title: 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.
authors.affiliation: Mineralized Tissue Research Laboratory, Hospital for Special Surgery , New York, NY , USA .
authors.forename: Eduardo
authors.initials: E
authors.lastname: Villarreal-Ramirez
authors.forename: Ramón
authors.initials: R
authors.lastname: Garduño-Juarez
authors.forename: Arne
authors.initials: A
authors.lastname: Gericke
authors.forename: Adele
authors.initials: A
authors.lastname: Boskey
mesh_terms: D000595:Amino Acid Sequence; D017886:Durapatite / Q000378:metabolism*; D016326:Extracellular Matrix Proteins / Q000378:metabolism*; D006801:Humans; D056004:Molecular Dynamics Simulation; D010455:Peptides / Q000737:chemistry / Q000378:metabolism; D010750:Phosphoproteins / Q000378:metabolism*; D010766:Phosphorylation; D017434:Protein Structure, Tertiary; D012795:Sialoglycoproteins / Q000378:metabolism*; D000099311:Dentin Sialophosphoprotein
chemical_list: D017886:Durapatite; D016326:Extracellular Matrix Proteins; D010455:Peptides; D010750:Phosphoproteins; D012795:Sialoglycoproteins; D000099311:Dentin Sialophosphoprotein
keywords: Biomineralization; bone dentin; dentin phosphoprotein; molecular dynamics; phosphophoryn