Protein-RNA interactions in belladonna mottle virus investigated by laser Raman spectroscopy

Raman difference spectroscopy of the belladonna mottle virus (BDMV) and its separated RNA and protein components indicates that molecular interaction occurs between the single-stranded RNA genome and capsid subunits. The molecular interactions that stabilize the virion at pH 5.0 are altered or eliminated at pH 8.0, even though release of the RNA from the capsid is prevented by the addition of divalent metal cations (Ca2+). From the perturbations that occur to Raman lines of cytosine and adenine rings of the encapsidated RNA molecule between pH values of 5.0 and 8.0, it is concluded that cytosines are protonated in significant numbers at the conditions which maintain the native virus structure and that the stacking of adenines is altered by changes in pH. The degree of protonation of RNA bases can be reduced by elevation of the pH to 8.0 for encapsidated RNA or by release of the RNA from the capsid at pH 5.0. Although the protein groups that interact with the viral RNA cannot be identified unambiguously from the Raman spectra, it is apparent that the molecular environments of aromatic amino acid side chains are altered with the same changes in pH (from 5.0 to 8.0) that perturb the cytosine and adenine ring structures. No significant change in secondary structures of the capsid subunit can be detected with changes in pH or with RNA release. On the other hand, the characteristic Raman lines of the phosphate groups of packaged RNA differ from those of naked RNA at all pH values examined, most likely as a result of specific electrostatic binding of divalent cations to RNA phosphates within the virus shell.