Hierarchical organic-inorganic hybrid structures, such as in tooth enamel and bone, are ubiquitous in biominerals, yet challenging to synthesize in vitro. In tooth enamel, mineralization is thought to begin with nucleation of amorphous calcium phosphate (ACP) in an amelogenin (Amel)-rich extracellular protein matrix and evolve to highly aligned bundles of apatite (AP) filaments with less than 2% residual protein1-3. Recent reports demonstrate that full-length Amel, an intrinsically disordered protein (IDP), can adopt an amyloid (cross β-sheet) quaternary structure and spontaneously self-assemble into nanoribbons (NR) 17 nm wide and a few nm in thickness4,5. In vivo studies revealed the presence of ribbon-like assemblies in the developing enamel matrix of various mammals, including humans4, 6-8, and these NR match the dimension and morphology of ribbons assembled from both recombinant human Amel (rH174)9 and synthetic peptides4. In vivo observations suggest Amel NR are involved in mineralization of AP filaments which form during secretory stage of amelogenesis4, while recent in vitro experiments demonstrate that synthetic NR can indeed template growth of AP filaments starting with an amorphous precursor formed in the presence of acidic macromolecules5. However, the mechanism that leads to NR templating of ACP and its basis in NR and mineral structure remain unknown.
To determine the mechanism of mineral templating by human Amel NR, we performed in situ AFM observations of calcium phosphate nucleation on self-assembled NR of the full-length protein, as well as evolutionarily-conserved sub-segments hypothesized to be important for: 1) self-assembly; 2) stabilizing ACP (i.e., phosphorylated serine-16); and 3) binding with the AP surface (i.e., the C-terminus)4,11,12. To relate mechanism to structure we performed molecular dynamics (MD) simulations of the conformational states of NR formed from these peptide sub-segments.
Five sequences were designed. Recombinant full-length human Amel (rH174) and two peptide analogs, consisting of the domain that drives self-assembly (14P2) and 14P2 with truncated C-terminus appended to it (14P2Cterm) shown in Fig. 1, a to c. In addition, phosphorylated versions of both peptides, p14P2 and p14P2Cterm, were also synthesized with phosphorylated serine sites highlighted in Fig. 1, a to c. The variable, histidine- and proline-rich central domain of Amel may also play a role in self-assembly or mineralization however its structure and function is unclear and was not investigated here.
All sequences assembled into NR on the surface of highly ordered pyrolytic graphite (HOPG) and remained stable in water (Fig. 1, d to g) for a pH range of 1.94 - 7.4 (Supplementary Fig. 1). NR dimensions for each sequence (Supplementary Table S1) were distinct, but films of the NR are similar in morphology, consisting of individual NR or islands with well aligned rows of NR. Further analysis of 14P2 (Fig. 1d) and other sequences (Supplementary Figs. 1b to e and 2) shows that, at high enough peptide or protein concentration, HOPG was completely covered, consisting of multiple layers of NR of 2 types, R1 and R2 (Fig. 1i) in contact with HOPG. R2 is the dominant morphology and can stack above one another (Fig 1j) whereas R1, rarely observed, forms a single highly crystalline layer (Fig 1k). R2 row widths and heights were roughly twice that of R1; e.g., for 14P2, the width and height of R1 rows are 2.51± 0.47 nm and 0.33±0.07 nm, respectively, while those of R2 rows are 5.81±0.60 nm and 0.65±0.04 nm. In all cases, the NR were aligned with the three HOPG directions (Fig. 1f and Supplementary Fig. 3).
Previous analysis of the β-sheet structure of amyloid ribbons by X-ray Diffraction (XRD) shows that dominant diffraction peaks lie at d-spacings of ~4.7 Å and ~10 Å13,14. The R2 NR prepared using our protocol exhibit similar diffraction patterns in bulk solution with and without HOPG, indicating that the structure is retained (Supplementary Fig. 4). To gain insight into the identity and distribution of exposed residues arising from the NR assembly, we performed MD simulations with the Interface-CHARMM force field with over 50 conformations for all peptides on HOPG, including virtual π electrons on graphite and aromatic amino acids which was shown to be critical to reproduce solvent and organic interfacial interactions (Supplementary Method 2)15-17.
