memble membrane protein systems: Martini 3 coarse-grained EGFR and rhodopsin in a refined-lipidome bilayer

This dataset contains the two membrane protein systems built and equilibrated with memble for the article "Building Martini 3 coarse-grained membrane protein systems from refined lipid parameters with memble" (Current Protocols). memble is an open-source tool that builds a Martini 3 membrane protein system by reading each lipid directly from its published topology file rather than from a fixed library, so that a refined or newly released lipid parameter set can be used as soon as it appears. The protein-free bilayers used to validate the lipid parameters are deposited separately (https://doi.org/10.5281/zenodo.20684875). Two systems are included. 1. EGFR transmembrane-juxtamembrane system (Basic Protocol 2, Figure 2 of the article). Four copies of the EGFR transmembrane-juxtamembrane construct, with the transmembrane core taken as residues 65 to 88 of each chain and the juxtamembrane left flexible (SS_MODE=tm), embedded in an asymmetric bilayer of the refined Martini 3 lipidome with cholesterol, DLPC, and PSM in the upper leaflet and cholesterol, DLPC, and DOPS in the lower leaflet. 2. Rhodopsin (GPCR) system (Basic Protocol 3, Figure 4 of the article). Bovine rhodopsin (PDB 1U19), one chain, with the retinal, sugars, palmitate, ions, and water removed, oriented on the mean axis of its seven membrane-spanning helices (MULTI_TM=1, NTERM_SIDE=up). The upper leaflet is CHOL:DLPC:PSM at 33:33:33 and the lower leaflet CHOL:DLPC:DOPS:POP2_45 at 33:33:33:1, placing phosphatidylinositol 4,5-bisphosphate on the cytoplasmic side, where it occurs in the cell. CONTENTS Each archive holds the built system and the production trajectory of one system. The trajectory files ending in _nw.xtc have the water and ion beads removed and carry one frame per 5 ns; the matching _nw.gro is the first frame of the same selection, so the pair can be opened on its own in VMD, PyMOL, or MDAnalysis with no other file. The complete system including water and ions is given as coordinates and topology (system.gro and system.top with the per-molecule topology files), together with the run input (.mdp) of every stage and the run scripts written by the build, so that the run can be reproduced in full from the deposited input. SIMULATION DETAILS Both systems were run in GROMACS with the Martini 3 force field, reaction-field electrostatics with a relative dielectric of 15, and a 1.1 nm cutoff for both the Coulomb and the Lennard-Jones interactions. Temperature was held at 310 K with the velocity-rescaling thermostat and a 1 ps coupling time, and pressure at 1 bar with semiisotropic coupling and a compressibility of 3 x 10^-4 bar^-1. Each system was energy minimized and then equilibrated in five stages of 0.5, 1, 1, 2, and 5 ns with the position restraints released step by step, 9.5 ns in total, and then run at a 20 fs timestep with the Parrinello-Rahman barostat. PARAMETERS AND PROVENANCE The Martini 3 force field, the refined Martini 3 lipidome, and the phosphatidylinositide headgroup parameters are the work of their original authors and are obtained from the sources below. They are not redistributed here. Martini 3 force field: Souza et al. (2021) Nat Methods 18, 382-388. https://doi.org/10.1038/s41592-021-01098-3 and https://cgmartini.nl Refined Martini 3 lipidome: Pedersen et al. (2025) ACS Cent Sci 11, 1598-1610. https://doi.org/10.1021/acscentsci.5c00755 and https://github.com/Martini-Force-Field-Initiative/M3-Lipid-Parameters Phosphatidylinositide headgroups: Borges-Araujo et al. (2022) J Chem Theory Comput 18, 357-373. https://doi.org/10.1021/acs.jctc.1c00615 SOFTWARE Built with memble (Apache License 2.0), https://github.com/takeshi-sato-dev/memble , archived at https://doi.org/10.5281/zenodo.20684812 . memble uses COBY for the lipid packing step and martinize2/vermouth for the coarse graining.```