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Reposted by Ioannis Skalidis

Friedrich Förster @fridof.bsky.social · 25/05/2026

The first cut is the deepest: Cleavable signal peptides direct thousands of different nascent proteins to the endoplasmic reticulum. Oddly, SPs are all different and nevertheless cleaved with exquisite specificity. Our new cryo-EM structures + MD solve this paradox: www.nature.com/articles/s41...

nature.com

Structural basis of signal peptide recognition by the signal peptidase complex - Nature Communications

Signal peptides are highly variable, yet the signal peptidase complex processes them with remarkable specificity. Here, authors combine cryo-EM, molecular dynamics simulations and modeling to reveal a...

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Ioannis Skalidis @johnskal.bsky.social · 06/03/2026

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

pnas.org

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...

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Ioannis Skalidis @johnskal.bsky.social · 16/10/2025

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

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Reposted by Ioannis Skalidis

cryoEM papers @cryoempapers.bsky.social · 02/09/2025

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

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Ioannis Skalidis @johnskal.bsky.social · 02/09/2025

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...

biorxiv.org

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 ...

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Ioannis Skalidis @johnskal.bsky.social · 23/03/2025

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

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Ioannis Skalidis @johnskal.bsky.social · 22/02/2025

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

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Ioannis Skalidis @johnskal.bsky.social · 11/02/2025

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!

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Ioannis Skalidis @johnskal.bsky.social · 17/01/2025

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

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