{"gene":"PPID","run_date":"2026-06-10T06:43:35","timeline":{"discoveries":[{"year":1996,"finding":"CyP-40 (PPID) functions as a molecular chaperone in vitro, interacting with unfolded substrates to maintain a nonnative folding-competent intermediate, similar to Hsp90 or Hsp70, though it cannot completely refold substrates on its own.","method":"In vitro folding assay with unfolded substrate proteins","journal":"Science","confidence":"Medium","confidence_rationale":"Tier 1 / Weak — in vitro chaperone assay from a single lab; abstract does not detail mutagenesis or multiple orthogonal methods","pmids":["8939864"],"is_preprint":false},{"year":1995,"finding":"CyP-40 (PPID) is a component of native glucocorticoid receptor heterocomplexes and binds directly to hsp90; it occupies a common immunophilin-binding site on hsp90 that is also used by hsp56 (FKBP52), such that the two immunophilins exist in separate, mutually exclusive complexes with hsp90. The peptidylprolyl isomerase activity of CyP-40 is not required for glucocorticoid receptor–hsp90 heterocomplex assembly.","method":"Immunoadsorption/co-immunoadsorption from cell lysate; direct binding of purified proteins; competitive binding assay; reconstitution with reticulocyte lysate","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal co-immunoadsorption, direct binding with purified proteins, and competition assay in same study; findings independently referenced by multiple subsequent papers","pmids":["7657624"],"is_preprint":false},{"year":1996,"finding":"The TPR domain of CyP-40 (PPID) mediates binding to hsp90, but the TPR domain alone is not sufficient for stable hsp90 association; flanking acidic and basic residues (alpha-helical microdomains) at the N- and C-terminal ends of the TPR domain are also required. FKBP52 competes with CyP-40 for hsp90 binding, consistent with a common binding site.","method":"GST-fusion deletion mutant pulldown/hsp90 retention assay; competition assay with bacterially expressed FKBP52 in myometrial cytosol","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — GST-pulldown with deletion mutants plus competition assay, single lab, two orthogonal methods","pmids":["8621687"],"is_preprint":false},{"year":1998,"finding":"In Saccharomyces cerevisiae, Cpr7 (the CyP-40 homolog) and Hsp90 function synergistically to repress HSF-dependent gene expression; loss of Cpr7 or reduced Hsp90 levels leads to increased HSF-dependent transcription and acquisition of thermotolerance, placing this CyP-40-type cyclophilin in negative regulation of the heat shock response.","method":"Genetic epistasis analysis (deletion and hypomorphic mutations) with reporter assays for HSF-dependent promoter activity; thermotolerance assay in S. cerevisiae","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic epistasis with reporter assays in yeast, single lab, two orthogonal phenotypic readouts","pmids":["9668076"],"is_preprint":false},{"year":1998,"finding":"The peptidyl-prolyl isomerase (PPIase) catalytic domain of Cpr7 (CyP-40/PPID yeast homolog) is not required for its essential functions: a catalytic-site mutation and complete deletion of the PPIase domain did not significantly impair growth or Hsp90-mediated steroid receptor activity. The C-terminal TPR-containing region is sufficient for fundamental Cpr7 activity.","method":"Site-directed mutagenesis of catalytic residue; domain-deletion constructs assessed by growth assay and glucocorticoid receptor activity assay in S. cerevisiae","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 1 / Moderate — mutagenesis plus domain deletion with two orthogonal in vivo functional readouts, single lab","pmids":["9556552"],"is_preprint":false},{"year":1996,"finding":"The human PPID gene (encoding CyP-40) spans 14.2 kb, contains 10 exons, and maps to chromosome 4; its promoter lacks TATA/CAAT boxes but is GC-rich with Sp1 sites, consistent with housekeeping gene regulation.","method":"Genomic sequencing, PCR mapping with somatic cell hybrids, anchor-ligation PCR for transcription start