On the Coupling between the Collective Dynamics of Proteins and Their Hydration Water

Nibali, Valeria Conti; D’Angelo, Giovanna; Paciaroni, Alessandro; Tobias, Douglas J.; Tarek, Mounir

doi:10.1021/jz500023e

Cited by 61 publications

(50 citation statements)

References 49 publications

(98 reference statements)

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“…It is worth of mention that the existence of short-lived coherent excitations with a speed of about 3500 m/s has been proven also for water at the interface with proteins and DNA 173,167,168 , in agreement with MD simulation results 155,174 . A distinct feature of water at the interface with biomolecules is the rapid overdamping of the high-frequency mode, which supports the glass-like behavior of bound water.…”

Section: Fast Soundsupporting

confidence: 81%

X-ray and Neutron Scattering of Water

et al. 2016

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International audienceThis review article focuses on the most recent advances in X-ray and neutron scattering studies of water structure, from ambient temperature to the deeply supercooled and amorphous states, and of water diffusive and collective dynamics, in disparate thermodynamic conditions and environments. In particular, the ability to measure X-ray and neutron diffraction of water with unprecedented high accuracy in an extended range of momentum transfers has allowed the derivation of detailed O–O pair correlation functions. A panorama of the diffusive dynamics of water in a wide range of temperatures (from 400 K down to supercooled water) and pressures (from ambient up to multiple gigapascals) is presented. The recent results obtained by quasi-elastic neutron scattering under high pressure are compared with the existing data from nuclear magnetic resonance, dielectric and infrared measurements, and modeling. A detailed description of the vibrational dynamics of water as measured by inelastic neutron scattering is presented. The dependence of the water vibrational density of states on temperature and pressure, and in the presence of biological molecules, is discussed. Results about the collective dynamics of water and its dispersion curves as measured by coherent inelastic neutron scattering and inelastic X-ray scattering in different thermodynamic conditions are reported

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Section: Fast Soundsupporting

confidence: 81%

X-ray and Neutron Scattering of Water

et al. 2016

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“…5b) and are located close to the surface of residues identified as conserved micro-switches in rhodopsin. Previous experimental63 and computational5364 investigations on protein hydration water have identified a peak at a similar frequency and in these instances it was described as a localized, water relaxation mode that fosters the propagation of collective, vibrational oscillations in hydrated proteins. The localized solvent-relaxation (LSR) mode would be expected to be a negligible component of the hydration water in rhodopsin and it is unlikely that such a mode would be detected experimentally.…”

Section: Resultsmentioning

confidence: 86%

Vibrational resonance, allostery, and activation in rhodopsin-like G protein-coupled receptors

Woods

Dutta

Klein‐Seetharaman

2016

Sci Rep

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G protein-coupled receptors are a large family of membrane proteins activated by a variety of structurally diverse ligands making them highly adaptable signaling molecules. Despite recent advances in the structural biology of this protein family, the mechanism by which ligands induce allosteric changes in protein structure and dynamics for its signaling function remains a mystery. Here, we propose the use of terahertz spectroscopy combined with molecular dynamics simulation and protein evolutionary network modeling to address the mechanism of activation by directly probing the concerted fluctuations of retinal ligand and transmembrane helices in rhodopsin. This approach allows us to examine the role of conformational heterogeneity in the selection and stabilization of specific signaling pathways in the photo-activation of the receptor. We demonstrate that ligand-induced shifts in the conformational equilibrium prompt vibrational resonances in the protein structure that link the dynamics of conserved interactions with fluctuations of the active-state ligand. The connection of vibrational modes creates an allosteric association of coupled fluctuations that forms a coherent signaling pathway from the receptor ligand-binding pocket to the G-protein activation region. Our evolutionary analysis of rhodopsin-like GPCRs suggest that specific allosteric sites play a pivotal role in activating structural fluctuations that allosterically modulate functional signals.

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“…The slope of the plot,

P \frac{f_{P A D}}{V_{m e s o}} = 0.031

, allows estimation of V meso , with the assumption of a comparable solvation interaction of TEMPOL with each phase ( P =1), and an estimated value of f PAD . An average thickness (Δ r ) of the water layer around a protein that displays dynamical properties distinct from bulk water has been identified as ~10 Å, 5–6 with an upper limit of 20 Å. 4 The accessible surface area of the EAL oligomer is 1.27΄10 5 Å 2 , as determined by using ASAView.…”

Section: Discussionmentioning

confidence: 99%

“…1–3 Reciprocally, water dynamics influenced by protein have been distinguished from bulk water at distances of up to 20 Å from the protein surface, 4 and computational studies suggest mechanistic features of distinct, protein-influenced water dynamics extending to 10 Å. 5–6 When water is removed by drying, protein fluctuations are lowered in frequency and suppressed in amplitude. 7–8 Restriction of solvent water motions, by lowering temperature to solidify the solvent, also suppresses protein fluctuations and eliminates function not associated with diffusive exchange of substrates/products.…”

Section: Introductionmentioning

confidence: 99%

Mesodomain and Protein-Associated Solvent Phases with Temperature-Tunable (200–265 K) Dynamics Surround Ethanolamine Ammonia-Lyase in Globally Polycrystalline Aqueous Solution Containing Dimethyl Sulfoxide

Nforneh

Warncke

2017

J. Phys. Chem. B

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Electron paramagnetic resonance (EPR) spectroscopy of the spin probe, TEMPOL, is used to resolve solvent phases that surround the ethanolamine ammonia-lyase (EAL) protein from Salmonella typhimurium at low-temperature (T) in frozen, globally polycrystalline aqueous solution, and to report on the T-dependence of their detectably rigid and fluid states. EAL plays a role in human gut microbiome-based disease conditions, and physical-chemical studies provide insight into protein structure and mechanism, toward potential therapeutics. Temperature dependences of the rotational correlation times (τc; detection range, 10−11≤τc ≤10−7 s) and corresponding weights of TEMPOL tumbling components from 200 to 265 K in the presence of EAL, are measured in two frozen systems: (1) water-only, and (2) 1% v/v dimethylsulfoxide (DMSO). In the water-only condition, a protein-vicinal solvent component detectably fluidizes at 230 K, and melts the surrounding ice-crystalline region with increasing T, creating a bounded, relatively high-viscosity aqueous solvent domain, up to 265 K. In the EAL, 1% DMSO condition, two distinct concentric solvent phases are resolved around EAL: protein-associated domain (PAD) and mesodomain. The DMSO-aqueous mesodomain fluidizes at 200 K, followed by PAD fluidization at 210 K. The interphase-dynamical coupling is consistent with the spatial arrangement and significant contact areas of the phases, indicated by the experimentally-determined mean volume ratio, V(mesodomain):V(PAD):V(protein) = 0.5:0.3:1.0. The results provide a rationale for native chemical reactions of EAL at T<250 K, and an advance toward precise control of solvent dynamics as a tunable parameter for quantifying the coupling between solvent and protein fluctuations and chemical reaction steps in EAL, and other enzymes.

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On the Coupling between the Collective Dynamics of Proteins and Their Hydration Water

Cited by 61 publications

References 49 publications

X-ray and Neutron Scattering of Water

X-ray and Neutron Scattering of Water

Vibrational resonance, allostery, and activation in rhodopsin-like G protein-coupled receptors

Mesodomain and Protein-Associated Solvent Phases with Temperature-Tunable (200–265 K) Dynamics Surround Ethanolamine Ammonia-Lyase in Globally Polycrystalline Aqueous Solution Containing Dimethyl Sulfoxide

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