{"gene":"PF3D7_1018300","run_date":"2026-09-08T12:51:28","timeline":{"discoveries":[{"year":2012,"finding":"PfSPP (signal peptide peptidase) is an ER-resident intramembrane protease that remains intracellular throughout erythrocyte invasion; SPP-specific chemical inhibition has no effect on erythrocyte invasion but inhibits intra-erythrocytic parasite development at low micromolar concentrations, demonstrating that PfSPP is required for growth but not invasion.","method":"Immunofluorescence microscopy (subcellular localization), SPP-specific chemical inhibitors (invasion and growth assays in cultured P. falciparum)","journal":"Traffic (Copenhagen, Denmark)","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct localization by IFA plus chemical-genetic functional dissection in a single lab with two orthogonal approaches (imaging + pharmacology)","pmids":["22844982"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2014,"finding":"PfSPP localizes to the endoplasmic reticulum (confirmed by immunofluorescence and immunogold electron microscopy), exists as monomer and dimer forms in parasite lysate, and cleaves malaria heat shock protein 101 (HSP101) as an in vivo substrate; partial inhibition of PfSPP correlates with gametocyte emergence.","method":"Immunofluorescence microscopy, immunogold electron microscopy, SDS-PAGE/western blot (monomer/dimer), transfection-based in vivo luminescence cleavage assay for substrate identification","journal":"Biochemical and biophysical research communications","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct localization by two imaging methods plus transfection-based substrate assay; single lab, multiple orthogonal methods","pmids":["25017910"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2007,"finding":"PfSP21, the catalytic subunit of the signal peptidase complex (SPC) from P. falciparum, cleaves a peptide substrate containing the signal peptidase cleavage site in vitro; it is phosphorylated by protein kinase C and its enzymatic activity is upregulated after this phosphorylation; it localizes to the ER by immunofluorescence; dsRNA knockdown of PfSP21 inhibits parasite growth in culture.","method":"In vitro peptide cleavage assay, protein kinase C phosphorylation assay, immunofluorescence assay (ER localization), dsRNA-mediated knockdown with growth inhibition readout","journal":"Molecular and biochemical parasitology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — in vitro enzymatic assay plus phosphorylation assay plus localization plus loss-of-function, all in a single lab; multiple orthogonal methods","pmids":["18054093"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2005,"finding":"Type I signal peptidase from P. falciparum is an intron-less, single-copy gene encoding a serine protease with a serine/lysine catalytic dyad; the enzyme undergoes self-cleavage and was demonstrated to possess type I signal peptidase activity by complementation of E. coli signal peptidase mutants (in vivo preprotein processing assay).","method":"Gene cloning and sequence analysis, E. coli complementation assay for in vivo signal peptidase activity, self-cleavage assay","journal":"Journal of biomedicine & biotechnology","confidence":"Medium","confidence_rationale":"Tier 1 / Weak — functional complementation assay establishes enzymatic activity; single lab, single study","pmids":["16489263"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""},{"species":"Plasmodium knowlesi","strain":""},{"species":"Plasmodium yoelii","strain":""}]},{"year":2009,"finding":"The gamma-secretase/SPP inhibitor LY411,575 prevents Plasmodium development in the liver (IC50 ~80 nM in hepatoma cells and primary hepatocytes) without affecting hepatocyte invasion, and decreases parasite liver load in vivo; the effect does not operate via the host Notch signaling pathway, suggesting it acts through inhibition of the parasite's signal peptide peptidase.","method":"Cell-based growth inhibition assay (human hepatoma lines and mouse primary hepatocytes), in vivo rodent malaria model (parasite liver load quantification), Notch pathway reporter assay (negative result for Notch involvement)","journal":"PloS one","confidence":"Low","confidence_rationale":"Tier 3 / Weak — pharmacological inhibitor with indirect inference about parasite SPP as target; no direct biochemical confirmation of target engagement in this study","pmids":["19337374"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"current_model":"PF3D7_1018300 encodes a putative peptidase in P. falciparum; the most specific corpus evidence indicates that the related signal peptide peptidase (PfSPP) is an ER-resident intramembrane aspartic protease that localizes exclusively intracellularly, exists as monomer and dimer forms, cleaves HSP101 as an in vivo substrate, is required for intra-erythrocytic growth but not erythrocyte invasion, and is inhibitable by gamma-secretase/SPP-class inhibitors; however, because the corpus mixes several peptidase family members (SPP, type I signal peptidase), the precise molecular identity of PF3D7_1018300 within this family cannot be definitively resolved from the available abstracts."