Homology modelling of general odorant binding proteins (ZcofGOBP1 and ZcofGOBP 2) in Zeuzera coffeae and their molecular docking with volatiles of Eucommia ulmoides
Author of the article:HUANG Xing-Rui1, 2** ZOU Jie1, 2 YANG Jie1 WEN Xi1 HUANG Xing-Long1, 2***
Author's Workplace:1. College of Biology and Environmental Sciences, Jishou University, Jishou 416000, China; 2. National and Local United Engineering Laboratory of Integrative Utilization of Eucommia Ulmoides, Jishou University, Jishou 416000, China
Key Words:Zeuzera coffeae; molecular docking; general odorant binding protein; Eucommia ulmoides; volatile
Abstract:
[Aim] To elucidate the olfactory mechanisms of the wood-boring
pest Zeuzera coffeae selecting Eucommia ulmoides as host plant. [Methods] General odorant binding
proteins (GOBPs) in Z. coffeae were identified by transcriptome data
analysis. Homology modelling and molecular docking were performed to predict
the binding properties of these proteins with volatile compounds from E. ulmoides. [Results] Two GOBP genes (ZcofGOBP1 and ZcofGOBP2) were identified in Z. coffeae. The proteins
encoded by these genes were soluble proteins with six α-helixes and six
conserved cysteine residues. Homology modelling indicated that the conserved
cysteine residues form three disulfide bonds and the α-helixes were fixed by
disulfide bonds to form a ligand-binding pocket with a mouth on the protein
surface. Molecular docking revealed prominent binding abilities (Free energy
lower than -7 kJ/mol) of ZcofGOBPs with several E. ulmoides volatile
compounds. For example, ZcofGOBP1 with phytol and methyl
cis-11,14,17-eicosatrienoate, and ZcofGOBP2 with ethyl palmitate and
damascenone. The interaction of ZcofGOBPs with ligands was strongly influenced
by hydrogen bonds, covalent bonds, and van der Waals forces. [Conclusion] ZcofGOBP1 and ZcofGOBP2
are soluble proteins with ligand binding pockets and may be involved in the
perception of E. ulmoides by binding and transporting the host
volatiles.