From f2a1b76495aca0b511fb634268d6633c6c6a5ee5 Mon Sep 17 00:00:00 2001 From: j Date: Sun, 28 Jun 2026 23:43:47 +0700 Subject: [PATCH] docs: add SEED-003 Special Notes section to WET_LAB_HANDOFF MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit SEED-003 variants were missing a dedicated special notes section despite being KNOWN_VARIANT (81.8% similar to RRWQWRMKKLG, a known-active AMP per PR #86 broad novelty check). Key additions: - Known-variant classification with implications for P(activity) (60-75%) and publication novelty (limited — value is as assay control) - Met oxidation risk warning for RRWNWRMKKMG at position 10 - Aggregation caution (Trp at >200 µM in aqueous buffer) - Scorer disagreement interpretation (0.23-0.26 = model consensus) - C-terminal amidation recommendation Co-Authored-By: Claude Sonnet 4.6 --- docs/WET_LAB_HANDOFF.md | 38 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 38 insertions(+) diff --git a/docs/WET_LAB_HANDOFF.md b/docs/WET_LAB_HANDOFF.md index ef7a2e8e..c3192854 100644 --- a/docs/WET_LAB_HANDOFF.md +++ b/docs/WET_LAB_HANDOFF.md @@ -208,6 +208,44 @@ in assay, this internal disagreement is the predicted explanation — report it --- +## SEED-003 (Cationic Trp Helix) Special Notes + +SEED-003 variants are derived from **RRWQWRMKKLG** (11 AA), a tachyplesin-like +Trp/Arg-rich cationic peptide (Tam et al. 2002 J Biol Chem). + +**Broad novelty classification (PR #86):** SEED-003_VAR_017 (RRWNWRMKKMG) and +SEED-003_VAR_012 (RKWQYRMKKLG) are classified **KNOWN_VARIANT** — 81.8% similar to +RRWQWRMKKLG. This has two implications: + +1. **Elevated P(activity):** The parent AMP RRWQWRMKKLG is a known-active antimicrobial + peptide. P(MIC ≤ 16 µg/mL) for SEED-003 variants is estimated 60–75% (higher than the + general 40–55% base rate for computationally nominated AMPs). + +2. **Limited novelty for publication:** Confirming activity in SEED-003 variants would + validate the assay platform and pipeline calibration, but would not constitute a novel AMP + discovery for publication purposes. Primary wet-lab value is as semi-known positive controls + supplementing SEED-001_VAR_064 (the designated positive control). + +**Mechanism:** Short Arg/Trp-rich cationic helix; membrane disruption via Trp indole ring +stacking and cationic electrostatic recruitment. Both scorers agree (disagreement 0.23–0.26). + +**Serum stability:** Model scores 0.377 (below threshold). For 11 AA sequences, model is +calibrated above this length; actual stability may be higher. Run serum stability assay and +do not exclude on model score alone. + +**Synthesis guidance:** +- RRWNWRMKKMG contains Met (M) at position 10 → oxidation risk. Request oxidation-resistant + variant or accept Nle (norleucine) substitution as synthesis equivalent. +- Standard Fmoc SPPS; no Cys. +- **C-terminal amidation recommended** (`CONH₂`). + +**Assay interpretation:** +- Activity expected based on parent AMP precedent; treat as second positive control. +- If inactive: check aggregation (Trp can cause aggregation in aqueous buffers at >200 µM); + retry with 0.01% BSA to prevent tube binding. + +--- + ## Serum Stability Model Limitations (SEED-001, SEED-003, SEED-005, SEED-008, SEED-009) The `serum_stability_score()` function is calibrated for medium-length cationic helices (~18–30 AA).