Insights into the binding mode of AS1411 aptamer to nucleolin
AS1411 aptamer can function as a recognition probe to detect the cell surface nucleolin overexpressed in cancer cells, however, little is known about their binding process. This study proposed a feasible binding mode for the first time and provided atomic-level descriptions for the high affinity and...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2022-10-01
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| Series: | Frontiers in Molecular Biosciences |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fmolb.2022.1025313/full |
| _version_ | 1811229933343604736 |
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| author | Lihua Bie Lihua Bie Lihua Bie Yue Wang Fuze Jiang Fuze Jiang Zhen Xiao Zhen Xiao Lianjun Zhang Lianjun Zhang Jing Wang Jing Wang |
| author_facet | Lihua Bie Lihua Bie Lihua Bie Yue Wang Fuze Jiang Fuze Jiang Zhen Xiao Zhen Xiao Lianjun Zhang Lianjun Zhang Jing Wang Jing Wang |
| author_sort | Lihua Bie |
| collection | DOAJ |
| description | AS1411 aptamer can function as a recognition probe to detect the cell surface nucleolin overexpressed in cancer cells, however, little is known about their binding process. This study proposed a feasible binding mode for the first time and provided atomic-level descriptions for the high affinity and specific binding of AS1411. The binding pose predicted by docking was screened using knowledge-based criteria, and a microsecond molecular dynamics (MD) simulation showed the stable existence of the predicted structure in the solution. Structural analysis shows that the unique capping of the 5′ end of AS1411 provides the specific binding with RBD1, and the interactions of hydrogen bond, salt bridge, and water-mediated network between AS1411 and RBD1,2 stabilize the binding. The calculation of per-residue decomposition emphasizes the dominant contribution of van der Waals energy and critical residues are screened. Our study provides the molecular basis of this specific binding and can guide rational AS1411-based aptamers design. Further insights require tight collaborations between the experiments and in silico studies. |
| first_indexed | 2024-04-12T10:21:31Z |
| format | Article |
| id | doaj.art-772d5f0ffde74fb887e2728a96d93145 |
| institution | Directory Open Access Journal |
| issn | 2296-889X |
| language | English |
| last_indexed | 2024-04-12T10:21:31Z |
| publishDate | 2022-10-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Molecular Biosciences |
| spelling | doaj.art-772d5f0ffde74fb887e2728a96d931452022-12-22T03:37:05ZengFrontiers Media S.A.Frontiers in Molecular Biosciences2296-889X2022-10-01910.3389/fmolb.2022.10253131025313Insights into the binding mode of AS1411 aptamer to nucleolinLihua Bie0Lihua Bie1Lihua Bie2Yue Wang3Fuze Jiang4Fuze Jiang5Zhen Xiao6Zhen Xiao7Lianjun Zhang8Lianjun Zhang9Jing Wang10Jing Wang11Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, ChinaLaboratory for Advanced Analytical Technologies, Empa, Swiss Federal Laboratories for Materials Science and Technology, Dübendorf, SwitzerlandInstitute of Environmental Engineering, ETH Zürich, Zürich, SwitzerlandHubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, ChinaLaboratory for Advanced Analytical Technologies, Empa, Swiss Federal Laboratories for Materials Science and Technology, Dübendorf, SwitzerlandInstitute of Environmental Engineering, ETH Zürich, Zürich, SwitzerlandInstitute of Systems Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, ChinaSuzhou Institute of Systems Medicine, Suzhou, ChinaInstitute of Systems Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, ChinaSuzhou Institute of Systems Medicine, Suzhou, ChinaLaboratory for Advanced Analytical Technologies, Empa, Swiss Federal Laboratories for Materials Science and Technology, Dübendorf, SwitzerlandInstitute of Environmental Engineering, ETH Zürich, Zürich, SwitzerlandAS1411 aptamer can function as a recognition probe to detect the cell surface nucleolin overexpressed in cancer cells, however, little is known about their binding process. This study proposed a feasible binding mode for the first time and provided atomic-level descriptions for the high affinity and specific binding of AS1411. The binding pose predicted by docking was screened using knowledge-based criteria, and a microsecond molecular dynamics (MD) simulation showed the stable existence of the predicted structure in the solution. Structural analysis shows that the unique capping of the 5′ end of AS1411 provides the specific binding with RBD1, and the interactions of hydrogen bond, salt bridge, and water-mediated network between AS1411 and RBD1,2 stabilize the binding. The calculation of per-residue decomposition emphasizes the dominant contribution of van der Waals energy and critical residues are screened. Our study provides the molecular basis of this specific binding and can guide rational AS1411-based aptamers design. Further insights require tight collaborations between the experiments and in silico studies.https://www.frontiersin.org/articles/10.3389/fmolb.2022.1025313/fullAS1411aptamernucleolindockingbinding mode |
| spellingShingle | Lihua Bie Lihua Bie Lihua Bie Yue Wang Fuze Jiang Fuze Jiang Zhen Xiao Zhen Xiao Lianjun Zhang Lianjun Zhang Jing Wang Jing Wang Insights into the binding mode of AS1411 aptamer to nucleolin Frontiers in Molecular Biosciences AS1411 aptamer nucleolin docking binding mode |
| title | Insights into the binding mode of AS1411 aptamer to nucleolin |
| title_full | Insights into the binding mode of AS1411 aptamer to nucleolin |
| title_fullStr | Insights into the binding mode of AS1411 aptamer to nucleolin |
| title_full_unstemmed | Insights into the binding mode of AS1411 aptamer to nucleolin |
| title_short | Insights into the binding mode of AS1411 aptamer to nucleolin |
| title_sort | insights into the binding mode of as1411 aptamer to nucleolin |
| topic | AS1411 aptamer nucleolin docking binding mode |
| url | https://www.frontiersin.org/articles/10.3389/fmolb.2022.1025313/full |
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