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Article ; Online: Structure of Amyloid Peptide Ribbons Characterized by Electron Microscopy, Atomic Force Microscopy, and Solid-State Nuclear Magnetic Resonance.

Thurber, Kent R / Yau, Wai-Ming / Tycko, Robert

The journal of physical chemistry. B

2024 Volume 128, Issue 7, Page(s) 1711–1723

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 ...

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 (Aβ
MeSH term(s)	Microscopy, Atomic Force ; Electrons ; Protein Structure, Secondary ; Nuclear Magnetic Resonance, Biomolecular/methods ; Amyloid/chemistry ; Amyloidogenic Proteins ; Amyloid beta-Peptides/chemistry
Chemical Substances	Amyloid ; Amyloidogenic Proteins ; Amyloid beta-Peptides
Language	English
Publishing date	2024-02-13
Publishing country	United States
Document type	Journal Article
ISSN	1520-5207
ISSN (online)	1520-5207
DOI	10.1021/acs.jpcb.3c07867
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Experimental Evidence for Millisecond-Timescale Structural Evolution Following the Microsecond-Timescale Folding of a Small Protein.

Wilson, C Blake / Yau, Wai-Ming / Tycko, Robert

Physical review letters

2024 Volume 132, Issue 4, Page(s) 48402

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 ... ...

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}.
MeSH term(s)	Protein Folding ; Magnetic Resonance Spectroscopy
Language	English
Publishing date	2024-02-09
Publishing country	United States
Document type	Journal Article
ZDB-ID	208853-8
ISSN	1079-7114 ; 0031-9007
ISSN (online)	1079-7114
ISSN	0031-9007
DOI	10.1103/PhysRevLett.132.048402
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Article ; Online: From Milliseconds to Minutes: Melittin Self-Assembly from Concerted Non-Equilibrium Pressure-Jump and Equilibrium Relaxation Nuclear Magnetic Resonance.

Gelenter, Martin D / Yau, Wai-Ming / Anfinrud, Philip A / Bax, Ad

The journal of physical chemistry letters

2024 Volume 15, Issue 7, Page(s) 1930–1935

Abstract: Non-equilibrium kinetics techniques like pressure-jump nuclear magnetic resonance (NMR) are powerful in tracking changes in oligomeric populations and are not limited by relaxation rates for the time scales of exchange that can be probed. However, these ... ...

Abstract	Non-equilibrium kinetics techniques like pressure-jump nuclear magnetic resonance (NMR) are powerful in tracking changes in oligomeric populations and are not limited by relaxation rates for the time scales of exchange that can be probed. However, these techniques are less sensitive to minor, transient populations than are Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion experiments. We integrated non-equilibrium pressure-jump and equilibrium CPMG relaxation dispersion data to fully map the kinetic landscape of melittin tetramerization. While monomeric peptides weakly form dimers (
MeSH term(s)	Melitten ; Nuclear Magnetic Resonance, Biomolecular/methods ; Models, Molecular ; Magnetic Resonance Spectroscopy ; Magnetic Resonance Imaging
Chemical Substances	Melitten (20449-79-0)
Language	English
Publishing date	2024-02-12
Publishing country	United States
Document type	Journal Article
ISSN	1948-7185
ISSN (online)	1948-7185
DOI	10.1021/acs.jpclett.3c03563
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Article ; Online: Early events in amyloid-β self-assembly probed by time-resolved solid state NMR and light scattering.

Jeon, Jaekyun / Yau, Wai-Ming / Tycko, Robert

Nature communications

2023 Volume 14, Issue 1, Page(s) 2964

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 ... ...

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.
MeSH term(s)	Humans ; Magnetic Resonance Imaging ; Amyloid beta-Peptides ; Alzheimer Disease ; Amyloidogenic Proteins ; Magnetic Resonance Spectroscopy
Chemical Substances	Amyloid beta-Peptides ; Amyloidogenic Proteins
Language	English
Publishing date	2023-05-23
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Intramural
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-023-38494-6
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Article ; Online: Structures of brain-derived 42-residue amyloid-β fibril polymorphs with unusual molecular conformations and intermolecular interactions.

