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
|
Wilson CB, Yau WM, Tycko R. Experimental Evidence for Millisecond-Timescale Structural Evolution Following the Microsecond-Timescale Folding of a Small Protein. Phys Rev Lett 2024; 132:048402. [PMID: 38335342 DOI: 10.1103/physrevlett.132.048402] [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] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 10/27/2023] [Indexed: 02/12/2024]
Abstract
Prior work has shown that small proteins can fold (i.e., convert from unstructured to structured states) within 10 μs. Here we use time-resolved solid state nuclear magnetic resonance (ssNMR) methods to show that full folding of the 35-residue villin headpiece subdomain (HP35) requires a slow annealing process that has not been previously detected. ^{13}C ssNMR spectra of frozen HP35 solutions, acquired with a variable time τ_{e} at 30 °C after rapid cooling from 95 °C and before rapid freezing, show changes on the 3-10 ms timescale, attributable to slow rearrangements of protein sidechains during τ_{e}.
Collapse
Affiliation(s)
- C Blake Wilson
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, USA
| | - Wai-Ming Yau
- 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
|
3
|
Gomez-Gutierrez R, Ghosh U, Yau WM, Gamez N, Do K, Kramm C, Shirani H, Vegas-Gomez L, Schulz J, Moreno-Gonzalez I, Gutierrez A, Nilsson KPR, Tycko R, Soto C, Morales R. Two structurally defined Aβ polymorphs promote different pathological changes in susceptible mice. EMBO Rep 2023:e57003. [PMID: 37424505 PMCID: PMC10398671 DOI: 10.15252/embr.202357003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 05/10/2023] [Accepted: 05/16/2023] [Indexed: 07/11/2023] Open
Abstract
Misfolded Aβ is involved in the progression of Alzheimer's disease (AD). However, the role of its polymorphic variants or conformational strains in AD pathogenesis is not fully understood. Here, we study the seeding properties of two structurally defined synthetic misfolded Aβ strains (termed 2F and 3F) using in vitro and in vivo assays. We show that 2F and 3F strains differ in their biochemical properties, including resistance to proteolysis, binding to strain-specific dyes, and in vitro seeding. Injection of these strains into a transgenic mouse model produces different pathological features, namely different rates of aggregation, formation of different plaque types, tropism to specific brain regions, differential recruitment of Aβ40 /Aβ42 peptides, and induction of microglial and astroglial responses. Importantly, the aggregates induced by 2F and 3F are structurally different as determined by ssNMR. Our study analyzes the biological properties of purified Aβ polymorphs that have been characterized at the atomic resolution level and provides relevant information on the pathological significance of misfolded Aβ strains.
Collapse
Grants
- AARGD-18-566576 Alzheimer's Association (AA)
- PI21/00915 European Union
- P18-RT-2233 Consejería de Economía, Conocimiento, Empresas y Universidad, Junta de Andalucía (Ministry of Economy, Knowledge, Business and University, Andalusia)
- UMA18-FEDERJA-211 Consejería de Economía, Innovación, Ciencia y Empleo, Junta de Andalucía (Ministry of Economy, Innovation, Science and Employment, Government of Andalucia)
- PI21/00915 MEC | Instituto de Salud Carlos III (ISCIII)
- R56AG061878 National Institutes of Health (USA)
- RF1AG059321 National Institutes of Health (USA)
- Z01-DK029061-14 National Institutes of Health (USA)
Collapse
Affiliation(s)
- Ruben Gomez-Gutierrez
- Department of Neurology, The University of Texas Health Science Center at Houston, Houston, TX, USA
- Dpto. Biología Celular, Genética y Fisiología, Instituto de Investigación Biomédica de Málaga-IBIMA, Facultad de Ciencias, Universidad de Málaga, Málaga, Spain
| | - Ujjayini Ghosh
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Wai-Ming Yau
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Nazaret Gamez
- Department of Neurology, The University of Texas Health Science Center at Houston, Houston, TX, USA
- Dpto. Biología Celular, Genética y Fisiología, Instituto de Investigación Biomédica de Málaga-IBIMA, Facultad de Ciencias, Universidad de Málaga, Málaga, Spain
| | - Katherine Do
- Department of Neurology, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Carlos Kramm
- Department of Neurology, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Hamid Shirani
- Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden
| | - Laura Vegas-Gomez
- Dpto. Biología Celular, Genética y Fisiología, Instituto de Investigación Biomédica de Málaga-IBIMA, Facultad de Ciencias, Universidad de Málaga, Málaga, Spain
| | - Jonathan Schulz
- Department of Neurology, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Ines Moreno-Gonzalez
- Department of Neurology, The University of Texas Health Science Center at Houston, Houston, TX, USA
- Dpto. Biología Celular, Genética y Fisiología, Instituto de Investigación Biomédica de Málaga-IBIMA, Facultad de Ciencias, Universidad de Málaga, Málaga, Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
- Centro Integrativo de Biologia y Quimica Aplicada (CIBQA), Universidad Bernardo O'Higgins, Santiago, Chile
| | - Antonia Gutierrez
- Dpto. Biología Celular, Genética y Fisiología, Instituto de Investigación Biomédica de Málaga-IBIMA, Facultad de Ciencias, Universidad de Málaga, Málaga, Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
| | - K Peter R Nilsson
- Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden
| | - Robert Tycko
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Claudio Soto
- Department of Neurology, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Rodrigo Morales
- Department of Neurology, The University of Texas Health Science Center at Houston, Houston, TX, USA
- Centro Integrativo de Biologia y Quimica Aplicada (CIBQA), Universidad Bernardo O'Higgins, Santiago, Chile
| |
Collapse
|
4
|
Jeon J, Yau WM, Tycko R. Early events in amyloid-β self-assembly probed by time-resolved solid state NMR and light scattering. Nat Commun 2023; 14:2964. [PMID: 37221174 DOI: 10.1038/s41467-023-38494-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 05/04/2023] [Indexed: 05/25/2023] Open
Abstract
Self-assembly of amyloid-β peptides leads to oligomers, protofibrils, and fibrils that are likely instigators of neurodegeneration in Alzheimer's disease. We report results of time-resolved solid state nuclear magnetic resonance (ssNMR) and light scattering experiments on 40-residue amyloid-β (Aβ40) that provide structural information for oligomers that form on time scales from 0.7 ms to 1.0 h after initiation of self-assembly by a rapid pH drop. Low-temperature ssNMR spectra of freeze-trapped intermediates indicate that β-strand conformations within and contacts between the two main hydrophobic segments of Aβ40 develop within 1 ms, while light scattering data imply a primarily monomeric state up to 5 ms. Intermolecular contacts involving residues 18 and 33 develop within 0.5 s, at which time Aβ40 is approximately octameric. These contacts argue against β-sheet organizations resembling those found previously in protofibrils and fibrils. Only minor changes in the Aβ40 conformational distribution are detected as larger assemblies develop.
