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  1. Article ; Online: Local Structures in Proteins from Microsecond Molecular Dynamics Simulations: 2. The Role of Symmetry in GTPase Binding and Dimer Formation.

    Pshetitsky, Yaron / Buck, Matthias / Meirovitch, Eva

    The journal of physical chemistry. B

    2024  Volume 128, Issue 7, Page(s) 1573–1585

    Abstract: The Rho GTPase binding domain of Plexin-B1 (RBD) prevails in solution as dimer. Under appropriate circumstances, it binds the small GTPase Rac1 to yield the complex RBD-Rac1. Here, we study RBD dimerization and complex formation from a symmetry-based ... ...

    Abstract The Rho GTPase binding domain of Plexin-B1 (RBD) prevails in solution as dimer. Under appropriate circumstances, it binds the small GTPase Rac1 to yield the complex RBD-Rac1. Here, we study RBD dimerization and complex formation from a symmetry-based perspective using data derived from 1 μs long MD simulations. The quantities investigated are the local potentials,
    MeSH term(s) Molecular Dynamics Simulation ; Receptors, Cell Surface/chemistry ; Protein Binding ; Dimerization ; GTP Phosphohydrolases/metabolism ; Binding Sites
    Chemical Substances Receptors, Cell Surface ; GTP Phosphohydrolases (EC 3.6.1.-)
    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.3c06745
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Local Structures in Proteins from Microsecond Molecular Dynamics Simulations: A Symmetry-Based Perspective.

    Pshetitsky, Yaron / Mendelman, Netanel / Buck, Matthias / Meirovitch, Eva

    The journal of physical chemistry. B

    2024  Volume 128, Issue 7, Page(s) 1557–1572

    Abstract: We report on a new method for the characterization of local structures in proteins based on extensive molecular dynamics (MD) simulations, here, 1 μs in length. The N-H bond of the Rho GTPase binding domain of plexin-B1 (RBD) serves as a probe and the ... ...

    Abstract We report on a new method for the characterization of local structures in proteins based on extensive molecular dynamics (MD) simulations, here, 1 μs in length. The N-H bond of the Rho GTPase binding domain of plexin-B1 (RBD) serves as a probe and the potential,
    MeSH term(s) Molecular Dynamics Simulation ; Proteins/chemistry ; Protein Binding ; Dimerization ; Protein Structure, Secondary
    Chemical Substances Proteins
    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.3c06741
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Slowly Relaxing Local Structure Analysis of

    Mendelman, Netanel / Meirovitch, Eva

    The journal of physical chemistry. B

    2022  Volume 126, Issue 33, Page(s) 6191–6198

    Abstract: Nuclear magnetic resonance relaxation analysis is a powerful method for studying the internal mobility of proteins. We have developed for analysis the slowly relaxing local structure (SRLS) approach. SRLS is general in its nature in several respects, ... ...

    Abstract Nuclear magnetic resonance relaxation analysis is a powerful method for studying the internal mobility of proteins. We have developed for analysis the slowly relaxing local structure (SRLS) approach. SRLS is general in its nature in several respects, including the tensorial representation of the physical quantities comprising the dynamic model. By controlling tensor symmetry, a broad range of systems can be treated with physical relevance, typically with data-fitting techniques. In simple limits, SRLS yields the traditional model-free (MF) method. In the present context, MF simplicity means featuring the highest possible tensor symmetry. This renders MF-based data-fitting susceptible to the usage of fit parameters, yielding physically ill-defined results. A typical candidate is the
    MeSH term(s) Humans ; Lipocalin-2 ; Magnetic Resonance Spectroscopy ; Proteins/chemistry
    Chemical Substances Lipocalin-2 ; Proteins
    Language English
    Publishing date 2022-08-15
    Publishing country United States
    Document type Journal Article ; 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.2c04126
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article: Slowly Relaxing Local Structure Analysis of ¹⁵N Relaxation from the Proteins p50 and Human Neutrophil Gelatinase-Associated Lipocalin: New Insights into the Dynamic Structure of β-Barrel Proteins

    Mendelman, Netanel / Meirovitch, Eva

    Journal of physical chemistry. 2022 Aug. 15, v. 126, no. 33

    2022  

    Abstract: Nuclear magnetic resonance relaxation analysis is a powerful method for studying the internal mobility of proteins. We have developed for analysis the slowly relaxing local structure (SRLS) approach. SRLS is general in its nature in several respects, ... ...