},"narrative":{"mechanistic_narrative":"The corpus does not resolve the precise molecular identity of PF3D7_1018300 within the P. falciparum peptidase family, because it mixes findings on signal peptide peptidase (PfSPP), the signal peptidase complex catalytic subunit (PfSP21), and type I signal peptidase. The most specific and best-supported evidence describes PfSPP, an endoplasmic reticulum-resident intramembrane protease that remains intracellular throughout erythrocyte invasion [PMID:22844982, PMID:25017910]. Chemical-genetic and pharmacological data establish that this activity is dispensable for erythrocyte invasion but required for intra-erythrocytic parasite development, since SPP-specific inhibitors block growth at low micromolar concentrations without affecting invasion [PMID:22844982]. PfSPP exists as monomer and dimer forms and cleaves malaria heat shock protein 101 (HSP101) as an in vivo substrate, with partial inhibition correlating with gametocyte emergence [PMID:25017910]. A gamma-secretase/SPP-class inhibitor also blocks Plasmodium liver-stage development without affecting hepatocyte invasion or host Notch signaling, consistent with a parasite SPP target [PMID:19337374]. Whether these SPP-attributed properties, or the distinct in vitro cleavage and E. coli complementation activities described for signal peptidase complex members [PMID:18054093, PMID:16489263], correspond to PF3D7_1018300 specifically cannot be determined from the available abstracts.","teleology":[{"year":2005,"claim":"Establishing that a Plasmodium type I signal peptidase is a catalytically active serine protease addressed whether the parasite encodes a functional preprotein-processing enzyme.","evidence":"Gene cloning, sequence analysis, E. coli signal peptidase complementation, and self-cleavage assay","pmids":["16489263"],"confidence":"Medium","gaps":["Does not identify whether this gene is PF3D7_1018300","No endogenous parasite substrate identified","Activity shown only by heterologous complementation"],"attribution":[{"species":"Plasmodium falciparum","strain":""},{"species":"Plasmodium knowlesi","strain":""},{"species":"Plasmodium yoelii","strain":""}]},{"year":2007,"claim":"Characterizing PfSP21, the catalytic subunit of the signal peptidase complex, addressed whether signal peptidase activity is enzymatically active, regulated, and required for growth.","evidence":"In vitro peptide cleavage assay, protein kinase C phosphorylation assay, immunofluorescence, and dsRNA knockdown growth assay in P. falciparum","pmids":["18054093"],"confidence":"Medium","gaps":["Does not establish that PfSP21 is PF3D7_1018300","Substrate specificity limited to a peptide model","Physiological relevance of PKC phosphorylation not resolved in vivo"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2009,"claim":"Testing a gamma-secretase/SPP inhibitor against liver-stage parasites addressed whether SPP-class protease activity is a druggable requirement for development in a stage other than blood.","evidence":"Cell-based growth inhibition in hepatoma lines and primary hepatocytes, in vivo rodent liver-load quantification, and Notch reporter assay","pmids":["19337374"],"confidence":"Low","gaps":["Pharmacological inference only; no direct target engagement demonstrated","Does not identify PF3D7_1018300 as the target","Effect attributed to parasite SPP by exclusion of Notch, not by direct assay"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2012,"claim":"Combining subcellular localization with SPP-specific inhibition addressed at which stage and compartment the peptidase acts, showing it is intracellular and required for growth but not invasion.","evidence":"Immunofluorescence localization and SPP-specific chemical inhibitor invasion/growth assays in cultured P. falciparum","pmids":["22844982"],"confidence":"Medium","gaps":["Does not confirm the ER identity biochemically in this study","Inhibitor specificity for a single family member unresolved","Does not tie the phenotype to PF3D7_1018300 by gene knockout"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2014,"claim":"Identifying HSP101 as an in vivo substrate and confirming ER residence and oligomeric state addressed the molecular function and cellular localization of PfSPP.","evidence":"Immunofluorescence, immunogold electron microscopy, western blot for monomer/dimer, and transfection-based in vivo cleavage assay in P. falciparum","pmids":["25017910"],"confidence":"Medium","gaps":["Substrate repertoire beyond HSP101 unknown","Does not resolve whether PfSPP corresponds to PF3D7_1018300","Mechanistic link between inhibition and gametocyte emergence uncharacterized"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":null,"claim":"The precise molecular identity of PF3D7_1018300 within the parasite peptidase family, and whether any of the SPP or signal peptidase activities in the corpus are attributable specifically to this gene, remain unestablished.","evidence":"","pmids":[],"confidence":"Low","gaps":["No study genetically ties any characterized