{"gene":"VDAC1","run_date":"2026-06-11T09:02:06","timeline":{"discoveries":[{"year":2010,"finding":"VDAC1 is a target for Parkin-mediated Lys27 poly-ubiquitylation during PINK1/Parkin-directed mitophagy; PINK1 kinase activity and mitochondrial localization are prerequisites for Parkin translocation to depolarized mitochondria, after which Parkin ubiquitylates VDAC1 to recruit the autophagic adaptor p62/SQSTM1 for mitochondrial clearance.","method":"siRNA knockdown, co-immunoprecipitation, ubiquitin chain-linkage analysis, cell-based mitophagy assays in non-neuronal and neuronal cells","journal":"Nature cell biology","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal Co-IP, siRNA loss-of-function with defined phenotypic readout, ubiquitin linkage analysis, replicated in multiple cell types; widely cited and consistent with subsequent studies","pmids":["20098416"],"is_preprint":false},{"year":2020,"finding":"VDAC1 can be either mono- or poly-ubiquitinated by Parkin in a PINK1-dependent manner; poly-ubiquitination is required for mitophagy induction, whereas mono-ubiquitination at K274 suppresses apoptosis by limiting mitochondrial calcium uptake through the MCU channel. VDAC1 K274R mutation (blocking monoubiquitination) promotes apoptosis and Parkinson disease-related phenotypes in Drosophila.","method":"Ubiquitin mutant expression, transgenic Drosophila genetics, mitochondrial calcium measurements, MCU suppression epistasis","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods (biochemistry, Drosophila genetics, calcium measurements, epistasis), mechanistic discrimination between mono- and poly-ubiquitination outcomes","pmids":["32047033"],"is_preprint":false},{"year":2005,"finding":"Influenza virus PB1-F2 protein physically interacts with VDAC1 on the outer mitochondrial membrane (and with ANT3 on the inner membrane), triggering mitochondrial permeability transition, cytochrome c release, and enhancement of tBid-induced membrane permeabilization; permeability transition pore blockers inhibit PB1-F2-induced permeabilization.","method":"GST pulldown with mass spectrometry, purified mitochondria permeabilization assay, pharmacological PTPC inhibition","journal":"PLoS pathogens","confidence":"High","confidence_rationale":"Tier 1-2 / Moderate — GST pulldown with MS identification, functional reconstitution with purified mitochondria, pharmacological rescue; single lab but multiple orthogonal methods","pmids":["16201016"],"is_preprint":false},{"year":2009,"finding":"Nek1 kinase physically associates with VDAC1 and phosphorylates it on serine 193; this phosphorylation is required to maintain normal mitochondrial membrane permeability and prevent excessive cell death. A phospho-mimetic S193E mutant rescues exaggerated MMP after DNA damage, while a non-phosphorylatable S193A mutant induces cell death.","method":"Yeast two-hybrid, GST pulldown, reciprocal immunoprecipitation, kinase-dead mutant expression, siRNA knockdown, mitochondrial membrane permeability assays, VDAC1 phospho-mutant rescue experiments","journal":"Cell cycle (Georgetown, Tex.)","confidence":"High","confidence_rationale":"Tier 2 / Moderate — reciprocal Co-IP, GST pulldown, phospho-site mutagenesis with functional rescue, multiple cell lines; single lab but multiple orthogonal methods","pmids":["19158487"],"is_preprint":false},{"year":2014,"finding":"TSPO binds VDAC1 on the outer mitochondrial membrane; this interaction reduces mitochondrial coupling, promotes ROS overproduction, and thereby counteracts PARK2-mediated ubiquitination of proteins, inhibiting PINK1-PARK2-dependent mitophagy and abolishing SQSTM1/p62 and LC3 recruitment to mitochondria.","method":"Co-immunoprecipitation, VDAC1 knockdown/overexpression, mitophagy flux assays, ROS measurements, PARK2-ubiquitination assays","journal":"Autophagy","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP, loss-of-function with defined phenotype, ROS measurements; single lab, two orthogonal methods","pmids":["25470454"],"is_preprint":false},{"year":2008,"finding":"In cisplatin-induced apoptosis, VDAC1 acts downstream of Bak and upstream of Bax in a hierarchical pathway governing mitochondrial membrane permeabilization; VDAC1 knockdown or chemical inhibition prevents Bax conformational activation without affecting Bak activation.","method":"siRNA screen, VDAC1 chemical inhibition (DIDS), Bax/Bak knockdown epistasis, mitochondrial membrane potential assay, plasma membrane permeabilization assay","journal":"Oncogene","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — siRNA knockdown, chemical inhibition, genetic epistasis; single lab, multiple orthogonal methods","pmids":["18362892"],"is_preprint":false},{"year":2012,"finding":"Bcl-xL directly interacts with VDAC1; the interaction requires specific VDAC1 residues including the N-terminal domain, reduces VDAC1 channel conductance in bilayer reconstitution, and mediates Bcl-xL antiapoptotic activity, since Bcl-xL fails to protect against apoptosis in cells expressing VDAC1 mutants that cannot bind Bcl-xL.","method":"Microscale thermophoresis, bilayer-reconstituted conductance assay, surface plasmon resonance, site-directed mutagenesis, cell viability assays with staurosporine","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 / Moderate — in vitro binding with MST, bilayer reconstitution with conductance measurement, SPR, functional mutagenesis; single lab but multiple Tier 1 orthogonal methods","pmids":["22589539"],"is_preprint":false},{"year":2003,"finding":"VDAC1 expressed in the plasma membrane functions as a NADH-ferricyanide reductase; purified VDAC1 from both plasma membrane and mitochondria fractions exhibits this enzymatic activity, and targeting VDAC1 to the plasma membrane via an N-terminal signal peptide significantly increases cellular NADH-ferricyanide reductase activity.","method":"Subcellular fractionation, immunoprecipitation of enzymatic activity, VDAC1-GFP plasma-membrane targeting construct, confocal microscopy, FACS, enzymatic activity assay","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — enzymatic activity assay on purified protein, immunoprecipitation, subcellular targeting construct with confocal confirmation; single lab, multiple methods","pmids":["14573604"],"is_preprint":false},{"year":2008,"finding":"Hexokinase I and II bind VDAC1 through charged residues in several beta-strands and the N-terminal domain; disrupting the HK-VDAC1 interaction by mutagenesis or VDAC1-based peptides detaches HK from mitochondria, diminishes HK antiapoptotic activity, and reduces tumor cell survival.","method":"Site-directed mutagenesis of VDAC1, VDAC1-based peptide expression, HK-I-GFP mitochondrial localization assay, apoptosis assays","journal":"Biochimica et biophysica acta","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — structure-guided mutagenesis, peptide-disruption of interaction, functional apoptosis readout; single lab, multiple orthogonal methods","pmids":["19094960"],"is_preprint":false},{"year":2008,"finding":"Phosphorylated StAR interacts with VDAC1 on the outer mitochondrial membrane; this interaction facilitates processing of 37-kDa phospho-StAR to the 32-kDa intermediate required for steroidogenesis. In the absence of VDAC1, phospho-StAR is degraded by cysteine proteases before mitochondrial import.","method":"Co-immunoprecipitation, VDAC1 knockdown, protease inhibitor experiments, biochemical processing assays","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP, loss-of-function with defined biochemical phenotype; single lab, two orthogonal methods","pmids":["18250166"],"is_preprint":false},{"year":2011,"finding":"VDAC1 oligomerization contact sites involve beta-strands 1, 2, 16, and 19; replacing hydrophobic residues in these strands with charged residues interferes with oligomerization. Cysteine-scanning cross-linking confirms proximity of these strands in dimers. VDAC1 exists as a dimer under physiological conditions and undergoes conformational changes to higher oligomers upon apoptosis induction.","method":"Structure-based mutagenesis, cysteine-replacement cross-linking with BMOE, chemical cross-linking, computation-guided dimerization interface prediction","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 / Moderate — site-directed mutagenesis, cysteine cross-linking with defined reagents, chemical cross-linking, structure-based approach; single lab but multiple Tier 1 orthogonal methods","pmids":["22117062"],"is_preprint":false},{"year":2010,"finding":"VDAC1 cysteine residues Cys127 and Cys232 have distinct topologies: one faces the pore (accessible to bulky 5-FM but blocked by prior NEM labeling) and one faces the lipid bilayer. However, cysteine-less VDAC1 (both Cys→Ala) retains normal channel activity and supports apoptosis when overexpressed, demonstrating that the cysteines are not required for channel gating or apoptotic function.","method":"Bilayer reconstitution conductance assay, thiol-modifying agents (NEM, 5-FM, BMOE), cysteine-to-alanine mutagenesis, cell apoptosis assay, mitochondrial localization by fluorescence","journal":"The Biochemical journal","confidence":"High","confidence_rationale":"Tier 1 / Moderate — in vitro reconstitution, specific thiol-modifying reagents, mutagenesis with functional readout; single lab, multiple Tier 1 methods","pmids":["20192921"],"is_preprint":false},{"year":2015,"finding":"Itraconazole targets VDAC1 as its primary molecular target in endothelial cells; VDAC1 inhibition disrupts mitochondrial metabolism, raises the AMP:ATP ratio, activates AMPK, and thereby inhibits mTOR signaling. VDAC1-knockout cells are resistant to AMPK activation and mTOR inhibition by itraconazole, demonstrating VDAC1 as the mediator.","method":"VDAC1 knockdown and knockout cell lines, cellular thermal shift assay (implied by target identification), AMPK/mTOR pathway western blots, AMP:ATP ratio measurements, VDAC1-KO rescue experiments","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 2 / Strong — VDAC1 KO rescue experiment, KD phenocopy, pathway measurements, independent validation with second VDAC-targeting compound (erastin); multiple orthogonal approaches","pmids":["26655341"],"is_preprint":false},{"year":2013,"finding":"Elevated intracellular Ca2+ promotes VDAC1 oligomerization and apoptosis; Ca2+ chelation with BAPTA-AM inhibits VDAC1 oligomerization and apoptosis, while Ca2+ ionophore treatment induces VDAC1 oligomerization in the absence of other apoptotic stimuli. Inhibition of mitochondrial Ca2+ transport decreases VDAC1 oligomerization, and increased [Ca2+]i upregulates VDAC1 expression.","method":"Chemical cross-linking to monitor oligomerization, Ca2+ chelator (BAPTA-AM), Ca2+ ionophore treatment, AzRu-mediated inhibition of mitochondrial Ca2+ transport, cell apoptosis assays","journal":"Biochimica et biophysica acta","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — pharmacological manipulation with defined biochemical readout (oligomerization), multiple Ca2+-modulating conditions; single lab, consistent results across conditions","pmids":["23542128"],"is_preprint":false},{"year":2016,"finding":"DIDS and related anion transport inhibitors (SITS, H2DIDS, DNDS, DPC) directly interact with VDAC1 (shown by microscale thermophoresis and reduced bilayer conductance), inhibit VDAC1 oligomerization, and consequently suppress pro-apoptotic protein release, apoptosis, Ca2+ elevation, ROS production, and mitochondrial membrane potential dissipation.","method":"Microscale thermophoresis, bilayer-reconstituted VDAC1 conductance, chemical cross-linking, BRET2 in living cells, apoptosis assays","journal":"Biochimica et biophysica acta","confidence":"High","confidence_rationale":"Tier 1 / Moderate — direct binding by MST, bilayer electrophysiology, BRET2 oligomerization assay in living cells; single lab but Tier 1 methods with multiple orthogonal approaches","pmids":["27064145"],"is_preprint":false},{"year":2016,"finding":"Novel compounds (VBIT-3 and VBIT-4) directly interact with VDAC1, prevent VDAC1 oligomerization, inhibit apoptosis, restore mitochondrial membrane potential, decrease ROS production, prevent hexokinase detachment from mitochondria, and normalize intracellular Ca2+ levels.","method":"High-throughput compound screening, direct VDAC1 binding assays, chemical cross-linking for oligomerization, mitochondrial membrane potential assay, ROS assay, hexokinase binding assay, cell viability assays","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct binding confirmation, oligomerization assay, multiple functional readouts; single lab, multiple orthogonal methods","pmids":["27738100"],"is_preprint":false},{"year":2015,"finding":"Cyathin-R, a fungal diterpene, promotes VDAC1 oligomerization to mediate cytochrome c release and apoptosis in Bax/Bak-deficient cells; VDAC1 silencing prevents cyathin-R-induced apoptosis, demonstrating that VDAC1 can mediate apoptosis independently of Bax/Bak.","method":"Bax/Bak-deficient MEF cells, VDAC1 siRNA knockdown, chemical