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

Li DZ, Yu GQ, Yi SC, Zhang Y, Kong DX, Wang MQ - Int. J. Biol. Sci. (2015)

Bottom Line: 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 Å(³) compared with ligands with a molecular volume between 160 and 185 Å(³).Ligand-binding experiments and cyber molecular docking assays indicated that hydrophobic interactions are more significant than hydrogen-bonding interactions.This study provides a basis to explore the ligand-binding mechanisms of Minus-C OBP.

View Article: PubMed Central - PubMed

Affiliation: 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.

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 Å(³) compared with ligands with a molecular volume between 160 and 185 Å(³). 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.

No MeSH data available.


Comparison of shape of DhelOBP21 and its mutants. The green areas express hydrophobicity and red areas express hydrophilia of binding cavity. The red atom is oxygen atom. The blue atom is nitrogen-atom. The gray molecule in the cavity is 1-NPN.
© Copyright Policy
Related In: Results  -  Collection


getmorefigures.php?uid=PMC4582152&req=5

Figure 8: Comparison of shape of DhelOBP21 and its mutants. The green areas express hydrophobicity and red areas express hydrophilia of binding cavity. The red atom is oxygen atom. The blue atom is nitrogen-atom. The gray molecule in the cavity is 1-NPN.

Mentions: We compared the binding cavity shapes using 1-NPN as a reference (Fig. 8). We found that the cavity shape was different, as was the pose of 1-NPN. It did not establish any hydrogen bonds, but instead maintained binding through hydrophobic contact with the cavity. By contrast, we found that the mutant protein S67A was more spacious and had a more hydrophobic cavity, so the binding ability of 1-NPN was the strongest. Because it induced spatial changes in conformation, the mutant I84N showed enhanced binding capacity. Although the cavity of mutant T119N became larger, a new area also appeared in the corner. Additionally, the polar atom “N” could enter the binding cavity, but it interacted with the hydrophobic area. Therefore, its binding ability did not change compared with the cavity of the wild-type protein.


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

Li DZ, Yu GQ, Yi SC, Zhang Y, Kong DX, Wang MQ - Int. J. Biol. Sci. (2015)

Comparison of shape of DhelOBP21 and its mutants. The green areas express hydrophobicity and red areas express hydrophilia of binding cavity. The red atom is oxygen atom. The blue atom is nitrogen-atom. The gray molecule in the cavity is 1-NPN.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC4582152&req=5

Figure 8: Comparison of shape of DhelOBP21 and its mutants. The green areas express hydrophobicity and red areas express hydrophilia of binding cavity. The red atom is oxygen atom. The blue atom is nitrogen-atom. The gray molecule in the cavity is 1-NPN.
Mentions: We compared the binding cavity shapes using 1-NPN as a reference (Fig. 8). We found that the cavity shape was different, as was the pose of 1-NPN. It did not establish any hydrogen bonds, but instead maintained binding through hydrophobic contact with the cavity. By contrast, we found that the mutant protein S67A was more spacious and had a more hydrophobic cavity, so the binding ability of 1-NPN was the strongest. Because it induced spatial changes in conformation, the mutant I84N showed enhanced binding capacity. Although the cavity of mutant T119N became larger, a new area also appeared in the corner. Additionally, the polar atom “N” could enter the binding cavity, but it interacted with the hydrophobic area. Therefore, its binding ability did not change compared with the cavity of the wild-type protein.

Bottom Line: 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 Å(³) compared with ligands with a molecular volume between 160 and 185 Å(³).Ligand-binding experiments and cyber molecular docking assays indicated that hydrophobic interactions are more significant than hydrogen-bonding interactions.This study provides a basis to explore the ligand-binding mechanisms of Minus-C OBP.

View Article: PubMed Central - PubMed

Affiliation: 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.

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 Å(³) compared with ligands with a molecular volume between 160 and 185 Å(³). 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.

No MeSH data available.