Toxins destroy membrane

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Martini simulations from the Hummer group show how toxic peptides form big pores in cholesterol containing membranes.

For details, see: Vogele et al., PNAS 2019, doi.org/10.1073/pnas.1904304116

MERMAID

A web server for setting up and running Martini membrane systems has just been launched:

M. Damre, A. Marchetto, A. Giorgetti. MERMAID: dedicated web server to prepare and run coarse-grained membrane protein dynamics. Nucleic Acids Research, gkz416, doi:10.1093/nar/gkz416.

Ceramide binding to VDAC

VDAC-ceramide.pngStarting as a simple tutorial excercise to demonstrate the power of Martini to study protein-lipid interactions, ending up as a full-blown paper with lots of experimental support and biological relevance ! Read all about the amazing ability of ceramides to bind to voltage dependent anion channels (VDAC) in mitochondrial membranes:

Dadsena et al., Ceramides bind VDAC2 to trigger mitochondrial apoptosis. Nature Commun. 10:1832, 2019. doi:10.1038/s41467-019-09654

Swinger

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Happy Easter with lots of swinging activities .... For inspiration, check out how to convert your CG water beads to real ones on-the-fly !

J. Zavadlav, S.J. Marrink M. Praprotnik, SWINGER: a clustering algorithm for concurrent coupling of atomistic and supramolecular liquids. Interface Focus 9:20180075, 2019. doi.org/10.1098/rsfs.2018.0075

Light Harvesting Complex II

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Martini simulations of the full trimeric light harvesting complex II, embedded in a thylakoid membrane, reveal interesting chromophore dynamics and lipid binding sites.

For details, check the paper which is now online: S. Thallmair, P.A. Vainikka, S.J. Marrink. Biophys. J., 116:1446-1455, 2019. doi:10.1016/j.bpj.2019.03.009

Less fuzzy lipids

lipid phase diagrams

A recent study by Carpenter, Lopez and coworkers nicely characterized the phase behavior of Martini DPPC/DOPC/cholesterol ternary mixtures. General Martini parameters correctly captured a large fraction of the phase diagram, but parameters optimized against CHARMM DOPC and DPPC simulations could better capture some of the details, especially close to the critical point.

The new lipid parameters specifically tuned to CHARMM DOPC and DPPC can be found here and in the Martini lipid parameter list: DPPC and DOPC.

For details see JCTC 2018, DOI:10.1021/acs.jctc.8b00496.