Lee, Myungwoon / Yau, Wai-Ming / Louis, John M / Tycko, Robert

Proceedings of the National Academy of Sciences of the United States of America

2023 Volume 120, Issue 11, Page(s) e2218831120

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 ...

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.
MeSH term(s)	Humans ; Amyloid beta-Peptides/metabolism ; Alzheimer Disease/metabolism ; Magnetic Resonance Spectroscopy ; Brain/metabolism ; Molecular Conformation ; Amyloid/chemistry ; Peptide Fragments/metabolism
Chemical Substances	Amyloid beta-Peptides ; Amyloid ; Peptide Fragments
Language	English
Publishing date	2023-03-09
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Intramural
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.2218831120
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Article ; Online: Nitroxide-based triradical dopants for efficient low-temperature dynamic nuclear polarization in aqueous solutions over a broad pH range.

Yau, Wai-Ming / Blake Wilson, C / Jeon, Jaekyun / Tycko, Robert

Journal of magnetic resonance (San Diego, Calif. : 1997)

2022 Volume 342, Page(s) 107284

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 ... ...

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.
MeSH term(s)	Hydrogen-Ion Concentration ; Nitrogen Oxides/chemistry ; Temperature ; Water
Chemical Substances	Nitrogen Oxides ; Water (059QF0KO0R) ; nitroxyl (GFQ4MMS07W)
Language	English
Publishing date	2022-08-12
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Intramural
ZDB-ID	1469665-4
ISSN	1096-0856 ; 1557-8968 ; 1090-7807 ; 0022-2364
ISSN (online)	1096-0856 ; 1557-8968
ISSN	1090-7807 ; 0022-2364
DOI	10.1016/j.jmr.2022.107284
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Article ; Online: Depletion of amyloid-β peptides from solution by sequestration within fibril-seeded hydrogels.

Yau, Wai-Ming / Tycko, Robert

Protein science : a publication of the Protein Society

2018 Volume 27, Issue 7, Page(s) 1218–1230

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 ... ...

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.
MeSH term(s)	Amyloid/chemistry ; Amyloid beta-Peptides/chemistry ; Humans ; Hydrogels/chemistry ; Peptide Fragments/chemistry ; Protein Aggregates ; Solutions ; Temperature
Chemical Substances	Amyloid ; Amyloid beta-Peptides ; Hydrogels ; Peptide Fragments ; Protein Aggregates ; Solutions ; amyloid beta-protein (1-40) ; amyloid beta-protein (1-42)
Language	English
Publishing date	2018-03-08
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	1106283-6
ISSN	1469-896X ; 0961-8368
ISSN (online)	1469-896X
ISSN	0961-8368
DOI	10.1002/pro.3387
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Zs.A 3407: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (2.OG) ab Jg. 2022: Lesesaal (EG)
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Article ; Online: 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.

Jeon, Jaekyun / Yau, Wai-Ming / Tycko, Robert

Journal of the American Chemical Society

2020 Volume 142, Issue 50, Page(s) 21220–21232

Abstract: Calmodulin (CaM) mediates a wide range of biological responses to changes in intracellular ... ...

Abstract	Calmodulin (CaM) mediates a wide range of biological responses to changes in intracellular Ca
MeSH term(s)	Calmodulin/chemistry ; Calmodulin/metabolism ; Kinetics ; Molecular Docking Simulation ; Myosin-Light-Chain Kinase/chemistry ; Nuclear Magnetic Resonance, Biomolecular ; Peptide Fragments/chemistry ; Peptide Fragments/metabolism ; Protein Domains
Chemical Substances	Calmodulin ; Peptide Fragments ; Myosin-Light-Chain Kinase (EC 2.7.11.18)
Language	English
Publishing date	2020-12-07
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Intramural ; Research Support, Non-U.S. Gov't
ZDB-ID	3155-0
ISSN	1520-5126 ; 0002-7863
ISSN (online)	1520-5126
ISSN	0002-7863
DOI	10.1021/jacs.0c11156
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Article ; Online: Structural differences in amyloid-β fibrils from brains of nondemented elderly individuals and Alzheimer's disease patients.

