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Traditional linear models depict mTOR signaling as a sequential phosphorylation cascade, but accumulating evidence supports a model that includes signaling through dynamic protein-protein interaction networks. To examine how neuronal mTOR signaling discriminates between distinct stimuli, we quantified phosphorylation events and protein co-association networks in primary mouse cortical neurons. Unexpectedly, neuronal mTOR activation by IGF or glutamate triggered dissociation\u2014rather than the anticipated assembly\u2014of protein complexes involving mTOR complex1 (TORC1), mTOR complex 2 (TORC2), and translational machinery, distinguishing neurons from proliferative cells. Applying in vitro homeostatic scaling paradigms revealed distinct combinatorial encoding of synaptic scaling direction: both up- and down-scaling induced dissociation of translational complexes, but downscaling uniquely included dissociation of upstream pathway regulators. Cortical neurons from Shank3B knockout mice, modeling autism-associated Phelan-McDermid Syndrome, displayed baseline hyperactivation of the mTOR network, which reduced the dynamic range of network responses to homeostatic scaling and pharmacological inhibition. These findings reveal that neuronal mTOR signaling employs stimulus-specific combinations of dissociative protein interaction modules to encode opposing forms of synaptic plasticity.<\/jats:p>","DOI":"10.1101\/2025.05.20.655155","type":"posted-content","created":{"date-parts":[[2025,5,23]],"date-time":"2025-05-23T20:30:21Z","timestamp":1748032221000},"source":"Crossref","is-referenced-by-count":2,"title":["Dissociation of the mTOR protein interaction network following neuronal activation is altered by Shank3 mutation"],"prefix":"10.64898","author":[{"given":"Devin T.","family":"Wehle","sequence":"first","affiliation":[{"name":"Graduate Program in Neuroscience, University of Washington, Seattle, WA, USA"},{"name":"Center for Integrative Brain Research, Seattle Children\u2019s Research Institute, Seattle, WA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Emily A.","family":"Brown","sequence":"additional","affiliation":[{"name":"Graduate Program in Neuroscience, University of Washington, Seattle, WA, USA"},{"name":"Center for Integrative Brain Research, Seattle Children\u2019s Research Institute, Seattle, WA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vera","family":"Stamenkovic","sequence":"additional","affiliation":[{"name":"Center for Integrative Brain Research, Seattle Children\u2019s Research Institute, Seattle, WA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Felicia","family":"Harsh","sequence":"additional","affiliation":[{"name":"Center for Integrative Brain Research, Seattle Children\u2019s Research Institute, Seattle, WA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4180-573X","authenticated-orcid":false,"given":"Stephen E.P.","family":"Smith","sequence":"additional","affiliation":[{"name":"Graduate Program in Neuroscience, University of Washington, Seattle, WA, USA"},{"name":"Center for Integrative Brain Research, Seattle Children\u2019s Research Institute, Seattle, WA, USA"},{"name":"Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"key":"2026041123065490000_2025.05.20.655155v1.1","doi-asserted-by":"publisher","DOI":"10.1007\/BF01076771"},{"key":"2026041123065490000_2025.05.20.655155v1.2","doi-asserted-by":"publisher","DOI":"10.1126\/science.1083653"},{"key":"2026041123065490000_2025.05.20.655155v1.3","doi-asserted-by":"publisher","DOI":"10.1016\/j.febslet.2012.04.054"},{"key":"2026041123065490000_2025.05.20.655155v1.4","doi-asserted-by":"publisher","DOI":"10.1002\/2211-5463.13619"},{"key":"2026041123065490000_2025.05.20.655155v1.5","doi-asserted-by":"publisher","DOI":"10.1038\/nature12122"},{"key":"2026041123065490000_2025.05.20.655155v1.6","doi-asserted-by":"publisher","DOI":"10.1016\/j.neuron.2014.09.034"},{"key":"2026041123065490000_2025.05.20.655155v1.7","doi-asserted-by":"crossref","unstructured":"L. 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