Bone sialoprotein (BSP) is a highly phosphorylated, acidic, noncollagenous protein in bone matrix. Although BSI has been proposed to be a nucleator of hydroxyapatite (Ca-5(PO4)(3)OH), the major mineral component of bone, no detailed mechanism for the nucleation process has been elucidated at the atomic level to date. In the present work, using a peptide model, we apply molecular dynamics (MD) simulations to study the conformational effect of a proposed nucleating motif of BSP (a phosphorylated, acidic, 10 amino-acid residue sequence) on controlling the distributions of Ca2+ and inorganic phosphate (Pi) ions in solution, and specifically, we explore whether a nucleating template for orientated hydroxyapatite could be formed in different peptide conformations. Both the alpha-helical conformation and the random coil structure have been studied, and inorganic solutions without the peptide are simulated as reference. Ca2+ distributions around the peptide surface and interactions between Ca2+ and Pi in the presence of the peptide are examined in detail. From the MD simulations, although in some cases for the a-helical conformation, we observe that a Ca2+ equilateral triangle forms around the surface of peptide, which matches the distribution of Ca2+ ions on the (001) face of the hydroxyapatite crystal, we do not consistently find a stable nucleating template formation in general for either the helical conformation or the random coil structure. Therefore, independent of conformations, the BSP nucleating motif is more likely to help nucleate an amorphous calcium phosphate cluster, which ultimately converts to crystalline hydroxyapatite.