GLDP1 (At4g33010) encodes one of the two Arabidopsis P proteins (glycine dehydrogenase (decarboxylating), EC 1.4.4.2) of the mitochondrial glycine decarboxylase complex (GDC, glycine cleavage system). The PLP-dependent homodimeric enzyme binds glycine through its pyridoxal phosphate cofactor, releases CO2 and transfers the remaining aminomethyl group to the lipoyl arm of the H protein; the T and L proteins then complete the conversion of glycine to 5,10-methylene-tetrahydrofolate, NH3 and NADH. GDC, with serine hydroxymethyltransferase, forms the mitochondrial part of the photorespiratory C2 cycle and also supplies one-carbon units. GLDP1 is the predominant P protein in leaves (about four-fold more than GLDP2 in the leaf complex) and carries the larger share of photorespiratory glycine decarboxylation, but it is functionally redundant with GLDP2: single mutants grow normally, whereas gldp1 gldp2 double mutants arrest as seedlings even at high CO2. GDC activity is inhibited by S-nitrosylation and glutathionylation of GLDP1 cysteines.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0003729 mRNA binding | IDA PMID:32344669 Discovering the RNA-Binding Proteome of Plant Leaves with an... | MARK AS OVER ANNOTATED | Summary: Leaf RNA interactome capture (ptRIC) recovered glycine dehydrogenase among UV-crosslinked poly(A) RNA-associated proteins. Reason: The paper reports the protein only as one of several metabolic enzymes newly captured in the leaf RBPome, with no follow-up validation, no mapped RNA-binding region and no defined mRNA target. The P protein is a mitochondrial matrix enzyme, and the observation does not establish a biological mRNA-binding function. The detection may be real but is not informative about gene function, so the annotation is kept but flagged as an over-interpretation of a screen. Supporting Evidence: PMID:32344669 Additional moonlighting enzymes were identified in the leaf RBPome, such as COBALAMIN-INDEPENDENT METHIONINE SYNTHASE, (S)-2-HYDROXY-ACID OXIDASE, GLYCINE DEHYDROGENASE and GLUTAMATE-GLYOXYLATE AMINOTRANSFERASE, which, to our knowledge, have not previously been linked to RNA biology |
| GO:0004375 glycine dehydrogenase (decarboxylating) activity | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT inference from node PTN000206531 (GcvP family) of glycine dehydrogenase (decarboxylating) activity for GLDP1. Reason: GLDP1 (At4g33010) is one of the two Arabidopsis P proteins of the glycine decarboxylase complex, the PLP-dependent enzyme that decarboxylates glycine and transfers the aminomethyl group to the lipoyl arm of the H protein (RHEA:24304, EC 1.4.4.2). It belongs to the GcvP family, and catalytic activity of both Arabidopsis GLDP isoforms is reported (GLDP2 weaker than GLDP1). This is the core molecular function. The IBA node placement is sound: the plant P proteins sit within the eukaryotic mitochondrial GcvP clade and retain the PLP-lysine. Supporting Evidence: PMID:22303256 P-protein (EC 1.4.4.2) is a pyridoxal-5-phosphate-containing homodimer, that catalyzes the actual glycine decarboxylation reaction file:ARATH/GLDP1/GLDP1-uniprot.txt CO(2) is released and the remaining methylamine moiety is then transferred to the lipoamide cofactor of the H protein file:ARATH/GLDP1/GLDP1-uniprot.txt Belongs to the GcvP family. PMID:33506579 GLDP2, a paralog of GLDP1 with weaker catalytic activity |
| GO:0004375 glycine dehydrogenase (decarboxylating) activity | IEA GO_REF:0000120 | ACCEPT | Summary: Combined IEA (InterPro GcvP signatures, RHEA:24304, EC 1.4.4.2) for glycine dehydrogenase (decarboxylating) activity. Reason: GLDP1 (At4g33010) is one of the two Arabidopsis P proteins of the glycine decarboxylase complex, the PLP-dependent enzyme that decarboxylates glycine and transfers the aminomethyl group to the lipoyl arm of the H protein (RHEA:24304, EC 1.4.4.2). It belongs to the GcvP family, and catalytic activity of both Arabidopsis GLDP isoforms is reported (GLDP2 weaker than GLDP1). This is the core molecular function. Supporting Evidence: PMID:22303256 P-protein (EC 1.4.4.2) is a pyridoxal-5-phosphate-containing homodimer, that catalyzes the actual glycine decarboxylation reaction file:ARATH/GLDP1/GLDP1-uniprot.txt CO(2) is released and the remaining methylamine moiety is then transferred to the lipoamide cofactor of the H protein PMID:33506579 GLDP2, a paralog of GLDP1 with weaker catalytic activity |
