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Lipids unplugged
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- Last Updated: Wednesday, 11 May 2022 18:27
Simulations 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
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.
Membrane permeability
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- Last Updated: Monday, 28 March 2022 11:51
