Browsing by Author "Hansen-Goos, Hendrik"

Now showing 1 - 1 of 1

Open Access
Entropic forces on bio-molecules
(2008) Hansen-Goos, Hendrik; Dietrich, Siegfried (Prof. Dr.)
In this thesis the influence of different solvent conditions on the formation of beta-sheet and helix motifs in protein folding is studied. Solvation free energies are calculated for proteins in the tube model using the concept of morphological thermodynamics. This approach allows for determining solvent properties in simple test geometries while the characteristics of complex protein conformations enter via only four geometric measures: excluded volume, solvent accessible surface, and surface integrals of the mean and Gaussian curvatures of a given protein conformation. Solvent properties are calculated using density functional theory of classical fluids. In order to assess entropic solvent contributions a hard-sphere solvent is considered. The hard-sphere fluid is modeled within a variation of Rosenfeld's fundamental measure theory which provides an accurate free energy model for inhomogeneous hard-sphere mixtures. In the first part of the thesis, which is preparatory to the treatment of protein solvation albeit containing independent results, an improved equation of state for the hard-sphere mixture is derived and, based thereon, an improved version of fundamental measure theory. In a further step, an improved generalization of fundamental measure theory to fluids of arbitrarily shaped hard particles is provided which, in contrast to previous attempts, is able to describe the isotropic-nematic phase transition. Based on these improvements a very accurate and efficient calculation of solvation free energies becomes possible. For the hard-sphere solvent we find that, in contrast to conclusions drawn in a less general study by Snir and Kamien, beta-sheets are connected with small solvent particles at large packing fractions. The unwinding transition from a tightly packed helix to a helix with larger radius upon increasing the size of the solvent particles, which was interpreted by Snir and Kamien as an indication of sheetlike folding in the regime of large solvent particles, is shown to be unrelated to beta-sheet formation. The study is extended to solvents with intermolecular attraction and different protein-solvent interactions. In this way, we can confirm in our model the role of hydrophobicity as a major driving force for protein folding.