(681c) Quantitative Characterization of Protein-Ligand and Protein-Protein Binding Processes Involved in Plant Hormone Signaling

Plant hormones are a series of small molecules that are naturally produced in plants, which regulate plant growth, development and responses to biotic and abiotic stresses. There are 9 major classes of plant hormones that have been identified, including auxin, abscisic acid, brassinosteroids, cytokinins, ethylene, gibberellins, jasmonates, salicylic acid, and strigolactones. Over the past decades, substantial research studies have been trying to answer a set of fundamental questions in plant biology: how do hormones work in plants?

Recently, the crystal structures of receptor proteins for 7 classes of plant hormones have been identified, except for ethylene and salicylic acid. These structural studies have led to a predominant ‘molecular glue’ hypothesis to explain the mode of actions of these hormones. According to this hypothesis, plant hormones act as ‘molecular glue’ after binding to their receptors, thereby promoting protein-protein interactions between the receptors and the binding partners, which triggers the downstream signaling cascades. While this hypothesis has been supported by a variety of experimental data, the nanoscale details of how plant hormones bind to their receptors and lead to the assembly of protein-protein complexes remain largely unknown.

In this work, we utilize large-scale all-atom molecular dynamics (MD) simulations and advanced free energy calculation methods to examine the mode of actions for 7 plant hormones, whose receptor structures are currently available. We have performed hundreds of microseconds MD simulations to capture the plant hormone binding processes. Coupled with Markov state models, we fully map out the protein-ligand binding pathways and the associated conformational changes of receptor proteins, along with thorough quantitative thermodynamic and kinetic characterization. Our results unravel the complete structural, dynamic, and energetic basis of the protein-ligand binding processes involved in plant signaling. In addition, we have investigated the solvation thermodynamics of these plant hormone receptors via MD simulations and inhomogeneous solvation theory. Our results highlight the essential role of water molecules in plant hormone perception and affinity, which can be exploited for receptor engineering and agrochemical design.

To test the ‘molecular glue’ hypothesis, we have employed replica exchange umbrella sampling (REUS) MD simulations to accurately estimate the standard protein-protein binding free energies for the complexes between the receptors and the binding partners. We quantify the free energy changes of protein-protein associations in the presence and the absence of bound hormones, allowing for a quantitative validation of the hypothesis. Altogether, our results have provided new insights into the fundamental mechanisms of plant hormone signaling and created avenues for engineering plant signaling pathways to control plant activities.

Reference: Shukla S.⁺, Zhao C.⁺, & Shukla D. (2019). Dewetting Controls Plant Hormone Perception and Initiation of Drought Resistance Signaling. Structure. 27, 692-702.