STRC h09 Phase 4m Kd Mono Soft Floor Result
Phase 4m PASS: WH2-family AF3 calibration gives R2=0.690 and h09 Kd_F=1.48 mM, below the 5 mM soft-floor gate.
Problem
Phase 4j held h09 at tentative-S because the conservative avidity model used the Husson Tbeta4 x F-actin 5-10 mM floor for single WH2 x filament binding, leaving the conservative Kd_eff case just above the 50 uM gate. Phase 4m tested the pre-registered cheaper route: use matched AF3 ipTM within the Chereau WH2 x G-actin family to place a soft Kd_mono floor for the h09 WH2 motif.
Method
- Script:
hypotheses/h09-hydrogel/scripts/phase4m_iptm_kd_analysis.py - Inputs: six AlphaFold Server ZIPs in
models/af3_results/h09_phase4k_4m_2026-04-27/ - Artifact:
hypotheses/h09-hydrogel/artifacts/phase4m_calibration_2026-04-27.json
| Parameter | Value | Source |
|---|---|---|
| WAVE2 WH2 x G-actin Kd | 52 nM | 2026-04-23-chereau-wh2-actin-pnas |
| WIP WH2 x G-actin Kd | 160 nM | 2026-04-23-chereau-wh2-actin-pnas |
| MIM WH2 x G-actin Kd | 230 nM | 2026-04-23-chereau-wh2-actin-pnas |
| WASP WH2 x G-actin Kd | 250 nM | 2026-04-23-chereau-wh2-actin-pnas |
| Tbeta4 x G-actin Kd | 760 nM | 2026-04-23-chereau-wh2-actin-pnas |
| Tbeta4 G-actin to F-actin scale | 10,000x | actin-kinetics |
Results
| Construct | AF3 ipTM | AF3 pTM | Kd input |
|---|---|---|---|
| WAVE2 | 0.64 | 0.73 | 52 nM |
| WIP | 0.59 | 0.69 | 160 nM |
| MIM | 0.61 | 0.71 | 230 nM |
| WASP | 0.53 | 0.65 | 250 nM |
| Tbeta4 | 0.53 | 0.65 | 760 nM |
| h09 WH2 | 0.60 | 0.70 | predicted |
Fit: log10(Kd_M) = -7.092 * ipTM - 2.574, R2 = 0.690.
Predicted h09 WH2 x G-actin Kd = 1.48e-7 M. After the pre-registered 10,000x Tbeta4 G-to-F scaling, predicted h09 WH2 x F-actin Kd = 1.48e-3 M = 1.48 mM.
Phase 4j conservative re-run with Kd_mono = 1.48 mM:
| C_eff | N | Kd_eff | Gate |
|---|---|---|---|
| 50 mM | 3 | 1.30 uM | PASS |
| 50 mM | 4 | 38.39 nM | PASS |
| 50 mM | 5 | 1.14 nM | PASS |
| 100 mM | 3 | 324.22 nM | PASS |
| 100 mM | 4 | 4.80 nM | PASS |
| 100 mM | 5 | 71.02 pM | PASS |
Verdict
- Outcome: PASS
- Key numbers: R2 = 0.690; h09 ipTM = 0.60; predicted Kd_F = 1.48 mM; Kd_eff at conservative C_eff=50 mM, N=3 = 1.30 uM.
- Interpretation: The pre-registered soft-floor gate clears: predicted h09 Kd_F is below 5 mM, and even N=3 at C_eff=50 mM is below the 50 uM therapeutic gate.
- Limitations: This is a within-family comparative AF3 calibration, not an absolute Kd measurement. The 10,000x G-to-F scaling remains a Tbeta4 analog conversion.
Ranking delta
- Hypothesis h09: tier tentative-S → S | mech 5 → 5 | deliv 4 → 4 | misha_fit 3 → 3
- Evidence: Phase 4m closes the dominant Kd_mono uncertainty from Phase 4n sensitivity and closes the Phase 4j conservative-FAIL case.
- Next step changes to: finish Phase 4k contact parse as a supporting geometry audit; Phase 4l remains optional unless a paper-grade C_eff estimate is needed.
Connections
[part-of]h09 hub[supports]STRC h09 Phase 4j Avidity Kd Model 2026-04-26[supports]STRC h09 Phase 4n Avidity Monte Carlo 2026-04-26[source]2026-04-23-chereau-wh2-actin-pnas[source]actin-kinetics