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The hydrophobic aggregating EMD protein was successfully immobilized both on top of and within the multilayer structures at pH 5.0. DPI measurements further indicated that the immobilization of EMD is influenced by the flow pattern during adsorption. The formed polypeptide−EMD multilayer films are of interest since it is known that EMD is able to trigger cell response and induce biomineralization. The multilayer films thus have potential to be useful as bioactive and biodegradable coatings for future dental implants.