The simulations predict the most favorable β-sheet conformation occurs in solution for both the basic 14P2 sequence (Fig. 2a) and the three modified versions (Supplementary Fig. 6). On HOPG, the standard β-sheet conformation is relatively less stable, with monomers beginning to spread after 7.5 ns (Supplementary Fig. 7). Further simulations with longer duration (10 ns) show that adopting a quasi-β-sheet conformation with a slightly larger backbone gap in the central YINFSY domain (~1 nm vs ~0.5 nm) and lower height (~0.8 nm vs. ~1.2 nm) — nearly identical to R2 NR AFM topography — is most favorable, stabilizing the otherwise transient sheet (Fig 2a and Supplementary Fig. 8).
In both the transient and stabilized states, phenyl residues in the 14P2 domain are bound to the surface by π-π interactions with graphite while adjacent, parallel ribbons formed hydrogen bonds between the N and C termini (Supplementary Fig. 8). In the stabilized conformation, hydrogen bonding is possible between -OH groups of Tyr5 and Tyr10 and the O=C- of the adjacent monomer backbone. Modification of 14P2 by phosphorylation (Fig. 2b) or appending the C-terminus (Fig. 2c and Supplementary Fig. 9) generated similar packing in the 14P2 domain. However, the DKTKREEVD domain extends into the solution, lacks the N and C terminus interaction with adjacent ribbons (Supplementary Fig. 8), and is more disordered than the 14P2 domain (Fig. 2c). Further analysis reveals that nearly all hydrophilic side chains (in both transient and stabilized conformations), including phosphorylated serine, protrude into the solution with a periodicity that transverses the long axis of the nanoribbon (thick lines in Fig. 2a, b and c).
To quantify the impact of this structural motif on calcium phosphate nucleation rates, we used in situ AFM to investigate nucleation using substrates with the dominant R2 NR, identical to those in Fig. 1, at pH 7.4 and 25 ºC for a range of supersaturations σ (Supplementary Tables 2 and 4) over timescales for which nucleation was absent both in solution and on bare HOPG (Supplementary Fig. 10). The value of σ was determined in two ways (Supplementary Table S4): from the value of the equilibrium constant Ksp reported previously at a different ionic strength18 and using the ionic activity product at which the post-nucleation growth rate extrapolated to zero (Supplementary Method 8).
Time-lapse images (Fig. 3, a to e and Supplementary Videos 1 to 5) revealed that ACP ((Ca2(HPO4)3)2-) was the first phase to form at all values of σ explored here for all five sequences, as validated by in situ AFM and electron microscopy (Supplementary Figs. 11 to 13) and observed previously for nucleation on a number of proteins18-20. The ACP particles grew in size (Supplementary Table S3) before transforming to fiber- or plate-shaped mineral (Fig. 3, a to e panel 5 and Supplementary Fig. 13).
Nucleation rates and total mineral coverage were highest on the phosphorylated peptides, p14P2 and p14P2Cterm (Fig. 3 f and Supplementary Fig. 14, Supplementary Tables 5 and 6), which had particles concentrated along the length and direction of the NR (Supplementary Video 6). In contrast, ACP growth rates on non-phosphorylated peptides were higher than on the phosphorylated versions (Fig. 3g and Supplementary Fig. 14, Supplementary Table S3). Furthermore, appending the C-terminus to 14P2 and p14P2 sequences resulted in an increase of 1.3 to 2 times in nucleation rates and a factor of 1.5 to 2.3 in (vertical) growth rates. Comparison to previous results using conformationally dissimilar Amel nanospheres and nanospheres co-assembled with highly charged enamelin (Enam) (Fig. 3h, Amel sph: Enam, 50:0 and 50:1)19 shows that all NR sequences drive higher nucleation rates than do nanospheres, and the phosphorylated NR outperform the mixed Amel nanosphere-Enam system, even at lower supersaturations and for the optimal Amel:Enam ratio. In addition, phosphorylated NR induced ACP nucleation rates 1.9 to 2.8 times larger than observed on collagen (Fig. 3h, Col. σACP = 0.128)18. These findings show that both sequence and conformation strongly impact template activity and that phosphorylated NR are the most potent ACP nucleators investigated to date.
To determine the mechanism and underlying energetic factors through which Amel NR drive ACP nucleation, the data on nucleation rates vs σ were analyzed using classical nucleation theory (CNT), which has been used previously to analyze heterogeneous nucleation on organic templates18, 19, 21-23 and has been shown to effectively describe ACP nucleation kinetics18. CNT predicts that the heterogeneous nucleation rate (Jo) varies exponentially with the effective interfacial energy (αACP) and σ ACP according to:
where A is the kinetic pre-factor, which depends on the density of possible nucleation sites (24), on attachment rates, and barriers to ion desolvation25, ωis volume of the ACP growth unit, k is Boltzmann’s constant and T is absolute temperature. (See Supplementary Method 10).
