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...

A general expression for the distribution of the fluctuating 2(l)-pole moment M(l) of a spherical sample of dielectric material is derived on the basis of dielectric theory combined with statistical mechanics. The formulas are compared with results from computer simulations of a weakly coupled Stockmayer fluid and the agreement is shown to be excellent. Furthermore, we calculate the size of the...

A practical potentiometric method was applied successfully to experimental electrochemical data in order to determine the autoprotolysis constants (pKap) of water + dimethyl sulfoxide mixtures containing 0-90 % of DMSO by volume at 25° C and 0.1 M ionic strength was maintained in each mixture by NaClO4 solution. The results indicated that water-DMSO mixtures are more basic media than pure water...

The highly anisotropic environment of the lipid bilayer membrane imposes significant constraints on the structures and functions of membrane proteins. However, NMR structure calculations typically use a simple repulsive potential that neglects the effects of solvation and electrostatics, because explicit atomic representation of the solvent and lipid molecules is computationally expensive and i...

As the field of structural genomics matures, new methods will be required that can accurately and rapidly distinguish reliable structure predictions from those that are more dubious. We present a method based on the CHARMM gas phase implicit hydrogen force field in conjunction with a generalized Born implicit solvation term that allows one to make such discrimination. We begin by analyzing pair...

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...

Reduction and oxidation potentials of a series of parasubstituted phenylselanyl radicals, XC(6)H(4)Se(*), have been measured using photomodulated voltammetry in acetonitrile. The thermodynamic significance of these data was substantiated through a study of the oxidation process of the pertinent selenolates in linear sweep voltammetry. Both the reduction and the oxidation potentials correlate li...