Setting up some coarse grain LPS systems

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. HsuB. M. H. BruininksD. JefferiesP. Cesar Telles de SouzaJ. LeeD. S. PatelS. J. MarrinkY. QiS. KhalidW. ImJ. Comput. Chem20173823542363. DOI: 10.1002/jcc.24895

Go Martini

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

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

Another fruitful Martini Workshop

Cherish this picture, for it will contain some nobel price winners in the future!group picture Martiniworkshop 2017

Sticky sugars

Be aware of the fact that self interactions of large biomolecules in Martini are sometimes too strong and may lead to arteficial aggregation - see for instance the recent work of the group of Sikora on polysaccharides:

P.S. Schmalhorst, F. Deluweit, R. Scherrers, C.P. Heisenberg, M. Sikora. JCTC, in press. DOI: 10.1021/acs.jctc.7b0037410.1021/acs.jctc.7b00374

 Note: with the forthcomng release of Martini 3.0, we aim to resolve this issue !

Supramolecular polymer dynamics

The group of Pavan has used Martini in combination with well-tempered metadynamics to study the self-healing capacity of bio-inspired supramolecular polymers. Cool !

D. Bochicchio, M. Salvalaglio, G. Pavan. Nature Commun. 8:147 (2017).