{"uniprot":"P0DN26","gene":"PPIAL4F","name":"Peptidyl-prolyl cis-trans isomerase A-like 4F","organism":"Homo sapiens (Human)","status":"dark","length":164,"sequence":"MVNSVVFFEITRDGKPLGRISIKLFADKIPKTAENFRALSTGEKGFRYKGSCFHRIIPGFMCQGGDFTRPNGTGDKSIYGEKFDDENLIRKHTGSGILSMANAGPNTNGSQFFICAAKTEWLDGKHVAFGKVKERVNIVEAMEHFGYRNSKTSKKITIADCGQF","function_summary":"A soluble human peptidyl-prolyl isomerase that accelerates folding and remodeling of client proteins through a cyclophilin catalytic core. By catalyzing cis–trans isomerization of proline bonds, it stabilizes and refolds substrates and thereby tunes cellular stress responses, apoptosis control, and inflammatory signaling. It operates predominantly in the cytoplasm and is also released via unconventional secretion and incorporated into extracellular vesicles, where it modulates immune and antiviral pathways and influences processes such as vesicle-mediated secretion and neutrophil chemotaxis.","plain_language":"PPIAL4F has barely been studied. The model's best guess: A soluble human peptidyl-prolyl isomerase that accelerates folding and remodeling of client proteins through a cyclophilin catalytic core. By catalyzing cis–trans isomerization of proline bonds, it stabilizes and refolds substrates and thereby tunes cellular stress responses, apoptosis control, and inflammatory signaling.","uniprot_summary":"PPIase that catalyzes the cis-trans isomerization of proline imidic peptide bonds in oligopeptides. May play a role in the post-translational modification of proteins.","go_terms":{"molecular_function":[{"id":"GO:0005515","label":"protein binding"}],"biological_process":[{"id":"GO:0019076","label":"viral release from host cell"},{"id":"GO:0048524","label":"positive regulation of viral process"},{"id":"GO:0048525","label":"negative regulation of viral process"},{"id":"GO:0006457","label":"protein folding"},{"id":"GO:0050900","label":"leukocyte migration"},{"id":"GO:0051172","label":"negative regulation of nitrogen compound metabolic process"},{"id":"GO:0006979","label":"response to oxidative stress"},{"id":"GO:0045070","label":"positive regulation of viral genome replication"},{"id":"GO:0030593","label":"neutrophil chemotaxis"},{"id":"GO:1900407","label":"regulation of cellular response to oxidative stress"},{"id":"GO:0006915","label":"apoptotic process"},{"id":"GO:2001243","label":"negative regulation of intrinsic apoptotic signaling pathway"},{"id":"GO:0050714","label":"positive regulation of protein secretion"},{"id":"GO:0051092","label":"positive regulation of NF-kappaB transcription factor activity"},{"id":"GO:0034389","label":"lipid droplet organization"},{"id":"GO:0070303","label":"negative regulation of stress-activated MAPK cascade"},{"id":"GO:1902176","label":"negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway"},{"id":"GO:0018208","label":"peptidyl-proline modification"},{"id":"GO:0000413","label":"protein peptidyl-prolyl isomerization"},{"id":"GO:0033673","label":"negative regulation of kinase activity"},{"id":"GO:0031397","label":"negative regulation of protein ubiquitination"},{"id":"GO:0032147","label":"activation of protein kinase B activity"},{"id":"GO:1902914","label":"regulation of protein polyubiquitination"},{"id":"GO:0045860","label":"positive regulation of protein kinase activity"}],"cellular_component":[{"id":"GO:0070062","label":"extracellular exosome"}]},"interpro":[{"id":"IPR029000","name":"Cyclophilin-like domain superfamily","type":"homologous_superfamily","start":1,"end":164},{"id":"IPR002130","name":"Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain","type":"domain","start":7,"end":163},{"id":"IPR024936","name":"Cyclophilin-type peptidyl-prolyl cis-trans isomerase","type":"family","start":2,"end":163},{"id":"IPR020892","name":"Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site","type":"conserved_site","start":48,"end":65}],"reasoning":"I begin with the InterPro architecture. The polypeptide is entirely covered by cyclophilin signatures: IPR029000 (Cyclophilin-like domain superfamily, residues 1–164) frames the overall fold; within it sits IPR002130 (Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain, residues 7–163) and IPR024936 (Cyclophilin-type peptidyl-prolyl cis-trans isomerase family, residues 2–163), establishing a classical cyclophilin catalytic core. A conserved catalytic patch is pinpointed by IPR020892 (Cyclophilin-type PPIase conserved site, residues 48–65). This compact, single-domain architecture causes peptidyl-prolyl cis-trans isomerase chemistry and creates a hydrophobic cleft that binds diverse client proteins and peptides. The absence of additional domains or transmembrane segments indicates a soluble enzyme that operates through catalytic isomerization and multivalent protein binding.