Coarse-grained simulation of CAV1-8S in a symmetric bilayer mixture

Simulation of CAV1-8S embedded in a symmetric bilayer mixture with a lipid composition modeling that of the cytoplasmic leaflet of mammlian plasma membranes (PAPS/PLPC/PDPE/Chol 26/18/16/40 mol%). The system has 3250 lipids in the protein-proximal leaflet and 3500 lipids in the protein-distal leaflet, 150 mM salt (Na and Cl ions), and was constructed with CHARMM-GUI with initial dimensions of 45 x 45 x 26 nm.

The simulation was run with the MARTINI 2.2 force field at 37C for a total of 10 us. Uploaded are the structure (.gro) file, the raw trajectory (.xtc) from the last 2 us (output every 0.1 ns), sample simulation parameters (.mdp) and the force field parameters (.itp).

More details and results from the simulation can be found in Doktorova et al. 2025. PNAS. In press (https://doi.org/10.1101/2024.08.28.610209)