The development of polymer-based structures is hindered due to the difficulties in realizing well-defined modulated structures without interpenetration of charged polymers. Two types of polyelectrolyte multilayer structures, with and without embedded layers of the biomolecule, glutamic acid, are compared using infrared spectroscopy and X-ray and neutron scattering techniques. Structure characterization of polyelectrolyte multilayers focuses usually on the arrangement along the surface normal. Using specular and off-specular neutron scattering we get insight into the in- and out-of-plane arrangement of the structure. A formation of well-defined, smooth layers is observed in the structure containing the biomolecule. This reduced roughness is associated with a drastic decrease in chain mobility responsible for interpenetration. In contrast, the multilayer without the biomolecule forms an island-like structure. Thus biomolecules can interrupt the propagation of island-like structures at such interfaces which can be effectively used in achieving well-defined supramolecular layer structures out of charged polymers.