Computational Interaction Analysis of Sirex noctilio Odorant-Binding Protein (SnocOBP7) Combined with Female Sex Pheromones and Symbiotic Fungal Volatiles

Abstract

Sirex noctilio, a major forestry quarantine pest, has spread rapidly and caused serious harm. However, existing methods still need to be improved because its olfactory interaction mechanisms are poorly understood. In order to study the role of male-specific protein SnocOBP7 in the protein–ligand interactions, we selected it as the object of computational simulation and analysis. By docking it with 11 ligands and evaluating free binding energy decomposition, the three best binding ligands were found to be female sex pheromones ((Z)-7-heptacosene and (Z)-7-nonacosene) and symbiotic fungal volatiles ((−)-globulol). Binding mode analysis and computational alanine scanning suggested that five residues play key roles in the binding of each female sex pheromone to SnocOBP7, whereas two residues play key roles in (−)-globulol binding. Phe108 and Leu36 may be the crucial sites via which SnocOBP7 binds female sex pheromones, whereas Met40 may regulate the courtship behavior of males, and Leu61 may be related to mating and host finding. Our studies predicted the function of SnocOBP7 and found that the interaction between SnocOBP7 and pheromone is a complex process, and we successfully predicted its binding key amino-acid sites, providing a basis for the development of new prevention and control methods relying on female sex pheromones and symbiotic fungi.

Expression Pattern, Molecular Docking and Dynamics Simulation Analysis of CSP4 from Sirex nitobei Provides Molecular Basis of CSP Bound to Scent Molecules

“…Among the 14 ligands, we identified two sex pheromone molecules, three host plant volatiles, and three symbiotic fungal volatiles with higher binding affinity, with (Z)-7-heptacosene, (Z)-9-nonacosene, and (-)-globulol binding most highly stable. In a molecular docking and molecular dynamics study of SnocOBP7 with 11 odorant molecules, Li et al found that SnocOBP7 bound most stably to (Z)-7-heptacosene, (Z)-7-nonacosene and (-)-globulol [52], which was consistent with our results. In the study of the interaction mechanism of RpadOBP3 from Rhopalosiphum padi with (E)-β-farnesene(EβF), Fan identified three amino acid residues in the hydrophobic structural domain, TRP71, TRP68, and PHE2, bound tightly to EβF [53].…”

Chemical and visual ecology of the Symphyta

“…Technological advances have the potential to facilitate the development of management tactics for forest insects, including the Symphyta (Slippers et al, 2020). More Symphyta genomes are available, which facilitates the development of new technology such as reverse chemical ecology (Li et al, 2021) or CRISPR‐Cas9 (Pickett, 2014). Accurate identification of Diprionidae pheromone isomers and an increase in compound purity can increase the number of insects caught in ‘attract and kill’ programmes.…”

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

“…The conformational changes when AgamOBP1 bound both N,N-diethyl-3-toluamide and 6-methyl-5-hepten-2-one were investigated by molecular dynamics [50]. According to the existing research, both SnocOBP12 and SnocOBP7 [23] can bind (−)-globuol well. The interaction between SnocOBPs remains to be explored.…”

“…The three best binding ligands were found to be female sex pheromones ((Z)-7-heptacosene and (Z)-7-nonacosene) and symbiotic fungal volatiles ((−)-globulol). Five residues played key roles in the binding of each female sex pheromone to SnocOBP7, whereas two residues play key roles in (−)-globulol binding [23].…”