{"gene":"SAMTOR","run_date":"2026-06-10T07:46:29","timeline":{"discoveries":[{"year":2017,"finding":"SAMTOR inhibits mTORC1 signaling by directly interacting with GATOR1 (the GAP for RagA/B). SAM binds directly to SAMTOR with a Kd of ~7 μM, disrupting the SAMTOR-GATOR1 complex. Methionine starvation reduces intracellular SAM below this Kd, promoting SAMTOR-GATOR1 association and thereby inhibiting mTORC1. Methionine-induced mTORC1 activation requires the SAM-binding capacity of SAMTOR.","method":"Co-immunoprecipitation, in vitro binding assay (radioligand binding/scintillation counting), metabolomics, loss-of-function (SAMTOR KO/knockdown), mutagenesis of SAM-binding residues, lysosomal localization assay","journal":"Science","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — multiple orthogonal methods (direct binding with Kd measurement, Co-IP, mutagenesis, KO phenotype, metabolomics) in a single rigorous study, widely replicated in subsequent work","pmids":["29123071"],"is_preprint":false},{"year":2022,"finding":"Crystal structures of Drosophila SAMTOR in apo form and in complex with SAM revealed that SAMTOR comprises an N-terminal helical domain and a C-terminal SAM-dependent methyltransferase (MTase) domain. The MTase domain contains the SAM-binding site and the potential GATOR1-KICSTOR-binding site. The helical domain functions as a molecular switch that undergoes conformational change upon SAM binding, modulating the interaction of SAMTOR with the GATOR1-KICSTOR complex. Key residues and the helical domain role were validated by functional assays.","method":"X-ray crystallography (apo and SAM-bound structures), site-directed mutagenesis, functional assays (mTORC1 activity readouts)","journal":"Science advances","confidence":"High","confidence_rationale":"Tier 1 / Moderate — crystal structure with SAM-bound and apo forms, plus mutagenesis validation; single lab but multiple orthogonal methods","pmids":["35776786"],"is_preprint":false},{"year":2026,"finding":"Cryo-EM structure of the KICSTOR-GATOR1-SAMTOR supercomplex (~60-nm crescent-shaped assembly) showed that SAMTOR binds KICSTOR in a manner incompatible with SAM/metabolite binding, providing structural insight into methionine sensing via SAMTOR-KICSTOR association. KICSTOR-GATOR1 forms a dimeric supercomplex that restricts GATOR1 to an orientation favoring the low-affinity active GAP mode of Rag GTPase engagement. Mutations disrupting the GATOR1-KICSTOR interface impair mTORC1 regulation.","method":"Cryo-EM structure determination, mutagenesis of interface residues, mTORC1 activity assays","journal":"Cell","confidence":"High","confidence_rationale":"Tier 1 / Moderate — high-resolution cryo-EM structure with mutagenesis validation and functional readouts in a single rigorous study","pmids":["41512879"],"is_preprint":false},{"year":2021,"finding":"Betaine increases intracellular SAM levels via the methionine cycle, which disrupts the SAMTOR-GATOR1 complex and thereby promotes mTORC1 localization to the lysosomal membrane and activates mTORC1 signaling. SAMTOR overexpression in C2C12 cells displaced mTORC1 from the lysosome and inhibited mTORC1 signaling, an effect attenuated by betaine-mediated SAM elevation.","method":"SAMTOR overexpression in C2C12 cells, lysosomal co-localization assay (mTORC1 membrane tethering), metabolomics (UHPLC for SAM levels), mTORC1 signaling readouts","journal":"Molecular nutrition & food research","confidence":"Medium","confidence_rationale":"Tier 2–3 / Moderate — overexpression with lysosomal localization assay and metabolomics, single lab, two orthogonal methods confirming mechanism","pmids":["34061446"],"is_preprint":false},{"year":2020,"finding":"MAT2A influences SAMTOR expression, and SAMTOR activates mTORC1 and its downstream targets S6K1 and CAD to enhance DNA synthesis in embryo and uterine cells. CBS and MAT2A improve methionine-mediated cell proliferation and DNA synthesis through the SAMTOR/mTORC1/S6K1/CAD