Conformational changes and proton uptake in the reversible aggregation of tobacco-mosaic-virus protein

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)

Polymerization of tobacco mosaic virus protein without and with hydrogen ion binding

When tobacco mosaic virus (TMV) protein is polymerized at pH values above 7 in unbuffered solutions, either by raising temperature at constant ionic strength or by increasing ionic strength at constant temperature, a 20 S component is formed having bound only the very small amount of H+ ion supplied by the unpolymerized protein. When hydrogen ion is added by titration during polymerization so as to keep pH constant, as would occur automatically if a buffer were present, a 20 S component is formed with one H+ ion bound each for half of the subunits. Thus, a 20 S form with and a 20 S form without bound H+ ion exist. Furthermore, the 20 S form without bound H+ ion binds H+ ion when supplied by titration to produce a 20 S form with the same amount of bound H+ ion as when H+ ion is supplied during the polymerization.

Scanning calorimetric investigation of the polymerization of the coat protein of tobacco mosaic virus

The endothermic polymerization of the coat protein of tobacco mosaic virus has been studied by high-sensitivity differential scanning calorimetry, with control experiments involving turbidimetry and sedimentation velocity measurements. The variation of the apparent extent of polymerization under conditions close to equilibrium as the temperature is raised follows a course which is difficult to duplicate on the basis of simple models for the process. The enthalpy of polymerization at low protein concentration varies from 12.5 kcal (mol of monomer)-1 (17500 daltons) under conditions where the product is largely a mixture of short helical rods to 6.0 kcal ol-1 for the formation of double disks containing 34 monomer units. In the former case, the polymerization is accompanied by a decrease in apparent heat capacity of 350 cal K-1 mol-1 while in the latter there is an increase of 150 cal K-1 mol-1. These results constitute evidence that these two types of polymerization involve intersubunit bonds of quite different chemical character.

Mechanism of RNA-protein interactions in tobacco mosaic virus: analysis of the pH stability of virus protein complexes with synthetic polynucleotides

TMV-like RNP complexes were reconstituted from TMV protein and synthetic polynucleotides. Analysis of the pH stability of RNP with polynucleotides containing U, G, or their analogues reveals a correlation between the stability of their structure and the pK values of the bases, and indicates that the -NH-CO-groups of U and G are involved in hydrogen bonding with protein. It is suggested that TMV protein has two U- and one G-specific binding sites which, according to the phase position of the protein subunits relative to the origin of TMV assembly (D. Zimmern (1977), Cell 11, 463) are likely to be organized as UGU. The binding of the A and C residues of RNA with TMV protein is nonspecific. TMV protein groups with pK 6.3, 7.5 and 9.7 were found to be essential in the protein-protein interactions in RNP. A group of the protein with pK 8.2 is also involved in RNP stabilization. Both protein-protein interactions and interactions of protein with RNA phosphate groups were shown to be mediated by a conformational change in the protein induced by base binding. The effect of bases on both types of interactions changes in the order G approximately equal to much greater than A, and incorporation of C in RNP proceeds in a compulsory way at the expense of interaction of the neighbouring nucleotide residues in polynucleotides with protein. The data obtained are used to discuss the principles of the cooperativity of the interactions between TMV components and the mechanism of initiation and elongation in TMV self-assembly.

Studies on the mechanism of assembly of tobacco mosaic virus

Sedimentation and proton binding studies on the endothermic self-association of tobacco mosaic virus (TMV) protein indicate that the so-called "20S" sedimenting protein is an interaction system involving at least the 34-subunit two-turn yield cylindrical disk aggregate and the 49-subunit three-turn helical rod. The pH dependence of this overall equilibrium suggests that disk formation is proton-linked through the binding of protons to the two-turn helix which is not present as significant concentrations near pH 7. There is a temperature-induced intramolecular conformation change in the protein leading to a difference spectrum which is complete in 5 x 10(-6) s at pH 7 and 20 degrees C and is dominated at 300 nm by tryptophan residues. Kinetics measurements of protein polymerization, from 10(-6) to 10(3) s, reveal three relaxation processes at pH 7.0, 20 degrees C, 0.10 M ionic strength K (H) PO4. The fastest relaxation time is a few milliseconds and represents reactions within the 4S protein distribution. The second fastest relaxation is 50-100 x 10(-3) s and represents elementary polymerization steps involved in the formation of the approximately 20 S protein. Analysis of the slowest relaxation, approximately 5 x 10(4) s, suggests that this very slow formation of approximately 20 S protein may be dominated by some first order process in the overall dissociation of approximately 20S protein. Sedimentation measurements of the rate of TMV reconstitution, under the same conditions, show by direct measurements of 4S and approximately 20S incorporation at various 4S to approximately 20S weight ratios that the relative rate of approximately 20S incorporation decreases almost linearly, from 0 to 50% 4S. There appears to be one or more regions of TMV-RNA, approximately 1-1.5 kilobases long, which incorporates approximately 20S protein exclusively. Solutions of approximately 95-100% approximately 20S protein have been prepared for the first time and used for reconstitution with RNA. Such protein solutions yield full size TMV, but at a slower rate than if 4S protein is added. Thus the elongation reaction in TMV assembly, following nucleation with approximately 20S protein, is not exclusively dependent upon the presence of either 4S or approximately 20S protein aggregates. The initial, maximum, rate of reconstitution increases about threefold when the protein composition is changed from 5% to 30% 4S protein, at constant total protein concentration at pH 7.0, 20 degrees C in 0.10 M ionic strength K (H)PO4. The probable binding frame at the internal assembly nucleation site of TMV-RNA has been determined by measuring the association constants for the binding of various trinucleoside diphosphates to helical TMV protein rods. The -CAG-AAG-AAG-sequence at the nucleation site is capable of providing at least 10-14 kcal/mol of sites of binding free energy for the nucleation event in TMV self-assembly.

Tobacco mosaic virus protein: sedimentation equilibrium studies of the initial stages of polymerization

The lowest stages of polymerization of tobacco mosaic virus protein were studied by means of high-speed sedimentation equilibrium experiments. Several distinct modes of polymerization were found. At pH 7.1 the expected monomer-trimer-higher polymer equilibrium was observed--very little dimer was detected at this pH. At pH 7.5, however, a strong dimerization was observed--neither monomer nor trimer was detected at this pH. An octamer appeared to be the only species present other than the dimer. When 0.01 M beta-mercaptoethanol was added to the solvent pH 7.5, the dimer was dissociated, resulting in a monomer-trimer association. The dimerization may be the basis for the larger "doubled" polymers formed by the protein at alkaline pH, while the octamer may correspond to the 8S peak frequently observed in sedimentation velocity experiments at alkaline pH. On the other hand, the monomer-trimer-higher polymer equilibrium may correspond to the single helix formed by the protein at slightly acid pH and to the combination of 4S and 20S peaks seen in sedimentation velocity experiments at slightly acid pH.

Hydrogen-ion binding by tobacco-mosaic-virus protein polymers

Hydrogen ion titration curves of tobacco mosaic virus protein have been measured in various conditions of protein concentration, temperature, ionic strength, and rate of pH change. The polymers present at each stage are deduced from turbidity and sedimentation data, plus published information. A simple semi-quantitative analysis of the curves is given, and the pK values of the two abnormal carboxylates in single helix are estimated as 6.4 and about 7.0. Disks, and some faster-forming unknown polymers in the same size range, have been abnormal carboxylate with pK 6.9. These results are most easily interpreted in terms of electrostatic interactions between carboxylates, probably at the axial ends of the protein subunits.

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.

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.