Assessing the Martini 3 protein model: A review of its path and potential

Borges-Araújo, Luís; Pereira, Gilberto P.; Valério, Mariana; Souza, Paulo C.T.

doi:10.1016/j.bbapap.2024.141014

Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics

2024

DOI: 10.1016/j.bbapap.2024.141014

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Assessing the Martini 3 protein model: A review of its path and potential

Luís Borges-Araújo,

Gilberto P. Pereira,

Mariana Valério

et al.

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2024

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Cited by 8 publications

References 98 publications

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Two cooperative lipid binding sites within the pleckstrin homology domain are necessary for AKT binding and stabilization to the plasma membrane

Soteriou,

Xu,

Connell

et al. 2024

Structure

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Two cooperative lipid binding sites within the pleckstrin homology domain are necessary for AKT binding and stabilization to the plasma membrane

Soteriou,

Xu,

Connell

et al. 2024

Structure

View full text Add to dashboard Cite

OLIVES: A Go̅-like Model for Stabilizing Protein Structure via Hydrogen Bonding Native Contacts in the Martini 3 Coarse-Grained Force Field

Pedersen,

Borges-Araújo,

Stange

et al. 2024

J. Chem. Theory Comput.

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Recalibration of MARTINI-3 Parameters for Improved Interactions between Peripheral Proteins and Lipid Bilayers

Soni,

Gupta,

Mandal

2024

J. Chem. Theory Comput.

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The MARTINI force field is one of the most used coarse-grained models for biomolecular simulations. Many limitations of the model including the protein−protein overaggregation have been improved in its latest version, MARTINI-3. In this study, we investigate the efficacy of the MARTINI-3 parameters for capturing the interactions of peripheral proteins with model plasma membranes. Particularly, we consider two classes of proteins, namely, annexin and epsin, which are known to generate negative and positive membrane curvatures, respectively. We find that current MARTINI-3 parameters are not able to correctly describe the protein−membrane interface and the protein-induced membrane curvatures for any of these proteins. The problem arises due to the lack of proper hydrophobic interactions between the protein residues and lipid tails. Making systematic adjustments, we show that a combination of reduction in the protein−water interactions and enhancement of protein−lipid hydrophobic interactions is essential for accurate prediction of the interfacial structure including the protein-induced membrane curvature. Next, we apply our model to a couple of other peripheral proteins, namely, Snf7, a core component of the ESCRT-III complex, and the PH domain of evectin-2. We find that our model captures the protein−membrane interfacial structure much more accurately than the MARTINI-3 model for all of the peripheral proteins considered in this study. However, the strategy described in this study may not be suitable for oligomeric transmembrane proteins where protein−protein hydrophobic interactions should be increased instead of protein−lipid hydrophobic interactions.

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Assessing the Martini 3 protein model: A review of its path and potential

Cited by 8 publications

References 98 publications

Two cooperative lipid binding sites within the pleckstrin homology domain are necessary for AKT binding and stabilization to the plasma membrane

Two cooperative lipid binding sites within the pleckstrin homology domain are necessary for AKT binding and stabilization to the plasma membrane

OLIVES: A Go̅-like Model for Stabilizing Protein Structure via Hydrogen Bonding Native Contacts in the Martini 3 Coarse-Grained Force Field

Recalibration of MARTINI-3 Parameters for Improved Interactions between Peripheral Proteins and Lipid Bilayers

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