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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.


Alignment of DhelOBP21 (KF984184) from Dastarcus helophoroides as well as other insects. Anopheles darlingi (AdarOBP, ETN64377.1) \ Agrotis ipsilon (AipsOBP5, AGR39568.1) \ Batocera horsfieldi (BhorOBP3, ADD82416.1) \ Batocera horsfieldi (BhorOBP4, ADD82417.1) \ Dendrolimus houi (DhouOBP,AII00983.1) \ Dendrolimus kikuchii (DkikOBP, AII01006.1) \ Danaus plexippus (DpleOBP, EHJ66992.1) \ Dendroctonus ponderosae (DponOBP29, AGI05182.1) \ Dendroctonus ponderosae (DponOBP30, AGI05176.1) \ Helicoverpa armigera (HarmOBP17, AFI57166.1) \ Helicoverpa assulta (HassOBP17, AGC92792.1) \ Monochamus alternatus (MaltOBP2, AHA39267.1) \ Monochamus alternatus (MaltOBP3, AHA39268.1) \ Monochamus alternatus (MaltOBP5, AHA39270.1) \ Manduca sexta (MsexABP8, AAL60426.1) \ Spodoptera exigua (SexiOBP, ADY17884.1) \ Spodoptera exigua (SexiOBP9, AGH70105.1) \ Tribolium castaneum (TcasOBP6, EFA04594.1) \ Tribolium castaneum (TcasOBP01, EFA07544.1)\ Tribolium castaneum (TcasOBP02, EFA07545.1) \ Tribolium castaneum (TcasOBP05, EFA07543.1) \ Tribolium castaneum (TcasOBP06, EFA07548.1) \ Tribolium castaneum (TcasOBP09, EFA07429.1).
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Figure 1: Alignment of DhelOBP21 (KF984184) from Dastarcus helophoroides as well as other insects. Anopheles darlingi (AdarOBP, ETN64377.1) \ Agrotis ipsilon (AipsOBP5, AGR39568.1) \ Batocera horsfieldi (BhorOBP3, ADD82416.1) \ Batocera horsfieldi (BhorOBP4, ADD82417.1) \ Dendrolimus houi (DhouOBP,AII00983.1) \ Dendrolimus kikuchii (DkikOBP, AII01006.1) \ Danaus plexippus (DpleOBP, EHJ66992.1) \ Dendroctonus ponderosae (DponOBP29, AGI05182.1) \ Dendroctonus ponderosae (DponOBP30, AGI05176.1) \ Helicoverpa armigera (HarmOBP17, AFI57166.1) \ Helicoverpa assulta (HassOBP17, AGC92792.1) \ Monochamus alternatus (MaltOBP2, AHA39267.1) \ Monochamus alternatus (MaltOBP3, AHA39268.1) \ Monochamus alternatus (MaltOBP5, AHA39270.1) \ Manduca sexta (MsexABP8, AAL60426.1) \ Spodoptera exigua (SexiOBP, ADY17884.1) \ Spodoptera exigua (SexiOBP9, AGH70105.1) \ Tribolium castaneum (TcasOBP6, EFA04594.1) \ Tribolium castaneum (TcasOBP01, EFA07544.1)\ Tribolium castaneum (TcasOBP02, EFA07545.1) \ Tribolium castaneum (TcasOBP05, EFA07543.1) \ Tribolium castaneum (TcasOBP06, EFA07548.1) \ Tribolium castaneum (TcasOBP09, EFA07429.1).

Mentions: DhelOBP21 was obtained from the antennal transcriptome. Using gene-specific primers, a full-length cDNA encoding DhelOBP21 was cloned. Sequence analysis showed that the full-length Open Reading Frame (ORF) consists of 405 nucleotides that encode 135 amino acid residues, with a predicted MW of 14.87 kD. For DhelOBP21, SignalP predicted a peptide with 18 amino acid residues, and ExPASy (http://web.expasy.org/compute_pi/) predicted an isoelectric point of 8.60. We conducted an alignment of the amino acid sequence of DhelOBP21 with the corresponding OBPs from other species (Fig. 1). DhelOBP21 has less than six Cys residues and belongs to the Minus-C insect OBP subfamily with a common pattern X33-C1-X30-C2-X39-C3-X16-C4-X12 (X denotes any amino acid).