cross-linking for oligomerization, cytochrome c release assay, xenograft mouse model","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic loss-of-function (siRNA), defined mechanistic readout (oligomerization + Cyto c release), Bax/Bak-null epistasis; single lab, multiple methods","pmids":["26253170"],"is_preprint":false},{"year":2019,"finding":"Mutant SOD1 (G93A and G85R, but not wild-type SOD1) directly interacts with the N-terminal domain of VDAC1, reducing its channel conductance; a VDAC1 N-terminal domain-derived peptide inhibits mutant SOD1 toxicity in motor neuron-like cells and mouse embryonic stem cell-derived motor neurons.","method":"Direct binding assay with purified VDAC1, bilayer conductance measurement, N-terminally truncated VDAC1 construct, cell viability assay with peptide treatment","journal":"Frontiers in cellular neuroscience","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct binding to purified protein, bilayer electrophysiology showing functional effect, truncation mutant to define binding region; single lab, multiple orthogonal methods","pmids":["31474832"],"is_preprint":false},{"year":2023,"finding":"Under hypoxia, GPCPD1 is depalmitoylated by LYPLA1 and relocates to the outer mitochondrial membrane where it binds VDAC1, interferes with VDAC1 oligomerization, increasing VDAC1 monomers, which provide more anchor sites for PRKN-mediated polyubiquitination and consequent mitophagy induction.","method":"Co-immunoprecipitation, VDAC1 oligomerization assay (chemical cross-linking), PRKN ubiquitination assay, GPCPD1 depalmitoylation/localization tracking, siRNA knockdown","journal":"Autophagy","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP, oligomerization assay, ubiquitination assay, subcellular localization by fractionation; single lab, multiple orthogonal methods","pmids":["36803235"],"is_preprint":false},{"year":2023,"finding":"Parkin ubiquitinates VDAC1 at lysine 53; this site-specific ubiquitination interrupts VDAC1 oligomerization and prevents mitochondrial DNA release into the cytoplasm. VDAC1 K53R mutant (ubiquitination-deficient) forms oligomers resistant to Parkin suppression and triggers STING pathway activation in hepatic stellate cells.","method":"Site-directed mutagenesis (K53R), E3 ligase activity assay, VDAC1 oligomerization assay, mtDNA release assay, STING signaling readout, Parkin knockout mice","journal":"Experimental & molecular medicine","confidence":"High","confidence_rationale":"Tier 2 / Strong — specific ubiquitination site identified by mutagenesis, Parkin KO in vivo, multiple functional readouts (oligomerization, mtDNA release, STING); single lab but multiple orthogonal Tier 2 methods with in vivo validation","pmids":["36658227"],"is_preprint":false},{"year":2021,"finding":"HKII and VDAC1 form a binary complex in which HKII partially (not completely) occludes VDAC1's permeation pathway after membrane insertion of HKII's H-anchor. Phosphorylation of VDAC1 disrupts HKII binding, as confirmed by electrophysiology.","method":"Molecular dynamics simulations, Brownian dynamics docking, electrophysiology (channel conductance in presence/absence of HKII), VDAC1 phosphorylation mimetics","journal":"Communications biology","confidence":"Medium","confidence_rationale":"Tier 1 / Moderate — structural modeling validated by electrophysiology, phosphorylation mutant functional test; computational-structural approach with experimental electrophysiological validation, single lab","pmids":["34083717"],"is_preprint":false},{"year":2020,"finding":"TLK1 phosphorylates Nek1 at T141, and this activating phosphorylation contributes to Nek1-mediated phosphorylation and stability of VDAC1, thereby maintaining mitochondrial membrane integrity. Cells overexpressing kinase-dead Nek1-T141A show reduced VDAC1 phosphorylation, exaggerated mitochondrial permeability, reduced mitochondrial respiration, and increased apoptosis.","method":"Nek1-T141A mutant overexpression, VDAC1 phosphorylation western blot, mitochondrial permeability/cytochrome c release assay, oxygen consumption measurements, drug sensitivity assays","journal":"Cell cycle (Georgetown, Tex.)","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — phospho-mutant functional analysis, mitochondrial function assays, cytochrome c release; single lab, multiple functional readouts","pmids":["31914854"],"is_preprint":false},{"year":2018,"finding":"VDAC1 and VDAC2 cysteine residues from rat liver mitochondria undergo over-oxidation and succination as post-translational modifications, with cysteine over-oxidation appearing to be an exclusive feature of VDACs not found in other transmembrane mitochondrial proteins.","method":"Tryptic and chymotryptic proteolysis, UHPLC/High-Resolution ESI-MS/MS","journal":"Biochimica et biophysica acta. Bioenergetics","confidence":"Medium","confidence_rationale":"Tier 1 / Moderate — high-resolution mass spectrometry on native mitochondrial protein, comparative analysis with control proteins; single lab, rigorous analytical method","pmids":["29890122"],"is_preprint":false},{"year":2010,"finding":"Loss of Drosophila Porin (VDAC) causes elongated mitochondria in indirect flight muscle, while Porin overexpression produces fragmented mitochondria. Genetic epistasis with Drp1 (fission) and mitofusins (fusion) demonstrates that Porin regulates mitochondrial morphology through the fission/fusion machinery, and increased mitochondrial fission rescues locomotor defects in porin mutants.","method":"Drosophila porin mutant generation, mitochondrial morphology imaging, genetic epistasis with Drp1 and mitofusin mutants, locomotor behavior assays","journal":"PloS one","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Drosophila loss-of-function with morphological readout, genetic epistasis with fission/fusion machinery; single lab, ortholog study with defined genetic interactions","pmids":["20949033"],"is_preprint":false},{"year":2019,"finding":"In yeast (Por1/VDAC ortholog), porin associates with Tom22 to act as a sink for newly imported Tom22, modulating Tom22 integration into the TOM complex and thereby regulating the dynamic equilibrium between trimeric (3-channel, Tom22-containing) and dimeric (2-channel) TOM complexes. Porin also facilitates import of TIM40/MIA-dependent proteins by promoting the dimeric TOM complex.","method":"Co-immunoprecipitation, in vitro import assays, TOM complex native gel analysis, cell-cycle-dependent Tom22 phosphorylation analysis","journal":"Molecular cell","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP of Por1-Tom22 interaction, import assays, native gel analysis of TOM complex composition; single study but multiple orthogonal methods in yeast ortholog","pmids":["30738703"],"is_preprint":false},{"year":2018,"finding":"Yeast porins (Por1/Por2) interact with Mdm31 and Mdm35, and their depletion destabilizes Ups1 and Ups2, decreases cardiolipin levels by ~90%, and abolishes Ups2-dependent phosphatidylethanolamine synthesis. Por1 mutations that disrupt Mdm31/Mdm35 interactions (without affecting respiratory growth) also decrease cardiolipin levels, demonstrating a specific role in mitochondrial phospholipid metabolism conserved to mammalian VDAC.","method":"Yeast two-hybrid, co-immunoprecipitation, lipidomic analysis, Por1 interaction-defective mutants, HeLa cell VDAC knockdown","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP, lipidomics, interaction-defective mutagenesis, conservation tested in HeLa cells; single lab, multiple orthogonal methods","pmids":["30237174"],"is_preprint":false},{"year":2022,"finding":"VDAC1 downregulation by shRNA in human erythroblasts accelerates early maturation but blocks differentiation at the orthochromatic stage, reducing enucleation and increasing cell death. VDAC1 is required for phagophore membrane recruitment to regulate selective mitophagy of functional mitochondria during terminal erythropoiesis.","method":"shRNA knockdown, erythroid differentiation staging, mitochondrial retention assay, mitophagy flux assay, confocal microscopy","journal":"Haematologica","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — shRNA knockdown with defined stage-specific phenotype, mitophagy assay; single lab, multiple readouts","pmids":["33406813"],"is_preprint":false},{"year":2022,"finding":"Wild-type ataxin-3 deubiquitinates VDAC1; in SCA3 patients with expanded ataxin-3, VDAC1 deubiquitination and Parkin recruitment to depolarized mitochondria are inhibited, leading to impaired canonical mitophagy and compensatory increase in p62-linked mitophagy and autophagy.","method":"Patient-derived fibroblast cell lines, VDAC1 ubiquitination assay, Parkin translocation assay, mitophagy flux, OXPHOS complex measurement, ATP production assay","journal":"International journal of molecular sciences","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — patient-derived cells, ubiquitination assay, Parkin translocation, mitophagy flux; single lab but multiple functional assays","pmids":["35682609"],"is_preprint":false},{"year":1991,"finding":"Porin (VDAC) interacts with hexokinase and glycerol kinase on the outer mitochondrial membrane surface, providing these enzymes with preferred access to mitochondrially-generated ATP through metabolic microcompartmentation.","method":"Biochemical interaction studies, mitochondrial outer membrane protein binding assays (review of primary experimental evidence)","journal":"Biochemical medicine and metabolic biology","confidence":"Low","confidence_rationale":"Tier 3 / Moderate — review paper summarizing prior biochemical binding data; underlying experimental evidence is single-method pulldown-type assays from multiple labs","pmids":["1710914"],"is_preprint":false},{"year":2023,"finding":"MCU upregulation by cadmium intensifies MCU-VDAC1 interaction, enhances VDAC1 dimerization and ubiquitination, causing excessive mitophagy and hepatotoxicity; MCU inhibition (siRNA or Ru360) attenuates VDAC1 dimerization, excessive mitophagy, and hepatocyte death.","method":"Co-immunoprecipitation, VDAC1 oligomerization assay, siRNA knockdown, MCU heterozygous knockout mice, mitophagy flux assay","journal":"Advanced science (Weinheim, Baden-Wurttemberg, Germany)","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP, VDAC1 oligomerization assay, genetic KO in vivo, multiple functional readouts; single lab, multiple orthogonal methods","pmids":["36642847"],"is_preprint":false},{"year":2025,"finding":"VSTM2L forms a complex with VDAC1 and hexokinase 2 (HK2), enhancing their binding affinity and preventing VDAC1 oligomerization, thereby inhibiting ferroptosis and maintaining mitochondrial homeostasis in prostate cancer cells.","method":"Co-immunoprecipitation, VDAC1 oligomerization assay, siRNA knockdown, in vitro and in vivo ferroptosis assays","journal":"Nature communications","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP of ternary complex, VDAC1 oligomerization assay, loss-of-function with ferroptosis readout; single lab, multiple orthogonal methods","pmids":["39880844"],"is_preprint":false},{"year":2018,"finding":"Zinc and p53 disrupt mitochondrial binding of HK2 to VDAC1 in prostate cancer cells by phosphorylating VDAC1, a process mediated through Akt inhibition and GSK3β activation.","method":"Mitochondrial fractionation, co-immunoprecipitation of HK2-VDAC1, VDAC1 phosphorylation western blot, Akt/GSK3β pharmacological inhibition, xenograft model","journal":"Experimental cell research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP of HK2-VDAC1 complex, VDAC1 phosphorylation assay, kinase pathway manipulation; single lab, multiple orthogonal methods","pmids":["30528266"],"is_preprint":false},{"year":2023,"finding":"BAP31 directly binds VDAC1 and affects its oligomerization and polyubiquitination; BAP31 knockdown increases lipid peroxidation and facilitates ferroptosis, while BAP31 overexpression inhibits ferroptosis. HNF4A binds the BAP31 promoter and increases its transcription, placing VDAC1 oligomerization downstream of this HNF4A-BAP31 axis.","method":"Co-immunoprecipitation, VDAC1 oligomerization assay, ubiquitination assay, siRNA knockdown, lipid peroxidation assay, ChIP for HNF4A-BAP31 promoter interaction","journal":"Cell death & disease","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP, oligomerization assay, ubiquitination, ChIP, functional ferroptosis readout; single lab, multiple orthogonal methods","pmids":["37296105"],"is_preprint":false},{"year":2021,"finding":"VDAC1 promotes cardiomyocyte autophagy in anoxia/reoxygenation injury via the PINK1/Parkin pathway; VDAC1 knockdown inhibits PINK1/Parkin activation and Parkin translocation to mitochondria, reducing autophagic vacuole formation, ROS burst, and mitochondrial dysfunction.","method":"siRNA knockdown, autophagic flux assay, Parkin translocation immunofluorescence, ROS measurement, mitochondrial membrane potential assay","journal":"Cell biology international","confidence":"Low","confidence_rationale":"Tier 3 / Weak — siRNA knockdown with