activity to the PF3D7_1018300 locus","Corpus conflates SPP, PfSP21, and type I signal peptidase","No direct knockout or tagging of PF3D7_1018300 reported"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":["Signal peptidase complex (SPC), catalytic subunit PfSP21 [#2]"],"partners":["HSP101 (IN VIVO SUBSTRATE OF PFSPP) [#1]"],"other_free_text":["PfSPP exists as monomer and dimer forms in parasite lysate [#1]","SPP-specific and gamma-secretase-class inhibitors block intra-erythrocytic and liver-stage development without affecting invasion [#0, #4]","Partial PfSPP inhibition correlates with gametocyte emergence [#1]","The corpus mixes SPP, PfSP21, and type I signal peptidase; specific identity of PF3D7_1018300 is not resolved by the available evidence"]}},"prefetch_data":{},"corpus_meta":[{"pmid":"19337374","id":"PMC_19337374","title":"A small molecule inhibitor of signal peptide peptidase inhibits Plasmodium development in the liver and decreases malaria severity.","date":"2009","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/19337374","citation_count":24,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["peptidase"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"20478341","id":"PMC_20478341","title":"Downstream effects of haemoglobinase inhibition in Plasmodium falciparum-infected erythrocytes.","date":"2010","source":"Molecular and biochemical parasitology","url":"https://pubmed.ncbi.nlm.nih.gov/20478341","citation_count":23,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["peptidase"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"22844982","id":"PMC_22844982","title":"Malaria parasite signal peptide peptidase is an ER-resident protease required for growth but not for invasion.","date":"2012","source":"Traffic (Copenhagen, Denmark)","url":"https://pubmed.ncbi.nlm.nih.gov/22844982","citation_count":23,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["peptidase"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"26584340","id":"PMC_26584340","title":"New directions for protease inhibitors directed drug discovery.","date":"2016","source":"Biopolymers","url":"https://pubmed.ncbi.nlm.nih.gov/26584340","citation_count":21,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["peptidase"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"18054093","id":"PMC_18054093","title":"Plasmodium falciparum signal peptidase is regulated by phosphorylation and required for intra-erythrocytic growth.","date":"2007","source":"Molecular and biochemical parasitology","url":"https://pubmed.ncbi.nlm.nih.gov/18054093","citation_count":19,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["peptidase"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"26046535","id":"PMC_26046535","title":"Differential Inhibition of Signal Peptide Peptidase Family Members by Established γ-Secretase Inhibitors.","date":"2015","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/26046535","citation_count":18,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["peptidase"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"23084821","id":"PMC_23084821","title":"Host targeting of virulence determinants and phosphoinositides in blood stage malaria parasites.","date":"2012","source":"Trends in parasitology","url":"https://pubmed.ncbi.nlm.nih.gov/23084821","citation_count":15,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["peptidase"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"24145449","id":"PMC_24145449","title":"Ferrous iron-dependent drug delivery enables controlled and selective release of therapeutic agents in vivo.","date":"2013","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/24145449","citation_count":15,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["peptidase"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"27784256","id":"PMC_27784256","title":"The Widespread Anti-Protozoal Action of HIV Aspartic Peptidase Inhibitors: Focus on Plasmodium spp., Leishmania spp. and Trypanosoma cruzi.","date":"2017","source":"Current topics in medicinal chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/27784256","citation_count":11,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["peptidase"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"29187532","id":"PMC_29187532","title":"Characterization of SPP inhibitors suppressing propagation of HCV and protozoa.","date":"2017","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/29187532","citation_count":10,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["peptidase"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"16489263","id":"PMC_16489263","title":"Isolation and characterization of type I signal peptidase of different malaria parasites.","date":"2005","source":"Journal of biomedicine & biotechnology","url":"https://pubmed.ncbi.nlm.nih.gov/16489263","citation_count":9,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["peptidase"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"25017910","id":"PMC_25017910","title":"Plasmodium falciparum signal peptide peptidase cleaves malaria heat shock protein 101 (HSP101). Implications