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
- Institute for Bioscience and Biotechnology Research, University of Maryland/National Institute of Standards and Technology, Rockville, MD, 20850, 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
| | - 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
|
5
|
Lee M, Yau WM, Louis JM, Tycko R. Structures of brain-derived 42-residue amyloid-β fibril polymorphs with unusual molecular conformations and intermolecular interactions. Proc Natl Acad Sci U S A 2023; 120:e2218831120. [PMID: 36893281 PMCID: PMC10089215 DOI: 10.1073/pnas.2218831120] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [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: 11/08/2022] [Accepted: 02/04/2023] [Indexed: 03/11/2023] Open
Abstract
Fibrils formed by the 42-residue amyloid-β peptide (Aβ42), a main component of amyloid deposits in Alzheimer's disease (AD), are known to be polymorphic, i.e., to contain multiple possible molecular structures. Previous studies of Aβ42 fibrils, including fibrils prepared entirely in vitro or extracted from brain tissue and using solid-state NMR (ssNMR) or cryogenic electron microscopy (cryo-EM) methods, have found polymorphs with differences in amino acid sidechain orientations, lengths of structurally ordered segments, and contacts between cross-β subunit pairs within a single filament. Despite these differences, Aβ42 molecules adopt a common S-shaped conformation in all previously described high-resolution Aβ42 fibril structures. Here we report two cryo-EM-based structures of Aβ42 fibrils that are qualitatively different, in samples derived from AD brain tissue by seeded growth. In type A fibrils, residues 12 to 42 adopt a ν-shaped conformation, with both intra-subunit and intersubunit hydrophobic contacts to form a compact core. In type B fibrils, residues 2 to 42 adopt an υ-shaped conformation, with only intersubunit contacts and internal pores. Type A and type B fibrils have opposite helical handedness. Cryo-EM density maps and molecular dynamics simulations indicate intersubunit K16-A42 salt bridges in type B fibrils and partially occupied K28-A42 salt bridges in type A fibrils. The coexistence of two predominant polymorphs, with differences in N-terminal dynamics, is supported by ssNMR data, as is faithful propagation of structures from first-generation to second-generation brain-seeded Aβ42 fibril samples. These results demonstrate that Aβ42 fibrils can exhibit a greater range of structural variations than seen in previous studies.
Collapse
Affiliation(s)
- Myungwoon Lee
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD20892-0520
| | - Wai-Ming Yau
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD20892-0520
| | - John M. Louis
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD20892-0520
| | - Robert Tycko
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD20892-0520
| |
Collapse
|
6
|
Tycko R, Jeon J, Lee M, Thurber K, Yau WM. Early stages and final results of amyloid-beta self-assembly. Biophys J 2023; 122:314a. [PMID: 36783580 DOI: 10.1016/j.bpj.2022.11.1764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023] Open
Affiliation(s)
- Robert Tycko
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Jaekyun Jeon
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Myungwoon Lee
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Kent Thurber
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Wai-Ming Yau
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| |
Collapse
|
7
|
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
|
8
|
Yau WM, Blake Wilson C, Jeon J, Tycko R. Nitroxide-based triradical dopants for efficient low-temperature dynamic nuclear polarization in aqueous solutions over a broad pH range. J Magn Reson 2022; 342:107284. [PMID: 35986970 PMCID: PMC9463097 DOI: 10.1016/j.jmr.2022.107284] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 08/05/2022] [Accepted: 08/09/2022] [Indexed: 05/31/2023]
Abstract
Dynamic nuclear polarization (DNP) can provide substantial sensitivity enhancements in solid state nuclear magnetic resonance (ssNMR) measurements on frozen solutions, thereby enabling experiments that would otherwise be impractical. Previous work has shown that nitroxide-based triradical compounds are particularly effective as dopants in DNP-enhanced measurements at moderate magic-angle spinning frequencies and moderate magnetic field strengths, generally leading to a more rapid build-up of nuclear spin polarizations under microwave irradiation than the more common biradical dopants at the same electron spin concentrations. Here we report the synthesis and DNP performance at 25 K and 9.41 T for two new triradical compounds, sulfoacetyl-DOTOPA and PEG12-DOTOPA. Under our experimental conditions, these compounds exhibit ssNMR signal enhancements and DNP build-up times that are nearly identical to those of previously described triradical dopants. Moreover, these compounds have high solubility in aqueous buffers and water/glycerol mixtures at both acidic and basic pH values, making them useful in a wide variety of experiments on biomolecular systems.
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
| | - C Blake Wilson
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, United States
| | - Jaekyun Jeon
- 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
|
Abstract
Elucidation of the detailed mechanisms by which biological macromolecules undergo major structural conversions, such as folding, complex formation, and self-assembly, is a central concern of biophysical chemistry that will benefit from new experimental methods. We describe a simple technique for initiating a structural conversion process by a rapid decrease in the temperature of a solution, i.e., a rapid inverse temperature jump. By pumping solutions through copper capillary tubes that are thermally anchored to heated and cooled blocks, solution temperatures can be switched from 95 to 30 °C (or lower) in about 0.8 ms. For time-resolved solid-state nuclear magnetic resonance (ssNMR), solutions can then be frozen rapidly by spraying into cold isopentane after a variable structural evolution time τe. As an initial demonstration, we use this "inverse T-jump" technique to characterize the kinetics and mechanism by which the 26-residue peptide melittin converts from its primarily disordered, monomeric state at 95 °C to its α-helical, tetrameric state at 30 °C. One- and two-dimensional ssNMR spectra of frozen solutions with various values of τe, recorded at 25 K with signal enhancements from dynamic nuclear polarization, show that both helical secondary structure and intermolecular contacts develop on the same time scale of about 6 ms. The dependences on τe of both intraresidue crosspeak patterns and inter-residue crosspeak volumes in two-dimensional spectra can be fit with a unidirectional dimerization model, consistent with dimerization being the rate-limiting step for melittin tetramer formation.
Collapse
Affiliation(s)
- C Blake Wilson
- 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
|
10
|
Ghosh U, Yau WM, Collinge J, Tycko R. Structural differences in amyloid-β fibrils from brains of nondemented elderly individuals and Alzheimer's disease patients. Proc Natl Acad Sci U S A 2021; 118:e2111863118. [PMID: 34725161 PMCID: PMC8609303 DOI: 10.1073/pnas.2111863118] [Citation(s) in RCA: 6] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Accepted: 09/20/2021] [Indexed: 02/05/2023] Open
Abstract
Although amyloid plaques composed of fibrillar amyloid-β (Aβ) assemblies are a diagnostic hallmark of Alzheimer's disease (AD), quantities of amyloid similar to those in AD patients are observed in brain tissue of some nondemented elderly individuals. The relationship between amyloid deposition and neurodegeneration in AD has, therefore, been unclear. Here, we use solid-state NMR to investigate whether molecular structures of Aβ fibrils from brain tissue of nondemented elderly individuals with high amyloid loads differ from structures of Aβ fibrils from AD tissue. Two-dimensional solid-state NMR spectra of isotopically labeled Aβ fibrils, prepared by seeded growth from frontal lobe tissue extracts, are similar in the two cases but with statistically significant differences in intensity distributions of cross-peak signals. Differences in solid-state NMR data are greater for 42-residue amyloid-β (Aβ42) fibrils than for 40-residue amyloid-β (Aβ40) fibrils. These data suggest that similar sets of fibril polymorphs develop in nondemented elderly individuals and AD patients but with different relative populations on average.
