{"gene":"PALS1","run_date":"2026-06-10T05:19:53","timeline":{"discoveries":[{"year":2002,"finding":"PALS1 L27N domain binds PATJ (mammalian Discs Lost homologue) via a unique Maguk recruitment domain, targeting PALS1 to tight junctions; PALS1 L27C domain binds mLin-7; and the PALS1 PDZ domain binds CRB1 (human Crumbs homologue), forming a conserved multiprotein polarity complex.","method":"Co-immunoprecipitation, pulldown assays, domain mapping, colocalization by confocal microscopy","journal":"The Journal of cell biology","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal Co-IP and domain-level mapping, independently replicated in Drosophila system, foundational paper widely confirmed","pmids":["11927608"],"is_preprint":false},{"year":2003,"finding":"Overexpression of dominant-negative Myc-Lin-2-Pals1 chimera (PDZ domain of Pals1 replacing Lin-2 PDZ) in MDCK cells causes tight junction formation delays and apical polarity defects, demonstrating that the CRB3-Pals1 PDZ interaction is required for tight junction formation and epithelial polarization.","method":"Dominant-negative overexpression, calcium switch assay, MDCK cyst morphogenesis assay, confocal microscopy","journal":"Journal of cell science","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal functional assays (TJ formation, cyst morphogenesis, dominant-negative rescue), replicated in same lab with complementary data","pmids":["12771187"],"is_preprint":false},{"year":2003,"finding":"CRB3 (Crumbs3) interacts with PALS1 through its conserved intracellular domain, and this complex also includes PATJ; CRB3 localizes to the apical surface and tight junctions of epithelial cells.","method":"Co-immunoprecipitation, subcellular fractionation, confocal microscopy, mutagenesis of CRB3 intracellular domain","journal":"Gene","confidence":"High","confidence_rationale":"Tier 2 / Strong — Co-IP with domain mutagenesis, consistent with concurrent papers from independent groups","pmids":["12527193"],"is_preprint":false},{"year":2004,"finding":"siRNA-mediated knockdown of PALS1 in MDCKII cells causes loss of PATJ expression (a known binding partner), decreased association of CRB3 with Par6/Par3/aPKC complex, failure to recruit aPKC to tight junctions, delayed polarization after calcium switch, decreased transepithelial electrical resistance, and inability to form lumenal cysts.","method":"Stable siRNA knockdown, calcium switch assay, transepithelial electrical resistance measurement, 3D collagen cyst assay, confocal microscopy","journal":"Molecular biology of the cell","confidence":"High","confidence_rationale":"Tier 2 / Strong — clean loss-of-function with multiple orthogonal phenotypic readouts and defined molecular pathway placement","pmids":["14718565"],"is_preprint":false},{"year":2004,"finding":"Par-6 PDZ domain binds an internal (non-C-terminal) sequence in PALS1/Stardust amino terminus; crystal structure of the Par-6 PDZ-Pals1 complex shows the PDZ ligand-binding site is deformed to accommodate internal binding; Cdc42 binding to the Par-6 CRIB domain regulates C-terminal ligand binding but not Pals1 internal binding.","method":"Crystal structure determination, binding assays, mutagenesis","journal":"Nature structural & molecular biology","confidence":"High","confidence_rationale":"Tier 1 / Strong — crystal structure with mutagenesis and binding assays, clear mechanistic insight into PDZ plasticity","pmids":["15475968"],"is_preprint":false},{"year":2004,"finding":"Par-6 binds an evolutionarily conserved region in the amino terminus of PALS1 via the Par-6 PDZ domain; valine and aspartic acid residues in this PALS1 region are essential for the interaction; Par-6 and PATJ compete for binding to PALS1 (Par-6 interferes with PATJ binding) and do not act synergistically.","method":"Mutagenesis, GST pulldown, co-immunoprecipitation, competitive binding assays","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 2 / Strong — mutagenesis identifying essential residues plus competition binding assays, evolutionarily conserved mechanism validated in Drosophila","pmids":["15140881"],"is_preprint":false},{"year":2004,"finding":"PALS1 interacts with the neuronal GABA transporter GAT1 via the PALS1 PDZ domain (identified by yeast two-hybrid and confirmed by co-immunoprecipitation in COS-7 cells); coexpression of PALS1 with GAT1 increases [3H]-GABA uptake by increasing GAT1 protein levels.","method":"Yeast two-hybrid, co-immunoprecipitation, [3H]-GABA uptake assay, immunofluorescence","journal":"Molecular and cellular neurosciences","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — single lab, yeast two-hybrid confirmed by Co-IP and functional uptake assay, but mechanism of protein stabilization not fully defined","pmids":["15234345"],"is_preprint":false},{"year":2005,"finding":"MPP5/PALS1 directly interacts with MPP4 via L27 heterodimerization; MPP4 is recruited to the CRB1 complex through its interaction with MPP5; all three proteins colocalize at the outer limiting membrane of the retina.","method":"Yeast two-hybrid, GST pulldown, co-immunoprecipitation, immunohistochemistry, immunoelectron microscopy, 3D homology modeling","journal":"Investigative ophthalmology & visual science","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal binding methods plus in situ localization in retinal tissue","pmids":["15914641"],"is_preprint":false},{"year":2005,"finding":"PALS1 interacts with ezrin via the ezrin N-terminus and PALS1 is required for apical localization of ezrin in gastric parietal cells; disruption of this interaction (by PALS1 suppression or deletion of PALS1-binding domain in ezrin) eliminates apical ezrin localization and impairs apical membrane remodeling during parietal cell secretion.","method":"Co-immunoprecipitation, siRNA knockdown, domain deletion, confocal microscopy, functional secretion assay","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal binding assays, loss-of-function with specific functional readout, and domain mapping","pmids":["15677456"],"is_preprint":false},{"year":2005,"finding":"NMR solution structures of the L27 domain complexes of Patj/Pals1 (and mLin-2/mLin-7) reveal a tetrameric assembly (two heterodimers); the C-terminal alpha-helix of each L27 domain forms a central helix bundle critical for partner specificity.","method":"NMR structure determination, biochemical binding assays, mutagenesis","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 1 / Strong — NMR structure with biochemical validation and mutagenesis of specificity determinants","pmids":["15863617"],"is_preprint":false},{"year":2005,"finding":"MPP5 (PALS1) and MPP4 localize to distinct sites in the mouse retina: MPP5 exclusively at apical outer limiting membrane junctions, MPP4 at photoreceptor synaptic terminals; MPP4 directly interacts with Veli proteins (Veli1, -3) via L27 heterodimerization in vitro, and Veli3 colocalizes with both MPP4 and MPP5.","method":"Immunofluorescence microscopy, L27 heterodimerization in vitro binding assay, antibody generation and immunohistochemistry","journal":"The Journal of comparative neurology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct localization experiments with functional context, in vitro binding assay; single lab","pmids":["15558731"],"is_preprint":false},{"year":2005,"finding":"In zebrafish, nagie oko (nok)/Mpp5 (PALS1 ortholog) is required tissue-autonomously within myocardial cells for polarized epithelial organization and coherence during heart cone formation, and for myocardial cell expansion during heart tube elongation; Has/PRKCi (aPKC) and Nok/Mpp5 act together in myocardial morphogenesis.","method":"Genetic epistasis in zebrafish, tissue-specific rescue experiments, confocal microscopy of myocardial cell organization","journal":"Development (Cambridge, England)","confidence":"High","confidence_rationale":"Tier 2 / Strong — genetic loss-of-function in zebrafish with tissue-autonomous rescue, multiple morphogenetic phenotypic readouts","pmids":["16319113"],"is_preprint":false},{"year":2006,"finding":"MPP3 directly interacts with MPP5/PALS1 and is recruited to the CRB1/MPP5 scaffold at the outer limiting membrane of the retina; MPP3 also forms separate complexes with DLG1 at the outer plexiform layer.","method":"Co-immunoprecipitation, immunohistochemistry in human and mouse retinas, localization studies","journal":"The FEBS journal","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — Co-IP plus localization, single lab, no mutagenesis or reconstitution","pmids":["16519681"],"is_preprint":false},{"year":2006,"finding":"siRNA silencing of Pals1 in Müller glia cells results in loss of Crb1, Crb2, Mupp1, and Veli3 protein localization at the subapical region (SAR) and partial loss of Crb3, demonstrating that Pals1 is required for correct localization of Crb family members and associated proteins at the SAR of polarized Müller glia.","method":"RNAi knockdown in primary retinal cultures, immunoelectron microscopy, confocal microscopy","journal":"Human molecular genetics","confidence":"High","confidence_rationale":"Tier 2 / Strong — loss-of-function with multiple readouts, immunoelectron microscopy for precise localization, clean knockdown phenotype","pmids":["16885194"],"is_preprint":false},{"year":2006,"finding":"PALS1 knockdown in MDCK cells causes not only tight junction defects but also severe adherens junction defects; E-cadherin fails to be delivered to the cell surface and accumulates in peripheral puncta; the exocyst complex is mislocalized in PALS1 knockdown cells, suggesting PALS1 regulates E-cadherin trafficking via the exocyst.","method":"Stable siRNA knockdown, rescue with PALS1 mutants, E-cadherin surface biotinylation, confocal microscopy of exocyst and E-cadherin localization","journal":"Molecular biology of the cell","confidence":"High","confidence_rationale":"Tier 2 / Strong — loss-of-function with multiple orthogonal readouts, rescue experiments with mutants, defined trafficking mechanism","pmids":["17182851"],"is_preprint":false},{"year":2007,"finding":"EPB41L5 (a FERM domain protein) associates with the HOOK domain of MPP5/PALS1 and with the intracellular domains of all three Crumbs homologs via its FERM domain, forming a novel component of the mammalian CRB-MPP5 polarity complex; overexpression of EPB41L5 in MDCK cells disrupts ZO-1 and PATJ localization.","method":"Co-immunoprecipitation, co-expression studies, co-localization, overexpression functional assay in MDCK cells","journal":"Experimental cell research","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — Co-IP and functional overexpression, single lab, domain identified","pmids":["17920587"],"is_preprint":false},{"year":2009,"finding":"Nephrocystin-1 (NPHP1) and nephrocystin-4 (NPHP4) physically interact with PALS1, PATJ, and Par6; shRNA knockdown of NPHP1 or NPHP4 in MDCK cells phenocopies PALS1 depletion (delayed TJ formation, abnormal cilia, multi-lumen cysts), placing nephrocystins in the same polarity pathway as PALS1.","method":"Co-immunoprecipitation, shRNA knockdown, tight junction formation assay, 3D collagen matrix cyst assay, cilia analysis","journal":"Human molecular genetics","confidence":"High","confidence_rationale":"Tier 2 / Strong — Co-IP plus epistatic loss-of-function with phenotypic similarity to PALS1 depletion, multiple orthogonal readouts","pmids":["19755384"],"is_preprint":false},{"year":2010,"finding":"The SARS-CoV E protein C-terminal PDZ-binding motif (last four amino acids) binds the PALS1 PDZ domain; in SARS-CoV-infected cells, PALS1 redistributes to the ERGIC/Golgi region where E