Max Bonomi
@bonomimax.bsky.social
1.4K followers 2.8K following 32 posts
Head of Computational Structural Biology Lab @pasteur.fr. ERC-CoG 2022. Research Director DR2 @cnrs.bsky.social. Founder/developer @plumed.org
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bonomimax.bsky.social
🚀 Super excited to share our new work, led by @vschnapka.bsky.social bAIes, a Bayesian framework for generating accurate atomic-resolution ensembles of IDPs using #AlphaFold info! Now on @biorxivpreprint.bsky.social → feedback welcome! @pasteur.fr @erc.europa.eu

www.biorxiv.org/content/10.1...
www.biorxiv.org
bonomimax.bsky.social
Yep I think this also is feasible!
bonomimax.bsky.social
Ahah I thought you were commenting on the other bioRxiv. My fault. In any case, the answer is yes!
bonomimax.bsky.social
Yes, if some low res density is actually there. Same for semi-ordered waters, lipids or glycans 🎉
bonomimax.bsky.social
❄️ Even high-resolution #cryoEM maps can still hide a few secrets 🔍 Discover how we uncover them in this exciting collaboration with @egreene.bsky.social @fraserlab.com @pasteur.fr @cnrsbiologie.bsky.social

📄 Preprint: www.biorxiv.org/content/10.1...
Product-stabilized filamentation by human glutamine synthetase allosterically tunes metabolic activity
To maintain metabolic homeostasis, enzymes must adapt to fluctuating nutrient levels through mechanisms beyond gene expression. Here, we demonstrate that human glutamine synthetase (GS) can reversibly polymerize into filaments aided by a composite binding site formed at the filament interface by the product, glutamine. Time-resolved cryo-electron microscopy (cryo-EM) confirms that glutamine binding stabilizes these filaments, which in turn exhibit reduced catalytic specificity for ammonia at physiological concentrations. This inhibition appears induced by a conformational change that remodulates the active site loop ensemble gating substrate entry. Metadynamics ensemble refinement revealed >10 Å conformational range for the active site loop and that the loop is stabilized by transient contacts. This disorder is significant, as we show that the transient contacts which stabilize this loop in a closed conformation are essential for catalysis both in vitro and in cells. We propose that GS filament formation constitutes a negative-feedback mechanism, directly linking product concentration to the structural and functional remodeling of the enzyme. ### Competing Interest Statement HY is an employee of JSR. J.S.F. is a consultant to, a shareholder of, and receives sponsored research support from Relay Therapeutics. National Institutes of Health, https://ror.org/01cwqze88, F32GM144982, R35GM145238
www.biorxiv.org
bonomimax.bsky.social
Any sticker left for a colleague? 😜
bonomimax.bsky.social
🔧 Try it now with the dev version of @plumed.org
📂 Reproducibility: www.plumed-nest.org/eggs/25/014
📚 Tutorial (coming soon): www.plumed-tutorials.org
bonomimax.bsky.social
🚀 Super excited to share our new work, led by @vschnapka.bsky.social bAIes, a Bayesian framework for generating accurate atomic-resolution ensembles of IDPs using #AlphaFold info! Now on @biorxivpreprint.bsky.social → feedback welcome! @pasteur.fr @erc.europa.eu

www.biorxiv.org/content/10.1...
www.biorxiv.org
Reposted by Max Bonomi
bussilab.org
Our integrative approach using #MD and #cryoEM data to construct structural ensembles of #RNA just published on @natcomms.bsky.social doi.org/10.1038/s414... Lead by Elisa Posani, with @magistratolab.bsky.social @bonomimax.bsky.social @pjanos.bsky.social @navtejtoor.bsky.social and Daniel Haack 🎉
Reposted by Max Bonomi
psb-grenoble.bsky.social
🧬PSB Symposium on " #MachineLearning in Cellular #StructuralBiology ", EPN Campus Grenoble, France, 26-27 June 2025🧬

📢Reminder - Call for abstracts (posters & short talks)
Submission & registration deadline 25 May: www.psb-grenoble.eu/psbsymposium...

