1
|
Thurber KR, Yau WM, Tycko R. Structure of Amyloid Peptide Ribbons Characterized by Electron Microscopy, Atomic Force Microscopy, and Solid-State Nuclear Magnetic Resonance. J Phys Chem B 2024; 128:1711-1723. [PMID: 38348474 DOI: 10.1021/acs.jpcb.3c07867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
Polypeptides often self-assemble to form amyloid fibrils, which contain cross-β structural motifs and are typically 5-15 nm in width and micrometers in length. In many cases, short segments of longer amyloid-forming protein or peptide sequences also form cross-β assemblies but with distinctive ribbon-like morphologies that are characterized by a well-defined thickness (on the order of 5 nm) in one lateral dimension and a variable width (typically 10-100 nm) in the other. Here, we use a novel combination of data from solid-state nuclear magnetic resonance (ssNMR), dark-field transmission electron microscopy (TEM), atomic force microscopy (AFM), and cryogenic electron microscopy (cryoEM) to investigate the structures within amyloid ribbons formed by residues 14-23 and residues 11-25 of the Alzheimer's disease-associated amyloid-β peptide (Aβ14-23 and Aβ11-25). The ssNMR data indicate antiparallel β-sheets with specific registries of intermolecular hydrogen bonds. Mass-per-area values are derived from dark-field TEM data. The ribbon thickness is determined from AFM images. For Aβ14-23 ribbons, averaged cryoEM images show a periodic spacing of β-sheets. The combined data support structures in which the amyloid ribbon growth direction is the direction of intermolecular hydrogen bonds between β-strands, the ribbon thickness corresponds to the width of one β-sheet (i.e., approximately the length of one molecule), and the variable ribbon width is a variable multiple of the thickness of one β-sheet (i.e., a multiple of the repeat distance in a stack of β-sheets). This architecture for a cross-β assembly may generally exist within amyloid ribbons.
Collapse
Affiliation(s)
- Kent R Thurber
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, United States
| | - Wai-Ming Yau
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, United States
| | - Robert Tycko
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, United States
| |
Collapse
|
2
|
Jeon J, Blake Wilson C, Yau WM, Thurber KR, Tycko R. Time-resolved solid state NMR of biomolecular processes with millisecond time resolution. J Magn Reson 2022; 342:107285. [PMID: 35998398 PMCID: PMC9463123 DOI: 10.1016/j.jmr.2022.107285] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Revised: 08/10/2022] [Accepted: 08/11/2022] [Indexed: 05/21/2023]
Abstract
We review recent efforts to develop and apply an experimental approach to the structural characterization of transient intermediate states in biomolecular processes that involve large changes in molecular conformation or assembly state. This approach depends on solid state nuclear magnetic resonance (ssNMR) measurements that are performed at very low temperatures, typically 25-30 K, with signal enhancements from dynamic nuclear polarization (DNP). This approach also involves novel technology for initiating the process of interest, either by rapid mixing of two solutions or by a rapid inverse temperature jump, and for rapid freezing to trap intermediate states. Initiation by rapid mixing or an inverse temperature jump can be accomplished in approximately-one millisecond. Freezing can be accomplished in approximately 100 microseconds. Thus, millisecond time resolution can be achieved. Recent applications to the process by which the biologically essential calcium sensor protein calmodulin forms a complex with one of its target proteins and the process by which the bee venom peptide melittin converts from an unstructured monomeric state to a helical, tetrameric state after a rapid change in pH or temperature are described briefly. Future applications of millisecond time-resolved ssNMR are also discussed briefly.
Collapse
Affiliation(s)
- Jaekyun Jeon
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA
| | - C Blake Wilson
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA
| | - Wai-Ming Yau
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA
| | - Kent R Thurber
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA
| | - Robert Tycko
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA.
