Extended Data Fig. 7: Collective variables for mABP simulations and free-energy landscapes of mABP simulations.
From: Cryo-EM structure of human rhodopsin bound to an inhibitory G protein
a, To bias movement between TM6 relative to that of the receptor bundle, two centre-of-geometry (COG) distance collective variables (CVs) were implemented into fABMACS66. CV1 and CV2 are COG distances between selected atoms of TM6 to TM1/2 and TM6 to TM3/4 respectively. Collective variable atoms for the rhodopsin simulation are highlighted. b, COG collective variable formula and the CV1 and CV2 distances. c, Potential energy surface reveals that CV1 and CV2 distances are larger in the Gs-coupled receptors (A2AR and β2AR) than those in the Gi-coupled receptors (mOR1 and rhodopsin).
