Effects of mechanical stress on the activation mechanism of the angiotensin II type 1 receptor (AT1)

Description

Data set for the article "Mechanical stress and anionic lipids synergistically stabilize an atypical structure of the angiotensin II type 1 receptor (AT1)" by Rym Ben Boubaker, Daniel Henrion and Marie Chabbert The data set includes - DATA: numerical values to generate graphs (DATA_FOR_FIGURES.xlsx) and the TM3-TM6 and TM3_TM7 distances for all the replicas to generate heatmaps and figures (DISTANCES_TM3_TM6_AT1_ALL.xlsx and DISTANCES_TM3_TM7_AT1_ALL.xlsx). - Classical MD trajectories: charmm-gui constructs and trajectories with 55 frames from 0 to 220 ns - Steered MD trajectories: For each replica, charmm-gui constructs, initial snapshots (.coor, .vel, .xsc and .pdb files) and a merged pdb file with 12 frames equidistant on the duration of the simulation (90ns), containing the receptor, water and ions molecules, and lipids within a distance of 8 Å, for straightforward visualization with Pymol - Scripts namd for classical and steered MD simulations and toppar files for Charmm36 forcefield - Scripts tcl for VMD analysis - Scripts for cross-section measurements (.tcl, .sh and .inp files) - Script .pl for quaternion calculation - Scripts for pressure profile measurements (include .tcl, .sh, .inp scripts and test data) - Scripts R for Bio3D analysis, heatmaps, boxplots, and statistical analysis

Steps to reproduce

Details are described in "Mechanical stress and anionic lipids synergistically stabilize an atypical structure of the angiotensin II type 1 receptor (AT1)" by Rym Ben Boubaker, Daniel Henrion and Marie Chabbert, Plos Comput Biol, in press.

Categories

Funding

Licence