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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.


Related in: MedlinePlus

3-D structure model and docking of DhelOBP21. (A) Superimposed secondary structures of DhelOBP21 and the template 1C3Y. The model of DhelOBP21 and crystal structure of 1C3Y are shown in red and yellow, respectively. (B) Predicted 3D model of DhelOBP21. The centre is the binding cavity within the ligands. The green area expresses hydrophobicity and red area hydrophilia. (C) Sequence alignment of DhelOBP21 and template. The secondary elements for DhelOBP21 are shown above the sequences. α-helices are displayed as squiggles. Identical residues are highlighted in white letters with a red background. Residues with similar physicochemical properties are shown in red letters and a blue frame. The stars are amino acid of forming the cavity, and the stars in yellow are mutation sites.
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Figure 2: 3-D structure model and docking of DhelOBP21. (A) Superimposed secondary structures of DhelOBP21 and the template 1C3Y. The model of DhelOBP21 and crystal structure of 1C3Y are shown in red and yellow, respectively. (B) Predicted 3D model of DhelOBP21. The centre is the binding cavity within the ligands. The green area expresses hydrophobicity and red area hydrophilia. (C) Sequence alignment of DhelOBP21 and template. The secondary elements for DhelOBP21 are shown above the sequences. α-helices are displayed as squiggles. Identical residues are highlighted in white letters with a red background. Residues with similar physicochemical properties are shown in red letters and a blue frame. The stars are amino acid of forming the cavity, and the stars in yellow are mutation sites.

Mentions: Based on the stereo-chemical optimization and energy minimization performed with MOE, a first-rank model with the minimum energy among the 250 intermediate models was inspected using the stereo-chemical quality evaluation tool in MOE—Protein Geometry. A pairwise RMSD of alpha C between the template 1C3Y and DhelOBP21 was 1.856 Å (Fig. 2A). As shown in Fig. S2, 97.2% of residues (107 residues) were located in the allowed region and 2.8% (three residues, Glu, Gln, and Ala) were located near the marginal region in a Ramachandran map, along with other stereochemical indices (including bond lengths, bond angles, and dihedrals), indicating that its overall stereochemical quality was generally reliable and acceptable.


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)

3-D structure model and docking of DhelOBP21. (A) Superimposed secondary structures of DhelOBP21 and the template 1C3Y. The model of DhelOBP21 and crystal structure of 1C3Y are shown in red and yellow, respectively. (B) Predicted 3D model of DhelOBP21. The centre is the binding cavity within the ligands. The green area expresses hydrophobicity and red area hydrophilia. (C) Sequence alignment of DhelOBP21 and template. The secondary elements for DhelOBP21 are shown above the sequences. α-helices are displayed as squiggles. Identical residues are highlighted in white letters with a red background. Residues with similar physicochemical properties are shown in red letters and a blue frame. The stars are amino acid of forming the cavity, and the stars in yellow are mutation sites.
© Copyright Policy
Related In: Results  -  Collection

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

Figure 2: 3-D structure model and docking of DhelOBP21. (A) Superimposed secondary structures of DhelOBP21 and the template 1C3Y. The model of DhelOBP21 and crystal structure of 1C3Y are shown in red and yellow, respectively. (B) Predicted 3D model of DhelOBP21. The centre is the binding cavity within the ligands. The green area expresses hydrophobicity and red area hydrophilia. (C) Sequence alignment of DhelOBP21 and template. The secondary elements for DhelOBP21 are shown above the sequences. α-helices are displayed as squiggles. Identical residues are highlighted in white letters with a red background. Residues with similar physicochemical properties are shown in red letters and a blue frame. The stars are amino acid of forming the cavity, and the stars in yellow are mutation sites.
Mentions: Based on the stereo-chemical optimization and energy minimization performed with MOE, a first-rank model with the minimum energy among the 250 intermediate models was inspected using the stereo-chemical quality evaluation tool in MOE—Protein Geometry. A pairwise RMSD of alpha C between the template 1C3Y and DhelOBP21 was 1.856 Å (Fig. 2A). As shown in Fig. S2, 97.2% of residues (107 residues) were located in the allowed region and 2.8% (three residues, Glu, Gln, and Ala) were located near the marginal region in a Ramachandran map, along with other stereochemical indices (including bond lengths, bond angles, and dihedrals), indicating that its overall stereochemical quality was generally reliable and acceptable.

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.


Related in: MedlinePlus