Adrien Schahl
@aschahl.bsky.social
📤 183
📥 270
📝 86
Postdoc in Delemotte group of Scilifelab and KTH. MD of proteins lipids and sugars.
Hey
@lindorfflarsen.bsky.social
we didn't choke out boxing day 🤩
15 days ago
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Adrien Schahl
Jean-Philip Piquemal
26 days ago
#compchem
#compbio
Last preprint of the year: "Fast, systematic and robust relative binding free energies for simple and complex transformations : dual-LAO".
arxiv.org/abs/2512.17624
Great work by N. Ansari.
@qubit-pharma.bsky.social
. Another nice collab with J. Hénin.
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Adrien Schahl
Jean-Philip Piquemal
about 1 month ago
💫 We just released the weights of the
#FeNNixBio1
foundation machine learning model for drug design! 💫 Weights:
github.com/FeNNol-tools...
FeNNol code:
github.com/FeNNol-tools...
The models are distributed under the open source ASL license (non-commercial academic research).
#compchem
#compbio
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GitHub - FeNNol-tools/FeNNol-PMC: FeNNol Pretrained Models Collection
FeNNol Pretrained Models Collection. Contribute to FeNNol-tools/FeNNol-PMC development by creating an account on GitHub.
https://github.com/FeNNol-tools/FeNNol-PMC
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Adrien Schahl
Dr. Jules Marien
about 1 month ago
New paper is out ! We show that all classical phosphorylation forcefields that we tested lead to an overbinding of phosphate groups to bulk sodium (Na+) and potassium (K+) cations. This assessment has serious implications for MD simulations of phosphorylated proteins !
doi.org/10.1021/acs....
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Sticky Salts: Overbinding of Monovalent Cations to Phosphorylations in All-Atom Force Fields
Phosphorylation is a major post-translational modification that is involved in the regulation of the dynamics and function of intrinsically disordered proteins (IDPs). We recently characterized a phen...
https://doi.org/10.1021/acs.jcim.5c02154
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Adrien Schahl
Syma Khalid
about 1 month ago
Our paper on polymyxin interacting with the E. coli outer membrane is out! Simulations by the very talented
@dheerajprakaash.bsky.social
www.nature.com/articles/s42...
To scale outer membrane protein island simulated at coarse-grained resolution with portions refined at all atom resolution.
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Polymyxins slow down lateral diffusion of proteins and lipopolysaccharide in the E. coli outer membrane - Communications Biology
Multi-scale molecular dynamics simulations reveal that polymyxins form polymyxin-protein aggregates upon associating with the E. coli outer membrane thereby reducing lateral mobility of outer membrane...
https://www.nature.com/articles/s42003-025-09161-x
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Adrien Schahl
Dr. Hab Sophie Sacquin-Mora
about 2 months ago
"Across (Conformational) Space and (Relaxation) Time",
@marienj.bsky.social
's latest work, is now out in J. Phys. Chem. B
@pubs.acs.org
. In this paper, we used coarse-grain simulations with the CALVADOS model to investigate the dynamics of a large IDP.
pubs.acs.org/doi/10.1021/...
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Across (Conformational) Space and (Relaxation) Time: Using Coarse-Grain Simulations to Probe the Intra- and Interdomain Dynamics of the Tau Protein
The biological importance of intrinsically disordered proteins (IDPs) has been established for over two decades, yet these systems remain difficult to characterize, as they are better described by conformational ensembles instead of a single reference structure for their folded counterparts. Tau is a prominent member of the IDP family, which sees its cellular function regulated by multiple phosphorylation sites and whose hyperphosphorylation is involved in neurodegenerative diseases such as Alzheimer’s. We used coarse-grain MD simulations with the CALVADOS model to investigate the conformational landscape of tau without and with phosphorylations. Characterizing the local compactness of IDPs allows us to highlight how disorder comes in various flavors, as we can define different domains along the tau sequence. We define the IDP’s Statistical Tertiary Organization (STO) as the average spatial arrangements of domains, which constitute an extension of the tertiary structure of folded proteins. We also use IDP-specific metrics to characterize the local curvature and flexibility of tau. Comparing the local flexibilities with T2 relaxation times from NMR experiments, we show how this metric is related to the protein dynamics. A curvature and flexibility pattern in the repeat domains can also be connected to tau binding properties, without having to explicitly model the protein’s interaction partner. Finally, we rediscuss the original paperclip model that describes the spatial organization of tau and how phosphorylations impact it. The resulting changes in the protein intradomain and interdomain interaction pattern allow us to propose experimental setups to test our hypothesis.
