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Article: The N-Terminal Domain of Aβ₄₀-Amyloid Fibril: The MOMD Perspective of its Dynamic Structure from NMR Lineshape Analysis

Meirovitch, Eva / Liang, Zhichun / Freed, Jack H.

Journal of physical chemistry. 2022 Feb. 05, v. 126, no. 6

2022

Abstract: We have developed the stochastic microscopic-order-macroscopic-disorder (MOMD) approach for elucidating dynamic structures in the solid-state from ²H NMR lineshapes. In MOMD, the probe experiences an effective/collective motional mode. The latter is ... ...

Abstract	We have developed the stochastic microscopic-order-macroscopic-disorder (MOMD) approach for elucidating dynamic structures in the solid-state from ²H NMR lineshapes. In MOMD, the probe experiences an effective/collective motional mode. The latter is described by a potential, u, which represents the local spatial-restrictions, a local-motional diffusion tensor, R, and key features of local geometry. Previously we applied MOMD to the well-structured core domain of the 3-fold-symmetric twisted polymorph of the Aβ₄₀-amyloid fibril. Here, we apply it to the N-terminal domain of this fibril. We find that the dynamic structures of the two domains are largely similar but differ in the magnitude and complexity of the key physical parameters. This interpretation differs from previous multisimple-mode (MSM) interpretations of the same experimental data. MSM used for the two domains different combinations of simple motional modes taken to be independent. For the core domain, MOMD and MSM disagree on the character of the dynamic structure. For the N-terminal domain, they even disagree on whether this chain segment is structurally ordered (MOMD finds that it is), and whether it undergoes a phase transition at 260 K where bulklike water located in the fibril matrix freezes (MOMD finds that it does not). These are major differences associated with an important system. While the MOMD description is a physically sound one, there are drawbacks in the MSM descriptions. The results obtained in this study promote our understanding of the dynamic structure of protein aggregates. Thus, they contribute to the effort to pharmacologically control neurodegenerative disorders believed to be caused by such aggregates.
Keywords	freezing ; geometry ; journals ; neurodegenerative diseases ; protein aggregates ; protein structure
Language	English
Dates of publication	2022-0205
Size	p. 1202-1211.
Publishing place	American Chemical Society
Document type	Article
ISSN	1520-5207
DOI	10.1021/acs.jpcb.1c10131
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: The N-Terminal Domain of Aβ

Meirovitch, Eva / Liang, Zhichun / Freed, Jack H

The journal of physical chemistry. B

2022 Volume 126, Issue 6, Page(s) 1202–1211

Abstract: We have developed the stochastic microscopic-order-macroscopic-disorder (MOMD) approach for elucidating dynamic structures in the solid-state ... ...

Abstract	We have developed the stochastic microscopic-order-macroscopic-disorder (MOMD) approach for elucidating dynamic structures in the solid-state from
MeSH term(s)	Amyloid/chemistry ; Amyloid beta-Peptides/chemistry ; Diffusion ; Magnetic Resonance Imaging ; Magnetic Resonance Spectroscopy ; Protein Aggregates
Chemical Substances	Amyloid ; Amyloid beta-Peptides ; Protein Aggregates
Language	English
Publishing date	2022-02-05
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ISSN	1520-5207
ISSN (online)	1520-5207
DOI	10.1021/acs.jpcb.1c10131
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Article: Structural Dynamics by NMR in the Solid State: II. The MOMD Perspective of the Dynamic Structure of Metal–Organic Frameworks Comprising Several Mobile Components

Meirovitch, Eva / Liang, Zhichun / Schurko, Robert W. / Loeb, Stephen J. / Freed, Jack H.

Journal of physical chemistry. 2022 Mar. 25, v. 126, no. 13

2022

Abstract: We describe the application of the microscopic-order-macroscopic-disorder (MOMD) approach, developed for the analysis of dynamic ²H NMR lineshapes in the solid state, to unravel interactions among the constituents of metal–organic frameworks (MOFs) that ... ...