Ghosh, Ujjayini / Yau, Wai-Ming / Collinge, John / Tycko, Robert

Proceedings of the National Academy of Sciences of the United States of America

2021 Volume 118, Issue 45

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. ... ...

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.
MeSH term(s)	Aged, 80 and over ; Alzheimer Disease/pathology ; Amyloid beta-Peptides/chemistry ; Case-Control Studies ; Female ; Frontal Lobe/pathology ; Humans ; Magnetic Resonance Spectroscopy ; Male ; Plaque, Amyloid/chemistry ; Plaque, Amyloid/pathology
Chemical Substances	Amyloid beta-Peptides
Language	English
Publishing date	2021-11-01
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, N.I.H., Intramural ; Research Support, Non-U.S. Gov't
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.2111863118
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Zs.A 1148: Show issues

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Article ; Online: Molecular structure of a prevalent amyloid-β fibril polymorph from Alzheimer's disease brain tissue.

Ghosh, Ujjayini / Thurber, Kent R / Yau, Wai-Ming / Tycko, Robert

Proceedings of the National Academy of Sciences of the United States of America

2021 Volume 118, Issue 4

Abstract: Amyloid-β (Aβ) fibrils exhibit self-propagating, molecular-level polymorphisms that may contribute to variations in clinical and pathological characteristics of Alzheimer's disease (AD). We report the molecular structure of a specific fibril polymorph, ... ...

Abstract	Amyloid-β (Aβ) fibrils exhibit self-propagating, molecular-level polymorphisms that may contribute to variations in clinical and pathological characteristics of Alzheimer's disease (AD). We report the molecular structure of a specific fibril polymorph, formed by 40-residue Aβ peptides (Aβ40), that is derived from cortical tissue of an AD patient by seeded fibril growth. The structure is determined from cryogenic electron microscopy (cryoEM) images, supplemented by mass-per-length (MPL) measurements and solid-state NMR (ssNMR) data. Previous ssNMR studies with multiple AD patients had identified this polymorph as the most prevalent brain-derived Aβ40 fibril polymorph from typical AD patients. The structure, which has 2.8-Å resolution according to standard criteria, differs qualitatively from all previously described Aβ fibril structures, both in its molecular conformations and its organization of cross-β subunits. Unique features include twofold screw symmetry about the fibril growth axis, despite an MPL value that indicates three Aβ40 molecules per 4.8-Å β-sheet spacing, a four-layered architecture, and fully extended conformations for molecules in the central two cross-β layers. The cryoEM density, ssNMR data, and MPL data are consistent with β-hairpin conformations for molecules in the outer cross-β layers. Knowledge of this brain-derived fibril structure may contribute to the development of structure-specific amyloid imaging agents and aggregation inhibitors with greater diagnostic and therapeutic utility.
MeSH term(s)	Alzheimer Disease/metabolism ; Alzheimer Disease/pathology ; Amyloid/metabolism ; Amyloid/ultrastructure ; Amyloid beta-Peptides/metabolism ; Amyloid beta-Peptides/ultrastructure ; Binding Sites ; Cerebral Cortex/chemistry ; Cerebral Cortex/pathology ; Cryoelectron Microscopy ; Humans ; Models, Molecular ; Nuclear Magnetic Resonance, Biomolecular ; Peptide Fragments/metabolism ; Peptide Fragments/ultrastructure ; Protein Binding ; Protein Conformation, beta-Strand ; Protein Interaction Domains and Motifs ; Thermodynamics
Chemical Substances	Amyloid ; Amyloid beta-Peptides ; Peptide Fragments ; amyloid beta-protein (1-40)
Language	English
Publishing date	2021-01-11
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Intramural
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.2023089118
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