相关论文: The structural order of protein hydration water

We report that protein confinement within nanoscopic vesicular compartments corresponds to a liquid-liquid phase transition with the protein/water within vesicle lumen interacting very differently than in bulk. We show this effect leads to…

In addition to the biologically active monomer of the protein Insulin circulating in human blood, the molecule also exists in dimeric and hexameric forms that are used as storage. The Insulin monomer contains two distinct surfaces, namely…

We investigate the curvature-dependence of water dynamics in the vicinity of hydrophobic spherical solutes using molecular dynamics simulations. For both, the lateral and perpendicular diffusivity as well as for H-bond kinetics of water in…

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…

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…

Here we reveal details of the interaction between human lysozyme proteins, both native and fibrils, and their water environment by intense terahertz time domain spectroscopy. With the aid of a rigorous dielectric model, we determine the…

At the fundamental level, our understanding of water hydrogen-bond dynamics has been largely built on the detailed analysis of classical molecular simulations. The latter served to develop a plethora of hydrogen bond definitions based on…

While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…

Predicting the asymmetric structure and dynamics of solvated hydroxide and hydronium in water has been a challenging task from ab initio molecular dynamics (AIMD). The difficulty mainly comes from a lack of accurate and efficient…

The coffee-ring effect is a universal feature of evaporating sessile droplets with pinned contact line, wherein solutes or particles are advected to the droplet's edge due to evaporation-driven flows. While existing models have successfully…

The process of ligand-protein unbinding is crucial in biophysics. Water is an essential part of any biological system and yet, many aspects of its role remain elusive. Here, we simulate with state-of-the-art enhanced sampling techniques the…

While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…

We use molecular dynamics computer simulations and nuclear magnetic resonance experiments to investigate the dynamics of water at interfaces of molecular roughness and low mobility. We find that, when approaching such interfaces, the…

The hydrophobic effect stabilizes the native structure of proteins by minimizing the unfavourable interactions between hydrophobic residues and water through the formation of a hydrophobic core. Here we include the entropic and enthalpic…

Radiation-induced damage of biological matter is an ubiquitous problem in nature. The influence of the hydration environment is widely discussed, but its exact role remains elusive. Utilising well defined solvated-molecule aggregates, we…

The behavior of proteins near interfaces is relevant for biological and medical purposes. Previous results in bulk show that, when the protein concentration increases, the proteins unfold and, at higher concentrations, aggregate. Here, we…

In a recent work we have briefly introduced a new structural index for water that, unlike previous indicators, was devised specifically for generic contexts beyond bulk conditions, making it suitable for hydration and nanoconfinement…

Despite widespread interest, a detailed understanding of the dynamics of proton transfer at interfaces is lacking. Here we use ab initio molecular dynamics to unravel the connection between interfacial water structure and proton transfer…

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…

We perform molecular dynamics simulation of water using the TIP5P model to quantify structural order in both the first shell (defined by four nearest neighbors)and second shell (defined by twelve next-nearest neighbors) of a central water…