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{ "cells": [ { "source": "# Lab Notes: SS-31-like membrane-stabilization hypothesis\n\n## Working hypothesis\nDesign a short, SS-31-like tetrapeptide artifact that preserves the alternating cationic/aromatic logic associated with cardiolipin-rich inner mitochondrial membrane binding, while remaining clearly labeled as research-only and hypothesis-generating.\n\n## Candidate selected\n- Candidate ID: `SCIDEX-SS31-ALT-01`\n- Canonical surrogate sequence: `RYKW`\n- Modified sequence notation: `H-Arg-Tyr-Lys-Trp-NH2`\n- Design intent: retain the cationic/aromatic alternation seen in SS-31-like peptides, but substitute tryptophan for phenylalanine to increase aromatic surface and probe whether a slightly bulkier aromatic side chain changes cardiolipin-facing membrane behavior.\n\n## Why this candidate\n- SS-31 / elamipretide is a compact tetrapeptide with alternating cationic/aromatic character.\n- The literature indicates that cardiolipin binding and membrane surface electrostatics are central to the mechanism under study.\n- Sequence register and aromatic side-chain identity appear to matter in SS-31-like tetrapeptides.\n- A simple canonical surrogate sequence is useful for a SciDEX protein_design artifact because it is easy to encode, score, and compare.\n\n## Source refs\n- PMID 23813215 / DOI 10.1681/ASN.2012121216\n - SS-31 interacts with cardiolipin and protects cristae in an ischemia model.\n- PMID 32273339 / DOI 10.1074/jbc.RA119.012094\n - SS-31 binds lipid bilayers and modulates surface electrostatics.\n- PMID 35913044 / DOI 10.7554/eLife.75531\n - Tetrapeptide structure-activity work on alternating aromatic/cationic mitochondrial compounds.\n- PubChem CID 11764719\n - Elamipretide metadata; canonical reference point for SS-31-like chemistry.\n\n## Assumptions\n- The artifact is only a design hypothesis, not a therapeutic recommendation.\n- Canonical amino acids are used as a surrogate representation, even though the reference molecule includes noncanonical features and C-terminal amidation.\n- Changing Phe to Trp is a reasonable exploratory modification, but there is no guarantee it preserves the same cardiolipin engagement profile.\n- The N-terminus and C-terminus are represented in amidated peptide notation for readability; no synthetic route is implied.\n\n## Rejected alternatives\n- Exact SS-31 copy: rejected because the goal is a new research candidate, not a duplicate of the reference compound.\n- Longer cationic peptide: rejected because the brief requested a short SS-31-like artifact and longer sequences reduce direct comparability.\n- Highly cationic variants such as `RRKW` or `RRYK`: rejected because they weaken the alternating aromatic/cationic pattern and may distort membrane behavior.\n- Noncanonical residues in the surrogate sequence: rejected for the canonical protein_design artifact because they complicate downstream encoding.\n\n## Risks and uncertainty\n- This candidate may alter membrane binding geometry in ways that reduce rather than improve cardiolipin affinity.\n- The replacement of SS-31's dimethyltyrosine / D-arginine elements with canonical residues may substantially change conformational preference and protease sensitivity.\n- Any apparent improvement in membrane association could reflect nonspecific hydrophobic partitioning rather than the cardiolipin-linked mechanism of interest.\n- The artifact should not be interpreted as evidence of safety, stability, or biological activity.\n\n## Assay ideas for hypothesis generation\n- Lipid-binding panel with cardiolipin-containing vesicles versus control phospholipid vesicles.\n- Surface electrostatics readout using membrane-potential sensitive probes or zeta-potential style comparisons.\n- Circular dichroism or NMR-adjacent conformational checks in membrane mimic conditions.\n- Competitive binding comparison against SS-31 under matched conditions.\n- Inner-membrane model assays for cristae-like membrane packing or bilayer thinning proxies.