Figure 4.

Schematic representation of the cylindrical restraint potential used in the free-energy calculations, similar to the funnel metadynamics protocol [30]. The carboxylate of the triterpenic acids (or C-17 hydroxyl of betulin) was subject to a restraining force when its distance from the cylindrical axis (centered on the Zn${}^{2+}$ ion) exceeded 4.5 Å. This distance was sufficiently large that the restraining force was never active when the carboxylate–Zn${}^{2+}$ distance was near the free energy minima ($r<3.5$ Å); therefore, it should not have influenced sampling of the bound state. The only exception was betulin, which possesses no carboxylate and exhibited marginal affinity for the active site. (A) An unbound state of belulinic acid and BaP1. The arrow represents the transition coordinate, r, defined as the distance between the carboxylate group and the Zn${}^{2+}$ ion. (B) A bound state of betulinic acid, with $r=2.8$ Å.