autophagy and pathway readouts; single lab, single main intervention method","pmids":["33675282"],"is_preprint":false},{"year":2023,"finding":"Alisol B directly binds VDAC1 at amino acid residues S196 and H184 in the ATP-binding region; mutations at these sites abolish the thermal stabilization effect of Alisol B on VDAC1, and VDAC1 binding mediates Alisol B's ability to decrease mitochondrial ATP production and activate AMPK independently of canonical upstream kinases.","method":"Cellular thermal shift assay (CETSA), molecular dynamics, ultrafiltration-LC/MS, site-directed mutagenesis of VDAC1 (S196 and H184 mutations), AMP:ATP ratio measurement","journal":"Phytomedicine : international journal of phytotherapy and phytopharmacology","confidence":"Medium","confidence_rationale":"Tier 1-2 / Moderate — CETSA binding assay, mutagenesis ablating binding, functional metabolic readout; single lab, multiple orthogonal methods","pmids":["38520833"],"is_preprint":false},{"year":1985,"finding":"Mitochondrial porin (VDAC) forms large pores permeable to hydrophilic substances up to ~6000 Da, with pore diameter of 1.2–2 nm, and pore conductance is controlled by electric fields and metabolic processes. These properties were established in early electrophysiological characterization.","method":"Planar lipid bilayer electrophysiology, molecular sieving assays","journal":"CRC critical reviews in biochemistry","confidence":"Medium","confidence_rationale":"Tier 1 / Strong — bilayer electrophysiology and permeability measurements, replicated across multiple laboratories over decades","pmids":["2415299"],"is_preprint":false}],"current_model":"VDAC1 is a voltage-dependent anion channel in the outer mitochondrial membrane that serves as a metabolite/ion gatekeeper (permeable to molecules up to ~6 kDa, gated by voltage) and acts as a central hub in mitochondria-mediated apoptosis: upon apoptotic stimulation, VDAC1 is overexpressed and oligomerizes via interfaces involving beta-strands 1, 2, 16, and 19—a Ca2+-promoted process—forming a large pore that releases cytochrome c and other pro-apoptotic proteins; VDAC1 oligomerization and apoptotic function are regulated by direct binding partners including hexokinase I/II (via N-terminal and charged beta-strand residues), anti-apoptotic Bcl-xL and Bcl-2, and the viral PB1-F2 protein (acting through the permeability transition pore), as well as by post-translational modifications including Parkin-mediated ubiquitination at K27 (poly-Ub, promotes mitophagy), K274 (mono-Ub, suppresses apoptosis via MCU/Ca2+), K53 (poly-Ub by Parkin, restricts oligomerization and mtDNA release), deubiquitination by ataxin-3, and phosphorylation at S193 by Nek1 (activated by TLK1) which maintains mitochondrial membrane integrity; at the plasma membrane, VDAC1 functions as a NADH-ferricyanide reductase; as an upstream regulator of the AMPK/mTOR axis, VDAC1 binding by itraconazole or alisol B (at H184/S196) disrupts mitochondrial ATP production, raises AMP:ATP ratio, and activates AMPK to inhibit mTOR; in yeast and Drosophila orthologs, porin additionally regulates mitochondrial morphology (fission/fusion balance), TOM complex assembly (by chaperoning Tom22), and mitochondrial phospholipid (cardiolipin) metabolism through interactions with Mdm31/Mdm35."},"narrative":{"mechanistic_narrative":"VDAC1 is a large voltage-gated channel of the outer mitochondrial membrane that forms a ~1.2–2 nm pore permeable to hydrophilic solutes up to ~6 kDa, gated by electric fields and metabolic state, positioning it as the principal gateway for metabolite and ion flux across the outer membrane [PMID:2415299]. Beyond conductance, VDAC1 is a central effector of mitochondria-mediated cell death: it dimerizes under physiological conditions through contacts involving beta-strands 1, 2, 16, and 19 and converts to higher-order oligomers upon apoptotic stimulation, a transition promoted by elevated intracellular Ca2+ and required for cytochrome c release [PMID:22117062, PMID:23542128]. VDAC1 oligomerization can drive apoptosis even in Bax/Bak-deficient cells, and in cisplatin-induced death VDAC1 acts downstream of Bak and upstream of Bax activation [PMID:18362892, PMID:26253170]. This oligomeric, death-promoting state is constrained by direct binding partners: hexokinase I/II dock onto charged beta-strand and N-terminal residues to partially occlude the pore and confer anti-apoptotic, pro-survival activity, while Bcl-xL binds the N-terminal domain to reduce channel conductance and mediate its protective effect [PMID:22589539, PMID:19094960, PMID:34083717]. Multiple chemical probes that bind VDAC1 directly—DIDS-class anion-transport inhibitors and the VBIT-3/VBIT-4 compounds—block oligomerization and suppress apoptosis, ROS, and Ca2+ elevation, validating oligomerization as the pharmacological lever [PMID:27064145, PMID:27738100]. VDAC1 is a major node in PINK1/Parkin mitophagy, undergoing site-specific ubiquitination by Parkin with opposing outcomes: K27 poly-ubiquitination recruits p62/SQSTM1 for mitochondrial clearance, K274 mono-ubiquitination suppresses apoptosis by limiting MCU-mediated Ca2+ uptake, and K53 poly-ubiquitination restricts oligomerization and blocks mtDNA release and downstream STING activation [PMID:20098416, PMID:32047033, PMID:36658227]. These modifications are countered by ataxin-3-mediated deubiquitination, whose loss in SCA3 impairs canonical mitophagy [PMID:35682609]. Phosphorylation of VDAC1 at Ser193 by Nek1—itself activated by TLK1—maintains membrane integrity and disrupts hexokinase binding [PMID:19158487, PMID:31914854]. VDAC1 also serves non-apoptotic roles, acting as the molecular target through which itraconazole and alisol B (binding H184/S196) lower mitochondrial ATP, raise the AMP:ATP ratio, and activate AMPK to inhibit mTOR [PMID:26655341, PMID:38520833], and functioning as a plasma-membrane NADH-ferricyanide reductase [PMID:14573604]. Studies of yeast and Drosophila orthologs extend its functions to mitochondrial morphology via the fission/fusion machinery, TOM complex assembly through chaperoning of Tom22, and cardiolipin/phospholipid metabolism via Mdm31/Mdm35 [PMID:20949033, PMID:30738703, PMID:30237174].","teleology":[{"year":1985,"claim":"Established the foundational biophysical identity of VDAC1 as a large, voltage- and metabolite-gated outer-membrane pore, defining the channel whose gating later studies would link to death and signaling.","evidence":"planar lipid bilayer electrophysiology and molecular sieving of purified mitochondrial porin","pmids":["2415299"],"confidence":"Medium","gaps":["Did not define the molecular determinants of gating","No connection to apoptosis or signaling at this stage"]},{"year":1991,"claim":"Framed VDAC as a scaffold for metabolic microcompartmentation by binding hexokinase and glycerol kinase at the outer membrane, an early concept of channel–enzyme coupling.","evidence":"review of biochemical outer-membrane binding assays for hexokinase and glycerol kinase","pmids":["1710914"],"confidence":"Low","gaps":["Review-level summary of single-method pulldown data","Binding residues and functional consequence not defined here"]},{"year":2003,"claim":"Showed VDAC1 has an enzymatic activity beyond pore conduction—NADH-ferricyanide reductase at the plasma membrane—indicating a moonlighting function distinct from its mitochondrial role.","evidence":"subcellular fractionation, immunoprecipitation of enzymatic activity, and plasma-membrane targeting constructs","pmids":["14573604"],"confidence":"Medium","gaps":["Physiological substrate/electron acceptor in vivo unclear","Relationship of this activity to mitochondrial VDAC1 function unresolved"]},{"year":2005,"claim":"Identified VDAC1 as a host target of influenza PB1-F2 that triggers permeability transition and cytochrome c release, linking VDAC1 to pathogen-induced apoptosis.","evidence":"GST pulldown with MS, purified-mitochondria permeabilization assay, and PTPC inhibitor rescue","pmids":["16201016"],"confidence":"High","gaps":["Binding interface on VDAC1 not mapped","Relative contribution of VDAC1 versus ANT3 not resolved"]},{"year":2008,"claim":"Placed VDAC1 in a hierarchical apoptotic pathway (downstream of Bak, upstream of Bax) and defined hexokinase docking residues, establishing VDAC1 as a regulated apoptotic checkpoint and HK as a survival ligand.","evidence":"siRNA, chemical inhibition (DIDS), Bax/Bak epistasis; VDAC1 mutagenesis and HK-detaching peptides with apoptosis readouts","pmids":["18362892","19094960"],"confidence":"Medium","gaps":["Mechanism coupling VDAC1 to Bax conformational change not defined","Whether HK binding acts solely by pore occlusion unresolved"]},{"year":2009,"claim":"Showed Nek1 phosphorylates VDAC1 at Ser193 to restrain excessive membrane permeability, revealing kinase control of VDAC1 death function.","evidence":"yeast two-hybrid, reciprocal Co-IP, kinase-dead and S193A/S193E phospho-mutant rescue of mitochondrial permeability","pmids":["19158487"],"confidence":"High","gaps":["Structural effect of S193 phosphorylation on the channel not defined","Upstream activation of Nek1 not addressed here"]},{"year":2010,"claim":"Defined VDAC1 as a Parkin substrate ubiquitinated at K27 to recruit p62 during PINK1/Parkin mitophagy, integrating VDAC1 into mitochondrial quality control.","evidence":"siRNA, reciprocal Co-IP, ubiquitin chain-linkage analysis, mitophagy assays in multiple cell types","pmids":["20098416"],"confidence":"High","gaps":["Whether VDAC1 ubiquitination is required versus accessory for mitophagy not fully resolved","Other Parkin sites not yet distinguished"]},{"year":2010,"claim":"Linked VDAC to mitochondrial morphology by demonstrating ortholog loss/overexpression shifts the fission/fusion balance via Drp1 and mitofusins.","evidence":"Drosophila porin mutants, morphology imaging, genetic epistasis with Drp1/mitofusins, locomotor assays","pmids":["20949033"],"confidence":"Medium","gaps":["Ortholog study; direct relevance to human VDAC1 not tested","Molecular mechanism connecting VDAC to fission/fusion machinery unknown"]},{"year":2010,"claim":"Mapped cysteine topology and showed cysteines are dispensable for channel and apoptotic function, ruling out a required redox-cysteine gating mechanism.","evidence":"bilayer conductance with thiol-modifying reagents and cysteine-to-alanine mutagenesis with apoptosis readout","pmids":["20192921"],"confidence":"High","gaps":["Does not exclude regulatory roles of cysteine oxidation under stress","Native redox state of cysteines in vivo not addressed"]},{"year":2011,"claim":"Identified the structural oligomerization interface (beta-strands 1, 2, 16, 19) and showed VDAC1 is a physiological dimer that climbs to higher oligomers upon apoptosis, providing the structural basis for pore-formation models.","evidence":"structure-based mutagenesis and cysteine cross-linking (BMOE) of dimer contacts","pmids":["22117062"],"confidence":"High","gaps":["Architecture of the apoptotic high-order oligomer not resolved at atomic level","How cargo such as cytochrome c traverses the oligomer unclear"]},{"year":2012,"claim":"Established direct Bcl-xL–VDAC1 binding via the N-terminal domain as a conductance-reducing, anti-apoptotic interaction, mechanistically distinct from HK binding.","evidence":"MST, SPR, bilayer conductance, site-directed mutagenesis, viability assays","pmids":["22589539"],"confidence":"High","gaps":["Whether Bcl-xL acts on monomer or blocks oligomerization not distinguished","In vivo relevance to tissue apoptosis not addressed"]},{"year":2013,"claim":"Showed Ca2+ is a direct trigger of VDAC1 oligomerization and apoptosis, connecting calcium signaling to pore formation.","evidence":"cross-linking oligomerization assays with Ca2+ chelator, ionophore, and mitochondrial Ca2+-transport inhibition","pmids":["23542128"],"confidence":"Medium","gaps":["Whether Ca2+ acts directly on VDAC1 or via partners not resolved","Ca2+ sensing site on VDAC1 not identified"]},{"year":2014,"claim":"Identified TSPO–VDAC1 binding as a negative regulator of mitophagy by promoting ROS and counteracting Parkin ubiquitination.","evidence":"Co-IP, VDAC1 knockdown/overexpression, mitophagy flux and ROS assays","pmids":["25470454"],"confidence":"Medium","gaps":["Single-lab Co-IP; binding interface unmapped","Mechanism by which TSPO–VDAC1 raises ROS not defined"]},{"year":2015,"claim":"Defined VDAC1 as the molecular target through which itraconazole lowers ATP and activates AMPK to inhibit mTOR, establishing VDAC1 as an upstream metabolic regulator.","evidence":"VDAC1 KO/KD rescue, AMPK/mTOR western blots, AMP:ATP measurements","pmids":["26655341"],"confidence":"High","gaps":["Drug binding site not mapped in this study","Whether AMPK activation requires channel inhibition versus oligomerization unclear"]},{"year":2015,"claim":"Demonstrated a small molecule (cyathin-R) can force VDAC1 oligomerization to drive apoptosis independently of Bax/Bak, reinforcing VDAC1 as an autonomous death