Antagonist binding actively disrupts interleukin-1 receptor dynamics to block co-receptor recruitment
Description
This dataset contains all-atom molecular dynamics (MD) simulation trajectories supporting the manuscript "Antagonist binding actively disrupts interleukin-1 receptor dynamics to block co-receptor recruitment." The data characterizes the intrinsic dynamics and allosteric pathways of the human interleukin-1 receptor (R1) in its unbound, agonist-bound, and antagonist-bound states. The repository includes production trajectories for the following systems (identified by their starting PDB entries). Here, we use Chain IDs to distinguish between components extracted from complexes for "apo" (ligand-removed) simulations. The following table maps the repository folders to the identifiers used in the manuscript and figure legends: Directory Component(s) Label used in the paper 1G0Y Unbound Receptor (R1) 1G0Y 1ILR Unbound Antagonist (Ra) 1ILR 9ILB Unbound Agonist (IL1) 9ILB 1IRA Antagonist-bound Complex 1IRA 1ITB Agonist-bound Complex 1ITB 4DEP Fully Assembled Ternary Complex 4DEP 4DEP_binary R1–IL1 binary subcomplex 4DEP_binary 1IRA_A Receptor (R1) freed from Ra 1IRA_apo 1ITB_A Receptor (R1) freed from IL1 1ITB_apo 4DEP_A Receptor (R1) freed from ternary complex 4DEP_apo 1IRA_B Antagonist (Ra) freed from R1 1IRA_Apo 1ITB_B Agonist (IL1) freed from R1 1ITB_Apo 4DEP_B Agonist (IL1) freed from ternary complex 4DEP_Apo These files can be analyzed using standard molecular modeling suites such as AMBER (cpptraj), VMD, MDAnalysis, or MDTraj. The provided topology files are essential for interpreting the coordinate data in the NetCDF files.
Files
Steps to reproduce
Initial protein coordinates were obtained from the Protein Data Bank (PDB IDs: 1G0Y, 1ILR, 9ILB, 1IRA, 1ITB, and 4DEP). Systems were prepared using the tleap module from AmberTools, solvated in TIP3P water, and neutralized with Na+/Cl- ions. All-atom MD simulations were performed using Amber 22 with the ff14SB force field. Production runs were conducted at 298 K and 1 atm using a Langevin thermostat and Monte Carlo barostat. Resulting trajectories were processed using cpptraj to strip water/ions and image the coordinates to the primary unit cell for the final shared files
Institutions
- Uniwersytet WarszawskiWarszawa