Structural investigation of selective binding dynamics for the pheromone‐binding protein 1 of the grapevine moth, Lobesia botrana

Abstract

The European grapevine moth, Lobesia botrana (Denis & Schiffermüller), is a serious pest in vineyards in North and South America. Mating disruption techniques have been used to control and monitor L. botrana on the basis of its sexual communication. This needs a well-tuned olfactory system, in which it is believed that pheromone-binding proteins (PBPs) are key players that transport pheromones in the antennae of moths. In this study, the selectivity of a PBP, named as LbotPBP1, was tested by fluorescence binding assays against 11 sex pheromone components and 6 host plant volatiles. In addition, its binding mechanism was predicted on the basis of Arch. Insect Biochem. Physiol. 2019;101:e21557.wileyonlinelibrary.com/journal/arch *These authors contributed equally to this work. structural analyses by molecular docking and complex and steered molecular dynamics (SMD). Our results indicate that LbotPBP1 binds selectively to sex pheromone components over certain host plant volatiles, according to both in vitro and in silico tests. Thus, chain length (14 carbon atoms) and functional groups (i.e., alcohol and ester) appear to be key features for stable binding. Likewise, residues such as Phe12, Phe36, and Phe118 could participate in unspecific binding processes, whilst Ser9, Ser56, and Trp114 could participate in the specific recognition and stabilization of sex pheromones instead of host plant volatiles. Moreover, our SMD approach supported 11-dodecenyl acetate as the best ligand for LbotPBP1. Overall, the dynamics simulations, contact frequency analysis and SMD shed light on the binding mechanism of LbotPBP1 and could overcome the imprecision of molecular docking, supporting the in vitro binding assays. Finally, the role of LbotPBP1 in the chemical ecology of L. botrana is discussed. K E Y W O R D S molecular modeling, odorant-binding protein, olfactory system, Tortricidae

Mating‐based regulation and ligand binding of an odorant‐binding protein support the inverse sexual communication of the greater wax moth, Galleria mellonella (Lepidoptera: Pyralidae)

“…Recombinant proteins were obtained according to the methodology reported by Venthur et al . (). Positive colonies for each construct were inoculated in 10 ml fresh Lysogeny Broth (LB)/ampicillin medium at 37°C.…”

“…In order to evaluate the results of the fluorescence binding assays from a structural point of view, a protein-ligand (ie complex) molecular dynamics protocol was performed according to the methodology reported by Venthur et al (2019). First, a three-dimensional (3D) structure was predicted for GOBP2 using homology modelling.…”

“…Cloned GOBP2 was synthesized by Biomatik (Wilmington, DE, USA) using the pET-28a expression vector. Recombinant proteins were obtained according to the methodology reported by Venthur et al (2019). Positive colonies for each construct were inoculated in 10 ml fresh Lysogeny Broth (LB)/ampicillin medium at 37 C. GOBP2 expression was induced by adding isopropyl β-D-1-thiogalactopyranoside (IPTG) to 0.5 mM final concentration when the Optical Density 600 (OD 600 ) reached 0.6-0.7.…”

“…Molecular dynamics simulations were performed using the NAMD v. 2.9 software and Chemistry at HARvard Macromolecular Mechanics (CHARMM36) force field for the six ligands bound to GOBP2 according to the methodology reported by Venthur et al (2019). First, Protein Structure Files (PSF) were created using a command line in the VMD software (Illinois, USA) including topology files for both the protein and ligands.…”

Field evaluation of sex pheromones and binding specificity of pheromone binding protein 4 in Tryporyza intacta (Lepidoptera: Crambidae)

“…Insects distinguish odorant molecules through their olfactory organ to seek food, mating partners and oviposition sites [1][2][3][4] . External chemicals including host-plant volatiles and sex pheromones enter into the chemosensilla and then are captured by odorant binding proteins (OBPs) in the antennae [5][6][7] .…”