effector.","evidence":"Bax/Bak-null MEFs, VDAC1 siRNA, cross-linking oligomerization, cytochrome c release, xenograft","pmids":["26253170"],"confidence":"Medium","gaps":["Direct binding of cyathin-R to VDAC1 not shown","Mechanism of oligomer induction not defined"]},{"year":2016,"claim":"Validated VDAC1 oligomerization as a druggable target through two compound classes (DIDS-type inhibitors and VBIT-3/4) that directly bind VDAC1 and block oligomerization and apoptosis.","evidence":"MST/direct binding, bilayer conductance, BRET2 oligomerization in living cells, apoptosis/ROS/Ca2+/HK assays","pmids":["27064145","27738100"],"confidence":"High","gaps":["Compound binding sites on VDAC1 not resolved structurally","Selectivity over VDAC2/3 not fully established"]},{"year":2018,"claim":"Showed kinase-pathway control of HK2–VDAC1 binding (zinc/p53 via Akt/GSK3β phosphorylating VDAC1) and reported VDAC-specific cysteine over-oxidation, expanding the PTM landscape regulating VDAC1.","evidence":"Co-IP, VDAC1 phosphorylation blots, kinase inhibition, xenograft; high-resolution MS of native VDAC cysteines","pmids":["30528266","29890122"],"confidence":"Medium","gaps":["Specific phospho-sites in the zinc/p53 axis not mapped","Functional consequence of cysteine over-oxidation/succination unknown"]},{"year":2018,"claim":"Established a conserved role for VDAC/porin in mitochondrial phospholipid metabolism through Mdm31/Mdm35 interactions controlling cardiolipin levels.","evidence":"yeast two-hybrid, Co-IP, lipidomics, interaction-defective Por1 mutants, validated in HeLa knockdown","pmids":["30237174"],"confidence":"Medium","gaps":["Mammalian VDAC1 partners equivalent to Mdm31/Mdm35 not identified","Mechanism linking VDAC to lipid-transfer machinery unclear"]},{"year":2019,"claim":"Defined a TOM-assembly function for porin as a Tom22 sink balancing trimeric/dimeric TOM complexes, extending VDAC's role into protein import.","evidence":"Co-IP, in vitro import assays, native-gel TOM analysis in yeast","pmids":["30738703"],"confidence":"Medium","gaps":["Conservation of the Tom22-chaperoning role in human VDAC1 not tested","Structural basis of the porin–Tom22 interaction unknown"]},{"year":2019,"claim":"Showed mutant SOD1 (ALS-associated) binds the VDAC1 N-terminus and reduces conductance, with an N-terminal peptide mitigating toxicity, implicating VDAC1 in motor neuron disease.","evidence":"direct binding to purified VDAC1, bilayer conductance, N-terminal truncation, motor-neuron viability with peptide","pmids":["31474832"],"confidence":"Medium","gaps":["In vivo relevance in ALS models not established here","Whether reduced conductance is the toxic mechanism unclear"]},{"year":2020,"claim":"Discriminated opposing outcomes of Parkin mono- versus poly-ubiquitination of VDAC1: poly-Ub drives mitophagy while K274 mono-Ub suppresses apoptosis by limiting MCU Ca2+ uptake, refining the ubiquitin code on VDAC1.","evidence":"ubiquitin mutants, transgenic Drosophila, mitochondrial Ca2+ measurements, MCU epistasis","pmids":["32047033"],"confidence":"High","gaps":["How K274 mono-Ub mechanistically limits MCU coupling not resolved","Mammalian in vivo confirmation of K274 phenotype pending"]},{"year":2020,"claim":"Placed the Nek1–VDAC1 axis under TLK1 control, showing TLK1 phosphorylation of Nek1-T141 supports VDAC1 phosphorylation, stability, and mitochondrial integrity.","evidence":"Nek1-T141A mutant, VDAC1 phosphorylation blots, mitochondrial permeability and respiration assays","pmids":["31914854"],"confidence":"Medium","gaps":["Direct TLK1→Nek1→VDAC1 chain not fully reconstituted","Quantitative contribution to VDAC1 stability unclear"]},{"year":2021,"claim":"Provided a structural model of the HKII–VDAC1 binary complex showing partial pore occlusion and phosphorylation-dependent disruption of binding, mechanistically uniting earlier HK and phospho-regulation findings.","evidence":"molecular/Brownian dynamics docking with electrophysiological validation and phospho-mimetics","pmids":["34083717"],"confidence":"Medium","gaps":["Computational model lacks experimental atomic structure","Which phospho-site drives disruption not pinned down"]},{"year":2022,"claim":"Linked ataxin-3-mediated VDAC1 deubiquitination to mitophagy, showing expanded ataxin-3 in SCA3 impairs Parkin recruitment and canonical mitophagy.","evidence":"SCA3 patient fibroblasts, VDAC1 ubiquitination and Parkin translocation assays, mitophagy flux, OXPHOS/ATP","pmids":["35682609"],"confidence":"Medium","gaps":["VDAC1 ubiquitin sites targeted by ataxin-3 not defined","Causality of VDAC1 deubiquitination in SCA3 pathology not established"]},{"year":2022,"claim":"Demonstrated a developmental requirement for VDAC1 in terminal erythropoiesis, recruiting phagophore membranes for selective mitophagy needed for enucleation.","evidence":"shRNA knockdown in human erythroblasts, differentiation staging, mitophagy flux, confocal","pmids":["33406813"],"confidence":"Medium","gaps":["Molecular basis of phagophore recruitment by VDAC1 unknown","Dependence on Parkin/PINK1 in this context not resolved"]},{"year":2023,"claim":"Defined K53 Parkin ubiquitination as a brake on VDAC1 oligomerization that prevents mtDNA release and STING-driven inflammation, connecting VDAC1 oligomerization to innate immune signaling.","evidence":"K53R mutagenesis, oligomerization and mtDNA-release assays, STING readout, Parkin-KO mice","pmids":["36658227"],"confidence":"High","gaps":["How K53 ubiquitination sterically blocks oligomerization unclear","Generality across cell types beyond hepatic stellate cells untested"]},{"year":2023,"claim":"Identified multiple oligomerization-regulating partners and contexts—GPCPD1 increasing monomers to enable mitophagy, MCU enhancing dimerization/ubiquitination, and BAP31 controlling oligomerization to gate ferroptosis—showing oligomeric state as a convergent regulatory hub.","evidence":"Co-IP, cross-linking oligomerization, ubiquitination and ferroptosis/mitophagy assays, MCU-KO mice, HNF4A ChIP","pmids":["36803235","36642847","37296105"],"confidence":"Medium","gaps":["Direct binding interfaces for these partners not mapped","Whether these regulators act independently or in shared complexes unknown"]},{"year":2023,"claim":"Mapped a defined small-molecule binding site (S196/H184 in the ATP-binding region) for alisol B that mediates AMPK activation via reduced ATP, refining the VDAC1–AMPK/mTOR mechanism.","evidence":"CETSA, ultrafiltration-LC/MS, site-directed mutagenesis ablating binding, AMP:ATP measurement","pmids":["38520833"],"confidence":"Medium","gaps":["Whether endogenous ligands occupy this site unknown","Relationship of this site to oligomerization not addressed"]},{"year":2025,"claim":"Showed VSTM2L stabilizes the HK2–VDAC1 complex to suppress VDAC1 oligomerization and inhibit ferroptosis, extending the survival-promoting role of HK binding to redox cell death.","evidence":"Co-IP of ternary complex, oligomerization assay, siRNA, in vitro/in vivo ferroptosis assays","pmids":["39880844"],"confidence":"Medium","gaps":["VSTM2L binding interface on the complex not mapped","Generality beyond prostate cancer cells untested"]},{"year":null,"claim":"The atomic architecture of the apoptotic high-order VDAC1 oligomer and the route by which it conducts cytochrome c and mtDNA remain undefined, as does the unifying logic by which the many partners, PTMs, and small molecules converge on a single oligomerization switch.","evidence":"","pmids":[],"confidence":"Low","gaps":["No high-resolution structure of the death-associated oligomer","No reconstituted system showing macromolecular cargo passage","Integration of competing ubiquitination/phosphorylation signals on oligomeric state unresolved"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0005215","term_label":"transporter activity","supporting_discovery_ids":[35,5]},{"term_id":"GO:0016491","term_label":"oxidoreductase activity","supporting_discovery_ids":[7]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[12,34]}],"localization":[{"term_id":"GO:0005739","term_label":"mitochondrion","supporting_discovery_ids":[35,24]},{"term_id":"GO:0005886","term_label":"plasma membrane","supporting_discovery_ids":[7]}],"pathway":[{"term_id":"R-HSA-5357801","term_label":"Programmed Cell Death","supporting_discovery_ids":[5,10,16]},{"term_id":"R-HSA-9612973","term_label":"Autophagy","supporting_discovery_ids":[0,1,19,26]},{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[12,34]},{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[24]},{"term_id":"R-HSA-1430728","term_label":"Metabolism","supporting_discovery_ids":[25,7]}],"complexes":["VDAC1 oligomer","VDAC1-hexokinase complex","TOM complex (yeast Por1)"],"partners":["HK1","HK2","BCL2L1","PRKN","NEK1","MCU","TSPO","ATXN3"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"P21796","full_name":"Non-selective voltage-gated ion channel VDAC1","aliases":["Outer mitochondrial membrane protein porin 1","Plasmalemmal porin","Porin 31HL","Porin 31HM","Voltage-dependent anion-selective channel protein 1","VDAC-1","hVDAC1"],"length_aa":283,"mass_kda":30.8,"function":"Non-selective voltage-gated ion channel that mediates the transport of anions and cations through the mitochondrion outer membrane and plasma membrane (PubMed:10661876, PubMed:11845315, PubMed:18755977, PubMed:30061676, PubMed:8420959). The channel at the outer mitochondrial membrane allows diffusion of small hydrophilic molecules; in the plasma membrane it is involved in cell volume regulation and apoptosis (PubMed:10661876, PubMed:11845315, PubMed:18755977, PubMed:8420959). It adopts an open conformation at low or zero membrane potential and a closed conformation at potentials above 30-40 mV (PubMed:10661876, PubMed:18755977, PubMed:8420959). The open state has a weak anion selectivity whereas the closed state is cation-selective (PubMed:18755977, PubMed:8420959). Binds various signaling molecules, including the sphingolipid ceramide, the phospholipid phosphatidylcholine, and the sterols cholesterol and oxysterol (PubMed:18755977, PubMed:31015432). In depolarized mitochondria, acts downstream of PRKN and PINK1 to promote mitophagy or prevent apoptosis; polyubiquitination by PRKN promotes mitophagy, while monoubiquitination by PRKN decreases mitochondrial calcium influx which ultimately inhibits apoptosis (PubMed:32047033). May participate in the formation of the permeability transition pore complex (PTPC) responsible for the release of mitochondrial products that triggers apoptosis (PubMed:15033708, PubMed:25296756). May mediate ATP export from cells (PubMed:30061676). Part of a complex composed of HSPA9, ITPR1 and VDAC1 that regulates mitochondrial calcium-dependent apoptosis by facilitating calcium transport from the ER lumen to the mitochondria intermembrane space thus providing calcium for the downstream calcium channel MCU that directly releases it into mitochondria matrix (By similarity). Mediates cytochrome c efflux (PubMed:20230784) Catalyzes the scrambling of phospholipids across the outer mitochondrial membrane; the mechanism is unrelated to channel activity and is capable of translocating both anionic and zwitterionic phospholipids","subcellular_location":"Mitochondrion outer membrane; Cell membrane; Membrane raft","url":"https://www.uniprot.org/uniprotkb/P21796/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/VDAC1","classification":"Common Essential","n_dependent_lines":939,"n_total_lines":1208,"dependency_fraction":0.777317880794702},"opencell":{"profiled":true,"resolved_as":"","ensg_id":"ENSG00000213585","cell_line_id":"CID000086","localizations":[{"compartment":"mitochondria","grade":3}],"interactors":[{"gene":"VDAC2","stoichiometry":10.0},{"gene":"VDAC3","stoichiometry":10.0},{"gene":"GK;GK3P","stoichiometry":4.0},{"gene":"NME2;NME1-NME2;NME1","stoichiometry":4.0},{"gene":"CALD1","stoichiometry":0.2},{"gene":"CYB5R3","stoichiometry":0.2},{"gene":"ELOVL1","stoichiometry":0.2},{"gene":"FKBP8","stoichiometry":0.2},{"gene":"MAPRE1","stoichiometry":0.2},{"gene":"PRKACA","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/target/CID000086","total_profiled":1310},"omim":[{"mim_id":"620751","title":"RETROTRANSPOSON GAG-LIKE 10; RTL10","url":"https://www.omim.org/entry/620751"},{"mim_id":"615664","title":"THYMOCYTE-EXPRESSED POSITIVE SELECTION-ASSOCIATED PROTEIN 1; TESPA1","url":"https://www.omim.org/entry/615664"},{"mim_id":"615239","title":"MICRO RNA 7-1; MIR7-1","url":"https://www.omim.org/entry/615239"},{"mim_id":"614520","title":"ENCEPHALOMYOPATHY, MITOCHONDRIAL, DUE TO VOLTAGE-DEPENDENT ANION CHANNEL DEFICIENCY","url":"https://www.omim.org/entry/614520"},{"mim_id":"610029","title":"VOLTAGE-DEPENDENT ANION CHANNEL 3; VDAC3","url":"https://www.omim.org/entry/610029"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"","locations":[],"tissue_specificity":"Tissue enhanced","tissue_distribution":"Detected in all","driving_tissues":[{"tissue":"skeletal muscle","ntpm":979.5},{"tissue":"tongue","ntpm":758.2}],"url":"https://www.proteinatlas.org/search/VDAC1"},"hgnc":{"alias_symbol":["MGC111064","PORIN"],"prev_symbol":[]},"alphafold":{"accession":"P21796","domains":[{"cath_id":"2.40.160.10","chopping":"6-281","consensus_level":"medium","plddt":93.5645,"start":6,"end":281}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/P21796","model_url":"https://alphafold.ebi.ac.uk/files/AF-P21796-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-P21796-F1-predicted_aligned_error_v6.png","plddt_mean":93.06},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=VDAC1","jax_strain_url":"https://www.jax.org/strain/search?query=VDAC1"},"sequence":{"accession":"P21796","fasta_url":"https://rest.uniprot.org/uniprotkb/P21796.