Martini 3 Coarse-Grained Force Field parameters for GM1 and GM2. Gromacs Topology files.
- 1. 1. Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
- 2. 2. Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) and Departamento de Química Orgánica, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
Description
With the release of the Martini 3 Force Field, one of the most widely used for Coarse-Grained molecular dynamics simulations, we present optimized parameters for the gangliosides GM1 and GM2, which play critical roles in different neurological conditions, such as in Alzheimer’s and Tay-Sachs diseases. Our model was built following the Martini carbohydrate guidelines and validated against atomistic simulations. The new parametrization of GM1 and GM2 reproduces key atomistic behaviours within a lipid bilayer. Using these new set of parameters, gangliosides remain as monomers in a lipid membrane, overcoming the issues of previous Martini versions related to the over aggregation. Moreover, they accurately reproduce the specific interaction of the cholera toxin with lipid membranes containing GM1, highlighting their validity. This model offers a reliable framework for investigating ganglioside interactions employing the Martini 3 Force Field, supporting disease-related research with enhanced computational efficiency.
In this repository, GROMACS-compatible topology files are available.
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