The role of phosphorylation in dentin phosphoprotein peptide absorption to hydroxyapatite surfaces: a molecular dynamics study

Abstract

Dentin phosphoprotein (DPP) is a protein expressed mainly in dentin and to a lesser extent in bone. DPP has a disordered structure, rich in glutamic acid, aspartic acid and phosphorylated serine/threonine residues. It has a high capacity for binding to calcium ions and to hydroxyapatite (HA) crystal surfaces. We used molecular dynamics (MD) simulations as a method for virtually screening interactions between DPP motifs and HA. The goal was to determine which motifs are absorbed to HA surfaces. For these simulations, we considered five peptides from the human DPP sequence. All-atom MD simulations were performed using GROMACS, the peptides were oriented parallel to the {100} HA crystal surface, the distance between the HA and the peptide was 3 nm. The system was simulated for 20 ns. Preliminary results show that for the unphosphorylated peptides, the acidic amino acids present an electrostatic attraction where their side chains are oriented towards HA. This attraction, however, is slow to facilitate bulk transport to the crystal surface. On the other hand, the phosphorylated (PP) peptides are rapidly absorbed on the surface of the HA with their centers of mass closer to the HA surface. More importantly, the root mean square fluctuation (RMSF) indicates that the average structures of the phosphorylated peptides are very inflexible and elongate, while that of the unphosphorylated peptides are flexible. Radius of gyration (Rg) analysis showed the compactness of un-phosphorylated peptides is lower than phosphorylated peptides. Phosphorylation of the DPP peptides is necessary for binding to HA surfaces.

Intrinsically disordered proteins and biomineralization

“…The structure of LRAP peptide absorbed to CAP was consistent with an α-helix, whereas when bound to HA the structure corresponded more to a random coil [107]. We studied DPP peptides by FTIR spectroscopy and found the phosphorylated peptides in solution in the presence of HA formed α-helical structures and lost their random coil characteristics [108]. Perhaps, through evolution, the most efficient strategy found by nature for protein-surface interactions, was using IDPs to bind to solid surfaces and in this way control the nucleation, growth and morphology of biominerals while still being able to interact with other partners.…”

“…The extent of phosphorylation of these proteins and their peptides affects their ability to bind to HA and to regulate mineralization [119]. Modeling of the most frequently appearing repeat peptide in DPP [108] by molecular dynamics simulations, showed the phosphorylated peptide bound with greater affinity and a more organized structure to the surface of hydroxyapatite (Figure 3A,B). The change to a more-ordered structure after phosphorylation and interactions with either calcium ions or hydroxyapatite was verified by circular dichroism, small angle scattering and vibrational spectroscopy (Figure 4).…”

“…Water is not shown but was included in the model. For details of the modeling procedures see Villarreal-Ramirez et al, 2014 [108]).…”

Phosphorylation regulates the secondary structure and function of dentin phosphoprotein peptides

“…These peptides cover, to a large extent, the complete motifs observed in DPP [22]. The different simplified DPP peptides were positioned at a distance of 3.0 nm from the HA surface.…”

“…Although the precise interactions between DPP and HA are also unknown, several studies have suggested that these proteins are generally adsorbed to surfaces by electrostatic forces of different strengths depending on the protein structure and surface charge [19–22]. Protein structures of IDPs with their partners have been characterized by nuclear magnetic resonance [23] and molecular modeling [24].…”