https://pubs.acs.org/doi/10.1021/acs.jpcb.5c06282
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Adrien Schahl
Siewert-Jan Marrink
2 months ago
An optimized contact map for GōMartini 3 enabling conformational changes in protein assemblies
www.biorxiv.org/content/10.1...
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Adrien Schahl
Anna Duncan
2 months ago
*If you would like to be considered for a talk at this workshop, please register & submit an abstract by 7 November* We also have a fantastic line-up of invited speakers: Matteo Degiacomi, Lucie Delemotte, Weria Pezeshkian, Mohsen Sadeghi & Ilpo Vattulainen Registration:
aias.au.dk/events/show/...
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Adrien Schahl
Wout Oosterheert
3 months ago
Very excited that my final postdoctoral work is now online in Cell
@cellpress.bsky.social
.
www.sciencedirect.com/science/arti...
Using 16 (!) cryo-EM structures, we uncovered how the three proteins coronin, cofilin and AIP1 work together to rapidly disassemble actin filaments.
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Adrien Schahl
Biophysical Society
4 months ago
Erdinc Sezgin to Receive 2026 Early Independent Career Award
www.biophysics.org/news-room/er...
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Adrien Schahl
CNRS
4 months ago
🔬 Sophie Sacquin-Mora, biochimiste, étudie les protéines pour comprendre leur fonctionnement et prédire leurs comportements liés à certaines maladies. Des recherches qui offrent l’espoir de trouver de nouveaux médicaments et traitements médicaux.
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Brève de science : au cœur des protéines
Faut-il forcément des microscopes et des tubes à essai pour observer des molécules ou des protéines ?
https://www.cnrs.fr/fr/actualite/breve-de-science-au-coeur-des-proteines
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Adrien Schahl
Olivier Neyrolles
4 months ago
Excited to share Wendy Le Mouëllic’s PhD work, now published in
@pnas.org
! It reveals that M. tuberculosis depends on inorganic sulfate import to survive inside host cells—fueling essential processes such as redox balance and stress resistance. Huge congrats to Wendy & colleagues!
shorturl.at/WbFQC
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Inorganic sulfate is critical for Mycobacterium tuberculosis lung tissue colonization and redox balance | PNAS
Tuberculosis remains the deadliest infectious disease caused by a single pathogen, highlighting the urgent need for novel therapies. A deeper under...
https://www.pnas.org/doi/10.1073/pnas.2503966122
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Michael Way
4 months ago
And now for something completely different
@tianyang22.bsky.social
&
#YanCao
uncover of how SPIN90 dimers activate Arp2/3 to nucleate bidirectional linear actin filaments. Great collaboration with
@romet-jegou-lab.bsky.social
&
@carolynmoores1.bsky.social
#Cryo-EM
#Arp2/3
rdcu.be/eGoH4
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Arp2/3-mediated bidirectional actin assembly by SPIN90 dimers
Nature Structural & Molecular Biology - Liu et al. show that SPIN90 dimerizes and binds two Arp2/3 complexes to nucleate two bidirectional actin filaments and the dimerization domain is...
https://rdcu.be/eGoH4
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Adrien Schahl
André Nadler
5 months ago
Out today in
@nature.com
: Together with the Honigmann, Shevchenko, Drobot and Hof labs, we present a general workflow for imaging the localization and transport of individual lipids in cells and mapping their metabolism.
www.nature.com/articles/s41...
