Antagonist binding actively disrupts interleukin-1 receptor dynamics to block co-receptor recruitment

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.