lamm-mit/keratin-pdb

Human Keratin AlphaFold PDB Structures

Curated human keratin AlphaFold PDB structure records with source metadata, raw PDB text, chain/residue/atom summaries, and pLDDT confidence statistics parsed from the B-factor column.

Keratin Protein Background and Study Significance

Keratins are structural proteins that form intermediate filaments in epithelial tissues, including hair, skin, and nails. In hair fibers, keratin proteins assemble into hierarchical structures that help determine mechanical properties such as strength, elasticity, toughness, and resistance to fracture. Keratins are commonly grouped into two complementary classes: Type I keratins, which are generally acidic, and Type II keratins, which are generally basic or neutral. These proteins pair to form coiled-coil heterodimers that further assemble into larger filament networks.

This work focuses on human hair keratins at the molecular scale. While hair-fiber mechanics are often studied experimentally at the macroscopic level, the molecular unfolding behavior of individual keratin proteins is less systematically characterized. The paper addresses this gap by curating 51 human keratin proteins, predicting or collecting their structures, and simulating their unfolding under controlled steered molecular dynamics conditions.

flowchart LR
    A["Human keratin sequences"] --> B["AlphaFold protein structures"]
    B --> C["Equilibration MD"]
    C --> D["Steered MD pulling"]
    D --> E["Force-displacement curves"]
    E --> F["Strength and toughness"]
    B --> G["Sequence and structure descriptors"]
    G --> H["Structure-property analysis"]
    F --> H
    H --> I["Molecular insight into hair-fiber mechanics"]

The significance of this study is that it provides a reproducible, dataset-scale molecular dynamics framework for comparing keratin unfolding mechanics across Type I and Type II keratins. By connecting sequence features, predicted structures, secondary-structure descriptors, and MD-derived mechanical properties, the study helps explain how molecular-scale protein behavior may contribute to the toughness and resilience of hierarchical hair fibers.

The steered molecular dynamics pulling velocities used in the study are accelerated computational probes, not direct reproductions of experimental hair-fiber strain rates. Their value is comparative: they reveal relative unfolding trends, rate-sensitive stiffening, strength-toughness coupling, and relationships between molecular descriptors such as sequence length, molecular weight, coil content, SASA, and energy absorption.

Dataset Summary

• Hub repo: lamm-mit/keratin-pdb

• Records: 51

• Organism: Homo sapiens (NCBI:txid9606)

• Keratin type counts: {"type_I": 25, "type_II": 26}

• Sequence length range: 394-644 amino acids

• Median sequence length: 493

• Sequence-string discrepancies flagged in records: ["KRT17", "KRT26", "KRT34"]

• Sequence length-field/string discrepancies flagged in records: ["KRT17", "KRT26"]

• Generated at: 2026-06-05T15:18:17.880019+00:00

Fields

• record_id/gene_symbol
• UniProt and AlphaFold URLs
• NCBI taxon and organism names
• keratin type
• raw PDB text
• header, title, COMPND, SOURCE, DBREF, SEQRES metadata
• chain, residue, atom, element, and coordinate summaries
• CA/all-atom pLDDT summary statistics and confidence bands
• file size, path, modification time, and SHA-256

Dataset Generation

The structures correspond to AlphaFold2/AlphaFold Database monomer predictions for the 51 curated human keratin proteins used in the accompanying keratin unfolding mechanics study. The paper used these folded structures as starting molecular models for downstream visualization, equilibration, and steered molecular dynamics simulations.

Each PDB record was parsed to retain the raw coordinate text and to expose searchable structural metadata: title/header fields, COMPND and SOURCE annotations, DBREF records, SEQRES sequences, chain identifiers, residue and atom counts, element counts, coordinate bounds, and AlphaFold confidence summaries. For AlphaFold-style PDB files, per-residue pLDDT values are encoded in the B-factor column; this dataset reports C-alpha and all-atom pLDDT statistics and confidence-band counts.

Sources and Attribution

Sequence records are linked to UniProtKB, and structure records are linked to AlphaFold Database entries where available. UniProt states that copyrightable parts of its databases are available under CC BY 4.0, and AlphaFold Database states that its data is available under CC BY 4.0 for academic and commercial use. Users should cite UniProt, AlphaFold Database, and the accompanying keratin unfolding mechanics manuscript as appropriate for downstream work.

Validation Notes

The upload workflow checks unique record identifiers, expected Type I/Type II coverage, expected velocity groups for simulation outputs, sequence lengths, force-vector lengths, and internal PDB residue/SEQRES consistency. Per-record boolean fields retain known source-sequence discrepancy flags instead of silently overwriting them.

Citation

Please cite as:

@article{LuLeonforteBuehler2026,
    title={Comparative Molecular Dynamics Characterization of Hair Keratin Unfolding Mechanics},
    author={Wei Lu, Fabien Leonforte, Markus J. Buehler},
    journal={xxx},
    year={2026},
    url={http://XYZ.XYZ},
}