Čeština
EnglishPlant protein-lipid interfaces studied by molecular dynamics simulations
Neubergerová M., Pleskot R.
JOURNAL OF EXPERIMENTAL BOTANY : erae228, 2024
Klíčová slova: Integral membrane protein; membrane; molecular dynamics simulations; peripheral membrane protein; protein-lipid interactions; structural modelling
Abstrakt: The delineation of protein-lipid interfaces is essential for understanding the mechanisms of various membrane-associated processes crucial to plant development and growth, including signalling, trafficking, and membrane transport. Due to their highly dynamic nature, the precise characterization of lipid-protein interactions is challenging by experimental techniques. Molecular dynamics (MD) simulations provide a powerful computational alternative with a spatial-temporal resolution allowing the atomistic-level description. In this review, we aim to introduce plant scientists to the MD simulations. We describe different steps of performing the MD simulations and provide a broad survey of the MD studies investigating plant protein-lipid interfaces. Our aim is also to illustrate that combining the MD simulations with artificial intelligence-based protein structure determination opens unprecedented possibilities for future investigations of dynamic plant protein-lipid interfaces.
DOI: 10.1093/jxb/erae228 Autoři z ÚEB: Michaela Neuberge..., Roman Pleskot
JOURNAL OF EXPERIMENTAL BOTANY : erae228, 2024
Klíčová slova: Integral membrane protein; membrane; molecular dynamics simulations; peripheral membrane protein; protein-lipid interactions; structural modelling
Abstrakt: The delineation of protein-lipid interfaces is essential for understanding the mechanisms of various membrane-associated processes crucial to plant development and growth, including signalling, trafficking, and membrane transport. Due to their highly dynamic nature, the precise characterization of lipid-protein interactions is challenging by experimental techniques. Molecular dynamics (MD) simulations provide a powerful computational alternative with a spatial-temporal resolution allowing the atomistic-level description. In this review, we aim to introduce plant scientists to the MD simulations. We describe different steps of performing the MD simulations and provide a broad survey of the MD studies investigating plant protein-lipid interfaces. Our aim is also to illustrate that combining the MD simulations with artificial intelligence-based protein structure determination opens unprecedented possibilities for future investigations of dynamic plant protein-lipid interfaces.
DOI: 10.1093/jxb/erae228 Autoři z ÚEB: Michaela Neuberge..., Roman Pleskot