Bulk and interfacial liquid water as a transient network

Graph-based analysis of H-bond networks and unsupervised learning reveal conformational coupling in prion peptide segments

In this study, we employed a comprehensive computational approach to investigate the physical chemistry of the water networks surrounding hydrated peptide segments, as derived from molecular dynamics simulations. Our analysis uncovers a complex interplay of direct and water-mediated hydrogen bonds that intricately weave through the peptides. We demonstrate that these hydrogen bond networks encode critical information about the peptides' conformational behavior, with the dimensionality of these networks showing sensitivity to the peptides' conformations. Additionally, we estimated the free-energy landscape of the peptides across various conformations, revealing that their structures are predominantly characterized by unfolded, partially folded, and folded configurations, resulting in broad and rugged free-energy surfaces due to the numerous degrees of freedom contributed by the surrounding solvent. Importantly, the structured nature of this free-energy landscape becomes obscured when conventional collective variables, such as the number of hydrogen bonds, are used. Our findings provide new insights into the molecular mechanisms that couple protein and solvent degrees of freedom, highlighting their significance in the functioning of biological systems.

Dipolar Dispersion Forces in Water-Methanol Mixtures: Enhancement of Water Interactions upon Dilution Drives Self-Association

Mixtures of short-chain alcohols and water produce anomalous thermodynamic and structural quantities, including molecular segregation into water-rich and alcohol-rich components. Herein, we used molecular dynamics simulations with polarizable models to investigate interactions that could drive the self-association of water molecules in mixtures with methanol (MeOH). As water was diluted with MeOH, significant changes in the distribution of molecules and solvation properties occurred, where water exhibited a clear preference for self-association. When common structural quantities were analyzed, it was found that there was a clear reduction in water-water hydrogen bonding and tetrahedral order (both in terms of typical bulk behavior), contrary to the observed water self-association. However, when dipolar dispersion forces between all molecules as a function of system composition were analyzed, it was found that water-water dipolar interactions became significantly stronger with dilution (6-fold stronger interaction in 75% MeOH compared to 0% MeOH). This was only observed for water, where MeOH-MeOH interactions became weaker as the systems were more dilute in MeOH. These forces result from specific dipole orientations, likely occurring to adopt lower energy configurations (i.e., head-to-tail or antiparallel). For water, this may result from lost other interactions (e.g., hydrogen bonding), leading to more rotational freedom between the dipole moments. These intriguing changes in dipolar interactions, which directly result from structural changes, can therefore explain, in part, the driving force for water self-association in MeOH-water mixtures.

Effect of Hydrogen Bonds on the Dielectric Properties of Interfacial Water

The dielectric constant for water is reduced under confinement. Although this phenomenon is well known, the underlying physical mechanism for the reduction is still in debate. In this work, we investigate the effect of the orientation of hydrogen bonds on the dielectric properties of confined water using molecular dynamics simulations. We find a reduced rotational diffusion coefficient for water molecules close to the solid surface. The reduced rotational diffusion arises due to the hindered rotation away from the plane parallel to the channel walls. The suppressed rotation in turn affects the orientational polarization of water, leading to a low value for the dielectric constant at the interface. We attribute the constrained out-of-plane rotation to originate from a higher density of planar hydrogen bonds formed by the interfacial water molecules.

Perturbation of hydration layer in solvated proteins by external electric and electromagnetic fields: Insights from non-equilibrium molecular dynamics

Given the fundamental role of water in governing the biochemistry of enzymes, and in regulating their wider biological activity (e.g., by local water concentration surrounding biomolecules), the influence of extraneous electric and electromagnetic (e/m) fields thereon is of central relevance to biophysics and, more widely, biology. With the increase in levels of local and atmospheric microwave-frequency radiation present in modern life, as well as other electric-field exposure, the impact upon hydration-water layers surrounding proteins, and biomolecules generally, becomes a particularly pertinent issue. Here, we present a (non-equilibrium) molecular-dynamics-simulation study on a model protein (hen egg-white lysozyme) hydrated in water, in which we determine, inter alia, translational self-diffusivities for both hen egg-white lysozyme and its hydration layer together with relaxation dynamics of the hydrogen-bond network between the protein and its hydration-layer water molecules on a residue-per-residue basis. Crucially, we perform this analysis both above and below the dynamical-transition temperature (at ∼220 K), at 300 and 200 K, respectively, and we compare the effects of external static-electric and e/m fields with linear-response-régime (r.m.s.) intensities of 0.02 V/Å. It was found that the translational self-diffusivity of hen egg-white lysozyme and its hydration-water layer are increased substantially in static fields, primarily due to the induced electrophoretic motion, whilst the water-protein hydrogen-bond-network-rearrangement kinetics can also undergo rather striking accelerations, primarily due to the enhancement of a larger-amplitude local translational and rotational motion by charged and dipolar residues, which serves to promote hydrogen-bond breakage and re-formation kinetics. These external-field effects are particularly evident at 200 K, where they serve to induce the protein- and solvation-layer-response effects redolent of dynamical transition at a lower temperature (∼200 K) vis-à-vis the zero-field case (∼220 K).

How water mediates the long-range interactions between remote protein molecules

A mechanism of the influence of the presence of one protein molecule on the internal dynamics of another is proposed.