Figure 4. Trajectory of the probability flux and the highest probability path in nAChR (PDB code: 2BG9).

(a) Trajectory of the probability flux over time for each residue of the α1 nAChR upon perturbation to the agonist-binding site (Y93, W149, Y190, and Y198). The color denotes the normalized intensity of the flux. Positive and negative signs describe the net signal flow into and out of the residue, respectively. (b) The signaling path with highest probability between Y190 of the C loop and the pore-lining residue L251 (9′) in the α1 nAChR. Perturbation starting and ending points are shown in green and red spheres, respectively. Residues comprising the path are shown in purple spheres. The labeled residues were identified previously in the mutagenesis and functional studies for transferring energy from the extracellular domain to the channel gating [25], [27], .