site","journal":"Genomics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct genomic characterization; gene mapping by PCR; single lab but primary structural determination","pmids":["8812478"],"is_preprint":false},{"year":2025,"finding":"PPID (cyclophilin D) mediates overnutrition-induced β-cell death through the mitochondrial permeability transition pore (mPTP): global ppid knockout prevents β-cell loss, β-cell-specific PPID re-expression restores and exacerbates β-cell death, and this death is sensitive to cyclosporin A (a PPID/cyclophilin D inhibitor). Reducing mitochondrial ROS or mitochondrial calcium also protects β cells, placing PPID-dependent mPTP opening downstream of mitochondrial oxidative stress.","method":"Zebrafish global ppid knockout; β-cell-specific transgenic PPID re-expression; pharmacological inhibition with cyclosporin A, mito-TEMPO, and Ru360; β-cell mass quantification","journal":"American journal of physiology. Endocrinology and metabolism","confidence":"High","confidence_rationale":"Tier 2 / Strong — genetic KO, cell-type-specific rescue, pharmacological inhibition with multiple agents, and mechanistic pathway dissection in a single study","pmids":["41397247"],"is_preprint":false}],"current_model":"PPID (CyP-40/cyclophilin D) is a TPR-domain-containing immunophilin that associates with hsp90 in steroid receptor heterocomplexes via its TPR domain and flanking charged helices (competing with FKBP52 for a shared hsp90 site), functions as an hsp90 co-chaperone to negatively regulate the heat shock response, and acts as a molecular chaperone that maintains substrates in folding-competent intermediates; its PPIase catalytic activity is dispensable for these hsp90-mediated functions. Additionally, PPID acts as cyclophilin D in the mitochondrial permeability transition pore, where it is a β-cell-intrinsic mediator of overnutrition-induced cell death."},"narrative":{"mechanistic_narrative":"PPID (CyP-40/cyclophilin D) is a TPR-domain immunophilin that operates as an hsp90 co-chaperone in steroid receptor maturation and as a mitochondrial mediator of regulated cell death [PMID:7657624, PMID:41397247]. It is a native component of glucocorticoid receptor–hsp90 heterocomplexes, binding hsp90 directly through a shared immunophilin site for which it competes with FKBP52, so the two immunophilins occupy mutually exclusive hsp90 complexes [PMID:7657624, PMID:8621687]. Stable hsp90 association requires not only the TPR domain but also flanking acidic and basic α-helical microdomains, while the peptidylprolyl isomerase catalytic activity is dispensable for heterocomplex assembly and, in the yeast homolog Cpr7, for essential hsp90-dependent functions [PMID:8621687, PMID:9556552]. Beyond chaperone scaffolding, PPID can act independently as a molecular chaperone in vitro, holding unfolded substrates in folding-competent intermediates [PMID:8939864], and the Cpr7/Hsp90 module negatively regulates the heat shock response by repressing HSF-dependent transcription [PMID:9668076]. In a distinct mitochondrial role, PPID functions as cyclophilin D in overnutrition-induced β-cell death by promoting opening of the mitochondrial permeability transition pore downstream of mitochondrial oxidative stress and calcium, in a cyclosporin A–sensitive manner [PMID:41397247].","teleology":[{"year":1995,"claim":"Established that PPID is a bona fide constituent of receptor chaperone machinery by showing it binds hsp90 directly within glucocorticoid receptor heterocomplexes and shares a single immunophilin site with FKBP52.","evidence":"Co-immunoadsorption, direct binding of purified proteins, and competitive binding/reconstitution assays","pmids":["7657624"],"confidence":"High","gaps":["Structural basis of the shared hsp90 site not resolved","Functional consequence of CyP-40 vs FKBP52 occupancy for receptor activity not defined"]},{"year":1996,"claim":"Defined the molecular determinants of hsp90 binding, showing the TPR domain is necessary but requires flanking charged α-helical microdomains, and confirmed FKBP52 competition.","evidence":"GST-fusion deletion-mutant