STRC Research

STRC TMEM145 Kd Experiment Plan

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STRC × TMEM145 Kd — Experiment Plan

Why this is the highest-leverage single experiment

Cross-hypothesis audit 2026-04-23 (STRC Cross-Hypothesis Parameter Audit 2026-04-23) confirmed: the STRC × TMEM145 binding affinity has no SPR, BLI, or ITC measurement published anywhere. CoIP + pull-down + nanoSPD only (Derstroff 2026 Neuron, Reimann NatComms 2025, Verpy 2011, Dulon 2019 SI — all checked).

This single number is load-bearing for:

HypothesisWhat it unlocks
STRC Mini-STRC Single-Vector Hypothesis (h03)AAV titer → OHC transduction → functional STRC occupancy at HTC
STRC Synthetic Peptide Hydrogel HTC (h09)Phase 4e dose window (KD_TMEM145_M); Phase 4h endogenous E1659A competition (STRC_NORMAL_OHC_M baseline)
STRC Engineered Homodimer Avidity (h26)Every 100×, 1000× avidity claim — applied to an unmeasured base
Future any-STRC-binder hypotheses (hN)Gate threshold for “therapeutic Kd” vs “insufficient”

Without this number, all four hypotheses produce numerics that are structurally-correct-but-parametrically-hollow. With it, every dose-occupancy calculation becomes defensible.

Three paths — pick by feasibility + time

Path A — Collaboration request (fastest if it lands, high variance)

Email SPR-capable labs with the exact reagents or with STRC/TMEM145 constructs ready to go:

LabInstitutionSPR capabilitySTRC expertiseNotes
Jeffrey HoltHarvard / Boston Children’sYes (standard)Yes — primary STRC investigatorAlready works on STRC AAV; hypothesis-critical partnership
Thomas ReimannUniv MarburgYesYes — parallel TMEM145 labNatComms 2025; would likely have reagents
Dominik OliverUniv Marburg / KU LeuvenYesYes — Derstroff 2026 senior authorDirect access to STRC clones
Guy RichardsonUniv SussexYesStereocilin/TM/mechanics expert (Tobin 2019 contributor)Stereocilia bundle biophysics line
Christine Petit / Elisabeth VerpyInstitut PasteurYesOriginal STRC discoverers (Verpy 2001, 2011)Original STRC molecular biology source

Pitch angle: computational work (AF3 models + thermodynamic predictions) is ready; single biophysics measurement closes multiple publications. Offer co-authorship. Propose sending in reagents; ask them to run SPR in their pipeline. Turnaround: 2-6 months if positive response, indefinite if silent.

Path B — Computational stopgap (fastest deterministic, lower quality)

AF3 ipTM → Kd empirical calibration on PDBbind / SKEMPI positive controls, then apply to STRC × TMEM145.

  • Pull 50-200 protein-protein complexes from PDBbind 2020 refined set with measured Kd (range 10 pM to 100 μM)
  • Run AF3 on each pair, extract ipTM + ipSAE (Dunbrack 2025 PMC 11844409 — better than vanilla ipTM for disordered regions)
  • Fit Kd = f(ipTM, interface_area, pLDDT-at-interface, shape-complementarity)
  • Apply fit + confidence intervals to STRC × TMEM145 AF3 output (ipTM 0.68-0.79)
  • Report as probabilistic estimate with explicit disclaimer

Known to be weak (ipTM-Kd correlation R² ≈ 0.06 in Chen 2013 data), so output is a wide posterior, not a point estimate. But defensible as “best computational stopgap pending experiment.”

Compute cost: ~200 AF3 runs (Egor’s quota) + fitting.

Path C — In-house measurement (most expensive, most valuable)

Set up SPR/BLI in Hong Kong with local biotech/academic partner.

  • Express recombinant STRC ZP + TMEM145 ectodomain fragments (both likely expressed in mammalian HEK293 given disulfide complexity)
  • HKU biochemistry dept, CUHK proteomics core, or contract CRO (BGI, WuXi)
  • Reagents: ~2-5k; 6-10 week timeline from clone order
  • Advantage: data belongs to us, publishable independently

Budget estimate: $15-20k total. Timeline: 8-12 weeks.

  1. Today / this week — Path A. Draft the outreach email. Cross-check against brain-writer for Egor-voice alignment. Send to 3 labs (Holt + Reimann + Oliver) with 2-week response deadline expectation.

  2. In parallel (today / next 2 weeks) — Path B. Set up AF3 calibration pipeline. This produces an interim estimate regardless of A outcome. Document output in models/strc_tmem145_kd_iptm_calibration.py.

  3. Trigger Path C — if neither A lab responds within 3 weeks with a clear yes, or if Path B gives a wide posterior that blocks therapeutic decisions. Requires Egor’s $15-20k approval + partner selection.

Deliverables once Kd is measured

  • Update literature-params/strc-tmem145-interactions.md with value, method, uncertainty
  • Re-run Phase 4e/4h of h09 with real Kd
  • Re-evaluate h26 avidity math: does measured base × avidity ratio land in therapeutic range?
  • Feed into h03 expression/occupancy model (when its audit is reauthorized)
  • Ranking delta across h03, h09, h26

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