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Adrien Schahl
Erdinc Sezgin
4 months ago
Previous preprint is now published in RSC Chemical Biology. If you are interested in plasma membrane labeling, see the paper! 👇
pubs.rsc.org/en/content/a...
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Adrien Schahl
Böckmann Lab
5 months ago
We're hiring! Join our team at
@fau.de
! We are seeking an enthusiastic candidate for a PhD position in our lab specializing in cutting-edge theoretical and computational membrane biophysics. Please send your CV, and a statement of research interests via email.
www.biomemphys.nat.fau.de/jobs/
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Adrien Schahl
Matthieu Chavent
5 months ago
our article "How PGL finds a sweet spot in phospholipid membranes: A combined multiscale MD and NMR study" is now freely available in its final version in
@biophysj.bsky.social
www.sciencedirect.com/science/arti...
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How PGL finds a sweet spot in phospholipid membranes: A combined multiscale MD and NMR study
Glycolipids from pathogenic Mycobacterium tuberculosis play important roles during the interaction of the pathogen with macrophages and can shape the …
https://www.sciencedirect.com/science/article/pii/S0006349525004898?dgcid=coauthor
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New preprint about my work done under the direction of
@sciezgin.bsky.social
,
@delemottelab.bsky.social
and Rebecca Howard. We studied the opening process of ADAM10 enhanced sampling MD, MSM and Fluorescence microscopy! Let us know what you think about it 😁
www.biorxiv.org/content/10.1...
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Lipid-facilitated opening of the ADAM10 sheddase revealed by enhanced sampling simulations
ADAM10 is a crucial membrane-bound metalloprotease that regulates cellular physiology by cleaving and releasing membrane-anchored proteins, including adhesion molecules and growth factor precursors, t...
https://www.biorxiv.org/content/10.1101/2025.08.17.670722v1
5 months ago
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Adrien Schahl
Siewert-Jan Marrink
5 months ago
Cool simulations from my former PhD student Petteri Vainikka now published: "Molecular Dynamics Simulation of Fatty Acid Extraction Using a Type V Deep Eutectic Solvent with Tunable Hydrophobicity" | The Journal of Physical Chemistry B
pubs.acs.org/doi/full/10....
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Molecular Dynamics Simulation of Fatty Acid Extraction Using a Type V Deep Eutectic Solvent with Tunable Hydrophobicity
Deep eutectic solvents (DESs) are often promoted as a more environmentally friendly alternative for ionic liquids and other ionic solvents. Like ionic liquids, DESs can be designed for specific tasks ...
https://pubs.acs.org/doi/full/10.1021/acs.jpcb.4c08261
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Weird lipids, weird effects on membranes ! Happy to see this story out 😄 If you like MD simulations, NMR spectroscopy and membranes this story will interest you 😊
add a skeleton here at some point
5 months ago
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Adrien Schahl
Siewert-Jan Marrink
6 months ago
A true community effort ! The Martini 3 Lipidome: Expanded and Refined Parameters Improve Lipid Phase Behavior | ACS Central Science
pubs.acs.org/doi/10.1021/...
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https://pubs.acs.org/doi/10.1021/acscentsci.5c00755
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Adrien Schahl
Kresten Lindorff-Larsen
6 months ago
Our paper on: A coarse-grained model for simulations of phosphorylated disordered proteins (aka parameters for phospho-serine and -threonine for CALVADOS) is now published in Biophysical Journal
authors.elsevier.com/a/1lTcE1SPTB...
@asrauh.bsky.social
@giuliotesei.bsky.social
& Gustav Hedemark
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Adrien Schahl
Paulo C. T. Souza
6 months ago
🚀 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
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Adrien Schahl
Cecilia Clementi
6 months ago
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.