Abstract	We describe the application of the microscopic-order-macroscopic-disorder (MOMD) approach, developed for the analysis of dynamic ²H NMR lineshapes in the solid state, to unravel interactions among the constituents of metal–organic frameworks (MOFs) that comprise mobile components. MOMD was applied recently to University of Windsor Dynamic Material (UWDM) MOFs with one mobile crown ether per cavity. In this work, we study UWDM-9-d₄, which comprises a mobile ²H-labeled phenyl-ring residue along with an isotopically unlabeled 24C8 crown ether. We also study UiO-68-d₄, which is structurally similar to UWDM-9-d₄ but lacks the crown ether. The physical picture consists of the NMR probe─the C–D bonds of the phenyl-d₄ rotor─diffusing locally (diffusion tensor R) in the presence of a local ordering potential, u. For UiO-68-d₄, we find it sufficient to expand u in terms of four real Wigner functions, D₀\|K\|ᴸ, overall 2–3 kT in magnitude, with R∥ relatively fast, and R⊥ in the (2.8–5.0) × 10² s–¹ range. For UWDM-9-d₄, u requires only two terms 2–3 kT in magnitude and slower rate constants R∥ and R⊥. In the more crowded macrocycle-containing UWDM-9-d₄ cavity, phenyl-d₄ dynamics is more isotropic and is described by a simpler ordering potential. This is ascribed to cooperative phenyl-ring/macrocycle motion, which yields a dynamic structure more uniform in character. The experimental ²H spectra used here were analyzed previously with a multi-simple-mode (MSM) approach where several independent simple motional modes are combined. Where possible, similar features have been identified and used to compare the two approaches.
Keywords	clothing ; cooperatives ; coordination polymers ; ethers ; isotropy ; journals ; physical chemistry ; universities
Language	English
Dates of publication	2022-0325
Size	p. 2452-2465.
Publishing place	American Chemical Society
Document type	Article
ISSN	1520-5207
DOI	10.1021/acs.jpcb.1c10120
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Article: Structural Dynamics by NMR in the Solid State: The Unified MOMD Perspective Applied to Organic Frameworks with Interlocked Molecules

Meirovitch, Eva / Liang, Zhichun / Freed, Jack H

Journal of physical chemistry. 2020 June 25, v. 124, no. 29

2020

Abstract: The microscopic-order-macroscopic-disorder (MOMD) approach for NMR lineshape analysis has been applied to the University of Windsor Dynamic Materials (UWDM) of types 1, 2, α-3, β-3, and 5, which are metal–organic frameworks (MOFs) comprising mobile ... ...

Abstract	The microscopic-order-macroscopic-disorder (MOMD) approach for NMR lineshape analysis has been applied to the University of Windsor Dynamic Materials (UWDM) of types 1, 2, α-3, β-3, and 5, which are metal–organic frameworks (MOFs) comprising mobile mechanically interlocked molecules (MIMs). The mobile MIM components are selectively deuterated crown ether macrocycles – 24C6, 22C6, and B24C6. Their motion is described in MOMD by an effective/collective dynamic mode characterized by a diffusion tensor, R, a restricting/ordering potential, u, expanded in the Wigner rotation matrix elements, D₀, Kᴸ, and features of local geometry. Experimental ²H lineshapes are available over 220 K (on average) and in some cases 320 K. They are reproduced with axial R, u given by the terms D₀,₀² and D₀,\|₂\|², and established local geometry. For UWDM of types 1, β-3, and 5, where the macrocycle resides in a relatively loose space, u is in the 1–3 kT, R∥ in the (1.0–2.5) × 10⁶ s–¹, and R⊥ in the (0.4–2.5) × 10⁴ s–¹ range; the deuterium atom is bonded to a carbon atom with tetrahedral coordination character. For UWDM of types 2 and α-3, where the macrocycle resides in a much tighter space, a substantial change in the symmetry of u and the coordination character of the ²H-bonded carbon are detected at higher temperatures. The activation energies for R∥ and R⊥ are characteristic of each system. The MOMD model is general; effective/collective dynamic modes are treated. The characteristics of motion, ordering, and geometry are physically well-defined; they differ from case to case in extent and symmetry but not in essence. Physical clarity and consistency provide new insights. A previous interpretation of the same experimental data used models consisting of collections of independent simple motions. These models are specific to each case and temperature. Within their scope, generating consistent physical pictures and comparing cases are difficult; possible collective modes are neglected.
Keywords	carbon ; deuterium ; geometry ; models ; physical chemistry ; temperature
Language	English
Dates of publication	2020-0625
Size	p. 6225-6235.
Publishing place	American Chemical Society
Document type	Article
Note	NAL-AP-2-clean
ISSN	1520-5207
DOI	10.1021/acs.jpcb.0c03687
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Article ; Online: Microsecond dynamics in proteins by two-dimensional ESR: Predictions.

