{"compile":"2026-10-10","canonical":"https://aaronspradlin.grok.me/wiki/p53-campaign","json":"https://aaronspradlin.grok.me/page.json?slug=p53-campaign","license":"Source-available for noncommercial research and evaluation only. No commercial, product, platform, or service use without written permission.","scientific_breakthrough":false,"slug":"p53-campaign","title":"p53 mutational mechanisms","dek":"Aug 2025 Labs/p53. 16 Sep 2026 README: further testing did not support the findings; lab materials withdrawn. Do not rely on them as validation. Restricted/Corrected.","updated":"2026-09-19","status":"applied","claim":"corrected","tags":["protein","p53","Y220C","R248Q","PhiKan083"],"related":["protein-audit","mecp2-rett","protein-bridge-v9","applied-stack","claim-ledger","for-researchers","open-science"],"packages":[{"id":"labs-p53","name":"Labs/p53","path":"Labs/p53","status":"restricted"},{"id":"wetlab-root","name":"WetLabEngine (root)","path":"/","status":"supported"}],"notes":[],"claims":[{"status":"restricted","text":"Inside this coarse-grained campaign, R248Q and Y220C reach similar misfolded globules by different routes (electrostatic network loss vs kinetic trap), and a contact-anneal + PhiKan083 protocol improved Y220C RMSD relative to ~25 Å baselines. Not native folding, not a crystal rescue, not a cancer therapy, not a TOE result."},{"status":"not-claimed","text":"This atlas does not claim that PhiKan083 rescues p53-Y220C in cells, or that UQCF-GEM replaces all-atom MD. The native-start drift is the campaign’s own limit."}],"text":"Labs/p53 is a 12-run coarse-grained campaign on the p53 DNA-binding domain, dated 22–23 Aug 2025 in the deliverable folders. The machine-readable contract is findings.json v2.2. The human manuscript (ReadMe.pd) is co-attributed to Gemini, ChatGPT, Grok, and Aaron Spradlin. There is no load-bearing X field note for this campaign in the current compile — it lives on GitHub. Cite the folder and the science contract, not a tweet.\n\nWild-type also collapses to a compact non-native globule (best RMSD 26.6 Å). The result is mechanism differentiation among misfolded globules, not native p53 folding. Contact-anneal + PhiKan083 improved Y220C from ~25 Å to 18.9 Å inside this force field. That is not a pharmacological proof and not a crystal-structure rescue.\n\nThesis in the contract\n\nAcross the UQCF-GEM campaign, p53-Y220C predominantly fails via a kinetic collapse trap, while p53-R248Q failure is electrostatic in nature. A protocol-level intervention—contact anneal with PhiKan083—achieves meaningful improvement (≤ 20 Å) relative to ~25 Å baselines. The campaign ultimately revealed a force-field limitation in the ligand model.\n\nTwelve-run scoreboard\n\nTwo failure modes, one globule\n\nFinal RMSD alone does not separate the mutants from wild-type. The mechanistic split is in the diagnostics. R248Q (DNA-contact mutant) loses the salt-bridge network (median 1.0 versus WT 7.0) while collapsing to the same 26.6 Å globule — electrostatic_failure. Y220C (pocket mutant) is diagnosed as a kinetic trap: genetic pocket patches Y220F and L221F do not improve RMSD; a gentler contact-anneal protocol plus the pharmacological chaperone PhiKan083 does, inside this model. The timing sweep says the ligand acts as a thermodynamic stabilizer of the collapsed state, not a kinetic folding guide.\n\nModel: coarse-grained, backbone-centric UQCF-GEM. Terms named in the manuscript: steric, directional H-bond, Ramachandran, Debye–Hückel electrostatics, tunable contact springs.\nProtocol: extended coil start unless marked native-start. pH 7.4, ionic strength 150 mM. k_hbond = 16.0, k_contact_springs = 0.05 as the posted sweet spot.\nNegative results are first-class: L221F and Y220F fail; the native-start ligand run drifts to 4.0 Å and is filed as a force-field limit, not hidden.\nPNG and PDB artifacts in Labs/ are Git LFS pointers in a plain clone. Markdown reports, raw CSVs, and findings.json are ordinary files.\n\nInside this coarse-grained campaign, R248Q and Y220C reach similar misfolded globules by different routes (electrostatic network loss vs kinetic trap), and a contact-anneal + PhiKan083 protocol improved Y220C RMSD relative to ~25 Å baselines. Not native folding, not a crystal rescue, not a cancer therapy, not a TOE result.\n\nThis atlas does not claim that PhiKan083 rescues p53-Y220C in cells, or that UQCF-GEM replaces all-atom MD. The native-start drift is the campaign’s own limit.\n\nLabs/p53 on GitHub\nfindings.json v2.2\nRun this first (MECP2 smoke)\nMECP2 campaign","howToCite":"Spradlin, A. (2026-10-10). p53 mutational mechanisms. Retained Atlas. https://aaronspradlin.grok.me/wiki/p53-campaign. Keep claim badge: corrected."}