Protein Dynamics in Tight Tunnels
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Abstract
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 significance. Furthermore, within the framework of protein degradation facilitated by the proteasome, we analyze how the presence of knots influences 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.
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