A. Orecchini

Translational diffusion of hydration water correlates with functional motions in folded and intrinsically disordered proteins

Hydration water is the natural matrix of biological macromolecules and is essential for their activity in cells. The coupling between water and protein dynamics has been intensively studied, yet it remains controversial. Here we combine protein perdeuteration, neutron scattering and molecular dynamics simulations to explore the nature of hydration water motions at temperatures between 200 and 300 K, across the so-called protein dynamical transition, in the intrinsically disordered human protein tau and the globular maltose binding protein. Quasi-elastic broadening is fitted with a model of translating, rotating and immobile water molecules. In both experiment and simulation, the translational component markedly increases at the protein dynamical transition (around 240 K), regardless of whether the protein is intrinsically disordered or folded. Thus, we generalize the notion that the translational diffusion of water molecules on a protein surface promotes the large-amplitude motions of proteins that are required for their biological activity.

Collective dynamics of protein hydration water by brillouin neutron spectroscopy.

By a detailed experimental study of THz dynamics in the ribonuclease protein, we could detect the propagation of coherent collective density fluctuations within the protein hydration shell. The emerging picture indicates the presence of both a dispersing mode, traveling with a speed greater than 3000 m/s, and a nondispersing one, characterized by an almost constant energy of 6-7 meV. In agreement with molecular dynamics simulations [Phys. Rev. Lett. 2002, 89, 275501], the features of the dispersion curves closely resemble those observed in pure liquid water [Phys. Rev. E: Stat. Phys., Plasmas, Fluids, Relat. Interdiscip. Top. 2004, 69, 061203]. On the contrary, the observed damping factors are much larger than in bulk water, with the dispersing mode becoming overdamped at Q = 0.6 A(-1) already. Such novel experimental findings are discussed as a dynamic signature of the disordering effect induced by the protein surface on the local structure of water.

Vibrational Collective Dynamics of Dry Proteins in the Terahertz Region

The coherent density fluctuations of a perdeuterated dry protein have been studied by Brillouin neutron spectroscopy. Besides a nearly wavevector-independent branch located around 5 meV, a propagating mode with a linear trend at low wavevector Q is revealed. The corresponding speed of 3780 ± 130 m/s is definitely higher than that of hydrated proteins. Above Q = 0.8 Å(-1), this mode becomes overdamped, with lifetimes shorter than 0.1 ps, in fashion similar to glassy materials. The present results indicate that dry proteins sustain coherent density fluctuations in the THz frequency regime. The trend of the longitudinal modulus indicates that in this frequency range dry biomolecules are more rigid than hydrated proteins.

Coupled relaxations at the protein-water interface in the picosecond time scale.

The spectral behaviour of a protein and its hydration water has been investigated through neutron scattering. The availability of both hydrogenated and perdeuterated samples of maltose-binding protein (MBP) allowed us to directly measure with great accuracy the signal from the protein and the hydration water alone. Both the spectra of the MBP and its hydration water show two distinct relaxations, a behaviour that is reminiscent of glassy systems. The two components have been described using a phenomenological model that includes two Cole–Davidson functions. In MBP and its hydration water, the two relaxations take place with similar average characteristic times of approximately 10 and 0.2 ps. The common time scales of these relaxations suggest that they may be a preferential route to couple the dynamics of the water hydrogen-bond network around the protein surface with that of protein fluctuations.

Quasielastic neutron scattering investigation of the pressure dependence of molecular motions in liquid water

We report on a high-resolution, high-statistics, quasielastic neutron scattering (QENS) experiment on liquid water, aimed at accurately measuring the pressure dependence of the single-particle dynamic response function at low wave vector transfers, namely, from 0.26 to 1.32 A(-1). High-pressure QENS data were collected along the T = 268 K isothermal path over the rather extended pressure range of 80 up to 350 MPa, a thermodynamic region so far unexplored by this microscopic technique. The analysis of the measured line shapes enabled us to draw a consistent picture of the wave vector and pressure dependences of the diffusion mechanisms in liquid water, against which the most recent models for water dynamics can be checked. In close similarity with the case of supercooled water, the relaxing-cage model was found to provide a quantitatively more accurate description of the molecular motions and their pressure evolution in liquid water.

Collective density fluctuations of DNA hydration water in the time-window below 1 ps

The coherent density fluctuations propagating through DNA hydration water were studied by neutron scattering spectroscopy. Two collective modes were found to be sustained by the aqueous solvent: a propagating excitation, characterised by a speed of about 3500 m/s, and another one placed at about 6 meV. These results globally agree with those previously found for the coherent excitations in bulk water, although in DNA hydration water the speed of propagating modes is definitely higher than that of the pure solvent. The short-wavelength collective excitations of DNA hydration water are reminiscent of those observed in protein hydration water and in the amorphous forms of ice.

