Ioannis Skalidis

Direct evidence of acid-driven protein desolvation | PNAS Water and its ability to modulate the protonation states of biomolecules govern the physical chemistry of life, dictating their metabolic functions...

One of the last works from my PhD is finally out!

We delved deep into water dynamics as a function of pH, in a series of high-resolution structures. The manuscript is now online at @pnas.org! If you're into high-res biochemical insights, I promise its worth the read!

#cryoEM #biochemistry #SPA

Thanks Pranav! In the meantime I already set up the pipeline, but still advice is welcome! Any settings you suggest I start with for pytom-tm and then filtering in warp?

Does anybody have a working protocol for a pipeline including aretomo3 to pytom-tm to warptools for #STA? I would ideally like to use M for the final refinements instead of being confined to relion5. Any suggestions/resources would be welcome! #teamtomo #cryoet #cryoem

Direct evidence of acid-driven protein desolvation www.biorxiv.org/content/10.1101/2025.09.01.673474v1 #cryoEM

Direct evidence of acid-driven protein desolvation | Panagiotis Kastritis Did you know that proteins lose bound waters upon acidification? We didn't as well. But we visualized this phenomenon in a series of high-resolution cryo-EM structures (~2 Å) across different pH value...

If you wanna read a nice resume of the work, here's the LinkedIn post: www.linkedin.com/posts/pkastr...

Direct evidence of acid-driven protein desolvation Water and its ability to modulate the protonation states of biomolecules govern the physical chemistry of life, dictating their metabolic functions. However, how amino acid protonation alters protein ...

A project that would never leave my mind during my PhD is finally out!

We used #cryo-em #spa #md to see how the solvation layer of a protein is affected during acidification!

Really cool insights and a truly fundamental work, congrats to all involved!

www.biorxiv.org/content/10.1...

The first project I worked on, right after joining @bijvoet-centre.bsky.social!

Damn, I'm sad I just found out about this one only now!

Thank you very much Andrea!

I have a couple of nice visualization snippets for chimerax that I have gathered from here, there, and my own stuff. Would be cool to have somewhere to deposit them!

Oh, forgot to tag @bijvoet-centre.bsky.social where the Structural Biochemistry group is a part of!

I guess I should have posted a bit earlier, but I'm very excited that my #MSCA application got accepted! I'll be working at @fridof.bsky.social lab @utrechtuniversity.bsky.social to develop my #teamtomo skills on my project: Protein ER-ways! Here's to gaining new insights on ER protein biogenesis!

Is this infographic true? Did these unis charge 60%+ for overheads????

EMDB/PDB code is not even necessary, and tbh I never require it. Just send me a chimerax session with everything inside. How hard is that to do?

Having now worked myself on tomo data collection and analysis makes me appreciate the enormity of this work even more! Amazing stuff...