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)

Alignment of DhelOBP21 (KF984184) from Dastarcus helophoroides as well as other insects. Anopheles darlingi (AdarOBP, ETN64377.1) \ Agrotis ipsilon (AipsOBP5, AGR39568.1) \ Batocera horsfieldi (BhorOBP3, ADD82416.1) \ Batocera horsfieldi (BhorOBP4, ADD82417.1) \ Dendrolimus houi (DhouOBP,AII00983.1) \ Dendrolimus kikuchii (DkikOBP, AII01006.1) \ Danaus plexippus (DpleOBP, EHJ66992.1) \ Dendroctonus ponderosae (DponOBP29, AGI05182.1) \ Dendroctonus ponderosae (DponOBP30, AGI05176.1) \ Helicoverpa armigera (HarmOBP17, AFI57166.1) \ Helicoverpa assulta (HassOBP17, AGC92792.1) \ Monochamus alternatus (MaltOBP2, AHA39267.1) \ Monochamus alternatus (MaltOBP3, AHA39268.1) \ Monochamus alternatus (MaltOBP5, AHA39270.1) \ Manduca sexta (MsexABP8, AAL60426.1) \ Spodoptera exigua (SexiOBP, ADY17884.1) \ Spodoptera exigua (SexiOBP9, AGH70105.1) \ Tribolium castaneum (TcasOBP6, EFA04594.1) \ Tribolium castaneum (TcasOBP01, EFA07544.1)\ Tribolium castaneum (TcasOBP02, EFA07545.1) \ Tribolium castaneum (TcasOBP05, EFA07543.1) \ Tribolium castaneum (TcasOBP06, EFA07548.1) \ Tribolium castaneum (TcasOBP09, EFA07429.1).
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Related In: Results  -  Collection

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Figure 1: Alignment of DhelOBP21 (KF984184) from Dastarcus helophoroides as well as other insects. Anopheles darlingi (AdarOBP, ETN64377.1) \ Agrotis ipsilon (AipsOBP5, AGR39568.1) \ Batocera horsfieldi (BhorOBP3, ADD82416.1) \ Batocera horsfieldi (BhorOBP4, ADD82417.1) \ Dendrolimus houi (DhouOBP,AII00983.1) \ Dendrolimus kikuchii (DkikOBP, AII01006.1) \ Danaus plexippus (DpleOBP, EHJ66992.1) \ Dendroctonus ponderosae (DponOBP29, AGI05182.1) \ Dendroctonus ponderosae (DponOBP30, AGI05176.1) \ Helicoverpa armigera (HarmOBP17, AFI57166.1) \ Helicoverpa assulta (HassOBP17, AGC92792.1) \ Monochamus alternatus (MaltOBP2, AHA39267.1) \ Monochamus alternatus (MaltOBP3, AHA39268.1) \ Monochamus alternatus (MaltOBP5, AHA39270.1) \ Manduca sexta (MsexABP8, AAL60426.1) \ Spodoptera exigua (SexiOBP, ADY17884.1) \ Spodoptera exigua (SexiOBP9, AGH70105.1) \ Tribolium castaneum (TcasOBP6, EFA04594.1) \ Tribolium castaneum (TcasOBP01, EFA07544.1)\ Tribolium castaneum (TcasOBP02, EFA07545.1) \ Tribolium castaneum (TcasOBP05, EFA07543.1) \ Tribolium castaneum (TcasOBP06, EFA07548.1) \ Tribolium castaneum (TcasOBP09, EFA07429.1).
Mentions: DhelOBP21 was obtained from the antennal transcriptome. Using gene-specific primers, a full-length cDNA encoding DhelOBP21 was cloned. Sequence analysis showed that the full-length Open Reading Frame (ORF) consists of 405 nucleotides that encode 135 amino acid residues, with a predicted MW of 14.87 kD. For DhelOBP21, SignalP predicted a peptide with 18 amino acid residues, and ExPASy (http://web.expasy.org/compute_pi/) predicted an isoelectric point of 8.60. We conducted an alignment of the amino acid sequence of DhelOBP21 with the corresponding OBPs from other species (Fig. 1). DhelOBP21 has less than six Cys residues and belongs to the Minus-C insect OBP subfamily with a common pattern X33-C1-X30-C2-X39-C3-X16-C4-X12 (X denotes any amino acid).

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.