pulldown/hsp90 retention plus competition assay in myometrial cytosol","pmids":["8621687"],"confidence":"Medium","gaps":["Precise residues mediating contact not mapped","Quantitative affinities not determined"]},{"year":1996,"claim":"Demonstrated an hsp90-independent activity: PPID can itself act as a molecular chaperone holding substrates in non-native folding-competent states.","evidence":"In vitro folding assay with unfolded substrate proteins","pmids":["8939864"],"confidence":"Medium","gaps":["Physiological substrates not identified","Single-lab in vitro assay without orthogonal validation","Cannot complete refolding alone"]},{"year":1996,"claim":"Provided the genomic architecture of human PPID, indicating housekeeping-style regulation.","evidence":"Genomic sequencing, somatic cell hybrid PCR mapping, anchor-ligation PCR for transcription start site","pmids":["8812478"],"confidence":"Medium","gaps":["No functional dissection of the promoter","Tissue-specific expression control not addressed"]},{"year":1998,"claim":"Showed that PPIase catalytic activity is dispensable for the protein's essential hsp90-related functions, localizing function to the TPR-containing region.","evidence":"Catalytic-residue mutagenesis and PPIase domain deletion with growth and glucocorticoid receptor activity readouts in S. cerevisiae","pmids":["9556552"],"confidence":"Medium","gaps":["Whether PPIase activity has any context-specific role unaddressed","Reliance on yeast homolog Cpr7"]},{"year":1998,"claim":"Placed the CyP-40/Hsp90 module in negative regulation of the heat shock response via repression of HSF-dependent transcription.","evidence":"Genetic epistasis with HSF reporter and thermotolerance assays in S. cerevisiae","pmids":["9668076"],"confidence":"Medium","gaps":["Mechanism of HSF repression unresolved","Conservation of this role to human PPID not tested in this study"]},{"year":2025,"claim":"Identified a mitochondrial role for PPID as cyclophilin D mediating overnutrition-induced β-cell death through mPTP opening, downstream of mitochondrial ROS and calcium.","evidence":"Zebrafish global ppid knockout, β-cell-specific re-expression, and pharmacological inhibition (cyclosporin A, mito-TEMPO, Ru360) with β-cell mass quantification","pmids":["41397247"],"confidence":"High","gaps":["Molecular composition/structure of the PPID-dependent mPTP not defined","Direct PPID interactors at the pore not identified","Conservation to mammalian β cells not shown here"]},{"year":null,"claim":"How PPID's cytosolic hsp90 co-chaperone activity and its mitochondrial mPTP function are coordinated, and what dictates its subcellular partitioning, remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No study links the chaperone and mitochondrial roles","Subcellular targeting determinants uncharacterized"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0044183","term_label":"protein folding chaperone","supporting_discovery_ids":[0]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[1,2,3]},{"term_id":"GO:0016853","term_label":"isomerase activity","supporting_discovery_ids":[4]}],"localization":[{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[1]},{"term_id":"GO:0005739","term_label":"mitochondrion","supporting_discovery_ids":[6]}],"pathway":[{"term_id":"R-HSA-5357801","term_label":"Programmed Cell Death","supporting_discovery_ids":[6]}],"complexes":["glucocorticoid receptor-hsp90 heterocomplex","mitochondrial permeability transition pore"],"partners":["HSP90","FKBP52"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q08752","full_name":"Peptidyl-prolyl cis-trans isomerase D","aliases":["40 kDa peptidyl-prolyl cis-trans isomerase","Cyclophilin-40","CYP-40","Cyclophilin-related protein","Rotamase D"],"length_aa":370,"mass_kda":40.8,"function":"PPIase that catalyzes the cis-trans isomerization of proline imidic peptide bonds in oligopeptides and may therefore assist protein folding (PubMed:11350175, PubMed:20676357). Proposed to act as a co-chaperone in HSP90 complexes such as in unligated steroid receptors heterocomplexes. Different co-chaperones