Gupta, Pranav / Liang, Zhichun / Freed, Jack H

The Journal of chemical physics

2020 Volume 152, Issue 21, Page(s) 214112

Abstract: Two-dimensional electron-electron double resonance (2D-ELDOR) provides extensive insight into molecular motions. Recent developments permitting experiments at higher frequencies (95 GHz) provide molecular orientational resolution, enabling a clearer ... ...

Abstract	Two-dimensional electron-electron double resonance (2D-ELDOR) provides extensive insight into molecular motions. Recent developments permitting experiments at higher frequencies (95 GHz) provide molecular orientational resolution, enabling a clearer description of the nature of the motions. In this work, simulations are provided for the example of domain motions within proteins that are themselves slowly tumbling in solution. These show the nature of the exchange cross-peaks that are predicted to develop in real time from such domain motions. However, we find that the existing theoretical methods for computing 2D-ELDOR experiments over a wide motional range begin to fail seriously when applied to very slow motions characteristic of proteins in solution. One reason is the failure to obtain accurate eigenvectors and eigenvalues of the complex symmetric stochastic Liouville matrices describing the experiment when computed by the efficient Lanczos algorithm in the range of very slow motion. Another, perhaps more serious, issue is that these matrices are "non-normal," such that for the very slow motional range even rigorous diagonalization algorithms do not yield the correct eigenvalues and eigenvectors. We have employed algorithms that overcome both these issues and lead to valid 2D-ELDOR predictions even for motions approaching the rigid limit. They are utilized to describe the development of cross-peaks in 2D-ELDOR at 95 GHz for a particular case of domain motion.
MeSH term(s)	Algorithms ; Electron Spin Resonance Spectroscopy ; Protein Conformation ; Proteins/chemistry ; Spin Labels
Chemical Substances	Proteins ; Spin Labels
Language	English
Publishing date	2020-06-25
Publishing country	United States
Document type	Journal Article
ZDB-ID	3113-6
ISSN	1089-7690 ; 0021-9606
ISSN (online)	1089-7690
ISSN	0021-9606
DOI	10.1063/5.0008094
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Article ; Online: Structural Dynamics by NMR in the Solid State: The Unified MOMD Perspective Applied to Organic Frameworks with Interlocked Molecules.

Meirovitch, Eva / Liang, Zhichun / Freed, Jack H

The journal of physical chemistry. B

2020 Volume 124, Issue 29, Page(s) 6225–6235

Abstract: The microscopic-order-macroscopic-disorder (MOMD) approach for NMR lineshape analysis has been applied to the University of Windsor Dynamic Materials (UWDM) of types 1, 2, α-3, β-3, and 5, which are metal-organic frameworks (MOFs) comprising mobile ... ...

Abstract	The microscopic-order-macroscopic-disorder (MOMD) approach for NMR lineshape analysis has been applied to the University of Windsor Dynamic Materials (UWDM) of types 1, 2, α-3, β-3, and 5, which are metal-organic frameworks (MOFs) comprising mobile mechanically interlocked molecules (MIMs). The mobile MIM components are selectively deuterated crown ether macrocycles - 24C6, 22C6, and B24C6. Their motion is described in MOMD by an effective/collective dynamic mode characterized by a diffusion tensor,
MeSH term(s)	Diffusion ; Magnetic Resonance Imaging ; Magnetic Resonance Spectroscopy ; Motion ; Temperature
Language	English
Publishing date	2020-07-14
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ISSN	1520-5207
ISSN (online)	1520-5207
DOI	10.1021/acs.jpcb.0c03687
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Article ; Online: Structural Dynamics by NMR in the Solid State: II. The MOMD Perspective of the Dynamic Structure of Metal-Organic Frameworks Comprising Several Mobile Components.