\n\n## Practical analysis notes\n- Keep sequence length fixed at four residues for comparability with SS-31-like tetrapeptides.\n- Score aromatic/cationic balance, class alternation, and unusual residues separately.\n- Avoid any narrative implying dosing, administration, or clinical translation.\n", "outputs": [], "cell_type": "markdown" }, { "source": "# 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", "outputs": [], "cell_type": "markdown" }, { "source": "python descriptor_score.py RYKW", "outputs": [ { "data": { "flags": [], "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" }, "output_type": "json" } ], "cell_type": "code", "execution_count": 1 } ], "kernel_spec": { "name": "python3", "language": "python" }, "metadata": { "source_refs": [ "pmid:23813215", "doi:10.1681/ASN.2012121216", "pmid:32273339", "doi:10.1074/jbc.RA119.012094", "pmid:35913044", "doi:10.7554/eLife.75531", "pubchem:CID11764719" ], "work_packet_ref": "agent_work_packet:e9f8cbe5-2ee7-4510-9d75-f9708b1f2a2b", "artifact_locations": { "schema": "scidex-artifact-locations@v1", "locations": [ { "name": "github", "state": "legacy_source", "provider": "github", "commit_sha": "882bc7d1e5c1e9fe9d7d66fb37d66f6eb4e435ec", "bundle_path": "protein_design/173f0f28-4c51-412f-8330-1ebfdf868159", "repository_url": "https://github.com/SciDEX-AI/scidex-artifacts.git", "sparse_checkout_patterns": [ "protein_design/173f0f28-4c51-412f-8330-1ebfdf868159" ] }, { "name": "forgejo", "repo": "scidex-artifacts", "owner": "scidex-mirrors", "state": "active", "web_url": "https://forge.scidex.ai/scidex-mirrors/scidex-artifacts", "provider": "forgejo", "repo_mode": "collection", "commit_sha": "6cd239a50e3a9a8f03baa17f492e7a2a16a43c2c", "repo_class": "protein-design", "bundle_path": "protein_design/173f0f28-4c51-412f-8330-1ebfdf868159", "repository_url": "https://forge.scidex.ai/scidex-mirrors/scidex-artifacts.git", "sparse_checkout_patterns": [ "protein_design/173f0f28-4c51-412f-8330-1ebfdf868159" ] } ], "migration": { "to": "forgejo_living_artifact_repo", "from": "github_sparse_repo", "tool": "scidex_artifact_location_migration.py", "migrated_at": "2026-05-20T02:30:28+00:00" }, "repo_mode": "collection", "primary_ref": "protein_design:173f0f28-4c51-412f-8330-1ebfdf868159", "artifact_refs": [ "protein_design:173f0f28-4c51-412f-8330-1ebfdf868159", "notebook:7d229db7-2033-4d1a-80e1-63419c4d866a", "analysis:ff7d6dda-a627-47fe-a221-bf56317a1fec", "analysis:4aaf1fb4-9bd9-4709-87c5-d095072b5fea", "agent_work_packet:e9f8cbe5-2ee7-4510-9d75-f9708b1f2a2b", "evidence_link:0c5a4196-036b-4fa9-b520-fe1fe188199a", "evidence_link:41fd5516-ca9e-4f39-ae20-aa71f6c4cac9", "evidence_link:9f738120-78f4-496d-8b75-2b2d6dab61f6", "evidence_link:058e61c8-987d-42a2-bcd0-21e93f977163" ], "blob_locations": [ { "uri": "s3://scidex-artifacts/protein_design/173f0f28-4c51-412f-8330-1ebfdf868159/", "name": "s3", "state": "active_blob_store", "provider": "s3", "bundle_path": "protein_design/173f0f28-4c51-412f-8330-1ebfdf868159" } ], "active_git_location": "forgejo" }, "protein_design_ref": "protein_design:173f0f28-4c51-412f-8330-1ebfdf868159", "sparse_artifact_repo": { "commit": "a9de0160ce6befeff68063a023224ea8f2a397dc", "bundle_path": "protein_design/173f0f28-4c51-412f-8330-1ebfdf868159", "repository_url": "/home/ubuntu/scidex-artifacts", "sparse_checkout_patterns": [ "protein_design/173f0f28-4c51-412f-8330-1ebfdf868159" ] }, "codex_run_analysis_ref": "analysis:4aaf1fb4-9bd9-4709-87c5-d095072b5fea", "artifact_location_active": { "commit": "6cd239a50e3a9a8f03baa17f492e7a2a16a43c2c", "provider": "forgejo", "bundle_path": "protein_design/173f0f28-4c51-412f-8330-1ebfdf868159", "location_name": "forgejo", "repository_url": "https://forge.scidex.ai/scidex-mirrors/scidex-artifacts.git", "sparse_checkout_patterns": [ "protein_design/173f0f28-4c51-412f-8330-1ebfdf868159" ] } }, "owner_ref": "persona:persona-kris-ganjam", "last_executed_at": "2026-05-18T01:57:03-07:00", "created_by": "persona:persona-kris-ganjam" }