Related papers: Effect of hydrogen bonds on protein stability
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…
Hydrogen bonds are of paramount importance in the chemistry of clays, mediating the interaction between the clay surface and water, and for some materials between separate layers. It is well-established that the accuracy of a computational…
The structures of proteins exhibit secondary elements composed of helices and loops. Comparison of several water-only hydrophobicity scales with the functionalities of two repeat proteins shows that these secondary elements possess…
1. Role of inter-domain water clusters in large-scale dynamics of proteins; 2. Description of large-scale dynamics of proteins based on generalized Stokes-Einstein and Eyring-Polany equation; 3. Dynamic model of protein-ligand complexes…
Water is a key ingredient for life and plays a central role as solvent in many biochemical reactions. However, the intrinsically quantum nature of the hydrogen nucleus, revealing itself in a large variety of physical manifestations,…
Water freezing is ubiquitous on Earth, affecting many areas from biology to climate science and aviation technology. Probing the atomic structure in the homogeneous ice nucleation process from scratch is of great value but still…
Hydrogen bonding plays a role in the microphase separation behavior of many block copolymers, such as those used in lithography, where the stronger interactions due to H-bonding can lead to a smaller period for the self-assembled…
The hydrogen-bond network of water is characterized by the presence of coordination defects relative to the ideal tetrahedral network of ice, whose fluctuations determine the static and time-dependent properties of the liquid. Because of…
We use appropriately defined short ranged reference models of liquid water to clarify the different roles local hydrogen bonding, van der Waals attractions, and long ranged electrostatic interactions play in the solvation and association of…
To analyze hydration effects on macromolecular diffusion, the friction coefficients of macromolecules were examined using molecular dynamics simulations with an all-atom model. In the present study, a method was introduced to decompose the…
We demonstrate for the first time a tight binding model for water incorporating polarizable anions. A novel aspect is that we adopt a "ground up" approach in that properties of the monomer and dimer only are fitted. Subsequently we make…
Methanol-water liquid mixtures have been investigated by high-energy synchrotron X-ray and neutron diffraction at low temperatures. We are thus able to report the first complete sets of both X-ray and neutron weighted total scattering…
A sequential of concepts developed in last decade has enabled a resolution to multiple anomalies of water ice and its low-dimensionality, particularly. Developed concepts include the coupled hydrogen bond oscillator pair, segmental specific…
Fluid polyamorphism, the existence of multiple amorphous fluid states in a single-component system, has been observed or predicted in a variety of substances. A remarkable example of this phenomenon is the fluid-fluid phase transition in…
In this Letter, we present a simple model of aqueous interfacial molecular structure and we use this model to isolate the effects of hydrogen bonding on the dielectric properties of the liquid water-vapor interface. By comparing this model…
Monte Carlo computer simulations in the canonical and grand canonical statistical ensemble were used to explore the properties of the central force (CF1) water model. The intramolecular structure of the H$_2$O molecule is well reproduced by…
Quantum-mechanical van der Waals dispersion interactions play an essential role for both intra-protein and protein-water interactions -- the two main driving forces for the structure and dynamics of proteins in aqueous solution. Typically,…
By taking into account base-base stacking interactions we improve the Generalized Model of Polypeptide Chain (GMPC). Based on a one-dimensional Potts-like model with many-particle interactions, the GMPC describes the helix-coil transition…
Water is an ubiquitous liquid that has several exotic and anomalous properties. Despite its apparent simple chemical formula, its capability of forming a dynamic network of hydrogen bonds leads to a rich variety of physics. Here we study…
We have performed a multicanonical molecular dynamics simulation on a simple model protein.We have studied a model protein composed of charged, hydrophobic, and neutral spherical bead monomers.Since the hydrophobic interaction is considered…