Membrane Composition and Raf[CRD]-Membrane Attachment Are Driving Forces for K-Ras4B Dimer Stability

RAS proteins are membrane-anchored GTPases that regulate key cellular signaling networks. It has been recently shown that different anionic lipid types can affect the properties of RAS in terms of dimerization/clustering on the cell membrane. To understand the effects of anionic lipids on key spatiotemporal properties of dimeric K-Ras4B, we perform all-atom molecular dynamics simulations of the dimer K-Ras4B in the presence and absence of Raf[CRD/RBD] effectors on two model anionic lipid membranes: one containing 78% mol. DOPC, 20% mol. DOPS, 2% mol. PIP2 and another one with enhanced concentration of anionic lipids containing 50% mol. DOPC, 40% mol. DOPS, 10% mol. PIP2. Analysis of our results unveils the orientational space of dimeric K-Ras4B, and shows that the stability of the dimer is enhanced on the membrane containing a high concentration of anionic lipids in the absence of Raf effectors. This enhanced stability is also observed in the presence of Raf[CRD/RBD] effectors although it is not influenced by the concentration of anionic lipids in the membrane, but rather on the ability of Raf[CRD] to anchor to the membrane. We generate dominant K-Ras4B conformations by Markov State Modeling and yield the population of states according to the K-Ras4B orientation on the membrane. For the membrane containing anionic lipids, we observe correlations between the diffusion of K-Ras4B and PIP2 and anchoring of anionic lipids to the Raf[CRD] domain. We conclude that the presence of effectors with the CRD domain anchoring on the membrane as well as the membrane composition both influence the conformational stability of the K-Ras4B dimer enabling the preservation of crucial interface interactions.