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Amelogenin is the main component of the organic matrix necessary to the formation of tooth enamel by directing the hydroxyapatite (HAP) growth. However, the detailed mechanism of adsorption between amelogenin and HAP is still not clear. In this report, simulations of the dynamic behavior of six different orientations of leucine-rich amelogenin protein (LRAP), the amelogenin splice variant, on a fixed hydrophilic HAP surface (001) were performed. Energy minimization, molecular dynamics (MD), and steered molecular dynamics (SMD) simulations were integrated in carrying this study. The results are highly consistent with the previous experimental findings. It was confirmed that the carboxyl groups contributed mainly to the adsorption of LRAP on the HAP (001) surface. Moreover, it was found that the −COO- claw of LRAP grasps the calcium ion with its two oxygen atoms in a special triangle form. This interaction form can resist external forces and is the key factor of the adsorption between LRAP and HAP.

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Understanding the mechanisms that govern the crystallization of natural minerals such as calcium carbonate, calcium oxalate, or hydroxyapatite and its control by biological and synthetic polymers can help to guide the design of new biomimetic materials. In this paper, the adsorption behavior of oligomers of polystyrene sulfonate (PSS) on calcite surfaces was investigated by molecular dynamics simulations. The binding strengths of PSS oligomers to different calcite surfaces were computed via potential of mean force calculations, and the binding modes were analyzed in detail. These results could be set in relation to and serve as a molecular-level explanation of the experimentally observed PSS-stabilized exposure of (001) surfaces during calcite mineralization. The simulations show that oligomers of PSS preferentially bind to the polar calcite (001) surface, much stronger than to the nonpolar (104) surface. While sharing in common a dominant role of solvent-induced forces, the mode of binding to the two surfaces is different. The interaction of the sulfonate group with the (001) surface is dominated by both direct and solvent-mediated binding, while the binding of the styrene sulfonate to the (104) surface is mediated by one or two layers of water molecules. Moreover, local solvent density variations at the interface impact the geometry of binding which vastly differs between the two surfaces. In particular, these last effects have important further implications for the preferential binding of PSS polymers (compared to monomers or oligomers) and specific material recognition by synthetic polymers and peptides in general.

Understanding the relation between structural and thermodynamic quantities obtained with simplified-e.g., coarse-grained (CG) or implicit-solvent-models is an ongoing challenge in the field of multiscale simulation. Assessing the transferability of such models to state points that differ from the one where the model was parametrized is important if one wants to apply these models to complex systems, which, for example, exhibit spatially varying compositions. Here, we investigate the transferability of CG (in this case implicit-solvent) ion models with effective pair potentials derived at very low concentrations to different ion concentrations in aqueous solution. We evaluate both thermodynamic and structural properties of systems of NaCl in aqueous solution both in atomistic explicit-solvent and CG simulations. For the explicit solvent simulations, osmotic coefficients have been calculated at a wide range of salt concentrations and agree very well with experimental data. It had been shown previously that a concentration-dependent dielectric permittivity can be used to make effective implicit-solvent pair potentials transferable since it accounts for the effect of ion concentration on solvent properties, resulting in very good osmotic properties of these models for a certain range of salt concentrations. We investigate the explicit and implicit solvent models also in terms of structural properties, where we can show how with a concentration-dependent dielectric constant one obtains very good structural agreement at low and intermediate salt concentrations, while for larger salt concentrations, multibody ion-ion correlations put a limit to straightforward transferability. We show how-guided by this structural analysis-the transferability of the implicit-solvent model can be improved for high ion concentrations. Doing so, we obtain transferable implicit-solvent effective pair potentials which are both structurally and thermodynamically consistent with an explicit solvent reference model.