Meirovitch, Eva / Liang, Zhichun / Schurko, Robert W / Loeb, Stephen J / Freed, Jack H

The journal of physical chemistry. B

2022 Volume 126, Issue 13, Page(s) 2452–2465

Abstract: We describe the application of the microscopic-order-macroscopic-disorder (MOMD) approach, developed for the analysis of ... ...

Abstract	We describe the application of the microscopic-order-macroscopic-disorder (MOMD) approach, developed for the analysis of dynamic
MeSH term(s)	Crown Ethers ; Diffusion ; Magnetic Resonance Imaging ; Magnetic Resonance Spectroscopy ; Metal-Organic Frameworks
Chemical Substances	Crown Ethers ; Metal-Organic Frameworks
Language	English
Publishing date	2022-03-25
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ISSN	1520-5207
ISSN (online)	1520-5207
DOI	10.1021/acs.jpcb.1c10120
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Phenyl-Ring Dynamics in Amyloid Fibrils and Proteins: The Microscopic-Order-Macroscopic-Disorder Perspective

Meirovitch, Eva / Liang, Zhichun / Freed, Jack H

Journal of physical chemistry. 2018 Aug. 24, v. 122, no. 37

2018

Abstract: We have developed the microscopic-order-macroscopic-disorder (MOMD) approach for studying internal mobility in polycrystalline proteins with 2H lineshape analysis. The motion itself is expressed by a diffusion tensor, R, the local spatial restraints by a ...

Abstract	We have developed the microscopic-order-macroscopic-disorder (MOMD) approach for studying internal mobility in polycrystalline proteins with 2H lineshape analysis. The motion itself is expressed by a diffusion tensor, R, the local spatial restraints by a potential, u, and the “local geometry” by the relative orientation of the model-related and nuclear magnetic resonance-related tensors. Here, we apply MOMD to phenyl-ring dynamics in several Αβ40-amyloid-fibrils, and the villin headpiece subdomain (HP36). Because the available data are limited in extent and sensitivity, we adjust u and R in the relevant parameter ranges, fixing the “local geometry” in accordance with standard stereochemistry. This yields a physically well-defined and consistent picture of phenyl-ring dynamics, enabling comparison between different systems. In the temperature range of 278–308 K, u has a strength of (1.7–1.8) kT and a rhombicity of (2.4–2.6) kT, and R has components of 5.0 × 102 ≤ R⊥ ≤ 2.0 × 103 s–1 and 6.3 × 105 ≤ R∥ ≤ 2.0 × 106 s–1. At 278 K, fibril hydration increases the axiality of both u and R; HP36 hydration has a similar effect at 295 K, reducing R⊥ considerably. The D23N mutation slows down the motion of the probe; Aβ40 polymorphism affects both this motion and the related local potential. The present study identifies the impact of various factors on phenyl-ring mobility in amyloid fibrils and globular proteins; the difference between the two protein forms is considerable. The distinctive impact of hydration on phenyl-ring motion and previously studied methyl-group motion is also examined. The 2H lineshapes considered here were analyzed previously with various multi-simple-mode (MSM) models, where several simple motional modes are combined. The MOMD and MSM interpretations differ in essence.
Keywords	amyloid ; deuterium ; models ; moieties ; mutation ; stable isotopes ; stereochemistry ; temperature
Language	English
Dates of publication	2018-0824
Size	p. 8675-8684.
Publishing place	American Chemical Society
Document type	Article
ISSN	1520-5207
DOI	10.1021/acs.jpcb.8b06330
Database	NAL-Catalogue (AGRICOLA)

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Article: MOMD Analysis of NMR Line Shapes from Aβ-Amyloid Fibrils: A New Tool for Characterizing Molecular Environments in Protein Aggregates

Meirovitch, Eva / Liang, Zhichun / Freed, Jack H

Journal of physical chemistry. 2018 Apr. 06, v. 122, no. 18

2018

Abstract: The microscopic-order-macroscopic-disorder (MOMD) approach for 2H NMR line shape analysis is applied to dry and hydrated 3-fold- and 2-fold-symmetric amyloid-Aβ40 fibrils and protofibrils of the D23N mutant. The methyl moieties of L17, L34, V36 (C–CD3), ... ...

