Regensburg 2019 – wissenschaftliches Programm

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BP: Fachverband Biologische Physik

BP 9: Computational biophysics

BP 9.2: Vortrag

Dienstag, 2. April 2019, 10:00–10:15, H11

Thermodynamics and conformations of homopolymeric polypeptides — •Arne Böker, Paul Käthner, and Wolfgang Paul — Martin-Luther-Universität Halle-Wittenberg

Although the number of structures in the PDB is continuously growing, the topic of protein folding still requires great attention and is being treated with a variety of methods. Especially the reasons for proteins to aggregate as amyloids are far from being understood. While aggregation is a collective feature of multiple molecules, the starting point must be a single chain, so understanding single molecule structure is a prerequisite for understanding aggregation. The stability of motifs such as β-sheets may give us insight into the formation and stability of aggregates.

For these reasons, we simulate different polypeptides (polyalanines/polyA, polyglutamines/polyQ and polyserines/polyS with 8 to 23 monomers) and investigate their thermodynamics and structure formation. We use a four-bead representation called PRIME20 (Cheon et al., 2010) together with a flat histogram Monte Carlo method (Liang et al., 2007) which provides full thermodynamic information over a broad temperature range.

We find that polyS and polyQ, disordered under physiological conditions, can fold into distinct ground states where polyS forms a helix similar to polyA while polyQ prefers a hairpin. β-type intermediates occur during folding of all our peptides. We also investigate the influence of end-attached spectroscopy dyes and solubility-enhancing residues and find significant deviations in the folded structures.