Version history

{
  "design_id": "SCIDEX-SS31-ALT-01",
  "sequence": "RYKW",
  "target_protein": "cardiolipin-rich mitochondrial inner membrane",
  "score": 1,
  "method": "codex-rosalind-agentic-design",
  "related_paper_id": "pmid:23813215",
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      {
        "id": "23813215",
        "doi": "10.1681/ASN.2012121216",
        "note": "SS-31 interacts with cardiolipin and protects cristae in an ischemia model.",
        "type": "pmid"
      },
      {
        "id": "32273339",
        "doi": "10.1074/jbc.RA119.012094",
        "note": "SS-31 binds lipid bilayers and modulates surface electrostatics.",
        "type": "pmid"
      },
      {
        "id": "35913044",
        "doi": "10.7554/eLife.75531",
        "note": "Tetrapeptide SAR for alternating aromatic/cationic mitochondrial compounds.",
        "type": "pmid"
      },
      {
        "cid": "11764719",
        "name": "elamipretide",
        "note": "Metadata anchor for the reference SS-31 compound.",
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      "length": 4,
      "sequence": "RYKW",
      "flag_score": 100,
      "total_score": 100,
      "length_score": 100,
      "balance_score": 100,
      "aromatic_count": 2,
      "cationic_count": 2,
      "alternation_score": 100,
      "canonical_sequence": "RYKW"
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    "modified_sequence_notation": "H-Arg-Tyr-Lys-Trp-NH2"
  },
  "target_function": "binder",
  "target_id": "cardiolipin",
  "target_family": "mitochondrial-lipid-binding-peptide",
  "fold": "short-aromatic-cationic-tetrapeptide",
  "domain": "mitochondrial membrane biophysics",
  "summary": "# Design Description\n\n## Artifact name\n`SCIDEX-SS31-ALT-01`\n\n## One-line description\nA research-only SS-31-like tetrapeptide surrogate, `H-Arg-Tyr-Lys-Trp-NH2` (`RYKW`), proposed as a hypothesis-generating cardiolipin-facing membrane binder for mitochondrial inner-membrane studies.\n\n## Rationale\nThis candidate preserves the core SS-31 design logic described in the source literature:\n\n- short tetrapeptide length\n- alternating cationic and aromatic side chains\n- compact sequence suitable for membrane interaction studies\n- emphasis on cardiolipin-rich inner mitochondrial membrane behavior\n\nThe specific change from the SS-31 reference motif is the use of tryptophan in place of phenylalanine to increase aromatic bulk and provide a different aromatic interaction surface. This is only a design hypothesis. It does not imply improved function, safety, or translational value.\n\n## Sequence representation\n- Canonical surrogate sequence: `RYKW`\n- Modified peptide notation: `H-Arg-Tyr-Lys-Trp-NH2`\n\n## What this is not\n- Not a medical recommendation\n- Not a therapeutic claim\n- Not a validated mitochondrial drug candidate\n- Not an optimized structure\n\n## Expected qualitative properties\n- Two cationic residues should support electrostatic interaction with anionic lipid environments.\n- Two aromatic residues should support membrane association and a compact SS-31-like pattern.\n- The alternating register should keep the sequence in the same design family as the reference compounds.\n\n## Uncertainty statement\nThe mechanistic link between sequence choice and cardiolipin stabilization remains uncertain. The reference literature supports the broader motif class, but not this exact surrogate sequence.\n\n## Suggested next experiments\n- Compare `RYKW` against SS-31 and a scrambled control in cardiolipin-containing membrane assays.\n- Measure binding or partitioning under matched salt and lipid-composition conditions.\n- Assess whether the candidate changes membrane electrostatics in a direction consistent with the SS-31 literature.\n- Check whether the peptide adopts a compact membrane-associated conformation or remains more extended than SS-31.\n"
}