51
|
Fragai M, Luchinat C, Parigi G, Ravera E. Practical considerations over spectral quality in solid state NMR spectroscopy of soluble proteins. JOURNAL OF BIOMOLECULAR NMR 2013; 57:155-66. [PMID: 23990200 DOI: 10.1007/s10858-013-9776-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2013] [Accepted: 08/23/2013] [Indexed: 05/09/2023]
Abstract
Great theoretical and methodological advances are pushing the limits of resolution and sensitivity in solid state NMR (SSNMR). However, sample preparation remains a critical issue for the success of an experiment. The factors affecting spectral quality in SSNMR samples are discussed, examining cases encountered in the literature and presenting new experimental data. A discussion on resolution and sensitivity in sedimented solutes is framed in this context.
Collapse
Affiliation(s)
- Marco Fragai
- Center for Magnetic Resonance (CERM), University of Florence, Via L. Sacconi 6, 50019, Sesto Fiorentino, FI, Italy
| | | | | | | |
Collapse
|
52
|
Lewandowski JR. Advances in solid-state relaxation methodology for probing site-specific protein dynamics. Acc Chem Res 2013; 46:2018-27. [PMID: 23621579 DOI: 10.1021/ar300334g] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Dynamics are intimately linked to protein stability and play a crucial role in important biological processes, such as ligand binding, allosteric regulation, protein folding, signaling, and enzymatic catalysis. Solid-state NMR relaxation measurements allow researchers to determine the amplitudes, time scales, and under favorable conditions, directionality of motions at atomic resolution over the entire range of dynamic processes from picoseconds to milliseconds. Because this method allows researchers to examine both the amplitudes and time scales of motions in this range, they can link different tiers of protein motions in protein energy landscapes. As a result, scientists can better understand the relationships between protein motions and functions. Such studies are possible both with the primary targets of solid-state NMR studies, such as amyloid fibrils, membrane proteins, or other heterogeneous systems, and others that researchers typically study by solution NMR and X-ray crystallography. In addition, solid-state NMR, with the absence of tumbling in solution, eliminates the intrinsic size limitation imposed by slow tumbling of large proteins. Thus, this technique allows researchers to characterize interdomain and intermolecular interactions in large complexes at the atomic scale. In this Account, we discuss recent advances in solid-state relaxation methodology for studying widespread site-specific protein dynamics. We focus on applications involving magic angle spinning, one of the primary methods used in high-resolution solid-state NMR. We give an overview of challenges and solutions for measuring (15)N and (13)C spin-lattice relaxation (R1) to characterize fast picosecond-nanosecond motions, spin-lattice in the rotating frame (R1ρ), and other related relaxation rates for characterization of picosecond-millisecond protein motions. In particular, we discuss the problem of separating incoherent effects caused by random motions from coherent effects arising from incomplete averaging of orientation-dependent NMR interactions. We mention a number of quantitative studies of protein dynamics based on solid-state relaxation measurements. Finally, we discuss the potential use of relaxation measurements for extracting the directionality of motions. Using the (15)N and (13)C R1 and R1ρ measurements, we illustrate the backbone and side-chain dynamics in the protein GB1 and comment on this emerging dynamic picture within the context of data from solution NMR measurements and simulations.
Collapse
|
53
|
Knight MJ, Felli IC, Pierattelli R, Emsley L, Pintacuda G. Magic angle spinning NMR of paramagnetic proteins. Acc Chem Res 2013; 46:2108-16. [PMID: 23506094 DOI: 10.1021/ar300349y] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Metal ions are ubiquitous in biochemical and cellular processes. Since many metal ions are paramagnetic due to the presence of unpaired electrons, paramagnetic molecules are an important class of targets for research in structural biology and related fields. Today, NMR spectroscopy plays a central role in the investigation of the structure and chemical properties of paramagnetic metalloproteins, linking the observed paramagnetic phenomena directly to electronic and molecular structure. A major step forward in the study of proteins by solid-state NMR came with the advent of ultrafast magic angle spinning (MAS) and the ability to use (1)H detection. Combined, these techniques have allowed investigators to observe nuclei that previously were invisible in highly paramagnetic metalloproteins. In addition, these techniques have enabled quantitative site-specific measurement of a variety of long-range paramagnetic effects. Instead of limiting solid-state NMR studies of biological systems, paramagnetism provides an information-rich phenomenon that can be exploited in these studies. This Account emphasizes state-of-the-art methods and applications of solid-state NMR in paramagnetic systems in biological chemistry. In particular, we discuss the use of ultrafast MAS and (1)H-detection in perdeuterated paramagnetic metalloproteins. Current methodology allows us to determine the structure and dynamics of metalloenzymes, and, as an example, we describe solid-state NMR studies of microcrystalline superoxide dismutase, a 32 kDa dimer. Data were acquired with remarkably short times, and these experiments required only a few milligrams of sample.
Collapse
Affiliation(s)
- Michael J. Knight
- Université de Lyon, Institut de Sciences Analytiques (CNRS / ENS-Lyon / UCB Lyon 1), Centre de RMN à Très Hauts Champs, 5 rue de la Doua, 69100 Villeurbanne, France
| | - Isabella C. Felli
- Department of Chemistry “Ugo Schiff“ and Magnetic Resonance Center (CERM), University of Florence, via Luigi Sacconi 6 − 50019 Sesto Fiorentino, FI, Italy
| | - Roberta Pierattelli
- Department of Chemistry “Ugo Schiff“ and Magnetic Resonance Center (CERM), University of Florence, via Luigi Sacconi 6 − 50019 Sesto Fiorentino, FI, Italy
| | - Lyndon Emsley
- Université de Lyon, Institut de Sciences Analytiques (CNRS / ENS-Lyon / UCB Lyon 1), Centre de RMN à Très Hauts Champs, 5 rue de la Doua, 69100 Villeurbanne, France
| | - Guido Pintacuda
- Université de Lyon, Institut de Sciences Analytiques (CNRS / ENS-Lyon / UCB Lyon 1), Centre de RMN à Très Hauts Champs, 5 rue de la Doua, 69100 Villeurbanne, France
| |
Collapse
|
54
|
Bertini I, Luchinat C, Parigi G, Ravera E. SedNMR: on the edge between solution and solid-state NMR. Acc Chem Res 2013; 46:2059-69. [PMID: 23470055 DOI: 10.1021/ar300342f] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Solid-state NMR (SS-NMR) of proteins requires that those molecules be immobilized, usually by crystallization, freezing, or lyophilization. However, self-crowding can also slow molecular rotation sufficiently to prevent the nuclear interactions from averaging. To achieve self-crowding, researchers can use a centrifugal field to create a concentration gradient or use regular ultracentrifugation to produce highly concentrated, gel-like solutions. Thus sedimented solute NMR (SedNMR) provides a simple method to prepare biological samples for SS-NMR experiments with minimal perturbation. This method may also give researchers a way to investigate species that are not otherwise accessible by NMR. We induce the sedimentation in one of two ways: (1) by the extreme centrifugal force exerted during magic angle spinning (MAS-induced sedimentation or in situ) or (2) by an ultracentrifuge (UC-induced sedimentation or ex situ). Sedimentation is particularly useful in situations where it is difficult to obtain protein crystals. Furthermore, because the proteins remain in a largely hydrated state, the sedimented samples may provide SS-NMR spectra that have better resolution than the spectra from frozen solutions or lyophilized powders. If sedimentation is induced in situ, the same protein sample can be used for both solution and SS-NMR studies. Finally, we show that in situ SedNMR can be used to detect the NMR signals of large molecular adducts that have binding constants that are too weak to allow for the selective isolation and crystallization of the complexed species. We can selectively induce sedimentation for the heaviest molecular species. Because the complexed molecules are subtracted from the bulk solution, the reaction proceeds further toward the formation of complexes.
