KRAS recognition by Src: Mechanistic insights from Molecular Dynamics Simulations

Abstract

c-Src, the first identified oncogene, and Ras, one of the most frequently mutated proteins in human cancers, can activate each other to promote tumorigenesis. Recent experimental work has found that c-Src can recognize and phosphorylate both GTP-bound and GDP-bound forms of KRas, as well as GTP-bound NRas and GDP-bound HRas. The molecular mechanisms underlying this specific recognition remain unknown. We leverage molecular simulation tools (eg. Molecular dynamics and Markov State Models analysis) to model a Src-KRas interaction in solution to identify the mechanisms underlying the c-Src recognition of the G12D mutant of KRas4B-G12D, the most prevalent in humans. We found that the most populated states of nucleotide-bound KRas maintain more open and dynamic switch regions, facilitating easier access of c-Src to the phosphorylation sites of KRas (Tyr32 for GTP-bound KRas and Tyr64 for GDP-bound KRas). We further identify two c-Src specific regions (residues 340-359 and 453-473), along with putative recognition hotspots at Leu347, Asp348, Lys351, Gly459, Arg460, and Val461, that may contribute to the stabilization of phosphorylation-competent KRas conformations. c-Src selectively recognizes and engages specific macrostates of KRas, which may constitute privileged targets for the rational design of peptide-based inhibitors.