相关论文: The structural order of protein hydration water
An accurate description of the structure and dynamics of interfacial water is essential for phospholipid membranes, since it determines their function and their interaction with other molecules. Here we consider water confined in stacked…
The interface between hemoglobin (Hb) and its environment, in particular water, is of great physiological relevance. Here, results from {\it in vitro}, {\it in vivo}, and computational experiments (molecular dynamics simulations) are…
The low-frequency collective vibrational modes in proteins as well as the protein-water interface have been suggested as dominant factors controlling the efficiency of biochemical reactions and biological energy transport. It is thus…
Water hydrating phospholipid membranes determine their stability and function, as well as their interaction with other molecules. In this article we study, using all-atom molecular dynamics simulations, the rotational and translational…
In order to inquire the microscopic origin of observed multiple time scales in solvation dynamics we carry out several computer experiments. We perform atomistic molecular dynamics simulations on three protein-water systems namely,…
The physical nature and the correct definition of hydrogen bond (H-bond) are considered.\,\,The influence of H-bonds on the thermodynamic, kinetic, and spectroscopic properties of water is analyzed.\,\,The conventional model of H-bonds as…
The effects of static electric field on the dynamics of lysozyme and its hydration water have been investigated by means of incoherent quasi-elastic neutron scattering (QENS). Measurements were performed on lysozyme samples, hydrated…
Protein-protein interactions (protein functionalities) are mediated by water, which compacts individual proteins and promotes close and temporarily stable large-area protein-protein interfaces. In their classic paper Kyte and Doolittle (KD)…
Water shapes and defines the properties of biological systems. Therefore, understanding the nature of the mutual interaction between water and biological systems is of primary importance for a proper assessment of biological activity and…
In a recent paper [PRL 91, 138103 (2003)] a new mechanism to explain the cold denaturation of proteins, based on the loss of local low-density water structure, has been proposed. In the present paper this mechanism is tested by means of…
We present a 2D lattice model of water to study the effects of ion hydration on the properties of water. We map the water molecules as lattice particles consisting of a single Oxygen at the center of a site and two Hydrogen atoms on each…
Water, a subject of human fascination for millennia, is likely the most studied substance on Earth, with an entire scientific field -- hydrodynamics -- dedicated to understanding water in motion. However, when water flows through…
In this manuscript, we present a general computational method for characterizing the molecular structure of liquid water interfaces as sampled from atomistic simulations. With this method, the interfacial structure is quantified based on…
A new statistical mechanics formulation of characterizing the structural fluctuation of protein correlated with that of water is presented based on the generalized Langevin equation and the 3D-RISM/RISM theory of molecular liquids. The…
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…
Understanding the molecular mechanism by which denaturants modulate protein structure remains a central challenge in protein biophysics. In this work, molecular dynamics simulations were employed to investigate the effects of urea on the…
Proteins tend to bury hydrophobic residues inside their core during the folding process to provide stability to the protein structure and to prevent aggregation. Nevertheless, proteins do expose some 'sticky' hydrophobic residues to the…
Ab initio molecular dynamics simulations of liquid water under equilibrium ambient conditions, together with a novel energy decomposition analysis, have recently shown that a substantial fraction of water molecules exhibit a significant…
At low temperatures proteins exist in a glassy state, a state which has no conformational flexibility and shows no biological functions. In a hydrated protein, at and above 220 K, this flexibility is restored and the protein is able to…
Since the pioneering works of Pethig, Grant and Wuthrich on protein hydration layer, many studies have been devoted to find out if there are any general and universal characteristic features that can distinguish water molecules inside the…