Long-lasting salt bridges provide the anchoring mechanism of oncogenic KRas-4B proteins at cell membranes

Abstract

Ras is a family of related proteins participating in all animal cell lineages and organs. Ras proteins work as GDP-GTP binary switches and regulate cytoplasmic signalling networks that are able to control several cellular processes, playing an essential role in signal transduction pathways involved in cell growth, differentiation and survival so that overacting Ras signalling can lead to cancer. One of the hardest challenges to face is, with more than hundred different missense mutations found in cancer, the design of mutation-selective therapeutic strategies. In this work, a G12D mutated farnesylated GTP bound KRas-4B protein has been simulated at the interface of a DOPC/DOPS/cholesterol model anionic cell membrane at the all-atom level. A specific long-lasting salt bridge connection between farnesyl and the hypervariable region of the protein has been identified as the main mechanism responsible of the binding of oncogenic farnesylated KRas-4B to the cell membrane, since this particular bond is absent in both wild-type and oncogenic methylated species of KRas-4B. This finding may lead to a deeper understanding of the mechanisms of protein binding and eventual growing and spreading inside cell membranes. From free energy landscapes obtained by well-tempered metadynamics simulations, we have characterised local and global minima of KRas-4B binding to the cell membrane revealing the main pathways between anchored and released states.