A melt-processed protein composition formed from a protein, plasticizer, and an electrophilic reagent is provided. The electrophilic reagent, for instance, may be selected to undergo a nucleophilic addition reaction with free sulfhydryl and/or thiyl radicals to help minimize the formation of disulfide crosslinking bonds that could otherwise lead to protein aggregation during melt processing. To enhance the degree to which the electrophilic reagent can limit crosslinking, a plasticizer is also employed that helps to mediate the adsorption of the electrophilic reagent into the internal structure of the protein, where it can be more stably retained. Furthermore, the temperature and shear rate employed during melt blending may also be selected to be relatively low to help limit polypeptide dissociation, thereby minimizing the impact of aggregation and embrittlement.