Collapse
Affiliation(s)
- Ivano Bertini
- CERM, University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy, and Department of Chemistry “U. Schiff”, University of Florence, via della Lastruccia 3, 50019, Sesto Fiorentino, Italy
| | - Claudio Luchinat
- CERM, University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy, and Department of Chemistry “U. Schiff”, University of Florence, via della Lastruccia 3, 50019, Sesto Fiorentino, Italy
| | - Giacomo Parigi
- CERM, University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy, and Department of Chemistry “U. Schiff”, University of Florence, via della Lastruccia 3, 50019, Sesto Fiorentino, Italy
| | - Enrico Ravera
- CERM, University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy, and Department of Chemistry “U. Schiff”, University of Florence, via della Lastruccia 3, 50019, Sesto Fiorentino, Italy
| |
Collapse
|
55
|
Gelis I, Vitzthum V, Dhimole N, Caporini MA, Schedlbauer A, Carnevale D, Connell SR, Fucini P, Bodenhausen G. Solid-state NMR enhanced by dynamic nuclear polarization as a novel tool for ribosome structural biology. JOURNAL OF BIOMOLECULAR NMR 2013; 56:85-93. [PMID: 23689811 DOI: 10.1007/s10858-013-9721-2] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Accepted: 03/07/2013] [Indexed: 06/02/2023]
Abstract
The impact of Nuclear Magnetic Resonance (NMR) on studies of large macromolecular complexes hinges on improvements in sensitivity and resolution. Dynamic nuclear polarization (DNP) in the solid state can offer improved sensitivity, provided sample preparation is optimized to preserve spectral resolution. For a few nanomoles of intact ribosomes and an 800 kDa ribosomal complex we demonstrate that the combination of DNP and magic-angle spinning NMR (MAS-NMR) allows one to overcome current sensitivity limitations so that homo- and heteronuclear (13)C and (15)N NMR correlation spectra can be recorded. Ribosome particles, directly pelleted and frozen into an NMR rotor, yield DNP signal enhancements on the order of ~25-fold and spectra that exhibit narrow linewidths, suitable for obtaining site-specific information. We anticipate that the same approach is applicable to other high molecular weight complexes.
Collapse
Affiliation(s)
- Ioannis Gelis
- Buchmann Institute for Molecular Life Sciences, Institute of Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | | | | | | | | | | | | | | | | |
Collapse
|
56
|
Banigan JR, Gayen A, Traaseth NJ. Combination of ¹⁵N reverse labeling and afterglow spectroscopy for assigning membrane protein spectra by magic-angle-spinning solid-state NMR: application to the multidrug resistance protein EmrE. JOURNAL OF BIOMOLECULAR NMR 2013; 55:391-9. [PMID: 23539118 PMCID: PMC3747971 DOI: 10.1007/s10858-013-9724-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Accepted: 03/15/2013] [Indexed: 05/20/2023]
Abstract
Magic-angle-spinning (MAS) solid-state NMR spectroscopy has emerged as a viable method to characterize membrane protein structure and dynamics. Nevertheless, the spectral resolution for uniformly labeled samples is often compromised by redundancy of the primary sequence and the presence of helical secondary structure that results in substantial resonance overlap. The ability to simplify the spectrum in order to obtain unambiguous site-specific assignments is a major bottleneck for structure determination. To address this problem, we used a combination of (15)N reverse labeling, afterglow spectroscopic techniques, and frequency-selective dephasing experiments that dramatically improved the ability to resolve peaks in crowded spectra. This was demonstrated using the polytopic membrane protein EmrE, an efflux pump involved in multidrug resistance. Residues preceding the (15)N reverse labeled amino acid were imaged using a 3D NCOCX afterglow experiment and those following were recorded using a frequency-selective dephasing experiment. Our approach reduced the spectral congestion and provided a sensitive way to obtain chemical shift assignments for a membrane protein where no high-resolution structure is available. This MAS methodology is widely applicable to the study of other polytopic membrane proteins in functional lipid bilayer environments.
Collapse
Affiliation(s)
| | | | - Nathaniel J. Traaseth
- Author for correspondence: Nathaniel J. Traaseth 100 Washington Square East New York, NY 10003 Phone: (212) 992-9784
| |
Collapse
|
57
|
Kulichikhin VG, Yampolskaya GP. Colloid-chemical aspects of protein crystallization. Russ Chem Bull 2013. [DOI: 10.1007/s11172-013-0045-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
|
58
|
Ikeda K, Egawa A, Fujiwara T. Secondary structural analysis of proteins based on (13)C chemical shift assignments in unresolved solid-state NMR spectra enhanced by fragmented structure database. JOURNAL OF BIOMOLECULAR NMR 2013; 55:189-200. [PMID: 23271376 DOI: 10.1007/s10858-012-9701-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Accepted: 12/21/2012] [Indexed: 06/01/2023]
Abstract
Magic-angle-spinning solid-state (13)C NMR spectroscopy is useful for structural analysis of non-crystalline proteins. However, the signal assignments and structural analysis are often hampered by the signal overlaps primarily due to minor structural heterogeneities, especially for uniformly-(13)C,(15)N labeled samples. To overcome this problem, we present a method for assigning (13)C chemical shifts and secondary structures from unresolved two-dimensional (13)C-(13)C MAS NMR spectra by spectral fitting, named reconstruction of spectra using protein local structures (RESPLS). The spectral fitting was conducted using databases of protein fragmented structures related to (13)C(α), (13)C(β), and (13)C' chemical shifts and cross-peak intensities. The experimental (13)C-(13)C inter- and intra-residue correlation spectra of uniformly isotope-labeled ubiquitin in the lyophilized state had a few broad peaks. The fitting analysis for these spectra provided sequence-specific C(α), C(β), and C' chemical shifts with an accuracy of about 1.5 ppm, which enabled the assignment of the secondary structures with an accuracy of 79 %. The structural heterogeneity of the lyophilized ubiquitin is revealed from the results. Test of RESPLS analysis for simulated spectra of five different types of proteins indicated that the method allowed the secondary structure determination with accuracy of about 80 % for the 50-200 residue proteins. These results demonstrate that the RESPLS approach expands the applicability of the NMR to non-crystalline proteins exhibiting unresolved (13)C NMR spectra, such as lyophilized proteins, amyloids, membrane proteins and proteins in living cells.
Collapse
Affiliation(s)
- Keisuke Ikeda
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, 565-0871, Japan
| | | | | |
Collapse
|
59
|
Shi X, Yarger JL, Holland GP. 2H-13C HETCOR MAS NMR for indirect detection of 2H quadrupole patterns and spin-lattice relaxation rates. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2013; 226:1-12. [PMID: 23174312 DOI: 10.1016/j.jmr.2012.10.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Revised: 10/17/2012] [Accepted: 10/22/2012] [Indexed: 06/01/2023]
Abstract
Two-dimensional (2D) cross-polarization magic angle spinning (CP-MAS) (2)H-(13)C heteronuclear correlation (HETCOR) experiments were utilized to indirectly detect site-specific deuterium MAS powder patterns. The (2)H-(13)C cross-polarization efficiency is orientation-dependent and non-uniform for all crystallites. This leads to difficulty in extracting the correct (2)H MAS quadrupole powder patterns. In order to obtain accurate deuterium line shapes, (13)C spin lock rf field, spin lock rf ramp and CP contact time were carefully calibrated with the assistance of theoretical simulations. The extracted quadrupole patterns for U-[(2)H/(13)C/(15)N]-alanine indicate that the methyl deuterium undergoes classic, three-site jumping in the fast motion regime (10(-8)-10(-12)s) and the methine deuterium has a rigid deuterium powder pattern. For U-[(2)H/(13)C/(15)N]-phenylalanine, indirectly detected deuterium line shapes illustrate that the aromatic ring undergoes 180° flips in the fast motion regime while (2)Hβ and (2)Hα are completely rigid. The experimental deuterium line shapes for U-[(2)H/(13)C/(15)N]-proline reflect that (2)Hβ, (2)Hγ and (2)Hδ are subjected to fast, two-site reorientations at an angle of (15±5)°, (30±5)° and (25±10)° respectively. In addition, an approach that combines a composite inversion pulse with (2)H-(13)C CP-MAS is applied to measure (2)H spin-lattice relaxation times in a site-specific, (13)C-detected fashion.
