Peculiarities of DNA Binding to Two-Dimensional Crystals of Bacterial Protein DPS from Escherichia coli Based on Molecular Dynamics Data
In this work, using coarse-grained molecular modeling methods, the interactions of DNA-binding protein from starved cells (Dps) of the bacterium Escherichia coli with DNA sections of various lengths and composition are investigated. The binding features in two-dimensional crystals of the Dps protein are studied. Using free energy search methods—thermodynamic integration and linear interaction energy—the most favorable conditions for the binding of DNA and Dps are determined.
Authors
- Н. Г. Лойко (ORCID: https://orcid.org/0000-0001-5204-007X)
- Э. В. Терешкин (ORCID: https://orcid.org/0000-0001-6091-7476)
- V. V. Kovalenko (ORCID: https://orcid.org/0000-0001-9851-8358)
- К. Б. Терешкина (ORCID: https://orcid.org/0000-0003-1165-5224)
- Yurii F. Krupyanskii (ORCID: https://orcid.org/0000-0002-2994-4799)
Institutions
- Russian Academy of Sciences (RU)
- Semenov Institute of Chemical Physics (RU)
- Federal Research Centre «Fundamentals of Biotechnology» of the Russian Academy of Sciences (RU)
Publication Details
- Journal
- Russian Journal of Physical Chemistry B
- Published
- 2024-12-01
- DOI
- https://doi.org/10.1134/s199079312470146x
- Citations
- 1
- Primary Topic
- Enzyme Structure and Function
- Type
- article
- Field-Weighted Citation Impact
- 0.12