| GO:0005515 protein binding | IPI PMID:19452453 Proteomic profiling of tandem affinity purified 14-3-3 prote... | REMOVE | Summary: Tandem affinity purification of 14-3-3 omega (At1g78300) complexes recovered GLDP1 among ~121 putative clients. Reason: Bare protein binding is uninformative. The 14-3-3 TAP-MS screen lists GLDP1 as a putative client but establishes no specific molecular function for GLDP1; whether a cytosolic 14-3-3 contacts the precursor or the mature matrix protein is not addressed. Removal reflects the protein-binding policy, not a claim that the co-purification is false. Supporting Evidence: PMID:19452453 The identification here of 121 putative clients provides support for in vivo 14-3-3 interactions with a diverse array of proteins |
| GO:0005739 mitochondrion | HDA PMID:14671022 Experimental analysis of the Arabidopsis mitochondrial prote... | ACCEPT | Summary: Identified in the LC-MS/MS proteome of isolated Arabidopsis mitochondria; this study is the experimental basis of the UniProt mitochondrial location. Reason: The P protein carries a mitochondrial transit peptide and functions in the glycine decarboxylase complex of the mitochondrial matrix; UniProt records an experimental mitochondrial location for GLDP1. Mitochondrion is the compartment established for the Arabidopsis protein itself; the matrix sub-location is inferred from plant GDC biochemistry (largely pea), and the complex-level annotation conveys it, so the general term is kept as the core location. Supporting Evidence: file:ARATH/GLDP1/GLDP1-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion {ECO:0000269|PubMed:14671022} PMID:11286922 In green leaves, this multienzyme system is present at tremendously high concentrations within the mitochondrial matrix. |
| GO:0005739 mitochondrion | HDA PMID:18385124 Heterogeneity of the mitochondrial proteome for photosynthet... | ACCEPT | Summary: Quantified in the mitochondrial proteome of photosynthetic shoots versus cell culture; the photorespiratory apparatus was elevated in shoot mitochondria. Reason: The P protein carries a mitochondrial transit peptide and functions in the glycine decarboxylase complex of the mitochondrial matrix; UniProt records an experimental mitochondrial location for GLDP1. Mitochondrion is the compartment established for the Arabidopsis protein itself; the matrix sub-location is inferred from plant GDC biochemistry (largely pea), and the complex-level annotation conveys it, so the general term is kept as the core location. Supporting Evidence: PMID:18385124 showed the elevated level of the photorespiratory apparatus file:ARATH/GLDP1/GLDP1-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion {ECO:0000269|PubMed:14671022} PMID:11286922 In green leaves, this multienzyme system is present at tremendously high concentrations within the mitochondrial matrix. |
| GO:0005739 mitochondrion | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT inference (PTN000206533) that the P protein is active in mitochondria. Reason: The P protein carries a mitochondrial transit peptide and functions in the glycine decarboxylase complex of the mitochondrial matrix; UniProt records an experimental mitochondrial location for GLDP1. Mitochondrion is the compartment established for the Arabidopsis protein itself; the matrix sub-location is inferred from plant GDC biochemistry (largely pea), and the complex-level annotation conveys it, so the general term is kept as the core location. Supporting Evidence: PMID:25862457 Gly decarboxylase P-protein2 (At2g26080 and At4g33010 file:ARATH/GLDP1/GLDP1-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion {ECO:0000269|PubMed:14671022} PMID:11286922 In green leaves, this multienzyme system is present at tremendously high concentrations within the mitochondrial matrix. |
