Computational Modeling Reveals that Signaling Lipids Modulate the Orientation of K-Ras4A at the Membrane Reflecting Protein Topology

The structural, dynamical, and functional characterization of the small GTPase K-Ras has become a research area of intense focus due to its high occurrence in human cancers. Ras proteins are only fully functional when they interact with the plasma membrane. Here we present all-atom molecular dynamics simulations (totaling 5.8 μs) to investigate the K-Ras4A protein at membranes that contain anionic lipids (phosphatidyl serine or phosphatidylinositol bisphosphate). We find that similarly to the homologous and highly studied K-Ras4B, K-Ras4A prefers a few distinct orientations at the membrane. Remarkably, the protein surface charge and certain lipids can strongly modulate the orientation preference. In a novel analysis, we reveal that the electrostatic interaction (attraction but also repulsion) between the protein's charged residues and anionic lipids determines the K-Ras4A orientation, but that this is also influenced by the topology of the protein, reflecting the geometry of its surfaces. [Display omitted] •Simulations predict the five major orientations of Ras with respect to the membrane•Lipid molecules modulate the orientation preference of the K-Ras catalytic domain•PIP2 converts the Ras-membrane complex to a more active form•Protein topology and electrostatics determine Ras orientations at the membrane K-Ras, a small GTPase linked to human cancers, is only fully functional when engaged with the plasma membrane. Li and Buck use all-atom molecular dynamics simulations to examine how K-Ras4A interacts with anionic lipid membranes and find that the protein surface charge as well as geometry, in contact with certain lipids can strongly modulate the orientation preference.