Matthieu Chavent

PhD positions in my lab (AI for Science), but with special preference for people who complement our current activities or are enthusiastic about contributing to our on going work. Looking for technically strong, independent and proactive candidates. www.chalmers.se/en/about-cha...

Structural basis for domain coupling in heteromeric glycine receptors revealed by an atypical allosteric agonist Counteracting ligands stabilize glycine receptor states revealing mechanisms of pentameric ligand-gated channel allostery.

Check out our latest paper on the glycine receptor with
@chakrapanilab.bsky.social

where we show the interplay between the orthosteric and allosteric binding sites.

www.science.org/doi/10.1126/...

New preprint: “When lipids embrace RNA”

www.biorxiv.org/content/10.6...

Using multiscale simulations (🍸 #Martini + constant-pH MD), we show that:

• Local pKa ≠ global pKa
• Endosomal escape is limited by persistent protonation.

#LNP #MolecularDynamics

Model of mitochondrial compartments. The assembly of the mitochondrial model based on an experimentally informed membrane structure (white), from an empty structure (left) into a mask representation of the IMS (yellow) and matrix (pink) compartments represented by 3 nm voxels. Structures are packed into their assigned compartments based on the mask. In the last section and the magnified inset, structures are colored by kind: Proteins (green), RNA (dark blue), metabolites (pale blue).

Our paper about Bentopy is now published in Protein Science!

Bentopy makes assembling large-scale MD models accessible and fast.

doi.org/10.1002/pro....

@janstevens.bsky.social, @cg-martini.bsky.social

Cutaway and close-up views of a Martini coarse-grained whole-cell model of JCVI-syn3A, showing the densely packed cytoplasm with proteins, RNA, metabolites, and chromosome inside a lipid membrane with embedded membrane proteins

Our paper on [Bentopy](doi.org/10.1002/pro....) is out in Protein Science! We developed Bentopy to make assembling large-scale MD models more accessible, building on what we learned from trying to simulate whole-cell models. Here's our updated Martini JCVI-syn3A cell model👇

Beautiful and extensive work from the @carobarisch.bsky.social and @soldatilab.bsky.social labs demonstrating that nutrient utilization in intracellular mycobacteria is dependent on their intracellular location.

Visionary work!!

www.biorxiv.org/content/10.6...

Happy that simulations, performed by Gabriel Diaz, stellar master student in the team, helped to decipher how PIP2 lipids help recruiting Munc13 protein to prime synaptic vesicle Collaborative work led by F. Pincet @normalesup.bsky.social

full story at @pnas.org : www.pnas.org/doi/10.1073/...

Lipids challenge ligands to control receptors

The behaviour of a receptor protein can be influenced by the presence of certain lipids in the membrane it is embedded in.

🔗 buff.ly/G1Zl6cZ

Excited to share the upcoming CECAM workshop: “Accessibility, Inclusivity & Visibility in Computational Chemistry”!

📅 Apr 22–24, 2026
📍 Lyon (hybrid)
💸 Free registratration: deadline Mar 31

Join us to discuss how to make #Compchem more inclusive & accessible. Contributed talks welcome!

YouTube video by Build-a-Cell Build-a-Cell seminar James Saenz: Harnessing minimal cells to understand the living membranes

How do lipids shape life? I explore this question in my recent talk for the Build-a-Cell 🦠 seminar series. Thanks to @kateadamala.bsky.social for hosting! Watch it here: youtu.be/JnF7hPCiSbI?...

Please share!!! I am looking for a postdoctoral researcher to join us. Focus will be on exciting collaborative projects on lipids and membrane biology, pushing the boundaries of in silico "reconstitutions". Previous experience with molecular dynamics simulations of biological systems a strong plus!

AGDG

This project is joint with fab computational biologist @mattbashton.bsky.social - great opportunity to learn computational and molecular biology skills

When cryo-EM modeling meets structure prediction Nature Structural & Molecular Biology, Published online: 23 January 2026; doi:10.1038/s41594-026-01744-4Accurately interpreting density maps into atomic models is a central yet challenging goal of cryo-EM. Two studies now reveal distinct ways in which protein structure prediction can be incorporated into cryo-EM model building to enable more accurate and robust automated construction of protein atomic models from density maps.

New online: When cryo-EM modeling meets structure prediction

Go #TeamTomo! 🧪 @wilflinglab.bsky.social & @nanigrotjahn.bsky.social are on a roll! Beautiful in-cell visualization of lysosome rupture 🎈💥

Have you registered yet? Early bird registration and abstract submission are open until January 31.
mosbacher-kolloquium.org

An off-brand Lego model of Terry Pratchett's Discworld

Got meself a wee project which took up my whole evening, I think people call this kind of thing a "timeline cleanse"?

A dynamic displacement mechanism drives protein import into mitochondria Most mitochondrial proteins are produced in the cytosol and imported through the translocase of the outer mitochondrial membrane (TOM) to reach their final destination. Although this protein entry gat...