Collapse
Affiliation(s)
- Ujjayini Ghosh
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD 20892-0520
- Department of Chemistry, Michigan State University, East Lansing, MI 48824
| | - Wai-Ming Yau
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD 20892-0520
| | - John Collinge
- Medical Research Council Prion Unit, University College London, London W1W 7FF, United Kingdom
- Institute of Prion Diseases, University College London, London W1W 7FF, United Kingdom
| | - Robert Tycko
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD 20892-0520;
| |
Collapse
|
11
|
Raskatov JA, Foley A, Louis JM, Yau WM, Tycko R. Constraints on the Structure of Fibrils Formed by a Racemic Mixture of Amyloid-β Peptides from Solid-State NMR, Electron Microscopy, and Theory. J Am Chem Soc 2021; 143:13299-13313. [PMID: 34375097 PMCID: PMC8456612 DOI: 10.1021/jacs.1c06339] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [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: 01/08/2023]
Abstract
Previous studies have shown that racemic mixtures of 40- and 42-residue amyloid-β peptides (d,l-Aβ40 and d,l-Aβ42) form amyloid fibrils with accelerated kinetics and enhanced stability relative to their homochiral counterparts (l-Aβ40 and l-Aβ42), suggesting a "chiral inactivation" approach to abrogating the neurotoxicity of Aβ oligomers (Aβ-CI). Here we report a structural study of d,l-Aβ40 fibrils, using electron microscopy, solid-state nuclear magnetic resonance (NMR), and density functional theory (DFT) calculations. Two- and three-dimensional solid-state NMR spectra indicate molecular conformations in d,l-Aβ40 fibrils that resemble those in known l-Aβ40 fibril structures. However, quantitative measurements of 13C-13C and 15N-13C distances in selectively labeled d,l-Aβ40 fibril samples indicate a qualitatively different supramolecular structure. While cross-β structures in mature l-Aβ40 fibrils are comprised of in-register, parallel β-sheets, our data indicate antiparallel β-sheets in d,l-Aβ40 fibrils, with alternation of d and l molecules along the fibril growth direction, i.e., antiparallel "rippled sheet" structures. The solid-state NMR data suggest the coexistence of d,l-Aβ40 fibril polymorphs with three different registries of intermolecular hydrogen bonds within the antiparallel rippled sheets. DFT calculations support an energetic preference for antiparallel alignments of the β-strand segments identified by solid-state NMR. These results provide insight into the structural basis for Aβ-CI and establish the importance of rippled sheets in self-assembly of full-length, naturally occurring amyloidogenic peptides.
Collapse
Affiliation(s)
- Jevgenij A. Raskatov
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
| | - Alejandro Foley
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
| | - John M. Louis
- 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
| | - 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
|
12
|
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
|
13
|
Jeon J, Yau WM, Tycko R. Millisecond Time-Resolved Solid-State NMR Reveals a Two-Stage Molecular Mechanism for Formation of Complexes between Calmodulin and a Target Peptide from Myosin Light Chain Kinase. J Am Chem Soc 2020; 142:21220-21232. [PMID: 33280387 DOI: 10.1021/jacs.0c11156] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Calmodulin (CaM) mediates a wide range of biological responses to changes in intracellular Ca2+ concentrations through its calcium-dependent binding affinities to numerous target proteins. Binding of two Ca2+ ions to each of the two four-helix-bundle domains of CaM results in major conformational changes that create a potential binding site for the CaM binding domain of a target protein, which also undergoes major conformational changes to form the complex with CaM. Details of the molecular mechanism of complex formation are not well established, despite numerous structural, spectroscopic, thermodynamic, and kinetic studies. Here, we report a study of the process by which the 26-residue peptide M13, which represents the CaM binding domain of skeletal muscle myosin light chain kinase, forms a complex with CaM in the presence of excess Ca2+ on the millisecond time scale. Our experiments use a combination of selective 13C labeling of CaM and M13, rapid mixing of CaM solutions with M13/Ca2+ solutions, rapid freeze-quenching of the mixed solutions, and low-temperature solid state nuclear magnetic resonance (ssNMR) enhanced by dynamic nuclear polarization. From measurements of the dependence of 2D 13C-13C ssNMR spectra on the time between mixing and freezing, we find that the N-terminal portion of M13 converts from a conformationally disordered state to an α-helix and develops contacts with the C-terminal domain of CaM in about 2 ms. The C-terminal portion of M13 becomes α-helical and develops contacts with the N-terminal domain of CaM more slowly, in about 8 ms. The level of structural order in the CaM/M13/Ca2+ complexes, indicated by 13C ssNMR line widths, continues to increase beyond 27 ms.
Collapse
Affiliation(s)
- Jaekyun Jeon
- 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
|
14
|
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
|
15
|
Chen HY, Tycko R. Slice selection in low-temperature, DNP-enhanced magnetic resonance imaging by Lee-Goldburg spin-locking and phase modulation. J Magn Reson 2020; 313:106715. [PMID: 32179432 PMCID: PMC7145747 DOI: 10.1016/j.jmr.2020.106715] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 03/03/2020] [Accepted: 03/07/2020] [Indexed: 06/01/2023]
Abstract
Large enhancements in nuclear magnetic resonance (NMR) signals provided by dynamic nuclear polarization (DNP) at low temperatures have the potential to enable inductively-detected 1H magnetic resonance imaging (MRI) with isotropic spatial resolution on the order of one micron, especially when low temperatures and DNP are combined with microcoils, three-dimensional (3D) phase encoding of image information, pulsed spin locking during NMR signal detection, and homonuclear dipolar decoupling by Lee-Goldburg (LG) irradiation or similar methods. However, the relatively slow build-up of nuclear magnetization under DNP leads to very long acquisition times for high-resolution 3D images unless the sample volume or field of view (FOV) is restricted. We have therefore developed a method for slice selection in low-temperature, DNP-enhanced MRI that limits the FOV to about 50 μm in one or more dimensions. This method uses small-amplitude phase modulation of LG irradiation in the presence of a strong magnetic field gradient to invert spin-locked 1H magnetization in the selected slice. Experimental results are reported, including effects of radio-frequency field inhomogeneity, variations in the amplitude of phase modulation, and shaped phase modulation.
Collapse
Affiliation(s)
- Hsueh-Ying Chen
- 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
|
16
|
Yau WM, Jeon J, Tycko R. Succinyl-DOTOPA: An effective triradical dopant for low-temperature dynamic nuclear polarization with high solubility in aqueous solvent mixtures at neutral pH. J Magn Reson 2020; 311:106672. [PMID: 31887554 PMCID: PMC6964257 DOI: 10.1016/j.jmr.2019.106672] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [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: 11/03/2019] [Revised: 12/10/2019] [Accepted: 12/18/2019] [Indexed: 05/05/2023]
Abstract
We report the synthesis of the nitroxide-based triradical compound succinyl-DOTOPA and the characterization of its performance as a dopant for dynamic nuclear polarization (DNP) experiments in frozen solutions at low temperatures. Compared with previously described DOTOPA derivatives, succinyl-DOTOPA has substantially greater solubility in glycerol/water mixtures with pH > 4 and therefore has wider applicability. Solid state nuclear magnetic resonance (ssNMR) measurements at 9.39 T and 25 K, with magic-angle spinning at 7.00 kHz, show that build-up times of DNP-enhanced, cross-polarized 13C ssNMR signals are shorter and that signal amplitudes are larger for glycerol/water solutions of L-proline containing succinyl-DOTOPA than for solutions containing the biradical AMUPol, with electron spin concentrations of 15 mM or 30 mM, resulting in greater net sensitivity gains from DNP. In similar measurements at 90 K, AMUPol yields greater net sensitivity, apparently due to its longer electron spin-lattice and spin-spin relaxation times. One- and two-dimensional 13C ssNMR measurements at 25 K on the complex of the 27-residue peptide M13 with the calcium-sensing protein calmodulin, in glycerol/water with 10 mM succinyl-DOTOPA, demonstrate the utility of this compound in DNP-enhanced ssNMR studies of biomolecular systems.