for gametocytogenesis.","date":"2014","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/25017910","citation_count":8,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["peptidase"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"9269721","id":"PMC_9269721","title":"Electrophoretic variations of peptidase E (PEPE) in characterizing clones and isolates of Plasmodium falciparum from different geographical areas.","date":"1997","source":"Folia parasitologica","url":"https://pubmed.ncbi.nlm.nih.gov/9269721","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["peptidase"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":8352,"output_tokens":2239,"usd":0.02932,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":6678,"output_tokens":2744,"usd":0.050995,"stage2_stop_reason":"end_turn"},"total_usd":0.080315,"stage1_batch_id":"msgbatch_01DisAaTypwmC8QwdMBuePHo","stage2_batch_id":"msgbatch_0184zxZTqxiEfdYYfPMfkqjb","note":"batch pricing = 50% of standard"},"stage1_raw":"I need to carefully identify which papers are about PF3D7_1018300 specifically. This gene is annotated as \"peptidase, putative\" in P. falciparum. I need to determine what gene this actually corresponds to based on the corpus.\n\nLooking at the papers:\n- Papers 3, 5, 11, 12 are about PfSPP (Signal Peptide Peptidase) or PfSP21 (signal peptidase complex subunit)\n- Paper 5 (PMID:18054093) is about PfSP21, the catalytic subunit of signal peptidase complex (SPC) - this is a type I signal peptidase\n- Paper 11 (PMID:16489263) is about type I signal peptidase from P. falciparum\n- Papers 3, 12 are about PfSPP (signal peptide peptidase, an intramembrane aspartic protease)\n- Paper 13 is about PEPE (Peptidase E), an aminopeptidase-type enzyme\n\nPF3D7_1018300 is annotated as \"peptidase, putative.\" I need to be careful not to assign findings from clearly different genes. The corpus seems to mix several peptidases. Without clear mapping of gene IDs, I should focus on papers that directly describe PF3D7_1018300 by its PlasmoDB ID or clearly correspond to it. Given the corpus appears to be retrieved specifically for this gene, and the top papers are most gene-specific first, I'll focus on papers 3, 5, 11, 12 which are most specific about Plasmodium peptidases, while being cautious about which specific gene they describe.\n\nPaper 13 about PEPE is likely a different enzyme (aminopeptidase E). Papers 1, 6, 10 are about SPP inhibitors but focus on human SPP. Papers 2, 4, 7, 8, 9 are about broader drug mechanisms.\n\nGiven PF3D7_1018300 is a \"peptidase, putative,\" and the most specific papers deal with PfSPP (intramembrane aspartic protease, papers 3, 12) or type I signal peptidase (papers 5, 11), I'll extract mechanistic findings from papers that are clearly about P. falciparum peptidases, noting that the corpus specificity ordering suggests papers 3, 12 (PfSPP) and 5, 11 (type I signal peptidase) are the most relevant.\n\n```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2012,\n      \"finding\": \"PfSPP (signal peptide peptidase) is an ER-resident intramembrane protease that remains intracellular throughout erythrocyte invasion; SPP-specific chemical inhibition has no effect on erythrocyte invasion but inhibits intra-erythrocytic parasite development at low micromolar concentrations, demonstrating that PfSPP is required for growth but not invasion.\",\n      \"method\": \"Immunofluorescence microscopy (subcellular localization), SPP-specific chemical inhibitors (invasion and growth assays in cultured P. falciparum)\",\n      \"journal\": \"Traffic (Copenhagen, Denmark)\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct localization by IFA plus chemical-genetic functional dissection in a single lab with two orthogonal approaches (imaging + pharmacology)\",\n      \"pmids\": [\"22844982\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"PfSPP localizes to the endoplasmic reticulum (confirmed by immunofluorescence and immunogold electron microscopy), exists as monomer and dimer forms in parasite lysate, and cleaves malaria heat shock protein 101 (HSP101) as an in vivo substrate; partial inhibition of PfSPP correlates with gametocyte emergence.\",\n      \"method\": \"Immunofluorescence microscopy, immunogold electron microscopy, SDS-PAGE/western blot (monomer/dimer), transfection-based in vivo luminescence cleavage assay for substrate identification\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct localization by two imaging methods plus transfection-based substrate assay; single lab, multiple orthogonal methods\",\n      \"pmids\": [\"25017910\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"PfSP21, the catalytic subunit of the signal peptidase complex (SPC) from P. falciparum, cleaves a peptide substrate containing the signal peptidase cleavage site in vitro; it is phosphorylated by protein kinase C and its enzymatic activity is upregulated after this phosphorylation; it localizes to the ER by immunofluorescence; dsRNA knockdown of PfSP21 inhibits parasite growth in culture.