The present work represents interactions between the core-shell nanoparticles and different proteins, exemplified by lysozyme (LSZ), pepsin, bovine serum albumin (BSA), thioredoxin (TRX) and yellow fluorescent protein (YFP). The core-shell morphology derives from the non-covalent deposition of polyethyleneimine (PEI) onto nanoprecipitated luminescent complex (AuCl)2L (L is cyclic PNNP ligand). Analysis of the data obtained by DLS, CD spectroscopy, luminescence derived from both (AuCl)2L and YFP reveal the electrostatically driven interaction of negatively charged proteins with the shell of PEI-(AuCl)2L. The fluorescence of YFP enables to reveal the inclusion of the protein molecules into the shell. The lack of any luminescent response of PEI-(AuCl)2L on TRX conforms its electrostatically driven interactions with the shell which, in turn, excludes a binding of the exposed thiol moieties with (AuCl)2L. The negatively charged surface of pepsin provides the greatest recharging of the PEI-based shell versus the other proteins, which is followed by the enhanced luminescence of (AuCl)2L. The significant effect of PEI-(AuCl)2L on the CD spectra of LSZ followed by the decreased intensity of (AuCl)2L-based luminescence points to specific interaction mode of PEI-(AuCl)2L with LSZ. The flow cytometry and fluorescent microscopy measurements revealed efficient internalization of PEI-(AuCl)2L into the Wi-38 cell samples resulting in the efficient staining of all cell organelles. The concentration dependent cytotoxicity of PEI-(AuCl)2L is detectably enhanced by LSZ, which is correlated with its interaction mode with the nanoparticles.