiang
- Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
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4
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Suiter CL, Paramasivam S, Hou G, Sun S, Rice D, Hoch JC, Rovnyak D, Polenova T. Sensitivity gains, linearity, and spectral reproducibility in nonuniformly sampled multidimensional MAS NMR spectra of high dynamic range. JOURNAL OF BIOMOLECULAR NMR 2014; 59:57-73. [PMID: 24752819 PMCID: PMC4142058 DOI: 10.1007/s10858-014-9824-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Accepted: 03/20/2014] [Indexed: 05/04/2023]
Abstract
Recently, we have demonstrated that considerable inherent sensitivity gains are attained in MAS NMR spectra acquired by nonuniform sampling (NUS) and introduced maximum entropy interpolation (MINT) processing that assures the linearity of transformation between the time and frequency domains. In this report, we examine the utility of the NUS/MINT approach in multidimensional datasets possessing high dynamic range, such as homonuclear (13)C-(13)C correlation spectra. We demonstrate on model compounds and on 1-73-(U-(13)C,(15)N)/74-108-(U-(15)N) E. coli thioredoxin reassembly, that with appropriately constructed 50% NUS schedules inherent sensitivity gains of 1.7-2.1-fold are readily reached in such datasets. We show that both linearity and line width are retained under these experimental conditions throughout the entire dynamic range of the signals. Furthermore, we demonstrate that the reproducibility of the peak intensities is excellent in the NUS/MINT approach when experiments are repeated multiple times and identical experimental and processing conditions are employed. Finally, we discuss the principles for design and implementation of random exponentially biased NUS sampling schedules for homonuclear (13)C-(13)C MAS correlation experiments that yield high-quality artifact-free datasets.
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Affiliation(s)
- Christopher L. Suiter
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Sivakumar Paramasivam
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
| | - Guangjin Hou
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Shangjin Sun
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
| | - David Rice
- Agilent Technologies Inc., Santa Clara, CA 95051, USA
| | - Jeffrey C. Hoch
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT 06030-3305, USA
| | - David Rovnyak
- Department of Chemistry, Bucknell University, Lewisburg, PA 17837, USA
| | - Tatyana Polenova
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
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5
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Lin EC, Opella SJ. Sampling scheme and compressed sensing applied to solid-state NMR spectroscopy. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2013; 237:40-48. [PMID: 24140622 PMCID: PMC3851314 DOI: 10.1016/j.jmr.2013.09.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Revised: 09/07/2013] [Accepted: 09/24/2013] [Indexed: 05/11/2023]
Abstract
We describe the incorporation of non-uniform sampling (NUS) compressed sensing (CS) into oriented sample (OS) solid-state NMR for stationary aligned samples and magic angle spinning (MAS) Solid-state NMR for unoriented 'powder' samples. Both simulated and experimental results indicate that 25-33% of a full linearly sampled data set is required to reconstruct two- and three-dimensional solid-state NMR spectra with high fidelity. A modest increase in signal-to-noise ratio accompanies the reconstruction.
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Affiliation(s)
- Eugene C Lin
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0307, United States
| | - Stanley J Opella
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0307, United States.
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6
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Sun S, Yan S, Guo C, Li M, Hoch JC, Williams JC, Polenova T. A time-saving strategy for MAS NMR spectroscopy by combining nonuniform sampling and paramagnetic relaxation assisted condensed data collection. J Phys Chem B 2012; 116:13585-96. [PMID: 23094591 DOI: 10.1021/jp3005794] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
We present a time-saving strategy for acquiring 3D magic angle spinning NMR spectra for chemical shift assignments in proteins and protein assemblies in the solid state. By simultaneous application of nonuniform sampling (NUS) and paramagnetic-relaxation-assisted condensed data collection (PACC), we can attain 16-fold time reduction in the 3D experiments without sacrificing the signal-to-noise ratio or the resolution. We demonstrate that with appropriate concentration of paramagnetic dopant introduced into the sample the overwhelming majority of chemical shifts are not perturbed, with the exception of a limited number of shifts corresponding to residues located at the surface of the protein, which exhibit small perturbations. This approach enables multidimensional MAS spectroscopy in samples of intrinsically low sensitivity and/or high spectral congestion where traditional experiments fail, and is especially beneficial for structural and dynamics studies of large proteins and protein assemblies.
