{ "map": "QBM-01", "title": "Mitochondrial electron transport and oxidative phosphorylation", "qbo_version": "0.1.0", "nodes": [ { "node_id": "NADH_POOL", "qbo": "QBO:NADH_POOL", "label": "NADH / NAD+", "kind": "simple_chemical", "compartment": "mitochondrial_matrix", "evidence_tier": "T4", "confidence": "verified", "quantum_class": [ "structural_context" ], "nuclei": [], "agi": [], "magnetically_addressable": false, "rationale": null, "caveat": null, "evidence": [] }, { "node_id": "SUCCINATE", "qbo": "QBO:SUCCINATE", "label": "Succinate", "kind": "simple_chemical", "compartment": "mitochondrial_matrix", "evidence_tier": "T4", "confidence": "verified", "quantum_class": [ "structural_context" ], "nuclei": [], "agi": [], "magnetically_addressable": false, "rationale": null, "caveat": null, "evidence": [] }, { "node_id": "O2", "qbo": "QBO:O2", "label": "O2", "kind": "simple_chemical", "compartment": "mitochondrial_matrix", "evidence_tier": "T4", "confidence": "verified", "quantum_class": [ "structural_context" ], "nuclei": [], "agi": [], "magnetically_addressable": false, "rationale": null, "caveat": null, "evidence": [] }, { "node_id": "COMPLEX_I", "qbo": "QBO:COMPLEX_I", "label": "Complex I (NADH:ubiquinone oxidoreductase)", "kind": "complex", "compartment": "mitochondrial_inner_membrane", "evidence_tier": "T3", "confidence": "inferred", "quantum_class": [ "flavin_semiquinone", "iron_sulfur_4Fe4S", "iron_sulfur_2Fe2S", "ros_leak_site" ], "nuclei": [ "1H", "14N", "57Fe", "33S" ], "agi": [ "AT5G37510", "AT5G08530", "AT4G02580", "AT5G11770" ], "magnetically_addressable": true, "rationale": "The FMN site forms a flavin semiquinone during turnover and is a known superoxide-producing leak site, and the Fe/S chain performs sequential one-electron transfers \u2014 both of the physical routes the radical-pair and hyperfine arguments require. No published experiment has applied a near-null field and measured plant complex I activity, so this is a hypothesis with a mechanism, not a result.\n", "caveat": "Electron transfer along the Fe/S chain is fast relative to plausible singlet-triplet mixing times, so a coherent radical-pair effect here is harder to argue than at the flavin. Treat the flavin and the cluster chain as separate hypotheses rather than one.\n", "evidence": [] }, { "node_id": "COMPLEX_I_FMN", "qbo": "QBO:COMPLEX_I_FMN", "label": "Complex I FMN site", "kind": "cofactor", "compartment": "mitochondrial_matrix", "evidence_tier": "T3", "confidence": "inferred", "quantum_class": [ "flavin_semiquinone", "radical_pair_acceptor", "ros_leak_site" ], "nuclei": [ "1H", "14N" ], "agi": [ "AT5G08530" ], "magnetically_addressable": true, "rationale": "A one-electron-reduced flavin is the best-characterised magnetosensitive species in biology; the same chemistry underlies the cryptochrome radical-pair model. The review's argument is precisely that this chemistry is not confined to photoreceptors.\n", "caveat": null, "evidence": [] }, { "node_id": "COMPLEX_II", "qbo": "QBO:COMPLEX_II", "label": "Complex II (succinate dehydrogenase)", "kind": "complex", "compartment": "mitochondrial_inner_membrane", "evidence_tier": "T3", "confidence": "inferred", "quantum_class": [ "flavin_semiquinone", "iron_sulfur_2Fe2S", "iron_sulfur_4Fe4S", "iron_sulfur_3Fe4S", "ros_leak_site" ], "nuclei": [ "1H", "14N", "57Fe", "33S" ], "agi": [ "AT5G66760", "AT3G27380", "AT5G40650", "AT5G09600", "AT2G46505" ], "magnetically_addressable": true, "rationale": "Carries all three cluster types plus a covalent flavin, and sits at the junction the review nominates as the bottleneck \u2014 a change here propagates into both TCA flux and respiratory electron flow.