Related papers: Effect of hydrogen bonds on protein stability
The structural, electronic, and spectroscopic properties of a high-pressure phase of methane hydrate (MH-III) are studied by first principles electronic structure calculations. A detailed analysis of the atomic positions suggests that {\it…
We study the thermodynamic behavior of a model protein with 54 amino acids that is designed to form a three-helix bundle in its native state. The model contains three types of amino acids and five to six atoms per amino acid, and has the…
Using a structure-based coarse-grained model of proteins, we study the mechanism of unfolding of knotted proteins through heating. We find that the dominant mechanisms of unfolding depend on the temperature applied and are generally…
Conformational transitions of flexible molecules, especially those driven by hydrophobic effects, tend to be hindered by desolvation barriers. For such transitions, it is thus important to characterize and understand the interplay between…
An open question is whether the liquid and glassy phases of water are thermodynamically distinct or continuous. Here we address this question using molecular dynamics simulations in comparison with neutron scattering experiments to study…
In our recent works, based on the structural studies on water and interfacial water (topmost water layer at the solute/water interface), hydration free energy is derived and utilized to investigate the physical origin of hydrophobic…
Most thermodynamic modeling of hydrogels focused on predicting their final volumes in equilibrium with water, built on Flory's theories for the entropy of mixing and rubber elasticity, and Donnan's equilibrium conditions if polyelectrolyte…
We consider the hydrodynamics of lipid bilayers containing transmembrane proteins of arbitrary shape. This biologically-motivated problem is relevant to the cell membrane, whose fluctuating dynamics play a key role in phenomena ranging from…
The hydrogen bond is a fundamental ingredient to stabilize the DNA and RNA macromolecules. The main contribution of this work is to describe quantitatively this interaction as a consequence of the quantum confinement of the hydrogen. The…
A single water molecule has nothing special. However, macroscopic water displays many anomalous properties at the interface, such as a high surface tension, hydrophobicity and hydrophillicity. Although the underlying mechanism is still…
The hydrogen peroxide is present in the living cell at small concentrations that increase under the action of the heavy ion beams in the process of anticancer therapy. The interactions of hydrogen peroxide with DNA, proteins and other…
Effects of chain length compatibility and molecular ratio on the two-dimensional crystallization of a binary mixed surfactant system with non-identical molecular size and its consequence on retardation to water evaporation are described via…
Hydrogen-bond forms a pair of asymmetric, coupled, H-bridged oscillators with ultra-short-range interactions and memory. hydrogen bond cooperative relaxation and the associated binding electron entrapment and nonbonding electron…
A coarse-grained off-lattice model that is not biased in any way to the native state is proposed to fold proteins. To predict the native structure in a reasonable time, the model has included the essential effects of water in an effective…
The some dynamic properties of a random heteropolymer in the condensed state are studied in the mode coupling approximation. In agreement with recent report a dynamic friction increasing is predicted for the random heteropolymer with…
An approach has been proposed to characterize the competitive association of D2O and to study the heterogeneity of hydration water adsorbed by the protein, immunoglobulin G, using methodology for determining of non-freezing water in mixed…
The adsorption of a collagen fragment on both a hydrophobic, hydrogen-terminated and a hydrophilic, natively oxidised Si surface is investigated using all-atom molecular dynamics. While favourable direct protein-surface interactions via…
Water and glycerol are well-known to facilitate the structural relaxation of amorphous protein matrices. However, several studies evidenced that they may also limit fast ($\sim$ pico-nanosecond, ps-ns) and small-amplitude ($\sim$ \AA )…
Thin films of binary mixtures that interact through isotropic forces and directionally specific "hydrogen bonding" are considered through Monte Carlo simulations. We show, in good agreement with experiment, that the single phase of these…
Collagen type I is well-known for its outstanding mechanical properties which it inherits from its hierarchical structure. Collagen type I fibrils may be viewed as an heterogeneous material made of protein, macromolecules (such as…