Collapse
Affiliation(s)
- Xiangyan Shi
- Department of Chemistry and Biochemistry, Magnetic Resonance Research Center, Arizona State University, Tempe, AZ 85287-1604, United States
| | | | | |
Collapse
|
60
|
Bhaumik A, Luchinat C, Parigi G, Ravera E, Rinaldelli M. NMR crystallography on paramagnetic systems: solved and open issues. CrystEngComm 2013. [DOI: 10.1039/c3ce41485j] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
61
|
Herbert-Pucheta JE, Chan-Huot M, Duma L, Abergel D, Bodenhausen G, Assairi L, Blouquit Y, Charbonnier JB, Tekely P. Probing Structural and Motional Features of the C-Terminal Part of the Human Centrin 2/P17-XPC Microcrystalline Complex by Solid-State NMR Spectroscopy. J Phys Chem B 2012. [DOI: 10.1021/jp3099472] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jose-Enrique Herbert-Pucheta
- Ecole Normale Supérieure, Département
de Chimie, 24 rue Lhomond, 75231 Paris, France
- Université Pierre-et-Marie Curie, Paris, France
- UMR 7203, Laboratoire des Biomolécules, CNRS/UPMC/ENS, Paris, France
| | - Monique Chan-Huot
- Ecole Normale Supérieure, Département
de Chimie, 24 rue Lhomond, 75231 Paris, France
- Université Pierre-et-Marie Curie, Paris, France
- UMR 7203, Laboratoire des Biomolécules, CNRS/UPMC/ENS, Paris, France
- Institut Curie - Centre de Recherche, 91405 Orsay, France
- INSERM U759, 91405 Orsay, France
| | - Luminita Duma
- Ecole Normale Supérieure, Département
de Chimie, 24 rue Lhomond, 75231 Paris, France
- Université Pierre-et-Marie Curie, Paris, France
- UMR 7203, Laboratoire des Biomolécules, CNRS/UPMC/ENS, Paris, France
| | - Daniel Abergel
- Ecole Normale Supérieure, Département
de Chimie, 24 rue Lhomond, 75231 Paris, France
- Université Pierre-et-Marie Curie, Paris, France
- UMR 7203, Laboratoire des Biomolécules, CNRS/UPMC/ENS, Paris, France
| | - Geoffrey Bodenhausen
- Ecole Normale Supérieure, Département
de Chimie, 24 rue Lhomond, 75231 Paris, France
- Université Pierre-et-Marie Curie, Paris, France
- UMR 7203, Laboratoire des Biomolécules, CNRS/UPMC/ENS, Paris, France
| | - Liliane Assairi
- Institut Curie - Centre de Recherche, 91405 Orsay, France
- INSERM U759, 91405 Orsay, France
| | - Yves Blouquit
- Institut Curie - Centre de Recherche, 91405 Orsay, France
- INSERM U759, 91405 Orsay, France
| | - Jean-Baptiste Charbonnier
- UMR 8221,
Laboratoire de Biologie Structurale
et Radiobiologie, iBiTec-S, CEA, 91191
Gif-sur-Yvette, France
| | - Piotr Tekely
- Ecole Normale Supérieure, Département
de Chimie, 24 rue Lhomond, 75231 Paris, France
- Université Pierre-et-Marie Curie, Paris, France
- UMR 7203, Laboratoire des Biomolécules, CNRS/UPMC/ENS, Paris, France
| |
Collapse
|
62
|
Vinther JM, Nielsen AB, Bjerring M, van Eck ERH, Kentgens APM, Khaneja N, Nielsen NC. Refocused continuous-wave decoupling: A new approach to heteronuclear dipolar decoupling in solid-state NMR spectroscopy. J Chem Phys 2012; 137:214202. [DOI: 10.1063/1.4768953] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
63
|
Shahid SA, Markovic S, Linke D, van Rossum BJ. Assignment and secondary structure of the YadA membrane protein by solid-state MAS NMR. Sci Rep 2012; 2:803. [PMID: 23150774 PMCID: PMC3495290 DOI: 10.1038/srep00803] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2012] [Accepted: 10/15/2012] [Indexed: 11/11/2022] Open
Abstract
We report the complete solid-state MAS NMR resonance assignment of a medium-sized, trimeric membrane protein, YadA-M. The protein YadA (Yersinia adhesin A) is an important virulence factor of enteropathogenic Yersinia species (such as Yersinia enterocolitica and Yersinia pseudotuberculosis). YadA is localized on the bacterial cell surface and is involved in adhesion to host cells and tissues. It is anchored in the outer membrane by a transmembrane anchor domain (YadA-M). This domain hosts the so-called autotransporter function of YadA: it transports its own N-terminal domain through the outer membrane. The assignment is based on a dataset that consisted of several MAS NMR correlation spectra, recorded on a single, uniformly (13)C, (15)N- labelled microcrystalline preparation. Except for the single C-terminal residue and the mobile strep tag, we were able to completely assign YadA-M. From this, secondary structure elements were predicted, which, combined with several long-range interstrand restraints, yielded the architecture of the β-sheet.
Collapse
Affiliation(s)
- Shakeel A. Shahid
- Leibniz-Institut für Molekulare Pharmakologie (FMP); Robert-Rössle-Straße 10, 13125 Berlin, Germany
- Max Planck Institute for Developmental Biology; Spemannstraße 35, 72076 Tübingen, Germany
| | - Stefan Markovic
- Leibniz-Institut für Molekulare Pharmakologie (FMP); Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Dirk Linke
- Max Planck Institute for Developmental Biology; Spemannstraße 35, 72076 Tübingen, Germany
| | - Barth-Jan van Rossum
- Leibniz-Institut für Molekulare Pharmakologie (FMP); Robert-Rössle-Straße 10, 13125 Berlin, Germany
| |
Collapse
|
64
|
Bertini I, Engelke F, Gonnelli L, Knott B, Luchinat C, Osen D, Ravera E. On the use of ultracentrifugal devices for sedimented solute NMR. JOURNAL OF BIOMOLECULAR NMR 2012; 54:123-7. [PMID: 22872367 DOI: 10.1007/s10858-012-9657-y] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2012] [Accepted: 07/26/2012] [Indexed: 05/09/2023]
Abstract
We have recently proposed sedimented solute NMR (SedNMR) as a solid-state method to access biomolecules without the need of crystallization or other sample manipulation. The drawback of SedNMR is that samples are intrinsically diluted and this is detrimental for the signal intensity. Ultracentrifugal devices can be used to increase the amount of sample inside the rotor, overcoming the intrinsic sensitivity limitation of the method. We designed two different devices and we here report the directions for using such devices and the relevant equations for determining the parameters for sedimentation.
Collapse
Affiliation(s)
- Ivano Bertini
- Center for Magnetic Resonance (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, FI, Italy.
| | | | | | | | | | | | | |
Collapse
|
65
|
Huang W, Bardaro MF, Varani G, Drobny GP. Preparation of RNA samples with narrow line widths for solid state NMR investigations. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2012; 223:51-54. [PMID: 22967888 DOI: 10.1016/j.jmr.2012.07.018] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2012] [Revised: 07/19/2012] [Accepted: 07/22/2012] [Indexed: 06/01/2023]
Abstract
Solid state NMR can provide detailed structural and dynamic information on biological systems that cannot be studied under solution conditions, and can investigate motions which occur with rates that cannot be fully studied by solution NMR. This approach has successfully been used to study proteins, but the application of multidimensional solid state NMR to RNA has been limited because reported line widths have been too broad to execute most multidimensional experiments successfully. A reliable method to generate spectra with narrow line widths is necessary to apply the full range of solid state NMR spectroscopic approaches to RNA. Using the HIV-1 transactivation response (TAR) RNA as a model, we present an approach based on precipitation with polyethylene glycol that improves the line width of (13)C signals in TAR from >6 ppm to about 1 ppm, making solid state 2D NMR studies of selectively enriched RNAs feasible at ambient temperature.
Collapse
Affiliation(s)
- Wei Huang
- Department of Chemistry, University of Washington, Box 351700, Seattle, WA 98195, USA
| | | | | | | |
Collapse
|
66
|
Spence JCH, Weierstall U, Chapman HN. X-ray lasers for structural and dynamic biology. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2012; 75:102601. [PMID: 22975810 DOI: 10.1088/0034-4885/75/10/102601] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Research opportunities and techniques are reviewed for the application of hard x-ray pulsed free-electron lasers (XFEL) to structural biology. These include the imaging of protein nanocrystals, single particles such as viruses, pump--probe experiments for time-resolved nanocrystallography, and snapshot wide-angle x-ray scattering (WAXS) from molecules in solution. The use of femtosecond exposure times, rather than freezing of samples, as a means of minimizing radiation damage is shown to open up new opportunities for the molecular imaging of biochemical reactions at room temperature in solution. This is possible using a 'diffract-and-destroy' mode in which the incident pulse terminates before radiation damage begins. Methods for delivering hundreds of hydrated bioparticles per second (in random orientations) to a pulsed x-ray beam are described. New data analysis approaches are outlined for the correlated fluctuations in fast WAXS, for protein nanocrystals just a few molecules on a side, and for the continuous x-ray scattering from a single virus. Methods for determining the orientation of a molecule from its diffraction pattern are reviewed. Methods for the preparation of protein nanocrystals are also reviewed. New opportunities for solving the phase problem for XFEL data are outlined. A summary of the latest results is given, which now extend to atomic resolution for nanocrystals. Possibilities for time-resolved chemistry using fast WAXS (solution scattering) from mixtures is reviewed, toward the general goal of making molecular movies of biochemical processes.
