Circular dichroism studies on coat proteins of some strains and mutants of tobacco mosaic virus

Two azurins with unusual redox and spectroscopic properties isolated from the Pseudomonas chlororaphis strains DSM 50083T and DSM 50135

Two azurins (Az624 and Az626) were isolated from the soluble extract of two strains of Pseudomonas chlororaphis, DSM 50083(T) and DSM 50135, respectively, grown under microaerobic conditions with nitrate as final electron acceptor. The azurins, purified to electrophoretic homogeneity in three chromatographic steps, exhibit several peculiar properties. They have high reduction potentials and lower pI than most azurins described in the literature. As previously observed for Pseudomonas aeruginosa azurin, their reduction potentials are pH-dependent, but the pK values of their oxidized forms are lower, which suggests that deeper structural changes are associated with the oxidation process of these novel azurins. A hitherto undescribed pH-dependence of the diffusion coefficient was observed in Az624, that could be caused either by conformational changes, or by the formation of supramolecular aggregates associated with a protonation process. Both azurins exhibit axial X-band electron paramagnetic resonance spectra in frozen solution showing a typical hyperfine with the copper nucleus (I=3/2) and a well-resolved superhyperfine structure with two equivalent 14N nucleus (I=1), which is not usually observed for azurins from other species.

Preparation and properties of recombinant DNA derived tobacco mosaic virus coat protein

Recombinant DNA derived tobacco mosaic virus (vulgare strain) coat protein (r-TMVP) was obtained by cloning and expression in Escherichia coli and was purified by column chromatography, self-assembly polymerization, and precipitation. SDS-PAGE, amino terminal sequencing, and immunoblotting with polyclonal antibodies raised against TMVP confirmed the identify and purity of the recombinant protein. Isoelectric focusing in 8 M urea and fast atom bombardment mass spectrometry demonstrated that the r-TMVP is not acetylated at the amino terminus, unlike the wild-type protein isolated from the tobacco plant derived virus. The characterization of r-TMVP with regard to its self-assembly properties revealed reversible endothermic polymerization as studied by analytical ultracentrifugation, circular dichroism, and electron microscopy. However, the details of the assembly process differed from those of the wild-type protein. At neutral pH, low ionic strength, and 20 degrees C, TMVP forms a 20S two-turn helical rod that acts as a nucleus for further assembly with RNA and additional TMVP to form TMV. Under more acidic conditions, this 20S structure also acts as a nucleus for protein self-assembly to form viruslike RNA-free rods. The r-TMVP that is not acetylated carries an extra positive charge at the amino terminus and does not appear to form the 20S nucleus. Instead, it forms a 28S four-layer structure, which resembles in size and structure the dimer of the bilayer disk formed by the wild-type protein at pH 8.0, high ionic strength, and 20 degrees C.(ABSTRACT TRUNCATED AT 250 WORDS)

Tobacco mosaic virus protein aggregates in solution: structural comparison of 20S aggregates with those near conditions for disk crystallization

Previous X-ray studies (2.8-A resolution) on the crystals of tobacco mosaic virus protein (TMVP) grown from solutions containing high salt have characterized the structure of the protein aggregate as a bilayered cylindrical disk formed by 34 identical subunits [Bloomer, A.C., Champness, J.N., Bricogne, G., Staden, R., & Klug, A. (1978) Nature (London) 276, 362-368]. Under low-salt conditions, 20S aggregates are in equilibrium with 4S species and involved in the efficient nucleation of TMV assembly in vitro [Butler, P.J.G. (1984) J. Gen. Virol. 65, 253-279]. We have investigated by sedimentation velocity and near-UV circular dichroism (CD) measurements the structure of 20S aggregates in low salt (I = 0.1 potassium phosphate at pH 7.0 and 20 degrees C) and the aggregates in high salt [0.2 M (NH4)2SO4 in I = 0.1 tris(hydroxymethyl)aminomethane hydrochloride at pH 8.0 and 20 degrees C, close to the conditions under which TMVP crystallizes as disk aggregates]. At high salt, we observe structures (presumably stacks of disks) having s20,w values around 40, 45, and 50 S, but not the 20S species present in low-salt buffers. The near-UV CD spectrum of 20S aggregates has been obtained for the first time, using computer techniques, from the spectra of the 4S-20S equilibrium mixture and the 4S species. This spectrum of 20S aggregates differs dramatically from that of the stacks of disks examined at both high and low salt (into which the stacks can be returned by dialysis), indicating that the difference is not a solvent effect.(ABSTRACT TRUNCATED AT 250 WORDS)