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Affiliation(s)
- Shangjin Sun
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
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7
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Paramasivam S, Suiter CL, Hou G, Sun S, Palmer M, Hoch JC, Rovnyak D, Polenova T. Enhanced sensitivity by nonuniform sampling enables multidimensional MAS NMR spectroscopy of protein assemblies. J Phys Chem B 2012; 116:7416-27. [PMID: 22667827 DOI: 10.1021/jp3032786] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We report dramatic sensitivity enhancements in multidimensional MAS NMR spectra by the use of nonuniform sampling (NUS) and introduce maximum entropy interpolation (MINT) processing that assures the linearity between the time and frequency domains of the NUS acquired data sets. A systematic analysis of sensitivity and resolution in 2D and 3D NUS spectra reveals that with NUS, at least 1.5- to 2-fold sensitivity enhancement can be attained in each indirect dimension without compromising the spectral resolution. These enhancements are similar to or higher than those attained by the newest-generation commercial cryogenic probes. We explore the benefits of this NUS/MaxEnt approach in proteins and protein assemblies using 1-73-(U-(13)C,(15)N)/74-108-(U-(15)N) Escherichia coli thioredoxin reassembly. We demonstrate that in thioredoxin reassembly, NUS permits acquisition of high-quality 3D-NCACX spectra, which are inaccessible with conventional sampling due to prohibitively long experiment times. Of critical importance, issues that hinder NUS-based SNR enhancement in 3D-NMR of liquids are mitigated in the study of solid samples in which theoretical enhancements on the order of 3-4 fold are accessible by compounding the NUS-based SNR enhancement of each indirect dimension. NUS/MINT is anticipated to be widely applicable and advantageous for multidimensional heteronuclear MAS NMR spectroscopy of proteins, protein assemblies, and other biological systems.
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Affiliation(s)
- Sivakumar Paramasivam
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
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8
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Eddy MT, Ruben D, Griffin RG, Herzfeld J. Deterministic schedules for robust and reproducible non-uniform sampling in multidimensional NMR. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2012; 214:296-301. [PMID: 22200565 PMCID: PMC3257378 DOI: 10.1016/j.jmr.2011.12.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2011] [Revised: 11/16/2011] [Accepted: 12/02/2011] [Indexed: 05/20/2023]
Abstract
We show that a simple, general, and easily reproducible method for generating non-uniform sampling (NUS) schedules preserves the benefits of random sampling, including inherently reduced sampling artifacts, while removing the pitfalls associated with choosing an arbitrary seed. Sampling schedules are generated from a discrete cumulative distribution function (CDF) that closely fits the continuous CDF of the desired probability density function. We compare random and deterministic sampling using a Gaussian probability density function applied to 2D HSQC spectra. Data are processed using the previously published method of Spectroscopy by Integration of Frequency and Time domain data (SIFT). NUS spectra from deterministic sampling schedules were found to be at least as good as those from random schedules at the SIFT critical sampling density, and significantly better at half that sampling density. The method can be applied to any probability density function and generalized to greater than two dimensions.
