相关论文: Putting Proteins back into Water

In this study, variations with respect to temperature of the increments of enthalpy and Gibbs energy, arising in the dissolution of proteins in water, have been investigated by the methods of statistical thermodynamics. In this formalism,…

Membrane and nuclear proteins of poor solubility have been separated by high resolution two-dimensional (2-D) gel electrophoresis. Isoelectric focusing with immobilized pH gradients leads to severe quantitative losses of proteins in the…

The free energy landscape of a protein-like chain in a fluid was studied by combining discontinuous molecular dynamics and parallel tempering. The model protein is a repeating sequence of four different beads, with interactions mimicking…

Understanding protein folding has been one of the great challenges in biochemistry and molecular biophysics. Over the past 50 years, many thermodynamic and kinetic studies have been performed addressing the stability of globular proteins.…

We have investigated the relaxational dynamics for a protein model at various temperatures. Theoretical analysis of this model in conjunction with numerical simulations suggests several relaxation regimes, including a single exponential, a…

New experiments for water at the surface of proteins at very low temperature display intriguing dynamic behaviors. The extreme conditions of these experiments make it difficult to explore the wide range of thermodynamic state points needed…

We establish three partial differential equation models describing the thermodynamics of the fluid, by combining the energetic variational approach, appropriate constitutive relations, and classical thermodynamics laws. What is more, by…

A simple lattice model, recently introduced as a generalization of the Wako--Sait\^o model of protein folding, is used to investigate the properties of widely studied molecules under external forces. The equilibrium properties of the model…

We construct a discrete model of fluid particles according to the GENERIC formalism. The model has the form of Smoothed Particle Hydrodynamics including correct thermal fluctuations. A slight variation of the model reproduces the…

Molecular dynamics simulations are performed to study the temperature-dependent dynamics and structures of the hydration shells of elastin-like and collagen-like peptides. For both model peptides, it is consistently observed that, upon…

The time sequences of the molecular dynamics simulation for the folding process of a protein is analyzed with the inherent structure landscape which focuses on configurational dynamics of the system. Time dependent energy and entropy for…

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 a simplified model which is based on the same physics as inherent in most statistical models for nuclear multifragmentation. The simplified model allows exact calculations for thermodynamic properties of systems of large number of…

Activated processes such as protein unfolding are highly sensitive to heterogeneity in the environment. We study a highly simplified model of a protein in a random heterogeneous environment, a model of the in vivo environment. It is found…

Metadynamics is a powerful computational tool to obtain the free energy landscape of complex systems. The Monte Carlo algorithm has proven useful to calculate thermodynamic quantities associated with simplified models of proteins, and thus…

The equilibrium free energy landscape of an off-lattice model protein as a function of an internal (reaction) coordinate is reconstructed from out-of-equilibrium mechanical unfolding manipulations. This task is accomplished via two…

We address the problem of predicting the solvation free energy and equilibrium solvent density profile in fews minutes from the molecular density functional theory beyond the usual hypernetted-chain approximation. We introduce a bridge…

The weighty evidences of specific transformations of the thermal motion in pure water in the physiological temperature interval (PTI) from (30 +(-) 3)o C to (42 +(-) 3)o C for warm-blooded organisms are presented. It is shown that near the…

Using simulations or experiments performed at some set of temperatures to learn about the physics or chemistry at some other arbitrary temperature is a problem of immense practical and theoretical relevance. Here we develop a framework…

A simple way to get insights about the possible functional motions of a protein is to perform a normal mode analysis (NMA). Indeed, it has been shown that low-frequency modes thus obtained are often closely related to domain motions…