Sequence-specific alteration of the ribosome-membrane junction exposes nascent secretory proteins to the cytosol.

Tight docking of the ribosome at the translocation channel ensures that nascent secretory proteins are shielded from the cytoplasm during transfer into the endoplasmic reticulum. Discrete pause transfer sequences mediate the transient stopping of translocation in certain proteins. Here we show that during a translocational pause, the junction between the ribosome and translocation channel is opened, exposing the nascent chain to the cytosol. While transient, this opening is sufficient to demonstrate macromolecular interactions between the translocating chain and molecules added to the cytosol, such as antibodies and site-specific proteases. Moreover, this opening is accompanied by alterations in the proteins that neighbor the nascent chain. These results demonstrate that specific sequences within a translocating nascent chain can elicit dramatic and reversible structural changes in the translocation machinery. Thus, the translocon is dynamic and can be regulated.