Room for Improvement in the Initial Martini 3 Parameterization of Peptide Interactions

2022/09/20 by J. Karl Spinti, Fernando Neiva Nunes, Manuel N. Melo · 1 voice
Biochemistry, Genetics and Molecular Biology · #Lipid Membrane Structure and Behavior #Mechanisms of cancer metastasis #RNA and protein synthesis mechanisms

paper · pdf · doi:10.26434/chemrxiv-2022-wgz1j

openalex publication_date 2022/09/20 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/22

Abstract

The Martini 3 coarse-grain force field has greatly improved upon its predecessor, having already been successfully employed in several applications. Here, we gauge the accuracy of Martini 2 and 3 protein interactions in two types of systems: coiled coil peptide dimers in water and transmembrane peptides. Coiled coil dimers form incorrectly under Martini 2 and not at all under Martini 3. With transmembrane peptides, Martini 3 represents better the membrane thickness–peptide tilt relationship, but shorter peptides do not remain transmembranar. We discuss related observations, and describe mitigation strategies involving either scaling interactions or restraining the system.

Citations

• Matplotlib: A 2D Graphics Environment
• Polymorphic transitions in single crystals: A new molecular dynamics method
• Array programming with NumPy
• Martini 3: a general purpose force field for coarse-grained molecular dynamics

Discussions

• Check out our preprint on some Martini 3 rough edges when modeling helical peptides in specifc dimeric or transmembrane conditions. Keeping it challenging for upcoming refinements to the force field b [bsky, 1 points, 0 comments]

Related

• Coarse-grained simulations of long intrinsically disordered proteins: a benchmark of Martini 3 force-fields
• The Martini Model in Materials Science
• Fast parameterization of Martini3 models for fragments and small molecules
• Martini 3 Coarse-Grained Force Field for Carbohydrates
• Martini 3 Limitations in Phospholipid Flip-Flop