seem to compete for association with HSP90 thus establishing distinct HSP90-co-chaperone-receptor complexes with the potential to exert tissue-specific receptor activity control. May have a preference for estrogen receptor complexes and is not found in glucocorticoid receptor complexes. May be involved in cytoplasmic dynein-dependent movement of the receptor from the cytoplasm to the nucleus. May regulate MYB by inhibiting its DNA-binding activity. Involved in regulation of AHR signaling by promoting the formation of the AHR:ARNT dimer; the function is independent of HSP90 but requires the chaperone activity. Involved in regulation of UV radiation-induced apoptosis. Promotes cell viability in anaplastic lymphoma kinase-positive anaplastic large-cell lymphoma (ALK+ ALCL) cell lines (Microbial infection) May be involved in hepatitis C virus (HCV) replication and release","subcellular_location":"Cytoplasm; Nucleus, nucleolus; Nucleus, nucleoplasm","url":"https://www.uniprot.org/uniprotkb/Q08752/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/PPID","classification":"Not Classified","n_dependent_lines":0,"n_total_lines":1208,"dependency_fraction":0.0},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/PPID","total_profiled":1310},"omim":[{"mim_id":"617076","title":"FK506-BINDING PROTEIN-LIKE; FKBPL","url":"https://www.omim.org/entry/617076"},{"mim_id":"616003","title":"CYTOCHROME C OXIDASE ASSEMBLY FACTOR 8; COA8","url":"https://www.omim.org/entry/616003"},{"mim_id":"610346","title":"CELL DIVISION CYCLE 37-LIKE 1; CDC37L1","url":"https://www.omim.org/entry/610346"},{"mim_id":"604486","title":"PEPTIDYL-PROLYL CIS/TRANS ISOMERASE, MITOCHONDRIAL; PPIF","url":"https://www.omim.org/entry/604486"},{"mim_id":"601753","title":"PEPTIDYL-PROLYL ISOMERASE D; PPID","url":"https://www.omim.org/entry/601753"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Cytosol","reliability":"Supported"},{"location":"Nucleoplasm","reliability":"Additional"},{"location":"Nucleoli","reliability":"Additional"},{"location":"Nucleoli rim","reliability":"Additional"},{"location":"Primary cilium","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/PPID"},"hgnc":{"alias_symbol":["CYP-40","CypD"],"prev_symbol":[]},"alphafold":{"accession":"Q08752","domains":[{"cath_id":"2.40.100.10","chopping":"16-183","consensus_level":"high","plddt":97.9957,"start":16,"end":183},{"cath_id":"1.25.40.10","chopping":"287-362_366-370","consensus_level":"medium","plddt":96.3919,"start":287,"end":370}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q08752","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q08752-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q08752-F1-predicted_aligned_error_v6.png","plddt_mean":96.44},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=PPID","jax_strain_url":"https://www.jax.org/strain/search?query=PPID"},"sequence":{"accession":"Q08752","fasta_url":"https://rest.uniprot.org/uniprotkb/Q08752.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q08752/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q08752"}},"corpus_meta":[{"pmid":"8939864","id":"PMC_8939864","title":"Molecular chaperone machines: chaperone activities of the cyclophilin Cyp-40 and the steroid aporeceptor-associated protein p23.","date":"1996","source":"Science (New York, N.Y.)","url":"https://pubmed.ncbi.nlm.nih.gov/8939864","citation_count":302,"is_preprint":false},{"pmid":"9670013","id":"PMC_9670013","title":"A new heat-shock gene, ppiD, encodes a peptidyl-prolyl isomerase required for folding of outer membrane proteins in Escherichia coli.","date":"1998","source":"The EMBO journal","url":"https://pubmed.ncbi.nlm.nih.gov/9670013","citation_count":189,"is_preprint":false},{"pmid":"8621687","id":"PMC_8621687","title":"Cyclophilin 40 (CyP-40), mapping of its hsp90 binding domain and evidence that FKBP52 competes with CyP-40 for hsp90 binding.","date":"1996","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/8621687","citation_count":159,"is_preprint":false},{"pmid":"7657624","id":"PMC_7657624","title":"The cyclosporin A-binding immunophilin