Collective Dynamics of Intracellular Water in Living Cells

Water dynamics plays a fundamental role for the fulfillment of biological functions in living organisms. Decades of hydrated protein powder studies have revealed the peculiar dynamical properties of hydration water with respect to pure water, due to close coupling interactions with the macromolecule. In such a framework, we have studied coherent collective dynamics in protein and DNA hydration water. State-of-the-art neutron instrumentation has allowed us to observe the propagation of coherent density fluctuations within the hydration shell of the biomolecules. The corresponding dispersion curves resulted to be only slightly affected by the coupling with the macromolecules. Nevertheless, the effects of the interaction appeared as a marked increase of the mode damping factors, which suggested a destructuring of the water hydrogen-bond network. Such results were interpreted as the signature of a glassy dynamical character of macromolecule hydration water, in agreement with indications from measurements of the density of vibrational states. Extending the investigations to living organisms at physiological conditions, we present here an in-vivo study of collective dynamics of intracellular water in Escherichia coli cells. The cells and water were fully deuterated to minimise the incoherent neutron scattering background. The water dynamics observed in the living cells is discussed in terms of the dynamics of pure bulk water and that of hydration water measured in powder samples.

Water dynamics as affected by interaction with biomolecules and change of thermodynamic state: a neutron scattering study

The dynamics of water as subtly perturbed by both the interaction with biomolecules and the variation of temperature and pressure has been investigated via neutron scattering spectroscopy. A measurement of inelastic neutron scattering devoted to the study of the coherent THz dynamics of water in a water-rich mixture with DNA (hydration level of 1 g DNA/15 g D(2)O) at room temperature is reported. The DNA hydration water coherent dynamics is characterised by the presence of collective modes, whose dispersion relations are similar to those observed in bulk water. These dispersion relations are well described by the interaction model developed in the case of bulk water, and the existence of a fast sound is experimentally demonstrated. The behaviour of the collective water dynamics was complemented by studying the single-particle dynamics of bulk water along the isotherm T = 298 K in the pressure range 0.1-350 MPa by means of incoherent scattering. This experiment is an attempt to simulate the change of the water molecular arrangement due to the interaction with DNA, by increasing the pressure as the presence of the biomolecule produces an increase in the density. An anomaly is found in the behaviour of the relaxation time derived from the quasi-elastic scattering signal, which can be related to the hypothetical second critical point in water. This anomaly and the transition from slow to fast sound take place in the same Q range, thus suggesting that the two phenomena could be related at some microscopic level.

Coupled thermal fluctuations of proteins and protein hydration water on the picosecond timescale

The mean square displacements (MSD) of a model protein, the maltose binding protein, and its hydration water have been estimated from the elastic neutron scattering intensity measured on the IN5 time-of-flight spectrometer. The availability of the protein in both fully deuterated and hydrogenated form allowed reliable separation of the contribution of the solvent interacting with the biomolecule from that of the hydrated biomolecule. The thermal fluctuations of hydration water and protein activate in the same temperature range between 200–220 K. This result supports a picture where the dynamical coupling between the biomolecule and the solvent is already effective in the picosecond timescale. A quantitative agreement of the MSD, with values from molecular dynamics simulations, is found.

Dynamics of water confined in fuel cell Nafion membranes containing zirconium phosphate nanofiller

A quasielastic neutron scattering investigation, to study the single particle dynamics of water absorbed in a Nafion/zirconium phosphate composite membrane hydrated at a saturation value, is herewith presented. The measurements were done on samples hydrated with both H2O and D2O to properly select the spectral contribution of the confined water. Both the elastic incoherent structure factor (EISF) and the linewidth of the quasielastic component are evaluated as a function of the momentum transfer. Their trend suggests that the motion of the system hydrogen atoms can be schematized as a random jumping inside a confining spherical region, which can be related to the boundaries of the cluster that water molecules form around the sulfonic and phosphate acid sites. The size of such a region, the characteristic time necessary to explore the region and the number of mobile protons involved in this motion are similar to those estimated for water absorbed in a simple Nafion membrane at a saturation water content. Also the calculated jump diffusion coefficient resembles that of water confined in a simple Nafion membrane, and both are consistent with the value of bulk water. The results indicate that the dynamical behaviour of water in Nafion membranes is nearly unaffected by the presence of zirconium phosphate nanoparticles.