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Int J Biol Sci 2015; 11(11):1281-1295. doi:10.7150/ijbs.12528

Research Paper

Structure-Based Analysis of the Ligand-Binding Mechanism for DhelOBP21, a C-minus Odorant Binding Protein, from Dastarcus helophoroides (Fairmaire; Coleoptera: Bothrideridae)

Dong-Zhen Li1, Guang-Qiang Yu2, Shan-Cheng Yi1, Yinan Zhang3, De-Xin Kong2, Man-Qun Wang1✉

1. Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, P. R. China
2. College of Informatics, Huazhong Agricultural University, Wuhan 430070, P. R. China
3. Department of Horticulture, Beijing Vocational College of Agriculture, Beijing 102442, PR China

Abstract

Odorant binding proteins (OBPs) transport hydrophobic odor molecules across the sensillar lymph to trigger a neuronal response. Herein, the Minus-C OBP (DhelOBP21) was characterized from Dastarcus helophoroides, the most important natural parasitic enemy insect that targets Monochamus alternatus. Homology modeling and molecular docking were conducted on the interaction between DhelOBP21 and 17 volatile molecules (including volatiles from pine bark, the larva of M. alternatus, and the faeces of the larva). The predicted three-dimensional structure showed only two disulfide bridges and a hydrophobic binding cavity with a short C-terminus. Ligand-binding experiments using N-phenylnaphthylamine (1-NPN) as a fluorescent probe showed that DhelOBP21 exhibited better binding affinities against those ligands with a molecular volume between 100 and 125 ų compared with ligands with a molecular volume between 160 and 185 ų. Molecules that are too big or too small are not conducive for binding. We mutated the amino acid residues of the binding cavity to increase either hydrophobicity or hydrophilia. Ligand-binding experiments and cyber molecular docking assays indicated that hydrophobic interactions are more significant than hydrogen-bonding interactions. Although hydrogen-bond interactions could be predicted for some binding complexes, the hydrophobic interactions had more influence on binding following hydrophobic changes that affected the cavity. The orientation of ligands affects binding by influencing hydrophobic interactions. The binding process is controlled by multiple factors. This study provides a basis to explore the ligand-binding mechanisms of Minus-C OBP.

Keywords: Odorant-binding proteins, fluorescence competitive binding assays, molecular docking, site-directed mutagenesis, molecular volume, hydrophobic interactions, Dastarcus helophoroides.

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How to cite this article:
Li DZ, Yu GQ, Yi SC, Zhang Y, Kong DX, Wang MQ. Structure-Based Analysis of the Ligand-Binding Mechanism for DhelOBP21, a C-minus Odorant Binding Protein, from Dastarcus helophoroides (Fairmaire; Coleoptera: Bothrideridae). Int J Biol Sci 2015; 11(11):1281-1295. doi:10.7150/ijbs.12528. Available from http://www.ijbs.com/v11p1281.htm