Siewert-Jan Marrink

Great experimental work backed up with Martini simulations from Chris Brasnett !

YouTube video by Marieke Bentopy tutorial walkthrough

I just uploaded a video walkthrough of the tutorial I recorded this morning.

youtu.be/C4LYZokS_t4

Building realistic models of cells means fitting proteins, RNA, and metabolites at experimental concentrations inside complex cellular architectures. Here's a movie showing how we pack the cytoplasmic space of the JCVI-Syn3A cell:

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👇

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

Let's safe the planet and get rid of PFAS! A good start is to perform simulations, now possible with:

Great work from Daniel Ramirez: Gradient-Based Optimization of Force Field Parameters for Martini Lipid Models | ChemRxiv - go.shr.lc/3YDOka5

Unlocking High-Throughput Investigation of Transport Tunnels in Enzymes Using Coarse-Grained Simulation Methods Transport tunnels in enzymes with buried active sites are critical gatekeepers of enzymatic function, controlling substrate access, product release, and catalytic efficiency. Despite their importance,...

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

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...

MemPrO: A Predictive Tool for Membrane Protein Orientation | Journal of Chemical Theory and Computation pubs.acs.org/doi/10.1021/...

Instead of a tree, I can offer a snowman! ☃️

Built using bentopy, based on David Naranjo's idea.

The input file can be found here: gist.github.com/ma3ke/723f9c....

Surely someone can make a better Martini X-mas tree?

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...

Martini 3 Building Blocks for Lipid Nanoparticle Design Lipid nanoparticles (LNPs) represent a promising platform for advanced drug and gene delivery, yet optimizing these particles for specific cargos and cell targets poses a complex multifaceted challeng...

Martini 3 Building Blocks for Lipid Nanoparticle Design | Journal of Chemical Theory and Computation pubs.acs.org/doi/full/10....

The Martini globe. The lipids of the globe are coloured by their continent based on the tectonic plates. The Kingdom of Denmark is coloured dark red.

By @fabianschuhmann.bsky.social @cg-martini.bsky.social @weria-lab.bsky.social et al in doi.org/10.1021/acs....

New on the Martini webportal (cgmartini.nl/docs/contact...): acknowledgment of all the people who contribute to the development. The list is still growing - if you feel your name should be added please let us know.

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...

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.

AI-Ready Cryo-Electron Tomography Simulations of the Whole Cell @ Young Scientists Symposium ISTA, in Klosterneuburg on 18 November 2025

Tomorrow, on 18 Nov, I'll again give a talk at YSS'25. This time, I will present our work on AI-Ready Cryo-Electron Tomography Simulations of the Whole Cell. This is a project I’m especially fond of. I had the idea years ago, and it’s finally taking shape at @istaresearch.bsky.social & @rug.nl

An optimized contact map for GōMartini 3 enabling conformational changes in protein assemblies www.biorxiv.org/content/10.1...

CCD2MD: A Suite of Packages for Preparing Co-Folded Outputs for Molecular Dynamics Simulations Protein–lipid interactions play a crucial role in the stability and function of membrane proteins. While experimental approaches to characterize these interactions in a native-like membrane environment can be challenging, computational techniques offer a powerful alternative for identifying and analyzing potential binding sites. Recent advances in cofolding methods now enable the prediction of holo protein structures, capturing conformational changes that may occur upon lipid binding and thereby improving the accuracy of binding site characterization. However, the outputs from these methods often require postprocessing to ensure compatibility with widely used molecular dynamics force fields. In this work, we introduce CCD2MD, a modular toolkit designed to convert cofolding outputs into simulation-ready systems for GROMACS. CCD2MD supports both atomistic and coarse-grained representations with or without membrane embedding. While CCD2MD is exemplified here with protein–lipid systems, its modular design allows for straightforward adaptation to other cofolded biomolecular assemblies, incorporating complexes with nucleic acids, small molecules, carbohydrates, or metal ions, thereby enabling a variety of simulation setups across multiple scales.

CCD2MD: A Suite of Packages for Preparing Co-Folded Outputs for Molecular Dynamics Simulations | Journal of Chemical Information and Modeling pubs.acs.org/doi/full/10....

📜 New preprint! We developed PoGö, an algorithm to optimize the essential dynamics of GöMartini proteins based on all-atom simulations: www.biorxiv.org/content/10.1...

the Martini Pumpkin by my PhD student Isabell Lindahl.
Too much fat though!

TS2CG, Martini3, Martini
@cg-martini.bsky.social

Allosteric pathway connects Zn(II) loss from SOD1 to known pathogenic mechanisms Cu,Zn superoxide dismutase (SOD1) is one of the proteins with mutations linked to hereditary forms of the amyotrophic lateral sclerosis neurodegenerat…

Allosteric pathway connects Zn(II) loss from SOD1 to known pathogenic ... www.sciencedirect.com/science/arti...

Coarse-Grained Martini 3 Model for Collagen Fibrils: Biophysical Journal www.cell.com/biophysj/ful...

Nobel Prize for Martini ! Terrific news ! Well deserved of course.
Oh shoot .... Martinis ...

Molecular basis for the regulation of membrane proteins through preferential lipid solvation - Nature Chemical Biology Static protein structures can capture the association of lipids, but it is unclear whether the association is due to lipids acting as long-lived ligands or the solvation of preferred lipids around the protein. A computational-experimental framework has now shown that for the protein CLC-ec1, it is the change in lipid solvation energies that drives dimerization, with preferred lipids around the protein modulating this driving force.

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...

How does Mycoplasma pneumoniae scavenge lipids from its host membranes? P116 is an adaptive, all-in-one lipid acquisition machinery fit for any host environment.

How does Mycoplasma pneumoniae scavenge lipids from its host membranes? | Science Advances www.science.org/doi/full/10....

Peptide Electrostatic Modulation Directs Human Neural Cell Fate This study explores the effect of charge on the bioactivity of peptide-based supramolecular materials. The design of a peptide library with varying charges that self-assemble into supramolecular fibe....

Cool paper from our former guest student Laura, combining fancy experiments with titratable Martini simulations on supramolecular self-assembled systems as versatile platforms for bio-engineering. Advanced Science, doi.org/10.1002/advs...

Martini 3 Coarse-Grained Models for Carbon Nanomaterials The Martini model is a coarse-grained force field allowing simulations of biomolecular systems as well as a range of materials including different types of nanomaterials of technological interest. Recently, a new version of the force field (version 3) has been released that includes new parameters for lipids, proteins, carbohydrates, and a number of small molecules, but not yet carbon nanomaterials. Here, we present new Martini models for three major types of carbon nanomaterials: fullerene, carbon nanotubes, and graphene. The new models were parametrized within the Martini 3 framework, and reproduce semiquantitatively a range of properties for each material. In particular, the model of fullerene yields excellent solid-state properties and good properties in solution, including correct trends in partitioning between different solvents and realistic translocation across lipid membranes. The models of carbon nanotubes reproduce the atomistic behavior of nanotube porins spanning lipid bilayers. The model of graphene reproduces structural and elastic properties, as well as trends in experimental adsorption enthalpies of organic molecules. All new models can be used in large-scale simulations to study the interaction with the wide variety of molecules already available in the Martini 3 force field, including biomolecular and synthetic systems.

Martini 3 Coarse-Grained Models for Carbon Nanomaterials | Journal of Chemical Theory and Computation pubs.acs.org/doi/full/10....