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, USA
| | - Jaekyun Jeon
- 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
|
17
|
Murray DT, Tycko R. Side Chain Hydrogen-Bonding Interactions within Amyloid-like Fibrils Formed by the Low-Complexity Domain of FUS: Evidence from Solid State Nuclear Magnetic Resonance Spectroscopy. Biochemistry 2020; 59:364-378. [PMID: 31895552 DOI: 10.1021/acs.biochem.9b00892] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In aqueous solutions, the 214-residue low-complexity domain of the FUS protein (FUS-LC) is known to undergo liquid-liquid phase separation and also to self-assemble into amyloid-like fibrils. In previous work based on solid state nuclear magnetic resonance (ssNMR) methods, a structural model for the FUS-LC fibril core was developed, showing that residues 39-95 form the fibril core. Unlike fibrils formed by amyloid-β peptides, α-synuclein, and other amyloid-forming proteins, the FUS-LC core is largely devoid of purely hydrophobic amino acid side chains. Instead, the core-forming segment contains numerous hydroxyl-bearing residues, including 18 serines, six threonines, and eight tyrosines, suggesting that the FUS-LC fibril structure may be stabilized in part by inter-residue hydrogen bonds among side chain hydroxyl groups. Here we describe ssNMR measurements, performed on 2H,15N,13C-labeled FUS-LC fibrils, that provide new information about the interactions of hydroxyl-bearing residues with one another and with water. The ssNMR data support the involvement of specific serine, threonine, and tyrosine residues in hydrogen-bonding interactions. The data also reveal differences in hydrogen exchange rates with water for different side chain hydroxyl groups, providing information about solvent exposure and penetration of water into the FUS-LC fibril core.
Collapse
Affiliation(s)
- Dylan T Murray
- Department of Chemistry , University of California , Davis , California 95616-5271 , 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
|
18
|
Morales R, Gomez-Gutierrez R, Kramm C, Tycko R, Soto C. O1‐03‐05: INDUCTION OF DIFFERENT BRAIN PATHOLOGY IN MICE TREATED WITH TWO MISFOLDED Aβ CONFORMERS. Alzheimers Dement 2019. [DOI: 10.1016/j.jalz.2019.06.4533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Rodrigo Morales
- The University of Texas Health Science Center at Houston Houston TX USA
| | - Ruben Gomez-Gutierrez
- Deptartment of Neurology The University of Texas Health Science Center at Houston Houston TX USA
- Deptartment of Cell Biology, Faculty of Sciences University of Malaga, CIBERNED, IBIMA Malaga Spain
| | - Carlos Kramm
- The University of Texas Health Science Center at Houston Houston TX USA
| | | | - Claudio Soto
- The University of Texas Health Science Center at Houston Houston TX USA
| |
Collapse
|
19
|
Zhang Z, Liu H, Deng J, Tycko R, Yang J. Optimization of band-selective homonuclear dipolar recoupling in solid-state NMR by a numerical phase search. J Chem Phys 2019; 150:154201. [PMID: 31005077 DOI: 10.1063/1.5092986] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Spin polarization transfers among aliphatic 13C nuclei, especially 13Cα-13Cβ transfers, permit correlations of their nuclear magnetic resonance (NMR) frequencies that are essential for signal assignments in multidimensional solid-state NMR of proteins. We derive and demonstrate a new radio-frequency (RF) excitation sequence for homonuclear dipolar recoupling that enhances spin polarization transfers among aliphatic 13C nuclei at moderate magic-angle spinning (MAS) frequencies. The phase-optimized recoupling sequence with five π pulses per MAS rotation period (denoted as PR5) is derived initially from systematic numerical simulations in which only the RF phases are varied. Subsequent theoretical analysis by average Hamiltonian theory explains the favorable properties of numerically optimized phase schemes. The high efficiency of spin polarization transfers in simulations is preserved in experiments, in part because the RF field amplitude in PR5 is only 2.5 times the MAS frequency so that relatively low 1H decoupling powers are required. Experiments on a microcrystalline sample of the β1 immunoglobulin binding domain of protein G demonstrate an average enhancement factor of 1.6 for 13Cα → 13Cβ polarization transfers, compared to the standard 13C-13C spin-diffusion method, implying a two-fold time saving in relevant 2D and 3D experiments.
Collapse
Affiliation(s)
- Zhengfeng Zhang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, People's Republic of China
| | - Hui Liu
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, People's Republic of China
| | - Jing Deng
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, People's Republic of China
| | - Robert Tycko
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, USA
| | - Jun Yang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, People's Republic of China
| |
Collapse
|
20
|
Jeon J, Thurber K, Yau WM, Tycko R. Site-Specific Characterization of Intermediates in Folding-Tetramerization of Melittin by the Rapid Mix/Freeze Method and Magic Angle Spinning Dynamic Nuclear Polarization (MAS-DNP) NMR at Low Temperature (25K). Biophys J 2019. [DOI: 10.1016/j.bpj.2018.11.1070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
|
21
|
Ghosh U, Tycko R. Fibril Structure of Abeta40 Visualized by Cryo-Electron Microscopy and Solid-State NMR. Biophys J 2019. [DOI: 10.1016/j.bpj.2018.11.932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
|
22
|
Chen HY, Tycko R. Temperature-Dependent Nuclear Spin Relaxation Due to Paramagnetic Dopants Below 30 K: Relevance to DNP-Enhanced Magnetic Resonance Imaging. J Phys Chem B 2018; 122:11731-11742. [PMID: 30277390 DOI: 10.1021/acs.jpcb.8b07958] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Dynamic nuclear polarization (DNP) can increase nuclear magnetic resonance (NMR) signal strengths by factors of 100 or more at low temperatures. In magnetic resonance imaging (MRI), signal enhancements from DNP potentially lead to enhancements in image resolution. However, the paramagnetic dopants required for DNP also reduce nuclear spin relaxation times, producing signal losses that may cancel the signal enhancements from DNP. Here we investigate the dependence of 1H NMR relaxation times, including T1ρ and T2, under conditions of Lee-Goldburg 1H-1H decoupling and pulsed spin locking, on temperature and dopant concentration in frozen solutions that contain the trinitroxide compound DOTOPA. We find that relaxation times become longer at temperatures below 10 K, where DOTOPA electron spins become strongly polarized at equilibrium in a 9.39 T magnetic field. We show that the dependences of relaxation times on temperature and DOTOPA concentration can be reproduced qualitatively (although not quantitatively) by detailed simulations of magnetic field fluctuations due to flip-flop transitions in a system of dipole-coupled electron spin magnetic moments. These results have implications for ongoing attempts to reach submicron resolution in inductively detected MRI at very low temperatures.
Collapse
Affiliation(s)
- Hsueh-Ying Chen
- 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
|
23
|
Murray DT, Zhou X, Kato M, Xiang S, Tycko R, McKnight SL. Structural characterization of the D290V mutation site in hnRNPA2 low-complexity-domain polymers. Proc Natl Acad Sci U S A 2018; 115:E9782-E9791. [PMID: 30279180 PMCID: PMC6196502 DOI: 10.1073/pnas.1806174115] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [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] [Indexed: 11/24/2022] Open
Abstract
Human genetic studies have given evidence of familial, disease-causing mutations in the analogous amino acid residue shared by three related RNA binding proteins causative of three neurological diseases. Alteration of aspartic acid residue 290 of hnRNPA2 to valine is believed to predispose patients to multisystem proteinopathy. Mutation of aspartic acid 262 of hnRNPA1 to either valine or asparagine has been linked to either amyotrophic lateral sclerosis or multisystem proteinopathy. Mutation of aspartic acid 378 of hnRNPDL to either asparagine or histidine has been associated with limb girdle muscular dystrophy. All three of these aspartic acid residues map to evolutionarily conserved regions of low-complexity (LC) sequence that may function in states of either intrinsic disorder or labile self-association. Here, we present a combination of solid-state NMR spectroscopy with segmental isotope labeling and electron microscopy on the LC domain of the hnRNPA2 protein. We show that, for both the wild-type protein and the aspartic acid 290-to-valine mutant, labile polymers are formed in which the LC domain associates into an in-register cross-β conformation. Aspartic acid 290 is shown to be charged at physiological pH and immobilized within the polymer core. Polymers of the aspartic acid 290-to-valine mutant are thermodynamically more stable than wild-type polymers. These observations give evidence that removal of destabilizing electrostatic interactions may be responsible for the increased propensity of the mutated LC domains to self-associate in disease-causing conformations.
