Unbiased picture of the ligand docking process for the hevein protein–oligosaccharide complex
Abstract The ligand-docking behavior of hevein, the major latex protein from the rubber tree Hevea brasiliensis (Euphorbiaceae), has been investigated by the unguided molecular dynamics (MD) simulation method. An oligosaccharide molecule, initially placed in an arbitrary position, was allowed to mov...
Saved in:
| Main Authors: | , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Nature Portfolio
2025-01-01
|
| Series: | Scientific Reports |
| Subjects: | |
| Online Access: | https://doi.org/10.1038/s41598-025-87407-8 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1832571720982069248 |
|---|---|
| author | Toshifumi Yui Takuya Uto |
| author_facet | Toshifumi Yui Takuya Uto |
| author_sort | Toshifumi Yui |
| collection | DOAJ |
| description | Abstract The ligand-docking behavior of hevein, the major latex protein from the rubber tree Hevea brasiliensis (Euphorbiaceae), has been investigated by the unguided molecular dynamics (MD) simulation method. An oligosaccharide molecule, initially placed in an arbitrary position, was allowed to move around hevein for a prolonged simulation time, on the order of microseconds, with the expectation of spontaneous ligand docking of the oligosaccharide molecule to the binding site of hevein. In the binary solution system consisting of a hevein molecule and a chito-trisaccharide (GlcNAc3) molecule, three out of the six separate simulation runs successfully reproduced the complex structure of the observed binding from. It appeared that the surface topology formed by two aromatic side chains of the hevein molecule played a role in orienting the GlcNAc3 molecule in the correct direction. We also performed MD simulations of the ternary solution system containing a cello-hexasaccharide (Glc6) molecule in addition to hevein and a chito-hexasaccharide (GlcNAc6) molecule. Formation of hevein–GlcNAc6 complex structures was exclusively observed, while the Glc6 molecule remained in the solvent phase throughout the simulations. Obviously, the acetamide groups of GlcNAc play a role in detecting the binding site and its vicinity on the protein surface. |
| format | Article |
| id | doaj-art-52d168ff71bc425cba5616651908df39 |
| institution | Kabale University |
| issn | 2045-2322 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj-art-52d168ff71bc425cba5616651908df392025-02-02T12:22:43ZengNature PortfolioScientific Reports2045-23222025-01-011511910.1038/s41598-025-87407-8Unbiased picture of the ligand docking process for the hevein protein–oligosaccharide complexToshifumi Yui0Takuya Uto1Department of Applied Chemistry, Faculty of Engineering, University of MiyazakiDepartment of Applied Chemistry, Faculty of Engineering, University of MiyazakiAbstract The ligand-docking behavior of hevein, the major latex protein from the rubber tree Hevea brasiliensis (Euphorbiaceae), has been investigated by the unguided molecular dynamics (MD) simulation method. An oligosaccharide molecule, initially placed in an arbitrary position, was allowed to move around hevein for a prolonged simulation time, on the order of microseconds, with the expectation of spontaneous ligand docking of the oligosaccharide molecule to the binding site of hevein. In the binary solution system consisting of a hevein molecule and a chito-trisaccharide (GlcNAc3) molecule, three out of the six separate simulation runs successfully reproduced the complex structure of the observed binding from. It appeared that the surface topology formed by two aromatic side chains of the hevein molecule played a role in orienting the GlcNAc3 molecule in the correct direction. We also performed MD simulations of the ternary solution system containing a cello-hexasaccharide (Glc6) molecule in addition to hevein and a chito-hexasaccharide (GlcNAc6) molecule. Formation of hevein–GlcNAc6 complex structures was exclusively observed, while the Glc6 molecule remained in the solvent phase throughout the simulations. Obviously, the acetamide groups of GlcNAc play a role in detecting the binding site and its vicinity on the protein surface.https://doi.org/10.1038/s41598-025-87407-8Carbohydrate-binding proteinChito-oligosaccharideUnbiased ligand dockingMolecular dynamics simulation |
| spellingShingle | Toshifumi Yui Takuya Uto Unbiased picture of the ligand docking process for the hevein protein–oligosaccharide complex Scientific Reports Carbohydrate-binding protein Chito-oligosaccharide Unbiased ligand docking Molecular dynamics simulation |
| title | Unbiased picture of the ligand docking process for the hevein protein–oligosaccharide complex |
| title_full | Unbiased picture of the ligand docking process for the hevein protein–oligosaccharide complex |
| title_fullStr | Unbiased picture of the ligand docking process for the hevein protein–oligosaccharide complex |
| title_full_unstemmed | Unbiased picture of the ligand docking process for the hevein protein–oligosaccharide complex |
| title_short | Unbiased picture of the ligand docking process for the hevein protein–oligosaccharide complex |
| title_sort | unbiased picture of the ligand docking process for the hevein protein oligosaccharide complex |
| topic | Carbohydrate-binding protein Chito-oligosaccharide Unbiased ligand docking Molecular dynamics simulation |
| url | https://doi.org/10.1038/s41598-025-87407-8 |
| work_keys_str_mv | AT toshifumiyui unbiasedpictureoftheliganddockingprocessfortheheveinproteinoligosaccharidecomplex AT takuyauto unbiasedpictureoftheliganddockingprocessfortheheveinproteinoligosaccharidecomplex |