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Reposted by Greg Chojnowski

Matthias Wilmanns @matthiaswilmanns.bsky.social · Sep 3

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 · Apr 19

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.

82 years since the Warsaw Ghetto Uprising

The doomed Uprising led to the complete annihilation of Jewish Warsaw.

tvpworld.com

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Greg Chojnowski @gchojnowski.bsky.social · Mar 27

There may be issues with mappings of some depositions, but the repo doesn't check/solve this. It only parses what's in the PDB already.

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Greg Chojnowski @gchojnowski.bsky.social · Mar 27

It seems to use the same ebi api as www.uniprot.org/id-mapping

UniProt

UniProt is the world's leading high-quality, comprehensive and freely accessible resource of protein sequence and functional information.

www.uniprot.org

Greg Chojnowski @gchojnowski.bsky.social · Feb 15

www.goodreads.com/quotes/99381...

a grim reflection on the past and a projection of the future that has just arrived.

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...

www.goodreads.com

Greg Chojnowski @gchojnowski.bsky.social · Feb 8

Finally!

Cooty McCootFace @cootymccootface.bsky.social · Feb 7

HOLE-y!
An implementation of Oliver Smart's HOLE now available in Coot 1
Linear Gramicidin D - 2y5m - behold the lipid phase!
Coot 1.1.12 out soon
#coot

Greg Chojnowski @gchojnowski.bsky.social · Feb 8

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

Greg Chojnowski @gchojnowski.bsky.social · Feb 6

code and a Colab notebok are avilable at
github.com/gchojnowski/...

GitHub - gchojnowski/gapTrick: rebuilds and completes models of protein complexes using AlphaFold2

rebuilds and completes models of protein complexes using AlphaFold2 - gchojnowski/gapTrick

github.com

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Greg Chojnowski @gchojnowski.bsky.social · Feb 6

- identifies crucial contacts; very useful for selecting mutagenesis targets

- fixes model geometry. In cryo-EM, stereochemistry is usually the best priors you have!

- helps predicting models of weak complexes that AlphaFold3 cannot

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Greg Chojnowski @gchojnowski.bsky.social · Feb 6

I’m happy to share gapTrick, an AlphaFold2-based tool for characterising protein-protein complexes

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

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...

www.biorxiv.org

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Greg Chojnowski @gchojnowski.bsky.social · Feb 1

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

Reposted by Greg Chojnowski

Randy Read 🇨🇦🇬🇧 @randyjread.bsky.social · Jan 18

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!

Basil Greber @bjgreber.bsky.social · Jan 18

Peer review pet peeve: I ask for maps & coordinates for review, editor says “yes, of course, we will get these to you”. And then nothing happens until the “your review is (over)due” reminders pour in. You want me to do a proper job or just submit whatever other ramblings I might have come up with?

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Reposted by Greg Chojnowski

jankosinski.bsky.social @jankosinski.bsky.social · Dec 4

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 · Nov 21

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

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...

www.embl.org

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Reposted by Greg Chojnowski

Arjen Jakobi @cryotud.bsky.social · Nov 18

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 · Nov 15

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 · Nov 14

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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Greg Chojnowski @gchojnowski.bsky.social · Nov 13

there are 2fofc/fofc maps in ccp4 format available in @pdbeurope.bsky.social (EDS map/difference map) and you can open them in coot. but why don't you just fetch them directly in moorhen.org?

Moorhen

Moorhen is a molecular graphics web application based on the Coot desktop program.

moorhen.org

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Greg Chojnowski @gchojnowski.bsky.social · Nov 13

Thanks!

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