phmathВестник Государственного университета просвещения. Серия: Физика-МатематикаBulletin of Federal State University of Education. Series: Physics and Mathematics2949-50832949-5067Federal State University of Education10.18384/2949-5067-2023-4-49-63phmath-605Research ArticleФИЗИКАPHYSICSМолекулярно-динамические расчёты адсорбции и подвижности биомолекул на поверхности графеновых подложекMolecular dynamic of the adsorption and mobility of biomolecules on graphene sheetsТерешкинЭ. В.TereshkinE. V.

Терешкин Эдуард Владимирович – научный сотрудник отдела строения вещества

119991, г. Москва, ул. Косыгина, д. 4

Eduard V. Tereshkin – Researcher, Department of Structure of Matter

ulitsa Kosygina 4, Moscow 119991

ramm@mail.ruТерешкинаК. Б.TereshkinaK. B.

Терешкина Ксения Борисовна – кандидат физико-математических наук, старший научный сотрудник отдела строения вещества

119991, г. Москва, ул. Косыгина, д. 4

Ksenia B. Tereshkina – Cand. Sci. (Phys.-Math.), Senior Researcher, Department of Structure of Matter

ulitsa Kosygina 4, Moscow 119991

ksenia.tereshkina@chph.ras.ruКрупянскийЮ. Ф.KrupyanskiiYu. F.

Крупянский Юрий Федорович – доктор физико–математических наук, заведующий отделом строения вещества

119991, г. Москва, ул. Косыгина, д. 4

Yurii F. Krupyanskii – Dr. Sci. (Phys.-Math.), Departmental Head, Department of Structure of Matter

ulitsa Kosygina 4, Moscow 119991

   

yuriifkru@gmail.comФедеральный исследовательский центр химической физики им. Н. Н. Семенова Российской академии наукРоссияN. N. Semenov Federal Research Center for Chemical PhysicsRussian Federation202330012024044963Copyright © Терешкин Э.В., Терешкина К.Б., Крупянский Ю.Ф., 20242024Терешкин Э.В., Терешкина К.Б., Крупянский Ю.Ф.Tereshkin E.V., Tereshkina K.B., Krupyanskii Y.F.Данная работа распространяется под лицензией Creative Commons Attribution 4.0.This work is licensed under a Creative Commons Attribution 4.0 License.https://www.physmathmgou.ru/jour/article/view/605Цель

Цель. Выявить различия в динамике дезоксирибонуклеиновой кислоты (ДНК) и стабилизирующего её белка на поверхности графена, оксида графена и в растворе.

Процедура

Процедура. Методом молекулярной динамики в полноатомном приближении проведены расчёты ДНК, связанной с ДНК-стабилизирующим белком DPS (DNA-binding protein from starved cells) на поверхности графена, оксида графена и в растворе. 

Результаты

Результаты. На основе проведённых исследований показано, что графеновые подложки могут оказывать влияние на динамику белков и ДНК. В частности, могут ограничивать подвижность свободных областей белка, затрудняя их взаимодействие с другими молекулами, и адсорбировать молекулы ДНК, изменяя структуру комплексов DPS –  ДНК.

Теоретическая и/или практическая значимость. Полученные данные представляют практический интерес для исследователей структуры биологических молекул и их комплексов на поверхности графеновых подложек. Также данные могут быть использованы при создании основанных на биологических молекулах наноматериалов с заданными свойствами.

Aim

Aim. To reveal the differences in the dynamics of deoxyribonucleic acid (DNA) and its stabilizing protein on the surface of graphene, graphene oxide and in solution.

Methodology

Methodology. Using the method of molecular dynamics in the all atom approximation, calculations of DNA bound to the DNA-stabilizing protein DPS (DNA-binding protein from starved cells) on the surface of graphene, graphene oxide and in solution were carried out.

Results

Results. Based on the studies performed, it was shown that graphene substrates can affect the dynamics of proteins and DNA. In particular, they can limit the mobility of free protein regions, hindering their interaction with other molecules, and adsorb DNA, changing the structure of DPS – DNA complexes.

Research implications

Research implications. The obtained data are of practical interest for researchers of the structure of biological molecules and their complexes on the surface of graphene substrates. Also, the data can be used to create bioinspired nanomaterials with desired properties. 

взаимодействие белков с графеномвзаимодействие ДНК с белком и графеномграфеноксид графенабактериальный белок DPSмоделирование биологических молекул на графенемолекулярная динамикаinteraction of proteins with grapheneinteraction of DNA with protein and graphenegraphenegraphene oxideDPS bacterial proteinsimulation of biological molecules on graphenemolecular dynamicsРасчёты проводились на высокопроизводительной вычислительной системе МВС-10П в Межведомственном суперкомпьютерном центре Российской академии наук (МСЦ РАН). Работа выполнена в рамках государственного задания Минобрнауки России (Тема FFZE-2022-0011, № 122040400089-6)The computations were carried out on MVS-10P at Joint Supercomputer Center of the Russian Academy of Sciences (JSCC RAS). This work was supported within frameworks of the state task for FRC CP RAS FFZE-2022-0011 (state registration No 122040400089-6)ReferencesLomonossoff G. P., Wege C. 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The authors declare that there are no conflicts of interest present.