Martini 3: A journey through development and future prospects

Paulo C. T. Souza


Laboratoire de Biologie et Modélisation de la Cellule, CNRS, UMR 5239, Inserm, U1293, Université Claude Bernard Lyon 1, Ecole Normale Supérieure de Lyon, Centre Blaise Pascal de Simulation et de Modélisation Numérique, 46 Allée d’Italie, 69364, Lyon, France.

The Martini model is among the most popular coarse-grained (CG) models in molecular simulations, widely recognized for its intuitive building block approach [1]. In Martini, two to four non-hydrogen atoms are represented by a single effective particle, or bead, with interactions parameterized primarily using thermodynamic data. Despite its extensive usage, identified limitations highlighted the need for significant updates [2], prompting a comprehensive reparametrization of the CG beads—something that had not been performed since 2007 [3].

This presentation introduces Martini 3, the latest iteration of the model, featuring improved interaction balances, new bead types, and enhanced treatment of specific interactions such as hydrogen bonding and electron polarizability [4]. Martini 3 provides more accurate predictions of molecular interactions and packing, significantly benefiting the study of complex biological systems. Through illustrative examples, I will demonstrate how Martini 3 can be effectively applied to the binding of small molecules to proteins [5,6] and the design and modeling of lipid nanoparticles [7]. Additionally, I will discuss ongoing and future developments aimed at further enhancing lipid [8] and protein models within Martini 3 [9], emphasizing its growing role and potential in computational research areas such as biophysics and structural biology, as well as industrial applications.

References:

  1. Marrink, S. J. et al. Two decades of Martini: Better beads, broader scope. Wiley Interdiscip. Rev. Comput. Mol. Sci. 13, (2023).
  2. Alessandri, R. et al. Pitfalls of the Martini Model. J Chem Theory Comput 15, 5448–5460 (2019).
  3. Marrink, S. J., Risselada, H. J., Yefimov, S., Tieleman, D. P. & de Vries, A. H. The MARTINI force field: coarse grained model for biomolecular simulations. J Phys Chem B 111, 7812–7824 (2007).
  4. Souza, P. C. T. et al. Martini 3: a general purpose force field for coarse-grained molecular dynamics. Nat Methods 18, 382–388 (2021).
  5. Souza, P. C. T. et al. Protein-ligand binding with the coarse-grained Martini model. Nat Commun 11, 3714 (2020).
  6. Bartocci, A. et al. A millisecond coarse-grained simulation approach to decipher allosteric cannabinoid binding at the glycine receptor α1. Nat Commun 15, 9040 (2024).
  7. Kjølbye, L. R. et al. Martini 3 building blocks for Lipid Nanoparticle design. ChemRxiv (2024) doi:10.26434/chemrxiv-2024-bf4n8.
  8. Pedersen, K. B. et al. The Martini 3 lipidome: Expanded and refined parameters improve lipid phase behavior. ChemRxiv (2024) doi:10.26434/chemrxiv-2024-8bjrr.
  9. Souza, P. C. T. et al. GōMartini 3: From large conformational changes in proteins to environmental bias corrections. bioRxiv (2024) doi:10.1101/2024.04.15.589479.

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