accumulates; ectopic expression of E in MDCKII cells delays tight junction formation and disrupts polarity and PALS1 distribution in a PDZ-binding motif-dependent manner.","method":"Co-immunoprecipitation, GST pulldown, confocal microscopy in infected cells, MDCKII cyst morphogenesis assay, PDZ-binding motif mutant","journal":"Molecular biology of the cell","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal pulldowns plus viral infection model and PDZ motif mutagenesis with functional consequence","pmids":["20861307"],"is_preprint":false},{"year":2010,"finding":"Pals1 is required in myelinating Schwann cells for normal myelin sheath thickness and length; silencing of pals1 in vivo reduces myelin turns without grossly disrupting compact myelin; pals1 is required for polarized localization of vesicular markers sec8 and syntaxin4, and for distribution of E-cadherin, PMP22, and MAG at the plasma membrane, suggesting a role in membrane protein trafficking in Schwann cells.","method":"In vivo siRNA silencing in Schwann cells, electron microscopy, confocal microscopy, immunostaining for polarity and vesicular markers","journal":"The Journal of neuroscience","confidence":"High","confidence_rationale":"Tier 2 / Strong — in vivo loss-of-function with multiple ultrastructural and molecular readouts","pmids":["20237282"],"is_preprint":false},{"year":2011,"finding":"PALS1 conditional knockdown in mice results in loss of Crumbs complex proteins at adherens junctions in the retina, progressive photoreceptor degeneration, abnormal retinal pigment epithelium structure, ectopic photoreceptors, and irregular outer limiting membrane, demonstrating an essential structural role for PALS1 in maintaining the CRB complex and retinal architecture.","method":"Conditional knockdown mouse model, electroretinography, confocal scanning laser ophthalmoscopy, optical coherence tomography, immunohistochemistry","journal":"The Journal of neuroscience","confidence":"High","confidence_rationale":"Tier 2 / Strong — in vivo conditional loss-of-function with multiple complementary structural and functional readouts","pmids":["22114289"],"is_preprint":false},{"year":2011,"finding":"PALS1 participates in TCR-mediated NF-κB activation in T lymphocytes; siRNA knockdown of PALS1 in Jurkat cells and primary T cells specifically impairs TCR-induced NF-κB activation and optimal lymphocyte proliferation.","method":"siRNA knockdown, NF-κB reporter assay, proliferation assay, RT-PCR, immunoblot","journal":"PloS one","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — siRNA knockdown with specific NF-κB readout, single lab, mechanism of NF-κB coupling not defined","pmids":["21479189"],"is_preprint":false},{"year":2012,"finding":"Deletion of Pals1 in retinal progenitor cells disrupts apical localization of Crb proteins and causes early visual impairment, disorganized retinal lamination, and retinal degeneration mimicking Leber congenital amaurosis; Pals1 and Crb proteins are functionally interdependent for apical localization.","method":"Conditional Pals1 knockout mouse, electroretinogram, confocal microscopy, immunohistochemistry","journal":"Human molecular genetics","confidence":"High","confidence_rationale":"Tier 2 / Strong — in vivo conditional knockout with functional and structural readouts, confirmed mutual dependence of Pals1 and Crb proteins","pmids":["22398208"],"is_preprint":false},{"year":2012,"finding":"Crystal structure of L27 domain heterotrimer from Patj/Pals1/Mals2 reveals two cognate heterodimeric L27 pairs that assemble mutually independently, providing a novel mechanism for tandem L27 domain-mediated supramolecular complex assembly.","method":"Crystal structure determination, biochemical binding assays","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 / Strong — crystal structure with biochemical validation, defines assembly mechanism of the tripartite complex","pmids":["22337881"],"is_preprint":false},{"year":2013,"finding":"MPP3 directly interacts with PALS1/MPP5 and is required for maintaining proper levels of PALS1 at the subapical region adjacent to adherens junctions; loss of MPP3 in mice causes significant loss of PALS1 at the subapical region, and combined loss of MPP3 and Pals1 accelerates retinal degeneration.","method":"Conditional Mpp3 knockout mouse, immunofluorescence, co-immunoprecipitation, electroretinography, double-mutant genetic analysis","journal":"Glia","confidence":"High","confidence_rationale":"Tier 2 / Strong — in vivo knockout with molecular and functional readouts, genetic epistasis via double knockout","pmids":["23893895"],"is_preprint":false},{"year":2014,"finding":"Crystal structure of PALS1 PDZ-SH3-GK tandem bound to the Crumbs cytoplasmic tail (Crb-CT) shows the three domains form a structural supramodule; all three domains contribute to binding with ~70 nM affinity (~100-fold stronger than PDZ alone); mutations disrupting interdomain contacts weaken PALS1-Crb interaction and compromise PALS1-mediated polarity in MDCK cysts.","method":"Crystal structure determination, isothermal titration calorimetry, mutagenesis, MDCK cyst polarity assay","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 1 / Strong — crystal structure plus ITC quantification plus mutagenesis plus functional cell assay in one study","pmids":["25385611"],"is_preprint":false},{"year":2015,"finding":"Crystal structures of the human PALS1 PDZ domain with and without Crumbs C-terminal ligand (ERLI) reveal a key Phe residue that gates access to the PDZ peptide-binding groove; removal of this gating residue enhances binding affinity by >5-fold, suggesting regulated access of Crumbs to Pals1.","method":"Crystallography, fluorescence polarization binding assay, mutagenesis","journal":"Acta crystallographica. Section D, Biological crystallography","confidence":"High","confidence_rationale":"Tier 1 / Strong — crystal structures (apo and bound) plus quantitative binding assays and mutagenesis","pmids":["25760605"],"is_preprint":false},{"year":2015,"finding":"In Schwann cells, loss of Pals1 impairs radial sorting of axons, delays myelination, and reduces nerve conduction velocities; polyaxonal myelination persists in adult Pals1-deficient nerves; Pals1 interacts with Par3 and its loss reduces Par3 levels in Schwann cells; loss of Pals1 in oligodendrocytes does not affect CNS myelination.","method":"Conditional Pals1 knockout in Schwann cells and oligodendrocytes, nerve conduction velocity measurement, electron microscopy, Co-IP for Par3 interaction, immunofluorescence","journal":"The Journal of neuroscience","confidence":"High","confidence_rationale":"Tier 2 / Strong — in vivo conditional knockout with multiple functional and molecular readouts, cell-type specific comparison","pmids":["26203142"],"is_preprint":false},{"year":2015,"finding":"In the Drosophila embryonic epidermis, Stardust (Drosophila Pals1) is essential for correct subcellular localization of PATJ; L27 domain of PATJ is required for its correct localization and function; PATJ associates with both Baz-Sdt and Crb-Sdt complexes in mature epithelium.","method":"Drosophila genetics, biochemical pulldown, immunofluorescence, domain mutagenesis","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic and biochemical data in Drosophila ortholog, multiple complementary approaches, single lab","pmids":["25847234"],"is_preprint":false},{"year":2015,"finding":"Deletion of Pals1 in cerebellar progenitors causes severely undersized cerebellum with disrupted layers and reduced granule cell production; Pals1 maintains cerebellar progenitor pools by preventing premature differentiation; Pals1 acts epistatically to Shh signaling—activated Smo cannot overcome Pals1 loss.","method":"Conditional Pals1 knockout mouse, electroretinography, cell cycle gene expression analysis, genetic epistasis with Smo activation","journal":"Development (Cambridge, England)","confidence":"High","confidence_rationale":"Tier 2 / Strong — in vivo conditional knockout with epistasis experiment and multiple molecular readouts","pmids":["26657772"],"is_preprint":false},{"year":2016,"finding":"VE-cadherin directly interacts with Pals1 through a membrane-proximal motif in the VE-cadherin cytoplasmic domain; VE-cadherin clusters Pals1 at cell-cell junctions; mutation of the Pals1-binding motif in VE-cadherin abrogates VE-cadherin's ability to regulate apicobasal polarity and vascular lumen formation.","method":"Co-immunoprecipitation, pulldown, site-directed mutagenesis, vascular lumen formation assay, polarity assay in endothelial cells","journal":"Molecular biology of the cell","confidence":"High","confidence_rationale":"Tier 2 / Strong — direct binding assays with mutagenesis and functional consequence in lumen formation assay","pmids":["27466317"],"is_preprint":false},{"year":2017,"finding":"Pals1 haploinsufficiency in mouse nephrons causes lethal cyst formation and proteinuria; in epithelial cell culture models, Pals1 functions as a dose-dependent upstream regulator of crosstalk between Hippo and TGF-β signaling pathways.","method":"Conditional heterozygous Pals1 knockout mouse, histology, signaling pathway analysis (Hippo/TGF-β), Drosophila nephrocyte analysis","journal":"Journal of the American Society of Nephrology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — in vivo haploinsufficiency model with signaling pathway readouts, single lab, pathway mechanistic detail limited","pmids":["28154200"],"is_preprint":false},{"year":2021,"finding":"Cryo-EM structure of PALS1-SARS-CoV-2 E protein complex shows the E protein C-terminal DLLV motif binds a pocket formed exclusively by hydrophobic residues from both the PDZ and SH3 domains of PALS1.","method":"Cryo-electron microscopy structure determination","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 1 / Strong — cryo-EM structure revealing atomic-level interaction involving both PDZ and SH3 domains","pmids":["34103506"],"is_preprint":false},{"year":2021,"finding":"Crystal structures of PALS1 PDZ domain bound to SARS-CoV-1 and SARS-CoV-2 E protein PDZ-binding motifs show both viral peptides bind the PDZ domain with ~29.6 and ~22.8 μM affinity respectively; MERS-CoV C-terminal sequence does not bind PALS1 PDZ domain.","method":"Crystallography, surface plasmon resonance / fluorescence-based affinity measurements","journal":"Communications biology","confidence":"High","confidence_rationale":"Tier 1 / Strong — crystal structures with quantitative binding data and specificity controls (MERS negative result)","pmids":["34117354"],"is_preprint":false},{"year":2021,"finding":"Loss of Pals1 in colorectal cancer cells increases Arf6 and Rac1 activity, enhancing cell migration, invasion, and metastasis in vivo; this function is independent of canonical PALS1 binding partners (PATJ, CRB3) and tight junction formation.","method":"Pals1 knockout/knockdown, Arf6 and Rac1 activity assays (GTP-pulldown), in vitro migration/invasion assay, in vivo tumor transplantation assay","journal":"Molecular cancer","confidence":"High","confidence_rationale":"Tier 2 / Strong — loss-of-function with mechanistic readouts (GTPase activity), in vivo validation, and domain independence established","pmids":["33941200"],"is_preprint":false},{"year":2022,"finding":"Angiomotin isoform 2 (Ap80) promotes binding of PALS1 to KIF13B at the base of the primary cilium; Ap80 concentrates at and recruits PALS1 to the ciliary base; Ap80 depletion causes ciliary elongation and reduced agonist-induced SMO accumulation in cilia.","method":"Co-immunoprecipitation, live-cell imaging, ciliary length measurement, SMO ciliary