I don't know yet- clearly something has to do with strength of intermolecular interactions (e.g. the Arg effect) but also I bet something has to do with refolding rates. Although surprisingly we don't see much correlation with topology (% alpha vs % beta) so maybe not folding rates... ???

That Savas lab looks cool, but this was actually done in collaboration with Jeff Savas's lab at Northwestern, who is not on bsky that I can find :) thanks for the highlight!

Thank you so much :)

Thanks! Yeah, lots to learn!

Thanks!!

I hope this is useful and we're excited to use this approach to explore more protein stresses- shelf life, vortexing, freeze-thaw, etc. I also love this paper because it's our lab's first time using quantitative proteomics! Congrats Cydney et al!!

All data are available on Zenodo and we'd love to see what you can do with it! Cydney also made a nice notebook to run the predictive model (including DMS scan) in Colab!

Preprint: biorxiv.org/content/10.1...
Colab: colab.research.google.com/drive/1KNWvG...
Data: docs.google.com/forms/d/e/1F...

There’s much more in the paper, including the surprising observation that higher folding stability correlates with aggregation even controlling for hydrophobicity (?!) Stabilities measured by Kotaro Tsuboyama!

Existing aggregation predictors show only modest correlations with our results, but fine tuning SaProt does well on our (carefully split) test set!

Arginine is strongly aggregation promoting! This was known in literature but not to me.

Hydrophobicity and isoelectric point (pI) are correlated with temp- and pH-propensity, but don’t tell the whole story. Other factors also influenced aggregation.

Really cool result: changes in soluble abundance from having all protein domains mixed together are nicely correlated with similar experiments on single, purified domains (also at 10 mg/mL).

Overall, 25-50% of the total protein became insoluble, but the proteomics revealed which proteins aggregated (became insoluble) more and which aggregated less.

We expressed the protein domains together as a mixture in one E. coli culture, purified our mixture of domains and concentrated to 10mg/mL, then used TMT proteomics to monitor the change in soluble protein abundance after high temp/low pH.

This work was led by the incredible Cydney Martell, who worked out the entire approach from scratch and did virtually all the experiments and computational analysis (and earned her own PhRMA fellowship)! phrmafoundation.org/grants-fello... With proteomics help from the Savas Lab at NU!

So sorry to hear, what an incredible tragedy 😢

FWIW my DP2 was GM funded so I'm eligible and I have an R35 with a score of 23 submitted May 2024 that is stuck Pending...

They never specifically told me it was because I had too much other funding, but fwiw I had 1 year left on a DP2 at the time and that was it. Plus a small amount of non-federal stuff.