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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...
https://doi.org/10.1038/s41557-025-01874-0
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Adrien Schahl
Chelsea Brown
6 months ago
It was great to help out the lipids with these two Mycobacterial enzymes. Fantastic work from the Mancia lab!
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Very nice presentation of
@eriklindahl.bsky.social
about his work to integrate AI, MD and experiments. 🤩
#EBSA2025
7 months ago
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Adrien Schahl
Mathieu M.J.E. Rebeaud
7 months ago
Hot off the press in JBC, here's the latest article started during my Ph.D in Prof. Goloubinoff's Lab and continued and completed at
@paolodelosrios.bsky.social
Lab. "Hsp110 Nucleotide Exchange Factors may amplify Hsp70-disaggregation by enhanced entropic pulling"
www.jbc.org/article/S002...
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Hsp110 Nucleotide Exchange Factors may amplify Hsp70-disaggregation by enhanced entropic pulling
Hsp70s use energy from ATP hydrolysis to unfold protein structures and solubilize stable aggregates and accumulate native species, even under adverse non-native conditions. To carry out its catalytic ...
https://www.jbc.org/article/S0021-9258(25)02300-2/fulltext
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Adrien Schahl
Heidi Klem
7 months ago
The Klem Lab at LSU is hiring a postdoctoral researcher in computational biochemistry! Application info:
klem-research-group.github.io/join/
♻️ Please share with anyone who might be interested!
#chemjobs
#postdoc
#compchem
#biochemistry
#enzymes
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Adrien Schahl
Mathieu M.J.E. Rebeaud
7 months ago
Subtle variations in a client protein determine bacterial Hsp90 dependence Et hop un nouveau preprint sur lequel j'ai beaucoup aimé travailler avec les copains de Marseille dont
@sebdementin.bsky.social
et Olivier. C'est Marseille-Lausanne connexion bébé.
www.biorxiv.org/content/10.1...
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Subtle variations in a client protein determine bacterial Hsp90 dependence
Chaperones ensure protein homeostasis and are conserved across species. The ATP-dependent chaperone Hsp90 is present from bacteria to eukaryotes, where it stabilizes and activates a wide range of subs...
https://www.biorxiv.org/content/10.1101/2025.07.01.662558v1
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@cg-martini.bsky.social
presenting the work of his lab about CG modelling of whole cell, notably with publications from
@janstevens.bsky.social
#EBSA2025
🤩
7 months ago
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Adrien Schahl
Elisa Fadda
7 months ago
When glycan recognition is linked to immune response, you need fine tuning! 😎 Here ⬇️ we show how human Siglecs act as molecular precision tools, recognising the glycan and also the biological environment (or context) these glycans are found in. A 1/5
#glycotime🧵
⬇️
doi.org/10.1101/2025...
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Adrien Schahl
Dr. Hab Sophie Sacquin-Mora
7 months ago
@marienj.bsky.social
's third PhD paper, where we investigated the impact of phosphorylations on the tau-tubulin interface, is now out in Biochemistry!
pubs.acs.org/doi/10.1021/...
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Impact of Multiple Phosphorylations on the Tau-R2/Tubulin Interface
The phosphorylation of the microtubule-associated tau protein plays a key role in the regulation of its physiological function. In particular, tau hyperphosphorylation affects its binding to the tubulin surface, destabilizing the tau-microtubule interface and leading to the accumulation of fibrillar aggregates in the brain. In this work, we performed classical molecular dynamics simulations for the tau-R2/tubulin assembly with various phosphorylation states of serines 285, 289, and 293. We analyze the resulting trajectories to obtain a detailed view of the protein interface in the complex and the impact of tau phosphorylations on the stability of this assembly and on the mobility of the tubulin disordered C-terminal tails (CTTs). We show how the tubulin CTTs help maintain the tau-R2 fragment on the tubulin surface despite the destabilizing effect induced by phosphorylations. Conversely, tau phosphorylation affects the CTTs’ flexibility and their potential activity as MAP-recruiting hooks. Furthermore, counterion-mediated bridges between the phosphate groups and tubulin glutamates also contribute to the binding of tau-R2 on the MT. Overall, the complex dynamics of this fuzzy phosphorylated assembly shed new light on the importance of the cytoplasmic environment in neurons in the context of Alzheimer’s disease.