Collapse
Affiliation(s)
- Dylan T Murray
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Disease, Bethesda, MD 20892
- Postdoctoral Research Associate Training Program, National Institute of General Medical Sciences, Bethesda, MD 20892
| | - Xiaoming Zhou
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Masato Kato
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Siheng Xiang
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Robert Tycko
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Disease, Bethesda, MD 20892;
| | - Steven L McKnight
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390
| |
Collapse
|
24
|
Morales R, Kramm-Barria C, Gomez-Gutierrez R, Tycko R, Soto C. P1‐115:
IN VIVO
PROPAGATION OF SYNTHETIC Aβ CONFORMATIONAL STRAINS. Alzheimers Dement 2018. [DOI: 10.1016/j.jalz.2018.06.118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Rodrigo Morales
- The University of Texas Health Science Center at HoustonHoustonTXUSA
| | | | | | | | - Claudio Soto
- The University of Texas Health Science Center at HoustonHoustonTXUSA
| |
Collapse
|
25
|
Ghosh U, Yau WM, Tycko R. Coexisting order and disorder within a common 40-residue amyloid-β fibril structure in Alzheimer's disease brain tissue. Chem Commun (Camb) 2018; 54:5070-5073. [PMID: 29707712 PMCID: PMC5953852 DOI: 10.1039/c8cc01967c] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [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: 01/04/2023]
Abstract
Fibrils formed by 40- and 42-residue amyloid-β (Aβ40 and Aβ42) peptides exhibit molecular-level structural polymorphisms. A recent screen of fibrils derived from brain tissue of Alzheimer's disease patients revealed a single predominant Aβ40 polymorph. We present solid state nuclear magnetic resonance (ssNMR) data that define its coexisting structurally ordered and disordered segments.
Collapse
Affiliation(s)
- Ujjayini Ghosh
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Building 5, Room 409, Bethesda, Maryland 20892-0520, USA.
| | | | | |
Collapse
|
26
|
Yau WM, Tycko R. Depletion of amyloid-β peptides from solution by sequestration within fibril-seeded hydrogels. Protein Sci 2018; 27:1218-1230. [PMID: 29417648 DOI: 10.1002/pro.3387] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Revised: 02/02/2018] [Accepted: 02/05/2018] [Indexed: 11/10/2022]
Abstract
Aggregation of amyloid-β (Aβ) peptides in brain tissue leads to neurodegeneration in Alzheimer's disease (AD). Regardless of the kinetics or detailed mechanisms of Aβ aggregation, aggregation can only occur if Aβ concentrations exceed their local equilibrium solubility values. We propose that excess Aβ peptides can be removed from supersaturated solutions, including solutions in biological fluids, by the addition of hydrogels that are seeded with Aβ fibril fragments. Fibril growth within the hydrogels then sequesters excess peptides until equilibrium concentrations are reached. Experiments with 40- and 42-residue Aβ peptides (Aβ40 and Aβ42) in phosphate buffer at 24°C and in filtered fetal bovine serum at 37°C, using crosslinked polyacrylamide hydrogels, demonstrate the validity of this concept. Aβ sequestration in fibril-seeded hydrogels (or other porous media) may prove to be a useful technique in experiments with animal models of AD and may represent a possible approach to preventing or slowing the progression of AD in humans.
Collapse
Affiliation(s)
- Wai-Ming Yau
- 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
|
27
|
Affiliation(s)
- 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
|
28
|
Chen HY, Tycko R. Low-temperature magnetic resonance imaging with 2.8 μm isotropic resolution. J Magn Reson 2018; 287:47-55. [PMID: 29288890 PMCID: PMC5803441 DOI: 10.1016/j.jmr.2017.12.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [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: 11/22/2017] [Revised: 12/18/2017] [Accepted: 12/20/2017] [Indexed: 05/16/2023]
Abstract
We demonstrate the feasibility of high-resolution 1H magnetic resonance imaging (MRI) at low temperatures by obtaining an MRI image of 20 μm diameter glass beads in glycerol/water at 28 K with 2.8 μm isotropic resolution. The experiments use a recently-described MRI apparatus (Moore and Tycko, 2015) with minor modifications. The sample is contained within a radio-frequency microcoil with 150 μm inner diameter. Sensitivity is additionally enhanced by paramagnetic doping, optimization of the sample temperature, three-dimensional phase-encoding of k-space data, pulsed spin-lock detection of 1H nuclear magnetic resonance signals, and spherical sampling of k-space. We verify that the actual image resolution is 2.7 ± 0.3 μm by quantitative comparisons of experimental and calculated images. Our imaging approach is compatible with dynamic nuclear polarization, providing a path to significantly higher resolution in future experiments.
Collapse
Affiliation(s)
- Hsueh-Ying Chen
- 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
|
29
|
Gupta S, Tycko R. Segmental isotopic labeling of HIV-1 capsid protein assemblies for solid state NMR. J Biomol NMR 2018; 70:103-114. [PMID: 29464399 PMCID: PMC5832360 DOI: 10.1007/s10858-017-0162-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [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: 09/15/2017] [Accepted: 12/28/2017] [Indexed: 05/09/2023]
Abstract
Recent studies of noncrystalline HIV-1 capsid protein (CA) assemblies by our laboratory and by Polenova and coworkers (Protein Sci 19:716-730, 2010; J Mol Biol 426:1109-1127, 2014; J Biol Chem 291:13098-13112, 2016; J Am Chem Soc 138:8538-8546, 2016; J Am Chem Soc 138:12029-12032, 2016; J Am Chem Soc 134:6455-6466, 2012; J Am Chem Soc 132:1976-1987, 2010; J Am Chem Soc 135:17793-17803, 2013; Proc Natl Acad Sci USA 112:14617-14622, 2015; J Am Chem Soc 138:14066-14075, 2016) have established the capability of solid state nuclear magnetic resonance (NMR) measurements to provide site-specific structural and dynamical information that is not available from other types of measurements. Nonetheless, the relatively high molecular weight of HIV-1 CA leads to congestion of solid state NMR spectra of fully isotopically labeled assemblies that has been an impediment to further progress. Here we describe an efficient protocol for production of segmentally labeled HIV-1 CA samples in which either the N-terminal domain (NTD) or the C-terminal domain (CTD) is uniformly 15N,13C-labeled. Segmental labeling is achieved by trans-splicing, using the DnaE split intein. Comparisons of two-dimensional solid state NMR spectra of fully labeled and segmentally labeled tubular CA assemblies show substantial improvements in spectral resolution. The molecular structure of HIV-1 assemblies is not significantly perturbed by the single Ser-to-Cys substitution that we introduce between NTD and CTD segments, as required for trans-splicing.
Collapse
Affiliation(s)
- Sebanti Gupta
- 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.