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Affiliation(s)
- Matthew T. Eddy
- Department of Chemistry Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - David Ruben
- Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Robert G. Griffin
- Department of Chemistry Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Judith Herzfeld
- Department of Chemistry, Brandeis University, Waltham, MA 02454, USA
- Corresponding author: voice 781-736-2538, fax 781-736-2516,
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9
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Kalaivani S, Narasimhaswamy T, Das BB, Lobo NP, Ramanathan K. Phase Characterization and Study of Molecular Order of a Three-Ring Mesogen by 13C NMR in Smectic C and Nematic Phases. J Phys Chem B 2011; 115:11554-65. [DOI: 10.1021/jp203388v] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- S. Kalaivani
- Polymer Laboratory, Central Leather Research Institute (Council of Scientific & Industrial Research, CSIR), Adyar, Chennai 600 020, India
| | - T. Narasimhaswamy
- Polymer Laboratory, Central Leather Research Institute (Council of Scientific & Industrial Research, CSIR), Adyar, Chennai 600 020, India
| | - Bibhuti B. Das
- Department of Physics and ‡NMR Research Center, Indian Institute of Science, Bangalore 560 012, India
| | - Nitin P. Lobo
- Department of Physics and ‡NMR Research Center, Indian Institute of Science, Bangalore 560 012, India
| | - K.V. Ramanathan
- Department of Physics and ‡NMR Research Center, Indian Institute of Science, Bangalore 560 012, India
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10
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Matsuki Y, Eddy MT, Griffin RG, Herzfeld J. Rapid three-dimensional MAS NMR spectroscopy at critical sensitivity. Angew Chem Int Ed Engl 2010; 49:9215-8. [PMID: 20957710 PMCID: PMC3495158 DOI: 10.1002/anie.201003329] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Yoh Matsuki
- Department of Chemistry, Brandeis University, Waltham MA 02454 (USA), Fax: (+1) 781 736 2538. Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge MA 02139 (USA)
| | - Matthew T. Eddy
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge MA 02139 (USA)
| | - Robert G. Griffin
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge MA 02139 (USA)
| | - Judith Herzfeld
- Department of Chemistry, Brandeis University, Waltham MA 02454 (USA), Fax: (+1) 781 736 2538
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11
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Matsuki Y, Eddy MT, Griffin RG, Herzfeld J. Rapid Three-Dimensional MAS NMR Spectroscopy at Critical Sensitivity. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201003329] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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12
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Knox RW, Lu GJ, Opella SJ, Nevzorov AA. A resonance assignment method for oriented-sample solid-state NMR of proteins. J Am Chem Soc 2010; 132:8255-7. [PMID: 20509649 DOI: 10.1021/ja102932n] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A general sequential assignment strategy for uniformly (15)N-labeled uniaxially aligned membrane proteins is proposed. Mismatched Hartmann-Hahn magnetization transfer is employed to establish proton-mediated correlations among the neighboring (15)N backbone spins. Magnetically aligned Pf1 phage coat protein was used to illustrate the method. Exchanged and nonexchanged separated local field spectra were acquired and overlaid to distinguish the cross-peaks from the main peaks. Most of the original assignments from the literature were confirmed without selectively labeled samples. This method is applicable to proteins with arbitrary topology and will find use in assigning solid-state NMR spectra of oriented membrane proteins for their subsequent structure determination.
