Thrilled to share our new Science paper! Predicting protein-protein interactions in the human proteome | Science www.science.org/doi/10.1126/...

And from other labs’ work this is really cool: www.science.org/doi/10.1126/...

New online: Cryo-EM structures reveal the molecular mechanism of SUMO E1–E2 thioester transfer

Allosteric activation of a ubiquitin ligase by an internal kinase domain! Congratulations to our team member Thornton Fokkens for this fascinating discovery in a neglected disease area with strong therapeutic need. Many thanks to all our great collaborators! www.sciencedirect.com/science/arti...

Are the lipids associated with static protein structures there as long-lived ligands or an effect of preferential solvation? This computational-experimental framework shows the way! #lipidtime #compchem www.nature.com/articles/s41...

The EMBO SUMO conference was great. A superb programme and atmosphere. Congratulations and thanks to the organisers!

Fantastic work coming out of Neil Hunter’s lab! www.nature.com/articles/s41...

Initial attempt at replicating in relion (parameters in next post). This is for Aca2-RNA, using a 100k subset of the 2D-classified particles (no prior 3D cleanup). A 1-class ab initio in relion, then local refinement in relion (1.8deg searches+blush) gives a nominally 3.3Å map; 3.5 Å w/out blush.

You’ve heard of ubiquitination, meet deazaguanylation: Doug Wassarman in our lab discovered phage defense pathways have co-opted Q nucleobase biosynthetic enzymes to catalyze a new form of protein conjugation chemistry @science.org www.science.org/doi/10.1126/...

Single-sequence deep learning delivers crystal-quality models of covalent K-Ras G12 hotspot complexes https://www.biorxiv.org/content/10.1101/2025.09.16.676163v1

Experimental verification is increasingly the bottleneck in protein design projects. In this paper, we develop a new mini-binder screening pipeline based on the microfluidic sizing technique called flow-induced dispersion analysis (FIDA). doi.org/10.1002/pro....

Happy to see that Spacedust is now published on Nature Methods! It combines sensitive Foldseek structure search and conserved neighborhood detection to discover functionally-associated gene clusters in prokaryotic & viral genomes. 1/6🧵

Liquid-liquid phase separation of HP1? Not in our mouse fibroblasts… This paper by the Fabian Erdel group offers a fresh perspective on how this can be reconciled with seemingly conflicting reports: The phase separation propensity of HP1 decreases from yeast → fly → mouse. doi.org/10.1038/s414...

Looks interesting (particularly for in silico affinity maturation) & code available on github: github.com/TencentAI4S/...

Thank you @aacrjournals.bsky.social for highlighting our recent study on PARP inhibitors and histone turnover! 🧬💊

I supervise an excellent postdoc who's looking for a postdoc or associate position in < 1 yr. Highly skilled in chem biol and biochem (peptide synthesis, native chem ligation, bacterial expression, purification, intein-based splicing, crystallography, interaction assays). Contact me if interested.

Sharing once again - and highly recommending - the postdoc positions with Antoni. One of the projects is a collaboration with us and the postdoc will include a sojourn in our lab.

Featuring #AlphaBridge features from @alvarezsalmoral.bsky.social, with @jonasteuwen.bsky.social and team, our new work from @nkinl.bsky.social nl.bsky.social @oncodeinstitute.bsky.social . Have a look at ahmpc.eu for more!

So happy to see these developments! Particularly the structure of the 29 kDa heterodimer of hemoglobin! Well done Oli & co! Of course can’t overlook the importance of sample prep and data collection - credit to Mark Herzik and Mengyu Wu

This review outlines how the ring-shaped RNA helicase Rho regulates bacterial gene expression, both genome-wide and at specific loci, using constitutive or alternative condition-dependent mechanisms bit.ly/4l22ICy

🔬 Postdoc in RNA Biology! Study Rho-dependent transcription termination in Helicobacter pylori using Helicase-SELEX for genome-wide mapping. 2-year position at the intersection of RNA biochemistry & bacterial genetics. 📩 Interested? DM to connect! #Postdoc #RNABiology #HelicobacterPylori #ScienceJob

Pleased to share our latest article on Rho-dependent transcription termination in Bacillus subtilis. Great collaboration with Sylvain Durand #IBPC and Elena and Vladimir Bidnenko #INRAE_DPT_MICA #CNRSchimie academic.oup.com/nar/article/...

OsSPT38 encodes a novel SUMO E3 ligase that enhances rice stress resilience and grain yield #research #MolecularPlant cell.com/molecular-pl...

New online: Computational design of sequence-specific DNA-binding proteins

Excited to share my postdoc work, out on bioRxiv today! Histones package DNA into nucleosomes to form the building blocks of chromatin, but how modular and programmable is this system? 1/9

E. coli transcription factors regulate promoter activity by a universal, homeostatic mechanism | Science www.science.org/doi/10.1126/...

I remember when, several years ago, we first discussed Ivan's idea that Ub may be covalently linked to ADPr in these cases. An interesting commentary on this new composite PTM, by Chatrin, Kang, and Ivan - some of the key people contributing to its detection in vitro and its ongoing study in cells.