Collapse
Affiliation(s)
- J C H Spence
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA.
| | | | | |
Collapse
|
67
|
Reif B. Ultra-high resolution in MAS solid-state NMR of perdeuterated proteins: implications for structure and dynamics. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2012; 216:1-12. [PMID: 22280934 DOI: 10.1016/j.jmr.2011.12.017] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2011] [Revised: 12/20/2011] [Accepted: 12/22/2011] [Indexed: 05/14/2023]
Abstract
High resolution proton spectra are obtained in MAS solid-state NMR in case samples are prepared using perdeuterated protein and D(2)O in the recrystallization buffer. Deuteration reduces drastically (1)H, (1)H dipolar interactions and allows to obtain amide proton line widths on the order of 20 Hz. Similarly, high-resolution proton spectra of aliphatic groups can be obtained if specifically labeled precursors for biosynthesis of methyl containing side chains are used, or if limited amounts of H(2)O in the bacterial growth medium is employed. This review summarizes recent spectroscopic developments to access structure and dynamics of biomacromolecules in the solid-state, and shows a number of applications to amyloid fibrils and membrane proteins.
Collapse
Affiliation(s)
- Bernd Reif
- Munich Center for Integrated Protein Science (CIPSM), Department Chemie, Technische Universität München, Lichtenbergstr. 4, 85747 Garching, Germany.
| |
Collapse
|
68
|
Reif B. Deuterated peptides and proteins: structure and dynamics studies by MAS solid-state NMR. Methods Mol Biol 2012; 831:279-301. [PMID: 22167680 DOI: 10.1007/978-1-61779-480-3_16] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Perdeuteration and back substitution of exchangeable protons in microcrystalline proteins, in combination with recrystallization from D(2)O-containing buffers, significantly reduce (1)H, (1)H dipolar interactions. This way, amide proton line widths on the order of 20 Hz are obtained. Aliphatic protons are accessible either via specifically protonated precursors or by using low amounts of H(2)O in the bacterial growth medium. The labeling scheme enables characterization of structure and dynamics in the solid-state without dipolar truncation artifacts.
Collapse
Affiliation(s)
- Bernd Reif
- Munich Center for Integrated Protein Science (CIPSM) at Department Chemie, Technische Universität München, Garching, Germany.
| |
Collapse
|
69
|
Hackel C, Zinkevich T, Belton P, Achilles A, Reichert D, Krushelnitsky A. The trehalose coating effect on the internal protein dynamics. Phys Chem Chem Phys 2012; 14:2727-34. [DOI: 10.1039/c2cp23098d] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
70
|
Chow WY, Taylor AM, Reid DG, Gallagher JA, Duer MJ. Collagen atomic scale molecular disorder in ochronotic cartilage from an alkaptonuria patient, observed by solid state NMR. J Inherit Metab Dis 2011; 34:1137-40. [PMID: 21735270 DOI: 10.1007/s10545-011-9373-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/21/2011] [Revised: 06/16/2011] [Accepted: 06/21/2011] [Indexed: 10/18/2022]
Abstract
UNLABELLED In pilot studies of the usefulness of solid state nuclear magnetic resonance spectroscopy in characterizing chemical and molecular structural effects of alkaptonuria on connective tissue, we have obtained (13) C spectra from articular cartilage from an AKU patient. An apparently normal anatomical location yielded a cross polarization magic angle spinning spectrum resembling literature spectra and dominated by collagen and glycosaminoglycan signals. All spectral linewidths from strongly pigmented ochronotic cartilage however were considerably increased relative to the control indicating a marked increase in collagen molecular disorder. This disordering of cartilage structural protein parallels, at the atomic level, the disordering revealed at higher length scales by microscopy. We also demonstrate that the abnormal spectra from ochronotic cartilage fit with the abnormality in the structure of collagen fibres at the ultrastructural level, whereby large ochronotic deposits appear to alter the structure of the collagen fibre by invasion and cross linking. SUMMARY Increased signal linewidths in solid state NMR spectra of ochronotic articular cartilage from an AKU patient relative to linewidths in normal, control, cartilage reveals a marked decrease in collagen molecular order in the diseased tissue. This atomic level disordering parallels higher length scale disorder revealed by microscopic techniques.
Collapse
Affiliation(s)
- Wing Ying Chow
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | | | | | | | | |
Collapse
|
71
|
Franks WT, Linden AH, Kunert B, van Rossum BJ, Oschkinat H. Solid-state magic-angle spinning NMR of membrane proteins and protein-ligand interactions. Eur J Cell Biol 2011; 91:340-8. [PMID: 22019511 DOI: 10.1016/j.ejcb.2011.09.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2011] [Revised: 09/09/2011] [Accepted: 09/09/2011] [Indexed: 10/15/2022] Open
Abstract
Structural biology is developing into a universal tool for visualizing biological processes in space and time at atomic resolution. The field has been built by established methodology like X-ray crystallography, electron microscopy and solution NMR and is now incorporating new techniques, such as small-angle X-ray scattering, electron tomography, magic-angle-spinning solid-state NMR and femtosecond X-ray protein nanocrystallography. These new techniques all seek to investigate non-crystalline, native-like biological material. Solid-state NMR is a relatively young technique that has just proven its capabilities for de novo structure determination of model proteins. Further developments promise great potential for investigations on functional biological systems such as membrane-integrated receptors and channels, and macromolecular complexes attached to cytoskeletal proteins. Here, we review the development and applications of solid-state NMR from the first proof-of-principle investigations to mature structure determination projects, including membrane proteins. We describe the development of the methodology by looking at examples in detail and provide an outlook towards future 'big' projects.
Collapse
Affiliation(s)
- W Trent Franks
- Leibniz-Institut für Molekulare Pharmakologie (FMP), Robert Rössle Str. 10, 13125 Berlin, Germany
| | | | | | | | | |
Collapse
|
72
|
Abstract
Relatively large proteins in solution, spun in NMR rotors for solid samples at typical ultracentrifugation speeds, sediment at the rotor wall. The sedimented proteins provide high-quality solid-state-like NMR spectra suitable for structural investigation. The proteins fully revert to the native solution state when spinning is stopped, allowing one to study them in both conditions. Transiently sedimented proteins can be considered a novel phase as far as NMR is concerned. NMR of transiently sedimented molecules under fast magic angle spinning has the advantage of overcoming protein size limitations of solution NMR without the need of sample crystallization/precipitation required by solid-state NMR.
Collapse
|
73
|
Solution- and solid-state NMR studies of GPCRs and their ligands. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2011; 1808:1462-75. [DOI: 10.1016/j.bbamem.2010.10.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2010] [Revised: 10/02/2010] [Accepted: 10/05/2010] [Indexed: 12/29/2022]
|
74
|
Tannin fingerprinting in vegetable tanned leather by solid state NMR spectroscopy and comparison with leathers tanned by other processes. Molecules 2011; 16:1240-52. [PMID: 21278677 PMCID: PMC6259749 DOI: 10.3390/molecules16021240] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2010] [Revised: 01/26/2011] [Accepted: 01/27/2011] [Indexed: 11/17/2022] Open
Abstract
Solid state 13C-NMR spectra of pure tannin powders from four different sources – mimosa, quebracho, chestnut and tara – are readily distinguishable from each other, both in pure commercial powder form, and in leather which they have been used to tan. Groups of signals indicative of the source, and type (condensed vs. hydrolyzable) of tannin used in the manufacture are well resolved in the spectra of the finished leathers. These fingerprints are compared with those arising from leathers tanned with other common tanning agents. Paramagnetic chromium (III) tanning causes widespread but selective disappearance of signals from the spectrum of leather collagen, including resonances from acidic aspartyl and glutamyl residues, likely bound to Cr (III) structures. Aluminium (III) and glutaraldehyde tanning both cause considerable leather collagen signal sharpening suggesting some increase in molecular structural ordering. The 27Al-NMR signal from the former material is consistent with an octahedral coordination by oxygen ligands. Solid state NMR thus provides easily recognisable reagent specific spectral fingerprints of the products of vegetable and some other common tanning processes. Because spectra are related to molecular properties, NMR is potentially a powerful tool in leather process enhancement and quality or provenance assurance.
