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Molecular Modeling of Signal Peptide Recognition by Eukaryotic Sec Complexes

Journal

Publisher

MDPI
DOI: 10.3390/ijms221910705

Keywords

signal peptide; Sec61 complex; protein translocation; nascent peptide chain; membrane insertion; molecular modelling; molecular dynamics simulations; molecular docking

Funding

  1. Deutsche Forschungsgemeinschaft [He3875/15-1]

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Recent molecular modeling and simulation studies have focused on the dynamics and mechanisms of the Sec translocon, exploring the process of protein translocation into the endoplasmic reticulum and bacterial periplasm. Computational studies have investigated the conformational dynamics of the translocon in various states and addressed mechanistic issues such as membrane insertion and peptide recognition. Additionally, simulations have examined how accessory proteins impact Sec61 conformation during translation pathways.
Here, we review recent molecular modelling and simulation studies of the Sec translocon, the primary component/channel of protein translocation into the endoplasmic reticulum (ER) and bacterial periplasm, respectively. Our focus is placed on the eukaryotic Sec61, but we also mention modelling studies on prokaryotic SecY since both systems operate in related ways. Cryo-EM structures are now available for different conformational states of the Sec61 complex, ranging from the idle or closed state over an inhibited state with the inhibitor mycolactone bound near the lateral gate, up to a translocating state with bound substrate peptide in the translocation pore. For all these states, computational studies have addressed the conformational dynamics of the translocon with respect to the pore ring, the plug region, and the lateral gate. Also, molecular simulations are addressing mechanistic issues of insertion into the ER membrane vs. translocation into the ER, how signal-peptides are recognised at all in the translocation pore, and how accessory proteins affect the Sec61 conformation in the co- and post-translational pathways.

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