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Electrical Stimulus Controlled Binding/Unbinding of Human Thrombin-Aptamer Complex
The binding/unbinding of the human thrombin and its 15-mer single stranded DNA aptamer, under the application of external stimulus in the form of electrostatic potential/electric field, is investigated by a combination of continuum analysis and atomistic molecular dynamics simulation. In agreement w...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group
2016
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5118750/ https://www.ncbi.nlm.nih.gov/pubmed/27874042 http://dx.doi.org/10.1038/srep37449 |
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author | Gosai, Agnivo Ma, Xiao Balasubramanian, Ganesh Shrotriya, Pranav |
author_facet | Gosai, Agnivo Ma, Xiao Balasubramanian, Ganesh Shrotriya, Pranav |
author_sort | Gosai, Agnivo |
collection | PubMed |
description | The binding/unbinding of the human thrombin and its 15-mer single stranded DNA aptamer, under the application of external stimulus in the form of electrostatic potential/electric field, is investigated by a combination of continuum analysis and atomistic molecular dynamics simulation. In agreement with the experiments that demonstrate the influence of electrostatic potential on the thrombin/aptamer complex, our computations show that the application of positive electric field successfully unbinds the thrombin from the aptamer. Results from umbrella sampling simulations reveal that there is a decrease in the free energy of binding between the thrombin and aptamer in presence of positive electric fields. Hydrogen bonding and non-bonded interaction energies, and hence the free energy of binding, between the thrombin and its aptamer reduce as the applied electric field is shifted from negative to positive values. Our analyses demonstrate that application of electrical stimulus modifies the molecular interactions within the complex and consequently, electrical field can be used to modulate the association between the thrombin and its aptamer. |
format | Online Article Text |
id | pubmed-5118750 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | Nature Publishing Group |
record_format | MEDLINE/PubMed |
spelling | pubmed-51187502016-11-28 Electrical Stimulus Controlled Binding/Unbinding of Human Thrombin-Aptamer Complex Gosai, Agnivo Ma, Xiao Balasubramanian, Ganesh Shrotriya, Pranav Sci Rep Article The binding/unbinding of the human thrombin and its 15-mer single stranded DNA aptamer, under the application of external stimulus in the form of electrostatic potential/electric field, is investigated by a combination of continuum analysis and atomistic molecular dynamics simulation. In agreement with the experiments that demonstrate the influence of electrostatic potential on the thrombin/aptamer complex, our computations show that the application of positive electric field successfully unbinds the thrombin from the aptamer. Results from umbrella sampling simulations reveal that there is a decrease in the free energy of binding between the thrombin and aptamer in presence of positive electric fields. Hydrogen bonding and non-bonded interaction energies, and hence the free energy of binding, between the thrombin and its aptamer reduce as the applied electric field is shifted from negative to positive values. Our analyses demonstrate that application of electrical stimulus modifies the molecular interactions within the complex and consequently, electrical field can be used to modulate the association between the thrombin and its aptamer. Nature Publishing Group 2016-11-22 /pmc/articles/PMC5118750/ /pubmed/27874042 http://dx.doi.org/10.1038/srep37449 Text en Copyright © 2016, The Author(s) http://creativecommons.org/licenses/by/4.0/ This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ |
spellingShingle | Article Gosai, Agnivo Ma, Xiao Balasubramanian, Ganesh Shrotriya, Pranav Electrical Stimulus Controlled Binding/Unbinding of Human Thrombin-Aptamer Complex |
title | Electrical Stimulus Controlled Binding/Unbinding of Human Thrombin-Aptamer Complex |
title_full | Electrical Stimulus Controlled Binding/Unbinding of Human Thrombin-Aptamer Complex |
title_fullStr | Electrical Stimulus Controlled Binding/Unbinding of Human Thrombin-Aptamer Complex |
title_full_unstemmed | Electrical Stimulus Controlled Binding/Unbinding of Human Thrombin-Aptamer Complex |
title_short | Electrical Stimulus Controlled Binding/Unbinding of Human Thrombin-Aptamer Complex |
title_sort | electrical stimulus controlled binding/unbinding of human thrombin-aptamer complex |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5118750/ https://www.ncbi.nlm.nih.gov/pubmed/27874042 http://dx.doi.org/10.1038/srep37449 |
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