Fitting the data for all values of σ ACP (Fig. 3i and Supplementary Fig. 15, Supplementary Tables 7 and 8) results in values of αACP for all NR sequences that are remarkably small, ranging from 1.4 - 2.4 mJ m-2 or 12 - 20 mJ m-2 (depending on the method used to determine Ksp), when compared to either nucleation on collagen18 (40 mJ m-2) or in bulk solution18 (~150 mJ m-2). Hence, we infer that nucleation is highly favorable on Amel NR due to the low interfacial energy. The data also show that both addition of the C-terminus to 14P2 and phosphorylation of the analogs have minor effects on αACP, with the induced change ranging from a factor of 0.9 to 1.5 (Fig. 3j and Supplementary Tables 7 and 8). In contrast, phosphorylation results in a 15 to 19-fold increase in the kinetic pre-factor A. Comparison of the value of A with the net charge of the peptide reveals a strong linear trend, likely reflecting rates of ion binding or the lifetime of bound ions.
To understand the structural reason for why phosphorylated 14P2 NR so dramatically enhances nucleation kinetics, we compared the geometric arrangement of the NR’s charged side chains with the dimers of the Ca(HPO4)34- multi-ion complexes shown previously to be the incipient species leading to formation of ACP through binding of an additional Ca2+ ion, as well as to octacalcium phosphate (OCP) and AP18 through further ion binding reactions. Superposition of Ca2+ ions in the dimeric complex onto the p14P2 NR conformation (stabilized or transient sheet) shows an excellent match with the spacing (~1 nm) of the periodic hydrophilic residues that span the long axis of the NR (Fig 4a). Thus, binding of Ca2+ ions to the periodic phosphorylation sites may provide a means to stabilize the calcium triphosphate dimers and promote formation of ACP beyond that afforded alone by a template of low interfacial energy.
The above experimental findings show that the amyloid structure of Amel NR, especially the evolutionarily conserved 14P2 self-assembly domain26, drastically lowers the thermodynamic barrier for nucleation of ACP, while the simulations predict that Amel NR present a periodic template of hydrophilic residues for mineral formation — without involvement of non-Amel proteins (Fig. 4b). Moreover, phosphorylation of the NRs dramatically enhances the kinetic pre-factor, likely through enhanced Ca2+ ion binding at charged residues. Addition of the Amel C-terminus has little impact on these two factors, suggesting that amyloid-like Amel NR can retain its structure and function even after C-terminal cleavage. Whether the C-terminus then independently acts to inhibit HAP (100) growth as previously proposed27, or acts as a highly charged macromolecule to produce the polymer induced liquid precursor (PILP) used in previous NR mineralization experiments to produce aligned AP filaments8, remains to be explored.
The results also provide evidence that one region of a matrix IDP can fold to drive self-assembly into a template that stabilizes a mineral phase while leaving another region unfolded to interact with non-matrix proteins, ions or crystals28,29. The use of such sequence-specific interfacial behavior towards crystal nucleation can, in principle, be expanded beyond proteins to block copolymers, peptoids and other amphiphilic polymers in which different domains can control distinct aspects of nucleation through reduction of mineral-binding energies by assembly into an ordered template and enhancement of ion-binding at exposed charged residues30-32.
The link between the self-assembled molecular structure of Amel NR templates and mineral nucleation points towards a range of translational opportunities. The ability to readily assemble peptides with control over orientation on crystalline surfaces like graphene33, mica34 or MoS216, or to array proteins on surfaces patterned at the nanoscale using block copolymers films35 or nanolithography37, provides a potential path to organize Amel NR for dental tissue engineering. Alternatively, the periodic organization of nucleation sites on the NRs suggests a means for creating patterns of quantum dots of other materials by tailoring the site chemistry. More broadly, achieving predictive hierarchical growth of inorganic crystalline arrays directed by organic scaffold, inspired by nature, is a long sought-after vision of bioinspired material science. The robust hierarchical design of amyloid NRs arrayed with modular functional groups around a self-assembling domain, provides a general scaffold design upon which that vision may be realized.