\",\n      \"method\": \"In vitro peptide cleavage assay, protein kinase C phosphorylation assay, immunofluorescence assay (ER localization), dsRNA-mediated knockdown with growth inhibition readout\",\n      \"journal\": \"Molecular and biochemical parasitology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — in vitro enzymatic assay plus phosphorylation assay plus localization plus loss-of-function, all in a single lab; multiple orthogonal methods\",\n      \"pmids\": [\"18054093\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2005,\n      \"finding\": \"Type I signal peptidase from P. falciparum is an intron-less, single-copy gene encoding a serine protease with a serine/lysine catalytic dyad; the enzyme undergoes self-cleavage and was demonstrated to possess type I signal peptidase activity by complementation of E. coli signal peptidase mutants (in vivo preprotein processing assay).\",\n      \"method\": \"Gene cloning and sequence analysis, E. coli complementation assay for in vivo signal peptidase activity, self-cleavage assay\",\n      \"journal\": \"Journal of biomedicine & biotechnology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Weak — functional complementation assay establishes enzymatic activity; single lab, single study\",\n      \"pmids\": [\"16489263\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}, {\"species\": \"Plasmodium knowlesi\", \"strain\": \"\"}, {\"species\": \"Plasmodium yoelii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"The gamma-secretase/SPP inhibitor LY411,575 prevents Plasmodium development in the liver (IC50 ~80 nM in hepatoma cells and primary hepatocytes) without affecting hepatocyte invasion, and decreases parasite liver load in vivo; the effect does not operate via the host Notch signaling pathway, suggesting it acts through inhibition of the parasite's signal peptide peptidase.\",\n      \"method\": \"Cell-based growth inhibition assay (human hepatoma lines and mouse primary hepatocytes), in vivo rodent malaria model (parasite liver load quantification), Notch pathway reporter assay (negative result for Notch involvement)\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — pharmacological inhibitor with indirect inference about parasite SPP as target; no direct biochemical confirmation of target engagement in this study\",\n      \"pmids\": [\"19337374\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    }\n  ],\n  \"current_model\": \"PF3D7_1018300 encodes a putative peptidase in P. falciparum; the most specific corpus evidence indicates that the related signal peptide peptidase (PfSPP) is an ER-resident intramembrane aspartic protease that localizes exclusively intracellularly, exists as monomer and dimer forms, cleaves HSP101 as an in vivo substrate, is required for intra-erythrocytic growth but not erythrocyte invasion, and is inhibitable by gamma-secretase/SPP-class inhibitors; however, because the corpus mixes several peptidase family members (SPP, type I signal peptidase), the precise molecular identity of PF3D7_1018300 within this family cannot be definitively resolved from the available abstracts.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"The corpus does not resolve the precise molecular identity of PF3D7_1018300 within the P. falciparum peptidase family, because it mixes findings on signal peptide peptidase (PfSPP), the signal peptidase complex catalytic subunit (PfSP21), and type I signal peptidase. The most specific and best-supported evidence describes PfSPP, an endoplasmic reticulum-resident intramembrane protease that remains intracellular throughout erythrocyte invasion [#0, #1]. Chemical-genetic and pharmacological data establish that this activity is dispensable for erythrocyte invasion but required for intra-erythrocytic parasite development, since SPP-specific inhibitors block growth at low micromolar concentrations without affecting invasion [#0]. PfSPP exists as monomer and dimer forms and cleaves malaria heat shock protein 101 (HSP101) as an in vivo substrate, with partial inhibition correlating with gametocyte emergence [#1]. A gamma-secretase/SPP-class inhibitor also blocks Plasmodium liver-stage development without affecting hepatocyte invasion or host Notch signaling, consistent with a parasite SPP target [#4]. Whether these SPP-attributed properties, or the distinct in vitro cleavage and E. coli complementation activities described for signal peptidase complex members [#2, #3], correspond to PF3D7_1018300 specifically cannot be determined from the available abstracts.\"\n  ,\n  \"teleology\": [\n    {\n      \"year\": 2005,\n      \"claim\": \"Establishing that a Plasmodium type I signal peptidase is a catalytically active serine protease addressed whether the parasite encodes a functional preprotein-processing enzyme.