How does Sec63 affect the conformation of Sec61 in yeast?

Pratiti Bhadra,Volkhard Helms,Lalitha Yadhanapudi,Karin Römisch,Alexander Mackerell

doi:10.1371/journal.pcbi.1008855

Abstract

The Sec complex catalyzes the translocation of proteins of the secretory pathway into the endoplasmic reticulum and the integration of membrane proteins into the endoplasmic reticulum membrane. Some substrate peptides require the presence and involvement of accessory proteins such as Sec63. Recently, a structure of the Sec complex from Saccharomyces cerevisiae, consisting of the Sec61 channel and the Sec62, Sec63, Sec71 and Sec72 proteins was determined by cryo-electron microscopy (cryo-EM). Here, we show by co-precipitation that the Sec61 channel subunit Sbh1 is not required for formation of stable Sec63-Sec61 contacts. Molecular dynamics simulations started from the cryo-EM conformation of Sec61 bound to Sec63 and of unbound Sec61 revealed how Sec63 affects the conformation of Sec61 lateral gate, plug, pore region and pore ring diameter via three intermolecular contact regions. Molecular docking of SRP-dependent vs. SRP-independent signal peptide chains into the Sec61 channel showed that the pore regions affected by presence/absence of Sec63 play a crucial role in positioning the signal anchors of SRP-dependent substrates nearby the lateral gate.

Highlights

In eukaryotes, newly synthesized polypeptide chains destined for the secretory pathway are translocated into the endoplasmic reticulum (ER) or laterally inserted into the ER membrane via a conserved hetero-trimeric complex, the Sec61 channel [1]
There is no large difference in the average radius of gyration values of Sec61 in ‘Sec63-bound’, as well as the ‘free’ states
In two independent free simulations, the radius of gyration (Rg) of Sec61 showed a drop in the value after 500 ns and a larger deviation among the unbound simulations, suggesting that Sec63 has a stabilizing role on Sec61

Summary

Introduction

Newly synthesized polypeptide chains destined for the secretory pathway are translocated into the endoplasmic reticulum (ER) or laterally inserted into the ER membrane via a conserved hetero-trimeric complex, the Sec channel [1]. Translocation of secretory proteins can occur either co-translationally or in a post-translational manner [2,3,4]. In the co-translational pathway, a newly synthesized protein bearing a signal sequence exits from the ribosome and a ribonucleoprotein particle called signal recognition particle (SRP) binds to the signal sequence. In the post-translational pathway, the fully synthesized secretory precursor or protein is released from the ribosome and supported by chaperones and/or SRP-independent machineries, enters into the Sec channel. The Sec complex is composed of two protein complexes, the Sec complex and the hetero-tetrameric Sec62-Sec complex comprising Sec, Sec, Sec and Sec. Sec and Sec are present in mammalian cells [9]

Methods

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Discussion

Conclusion