The Plasma Membrane as a Competitive Inhibitor and Positive Allosteric Modulator of KRas4B Signaling

Mutant Ras proteins are important drivers of human cancers, yet no approved drugs act directly on this difficult target. Over the last decade, the idea has emerged that oncogenic signaling can be diminished by molecules that drive Ras into orientations in which effector binding interfaces are occluded by the cell membrane. To support this approach to drug discovery, we characterize the orientational preferences of membrane-bound K-Ras4B in 1.45 milliseconds aggregate time of atomistic molecular dynamics simulations. Individual simulations probe active or inactive states of Ras on membranes with or without anionic lipids. We find that the membrane orientation of Ras is relatively insensitive to its bound guanine nucleotide and activation state but depends strongly on interactions with anionic phosphatidylserine lipids. These lipids slow Ras’ translational and orientational diffusion and promote a discrete population in which small changes in orientation control Ras’ competence to bind multiple regulator and effector proteins. Our results suggest that compound-directed conversion of constitutively active mutant Ras into functionally inactive forms may be accessible via subtle perturbations of Ras’ orientational preferences at the membrane surface.Statement of SignificanceMutations that lock Ras proteins in active states can undermine cellular decision making and drive cancer. Because there are no drugs to deactivate Ras, we use simulations to relate Ras’ three-dimensional orientation at the membrane surface to its signaling competence. Data shows that Ras reorientation is generally rapid, but can be trapped in one of three states by membrane adhesion of the globular signaling domain. One of these states is stabilized by negatively charged lipids and brings an effector binding interface toward the membrane surface, potentially obstructing protein-protein interactions required for propagation of the growth signal. Rare events drive a second type of membrane-based signaling obstruction that correlate with configurational changes in Ras’ globular domain, yielding a potential drug target.