The remarkable properties of bone derive from a highly organized arrangement of coaligned nanometer-scale apatite platelets within a fibrillar collagen matrix. The origin of this arrangement is poorly understood and the crystal structures of hydroxyapatite (HAP) and the nonmineralized collagen fibrils alone do not provide an explanation. Moreover, little is known about collagen-apatite interaction energies, which should strongly influence both the molecular-scale organization and the resulting mechanical properties of the composite. We investigated collagen-mineral interactions by combining dynamic force spectroscopy (DFS) measurements of binding energies with molecular dynamics (MD) simulations of binding and atomic force microscopy (AFM) observations of collagen adsorption on single crystals of calcium phosphate for four mineral phases of potential importance in bone formation. In all cases, we observe a strong preferential orientation of collagen binding, but comparison between the observed orientations and transmission electron microscopy (TEM) analyses of native tissues shows that only calcium-deficient apatite (CDAP) provides an interface with collagen that is consistent with both. MD simulations predict preferred collagen orientations that agree with observations, and results from both MD and DFS reveal large values for the binding energy due to multiple binding sites. These findings reconcile apparent contradictions inherent in a hydroxyapatite or carbonated apatite (CAP) model of bone mineral and provide an energetic rationale for the molecular-scale organization of bone.biomineralization | bone | protein-mineral interface | dynamic force spectroscopy B one is a natural protein-mineral composite consisting of nonstoichiometric nanometer-scale carbonated apatite crystallites inside a fibrillar protein matrix. The matrix is mainly composed of type I collagen and is organized on multiple length scales (1, 2). At the shortest scale, three polypeptide chains form a triple helix referred to as a tropocollagen molecule that is ∼300 nm in length and 1.5 nm in diameter. These helices are arranged in a quasi-hexagonal bundle in which they overlap and intertwine to form microfibrils containing "hole zones," where there is a gap between the N termini of one helix and the C termini of another (3-5). These microfibrils are further bundled both laterally and longitudinally to form native collagen (3, 4).Within this highly organized scaffold, apatite crystallites form nanometer-scale platelets (6-9) with their [001] axes preferentially aligned parallel to the fibril axis (10-15) and the platelet faces defined by {100} crystal planes (16). Recent in vitro investigations of hydroxyapatite (HAP) formation within collagen fibrils revealed a multistage process in which amorphous calcium phosphate (ACP) first infiltrated through the hole zones and then converted into HAP platelets with initial mineral deposition occurring near the hole zones (11, 13). In vitro transmission electron microscopy (TEM) and atomic force microscop...