Compositions comprise a flagellin component or a Toll-like Receptor agonist component that is at least a portion of a flagellin or a Toll-like Receptor agonist, wherein the flagellin component or Toll-like Receptor agonist component includes at least one cysteine residue and whereby the flagellin component or Toll-like Receptor agonist component activates a Toll-like Receptor 5 or Toll-like Receptor. Compositions comprise a flagellin component that is at least a portion of a flagellin, wherein at least one lysine of the flagellin component has been substituted with at least one arginine, serine and histidine, whereby the flagellin component activates Toll-like Receptor 5. Compositions can further include an antigen, such as an influenza antigen, a flavivirus antigen, a pathogen-related antigen, a bacterial capsular antigen and a carrier protein. The compositions are used to stimulate an immune response and a protective immune response in a subject.