| |
Collapse
|
3
|
Thurber KR, Yin Y, Tycko R. Automated picking of amyloid fibrils from cryo-EM images for helical reconstruction with RELION. J Struct Biol 2021; 213:107736. [PMID: 33831509 DOI: 10.1016/j.jsb.2021.107736] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 03/31/2021] [Accepted: 04/01/2021] [Indexed: 11/16/2022]
Abstract
Cryogenic electron microscopy (cryo-EM) is an important tool for determining the molecular structure of proteins and protein assemblies, including helical assemblies such as amyloid fibrils. In reconstruction of amyloid fibril structures from cryo-EM images, an important early step is the selection of fibril locations. This fibril picking step is typically done by hand, a tedious process when thousands of images need to be analyzed. Here we present a computer program called FibrilFinder that identifies the locations and directions of fibril segments in cryo-EM images, by using the properties that the fibrils should be linear objects and have widths within a specified range. The program outputs the fibril locations in text files compatible with the RELION density reconstruction program. After RELION is used to extract the particle image boxes contained in the fibril segments identified by FibrilFinder, a second program called FibrilFixer removes boxes that contain more than one fibril, for instance because two fibrils cross each other. As concrete and realistic examples, we describe the application of the two programs to cryo-EM images of two different amyloid fibrils, namely 40-residue amyloid-β fibrils derived from human brain tissue by seeded growth and fibrils formed by the C-terminal half of the low-complexity domain of the RNA-binding protein FUS. Both examples of amyloid fibrils can be picked from cryo-EM images using the same set of FibrilFinder and FibrilFixer parameters, showing that this software does not require re-optimization for each sample. A set of 1337 cryo-EM images was analyzed in 17 min with one multi-core computer. The new fibril picking software should enable the rapid analysis and comparison of more helical structures using cryo-EM, and perhaps serve as part of the greater automation of the entire structure determination process.
Collapse
Affiliation(s)
- Kent R Thurber
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA.
| | - Yi Yin
- Nuffield Department of Women's & Reproductive Health, University of Oxford, Oxford OX3 9DU, UK
| | - Robert Tycko
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA
| |
Collapse
|
4
|
Lee M, Ghosh U, Thurber KR, Kato M, Tycko R. Molecular structure and interactions within amyloid-like fibrils formed by a low-complexity protein sequence from FUS. Nat Commun 2020; 11:5735. [PMID: 33184287 PMCID: PMC7665218 DOI: 10.1038/s41467-020-19512-3] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 10/14/2020] [Indexed: 12/13/2022] Open
Abstract
Protein domains without the usual distribution of amino acids, called low complexity (LC) domains, can be prone to self-assembly into amyloid-like fibrils. Self-assembly of LC domains that are nearly devoid of hydrophobic residues, such as the 214-residue LC domain of the RNA-binding protein FUS, is particularly intriguing from the biophysical perspective and is biomedically relevant due to its occurrence within neurons in amyotrophic lateral sclerosis, frontotemporal dementia, and other neurodegenerative diseases. We report a high-resolution molecular structural model for fibrils formed by the C-terminal half of the FUS LC domain (FUS-LC-C, residues 111-214), based on a density map with 2.62 Å resolution from cryo-electron microscopy (cryo-EM). In the FUS-LC-C fibril core, residues 112-150 adopt U-shaped conformations and form two subunits with in-register, parallel cross-β structures, arranged with quasi-21 symmetry. All-atom molecular dynamics simulations indicate that the FUS-LC-C fibril core is stabilized by a plethora of hydrogen bonds involving sidechains of Gln, Asn, Ser, and Tyr residues, both along and transverse to the fibril growth direction, including diverse sidechain-to-backbone, sidechain-to-sidechain, and sidechain-to-water interactions. Nuclear magnetic resonance measurements additionally show that portions of disordered residues 151-214 remain highly dynamic in FUS-LC-C fibrils and that fibrils formed by the N-terminal half of the FUS LC domain (FUS-LC-N, residues 2-108) have the same core structure as fibrils formed by the full-length LC domain. These results contribute to our understanding of the molecular structural basis for amyloid formation by FUS and by LC domains in general.
Collapse
Affiliation(s)
- Myungwoon Lee
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, 20892-0520, USA
| | - Ujjayini Ghosh
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, 20892-0520, USA
| | - Kent R Thurber
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, 20892-0520, USA
| | - Masato Kato
- Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas, 75390-9152, USA
- Institute for Quantum Life Science, National Institutes for Quantum and Radiological Science and Technology, Chiba, 263-8555, Japan
| | - Robert Tycko
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, 20892-0520, USA.
