Protein prediction tool

Question

[nickmarinakis92]

Hello,

I would like to ask you if there is a prediction tool for stop loss mutations. I have a stop loss variant that is calculated to expand my protein for 8 more amino acids. Do you have any idea to predict it's impact.

Nikos

Answer 1

[Collin]

One possibility is that the stop loss could induce or prevent the degradation of the protein. A previous paper has shown that an extension sequence could contain a degron motif that is recognized by the Ubiquitin-Proteasome System (https://europepmc.org/article/med/32719554), which then targets that protein for degradation. I've previously developed a tool named deepDegron to predict whether mutations may result in the loss/gain of c-terminal degrons (https://deepdegron.readthedocs.io/en/latest/index.html). Since the stop loss mutations would affect the c-terminus, it might be worth checking. You can find more about deepDegron from our paper in Molecular Cell (https://www.sciencedirect.com/science/article/abs/pii/S109727652100040X).