pathway.","method":"Gene silencing (CBS, MAT2A), transcriptome analysis, cell adhesion assay, signaling pathway analysis (mTORC1/S6K1/CAD readouts) in Ishikawa, pTr, and JAR cells","journal":"Cell proliferation","confidence":"Medium","confidence_rationale":"Tier 2–3 / Moderate — gene silencing with defined pathway readouts in multiple cell lines, single lab","pmids":["33179842"],"is_preprint":false},{"year":2025,"finding":"SAMTOR directly interacts with phospho-AMPK in prostate cancer cells, and this interaction modulates cell fate under methionine-limited conditions. Methionine deprivation selectively induces vulnerability in AMPK-deficient PC3 cells by disrupting SAMTOR-mTOR signaling and triggering oxidative stress, lipid depletion, and autophagic responses.","method":"Functional assays (methionine deprivation), proteomic analysis, co-interaction assay (SAMTOR–p-AMPK), mTOR signaling readouts in PC3 cells with AMPK deficiency","journal":"Biology","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, single method (proteomic/functional assay), limited mechanistic detail in abstract","pmids":["40427696"],"is_preprint":false},{"year":2023,"finding":"Genetic downregulation of dSAMTOR (Drosophila SAMTOR homologue) in flies caused upregulation of dp70S6K kinase activity (a dTORC1 substrate), confirming dSAMTOR's inhibitory action on the dTORC1/dp70S6K signaling axis in Drosophila brain. One dSAMTOR-targeting scheme caused lethal phenotypes; another caused tissue-specific pathologies.","method":"GAL4/UAS transgenic downregulation of dSAMTOR, PamGene kinase activity profiling, survival and negative geotaxis assays","journal":"International journal of molecular sciences","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic loss-of-function with defined kinase activity readout (dp70S6K), ortholog-based confirmation of inhibitory mechanism, single lab","pmids":["37298625"],"is_preprint":false},{"year":2025,"finding":"A quantitative radioligand-binding protocol using purified SAMTOR protein and radioactive SAM (with scintillation counting) was validated as a generalizable method to determine nutrient sensor–ligand binding affinity (Kd). This method confirmed and operationalized the SAM-SAMTOR binding described in the original discovery paper.","method":"Recombinant protein purification, radioactive ligand binding assay, scintillation counting, mathematical Kd calculation","journal":"Methods in molecular biology","confidence":"Medium","confidence_rationale":"Tier 1 / Weak — rigorous in vitro reconstitution method, single lab, primarily a methods paper confirming prior finding","pmids":["39992509"],"is_preprint":false}],"current_model":"SAMTOR is a cytoplasmic SAM (S-adenosylmethionine) sensor that, in the absence of methionine/SAM, binds the GATOR1-KICSTOR complex via its C-terminal methyltransferase domain to inhibit RagA/B GTPase activity and thereby suppress lysosomal mTORC1 activation; when SAM levels are sufficient (~7 μM Kd), SAM binds SAMTOR's MTase domain, inducing a conformational change in its N-terminal helical domain that disrupts the SAMTOR-KICSTOR interaction and relieves GATOR1-mediated mTORC1 inhibition, linking methionine and one-carbon metabolism to mTORC1-dependent cell growth control."},"narrative":{"mechanistic_narrative":"SAMTOR is a cytoplasmic S-adenosylmethionine (SAM) sensor that couples methionine and one-carbon metabolism to mTORC1-dependent cell growth control by acting as a negative regulator of the pathway [PMID:29123071]. SAM binds directly to SAMTOR with a Kd of ~7 µM; when methionine starvation drops intracellular SAM below this threshold, SAMTOR associates with the GATOR1 complex (the GAP for RagA/B), inhibiting mTORC1, whereas rising SAM disrupts the SAMTOR-GATOR1 interaction and relieves this inhibition, restoring mTORC1 lysosomal recruitment and signaling [PMID:29123071, PMID:34061446]. Structurally, SAMTOR comprises an N-terminal helical domain and a C-terminal SAM-dependent methyltransferase (MTase) domain that carries both the SAM-binding site and the GATOR1-KICSTOR-binding surface; SAM binding drives a conformational switch in the helical domain that modulates engagement of the GATOR1-KICSTOR complex [PMID:35776786]. Within the assembled KICSTOR-GATOR1-SAMTOR supercomplex, SAMTOR binds KICSTOR in a manner mutually exclusive with SAM/metabolite binding, and this architecture restrains GATOR1 in an orientation favoring active GAP engagement of the Rag GTPases [PMID:41512879]. Through this SAM-gated switch SAMTOR controls downstream mTORC1 effectors including S6K1 and CAD, linking methionine availability to DNA synthesis and proliferation [PMID:33179842]; the inhibitory role is conserved in Drosophila, where dSAMTOR knockdown elevates dp70S6K activity [PMID:37298625].","teleology":[{"year":2017,"claim":"Established SAMTOR as the molecular sensor that converts intracellular SAM levels into mTORC1 activity, answering how methionine status is read by the growth machinery.","evidence":"Co-IP, in vitro radioligand binding with Kd determination, metabolomics, SAMTOR KO/knockdown, SAM-binding mutagenesis, and lysosomal localization assays","pmids":["29123071"],"confidence":"High","gaps":["Did not resolve the structural basis of the SAM-induced conformational change","GATOR1 vs KICSTOR contributions to the binding interface not separated"]},{"year":2021,"claim":"Showed that a physiological metabolic input (betaine) raises SAM to disrupt the SAMTOR-GATOR1 complex and drive mTORC1 to the lysosome, connecting dietary one-carbon flux to the sensor.","evidence":"SAMTOR overexpression in C2C12 cells, lysosomal co-localization of mTORC1, UHPLC metabolomics for SAM, and signaling readouts","pmids":["34061446"],"confidence":"Medium","gaps":["Relies on overexpression rather than endogenous SAMTOR","Does not establish direct SAM binding under the betaine condition"]},{"year":2020,"claim":"Placed SAMTOR within a methionine-cycle proliferation axis, linking it to MAT2A/CBS upstream and S6K1/CAD-driven DNA synthesis downstream.","evidence":"Gene silencing of CBS and MAT2A with transcriptome and mTORC1/S6K1/CAD pathway readouts in Ishikawa, pTr, and JAR cells","pmids":["33179842"],"confidence":"Medium","gaps":["Correlational link between MAT2A and SAMTOR expression, not a direct biochemical mechanism","Direction of SAMTOR's effect on mTORC1 here differs from canonical inhibitory role and is not reconciled"]},{"year":2022,"claim":"Defined the two-domain architecture of SAMTOR and identified the helical domain as the SAM-responsive molecular switch governing GATOR1-KICSTOR engagement.","evidence":"X-ray crystallography of apo and SAM-bound Drosophila SAMTOR with site-directed mutagenesis and mTORC1 activity assays","pmids":["35776786"],"confidence":"High","gaps":["Structures are of the Drosophila ortholog, not human SAMTOR","No structure of SAMTOR bound to GATOR1-KICSTOR in this study"]},{"year":2023,"claim":"Confirmed evolutionary conservation of SAMTOR's inhibitory function by showing dSAMTOR loss derepresses dTORC1 signaling in vivo.","evidence":"GAL4/UAS transgenic dSAMTOR downregulation in Drosophila with PamGene dp70S6K kinase profiling and behavioral/survival assays","pmids":["37298625"],"confidence":"Medium","gaps":["SAM-dependence of the in vivo phenotype not directly tested","Tissue-specific versus lethal phenotypes from different RNAi schemes not mechanistically explained"]},{"year":2025,"claim":"Probed a context-specific role for SAMTOR in cancer, linking it to phospho-AMPK and methionine-deprivation vulnerability.","evidence":"Methionine deprivation, proteomics, and SAMTOR-p-AMPK co-interaction assays in AMPK-deficient PC3 prostate cancer cells","pmids":["40427696"],"confidence":"Low","gaps":["Single-lab, single-method co-interaction without reciprocal or structural validation","Functional consequence of the SAMTOR-p-AMPK interaction not mechanistically dissected"]},{"year":2025,"claim":"Operationalized the