Biology Reference
In-Depth Information
FIGURE 3.5
Global meta paths. 3D representations of the global meta paths concerning dark and MII states
are shown inpanels (A) and (B), respectively. The receptors are represented as cartoons colored
according to the receptor portion (see the legend to
Fig. 3.3
for the coloring scheme).Meta paths
are black. Nodes are represented as spheres centered on the C
-atoms of the protein, on the C8
atom of retinal, and the O atom of the structural water molecules. Node diameter and link
thickness are proportional to node and link recurrence in the global pool of paths. A recurrence
cutoff
a
20% is employed for both nodes and links. In panel (C), the difference meta path is
shown onto the dark rhodopsin structure. Meta path nodes and links specific to the dark andMII
states are orange and green, respectively, whereas those shared by the two different states are
green. The contribution of each receptor portion to thosemeta path links that are specific to dark
(orange) andMII (violet) states, as well as thosemeta path links that are shared by the two forms
(green) is plotted as well in panel (D).
