Interaction Analysis of Odorant-Binding Protein 12 from Sirex noctilio and Volatiles from Host Plants and Symbiotic Fungi Based on Molecule Dynamics Simulation

Abstract

As a quarantine pest of conifer, Sirex noctilio has caused widespread harm around the world. It is expected that the molecular mechanism of protein–ligand binding can be elucidated to carry out the pest control. Through studies of SnocOBP12–ligand hydrophobic binding and dynamics and responsible amino acid residues identification, we got some promising results. SnocOBP12 had a general and excellent affinity for host plant volatiles, and may be a key protein for S. noctilio to find host plants. Among the many odor molecules that are bound to SnocOBP12, (−)-α-cedrene and (E)-β-farnesene from host plants and (−)-globuol from the symbiotic fungi of Sirex noctilio stood out and formed highly stable complexes with SnocOBP12. By the molecular mechanics Poisson–Boltzmann surface area (MM-PBSA) method, the calculated free binding energy of the three complexes was −30.572 ± 0.101 kcal/mol, −28.349 ± 0.119 kcal/mol and −25.244 ± 0.152 kcal/mol, respectively. It was found that the van der Waals energy contributed to the stability of the complexes. Some key amino acid residues were also found: LEU74 and TYR109 were very important for SnocOBP12 to stably bind (−)-α-cedrene, while for (E)-β-farnesene, ILE6, MET10, and LEU74 were very important for the stable binding system. We discovered three potential ligands and analyzed the interaction pattern of the protein with them, this paper provides a favorable molecular basis for optimizing the attractant formulation. Investigation of the binding characteristics in the olfactory system at the molecular level is helpful to understand the behavior of S. noctilio and develop new methods for more effective and environmentally friendly pest control.