Computational redesign of a fluorogen activating protein with Rosetta
Fig 5
Comparison of the initial docking and modeling results with the later obtained DiB1:M739 co-crystal structure.
(A) Binding pockets in the apo Blc structures showed as green (PDB ID 1QWD) or orange (PDB ID 3MBT) mesh. (B) Position of vaccenic acid (shown as blue sticks) and M739 (shown as yellow sticks) in the binding pocket of the lipocalin Blc (shown as a blue cartoon, PDB ID 2ACO) or DiB1 (shown as a yellow cartoon, PDB ID 6UBO), correspondingly. (C) The side and the top views on the overlay of the DiB1 complex (shown in yellow) with the DiB-RM apo structure (shown in light gray). The side chains of the amino acids in the positions that differ between DiB1 and DiB-RM as well as M739 are shown as sticks. Positions of the ligand in 50 top-scored structures after redocking of the chromophore M739 into (D) DiB1 crystal structure or (E) the DiB1 crystal structure-based DiB-RM model starting from the position of the ligand found in the DiB1:M739 co-crystal structure. The M739 chromophore from the co-crystal structure is shown as yellow sticks. All docked chromophores are shown as green lines.