Vibrational Density of States of Hydration Water at Biomolecular Sites: Hydrophobicity Promotes Low Density Amorphous Ice Behavior

Russo, Daniela; Teixeira, J.; Kneller, Larry R.; Copley, J. R. D.; Ollivier, Jacques; Perticaroli, Stefania; Pellegrini, E.; Ma, González

doi:10.1021/ja109610f

Cited by 53 publications

(56 citation statements)

References 40 publications

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“…Vibrational density of states of supercooled water measured on the IN6 spectrometer (Institut Laue-Langevin, Grenoble) 136 and water at the interface with maltose binding protein (MBP) 16,147 , , NALMA and NAGMA molecules 17 , measured on the IN5 spectrometer (Institut Laue-Langevin, Grenoble). The VDOS curves have been normalised to the first inelastic peak at 6 meV.…”

Section: Intermolecular Vibrationsmentioning

confidence: 99%

“…At low-temperature water at the interface with proteins 147 or with moieties with a more or less predominant hydrophobic character, such as N-acetyl-leucine-methylamide (NALMA) and Nacetyl-glycinemethylamide (NAGMA) respectively 17 , shows a HBB band whose shape is very similar to amorphous ice and quite different from the crystalline phase. In general, the HBB peak seems to be quite sensitive to the local topology of water molecules.…”

Section: Intermolecular Vibrationsmentioning

confidence: 99%

“…Several review articles have reported on water structure and dynamics 5,6,7,8,9,10 , but the recent advances in instrumentation for x-ray diffraction both at synchrotron and Linac Coherent Light Source (LCLS) facilities, and for neutron diffusion at reactor sources and pulsed sources facilities provide nowadays extremely accurate data on water structure 11 , and gave access to previously unexplored states 12,13 , thermodynamic conditions 12,14,3,15 , and environments 16,17,18 . In particular, the present article reviews the most recent x-ray and neutron diffraction results about the structure of liquid water and amorphous ice.…”

Section: Introductionmentioning

confidence: 99%

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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: Intermolecular Vibrationsmentioning

confidence: 99%

Section: Intermolecular Vibrationsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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X-ray and Neutron Scattering of Water

et al. 2016

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“…(19) in terms of the water and protein components is more non-trivial and requires considering cross-correlations between the protein and water fluctuations. The individual components λ var p and λ var w are often found to be significantly larger than the total λ var .…”

Section: Electro-elastic Fluctuations Of the Protein-water Interfacementioning

confidence: 99%

“…10,11 Water is known to orient its dipoles parallel to the dividing surface at hydrophobic patches 12,13 and flip its dipoles inward or outward depending on the surface charged group. [14][15][16] These heterogeneously polarized, heterogeneously compressed, [17][18][19] and potentially mutually frustrated interfacial water domains merge into an interfacial sub-ensemble involving several hundreds of water molecules, with its properties quite distinct from the bulk. 20,21 The bulk perspective does not apply just to the protein part of the thermal bath, but to the hydration shell as well.…”

Section: Introductionmentioning

confidence: 99%

Protein electron transfer: Dynamics and statistics

Matyushov

2013

The Journal of Chemical Physics

121

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A statistical-mechanical analysis on the hypermobile water around a large solute with high surface charge density J. Chem. Phys. 130, 014707 (2009) Electron transfer between redox proteins participating in energy chains of biology is required to proceed with high energetic efficiency, minimizing losses of redox energy to heat. Within the standard models of electron transfer, this requirement, combined with the need for unidirectional (preferably activationless) transitions, is translated into the need to minimize the reorganization energy of electron transfer. This design program is, however, unrealistic for proteins whose active sites are typically positioned close to the polar and flexible protein-water interface to allow inter-protein electron tunneling. The high flexibility of the interfacial region makes both the hydration water and the surface protein layer act as highly polar solvents. The reorganization energy, as measured by fluctuations, is not minimized, but rather maximized in this region. Natural systems in fact utilize the broad breadth of interfacial electrostatic fluctuations, but in the ways not anticipated by the standard models based on equilibrium thermodynamics. The combination of the broad spectrum of static fluctuations with their dispersive dynamics offers the mechanism of dynamical freezing (ergodicity breaking) of subsets of nuclear modes on the time of reaction/residence of the electron at a redox cofactor. The separation of time-scales of nuclear modes coupled to electron transfer allows dynamical freezing. In particular, the separation between the relaxation time of electro-elastic fluctuations of the interface and the time of conformational transitions of the protein caused by changing redox state results in dynamical freezing of the latter for sufficiently fast electron transfer. The observable consequence of this dynamical freezing is significantly different reorganization energies describing the curvature at the bottom of electron-transfer free energy surfaces (large) and the distance between their minima (Stokes shift, small). The ratio of the two reorganization energies establishes the parameter by which the energetic efficiency of protein electron transfer is increased relative to the standard expectations, thus minimizing losses of energy to heat. Energetically efficient electron transfer occurs in a chain of conformationally quenched cofactors and is characterized by flattened free energy surfaces, reminiscent of the flat and rugged landscape at the stability basin of a folded protein.

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THz frequency spectrum of protein–solvent interaction energy using a recurrence plot‐based Wiener–Khinchin method

Karain

2016

Proteins

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The dynamics of a protein and the water surrounding it are coupled via nonbonded energy interactions. This coupling can exhibit a complex, nonlinear, and nonstationary nature. The THz frequency spectrum for this interaction energy characterizes both the vibration spectrum of the water hydrogen bond network, and the frequency range of large amplitude modes of proteins. We use a Recurrence Plot based Wiener-Khinchin method RPWK to calculate this spectrum, and the results are compared to those determined using the classical auto-covariance-based Wiener-Khinchin method WK. The frequency spectra for the total nonbonded interaction energy extracted from molecular dynamics simulations between the β-Lactamase Inhibitory Protein BLIP, and water molecules within a 10 Å distance from the protein surface, are calculated at 150, 200, 250, and 310 K, respectively. Similar calculations are also performed for the nonbonded interaction energy between the residues 49ASP, 53TYR, and 142PHE in BLIP, with water molecules within 10 Å from each residue respectively at 150, 200, 250, and 310 K. A comparison of the results shows that RPWK performs better than WK, and is able to detect some frequency data points that WK fails to detect. This points to the importance of using methods capable of taking the complex nature of the protein-solvent energy landscape into consideration, and not to rely on standard linear methods. In general, RPWK can be a valuable addition to the analysis tools for protein molecular dynamics simulations. Proteins 2016; 84:1549-1557. © 2016 Wiley Periodicals, Inc.

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Vibrational Density of States of Hydration Water at Biomolecular Sites: Hydrophobicity Promotes Low Density Amorphous Ice Behavior

Cited by 53 publications

References 40 publications

X-ray and Neutron Scattering of Water

X-ray and Neutron Scattering of Water

Protein electron transfer: Dynamics and statistics

THz frequency spectrum of protein–solvent interaction energy using a recurrence plot‐based Wiener–Khinchin method

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