Improved Parameters for the Martini Coarse-Grained Protein Force Field

TLDR

The Martini coarse‑grained force field has been widely applied to biomolecular simulations, yet recent comparisons with atomistic models have exposed deficiencies in residue behavior. This study aims to reparametrize problematic residues to correct their hydrophobicity and dimerization properties. The authors reassigned particle types or added embedded charges, then validated the new parameters through lipid‑bilayer partitioning, membrane binding of Wimley‑White peptides, and solvent‑dependent dimerization free energies, while also refining bonded terms for more realistic α‑helix lengths and numerical stability. The resulting parameter set, Martini v2.2, improves residue behavior and overall force‑field performance.

Abstract

The Martini coarse-grained force field has been successfully used for simulating a wide range of (bio)molecular systems. Recent progress in our ability to test the model against fully atomistic force fields, however, has revealed some shortcomings. Most notable, phenylalanine and proline were too hydrophobic, and dimers formed by polar residues in apolar solvents did not bind strongly enough. Here, we reparametrize these residues either through reassignment of particle types or by introducing embedded charges. The new parameters are tested with respect to partitioning across a lipid bilayer, membrane binding of Wimley-White peptides, and dimerization free energy in solvents of different polarity. In addition, we improve some of the bonded terms in the Martini protein force field that lead to a more realistic length of α-helices and to improved numerical stability for polyalanine and glycine repeats. The new parameter set is denoted Martini version 2.2.