| |
Collapse
|
5
|
Thurber KR, Le TN, Changcoco V, Brook DJR. Verdazyl-ribose: A new radical for solid-state dynamic nuclear polarization at high magnetic field. J Magn Reson 2018; 289:122-131. [PMID: 29501956 PMCID: PMC5856651 DOI: 10.1016/j.jmr.2018.02.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 02/20/2018] [Accepted: 02/21/2018] [Indexed: 06/08/2023]
Abstract
Solid-state dynamic nuclear polarization (DNP) using the cross-effect relies on radical pairs whose electron spin resonance (ESR) frequencies differ by the nuclear magnetic resonance (NMR) frequency. We measure the DNP provided by a new water-soluble verdazyl radical, verdazyl-ribose, under both magic-angle spinning (MAS) and static sample conditions at 9.4 T, and compare it to a nitroxide radical, 4-hydroxy-TEMPO. We find that verdazyl-ribose is an effective radical for cross-effect DNP, with the best relative results for a non-spinning sample. Under non-spinning conditions, verdazyl-ribose provides roughly 2× larger 13C cross-polarized (CP) NMR signal than the nitroxide, with similar polarization buildup times, at both 29 K and 76 K. With MAS at 7 kHz and 1.5 W microwave power, the verdazyl-ribose does not provide as much DNP as the nitroxide, with the verdazyl providing less NMR signal and a longer polarization buildup time. When the microwave power is decreased to 30 mW with 5 kHz MAS, the two types of radical are comparable, with the verdazyl-doped sample having a larger NMR signal which compensates for its longer polarization buildup time. We also present electron spin relaxation measurements at Q-band (1.2 T) and ESR lineshapes at 1.2 and 9.4 T. Most notably, the verdazyl radical has a longer T1e than the nitroxide (9.9 ms and 1.3 ms, respectively, at 50 K and 1.2 T). The verdazyl electron spin lineshape is significantly affected by the hyperfine coupling to four 14N nuclei, even at 9.4 T. We also describe 3000-spin calculations to illustrate the DNP potential of possible radical pairs: verdazyl-verdazyl, verdazyl-nitroxide, or nitroxide-nitroxide pairs. These calculations suggest that the verdazyl radical at 9.4 T has a narrower linewidth than optimal for cross-effect DNP using verdazyl-verdazyl pairs. Because of the hyperfine coupling contribution to the electron spin linewidth, this implies that DNP using the verdazyl radical would improve at lower magnetic field. Another conclusion from the calculations is that a verdazyl-nitroxide bi-radical would be expected to be slightly better for cross-effect DNP than the nitroxide-nitroxide bi-radicals commonly used now, assuming the same spin-spin coupling constants.
Collapse
Affiliation(s)
- Kent R Thurber
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, United States.
| | - Thanh-Ngoc Le
- Department of Chemistry, San José State University, One Washington Square, San José, CA 95192, United States
| | - Victor Changcoco
- Department of Chemistry, San José State University, One Washington Square, San José, CA 95192, United States
| | - David J R Brook
- Department of Chemistry, San José State University, One Washington Square, San José, CA 95192, United States
| |
Collapse
|
6
|
Murray DT, Kato M, Lin Y, Thurber KR, Hung I, McKnight SL, Tycko R. Structure of FUS Protein Fibrils and Its Relevance to Self-Assembly and Phase Separation of Low-Complexity Domains. Cell 2017; 171:615-627.e16. [PMID: 28942918 PMCID: PMC5650524 DOI: 10.1016/j.cell.2017.08.048] [Citation(s) in RCA: 473] [Impact Index Per Article: 67.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2017] [Revised: 08/10/2017] [Accepted: 08/25/2017] [Indexed: 12/22/2022]
Abstract
Polymerization and phase separation of proteins containing low-complexity (LC) domains are important factors in gene expression, mRNA processing and trafficking, and localization of translation. We have used solid-state nuclear magnetic resonance methods to characterize the molecular structure of self-assembling fibrils formed by the LC domain of the fused in sarcoma (FUS) RNA-binding protein. From the 214-residue LC domain of FUS (FUS-LC), a segment of only 57 residues forms the fibril core, while other segments remain dynamically disordered. Unlike pathogenic amyloid fibrils, FUS-LC fibrils lack hydrophobic interactions within the core and are not polymorphic at the molecular structural level. Phosphorylation of core-forming residues by DNA-dependent protein kinase blocks binding of soluble FUS-LC to FUS-LC hydrogels and dissolves phase-separated, liquid-like FUS-LC droplets. These studies offer a structural basis for understanding LC domain self-assembly, phase separation, and regulation by post-translational modification.