- National Institutes of Health, Building 5, Room 409, Bethesda, MD, 20892-0520, USA.
| |
Collapse
|
30
|
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: 477] [Impact Index Per Article: 68.1] [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
|
31
|
Nagy-Smith K, Beltramo PJ, Moore E, Tycko R, Furst EM, Schneider JP. Molecular, Local, and Network-Level Basis for the Enhanced Stiffness of Hydrogel Networks Formed from Coassembled Racemic Peptides: Predictions from Pauling and Corey. ACS Cent Sci 2017; 3:586-597. [PMID: 28691070 PMCID: PMC5492410 DOI: 10.1021/acscentsci.7b00115] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Indexed: 05/20/2023]
Abstract
Hydrogels prepared from self-assembling peptides are promising materials for medical applications, and using both l- and d-peptide isomers in a gel's formulation provides an intuitive way to control the proteolytic degradation of an implanted material. In the course of developing gels for delivery applications, we discovered that a racemic mixture of the mirror-image β-hairpin peptides, named MAX1 and DMAX1, provides a fibrillar hydrogel that is four times more rigid than gels formed by either peptide alone-a puzzling observation. Herein, we use transmission electron microscopy, small angle neutron scattering, solid state NMR, diffusing wave, infrared, and fluorescence spectroscopies, and modeling to determine the molecular basis for the increased mechanical rigidity of the racemic gel. We find that enantiomeric peptides coassemble in an alternating fashion along the fibril long axis, forming an extended heterochiral pleat-like β-sheet, a structure predicted by Pauling and Corey in 1953. Hydrogen bonding between enantiomers within the sheet dictates the placement of hydrophobic valine side chains in the fibrils' dry interior in a manner that allows the formation of nested hydrophobic interactions between enantiomers, interactions not accessible within enantiomerically pure fibrils. Importantly, this unique molecular arrangement of valine side chains maximizes inter-residue contacts within the core of the fibrils resulting in their local stiffening, which in turn, gives rise to the significant increase in bulk mechanical rigidity observed for the racemic hydrogel.
Collapse
Affiliation(s)
- Katelyn Nagy-Smith
- Chemical
Biology Laboratory, National Cancer Institute, Frederick, Maryland 21702, United States
- Department of Chemistry and Biochemistry and Department of Chemical
and Biomolecular
Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Peter J. Beltramo
- Department of Chemistry and Biochemistry and Department of Chemical
and Biomolecular
Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Eric Moore
- 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
| | - Eric M. Furst
- Department of Chemistry and Biochemistry and Department of Chemical
and Biomolecular
Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Joel P. Schneider
- Chemical
Biology Laboratory, National Cancer Institute, Frederick, Maryland 21702, United States
| |
Collapse
|
32
|
Affiliation(s)
- 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
|
33
|
Bayro MJ, Ganser-Pornillos BK, Zadrozny KK, Yeager M, Tycko R. Helical Conformation in the CA-SP1 Junction of the Immature HIV-1 Lattice Determined from Solid-State NMR of Virus-like Particles. J Am Chem Soc 2016; 138:12029-32. [PMID: 27593947 DOI: 10.1021/jacs.6b07259] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Maturation of HIV-1 requires disassembly of the Gag polyprotein lattice, which lines the viral membrane in the immature state, and subsequent assembly of the mature capsid protein lattice, which encloses viral RNA in the mature state. Metastability of the immature lattice has been proposed to depend on the existence of a structurally ordered, α-helical segment spanning the junction between capsid (CA) and spacer peptide 1 (SP1) subunits of Gag, a segment that is dynamically disordered in the mature capsid lattice. We report solid state nuclear magnetic resonance (ssNMR) measurements on the immature lattice in noncrystalline, spherical virus-like particles (VLPs) derived from Gag. The ssNMR data provide definitive evidence for this critical α-helical segment in the VLPs. Differences in ssNMR chemical shifts and signal intensities between immature and mature lattice assemblies also support a major rearrangement of intermolecular interactions in the maturation process, consistent with recent models from electron cryomicroscopy and X-ray crystallography.
Collapse
Affiliation(s)
- Marvin J Bayro
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland 20892-0520, United States
| | - Barbie K Ganser-Pornillos
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine , Seridan G. Snyder Translational Research Building, 480 Ray C. Hunt Drive, Charlottesville, Virginia 22908, United States
| | - Kaneil K Zadrozny
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine , Seridan G. Snyder Translational Research Building, 480 Ray C. Hunt Drive, Charlottesville, Virginia 22908, United States
| | - Mark Yeager
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine , Seridan G. Snyder Translational Research Building, 480 Ray C. Hunt Drive, Charlottesville, Virginia 22908, United States.,Department of Medicine, Division of Cardiovascular Medicine, University of Virginia Health System , Charlottesville, Virginia 22908, United States.,Center for Membrane and Cell Physiology, University of Virginia School of Medicine , Charlottesville, Virginia 22908, 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
|
34
|
Abstract
Amyloid-β (Aβ) peptides aggregate to form polymorphic amyloid fibrils and a variety of intermediate assemblies, including oligomers and protofibrils, both in vitro and in human brain tissue. Since the beginning of the 21st century, considerable progress has been made to characterize the molecular structures of Aβ aggregates. Full molecular structural models based primarily on data from measurements using solid-state nuclear magnetic resonance (ssNMR) have been developed for several in vitro Aβ fibrils and one metastable protofibril. Partial structural characterization of other aggregation intermediates has been achieved. One full structural model for fibrils derived from brain tissue has also been reported. Future work is likely to focus on additional structures from brain tissue and on further clarification of nonfibrillar Aβ aggregates.
Collapse
Affiliation(s)
- Robert Tycko
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520
| |
Collapse
|
35
|
Abstract
The HIV-1 capsid protein (CA) forms the capsid shell that encloses RNA within a mature HIV-1 virion. Previous studies by electron microscopy have shown that the capsid shell is primarily a triangular lattice of CA hexamers, with variable curvature that destroys the ideal symmetry of a planar lattice. The mature CA lattice depends on CA dimerization, which occurs through interactions between helix 9 segments of the C-terminal domain (CTD) of CA. Several high-resolution structures of the CTD-CTD dimerization interface have been reported, based on X-ray crystallography and multidimensional solution nuclear magnetic resonance (NMR), with significant differences in amino acid side chain conformations and helix 9-helix 9 orientations. In a structural model for tubular CA assemblies based on cryogenic electron microscopy (cryoEM) [Zhao et al. Nature, 2013, 497, 643-646], the dimerization interface is substantially disordered. The dimerization interface structure in noncrystalline CA assemblies and the extent to which this interface is structurally ordered within a curved lattice have therefore been unclear. Here we describe solid state NMR measurements on the dimerization interface in tubular CA assemblies, which contain the curved triangular lattice of a mature virion, including quantitative measurements of intermolecular and intramolecular distances using dipolar recoupling techniques, solid state NMR chemical shifts, and long-range side chain-side chain contacts. When combined with restraints on the distance and orientation between helix 9 segments from the cryoEM study, the solid state NMR data lead to a unique high-resolution structure for the dimerization interface in the noncrystalline lattice of CA tubes. These results demonstrate that CA lattice curvature is not dependent on disorder or variability in the dimerization interface. This work also demonstrates the feasibility of local structure determination within large noncrystalline assemblies formed by high-molecular-weight proteins, using modern solid state NMR methods.
Collapse
Affiliation(s)
- Marvin J. Bayro
- 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
|
36
|
Lu JX, Bayro MJ, Tycko R. Major Variations in HIV-1 Capsid Assembly Morphologies Involve Minor Variations in Molecular Structures of Structurally Ordered Protein Segments. J Biol Chem 2016; 291:13098-112. [PMID: 27129282 DOI: 10.1074/jbc.m116.720557] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2016] [Indexed: 12/13/2022] Open
Abstract
We present the results of solid state nuclear magnetic resonance (NMR) experiments on HIV-1 capsid protein (CA) assemblies with three different morphologies, namely wild-type CA (WT-CA) tubes with 35-60 nm diameters, planar sheets formed by the Arg(18)-Leu mutant (R18L-CA), and R18L-CA spheres with 20-100 nm diameters. The experiments are intended to elucidate molecular structural variations that underlie these variations in CA assembly morphology. We find that multidimensional solid state NMR spectra of (15)N,(13)C-labeled CA assemblies are remarkably similar for the three morphologies, with only small differences in (15)N and (13)C chemical shifts, no significant differences in NMR line widths, and few differences in the number of detectable NMR cross-peaks. Thus, the pronounced differences in morphology do not involve major differences in the conformations and identities of structurally ordered protein segments. Instead, morphological variations are attributable to variations in conformational distributions within disordered segments, which do not contribute to the solid state NMR spectra. Variations in solid state NMR signals from certain amino acid side chains are also observed, suggesting differences in the intermolecular dimerization interface between curved and planar CA lattices, as well as possible differences in intramolecular helix-helix packing.
