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Молекулярное моделирование диффузионных процессов в мембранных структурах на примере ионного канала серотонинового рецепторастатья
Дата последнего поиска статьи во внешних источниках: 10 июля 2024 г.
- Авторы: АНТОНОВ М.Ю., ПОПИНАКО А.В., НИКОЛАЕВ И.Н.
- Журнал: Вестник Северо-Восточного федерального университета имени М.К. Аммосова
- Том: 71
- Номер: 3
- Год издания: 2019
- Издательство: Северо-Восточный федеральный университет имени М.К. Аммосова
- Местоположение издательства: Якутск
- Первая страница: 5
- Последняя страница: 15
- DOI: 10.25587/svfu.2019.71.31940
- Аннотация: Abstract. Studying dynamics and function of ion channels is a field of interest of modernexperimental molecular biology. At the same time, there are limited number of methods that allowstudying the processes on molecular level with atomic precision. The most accurate methods that providedata on the atomic structure of molecules are the X-ray crystallography (XRC) and the nuclear magneticresonance spectroscopy (NMR) methods. However, the XRC method provides data on the atomic structureof the crystallized molecule, while the crystallization conditions are usually far from physiological. Usingstructural data, obtained from the XRC/NMR methods, it is impossible to determine the state of thechannel (open or closed) and analyze the dynamic of the processes under study. In this article, themolecular simulation methods are used to study the structure, dynamics and the diffusion processeson the water-membrane interface, as well as the process of ion transportation in 5-HT3 mouse serotonin5HT-3 receptor, the spatial structure of which was determined in 2014. Based on the full-atom structure ofthe ion channel, we constructed the model, containing transmembrane domain of the 5-HT3 receptorwith lipid bilayer and solvent. Molecular dynamics protocols for simulation of the transmebrane domainof the ion channel were developed. We used steered molecular dynamics for simulation of thetransmembrane Na+ ion transport under external electric field. Using the umbrella sampling method, weestimated the free energy profile of Na+ ions transfer through the channel. Using the computer simulationmethods (including molecular dynamics method) allowed us making reasonable assumptions about theconformation and conductive state of the ion channel under study.Keywords: molecular modelling, molecular dynamics, steered molecular dynamics, diffusion,biomembranes, lipid bilayers, ion channels, serotonin receptor, transmembrane transport, membranepotential.
- Добавил в систему: Попинако Анна Владимировна