Collapse
|
75
|
Moseley HNB, Sperling LJ, Rienstra CM. Automated protein resonance assignments of magic angle spinning solid-state NMR spectra of β1 immunoglobulin binding domain of protein G (GB1). JOURNAL OF BIOMOLECULAR NMR 2010; 48:123-8. [PMID: 20931264 PMCID: PMC2962796 DOI: 10.1007/s10858-010-9448-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2010] [Accepted: 08/18/2010] [Indexed: 05/11/2023]
Abstract
Magic-angle spinning solid-state NMR (MAS SSNMR) represents a fast developing experimental technique with great potential to provide structural and dynamics information for proteins not amenable to other methods. However, few automated analysis tools are currently available for MAS SSNMR. We present a methodology for automating protein resonance assignments of MAS SSNMR spectral data and its application to experimental peak lists of the β1 immunoglobulin binding domain of protein G (GB1) derived from a uniformly ¹³C- and ¹⁵N-labeled sample. This application to the 56 amino acid GB1 produced an overall 84.1% assignment of the N, CO, CA, and CB resonances with no errors using peak lists from NCACX 3D, CANcoCA 3D, and CANCOCX 4D experiments. This proof of concept demonstrates the tractability of this problem.
Collapse
|
76
|
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.
Collapse
Affiliation(s)
- Jean-Philippe Demers
- Max Planck Institute for Biophysical Chemistry, Solid-state NMR, Göttingen 37077, Germany
| | | | | | | |
Collapse
|
77
|
Jehle S, Falb M, Kirkpatrick JP, Oschkinat H, Rossum BJV, Althoff G, Carlomagno T. Intermolecular Protein−RNA Interactions Revealed by 2D 31P−15N Magic Angle Spinning Solid-State NMR Spectroscopy. J Am Chem Soc 2010; 132:3842-6. [DOI: 10.1021/ja909723f] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Stefan Jehle
- Computational and Structural Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany, Leibniz-Institut für Molekulare Pharmakologie, Robert-Rössle-Strasse 10, 13125 Berlin, Germany, and Bruker Biospin, Im Silberstreifen 4, 76287 Rheinstetten, Germany
| | - Melanie Falb
- Computational and Structural Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany, Leibniz-Institut für Molekulare Pharmakologie, Robert-Rössle-Strasse 10, 13125 Berlin, Germany, and Bruker Biospin, Im Silberstreifen 4, 76287 Rheinstetten, Germany
| | - John P. Kirkpatrick
- Computational and Structural Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany, Leibniz-Institut für Molekulare Pharmakologie, Robert-Rössle-Strasse 10, 13125 Berlin, Germany, and Bruker Biospin, Im Silberstreifen 4, 76287 Rheinstetten, Germany
| | - Hartmut Oschkinat
- Computational and Structural Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany, Leibniz-Institut für Molekulare Pharmakologie, Robert-Rössle-Strasse 10, 13125 Berlin, Germany, and Bruker Biospin, Im Silberstreifen 4, 76287 Rheinstetten, Germany
| | - Barth-Jan van Rossum
- Computational and Structural Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany, Leibniz-Institut für Molekulare Pharmakologie, Robert-Rössle-Strasse 10, 13125 Berlin, Germany, and Bruker Biospin, Im Silberstreifen 4, 76287 Rheinstetten, Germany
| | - Gerhard Althoff
- Computational and Structural Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany, Leibniz-Institut für Molekulare Pharmakologie, Robert-Rössle-Strasse 10, 13125 Berlin, Germany, and Bruker Biospin, Im Silberstreifen 4, 76287 Rheinstetten, Germany
| | - Teresa Carlomagno
- Computational and Structural Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany, Leibniz-Institut für Molekulare Pharmakologie, Robert-Rössle-Strasse 10, 13125 Berlin, Germany, and Bruker Biospin, Im Silberstreifen 4, 76287 Rheinstetten, Germany
| |
Collapse
|
78
|
Diakova G, Goddard YA, Korb JP, Bryant RG. Water and backbone dynamics in a hydrated protein. Biophys J 2010; 98:138-46. [PMID: 20085726 PMCID: PMC2800973 DOI: 10.1016/j.bpj.2009.09.054] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2009] [Revised: 09/24/2009] [Accepted: 09/28/2009] [Indexed: 11/26/2022] Open
Abstract
Rotational immobilization of proteins permits characterization of the internal peptide and water molecule dynamics by magnetic relaxation dispersion spectroscopy. Using different experimental approaches, we have extended measurements of the magnetic field dependence of the proton-spin-lattice-relaxation rate by one decade from 0.01 to 300 MHz for (1)H and showed that the underlying dynamics driving the protein (1)H spin-lattice relaxation is preserved over 4.5 decades in frequency. This extension is critical to understanding the role of (1)H(2)O in the total proton-spin-relaxation process. The fact that the protein-proton-relaxation-dispersion profile is a power law in frequency with constant coefficient and exponent over nearly 5 decades indicates that the characteristics of the native protein structural fluctuations that cause proton nuclear spin-lattice relaxation are remarkably constant over this wide frequency and length-scale interval. Comparison of protein-proton-spin-lattice-relaxation rate constants in protein gels equilibrated with (2)H(2)O rather than (1)H(2)O shows that water protons make an important contribution to the total spin-lattice relaxation in the middle of this frequency range for hydrated proteins because of water molecule dynamics in the time range of tens of ns. This water contribution is with the motion of relatively rare, long-lived, and perhaps buried water molecules constrained by the confinement. The presence of water molecule reorientational dynamics in the tens of ns range that are sufficient to affect the spin-lattice relaxation driven by (1)H dipole-dipole fluctuations should make the local dielectric properties in the protein frequency dependent in a regime relevant to catalytically important kinetic barriers to conformational rearrangements.
Collapse
Affiliation(s)
- Galina Diakova
- Chemistry Department, University of Virginia, Charlottesville, Virginia
| | - Yanina A. Goddard
- Chemistry Department, University of Virginia, Charlottesville, Virginia
| | - Jean-Pierre Korb
- Physique de la Matière Condensée, Ecole Polytechnique, CNRS, Palaiseau, France
| | - Robert G. Bryant
- Chemistry Department, University of Virginia, Charlottesville, Virginia
| |
Collapse
|
79
|
Schneider R, Seidel K, Etzkorn M, Lange A, Becker S, Baldus M. Probing Molecular Motion by Double-Quantum (13C,13C) Solid-State NMR Spectroscopy: Application to Ubiquitin. J Am Chem Soc 2009; 132:223-33. [DOI: 10.1021/ja906283h] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Robert Schneider
- Department for NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany, and Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Karsten Seidel
- Department for NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany, and Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Manuel Etzkorn
- Department for NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany, and Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Adam Lange
- Department for NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany, and Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Stefan Becker
- Department for NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany, and Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Marc Baldus
- Department for NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany, and Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| |
Collapse
|
80
|
Farnet AM, Prudent P, Ziarelli F, Domeizel M, Gros R. Solid-state 13C NMR to assess organic matter transformation in a subsurface wetland under cheese-dairy farm effluents. BIORESOURCE TECHNOLOGY 2009; 100:4899-4902. [PMID: 19481928 DOI: 10.1016/j.biortech.2009.05.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2009] [Revised: 05/05/2009] [Accepted: 05/06/2009] [Indexed: 05/27/2023]
Abstract
Solid-state (13)C NMR were used to follow organic matter transformation in a subsurface wetland under the effluent of a small cheese-dairy farm under a Mediterranean climate. The results showed that the ratios commonly used to quantify humification, (aromaticity and Alkyl-C/O-Alkyl-C ratios) can be considered as relevant chemical indicators of organic matter transformation. Polysaccharides were transformed throughout the subsurface wetland whereas aromatic, phenolic and alkyl compounds accumulated. Furthermore, Phenolic-C signal and O-Alkyl-C signal were negatively correlated to proteases and beta-galactosidase activities showing that recalcitrant molecules actually accumulated. These results were correlated with high purification yields: the average decrease in chemical demand in oxygen was 90.75% and that in Total Kjeldahl Nitrogen was 75.65%. Thus subsurface wetlands can be considered as an efficient technology to purify effluents with high organic matter contents, such as cheese-dairy effluent, under drastic climate conditions. Furthermore this study highlights the fact that solid-state (13)C NMR is a suitable tool to follow organic matter transformation.