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/P21796/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/P21796"}},"corpus_meta":[{"pmid":"20098416","id":"PMC_20098416","title":"PINK1/Parkin-mediated 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\"siRNA knockdown, co-immunoprecipitation, ubiquitin chain-linkage analysis, cell-based mitophagy assays in non-neuronal and neuronal cells\",\n      \"journal\": \"Nature cell biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal Co-IP, siRNA loss-of-function with defined phenotypic readout, ubiquitin linkage analysis, replicated in multiple cell types; widely cited and consistent with subsequent studies\",\n      \"pmids\": [\"20098416\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"VDAC1 can be either mono- or poly-ubiquitinated by Parkin in a PINK1-dependent manner; poly-ubiquitination is required for mitophagy induction, whereas mono-ubiquitination at K274 suppresses apoptosis by limiting mitochondrial calcium uptake through the MCU channel. VDAC1 K274R mutation (blocking monoubiquitination) promotes apoptosis and Parkinson disease-related phenotypes in Drosophila.\",\n      \"method\": \"Ubiquitin mutant expression, transgenic Drosophila genetics, mitochondrial calcium measurements, MCU suppression epistasis\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods (biochemistry, Drosophila genetics, calcium measurements, epistasis), mechanistic discrimination between mono- and poly-ubiquitination outcomes\",\n      \"pmids\": [\"32047033\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2005,\n      \"finding\": \"Influenza virus PB1-F2 protein physically interacts with VDAC1 on the outer mitochondrial membrane (and with ANT3 on the inner membrane), triggering mitochondrial permeability transition, cytochrome c release, and enhancement of tBid-induced membrane permeabilization; permeability transition pore blockers inhibit PB1-F2-induced permeabilization.\",\n      \"method\": \"GST pulldown with mass spectrometry, purified mitochondria permeabilization assay, pharmacological PTPC inhibition\",\n      \"journal\": \"PLoS pathogens\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Moderate — GST pulldown with MS identification, functional reconstitution with purified mitochondria, pharmacological rescue; single lab but multiple orthogonal methods\",\n      \"pmids\": [\"16201016\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"Nek1 kinase physically associates with VDAC1 and phosphorylates it on serine 193; this phosphorylation is required to maintain normal mitochondrial membrane permeability and prevent excessive cell death. A phospho-mimetic S193E mutant rescues exaggerated MMP after DNA damage, while a non-phosphorylatable S193A mutant induces cell death.\",\n      \"method\": \"Yeast two-hybrid, GST pulldown, reciprocal immunoprecipitation, kinase-dead mutant expression, siRNA knockdown, mitochondrial membrane permeability assays, VDAC1 phospho-mutant rescue experiments\",\n      \"journal\": \"Cell cycle (Georgetown, Tex.)\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal Co-IP, GST pulldown, phospho-site mutagenesis with functional rescue, multiple cell lines; single lab but multiple orthogonal methods\",\n      \"pmids\": [\"19158487\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"TSPO binds VDAC1 on the outer mitochondrial membrane; this interaction reduces mitochondrial coupling, promotes ROS overproduction, and thereby counteracts PARK2-mediated ubiquitination of proteins, inhibiting PINK1-PARK2-dependent mitophagy and abolishing SQSTM1/p62 and LC3 recruitment to mitochondria.\",\n      \"method\": \"Co-immunoprecipitation, VDAC1 knockdown/overexpression, mitophagy flux assays, ROS measurements, PARK2-ubiquitination assays\",\n      \"journal\": \"Autophagy\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP, loss-of-function with defined phenotype, ROS measurements; single lab, two orthogonal methods\",\n      \"pmids\": [\"25470454\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"In cisplatin-induced apoptosis, VDAC1 acts downstream of Bak and upstream of Bax in a hierarchical pathway governing mitochondrial membrane permeabilization; VDAC1 knockdown or chemical inhibition prevents Bax conformational activation without affecting Bak activation.\",\n      \"method\": \"siRNA screen, VDAC1 chemical inhibition (DIDS), Bax/Bak knockdown epistasis, mitochondrial membrane potential assay, plasma membrane permeabilization assay\",\n      \"journal\": \"Oncogene\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — siRNA knockdown, chemical inhibition, genetic epistasis; single lab, multiple orthogonal methods\",\n      \"pmids\": [\"18362892\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"Bcl-xL directly interacts with VDAC1; the interaction requires specific VDAC1 residues including the N-terminal domain, reduces VDAC1 channel conductance in bilayer reconstitution, and mediates Bcl-xL antiapoptotic activity, since Bcl-xL fails to protect against apoptosis in cells expressing VDAC1 mutants that cannot bind Bcl-xL.\",\n      \"method\": \"Microscale thermophoresis, bilayer-reconstituted conductance assay, surface plasmon resonance, site-directed mutagenesis, cell viability assays with staurosporine\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — in vitro binding with MST, bilayer reconstitution with conductance measurement, SPR, functional mutagenesis; single lab but multiple Tier 1 orthogonal methods\",\n      \"pmids\": [\"22589539\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2003,\n      \"finding\": \"VDAC1 expressed in the plasma membrane functions as a NADH-ferricyanide reductase; purified VDAC1 from both plasma membrane and mitochondria fractions exhibits this enzymatic activity, and targeting VDAC1 to the plasma membrane via an N-terminal signal peptide significantly increases cellular NADH-ferricyanide reductase activity.\",\n      \"method\": \"Subcellular fractionation, immunoprecipitation of enzymatic activity, VDAC1-GFP plasma-membrane targeting construct, confocal microscopy, FACS, enzymatic activity assay\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — enzymatic activity assay on purified protein, immunoprecipitation, subcellular targeting construct with confocal confirmation; single lab, multiple methods\",\n      \"pmids\": [\"14573604\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"Hexokinase I and II bind VDAC1 through charged residues in several beta-strands and the N-terminal domain; disrupting the HK-VDAC1 interaction by mutagenesis or VDAC1-based peptides detaches HK from mitochondria, diminishes HK antiapoptotic activity, and reduces tumor cell survival.\",\n      \"method\": \"Site-directed mutagenesis of VDAC1, VDAC1-based peptide expression, HK-I-GFP mitochondrial localization assay, apoptosis assays\",\n      \"journal\": \"Biochimica et biophysica acta\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — structure-guided mutagenesis, peptide-disruption of interaction, functional apoptosis readout; single lab, multiple orthogonal methods\",\n      \"pmids\": [\"19094960\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"Phosphorylated StAR interacts with VDAC1 on the outer mitochondrial membrane; this interaction facilitates processing of 37-kDa phospho-StAR to the 32-kDa intermediate required for steroidogenesis. In the absence of VDAC1, phospho-StAR is degraded by cysteine proteases before mitochondrial import.\",\n      \"method\": \"Co-immunoprecipitation, VDAC1 knockdown, protease inhibitor experiments, biochemical processing assays\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP, loss-of-function with defined biochemical phenotype; single lab, two orthogonal methods\",\n      \"pmids\": [\"18250166\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"VDAC1 oligomerization contact sites involve beta-strands 1, 2, 16, and 19; replacing hydrophobic residues in these strands with charged residues interferes with oligomerization. Cysteine-scanning cross-linking confirms proximity of these strands in dimers. VDAC1 exists as a dimer under physiological conditions and undergoes conformational changes to higher oligomers upon apoptosis induction.\",\n      \"method\": \"Structure-based mutagenesis, cysteine-replacement cross-linking with BMOE, chemical cross-linking, computation-guided dimerization interface prediction\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — site-directed mutagenesis, cysteine cross-linking with defined reagents, chemical cross-linking, structure-based approach; single lab but multiple Tier 1 orthogonal methods\",\n      \"pmids\": [\"22117062\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"VDAC1 cysteine residues Cys127 and Cys232 have distinct topologies: one faces the pore (accessible to bulky 5-FM but blocked by prior NEM labeling) and one faces the lipid bilayer. However, cysteine-less VDAC1 (both Cys→Ala) retains normal channel activity and supports apoptosis when overexpressed, demonstrating that the cysteines are not required for channel gating or apoptotic function.\",\n      \"method\": \"Bilayer reconstitution conductance assay, thiol-modifying agents (NEM, 5-FM, BMOE), cysteine-to-alanine mutagenesis, cell apoptosis assay, mitochondrial localization by fluorescence\",\n      \"journal\": \"The Biochemical journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — in vitro reconstitution, specific thiol-modifying reagents, mutagenesis with functional readout; single lab, multiple Tier 1 methods\",\n      \"pmids\": [\"20192921\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"Itraconazole targets VDAC1 as its primary molecular target in endothelial cells; VDAC1 inhibition disrupts mitochondrial metabolism, raises the AMP:ATP ratio, activates AMPK, and thereby inhibits mTOR signaling. VDAC1-knockout cells are resistant to AMPK activation and mTOR inhibition by itraconazole, demonstrating VDAC1 as the mediator.\",\n      \"method\": \"VDAC1 knockdown and knockout cell lines, cellular thermal shift assay (implied by target identification), AMPK/mTOR pathway western blots, AMP:ATP ratio measurements, VDAC1-KO rescue experiments\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — VDAC1 KO rescue experiment, KD phenocopy, pathway measurements, independent validation with second VDAC-targeting compound (erastin); multiple orthogonal approaches\",\n      \"pmids\": [\"26655341\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"Elevated intracellular Ca2+ promotes VDAC1 oligomerization and apoptosis; Ca2+ chelation with BAPTA-AM inhibits VDAC1 oligomerization and apoptosis, while Ca2+ ionophore treatment induces VDAC1 oligomerization in the absence of other apoptotic stimuli. Inhibition of mitochondrial Ca2+ transport decreases VDAC1 oligomerization, and increased [Ca2+]i upregulates VDAC1 expression.\",\n      \"method\": \"Chemical cross-linking to monitor oligomerization, Ca2+ chelator (BAPTA-AM), Ca2+ ionophore treatment, AzRu-mediated inhibition of mitochondrial Ca2+ transport, cell apoptosis assays\",\n      \"journal\": \"Biochimica et biophysica acta\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — pharmacological manipulation with defined biochemical readout (oligomerization), multiple Ca2+-modulating conditions; single lab, consistent results across conditions\",\n      \"pmids\": [\"23542128\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"DIDS and related anion transport inhibitors (SITS, H2DIDS, DNDS, DPC) directly interact with VDAC1 (shown by microscale thermophoresis and reduced bilayer conductance), inhibit VDAC1 oligomerization, and consequently suppress pro-apoptotic protein release, apoptosis, Ca2+ elevation, ROS production, and mitochondrial membrane potential dissipation.\",\n      \"method\": \"Microscale thermophoresis, bilayer-reconstituted VDAC1 conductance, chemical cross-linking, BRET2 in living cells, apoptosis assays\",\n      \"journal\": \"Biochimica et biophysica acta\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — direct binding by MST, bilayer electrophysiology, BRET2 oligomerization assay in living cells; single lab but Tier 1 methods with multiple orthogonal approaches\",\n      \"pmids\": [\"27064145\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"Novel compounds (VBIT-3 and VBIT-4) directly interact with VDAC1, prevent VDAC1 oligomerization, inhibit apoptosis, restore mitochondrial membrane potential, decrease ROS production, prevent hexokinase detachment from mitochondria, and normalize intracellular Ca2+ levels.