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. 2011 Jul 7;286(36):31232–31240. doi: 10.1074/jbc.M110.212613

FIGURE 1.

FIGURE 1.

Trypan dyes and other sulfonic acid compounds have similar structural features. a, two-dimensional representation of one symmetrical half (as indicated by the dashed symmetry line) of trypan blue and trypan red (trypan red contains one additional sulfono group, indicated by red lettering). b, BDS bound in the active site of LmPYK (i). The BDS molecule is shown with an unbiased Fo − Fc electron density map contoured at 3 σ (green). Hydrogen bonds are shown as dashed red lines, and stacking interactions are shown as dashed purple lines. c, one symmetrical half of the colorless trypan analog, suramin. d, co-crystal (i) of Ponceau S bound in the active site of TcPYK (ii). e, co-crystal (i) of LmPYK and the AB80 molecule. f, a superimposition between dye-like molecules and suramin. Common groups superimpose onto the structure of suramin, highlighting the chemical relationships within the series of molecules. This figure highlights two-dimensional chemical similarities and not necessarily three-dimensional binding similarities (as illustrated by the shaded ellipses in panels a–e). g, a superimposition between Cibacron blue (a molecule commonly used for affinity purification of PYK) and AB80. Shaded ellipses in panels a–e highlight key binding characteristics observed in the LmPYK-sulfonic acid structures obtained: site S1, pink ellipse, a sulfono group (S(i)) is observed bound in a near identical position in all complexes; site S2, green ellipse, a stacking interaction with His-54 is conserved in all structures; site S3, green ellipse, a second stacking interaction with Tyr-59 and Pro-29 is observed for suramin, Ponceau S, and AB80; site S4, blue ellipse, a hydrogen bound acceptor/donor is also commonly observed. In the LmPYK-Ponceau S, the azo group forms a hydrogen bond via the hydroxyl group of Tyr-59. Only microcrystals were obtained with trypan blue, but the common PYK binding characteristics are also observed. Suramin and trypan blue are symmetrical molecules, and only half the molecule is shown (as indicated by the dashed symmetry lines).