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Ioannis Skalidis

@johnskal.bsky.social
140 followers 373 following 14 posts

MSCA post-doctoral researcher at Förster lab, Utrecht university. SPA guy trying to navigate Tomo. Lover of big protein complexes and even bigger scopes. I'm new here. #structuralbiology #cryoem

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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
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?
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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
If you wanna read a nice resume of the work, here's the LinkedIn post: www.linkedin.com/posts/pkastr...
linkedin.com
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...
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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 · 17/02/2025
Thank you very much Andrea!
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Ioannis Skalidis @johnskal.bsky.social · 12/02/2025
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!
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Ioannis Skalidis @johnskal.bsky.social · 11/02/2025
Oh, forgot to tag @bijvoet-centre.bsky.social where the Structural Biochemistry group is a part of!
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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 · 08/02/2025
Is this infographic true? Did these unis charge 60%+ for overheads????
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Ioannis Skalidis @johnskal.bsky.social · 18/01/2025
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?
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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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