Sticky proteins

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Last Updated: Thursday, 16 November 2017 19:50

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.

Membrane fusion

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Last Updated: Monday, 06 November 2017 21:34

fusion nature

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

High-throughput drug screening

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Last Updated: Tuesday, 26 September 2017 09:10

The group of Tristan Bereau uses truly high-throughput Martini simulations to screen thermodynamic properties of drug-membrane interactions. They establish linear relationships between partitioning coefficients and key features of the potential of mean force, allowing them to predict the structure of the insertion from bulk experimental measurements for more than 400 000 (!!) compounds. Details can be found here:

R. Menichetti, K.H. Kanekal, K. Kremer, T. Bereau. J. Chem. Phys. 147, 125101 (2017); http://dx.doi.org/10.1063/1.4987012
 
And ... Tristan is looking for new PhD students and postdocs to work on this topic, so send him an email if you are interested (This email address is being protected from spambots. You need JavaScript enabled to view it.)

Setting up some coarse grain LPS systems

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Last Updated: Monday, 18 September 2017 10:46

Journal cover image of LPS martini builder

This is the first paper of a fresh PhD student in our lab (Bart). We are proud to say that we made it to the cover! In this paper we show that we can build intial structures for all kind of membrane motives using the CHARMM-GUI interface and the Martini CG force field.

P.-C. Hsu, B. M. H. Bruininks, D. Jefferies, P. Cesar Telles de Souza, J. Lee, D. S. Patel, S. J. Marrink, Y. Qi, S. Khalid, W. Im. J. Comput. Chem. 2017, 38, 2354–2363. DOI: 10.1002/jcc.24895

Go Martini

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Last Updated: Monday, 18 September 2017 10:39

Looking for a way to model foldable Martini proteins? Try Go Martini, a clever combination of Martini and Go potentials developed by the group of Theodorakis. Further details on the method can be found in the publication:

A.B. Poma, M. Cieplak, P.E. Theodorakis, JCTC, 13:1366–1374, 2017. DOI:10.1021/acs.jctc.6b00986

Crowds slow you down

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Last Updated: Monday, 18 September 2017 10:39

What happens to the famous Saffman-Delbruck model when your membrane is crowded with proteins ? Read all about it in this exciting new paper from the Vattulainen group, featuring Martini simulations of very crowded membranes:

M. Javanainen, H. Martinez-Seara, R. Metzler, I. Vattulainen, J. Phys. Chem. Lett. 2017, available online