Data and code for: Elucidation of a dynamic interplay between a beta-2 adrenergic receptor, its agonist and stimulatory G protein

G protein-coupled receptors (GPCRs) belong to the largest group of
membrane receptors for transmembrane signal transduction. Ligand-induced
activation of GPCRs triggers G protein activation followed by various
signaling cascades. The uploaded data set help to understand structural
and energetic determinants of ligand binding to GPCRs and GPCRs to G
proteins.  In this dataset we presented the way how we
performed molecular dynamics (MD) simulations by using both Anton 2
supercomputer and Gaussian accelerated MD method for production runs.
Before the production runs, we run 90 ns equilibration with gradually
reducing protein restraints in the first 40 ns using NAMD. We simulated
two systems, beta-2 adrenergic receptor with norepinephrine bound
(β2AR-only) and the NE bound β2AR further bound with stimulatory G protein
(Gs) (β2AR-Gs). For the β2AR-only system, one Anton simulation and three
repeat GaMD simulations were performed. For the β2AR-Gs systems, four
Anton simulations and three repeat GaMD simulations were performed. The
repeat runs for the same system are identical except the starting
velocities. The needed restraint files used in equilibration, the
simulation input files, forcefield parameters and structure files for both
Anton 2 and GaMD simulations were provided. Short trajectories for each
run of each system were uploaded as well. For each system, we analyzed the
binding poses of NE, interaction energies between NE and β2AR,
 the conformational changes of the Gs protein, and the 2D
potential of mean force (PMF). The original data related to the analyses
and the codes for performing the analyses were provided as well. The codes
proved in this data set can be reused free of charge. This data set
corresponds to the paper "Elucidation of a dynamic interplay between
a beta-2 adrenergic receptor, its agonist and stimulatory G
protein"  (https://doi.org/10.1073/pnas.2215916120)