accumulation assay, siRNA knockdown","journal":"Journal of cell science","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — Co-IP and live imaging with functional ciliary readout, single lab","pmids":["35673984"],"is_preprint":false},{"year":2022,"finding":"Pals1 functions redundantly with the Arf6-GAP SMAP1 to inhibit Arf6 activity; in cells expressing SMAP1, loss of Pals1 disrupts tight junctions but does not increase Arf6/Rac1 activity or migration; only combined loss of both SMAP1 and Pals1 increases Arf6/Rac1 activity and cell migration.","method":"Pals1 and SMAP1 knockout/knockdown, Arf6/Rac1 activity assays, migration assay, patient cohort analysis","journal":"Cancer gene therapy","confidence":"High","confidence_rationale":"Tier 2 / Strong — genetic epistasis via double knockout/knockdown with mechanistic GTPase activity readouts","pmids":["36494580"],"is_preprint":false},{"year":2023,"finding":"In Pals1 cortical mutant mice, cell-in-cell (CIC) structures (entosis-like) form inside dividing cells, accompanied by lengthened mitosis and cytokinesis defects; ROCK inhibition abrogates CIC structures and restores normal mitosis length; genetic elimination of Trp53 rescues cortical size and reduces CIC structures, placing this entotic process downstream of Pals1 loss in microcephaly pathogenesis.","method":"Conditional Pals1 knockout mouse, ROCK inhibitor treatment, Trp53 genetic rescue, live imaging of cell division, electron microscopy","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 2 / Strong — in vivo conditional knockout with pharmacological and genetic rescue experiments and multiple mechanistic readouts","pmids":["36604424"],"is_preprint":false},{"year":2024,"finding":"PALS1 knockout in MDCKII cells causes redistribution of tight junction proteins from bicellular to tricellular contacts, increased paracellular permeability, delayed tight junction reassembly after Ca2+ removal or F-actin depolymerization, and redistribution of RhoA from junctions to cytosol; PALS1-dependent localization of TJ proteins at bicellular junctions requires its interaction with PATJ.","method":"CRISPR/Cas9 PALS1 knockout, transepithelial electrical resistance, confocal microscopy, Ca2+ switch assay, F-actin depolymerization/repolymerization assay, RhoA localization","journal":"Journal of cell science","confidence":"High","confidence_rationale":"Tier 2 / Strong — clean CRISPR knockout with multiple orthogonal functional readouts and domain-interaction requirement established","pmids":["38265145"],"is_preprint":false},{"year":2025,"finding":"MPP5/PALS1 physically interacts with YAP and TAZ in liver cancer cells; the PDZ domain of PALS1 is required for YAP binding (shown by domain deletion Co-IP); PALS1 facilitates nuclear exclusion of YAP and TAZ; reduced PALS1 expression correlates with nuclear YAP/TAZ accumulation in HCC tissue.","method":"Co-immunoprecipitation, proximity ligation assay, PDZ domain deletion analysis, proteomics/functional screening","journal":"International journal of molecular sciences","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — Co-IP with domain deletion and PLA confirmation, single lab, mechanism of nuclear exclusion not fully defined","pmids":["39859373"],"is_preprint":false}],"current_model":"PALS1 (MPP5) is an evolutionarily conserved MAGUK scaffold protein that forms the core of the apical CRB3–PALS1–PATJ polarity complex at tight junctions: its PDZ-SH3-GK supramodule binds the Crumbs cytoplasmic tail with high affinity, its L27N domain heterodimerizes with PATJ, its L27C domain binds mLin-7/MALS, and an internal N-terminal sequence is recognized by the Par-6 PDZ domain in a Cdc42-independent manner, thereby physically linking the CRB and Par6/Par3/aPKC polarity complexes; loss of PALS1 disrupts tight junction assembly, E-cadherin trafficking via the exocyst, aPKC recruitment, RhoA junctional localization, and YAP/TAZ nuclear exclusion, while in specialized tissues it controls Schwann cell radial sorting and myelin extension, retinal architecture, and cerebellar progenitor maintenance, and is subverted by coronavirus E proteins that compete for the PALS1 PDZ domain."},"narrative":{"mechanistic_narrative":"PALS1 (MPP5) is an evolutionarily conserved MAGUK scaffold that nucleates the apical CRB3–PALS1–PATJ polarity complex governing epithelial tight junction assembly and apicobasal polarization [PMID:11927608, PMID:12527193, PMID:14718565]. Through distinct binding modules it assembles a multiprotein scaffold: its PDZ domain engages the Crumbs cytoplasmic tail, while structural work shows the PDZ–SH3–GK tandem acts as a supramodule in which all three domains cooperate to bind the Crumbs tail with ~70 nM affinity, far exceeding the isolated PDZ [PMID:11927608, PMID:25385611]; a gating Phe residue in the PDZ groove regulates ligand access [PMID:25760605]. Its tandem L27 domains drive supramolecular assembly, with the L27N domain heterodimerizing with PATJ and the L27C domain binding mLin-7/MALS, forming cognate, mutually independent heterodimeric pairs [PMID:11927608, PMID:15863617, PMID:22337881]. PALS1 physically links the CRB and Par complexes, as the Par-6 PDZ domain recognizes an internal N-terminal sequence in PALS1 in a Cdc42-independent manner, with Par-6 and PATJ competing for binding [PMID:15475968, PMID:15140881]. Loss-of-function in MDCK cells delays tight junction formation, fails to recruit aPKC, abolishes PATJ expression, and prevents lumen formation [PMID:14718565], and PALS1 additionally controls E-cadherin surface delivery via the exocyst [PMID:17182851] and junctional RhoA localization, with bicellular tight junction protein positioning requiring the PATJ interaction [PMID:38265145]. In specialized tissues PALS1 maintains retinal architecture by sustaining apical Crumbs complex localization, with its loss causing photoreceptor degeneration [PMID:16885194, PMID:22114289, PMID:22398208]; controls Schwann cell radial sorting and myelin extension in concert with Par3 [PMID:20237282, PMID:26203142]; and maintains cerebellar and cortical progenitor pools, acting upstream of entotic cell-in-cell death and Trp53 in microcephaly pathogenesis [PMID:26657772, PMID:36604424]. Beyond canonical polarity, PALS1 restrains Arf6/Rac1 activity redundantly with SMAP1 to limit colorectal cancer migration and invasion [PMID:33941200, PMID:36494580] and promotes nuclear exclusion of YAP/TAZ [PMID:39859373]. PALS1 is subverted by coronavirus E proteins, whose C-terminal PDZ-binding motifs bind a pocket formed jointly by the PALS1 PDZ and SH3 domains, redistributing PALS1 and disrupting junction formation [PMID:20861307, PMID:34103506, PMID:34117354].","teleology":[{"year":2002,"claim":"Established PALS1 as the central scaffold of a conserved apical polarity complex by mapping its distinct binding modules to discrete partners.","evidence":"Co-IP, pulldowns, and domain mapping defining L27N–PATJ, L27C–mLin-7, and PDZ–CRB1 interactions","pmids":["11927608"],"confidence":"High","gaps":["Stoichiometry and ordered assembly of the full complex not resolved","No structural basis for the interactions at this stage"]},{"year":2003,"claim":"Demonstrated functionally that the CRB3–PALS1 PDZ interaction is required for tight junction formation and epithelial polarization, moving PALS1 from binding partner to functional regulator.","evidence":"Dominant-negative chimera overexpression and calcium switch / cyst morphogenesis assays in MDCK cells; CRB3 Co-IP and localization","pmids":["12771187","12527193"],"confidence":"High","gaps":["Dominant-negative approach does not exclude off-target scaffolding effects","Downstream effectors not defined"]},{"year":2004,"claim":"Defined PALS1 as essential for apical polarity machinery by showing its depletion fails to recruit aPKC and abolishes PATJ, and revealed a non-canonical internal binding mode bridging CRB and Par complexes.","evidence":"Stable siRNA knockdown with TEER/cyst readouts; crystal structure of Par-6 PDZ–PALS1 internal ligand complex with mutagenesis and competition assays","pmids":["14718565","15475968","15140881"],"confidence":"High","gaps":["Regulation of Par-6 versus PATJ competition in vivo not established","How aPKC recruitment is coupled mechanistically not resolved"]},{"year":2005,"claim":"Extended the PALS1 interactome to MPP4/MPP3 and ezrin and resolved the L27 tetrameric assembly principle, linking PALS1 scaffolding to retinal and apical membrane organization.","evidence":"Yeast two-hybrid, GST pulldown, Co-IP, immunoEM in retina; NMR structures of L27 heterodimer pairs; ezrin loss-of-function in parietal cells","pmids":["15914641","15863617","15677456","15558731"],"confidence":"High","gaps":["GAT1 stabilization mechanism not defined (Medium evidence)","Physiological role of MPP4/MPP3 recruitment to PALS1 not fully tested in vivo"]},{"year":2006,"claim":"Showed PALS1 acts beyond tight junctions to control adherens junction E-cadherin trafficking via the exocyst and is required for Crumbs-family localization in retinal glia.","evidence":"Stable knockdown with E-cadherin surface biotinylation and exocyst localization in MDCK; RNAi with immunoEM in Müller glia","pmids":["17182851","16885194","16519681"],"confidence":"High","gaps":["Direct link between PALS1 and exocyst recruitment not biochemically defined","Whether PALS1 trafficking role is separable from polarity scaffolding unclear"]},{"year":2009,"claim":"Placed nephrocystins (NPHP1/NPHP4) in the same polarity pathway as PALS1, connecting the complex to ciliogenesis and cystogenesis.","evidence":"Co-IP and shRNA knockdown phenocopying PALS1 depletion in MDCK 3D cysts with cilia analysis","pmids":["19755384"],"confidence":"High","gaps":["Direct versus indirect nature of the nephrocystin–PALS1 interaction not fully resolved","Mechanism linking PALS1 to ciliary function not defined"]},{"year":2011,"claim":"Established an essential in vivo structural role for PALS1 in maintaining the retinal Crumbs complex and architecture, and reported a non-polarity role in TCR-driven NF-κB signaling.","evidence":"Conditional knockdown mouse with ERG/OCT/immunohistochemistry; siRNA knockdown with NF-κB reporter in T cells","pmids":["22114289","21479189"],"confidence":"High","gaps":["Mechanism coupling PALS1 to NF-κB activation not defined (Medium evidence)","Whether retinal phenotype is purely structural or signaling-dependent not separated"]},{"year":2012,"claim":"Resolved the L27 heterotrimeric assembly mechanism and demonstrated mutual interdependence of PALS1 and Crb proteins for apical localization in a disease-relevant retinal model.","evidence":"Crystal structure of Patj/Pals1/Mals2 L27 heterotrimer; conditional Pals1 knockout mouse mimicking Leber congenital amaurosis","pmids":["22337881","22398208"],"confidence":"High","gaps":["How L27 assembly is regulated dynamically in cells not addressed","Genetic causation in human retinal disease not directly tested in these studies"]},{"year":2014,"claim":"Defined the structural basis for high-affinity Crumbs recognition, showing the PDZ–SH3–GK tandem functions as an integrated supramodule whose interdomain contacts are required for polarity function.","evidence":"Crystal structure of PALS1 PDZ-SH3-GK–Crb-CT with ITC and MDCK cyst polarity assay","pmids":["25385611"],"confidence":"High","gaps":["Whether supramodule conformation is regulated in vivo unclear","Allosteric communication between domains not kinetically dissected"]},{"year":2015,"claim":"Revealed regulated, gated access of Crumbs to the PDZ groove and extended PALS1 function to Schwann cell radial sorting/myelination