Leaf-specific pathogenesis-related 10 homolog, PgPR-10.3, shows in silico binding affinity with several biologically important molecules
Background: Pathogenesis-related 10 (PR-10) proteins are small, cytosolic proteins with a similar three-dimensional structure. Crystal structures for several PR-10 homologs have similar overall folding patterns, with an unusually large internal cavity that is a binding site for biologically importan...
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Format: | Article |
Language: | English |
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Elsevier
2015-10-01
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Series: | Journal of Ginseng Research |
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Online Access: | http://www.sciencedirect.com/science/article/pii/S1226845315000524 |
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author | Jin Haeng Han Jin Hee Lee Ok Ran Lee |
author_facet | Jin Haeng Han Jin Hee Lee Ok Ran Lee |
author_sort | Jin Haeng Han |
collection | DOAJ |
description | Background: Pathogenesis-related 10 (PR-10) proteins are small, cytosolic proteins with a similar three-dimensional structure. Crystal structures for several PR-10 homologs have similar overall folding patterns, with an unusually large internal cavity that is a binding site for biologically important molecules. Although structural information on PR-10 proteins is substantial, understanding of their biological function remains limited. Here, we showed that one of the PgPR-10 homologs, PgPR-10.3, shares binding properties with flavonoids, kinetin, emodin, deoxycholic acid, and ginsenoside Re (1 of the steroid glycosides).
Methods: Gene expression patterns of PgPR-10.3 were analyzed by quantitative real-time PCR. The three-dimensional structure of PgPR-10 proteins was visualized by homology modeling, and docking to retrieve biologically active molecules was performed using AutoDock4 program.
Results: Transcript levels of PgPR-10.3 expressed in leaves, stems, and roots of 3-wk-old ginseng plantlets were on average 86-fold lower than those of PgPR-10.2. In mature 2-yr-old ginseng plants, the mRNA of PgPR-10.3 is restricted to leaves. Ginsenoside Re production is especially prominent in leaves of Panax ginseng Meyer, and the binding property of PgPR-10.3 with ginsenoside Re suggests that this protein has an important role in the control of secondary metabolism.
Conclusion: Although ginseng PR-10.3 gene is expressed in all organs of 3-wk-old plantlets, its expression is restricted to leaves in mature 2-yr-old ginseng plants. The putative binding property of PgPR-10.3 with Re is intriguing. Further verification of binding affinity with other biologically important molecules in the large hydrophobic cavity of PgPR-10.3 may provide an insight into the biological features of PR-10 proteins. |
first_indexed | 2024-12-12T19:24:10Z |
format | Article |
id | doaj.art-10587668902d43e59d99f790d77fff84 |
institution | Directory Open Access Journal |
issn | 1226-8453 |
language | English |
last_indexed | 2024-12-12T19:24:10Z |
publishDate | 2015-10-01 |
publisher | Elsevier |
record_format | Article |
series | Journal of Ginseng Research |
spelling | doaj.art-10587668902d43e59d99f790d77fff842022-12-22T00:14:32ZengElsevierJournal of Ginseng Research1226-84532015-10-0139440641310.1016/j.jgr.2015.06.002Leaf-specific pathogenesis-related 10 homolog, PgPR-10.3, shows in silico binding affinity with several biologically important moleculesJin Haeng HanJin Hee LeeOk Ran LeeBackground: Pathogenesis-related 10 (PR-10) proteins are small, cytosolic proteins with a similar three-dimensional structure. Crystal structures for several PR-10 homologs have similar overall folding patterns, with an unusually large internal cavity that is a binding site for biologically important molecules. Although structural information on PR-10 proteins is substantial, understanding of their biological function remains limited. Here, we showed that one of the PgPR-10 homologs, PgPR-10.3, shares binding properties with flavonoids, kinetin, emodin, deoxycholic acid, and ginsenoside Re (1 of the steroid glycosides). Methods: Gene expression patterns of PgPR-10.3 were analyzed by quantitative real-time PCR. The three-dimensional structure of PgPR-10 proteins was visualized by homology modeling, and docking to retrieve biologically active molecules was performed using AutoDock4 program. Results: Transcript levels of PgPR-10.3 expressed in leaves, stems, and roots of 3-wk-old ginseng plantlets were on average 86-fold lower than those of PgPR-10.2. In mature 2-yr-old ginseng plants, the mRNA of PgPR-10.3 is restricted to leaves. Ginsenoside Re production is especially prominent in leaves of Panax ginseng Meyer, and the binding property of PgPR-10.3 with ginsenoside Re suggests that this protein has an important role in the control of secondary metabolism. Conclusion: Although ginseng PR-10.3 gene is expressed in all organs of 3-wk-old plantlets, its expression is restricted to leaves in mature 2-yr-old ginseng plants. The putative binding property of PgPR-10.3 with Re is intriguing. Further verification of binding affinity with other biologically important molecules in the large hydrophobic cavity of PgPR-10.3 may provide an insight into the biological features of PR-10 proteins.http://www.sciencedirect.com/science/article/pii/S1226845315000524abiotic stressligand bindingPanax ginseng Meyerpathogenesis-related-10salicylic acid |
spellingShingle | Jin Haeng Han Jin Hee Lee Ok Ran Lee Leaf-specific pathogenesis-related 10 homolog, PgPR-10.3, shows in silico binding affinity with several biologically important molecules Journal of Ginseng Research abiotic stress ligand binding Panax ginseng Meyer pathogenesis-related-10 salicylic acid |
title | Leaf-specific pathogenesis-related 10 homolog, PgPR-10.3, shows in silico binding affinity with several biologically important molecules |
title_full | Leaf-specific pathogenesis-related 10 homolog, PgPR-10.3, shows in silico binding affinity with several biologically important molecules |
title_fullStr | Leaf-specific pathogenesis-related 10 homolog, PgPR-10.3, shows in silico binding affinity with several biologically important molecules |
title_full_unstemmed | Leaf-specific pathogenesis-related 10 homolog, PgPR-10.3, shows in silico binding affinity with several biologically important molecules |
title_short | Leaf-specific pathogenesis-related 10 homolog, PgPR-10.3, shows in silico binding affinity with several biologically important molecules |
title_sort | leaf specific pathogenesis related 10 homolog pgpr 10 3 shows in silico binding affinity with several biologically important molecules |
topic | abiotic stress ligand binding Panax ginseng Meyer pathogenesis-related-10 salicylic acid |
url | http://www.sciencedirect.com/science/article/pii/S1226845315000524 |
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