The signal sequence moves through a ribosomal tunnel into a noncytoplasmic aqueous environment at the ER membrane early in translocation.

The signal sequence is in an aqueous milieu at an early stage in the translocation of a nascent secretory protein across the endoplasmic reticulum membrane. This was determined using fluorescent probes incorporated into the signal sequence of fully assembled ribosome-nascent chain-membrane complexes: the fluorescence lifetimes revealed that the probes were in an aqueous environment rather than buried in the nonpolar core of the membrane. Since these membrane-bound probes were not susceptible to collisional quenching by iodide ions, the space containing the signal sequence is sealed off from the cytoplasm by a tight ribosome-membrane junction. The nascent chain inside the ribosome is also not exposed to the cytoplasm and apparently passes through an aqueous tunnel in the ribosome.