Being picky: Mechanism for PLAFP picking up the signaling lipid PA from plasma membranes

Plants must adapt to changing environmental conditions across days, weeks, and seasons. Responding to environmental stimuli occurs mainly through metabolic changes in response to signals triggered by available resources or external stress factors. Most signals a plant experiences are local, such as nutrients in the root zone or the exposure of leaves to intense sunlight. But, especially in the case of stress factors such as drought, a global metabolic response must occur across plant tissues, which requires signal transport over longer distances. We are specifically interested in the transport of the drought stress signaling lipids by the phloem lipid-associated family protein (PLAFP) from Arabidopsis thaliana. During signaling, PLAFP picks up one phosphatidic acid (PA) from the plasma membrane and inserts the lipid into its stacked β-sheet. With free energy calculations in aqueous solution using molecular dynamics simulations, we quantified in agreement to experiment that PA's insertion into PLAFP is not unique to PA, but that all charged lipids have strongly negative binding free energies. This suggests that PLAFP's PA-specificity depends on the mechanism for picking up the lipid from the membrane instead of binding pocket interactions. Using adaptive sampling and hidden Markov models, we analyze the entire mechanism for PA desorption from the plasma membrane, through protein-membrane association to the insertion of PA into PLAFP, to membrane dissociation. The process is guided by the amino acids W41, W141, H112 and H113 with which the PA head group interacts in sequence. The amino acids are arranged like a ladder on the protein surface with each established interaction pulling the lipid further out of the plasma membrane. We propose that this interaction sequence is precisely tuned to PA and is the cause of PLAFP's specificity.