Collapse
Affiliation(s)
- A M Farnet
- Equipe Ecologie Microbienne et Biotechnologies, Institut Méditerranéen d'Ecologie et de Paléoécologie, UMR CNRS 6116, Université Paul Cézanne, Faculté des Sciences et Techniques de St Jérôme, Marseille Cedex 20, France.
| | | | | | | | | |
Collapse
|
81
|
Krushelnitsky A, Zinkevich T, Mukhametshina N, Tarasova N, Gogolev Y, Gnezdilov O, Fedotov V, Belton P, Reichert D. 13C and 15N NMR study of the hydration response of T4 lysozyme and alphaB-crystallin internal dynamics. J Phys Chem B 2009; 113:10022-34. [PMID: 19603846 DOI: 10.1021/jp900337x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The response to hydration of the internal protein dynamics was studied by the means of solid state NMR relaxation and magic angle spinning exchange techniques. Two proteins, lysozyme from bacteriophage T4 and human alphaB-crystallin were used as exemplars. The relaxation rates R1 and R1rho of 13C and 15N nuclei were measured as a function of a hydration level of the proteins in the range 0-0.6 g of water/g of protein. Both proteins were totally 15N-enriched with natural 13C abundance. The relaxation rates were measured for different spectral bands (peaks) that enabled the characterization of the dynamics separately for the backbone, side chains, and CH3 and NH3+ groups. The data obtained allowed a comparative analysis of the hydration response of the protein dynamics in different frequency ranges and different sites in the protein for two different proteins and two magnetic nuclei. The most important result is a demonstration of a qualitatively different response to hydration of the internal dynamics in different frequency ranges. The amplitude of the fast (nanosecond time scale) motion gradually increases with increasing hydration, whereas that of the slow (microsecond time scale) motion increases only until the hydration level 0.2-0.3 g of water/g of protein and then shows almost no hydration dependence. The reason for such a difference is discussed in terms of the different physical natures of these two dynamic processes. Backbone and side chain nuclei show the same features of the response of dynamics with hydration despite the fact that the backbone motional amplitudes are much smaller than those of side chains. Although T4 lysozyme and alphaB-crystallin possess rather different structural and biochemical properties, both proteins show qualitatively very similar hydration responses. In addition to the internal motions, exchange NMR data enabled the identification of one more type of motion in the millisecond to second time scale that appears only at high hydration levels. This motion was attributed to the restricted librations of the protein as a whole.
Collapse
Affiliation(s)
- A Krushelnitsky
- Kazan Institute of Biochemistry and Biophysics, Kazan, Russia.
| | | | | | | | | | | | | | | | | |
Collapse
|
82
|
Lewandowski JR, De Paëpe G, Eddy MT, Griffin RG. (15)N-(15)N proton assisted recoupling in magic angle spinning NMR. J Am Chem Soc 2009; 131:5769-76. [PMID: 19334788 PMCID: PMC2754755 DOI: 10.1021/ja806578y] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We describe a new magic angle spinning (MAS) NMR experiment for obtaining (15)N-(15)N correlation spectra. The approach yields direct information about the secondary and tertiary structure of proteins, including identification of alpha-helical stretches and interstrand connectivity in antiparallel beta-sheets, which are of major interest for structural studies of membrane proteins and amyloid fibrils. The method, (15)N-(15)N proton assisted recoupling (PAR), relies on a second-order mechanism, third spin assisted recoupling (TSAR), used previously in the context of (15)N-(13)C and (13)C-(13)C polarization transfer schemes. In comparison to (15)N-(15)N proton-driven spin diffusion experiments, the PAR technique accelerates polarization transfer between (15)N's by a factor of approximately 10(2)-10(3) and is furthermore applicable over the entire range of currently available MAS frequencies (10-70 kHz).
Collapse
Affiliation(s)
- Józef R Lewandowski
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | | | | | | |
Collapse
|
83
|
Bajaj VS, van der Wel PC, Griffin RG. Observation of a low-temperature, dynamically driven structural transition in a polypeptide by solid-state NMR spectroscopy. J Am Chem Soc 2009; 131:118-28. [PMID: 19067520 PMCID: PMC2651395 DOI: 10.1021/ja8045926] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
At reduced temperatures, proteins and other biomolecules are generally found to exhibit dynamic as well as structural transitions. This includes a so-called protein glass transition that is universally observed in systems cooled between 200 and 230 K, and which is generally attributed to interactions between hydrating solvent molecules and protein side chains. However, there is also experimental and theoretical evidence for a low-temperature transition in the intrinsic dynamics of the protein itself, absent any solvent. Here, we use low-temperature solid-state NMR to examine site-specific fluctuations in atomic structure and dynamics in the absence of solvents. In particular, we employ magic angle spinning NMR to examine a structural phase transition associated with dynamic processes in a solvent-free polypeptide, N-f-MLF-OH, lattice at temperatures as low as 90 K. This transition is characterized by the appearance of an extra set of lines in 1D (15)N spectra as well as additional cross peaks in 2D (13)C-(13)C and (13)C-(15)N spectra. Interestingly, the gradual, temperature-dependent appearance of the new spectral component is not accompanied by the line broadening typical of dynamic transitions. A direct comparison between the spectra of N-f-MLF-OH and the analog N-f-MLF-OMe, which does not display this transition, indicates a correlation of the structural transition to the temperature dependent motion of the aromatic phenylalanine side chain. Several quantitative solid state NMR experiments were employed to provide site-specific measurements of structural and motional features of the observed transition.
Collapse
Affiliation(s)
| | | | - Robert G. Griffin
- Francis Bitter Magnet Laboratory and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139 USA
| |
Collapse
|
84
|
Thurber KR, Tycko R. Biomolecular solid state NMR with magic-angle spinning at 25K. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2008; 195:179-86. [PMID: 18922715 PMCID: PMC2632798 DOI: 10.1016/j.jmr.2008.09.015] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2008] [Revised: 08/19/2008] [Accepted: 09/10/2008] [Indexed: 05/05/2023]
Abstract
A magic-angle spinning (MAS) probe has been constructed which allows the sample to be cooled with helium, while the MAS bearing and drive gases are nitrogen. The sample can be cooled to 25K using roughly 3 L/h of liquid helium, while the 4-mm diameter rotor spins at 6.7 kHz with good stability (+/-5 Hz) for many hours. Proton decoupling fields up to at least 130 kHz can be applied. This helium-cooled MAS probe enables a variety of one-dimensional and two-dimensional NMR experiments on biomolecular solids and other materials at low temperatures, with signal-to-noise proportional to 1/T. We show examples of low-temperature (13)C NMR data for two biomolecular samples, namely the peptide Abeta(14-23) in the form of amyloid fibrils and the protein HP35 in frozen glycerol/water solution. Issues related to temperature calibration, spin-lattice relaxation at low temperatures, paramagnetic doping of frozen solutions, and (13)C MAS NMR linewidths are discussed.
Collapse
Affiliation(s)
| | - Robert Tycko
- corresponding author: Dr. Robert Tycko, National Institutes of Health, Building 5, Room 112, Bethesda, MD 20892-0520. phone: 301-402-8272. fax: 301-496-0825. e-mail:
| |
Collapse
|
85
|
Montalvao RW, Cavalli A, Salvatella X, Blundell TL, Vendruscolo M. Structure Determination of Protein−Protein Complexes Using NMR Chemical Shifts: Case of an Endonuclease Colicin−Immunity Protein Complex. J Am Chem Soc 2008; 130:15990-6. [DOI: 10.1021/ja805258z] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Rinaldo W. Montalvao
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K., and Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, U.K
| | - Andrea Cavalli
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K., and Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, U.K
| | - Xavier Salvatella
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K., and Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, U.K
| | - Tom L. Blundell
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K., and Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, U.K
| | - Michele Vendruscolo
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K., and Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, U.K
| |
Collapse
|
86
|
Etzkorn M, Kneuper H, Dünnwald P, Vijayan V, Krämer J, Griesinger C, Becker S, Unden G, Baldus M. Plasticity of the PAS domain and a potential role for signal transduction in the histidine kinase DcuS. Nat Struct Mol Biol 2008; 15:1031-9. [DOI: 10.1038/nsmb.1493] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2008] [Accepted: 08/29/2008] [Indexed: 11/09/2022]
|
87
|
Knight JD, Williamson JA, Miranker AD. Interaction of membrane-bound islet amyloid polypeptide with soluble and crystalline insulin. Protein Sci 2008; 17:1850-6. [PMID: 18765820 DOI: 10.1110/ps.036350.108] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Islet amyloid polypeptide (IAPP, also known as amylin) is the major protein component of pancreatic amyloid fibers in type II diabetes and is normally cosecreted with insulin from the beta-cells of the pancreas. IAPP forms amyloid fibrils rapidly at concentrations well below those found in vivo, yet progression of type II diabetes occurs over many years. Insulin, a known inhibitor of IAPP fibrillogenesis, exists as a dense crystalline or near-crystalline core in the secretory vesicle, while IAPP localizes to the region between the crystal and the secretory vesicle membrane. In vitro, IAPP fibrillogenesis is both accelerated by lipid membranes and inhibited by monomeric insulin. In this work, we investigate insulin-IAPP-lipid interactions in vitro under conditions chosen to approximate native secretory vesicle physiology and the amyloid disease state. The effect of insulin on IAPP fibrillogenesis is investigated using fluorescence spectrometry. Additionally, interactions of IAPP and lipids with crystalline insulin are studied using fluorescence microscopy. We find that, while soluble states of insulin and IAPP do not interact significantly, large assemblies of either insulin (crystals) or IAPP (fibers) can lead to stable IAPP-insulin interactions. The results raise the possibility of multiple physiological interactions between these two beta-cell hormones.
