9UV5

ligament intra-crystalline peptide (LICP)

Summary for 9UV5

• Entry DOI: 10.2210/pdb9uv5/pdb
• Descriptor: PCA-PRO-ASP-HIS-GLU-GLY-THR-TYR-ASP-TYR (1 entity in total)
• Functional Keywords: biomineral protein, biosynthetic protein
• Biological source: Pinctada fucata
• Total number of polymer chains: 1
• Total formula weight: 1208.17

Authors

Futagawa, K.,Suzuki, M. (deposition date: 2025-05-09, release date: 2025-05-28, Last modification date: 2026-06-17)

Primary citation

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.
Elucidation of the aragonite nanofiber formation mechanism of LICP contained in the hinge ligament of Pinctada fucata.
Proc.Natl.Acad.Sci.USA, 123:e2522686123-e2522686123, 2026

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 -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.

PubMed: 41945435
DOI: 10.1073/pnas.2522686123

Experimental method

SOLUTION NMR