• 1. Enzyme Family Background
    • 1.1 Classification
    • 1.2 Reaction chemistry
    • 1.3 Substrate scope terminology
    • 1.4 Why substrate specificity is structurally interesting
  • 2. Structural Information
    • 2.1 Available experimental structures
    • 2.2 AlphaFold models
    • 2.3 Key structural regions
    • 2.4 Known substrate-contacting / selectivity residues
    • 2.5 Tunnel geometry notes
  • 3. Sequence Dataset Summary
    • 3.1 Dataset composition
    • 3.2 Taxonomic distribution
    • 3.3 Alignment properties
    • 3.4 Top mutual information positions
  • 4. Experimental Mutation Database
    • 4.1 Key literature to mine
    • 4.2 Gain-of-function mutations (toward mcl/broader specificity)
    • 4.3 Loss-of-function / specificity-narrowing mutations
    • 4.4 Combinatorial / double mutants
    • 4.5 Thermostability mutations
    • 4.6 Notes on data quality and comparability
  • 5. Your Starting Enzyme (Wild-Type)
    • 5.1 Identity
    • 5.2 Known properties
    • 5.3 Sequence — full
    • 5.4 Sequence — substrate-binding pocket region
    • 5.5 Alignment position mapping
  • 6. Engineering Target
    • 6.1 Primary goal
    • 6.2 Secondary goals
    • 6.3 Acceptable tradeoffs
    • 6.4 Hard constraints — DO NOT VIOLATE
    • 6.5 What has already been tested
  • 7. Production and Assay Context
    • 7.1 Expression system
    • 7.2 PHA production conditions
    • 7.3 Analytical method
  • 8. Reasoning Guidelines for LLM
    • 8.1 Prioritization criteria (in order)
    • 8.2 Required output format for mutation suggestions
    • 8.3 Reasoning I do NOT want
    • 8.4 When hypotheses conflict
    • 8.5 My background
  • 9. Session Log
    • Session [DATE]
    • Session [DATE]
  • 10. Experimental Results Log
    • Experiment [DATE / ID]
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