| GO:0005739 mitochondrion | IEA GO_REF:0000044 | ACCEPT | Summary: UniProt subcellular-location mapping (SL-0173 Mitochondrion). Reason: The P protein carries a mitochondrial transit peptide and functions in the glycine decarboxylase complex of the mitochondrial matrix; UniProt records an experimental mitochondrial location for GLDP1. Mitochondrion is the compartment established for the Arabidopsis protein itself; the matrix sub-location is inferred from plant GDC biochemistry (largely pea), and the complex-level annotation conveys it, so the general term is kept as the core location. Supporting Evidence: file:ARATH/GLDP1/GLDP1-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion {ECO:0000269|PubMed:14671022} PMID:11286922 In green leaves, this multienzyme system is present at tremendously high concentrations within the mitochondrial matrix. |
| GO:0005739 mitochondrion | ISM GO_REF:0000122 | ACCEPT | Summary: AtSubP sequence-based prediction of mitochondrial targeting, consistent with the N-terminal transit peptide. Reason: The P protein carries a mitochondrial transit peptide and functions in the glycine decarboxylase complex of the mitochondrial matrix; UniProt records an experimental mitochondrial location for GLDP1. Mitochondrion is the compartment established for the Arabidopsis protein itself; the matrix sub-location is inferred from plant GDC biochemistry (largely pea), and the complex-level annotation conveys it, so the general term is kept as the core location. Supporting Evidence: file:ARATH/GLDP1/GLDP1-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion {ECO:0000269|PubMed:14671022} PMID:11286922 In green leaves, this multienzyme system is present at tremendously high concentrations within the mitochondrial matrix. |
| GO:0005829 cytosol | HDA PMID:25293756 A proteomic strategy for global analysis of plant protein co... | MARK AS OVER ANNOTATED | Summary: High-throughput proteomic detection of GLDP1 in a crude leaf cytosolic (size-exclusion) fraction preparation. Reason: GLDP1 is an abundant mitochondrial matrix enzyme with a mitochondrial transit peptide and an experimentally established mitochondrial location. A single bulk-proteomics detection in a crude leaf cytosolic (size-exclusion) fraction fraction is best explained by carry-over of this very abundant leaf protein, and no targeted study places the P protein in this compartment. The crude cytosolic fraction is not depleted of broken-organelle matrix proteins. Under the ARATH corpus convention (projects/ARATH/organelle-audit.md, rule 3) a high-throughput proteomics hit for a protein localized elsewhere is marked as over-annotated rather than removed: the detection is a real observation, most likely contamination, but no targeted experiment excludes the compartment. Supporting Evidence: PMID:25293756 Applying this approach to the crude cytosolic fraction of Arabidopsis thaliana leaves using size exclusion chromatography file:ARATH/GLDP1/GLDP1-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion {ECO:0000269|PubMed:14671022} |
| GO:0005886 plasma membrane | HDA PMID:28887381 Global Analysis of Membrane-associated Protein Oligomerizati... | MARK AS OVER ANNOTATED | Summary: High-throughput proteomic detection of GLDP1 in a washed microsomal (membrane-associated) fraction preparation. Reason: GLDP1 is an abundant mitochondrial matrix enzyme with a mitochondrial transit peptide and an experimentally established mitochondrial location. A single bulk-proteomics detection in a washed microsomal (membrane-associated) fraction fraction is best explained by carry-over of this very abundant leaf protein, and no targeted study places the P protein in this compartment. The study itself notes that abundant soluble complexes contaminate the washed microsomes. Under the ARATH corpus convention (projects/ARATH/organelle-audit.md, rule 3) a high-throughput proteomics hit for a protein localized elsewhere is marked as over-annotated rather than removed: the detection is a real observation, most likely contamination, but no targeted experiment excludes the compartment. Supporting Evidence: PMID:28887381 The uncapped proteasome is an abundant, predominantly cytosolic complex that is a likely contaminant in the washed microsomes. file:ARATH/GLDP1/GLDP1-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion {ECO:0000269|PubMed:14671022} |
