Figure 1.
Chemical structures of selected barbiturates.
Table 1.
Binding, physical, and activity data for barbiturates.
Table 2.
Crystallographic data collection and refinement statistics.
Figure 2.
Stereoviews showing the anesthetic binding site of apoferritin with A) thiopental and B) pentobarbital.
The hydrogen bond between the drug and Ser-27 is shown as a black dashed line. In both images the ligands are depicted as sticks; color code: carbon, yellow; nitrogen, blue; oxygen, red; and sulfur, magenta. The electron density shown is 2Fo-Fc density calculated from the final refined structures, contoured at sigma level of 0.8 and carved around the ligands. Figures 2 and 3 were generated using PyMOL (The PyMOL Molecular Graphics System, Schrödinger, LLC).
Figure 3.
Diverse general anesthetics utilize a common binding site in apoferritin.
A) Orthogonal views of the apoferritin dimer, shown as a partially transparent molecular surface encasing a cartoon representation of the backbone. The anesthetic binding site is marked by thiopental, which is shown in a red space-filling representation. B) Stereo view showing a close-up of the anesthetic binding site, in an orientation similar to that seen in the left half of the upper panel. Four different general anesthetics are shown in ball-and-stick representations: Thiopental (yellow); propofol (magenta); isoflurane (cyan); and halothane (orange). The protein backbone is shown in blue, while selected protein side chains are shown in light gray. All four compounds, despite belonging to different chemotypes, utilize the same binding cavity, in which their positions overlap extensively.
Figure 4.
The packing density/affinity relationship for barbiturates is offset from that of the propofol-like compounds, interpreted here as the addition of an entropic penalty offset by new enthalpic gains.
Shown is the relationship between packing volume (fraction of cavity volume occupied by ligand) and affinity (dissociation constant, Kd) for apoferritin. The filled triangles represent a series of propofol analogs, for which a linear dependence of affinity upon packing density has been documented [21]. The open circles represent the barbiturates (P, pentobarbital; T, thiopental).