\",\n      \"evidence\": \"Gene cloning, sequence analysis, E. coli signal peptidase complementation, and self-cleavage assay\",\n      \"pmids\": [\"16489263\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Does not identify whether this gene is PF3D7_1018300\", \"No endogenous parasite substrate identified\", \"Activity shown only by heterologous complementation\"],\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"},\n        {\"species\": \"Plasmodium knowlesi\", \"strain\": \"\"},\n        {\"species\": \"Plasmodium yoelii\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": 2007,\n      \"claim\": \"Characterizing PfSP21, the catalytic subunit of the signal peptidase complex, addressed whether signal peptidase activity is enzymatically active, regulated, and required for growth.\",\n      \"evidence\": \"In vitro peptide cleavage assay, protein kinase C phosphorylation assay, immunofluorescence, and dsRNA knockdown growth assay in P. falciparum\",\n      \"pmids\": [\"18054093\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Does not establish that PfSP21 is PF3D7_1018300\", \"Substrate specificity limited to a peptide model\", \"Physiological relevance of PKC phosphorylation not resolved in vivo\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2009,\n      \"claim\": \"Testing a gamma-secretase/SPP inhibitor against liver-stage parasites addressed whether SPP-class protease activity is a druggable requirement for development in a stage other than blood.\",\n      \"evidence\": \"Cell-based growth inhibition in hepatoma lines and primary hepatocytes, in vivo rodent liver-load quantification, and Notch reporter assay\",\n      \"pmids\": [\"19337374\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Pharmacological inference only; no direct target engagement demonstrated\", \"Does not identify PF3D7_1018300 as the target\", \"Effect attributed to parasite SPP by exclusion of Notch, not by direct assay\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Combining subcellular localization with SPP-specific inhibition addressed at which stage and compartment the peptidase acts, showing it is intracellular and required for growth but not invasion.\",\n      \"evidence\": \"Immunofluorescence localization and SPP-specific chemical inhibitor invasion/growth assays in cultured P. falciparum\",\n      \"pmids\": [\"22844982\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Does not confirm the ER identity biochemically in this study\", \"Inhibitor specificity for a single family member unresolved\", \"Does not tie the phenotype to PF3D7_1018300 by gene knockout\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Identifying HSP101 as an in vivo substrate and confirming ER residence and oligomeric state addressed the molecular function and cellular localization of PfSPP.\",\n      \"evidence\": \"Immunofluorescence, immunogold electron microscopy, western blot for monomer/dimer, and transfection-based in vivo cleavage assay in P. falciparum\",\n      \"pmids\": [\"25017910\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Substrate repertoire beyond HSP101 unknown\", \"Does not resolve whether PfSPP corresponds to PF3D7_1018300\", \"Mechanistic link between inhibition and gametocyte emergence uncharacterized\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The precise molecular identity of PF3D7_1018300 within the parasite peptidase family, and whether any of the SPP or signal peptidase activities in the corpus are attributable specifically to this gene, remain unestablished.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No study genetically ties any characterized activity to the PF3D7_1018300 locus\", \"Corpus conflates SPP, PfSP21, and type I signal peptidase\", \"No direct knockout or tagging of PF3D7_1018300 reported\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0004190\", \"supporting_discovery_ids\": [0, 1]},\n      {\"term_id\": \"GO:0004252\", \"supporting_discovery_ids\": [2, 3]},\n      {\"term_id\": \"GO:0042500\", \"supporting_discovery_ids\": [3]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005789\", \"supporting_discovery_ids\": [0, 1, 2]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"GO:0006465\", \"supporting_discovery_ids\": [2, 3]},\n      {\"term_id\": \"GO:0006508\", \"supporting_discovery_ids\": [0, 1]}\n    ],\n    \"complexes\": [\n      \"Signal peptidase complex (SPC), catalytic subunit PfSP21 [#2]\"\n    ],\n    \"partners\": [\n      \"HSP101 (in vivo substrate of PfSPP) [#1]\"\n    ],\n    \"other_free_text\": [\n      \"PfSPP exists as monomer and dimer forms in parasite lysate [#1]\",\n      \"SPP-specific and gamma-secretase-class inhibitors block intra-erythrocytic and liver-stage development without affecting invasion [#0, #4]\",\n      \"Partial PfSPP inhibition correlates with gametocyte emergence [#1]\",\n      \"The corpus mixes SPP, PfSP21, and type I signal peptidase; specific identity of PF3D7_1018300 is not resolved by the available evidence\"\n    ]\n  }\n}","audit_flag":null,"strains":[{"strain":"Pf3D7","gene_id":"PF3D7_1018300","name":null,"product":"peptidase, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PbANKA","gene_id":"PBANKA_0502600","name":null,"product":"peptidase, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PkH","gene_id":"PKNH_0602500","name":null,"product":"peptidase, putative","uniprot_acc":null,"chromosome":null,"start_pos":null}],"gene_symbol":"","evaluation":null}