https://pubs.acs.org/doi/10.1021/acs.biochem.5c00109
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Adrien Schahl
Matthieu Chavent
7 months ago
Very happy to release AutoMartiniM3 for Martini3 to automatize CG modelling of small molecules and fragments. Great work from M Szczuka in my lab in collab with
@pauloctsouza.bsky.social
and
@tbereau.bsky.social
teams! Give it a try:
github.com/Martini-Forc...
poke
@cg-martini.bsky.social
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Adrien Schahl
Abishek Arora, PhD
7 months ago
📢 Happy to share our latest preprint investigating how prenatal
#SSRI
exposure may effect early
#neurodevelopment
by inducing
#metabolic
changes in iPSC-derived neural cells 🧠 and human cord-blood samples 🧪
tinyurl.com/y3n4amz6
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Lysophosphatidylcholines are elevated after selective serotonin reuptake inhibitor exposure during neural differentiation and correlate with early neurodevelopmental symptoms
Selective serotonin reuptake inhibitors (SSRIs) are often prescribed during pregnancy. Yet, epidemiological studies associate in-utero SSRI exposure with neurodevelopmental disorders, such as autism a...
https://tinyurl.com/y3n4amz6
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Adrien Schahl
Matthieu Chavent
8 months ago
Our joint paper with Wonpil Im lab is now available as a preprint: "Dynamic Architecture of Mycobacterial Outer Membranes Revealed by All-Atom Simulations"
www.biorxiv.org/content/10.1...
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Adrien Schahl
Paulo C. T. Souza
9 months ago
New paper out in Nature Communications from
@natureportfolio.nature.com
: We present
#GōMartini
3 — combining structure-based Gōwith
#Martini3
to better capture
#protein
conformational changes and environmental effects. 📄
www.nature.com/articles/s41...
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GōMartini 3: From large conformational changes in proteins to environmental bias corrections - Nature Communications
This work presents GōMartini 3, an improved coarse-grained protein model combining physics- and structure-based approaches. It boosts computational efficiency and accuracy for structured soluble and m...
https://www.nature.com/articles/s41467-025-58719-0
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Adrien Schahl
Matthieu Chavent
9 months ago
With my colleague
@pierrepo.bsky.social
, we have an open position related to the
@lumen-eu.bsky.social
project If you are interested by rendering MD data more FAIR and co-developing new discovery platform for MD and beyond please apply: en:
emploi.cnrs.fr/Offres/CDD/U...
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Portail Emploi CNRS - Offre d'emploi - Molecular Dynamics Simulation Data Engineer (M/F)
https://emploi.cnrs.fr/Offres/CDD/UPR9080-PIEPOU-001/Default.aspx?Lang=EN
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Adrien Schahl
FX Coudert
9 months ago
Large-Scale Characterization of Chemical Bonding and Topology in the Materials Project Database, now out in Chem Mater!
#chemsky
#compchem
#inorgchem
#topology
pubs.acs.org/doi/10.1021/...
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Adrien Schahl
Rommie Amaro
10 months ago
✨✨ It's
#glycotime
for
#HIV
Env ✨✨ N-linked glycans modulate flexibility & MPER epitope exposure
#glycotime
Huge effort by
@shehata92.bsky.social
@lcasalino88.bsky.social
with cryoET of Env in VLPs by
@thevillalab.bsky.social
& team 💪 Would love feedback!
www.biorxiv.org/content/10.1...
