Doctoral students seminar (April 30, 2019)

Mareen Schäfer on “Structure and dynamics of the nanophase separated comb-like polymer PPDOT as investigated by solid-state NMR”
Arne Böker on “Simulations of protein thermodynamics and structures with the PRIME20 model”

Martin-Luther-Universität Halle-Wittenberg 
Von-Danckelmann-Platz 3, SR 1.03 06120 Halle (Saale) 
Time: 3.30pm - 5.00pm 

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Structure and dynamics of the nanophase separated comb-like polymer PPDOT as investigated by solid-state NMR

Mareen Schäfer

We investigate the structure and molecular motions of the side and main-chains in the comb-like polymer, poly(1,4- phenylene-2,5-n-didecyloxy terephthalate) with 10 carbons in the alkyl side chain (PPDOT) with respect to its two polymorphic states by means of 13C MAS NMR spectroscopy. Both modifications, called A and B, exhibit a morphology with well-ordered backbones in π − π-stacks separated by nanodomains which are formed by the methylene sequences. A change form the as-synthesized PPDOT-B to PPDOT-A occurs through a solid-solid phase transition above 70°C. At ambient temperatures, the polymorph A slowly converts back to the thermodynamically more stable state B. We use 13C CP MAS spectra to observe the structural changes during the phase transition and the differences in both modifications. The 13C DIPSHIFT experiments yield information about the motionally averaged 1H – 13C dipole-dipole coupling. In the recorded spectra, we do not see any indication of an amorphous backbone phase and therefore we emphasize that the complete sample exhibits a well ordered π-π-stacking for T < 180C. The methylene sequences in modification B exist in trans- and gauche-rich conformations, in contrast to modification A where all side chains are in a gauche-rich environment with molecular motions in the intermediate regime at ambient temperatures and fast molecular dynamics at 120C. Above 180C we detect the formation of a liquid crystal phase, characterized by the loss of the π-π-stacking and molecular motions of the side chains with correlation times τc < 0.01 μs.

Simulations of protein thermodynamics and structures with the PRIME20 model

Arne Böker

The structure formation of small, simple polypeptides is of great medical relevance. Many of these polypeptides are known to cause hereditary diseases linked to a general tendency to aggregate as amyloids. Among the simplest sequences, homopolymers like polyalanine (polyA) and polyglutamine (polyQ) are notorious for their aggregation behaviour, and Huntington’s chorea (caused by a polyQ sequence) is among the most well-known example of a homopolymer amyloid disease.
In order to understand the formation of amyloids, the thermodynamic behaviour of single molecules – their basic building blocks – is a prerequisite. Hence, this project compares the thermodynamics and configurations of polyA, polyQ and polyserine (polyS) using a generalised-ensemble simulation algorithm called Stochastic Approximation Monte Carlo in combination with a mildly coarse-grained protein representation called PRIME20.
During the simulations, PRIME20 as it is described in literature turned out to be unable to produce realistic Ramachandran plots or α-helices, the most important secondary structure motif of proteins. Instead, polyA and polyS fold into γ-helix configurations which have never been observed experimentally, while polyQ forms a β-like hairpin. An analysis of idealised Ramachandran plots identifies the model parameters responsible for the unexpected helix type, and an updated version of the model produces better Ramachandran plots as well as the desired α-helices without changing central observations like the preference for hairpins by polyQ.
Furthermore, the influence of spectroscopy dyes attached to the peptide termini and of a tail which enhances solubility was studied using the same methods. The folded states are severely disturbed by these modifications, but at physiological temperatures the effect on the intrinsically disordered polyS and polyQ is small, justifying the experimental use of this set-up.

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