Deciphering the structural and dynamic effects of SHP2-E76 mutations: mechanistic insights into oncogenic activation

The tyrosine phosphatase known as SHP2 is a cytoplasmic protein and encodes by proto-oncogene PTPN11. This protein is essential for the regulation of cell growth, differentiation, programed cell death, and survival. This regulation is achieved through the release of intramolecular autoinhibition and the modulation of several signaling pathways, including the signaling cascade of Ras-MAPK. Mutations in SHP2 are frequently associated with human malignancies and neurodevelopmental disorders (NDDs). Specifically, a germline mutation (E76D) in SHP2 is linked to neurodevelopmental disorders, such as Noonan syndrome, while somatic mutations (E76G and E76A) and altered SHP2 expression are implicated in several forms of leukemia. These mutations disrupt the closed conformation, which normally keeps SHP2 in an inactive, auto-inhibited state, thereby enhancing phosphatase activity and activating SHP2, leading to a gain-of-function effect. However, the structural and functional implications of these disease-related mutants are not well elucidated. Therefore, in this study, we investigate the structural mechanisms underlying three distinct gain-of-function SHP2 mutations (E76D, E76G, and E76A) through the application of molecular dynamics (MD) simulations, focusing on how a single amino acid mutation at the same position result in different disease phenotypes, either cause cancer or NDDs. Notably, Patients with Noonan Syndrome have an increased risk of developing cancer, suggesting a potential link between these diseases and their mutations. MD simulation was employed to elucidate this mechanism, examining four distinct states: Apo-state (E76), M1-state (E76D), M2-state (E76G), and M3-state (E76A). The dynamics and conformational changes of SHP2 in both its Apo-state and mutant states (M1, M2, and M3) were compared. Our findings indicate that both cancer-related and NDD-related mutations destabilize the N-SH2 and PTP interface, facilitating SHP2 activation. However, the cancer-associated mutations induce more severe disruption at the N-SH2 and PTP interface than the NDD mutations. Additionally, dynamic analyses revealed that mutations at the interface (M1, M2, and M3) not only alter the native folded conformation of SHP2 but also significantly enhance the C-distance between the N-SH2 and PTP domains. Overall, this study provides a comprehensive understanding of the structural dynamics of SHP2 at the atomic level, revealing how mutations disrupt its auto-inhibition and increase PTP activity, providing valuable insights into the molecular mechanisms driving both cancer and neurodevelopmental disorders.