Protein Dynamics in Tight Tunnels

M. Wojciechowski, M. Chwastyk Institute of Physics, Polish Academy of Sciences, al. Lotników 32/46, PL-02668 Warsaw, Poland

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We investigate the impact of narrow tunnels, such as the ribosomal exit tunnel and the entrance of the proteasome channel, on the dynamics of proteins with and without knots. Our exploration delves into the potential driving forces behind protein chain movement and their individual signi cance. Furthermore, within the framework of protein degradation facilitated by the proteasome, we analyze how the presence of knots inuences the protein's entry into the proteasome chamber through diverse approaches. This discussion illustrates how molecular dynamics simulations within a coarse-grained structure-based model provide valuable insights into these intricate molecular processes.

DOI:10.12693/APhysPolA.145.S61 topics: molecular dynamics simulations, knots, ribosome, proteasome