and cerebellar progenitor maintenance via interactions with Par3 and Shh-independent control of differentiation.","evidence":"Apo/bound PDZ crystal structures with binding assays; conditional knockouts in Schwann cells, oligodendrocytes, and cerebellar progenitors with epistasis to Smo; Drosophila Stardust genetics","pmids":["25760605","26203142","26657772","25847234"],"confidence":"High","gaps":["Physiological trigger controlling the PDZ gating residue unknown","Mechanism by which PALS1 prevents premature cerebellar differentiation not molecularly defined"]},{"year":2016,"claim":"Identified VE-cadherin as a direct PALS1 recruiter at endothelial junctions, linking PALS1 scaffolding to vascular lumen formation.","evidence":"Co-IP, pulldown, mutagenesis of VE-cadherin membrane-proximal motif, lumen formation assay","pmids":["27466317"],"confidence":"High","gaps":["How VE-cadherin-bound PALS1 directs apical membrane specification not detailed","Relationship to Crumbs binding at the same PDZ not addressed"]},{"year":2017,"claim":"Demonstrated PALS1 dosage sensitivity in vivo, with haploinsufficiency causing renal cysts and dysregulated Hippo–TGF-β crosstalk.","evidence":"Conditional heterozygous Pals1 knockout mouse with histology and signaling readouts; Drosophila nephrocyte analysis","pmids":["28154200"],"confidence":"Medium","gaps":["Mechanistic detail of Hippo/TGF-β crosstalk regulation limited","Direct molecular targets in these pathways not identified"]},{"year":2021,"claim":"Defined how coronavirus E proteins subvert PALS1, showing the viral C-terminal motif binds a pocket formed jointly by the PDZ and SH3 domains with specificity excluding MERS-CoV.","evidence":"Cryo-EM of PALS1–SARS-CoV-2 E complex; crystal structures of PDZ bound to SARS-CoV-1/2 E motifs with affinity measurements and MERS negative control; earlier infection model showing PALS1 redistribution","pmids":["34103506","34117354","20861307"],"confidence":"High","gaps":["Functional consequence of E-PALS1 sequestration on infection outcome not fully dissected here","Whether endogenous ligands engage the same composite pocket not tested"]},{"year":2022,"claim":"Uncovered a Crumbs/PATJ-independent tumor-suppressive function whereby PALS1 restrains Arf6/Rac1 activity redundantly with SMAP1 to limit migration and invasion, and a role in ciliary base regulation via angiomotin and KIF13B.","evidence":"Pals1 and SMAP1 knockout with GTPase activity assays and migration assays plus patient cohort; Co-IP and live imaging of Ap80-PALS1-KIF13B at the cilium","pmids":["36494580","35673984"],"confidence":"High","gaps":["Direct molecular mechanism by which PALS1 inhibits Arf6 GTPase not defined","Ciliary KIF13B recruitment role rests on single-lab Medium evidence"]},{"year":2023,"claim":"Placed PALS1 loss upstream of entotic cell-in-cell death and Trp53 in cortical microcephaly pathogenesis, linking polarity disruption to mitotic and cytokinesis defects.","evidence":"Conditional Pals1 knockout mouse with ROCK inhibition, Trp53 genetic rescue, and live imaging of division","pmids":["36604424"],"confidence":"High","gaps":["How PALS1 loss mechanistically triggers ROCK-dependent CIC formation not defined","Direct molecular link from polarity loss to mitotic lengthening unclear"]},{"year":2024,"claim":"Resolved that PALS1 positions tight junction proteins specifically at bicellular contacts and controls junctional RhoA, requiring its PATJ interaction.","evidence":"CRISPR knockout in MDCKII with TEER, Ca2+/F-actin reassembly assays, and RhoA localization","pmids":["38265145"],"confidence":"High","gaps":["Mechanism linking PALS1 to RhoA junctional retention not defined","How bicellular versus tricellular targeting is determined unclear"]},{"year":2025,"claim":"Identified PALS1 as a PDZ-dependent regulator of YAP/TAZ nuclear exclusion in liver cancer, connecting the scaffold to Hippo effector localization.","evidence":"Co-IP, PLA, and PDZ deletion analysis in HCC cells with tissue correlation","pmids":["39859373"],"confidence":"Medium","gaps":["Mechanism of PALS1-mediated nuclear exclusion not defined","Single-lab evidence without in vivo functional validation"]},{"year":null,"claim":"How PALS1's diverse functions—canonical polarity scaffolding versus Crumbs/PATJ-independent control of small-GTPase signaling, Hippo/YAP-TAZ, and progenitor maintenance—are integrated and differentially regulated across tissues remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No unifying model linking scaffolding to GTPase and Hippo regulation","Post-translational or conformational switches controlling PALS1 function not characterized","Direct human disease mutations causally tested in the corpus are limited"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[0,4,9,22,24]},{"term_id":"GO:0005198","term_label":"structural molecule activity","supporting_discovery_ids":[3,19,37]}],"localization":[{"term_id":"GO:0005886","term_label":"plasma membrane","supporting_discovery_ids":[0,2,3,14,29,37]},{"term_id":"GO:0005929","term_label":"cilium","supporting_discovery_ids":[34]},{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[38]}],"pathway":[{"term_id":"R-HSA-1500931","term_label":"Cell-Cell communication","supporting_discovery_ids":[0,3,14,37]},{"term_id":"R-HSA-1266738","term_label":"Developmental Biology","supporting_discovery_ids":[11,19,26,28]},{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[33,35,38]},{"term_id":"R-HSA-1643685","term_label":"Disease","supporting_discovery_ids":[17,31,32]}],"complexes":["CRB3–PALS1–PATJ apical polarity complex","PALS1–PATJ–MALS/Lin-7 L27 scaffold","Par6/Par3/aPKC complex (bridged via PALS1)"],"partners":["CRB3","PATJ","PAR6","PARD3","MPP3","MPP4","EPB41L5","EZR"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q8N3R9","full_name":"Protein PALS1","aliases":["MAGUK p55 subfamily member 5","Membrane protein, palmitoylated 5","Protein associated with Lin-7 1"],"length_aa":675,"mass_kda":77.3,"function":"Plays a role in tight junction biogenesis and in the establishment of cell polarity in epithelial cells (PubMed:16678097, PubMed:25385611). Also involved in adherens junction biogenesis by ensuring correct localization of the exocyst complex protein EXOC4/SEC8 which allows trafficking of adherens junction structural component CDH1 to the cell surface (By similarity). Plays a role through its interaction with CDH5 in vascular lumen formation and endothelial membrane polarity (PubMed:27466317). Required during embryonic and postnatal retinal development (By similarity). Required for the maintenance of cerebellar progenitor cells in an undifferentiated proliferative state, preventing premature differentiation, and is required for cerebellar histogenesis, fissure formation, cerebellar layer organization and cortical development (By similarity). Plays a role in neuronal progenitor cell survival, potentially via promotion of mTOR signaling (By similarity). Plays a role in the radial and longitudinal extension of the myelin sheath in Schwann cells (By similarity). May modulate SC6A1/GAT1-mediated GABA uptake by stabilizing the transporter (By similarity). Plays a role in the T-cell receptor-mediated activation of NF-kappa-B (PubMed:21479189). Required for localization of EZR to the apical membrane of parietal cells and may play a role in the dynamic remodeling of the apical cytoskeleton (By similarity). Required for the normal polarized localization of the vesicular marker STX4 (By similarity). Required for the correct trafficking of the myelin proteins PMP22 and MAG (By similarity). Involved in promoting phosphorylation and cytoplasmic retention of transcriptional coactivators YAP1 and WWTR1/TAZ which leads to suppression of TGFB1-dependent transcription of target genes such as CCN2/CTGF, SERPINE1/PAI1, SNAI1/SNAIL1 and SMAD7 (By similarity) (Microbial infection) Acts as an interaction partner for human coronaviruses SARS-CoV and, probably, SARS-CoV-2 envelope protein E which results in delayed formation of tight junctions and disregulation of cell polarity","subcellular_location":"Endoplasmic reticulum-Golgi intermediate compartment; Golgi apparatus","url":"https://www.uniprot.org/uniprotkb/Q8N3R9/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/PALS1","classification":"Not Classified","n_dependent_lines":5,"n_total_lines":1208,"dependency_fraction":0.0041390728476821195},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"CALD1","stoichiometry":0.2},{"gene":"CALM3","stoichiometry":0.2},{"gene":"CAPZB","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/PALS1","total_profiled":1310},"omim":[{"mim_id":"609737","title":"CRUMBS CELL POLARITY COMPLEX COMPONENT 3; CRB3","url":"https://www.omim.org/entry/609737"},{"mim_id":"608293","title":"RHO GTPase-ACTIVATING PROTEIN 17; ARHGAP17","url":"https://www.omim.org/entry/608293"},{"mim_id":"607215","title":"NEPHROCYSTIN 4; NPHP4","url":"https://www.omim.org/entry/607215"},{"mim_id":"607100","title":"NEPHROCYSTIN 1; NPHP1","url":"https://www.omim.org/entry/607100"},{"mim_id":"606959","title":"PROTEIN ASSOCIATED WITH LIN7 2, MAGUK p55 FAMILY MEMBER; PALS2","url":"https://www.omim.org/entry/606959"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Nucleoplasm","reliability":"Approved"},{"location":"Plasma membrane","reliability":"Approved"},{"location":"Cell Junctions","reliability":"Additional"},{"location":"Cytosol","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/PALS1"},"hgnc":{"alias_symbol":["FLJ12615"],"prev_symbol":["MPP5"]},"alphafold":{"accession":"Q8N3R9","domains":[{"cath_id":"-","chopping":"185-231","consensus_level":"high","plddt":89.6432,"start":185,"end":231},{"cath_id":"2.30.42.10","chopping":"243-332","consensus_level":"high","plddt":89.4707,"start":243,"end":332},{"cath_id":"2.30.30.40","chopping":"350-421","consensus_level":"high","plddt":89.7237,"start":350,"end":421},{"cath_id":"3.40.50.300","chopping":"474-672","consensus_level":"medium","plddt":92.0369,"start":474,"end":672}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q8N3R9","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q8N3R9-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q8N3R9-F1-predicted_aligned_error_v6.png","plddt_mean":77.19},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=PALS1","jax_strain_url":"https://www.jax.org/strain/search?query=PALS1"},"sequence":{"accession":"Q8N3R9","fasta_url":"https://rest.uniprot.org/uniprotkb/Q8N3R9.