Missense mutations on SynGAP C2 domain impair membrane diffusion

SYNGAP1 mutations have been linked to a range of neuropathological disorders and, more recently, to the insurgence of cancer. SynGAP is a postsynaptic Ras GTPase-activating protein that regulates Ras/ERK signaling and synaptic plasticity. All SynGAP isoforms share a conserved C2-RasGAP core, where the C2 domain may mediate interactions with phospholipid membranes that influence SynGAP localization and signaling at synapses. However, how the C2 domain associates with membranes and how disease-associated missense mutations affect this process remain poorly understood. Here, using extensive molecular dynamics simulations integrated with structural analysis, we define how the SynGAP C2 domain associates with lipid bilayers. In particular, we observed spontaneous membrane binding of the domain in two distinct orientations, top and side, defined by the relative positioning of the C2 domain to its fold. These modes display markedly different dynamical properties: the top mode enables faster lateral diffusion on the membrane surface, whereas the side mode establishes more stable but less mobile contacts. Interestingly, pathogenic missense mutations mapping to the membrane-facing loops of SynGAP C2 disrupt these dynamics, leading to reduced diffusivity and altered membrane avidity. Our findings reveal a dual binding mechanism that underlies SynGAP's membrane versatility and offer a general framework for how diverse mutations may perturb SynGAP activity across its polyhedric biological functions.