Plant protein-lipid interfaces studied by molecular dynamics simulations.

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.

Regulation of the microsomal proteome by salicylic acid and deficiency of phosphatidylinositol-4-kinases ß1 and ß2 in Arabidopsis thaliana.

Phosphatidylinositol-4-kinases ß1 and ß2 (PI4Kß1/PI4Kß2), which are responsible for phosphorylation of phosphatidylinositol to phosphatidylinositol-4-phosphate, have important roles in plant vesicular trafficking. Moreover, PI4Kß1/PI4Kß2 negatively regulates biosynthesis of phytohormone salicylic acid (SA), a key player in plant immune responses. The study focused on the effect of PI4Kß1/PI4Kß2 deficiency and SA level on the proteome of microsomal fraction. For that purpose we used four Arabidopsis thaliana genotypes: wild type; double mutant with impaired function of PI4Kß1/PI4Kß2 (pi4kß1/pi4kß2) exhibiting high SA level; sid2 mutant with impaired SA biosynthesis depending on the isochorismate synthase 1 and triple mutant sid2/pi4kß1/pi4kß2. We identified 1797 proteins whose levels were changed between genotypes. We showed that increased SA concentration affected the levels of 473 proteins. This includes typical SA pathway markers but also points to connections between SA pathway and clathrin-independent endocytosis (flotillins) and exocytosis/protein secretion (syntaxins, tetraspanin) to be investigated in future. In contrast to SA, the absence of PI4Kß1/PI4Kß2 itself affected only 27 proteins. Among them we identified CERK1, a receptor for chitin. Although PI4Kß1/PI4Kß2 deficiency itself did not have a substantial impact on the proteome of the microsomal fraction, our data clearly show that it enhances proteome changes when SA pathway is modulated in parallel.