Simulation of an entire organelle

Simulation of the membranes of an entire mitochondrion ! See how more than 5 million lipids are organized in this amazingly complex organelle, obtained with our new backmapping tool TS2CG.

Pezeshkian, Konig, Wassenaar, Marrink, Nature Commun. 11, 2296 (2020). TS2CG2.jpg


Hybrid membranes



On (rare) occasions Martini membranes are not good enough, and you might want to simulate with atomistic resolution. But then your system size explodes and you don't have this Anton machine on your desk. What next? Liu Yang figured a way to combine the best of both worlds:

Y. Liu et al., Dual Resolution Membrane Simulations Using Virtual Sites, JPC-B, 2020. doi:10.1021/acs.jpcb.0c01842

Escape from the endosome


 Now in the theaters !!!

Read all about the amazing story of these poor little Martini genes, seemingly gagged and trapped inside an endosome waiting for degradation ... will they manage to escape ?

Bruininks et al., A molecular view on the escape of lipoplexed DNA from the endosome, eLife, online.

Martini at school

It may not sound such a good idea, bringing Martini to the schools. But check out this paper, explaining at high school level the molecular basis for some cool fat-featuring experiments, with the help of Martini simulations. Ideal also for online education !

Fats’ Love–Hate Relationships: A Molecular Dynamics Simulation and Hands-On Experiment Outreach Activity to Introduce the Amphiphilic Nature and Biological Functions of Lipids to Young Students and the General Public. A.S. Tascini, S. Wang, J.M. Seddon, F. Bresme, R. Chen. J. Chem. Educ. (2020). Online.

Lipid dependent protein-protein binding



Martini based simulations reveal the molecular mechanism for bidirectional regulation of CD44 for lipid raft affiliation by palmitoylations and PIP2, and how this affects binding to FERM. Check for details:

Sun, Schroer, Palacios, et al., PLoS Comp. Biol., online.

Membrane assisted toppling


Remarkable lipid gymnastics: collective bending of the membrane around an energy coupling factor (ECF) transporter facilitates toppling of the mobile (S-) component mediating substrate transport. Predictions of the simulations concerning the importance of certain lipid types are nicely confirmed experimentally. For details, see:

Faustino, Abdizadeh et al., Nature Commun. 11, 1763 (2020). doi:10.1038/s41467-020-15554-9