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Affiliation(s)
- Robert W Knox
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, North Carolina 27695-8204, USA
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Bertelsen K, Pedersen JM, Rasmussen BS, Skrydstrup T, Nielsen NC, Vosegaard T. Membrane-Bound Conformation of Peptaibols with Methyl-Deuterated α-Amino Isobutyric Acids by 2H Magic Angle Spinning Solid-State NMR Spectroscopy. J Am Chem Soc 2007; 129:14717-23. [DOI: 10.1021/ja0749690] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kresten Bertelsen
- Contribution from the Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry, University of Aarhus, Langelandsgade 140, DK-8000 Aarhus C, Denmark
| | - Jan M. Pedersen
- Contribution from the Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry, University of Aarhus, Langelandsgade 140, DK-8000 Aarhus C, Denmark
| | - Brian S. Rasmussen
- Contribution from the Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry, University of Aarhus, Langelandsgade 140, DK-8000 Aarhus C, Denmark
| | - Troels Skrydstrup
- Contribution from the Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry, University of Aarhus, Langelandsgade 140, DK-8000 Aarhus C, Denmark
| | - Niels Chr. Nielsen
- Contribution from the Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry, University of Aarhus, Langelandsgade 140, DK-8000 Aarhus C, Denmark
| | - Thomas Vosegaard
- Contribution from the Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry, University of Aarhus, Langelandsgade 140, DK-8000 Aarhus C, Denmark
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14
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Gehman JD, Separovic F, Lu K, Mehta AK. Boltzmann statistics rotational-echo double-resonance analysis. J Phys Chem B 2007; 111:7802-11. [PMID: 17583943 DOI: 10.1021/jp072504q] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A new approach to rotational-echo double-resonance (REDOR) data analysis, analogous to Boltzmann maximum entropy statistics, is reported. This Boltzmann statistics REDOR (BS-REDOR) approach is useful for reconstructing an unbiased internuclear distance distribution for multiple internuclear distances from experimentally limited REDOR data sets on isolated spin pairs. The analysis is characterized by exploring reconstructions on model data and applied to both [1-(13)C,15N]-glycine and a long intramolecular distance in Abeta (16-22) peptide nanotubes. The approach also provides insight into the minimal number of REDOR data points required to allow faithful determination of dipolar couplings in systems with multiple internuclear distances.
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Affiliation(s)
- John D Gehman
- School of Chemistry, Bio21 Institute, University of Melbourne, Melbourne, Victoria 3010, Australia
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15
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Bertelsen K, Pedersen JM, Nielsen NC, Vosegaard T. 2D separated-local-field spectra from projections of 1D experiments. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2007; 184:330-6. [PMID: 17084651 DOI: 10.1016/j.jmr.2006.10.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2006] [Revised: 10/02/2006] [Accepted: 10/16/2006] [Indexed: 05/12/2023]
Abstract
A novel procedure for reconstruction of 2D separated-local-field (SLF) NMR spectra from projections of 1D NMR data is presented. The technique, dubbed SLF projection reconstruction from one-dimensional spectra (SLF-PRODI), is particularly useful for uniaxially oriented membrane protein samples and represents a fast and robust alternative to the popular PISEMA experiment which correlates (1)H-(15)N dipole-dipole couplings with (15)N chemical shifts. The different 1D projections in the SLF-PRODI experiment are obtained from 1D spectra recorded under influence of homonuclear decoupling sequences with different scaling factors for the heteronuclear dipolar couplings. We demonstrate experimentally and numerically that as few as 2-4 1D projections will normally be sufficient to reconstruct a 2D SLF-PRODI spectrum with a quality resembling typical PISEMA spectra, leading to significant reduction of the acquisition time.
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Affiliation(s)
- Kresten Bertelsen
- Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO), University of Aarhus, DK-8000 Aarhus C, Denmark
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16
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Nevzorov AA, Park SH, Opella SJ. Three-dimensional experiment for solid-state NMR of aligned protein samples in high field magnets. JOURNAL OF BIOMOLECULAR NMR 2007; 37:113-6. [PMID: 17216304 DOI: 10.1007/s10858-006-9121-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2006] [Accepted: 10/27/2006] [Indexed: 05/13/2023]
Abstract
A pulse sequence that yields three-dimensional (1)H chemical shift/(1)H-(15)N heteronuclear dipolar coupling/(15)N chemical shift solid-state NMR spectra is demonstrated on a uniformly (15)N labeled membrane protein in magnetically aligned phospholipid bilayers. Based on SAMPI4, the pulse sequence yields high resolution in all three dimensions at a (1)H resonance frequency of 900 MHz with the relatively low rf field strength (33 kHz) available for a lossy aqueous sample with a commercial spectrometer and probe. The (1)H chemical shift frequency dimension is shown to select among amide resonances, which will be useful in studies of larger polytopic membrane proteins where the resonances overlap in two-dimensional spectra. Moreover, the (1)H chemical shift, which can be measured from these spectra, provides an additional orientationally dependent frequency as input for structure calculations.
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Affiliation(s)
- Alexander A Nevzorov
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0307, USA
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