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Abstract
Cholesterol plays a crucial role in biomembranes by regulating various properties such as fluidity, rigidity, permeability, and organization of lipid bilayers. The latest version of the Martini model, Martini 3, offers significant improvements in interaction balance, molecular packing, and the inclusion of new bead types and sizes. However, the release of the new model resulted in the need to re-parameterize many core molecules, including cholesterol. Here, we describe the development and validation of a Martini 3 cholesterol model, addressing issues related to its bonded setup, shape, volume and hydrophobicity. The proposed model mitigates some limitations of its Martini 2 predecessor while maintaining or improving overall behavior.
Supplementary materials
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Supplementary Information
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Additional analysis and information.
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Title
Supplementary Video S1
Description
Top view of Martini 3 70:30 DPPC:CHOL, 85:15 DPPC:CHOL and 85:15 DOPC:CHOL lipid bilayer simulations at 300 K. DPPC first acyl-chain beads (C1A, C1B) are represented in grey. Cholesterol hydroxyl bead (ROH) is represented in red. Note the transient formation of DPPC gel domains (visible through the hexagonal acyl-chain arrangement) over the course of the simulation. The last 500 ns are shown.
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