La-Proteina from NVidia to do co-design of fully atomistic protein structures (sequence + side-chains + backbone) for up to 800 residues is now open source with permissive licensing 🖥️ github.com/NVIDIA-Digit... 🗎 arxiv.org/abs/2507.09466

Read our comment on the rise of ADP-ribose-Ubiquitin hybrid modification. It's been fun to see it grows :)

Update: RareFold 🧬 Our AI framework for protein design with 29 noncanonical AAs now shows designed binders (linear + cyclic) are non-immunogenic in patient-derived assays — paving the way for safe next-gen peptide therapeutics. 👉https://www.biorxiv.org/content/10.1101/2025.05.19.654846v2

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

📢 New preprint: Aromatic Ring Flips Reveal Reshaping of Protein Dynamics in Crystals and Complexes. We addressed a long-standing question that people debated already in the 1970s - but it still remained open: Do proteins in crystals move as they do in solution? We used ring flips to find out. 1/n

WARM congratulations to: Tom DENDOOVEN, @martinpacesa.bsky.social, @mschuhmacher.bsky.social , @lfmilles.bsky.social, @preinerin.bsky.social,Markus Hopfler, @charleneboumendil.bsky.social, Gergo Gogl, @shifralansky.bsky.social, @alexanderbelyy.bsky.social,Erik Benson, @dbojar.bsky.social! 🤩 #ERCStG

Pre-print: our description of RZ affiliate ZNFX1 is now online. On binding viral RNA, ZNFX1 generates parallel Ub currents, coordinating Ub-dependent RNA silencing and aggregate resolution. Huge effort from first authors Dan Squair and @eilidhrivers.bsky.social www.biorxiv.org/content/10.1...

🚨 We're hiring, please share! The FMI seeks a tenure-track Group Leader (Assistant Prof) in Structural Biology 🔬 Innovative scientists in genome regulation, RNA metabolism, or protein homeostasis—especially using cutting-edge approaches—apply now at www.fmi.ch/education-ca...

We’re happy to share that our labs first #ALS and #FTD study “A stress-dependent TDP-43 SUMOylation program preserves neuronal function” is now online at Molecular Neurodegeneration! doi.org/10.1186/s130...

VEL-dependent polymerization maintains the chromatin association of Polycomb proteins for the switch to epigenetic silencing

I supervise an excellent postdoc who's looking for a postdoc or associate position in < 1 yr. Highly skilled in chem biol and biochem (peptide synthesis, native chem ligation, bacterial expression, purification, intein-based splicing, crystallography, interaction assays). Contact me if interested.

Was fun to work on this manuscript - never would have thought that an E1 enzyme could be involved in selecting a particular #ubiquitin -like protein isoform over another!

Amazing work with solid experimental backing and crystal structures. BindCraft is here to stay.

A reminder that our lovely Centre de Biophysique Moléculaire is here: @cbm-upr4301.bsky.social. Started by Charles Sadron in the 1960s, it has been part of an effort to decentralise French science and one of the pioneering places for biophysics. Now a medium-sized lab at the bio/chem/phys interface.

Delighted to share our work on cellular ubiquitination of drug-like compounds by HUWE1 - a surprising journey! Kudos to all contributors & first authors, Barbara Orth and Pavel Pohl. Sincere thanks to @ireserra.bsky.social ‬ #NatCommun for expertly guiding the winding publishing path. rdcu.be/eDzPk

Quite proud of this one. Our review on AI-designed de novo binders out now in Structure. We give a brief history, outline the current ecosystem, highlight some standout applications and discuss the need for regulatory discussions. 🤖🧪🔬

Are you a postdoc interested in the mechanisms of disease? Do you have a great record and an exciting vision? Come and start your own lab @dunnschool.bsky.social by applying for sponsorship for early career fellowships. Deadline 30th September...pass it on! www.path.ox.ac.uk/work-with-us...

We are happy to have contributed a protocol to a book on SUMO methods (work mainly by postdoc El Hadji Cisse and engineer Stéphane Goffinont): link.springer.com/protocol/10....

📣 Happy to share our last publication on SUMOylation and Natural Killers in AML. aacrjournals.org/mct/article-...

Scientists uncovered how the immune protein ZNFX1 enables cells to walk the fine line between fighting infection & avoiding autoimmune damage. ZNFX1 can ubiquitinate & compact host & viral RNA into molecular condensates, extending ubiquitin biology to RNA itself. More: www.imp.ac.at/news/article...

Researchers around @clausenlab.bsky.social & @dangrabarczyk.bsky.social have unveiled the three-dimensional structure of UBR4, a giant protein complex that safeguards cells by targeting defective proteins for destruction—offering fresh insights into health & disease. www.science.org/doi/10.1126/...

For life to emerge on Earth, peptides must first have formed without the aid of enzymes — but how? Reactions of sulfur-containing molecules might have been key go.nature.com/4oX04jC

Happy to share our work on the structure and function of the unusual E3 ligase ZNFX1 @cp-cell.bsky.social. It uses a nucleic acid-activated transthiolation mechanism, ubiquitinating and clustering RNA to protect cells in an immune response. @clausenlab.bsky.social www.cell.com/cell/fulltex...