Compositions that include a fusion protein comprising flagellin and at least one antigen that has an isoelectric point greater than about 7.0 and that is fused to at least one domain 3 of the flagellin activate Toll-like Receptor 5. Methods of stimulating an immune response, in particular, a protective immune response include administering a composition that includes an antigen fused to a loop of domain 3 of flagellin.