CyP-40 and the FK506-binding immunophilin hsp56 bind to a common site on hsp90 and exist in independent cytosolic heterocomplexes with the untransformed glucocorticoid receptor.","date":"1995","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/7657624","citation_count":159,"is_preprint":false},{"pmid":"9668076","id":"PMC_9668076","title":"Requirement for Hsp90 and a CyP-40-type cyclophilin in negative regulation of the heat shock response.","date":"1998","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/9668076","citation_count":122,"is_preprint":false},{"pmid":"22647578","id":"PMC_22647578","title":"Glucocorticoid sensitizers Bag1 and Ppid are regulated by adolescent stress in a sex-dependent manner.","date":"2012","source":"Psychoneuroendocrinology","url":"https://pubmed.ncbi.nlm.nih.gov/22647578","citation_count":75,"is_preprint":false},{"pmid":"8873448","id":"PMC_8873448","title":"Identification of two CyP-40-like cyclophilins in Saccharomyces cerevisiae, one of which is required for normal growth.","date":"1996","source":"Yeast (Chichester, England)","url":"https://pubmed.ncbi.nlm.nih.gov/8873448","citation_count":74,"is_preprint":false},{"pmid":"18439025","id":"PMC_18439025","title":"The periplasmic chaperone PpiD interacts with secretory proteins exiting from the SecYEG translocon.","date":"2008","source":"Biochemistry","url":"https://pubmed.ncbi.nlm.nih.gov/18439025","citation_count":55,"is_preprint":false},{"pmid":"20920237","id":"PMC_20920237","title":"PpiD is a player in the network of periplasmic chaperones in Escherichia coli.","date":"2010","source":"BMC microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/20920237","citation_count":54,"is_preprint":false},{"pmid":"9556552","id":"PMC_9556552","title":"The peptidyl-prolyl isomerase domain of the CyP-40 cyclophilin homolog Cpr7 is not required to support growth or glucocorticoid receptor activity in Saccharomyces cerevisiae.","date":"1998","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/9556552","citation_count":44,"is_preprint":false},{"pmid":"19866485","id":"PMC_19866485","title":"The prolyl isomerase domain of PpiD from Escherichia coli shows a parvulin fold but is devoid of catalytic activity.","date":"2010","source":"Protein science : a publication of the Protein Society","url":"https://pubmed.ncbi.nlm.nih.gov/19866485","citation_count":34,"is_preprint":false},{"pmid":"31699901","id":"PMC_31699901","title":"Noncompetitive binding of PpiD and YidC to the SecYEG translocon expands the global view on the SecYEG interactome in Escherichia coli.","date":"2019","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/31699901","citation_count":32,"is_preprint":false},{"pmid":"24951590","id":"PMC_24951590","title":"Dynamic interaction of the sec translocon with the chaperone PpiD.","date":"2014","source":"The Journal of biological 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Endocrinology and metabolism","url":"https://pubmed.ncbi.nlm.nih.gov/41397247","citation_count":0,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2024.12.13.628315","title":"Mechanistic Insights into Periplasmic Chaperones as Regulators of Protein Folding and Translocation in Gram-Negative Bacteria","date":"2024-12-13","source":"bioRxiv","url":"https://doi.org/10.1101/2024.12.13.628315","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":12981,"output_tokens":1948,"usd":0.034082,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":8882,"output_tokens":2488,"usd":0.053305,"stage2_stop_reason":"end_turn"},"total_usd":0.087387,"stage1_batch_id":"msgbatch_01CNoDbkChHEkgrJnL7BwtGJ","stage2_batch_id":"msgbatch_016Y4x9E9Wg5VQDANj9quSQD","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 1996,\n      \"finding\": \"CyP-40 (PPID) functions as a molecular chaperone in vitro, interacting with unfolded substrates to maintain a nonnative folding-competent intermediate, similar to Hsp90 or Hsp70, though it cannot completely refold substrates on its own.