Martini 3 force field parameters for protein lipidation post-translational modifications

Data for the publication "Martini 3 force field parameters for protein lipidation post-translational modifications" in the Journal of Chemical Theory and Computation

Protein lipidations are vital co-translational or post-translational modifications that tether lipid tails to specific protein aminoacids to allow them to anchor to biological membranes, switch their subcellular localizations, and modulate association with other proteins. Such lipidations are thus crucial for multiple biological processes such as signal transduction, protein trafficking and membrane localization, and are implicated in various diseases as well. Examples of such lipid-anchored proteins include the Ras family of proteins that undergo farnesylation, actin and gelsolin, which are myristoylated, phospholipase D, which is palmitoylated, glycosylphosphatidylinositol-anchored proteins and others.  

Here, we develop parameters for the latest version of the Martini 3 coarse-grained force field for cysteine-targeting farnesylation, geranylgeranylation and palmitoylation as well as the glycine-targeting myristoylation due to the importance of these lipidations in disease and in particular for studying cancer and anti-cancer drug discovery. The parameters are developed using the CHARMM36m all-atom force field parameters as reference. The behavior of the coarse-grained models is consistent with that of the all-atom force field for all lipidations and reproduces key dynamical and structural features  such as solvent-accessible surface area, bilayer penetration depth, and cluster representative conformations.  The parameters, along with mapping schemes for the popular martinize2 tool, are immediately available for download.