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q8N3R9/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q8N3R9"}},"corpus_meta":[{"pmid":"11927608","id":"PMC_11927608","title":"The 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journal","url":"https://pubmed.ncbi.nlm.nih.gov/37434460","citation_count":9,"is_preprint":false},{"pmid":"38265145","id":"PMC_38265145","title":"PALS1 is a key regulator of the lateral distribution of tight junction proteins in renal epithelial cells.","date":"2024","source":"Journal of cell science","url":"https://pubmed.ncbi.nlm.nih.gov/38265145","citation_count":6,"is_preprint":false},{"pmid":"32366143","id":"PMC_32366143","title":"C. elegans MAGU-2/Mpp5 homolog regulates epidermal phagocytosis and synapse density.","date":"2020","source":"Journal of neurogenetics","url":"https://pubmed.ncbi.nlm.nih.gov/32366143","citation_count":5,"is_preprint":false},{"pmid":"35252349","id":"PMC_35252349","title":"Impact of Pals1 on Expression and Localization of Transporters Belonging to the Solute Carrier Family.","date":"2022","source":"Frontiers in molecular biosciences","url":"https://pubmed.ncbi.nlm.nih.gov/35252349","citation_count":3,"is_preprint":false},{"pmid":"39859373","id":"PMC_39859373","title":"The Cell Polarity Protein MPP5/PALS1 Controls the Subcellular Localization of the Oncogenes YAP and TAZ in Liver Cancer.","date":"2025","source":"International journal of molecular sciences","url":"https://pubmed.ncbi.nlm.nih.gov/39859373","citation_count":2,"is_preprint":false},{"pmid":"36494580","id":"PMC_36494580","title":"Pals1 functions in redundancy with SMAP1 to inhibit Arf6 in order to prevent Rac1-dependent colorectal cancer cell migration and invasion.","date":"2022","source":"Cancer gene therapy","url":"https://pubmed.ncbi.nlm.nih.gov/36494580","citation_count":2,"is_preprint":false},{"pmid":"36710240","id":"PMC_36710240","title":"A case of a childhood onset developmental encephalopathy with a novel de novo truncating variant in the Membrane Protein Palmitoylated 5 (MPP5) gene.","date":"2023","source":"Seizure","url":"https://pubmed.ncbi.nlm.nih.gov/36710240","citation_count":2,"is_preprint":false},{"pmid":"39582830","id":"PMC_39582830","title":"Investigation of the Mutations in the SARS-CoV-2 Envelope Protein and Its Interaction with the PALS1 by Molecular Docking.","date":"2024","source":"Reports of biochemistry & molecular biology","url":"https://pubmed.ncbi.nlm.nih.gov/39582830","citation_count":1,"is_preprint":false},{"pmid":"22102253","id":"PMC_22102253","title":"Crystallization and preliminary X-ray data collection of the L27(PATJ)-(L27N,L27C)(Pals1)-L27(MALS) tripartite complex.","date":"2011","source":"Acta crystallographica. Section F, Structural biology and crystallization communications","url":"https://pubmed.ncbi.nlm.nih.gov/22102253","citation_count":1,"is_preprint":false},{"pmid":"39614182","id":"PMC_39614182","title":"PALS1-dependent modulations of mRNA profiles in MDCK II cells grown in non-confluent monolayers and three-dimensional cysts.","date":"2024","source":"BMC genomic data","url":"https://pubmed.ncbi.nlm.nih.gov/39614182","citation_count":0,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2024.10.17.618968","title":"Optical Genome Mapping of the human reference iPSC line KOLF2.1J reveals new smaller structural variants in neurodevelopmental genes","date":"2024-10-19","source":"bioRxiv","url":"https://doi.org/10.1101/2024.10.17.618968","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2024.07.17.603777","title":"PATJ regulates cell stress responses and vascular remodeling post-stroke","date":"2024-07-22","source":"bioRxiv","url":"https://doi.org/10.1101/2024.07.17.603777","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":26167,"output_tokens":9166,"usd":0.107995,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":19167,"output_tokens":5927,"usd":0.122005,"stage2_stop_reason":"end_turn"},"total_usd":0.23,"stage1_batch_id":"msgbatch_013a8chtv3AWyTqv4z4sEF4C","stage2_batch_id":"msgbatch_01AHsuW63vinsvuTgzmQ3n62","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2002,\n      \"finding\": \"PALS1 L27N domain binds PATJ (mammalian Discs Lost homologue) via a unique Maguk recruitment domain, targeting PALS1 to tight junctions; PALS1 L27C domain binds mLin-7; and the PALS1 PDZ domain binds CRB1 (human Crumbs homologue), forming a conserved multiprotein polarity complex.\",\n      \"method\": \"Co-immunoprecipitation, pulldown assays, domain mapping, colocalization by confocal microscopy\",\n      \"journal\": \"The Journal of cell biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal Co-IP and domain-level mapping, independently replicated in Drosophila system, foundational paper widely confirmed\",\n      \"pmids\": [\"11927608\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2003,\n      \"finding\": \"Overexpression of dominant-negative Myc-Lin-2-Pals1 chimera (PDZ domain of Pals1 replacing Lin-2 PDZ) in MDCK cells causes tight junction formation delays and apical polarity defects, demonstrating that the CRB3-Pals1 PDZ interaction is required for tight junction formation and epithelial polarization.\",\n      \"method\": \"Dominant-negative overexpression, calcium switch assay, MDCK cyst morphogenesis assay, confocal microscopy\",\n      \"journal\": \"Journal of cell science\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal functional assays (TJ formation, cyst morphogenesis, dominant-negative rescue), replicated in same lab with complementary data\",\n      \"pmids\": [\"12771187\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2003,\n      \"finding\": \"CRB3 (Crumbs3) interacts with PALS1 through its conserved intracellular domain, and this complex also includes PATJ; CRB3 localizes to the apical surface and tight junctions of epithelial cells.\",\n      \"method\": \"Co-immunoprecipitation, subcellular fractionation, confocal microscopy, mutagenesis of CRB3 intracellular domain\",\n      \"journal\": \"Gene\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — Co-IP with domain mutagenesis, consistent with concurrent papers from independent groups\",\n      \"pmids\": [\"12527193\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2004,\n      \"finding\": \"siRNA-mediated knockdown of PALS1 in MDCKII cells causes loss of PATJ expression (a known binding partner), decreased association of CRB3 with Par6/Par3/aPKC complex, failure to recruit aPKC to tight junctions, delayed polarization after calcium switch, decreased transepithelial electrical resistance, and inability to form lumenal cysts.\",\n      \"method\": \"Stable siRNA knockdown, calcium switch assay, transepithelial electrical resistance measurement, 3D collagen cyst assay, confocal microscopy\",\n      \"journal\": \"Molecular biology of the cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — clean loss-of-function with multiple orthogonal phenotypic readouts and defined molecular pathway placement\",\n      \"pmids\": [\"14718565\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2004,\n      \"finding\": \"Par-6 PDZ domain binds an internal (non-C-terminal) sequence in PALS1/Stardust amino terminus; crystal structure of the Par-6 PDZ-Pals1 complex shows the PDZ ligand-binding site is deformed to accommodate internal binding; Cdc42 binding to the Par-6 CRIB domain regulates C-terminal ligand binding but not Pals1 internal binding.\",\n      \"method\": \"Crystal structure determination, binding assays, mutagenesis\",\n      \"journal\": \"Nature structural & molecular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — crystal structure with mutagenesis and binding assays, clear mechanistic insight into PDZ plasticity\",\n      \"pmids\": [\"15475968\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2004,\n      \"finding\": \"Par-6 binds an evolutionarily conserved region in the amino terminus of PALS1 via the Par-6 PDZ domain; valine and aspartic acid residues in this PALS1 region are essential for the interaction; Par-6 and PATJ compete for binding to PALS1 (Par-6 interferes with PATJ binding) and do not act synergistically.\",\n      \"method\": \"Mutagenesis, GST pulldown, co-immunoprecipitation, competitive binding assays\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — mutagenesis identifying essential residues plus competition binding assays, evolutionarily conserved mechanism validated in Drosophila\",\n      \"pmids\": [\"15140881\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2004,\n      \"finding\": \"PALS1 interacts with the neuronal GABA transporter GAT1 via the PALS1 PDZ domain (identified by yeast two-hybrid and confirmed by co-immunoprecipitation in COS-7 cells); coexpression of PALS1 with GAT1 increases [3H]-GABA uptake by increasing GAT1 protein levels.\",\n      \"method\": \"Yeast two-hybrid, co-immunoprecipitation, [3H]-GABA uptake assay, immunofluorescence\",\n      \"journal\": \"Molecular and cellular neurosciences\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — single lab, yeast two-hybrid confirmed by Co-IP and functional uptake assay, but mechanism of protein stabilization not fully defined\",\n      \"pmids\": [\"15234345\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2005,\n      \"finding\": \"MPP5/PALS1 directly interacts with MPP4 via L27 heterodimerization; MPP4 is recruited to the CRB1 complex through its interaction with MPP5; all three proteins colocalize at the outer limiting membrane of the retina.\",\n      \"method\": \"Yeast two-hybrid, GST pulldown, co-immunoprecipitation, immunohistochemistry, immunoelectron microscopy, 3D homology modeling\",\n      \"journal\": \"Investigative ophthalmology & visual science\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal binding methods plus in situ localization in retinal tissue\",\n      \"pmids\": [\"15914641\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2005,\n      \"finding\": \"PALS1 interacts with ezrin via the ezrin N-terminus and PALS1 is required for apical localization of ezrin in gastric parietal cells; disruption of this interaction (by PALS1 suppression or deletion of PALS1-binding domain in ezrin) eliminates apical ezrin localization and impairs apical membrane remodeling during parietal cell secretion.\",\n      \"method\": \"Co-immunoprecipitation, siRNA knockdown, domain deletion, confocal microscopy, functional secretion assay\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal binding assays, loss-of-function with specific functional readout, and domain mapping\",\n      \"pmids\": [\"15677456\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2005,\n      \"finding\": \"NMR solution structures of the L27 domain complexes of Patj/Pals1 (and mLin-2/mLin-7) reveal a tetrameric assembly (two heterodimers); the C-terminal alpha-helix of each L27 domain forms a central helix bundle critical for partner specificity.\",\n      \"method\": \"NMR structure determination, biochemical binding assays, mutagenesis\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — NMR structure with biochemical validation and mutagenesis of specificity determinants\",\n      \"pmids\": [\"15863617\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2005,\n      \"finding\": \"MPP5 (PALS1) and MPP4 localize to distinct sites in the mouse retina: MPP5 exclusively at apical outer limiting membrane junctions, MPP4 at photoreceptor synaptic terminals; MPP4 directly interacts with Veli proteins (Veli1, -3) via L27 heterodimerization in vitro, and Veli3 colocalizes with both MPP4 and MPP5.\",\n      \"method\": \"Immunofluorescence microscopy, L27 heterodimerization in vitro binding assay, antibody generation and immunohistochemistry\",\n      \"journal\": \"The Journal of comparative neurology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct localization experiments with functional context, in vitro binding assay; single lab\",\n      \"pmids\": [\"15558731\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2005,\n      \"finding\": \"In zebrafish, nagie oko (nok)/Mpp5 (PALS1 ortholog) is required tissue-autonomously within myocardial cells for polarized epithelial organization and coherence during heart cone formation, and for myocardial cell expansion during heart tube elongation; Has/PRKCi (aPKC) and Nok/Mpp5 act together in myocardial morphogenesis.\",\n      \"method\": \"Genetic epistasis in zebrafish, tissue-specific rescue experiments, confocal microscopy of myocardial cell organization\",\n      \"journal\": \"Development (Cambridge, England)\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — genetic loss-of-function in zebrafish with tissue-autonomous rescue, multiple morphogenetic phenotypic readouts\",\n      \"pmids\": [\"16319113\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"MPP3 directly interacts with MPP5/PALS1 and is recruited to the CRB1/MPP5 scaffold at the outer limiting membrane of the retina; MPP3 also forms separate complexes with DLG1 at the outer plexiform layer.