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Lack of structure as a challenge for protein simulations: the cases of nuclear transport and spider silk

Lack of structure as a challenge for protein simulations: the cases of nuclear transport and spider silk

Datum: 9. Juni 2016 16:00

Ort: Allmandring 3, Seminarraum 1.079

Veranstalter: ICP

Lack of structure as a challenge for protein simulations: the cases of nuclear transport and spider silk

Frauke Gräter, Heidelberg Institut für Theoretische Studien

Intrinsically disordered proteins (IDPs) are highly flexible and dynamic molecules. Their fast dynamics are recognized to be critical for their biological function but pose a formidable challenge to both experimental studies and molecular simulations.

I will present two case studies, in which we tackled the problem of the sampling of disordered proteins by extensive Molecular Dynamics (MD) simulations. First, I will present our recent results on the interaction of nucleoporins, IDPs at nuclear pores, with their receptors. Our simulations predicted a surprisingly fast association of this IDP with its folded binding partner, in spite – or rather because of – its high flexibility. [1] Secondly, we quantified the viscoelastic properties of silk disordered peptides by bridging atomistic simulations to finite element analyses of spider silk fibers. [2] We discovered a stretch-induced ordering mechanism that hinges upon the disorder of silk proteins and increases the fiber’s toughness. [3] Finally, I will give insight into our ideas to rescue the overcollapse commonly observed for IDPs when simulated with state of the art protein force fields. [4]

[1] Milles et al, Cell 2015

[2] Patil et al, BJ 2014 & PLoS One, 2014

[3] Wagner et al, in preparation

[4] Mercadante et al, JPCB 2015

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