Ceramide binding to VDAC

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Last Updated: Tuesday, 23 April 2019 12:19

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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Last Updated: Saturday, 20 April 2019 19:56

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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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Last Updated: Tuesday, 23 April 2019 18:24

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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

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Last Updated: Wednesday, 20 February 2019 12:00

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.

Protein-Lipid Interactions

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Last Updated: Thursday, 14 February 2019 18:22

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In collaboration with the Tieleman group we published another comprehensive review, focussing on the diversity of protein-lipid interactions. More than 800 references, including many Martini-based studies. sincere apologies if your paper was not included.

V. Corradi, B.I. Sejdiu, H. Mesa-Galloso, H. Abdizadeh, S.Y. Noskov, S.J. Marrink, D.P. Tieleman. "Emerging Diversity in Lipid–Protein Interactions", Chem. Review, 2019. DOI:10.1021/acs.chemrev.8b00451

Complex Membranes

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Last Updated: Thursday, 24 January 2019 12:23

TOC Figure

Together with several co-authors, we wrote a comprehensive review (>700 references) on computer simulations of cell membranes. In this field, we are witnessing a transition from simulations of simpler membrane models to multicomponent systems, culminating in realistic models of an increasing variety of cell types and organelles. Here, we review the state of the art in the field of realistic membrane simulations and discuss the current limitations and challenges ahead.

S.J.Marrink, V. Corradi, P.C.T. Souza, H.I. Ingolfsson, D.P. Tieleman, M.S.P. Sansom. "Computational Modeling of Realistic Cell Membranes". Chem. Review, 2019. DOI:10.1021/acs.chemrev.8b00460