Plants must respond to their environment, relying on multiple signaling mechanisms to coordinate responses across the organism. In Arabidopsis thaliana , phloem-lipid associated family protein (PLAFP) has been found to transport lipids through the aqueous environment of the phloem, most particularly phosphatidic acid, a known signaling lipid. In a previous work, we have identified and validated a mechanism by which PLAFP may extract PA from the plasma membrane. Here, we use enhanced sampling, extreme timescale simulations, and alchemical transformations to investigate the timescale, limitations and possible requirements of this interaction. Long timescale (90 μs) simulation carried out on Anton2 was used to calculate residence time of PLAFP on the plasma membrane, the lateral diffusion of the protein across the membrane, and to quantify lipid association to PLAFP. Replica-exchange umbrella sampling simulations were used to enhance sampling across the lipid adsorption reaction mechanism identified in steered molecular dynamics simulations along a contact-driven reaction coordinate. Using these data, we describe the movement of PLAFP across the plasma membrane prior to lipid extraction, calculate the free energy landscape along the desorption-association pathway for a lipid to PLAFP, and estimate binding/unbinding kinetics. This research provides a better understanding of the rate at which plants may respond to external stimuli, and the mechanisms which allow them to do so.
Boren et al. (Sun,) studied this question.