Fluorescamine-labeled structural proteins of viruses in the Venezuelan equine encephalitis (VEE) serologic complex were purified by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Purified [14C]lysine-labeled capsid protein and El and E2 envelope glycoproteins of TC-83 (serologic subtype-variant I-A) virus were mixed with the corresponding [3H]lysine-labeled structural proteins of TC-83, PTF-39 (I-B), P676 (I-C), 3880 (I-D), Mena II (I-E), Everglades Fe 3-7c (II), Mucambo BeAn 8 (III), and Pixuna BeAr 35645 (IV) viruses and codigested with trypsin. Tryptic peptides were resolved by reverse-phase high-pressure liquid chromatography. The capsid and El proteins of I-A, I-B, I-C, and I-D viruses produced identical or nearly identical tryptic peptide maps, whereas the maps of I-E, II, III, and IV capsid and El proteins were distinct from the maps of the corresponding I-A proteins. The tryptic peptide maps of the type-specific protein, E2, of the various viruses showed the most variation and correlated well with the serologic and genetic homologies determined by oligonucleotide fingerprinting of VEE 42 S RNA. Fluorescamine derivatization of viral proteins was shown to have little or no effect on the specificity of trypsin. Trypsin was shown to cleave these proteins at both lysine and arginine residues.
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