Coarse Grain Forcefield for Biomolecules Interested to hear about the ins and outs of the Martini model ? Register for the forthcoming Martini webinar, April 18th !
Update: in case you missed it, you can find the recorded webinar on youtube
A nice example of how Martini can help you improving your performance, featuring the first Martini 3.0 dope:
Liu, Qiu, Alessandri, et al., Enhancing Molecular n-Type Doping of Donor–Acceptor Copolymers by Tailoring Side Chains. Advanced Materials, 2018, online.
Adding a lipid to your protein will be a piece of cake from now on.
Yoav Atsmon-Raz, and D. Peter Tieleman. Parameterization of Palmitoylated Cysteine, Farnesylated Cysteine, Geranylgeranylated Cysteine and Myristoylated Glycine for the Martini Force Field J. Phys. Chem. B,16 Nov 2017. article
The adapted martinize.py they used for adding the tails.
Lipid organization and dynamics of biologically complex plasma membranes; comparison of on idealized brain to an average membrane mixture.
H.I. Ingólfsson, T.S. Carpenter, H. Bhatia, P.T. Bremer, S.J. Marrink, F.C. Lightstone. Computational Lipidomics of the Neuronal Plasma Membrane. Biophys. J. 113:2271–2280, 2017. open access
For simulation files and parameters, see bbs.llnl.gov/neuronal-membrane-data.html
Current force fields tend to overstabilize protein-protein interactions, and Martini is no exception. A recent paper by the Vattulainen group shows the stickiness is also haunting membrane embedded proteins:
M. Javanainen, H. Martinez-Seara, I. Vattulainen. PLoS ONE 12:e0187936, 2017. https://doi.org/10.1371/journal.pone.0187936
We are working hard to improve the protein-protein interactions in the forthcoming Martini 3.0 force field, featuring a thoroughly recalibrated interaction matrix, with a planned release early 2018.
Our former PhD student Jelger Risselada has performed large scale Martini simulations of SNARE-mediated membrane fusion and teamed up with experimentalists to explain how tethering proteins facilitate opening of the fusion pore. The exciting results are published in Nature:
M. D’Agostino, H.J. Risselada, A. Lürick, C. Ungermann, A. Mayer. A tethering complex drives the terminal stage of SNARE-dependent membrane fusion. Nature, doi:10.1038/nature24469