Optical and hydrodynamic studies of the structure of bacteriophage f2

Urea and guanidine hydrochloride induced dissociation and denaturation of bacteriophage F2 capsid

A single, low molecular weight protein is found after urea or guanidine hydrochloride (Gdn.HCl) treatment of empty capsids derived from bacteriophage f2. The final product of denaturation is apparently a monomer, existing as a random coil in larger than or equal to 4.0 M Gdn.HCl but in a less extended form in 8.0 M urea. In contrast, an 11 S protein component is isolated after treatment of the intact virus with 4.0 M Gdn.HCl (Zelazo & Haschemeyer, 1969), indicating that RNA plays a role in stabilizing larger subunits. Denaturation by Gdn.HCl occurs in two stages as measured by changes in CD and Stokes radius: dissociation that involves a structural perturbation of aromatic side chains, followed by a major, cooperative transition that evidently results in the loss of all noncovalent structure. Denaturation by urea appears to be a much less cooperative process that occurs in several steps over a wide range of urea concentration (1--7 M). In both urea and Gdn.HCl, dissociation into subunits begins at a lower concentration of denaturant than the major changes in conformation.

Optical and hydrodynamic studies of the structure of bacteriophage f2. II. Fluorescence of the capsid

Fluorescence properties of the icosahedral RNA virus bacteriophage f2 and its empty capsid are reported. Emission is dominated by tryptophan with a maximum wavelength of 320 nm for f2 and its empty capsid. In addition to this short wavelength maximum, perturbation and denaturation studies indicate the inaccessibility of the tryptophan residues. However a high degree of thermal quenching and a red shift in fluorescence emission on heating suggest a noncooperative structural transition, not a denaturation, which allows buried tryptophans to become exposed to solvent. Therefore the tryptophan residues may be located between subunits. Fluorescence from tyrosine is detected near 315 nm for both f2 and its empty capsid, and may indicate an unusual tyrosine environment. Sensitization of tryptophan fluorescence by tyrosine absorption and low values of polarization indicate tyrosine leads to tryptophan and tryptophan leads to tryptophan energy transfer. The presence of RNA in f2 decreases the efficiency of these transfer processes, but does not significantly affect the other reported fluorescence properties.

Determination of secondary structure in rabbit globin messenger RNA by thermal denaturation

The secondary structure of highly purified globin messenger RNA has been investigated by alkaline hydrolysis, nuclease digestion, and thermal denaturation. The thermal denaturation properties of globin messenger have been compared to poly(U), poly (A), and a synthetic random sequence RNA copolymer. From these studies it is concluded that globin mRNA contains considerable secondary structure and that the amount of helical structure is greater than that which occurs with a random sequence polyribonucleotide. Globin mRNA contains, by comparison to the secondary structures of native DNA, tRNAs, or 18S rRNA, helices with involve 55-62% of the bases or 58-68% if a correction is made for the 3'-terminal poly(A) segment. The helices of globin mRNA appear to be unique as differences in the NaCl stabilization of this RNA have been noted when compared to other naturally ooccurring and synthetic RNAs. Comparison of the hyperchromicity maxima, obtained at 260 and 280 nm for globin mRNA and 18S rRNA, indicates that the helices of the two RNAs contain similar numbers of G-C base pairs. Differential analysis of NaCl stabilization curves indicate three discrete thermally denaturable helix types in globin mRNA.