Detailed Analysis of 17β-Estradiol-Aptamer Interactions: A Molecular Dynamics Simulation Study
Faculty of Applied Computer and Biosciences, University of Applied Sciences Mittweida, Technikumplatz 17, 09648 Mittweida, Germany
Institute for Organic Chemistry, Technische Universität Bergakademie Freiberg, Leipziger Straße 29, 09599 Freiberg, Germany
Author to whom correspondence should be addressed.
Received: 1 June 2018 / Revised: 6 July 2018 / Accepted: 9 July 2018 / Published: 11 July 2018
Micro-pollutants such as 17
-Estradiol (E2) have been detected in different water resources and their negative effects on the environment and organisms have been observed. Aptamers are established as a possible detection tool, but the underlying ligand binding is largely unexplored. In this study, a previously described 35-mer E2-specific aptamer was used to analyse the binding characteristics between E2 and the aptamer with a MD simulation in an aqueous medium. Because there is no 3D structure information available for this aptamer, it was modeled using coarse-grained modeling method. The E2 ligand was positioned inside a potential binding area of the predicted aptamer structure, the complex was used for an 25 ns MD simulation, and the interactions were examined for each time step. We identified E2-specific bases within the interior loop of the aptamer and also demonstrated the influence of frequently underestimated water-mediated hydrogen bonds. The study contributes to the understanding of the behavior of ligands binding with aptamer structure in an aqueous solution. The developed workflow allows generating and examining further appealing ligand-aptamer complexes.
This is an open access article distributed under the Creative Commons Attribution License
which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).
Share & Cite This Article
MDPI and ACS Style
Eisold, A.; Labudde, D. Detailed Analysis of 17β-Estradiol-Aptamer Interactions: A Molecular Dynamics Simulation Study. Molecules 2018, 23, 1690.
Eisold A, Labudde D. Detailed Analysis of 17β-Estradiol-Aptamer Interactions: A Molecular Dynamics Simulation Study. Molecules. 2018; 23(7):1690.
Eisold, Alexander; Labudde, Dirk. 2018. "Detailed Analysis of 17β-Estradiol-Aptamer Interactions: A Molecular Dynamics Simulation Study." Molecules 23, no. 7: 1690.
Show more citation formats
Show less citations formats
Note that from the first issue of 2016, MDPI journals use article numbers instead of page numbers. See further details here.
[Return to top]
For more information on the journal statistics, click here
Multiple requests from the same IP address are counted as one view.