Collapse
Affiliation(s)
- Dylan T Murray
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA; Postdoctoral Research Associate Program, National Institute of General Medical Sciences, National Institutes of Health, Bethesda, MD 20892-6200, USA
| | - Masato Kato
- Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-9152, USA
| | - Yi Lin
- Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-9152, USA
| | - Kent R Thurber
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA
| | - Ivan Hung
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32310, USA
| | - Steven L McKnight
- Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-9152, USA.
| | - Robert Tycko
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA.
| |
Collapse
|
7
|
Potapov A, Yau WM, Ghirlando R, Thurber KR, Tycko R. Successive Stages of Amyloid-β Self-Assembly Characterized by Solid-State Nuclear Magnetic Resonance with Dynamic Nuclear Polarization. J Am Chem Soc 2015; 137:8294-307. [PMID: 26068174 PMCID: PMC5559291 DOI: 10.1021/jacs.5b04843] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Self-assembly of amyloid-β (Aβ) peptides in human brain tissue leads to neurodegeneration in Alzheimer's disease (AD). Amyloid fibrils, whose structures have been extensively characterized by solid state nuclear magnetic resonance (ssNMR) and other methods, are the thermodynamic end point of Aβ self-assembly. Oligomeric and protofibrillar assemblies, whose structures are less well-understood, are also observed as intermediates in the assembly process in vitro and have been implicated as important neurotoxic species in AD. We report experiments in which the structural evolution of 40-residue Aβ (Aβ40) is monitored by ssNMR measurements on frozen solutions prepared at four successive stages of the self-assembly process. Measurements on transient intermediates are enabled by ssNMR signal enhancements from dynamic nuclear polarization (DNP) at temperatures below 30 K. DNP-enhanced ssNMR data reveal a monotonic increase in conformational order from an initial state comprised primarily of monomers and small oligomers in solution at high pH, to larger oligomers near neutral pH, to metastable protofibrils, and finally to fibrils. Surprisingly, the predominant molecular conformation, indicated by (13)C NMR chemical shifts and by side chain contacts between F19 and L34 residues, is qualitatively similar at all stages. However, the in-register parallel β-sheet supramolecular structure, indicated by intermolecular (13)C spin polarization transfers, does not develop before the fibril stage. This work represents the first application of DNP-enhanced ssNMR to the characterization of peptide or protein self-assembly intermediates.
Collapse
Affiliation(s)
- Alexey Potapov
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520
| | - Wai-Ming Yau
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520
| | - Rodolfo Ghirlando
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520
| | - Kent R. Thurber
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520
| | - Robert Tycko
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520
| |
Collapse
|
8
|
Yau WM, Thurber KR, Tycko R. Synthesis and evaluation of nitroxide-based oligoradicals for low-temperature dynamic nuclear polarization in solid state NMR. J Magn Reson 2014; 244:98-106. [PMID: 24887201 PMCID: PMC4106245 DOI: 10.1016/j.jmr.2014.05.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Revised: 05/02/2014] [Accepted: 05/03/2014] [Indexed: 05/05/2023]
Abstract
We describe the synthesis of new nitroxide-based biradical, triradical, and tetraradical compounds and the evaluation of their performance as paramagnetic dopants in dynamic nuclear polarization (DNP) experiments in solid state nuclear magnetic resonance (NMR) spectroscopy with magic-angle spinning (MAS). Under our experimental conditions, which include temperatures in the 25-30 K range, a 9.4 T magnetic field, MAS frequencies of 6.2-6.8 kHz, and microwave irradiation at 264.0 GHz from a 800 mW extended interaction oscillator source, the most effective compounds are triradicals that are related to the previously-described compound DOTOPA-TEMPO (see Thurber et al., 2010), but have improved solubility in glycerol/water solvent near neutral pH. Using these compounds at 30 mM total nitroxide concentration, we observe DNP enhancement factors of 92-128 for cross-polarized (13)C NMR signals from (15)N,(13)C-labeled melittin in partially protonated glycerol/water, and build-up times of 2.6-3.8s for (1)H spin polarizations. Net sensitivity enhancements with biradical and tetraradical dopants, taking into account absolute (13)C NMR signal amplitudes and build-up times, are approximately 2-4 times lower than with the best triradicals.