Structure of single-stranded virus RNA in situ. II. Optical activity of five tobacco mosaic-like viruses and their components

ORD and CD spectra of some TM-like viruses and their coat proteins were measured to study a possible role of tryptophan residues in RNA-protein interactions in these viruses. Five viruses of this group, differing in tryptophan content of their coat proteins, were used: v-TM virus (3 tryptophan residues per protein subunit), strains HR and U2 (2 tryptophan residues per subunit), dolihos enation mosaic virus and cucumber virus 4(1 tryptophan residue per subunit). The viruses differ significantly in their ORD and CD spectra and some correlation between these spectra and tryptophan content of coat proteins seems to exist. But an analysis of "intravirus RNA" CD spectra, obtained by subtraction of CD spectra of virus -like protein assemblies from the spectra of intact viruses, shows that the observed differences in optical activity can hardly be explained by tryptophan participation in RNA-protein interactions. The presence of the "additional" peak at 293 nm in the ORD of TM virus had been considered as evidence of tryptophan-RNA interactions in this virus. In the present work such a peak at 293 nm was observed in the ORD of all the 5 viruses studied, irrespective of the tryptophan content in their coat proteins. Besides, we managed to obtain the virus-like protein assemblies preparations which also showed a peak at 293 nm. All these data show that, in all probability, the 293 nm peak in the ORD of TM virus does not result from tryptophan-RNA interactions. It is believed that the difference in the optical activity of RNA particles of TM-like viruses do originate from the differences in the RNA-protein interactions in these viruses, but these interactions can hardly involve tryptophan residues of virus coat proteins.

A pH-dependent conformational change in the coat protein subunits from potato virus X

Both the circular dichroism and fluorescence spectra of the dissociated coat protein subunits from potato virus X changed substantially over the pH range 8 to 4, irreversible changes resulted below pH 4, with tyrosyl and tryptophanyl residues affected most. The titration curves show a pKa of about 5.6 and do not require cooperative interactions between the coat protein subunits, thus they are in marked contrast to titrations of tobacco mosaic virus A-protein. The spectra of the intact virus were little changed between pH 8 and 4 and suggested that the coat protein was locked into a conformation similar to that of the subunits in solution at pH 7. It is proposed that the pH induced conformational change is responsible for determining the acidic branch of the pH profile for reconstitution of potato virus X from its dissociated coat protein subunits and RNA.

Circular-dichroism and absorption spectroscopic studies on specific aromatic residues involved in the different modes of aggregation of tobacco-mosaic-virus protein

Conformational changes accompanying the different modes of aggregation of tobacco mosaic virus protein (TMV-protein) were investigated using circular dichroism (CD) and absorption difference spectra in the range of aromatic absorption. Comparing wild-type protein and mutant Ni 2068 (Tyr-139 leads to Cys-139) a tentative localization of aromatic amino acids in the three-dimensional structure is rendered possible. In all modes of aggregation the CD spectra are determined by intrasubunit interactions between aromatic residues, in particular Trp-17 and Trp-52 as well as Tyr-70, Tyr-72 and Tyr-139. The Trp-17-Trp-52 interaction was found to be highly sensitive towards changes of the quaternary structure especially with respect to helical aggregates. This suggests that the environment of the two tryptophan residues is of crucial importance in the three-dimensional structure of the subunit; in the course of aggregation intersubunit interactions compete with the specific intrasubunit Trp-17--Trp52 interactions. It is suggested that Try-70 and Tyr-72 form hydrogen bonds in a strongly hydrophobic environment. Formation of the double disc decreases the rotatory strength, pointing to an increase in conformational flexibility. Spectroscopic and chemical evidence prove that Tyr-70, Tyr-72 and Tyr-139 are in close neighbourhood. Double disc formation by lowering the pH (pH 8 LEADS TO 6.9, I = 0.1 M) or increasing the ionic strength (pH 8, I = 0.1 LEADS TO 0.6 M) is reflected by identical spectral effects in the environment of Tyr-70 - Tyr-72. However the interaction between Trp-17 and Trp-52 indicates significant differences in the conformation which may be important for the formation of higher aggregates, i.e. 'lockwashers', helices, and 'stacked discs'.

