Binding Properties of Odorant-Binding Protein 7 to Host Volatiles in Larvae of <i>Spodoptera frugiperda</i>

Liu, XiaoLong; Liao, Wang; Wu, ZheRan; Pei, YiWen; Wei, ZhiQiang; Lu, Min

doi:10.1021/acs.jafc.3c06833

Cited by 6 publications

(8 citation statements)

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“…The homology modeling method was first used to construct the 3D structure of SfruOBP7. Amino acid sequence of SfruOBP7 in Sfru's larval stage was obtained from the study by Lu et al 18 BLAST program 31 (http://blast.ncbi.nlm.nih.gov) was used to find the protein structure most similar to the residue sequence in the target protein SfruOBP7. Finally, Anopheles gambiae odorant binding protein7 (AgamOBP7) was found in Protein Data Bank (https:// www.rcsb.org/) as the template (PDB ID: 3R1V) 32 for homology modeling.…”

Section: Homology Modeling and Molecular Dockingmentioning

confidence: 99%

“…The grid box was defined according to the binding pocket of linalool. 18 The size was set as 60 Å × 60 Å × 60 Å, and spacing between the grid points was 0.375 Å. Docking was performed with Lamarckian genetic algorithm and default parameters. And then, by comparing the binding affinity, the best pose with the lowest docking energy was selected, and its initial coordinates were used as the original structure for subsequent simulations.…”

Section: Homology Modeling and Molecular Dockingmentioning

confidence: 99%

“…17 Whereas, many of the mechanisms by which OBPs recognize external volatile molecules remain unclear, especially the volatile molecule binding mechanism of SfruOBP7 in larvae, although SfruOBP7 is expressed in all stages of life, including eggs, larvae, pupae and adults. 18 Previous study using fluorescence competitive binding assay reported that the K i values between SfruOBP7 in larvae and different plant volatiles were in the range of 2-20 μmol L −1 . And the K i values for binding of (E)-2-hexenol (E2H; PubChem ID: 5318042), ⊍-pinene (⊍PI; PubChem ID: 2723720), (Z)-3-hexenyl acetate (Z3H; PubChem ID: 5363388), lauric acid (LAU; PubChem ID: 3893), O-cymene (OCY; PubChem ID: 10703) and 1-octanol (1OC; PubChem ID: 957) were 4.18, 13.92, 11.81, 6.75, 5.41 and 12.62 μmol L −1 , respectively.…”

Section: Introductionmentioning

confidence: 98%

“…And the K i values for binding of (E)-2-hexenol (E2H; PubChem ID: 5318042), ⊍-pinene (⊍PI; PubChem ID: 2723720), (Z)-3-hexenyl acetate (Z3H; PubChem ID: 5363388), lauric acid (LAU; PubChem ID: 3893), O-cymene (OCY; PubChem ID: 10703) and 1-octanol (1OC; PubChem ID: 957) were 4.18, 13.92, 11.81, 6.75, 5.41 and 12.62 μmol L −1 , respectively. 18 Although there is evidence that SfruOBP7 can bind with these different plant volatiles, little else is known about the dynamic interactions of plant volatiles with SfruOBP7 and the binding pattern between them.…”

Section: Introductionmentioning

confidence: 99%

“…However, so far, methods using experimental crystallizations have not determined the crystal structure of SfruOBP7. 18 This has, to some extent, hindered the comprehension of the interactions between SfruOBP7 and different chemical volatile molecules. Therefore, in our work, we first used the homology modeling method to construct the 3D structure of SfruOBP7, then used the molecule docking method [24][25][26][27] to obtain complex models of SfruOBP7 and different chemical volatile molecules (Fig.…”

Section: Introductionmentioning

confidence: 99%

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Molecular recognition between volatile molecules and odorant binding proteins 7 by homology modeling, molecular docking and molecular dynamics simulation

Wang,

Duan,

Zhao

et al. 2024

J Sci Food Agric

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BACKGROUNDOdorant‐binding proteins (OBPs) in insects are key to detection and recognition of external chemical signals associated with survival. OBP7 in Spodoptera frugiperda's larval stage (SfruOBP7) may search for host plants by sensing plant volatiles, which are important sources of pest attractants and repellents. However, the atomic‐level basis of binding modes remains elusive.RESULTSSfruOBP7 structure was constructed through homology modeling, and complex models of six plant volatiles ((E)‐2‐hexenol, α‐pinene, (Z)‐3‐hexenyl acetate, lauric acid, O‐cymene and 1‐octanol) and SfruOBP7 were obtained through molecular docking. To study the detailed interactions between the six plant volatile molecules and SfruOBP7, we conducted three 300 ns molecular dynamics simulations for each study object. The correlation coefficients between binding free energy obtained by molecular mechanics/generalized Born surface area together with solvated interaction energy methods and experimental values are 0.90 and 0.88, respectively, showing a good correlation. By comparing binding free energy along with interaction patterns between SfruOBP7 and the six volatile molecules, hotspot residues of SfruOBP7 when binding with different volatile molecules were determined. Hydrophobic interactions stemming from van der Waals interactions play a significant role in SfruOBP7 and these plant volatile systems.CONCLUSIONThe optimized three‐dimensional structure of SfruOBP7 and its binding modes with six plant volatiles revealed their interactions, thus providing a means for estimating the binding energies of other plant volatiles. Our study will help to guide the rational design of effective and selective insect attractants. © 2024 Society of Chemical Industry.

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Section: Homology Modeling and Molecular Dockingmentioning

confidence: 99%

Section: Homology Modeling and Molecular Dockingmentioning

confidence: 99%