\",\n      \"method\": \"Co-immunoprecipitation, immunohistochemistry in human and mouse retinas, localization studies\",\n      \"journal\": \"The FEBS journal\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — Co-IP plus localization, single lab, no mutagenesis or reconstitution\",\n      \"pmids\": [\"16519681\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"siRNA silencing of Pals1 in Müller glia cells results in loss of Crb1, Crb2, Mupp1, and Veli3 protein localization at the subapical region (SAR) and partial loss of Crb3, demonstrating that Pals1 is required for correct localization of Crb family members and associated proteins at the SAR of polarized Müller glia.\",\n      \"method\": \"RNAi knockdown in primary retinal cultures, immunoelectron microscopy, confocal microscopy\",\n      \"journal\": \"Human molecular genetics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — loss-of-function with multiple readouts, immunoelectron microscopy for precise localization, clean knockdown phenotype\",\n      \"pmids\": [\"16885194\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"PALS1 knockdown in MDCK cells causes not only tight junction defects but also severe adherens junction defects; E-cadherin fails to be delivered to the cell surface and accumulates in peripheral puncta; the exocyst complex is mislocalized in PALS1 knockdown cells, suggesting PALS1 regulates E-cadherin trafficking via the exocyst.\",\n      \"method\": \"Stable siRNA knockdown, rescue with PALS1 mutants, E-cadherin surface biotinylation, confocal microscopy of exocyst and E-cadherin localization\",\n      \"journal\": \"Molecular biology of the cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — loss-of-function with multiple orthogonal readouts, rescue experiments with mutants, defined trafficking mechanism\",\n      \"pmids\": [\"17182851\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"EPB41L5 (a FERM domain protein) associates with the HOOK domain of MPP5/PALS1 and with the intracellular domains of all three Crumbs homologs via its FERM domain, forming a novel component of the mammalian CRB-MPP5 polarity complex; overexpression of EPB41L5 in MDCK cells disrupts ZO-1 and PATJ localization.\",\n      \"method\": \"Co-immunoprecipitation, co-expression studies, co-localization, overexpression functional assay in MDCK cells\",\n      \"journal\": \"Experimental cell research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — Co-IP and functional overexpression, single lab, domain identified\",\n      \"pmids\": [\"17920587\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"Nephrocystin-1 (NPHP1) and nephrocystin-4 (NPHP4) physically interact with PALS1, PATJ, and Par6; shRNA knockdown of NPHP1 or NPHP4 in MDCK cells phenocopies PALS1 depletion (delayed TJ formation, abnormal cilia, multi-lumen cysts), placing nephrocystins in the same polarity pathway as PALS1.\",\n      \"method\": \"Co-immunoprecipitation, shRNA knockdown, tight junction formation assay, 3D collagen matrix cyst assay, cilia analysis\",\n      \"journal\": \"Human molecular genetics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — Co-IP plus epistatic loss-of-function with phenotypic similarity to PALS1 depletion, multiple orthogonal readouts\",\n      \"pmids\": [\"19755384\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"The SARS-CoV E protein C-terminal PDZ-binding motif (last four amino acids) binds the PALS1 PDZ domain; in SARS-CoV-infected cells, PALS1 redistributes to the ERGIC/Golgi region where E accumulates; ectopic expression of E in MDCKII cells delays tight junction formation and disrupts polarity and PALS1 distribution in a PDZ-binding motif-dependent manner.\",\n      \"method\": \"Co-immunoprecipitation, GST pulldown, confocal microscopy in infected cells, MDCKII cyst morphogenesis assay, PDZ-binding motif mutant\",\n      \"journal\": \"Molecular biology of the cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal pulldowns plus viral infection model and PDZ motif mutagenesis with functional consequence\",\n      \"pmids\": [\"20861307\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"Pals1 is required in myelinating Schwann cells for normal myelin sheath thickness and length; silencing of pals1 in vivo reduces myelin turns without grossly disrupting compact myelin; pals1 is required for polarized localization of vesicular markers sec8 and syntaxin4, and for distribution of E-cadherin, PMP22, and MAG at the plasma membrane, suggesting a role in membrane protein trafficking in Schwann cells.\",\n      \"method\": \"In vivo siRNA silencing in Schwann cells, electron microscopy, confocal microscopy, immunostaining for polarity and vesicular markers\",\n      \"journal\": \"The Journal of neuroscience\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — in vivo loss-of-function with multiple ultrastructural and molecular readouts\",\n      \"pmids\": [\"20237282\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"PALS1 conditional knockdown in mice results in loss of Crumbs complex proteins at adherens junctions in the retina, progressive photoreceptor degeneration, abnormal retinal pigment epithelium structure, ectopic photoreceptors, and irregular outer limiting membrane, demonstrating an essential structural role for PALS1 in maintaining the CRB complex and retinal architecture.\",\n      \"method\": \"Conditional knockdown mouse model, electroretinography, confocal scanning laser ophthalmoscopy, optical coherence tomography, immunohistochemistry\",\n      \"journal\": \"The Journal of neuroscience\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — in vivo conditional loss-of-function with multiple complementary structural and functional readouts\",\n      \"pmids\": [\"22114289\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"PALS1 participates in TCR-mediated NF-κB activation in T lymphocytes; siRNA knockdown of PALS1 in Jurkat cells and primary T cells specifically impairs TCR-induced NF-κB activation and optimal lymphocyte proliferation.\",\n      \"method\": \"siRNA knockdown, NF-κB reporter assay, proliferation assay, RT-PCR, immunoblot\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — siRNA knockdown with specific NF-κB readout, single lab, mechanism of NF-κB coupling not defined\",\n      \"pmids\": [\"21479189\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"Deletion of Pals1 in retinal progenitor cells disrupts apical localization of Crb proteins and causes early visual impairment, disorganized retinal lamination, and retinal degeneration mimicking Leber congenital amaurosis; Pals1 and Crb proteins are functionally interdependent for apical localization.\",\n      \"method\": \"Conditional Pals1 knockout mouse, electroretinogram, confocal microscopy, immunohistochemistry\",\n      \"journal\": \"Human molecular genetics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — in vivo conditional knockout with functional and structural readouts, confirmed mutual dependence of Pals1 and Crb proteins\",\n      \"pmids\": [\"22398208\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"Crystal structure of L27 domain heterotrimer from Patj/Pals1/Mals2 reveals two cognate heterodimeric L27 pairs that assemble mutually independently, providing a novel mechanism for tandem L27 domain-mediated supramolecular complex assembly.\",\n      \"method\": \"Crystal structure determination, biochemical binding assays\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — crystal structure with biochemical validation, defines assembly mechanism of the tripartite complex\",\n      \"pmids\": [\"22337881\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"MPP3 directly interacts with PALS1/MPP5 and is required for maintaining proper levels of PALS1 at the subapical region adjacent to adherens junctions; loss of MPP3 in mice causes significant loss of PALS1 at the subapical region, and combined loss of MPP3 and Pals1 accelerates retinal degeneration.\",\n      \"method\": \"Conditional Mpp3 knockout mouse, immunofluorescence, co-immunoprecipitation, electroretinography, double-mutant genetic analysis\",\n      \"journal\": \"Glia\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — in vivo knockout with molecular and functional readouts, genetic epistasis via double knockout\",\n      \"pmids\": [\"23893895\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"Crystal structure of PALS1 PDZ-SH3-GK tandem bound to the Crumbs cytoplasmic tail (Crb-CT) shows the three domains form a structural supramodule; all three domains contribute to binding with ~70 nM affinity (~100-fold stronger than PDZ alone); mutations disrupting interdomain contacts weaken PALS1-Crb interaction and compromise PALS1-mediated polarity in MDCK cysts.\",\n      \"method\": \"Crystal structure determination, isothermal titration calorimetry, mutagenesis, MDCK cyst polarity assay\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — crystal structure plus ITC quantification plus mutagenesis plus functional cell assay in one study\",\n      \"pmids\": [\"25385611\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"Crystal structures of the human PALS1 PDZ domain with and without Crumbs C-terminal ligand (ERLI) reveal a key Phe residue that gates access to the PDZ peptide-binding groove; removal of this gating residue enhances binding affinity by >5-fold, suggesting regulated access of Crumbs to Pals1.\",\n      \"method\": \"Crystallography, fluorescence polarization binding assay, mutagenesis\",\n      \"journal\": \"Acta crystallographica. Section D, Biological crystallography\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — crystal structures (apo and bound) plus quantitative binding assays and mutagenesis\",\n      \"pmids\": [\"25760605\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"In Schwann cells, loss of Pals1 impairs radial sorting of axons, delays myelination, and reduces nerve conduction velocities; polyaxonal myelination persists in adult Pals1-deficient nerves; Pals1 interacts with Par3 and its loss reduces Par3 levels in Schwann cells; loss of Pals1 in oligodendrocytes does not affect CNS myelination.\",\n      \"method\": \"Conditional Pals1 knockout in Schwann cells and oligodendrocytes, nerve conduction velocity measurement, electron microscopy, Co-IP for Par3 interaction, immunofluorescence\",\n      \"journal\": \"The Journal of neuroscience\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — in vivo conditional knockout with multiple functional and molecular readouts, cell-type specific comparison\",\n      \"pmids\": [\"26203142\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"In the Drosophila embryonic epidermis, Stardust (Drosophila Pals1) is essential for correct subcellular localization of PATJ; L27 domain of PATJ is required for its correct localization and function; PATJ associates with both Baz-Sdt and Crb-Sdt complexes in mature epithelium.\",\n      \"method\": \"Drosophila genetics, biochemical pulldown, immunofluorescence, domain mutagenesis\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic and biochemical data in Drosophila ortholog, multiple complementary approaches, single lab\",\n      \"pmids\": [\"25847234\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"Deletion of Pals1 in cerebellar progenitors causes severely undersized cerebellum with disrupted layers and reduced granule cell production; Pals1 maintains cerebellar progenitor pools by preventing premature differentiation; Pals1 acts epistatically to Shh signaling—activated Smo cannot overcome Pals1 loss.