\",\n      \"method\": \"High-throughput compound screening, direct VDAC1 binding assays, chemical cross-linking for oligomerization, mitochondrial membrane potential assay, ROS assay, hexokinase binding assay, cell viability assays\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct binding confirmation, oligomerization assay, multiple functional readouts; single lab, multiple orthogonal methods\",\n      \"pmids\": [\"27738100\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"Cyathin-R, a fungal diterpene, promotes VDAC1 oligomerization to mediate cytochrome c release and apoptosis in Bax/Bak-deficient cells; VDAC1 silencing prevents cyathin-R-induced apoptosis, demonstrating that VDAC1 can mediate apoptosis independently of Bax/Bak.\",\n      \"method\": \"Bax/Bak-deficient MEF cells, VDAC1 siRNA knockdown, chemical cross-linking for oligomerization, cytochrome c release assay, xenograft mouse model\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic loss-of-function (siRNA), defined mechanistic readout (oligomerization + Cyto c release), Bax/Bak-null epistasis; single lab, multiple methods\",\n      \"pmids\": [\"26253170\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"Mutant SOD1 (G93A and G85R, but not wild-type SOD1) directly interacts with the N-terminal domain of VDAC1, reducing its channel conductance; a VDAC1 N-terminal domain-derived peptide inhibits mutant SOD1 toxicity in motor neuron-like cells and mouse embryonic stem cell-derived motor neurons.\",\n      \"method\": \"Direct binding assay with purified VDAC1, bilayer conductance measurement, N-terminally truncated VDAC1 construct, cell viability assay with peptide treatment\",\n      \"journal\": \"Frontiers in cellular neuroscience\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct binding to purified protein, bilayer electrophysiology showing functional effect, truncation mutant to define binding region; single lab, multiple orthogonal methods\",\n      \"pmids\": [\"31474832\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"Under hypoxia, GPCPD1 is depalmitoylated by LYPLA1 and relocates to the outer mitochondrial membrane where it binds VDAC1, interferes with VDAC1 oligomerization, increasing VDAC1 monomers, which provide more anchor sites for PRKN-mediated polyubiquitination and consequent mitophagy induction.\",\n      \"method\": \"Co-immunoprecipitation, VDAC1 oligomerization assay (chemical cross-linking), PRKN ubiquitination assay, GPCPD1 depalmitoylation/localization tracking, siRNA knockdown\",\n      \"journal\": \"Autophagy\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP, oligomerization assay, ubiquitination assay, subcellular localization by fractionation; single lab, multiple orthogonal methods\",\n      \"pmids\": [\"36803235\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"Parkin ubiquitinates VDAC1 at lysine 53; this site-specific ubiquitination interrupts VDAC1 oligomerization and prevents mitochondrial DNA release into the cytoplasm. VDAC1 K53R mutant (ubiquitination-deficient) forms oligomers resistant to Parkin suppression and triggers STING pathway activation in hepatic stellate cells.\",\n      \"method\": \"Site-directed mutagenesis (K53R), E3 ligase activity assay, VDAC1 oligomerization assay, mtDNA release assay, STING signaling readout, Parkin knockout mice\",\n      \"journal\": \"Experimental & molecular medicine\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — specific ubiquitination site identified by mutagenesis, Parkin KO in vivo, multiple functional readouts (oligomerization, mtDNA release, STING); single lab but multiple orthogonal Tier 2 methods with in vivo validation\",\n      \"pmids\": [\"36658227\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"HKII and VDAC1 form a binary complex in which HKII partially (not completely) occludes VDAC1's permeation pathway after membrane insertion of HKII's H-anchor. Phosphorylation of VDAC1 disrupts HKII binding, as confirmed by electrophysiology.\",\n      \"method\": \"Molecular dynamics simulations, Brownian dynamics docking, electrophysiology (channel conductance in presence/absence of HKII), VDAC1 phosphorylation mimetics\",\n      \"journal\": \"Communications biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — structural modeling validated by electrophysiology, phosphorylation mutant functional test; computational-structural approach with experimental electrophysiological validation, single lab\",\n      \"pmids\": [\"34083717\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"TLK1 phosphorylates Nek1 at T141, and this activating phosphorylation contributes to Nek1-mediated phosphorylation and stability of VDAC1, thereby maintaining mitochondrial membrane integrity. Cells overexpressing kinase-dead Nek1-T141A show reduced VDAC1 phosphorylation, exaggerated mitochondrial permeability, reduced mitochondrial respiration, and increased apoptosis.\",\n      \"method\": \"Nek1-T141A mutant overexpression, VDAC1 phosphorylation western blot, mitochondrial permeability/cytochrome c release assay, oxygen consumption measurements, drug sensitivity assays\",\n      \"journal\": \"Cell cycle (Georgetown, Tex.)\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — phospho-mutant functional analysis, mitochondrial function assays, cytochrome c release; single lab, multiple functional readouts\",\n      \"pmids\": [\"31914854\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"VDAC1 and VDAC2 cysteine residues from rat liver mitochondria undergo over-oxidation and succination as post-translational modifications, with cysteine over-oxidation appearing to be an exclusive feature of VDACs not found in other transmembrane mitochondrial proteins.\",\n      \"method\": \"Tryptic and chymotryptic proteolysis, UHPLC/High-Resolution ESI-MS/MS\",\n      \"journal\": \"Biochimica et biophysica acta. Bioenergetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — high-resolution mass spectrometry on native mitochondrial protein, comparative analysis with control proteins; single lab, rigorous analytical method\",\n      \"pmids\": [\"29890122\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"Loss of Drosophila Porin (VDAC) causes elongated mitochondria in indirect flight muscle, while Porin overexpression produces fragmented mitochondria. Genetic epistasis with Drp1 (fission) and mitofusins (fusion) demonstrates that Porin regulates mitochondrial morphology through the fission/fusion machinery, and increased mitochondrial fission rescues locomotor defects in porin mutants.\",\n      \"method\": \"Drosophila porin mutant generation, mitochondrial morphology imaging, genetic epistasis with Drp1 and mitofusin mutants, locomotor behavior assays\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Drosophila loss-of-function with morphological readout, genetic epistasis with fission/fusion machinery; single lab, ortholog study with defined genetic interactions\",\n      \"pmids\": [\"20949033\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"In yeast (Por1/VDAC ortholog), porin associates with Tom22 to act as a sink for newly imported Tom22, modulating Tom22 integration into the TOM complex and thereby regulating the dynamic equilibrium between trimeric (3-channel, Tom22-containing) and dimeric (2-channel) TOM complexes. Porin also facilitates import of TIM40/MIA-dependent proteins by promoting the dimeric TOM complex.\",\n      \"method\": \"Co-immunoprecipitation, in vitro import assays, TOM complex native gel analysis, cell-cycle-dependent Tom22 phosphorylation analysis\",\n      \"journal\": \"Molecular cell\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP of Por1-Tom22 interaction, import assays, native gel analysis of TOM complex composition; single study but multiple orthogonal methods in yeast ortholog\",\n      \"pmids\": [\"30738703\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"Yeast porins (Por1/Por2) interact with Mdm31 and Mdm35, and their depletion destabilizes Ups1 and Ups2, decreases cardiolipin levels by ~90%, and abolishes Ups2-dependent phosphatidylethanolamine synthesis. Por1 mutations that disrupt Mdm31/Mdm35 interactions (without affecting respiratory growth) also decrease cardiolipin levels, demonstrating a specific role in mitochondrial phospholipid metabolism conserved to mammalian VDAC.\",\n      \"method\": \"Yeast two-hybrid, co-immunoprecipitation, lipidomic analysis, Por1 interaction-defective mutants, HeLa cell VDAC knockdown\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP, lipidomics, interaction-defective mutagenesis, conservation tested in HeLa cells; single lab, multiple orthogonal methods\",\n      \"pmids\": [\"30237174\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"VDAC1 downregulation by shRNA in human erythroblasts accelerates early maturation but blocks differentiation at the orthochromatic stage, reducing enucleation and increasing cell death. VDAC1 is required for phagophore membrane recruitment to regulate selective mitophagy of functional mitochondria during terminal erythropoiesis.\",\n      \"method\": \"shRNA knockdown, erythroid differentiation staging, mitochondrial retention assay, mitophagy flux assay, confocal microscopy\",\n      \"journal\": \"Haematologica\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — shRNA knockdown with defined stage-specific phenotype, mitophagy assay; single lab, multiple readouts\",\n      \"pmids\": [\"33406813\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"Wild-type ataxin-3 deubiquitinates VDAC1; in SCA3 patients with expanded ataxin-3, VDAC1 deubiquitination and Parkin recruitment to depolarized mitochondria are inhibited, leading to impaired canonical mitophagy and compensatory increase in p62-linked mitophagy and autophagy.\",\n      \"method\": \"Patient-derived fibroblast cell lines, VDAC1 ubiquitination assay, Parkin translocation assay, mitophagy flux, OXPHOS complex measurement, ATP production assay\",\n      \"journal\": \"International journal of molecular sciences\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — patient-derived cells, ubiquitination assay, Parkin translocation, mitophagy flux; single lab but multiple functional assays\",\n      \"pmids\": [\"35682609\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1991,\n      \"finding\": \"Porin (VDAC) interacts with hexokinase and glycerol kinase on the outer mitochondrial membrane surface, providing these enzymes with preferred access to mitochondrially-generated ATP through metabolic microcompartmentation.\",\n      \"method\": \"Biochemical interaction studies, mitochondrial outer membrane protein binding assays (review of primary experimental evidence)\",\n      \"journal\": \"Biochemical medicine and metabolic biology\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — review paper summarizing prior biochemical binding data; underlying experimental evidence is single-method pulldown-type assays from multiple labs\",\n      \"pmids\": [\"1710914\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"MCU upregulation by cadmium intensifies MCU-VDAC1 interaction, enhances VDAC1 dimerization and ubiquitination, causing excessive mitophagy and hepatotoxicity; MCU inhibition (siRNA or Ru360) attenuates VDAC1 dimerization, excessive mitophagy, and hepatocyte death.\",\n      \"method\": \"Co-immunoprecipitation, VDAC1 oligomerization assay, siRNA knockdown, MCU heterozygous knockout mice, mitophagy flux assay\",\n      \"journal\": \"Advanced science (Weinheim, Baden-Wurttemberg, Germany)\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP, VDAC1 oligomerization assay, genetic KO in vivo, multiple functional readouts; single lab, multiple orthogonal methods\",\n      \"pmids\": [\"36642847\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"VSTM2L forms a complex with VDAC1 and hexokinase 2 (HK2), enhancing their binding affinity and preventing VDAC1 oligomerization, thereby inhibiting ferroptosis and maintaining mitochondrial homeostasis in prostate cancer cells.\",\n      \"method\": \"Co-immunoprecipitation, VDAC1 oligomerization assay, siRNA knockdown, in vitro and in vivo ferroptosis assays\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP of ternary complex, VDAC1 oligomerization assay, loss-of-function with ferroptosis readout; single lab, multiple orthogonal methods\",\n      \"pmids\": [\"39880844\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"Zinc and p53 disrupt mitochondrial binding of HK2 to VDAC1 in prostate cancer cells by phosphorylating VDAC1, a process mediated through Akt inhibition and GSK3β activation.