Happy to re-share Giacomo Pedrelli's paper published in PNAS with contributions from a few of us from the Vorobieva lab:

"Negative design enables cell-free expression and folding of designed transmembrane β-barrels"

#proteindesign #denovodesign #nanopores #TMBs #OMPs #porins #membraneproteins

"Negative design enables cell-free expression and folding of designed transmembrane β-barrels" published in @pnas.org

Now that I know it will advance all sciences, I have to learn more about the "DNA wall". Google only finds wallpapers depicting DNA...

"H2O2-assisted plasma discharge caused a reduction in colony-forming units (CFUs) and disabled the process of the regeneration of V. cholera, as well as DNA wall distortion. [...] This research will provide baseline data for the advance of the biological, medical, and agricultural fields [...]"

Honoured to be selected as a new member of the Jonge Academie! 🎓
I look forward to contributing to science & tech policy through surveys and stakeholder consultations. I’m also eager to leverage international networks to shape a fair, safe, and sustainable future for academia in Belgium & Europe 🇧🇪 🇪🇺

Australian tropical rainforest trees switch in world first from carbon sink to emissions source Researchers say carbon emissions change in Queensland tropical rainforests may have global climate implications

This research paper is the first time that a tipping point of a switch from a carbon sink to a carbon emission source in tropical rainforests has been identified clearly – not just for one year but for the last 20 years. Cause is a change in the local climate. www.theguardian.com/environment/...

I'm excited to announce that from today I will work in the @bio2byte.bsky.social research group at the (IB)2 ULB-VUB Interuniversity Institute for Bioinformatics and @vubrussel.bsky.social DBIT-SBB as a Senior Postdoctoral Researcher.

Link to the article: doi.org/10.3390/biom...

Excited to share our latest work on tandem #SH3 binding among the p47phox-related proteins. We define the optimal binding preference of tandemly arranged SH3 domains and propose new #motif instances. Structure predictions suggest the possibility of a reverse binding mode for certain #SLiM instances.

Phase-separating fusion proteins drive cancer by upsetting transcription regulation - Genome Biology Background Numerous cellular processes rely on biomolecular condensates formed through liquid–liquid phase separation (LLPS). Recently, it has become evident that somatic mutations can interfere with ...

Catching up after not being too active recently:
In one of our most #interdisciplinary #multimodal research articles published last year, we demonstrated that #LLPS #condensate dysregulation is very widespread in somatic #cancer. We also provided mechanistic explanations for #oncofusion #proteins.

Great news!!!

Is it close to PhD level? 😁

GPT-5:

You’d like a sentence pair where the English sentence has at least 6 words, and the German translation is about twice as long in characters:

English (44 characters, 7 words):
She always takes the train to work.

German (90 characters, 9 words):
Sie fährt immer mit der Eisenbahn zur Arbeit.

The field is huge, I just meant how commonly this term has been used as of now... Tbh, I would really mind seeing back this term more often, as long as it is well defined somewhere in the manuscripts.

I just checked if people use the term epiproteomics, and actually I see 11 publications in PubMed with this term. Global changes in the PTMs of the proteome could be called epiproteomics, I guess...

I tried Mongozo buckwheat white beer and it was quite good :)

Targeting disordered proteins

Targeting protein disorder: the next hurdle in drug discovery www.nature.com/articles/s41...
rdcu.be/eqaY3

Intrinsically disordered proteins are often dysregulated in disease, but have been considered ‘undruggable’. This new Review discusses approaches that could tackle this barrier

#NatureReviews #DrugDiscovery #ProteinDisorder #ProteinEnsembles #TranscriptionFactors #BiomolecularCondensates #LLPS #imods #IDP #IDPs #HTS #HCS #Biophysics #StructuralBiology #Bioinformatics #ComputationalModeling #MolecularDynamics @viblifesciences.bsky.social @vubrussel.bsky.social

Targeting protein disorder: the next hurdle in drug discovery - Nature Reviews Drug Discovery Intrinsically disordered proteins are frequently dysregulated in many diseases, but because of their heterogeneous, highly dynamic structural states they have been considered largely ‘undruggable’ by ...

🚨 New Review in @natrevdrugdiscov.nature.com!

We reviewed how to #drug intrinsically disordered proteins ( #IDPs) 🧬

Among many others, we touch upon:
🧪 IDP modulators (i-mods) in clinical trials;
🔬 Exp.+comp. synergy;
🚀 A path forward to target IDPs

📖 Read more: doi.org/10.1038/s41573-025-01220-6

This is very cool! 🤩

I think it is around 45 minutes for lecture, then I usually change the topic or have interactions (or have a short break) to freshen up, and then use the second part of the 2h slot of teaching for a slightly or totally different topic. But anyway I prefer the maximally interactive format 🙂

Basically describes something like AF2-3 with either atom coordinate prediction or torsion angle prediction for modeling a protein structure or protein-ligand complex.

Wow, this surprised me!

It's back for us!

Nothing from the #NIH domain seems to be accessible to me (from Belgium)

I cannot access #PubMed or #PubChem. Are they down???

The author rather used a Proton Mail address for contact info than the EPFL email address. It tells me something... 😏

From 2012 to 2019, the retraction rate was relatively stable, with an average retraction rate of 0.10%. However, the retraction rate rose sharply after 2019 and reached 0.53% in 2023, and the growth rate of retracted articles (91.92%) outpaced the growth rate of published papers (32.3%) during 2019–2023

In #China, the #publication #retractation rate is ~10x higher than 5 years ago. 😮
Some of the reasons why this is happening are well-understood.

📰 Source: journals.plos.org/plosone/arti...

C9orf72-linked arginine-rich dipeptide repeats aggravate pathological phase separation of G3BP1 | PNAS The toxic effects of C9orf72-derived arginine-rich dipeptide repeats (R-DPRs) on cellular stress granules in amyotrophic lateral sclerosis (ALS) an...

Our latest #C9orf72 ALS paper is out demonstrating biomolecular #condensation of #G3BP1 driven by R-DPRs:
📰 C9orf72-linked arginine-rich dipeptide repeats aggravate pathological phase separation of G3BP1 🔬
www.pnas.org/doi/10.1073/...

#neurodegeneration #MND #ALS #endALS #FTD #LLPS

You can also find the shorter forms of these in AFDB:
alphafold.com/entry/H9T8G6
alphafold.com/entry/A0A3C0...
and I'm wondering if the one below is a different evolutionary path where the beta-helix "spiky" part is followed by more than a dozen MBG adhesin(?) domains:
alphafold.com/entry/Q9HVG6