@esrf.fr @embl.org @illneutrons.bsky.social
bonomimax.bsky.social
AlphaFold’s success builds on decades of tech advances, massive efforts to collect, curate, and share structural data, and rigorous benchmarking. What will it take to see a similar leap in structural ensemble prediction? @stephanieaw.bsky.social and I share some thoughts here 👇 Feedback is welcome!
stephanieaw.bsky.social
Predicting macromolecular ensembles is incredibly promising. However, as no single experimental method can map a conformational ensemble’s full atomistic landscape, there are foundational questions: What exactly are we trying to predict, and how will we know when we have succeeded?
From Possibility to Precision in Macromolecular Ensemble Prediction
Proteins and other macromolecules do not exist in a single state but as dynamic ensembles of interconverting conformations, which are essential for functions such as catalysis, allosteric regulation, ...
arxiv.org
bonomimax.bsky.social
Last session is about "Ethics and AI", with a fantastic lecture from Julie Allouche @pasteur.fr and Pierre Noro @pierrenoro.bsky.social @sciencespo.bsky.social
bonomimax.bsky.social
Next is technical challenges related to developing/using AI with Youssef Ghorbal and Thomas Menard
bonomimax.bsky.social
Last day of our "AI for Life Sciences" course @pasteuredu.bsky.social This morning we talk about Intellectual Property & AI with Nicolas Torno and Helene Chommy from DARRI @pasteur.fr
bonomimax.bsky.social
Final thematic session of our "AI for Life Sciences" is "AI in Neuroscience" with Jean-Baptiste Masson @pasteur.fr
@pasteuredu.bsky.social
bonomimax.bsky.social
It is now time for "AI in Structural Biology" with Guillaume Bouvier: AlphaFold and beyond! Short talks by @bardiauxb.bsky.social Ludovic Sauguet Vincent Schnapka and @duyvd.bsky.social @pasteur.fr @pasteuredu.bsky.social
Reposted by Max Bonomi
cantinilab.bsky.social
AI for life sciences day 2 started!

@m-albert.bsky.social is now teaching AI for image analysis. Felipe Llinares from Bioptimus will then talk about LLMs, with short talks from @jkobject.com from my team and @emordret.bsky.social from @audeber.bsky.social team.

@pasteur.fr @pasteuredu.bsky.social
bonomimax.bsky.social
We are back with our "AI for life sciences" course @pasteur.fr @pasteuredu.bsky.social with a deep dive into Neural Networks with @vincentmallet.bsky.social
Reposted by Max Bonomi
cantinilab.bsky.social
📢Here WE go!!! AI for life sciences course kicking off at @pasteur.fr with a lecture from @laineelodie.bsky.social.

Happy to see so many students on campus interested in AI!
@bonomimax.bsky.social @pasteuredu.bsky.social
bonomimax.bsky.social
If you are at @pasteur.fr today, come see @bussigio.bsky.social at 11AM in Salle Retrovirus. You won’t regret it #rna #cryoEM #coolscience @ipdbsc.bsky.social
bussilab.org
Our research presented today at @pasteur.fr ! @bussigio.bsky.social will give a seminar sharing our approaches to reconstruct #RNA dynamics using #moleculardynamics, #cryoEM, secondary structure prediction, and #DMS probing. Host @bonomimax.bsky.social
bonomimax.bsky.social
Looking forward!!!
Reposted by Max Bonomi
bonomimax.bsky.social
Always a pleasure Paul!!!
bonomimax.bsky.social
This might be controversial: what can we learn about IDPs from Alphafold? Starting soon in Room 502B #bps2025
bonomimax.bsky.social
Thanks Nadia! I was fighting the jet-lag 🏋️‍♀️