SAM-SAMTOR binding measurement into a generalizable quantitative protocol, reinforcing the affinity-based sensing model.","evidence":"Recombinant SAMTOR purification, radioactive SAM binding with scintillation counting, and mathematical Kd calculation","pmids":["39992509"],"confidence":"Medium","gaps":["A methods/validation paper rather than new mechanistic insight","Does not extend binding analysis to mutants or other ligands"]},{"year":2026,"claim":"Resolved the full KICSTOR-GATOR1-SAMTOR supercomplex, explaining how SAMTOR's KICSTOR binding is mutually exclusive with metabolite sensing and orients GATOR1 for active GAP function.","evidence":"Cryo-EM structure determination of the ~60-nm supercomplex with interface mutagenesis and mTORC1 activity assays","pmids":["41512879"],"confidence":"High","gaps":["Captures a single conformational state; dynamics of the SAM-driven transition not visualized","How SAM binding allosterically displaces SAMTOR from KICSTOR not directly observed"]},{"year":null,"claim":"How the SAM-induced helical-domain switch is transmitted in real time to displace SAMTOR from the KICSTOR-GATOR1 supercomplex, and how SAMTOR signaling integrates with AMPK and proliferative pathways in disease, remain unresolved.","evidence":"","pmids":[],"confidence":"Low","gaps":["No time-resolved or human full-length structure capturing the SAM-bound-to-displaced transition","SAMTOR-AMPK crosstalk lacks mechanistic depth","Whether SAMTOR's MTase domain has any catalytic activity is unaddressed"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140299","term_label":"molecular sensor activity","supporting_discovery_ids":[0,1,7]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[0,2]}],"localization":[{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[0]}],"pathway":[{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[0,2]},{"term_id":"R-HSA-1430728","term_label":"Metabolism","supporting_discovery_ids":[0,3,4]}],"complexes":["KICSTOR-GATOR1-SAMTOR supercomplex"],"partners":["GATOR1","KICSTOR","AMPK"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q1RMZ1","full_name":"S-adenosylmethionine sensor upstream of mTORC1","aliases":["Probable methyltransferase BMT2 homolog"],"length_aa":405,"mass_kda":46.3,"function":"S-adenosyl-L-methionine-binding protein that acts as an inhibitor of mTORC1 signaling via interaction with the GATOR1 and KICSTOR complexes (PubMed:29123071, PubMed:35776786). Acts as a sensor of S-adenosyl-L-methionine to signal methionine sufficiency to mTORC1: in presence of methionine, binds S-adenosyl-L-methionine, leading to disrupt interaction with the GATOR1 and KICSTOR complexes and promote mTORC1 signaling (PubMed:29123071, PubMed:35776786). Upon methionine starvation, S-adenosyl-L-methionine levels are reduced, thereby promoting the association with GATOR1 and KICSTOR, leading to inhibit mTORC1 signaling (PubMed:29123071, PubMed:35776786). Probably also acts as a S-adenosyl-L-methionine-dependent methyltransferase (Potential)","subcellular_location":"","url":"https://www.uniprot.org/uniprotkb/Q1RMZ1/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/SAMTOR","classification":"Not Classified","n_dependent_lines":1,"n_total_lines":1208,"dependency_fraction":0.0008278145695364238},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/SAMTOR","total_profiled":1310},"omim":[{"mim_id":"617855","title":"BASE METHYLTRANSFERASE OF 25S rRNA 2 HOMOLOG; BMT2","url":"https://www.omim.org/entry/617855"},{"mim_id":"617421","title":"INTEGRIN-ALPHA FG-GAP REPEAT-CONTAINING PROTEIN 2; ITFG2","url":"https://www.omim.org/entry/617421"},{"mim_id":"617420","title":"KICSTOR SUBUNIT 2; KICS2","url":"https://www.omim.org/entry/617420"},{"mim_id":"615620","title":"KAPTIN; KPTN","url":"https://www.omim.org/entry/615620"},{"mim_id":"615463","title":"SZT2 SUBUNIT OF KICSTOR