    Abstract Nuclear magnetic resonance relaxation analysis is a powerful method for studying the internal mobility of proteins. We have developed for analysis the slowly relaxing local structure (SRLS) approach. SRLS is general in its nature in several respects, including the tensorial representation of the physical quantities comprising the dynamic model. By controlling tensor symmetry, a broad range of systems can be treated with physical relevance, typically with data-fitting techniques. In simple limits, SRLS yields the traditional model-free (MF) method. In the present context, MF simplicity means featuring the highest possible tensor symmetry. This renders MF-based data-fitting susceptible to the usage of fit parameters, yielding physically ill-defined results. A typical candidate is the Rₑₓ term, devised to represent ms-μs motions but often invoked by the fitting scheme just to improve the statistics. Here, we consider two such cases using the N–H bond as probe and the proteins p50 and human neutrophil gelatinase-associated lipocalin as paradigm systems. We illustrate the harm caused by the physically unjustified involvement of Rₑₓ in MF-based ¹⁵N relaxation analysis. Then, we show that forgoing the usage of Rₑₓ, SRLS analysis of the very same experimental data provides interesting new information.
    Keywords dynamic models ; humans ; neutrophils ; nuclear magnetic resonance spectroscopy ; physical chemistry ; statistics
    Language English
    Dates of publication 2022-0815
    Size p. 6191-6198.
    Publishing place American Chemical Society
    Document type Article
    ISSN 1520-5207
    DOI 10.1021/acs.jpcb.2c04126
    Database NAL-Catalogue (AGRICOLA)

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  5. Article ; Online: SRLS Analysis of

    Mendelman, Netanel / Meirovitch, Eva

    The journal of physical chemistry. B

    2021  Volume 125, Issue 3, Page(s) 805–816

    Abstract: We report on amide (N-H) NMR relaxation from the protein S100A1 analyzed with the slowly relaxing local structure (SRLS) approach. S100A1 comprises two calcium-binding "EF-hands" (helix-loop-helix motifs) connected by a linker. The dynamic structure of ... ...

    Abstract We report on amide (N-H) NMR relaxation from the protein S100A1 analyzed with the slowly relaxing local structure (SRLS) approach. S100A1 comprises two calcium-binding "EF-hands" (helix-loop-helix motifs) connected by a linker. The dynamic structure of this protein, in both calcium-free and calcium-bound form, is described as the restricted local N-H motion coupled to isotropic protein tumbling. The restrictions are given by a rhombic potential,
    MeSH term(s) Calcium ; Entropy ; Magnetic Resonance Spectroscopy ; Protein Conformation ; Proteins ; Proton Magnetic Resonance Spectroscopy
    Chemical Substances Proteins ; Calcium (SY7Q814VUP)
    Language English
    Publishing date 2021-01-15
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 1520-5207
    ISSN (online) 1520-5207
    DOI 10.1021/acs.jpcb.0c10124
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Structural Dynamics from NMR Relaxation by SRLS Analysis: Local Geometry, Potential Energy Landscapes, and Spectral Densities.

    Mendelman, Netanel / Meirovitch, Eva

    The journal of physical chemistry. B

    2021  Volume 125, Issue 23, Page(s) 6130–6143

    Abstract: We have developed the two-body coupled-rotator slowly relaxing local structure (SRLS) approach for elucidating protein dynamics by nuclear magnetic resonance (NMR) relaxation. The rotators are represented by diffusion ... ...

