Matthieu Chavent

Han, Connolly, Ohi, Kenworthy et al. explore the evolutionary history of #caveolins. Using computational predictions & #CryoEM, the authors show both animal & choanoflagellate caveolins assemble into amphipathic disks composed of seven conserved structural elements. rupress.org/jcb/article/...

How PGL finds a sweet spot in phospholipid membranes – a combined multiscale MD and NMR study Glycolipids from pathogenic Mycobacterium tuberculosis (Mtb) play important roles during the interaction of the pathogen with macrophages, and can shape the host cell’s immune response by modulating i...

our new article combining MD and NMR to understand the positioning of phenolic glycolipids from mycobacteria in phospholipid membranes is now in @biophysj.bsky.social ! 🥳

"How PGL finds a sweet spot in phospholipid membranes – a combined multiscale MD and NMR study"

www.cell.com/biophysj/abs...

We are proud to be a founding contributor to lipidinteractome.org, a repository developed by @tafesselab.bsky.social & Schultz lab to increase accessibility to proteomics data from multi-functionalized lipid analogs! Check out the website & preprint: arxiv.org/abs/2507.23101 #lipidtime

Miam!! 🤤

Cardiolipin acyl chain composition tailors the conformation of mammalian ATP synthase dimers - Communications Chemistry Structure and function in mitochondrial cristae are shaped by interactions between ATP synthase dimers and cardiolipin lipids, but the underlying mechanisms remain unclear. Here, using molecular dynam...

Cardiolipin acyl chain composition tailors the conformation of mammalian ATP synthase dimers

www.nature.com/articles/s42...

Enhanced Sampling and Tailored Collective Variables Yield Reproducible Free Energy Landscapes of Beta-1 Adrenergic Receptor Activation The beta-1 adrenergic receptor (ADRB1) is a critical target for cardiovascular drugs, yet our understanding of how it is activated remains incomplete. Capturing the concerted interplay of agonists, solvent, ions, and protein microswitches is a significant challenge for conventional simulation methods and is essential for unraveling this process. Here, we address this challenge by implementing a powerful enhanced sampling framework that integrates the OneOPES enhanced sampling algorithm with a set of biologically motivated collective variables (CVs). These CVs are designed to track several key features of the activation process simultaneously, including rearrangement of conserved microswitches, the state of the sodium ion binding pocket, and dynamics of critical water molecules. Using this framework, we mapped the multidimensional free energy landscapes of the ADRB1 receptor in both its apo- and adrenaline-bound holo states. Our analysis reveals a detailed, stepwise activation pathway that quantifies the known modulatory roles of sodium ions and protonation states and identifies essential water-mediated networks that stabilize the active conformation. This work provides a detailed overview of ADRB1 activation and establishes the robustness of our OneOPES approach for investigating complex activation mechanisms with the potential for application to other Class A GPCRs.

New in @pubs.acs.org JCTC: We've mapped the complete activation pathway of the β1-adrenergic receptor using our OneOPES enhanced sampling method and tailored CVs. Our approach reveals how sodium ions, water networks & protein microswitches work together. pubs.acs.org/doi/full/10.... #GPCR

We have two open Post-Doc positions in my group at the interface with:
1- @ataly.bsky.social for molecular dynamics
2- Bruno Guillotin from protein mobility

Apply by sending CV, two ref letters and a short motivation letter to me : emmanuelle.bayer@u-bordeaux.fr. Deadline 15 sept.

2 yrs ago @yiechanglin.bsky.social sent me this movie of lipid scrambling by OSCA1.2. Now we show it’s common to WT OSCA/TMEM63 proteins, mechanically activated, cholesterol dependent, and protects cells from damaging forces. Awesome collab with @charlesdcox.bsky.social &Zhang lab. tiny.cc/tmem63

🚀 New preprint out!

"Fast Parameterization of #Martini3 Models for Fragments and Small Molecules" is now on #bioRxiv

👉 doi.org/10.1101/2025...

#AutoMartiniM3 – tool for automated #CG modeling. With @matthchavent.bsky.social, @tbereau.bsky.social and others.

#CoarseGraining #MD #DrugDiscovery

@cg-martini.bsky.social this may interest the MARTINI community! 😃

GitHub - Martini-Force-Field-Initiative/Automartini_M3 Contribute to Martini-Force-Field-Initiative/Automartini_M3 development by creating an account on GitHub.

code available here: github.com/Martini-Forc...

Fast parameterization of Martini3 models for fragments and small molecules Coarse-grained molecular dynamics simulations, such as those performed with the recently parametrized Martini 3 force field, simplify molecular models and enable the study of larger systems over longe...

