Structure and Dynamics of the HIV-1 Envelope Protein on the Virion Envelope

Here we provide the structures, trajectories, and model parameters of HIV-1 envelope protein (Env) embedded in membrane bilayers composed of POPC, LSM, cholesterol, POPS, POPE, and PIP2 at both all-atom (AA) and coarse-grained (CG) resolutions, as used in the study "Structure and Dynamics of the HIV-1 Envelope Protein on the Virion Envelope" by Ayan Majumder, Mandira Dutta, Levi Cherek, and Gregory A. Voth. The CG folder contains: CG/CG_model: CG model of the Env protein embedded in an asymmetric bilayer, along with LAMMPS scripts used to perform CG simulations. CG/flat_bilayer_nineEnv: CG trajectories from three independent replica simulations of nine Env proteins embedded in a flat asymmetric bilayer. CG/flat_bilayer_noPIP2_nineEnv: CG trajectory from a simulation of nine Env proteins embedded in a flat asymmetric lipid bilayer containing no PIP2 lipids. CG/flat_bilayer_oneEnv: CG trajectory from a simulation of one Env protein embedded in a flat asymmetric bilayer. CG/full_virion_envelope: CG trajectories from two independent replica simulations of 14 Env proteins in the full virion envelope. The AA folder contains: AA/Env_glycan: CHARMM36 (lipid)/CHARMM36m (protein) force field files for glycosylated Env protein embedded in an asymmetric bilayer; initial and final structures obtained from three independent replica simulations; GROMACS input files (MDP, TPR) required to rerun all simulations. AA/Env_without_glycan: CHARMM36 (lipid)/CHARMM36m (protein) force field files for Env protein without glycans embedded in an asymmetric bilayer; initial and final structures obtained from three independent replica simulations; GROMACS input files (MDP, TPR) required to rerun all simulations. AA/Env_dimer_glycan: CHARMM36 (lipid)/CHARMM36m (protein) force field files for glycosylated Env dimer embedded in an asymmetric bilayer; initial and final structures obtained from two independent replica simulations; GROMACS input files (MDP, TPR) required to rerun all simulations.