Related papers: Effect of hydrogen bonds on protein stability
The effect of glycerol, water and glycerol-water binary mixtures on the structure and dynamics of biomolecules has been well studied. However, a lot remains to be learned about the effect of varying glycerol concentration and temperature on…
Hydrogen bonding is modeled in terms of virtual exchange of protons between water molecules. A simple lattice model is analyzed, using ideas and techniques from the theory of correlated electrons in metals. Reasonable parameters reproduce…
We have performed Molecular Dynamics simulations of ectoine, hydroxyectoine and urea in explicit solvent. Special attention has been spent on the local surrounding structure of water molecules. Our results indicate that ectoine and…
Equilibrium properties of hydrogen-helium mixtures under thermodynamic conditions found in the interior of giant gas planets are studied by means of density functional theory molecular dynamics simulations. Special emphasis is placed on the…
Numerical simulations of hydrated proteins show that protein hydration shells are polarized into a ferroelectric cluster with a large magnitude of its average dipole moment. The emergence of this new mesophase dramatically alters the…
A simple model of globular proteins which incorporates anisotropic attractions is proposed. It is closely related to models used to model simple hydrogen-bonding molecules such as water. Theories for both the fluid and solid phases are…
The water impact of an inclined flat plate and at high horizontal velocity is experimentally investigated with focus on the fluid-structure interaction aspects. Several test conditions have been examined by varying the vertical to…
The water hydration shell has decisive impact on the structural and functional properties of RNA. Changes of RNA structure upon melting and in biochemical processes are accompanied by a change of hydration patterns, a process which is…
The peculiar structuring of liquid water stems from a fine-tuned molecular principle embodying the two different interaction demands of the water molecule: The formation of hydrogen bonds or the compensation for coordination defects. Here…
The self-organization of proteins into enriched compartments and the formation of complex patterns are crucial processes for life on the cellular level. Liquid-liquid phase separation is one mechanism for forming such enriched compartments.…
Microgels are soft colloidal particles constituted by cross-linked polymer networks with a high potential for applications. In particular, after adsorption at a fluid interface, interfacial tension provides two-dimensional (2D) confinement…
We have used computer simulation to study the collapse of a hydrophobic chain in water. We find that the mechanism of collapse is much like that of a first order phase transition. The evaporation of water in the vicinity of the polymer…
Fluids under extreme confinement exhibit unique structures and intermolecular bonding, distinct from their bulk analogs, driving innovative applications at the water-energy nexus. Probing confined water experimentally at the length scale of…
We use molecular dynamics simulations to study the diffusion of water inside deformed carbon nanotubes with different degrees of deformation at 300 K. We found that the number of hydrogen bonds that water forms depends on nanotube topology,…
Among the various features of amino acids, the hydrophobic property has most visible impact on stability of a sequence folding. This is mentioned in many protein folding related work, in this paper we more elaborately discuss the…
We incorporate hydrodynamic interactions (HI) in a coarse-grained and structure-based model of proteins by employing the Rotne-Prager hydrodynamic tensor. We study several small proteins and demonstrate that HI facilitate folding. We also…
Water molecules and molecular chaperones efficiently help the protein folding process. Here we describe their action in the context of the energy and topological networks of proteins. In energy terms water and chaperones were suggested to…
The dynamics of hydrogen bonds among water molecules themselves and with the polar head groups (PHG) at a micellar surface have been investigated by long molecular dynamics simulations. The lifetime of the hydrogen bond between a PHG and a…
Understanding protein folding has been one of the great challenges in biochemistry and molecular biophysics. Over the past 50 years, many thermodynamic and kinetic studies have been performed addressing the stability of globular proteins.…
To elucidate the possible role of structural waters in stabilizing bent DNA, various conformations of AT-containing decamers, (A5T5)2 and A10:T10, were studied by Monte Carlo simulations. The duplexes were constrained to reproduce the NMR…