The docked active site structures, with (magenta) or without (silver) the putative placeholder F99, are superimposed.
In our docking analysis of AgPPO8, substrates could be accommodated in the putative binding pocket Site II without displacing the placeholder F99.
This model apparently does not need the withdrawal of the placeholder F99, which is buried in the core of the protein.
Notably, when we manually removed the placeholder F99 from the structure of AgPPO8 in the docking experiment, the phenolic substrate still docked to Site II (Additional file 7), further supporting its preferential binding of substrate.
For example, the structural comparison of L. polyphemus hemocyanin subunit II of oxygenated state with deoxygenated Panulirus interruptus hemocyanin revealed an 8° rotation of domain I upon oxygen binding, pulling the placeholder F49 away from the active site [ 49, 50].
Each target on the stereoscopic SL task appeared at the centre of one of four placeholders circumscribed by two horizontally aligned figure-of-eights (read from left to right, placeholders 1 and 2 were in the left figure-of-eight and placeholders 3 and 4 were in the right figure-of-eight; targets appeared for 1000 ms; see Figure 1a).
In particular, participants were informed that the left figure-of-eight circumscribed placeholder locations 1 and 2 and projected to the left eye, whereas the right figure-of-eight circumscribed locations 3 and 4 and projected to the right eye.
In arthropod PPOs, a conserved Phe residue from the N-terminal domain I was considered as the substrate placeholder [ 26, 27].
Noting enrichment of Forkhead motifs at these sites and evidence that another Forkhead family member, FOXO1, also functions in Tregs, the authors found that FOXO1 acts as a placeholder for FOXP3, occupying sites in FOXP3-negative CD4 T cells that are subsequently bound by FOXP3.
A brief 100 ms color change of the placeholders, 700 ms to 850 ms after trial initiation, acted as the cue display.
