Investigating the effects of missense mutations on the dual Ras/Rap activation mechanism of SYNGAP1 using molecular modelling

SynGAP (Synaptic GTPase-Activating Protein) is enriched in the postsynaptic density, where it accelerates GTP hydrolysis by Ras- and Rap-GTPases. In forebrain, SynGAP is essential for synaptic plasticity and cognitive development, and de novo mutations in SYNGAP1 gene cause SynGAP-related disorder (SRD), characterized by intellectual disability, autism, and epilepsy. Beyond the nervous system, SynGAP regulates cell growth, differentiation, and cytoskeletal dynamics, and loss of its GAP activity has been implicated in tumorigenesis and cancer metastasis. Although classified as a RasGAP based on homology, SynGAP efficiently promotes GTP hydrolysis of both Ras and Rap1b. Here, a combination of modelling approaches, including in silico mutagenesis, free-energy calculations, and atomistic molecular dynamics simulations, were used to define the structural basis of this dual specificity. Cancer-associated and SRD-associated missense variants were analyzed to assess their effects on SynGAP interactions with Ras and Rap and, by extension, on GAP-mediated GTP hydrolysis. Modelling suggests that SynGAP regulates Ras through a canonical RasGAP mechanism, whereas Rap1b is controlled through a Plexin-like mechanism involving opening of Rap-Switch II and engagement of a previously uncharacterized region termed the SynGAP activation-segment. The modelling supports the established role of the C2-domain residue Arg401, possibly stabilizing an open Rap-Switch II conformation, and suggests new testable hypotheses that some variants could differentially affect Ras and Rap. Enhanced GTP stabilization is proposed to explain the greater potency of SynGAP toward Rap1b. Overall, 33 missense variants, including eight ClinVar and 18 cancer-associated variants, were predicted to potentially impair SynGAP-GTPase complex formation.

We study SynGAP, a protein essential for how brain cells communicate, learn, and develop. Changes in the SYNGAP1 gene are known to cause a neurodevelopmental disorder causing intellectual disability, autism, and epilepsy. SynGAP also helps regulate cell-growth pathways, and its dysfunction can contribute to cancer. In this work, we use computer-based approaches, including molecular dynamics simulations, to investigate how SynGAP interacts with the signaling GTPases Ras and Rap1b, which control key cellular processes. We show that SynGAP engages these proteins through two distinct interaction modes and model both at atom-level resolution. We also examine disease-associated missense variants and predict how they may disrupt these interactions. Our results help explain previously reported experimental findings and highlight regions of SynGAP that are critical for its function. By improving our understanding of how SynGAP regulates Ras and Rap1b, this work provides insight into SynGAP-related disorders and cancer as well as suggesting testable hypotheses for future experimental studies.