Rewiring of RSK–PDZ Interactome by Linear Motif Phosphorylation Phosphorylation of short linear peptide motifs is a widespread process for the dynamic regulation of protein–protein interactions. However, the global…

www.sciencedirect.com/science/arti...
Some are more and others are less. In both directions of binding energy spectrum.

Thank you for this nice summary!

We also think that a major source of the inactive fraction is coming from nucleic acid content in the extract, however this is quite tricky to prove. Anyhow, this is not affecting the affinity so it is not causing a huge headache for most cases.

Just finished reading this lovely paper by @zbobo2.bsky.social , @teamgogl.bsky.social , Gilles Travé, and collaborators, describing a new technique for quantifying transcription factor:DNA binding without protein purification. A short reader's summary follows.

I think they are pretty much invisible for standard proteomics because of their small size, but the most common should be HPV E6/E7 oncoproteins in HeLa cell lines.

These are also class 3 PDZ binding motifs.

🧬 New paper in Nature Communications!
We found that POLE2,part of DNA polymerase ε,moonlights as a receptor for NPF motifs, binding 70+ proteins across replication, transcription & repair.
The interactome is more interconnected than thought.
@teamgogl.bsky.social 🇫🇮🇫🇷🇭🇺🇬🇧

www.nature.com/articles/s41...

Fantastic collaboration led by co-first authors Salla Keskitalo and Boglárka Zámbó, with colleagues in Helsinki, Nice, Strasbourg, Budapest & London. First paper from our independent team supported by ATIP-Avenir, ANR & Fondation ARC

NPF motifs were thought to mainly bind EH domains. Instead, we uncover a highly degenerate and interconnected NPF-mediated network — suggesting similar hidden complexity may exist for other short linear motifs.

We show that the non-catalytic subunit of DNA polymerase ε binds NPF tripeptide motifs in many proteins. Beyond leading-strand DNA synthesis, this reveals unexpected interaction networks linked to replication and genome maintenance.

Happy to share that our paper describing a new motif-mediated interactome is out in Nature Communications

www.nature.com/articles/s41...

👏 Félicitations à Gergő Gógl, chercheur @insermpacacorse.bsky.social à l'institut de Biologie Valrose, lauréat du programme Impulscience® de la Fondation Bettencourt Schueller.

👉 Découvrez les 7 scientifiques @cnrs.fr récompensés : www.cote-azur.cnrs.fr/fr/cnrsinfo/...

@teamgogl.bsky.social

ERC-Plus: jackpot science or missed chance to fix academia? My reflections on ERC-Plus, Europe’s newest ultra-competitive research grant and what it tells us about the academic culture we’re…

I just published: ERC-Plus: jackpot science or missed chance to fix academia?

My reflections on ERC-Plus, Europe’s newest ultra-competitive research grant and what it tells us about the academic culture we’re building.

medium.com/p/erc-plus-j...

6000 expectedly unsupported application is wrong resource management. Counting with a 20 page application that is 120,000 pages of refined scientific text. I may be slow, but it takes me a day to refine a page. 120k page would take me 330 years of work. Every year. Plus the work of the reviewers...

Thermodynamic principles link in vitro transcription factor affinities to single-molecule chromatin states in cells In vitro-derived insights into features that drive transcription factor binding to DNA, including motif-adjacent sequence, enable prediction of chromatin states and transcription factor occupancy in cells.

Now online! Thermodynamic principles link in vitro transcription factor affinities to single-molecule chromatin states in cells

The second part of our (with @origichals.bsky.social and El Hadji) two-part review on non-covalent SUMO interactions is now published, focussing on SUMO-interacting motifs (SIMs), but discussing also other confirmed or potential SUMO-interacting elements.

According to ChatGPT, this is a three-stranded coiled coil.

profaff.fr

The new ProfAff database is up and running. Although there are still many things to improve, it is a major upgrade.

This is great, so we are not the only one who saw this! But if this is a common observation, I am super puzzled why we find so many completely homogenous gfp localizations in the literature.

We are seeing this in multiple cell lines in confocal or TIRF microscopy. In the attached TIRF image you can see a non transfected cell with no GFP signal.

Bluesky, we need your help! Why does plain eGFP partially colocalize with actin filaments in cells? (No bleed-through, observed in multiple cell lines. Whole plasmid sequenced.) #FluorescenceFriday #Microscopy

Applicants should have a recent PhD completion (<6 months before recruitment) and proven skills in protein production and purification.
📍 Start: January | ⏳ 6-month contract (extendable)

The project focuses on mapping motif-mediated protein–protein interactions involved in key cellular processes like signaling and cancer, using cutting-edge biophysical interactomics approaches such as the native holdup assay.

The Quantitative Interactomics and Disease-Related Networks team at iBV (Nice, France) is recruiting a Postdoctoral Researcher with expertise in recombinant protein technologies and biochemistry.

The old ProfAff server served us well, but it’s time for an upgrade! Can’t wait to launch the new version from our new institute!

I am incredibly grateful to the ERC reviewers for their time and support. This recognition is a true honor and means a great deal to me. Excited to keep pushing forward the characterization of so-far unexplored motif-mediated protein–protein interactions!

GPT-5 seems like a pretty significant step towards PhD level. But a PhD-level researcher knows the literature, i.e., names of researchers and contents of key papers, much better. Or maybe it's only because we are working in a very niche field?

Today we got immediate desk rejection .... almost 8 weeks after submission! I think respectful journals could do better than this.

I’m thrilled to share that I have secured a permanent position within Section 20 of the CNRS. I will do my utmost to advance our understanding of the intricate interactome of transcription factors, an area of research I am deeply passionate about. 🎆

This is outstanding news for our lab, but maybe it's even more important in our personal lives! As an academic couple, we had to face the infamous #TwoBodyProblem. Not anymore, thanks to the French scientific system! Thank you @cnrs.fr and @inserm.fr for supporting us!#academiclife

Congratulations to Boglarka for obtaining a CNRS permanent position! 🎉🥂 She will start a new line of research in the Gogl lab focusing on the quantitative interactomics and biophysics of protein-DNA interactions and their consequences on transcription regulation and chromatin organization.