Cholesterol-Enriched Membranes Reshape the Conformational Ensemble and Interfacial Mechanics of ACE2

Dataset Overview This repository contains raw simulation data, topologies, trajectories, umbrella sampling (US) window outputs, frame-selection workflows, and analysis scripts associated with molecular dynamics studies of Angiotensin-Converting Enzyme 2 (ACE2). The dataset investigates both monomeric and dimeric forms of ACE2 across three lipid membrane environments representing different biophysical regimes: Fluid membrane: POPC100 Intermediate membrane: POPC80:CHL20 (80% POPC, 20% Cholesterol) Raft-like membrane: POPC30:CHL50:PSM20 (30% POPC, 50% Cholesterol, 20% Sphingomyelin) File Descriptions Unbiased Molecular Dynamics Simulations & Topologies ACE2_mon_POPC100.tar.xz: GROMACS trajectory and setup files for ACE2 monomer in a POPC100 membrane. ACE2_mon_POPC80-CHL20.tar.xz: GROMACS trajectory and setup files for ACE2 monomer in a POPC80:CHL20 membrane. ACE2_mon_POPC30-CHL50-PSM20.tar.xz: GROMACS trajectory and setup files for ACE2 monomer in a POPC30:CHL50:PSM20 membrane. ACE2_dim_POPC100.tar.xz: GROMACS trajectory and setup files for ACE2 dimer in a POPC100 membrane. ACE2_dim_POPC80-CHL20.tar.xz: GROMACS trajectory and setup files for ACE2 dimer in a POPC80:CHL20 membrane. ACE2_dim_POPC30-CHL50-PSM20.tar.xz: GROMACS trajectory and setup files for ACE2 dimer in a POPC30:CHL50:PSM20 membrane. gromacs_index_files.tar.xz: Archive containing all GROMACS index (.ndx) files used across the simulation systems. Umbrella Sampling (US) & Potential of Mean Force (PMF) Data PMF_profiles_umbrella_frames.tar.xz: Initial frames extracted from unbiased simulations used to seed Umbrella Sampling windows, along with the extraction scripts. ACE2 Transmembrane (TM) Helix Tilt PMF Data: PMF_US_data_TM_tilt_POPC100.tar.xz: US parameters and collective variable data for TM helix tilt in POPC100. PMF_US_data_TM_tilt_POPC80_CHL20.tar.xz: US parameters and collective variable data for TM helix tilt in POPC80:CHL20. PMF_US_data_TM_tilt_POPC30_CHL50_PSM20.tar.xz: US parameters and collective variable data for TM helix tilt in POPC30:CHL50:PSM20. ACE2 Extracellular-Domain (ECD) Bending PMF Data: PMF_US_data_ECD_bending_POPC100.tar.xz: US parameters and collective variable data for ECD bending in POPC100. PMF_US_data_ECD_bending_POPC80_CHL20.tar.xz: US parameters and collective variable data for ECD bending in POPC80:CHL20. PMF_US_data_ECD_bending_POPC30_CHL50_PSM20.tar.xz: US parameters and collective variable data for ECD bending in POPC30:CHL50:PSM20. Analysis & Processing analysis.tar.xz: Python and Bash scripts used for data analysis, figure generation, and PMF calculation (e.g., WHAM/MBAR analysis).