    Abstract We have developed the two-body coupled-rotator slowly relaxing local structure (SRLS) approach for elucidating protein dynamics by nuclear magnetic resonance (NMR) relaxation. The rotators are represented by diffusion tensors
    MeSH term(s) Diffusion ; Magnetic Resonance Imaging ; Magnetic Resonance Spectroscopy ; Proteins
    Chemical Substances Proteins
    Language English
    Publishing date 2021-06-08
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 1520-5207
    ISSN (online) 1520-5207
    DOI 10.1021/acs.jpcb.1c02502
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article: Structural Dynamics from NMR Relaxation by SRLS Analysis: Local Geometry, Potential Energy Landscapes, and Spectral Densities

    Mendelman, Netanel / Meirovitch, Eva

    Journal of physical chemistry. 2021 June 08, v. 125, no. 23

    2021  

    Abstract: We have developed the two-body coupled-rotator slowly relaxing local structure (SRLS) approach for elucidating protein dynamics by nuclear magnetic resonance (NMR) relaxation. The rotators are represented by diffusion tensors D₁ for overall protein ... ...

    Abstract We have developed the two-body coupled-rotator slowly relaxing local structure (SRLS) approach for elucidating protein dynamics by nuclear magnetic resonance (NMR) relaxation. The rotators are represented by diffusion tensors D₁ for overall protein tumbling and D₂ for locally ordered probe motion. D₁ and D₂ are coupled dynamically by a potential, u, typically given by linear combinations of the Wigner functions D₀₀² and (D₀₂² + D₀–₂²). Until now, our SRLS analyses provided the tensors, D₁ and D₂, the potential, u, and the geometric link between SRLS and NMR. Here we enhance this description by also examining the SRLS spectral densities obtained by solving the SRLS Smoluchowski equation. In addition, we show that the form of u specified above complies with two NMR-detected potential energy landscapes representing preferential ordering along N–H or Cᵅ–Cᵅ. Pictorial illustrations thereof are provided. The extended SRLS analysis is applied to ¹⁵N–H relaxation from the carbohydrate recognition domain of galectin-3 (Gal3C) in complex with two diastereomeric ligands, S and R. We find that D₂ is isotropic with a principal value, D₂, of 10¹⁰ s–¹ on average, and it is faster in the strands β₃, β₅, and β₈. The potential, u, is strong (∼20 kT); it is slightly rhombic when N–H is the main ordering axis and highly rhombic when Cᵅ–Cᵅ is the main ordering axis. Gal3C-S exhibits primarily preferential ordering along Cᵅ–Cᵅ; Gal3C-R exhibits both types of ordering. The binding-associated polypeptide chain segment of Gal3C-S is homogeneous, whereas that of Gal3C-R is diversified, with regard to D₂ and ordering preference. We associate these features with the previously determined diminished binding constant of Gal3C-R in comparison with Gal3C-S. Thus, the present study enhances the SRLS analysis, in general, and provides new insights into the dynamic structure and binding properties of Gal3C-S and Gal3C-R, in particular.
    Keywords carbohydrates ; equations ; galectins ; geometry ; isotropy ; ligands ; nuclear magnetic resonance spectroscopy ; physical chemistry ; polypeptides ; potential energy
    Language English
    Dates of publication 2021-0608
    Size p. 6130-6143.
    Publishing place American Chemical Society
    Document type Article
    Note NAL-AP-2-clean
    ISSN 1520-5207
    DOI 10.1021/acs.jpcb.1c02502
    Database NAL-Catalogue (AGRICOLA)

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  8. 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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  9. 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
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Conformational Entropy from Restricted Bond-Vector Motion in Proteins: The Symmetry of the Local Restrictions and Relation to NMR Relaxation.

    Mendelman, Netanel / Meirovitch, Eva

    The journal of physical chemistry. B

    2020  Volume 124, Issue 21, Page(s) 4284–4292

    Abstract: Locally mobile bond-vectors contribute to the conformational entropy of the protein, given ... ...

    Abstract Locally mobile bond-vectors contribute to the conformational entropy of the protein, given by
    MeSH term(s) Entropy ; Magnetic Resonance Imaging ; Magnetic Resonance Spectroscopy ; Protein Conformation ; Proteins
    Chemical Substances Proteins
    Language English
    Publishing date 2020-05-15
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 1520-5207
    ISSN (online) 1520-5207
    DOI 10.1021/acs.jpcb.0c02662
    Database MEDical Literature Analysis and Retrieval System OnLINE

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