相关论文: Putting Proteins back into Water

We present a coarse-grained lattice model to study the influence of water on the recognition process of two rigid proteins. The basic model is formulated in terms of the hydrophobic effect. We then investigate several modifications of our…

A large number of water models exists for molecular simulations. They differ in the ability to reproduce specific features of real water instead of others, like the correct temperature for the density maximum or the diffusion coefficient.…

The process of protein folding from an unfolded state to a biologically active, folded conformation is governed by many parameters e.g the sequence of amino acids, intermolecular interactions, the solvent, temperature and chaperon…

The molecular mechanism of the solvent motion that is required to instigate the protein structural relaxation above a critical hydration level or transition temperature has yet to be determined. In this work we use quasi-elastic neutron…

Proteins work only if folded in their native state, but changes in temperature T and pressure P induce their unfolding. Therefore for each protein there is a stability region (SR) in the T-P thermodynamic plane outside which the biomolecule…

A simple and surprisingly accurate description of spectral diffusion in deeply frozen globular proteins is constructed directly using the concept of ultrametricity of protein dynamics. Earlier the similar concept has been used for…

The thermodynamics of proteins indicate that folding/unfolding takes place either through stable intermediates or through a two-state process without intermediates. The rather short folding times of the two-state process indicate that…

The interactions of a protein, its phase behavior, and ultimately, its ability to function, are all influenced by the interactions between the protein and its hydration waters. Here we study proteins with a variety of sizes, shapes,…

We study the behavior of five proteins at the air-water and oil-water interfaces by all-atom molecular dynamics. The proteins are found to get distorted when pinned to the interface. This behavior is consistent with the phenomenological way…

Folding and aggregation of proteins, the interaction between proteins and membranes, as well as the adsorption of organic soft matter to inorganic solid substrates belong to the most interesting challenges in understanding structure and…

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…

The interplay between structure-search of the native structure and desolvation in protein folding has been explored using a minimalist model. These results support a folding mechanism where most of the structural formation of the protein is…

The theory of biochemical processes needs simple but realistic models of phenomena underlying microscopic dynamics of proteins. Many experiments performed in the 1980s have demonstrated that within the protein native state, apart from usual…

We develop a multi-scale approach to simulate hydrated nanobio systems under realistic condi- tions (e.g., nanoparticles and protein solutions at physiological conditions over time-scales up to hours). We combine atomistic simulations of…

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…

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)…

The concept of the surface of a protein in solution, as well of the interface between protein and 'bulk solution', is introduced. The experimental technique of small angle X-ray and neutron scattering is introduced and described briefly.…

Prompted by results that showed that a simple protein model, the frustrated G\=o model, appears to exhibit a transition reminiscent of the protein dynamical transition, we examine the validity of this model to describe the low-temperature…

We present a thermodynamically consistent mesoscopic model of protein adsorption at liquid-solid interfaces. First describing the equilibrium state under varying protein concentration of the solution and binding conditions, we predict a…

Water plays a fundamental role in the structure and function of proteins and other biomolecules. The thermodynamic profile of water molecules surrounding a protein are critical for ligand binding and recognition. Therefore, identifying the…