This disclosure relates to particles comprising recombinant proteins, pharmaceutical composition comprising the particles, and therapeutic uses related thereto. In certain embodiments, the particles are made by the process of producing recombinant proteins and conjugating the recombinant proteins to form nanoparticles with a linking reagent comprising disulfide bonds. Typically the recombinant protein has a polypeptide of viral, fungal, or bacterial origin such as secreted effector proteins AvrA and YopJ. In certain embodiments, the disclosure relates to treating or preventing autoimmune diseases, cancer, or inflammatory diseases, or conditions such as inflammatory bowel disease (IBD).