| GO:0006544 glycine metabolic process | IEA GO_REF:0000002 | TOO GENERAL | Summary: InterPro2GO (IPR003437 GcvP) mapping to glycine metabolic process. Reason: True but uninformative: glycine decarboxylation via glycine cleavage system (GO:0019464) and glycine catabolic process (GO:0006546), both accepted in this review, already entail it. Supporting Evidence: PMID:17496108 The mitochondrial multienzyme glycine decarboxylase (GDC) catalyzes the tetrahydrofolate-dependent catabolism of glycine |
| GO:0006546 glycine catabolic process | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro2GO (GcvP signature) mapping to glycine catabolic process. Reason: The P protein catalyses the first step of glycine catabolism by the glycine cleavage system. The more specific GO:0019464 is also accepted; this broader process term is still informative and consistent with the genetic evidence. Supporting Evidence: PMID:17496108 The mitochondrial multienzyme glycine decarboxylase (GDC) catalyzes the tetrahydrofolate-dependent catabolism of glycine PMID:22303256 P-protein (EC 1.4.4.2) is a pyridoxal-5-phosphate-containing homodimer, that catalyzes the actual glycine decarboxylation reaction |
| GO:0006546 glycine catabolic process | IMP PMID:17496108 Deletion of glycine decarboxylase in Arabidopsis is lethal u... | ACCEPT | Summary: gldp1 T-DNA mutants accumulate glycine under photorespiratory conditions, and gldp1 gldp2 double mutants (no GDC) arrest at the cotyledon stage even at 0.9% CO2. Reason: Direct genetic evidence (full text read) that GLDP1 contributes to glycine breakdown: leaf glycine is significantly elevated in two independent gldp1 alleles under photorespiratory conditions, and GLDP1 carries the larger share of the photorespiratory load. Consistent with its catalytic role. Supporting Evidence: PMID:17496108 which were significantly elevated under photorespiratory conditions PMID:17496108 While AtGLDP1 clearly carries a somewhat higher photorespiratory workload than AtGLDP2 PMID:17496108 the double mutant does not develop beyond the cotyledon stage |
| GO:0009507 chloroplast | HDA PMID:18431481 Sorting signals, N-terminal modifications and abundance of t... | MARK AS OVER ANNOTATED | Summary: High-throughput proteomic detection of GLDP1 in a chloroplast stroma preparation. Reason: GLDP1 is an abundant mitochondrial matrix enzyme with a mitochondrial transit peptide and an experimentally established mitochondrial location. A single bulk-proteomics detection in a chloroplast stroma fraction is best explained by carry-over of this very abundant leaf protein, and no targeted study places the P protein in this compartment. The authors themselves estimate hundreds of false positives or non-chloroplast contaminants in the unfiltered chloroplast data set. Under the ARATH corpus convention (projects/ARATH/organelle-audit.md, rule 3) a high-throughput proteomics hit for a protein localized elsewhere is marked as over-annotated rather than removed: the detection is a real observation, most likely contamination, but no targeted experiment excludes the compartment. Supporting Evidence: PMID:18431481 proteins likely represent false positive identifications and/or non-chloroplast contaminations file:ARATH/GLDP1/GLDP1-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion {ECO:0000269|PubMed:14671022} |
| GO:0009534 chloroplast thylakoid | HDA PMID:20061580 AT_CHLORO, a comprehensive chloroplast proteome database wit... | MARK AS OVER ANNOTATED | Summary: High-throughput proteomic detection of GLDP1 in a chloroplast thylakoid preparation. Reason: GLDP1 is an abundant mitochondrial matrix enzyme with a mitochondrial transit peptide and an experimentally established mitochondrial location. A single bulk-proteomics detection in a chloroplast thylakoid fraction is best explained by carry-over of this very abundant leaf protein, and no targeted study places the P protein in this compartment. Under the ARATH corpus convention (projects/ARATH/organelle-audit.md, rule 3) a high-throughput proteomics hit for a protein localized elsewhere is marked as over-annotated rather than removed: the detection is a real observation, most likely contamination, but no targeted experiment excludes the compartment. Supporting Evidence: file:ARATH/GLDP1/GLDP1-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion {ECO:0000269|PubMed:14671022} |
