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The protein ligand shells of fluorescent protein-protected gold nanoclusters play an important role in the physiochemical properties and sensing applications of the nanoclusters. Recently, more and more attention has been paid to the investigation of the changes in the protein structure elements induced by the introduction of the nanoclusters in the proteins. In this work, the strategy of removal of the encapsulated gold nanoclusters from the protein ligand cages has been proposed, producing the “hollow” (or possibly “imprinted”) proteins for investigations for the first time. Nontoxic cysteamine was used as the etchant of the gold nanoclusters. With bovine serum albumin, lysozyme, and ovalbumin as model proteins, it was found that the luminescent dityrosine cross-links exist in the protein-protected gold nanoclusters, however, inner filter effect caused by the gold nanoclusters hide them.