9UV5 | pdb_00009uv5

ligament intra-crystalline peptide (LICP)

PDB DOI: https://doi.org/10.2210/pdb9UV5/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Pinctada fucata
Mutation(s): No

Deposited: 2025-05-09 Released: 2025-05-28
Deposition Author(s): Futagawa, K., Suzuki, M.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: SOLUTION NMR
Conformers Calculated: 200
Conformers Submitted: 20
Selection Criteria: structures with the least restraint violations

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Elucidation of the aragonite nanofiber formation mechanism of LICP contained in the hinge ligament of Pinctada fucata.

Futagawa, K., Namikawa, Y., Morioka, T., Meguro, H., Shida, A., Nagano, Y., Furihata, K., Watanabe, H., Nudelman, F., Okumura, T., Kogure, T., Ikeya, T., Ito, Y., Katayama, H., Nagata, K., Suzuki, M.

(2026) Proc Natl Acad Sci U S A 123: e2522686123-e2522686123

PubMed: 41945435 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1073/pnas.2522686123
Primary Citation Related Structures:
9UV5

PubMed Abstract:
The hinge ligament of bivalves exhibits remarkable flexibility and compressive strength due to its composite structure of aragonite nanofibers embedded in an organic matrix. While these nanofibers are crucial for shell mechanics, the molecular mechanisms underlying their formation remain unclear. We investigated the function of a 10-residue intracrystalline peptide, ligament intracrystalline peptide (LICP), in regulating aragonite crystal growth. Using a solution-state NMR technique optimized for biomineral systems with dispersive calcium carbonate particles, we showed that LICP adopted a planar, elongated conformation in binding to aragonite. This structure features a coplanar arrangement of carboxyl and aromatic side chains-particularly tyrosines-that enables selective interaction with the aragonite {110}. Saturation transfer difference NMR and dose-dependent structural analyses confirmed that this conformational change is triggered by solid-phase contact, rather than free calcium ions. Molecular dynamics simulations revealed enhanced binding stability of LICP to the {110} surface through multiple carboxyl and aromatic residues. Furthermore, in vitro crystallization assays showed that LICP promoted elongation of aragonite crystals along the c -axis, consistent with its selective surface binding. These findings demonstrated that conformational plasticity in short, disordered peptides enabled specific recognition of crystal faces and directed modulation of mineral growth. LICP serves as a minimal yet powerful model for exploring protein-mineral interfaces, offering broader insights into the structural principles by which intrinsically disordered peptides function in solid-phase biological systems.