Structural studies of tobacco mosaic virus and its components by laser Raman spectroscopy.

Raman spectra have been recorded for oriented gels of tobacco mosaic virus, aqueous solutions of TMV protein in the form of capsid and disk, and protein-free TMV RNA. The protein-free RNA molecule contains about 80% ordered type-A structure, which is similar to other RNA molecules in solution. RNA in the virus particle does not exhibit the base stacking and pairing normally found in protein-free RNA but instead shows at least two distinct structures characterized by different phosphodiester group frequencies in the Raman spectrum. Approximately one out of three such linkages retains the type-A geometry characteristic of aqueous RNA, while two out of three appear to have a different geometry not encountered previously for RNA. The secondary structure of the TMV coat protein molecule is similar for the three aggregation states studied (virus, capsid, and disk) and consists of 40-50% alpha helix, 40-50% irregular structure, and 0-20% beta sheet. Two of the three tryptophan residues per protein molecule reside in hydrophobic regions, and the third is in contact with water. The distribution of the four tyrosine residues per protein molecule among hydrogen-bonding states is the same for capsid and virus but different for the disk. The latter could be a consequence of the presence of Cl- ions which may form hydrogen bonds with one or more p-hydroxyl groups of tyrosine residues.