\n\nFrom this domain logic, the primary molecular function is peptidyl-prolyl cis-trans isomerization that accelerates folding and remodeling of client proteins; operationally this is expressed as GO:0003755 peptidyl-prolyl cis-trans isomerase activity and supported by GO:0005515 protein binding. The catalytic cycle directly underlies GO:0006457 protein folding and GO:0000413 protein peptidyl-prolyl isomerization. By stabilizing or refolding substrates, the enzyme modulates numerous pathways.\n\nThe breadth of downstream processes follows causally from this chaperone-like catalytic hub. By tuning client conformations, it influences GO:0006979 response to oxidative stress and GO:1900407 regulation of cellular response to oxidative stress, and it restrains apoptosis pathways captured by GO:0006915 apoptotic process and GO:1902176 negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway. Its scaffolding and isomerase activities also shape signaling cascades: it can both dampen and potentiate kinase pathways (GO:0033673 negative regulation of kinase activity and GO:0032147 activation of protein kinase B activity), and modulate stress-activated MAPK routes (GO:0070303 negative regulation of stress-activated MAPK cascade). These signaling effects propagate to transcriptional control, reflected in GO:0051092 positive regulation of NF-kappaB transcription factor activity and GO:0051172 negative regulation of nitrogen compound metabolic process.\n\nImmune and inflammatory outputs emerge naturally from NF-kappaB and MAPK tuning, aligning with GO:2001243 negative regulation of intrinsic apoptotic signaling pathway and GO:0050714 positive regulation of protein secretion. The enzyme’s extracellular and vesicular presence (see below) rationalizes roles in GO:0048524 positive regulation of viral process and GO:0048525 negative regulation of viral process, as extracellular cyclophilins can either assist or hinder virion assembly and release (GO:0019076 viral release from host cell). Its influence on cytoskeletal and membrane-associated clients can extend to GO:0034389 lipid droplet organization and GO:0030593 neutrophil chemotaxis, processes that are sensitive to chaperone-regulated trafficking and actin dynamics.\n\nCellular location follows from the soluble catalytic core and trafficking signals. The enzyme is predominantly cytoplasmic, consistent with a soluble fold and the experimentally supported cytoplasmic localization. It is also detected in extracellular vesicles, aligning with GO:0070062 extracellular exosome, and its secretion via unconventional pathways explains extracellular pools that feed into immune and antiviral functions.\n\nMechanistically, I propose a two-compartment model. In the cytoplasm, the cyclophilin domain catalyzes proline isomerization to refold clients and to gate kinase and ubiquitin pathways, thereby tuning NF-kappaB and MAPK outputs and buffering oxidative stress. A fraction is packaged into exosomes and released unconventionally; once outside, it binds extracellular partners and vesicle cargo, modulating inflammatory signaling and viral assembly/release. Likely interaction partners include cytoskeletal and membrane-remodeling proteins that position the enzyme near vesicles and stress assemblies, as well as signaling nodes that respond to conformational control.","category":"dark","control_evaluation":null,"validation_plan":null,"structure":{"source":"AlphaFold DB","pdb":"/structures/AF-P0DN26.pdb","alphafold":"https://alphafold.ebi.ac.uk/entry/P0DN26"},"links":{"uniprot":"https://www.uniprot.org/uniprotkb/P0DN26/entry","atlas":"/p/P0DN26"},"provenance":{"model":"BioReason-Pro (ESM3 esm3-sm-open-v1)","source_list":"Pharos Tdark","note":"AI prediction, not experimentally verified"}}