Coarse Grain Force Field for Biomolecular Simulations

Complexity of the photosynthetic machinery captured by Martini

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Last Updated on Monday, 26 September 2016 11:55

We proudly present the final work of F. J. van Eerden a PhD student in our lab, soon to graduate.

F.J. van Eerden, T. van den Berg, P.W.J.M. Frederix, D.H. de Jong, X. Periole, S.J. Marrink. Molecular dynamics of photosystem II embedded in the thylakoid membrane. JPCB,2016, Accepted Manuscript. doi:10.1021/acs.jpcb.6b06865

Martini metadynamics

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Last Updated on Tuesday, 09 August 2016 12:45

Check out this paper, a nice example of how metadynamics can be combined with Martini for efficient sampling of protein-protein binding free energies:

Protein side chains

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Last Updated on Monday, 09 May 2016 08:14

The team of Prof. Vogel has developed a fix to prevent side chains from flipping to the wrong side of beta strands. Soon to be implemented in martinize. For details, see:

F.A. Herzog, L. Braun, I. Schoen, V. Vogel. Improved side chain dynamics in Martini simulations of protein-lipid interfaces. JCTC, online. doi:10.1021/acs.jctc.6b00122

Curvature

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Last Updated on Friday, 19 August 2016 13:04

A nice study by Wang and Deserno show that the pivotal plane in a Martini DMPC bilayer is located closer to the bilayer center in comparison to an atomistic bilayer. This has important consequences for the interpretation of the effect of curvature on membrane properties. For details, please consult the full paper:

X. Wang, M. Deserno. Determining the tilt modulus by simulating membrane buckles. JPCB, online. doi: 10.1021/acs.jpcb.6b02016

Supercomplex formation

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Last Updated on Friday, 18 March 2016 23:45

Curious to see what a crowded membrane really looks like? Check out Clement's masterpiece:

C. Arnarez, S.J. Marrink, X. Periole. Molecular mechanism of cardiolipin-mediated assembly of respiratory chain supercomplexes. Chem. Sci., 2016, online. doi: 10.1039/C5SC04664E