Collapse
Affiliation(s)
- Wai-Ming Yau
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, United States
| | - Kent R Thurber
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, United States
| | - Robert Tycko
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, United States.
| |
Collapse
|
9
|
Thurber KR, Tycko R. Perturbation of nuclear spin polarizations in solid state NMR of nitroxide-doped samples by magic-angle spinning without microwaves. J Chem Phys 2014; 140:184201. [PMID: 24832263 PMCID: PMC4032438 DOI: 10.1063/1.4874341] [Citation(s) in RCA: 113] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Accepted: 04/21/2014] [Indexed: 01/17/2023] Open
Abstract
We report solid state (13)C and (1)H nuclear magnetic resonance (NMR) experiments with magic-angle spinning (MAS) on frozen solutions containing nitroxide-based paramagnetic dopants that indicate significant perturbations of nuclear spin polarizations without microwave irradiation. At temperatures near 25 K, (1)H and cross-polarized (13)C NMR signals from (15)N,(13)C-labeled L-alanine in trinitroxide-doped glycerol/water are reduced by factors as large as six compared to signals from samples without nitroxide doping. Without MAS or at temperatures near 100 K, differences between signals with and without nitroxide doping are much smaller. We attribute most of the reduction of NMR signals under MAS near 25 K to nuclear spin depolarization through the cross-effect dynamic nuclear polarization mechanism, in which three-spin flips drive nuclear polarizations toward equilibrium with spin polarization differences between electron pairs. When T1e is sufficiently long relative to the MAS rotation period, the distribution of electron spin polarization across the nitroxide electron paramagnetic resonance lineshape can be very different from the corresponding distribution in a static sample at thermal equilibrium, leading to the observed effects. We describe three-spin and 3000-spin calculations that qualitatively reproduce the experimental observations.
Collapse
Affiliation(s)
- Kent R Thurber
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, USA
| | - Robert Tycko
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, USA
| |
Collapse
|
10
|
|
11
|
Thurber KR, Potapov A, Yau WM, Tycko R. Solid state nuclear magnetic resonance with magic-angle spinning and dynamic nuclear polarization below 25 K. J Magn Reson 2013; 226:100-6. [PMID: 23238592 PMCID: PMC3529848 DOI: 10.1016/j.jmr.2012.11.009] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2012] [Revised: 11/10/2012] [Accepted: 11/13/2012] [Indexed: 05/05/2023]
Abstract
We describe an apparatus for solid state nuclear magnetic resonance (NMR) with dynamic nuclear polarization (DNP) and magic-angle spinning (MAS) at 20-25 K and 9.4 Tesla. The MAS NMR probe uses helium to cool the sample space and nitrogen gas for MAS drive and bearings, as described earlier, but also includes a corrugated waveguide for transmission of microwaves from below the probe to the sample. With a 30 mW circularly polarized microwave source at 264 GHz, MAS at 6.8 kHz, and 21 K sample temperature, greater than 25-fold enhancements of cross-polarized (13)C NMR signals are observed in spectra of frozen glycerol/water solutions containing the triradical dopant DOTOPA-TEMPO when microwaves are applied. As demonstrations, we present DNP-enhanced one-dimensional and two-dimensional (13)C MAS NMR spectra of frozen solutions of uniformly (13)C-labeled l-alanine and melittin, a 26-residue helical peptide that we have synthesized with four uniformly (13)C-labeled amino acids.
Collapse
Affiliation(s)
- Kent R Thurber
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, United States.
| | | | | | | |
Collapse
|
12
|
Thurber KR, Tycko R. Theory for cross effect dynamic nuclear polarization under magic-angle spinning in solid state nuclear magnetic resonance: the importance of level crossings. J Chem Phys 2012; 137:084508. [PMID: 22938251 PMCID: PMC3443114 DOI: 10.1063/1.4747449] [Citation(s) in RCA: 169] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2012] [Accepted: 08/07/2012] [Indexed: 12/14/2022] Open
Abstract
We present theoretical calculations of dynamic nuclear polarization (DNP) due to the cross effect in nuclear magnetic resonance under magic-angle spinning (MAS). Using a three-spin model (two electrons and one nucleus), cross effect DNP with MAS for electron spins with a large g-anisotropy can be seen as a series of spin transitions at avoided crossings of the energy levels, with varying degrees of adiabaticity. If the electron spin-lattice relaxation time T(1e) is large relative to the MAS rotation period, the cross effect can happen as two separate events: (i) partial saturation of one electron spin by the applied microwaves as one electron spin resonance (ESR) frequency crosses the microwave frequency and (ii) flip of all three spins, when the difference of the two ESR frequencies crosses the nuclear frequency, which transfers polarization to the nuclear spin if the two electron spins have different polarizations. In addition, adiabatic level crossings at which the two ESR frequencies become equal serve to maintain non-uniform saturation across the ESR line. We present analytical results based on the Landau-Zener theory of adiabatic transitions, as well as numerical quantum mechanical calculations for the evolution of the time-dependent three-spin system. These calculations provide insight into the dependence of cross effect DNP on various experimental parameters, including MAS frequency, microwave field strength, spin relaxation rates, hyperfine and electron-electron dipole coupling strengths, and the nature of the biradical dopants.