\n", "caveat": null, "evidence": [] }, { "node_id": "ALT_NADH_DH", "qbo": "QBO:ALT_NADH_DH", "label": "Alternative NAD(P)H dehydrogenases (NDA/NDB)", "kind": "macromolecule", "compartment": "mitochondrial_inner_membrane", "evidence_tier": "T3", "confidence": "inferred", "quantum_class": [ "flavin_semiquinone" ], "nuclei": [ "1H", "14N" ], "agi": [ "AT1G07180", "AT2G29990", "AT4G28220", "AT4G05020", "AT2G20800" ], "magnetically_addressable": true, "rationale": "FAD-dependent, so the same flavin semiquinone chemistry applies. Included mainly as the second confounder alongside AOX \u2014 a plant can route around a complex I lesion, which blunts any phenotype and must be controlled for.\n", "caveat": null, "evidence": [] }, { "node_id": "UBIQUINONE_POOL", "qbo": "QBO:UBIQUINONE_POOL", "label": "Ubiquinone pool (UQ / UQH2)", "kind": "simple_chemical", "compartment": "mitochondrial_inner_membrane", "evidence_tier": "T4", "confidence": "verified", "quantum_class": [ "structural_context" ], "nuclei": [], "agi": [], "magnetically_addressable": false, "rationale": null, "caveat": null, "evidence": [] }, { "node_id": "UBISEMIQUINONE", "qbo": "QBO:UBISEMIQUINONE", "label": "Ubisemiquinone (UQ\u00b7\u2212)", "kind": "simple_chemical", "compartment": "mitochondrial_inner_membrane", "evidence_tier": "T3", "confidence": "inferred", "quantum_class": [ "semiquinone_radical", "radical_pair_donor", "ros_leak_site" ], "nuclei": [ "1H" ], "agi": [], "magnetically_addressable": true, "rationale": "A free-radical intermediate held in a protein pocket. If any respiratory species supports spin-correlated chemistry, this is the leading candidate.\n", "caveat": null, "evidence": [] }, { "node_id": "AOX", "qbo": "QBO:AOX", "label": "Alternative oxidase (AOX)", "kind": "macromolecule", "compartment": "mitochondrial_inner_membrane", "evidence_tier": "T4", "confidence": "inferred", "quantum_class": [ "structural_context" ], "nuclei": [], "agi": [ "AT3G22370", "AT3G22360", "AT3G27620", "AT1G32350", "AT5G64210" ], "magnetically_addressable": false, "rationale": null, "caveat": null, "evidence": [] }, { "node_id": "RIESKE_FES", "qbo": "QBO:RIESKE_FES", "label": "Rieske [2Fe-2S] centre (complex III)", "kind": "macromolecule", "compartment": "mitochondrial_inner_membrane", "evidence_tier": "T3", "confidence": "inferred", "quantum_class": [ "rieske_2Fe2S", "semiquinone_radical", "ros_leak_site" ], "nuclei": [ "57Fe", "33S", "1H" ], "agi": [ "AT5G13430", "AT5G13440" ], "magnetically_addressable": true, "rationale": "The Qo site generates a kinetically stabilised ubisemiquinone \u2014 a genuine, comparatively long-lived organic radical in a defined protein pocket, which is the most favourable setting for a field-dependent branching effect anywhere in the respiratory chain.\n", "caveat": "Qo-site semiquinone is short-lived and its occupancy is debated; a field effect here would be easier to argue if lifetime were measured under the relevant conditions.\n", "evidence": [] }, { "node_id": "CYTOCHROME_C", "qbo": "QBO:CYTOCHROME_C", "label": "Cytochrome c", "kind": "macromolecule", "compartment": "mitochondrial_intermembrane_space", "evidence_tier": "T3", "confidence": "inferred", "quantum_class": [ "heme_electron_carrier" ], "nuclei": [ "57Fe", "1H" ], "agi": [ "AT1G22840", "AT4G10040" ], "magnetically_addressable": true, "rationale": "A one-electron heme carrier, paramagnetic in the ferric state. Included because Racca et al. place cytochrome c on the path from mitochondrial state to germination timing, which is the developmental window the review argues matters most.\n", "caveat": null, "evidence": [ { "ref": "Racca2022", "doi": "10.1111/nph.18287", "claim": "Cytochrome c and the transcription factor ABI4 link mitochondrial status to ABA-dependent seed germination.\n", "direction": "altered", "field_regime": null, "species": "Arabidopsis thaliana" } ] }, { "node_id": "COMPLEX_IV", "qbo": "QBO:COMPLEX_IV", "label": "Complex IV (cytochrome c oxidase)", "kind": "complex", "compartment": "mitochondrial_inner_membrane", "evidence_tier": "T3", "confidence": "inferred", "quantum_class": [ "heme_copper_binuclear", "cu_a_binuclear", "heme_electron_carrier" ], "nuclei": [ "57Fe", "1H" ], "agi": [], "magnetically_addressable": true, "rationale": "The review names cytochrome oxidase explicitly as a candidate direct metabolic target. The heme a3/CuB centre passes through paramagnetic oxygen intermediates (P, F, oxoferryl) whose spin states are, in principle, field-addressable.