Regensburg 2016 – wissenschaftliches Programm

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BP: Fachverband Biologische Physik

BP 27: Computational Biophysics

BP 27.4: Vortrag

Dienstag, 8. März 2016, 10:30–10:45, H43

Folding of small knotted proteins: Insights from a mean field coarse-grained model — Saeed Najafi and •Raffaello Potestio — Max Planck Institute for Polymer Research, Mainz, Germany

A small but relevant number of known protein structures features a knot. Understanding the process of folding from a swollen unknotted state to the biologically relevant native conformation is, for these proteins, particularly difficult, due to their rate-limiting topological entanglement. In this talk I will present and discuss a novel coarse-grained model, dubbed Elastic Folder Model (EFM), developed to contribute shedding some light on the problem of knotted protein folding. The EFM is a minimalistic, structure-based model where the information about the knotted conformation is encoded in bonded angular interactions only; this potential, which does not favor the formation of native contacts, is parametrized through a stochastic search scheme in parameter space. The optimal knotting pathways of the two smallest known proteins, obtained through this approach, are consistent with the results derived by means of coarse-grained as well as full atomistic simulations.