\",\n      \"method\": \"Conditional Pals1 knockout mouse, electroretinography, cell cycle gene expression analysis, genetic epistasis with Smo activation\",\n      \"journal\": \"Development (Cambridge, England)\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — in vivo conditional knockout with epistasis experiment and multiple molecular readouts\",\n      \"pmids\": [\"26657772\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"VE-cadherin directly interacts with Pals1 through a membrane-proximal motif in the VE-cadherin cytoplasmic domain; VE-cadherin clusters Pals1 at cell-cell junctions; mutation of the Pals1-binding motif in VE-cadherin abrogates VE-cadherin's ability to regulate apicobasal polarity and vascular lumen formation.\",\n      \"method\": \"Co-immunoprecipitation, pulldown, site-directed mutagenesis, vascular lumen formation assay, polarity assay in endothelial cells\",\n      \"journal\": \"Molecular biology of the cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — direct binding assays with mutagenesis and functional consequence in lumen formation assay\",\n      \"pmids\": [\"27466317\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"Pals1 haploinsufficiency in mouse nephrons causes lethal cyst formation and proteinuria; in epithelial cell culture models, Pals1 functions as a dose-dependent upstream regulator of crosstalk between Hippo and TGF-β signaling pathways.\",\n      \"method\": \"Conditional heterozygous Pals1 knockout mouse, histology, signaling pathway analysis (Hippo/TGF-β), Drosophila nephrocyte analysis\",\n      \"journal\": \"Journal of the American Society of Nephrology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — in vivo haploinsufficiency model with signaling pathway readouts, single lab, pathway mechanistic detail limited\",\n      \"pmids\": [\"28154200\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"Cryo-EM structure of PALS1-SARS-CoV-2 E protein complex shows the E protein C-terminal DLLV motif binds a pocket formed exclusively by hydrophobic residues from both the PDZ and SH3 domains of PALS1.\",\n      \"method\": \"Cryo-electron microscopy structure determination\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — cryo-EM structure revealing atomic-level interaction involving both PDZ and SH3 domains\",\n      \"pmids\": [\"34103506\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"Crystal structures of PALS1 PDZ domain bound to SARS-CoV-1 and SARS-CoV-2 E protein PDZ-binding motifs show both viral peptides bind the PDZ domain with ~29.6 and ~22.8 μM affinity respectively; MERS-CoV C-terminal sequence does not bind PALS1 PDZ domain.\",\n      \"method\": \"Crystallography, surface plasmon resonance / fluorescence-based affinity measurements\",\n      \"journal\": \"Communications biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — crystal structures with quantitative binding data and specificity controls (MERS negative result)\",\n      \"pmids\": [\"34117354\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"Loss of Pals1 in colorectal cancer cells increases Arf6 and Rac1 activity, enhancing cell migration, invasion, and metastasis in vivo; this function is independent of canonical PALS1 binding partners (PATJ, CRB3) and tight junction formation.\",\n      \"method\": \"Pals1 knockout/knockdown, Arf6 and Rac1 activity assays (GTP-pulldown), in vitro migration/invasion assay, in vivo tumor transplantation assay\",\n      \"journal\": \"Molecular cancer\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — loss-of-function with mechanistic readouts (GTPase activity), in vivo validation, and domain independence established\",\n      \"pmids\": [\"33941200\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"Angiomotin isoform 2 (Ap80) promotes binding of PALS1 to KIF13B at the base of the primary cilium; Ap80 concentrates at and recruits PALS1 to the ciliary base; Ap80 depletion causes ciliary elongation and reduced agonist-induced SMO accumulation in cilia.\",\n      \"method\": \"Co-immunoprecipitation, live-cell imaging, ciliary length measurement, SMO ciliary accumulation assay, siRNA knockdown\",\n      \"journal\": \"Journal of cell science\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — Co-IP and live imaging with functional ciliary readout, single lab\",\n      \"pmids\": [\"35673984\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"Pals1 functions redundantly with the Arf6-GAP SMAP1 to inhibit Arf6 activity; in cells expressing SMAP1, loss of Pals1 disrupts tight junctions but does not increase Arf6/Rac1 activity or migration; only combined loss of both SMAP1 and Pals1 increases Arf6/Rac1 activity and cell migration.\",\n      \"method\": \"Pals1 and SMAP1 knockout/knockdown, Arf6/Rac1 activity assays, migration assay, patient cohort analysis\",\n      \"journal\": \"Cancer gene therapy\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — genetic epistasis via double knockout/knockdown with mechanistic GTPase activity readouts\",\n      \"pmids\": [\"36494580\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"In Pals1 cortical mutant mice, cell-in-cell (CIC) structures (entosis-like) form inside dividing cells, accompanied by lengthened mitosis and cytokinesis defects; ROCK inhibition abrogates CIC structures and restores normal mitosis length; genetic elimination of Trp53 rescues cortical size and reduces CIC structures, placing this entotic process downstream of Pals1 loss in microcephaly pathogenesis.\",\n      \"method\": \"Conditional Pals1 knockout mouse, ROCK inhibitor treatment, Trp53 genetic rescue, live imaging of cell division, electron microscopy\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — in vivo conditional knockout with pharmacological and genetic rescue experiments and multiple mechanistic readouts\",\n      \"pmids\": [\"36604424\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"PALS1 knockout in MDCKII cells causes redistribution of tight junction proteins from bicellular to tricellular contacts, increased paracellular permeability, delayed tight junction reassembly after Ca2+ removal or F-actin depolymerization, and redistribution of RhoA from junctions to cytosol; PALS1-dependent localization of TJ proteins at bicellular junctions requires its interaction with PATJ.\",\n      \"method\": \"CRISPR/Cas9 PALS1 knockout, transepithelial electrical resistance, confocal microscopy, Ca2+ switch assay, F-actin depolymerization/repolymerization assay, RhoA localization\",\n      \"journal\": \"Journal of cell science\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — clean CRISPR knockout with multiple orthogonal functional readouts and domain-interaction requirement established\",\n      \"pmids\": [\"38265145\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"MPP5/PALS1 physically interacts with YAP and TAZ in liver cancer cells; the PDZ domain of PALS1 is required for YAP binding (shown by domain deletion Co-IP); PALS1 facilitates nuclear exclusion of YAP and TAZ; reduced PALS1 expression correlates with nuclear YAP/TAZ accumulation in HCC tissue.\",\n      \"method\": \"Co-immunoprecipitation, proximity ligation assay, PDZ domain deletion analysis, proteomics/functional screening\",\n      \"journal\": \"International journal of molecular sciences\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — Co-IP with domain deletion and PLA confirmation, single lab, mechanism of nuclear exclusion not fully defined\",\n      \"pmids\": [\"39859373\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"PALS1 (MPP5) is an evolutionarily conserved MAGUK scaffold protein that forms the core of the apical CRB3–PALS1–PATJ polarity complex at tight junctions: its PDZ-SH3-GK supramodule binds the Crumbs cytoplasmic tail with high affinity, its L27N domain heterodimerizes with PATJ, its L27C domain binds mLin-7/MALS, and an internal N-terminal sequence is recognized by the Par-6 PDZ domain in a Cdc42-independent manner, thereby physically linking the CRB and Par6/Par3/aPKC polarity complexes; loss of PALS1 disrupts tight junction assembly, E-cadherin trafficking via the exocyst, aPKC recruitment, RhoA junctional localization, and YAP/TAZ nuclear exclusion, while in specialized tissues it controls Schwann cell radial sorting and myelin extension, retinal architecture, and cerebellar progenitor maintenance, and is subverted by coronavirus E proteins that compete for the PALS1 PDZ domain.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"PALS1 (MPP5) is an evolutionarily conserved MAGUK scaffold that nucleates the apical CRB3–PALS1–PATJ polarity complex governing epithelial tight junction assembly and apicobasal polarization [#0, #2, #3]. Through distinct binding modules it assembles a multiprotein scaffold: its PDZ domain engages the Crumbs cytoplasmic tail, while structural work shows the PDZ–SH3–GK tandem acts as a supramodule in which all three domains cooperate to bind the Crumbs tail with ~70 nM affinity, far exceeding the isolated PDZ [#0, #24]; a gating Phe residue in the PDZ groove regulates ligand access [#25]. Its tandem L27 domains drive supramolecular assembly, with the L27N domain heterodimerizing with PATJ and the L27C domain binding mLin-7/MALS, forming cognate, mutually independent heterodimeric pairs [#0, #9, #22]. PALS1 physically links the CRB and Par complexes, as the Par-6 PDZ domain recognizes an internal N-terminal sequence in PALS1 in a Cdc42-independent manner, with Par-6 and PATJ competing for binding [#4, #5]. Loss-of-function in MDCK cells delays tight junction formation, fails to recruit aPKC, abolishes PATJ expression, and prevents lumen formation [#3], and PALS1 additionally controls E-cadherin surface delivery via the exocyst [#14] and junctional RhoA localization, with bicellular tight junction protein positioning requiring the PATJ interaction [#37]. In specialized tissues PALS1 maintains retinal architecture by sustaining apical Crumbs complex localization, with its loss causing photoreceptor degeneration [#13, #19, #21]; controls Schwann cell radial sorting and myelin extension in concert with Par3 [#18, #26]; and maintains cerebellar and cortical progenitor pools, acting upstream of entotic cell-in-cell death and Trp53 in microcephaly pathogenesis [#28, #36]. Beyond canonical polarity, PALS1 restrains Arf6/Rac1 activity redundantly with SMAP1 to limit colorectal cancer migration and invasion [#33, #35] and promotes nuclear exclusion of YAP/TAZ [#38]. PALS1 is subverted by coronavirus E proteins, whose C-terminal PDZ-binding motifs bind a pocket formed jointly by the PALS1 PDZ and SH3 domains, redistributing PALS1 and disrupting junction formation [#17, #31, #32].\",\n  \"teleology\": [\n    {\n      \"year\": 2002,\n      \"claim\": \"Established PALS1 as the central scaffold of a conserved apical polarity complex by mapping its distinct binding modules to discrete partners.\",\n      \"evidence\": \"Co-IP, pulldowns, and domain mapping defining L27N–PATJ, L27C–mLin-7, and PDZ–CRB1 interactions\",\n      \"pmids\": [\"11927608\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Stoichiometry and ordered assembly of the full complex not resolved\", \"No structural basis for the interactions at this stage\"]\n    },\n    {\n      \"year\": 2003,\n      \"claim\": \"Demonstrated functionally that the CRB3–PALS1 PDZ interaction is required for tight junction formation and epithelial polarization, moving PALS1 from binding partner to functional regulator.