Collapse
Affiliation(s)
- Kent R Thurber
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, USA.
| | | |
Collapse
|
13
|
Potapov A, Thurber KR, Yau WM, Tycko R. Dynamic nuclear polarization-enhanced ¹H-¹³C double resonance NMR in static samples below 20 K. J Magn Reson 2012; 221:32-40. [PMID: 22743540 PMCID: PMC3727229 DOI: 10.1016/j.jmr.2012.05.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2012] [Revised: 05/07/2012] [Accepted: 05/09/2012] [Indexed: 05/21/2023]
Abstract
We demonstrate the feasibility of one-dimensional and two-dimensional ¹H-¹³C double resonance NMR experiments with dynamic nuclear polarization (DNP) at 9.4 T and temperatures below 20 K, including both ¹H-¹³C cross-polarization and ¹H decoupling, and discuss the effects of polarizing agent type, polarizing agent concentration, temperature, and solvent deuteration. We describe a two-channel low-temperature DNP/NMR probe, capable of carrying the radio-frequency power load required for ¹H-¹³C cross-polarization and high-power proton decoupling. Experiments at 8 K and 16 K reveal a significant T₂ relaxation of ¹³C, induced by electron spin flips. Carr-Purcell experiments and numerical simulations of Carr-Purcell dephasing curves allow us to determine the effective correlation time of electron flips under our experimental conditions. The dependence of the DNP signal enhancement on electron spin concentration shows a maximum near 80 mM. Although no significant difference in the absolute DNP enhancements for triradical (DOTOPA-TEMPO) and biradical (TOTAPOL) dopants was found, the triradical produced greater DNP build-up rates, which are advantageous for DNP experiments. Additionally the feasibility of structural measurements on ¹³C-labeled biomolecules was demonstrated with a two-dimensional ¹³C-¹³C exchange spectrum of selectively ¹³C-labeled β-amyloid fibrils.
Collapse
Affiliation(s)
- Alexey Potapov
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institute of Health, Bethesda, MD 20892-0520, USA.
| | | | | | | |
Collapse
|
14
|
Thurber KR, Tycko R. Prospects for sub-micron solid state nuclear magnetic resonance imaging with low-temperature dynamic nuclear polarization. Phys Chem Chem Phys 2010; 12:5779-85. [PMID: 20458431 PMCID: PMC2883786 DOI: 10.1039/c0cp00157k] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We evaluate the feasibility of (1)H nuclear magnetic resonance (NMR) imaging with sub-micron voxel dimensions using a combination of low temperatures and dynamic nuclear polarization (DNP). Experiments are performed on nitroxide-doped glycerol-water at 9.4 T and temperatures below 40 K, using a 30 mW tunable microwave source for DNP. With DNP at 7 K, a 0.5 microL sample yields a (1)H NMR signal-to-noise ratio of 770 in two scans with pulsed spin-lock detection and after 80 db signal attenuation. With reasonable extrapolations, we infer that (1)H NMR signals from 1 microm(3) voxel volumes should be readily detectable, and voxels as small as 0.03 microm(3) may eventually be detectable. Through homonuclear decoupling with a frequency-switched Lee-Goldburg spin echo technique, we obtain 830 Hz (1)H NMR linewidths at low temperatures, implying that pulsed field gradients equal to 0.4 G/d or less would be required during spatial encoding dimensions of an imaging sequence, where d is the resolution in each dimension.
Collapse
Affiliation(s)
- Kent R. Thurber
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520
| | - Robert Tycko
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520
| |
Collapse
|
15
|
Thurber KR, Yau WM, Tycko R. Low-temperature dynamic nuclear polarization at 9.4 T with a 30 mW microwave source. J Magn Reson 2010; 204:303-13. [PMID: 20392658 PMCID: PMC2874615 DOI: 10.1016/j.jmr.2010.03.016] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2010] [Revised: 03/11/2010] [Accepted: 03/18/2010] [Indexed: 05/05/2023]
Abstract
Dynamic nuclear polarization (DNP) can provide large signal enhancements in nuclear magnetic resonance (NMR) by transfer of polarization from electron spins to nuclear spins. We discuss several aspects of DNP experiments at 9.4 T (400 MHz resonant frequency for (1)H, 264 GHz for electron spins in organic radicals) in the 7-80K temperature range, using a 30 mW, frequency-tunable microwave source and a quasi-optical microwave bridge for polarization control and low-loss microwave transmission. In experiments on frozen glycerol/water doped with nitroxide radicals, DNP signal enhancements up to a factor of 80 are observed (relative to (1)H NMR signals with thermal equilibrium spin polarization). The largest sensitivity enhancements are observed with a new triradical dopant, DOTOPA-TEMPO. Field modulation with a 10 G root-mean-squared amplitude during DNP increases the nuclear spin polarizations by up to 135%. Dependencies of (1)H NMR signal amplitudes, nuclear spin relaxation times, and DNP build-up times on the dopant and its concentration, temperature, microwave power, and modulation frequency are reported and discussed. The benefits of low-temperature DNP can be dramatic: the (1)H spin polarization is increased approximately 1000-fold at 7 K with DNP, relative to thermal polarization at 80K.