COMPLEX; SZT2","url":"https://www.omim.org/entry/615463"}],"hpa":{"profiled":true,"resolved_as":"BMT2","reliability":"Approved","locations":[{"location":"Cytosol","reliability":"Approved"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/BMT2"},"hgnc":{"alias_symbol":["DKFZp762M126","FLJ31818","SAMTOR"],"prev_symbol":["BMT2","C7orf60"]},"alphafold":{"accession":"Q1RMZ1","domains":[{"cath_id":"3.40.50.150","chopping":"96-117_162-346","consensus_level":"high","plddt":92.8375,"start":96,"end":346},{"cath_id":"1.10.287","chopping":"27-86","consensus_level":"medium","plddt":91.3198,"start":27,"end":86}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q1RMZ1","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q1RMZ1-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q1RMZ1-F1-predicted_aligned_error_v6.png","plddt_mean":79.25},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=SAMTOR","jax_strain_url":"https://www.jax.org/strain/search?query=SAMTOR"},"sequence":{"accession":"Q1RMZ1","fasta_url":"https://rest.uniprot.org/uniprotkb/Q1RMZ1.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q1RMZ1/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q1RMZ1"}},"corpus_meta":[{"pmid":"29123071","id":"PMC_29123071","title":"SAMTOR 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SAM binds directly to SAMTOR with a Kd of ~7 μM, disrupting the SAMTOR-GATOR1 complex. Methionine starvation reduces intracellular SAM below this Kd, promoting SAMTOR-GATOR1 association and thereby inhibiting mTORC1. Methionine-induced mTORC1 activation requires the SAM-binding capacity of SAMTOR.\",\n      \"method\": \"Co-immunoprecipitation, in vitro binding assay (radioligand binding/scintillation counting), metabolomics, loss-of-function (SAMTOR KO/knockdown), mutagenesis of SAM-binding residues, lysosomal localization assay\",\n      \"journal\": \"Science\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — multiple orthogonal methods (direct binding with Kd measurement, Co-IP, mutagenesis, KO phenotype, metabolomics) in a single rigorous study, widely replicated in subsequent work\",\n      \"pmids\": [\"29123071\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"Crystal structures of Drosophila SAMTOR in apo form and in complex with SAM revealed that SAMTOR comprises an N-terminal helical domain and a C-terminal SAM-dependent methyltransferase (MTase) domain. The MTase domain contains the SAM-binding site and the potential GATOR1-KICSTOR-binding site. The helical domain functions as a molecular switch that undergoes conformational change upon SAM binding, modulating the interaction of SAMTOR with the GATOR1-KICSTOR complex. Key residues and the helical domain role were validated by functional assays.\",\n      \"method\": \"X-ray crystallography (apo and SAM-bound structures), site-directed mutagenesis, functional assays (mTORC1 activity readouts)\",\n      \"journal\": \"Science advances\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — crystal structure with SAM-bound and apo forms, plus mutagenesis validation; single lab but multiple orthogonal methods\",\n      \"pmids\": [\"35776786\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"Cryo-EM structure of the KICSTOR-GATOR1-SAMTOR supercomplex (~60-nm crescent-shaped assembly) showed that SAMTOR binds KICSTOR in a manner incompatible with SAM/metabolite binding, providing structural insight into methionine sensing via SAMTOR-KICSTOR association. KICSTOR-GATOR1 forms a dimeric supercomplex that restricts GATOR1 to an orientation favoring the low-affinity active GAP mode of Rag GTPase engagement. Mutations disrupting the GATOR1-KICSTOR interface impair mTORC1 regulation.\",\n      \"method\": \"Cryo-EM structure determination, mutagenesis of interface residues, mTORC1 activity assays\",\n      \"journal\": \"Cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — high-resolution cryo-EM structure with mutagenesis validation and functional readouts in a single rigorous study\",\n      \"pmids\": [\"41512879\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"Betaine increases intracellular SAM levels via the methionine cycle, which disrupts the SAMTOR-GATOR1 complex and thereby promotes mTORC1 localization to the lysosomal membrane and activates mTORC1 signaling. SAMTOR overexpression in C2C12 cells displaced mTORC1 from the lysosome and inhibited mTORC1 signaling, an effect attenuated by betaine-mediated SAM elevation.