Current rectification hemolysin

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Last Updated: Wednesday, 08 June 2022 12:41

hemolysin.jpgThe group of Basdevant performed Martini simulations of the ionic transport through the α-hemolysin protein nanopore, using the polarizable water model. The electric potential difference applied experimentally was mimicked by the application of an electric field to the system. They were able to observe current asymmetry and anion selectivity, in agreement with previous studies and experiments, and identified the charged amino acids responsible for these current behaviors.

For details, see Dessaux et al., JPCB, 2022.

Penetrating PEGylated lipid nanodiscs

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Last Updated: Wednesday, 08 June 2022 08:59

Impressive work on using lipid nanoparticles to deliver drugs to tumour cells, featuring large scale Martini simulations. Snapshots show the difference in penetration efficiency between a PEGylated lipid nanodisc (a) and a PEGylated liposome (b), both with a diameter of 40 nm, before (t = 0 ns) and after (t = 1,750 ns) being pulled through a 20 nm pore. For details, see Dane et al., Nature Materials, 2022.LNP-pore.jpg

Lipids unplugged

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Last Updated: Wednesday, 11 May 2022 18:27
leakage_vs_nanodics.jpgSimulations with Martini 3 reveal how lipids unplug pyroptotic pores formed by gasdermin-A3.
 
To see by which mechanism this happens, as well as to see how the pore shape of small and large oligomers adapts to preferred shapes in accord with atomic-force-microscopy, see the latest publication of Mari & Pluhackova et al. in Nat. Comm. 

Happy Easter

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Last Updated: Friday, 15 April 2022 09:42

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Improved parameters for IDPs

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Last Updated: Saturday, 09 April 2022 14:07

The group of Lindorff-Larsen performed a systematic study on the behavior of intrinsically disordered proteins (IDPs) with Martini 3. Comparing to SAXS data, they show that Martini 3 generally underestimates the global dimensions of the IDPs, which can be fixed by slightly increasing protein-water interactions. Although not an ideal solution, for the time being this seems like a pragmatic approach when modeling IDPs (as well as multi-domain proteins that are connected via flexible linkers) with Martini 3. For details, read the paper ! Thomasen et al, JCTC, 2022.

Sticky Martini

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Last Updated: Monday, 28 March 2022 11:58

No worries, Martini 3 is not too sticky, but 'Sticky Martini' here refers to a novel way of letting Martini beads stick together on purpose, to mimic chemical reactions. See the work of Carvalho et al., just published in Npj Computational Materials.