Collapse
Affiliation(s)
- Kent R. Thurber
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520
| | - Wai-Ming Yau
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520
| | - Robert Tycko
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520
| |
Collapse
|
16
|
Shewmaker F, McGlinchey RP, Thurber KR, McPhie P, Dyda F, Tycko R, Wickner RB. The functional curli amyloid is not based on in-register parallel beta-sheet structure. J Biol Chem 2009; 284:25065-76. [PMID: 19574225 DOI: 10.1074/jbc.m109.007054] [Citation(s) in RCA: 109] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The extracellular curli proteins of Enterobacteriaceae form fibrous structures that are involved in biofilm formation and adhesion to host cells. These curli fibrils are considered a functional amyloid because they are not a consequence of misfolding, but they have many of the properties of protein amyloid. We confirm that fibrils formed by CsgA and CsgB, the primary curli proteins of Escherichia coli, possess many of the hallmarks typical of amyloid. Moreover we demonstrate that curli fibrils possess the cross-beta structure that distinguishes protein amyloid. However, solid state NMR experiments indicate that curli structure is not based on an in-register parallel beta-sheet architecture, which is common to many human disease-associated amyloids and the yeast prion amyloids. Solid state NMR and electron microscopy data are consistent with a beta-helix-like structure but are not sufficient to establish such a structure definitively.
Collapse
Affiliation(s)
- Frank Shewmaker
- Laboratory of Biochemistry and Genetics, NIDDK, National Institutes of Health, Bethesda, Maryland 20892-0830, USA
| | | | | | | | | | | | | |
Collapse
|
17
|
Thurber KR, Tycko R. Measurement of sample temperatures under magic-angle spinning from the chemical shift and spin-lattice relaxation rate of 79Br in KBr powder. J Magn Reson 2009; 196:84-7. [PMID: 18930418 PMCID: PMC2632797 DOI: 10.1016/j.jmr.2008.09.019] [Citation(s) in RCA: 184] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2008] [Revised: 09/22/2008] [Accepted: 09/22/2008] [Indexed: 05/06/2023]
Abstract
Accurate determination of sample temperatures in solid state nuclear magnetic resonance (NMR) with magic-angle spinning (MAS) can be problematic, particularly because frictional heating and heating by radio-frequency irradiation can make the internal sample temperature significantly different from the temperature outside the MAS rotor. This paper demonstrates the use of (79)Br chemical shifts and spin-lattice relaxation rates in KBr powder as temperature-dependent parameters for the determination of internal sample temperatures. Advantages of this method include high signal-to-noise, proximity of the (79)Br NMR frequency to that of (13)C, applicability from 20 K to 320 K or higher, and simultaneity with adjustment of the MAS axis direction. We show that spin-lattice relaxation in KBr is driven by a quadrupolar mechanism. We demonstrate a simple approach to including KBr powder in hydrated samples, such as biological membrane samples, hydrated amyloid fibrils, and hydrated microcrystalline proteins, that allows direct assessment of the effects of frictional and radio-frequency heating under experimentally relevant conditions.
