That New Nanopore Protein Sequencing Paper
There’s a new nanopore protein sequencing BioRxiv out! It’s well worth a read. But here are my high level thoughts...
What They Did
They design a bunch of synthetic proteins with a bit on the end which the ClpX unfoldase can attach to. This allows them to use ClpX to ratchet the protein through a nanopore (they use regular ONT MinION kits). ClpX is essentially performing the same function as the motor proteins in ONTs DNA sequencing approach. By adding a sequence which causes the ClpX to slip they can re-read the same region multiple times.
What do the results look like?
Pretty OK. It seems like we’re still looking at single AA changes in a static context. We’ve seen this before in the context of a peptide linked to a DNA strand. Here it seems to work reasonably well, showing somewhat reasonable classification efficiency1.
The fact that they can re-read the same region is also neat! But there are clearly several issues that need to be solved to make the whole thing workable. In particular the paper contains this statement which is pretty worrying:
This hypothesis was grounded on prior observations indicating that around 20 amino acids can occupy the CsgG sensing region when in a stretched conformation2