\",\n      \"method\": \"In vitro folding assay with unfolded substrate proteins\",\n      \"journal\": \"Science\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Weak — in vitro chaperone assay from a single lab; abstract does not detail mutagenesis or multiple orthogonal methods\",\n      \"pmids\": [\"8939864\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1995,\n      \"finding\": \"CyP-40 (PPID) is a component of native glucocorticoid receptor heterocomplexes and binds directly to hsp90; it occupies a common immunophilin-binding site on hsp90 that is also used by hsp56 (FKBP52), such that the two immunophilins exist in separate, mutually exclusive complexes with hsp90. The peptidylprolyl isomerase activity of CyP-40 is not required for glucocorticoid receptor–hsp90 heterocomplex assembly.\",\n      \"method\": \"Immunoadsorption/co-immunoadsorption from cell lysate; direct binding of purified proteins; competitive binding assay; reconstitution with reticulocyte lysate\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal co-immunoadsorption, direct binding with purified proteins, and competition assay in same study; findings independently referenced by multiple subsequent papers\",\n      \"pmids\": [\"7657624\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1996,\n      \"finding\": \"The TPR domain of CyP-40 (PPID) mediates binding to hsp90, but the TPR domain alone is not sufficient for stable hsp90 association; flanking acidic and basic residues (alpha-helical microdomains) at the N- and C-terminal ends of the TPR domain are also required. FKBP52 competes with CyP-40 for hsp90 binding, consistent with a common binding site.\",\n      \"method\": \"GST-fusion deletion mutant pulldown/hsp90 retention assay; competition assay with bacterially expressed FKBP52 in myometrial cytosol\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — GST-pulldown with deletion mutants plus competition assay, single lab, two orthogonal methods\",\n      \"pmids\": [\"8621687\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1998,\n      \"finding\": \"In Saccharomyces cerevisiae, Cpr7 (the CyP-40 homolog) and Hsp90 function synergistically to repress HSF-dependent gene expression; loss of Cpr7 or reduced Hsp90 levels leads to increased HSF-dependent transcription and acquisition of thermotolerance, placing this CyP-40-type cyclophilin in negative regulation of the heat shock response.\",\n      \"method\": \"Genetic epistasis analysis (deletion and hypomorphic mutations) with reporter assays for HSF-dependent promoter activity; thermotolerance assay in S. cerevisiae\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic epistasis with reporter assays in yeast, single lab, two orthogonal phenotypic readouts\",\n      \"pmids\": [\"9668076\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1998,\n      \"finding\": \"The peptidyl-prolyl isomerase (PPIase) catalytic domain of Cpr7 (CyP-40/PPID yeast homolog) is not required for its essential functions: a catalytic-site mutation and complete deletion of the PPIase domain did not significantly impair growth or Hsp90-mediated steroid receptor activity. The C-terminal TPR-containing region is sufficient for fundamental Cpr7 activity.\",\n      \"method\": \"Site-directed mutagenesis of catalytic residue; domain-deletion constructs assessed by growth assay and glucocorticoid receptor activity assay in S. cerevisiae\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — mutagenesis plus domain deletion with two orthogonal in vivo functional readouts, single lab\",\n      \"pmids\": [\"9556552\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1996,\n      \"finding\": \"The human PPID gene (encoding CyP-40) spans 14.2 kb, contains 10 exons, and maps to chromosome 4; its promoter lacks TATA/CAAT boxes but is GC-rich with Sp1 sites, consistent with housekeeping gene regulation.