Non-Brownian transport in complex systems

Dynamics at the protein-water interface from 17O spin relaxation in deeply supercooled solutions

Most of the decisive molecular events in biology take place at the protein-water interface. The dynamical properties of the hydration layer are therefore of fundamental importance. To characterize the dynamical heterogeneity and rotational activation energy in the hydration layer, we measured the (17)O spin relaxation rate in dilute solutions of three proteins in a wide temperature range extending down to 238 K. We find that the rotational correlation time can be described by a power-law distribution with exponent 2.1-2.3. Except for a small fraction of secluded hydration sites, the dynamic perturbation in the hydration layer is the same for all proteins and does not differ in any essential way from the hydration shell of small organic solutes. In both cases, the dynamic perturbation factor is <2 at room temperature and exhibits a maximum near 262 K. This maximum implies that, at low temperatures, the rate of water molecule rotation has a weaker temperature dependence in the hydration layer than in bulk water. We attribute this difference to the temperature-independent constraints that the protein surface imposes on the water H-bond network. The free hydration layer studied here differs qualitatively from confined water in solid protein powder samples.

Water/hydrocarbon interfaces: effect of hydrocarbon branching on single-molecule relaxation

Water/hydrocarbon interfaces are studied using molecular dynamics simulations in order to understand the effect of hydrocarbon branching on the dynamics of the system at and away from the interface. A recently proposed procedure for studying the intrinsic structure of the interface in such systems is utilized, and dynamics are probed in the usual laboratory frame as well as the intrinsic frame. The use of these two frames of reference leads to insight into the effect of capillary waves at the interface on dynamics. The systems were partitioned into zones with a width of 5 A, and a number of quantities of dynamical relevance, namely, the residence times, mean squared displacements, the velocity auto correlation functions, and orientational time correlations for molecules of both phases, were calculated in the laboratory and intrinsic frames at and away from the interface. For the aqueous phase, translational motion is found to be (a) diffusive at long times and not anomalous as in proteins or micelles, (b) faster at the interface than in the bulk, and (c) faster upon reduction of the effect of capillary waves. The rotational motion of water is (a) more anisotropic at the interface than in the bulk and (b) dependent on the orientation of the covalent O-H bond with respect to the plane of the interface. The effect of hydrocarbon branching on aqueous dynamics was found to be small, a result similar to the effect on the interfacial water structure. The hydrocarbon phase shows a larger variation for all dynamical probes, a trend consistent with their interfacial structure.

How protein surfaces induce anomalous dynamics of hydration water

Water around biomolecules slows down with respect to pure water, and both rotation and translation exhibit anomalous time dependence in the hydration shell. The origin of such behavior remains elusive. We use molecular dynamics simulations of water dynamics around several designed protein models to establish the connection between the appearance of the anomalous dynamics and water-protein interactions. For the first time we quantify the separate effect of protein topological and energetic disorder on the hydration water dynamics. When a static protein structure is simulated, we show that both types of disorder contribute to slow down water diffusion, and that allowing for protein motion, increasing the spatial dimensionality of the interface, reduces the anomalous character of hydration water. The rotation of water is, instead, altered by the energetic disorder only; indeed, when electrostatic interactions between the protein and water are switched off, water reorients even faster than in the bulk. The dynamics of water is also related to the collective structure--à voir the hydrogen bond (H-bond) network--formed by the solvent enclosing the protein surface. We show that, as expected for a full hydrated protein, when the protein surface offers pinning sites (charged or polar sites), the superficial water-water H-bond network percolates throughout the whole surface, hindering the water diffusion, whereas it does not when the protein surface lacks electrostatic interactions with water and the water diffusion is enhanced.

Anomalous behavior of water around sodium dodecyl sulphate micelles

The dynamics, structural properties, and energetics of hydration water around a sodium dodecyl sulphate micelle have been investigated using molecular dynamics simulation. A clear revelation of the slow dynamics of the hydration water has been made by separate measurements of the rotational and translational properties. Calculated diffusion coefficients fall within the range of experimentally observed quantities. The water-micelle head group (MHG) hydrogen bond is more stable (by an amount approximately 7.0 kcal/mol) compared to the water-water hydrogen bond. The difference in stability of the water monomers forming different numbers of hydrogen bonds (n=0,1,2) with the MHG has clearly been shown from the analyses of their rotational relaxation, residence times, as well as the energy of interaction with different components of the system. The singly hydrogen-bonded water species is the most abundant and stable. The entropy plays the key role in controlling the relative abundance of the different species.

