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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.


Comparison of binding affinities (indicated by 1/Ki*1000) between DhelOBP21 and its mutant at different pH. (A, B) The binding ability of ligands with the molecular volume between 100 and 125 ų. (C, D) The binding ability of ligands with the molecular volume between 160 and 185 ų.
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Figure 7: Comparison of binding affinities (indicated by 1/Ki*1000) between DhelOBP21 and its mutant at different pH. (A, B) The binding ability of ligands with the molecular volume between 100 and 125 ų. (C, D) The binding ability of ligands with the molecular volume between 160 and 185 ų.

Mentions: To gain deeper insights into the relationship between binding affinity and the nature of cavity, the binding profiles of mutant proteins S67A, I84N, and T119N were compared with DhelOBP-WT at pH 7.4 and 5.0 (Fig. 7). At pH 7.4, only (-)-caryophyllene oxide exhibited a stronger binding ability when the mutant protein S67A was compared with DhelOBP-WT, whereas the others are weaker. The binding affinity of terpinolene with mutant protein I84N was better than with DhelOBP-WT, and a slight enhancement was achieved between (+)-α-pinene and protein I84N compared with the wild-type protein. Mutant protein T119N had a greater binding ability towards Butylated hydroxytoluene and equivalent binding affinity for S-(-)-limomeme and 2-methoxy-4-vinylphenol Kosher compared with DhelOBP-WT. The binding abilities of the other ligands were reduced to a variable extent, especially for three ligands—3-canene, myrcene and camphene—for which their binding abilities declined significantly. By contrast, at pH 5.0, mutant protein S67A showed a stronger binding ability against most ligands. The binding performance of ligand S-(-)-limomeme was clearly weaker for DhelOBP-WT compared with the three mutant proteins. Binding of Camphene, Camphor, and (-)-Fenchone with DhelOBP-WT or mutant proteins I84N or T119N did not show any apparent difference. Compared with the binding abilities of DhelOBP-WT, butylated hydroxytoluene and (+)-α-pinene showed relatively higher affinities towards the mutant protein I84N, whereas terpinolene and 3-canene showed a relatively higher affinity towards the mutant protein T119N. Additionally, the effects of pH for the four proteins were each distinct. In addition to (-)-Caryophyllene oxide, DhelOBP-WT displayed weaker binding affinity at pH 5.0 than at pH 7.4, especially the S-(-)-limomeme. However, mutant protein S64A displayed a higher binding affinity at pH 5.0 than at pH 7.4. The mutant protein I84N showed a different change for each ligand, as did the mutant protein T119N.


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 binding affinities (indicated by 1/Ki*1000) between DhelOBP21 and its mutant at different pH. (A, B) The binding ability of ligands with the molecular volume between 100 and 125 ų. (C, D) The binding ability of ligands with the molecular volume between 160 and 185 ų.
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4582152&req=5

Figure 7: Comparison of binding affinities (indicated by 1/Ki*1000) between DhelOBP21 and its mutant at different pH. (A, B) The binding ability of ligands with the molecular volume between 100 and 125 ų. (C, D) The binding ability of ligands with the molecular volume between 160 and 185 ų.
Mentions: To gain deeper insights into the relationship between binding affinity and the nature of cavity, the binding profiles of mutant proteins S67A, I84N, and T119N were compared with DhelOBP-WT at pH 7.4 and 5.0 (Fig. 7). At pH 7.4, only (-)-caryophyllene oxide exhibited a stronger binding ability when the mutant protein S67A was compared with DhelOBP-WT, whereas the others are weaker. The binding affinity of terpinolene with mutant protein I84N was better than with DhelOBP-WT, and a slight enhancement was achieved between (+)-α-pinene and protein I84N compared with the wild-type protein. Mutant protein T119N had a greater binding ability towards Butylated hydroxytoluene and equivalent binding affinity for S-(-)-limomeme and 2-methoxy-4-vinylphenol Kosher compared with DhelOBP-WT. The binding abilities of the other ligands were reduced to a variable extent, especially for three ligands—3-canene, myrcene and camphene—for which their binding abilities declined significantly. By contrast, at pH 5.0, mutant protein S67A showed a stronger binding ability against most ligands. The binding performance of ligand S-(-)-limomeme was clearly weaker for DhelOBP-WT compared with the three mutant proteins. Binding of Camphene, Camphor, and (-)-Fenchone with DhelOBP-WT or mutant proteins I84N or T119N did not show any apparent difference. Compared with the binding abilities of DhelOBP-WT, butylated hydroxytoluene and (+)-α-pinene showed relatively higher affinities towards the mutant protein I84N, whereas terpinolene and 3-canene showed a relatively higher affinity towards the mutant protein T119N. Additionally, the effects of pH for the four proteins were each distinct. In addition to (-)-Caryophyllene oxide, DhelOBP-WT displayed weaker binding affinity at pH 5.0 than at pH 7.4, especially the S-(-)-limomeme. However, mutant protein S64A displayed a higher binding affinity at pH 5.0 than at pH 7.4. The mutant protein I84N showed a different change for each ligand, as did the mutant protein T119N.

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.