The molecular dynamics (MD) simulation method is used to assess structural details for humanprion protein (hereafter PrPN) and its Asp178 Asn mutant (hereafter PrPm) which causes fatalfamilial insomnia disease. The results reveal that the flexibility and instability increase in PrPmcould be related to specific amino acids exposed to the solvent. Solvation free energy of PrPm is 20kjmot1nni2 mor...

An efficient method for calculating the free energy of solvation of a (macro)molecule embedded in a continuum solvent is presented. It is based on the fully analytical evaluation of the volume and spatial symmetry of the solvent that is displaced from around a solute atom by its neighboring atoms. The two measures of solvent displacement are combined in empirical equations to approximate the at...

A global optimization method is described for identifying the global minimum energy conformation, as well as lower and upper bounds on the global minimum conformer of solvated peptides. Potential energy contributions are calculated using the ECEPP/3 force eld model. In considering the eeects of hydration, two implicit free energy models are compared. One method is based on the calculation of so...

Previous work describes a computational solvation model called semi-explicit assembly (SEA). The SEA water model computes the free energies of solvation of nonpolar and polar solutes in water with good efficiency and accuracy. However, SEA gives systematic errors in the solvation free energies of ions and charged solutes. Here, we describe field-SEA, an improved treatment that gives accurate so...

This article explores the impact of surface area, volume, curvature, and Lennard-Jones (LJ) potential on solvation free energy predictions. Rigidity surfaces are utilized to generate robust analytical expressions for maximum, minimum, mean, and Gaussian curvatures of solvent-solute interfaces, and define a generalized Poisson-Boltzmann (GPB) equation with a smooth dielectric profile. Extensive ...

The solvation and rotational relaxation dynamics of coumarin 153 have been investigated in a dicationic ionic liquid (IL), 1,6-bis-(3-methylimidazolium-1-yl)hexane bis-(trifluoromethylsulfonyl)amide ([C6(MIm)2][NTf2]2), for the first time to provide a comprehensive and a quantitative understanding of the nature of the ionic fluid and its influence on the average solvation and rotational relaxat...

Proteins respond to electrostatic perturbations through complex reorganizations of their charged and polar groups, as well as those of the surrounding media. These solvation responses occur both in the protein interior and on its surface, though the exact mechanisms of solvation are not well understood, in part because of limited data on the solvation responses for any given protein. Here, we c...

The formation of micelles by dodecylphosphocholine (DPC) is modeled by treating the surfactants in atomic detail and the solvent implicitly, in the spirit of the EEF1 solvation model for proteins. The solvation parameters of the DPC atoms are carried over from those of similar atoms in proteins. A slight adjustment of the parameters for the headgroup was found necessary for obtaining an aggrega...

The enthalpies of solution of the cyclic ethers 1,4-dioxane, 12-crown-4 and 18-crown-6 in mixtures of ethanol and water have been measured within the whole mole fraction range at T = 298.15 K. The enthalpy of solvation has been calculated. In pure ethanol and pure water, the solvation enthalpy of the investigated cyclic ethers depends linearity on the number of -CH2CH2- groups in the cyclic eth...

Binary mixtures of the protic ionic liquid ethylammonium nitrate (EAN) and acetonitrile (AN) were studied at 25 1C over the entire composition range by means of broadband dielectric spectroscopy covering 0.2 r n/GHz r 89. The dielectric spectra could be decomposed into two relaxation processes, both of which proved to be composite modes. For dilute solutions the higher-frequency Debye relaxatio...