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bioRxiv · 10.1101/2021.03.25.437005

CG2AT2: An Enhanced Fragment-based approach for Serial Multi-scale Molecular Dynamics simulations

Vickery, O. N.·Stansfeld, P. J.
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Abstract

Coarse-grained molecular dynamics provides a means for simulating the assembly and interactions of macromolecular complexes at a reduced level of representation, thereby allowing both longer timescale and larger sized simulations. Here, we describe an enhanced fragment-based protocol for converting macromolecular complexes from coarse-grained to atomistic resolution, for further refinement and analysis. While the focus is upon systems that comprise an integral membrane protein embedded in a phospholipid bilayer, the technique is also suitable for e.g. membrane-anchored and soluble protein/nucleotide complexes. Overall, this provides a method for generating an accurate and well equilibrated atomic-level description of a macromolecular complex. The approach is evaluated using a diverse test set of eleven system configurations of vary size and complexity. Simulations are assessed in terms of protein stereochemistry, conformational drift, lipid/protein interactions, and lipid dynamics.

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Vickery, O. N., Stansfeld, P. J.. 2021-03-26. CG2AT2: An Enhanced Fragment-based approach for Serial Multi-scale Molecular Dynamics simulations. https://doi.org/10.1101/2021.03.25.437005

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