Light Harvesting Complex II



Martini simulations of the full trimeric light harvesting complex II, embedded in a thylakoid membrane, reveal interesting chromophore dynamics and lipid binding sites.

For details, check the paper which is now online: S. Thallmair, P.A. Vainikka, S.J. Marrink. Biophys. J., 116:1446-1455, 2019. doi:10.1016/j.bpj.2019.03.009

Less fuzzy lipids

lipid phase diagrams

A recent study by Carpenter, Lopez and coworkers nicely characterized the phase behavior of Martini DPPC/DOPC/cholesterol ternary mixtures. General Martini parameters correctly captured a large fraction of the phase diagram, but parameters optimized against CHARMM DOPC and DPPC simulations could better capture some of the details, especially close to the critical point.

The new lipid parameters specifically tuned to CHARMM DOPC and DPPC can be found here and in the Martini lipid parameter list: DPPC and DOPC.

For details see JCTC 2018, DOI:10.1021/acs.jctc.8b00496.

Protein-Lipid Interactions


In collaboration with the Tieleman group we published another comprehensive review, focussing on the diversity of protein-lipid interactions. More than 800 references, including many Martini-based studies. sincere apologies if your paper was not included.

V. Corradi, B.I. Sejdiu, H. Mesa-Galloso, H. Abdizadeh, S.Y. Noskov, S.J. Marrink, D.P. Tieleman. "Emerging Diversity in Lipid–Protein Interactions", Chem. Review, 2019. DOI:10.1021/acs.chemrev.8b00451

Complex Membranes

TOC Figure

Together with several co-authors, we wrote a comprehensive review (>700 references) on computer simulations of cell membranes. In this field, we are witnessing a transition from simulations of simpler membrane models to multicomponent systems, culminating in realistic models of an increasing variety of cell types and organelles. Here, we review the state of the art in the field of realistic membrane simulations and discuss the current limitations and challenges ahead.

S.J.Marrink, V. Corradi, P.C.T. Souza, H.I. Ingolfsson, D.P. Tieleman, M.S.P. Sansom. "Computational Modeling of Realistic Cell Membranes". Chem. Review, 2019. DOI:10.1021/acs.chemrev.8b00460

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);