Cotransin

Cotransin is a relatively new probe for Sec61-dependent protein translocation. This probe is the best we have so far, but there is scant information regarding precise mode of on-target action and potential sites of off-target activity. Use of this probe seems limited to lysate-based experiments.

There has been 2015 mechanistic study “Defining a Conformational Consensus Motif in Cotransin-Sensitive Signal Sequences: PMC4373898 but the specificity does not have extensive SAR in particular for an obvious negative control. While more recent studies are optimistic on the possibility of specificity (e.g. “The signal peptide as a new target for drug design” PMID: 32209293) caution is warranted and reported concentrations are high enough to be in a vast stoichiometric excess to the target proteins in the in vitro systems. With more a physical mechanism rather than a specific protein binding pocket interaction this is not a classical probe.

Because Cotransin is signal sequence specific, it only blocks a certain subset of proteins which are translocated by SEC61. Cotransin analogues have been made which target different proteins which are translocated by SEC61. The Cotransin family of molecules are the best available tools to study SEC61 (Apratoxin, listed in references also targets SEC61 but is cytotoxic), but a better understanding of their selectivity for signal sequences or a comprehensive screen of which proteins are affected by each Cotransin analogue would be necessary to make the use of Cotransin as probes for SEC61 more general. Cotransin has been used at 5µM to block Cotransin sensitive proteins and at 30µM to block the majority of secreted proteins. Membrane integral proteins are not affected by Cotransin at these concentrations.