Collapse
Affiliation(s)
- Jefferson D Knight
- Department of Pharmacology, Yale University, New Haven, Connecticut 06520-8066, USA
| | | | | |
Collapse
|
88
|
Lesage A, Gardiennet C, Loquet A, Verel R, Pintacuda G, Emsley L, Meier B, Böckmann A. Polarisationstransfer über die Wasser‐Protein‐Grenzfläche im Festkörper. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200801110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
89
|
|
90
|
Loquet A, Laage S, Gardiennet C, Elena B, Emsley L, Böckmann A, Lesage A. Methyl Proton Contacts Obtained Using Heteronuclear Through-Bond Transfers in Solid-State NMR Spectroscopy. J Am Chem Soc 2008; 130:10625-32. [DOI: 10.1021/ja801464g] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Antoine Loquet
- Institut de Biologie et Chimie des Protéines, UMR 5086 CNRS/Université de Lyon 1, 7 passage du Vercors, 69367 Lyon, France, and Centre RMN à Très Hauts Champs, Université de Lyon, CNRS/ENS Lyon/UCB-Lyon 1, 5 rue de la Doua, 69100 Villeurbanne, France
| | - Ségolène Laage
- Institut de Biologie et Chimie des Protéines, UMR 5086 CNRS/Université de Lyon 1, 7 passage du Vercors, 69367 Lyon, France, and Centre RMN à Très Hauts Champs, Université de Lyon, CNRS/ENS Lyon/UCB-Lyon 1, 5 rue de la Doua, 69100 Villeurbanne, France
| | - Carole Gardiennet
- Institut de Biologie et Chimie des Protéines, UMR 5086 CNRS/Université de Lyon 1, 7 passage du Vercors, 69367 Lyon, France, and Centre RMN à Très Hauts Champs, Université de Lyon, CNRS/ENS Lyon/UCB-Lyon 1, 5 rue de la Doua, 69100 Villeurbanne, France
| | - Bénédicte Elena
- Institut de Biologie et Chimie des Protéines, UMR 5086 CNRS/Université de Lyon 1, 7 passage du Vercors, 69367 Lyon, France, and Centre RMN à Très Hauts Champs, Université de Lyon, CNRS/ENS Lyon/UCB-Lyon 1, 5 rue de la Doua, 69100 Villeurbanne, France
| | - Lyndon Emsley
- Institut de Biologie et Chimie des Protéines, UMR 5086 CNRS/Université de Lyon 1, 7 passage du Vercors, 69367 Lyon, France, and Centre RMN à Très Hauts Champs, Université de Lyon, CNRS/ENS Lyon/UCB-Lyon 1, 5 rue de la Doua, 69100 Villeurbanne, France
| | - Anja Böckmann
- Institut de Biologie et Chimie des Protéines, UMR 5086 CNRS/Université de Lyon 1, 7 passage du Vercors, 69367 Lyon, France, and Centre RMN à Très Hauts Champs, Université de Lyon, CNRS/ENS Lyon/UCB-Lyon 1, 5 rue de la Doua, 69100 Villeurbanne, France
| | - Anne Lesage
- Institut de Biologie et Chimie des Protéines, UMR 5086 CNRS/Université de Lyon 1, 7 passage du Vercors, 69367 Lyon, France, and Centre RMN à Très Hauts Champs, Université de Lyon, CNRS/ENS Lyon/UCB-Lyon 1, 5 rue de la Doua, 69100 Villeurbanne, France
| |
Collapse
|
91
|
Shi L, Peng X, Ahmed MAM, Edwards D, Brown LS, Ladizhansky V. Resolution enhancement by homonuclear J-decoupling: application to three-dimensional solid-state magic angle spinning NMR spectroscopy. JOURNAL OF BIOMOLECULAR NMR 2008; 41:9-15. [PMID: 18404253 DOI: 10.1007/s10858-008-9233-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2008] [Revised: 03/17/2008] [Accepted: 03/20/2008] [Indexed: 05/26/2023]
Abstract
We describe a simple protocol to achieve homonuclear J-decoupling in the indirect dimensions of multidimensional experiments, and to enhance spectral resolution of the backbone Calpha carbons in the 3D NCACX experiment. In the proposed protocol, the refocusing of the Calpha-CO homonuclear J-couplings is achieved by applying an off-resonance selective pi pulse to the CO spectral region in the middle of Calpha chemical shift evolution. As is commonly used in solution NMR, a compensatory echo period is used to refocus the unwanted chemical shift evolution of Calpha spins, which takes place during the off-resonance selective pulse. The experiments were carried out on the beta1 immunoglobulin binding domain of protein G (GB1). In GB1, such implementation results in significantly reduced line widths, and leads to an overall sensitivity enhancement.
Collapse
Affiliation(s)
- Lichi Shi
- Department of Physics and Biophysics Interdepartmental Group, University of Guelph, 50 Stone Road East, Guelph, ON, Canada N1G 2W1
| | | | | | | | | | | |
Collapse
|
92
|
Yang J, Tasayco ML, Polenova T. Magic Angle Spinning NMR Experiments for Structural Studies of Differentially Enriched Protein Interfaces and Protein Assemblies. J Am Chem Soc 2008; 130:5798-807. [DOI: 10.1021/ja711304e] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jun Yang
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, and Department of Chemistry, The City College of New York, Convent Avenue at 138th Street, New York, New York 10031
| | - Maria Luisa Tasayco
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, and Department of Chemistry, The City College of New York, Convent Avenue at 138th Street, New York, New York 10031
| | - Tatyana Polenova
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, and Department of Chemistry, The City College of New York, Convent Avenue at 138th Street, New York, New York 10031
| |
Collapse
|
93
|
Helmus JJ, Nadaud PS, Höfer N, Jaroniec CP. Determination of methyl 13C-15N dipolar couplings in peptides and proteins by three-dimensional and four-dimensional magic-angle spinning solid-state NMR spectroscopy. J Chem Phys 2008; 128:052314. [PMID: 18266431 DOI: 10.1063/1.2817638] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
We describe three- and four-dimensional semiconstant-time transferred echo double resonance (SCT-TEDOR) magic-angle spinning solid-state nuclear magnetic resonance (NMR) experiments for the simultaneous measurement of multiple long-range (15)N-(13)C(methyl) dipolar couplings in uniformly (13)C, (15)N-enriched peptides and proteins with high resolution and sensitivity. The methods take advantage of (13)C spin topologies characteristic of the side-chain methyl groups in amino acids alanine, isoleucine, leucine, methionine, threonine, and valine to encode up to three distinct frequencies ((15)N-(13)C(methyl) dipolar coupling, (15)N chemical shift, and (13)C(methyl) chemical shift) within a single SCT evolution period of initial duration approximately 1(1)J(CC) (where (1)J(CC) approximately 35 Hz, is the one-bond (13)C(methyl)-(13)C J-coupling) while concurrently suppressing the modulation of NMR coherences due to (13)C-(13)C and (15)N-(13)C J-couplings and transverse relaxation. The SCT-TEDOR schemes offer several important advantages over previous methods of this type. First, significant (approximately twofold to threefold) gains in experimental sensitivity can be realized for weak (15)N-(13)C(methyl) dipolar couplings (corresponding to structurally interesting, approximately 3.5 A or longer, distances) and typical (13)C(methyl) transverse relaxation rates. Second, the entire SCT evolution period can be used for (13)C(methyl) and/or (15)N frequency encoding, leading to increased spectral resolution with minimal additional coherence decay. Third, the experiments are inherently "methyl selective," which results in simplified NMR spectra and obviates the use of frequency-selective pulses or other spectral filtering techniques. Finally, the (15)N-(13)C cross-peak buildup trajectories are purely dipolar in nature (i.e., not influenced by J-couplings or relaxation), which enables the straightforward extraction of (15)N-(13)C(methyl) distances using an analytical model. The SCT-TEDOR experiments are demonstrated on a uniformly (13)C, (15)N-labeled peptide, N-acetyl-valine, and a 56 amino acid protein, B1 immunoglobulin-binding domain of protein G (GB1), where the measured (15)N-(13)C(methyl) dipolar couplings provide site-specific information about side-chain dihedral angles and the packing of protein molecules in the crystal lattice.
