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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.


Sketch of binding state. The yellow graphics express the different ligands. The green graphics express the binding cavity. And the red circles mean the oxygen atom and the blue circles mean the hydrogen atom, they form the hydrones. The dashed lines express the hydrophobic interaction.
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Figure 10: Sketch of binding state. The yellow graphics express the different ligands. The green graphics express the binding cavity. And the red circles mean the oxygen atom and the blue circles mean the hydrogen atom, they form the hydrones. The dashed lines express the hydrophobic interaction.

Mentions: Based on our findings, we can form a model to explain the binding state (Fig. 10). Before binding, hydrophobic ligands and cavity were surrounded by water, and water forms a cage that wraps around the ligands. When ligands enter the binding cavity, hydrophobic interactions make the hydrophobic ligands and cavity draw close together. Additionally, the aqueous phase concentrates to become more structured. The cage hydrates bound the ligands in cavity. In this process, the characteristics of the ligands can influence binding. The shape of ligand A conforms to the shape of the binding cavity, and establishes remarkable hydrophobic interactions. The volume of ligand B is too big to fit the binding cavity, so more collisions between the atoms of the ligand and cavity could occur when it enters the binding cavity. Ligand C is small, so it can 'roam around' the cavity and bind with the amino acid residues in various conformations and, because of that, it can be released easily. The binding process is dynamic.


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)

Sketch of binding state. The yellow graphics express the different ligands. The green graphics express the binding cavity. And the red circles mean the oxygen atom and the blue circles mean the hydrogen atom, they form the hydrones. The dashed lines express the hydrophobic interaction.
© Copyright Policy
Related In: Results  -  Collection

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

Figure 10: Sketch of binding state. The yellow graphics express the different ligands. The green graphics express the binding cavity. And the red circles mean the oxygen atom and the blue circles mean the hydrogen atom, they form the hydrones. The dashed lines express the hydrophobic interaction.
Mentions: Based on our findings, we can form a model to explain the binding state (Fig. 10). Before binding, hydrophobic ligands and cavity were surrounded by water, and water forms a cage that wraps around the ligands. When ligands enter the binding cavity, hydrophobic interactions make the hydrophobic ligands and cavity draw close together. Additionally, the aqueous phase concentrates to become more structured. The cage hydrates bound the ligands in cavity. In this process, the characteristics of the ligands can influence binding. The shape of ligand A conforms to the shape of the binding cavity, and establishes remarkable hydrophobic interactions. The volume of ligand B is too big to fit the binding cavity, so more collisions between the atoms of the ligand and cavity could occur when it enters the binding cavity. Ligand C is small, so it can 'roam around' the cavity and bind with the amino acid residues in various conformations and, because of that, it can be released easily. The binding process is dynamic.

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.