Structural Basis for Negative Regulation of ABA Signaling by ROP11 GTPase
Published in Journal of Chemical Information and Modeling, 2025
Recommended citation: Chuankai Zhao, Hassan Nadeem, and Diwakar Shukla Journal of Chemical Information and Modeling 2025 DOI: 10.1021/acs.jcim.5c02002 https://pubs.acs.org/doi/abs/10.1021/acs.jcim.5c02002
Abstract
Abscisic acid (ABA) is an essential plant hormone that is responsible for plant development and stress responses. Recent structural and biochemical studies have identified the key components involved in the ABA signaling cascade, including PYR/PYL/RCAR receptors, protein phosphatases PP2C, and protein kinases SnRK2. The plant-specific Rho-like (ROPs) small GTPases are negative regulators of ABA signal transduction by interacting with PP2C, which can shut off “leaky” ABA signal transduction caused by the constitutive activity of monomeric PYR/PYL/RCAR receptors. However, the structural basis for the negative regulation of ABA signaling by ROP GTPases remains elusive. In this study, we have utilized large-scale coarse-grained (10.05 ms) and all-atom molecular dynamics simulations and standard protein–protein binding free energy calculations to predict the complex structure of AtROP11 and phosphatase AtABI1. In addition, we have predicted the detailed complex association pathway and identified the critical residue pairs in AtROP11 and AtABI1 for complex stability. Overall, this study established a powerful framework for using large-scale molecular simulations to predict unknown protein complex structures and suggested the molecular mechanism of the negative regulation of ABA signal transduction by small GTPases.. 