Collapse
Affiliation(s)
- Jonathan J Helmus
- Department of Chemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | | | | | | |
Collapse
|
94
|
Wylie BJ, Rienstra CM. Multidimensional solid state NMR of anisotropic interactions in peptides and proteins. J Chem Phys 2008; 128:052207. [PMID: 18266412 DOI: 10.1063/1.2834735] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Accurate determinations of chemical shift anisotropy (CSA) tensors are valuable for NMR of biological systems. In this review we describe recent developments in CSA measurement techniques and applications, particularly in the context of peptides and proteins. These techniques include goniometeric measurements of single crystals, slow magic-angle spinning studies of powder samples, and CSA recoupling under moderate to fast MAS. Experimental CSA data can be analyzed by comparison with ab initio calculations for structure determination and refinement. This approach has particularly high potential for aliphatic (13)C analysis, especially Calpha tensors which are directly related to structure. Carbonyl and (15)N CSA tensors demonstrate a more complex dependence upon hydrogen bonding and electrostatics, in addition to conformational dependence. The improved understanding of these tensors and the ability to measure them quantitatively provide additional opportunities for structure determination, as well as insights into dynamics.
Collapse
Affiliation(s)
- Benjamin J Wylie
- Department of Chemistry, Department of Biochemistry and Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
| | | |
Collapse
|
95
|
Wickramasinghe NP, Shaibat MA, Jones CR, Casabianca LB, de Dios AC, Harwood JS, Ishii Y. Progress in C13 and H1 solid-state nuclear magnetic resonance for paramagnetic systems under very fast magic angle spinning. J Chem Phys 2008; 128:052210. [DOI: 10.1063/1.2833574] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
96
|
Schmidt HLF, Sperling LJ, Gao YG, Wylie BJ, Boettcher JM, Wilson SR, Rienstra CM. Crystal polymorphism of protein GB1 examined by solid-state NMR spectroscopy and X-ray diffraction. J Phys Chem B 2007; 111:14362-9. [PMID: 18052145 PMCID: PMC2774121 DOI: 10.1021/jp075531p] [Citation(s) in RCA: 97] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The study of micro- or nanocrystalline proteins by magic-angle spinning (MAS) solid-state NMR (SSNMR) gives atomic-resolution insight into structure in cases when single crystals cannot be obtained for diffraction studies. Subtle differences in the local chemical environment around the protein, including the characteristics of the cosolvent and the buffer, determine whether a protein will form single crystals. The impact of these small changes in formulation is also evident in the SSNMR spectra; however, the changes lead only to correspondingly subtle changes in the spectra. Here, we demonstrate that several formulations of GB1 microcrystals yield very high quality SSNMR spectra, although only a subset of conditions enable growth of single crystals. We have characterized these polymorphs by X-ray powder diffraction and assigned the SSNMR spectra. Assignments of the 13C and 15N SSNMR chemical shifts confirm that the backbone structure is conserved, indicative of a common protein fold, but side chain chemical shifts are changed on the surface of the protein, in a manner dependent upon crystal packing and electrostatic interactions with salt in the mother liquor. Our results demonstrate the ability of SSNMR to reveal minor structural differences among crystal polymorphs. This ability has potential practical utility for studying the formulation chemistry of industrial and therapeutic proteins, as well as for deriving fundamental insights into the phenomenon of single-crystal growth.
Collapse
Affiliation(s)
- Heather L Frericks Schmidt
- Department of Chemistry, University of Illinois Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61821, USA
| | | | | | | | | | | | | |
Collapse
|
97
|
Peng X, Libich D, Janik R, Harauz G, Ladizhansky V. Dipolar Chemical Shift Correlation Spectroscopy for Homonuclear Carbon Distance Measurements in Proteins in the Solid State: Application to Structure Determination and Refinement. J Am Chem Soc 2007; 130:359-69. [DOI: 10.1021/ja076658v] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Xiaohu Peng
- Department of Physics, Department of Molecular and Cellular Biology, and Biophysics Interdepartmental Group, University of Guelph, 50 Stone Road East, Guelph, Ontario, Canada, N1G 2W1
| | - David Libich
- Department of Physics, Department of Molecular and Cellular Biology, and Biophysics Interdepartmental Group, University of Guelph, 50 Stone Road East, Guelph, Ontario, Canada, N1G 2W1
| | - Rafal Janik
- Department of Physics, Department of Molecular and Cellular Biology, and Biophysics Interdepartmental Group, University of Guelph, 50 Stone Road East, Guelph, Ontario, Canada, N1G 2W1
| | - George Harauz
- Department of Physics, Department of Molecular and Cellular Biology, and Biophysics Interdepartmental Group, University of Guelph, 50 Stone Road East, Guelph, Ontario, Canada, N1G 2W1
| | - Vladimir Ladizhansky
- Department of Physics, Department of Molecular and Cellular Biology, and Biophysics Interdepartmental Group, University of Guelph, 50 Stone Road East, Guelph, Ontario, Canada, N1G 2W1
| |
Collapse
|
98
|
Kotecha M, Wickramasinghe NP, Ishii Y. Efficient low-power heteronuclear decoupling in 13C high-resolution solid-state NMR under fast magic angle spinning. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2007; 45 Suppl 1:S221-30. [PMID: 18157841 DOI: 10.1002/mrc.2151] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The use of a low-power two-pulse phase modulation (TPPM) sequence is proposed for efficient (1)H radio frequency (rf) decoupling in high-resolution (13)C solid-state NMR (SSNMR) under fast MAS conditions. Decoupling efficiency for different low-power decoupling sequences such as continuous-wave (cw), TPPM, XiX, and π-pulse (PIPS) train decoupling has been investigated at a spinning speed of 40 kHz for (13)C CPMAS spectra of uniformly (13)C- and (15)N-labeled L-alanine. It was found that the TPPM decoupling sequence, which was originally designed for high-power decoupling, provides the best decoupling efficiency at low power among all the low-power decoupling sequences examined here. Optimum performance of the low-power TPPM sequence was found to be obtained at a decoupling field intensity (ω(1)) of ~ω(R)/4 with a pulse flip angle of ~π and a phase alternation between ± [Symbol: see text]([Symbol: see text] = 20° ), where ω(R)/2π is the spinning speed. The sensitivity obtained for (13) CO(2)(-), (13)CH, and (13)CH(3) in L-alanine under low-power TPPM at ω(1)/2π of 10 kHz was only 5-15% less than that under high-power TPPM at ω(1) /2π of 200 kHz, despite the fact that only 0.25% of the rf power was required in low-power TPPM. Analysis of the (13)CH(2) signals for uniformly (13) C- and (15) N-labeled L-isoleucine under various low-power decoupling sequences also confirmed superior performance of the low-power TPPM sequence, although the intensity obtained by low-power TPPM was 61% of that obtained by high-power TPPM. (13)C CPMAS spectra of (13)C-labeled ubiquitin micro crystals obtained by low-power TPPM demonstrates that the low-power TPPM sequence is a practical option that provides excellent resolution and sensitivity in (13)C SSNMR for hydrated proteins.
Collapse
Affiliation(s)
- Mrignayani Kotecha
- Department of Chemistry, University of Illinois at Chicago, 845 W Taylor Street, Chicago, IL 60607, USA
| | | | | |
Collapse
|
99
|
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.
Collapse
Affiliation(s)
- Jun Yang
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
| | | | | | | | | | | |
Collapse
|
100
|
McNeill SA, Gor'kov PL, Struppe J, Brey WW, Long JR. Optimizing ssNMR experiments for dilute proteins in heterogeneous mixtures at high magnetic fields. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2007; 45 Suppl 1:S209-20. [PMID: 18157844 DOI: 10.1002/mrc.2146] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Solid-state NMR spectroscopy at high magnetic fields is proving to be an effective technique in structural biology, particularly for proteins which are not amenable to traditional X-ray and solution NMR approaches. Several parameters can be selected to provide optimal sensitivity, improve sample stability, and ensure biological relevance for ssNMR measurements on protein samples. These include selection of sample conditions, NMR probe design, and design of pulse experiments. Here, we demonstrate and evaluate several engineering and experimental approaches for pursuing measurements on dilute proteins in heterogeneous mixtures.
Collapse
Affiliation(s)
- Seth A McNeill
- Department of Biochemistry and Molecular Biology, McKnight Brain Institute, University of Florida, Gainesville, FL 32610, USA
| | | | | | | | | |
Collapse
|