Collapse
Affiliation(s)
- Jun-Xia Lu
- From the Laboratory of Chemical Physics, NIDKK, National Institutes of Health, Bethesda, Maryland 20892-0520
| | - Marvin J Bayro
- From the Laboratory of Chemical Physics, NIDKK, National Institutes of Health, Bethesda, Maryland 20892-0520
| | - Robert Tycko
- From the Laboratory of Chemical Physics, NIDKK, National Institutes of Health, Bethesda, Maryland 20892-0520
| |
Collapse
|
37
|
Thurber K, Tycko R. Low-temperature dynamic nuclear polarization with helium-cooled samples and nitrogen-driven magic-angle spinning. J Magn Reson 2016; 264:99-106. [PMID: 26920835 PMCID: PMC4769783 DOI: 10.1016/j.jmr.2016.01.011] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [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: 12/11/2015] [Revised: 01/18/2016] [Accepted: 01/19/2016] [Indexed: 05/05/2023]
Abstract
We describe novel instrumentation for low-temperature solid state nuclear magnetic resonance (NMR) with dynamic nuclear polarization (DNP) and magic-angle spinning (MAS), focusing on aspects of this instrumentation that have not been described in detail in previous publications. We characterize the performance of an extended interaction oscillator (EIO) microwave source, operating near 264 GHz with 1.5 W output power, which we use in conjunction with a quasi-optical microwave polarizing system and a MAS NMR probe that employs liquid helium for sample cooling and nitrogen gas for sample spinning. Enhancement factors for cross-polarized (13)C NMR signals in the 100-200 range are demonstrated with DNP at 25K. The dependences of signal amplitudes on sample temperature, as well as microwave power, polarization, and frequency, are presented. We show that sample temperatures below 30K can be achieved with helium consumption rates below 1.3 l/h. To illustrate potential applications of this instrumentation in structural studies of biochemical systems, we compare results from low-temperature DNP experiments on a calmodulin-binding peptide in its free and bound states.
Collapse
Affiliation(s)
- Kent 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
|
38
|
Abstract
Seeding of amyloid fibrils into fresh solutions of the same peptide or protein in disaggregated form leads to the formation of replicate fibrils, with close structural similarity or identity to the original fibrillar seeds. Here we describe procedures for isolating fibrils composed mainly of β-amyloid (Aβ) from human brain and from leptomeninges, a source of cerebral blood vessels, for investigating Alzheimer's disease and cerebral amyloid angiopathy. We also describe methods for seeding isotopically labeled, disaggregated Aβ peptide solutions for study using solid-state NMR and other techniques. These methods should be applicable to other types of amyloid fibrils, to Aβ fibrils from mice or other species, tissues other than brain, and to some non-fibrillar aggregates. These procedures allow for the examination of authentic amyloid fibrils and other protein aggregates from biological tissues without the need for labeling the tissue.
Collapse
Affiliation(s)
- Kathryn P Scherpelz
- Department of Biochemistry and Molecular Biology, The University of Chicago, AMB N314, 5841 South Maryland Avenue, Chicago, IL, 60637, USA
| | - Jun-Xia Lu
- Laboratory of Chemical Physics, NIDDK, National Institutes of Health, Bethesda, MD, USA
| | - Robert Tycko
- Laboratory of Chemical Physics, NIDDK, National Institutes of Health, Bethesda, MD, USA
| | - Stephen C Meredith
- Department of Biochemistry and Molecular Biology, The University of Chicago, AMB N314, 5841 South Maryland Avenue, Chicago, IL, 60637, USA.
- Department of Pathology, The University of Chicago, Chicago, IL, 60637, USA.
| |
Collapse
|
39
|
Moore E, Tycko R. Micron-scale magnetic resonance imaging of both liquids and solids. J Magn Reson 2015; 260:1-9. [PMID: 26397215 PMCID: PMC4628880 DOI: 10.1016/j.jmr.2015.09.001] [Citation(s) in RCA: 6] [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: 07/24/2015] [Revised: 08/31/2015] [Accepted: 09/02/2015] [Indexed: 05/16/2023]
Abstract
We describe and demonstrate a novel apparatus for magnetic resonance imaging (MRI), suitable for imaging of both liquid and solid samples with micron-scale isotropic resolution. The apparatus includes a solenoidal radio-frequency microcoil with 170 μm inner diameter and a set of planar gradient coils, all wound by hand and supported on a series of stacked sapphire plates. The design ensures efficient heat dissipation during gradient pulses and also facilitates disassembly, sample changes, and reassembly. To demonstrate liquid state (1)H MRI, we present an image of polystyrene beads within CuSO4-doped water, contained within a capillary tube with 100 μm inner diameter, with 5.0 μm isotropic resolution. To demonstrate solid state (1)H MRI, we present an image of NH4Cl particles within the capillary tube, with 8.0 μm isotropic resolution. High-resolution solid state MRI is enabled by frequency-switched Lee-Goldburg decoupling, with an effective rotating frame field amplitude of 289 kHz. At room temperature, pulsed gradients of 4 T/m (i.e., 170 Hz/μm for (1)H MRI) are achievable in all three directions with currents of 10 A or less. The apparatus is contained within a variable-temperature liquid helium cryostat, which will allow future efforts to obtain MRI images at low temperatures with signal enhancement by dynamic nuclear polarization.
Collapse
Affiliation(s)
- Eric Moore
- 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
|
40
|
Nagy-Smith K, Moore E, Schneider J, Tycko R. Molecular structure of monomorphic peptide fibrils within a kinetically trapped hydrogel network. Proc Natl Acad Sci U S A 2015; 112:9816-21. [PMID: 26216960 PMCID: PMC4538636 DOI: 10.1073/pnas.1509313112] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [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] [Indexed: 01/10/2023] Open
Abstract
Most, if not all, peptide- and protein-based hydrogels formed by self-assembly can be characterized as kinetically trapped 3D networks of fibrils. The propensity of disease-associated amyloid-forming peptides and proteins to assemble into polymorphic fibrils suggests that cross-β fibrils comprising hydrogels may also be polymorphic. We use solid-state NMR to determine the molecular and supramolecular structure of MAX1, a de novo designed gel-forming peptide, in its fibrillar state. We find that MAX1 adopts a β-hairpin conformation and self-assembles with high fidelity into a double-layered cross-β structure. Hairpins assemble with an in-register Syn orientation within each β-sheet layer and with an Anti orientation between layers. Surprisingly, although the MAX1 fibril network is kinetically trapped, solid-state NMR data show that fibrils within this network are monomorphic and most likely represent the thermodynamic ground state. Intermolecular interactions not available in alternative structural arrangements apparently dictate this monomorphic behavior.