| GO:0009570 chloroplast stroma | HDA PMID:20061580 AT_CHLORO, a comprehensive chloroplast proteome database wit... | MARK AS OVER ANNOTATED | Summary: High-throughput proteomic detection of GLDP1 in a chloroplast stroma preparation. Reason: GLDP1 is an abundant mitochondrial matrix enzyme with a mitochondrial transit peptide and an experimentally established mitochondrial location. A single bulk-proteomics detection in a chloroplast stroma fraction is best explained by carry-over of this very abundant leaf protein, and no targeted study places the P protein in this compartment. Under the ARATH corpus convention (projects/ARATH/organelle-audit.md, rule 3) a high-throughput proteomics hit for a protein localized elsewhere is marked as over-annotated rather than removed: the detection is a real observation, most likely contamination, but no targeted experiment excludes the compartment. Supporting Evidence: file:ARATH/GLDP1/GLDP1-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion {ECO:0000269|PubMed:14671022} |
| GO:0009941 chloroplast envelope | HDA PMID:12938931 Proteomic study of the Arabidopsis thaliana chloroplastic en... | MARK AS OVER ANNOTATED | Summary: High-throughput proteomic detection of GLDP1 in a chloroplast envelope membrane preparation. Reason: GLDP1 is an abundant mitochondrial matrix enzyme with a mitochondrial transit peptide and an experimentally established mitochondrial location. A single bulk-proteomics detection in a chloroplast envelope membrane fraction is best explained by carry-over of this very abundant leaf protein, and no targeted study places the P protein in this compartment. The P protein is a soluble matrix protein with no membrane anchor. Under the ARATH corpus convention (projects/ARATH/organelle-audit.md, rule 3) a high-throughput proteomics hit for a protein localized elsewhere is marked as over-annotated rather than removed: the detection is a real observation, most likely contamination, but no targeted experiment excludes the compartment. Supporting Evidence: PMID:12938931 membrane proteins localized to the Arabidopsis thaliana chloroplastic envelope membrane file:ARATH/GLDP1/GLDP1-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion {ECO:0000269|PubMed:14671022} |
| GO:0019464 glycine decarboxylation via glycine cleavage system | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT inference (PTN000206531) of glycine decarboxylation via glycine cleavage system. Reason: Core process. GLDP1 is the glycine-decarboxylating subunit of the Arabidopsis glycine decarboxylase complex; loss of both P-protein genes abolishes GDC and is lethal even under non-photorespiratory conditions. Supporting Evidence: PMID:17496108 The mitochondrial multienzyme glycine decarboxylase (GDC) catalyzes the tetrahydrofolate-dependent catabolism of glycine PMID:17496108 The presence of all four proteins is necessary for catalytic activity of the complex. PMID:17496108 the double mutant does not develop beyond the cotyledon stage PMID:17496108 The corresponding P proteins, AtGLDP1 and AtGLDP2, can more or less fully substitute each other under standard growth conditions. |
| GO:0046686 response to cadmium ion | IEP PMID:20005002 Leaf proteome responses of Arabidopsis thaliana exposed to m... | MARK AS OVER ANNOTATED | Summary: 2D-gel leaf proteomics of Cd-exposed seedlings reported changed abundance of a set of proteins, from which this expression-pattern annotation was made. Reason: Abstract-only cache; the GLDP1-specific result cannot be checked. Even taken at face value, an abundance change of a highly expressed photorespiratory enzyme under Cd-induced chlorosis and growth reduction reflects general metabolic adjustment, not a role of GLDP1 in responding to cadmium. Retained only as a non-informative expression observation. Supporting Evidence: PMID:20005002 Of the 730 reproducible proteins among all gels, 21 were statistically upregulated in response to Cd. |