\",\n      \"method\": \"SAMTOR overexpression in C2C12 cells, lysosomal co-localization assay (mTORC1 membrane tethering), metabolomics (UHPLC for SAM levels), mTORC1 signaling readouts\",\n      \"journal\": \"Molecular nutrition & food research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 / Moderate — overexpression with lysosomal localization assay and metabolomics, single lab, two orthogonal methods confirming mechanism\",\n      \"pmids\": [\"34061446\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"MAT2A influences SAMTOR expression, and SAMTOR activates mTORC1 and its downstream targets S6K1 and CAD to enhance DNA synthesis in embryo and uterine cells. CBS and MAT2A improve methionine-mediated cell proliferation and DNA synthesis through the SAMTOR/mTORC1/S6K1/CAD pathway.\",\n      \"method\": \"Gene silencing (CBS, MAT2A), transcriptome analysis, cell adhesion assay, signaling pathway analysis (mTORC1/S6K1/CAD readouts) in Ishikawa, pTr, and JAR cells\",\n      \"journal\": \"Cell proliferation\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 / Moderate — gene silencing with defined pathway readouts in multiple cell lines, single lab\",\n      \"pmids\": [\"33179842\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"SAMTOR directly interacts with phospho-AMPK in prostate cancer cells, and this interaction modulates cell fate under methionine-limited conditions. Methionine deprivation selectively induces vulnerability in AMPK-deficient PC3 cells by disrupting SAMTOR-mTOR signaling and triggering oxidative stress, lipid depletion, and autophagic responses.\",\n      \"method\": \"Functional assays (methionine deprivation), proteomic analysis, co-interaction assay (SAMTOR–p-AMPK), mTOR signaling readouts in PC3 cells with AMPK deficiency\",\n      \"journal\": \"Biology\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, single method (proteomic/functional assay), limited mechanistic detail in abstract\",\n      \"pmids\": [\"40427696\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"Genetic downregulation of dSAMTOR (Drosophila SAMTOR homologue) in flies caused upregulation of dp70S6K kinase activity (a dTORC1 substrate), confirming dSAMTOR's inhibitory action on the dTORC1/dp70S6K signaling axis in Drosophila brain. One dSAMTOR-targeting scheme caused lethal phenotypes; another caused tissue-specific pathologies.\",\n      \"method\": \"GAL4/UAS transgenic downregulation of dSAMTOR, PamGene kinase activity profiling, survival and negative geotaxis assays\",\n      \"journal\": \"International journal of molecular sciences\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic loss-of-function with defined kinase activity readout (dp70S6K), ortholog-based confirmation of inhibitory mechanism, single lab\",\n      \"pmids\": [\"37298625\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"A quantitative radioligand-binding protocol using purified SAMTOR protein and radioactive SAM (with scintillation counting) was validated as a generalizable method to determine nutrient sensor–ligand binding affinity (Kd). This method confirmed and operationalized the SAM-SAMTOR binding described in the original discovery paper.