Involvement of tyrosine residues in the protomer-protomer interaction of Proteus mirabilis flagella as studied by spectroscopic methods, chemical modification and aggregation experiments

Using spectrophotometrical titration, chemical modification, and ultraviolet difference spectral methods, the existence of at least two distinct tyrosine groups in the isolated flagellin of Proteus mirabilis flagella has been established. Three of the five flagellin tyrosines are buried in the protein matrix, whereas the other two seem to lie on the protein surface accessible to perturbants. Also about two tyrosine residues, presumably the latter ones exposed to the environment, can be nitrated with tetranitromethane in the monomeric flagellin with a concomitant loss of the polymerization ability after about one tyrosine per mol flagellin has been nitrated. Nitrated flagellin, homogeneous with respect to molecular weight, degree of nitration and isoelectric point, could be isolated and characterized. On the other hand, it could be shown that in the polymeric flagellum the phenolic groups of all five tyrosine residues are inaccessible to perturbing and modifying reagents. It seems, therefore, that the integrity of the phenolic groups is necessary for the proper folding and aggregation of the flagellin subunits to form the stable helical flagella.

A prediction of the structure of tobacco-mosaic-virus protein

The location of amino acid residues within the tobacco mosaic virus protein subunit is discussed. Sequence data, X-ray crystallographic measurements, and the availability of specific residues for enzymic, immunological or chemical reaction are amongst the information used to trace roughly how the tobacco mosaic virus polypeptide chain winds in and out from the virus axis. Published rules for predicting secondary structure are then applied to obtain a diagram of the course of the polypeptide chain. This map should be useful for the interpretation of X-ray diffraction data and already permits an outline of the main features of the inner third of subunit to be suggested.

Thermally induced conformational changes of tobacco mosaic virus and their protein assemblies

The measurement of the fluorescence intensity of tryptophan residues showed that a reversible transition in the local structure took place between 20 degrees C and 30c in intact virus particles and reconstituted protein assemblies of the ordinary strain and the tomato strain of tobacco mosaic virus. During this transition the overall polymer structure was maintained. In the case of the bean strain of tobacco mosaic virus, however, the fluorescence intensity did not show any transition in the same temperature range. Such a difference between different strains gave some information on the location of tryptophan residues possibly involved in the local structure change. The fluorescence polarization of intact virus particles showed no change in the whole temperature range, but the polarization of the reconstituted protein assembly of the ordinary strain showed a transition at the same temperature as the fluorescence intensity. This suggested a difference in the freedom of the local structure between intact virus particles and reconstituted protein assemblies. Oligomers of these virus proteins were stable up to 45c and above this temperature, began to make an irreversible transition where the secondary structure of the monomer was partially broken but the oligomer structure was retained.

Circular dichroism and fluorescence studies on potato virus X and its structural components

Circular dichroism (DC) measurements of the coat protein subunits of potato virus X show that native subunits that can reassemble with RNA to form infectious virus particles have appreciable alpha-helical structure. The CD of intact potato virus X was less intense below and more intense above 250 nm, and the maxima and minima were at longer wavelengths, than those of a CD spectrum computed from the individual contributions of the coat protein and RNA. The differences between the measured and computed spectra below 250 nm were attributed to the effects of differential light scattering and absorption flattening on measurements of the virus particle CD. The differences at longer wavelengths, were the CD contribution of the nucleic acid predominates, probably reflect the difference between a base-paired conformation of the RNA in solution and the more rigid single-stranded conformation imposed by the structure of the virus. The CD evidence suggests that the tertiary structure and potato virus X coat protein subunits in solution and in intact virus particles is similar. Both CD and fluorescence emission results indicate differences between the tryptophan environment in dissociated protein subunits and that in intact virus. These are attributed to local differences in subunit conformation or to the occurrence of intersubunit interactions involving tryptophan in the intact virus.