Getting your membranes curved

Boyd and May have deleloped a new tool called BUMPy. The tool allows you to create curved lipid bilayers, combining flexibility of shape, force field, model resolution, and bilayer composition. The tool is avialable online. For details, including many Martini based applications, check the paper: Boyd & May, JCTC, in press, DOI:10.1021/acs.jctc.8b00765

A polarizable MARTINI model for monovalent ions in aqueous solution

FigureIons are known to be tricky when it comes to molecular dynamics. A new polarizable model has been proposed which should have improved behaviour for highly charged models such as DNA and polyelectrolytes. The authors recommend its usage in combination with the refPol forcefield for Martini for best behaviour.

J. Michalowsky, J. Zeman, C. Holm, J. Smiatek, J. Chem. Phys. 149, 163319 (2018);

Martini 3 open-beta release

martini cocktailWe gladly announce the release of the open beta version of MARTINI 3. This first glance of the new MARTINI includes all the necessary files to perform CG simulations of phospholipid bilayers and proteins. In the near future, new models for other molecules will also be included in this open beta. So, continue visiting our website to be updated with the news. The main goal of this release is to get feedback from the scientific community. Reporting problems in our forum will help us in the improvement of the force field, which also increase the chances of your favorite system be properly working in the near future. Good feedback is also welcome for the sake of the developers. Be aware, the parametrization is still on-the-fly, which means that the CG models used (from the interaction between beads to the bonded parameters) can/will change until the release and publication of the definitive version.

You can find the open-beta input parameters here.

Formation of SMALPs


Experimental characterization of membrane proteins often requires their solubilization. A recent approach is to use styrene maleic acid (SMA) copolymers to isolate membrane proteins in nanometer-sized membrane discs, so called SMA lipid particles (SMALPs). The approach has the advantage of allowing direct extraction of proteins, keeping their native lipid environment. Despite the growing popularity of using SMALPs, the molecular mechanism behind the process remains poorly understood.

In this paper, we unravel the molecular details of the nanodisc formation based on Martini simulations:

M. Xue, L. Cheng, I. Faustino, W. Guo, S.J. Marrink, Biophys. J., 2018, online.

Lipid fingerprints

fingerprintThe large variety of lipids in the plasma membrane gives rise to very complex protein-lipid interactions. These interactions, coined fingeprints, are analyzed in the following paper, based on the Martini model (what else?):

V. Corradi et al. Lipid–Protein Interactions Are Unique Fingerprints for Membrane Proteins. ACS Cent. Sci., asap, 2018. DOI:10.1021/acscentsci.8b00143

Curvature-induced lipid sorting

PM tehters cover 02c(1)

By pulling tethers from realistic plasma membranes we have been able to identify to what extent lipids are being sorted as a result of curvature. We show that some lipids are depleted from highly curved regions, whereas other are being enriched. But everything also depends on the pulling direction, as the plasma membrane is asymmetric. For details, see the paper which is now available online in the new flagship journal of Wiley:

S. Baoukina, H.I. Ingólfsson, S.J. Marrink, D.P. Tieleman. Curvature‐Induced Sorting of Lipids in Plasma Membrane Tethers. Advanced Theory and Simulations,