\n", "caveat": "Strongly exchange-coupled metal centres relax very fast, which argues against coherent spin effects. This is a mechanistically attractive but physically demanding hypothesis, and is labelled T3 for that reason.\n", "evidence": [] }, { "node_id": "ATP_SYNTHASE", "qbo": "QBO:ATP_SYNTHASE", "label": "ATP synthase (complex V)", "kind": "complex", "compartment": "mitochondrial_inner_membrane", "evidence_tier": "T4", "confidence": "inferred", "quantum_class": [ "structural_context" ], "nuclei": [], "agi": [], "magnetically_addressable": false, "rationale": null, "caveat": null, "evidence": [] }, { "node_id": "MITO_SUPEROXIDE", "qbo": "QBO:MITO_SUPEROXIDE", "label": "Mitochondrial superoxide / H2O2", "kind": "simple_chemical", "compartment": "mitochondrial_matrix", "evidence_tier": "T2", "confidence": "reported", "quantum_class": [ "ros_leak_site" ], "nuclei": [], "agi": [ "AT3G10920" ], "magnetically_addressable": false, "rationale": "Not a magnetosensitive mechanism itself \u2014 it is the amplifier. A field effect too small to measure as a rate change can still register here, because ROS signalling is threshold-like.\n", "caveat": null, "evidence": [ { "ref": "Parmagnani2022", "doi": "10.3390/biom12121824", "claim": "Near-null magnetic field exposure alters ROS-associated transcriptomic and metabolomic programmes in Arabidopsis.\n", "direction": "altered", "field_regime": "NNMF", "species": "Arabidopsis thaliana" }, { "ref": "Farooq2021", "doi": "10.3389/fpls.2021.781734", "claim": "Reactive oxygen species and mitochondria jointly regulate seed germination, establishing the route from mitochondrial ROS to a developmental outcome.\n", "direction": "altered", "field_regime": null, "species": "multiple" } ] }, { "node_id": "ACONITASE", "qbo": "QBO:ACONITASE", "label": "Aconitase (ACO1/2/3)", "kind": "macromolecule", "compartment": "mitochondrial_matrix", "evidence_tier": "T3", "confidence": "inferred", "quantum_class": [ "iron_sulfur_4Fe4S" ], "nuclei": [ "57Fe", "33S" ], "agi": [ "AT4G35830", "AT4G26970", "AT2G05710" ], "magnetically_addressable": true, "rationale": "The review nominates aconitase as the sentinel of Fe/S integrity, and the biochemistry supports it: the exposed cluster iron makes aconitase the first TCA activity to fall under oxidative stress, so it reports cluster damage before anything else does.\n", "caveat": "Precisely because aconitase responds to any oxidative insult, a change under NNMF would NOT by itself implicate a magnetic mechanism. It is a sensitive readout and a poor discriminator; it needs a paired ROS-independent control.\n", "evidence": [] }, { "node_id": "LIPOYL_SYNTHASE", "qbo": "QBO:LIPOYL_SYNTHASE", "label": "Lipoyl synthase (LIP1)", "kind": "macromolecule", "compartment": "mitochondrial_matrix", "evidence_tier": "T3", "confidence": "inferred", "quantum_class": [ "iron_sulfur_4Fe4S", "radical_pair_donor" ], "nuclei": [ "57Fe", "33S", "1H" ], "agi": [ "AT2G20860" ], "magnetically_addressable": true, "rationale": "A radical-SAM enzyme generating a 5'-deoxyadenosyl radical from a [4Fe-4S] cluster \u2014 genuine organic radical chemistry on an iron-sulfur centre, which is the tightest coupling of the review's two proposed mechanisms found anywhere in primary metabolism. Its product lipoylates pyruvate dehydrogenase and the 2-oxoglutarate dehydrogenase complex, so a defect propagates straight into TCA flux.\n", "caveat": "The radical is generated inside the active site and quenched within one turnover; whether a spin-correlated pair with a long enough lifetime to be field-sensitive ever forms is untested.\n", "evidence": [] } ] }