📢 New preprint alert!
How do proteins enter mitochondria? We uncovered a surprising mechanism at the mitochondrial entry gate—using #NMR, in vivo single-particle tracking, yeast experiments, and MD simulations to crack the code.
www.biorxiv.org/content/10.6...
#StructuralBiology #Mitochondria
🧵 1/8

OpenBind is a new open science effort to dramatically increase the number of protein:ligand structures in the PDB, pairing this with high-quality affinity data to enable a new generation of predictive structure and affinity models for drug discovery. Check it out: openbind.ai

🧐”Study reveals how #tuberculosis exploits immune defenses to promote infection.”
🔗to study published in Science Immunology ⬇️
Mycobacterial α-glucans hijack dectin-1 to facilitate intracellular bacterial survival
www.science.org/doi/10.1126/...

Experimental tour-de-force from Anne-Claude Gavin's lab: selectivity mapping of 39 lipid transfer proteins reveals ~500 new LTP-lipid pairs. Molecular modeling by @mahmoudmoqadam.bsky.social, @rezatalandahti.bsky.social & Florian Echelard. @cbubergen.bsky.social
www.nature.com/articles/s41...

Insights into the Electronic and Structural Properties of Cellulose and Amylose: A Comparative Force Field Study Amylose and cellulose are important biopolymers with diverse applications in biotechnology and materials science. Understanding their structural, dynamic, and solvation properties at the molecular level is critical for harnessing their potential. This study investigates the electronic and structural properties of single-chain cellulose and single- and double-chain amylose in aqueous solution using molecular dynamics simulations with both nonpolarizable (CHARMM) and polarizable (Drude) force fields. CHARMM simulations show stable hydrogen bonding between amylose and water, higher glucose ring dipole moments, increased rigidity, adoption of chair conformations, and less variation in dihedral angles. In contrast, Drude simulations captured dynamic electronic polarization, enhanced conformational flexibility, and resulted in heterogeneous inter- and intramolecular hydrogen bonds. For cellulose, structural and solvation behaviors were largely similar between CHARMM and Drude. These findings highlight molecular interactions and solvation dynamics of amylose and cellulose, with potential relevance in materials science and biotechnology.

First article of 2026! Happy to have our first real foray into carbohydrates out in J Phys Chem B. Excellent work by PhD candidate Esmat Mohammadi.

pubs.acs.org/doi/full/10....

Sebinelli, Syska, Razmazma et al. @umontpellier.bsky.social show that the yeast protein Ist2, which localizes to ER–PM contact sites, possesses a #phospholipid scramblase activity in its ER-localized transmembrane domain that is important for several ER-related processes. rupress.org/jcb/article/...

Pitfalls in the Modeling of Maltoside Detergents in Protein Structures This publication is Open Access under the license indicated. Learn More

🚨Excellent editorial in ACS Central Sci 📣

Thank you @carolynbertozzi.bskyverified.social for your support and to @louisflwilson.bsky.social for spotting these mistakes + drafting an excellent manuscript

#CryoEM #StructuralBiology
#vidalized

ACS Central Science pubs.acs.org/doi/full/10....

Happy new year! I've so enjoyed the end-of-year lists of people's favorite papers from 2025, so I made a list of 16 #lipidtime studies from 2025 that I found interesting. Here they are in no particular order (please add more if you would like!), and here's to much more exciting science in 2026! 🧪

Happy New Year!

We began the year by reading this amazing Chemistry World article by @robinson-julia.bsky.social on how AI agents are democratising computational chemistry.

🔗 www.chemistryworld.com/news/ai-agen...

Image source: © Caroline Chapple, Courtesy of Chemistry World.
[1/5]

Membrane microdomains are crucial for Mycobacterium marinum EsxA-dependent membrane damage, escape to the cytosol, and infection Sterol-rich microdomain accumulation at the MCV is crucial for Mm-induced damage and infection in D. discoideum and BV-2 cells.

🚨 Want to know how we demonstrated the importance of sterol-rich membrane microdomains for M. marinum infection?

Check out our latest paper published in Science Advances 👇
www.science.org/doi/10.1126/...

✨ Big thanks to everyone, especially Cristina Boehm-Bosmani, @soldatilab.bsky.social ! ✨

I'm really excited to break up the holiday relaxation time with a new preprint that benchmarks AlphaFold3 (AF3)/“co-folding” methods with 2 new stringent performance tests.

Thread below - but first some links:
A longer take:
fraserlab.com/2025/12/29/k...

Preprint:
www.biorxiv.org/content/10.6...

MemPrO: A Predictive Tool for Membrane Protein Orientation Membrane proteins play a vital role in numerous cellular processes, including ion transport, intercellular communication, and antibiotic resistance. Ensuring their accurate orientation within lipid bi...

🌟 New Tool Alert!

We present MemPrO – a toolkit for orienting and building membrane protein systems:

✅ Membrane protein orientation 
✅ Mixed membrane building 
✅ Double membranes & curvature 
✅ Peptidoglycan cell wall support

🔗 github.com/pstansfeld/mempro 
📖 pubs.acs.org/doi/10.1021/...

Opportunity: postdoctoral fellowships at the center for Quantitative Cell Biology (QCB), Univ. of Illinois, in close collaboration with our group. Your ticket to become an expert in whole-cell Martini simulations !
qcb.illinois.edu/postdoctoral...