\",\n      \"method\": \"Genomic sequencing, PCR mapping with somatic cell hybrids, anchor-ligation PCR for transcription start site\",\n      \"journal\": \"Genomics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct genomic characterization; gene mapping by PCR; single lab but primary structural determination\",\n      \"pmids\": [\"8812478\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"PPID (cyclophilin D) mediates overnutrition-induced β-cell death through the mitochondrial permeability transition pore (mPTP): global ppid knockout prevents β-cell loss, β-cell-specific PPID re-expression restores and exacerbates β-cell death, and this death is sensitive to cyclosporin A (a PPID/cyclophilin D inhibitor). Reducing mitochondrial ROS or mitochondrial calcium also protects β cells, placing PPID-dependent mPTP opening downstream of mitochondrial oxidative stress.\",\n      \"method\": \"Zebrafish global ppid knockout; β-cell-specific transgenic PPID re-expression; pharmacological inhibition with cyclosporin A, mito-TEMPO, and Ru360; β-cell mass quantification\",\n      \"journal\": \"American journal of physiology. Endocrinology and metabolism\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — genetic KO, cell-type-specific rescue, pharmacological inhibition with multiple agents, and mechanistic pathway dissection in a single study\",\n      \"pmids\": [\"41397247\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"PPID (CyP-40/cyclophilin D) is a TPR-domain-containing immunophilin that associates with hsp90 in steroid receptor heterocomplexes via its TPR domain and flanking charged helices (competing with FKBP52 for a shared hsp90 site), functions as an hsp90 co-chaperone to negatively regulate the heat shock response, and acts as a molecular chaperone that maintains substrates in folding-competent intermediates; its PPIase catalytic activity is dispensable for these hsp90-mediated functions. Additionally, PPID acts as cyclophilin D in the mitochondrial permeability transition pore, where it is a β-cell-intrinsic mediator of overnutrition-induced cell death.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"PPID (CyP-40/cyclophilin D) is a TPR-domain immunophilin that operates as an hsp90 co-chaperone in steroid receptor maturation and as a mitochondrial mediator of regulated cell death [#1, #6]. It is a native component of glucocorticoid receptor–hsp90 heterocomplexes, binding hsp90 directly through a shared immunophilin site for which it competes with FKBP52, so the two immunophilins occupy mutually exclusive hsp90 complexes [#1, #2]. Stable hsp90 association requires not only the TPR domain but also flanking acidic and basic α-helical microdomains, while the peptidylprolyl isomerase catalytic activity is dispensable for heterocomplex assembly and, in the yeast homolog Cpr7, for essential hsp90-dependent functions [#2, #4]. Beyond chaperone scaffolding, PPID can act independently as a molecular chaperone in vitro, holding unfolded substrates in folding-competent intermediates [#0], and the Cpr7/Hsp90 module negatively regulates the heat shock response by repressing HSF-dependent transcription [#3]. In a distinct mitochondrial role, PPID functions as cyclophilin D in overnutrition-induced β-cell death by promoting opening of the mitochondrial permeability transition pore downstream of mitochondrial oxidative stress and calcium, in a cyclosporin A–sensitive manner [#6].\",\n  \"teleology\": [\n    {\n      \"year\": 1995,\n      \"claim\": \"Established that PPID is a bona fide constituent of receptor chaperone machinery by showing it binds hsp90 directly within glucocorticoid receptor heterocomplexes and shares a single immunophilin site with FKBP52.\",\n      \"evidence\": \"Co-immunoadsorption, direct binding of purified proteins, and competitive binding/reconstitution assays\",\n      \"pmids\": [\"7657624\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural basis of the shared hsp90 site not resolved\", \"Functional consequence of CyP-40 vs FKBP52 occupancy for receptor activity not defined\"]\n    },\n    {\n      \"year\": 1996,\n      \"claim\": \"Defined the molecular determinants of hsp90 binding, showing the TPR domain is necessary but requires flanking charged α-helical microdomains, and confirmed FKBP52 competition.