High Resolution Solvated Models Reveal Mechanisms of Allosteric Activation of mTORC1 by RHEB

Abstract The mechanistic target of rapamycin complex 1 (mTORC1) is a ∼1.2 MDa dimeric assembly comprising mTOR, mLST8, and RAPTOR that integrates nutrient, energy, and stress signals to regulate cell growth. While Cryo-EM structures have provided insights into allosteric activation of the complex by the small GTPase RHEB, their limited resolution has constrained a full mechanistic understanding. Here, we combine deep learning–based AlphaFold-3 models with Molecular Dynamics Flexible Fitting and simulations to generate refined, atomistic solvated models of mTORC1±ATP±RHEB. Simulations reveal a global remodelling of the complex by RHEB, which strengthens mTOR–RAPTOR interactions while weakening mTOR–mLST8 contacts. These drive the reorganization of Kinase N- and C-lobes into a catalytically competent state in which ATP binding is stabilized enthalpically with improved Mg²⁺ coordination. Our studies present structural, energetic and dynamic changes induced by RHEB binding which collectively cause allosteric preorganization of mTORC1 for catalysis prior to substrate binding.