相关论文: The structural order of protein hydration water
While a monomer of the ubiquitous hormone insulin is the biologically active form in the human body, its hexameric assembly acts as an efficient storage unit. However, the role of water molecules in the structure, stability and dynamics of…
We present results of molecular dynamics simulations of water confined in a silica pore. A cylindrical cavity is created inside a vitreous silica cell with geometry and size similar to the pores of real Vycor glass. The simulations are…
The resistance of hydrogen-bond networks to ambient flow in water produces viscoelectric stresses and contributes to electrostrictive pressure. Within Onsager's nonequilibrium thermodynamic framework, a lattice-gas description of aqueous…
Confinement can modify the dynamics, the thermodynamics and the structural properties of liquid water, the prototypical anomalous liquid. By considering a general anomalous liquid, suitable for globular proteins, colloids or liquid metals,…
Interpretation of the X-ray spectra of water as evidence for its asymmetric structure has challenged the conventional symmetric nearly-tetrahedral model and initiated an intense debate about the order and symmetry of the hydrogen bond…
Hydrophobicity is thought to be one of the primary forces driving the folding of proteins. On average, hydrophobic residues occur preferentially in the core, whereas polar residues tends to occur at the surface of a folded protein. By…
Path-integral molecular dynamics simulations and electronic structure-based energy decomposition analysis (EDA) are employed to connect hydrogen bond (H-bond) strength, its asymmetry, and the total delocalization energy at the water/air…
Experiments in bulk water confirm the existence of two local arrangements of water molecules with different densities, but, because of inevitable freezing at low temperature $T$, can not ascertain whether the two arrangements separate in…
Two-dimensional infrared spectroscopy experiments have presented new results regarding the dynamics of the hydrated excess proton (aka <q>hydronium</q> cation solvated in water). It has been suggested by these experiments that the hydrated…
We discern hydration geometries around the sugar-phosphate-backbone of an RNA double helix at the molecular level. RNA disordering upon melting is connected with a transition from ordered water structures towards local phosphate group…
Exploring and understanding the protein-folding problem has been a long-standing challenge in molecular biology. Here, using molecular dynamics simulation, we reveal how parallel distributed adjacent planar peptide groups of unfolded…
We refine a protein model that reproduces fundamental aspects of protein thermodynamics. The model exhibits two transitions, hot and cold unfolding. The number of relevant parameters is reduced to three: 1) binding energy of folding…
Water confinement inside a carbon nanotube (CNT) has been one of the most exciting subjects of both experimental and theoretical interest. Most of the previous studies, however, considered CNT structures with simple cylindrical shapes. In…
The contribution of a specific hydrogen bond in apoflavodoxin to protein stability is investigated by combining theory, experiment and simulation. Although hydrogen bonds are major determinants of protein structure and function, their…
The splitting of the principal peak in the structure factor of liquid water is commonly interpreted as evidence of a competition between two distinct local environments. Here, we show that this peak splitting arises from medium-range…
During compression of a water dimer calculated with high-precision first-principles methods, the trends of H-bond and O-H bond lengths show quantum effect of the electronic structure. We found that the H-bond length keeps decreasing, while…
The existence of water dimers in equilibrium water vapor at room temperature and their anomalous properties revealed by recent studies suggest the benchmark role of water dimer in both experiment and theory. However, there has been a…
We present a coarse-grained lattice model to study the influence of water on the recognition process of two rigid proteins. The basic model is formulated in terms of the hydrophobic effect. We then investigate several modifications of our…
The influence of three well-known disaccharides, namely trehalose, maltose and sucrose, on some structural and dynamical properties of lysozyme has been investigated by means of molecular dynamics computer simulations in the 37-60 wt %…
Hydrogen bonds are typically treated as sufficiently localized directional intermolecular bonds, in which dispersion and electrostatic contributions can be distinguished. However, being formed chiefly due to the overlapping of p orbitals of…