Structural Insights into Two Representative Conformations of the Complex Formed by Grapholita molesta (Busck) Pheromone Binding Protein 2 and Z-8-Dodecenyl Acetate.

Grapholita molesta is a notorious fruit borer globally, causing severe damage to fruit production. To control the pest, one commonly used mean is pheromone-mediated management. As an important sex pheromone, Z-8-dodecenyl acetate (Z8-12: Ac), is often coformulated with other active ingredients to regulate the behavior of G. molesta. To uncover its interactions with G. molesta pheromone binding protein 2 (GmolPBP2) is used to help develop insect attractants. During 200 ns molecular dynamics simulations, two representative conformations of the GmolPBP2-Z8-12: Ac complex are selected. Conformation II at the time of 14-106 ns is dominantly maintained by the hydrophobic interactions and hydrogen bond. In Conformation I, which lasts from 106 to 200 ns, the hydrophobic interactions are enhanced while the hydrogen bond is quite weakened, due to the formation of a more sophisticated hydrophobic binding pocket and the enlargement of hydrogen bond distance. Taking the two conformations as a whole, the affinity between GmolPBP2 and Z8-12: Ac is crucially determined by three hot-spots including Phe11, Trp36, and Ile51. These results would provide a basis for the discovery, optimization, and design of leading compounds potentially active to attract G. molesta.