Abstract	The microscopic-order-macroscopic-disorder (MOMD) approach for 2H NMR line shape analysis is applied to dry and hydrated 3-fold- and 2-fold-symmetric amyloid-Aβ40 fibrils and protofibrils of the D23N mutant. The methyl moieties of L17, L34, V36 (C–CD3), and M35 (S–CD3) serve as probes. Experimental 2H spectra acquired previously in the 147–310 K range are used. MOMD describes local probe motion as axial diffusion (R tensor) in the presence of a potential, u, which represents the spatial restrictions exerted by the molecular surroundings. We find that R∥ = (0.2–3.3) × 104 s–1, R⊥ = (2.2–2.5) × 102 s–1, and R is tilted from the 2H quadrupolar tensor at 60–75°. The strength of u is in the (2.0–2.4) kT range; its rhombicity is substantial. The only methyl moieties affected by fibril hydration are those of M35, located at fibril interfaces. The associated local potentials change form abruptly around 260 K, where massive water freezing occurs. An independent study revealed unfrozen “tightly-peptide-bound” water residing at the interfaces of the 3-fold-symmetric Aβ40 fibrils and at the interfaces of the E22G and E22Δ Aβ40-mutant fibrils. Considering this to be the case in general for Aβ40-related fibrils, the following emerges. The impact of water freezing is transmitted selectively to the fibril structure through interactions with tightly-peptide-bound water, in this case of M35 methyl moieties. The proof that such waters reside at the interfaces of the 2-fold-symmetric fibril, and the protofibril of the D23N mutant, is new. MOMD provides information on the surroundings of the NMR probe directly via the potential, u, which is inherent to the model; a prior interpretation of the same experimental data does so partially and indirectly (see below). Thus, MOMD analysis of NMR line shapes as applied to amyloid fibrils/protein aggregates emerges as a consistent new tool for elucidating the properties of, and processes associated with, molecular environments in the fibril.
Keywords	amyloid ; deuterium ; freezing ; models ; moieties ; mutants ; nuclear magnetic resonance spectroscopy ; protein aggregates
Language	English
Dates of publication	2018-0406
Size	p. 4793-4801.
Publishing place	American Chemical Society
Document type	Article
ISSN	1520-5207
DOI	10.1021/acs.jpcb.8b02181
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Article ; Online: Phenyl-Ring Dynamics in Amyloid Fibrils and Proteins: The Microscopic-Order-Macroscopic-Disorder Perspective.

Meirovitch, Eva / Liang, Zhichun / Freed, Jack H

The journal of physical chemistry. B

2018 Volume 122, Issue 37, Page(s) 8675–8684

Abstract: We have developed the microscopic-order-macroscopic-disorder (MOMD) approach for studying internal mobility in polycrystalline proteins ... ...

Abstract	We have developed the microscopic-order-macroscopic-disorder (MOMD) approach for studying internal mobility in polycrystalline proteins with
MeSH term(s)	Amyloid beta-Peptides/chemistry ; Deuterium ; Magnetic Resonance Spectroscopy/statistics & numerical data ; Models, Chemical ; Models, Molecular ; Neurofilament Proteins/chemistry ; Peptide Fragments/chemistry ; Protein Conformation ; Protein Domains
Chemical Substances	Amyloid beta-Peptides ; Neurofilament Proteins ; Peptide Fragments ; amyloid beta-protein (1-40) ; villin headpiece subdomain peptide ; Deuterium (AR09D82C7G)
Language	English
Publishing date	2018-09-10
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ISSN	1520-5207
ISSN (online)	1520-5207
DOI	10.1021/acs.jpcb.8b06330
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