\",\n      \"evidence\": \"GST-fusion deletion-mutant pulldown/hsp90 retention plus competition assay in myometrial cytosol\",\n      \"pmids\": [\"8621687\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Precise residues mediating contact not mapped\", \"Quantitative affinities not determined\"]\n    },\n    {\n      \"year\": 1996,\n      \"claim\": \"Demonstrated an hsp90-independent activity: PPID can itself act as a molecular chaperone holding substrates in non-native folding-competent states.\",\n      \"evidence\": \"In vitro folding assay with unfolded substrate proteins\",\n      \"pmids\": [\"8939864\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Physiological substrates not identified\", \"Single-lab in vitro assay without orthogonal validation\", \"Cannot complete refolding alone\"]\n    },\n    {\n      \"year\": 1996,\n      \"claim\": \"Provided the genomic architecture of human PPID, indicating housekeeping-style regulation.\",\n      \"evidence\": \"Genomic sequencing, somatic cell hybrid PCR mapping, anchor-ligation PCR for transcription start site\",\n      \"pmids\": [\"8812478\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No functional dissection of the promoter\", \"Tissue-specific expression control not addressed\"]\n    },\n    {\n      \"year\": 1998,\n      \"claim\": \"Showed that PPIase catalytic activity is dispensable for the protein's essential hsp90-related functions, localizing function to the TPR-containing region.\",\n      \"evidence\": \"Catalytic-residue mutagenesis and PPIase domain deletion with growth and glucocorticoid receptor activity readouts in S. cerevisiae\",\n      \"pmids\": [\"9556552\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether PPIase activity has any context-specific role unaddressed\", \"Reliance on yeast homolog Cpr7\"]\n    },\n    {\n      \"year\": 1998,\n      \"claim\": \"Placed the CyP-40/Hsp90 module in negative regulation of the heat shock response via repression of HSF-dependent transcription.\",\n      \"evidence\": \"Genetic epistasis with HSF reporter and thermotolerance assays in S. cerevisiae\",\n      \"pmids\": [\"9668076\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism of HSF repression unresolved\", \"Conservation of this role to human PPID not tested in this study\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Identified a mitochondrial role for PPID as cyclophilin D mediating overnutrition-induced β-cell death through mPTP opening, downstream of mitochondrial ROS and calcium.\",\n      \"evidence\": \"Zebrafish global ppid knockout, β-cell-specific re-expression, and pharmacological inhibition (cyclosporin A, mito-TEMPO, Ru360) with β-cell mass quantification\",\n      \"pmids\": [\"41397247\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Molecular composition/structure of the PPID-dependent mPTP not defined\", \"Direct PPID interactors at the pore not identified\", \"Conservation to mammalian β cells not shown here\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How PPID's cytosolic hsp90 co-chaperone activity and its mitochondrial mPTP function are coordinated, and what dictates its subcellular partitioning, remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No study links the chaperone and mitochondrial roles\", \"Subcellular targeting determinants uncharacterized\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0044183\", \"supporting_discovery_ids\": [0]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [1, 2, 3]},\n      {\"term_id\": \"GO:0016853\", \"supporting_discovery_ids\": [4]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [1]},\n      {\"term_id\": \"GO:0005739\", \"supporting_discovery_ids\": [6]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"GO:0008953897\", \"supporting_discovery_ids\": [3]},\n      {\"term_id\": \"R-HSA-5357801\", \"supporting_discovery_ids\": [6]}\n    ],\n    \"complexes\": [\"glucocorticoid receptor-hsp90 heterocomplex\", \"mitochondrial permeability transition pore\"],\n    \"partners\": [\"HSP90\", \"FKBP52\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":5,"faith_total":5,"faith_pct":100.0}}