Lipid shape and tuberculosis

The team of Matthieu Chavent has elucidated the role of a specific class of lipids, phthiocerol dimycocerosate (DIM), in phagocytosis of macrophages such as mycobacterium tuberculosis. Read all about it in: Augenstreich et al., The conical shape of DIM lipids promotes Mycobacterium tuberculosis infection of macrophages, PNAS 2019, in press.

Allosteric pathway unravelled

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Martini-based simulations of a superoxide dismutase protein reveal an allosteric pathway involving an important mutation site. Apart from the biological relevance of this finding, the study is a showcase of how the new Martini 3.0 model is able to capture allosteric coupling in proteins.  For details, see: P.C.T. Souza, S. Thallmair, S.J. Marrink, R. Mera-Adasme. An Allosteric Pathway in SOD1 Unravels the Molecular Mechanism of the G93A ALS-Linked Mutation. J. Phys. Chem. Letters, Just Accepted, 2019. doi.org/10.1021/acs.jpclett.9b02868

Coupling Dry Martini with Lattice Boltzmann

Brandner et al. developed a cool new method for the coupling between Dry Martini and Lattice Boltzmann Molecular Dynamics in order to include naturally hydrodynamic interactions in implicit solvent simulations of lipid systems. For details, see: Brandner et al., Scientific Reports 9, 16450 (2019). 

Chemical compound space

The team of Bereau published an interesting evaluation of the chemical space that can be represented by the MARTINI bead family. For details, see: Kanakal & Bereau, J. Chem. Phys. 51, 164106 (2019); https://doi.org/10.1063/1.5119101

In memoriam Herman Berendsen

Herman_Berendsen.jpgHerman Berendsen, one of the founding fathers of molecular modeling, passed away last Monday at the respectable age of 85.

We will miss him, but his legacy is large and will last for generations to come.

MARTINI practical guide

If you would like some guidance on how to setup complex MARTINI simulations, the tips and tricks behhind the scene, have a look at this book chapter: Bruininks et al., "A Practical View of the Martini Force Field", Biomolecular Simulations, 105-127, 2019. pdf-reprint.