STRC Research

STRC TECTA Chimera Phase 1 Fold Check

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STRC TECTA Chimera Phase 1 Fold Check

First compute on STRC Engineered TECTA Chimera (B-tier, was 0 compute). Tests whether a TECTA-STRC fusion adopts a plausible two-domain fold and preserves the TMEM145 binding interface.

Motivation

TECTA (alpha-tectorin) is a major component of the tectorial membrane, anchored there via its C-terminal ZP-C domain which self-polymerises with other ZP-containing proteins (TECTB, otogelin). STRC’s job is to connect OHC stereocilia to the TM via horizontal top connectors and attachment crowns — it must be localised correctly. The E1659A and 98 kb deletion variants lose STRC expression or localisation.

Idea: fuse STRC’s functional C-terminal (Ultra-Mini 1075-1775) to TECTA’s ZP anchor. Result: a chimeric protein that

  • is naturally integrated into the tectorial matrix via TECTA ZP polymerisation
  • presents the STRC TMEM145-binding surface on the TM side, facing OHC stereocilia
  • bypasses STRC’s native signal peptide, GPI anchoring, and all regulatory complexity that E1659A may disrupt

Speculative. But cheap to test geometrically.

Construct design

TECTA 1655-2155 (C-terminal 500 aa, ZP-N + ZP-C + CFCS)
+ GGSGSG linker (6 aa)
+ STRC 1075-1775 (Ultra-Mini, 701 aa)
= 1207 aa chimera

Fusion order: TECTA first (N-terminal), STRC second (C-terminal). TECTA ZP-C is at its natural C-terminus where it self-polymerises in-situ; placing STRC after the ZP domain may interfere with polymerisation. Alternative to test later: STRC first, TECTA second (STRC N-term, TECTA C-term); but this puts STRC’s signal peptide in the middle — problematic. First version keeps TECTA secretion/anchoring intact.

TECTA 1655-2155 slice includes:

  • ZP-N module (~aa 1700-1825)
  • ZP-C module (~aa 1850-2000)
  • CFCS cleavage (~aa 2050) — may or may not fire in chimera
  • GPI attachment signal (~aa 2100-2155) — may or may not be used

Phase 1 AF3 tests

Batch: ~/STRC/models/af3_jobs_2026-04-22/.

Job 1: strc_tecta_chimera_fold

Single-chain 1207 aa. Does the chimera adopt a stable two-domain fold?

Pass: pTM ≥ 0.55. TECTA region (positions 1-500) adopts ZP-fold. STRC region (positions 507-1207) adopts ARM-repeat fold matching Ultra-Mini solo.

Fail: pTM < 0.40, OR domains clash, OR linker forces non-native fold → TECTA-STRC fusion incompatible at this junction → try alternate TECTA region (e.g. VWF D domain earlier in TECTA) or kill.

Job 2: strc_tecta_chimera_x_tmem145

Chimera (1207 aa) + TMEM145 full (493 aa) = 1700 aa.

Pass: ipTM ≥ 0.40. The STRC region of the chimera engages the TMEM145 interface. TECTA ZP region does NOT dominate the interface (critical — TECTA ZP could form a false-positive binder with TMEM145 since both have ECD-type folds).

Fail: interface lost OR TECTA ZP dominates the interface → chimera architecturally unsuitable → kill.

Decision gates

Phase 1 AF3
    │
    ├─ both pass                  → Phase 2: tectorial membrane
    │                               self-assembly model. Can chimera
    │                               integrate into TECTA/TECTB/
    │                               otogelin matrix in silico?
    │                               (coarse-grained MD, weeks)
    │
    ├─ fold ok, interface on TECTA → wrong architecture; test
    │                               alternative order or alternate
    │                               TECTA region
    │
    ├─ fold fails                  → kill; TECTA scaffold idea needs
    │                               fundamentally different construct
    │                               (e.g. TECTA VWF-D + STRC, or
    │                               TECTB anchor instead)
    │
    └─ ambiguous                   → increase seed count, try different
                                     linker

Risks vs payoffs

Risks:

  • TECTA 1655-2155 may include cleavage/GPI signals that disrupt chimera biogenesis — AF3 will model the sequence as-is; biological reality may differ (proteolytic processing, etc.)
  • ZP-C self-polymerisation may trap the chimera in aggregates, making OHC function impossible
  • Speculative enough that most reviewers would call this high-risk even if AF3 passes

Payoffs:

  • Delivery-independent: does not need AAV targeting OHC specifically; chimera integrates into TECTA wherever TECTA is made (supporting cells, reticular lamina producers)
  • Bypasses all STRC regulatory biology (signal peptide, GPI, trafficking) that E1659A may disrupt
  • Single-gene product, much smaller than full STRC (1207 vs 1775) — fits single AAV easily

Phase 1 AF3 Results (2026-04-23)

Both jobs returned. Results: fold marginal PASS, binding CLEAN FAIL.

JobBest pTMBest ipTMGateVerdictMargin
Chimera fold0.58—pTM ≥ 0.55PASS+0.03
Chimera + TMEM1450.420.21 (chain-pair)ipTM ≥ 0.40CLEAN FAIL−0.19

Model spread: pTM 0.56-0.58 (consistent), binding ipTM 0.17-0.21 across models. Chain-pair decomposition for binding job: chimera self-iptm 0.50 (decent), TMEM145 self-iptm 0.58 (good), chimera–TMEM145 cross 0.21 (half the gate threshold). PAE min between chains 21.7 Å — the chains are effectively not docking. TMEM145 sits far from the chimera’s expected binding surface.

Interpretation: the TECTA ZP scaffold DOES support a stable two-domain fold (this is the chimera-fold PASS), but it positions the STRC Ultra-Mini portion away from the TMEM145 recognition surface. The ZP C-terminal anchor dominates the chimera’s surface topology, and the linker (GGSGSG) holds STRC in an orientation where its ARM-repeat 1669-1680 contact residues are buried or occluded. TMEM145 can’t find a productive docking pose — PAE 21.7 Å confirms chains drift apart rather than engage.

This is an architecture-level failure, not a refinement problem. No linker tweak is going to rescue an orientation-disrupted binding surface. TECTA-as-scaffold idea needs a fundamentally different construct.

Ranking delta

STRC Engineered TECTA Chimera (#11): Tier B → C.

Scoring:

  • Mechanism 2: unchanged (speculative from the start)
  • Delivery 2: unchanged
  • Misha-fit 3 → 2: this specific fusion architecture doesn’t preserve the STRC function

Not killed. Alternate TECTA scaffolds remain theoretically viable:

  • TECTA VWF D-domain region (earlier in the protein) instead of ZP C-terminal anchor — different anchoring mechanism
  • TECTB instead of TECTA — smaller ZP-family protein, may position STRC differently
  • Reversed fusion order (STRC N-term, TECTA C-term) — despite signal peptide complications

Each alternate would need its own Phase 1 AF3 pass. Given hypothesis #11 was B-tier (2/3/2 scoring) and the tested architecture failed cleanly, defer further Phase 1 variants to when S-tier work (Mini-STRC Shanghai mouse) provides bandwidth. Kept in register as “explored, current architecture failed, alternates available.”

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