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Greg Chojnowski

@gchojnowski.bsky.social
92 followers 239 following 14 posts

I build EM and MX models and write software to make it a bit less of a hassle. Some of the code I wrote is a part of CCP4 and CCP-EM. gchojnowski.github.io

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Greg Chojnowski @gchojnowski.bsky.social · 31/03/2026
Two homologous proteins were independently solved using cryo-EM. The high-resolution structure is correct but incomplete; the lower-resolution structure has a hard-to-spot error. Only together do they provide a complete picture!
Side-by-side comparison of the matching regions of two homologous proteins. The corresponding cryo-EM maps are shown in grey. The model on the left has a higher resolution (2.8 Å) but is truncated compared to the lower-resolution model on the right (3.4 Å). The dashed circle highlights a modelling issue (sequence register shift) in the structure on the right.
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Reposted by Greg Chojnowski
Matthias Wilmanns @matthiaswilmanns.bsky.social · 03/09/2025
We are excited to share our latest work, where we unravel the structural and functional secrets of the once-mysterious protein Pex8 revealing how it controls the peroxisomal cargo import receptor Pex5. Read more here: www.biorxiv.org/content/10.1101/2025.08.30.673231v1
Ensemble model of the full length Pex5 receptor (different blue color) in complex with Pex8 (green colors).

Key Findings:

Pex8 binds to a novel site on the mostly unfolded N-terminal region of the Pex5 receptor. This interaction is essential for peroxisomal protein import.

Computational modelling reveals the formation of an assembly with the trimeric peroxisomal E3-ubiquitin ligase.

We propose that this action positions the Pex5 receptor for its recycling, a step essential for the entire protein import process.

Why this matters:

Peroxisomes rely entirely on the import of folded proteins to function. Impaired peroxisome function is linked to severe disorders, and recent data show their crucial roles in carcinogenesis and the immune response. Our work elevates Pex8 from an enigma to a central player in this critical biological process.

Read the full story and see the structures here: https://www.biorxiv.org/content/10.1101/2025.08.30.673231v1

#CellBiology #StructuralBiology #Peroxisome #ProteinImport #bioRxiv #Biochemistry
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Reposted by Greg Chojnowski
TVP World @tvpworld.bsky.social · 19/04/2025
Today marks the 82nd anniversary of the Warsaw Ghetto Uprising, recognized as the largest act of armed resistance undertaken by Jews during WWII. Launched against insurmountable odds, the rebellion is often cited as one of the defining moments in modern Jewish history.
tvpworld.com
82 years since the Warsaw Ghetto Uprising
The doomed Uprising led to the complete annihilation of Jewish Warsaw.
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Greg Chojnowski @gchojnowski.bsky.social · 15/02/2025
www.goodreads.com/quotes/99381... a grim reflection on the past and a projection of the future that has just arrived.
goodreads.com
A quote from A People’s History of the United States
The problem of democracy in the post-Revolutionary society was not, however, the Constitutional limitations on voting. It lay deeper, beyond the Constitu...
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Greg Chojnowski @gchojnowski.bsky.social · 08/02/2025
Finally!
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Greg Chojnowski @gchojnowski.bsky.social · 08/02/2025
High time to understand what's going on in there. Sadly, the historian's perspective is as depressing as that of Faulkner, Steinbeck or Bukowski.
Cover of the book of "A People's History of the United States" by Howard Zinn
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Greg Chojnowski @gchojnowski.bsky.social · 06/02/2025
I’m happy to share gapTrick, an AlphaFold2-based tool for characterising protein-protein complexes www.biorxiv.org/content/10.1...
biorxiv.org
gapTrick - Structural characterisation of protein-protein interactions using AlphaFold with multimeric templates
The structural characterisation of protein-protein interactions is a key step in understanding the functions of living cells. Models of protein complexes provide important insights into interaction me...
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Greg Chojnowski @gchojnowski.bsky.social · 01/02/2025
The book doesn't really explain why we sleep, but the message is very simple and convincing: "Go the f*k to sleep!". Highly recommended (the book too).
The cover of the book Why We Sleep by Matthew Walker
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Reposted by Greg Chojnowski
Randy Read 🇨🇦🇬🇧 @randyjread.bsky.social · 18/01/2025
This might be a good opportunity to remind people that experimental data (diffraction or cryoEM maps) have to be provided with the submission of papers to the IUCr society journals on Structural Biology, Acta Cryst D and F. So referees don’t even have to ask any more!
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Reposted by Greg Chojnowski
jankosinski.bsky.social @jankosinski.bsky.social · 04/12/2024
We have released version 2 of AlphaPulldown - a general pipeline for high-throughput structural modeling! Software: github.com/KosinskiLab/... Preprint: biorxiv.org/content/10.1...
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Reposted by Greg Chojnowski
EMBL @embl.org · 21/11/2024
EMBL is Europe’s life sciences laboratory. 🧬🧪 At our sites in Barcelona,​​ Grenoble, Hamburg, Heidelberg, Hinxton, and Rome, we seek to understand life in context, from molecules to ecosystems. 🔬🌍 Follow us for our latest news and updates about research, training, services and more. www.embl.org
embl.org
European Molecular Biology Laboratory
With 29 member states, laboratories at six locations across Europe and thousands of scientists and engineers working together, the European Molecular Biology Laboratory is a powerhouse of biological e...
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Reposted by Greg Chojnowski
Arjen Jakobi @cryotud.bsky.social · 18/11/2024
Really looking forward to welcoming & meeting the participants of our #EMBOStructBio course this morning! Many of our speakers/tutors are here: @moalquraishi.bsky.social @sykhalid.bsky.social @ezgikaraca.bsky.social @amjjbonvin.bsky.social @gchojnowski.bsky.social @drmelissagraewert.bsky.social
https://www.embl.org/about/info/course-and-conference-office/events/stb24-01/#vf-tabs__section-programme
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Reposted by Greg Chojnowski
Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 15/11/2024
New GPU-based MMseqs2: 20x faster searches on a single L40S (approx. as fast as a RTX 4090) vs. a 128-core CPU. This work enables to set up a very cost-efficient ColabFold MSA GPU server. 🧵🧵 📄 www.biorxiv.org/content/10.1... 💾 mmseqs.com 🗞️ developer.nvidia.com/blog/boost-a...
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Reposted by Greg Chojnowski
Structural Biology @actacrystd.iucr.org · 14/11/2024
How many of the PDB models that were solved using experimental phasing could have been solved by molecular replacement using models obtained from AlphaFold? #MolecularReplacement #AlphaFold2 #ComputationalMethods t.co/s6EahtcYms
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