| GO:0048046 apoplast | HDA PMID:18538804 Hydroponic isotope labelling of entire plants (HILEP) for qu... | MARK AS OVER ANNOTATED | Summary: High-throughput proteomic detection of GLDP1 in a apoplast preparation. Reason: GLDP1 is an abundant mitochondrial matrix enzyme with a mitochondrial transit peptide and an experimentally established mitochondrial location. A single bulk-proteomics detection in a apoplast fraction is best explained by carry-over of this very abundant leaf protein, and no targeted study places the P protein in this compartment. GLDP1 has no signal peptide; detection of an abundant intracellular enzyme in apoplastic extracts is typical of cell-damage carry-over. Under the ARATH corpus convention (projects/ARATH/organelle-audit.md, rule 3) a high-throughput proteomics hit for a protein localized elsewhere is marked as over-annotated rather than removed: the detection is a real observation, most likely contamination, but no targeted experiment excludes the compartment. Supporting Evidence: PMID:18538804 it was possible to show differential protein expression in the apoplast of plants submitted to oxidative stress file:ARATH/GLDP1/GLDP1-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion {ECO:0000269|PubMed:14671022} |
| GO:0005960 glycine cleavage complex | IDA PMID:32311173 Stoichiometry of two plant glycine decarboxylase complexes a... | NEW | Summary: Mass-spectrometric stoichiometry of the Arabidopsis leaf glycine decarboxylase complex detects both P-protein isoforms (GCS-P1 = GLDP1, GCS-P2 = GLDP2) as components of the complex. Reason: GLDP1 has no cellular-component annotation to the glycine cleavage complex in GOA, although its paralogous H protein (GDCH) does. The P protein is a defining subunit of the P/H/T/L complex, all four proteins are required for activity, and the Arabidopsis leaf GDC contains GLDP1 and GLDP2 in a 4:1 ratio. Abstract-only cache, but the abstract states the measurement directly. Supporting Evidence: PMID:32311173 The Arabidopsis GDC contains four times more of the isoforms GCS-P1 and GCS-L1 in comparison with GCS-P2 and GCS-L2 PMID:17496108 The presence of all four proteins is necessary for catalytic activity of the complex. |
| GO:0009853 photorespiration | IMP PMID:17496108 Deletion of glycine decarboxylase in Arabidopsis is lethal u... | NEW | Summary: gldp1 mutants accumulate leaf glycine under photorespiratory conditions; GLDP1 carries most of the photorespiratory glycine decarboxylation load. Reason: Participation test: GLDP1 catalyses a step of the photorespiratory C2 cycle (mitochondrial glycine decarboxylation), so it does part of the work of the process rather than being required for or consumed by it. Comparator check (QuickGO, Arabidopsis, GO:0009853): enzymes catalysing other C2-cycle steps carry the term (SHM1 IMP, GLYK IMP/IBA, HPR TAS, GGAT1 TAS, PLGG1 IMP), whereas none of the GDC subunits (GLDP1, GLDP2, GDCH, GDCST) do; this absence looks like a gap rather than a convention. The term is not an ancestor or descendant of GO:0019464. Supporting Evidence: PMID:22303256 The combined reaction of glycine decarboxylase (GLD) and serine hydroxymethyltransferase (SHM) represents the mitochondrial part of the major photorespiratory pathway. PMID:17496108 While AtGLDP1 clearly carries a somewhat higher photorespiratory workload than AtGLDP2 PMID:17496108 which were significantly elevated under photorespiratory conditions |
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Download this section (compressed HTML)Q: Do GLDP1 and GLDP2 differ in kinetic properties or regulation (e.g. InLYP1-dependent turnover of GLDP2, redox modification) in ways that matter for non-photosynthetic one-carbon metabolism in roots, where GLDP2 transcripts dominate?
Q: Should the GDC subunits (P, H, T, L) be annotated to GO:0009853 photorespiration in Arabidopsis, as other C2-cycle enzymes are, or is GO:0019464 considered sufficient by TAIR curators?
Experiment: Purify recombinant GLDP1, GLDP2 and co-expressed heterodimers and measure H-protein-dependent glycine decarboxylation kinetics.
Hypothesis: GLDP1 and GLDP2 homo- and heterodimers differ in glycine decarboxylase activity and in their interaction with the H protein.
Type: enzyme kinetics
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