Elucidation of the aragonite nanofiber formation mechanism of LICP contained in the hinge ligament of <i>Pinctada fucata</i>
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.
Article Details
Journal Info
Proceedings of the National Academy of Sciences
National Academy of Sciences
Authors (16)
Kei Futagawa
Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo
Yuto Namikawa
Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo
Taichi Morioka
Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo
Haruki Meguro
Photon Science Innovation Center
Akira Shida
Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo
Yuki Nagano
Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo
Kazuo Furihata
Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo
Hiroyuki Watanabe
Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo
Fabio Nudelman
School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster Road
Taiga Okumura
Department of Earth and Planetary Science, Graduate School of Science, The University of Tokyo
Toshihiro Kogure
Department of Earth and Planetary Science, Graduate School of Science, University of Tokyo
Teppei Ikeya
Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, 1-1 minamiosawa, Hachioji, Tokyo 192-0397, Japan
Yutaka Ito
Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, 1-1 minamiosawa, Hachioji, Tokyo 192-0397, Japan
Hidekazu Katayama
Liberal Arts Center, Teikyo University, Toyosatodai 1-1, Utsunomiya, Tochigi 320-8551, Japan
Koji Nagata
Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo
Michio Suzuki
Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo