Enzyme hydration, activity and flexibility: A neutron scattering approach

Kurkal-Siebert, Vandana; Daniel, Roy M.; Finney, John; Tehei, Moeava; Dunn, Rachel V.; Smith, Jeremy C.

doi:10.1016/j.jnoncrysol.2006.01.115

Cited by 6 publications

(7 citation statements)

References 43 publications

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“…Because the rotational correlation time ρ global is approximately proportional to the total effective volume (∼ R h 3 ) and the effective hydration layer contributes about 50% to the total effective volume of a protein like GABARAP, the effective relative hydration, h hyd , can be estimated quite accurately if the molecular shape is known. These results support the findings of Bellissent-Funel et al that the interactions between soluble proteins and surrounding water molecules are an essential determinant for the structure, stability, flexibility, and dynamics of proteins.…”

Section: Discussionsupporting

confidence: 92%

Integrated NMR, Fluorescence, and Molecular Dynamics Benchmark Study of Protein Mechanics and Hydrodynamics

et al. 2018

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Understanding the function of a protein requires not only knowledge of its tertiary structure but also an understanding of its conformational dynamics. Nuclear magnetic resonance (NMR) spectroscopy, polarization-resolved fluorescence spectroscopy and molecular dynamics (MD) simulations are powerful methods to provide detailed insight into protein dynamics on multiple time scales by monitoring global rotational diffusion and local flexibility (order parameters) that are sensitive to inter-and intramolecular interactions, respectively. We present an integrated approach where data from these techniques are analyzed and interpreted within a joint theoretical description of depolarization and diffusion, demonstrating their conceptual similarities. This integrated approach is then applied to the autophagy-related protein GABARAP in its cytosolic form, elucidating its dynamics on the pico-to nanosecond time scale and its rotational and translational diffusion for protein concentrations spanning 9 orders of magnitude. We compare the dynamics of GABARAP as monitored by 15 N spin relaxation of the backbone amide groups, fluorescence anisotropy decays and fluorescence correlation spectroscopy of side chains labeled with BODIPY FL, and molecular movies of the protein from MD simulations. The recovered parameters agree very well between the distinct techniques if the different measurement conditions (probe localization, sample concentration) are taken into account. Moreover, we propose a method that compares the order parameters of the backbone and side chains to identify potential hinges for large-scale, functionally relevant intradomain motions, such as residues 27/28 at the interface between the two subdomains of GABARAP. In conclusion, the integrated concept of cross-fertilizing techniques presented here is fundamental to obtaining a comprehensive quantitative picture of multiscale protein dynamics and solvation. The possibility to employ these validated techniques under cellular conditions and combine them with fluorescence imaging opens up the perspective of studying the functional dynamics of GABARAP or other proteins in live cells.

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Section: Discussionsupporting

confidence: 92%

Integrated NMR, Fluorescence, and Molecular Dynamics Benchmark Study of Protein Mechanics and Hydrodynamics

et al. 2018

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“…The method that has been most commonly used for deriving the MSD from EINS measurements involves two approximations. , First, it is assumed that all hydrogen atoms have identical MSDs such that eq can be rewritten as S e l ( q⃗ , ω = 0 ) = 1 N ∑ α ⟨ e i q⃗ · Δ r⃗ α false( t R false) ⟩ ≈ ⟨ e i q⃗ · Δ r⃗ false( t R false) ⟩ where the mean-square displacements of individual atoms, ⟨Δ r⃗ α 2 ⟩, are replaced by the average mean square displacement ⟨Δ r⃗ 2 ⟩ . Then, using the cumulant expansion, , we have ⟨ e i q⃗ · Δ r⃗ false( t R false) ] ⟩ = normale − q⃗ 2 ρ 2 ( t R ) + q⃗ 4 ρ 4 ( t R ) …”

Section: Theoretical Approachmentioning

confidence: 99%

Derivation of Mean-Square Displacements for Protein Dynamics from Elastic Incoherent Neutron Scattering

et al. 2012

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The derivation of mean-square displacements from elastic incoherent neutron scattering (EINS) of proteins is examined, with the aid of experiments on camphor-bound cytochrome P450cam and complementary molecular dynamics simulations. It is shown that a q(4) correction to the elastic incoherent structure factor (where q is the scattering vector) can be simply used to reliably estimate from the experiment both the average mean-square atomic displacement, <Δr(2)> of the nonexchanged hydrogen atoms in the protein and its variance, σ(2). The molecular dynamics simulation results are in broad agreement with the experimentally derived <Δr(2)> and σ(2) derived from EINS on instruments at two different energy resolutions, corresponding to dynamics on the ∼100 ps and ∼1 ns time scales. Significant dynamical heterogeneity is found to arise from methyl-group rotations. The easy-to-apply q(4) correction extends the information extracted from elastic incoherent neutron scattering experiments and should be of wide applicability.

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“…3,7 The precise connection between biological function and fast protein conformational fluctuations is only beginning to be understood, and continues to be a subject of ongoing research and debate. [8][9][10][11][12][13] The fast fluctuations are generally considered to provide the lubrication that promotes larger-scale conformational changes and are, as such, a prerequisite to function. 3 A concrete example of the interplay of fast (ps-ns) dynamics and slow (ms-ms), large-scale conformational changes in an enzyme, demonstrated by a combination of NMR experiments and molecular dynamics (MD) simulations, was recently reported.…”

Section: Introductionmentioning

confidence: 99%

Hydration dynamics of purple membranes

2009

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Protein motions occur over many decades of time, from femtoseconds to seconds and longer. Fast (ps-ns) protein motion enabled by water dynamics on the surfaces of protein molecules is generally believed to be required for biological function. The coupling between water and protein dynamics for soluble proteins in aqueous solution is relatively well understood, while the couplings between protein, lipid, and water dynamics in membranes are only beginning to be unravelled. We report a molecular dynamics simulation study of the dynamics of water hydrating purple membranes (PM). We validate our simulations by comparing the temperature and hydration dependence of crystal lattice parameters and water and protein/lipid dynamics with neutron diffraction and spectroscopic data. We proceed to examine the temperature dependence of several time-dependent quantities describing different aspects of water dynamics, and identify and characterize the correlations between water dynamics and the motion of the protein and lipid components of PM. Our results point to a correlation between the solvation dynamics of lipid molecules and the dynamics of both the protein and lipid components.

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Enzyme hydration, activity and flexibility: A neutron scattering approach

Cited by 6 publications

References 43 publications

Integrated NMR, Fluorescence, and Molecular Dynamics Benchmark Study of Protein Mechanics and Hydrodynamics

Integrated NMR, Fluorescence, and Molecular Dynamics Benchmark Study of Protein Mechanics and Hydrodynamics

Derivation of Mean-Square Displacements for Protein Dynamics from Elastic Incoherent Neutron Scattering

Hydration dynamics of purple membranes

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