Skip to content

comp-001 — Uricase Shio-Koji Protease Stability

Question: Will A. flavus uricase (Q00511) survive the protease environment of a shio-koji ferment (15–20% NaCl, pH 4.5–5.0, RT, 7–14 days) with meaningful activity retained?

Short answer: Computational analysis predicts low risk. All protease recognition sites are in confidently-folded regions (100% of residues pLDDT > 80). Combined with strong salt inhibition of the dominant protease (ALP retains ~19% activity at shio-koji NaCl concentrations), the structural evidence argues against significant proteolytic degradation.

Verdict: §1.10 wet-lab stability experiment should still run — this analysis shifts the prior from "unknown" to "probably fine," reframing §1.10 as confirmation rather than feasibility gate.

How to reproduce

python3 analyze.py
# Outputs: outputs/cleavage_sites.json, outputs/summary.md

Requirements: Python 3.8+, stdlib only (json, pathlib, os). No packages to install.

Re-running with updated data

  • New AlphaFold model: Download updated PDB from https://alphafold.ebi.ac.uk/files/AF-Q00511-F1-model_v<version>.pdb, re-extract pLDDT values into inputs/alphafold_Q00511_plddt.json, update inputs/provenance.md, re-run.
  • Updated protease specificities: Edit inputs/protease_specificities.json and update _source field with new MEROPS reference.
  • Different protein: Replace Q00511.fasta and alphafold_Q00511_plddt.json with inputs for the new target.

File index

inputs/
  Q00511.fasta                    UniProt sequence (fetched 2026-05-05)
  alphafold_Q00511_plddt.json     Per-residue pLDDT from AlphaFold v6 PDB (fetched 2026-05-05)
  protease_specificities.json     P1/P1' rules + salt inhibition data (MEROPS + primary literature)
  provenance.md                   Data sources, fetch dates, version notes
outputs/
  cleavage_sites.json             Full machine-readable results
  summary.md                      Human-readable findings — this is the artifact cited in the wiki
analyze.py                        Analysis script
README.md                         This file