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Olivier Neyrolles
10 months ago
Shout-out to
@pierredupuy.bsky.social
and colleagues! Excited to share our latest study, where we uncovered a previously unknown bacterial defense system in M.
#tuberculosis
: effluxosomes — dynamic membrane clusters that coordinate resistance to multiple toxic metals.
shorturl.at/Ek0HD
#MicroSky
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Adrien Schahl
Chris Brasnett
10 months ago
Happy that MartiniGlass has found a home in JCIM. I hope the tool will be useful for everyone in the user community, whether you’re trying to make nice coherent images of your system, or just make sense of instabilities!
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Adrien Schahl
Kresten Lindorff-Larsen
10 months ago
Gemma Solomon and I are looking for a postdoc to work across the two groups on modelling biological systems with a view to applications for quantum computing More details about the project including how to apply in the link below. Deadline April 9 2025
candidate.hr-manager.net/ApplicationI...
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Bien présent, en ces moments de retour a l'obscurantisme. Évidemment présent demain pour la journée des droits des femmes, qui sont d'autant plus menacés actuellement.
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11 months ago
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Usually, you just want to model a protein, and everything works nicely. Sometimes, biology annoys you with an unexpected PTM. Turns out, this PTM was more interesting than what we thought. I'm super thankful to
@matthchavent.bsky.social
and
@jppiquem.bsky.social
for letting me investigate this.
add a skeleton here at some point
11 months ago
0
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Adrien Schahl
Filipe De Vadder
12 months ago
GLP-1’s lesser-known brother, GLP-2, is stirring up trouble! Excess fructose ramps up GLP-2, boosting gut glucose absorption before glucose intolerance sets in. Blocking GLP-2R prevents metabolic havoc. Time to give GLP-2 the attention it deserves!
www.sciencedirect.com/science/arti...
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High fructose rewires gut glucose sensing via glucagon-like peptide 2 to impair metabolic regulation in mice
Increased fructose consumption contributes to type 2 diabetes (T2D) and metabolic dysfunction-associated steatotic liver disease (MASLD), but the mech…
https://www.sciencedirect.com/science/article/pii/S2212877825000080
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Adrien Schahl
BioExcel CoE
12 months ago
This year's version of GROMACS is out! If you want to hear about the new features and performance improvements join our
#webinar
on 18 February 2025 Registration ➡️
bit.ly/40Ebbme
#moleculardynamics
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Adrien Schahl
Justin Lemkul
12 months ago
We have a new
#tutorial
posted online, this time for Gaussian-accelerated MD as implemented in NAMD. Article has been submitted to LiveCoMS, a great venue for such efforts. We welcome feedback! Yes, it's alanine dipeptide, but you have to start somewhere :)
#compchem
github.com/Lemkul-Lab/g...
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GitHub - Lemkul-Lab/gamd_livecoms_tutorial
Contribute to Lemkul-Lab/gamd_livecoms_tutorial development by creating an account on GitHub.
https://github.com/Lemkul-Lab/gamd_livecoms_tutorial
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#HelloESR
👋 Post-doc à Stockholm, j'étudie principalement le comportement de protéines en utilisant des méthodes de chimie/physique (Dynamique moléculaire), avec comme intérêt principal les applications sur la santé.
12 months ago
0
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For the record, it appears to work better than electric shock treatment 🤭
www.annemergmed.com/article/S019...
Congratulations for the paper 👏🏻
add a skeleton here at some point
about 1 year ago
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Adrien Schahl
Willow Coyote-Maestas
about 1 year ago
Check out our work, where we discover how receptor GPCR senses pH! We solved a longstanding question by developing foundational GPCR DMS tech dev + structural bio! Led by brilliant PhD student
@matthewkhoward.bsky.social
and Nick Hoppe w/
@amanglik.bsky.social
!
www.cell.com/cell/fulltex...
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