|
This article is cited in 1 scientific paper (total in 1 paper)
ANALYSIS AND MODELING OF COMPLEX LIVING SYSTEMS
Molecular dynamics study of complexes of a DNA aptamer with AMP and GMP
R. R. Ramazanova, P. A. Sokolovb a Sevastopol State University,
33 Universitetskaya st., Sevastopol, 299053, Russia
b Department of Physics, St. Petersburg State University,
1 Ulyanovskaya st., St. Petersburg, 198504, Russia
Abstract:
This study is devoted to a comparative study of the conformational stability of the DNA aptamer to adenosine derivatives in a free state and in a complex with AMP and HMP molecules by use of molecular dynamics. It was shown that, in the free state, the structure of the inner loop of the DNA aptamer hairpin, due to the special packing of guanines, closes the cavity of the binding site from external ligands, and the condition for the specific selection of adenosine derivatives in comparison with guanine arises. New stabilization factors of the AMP and aptamer complex have been revealed — hydrogen bonds between the O3' of the ribose atom of the ligands with the oxygen of the nearest phosphate group. It was also shown that guanines, which form hydrogen bonds with AMP within the binding site, are additionally stabilized by hydrogen bonds with phosphate groups opposing along the chain. The proposed scheme is in qualitative agreement with the experimental data, according to which the aptamer in solution acquires a hairpin conformation with the formation of a binding site, while the formed site exhibits high specificity when interacting only with adenosine derivatives.
Keywords:
ìolecular dynamics, DNA aptamer, AMP, ìolecular recognition.
Received: 05.05.2021 Revised: 05.09.2021 Accepted: 18.10.2021
Citation:
R. R. Ramazanov, P. A. Sokolov, “Molecular dynamics study of complexes of a DNA aptamer with AMP and GMP”, Computer Research and Modeling, 13:6 (2021), 1191–1203
Linking options:
https://www.mathnet.ru/eng/crm944 https://www.mathnet.ru/eng/crm/v13/i6/p1191
|
Statistics & downloads: |
Abstract page: | 86 | Full-text PDF : | 24 | References: | 16 |
|