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
|
18
|
Thurber KR, Tycko R. Biomolecular solid state NMR with magic-angle spinning at 25K. J Magn Reson 2008; 195:179-86. [PMID: 18922715 PMCID: PMC2632798 DOI: 10.1016/j.jmr.2008.09.015] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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
|
19
|
Thurber KR, Sauer KL, Buess ML, Klug CA, Miller JB. Increasing 14N NQR signal by 1H-14N level crossing with small magnetic fields. J Magn Reson 2005; 177:118-28. [PMID: 16122957 DOI: 10.1016/j.jmr.2005.07.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2005] [Revised: 07/22/2005] [Accepted: 07/22/2005] [Indexed: 05/04/2023]
Abstract
NQR detection of materials, such as TNT, is hindered by the low signal-to-noise ratio at low NQR frequencies. Sweeping small (0-26 mT) magnetic fields to shift the (1)H NMR frequency relative to the (14)N NQR frequencies can provide a significant increase of the (14)N NQR signal-to-noise ratio. Three effects of (1)H-(14)N level crossing are demonstrated in diglycine hydrochloride and TNT. These effects are (1) transferring (1)H polarization to one or more of the (14)N transitions, including the use of an adiabatic flip of the (1)H polarization during the field sweep, (2) shortening the effective (14)N T(1) by the interaction of (1)H with the (14)N transitions, (3) "level transfer" effect where the third (14)N (spin 1) energy level or other (14)N sites with different NQR frequency are used as a reservoir of polarization which is transferred to the measured (14)N transition by the (1)H. The (14)N NQR signal-to-noise ratio can be increased by a factor of 2.5 for one (14)N site in diglycine hydrochloride (and 2.2 in TNT), even though the maximum (1)H frequency used in this work, 111 6 kHz, is only 30% larger than the measured (14)N frequencies (834 kHz for diglycine hydrochloride and 843 kHz for TNT).
Collapse
Affiliation(s)
- Kent R Thurber
- US Naval Research Laboratory, Washington, DC 20375, USA.
| | | | | | | | | |
Collapse
|
20
|
Abstract
We demonstrate one-dimensional nuclear magnetic resonance imaging of the semiconductor GaAs with 170 nm slice separation and resolve two regions of reduced nuclear spin polarization density separated by only 500 nm. This was achieved by force detection of the magnetic resonance, magnetic resonance force microscopy (MRFM), in combination with optical pumping to increase the nuclear spin polarization. Optical pumping of the GaAs created spin polarization up to 12 times larger than the thermal nuclear spin polarization at 5K and 4T. The experiment was sensitive to sample volumes of 50 microm(3) containing approximately 4 x 10(11)71 Ga/Hz. These results demonstrate the ability of force-detected magnetic resonance to apply magnetic resonance imaging to semiconductor devices and other nanostructures.
Collapse
|
21
|
Thurber KR, Hunt AW, Imai T, Chou FC. 17O NMR study of q = 0 spin excitations in a nearly ideal S = 1 / 2 1D Heisenberg antiferromagnet, Sr2CuO3, up to 800 K. Phys Rev Lett 2001; 87:247202. [PMID: 11736538 DOI: 10.1103/physrevlett.87.247202] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2001] [Indexed: 05/23/2023]
Abstract
We used 17O NMR to probe the uniform (wave vector q = 0) electron spin excitations up to 800 K in Sr2CuO3 and separate the q = 0 from the q = +/-pi / a staggered components. Our results support the logarithmic decrease of the uniform spin susceptibility below T approximately 0.015J, where J = 2200 K. From measurement of the dynamical spin susceptibility for q = 0 by the spin-lattice relaxation rate 1/T(1), we demonstrate that the q = 0 mode of spin transport is ballistic at the T = 0 limit, but has a diffusion-like contribution at finite temperatures even for T<<J.
Collapse
Affiliation(s)
- K R Thurber
- Department of Physics, MIT, Cambridge, Massachusetts 02139 and Center for Materials Science and Engineering, MIT, Cambridge, Massachusetts 02139
| | | | | | | |
Collapse
|
22
|
Thurber KR, Imai T, Saitoh T, Azuma M, Takano M, Chou FC. 63Cu NQR evidence of dimensional crossover to anisotropic 2D regime in S = 1 / 2 three-Leg ladder Sr2Cu3O5. Phys Rev Lett 2000; 84:558-561. [PMID: 11015963 DOI: 10.1103/physrevlett.84.558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/1999] [Indexed: 05/23/2023]
Abstract
We probed spin-spin correlations up to 725 K with 63Cu nuclear quadrupole resonance in the S = 1 / 2 three-leg ladder Sr2Cu3O5. We present experimental evidence that below 300 K weak interladder coupling causes dimensional crossover of the spin-spin correlation length xi from the quasi-1D (xi approximately 1 / T) to the anisotropic 2D regime ( xi approximately exp2pirho(s) / T, where 2pirho(s) = 290+/-30 K is the effective spin stiffness).
Collapse
Affiliation(s)
- KR Thurber
- Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 and Center for Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | | | | | | | | | | |
Collapse
|