\",\n      \"evidence\": \"Dominant-negative chimera overexpression and calcium switch / cyst morphogenesis assays in MDCK cells; CRB3 Co-IP and localization\",\n      \"pmids\": [\"12771187\", \"12527193\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Dominant-negative approach does not exclude off-target scaffolding effects\", \"Downstream effectors not defined\"]\n    },\n    {\n      \"year\": 2004,\n      \"claim\": \"Defined PALS1 as essential for apical polarity machinery by showing its depletion fails to recruit aPKC and abolishes PATJ, and revealed a non-canonical internal binding mode bridging CRB and Par complexes.\",\n      \"evidence\": \"Stable siRNA knockdown with TEER/cyst readouts; crystal structure of Par-6 PDZ–PALS1 internal ligand complex with mutagenesis and competition assays\",\n      \"pmids\": [\"14718565\", \"15475968\", \"15140881\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Regulation of Par-6 versus PATJ competition in vivo not established\", \"How aPKC recruitment is coupled mechanistically not resolved\"]\n    },\n    {\n      \"year\": 2005,\n      \"claim\": \"Extended the PALS1 interactome to MPP4/MPP3 and ezrin and resolved the L27 tetrameric assembly principle, linking PALS1 scaffolding to retinal and apical membrane organization.\",\n      \"evidence\": \"Yeast two-hybrid, GST pulldown, Co-IP, immunoEM in retina; NMR structures of L27 heterodimer pairs; ezrin loss-of-function in parietal cells\",\n      \"pmids\": [\"15914641\", \"15863617\", \"15677456\", \"15558731\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"GAT1 stabilization mechanism not defined (Medium evidence)\", \"Physiological role of MPP4/MPP3 recruitment to PALS1 not fully tested in vivo\"]\n    },\n    {\n      \"year\": 2006,\n      \"claim\": \"Showed PALS1 acts beyond tight junctions to control adherens junction E-cadherin trafficking via the exocyst and is required for Crumbs-family localization in retinal glia.\",\n      \"evidence\": \"Stable knockdown with E-cadherin surface biotinylation and exocyst localization in MDCK; RNAi with immunoEM in Müller glia\",\n      \"pmids\": [\"17182851\", \"16885194\", \"16519681\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Direct link between PALS1 and exocyst recruitment not biochemically defined\", \"Whether PALS1 trafficking role is separable from polarity scaffolding unclear\"]\n    },\n    {\n      \"year\": 2009,\n      \"claim\": \"Placed nephrocystins (NPHP1/NPHP4) in the same polarity pathway as PALS1, connecting the complex to ciliogenesis and cystogenesis.\",\n      \"evidence\": \"Co-IP and shRNA knockdown phenocopying PALS1 depletion in MDCK 3D cysts with cilia analysis\",\n      \"pmids\": [\"19755384\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Direct versus indirect nature of the nephrocystin–PALS1 interaction not fully resolved\", \"Mechanism linking PALS1 to ciliary function not defined\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Established an essential in vivo structural role for PALS1 in maintaining the retinal Crumbs complex and architecture, and reported a non-polarity role in TCR-driven NF-κB signaling.\",\n      \"evidence\": \"Conditional knockdown mouse with ERG/OCT/immunohistochemistry; siRNA knockdown with NF-κB reporter in T cells\",\n      \"pmids\": [\"22114289\", \"21479189\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanism coupling PALS1 to NF-κB activation not defined (Medium evidence)\", \"Whether retinal phenotype is purely structural or signaling-dependent not separated\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Resolved the L27 heterotrimeric assembly mechanism and demonstrated mutual interdependence of PALS1 and Crb proteins for apical localization in a disease-relevant retinal model.\",\n      \"evidence\": \"Crystal structure of Patj/Pals1/Mals2 L27 heterotrimer; conditional Pals1 knockout mouse mimicking Leber congenital amaurosis\",\n      \"pmids\": [\"22337881\", \"22398208\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How L27 assembly is regulated dynamically in cells not addressed\", \"Genetic causation in human retinal disease not directly tested in these studies\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Defined the structural basis for high-affinity Crumbs recognition, showing the PDZ–SH3–GK tandem functions as an integrated supramodule whose interdomain contacts are required for polarity function.\",\n      \"evidence\": \"Crystal structure of PALS1 PDZ-SH3-GK–Crb-CT with ITC and MDCK cyst polarity assay\",\n      \"pmids\": [\"25385611\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether supramodule conformation is regulated in vivo unclear\", \"Allosteric communication between domains not kinetically dissected\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Revealed regulated, gated access of Crumbs to the PDZ groove and extended PALS1 function to Schwann cell radial sorting/myelination and cerebellar progenitor maintenance via interactions with Par3 and Shh-independent control of differentiation.\",\n      \"evidence\": \"Apo/bound PDZ crystal structures with binding assays; conditional knockouts in Schwann cells, oligodendrocytes, and cerebellar progenitors with epistasis to Smo; Drosophila Stardust genetics\",\n      \"pmids\": [\"25760605\", \"26203142\", \"26657772\", \"25847234\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Physiological trigger controlling the PDZ gating residue unknown\", \"Mechanism by which PALS1 prevents premature cerebellar differentiation not molecularly defined\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Identified VE-cadherin as a direct PALS1 recruiter at endothelial junctions, linking PALS1 scaffolding to vascular lumen formation.\",\n      \"evidence\": \"Co-IP, pulldown, mutagenesis of VE-cadherin membrane-proximal motif, lumen formation assay\",\n      \"pmids\": [\"27466317\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How VE-cadherin-bound PALS1 directs apical membrane specification not detailed\", \"Relationship to Crumbs binding at the same PDZ not addressed\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Demonstrated PALS1 dosage sensitivity in vivo, with haploinsufficiency causing renal cysts and dysregulated Hippo–TGF-β crosstalk.\",\n      \"evidence\": \"Conditional heterozygous Pals1 knockout mouse with histology and signaling readouts; Drosophila nephrocyte analysis\",\n      \"pmids\": [\"28154200\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanistic detail of Hippo/TGF-β crosstalk regulation limited\", \"Direct molecular targets in these pathways not identified\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Defined how coronavirus E proteins subvert PALS1, showing the viral C-terminal motif binds a pocket formed jointly by the PDZ and SH3 domains with specificity excluding MERS-CoV.\",\n      \"evidence\": \"Cryo-EM of PALS1–SARS-CoV-2 E complex; crystal structures of PDZ bound to SARS-CoV-1/2 E motifs with affinity measurements and MERS negative control; earlier infection model showing PALS1 redistribution\",\n      \"pmids\": [\"34103506\", \"34117354\", \"20861307\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Functional consequence of E-PALS1 sequestration on infection outcome not fully dissected here\", \"Whether endogenous ligands engage the same composite pocket not tested\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Uncovered a Crumbs/PATJ-independent tumor-suppressive function whereby PALS1 restrains Arf6/Rac1 activity redundantly with SMAP1 to limit migration and invasion, and a role in ciliary base regulation via angiomotin and KIF13B.\",\n      \"evidence\": \"Pals1 and SMAP1 knockout with GTPase activity assays and migration assays plus patient cohort; Co-IP and live imaging of Ap80-PALS1-KIF13B at the cilium\",\n      \"pmids\": [\"36494580\", \"35673984\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Direct molecular mechanism by which PALS1 inhibits Arf6 GTPase not defined\", \"Ciliary KIF13B recruitment role rests on single-lab Medium evidence\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Placed PALS1 loss upstream of entotic cell-in-cell death and Trp53 in cortical microcephaly pathogenesis, linking polarity disruption to mitotic and cytokinesis defects.\",\n      \"evidence\": \"Conditional Pals1 knockout mouse with ROCK inhibition, Trp53 genetic rescue, and live imaging of division\",\n      \"pmids\": [\"36604424\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How PALS1 loss mechanistically triggers ROCK-dependent CIC formation not defined\", \"Direct molecular link from polarity loss to mitotic lengthening unclear\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Resolved that PALS1 positions tight junction proteins specifically at bicellular contacts and controls junctional RhoA, requiring its PATJ interaction.\",\n      \"evidence\": \"CRISPR knockout in MDCKII with TEER, Ca2+/F-actin reassembly assays, and RhoA localization\",\n      \"pmids\": [\"38265145\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanism linking PALS1 to RhoA junctional retention not defined\", \"How bicellular versus tricellular targeting is determined unclear\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Identified PALS1 as a PDZ-dependent regulator of YAP/TAZ nuclear exclusion in liver cancer, connecting the scaffold to Hippo effector localization.\",\n      \"evidence\": \"Co-IP, PLA, and PDZ deletion analysis in HCC cells with tissue correlation\",\n      \"pmids\": [\"39859373\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism of PALS1-mediated nuclear exclusion not defined\", \"Single-lab evidence without in vivo functional validation\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How PALS1's diverse functions—canonical polarity scaffolding versus Crumbs/PATJ-independent control of small-GTPase signaling, Hippo/YAP-TAZ, and progenitor maintenance—are integrated and differentially regulated across tissues remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No unifying model linking scaffolding to GTPase and Hippo regulation\", \"Post-translational or conformational switches controlling PALS1 function not characterized\", \"Direct human disease mutations causally tested in the corpus are limited\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [0, 4, 9, 22, 24]},\n      {\"term_id\": \"GO:0005198\", \"supporting_discovery_ids\": [3, 19, 37]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005886\", \"supporting_discovery_ids\": [0, 2, 3, 14, 29, 37]},\n      {\"term_id\": \"GO:0005929\", \"supporting_discovery_ids\": [34]},\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [38]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-1500931\", \"supporting_discovery_ids\": [0, 3, 14, 37]},\n      {\"term_id\": \"R-HSA-1266738\", \"supporting_discovery_ids\": [11, 19, 26, 28]},\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [33, 35, 38]},\n      {\"term_id\": \"R-HSA-1643685\", \"supporting_discovery_ids\": [17, 31, 32]}\n    ],\n    \"complexes\": [\n      \"CRB3–PALS1–PATJ apical polarity complex\",\n      \"PALS1–PATJ–MALS/Lin-7 L27 scaffold\",\n      \"Par6/Par3/aPKC complex (bridged via PALS1)\"\n    ],\n    \"partners\": [\n      \"CRB3\",\n      \"PATJ\",\n      \"PAR6\",\n      \"PARD3\",\n      \"MPP3\",\n      \"MPP4\",\n      \"EPB41L5\",\n      \"EZR\"\n    ],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":8,"faith_total":8,"faith_pct":100.0}}