\",\n      \"method\": \"Mitochondrial fractionation, co-immunoprecipitation of HK2-VDAC1, VDAC1 phosphorylation western blot, Akt/GSK3β pharmacological inhibition, xenograft model\",\n      \"journal\": \"Experimental cell research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP of HK2-VDAC1 complex, VDAC1 phosphorylation assay, kinase pathway manipulation; single lab, multiple orthogonal methods\",\n      \"pmids\": [\"30528266\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"BAP31 directly binds VDAC1 and affects its oligomerization and polyubiquitination; BAP31 knockdown increases lipid peroxidation and facilitates ferroptosis, while BAP31 overexpression inhibits ferroptosis. HNF4A binds the BAP31 promoter and increases its transcription, placing VDAC1 oligomerization downstream of this HNF4A-BAP31 axis.\",\n      \"method\": \"Co-immunoprecipitation, VDAC1 oligomerization assay, ubiquitination assay, siRNA knockdown, lipid peroxidation assay, ChIP for HNF4A-BAP31 promoter interaction\",\n      \"journal\": \"Cell death & disease\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP, oligomerization assay, ubiquitination, ChIP, functional ferroptosis readout; single lab, multiple orthogonal methods\",\n      \"pmids\": [\"37296105\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"VDAC1 promotes cardiomyocyte autophagy in anoxia/reoxygenation injury via the PINK1/Parkin pathway; VDAC1 knockdown inhibits PINK1/Parkin activation and Parkin translocation to mitochondria, reducing autophagic vacuole formation, ROS burst, and mitochondrial dysfunction.\",\n      \"method\": \"siRNA knockdown, autophagic flux assay, Parkin translocation immunofluorescence, ROS measurement, mitochondrial membrane potential assay\",\n      \"journal\": \"Cell biology international\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — siRNA knockdown with autophagy and pathway readouts; single lab, single main intervention method\",\n      \"pmids\": [\"33675282\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"Alisol B directly binds VDAC1 at amino acid residues S196 and H184 in the ATP-binding region; mutations at these sites abolish the thermal stabilization effect of Alisol B on VDAC1, and VDAC1 binding mediates Alisol B's ability to decrease mitochondrial ATP production and activate AMPK independently of canonical upstream kinases.\",\n      \"method\": \"Cellular thermal shift assay (CETSA), molecular dynamics, ultrafiltration-LC/MS, site-directed mutagenesis of VDAC1 (S196 and H184 mutations), AMP:ATP ratio measurement\",\n      \"journal\": \"Phytomedicine : international journal of phytotherapy and phytopharmacology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1-2 / Moderate — CETSA binding assay, mutagenesis ablating binding, functional metabolic readout; single lab, multiple orthogonal methods\",\n      \"pmids\": [\"38520833\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1985,\n      \"finding\": \"Mitochondrial porin (VDAC) forms large pores permeable to hydrophilic substances up to ~6000 Da, with pore diameter of 1.2–2 nm, and pore conductance is controlled by electric fields and metabolic processes. These properties were established in early electrophysiological characterization.\",\n      \"method\": \"Planar lipid bilayer electrophysiology, molecular sieving assays\",\n      \"journal\": \"CRC critical reviews in biochemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Strong — bilayer electrophysiology and permeability measurements, replicated across multiple laboratories over decades\",\n      \"pmids\": [\"2415299\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"VDAC1 is a voltage-dependent anion channel in the outer mitochondrial membrane that serves as a metabolite/ion gatekeeper (permeable to molecules up to ~6 kDa, gated by voltage) and acts as a central hub in mitochondria-mediated apoptosis: upon apoptotic stimulation, VDAC1 is overexpressed and oligomerizes via interfaces involving beta-strands 1, 2, 16, and 19—a Ca2+-promoted process—forming a large pore that releases cytochrome c and other pro-apoptotic proteins; VDAC1 oligomerization and apoptotic function are regulated by direct binding partners including hexokinase I/II (via N-terminal and charged beta-strand residues), anti-apoptotic Bcl-xL and Bcl-2, and the viral PB1-F2 protein (acting through the permeability transition pore), as well as by post-translational modifications including Parkin-mediated ubiquitination at K27 (poly-Ub, promotes mitophagy), K274 (mono-Ub, suppresses apoptosis via MCU/Ca2+), K53 (poly-Ub by Parkin, restricts oligomerization and mtDNA release), deubiquitination by ataxin-3, and phosphorylation at S193 by Nek1 (activated by TLK1) which maintains mitochondrial membrane integrity; at the plasma membrane, VDAC1 functions as a NADH-ferricyanide reductase; as an upstream regulator of the AMPK/mTOR axis, VDAC1 binding by itraconazole or alisol B (at H184/S196) disrupts mitochondrial ATP production, raises AMP:ATP ratio, and activates AMPK to inhibit mTOR; in yeast and Drosophila orthologs, porin additionally regulates mitochondrial morphology (fission/fusion balance), TOM complex assembly (by chaperoning Tom22), and mitochondrial phospholipid (cardiolipin) metabolism through interactions with Mdm31/Mdm35.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"VDAC1 is a large voltage-gated channel of the outer mitochondrial membrane that forms a ~1.2–2 nm pore permeable to hydrophilic solutes up to ~6 kDa, gated by electric fields and metabolic state, positioning it as the principal gateway for metabolite and ion flux across the outer membrane [#35]. Beyond conductance, VDAC1 is a central effector of mitochondria-mediated cell death: it dimerizes under physiological conditions through contacts involving beta-strands 1, 2, 16, and 19 and converts to higher-order oligomers upon apoptotic stimulation, a transition promoted by elevated intracellular Ca2+ and required for cytochrome c release [#10, #13]. VDAC1 oligomerization can drive apoptosis even in Bax/Bak-deficient cells, and in cisplatin-induced death VDAC1 acts downstream of Bak and upstream of Bax activation [#5, #16]. This oligomeric, death-promoting state is constrained by direct binding partners: hexokinase I/II dock onto charged beta-strand and N-terminal residues to partially occlude the pore and confer anti-apoptotic, pro-survival activity, while Bcl-xL binds the N-terminal domain to reduce channel conductance and mediate its protective effect [#6, #8, #20]. Multiple chemical probes that bind VDAC1 directly—DIDS-class anion-transport inhibitors and the VBIT-3/VBIT-4 compounds—block oligomerization and suppress apoptosis, ROS, and Ca2+ elevation, validating oligomerization as the pharmacological lever [#14, #15]. VDAC1 is a major node in PINK1/Parkin mitophagy, undergoing site-specific ubiquitination by Parkin with opposing outcomes: K27 poly-ubiquitination recruits p62/SQSTM1 for mitochondrial clearance, K274 mono-ubiquitination suppresses apoptosis by limiting MCU-mediated Ca2+ uptake, and K53 poly-ubiquitination restricts oligomerization and blocks mtDNA release and downstream STING activation [#0, #1, #19]. These modifications are countered by ataxin-3-mediated deubiquitination, whose loss in SCA3 impairs canonical mitophagy [#27]. Phosphorylation of VDAC1 at Ser193 by Nek1—itself activated by TLK1—maintains membrane integrity and disrupts hexokinase binding [#3, #21]. VDAC1 also serves non-apoptotic roles, acting as the molecular target through which itraconazole and alisol B (binding H184/S196) lower mitochondrial ATP, raise the AMP:ATP ratio, and activate AMPK to inhibit mTOR [#12, #34], and functioning as a plasma-membrane NADH-ferricyanide reductase [#7]. Studies of yeast and Drosophila orthologs extend its functions to mitochondrial morphology via the fission/fusion machinery, TOM complex assembly through chaperoning of Tom22, and cardiolipin/phospholipid metabolism via Mdm31/Mdm35 [#23, #24, #25].\",\n  \"teleology\": [\n    {\n      \"year\": 1985,\n      \"claim\": \"Established the foundational biophysical identity of VDAC1 as a large, voltage- and metabolite-gated outer-membrane pore, defining the channel whose gating later studies would link to death and signaling.\",\n      \"evidence\": \"planar lipid bilayer electrophysiology and molecular sieving of purified mitochondrial porin\",\n      \"pmids\": [\"2415299\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Did not define the molecular determinants of gating\", \"No connection to apoptosis or signaling at this stage\"]\n    },\n    {\n      \"year\": 1991,\n      \"claim\": \"Framed VDAC as a scaffold for metabolic microcompartmentation by binding hexokinase and glycerol kinase at the outer membrane, an early concept of channel–enzyme coupling.\",\n      \"evidence\": \"review of biochemical outer-membrane binding assays for hexokinase and glycerol kinase\",\n      \"pmids\": [\"1710914\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Review-level summary of single-method pulldown data\", \"Binding residues and functional consequence not defined here\"]\n    },\n    {\n      \"year\": 2003,\n      \"claim\": \"Showed VDAC1 has an enzymatic activity beyond pore conduction—NADH-ferricyanide reductase at the plasma membrane—indicating a moonlighting function distinct from its mitochondrial role.\",\n      \"evidence\": \"subcellular fractionation, immunoprecipitation of enzymatic activity, and plasma-membrane targeting constructs\",\n      \"pmids\": [\"14573604\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Physiological substrate/electron acceptor in vivo unclear\", \"Relationship of this activity to mitochondrial VDAC1 function unresolved\"]\n    },\n    {\n      \"year\": 2005,\n      \"claim\": \"Identified VDAC1 as a host target of influenza PB1-F2 that triggers permeability transition and cytochrome c release, linking VDAC1 to pathogen-induced apoptosis.\",\n      \"evidence\": \"GST pulldown with MS, purified-mitochondria permeabilization assay, and PTPC inhibitor rescue\",\n      \"pmids\": [\"16201016\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Binding interface on VDAC1 not mapped\", \"Relative contribution of VDAC1 versus ANT3 not resolved\"]\n    },\n    {\n      \"year\": 2008,\n      \"claim\": \"Placed VDAC1 in a hierarchical apoptotic pathway (downstream of Bak, upstream of Bax) and defined hexokinase docking residues, establishing VDAC1 as a regulated apoptotic checkpoint and HK as a survival ligand.\",\n      \"evidence\": \"siRNA, chemical inhibition (DIDS), Bax/Bak epistasis; VDAC1 mutagenesis and HK-detaching peptides with apoptosis readouts\",\n      \"pmids\": [\"18362892\", \"19094960\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism coupling VDAC1 to Bax conformational change not defined\", \"Whether HK binding acts solely by pore occlusion unresolved\"]\n    },\n    {\n      \"year\": 2009,\n      \"claim\": \"Showed Nek1 phosphorylates VDAC1 at Ser193 to restrain excessive membrane permeability, revealing kinase control of VDAC1 death function.\",\n      \"evidence\": \"yeast two-hybrid, reciprocal Co-IP, kinase-dead and S193A/S193E phospho-mutant rescue of mitochondrial permeability\",\n      \"pmids\": [\"19158487\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural effect of S193 phosphorylation on the channel not defined\", \"Upstream activation of Nek1 not addressed here\"]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"Defined VDAC1 as a Parkin substrate ubiquitinated at K27 to recruit p62 during PINK1/Parkin mitophagy, integrating VDAC1 into mitochondrial quality control.\",\n      \"evidence\": \"siRNA, reciprocal Co-IP, ubiquitin chain-linkage analysis, mitophagy assays in multiple cell types\",\n      \"pmids\": [\"20098416\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether VDAC1 ubiquitination is required versus accessory for mitophagy not fully resolved\", \"Other Parkin sites not yet distinguished\"]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"Linked VDAC to mitochondrial morphology by demonstrating ortholog loss/overexpression shifts the fission/fusion balance via Drp1 and mitofusins.\",\n      \"evidence\": \"Drosophila porin mutants, morphology imaging, genetic epistasis with Drp1/mitofusins, locomotor assays\",\n      \"pmids\": [\"20949033\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Ortholog study; direct relevance to human VDAC1 not tested\", \"Molecular mechanism connecting VDAC to fission/fusion machinery unknown\"]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"Mapped cysteine topology and showed cysteines are dispensable for channel and apoptotic function, ruling out a required redox-cysteine gating mechanism.\",\n      \"evidence\": \"bilayer conductance with thiol-modifying reagents and cysteine-to-alanine mutagenesis with apoptosis readout\",\n      \"pmids\": [\"20192921\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Does not exclude regulatory roles of cysteine oxidation under stress\", \"Native redox state of cysteines in vivo not addressed\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Identified the structural oligomerization interface (beta-strands 1, 2, 16, 19) and showed VDAC1 is a physiological dimer that climbs to higher oligomers upon apoptosis, providing the structural basis for pore-formation models.