Collapse
Affiliation(s)
- Katelyn Nagy-Smith
- Chemical Biology Laboratory, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD 21702; Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716
| | - Eric Moore
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520
| | - Joel Schneider
- Chemical Biology Laboratory, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD 21702
| | - Robert Tycko
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520
| |
Collapse
|
41
|
Abstract
Our understanding of the molecular structures of amyloid fibrils that are associated with neurodegenerative diseases, of mechanisms by which disease-associated peptides and proteins aggregate into fibrils, and of structural properties of aggregation intermediates has advanced considerably in recent years. Detailed molecular structural models for certain fibrils and aggregation intermediates are now available. It is now well established that amyloid fibrils are generally polymorphic at the molecular level, with a given peptide or protein being capable of forming a variety of distinct, self-propagating fibril structures. Recent results from structural studies and from studies involving cell cultures, transgenic animals, and human tissue provide initial evidence that molecular structural variations in amyloid fibrils and related aggregates may correlate with or even produce variations in disease development. This article reviews our current knowledge of the structural and mechanistic aspects of amyloid formation, as well as current evidence for the biological relevance of structural variations.
Collapse
Affiliation(s)
- 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
|
42
|
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
|
43
|
Tycko R. On the problem of resonance assignments in solid state NMR of uniformly ¹⁵N,¹³C-labeled proteins. J Magn Reson 2015; 253:166-172. [PMID: 25797013 PMCID: PMC4371143 DOI: 10.1016/j.jmr.2015.02.006] [Citation(s) in RCA: 6] [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: 01/09/2015] [Revised: 02/05/2015] [Accepted: 02/08/2015] [Indexed: 05/31/2023]
Abstract
Determination of accurate resonance assignments from multidimensional chemical shift correlation spectra is one of the major problems in biomolecular solid state NMR, particularly for relative large proteins with less-than-ideal NMR linewidths. This article investigates the difficulty of resonance assignment, using a computational Monte Carlo/simulated annealing (MCSA) algorithm to search for assignments from artificial three-dimensional spectra that are constructed from the reported isotropic (15)N and (13)C chemical shifts of two proteins whose structures have been determined by solution NMR methods. The results demonstrate how assignment simulations can provide new insights into factors that affect the assignment process, which can then help guide the design of experimental strategies. Specifically, simulations are performed for the catalytic domain of SrtC (147 residues, primarily β-sheet secondary structure) and the N-terminal domain of MLKL (166 residues, primarily α-helical secondary structure). Assuming unambiguous residue-type assignments and four ideal three-dimensional data sets (NCACX, NCOCX, CONCA, and CANCA), uncertainties in chemical shifts must be less than 0.4 ppm for assignments for SrtC to be unique, and less than 0.2 ppm for MLKL. Eliminating CANCA data has no significant effect, but additionally eliminating CONCA data leads to more stringent requirements for chemical shift precision. Introducing moderate ambiguities in residue-type assignments does not have a significant effect.
Collapse
Affiliation(s)
- 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
|
44
|
|
45
|
Tycko R. Physical and structural basis for polymorphism in amyloid fibrils. Protein Sci 2014; 23:1528-39. [PMID: 25179159 DOI: 10.1002/pro.2544] [Citation(s) in RCA: 176] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Revised: 08/28/2014] [Accepted: 08/29/2014] [Indexed: 12/24/2022]
Abstract
As our understanding of the molecular structures of amyloid fibrils has matured over the past 15 years, it has become clear that, while amyloid fibrils do have well-defined molecular structures, their molecular structures are not uniquely determined by the amino acid sequences of their constituent peptides and proteins. Self-propagating molecular-level polymorphism is a common phenomenon. This article reviews current information about amyloid fibril structures, variations in molecular structures that underlie amyloid polymorphism, and physical considerations that explain the development and persistence of amyloid polymorphism. Much of this information has been obtained through solid state nuclear magnetic resonance measurements. The biological significance of amyloid polymorphism is also discussed briefly. Although this article focuses primarily on studies of fibrils formed by amyloid-β peptides, the same principles apply to many amyloid-forming peptides and proteins.
Collapse
Affiliation(s)
- Robert Tycko
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, 20892-0520
| |
Collapse
|
46
|
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
|
47
|
Tycko R. Remote sensing of sample temperatures in nuclear magnetic resonance using photoluminescence of semiconductor quantum dots. J Magn Reson 2014; 244:64-7. [PMID: 24859817 PMCID: PMC4090140 DOI: 10.1016/j.jmr.2014.04.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [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: 04/24/2014] [Accepted: 04/30/2014] [Indexed: 05/22/2023]
Abstract
Knowledge of sample temperatures during nuclear magnetic resonance (NMR) measurements is important for acquisition of optimal NMR data and proper interpretation of the data. Sample temperatures can be difficult to measure accurately for a variety of reasons, especially because it is generally not possible to make direct contact to the NMR sample during the measurements. Here I show that sample temperatures during magic-angle spinning (MAS) NMR measurements can be determined from temperature-dependent photoluminescence signals of semiconductor quantum dots that are deposited in a thin film on the outer surface of the MAS rotor, using a simple optical fiber-based setup to excite and collect photoluminescence. The accuracy and precision of such temperature measurements can be better than ±5K over a temperature range that extends from approximately 50K (-223°C) to well above 310K (37°C). Importantly, quantum dot photoluminescence can be monitored continuously while NMR measurements are in progress. While this technique is likely to be particularly valuable in low-temperature MAS NMR experiments, including experiments involving dynamic nuclear polarization, it may also be useful in high-temperature MAS NMR and other forms of magnetic resonance.
Collapse
Affiliation(s)
- 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
|
48
|
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
|
49
|
|
50
|
Bayro MJ, Chen B, Yau WM, Tycko R. Site-specific structural variations accompanying tubular assembly of the HIV-1 capsid protein. J Mol Biol 2013; 426:1109-27. [PMID: 24370930 DOI: 10.1016/j.jmb.2013.12.021] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Revised: 12/16/2013] [Accepted: 12/17/2013] [Indexed: 10/25/2022]
Abstract
The 231-residue capsid (CA) protein of human immunodeficiency virus type 1 (HIV-1) spontaneously self-assembles into tubes with a hexagonal lattice that is believed to mimic the surface lattice of conical capsid cores within intact virions. We report the results of solid-state nuclear magnetic resonance (NMR) measurements on HIV-1 CA tubes that provide new information regarding changes in molecular structure that accompany CA self-assembly, local dynamics within CA tubes, and possible mechanisms for the generation of lattice curvature. This information is contained in site-specific assignments of signals in two- and three-dimensional solid-state NMR spectra, conformation-dependent (15)N and (13)C NMR chemical shifts, detection of highly dynamic residues under solution NMR conditions, measurements of local variations in transverse spin relaxation rates of amide (1)H nuclei, and quantitative measurements of site-specific (15)N-(15)N dipole-dipole couplings. Our data show that most of the CA sequence is conformationally ordered and relatively rigid in tubular assemblies and that structures of the N-terminal domain (NTD) and the C-terminal domain (CTD) observed in solution are largely retained. However, specific segments, including the N-terminal β-hairpin, the cyclophilin A binding loop, the inter-domain linker, segments involved in intermolecular NTD-CTD interactions, and the C-terminal tail, have substantial static or dynamical disorder in tubular assemblies. Other segments, including the 310-helical segment in CTD, undergo clear conformational changes. Structural variations associated with curvature of the CA lattice appear to be localized in the inter-domain linker and intermolecular NTD-CTD interface, while structural variations within NTD hexamers, around local 3-fold symmetry axes, and in CTD-CTD dimerization interfaces are less significant.
Collapse
Affiliation(s)
- Marvin J Bayro
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA
| | - Bo Chen
- Department of Physics, University of Central Florida, Orlando, FL 32816, 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
| | - 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
|