Structure, dynamics, and energetics of water at the surface of a small globular protein: a molecular dynamics simulation

The dynamics of water around a biomolecular surface has attracted a lot of attention recently. We report here protein-solvent simulation studies of the small globular protein ubiquitin (human). The simulations are run unconstrained, without freezing the bonds. The mean square displacements of the water oxygen atoms show a sublinear trend with time. The diffusion coefficient data indicate that the water in the first hydration layer behaves like water at a temperature that is roughly 12 degrees C lower than the average temperature of the system (27 degrees C). Both the dipolar second-rank relaxation and the survival time correlation function of the water layers show two decay constants, indicating contributions from fast and slow dynamics. A calculation of the interaction energy between the water layers and protein indicates that the interaction energy sharply decreases beyond 4 A from the protein surface.

Nucleosome repositioning via loop formation

Active (catalyzed) and passive (intrinsic) nucleosome repositioning is known to be a crucial event during the transcriptional activation of certain eukaryotic genes. Here we consider theoretically the intrinsic mechanism and study in detail the energetics and dynamics of DNA-loop-mediated nucleosome repositioning, as previously proposed by earlier works. The surprising outcome of the present study is the inherent nonlocality of nucleosome motion within this model-being a direct physical consequence of the loop mechanism. On long enough DNA templates the longer jumps dominate over the previously predicted local motion, a fact that contrasts simple diffusive mechanisms considered before. The possible experimental outcome resulting from the considered mechanism is predicted, discussed, and compared to existing experimental findings.

Glasslike dynamical behavior of the plastocyanin hydration water

The dynamical behavior of water around plastocyanin has been investigated in a wide temperature range by molecular dynamics simulation. The mean square displacements of water oxygen atoms show, at long times, a t(alpha) trend for all temperatures. Below 150 K, alpha is constant and equal to 1; at higher temperatures it drops to a value significantly smaller than 1, and thereafter decreases with increasing temperature. The occurrence of such an anomalous diffusion matches the onset of the dynamical transition observed in the protein. The intermediate scattering function of water is characterized, at high temperature, by a stretched exponential decay evolving, at low temperature, toward a two step relaxation behavior, which becomes more evident on increasing the exchanged wave vector q. Both the mean square displacements and the intermediate scattering functions show, beyond the ballistic regime, a plateau, which progressively extends for longer times as long as the temperature is lowered, such behavior reflecting trapping of water molecules within a cage formed by the nearest neighbors. At low temperature, a low frequency broad inelastic peak is observed in the dynamical structure factor of hydration water; such an excess of vibrational modes being reminiscent of the boson peak, characteristic of disordered, amorphous systems. All these features, which are typical of complex systems, can be traced back to the glassy character of the hydration water and suggest a dynamical coupling occurring at the macromolecule-solvent interface.

A synthetic picture of intramolecular dynamics of proteins. Towards a contemporary statistical theory of biochemical processes

An increasing body of experimental evidence indicates the slow character of internal dynamics of native proteins. The important consequence of this is that theories of chemical reactions, used hitherto, appear inadequate for description of most biochemical reactions. Construction of a contemporary, truly advanced statistical theory of biochemical processes will need simple but realistic models of microscopic dynamics of biomolecules. In this review, intended to be a contribution towards this direction, three topics are considered. First, an intentionally simplified picture of dynamics of native proteins which emerges from recent investigations is presented. Fast vibrational modes of motion, of periods varying from 10(-14) to 10(-11) s, are contrasted with purely stochastic conformational transitions. Significant evidence is adduced that the relaxation time spectrum of the latter spreads in the whole range from 10(-11) to 10(5) s or longer, and up to 10(-7) s it is practically quasi-continuous. Next, the essential ideas of the theory of reaction rates based on stochastic models of intramolecular dynamics are outlined. Special attention is paid to reactions involving molecules in the initial conformational substrates confirmed to the transition state, which is realized in actual experimental situations. And finally, the two best experimentally justified classes of models of conformational transition dynamics, symbolically referred to as "protein glass" and "protein machine", are described and applied to the interpretation of a few simple biochemical processes, perhaps the most important result reported is the demonstration of the possibility of predominance of the short initial condition-dependent stage of protein involved reactions over the main stage described by the standard kinetics. This initial stage, and not the latter, is expected to be responsible for the coupling of component reactions in the complete enzymatic cycles as well as more complex processes of biological free energy transduction.