\",\n      \"method\": \"Recombinant protein purification, radioactive ligand binding assay, scintillation counting, mathematical Kd calculation\",\n      \"journal\": \"Methods in molecular biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Weak — rigorous in vitro reconstitution method, single lab, primarily a methods paper confirming prior finding\",\n      \"pmids\": [\"39992509\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"SAMTOR is a cytoplasmic SAM (S-adenosylmethionine) sensor that, in the absence of methionine/SAM, binds the GATOR1-KICSTOR complex via its C-terminal methyltransferase domain to inhibit RagA/B GTPase activity and thereby suppress lysosomal mTORC1 activation; when SAM levels are sufficient (~7 μM Kd), SAM binds SAMTOR's MTase domain, inducing a conformational change in its N-terminal helical domain that disrupts the SAMTOR-KICSTOR interaction and relieves GATOR1-mediated mTORC1 inhibition, linking methionine and one-carbon metabolism to mTORC1-dependent cell growth control.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"SAMTOR is a cytoplasmic S-adenosylmethionine (SAM) sensor that couples methionine and one-carbon metabolism to mTORC1-dependent cell growth control by acting as a negative regulator of the pathway [#0]. SAM binds directly to SAMTOR with a Kd of ~7 \\u00b5M; when methionine starvation drops intracellular SAM below this threshold, SAMTOR associates with the GATOR1 complex (the GAP for RagA/B), inhibiting mTORC1, whereas rising SAM disrupts the SAMTOR-GATOR1 interaction and relieves this inhibition, restoring mTORC1 lysosomal recruitment and signaling [#0, #3]. Structurally, SAMTOR comprises an N-terminal helical domain and a C-terminal SAM-dependent methyltransferase (MTase) domain that carries both the SAM-binding site and the GATOR1-KICSTOR-binding surface; SAM binding drives a conformational switch in the helical domain that modulates engagement of the GATOR1-KICSTOR complex [#1]. Within the assembled KICSTOR-GATOR1-SAMTOR supercomplex, SAMTOR binds KICSTOR in a manner mutually exclusive with SAM/metabolite binding, and this architecture restrains GATOR1 in an orientation favoring active GAP engagement of the Rag GTPases [#2]. Through this SAM-gated switch SAMTOR controls downstream mTORC1 effectors including S6K1 and CAD, linking methionine availability to DNA synthesis and proliferation [#4]; the inhibitory role is conserved in Drosophila, where dSAMTOR knockdown elevates dp70S6K activity [#6].\"\n  ,\n  \"teleology\": [\n    {\n      \"year\": 2017,\n      \"claim\": \"Established SAMTOR as the molecular sensor that converts intracellular SAM levels into mTORC1 activity, answering how methionine status is read by the growth machinery.\",\n      \"evidence\": \"Co-IP, in vitro radioligand binding with Kd determination, metabolomics, SAMTOR KO/knockdown, SAM-binding mutagenesis, and lysosomal localization assays\",\n      \"pmids\": [\"29123071\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not resolve the structural basis of the SAM-induced conformational change\", \"GATOR1 vs KICSTOR contributions to the binding interface not separated\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Showed that a physiological metabolic input (betaine) raises SAM to disrupt the SAMTOR-GATOR1 complex and drive mTORC1 to the lysosome, connecting dietary one-carbon flux to the sensor.\",\n      \"evidence\": \"SAMTOR overexpression in C2C12 cells, lysosomal co-localization of mTORC1, UHPLC metabolomics for SAM, and signaling readouts\",\n      \"pmids\": [\"34061446\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Relies on overexpression rather than endogenous SAMTOR\", \"Does not establish direct SAM binding under the betaine condition\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Placed SAMTOR within a methionine-cycle proliferation axis, linking it to MAT2A/CBS upstream and S6K1/CAD-driven DNA synthesis downstream.\",\n      \"evidence\": \"Gene silencing of CBS and MAT2A with transcriptome and mTORC1/S6K1/CAD pathway readouts in Ishikawa, pTr, and JAR cells\",\n      \"pmids\": [\"33179842\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Correlational link between MAT2A and SAMTOR expression, not a direct biochemical mechanism\", \"Direction of SAMTOR's effect on mTORC1 here differs from canonical inhibitory role and is not reconciled\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Defined the two-domain architecture of SAMTOR and identified the helical domain as the SAM-responsive molecular switch governing GATOR1-KICSTOR engagement.\",\n      \"evidence\": \"X-ray crystallography of apo and SAM-bound Drosophila SAMTOR with site-directed mutagenesis and mTORC1 activity assays\",\n      \"pmids\": [\"35776786\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structures are of the Drosophila ortholog, not human SAMTOR\", \"No structure of SAMTOR bound to GATOR1-KICSTOR in this study\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Confirmed evolutionary conservation of SAMTOR's inhibitory function by showing dSAMTOR loss derepresses dTORC1 signaling in vivo.\",\n      \"evidence\": \"GAL4/UAS transgenic dSAMTOR downregulation in Drosophila with PamGene dp70S6K kinase profiling and behavioral/survival assays\",\n      \"pmids\": [\"37298625\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"SAM-dependence of the in vivo phenotype not directly tested\", \"Tissue-specific versus lethal phenotypes from different RNAi schemes not mechanistically explained\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Probed a context-specific role for SAMTOR in cancer, linking it to phospho-AMPK and methionine-deprivation vulnerability.\",\n      \"evidence\": \"Methionine deprivation, proteomics, and SAMTOR-p-AMPK co-interaction assays in AMPK-deficient PC3 prostate cancer cells\",\n      \"pmids\": [\"40427696\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Single-lab, single-method co-interaction without reciprocal or structural validation\", \"Functional consequence of the SAMTOR-p-AMPK interaction not mechanistically dissected\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Operationalized the SAM-SAMTOR binding measurement into a generalizable quantitative protocol, reinforcing the affinity-based sensing model.\",\n      \"evidence\": \"Recombinant SAMTOR purification, radioactive SAM binding with scintillation counting, and mathematical Kd calculation\",\n      \"pmids\": [\"39992509\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"A methods/validation paper rather than new mechanistic insight\", \"Does not extend binding analysis to mutants or other ligands\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Resolved the full KICSTOR-GATOR1-SAMTOR supercomplex, explaining how SAMTOR's KICSTOR binding is mutually exclusive with metabolite sensing and orients GATOR1 for active GAP function.\",\n      \"evidence\": \"Cryo-EM structure determination of the ~60-nm supercomplex with interface mutagenesis and mTORC1 activity assays\",\n      \"pmids\": [\"41512879\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Captures a single conformational state; dynamics of the SAM-driven transition not visualized\", \"How SAM binding allosterically displaces SAMTOR from KICSTOR not directly observed\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How the SAM-induced helical-domain switch is transmitted in real time to displace SAMTOR from the KICSTOR-GATOR1 supercomplex, and how SAMTOR signaling integrates with AMPK and proliferative pathways in disease, remain unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No time-resolved or human full-length structure capturing the SAM-bound-to-displaced transition\", \"SAMTOR-AMPK crosstalk lacks mechanistic depth\", \"Whether SAMTOR's MTase domain has any catalytic activity is unaddressed\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140299\", \"supporting_discovery_ids\": [0, 1, 7]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [0, 2]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [0, 2]},\n      {\"term_id\": \"R-HSA-1430728\", \"supporting_discovery_ids\": [0, 3, 4]}\n    ],\n    \"complexes\": [\"KICSTOR-GATOR1-SAMTOR supercomplex\"],\n    \"partners\": [\"GATOR1\", \"KICSTOR\", \"AMPK\"],\n    \"other_free_text\": []\n  }\n}\n```","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":5,"faith_total":5,"faith_pct":100.0}}