\",\n      \"evidence\": \"structure-based mutagenesis and cysteine cross-linking (BMOE) of dimer contacts\",\n      \"pmids\": [\"22117062\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Architecture of the apoptotic high-order oligomer not resolved at atomic level\", \"How cargo such as cytochrome c traverses the oligomer unclear\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Established direct Bcl-xL–VDAC1 binding via the N-terminal domain as a conductance-reducing, anti-apoptotic interaction, mechanistically distinct from HK binding.\",\n      \"evidence\": \"MST, SPR, bilayer conductance, site-directed mutagenesis, viability assays\",\n      \"pmids\": [\"22589539\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether Bcl-xL acts on monomer or blocks oligomerization not distinguished\", \"In vivo relevance to tissue apoptosis not addressed\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Showed Ca2+ is a direct trigger of VDAC1 oligomerization and apoptosis, connecting calcium signaling to pore formation.\",\n      \"evidence\": \"cross-linking oligomerization assays with Ca2+ chelator, ionophore, and mitochondrial Ca2+-transport inhibition\",\n      \"pmids\": [\"23542128\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether Ca2+ acts directly on VDAC1 or via partners not resolved\", \"Ca2+ sensing site on VDAC1 not identified\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Identified TSPO–VDAC1 binding as a negative regulator of mitophagy by promoting ROS and counteracting Parkin ubiquitination.\",\n      \"evidence\": \"Co-IP, VDAC1 knockdown/overexpression, mitophagy flux and ROS assays\",\n      \"pmids\": [\"25470454\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single-lab Co-IP; binding interface unmapped\", \"Mechanism by which TSPO–VDAC1 raises ROS not defined\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Defined VDAC1 as the molecular target through which itraconazole lowers ATP and activates AMPK to inhibit mTOR, establishing VDAC1 as an upstream metabolic regulator.\",\n      \"evidence\": \"VDAC1 KO/KD rescue, AMPK/mTOR western blots, AMP:ATP measurements\",\n      \"pmids\": [\"26655341\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Drug binding site not mapped in this study\", \"Whether AMPK activation requires channel inhibition versus oligomerization unclear\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Demonstrated a small molecule (cyathin-R) can force VDAC1 oligomerization to drive apoptosis independently of Bax/Bak, reinforcing VDAC1 as an autonomous death effector.\",\n      \"evidence\": \"Bax/Bak-null MEFs, VDAC1 siRNA, cross-linking oligomerization, cytochrome c release, xenograft\",\n      \"pmids\": [\"26253170\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct binding of cyathin-R to VDAC1 not shown\", \"Mechanism of oligomer induction not defined\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Validated VDAC1 oligomerization as a druggable target through two compound classes (DIDS-type inhibitors and VBIT-3/4) that directly bind VDAC1 and block oligomerization and apoptosis.\",\n      \"evidence\": \"MST/direct binding, bilayer conductance, BRET2 oligomerization in living cells, apoptosis/ROS/Ca2+/HK assays\",\n      \"pmids\": [\"27064145\", \"27738100\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Compound binding sites on VDAC1 not resolved structurally\", \"Selectivity over VDAC2/3 not fully established\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Showed kinase-pathway control of HK2–VDAC1 binding (zinc/p53 via Akt/GSK3β phosphorylating VDAC1) and reported VDAC-specific cysteine over-oxidation, expanding the PTM landscape regulating VDAC1.\",\n      \"evidence\": \"Co-IP, VDAC1 phosphorylation blots, kinase inhibition, xenograft; high-resolution MS of native VDAC cysteines\",\n      \"pmids\": [\"30528266\", \"29890122\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Specific phospho-sites in the zinc/p53 axis not mapped\", \"Functional consequence of cysteine over-oxidation/succination unknown\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Established a conserved role for VDAC/porin in mitochondrial phospholipid metabolism through Mdm31/Mdm35 interactions controlling cardiolipin levels.\",\n      \"evidence\": \"yeast two-hybrid, Co-IP, lipidomics, interaction-defective Por1 mutants, validated in HeLa knockdown\",\n      \"pmids\": [\"30237174\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mammalian VDAC1 partners equivalent to Mdm31/Mdm35 not identified\", \"Mechanism linking VDAC to lipid-transfer machinery unclear\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Defined a TOM-assembly function for porin as a Tom22 sink balancing trimeric/dimeric TOM complexes, extending VDAC's role into protein import.\",\n      \"evidence\": \"Co-IP, in vitro import assays, native-gel TOM analysis in yeast\",\n      \"pmids\": [\"30738703\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Conservation of the Tom22-chaperoning role in human VDAC1 not tested\", \"Structural basis of the porin–Tom22 interaction unknown\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Showed mutant SOD1 (ALS-associated) binds the VDAC1 N-terminus and reduces conductance, with an N-terminal peptide mitigating toxicity, implicating VDAC1 in motor neuron disease.\",\n      \"evidence\": \"direct binding to purified VDAC1, bilayer conductance, N-terminal truncation, motor-neuron viability with peptide\",\n      \"pmids\": [\"31474832\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"In vivo relevance in ALS models not established here\", \"Whether reduced conductance is the toxic mechanism unclear\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Discriminated opposing outcomes of Parkin mono- versus poly-ubiquitination of VDAC1: poly-Ub drives mitophagy while K274 mono-Ub suppresses apoptosis by limiting MCU Ca2+ uptake, refining the ubiquitin code on VDAC1.\",\n      \"evidence\": \"ubiquitin mutants, transgenic Drosophila, mitochondrial Ca2+ measurements, MCU epistasis\",\n      \"pmids\": [\"32047033\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How K274 mono-Ub mechanistically limits MCU coupling not resolved\", \"Mammalian in vivo confirmation of K274 phenotype pending\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Placed the Nek1–VDAC1 axis under TLK1 control, showing TLK1 phosphorylation of Nek1-T141 supports VDAC1 phosphorylation, stability, and mitochondrial integrity.\",\n      \"evidence\": \"Nek1-T141A mutant, VDAC1 phosphorylation blots, mitochondrial permeability and respiration assays\",\n      \"pmids\": [\"31914854\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct TLK1→Nek1→VDAC1 chain not fully reconstituted\", \"Quantitative contribution to VDAC1 stability unclear\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Provided a structural model of the HKII–VDAC1 binary complex showing partial pore occlusion and phosphorylation-dependent disruption of binding, mechanistically uniting earlier HK and phospho-regulation findings.\",\n      \"evidence\": \"molecular/Brownian dynamics docking with electrophysiological validation and phospho-mimetics\",\n      \"pmids\": [\"34083717\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Computational model lacks experimental atomic structure\", \"Which phospho-site drives disruption not pinned down\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Linked ataxin-3-mediated VDAC1 deubiquitination to mitophagy, showing expanded ataxin-3 in SCA3 impairs Parkin recruitment and canonical mitophagy.\",\n      \"evidence\": \"SCA3 patient fibroblasts, VDAC1 ubiquitination and Parkin translocation assays, mitophagy flux, OXPHOS/ATP\",\n      \"pmids\": [\"35682609\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"VDAC1 ubiquitin sites targeted by ataxin-3 not defined\", \"Causality of VDAC1 deubiquitination in SCA3 pathology not established\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Demonstrated a developmental requirement for VDAC1 in terminal erythropoiesis, recruiting phagophore membranes for selective mitophagy needed for enucleation.\",\n      \"evidence\": \"shRNA knockdown in human erythroblasts, differentiation staging, mitophagy flux, confocal\",\n      \"pmids\": [\"33406813\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Molecular basis of phagophore recruitment by VDAC1 unknown\", \"Dependence on Parkin/PINK1 in this context not resolved\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Defined K53 Parkin ubiquitination as a brake on VDAC1 oligomerization that prevents mtDNA release and STING-driven inflammation, connecting VDAC1 oligomerization to innate immune signaling.\",\n      \"evidence\": \"K53R mutagenesis, oligomerization and mtDNA-release assays, STING readout, Parkin-KO mice\",\n      \"pmids\": [\"36658227\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How K53 ubiquitination sterically blocks oligomerization unclear\", \"Generality across cell types beyond hepatic stellate cells untested\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Identified multiple oligomerization-regulating partners and contexts—GPCPD1 increasing monomers to enable mitophagy, MCU enhancing dimerization/ubiquitination, and BAP31 controlling oligomerization to gate ferroptosis—showing oligomeric state as a convergent regulatory hub.\",\n      \"evidence\": \"Co-IP, cross-linking oligomerization, ubiquitination and ferroptosis/mitophagy assays, MCU-KO mice, HNF4A ChIP\",\n      \"pmids\": [\"36803235\", \"36642847\", \"37296105\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct binding interfaces for these partners not mapped\", \"Whether these regulators act independently or in shared complexes unknown\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Mapped a defined small-molecule binding site (S196/H184 in the ATP-binding region) for alisol B that mediates AMPK activation via reduced ATP, refining the VDAC1–AMPK/mTOR mechanism.\",\n      \"evidence\": \"CETSA, ultrafiltration-LC/MS, site-directed mutagenesis ablating binding, AMP:ATP measurement\",\n      \"pmids\": [\"38520833\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether endogenous ligands occupy this site unknown\", \"Relationship of this site to oligomerization not addressed\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Showed VSTM2L stabilizes the HK2–VDAC1 complex to suppress VDAC1 oligomerization and inhibit ferroptosis, extending the survival-promoting role of HK binding to redox cell death.\",\n      \"evidence\": \"Co-IP of ternary complex, oligomerization assay, siRNA, in vitro/in vivo ferroptosis assays\",\n      \"pmids\": [\"39880844\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"VSTM2L binding interface on the complex not mapped\", \"Generality beyond prostate cancer cells untested\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The atomic architecture of the apoptotic high-order VDAC1 oligomer and the route by which it conducts cytochrome c and mtDNA remain undefined, as does the unifying logic by which the many partners, PTMs, and small molecules converge on a single oligomerization switch.\",\n      \"evidence\": null,\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No high-resolution structure of the death-associated oligomer\", \"No reconstituted system showing macromolecular cargo passage\", \"Integration of competing ubiquitination/phosphorylation signals on oligomeric state unresolved\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0005215\", \"supporting_discovery_ids\": [35, 5]},\n      {\"term_id\": \"GO:0140110\", \"supporting_discovery_ids\": []},\n      {\"term_id\": \"GO:0016491\", \"supporting_discovery_ids\": [7]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [12, 34]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005741\", \"supporting_discovery_ids\": [10, 2]},\n      {\"term_id\": \"GO:0005739\", \"supporting_discovery_ids\": [35, 24]},\n      {\"term_id\": \"GO:0005886\", \"supporting_discovery_ids\": [7]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-5357801\", \"supporting_discovery_ids\": [5, 10, 16]},\n      {\"term_id\": \"R-HSA-9612973\", \"supporting_discovery_ids\": [0, 1, 19, 26]},\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [12, 34]},\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [24]},\n      {\"term_id\": \"R-HSA-1430728\", \"supporting_discovery_ids\": [25, 7]}\n    ],\n    \"complexes\": [\n      \"VDAC1 oligomer\",\n      \"VDAC1-hexokinase complex\",\n      \"TOM complex (yeast Por1)\"\n    ],\n    \"partners\": [\n      \"HK1\",\n      \"HK2\",\n      \"BCL2L1\",\n      \"PRKN\",\n      \"NEK1\",\n      \"MCU\",\n      \"TSPO\",\n      \"ATXN3\"\n    ],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":9,"faith_total":10,"faith_pct":90.0}}