Amyloid-like amelogenin nanoribbons template mineralization via a low energy interface of ion binding sites

Abstract

Protein scaffolds direct the organization of amorphous precursors that transform into mineralized tissues, but the templating mechanism remains elusive. Inspired by a model of tooth enamel, wherein amyloid-like amelogenin nanoribbons guide apatite mineralization, we investigated the impact of nanoribbon structure and chemistry on amorphous calcium phosphate (ACP) nucleation. Using amelogenin sub-segments including an amyloid-like domain, nanoribbon conformation and function were determined by in situ atomic force microscopy and molecular dynamics simulations. All sequences substantially reduce nucleation barriers by creating low-energy interfaces, while phosphorylation dramatically enhances kinetic factors associated with ion binding. Furthermore, the predicted distribution of hydrophilic residues in the amyloid domain matches the structure of the multi-ion clusters comprising ACP. These findings provide crucial insights into structure-function relationships underlying amelogenin biomineralization and a generalizable system for synthesizing hybrid materials for various applications.

Accurate and Ultrafast Simulation of Molecular Recognition and Assembly on Metal Surfaces in Four Dimensions

“…9,10 MD simulations using IFF reproduce lattice parameters of Pt with less than 0.1% deviation from experimental data and the geometry of the hydrocarbon molecules with less than 2% deviation in bond lengths and angles (Table S3 and Section S3 in the Supporting Information). 34 The inclusion of virtual π electrons for the aromatic hydrocarbons in IFF 35,36 enables up to 2 orders of magnitude higher accuracy for predictions of binding energies relative to other force fields, e.g., CHARMM36 and ReaxFF, which neglect the role of π electron clouds and associated multipolar interactions with neighbor molecules, or cannot provide physical binding information, respectively (Figures S2, S3, S5, and Section S4 in the Supporting Information). Dynamics over durations >10 ns also helps to determine the surface coverage with low uncertainties of ∼1%, much smaller than ∼10% uncertainty in experiments (Figures S6 to S8 and Table S5 in the Supporting Information).…”

Calcium interactions in amelogenin-derived peptide assembly

“…We surveyed the 31 P-31 P distance in brushite and HAP crystal (Supplementary Figure S8), showing that the shortest 31 P-31 P distance for brushite is 3.8 Å while 31 P-31 P distances along the c axis for HAP are between 4.0 and 4.2 Å, very close to the experimental results, although here the experimental results were on the organic phosphate. These distances indicate that the organic phosphate-calcium interaction network would be a good starting point for the inorganic ions to interact with and to promote a phase transformation from amorphous calcium phosphate to crystalline mineral oriented with the organic supramolecular template (Akkineni et al, 2022). The organic phosphate interaction network could coordinate with the calcium ions, reduce the calcium ion concentrations in solution, and bring water molecules into proper positions, all of which are necessary for a controlled calcium mineralization process.…”

“…Although amyloid is usually associated with cell toxicity and neurodegeneration, many functional amyloids have also been discovered these years playing key roles in regulating biosynthetic pathways (Fowler et al, 2007;Wu et al, 2021). The amyloid-like assemblies formed by the full-length amelogenin have proved to be able to template apatite crystal mineralization in vitro (Bai et al, 2020;Akkineni et al, 2022). In this work, the self-assembly of 14P2 and phosphorylated 14P2 at Ser16 (p14P2) were investigated in different solution conditions with variations in calcium and phosphate ion concentrations, since both ions are essential to enamel formation (Aoba and Moreno, 1987) and the concentrations of ions may have an effect on the status of protein assembly (Martinez Avila et al, 2012;Carneiro et al, 2016;Engelberth et al, 2018).…”