The preprint of @szczukam.bsky.social presenting our collaborative work with @pauloctsouza.bsky.social and @tbereau.bsky.social labs is now online!

You want to parametrize small molecules with Martini3 ff try our automatized approach!

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

Navigating protein landscapes with a machine-learned transferable coarse-grained model - Nature Chemistry The development of a universal protein coarse-grained model has been a long-standing challenge. A coarse-grained model with chemical transferability has now been developed by combining deep-learning m...

Our development of machine-learned transferable coarse-grained models in now on Nat Chem! doi.org/10.1038/s415...
I am so proud of my group for this work! Particularly first authors Nick Charron, Klara Bonneau, Aldo Pasos-Trejo, Andrea Guljas.

1/6 One of the key features of functional proteins is their inherent structural flexibility. In our recent work at #ICML, we introduce flexibility to protein structure design! More in a thread below.

Code / Tutorial: github.com/graeter-grou...
Poster: W-109, Thu 17 Jul 11 a.m. PDT — 1:30 p.m. PDT

Complete collection of the COSB edition on New Concepts in Drug Discoverythat Rod Hubbard and I edited is now online. My deepest thanks to all authors for their excellent articles!

www.sciencedirect.com/special-issu...

MDAnalysis User Group Meeting (logo)

Come to the @mdanalysis.bsky.social User Group Meeting at Arizona State University in November. See www.mdanalysis.org/2025/07/15/u... for our keynote speakers and more updates.

Great opportunity for junior researchers to present their work and to network with the MDAnalysis community.

Colin Kleanthous' fundraiser for Motor Neurone Disease Association Help Colin Kleanthous raise money to support Motor Neurone Disease Association

My wonderful colleage Colin Kleanthous is raising money for the MND association. Please support Colin in this worthy endeavor! www.justgiving.com/page/colin-k...
(Please repost!)

🚨 If you haven’t seen it yet…

📢 The NIH BioArt Source provides a library of FREE professionally designed illustrations and icons, available for anyone to use. They can be Downloaded in High Definition.

Check it out at bioart.niaid.nih.gov

High‐Speed Atomic Force Microscopy Reveals the Dynamic Interplay of Membrane Proteins is Lipid‐Modulated High-speed atomic force microscopy captures the lipid-dependent clustering dynamics of pentameric FocA and tetrameric GlpF in supported lipid bilayers. Protein mobility, cluster stability, and packin....

onlinelibrary.wiley.com/doi/10.1002/...

Scalable emulation of protein equilibrium ensembles with generative deep learning Following the sequence and structure revolutions, predicting functionally relevant protein structure changes at scale remains an outstanding challenge. We introduce BioEmu, a deep learning system that...

BioEmu is now on @science.org ! The revised version includes an upgraded model and makes a lot of MD simulation data internally generated at MSR available to the public. This took a lot of firepower from us in the last two years.
www.science.org/doi/10.1126/...

@biophysicalsoc.bsky.social T&C Subgroup, nominations due in a few weeks! Let's celebrate the contributions that are shaping our field 🎉🧬💻🔬

It was great to help out the lipids with these two Mycobacterial enzymes. Fantastic work from the Mancia lab!

An Evaluation of Biomolecular Energetics Learned by AlphaFold
by Lyu, Herschlag et al
doi.org/10.1101/2025...

Interesting comparison of AF2/3 structures with the PDB (AF2 appears better)

Reminder: The PDB itself is probably biased relative to solution conformational ensembles and energetics

Thank you Serge! CNRS concours are done for me! I have to say: quite a relief! 😅

Merci Robin! 😄

Thank you Stefano! :)

This is now official: I got a CNRS "Directeur de Recherche" position!

I would like to thank all my collaborators and colleagues as well as the members of my team with whom I have the chance to do great science that was credited by this position. 🙏

A stylized image of the molecular model of a mitochondrial crista, with proteins and lipids shown

What better way to use my first proper post than to share my first big piece of post-doctoral work with @cg-martini.bsky.social!
Here, we used integrative modelling to build and simulate a mitochondrial cristae.
Find the paper here (rdcu.be/eujAC) or see below for a quick overview 👇

Join our data curation team!

We are looking for a talented structural biologist or bioinformatician to join the data curation team at PDBe.

Location:
Hinxton, Cambridgeshire, UK

Last date to apply: 03/08/2025

Apply here: embl.wd103.myworkdayjobs.com/en-US/EMBL/j...