A. Böker and W. Paul
Martin-Luther-Universität Halle-Wittenberg, 06099 Halle
The relation between conformations of a polypeptide is governed by local minima in the free energy function. Coarse-grained models tend to simplify the free energy in such a way that these local minima are ignored. To circumvent this problem, the level of coarse graining needs to be chosen appropriately. PRIME20  provides reasonable detail by mapping each amino acid to four beads, but keeps parameter space simple with the set of interactions reduced to 19 energy parameters.
Poly-Glutamines (polyQ) are associated with Huntington’s disease due to their ability to aggregate into an amyloid state. Single polyQ chains have been found to form a beta hairpin as a precursor to these aggregates. We will discuss the temperature dependent end-to-end distance of the chains in relation to TTET and FRET experiments performed on polyQ chains.
We perform thermodynamic simulations of single PRIME20 chains using the “SAMC”  variation of Wang-Landau Monte Carlo sampling which provides insight in different statistical ensembles at the expense of dynamic information. The aforementioned polyQ are compared to poly-Alanines with a lower tendency to form beta structure motifs.