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

Visualization of protein-nucleic acid interactions in a virus. Refined structure of intact tobacco mosaic virus at 2.9 A resolution by X-ray fiber diffraction

The structure of tobacco mosaic virus (TMV) has been determined by fiber diffraction methods at 2.9 A resolution, and refined by restrained least-squares to an R-factor of 0.096. Protein-nucleic acid interactions are clearly visible. The final model contains all of the non-hydrogen atoms of the RNA and the protein, 71 water molecules, and two calcium-binding sites. Viral disassembly is driven by electrostatic repulsions between the charges in two carboxyl-carboxylate pairs and a phosphate-carboxylate pair. The phosphate-carboxylate pair and at least one of the carboxyl-carboxylate pairs appear to be calcium-binding sites. Nucleotide specificity, enabling TMV to recognize its own RNA by a repeating pattern of guanine residues, is provided by two guanine-specific hydrogen bonds in one of the three base-binding sites.

Ultrasonic absorption in tobacco mosaic virus and its protein aggregates

The structural fluctuations specific to self-assembled biological systems have been investigated further with ultrasonic techniques by using two strains of tobacco mosaic virus (TMV), as well as the helical aggregate of the common strain protein and subassemblies of it. We confirmed our earlier conclusion that protein assemblies exhibit specific structural fluctuations detected in ultrasonic experiments. As in spherical viruses, the fluctuations exhibited by the protein aggregates having a quaternary structure similar to that of the virion were modified in the virus by interaction with the RNA strand. It is unlikely that the origin for the observed effect is due either to: (1) the difference in local mobility of the segment 89 to 113 of the polypeptide chain in TMV and in the helical aggregate on the one hand, and in smaller aggregates, on the other hand; or (2) a local fluctuation associated with proton transfer reactions or ion-pair interactions. The most remarkable feature in the TMV system is the fact that the two-ring disk showed no excess of ultrasonic absorption with respect to the A-protein oligomer, while a large increase of ultrasonic absorption was observed in the rod-like aggregate that had undergone the disk-helix transition.

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.

Sequence specificity of trinucleoside diphosphate binding to polymerized tobacco mosaic virus protein

The binding of trinucleoside diphosphates to long helical rods of tobacco mosaic virus (TMV) protein is shown to depend on base sequence, 5' AAG 3' binding being the strongest of the 25 trinucleoside diphosphate sequences measured. As TMV has a stoichiometry of three nucleotides per protein subunit, the sequence of TMV RNA suggested to be the nucleation site for self-assembly of the virus has three possible binding frames. From our binding constant data the most likely frame is predicted and shown to have two contiguous AAG sequences in a hairpin loop region.

The generality of cation-binding sites in rod-shaped viruses

Hydrogen-ion titration curves have been measured for two filamentous plant viruses (clover yellow mosaic virus and potato virus X) and two filamentous bacterial viruses (fd and Pf1) with and without Ca2+ or Mg2+ ions present, and for the protein of the PM6 mutant of tobacco mosaic virus. The bacterial viruses do not possess the 'strong' cation-binding sites found in all plant viruses, but they have 'weak' sites that can be assigned to juxtaposed carboxylate groups on their external surfaces. The strong sites in plant viruses still cannot be assigned to any particular amino-acid side chains, but they must be located in the region of high electronegativity near the axis.

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.

Titration behaviour of three strains of tobacco mosaic virus

Hydrogen ion titration curves of the virions and proteins of three strains of tobacco mosaic virus (Y-TAMV, U2, and cowpea) were measured in the absence and the presence of Ca2+, Mg2+, or Mn2+ ions, and compared with the analogous curves for the type strain (vulgare). Extinction coefficients were also measured for all four strains' virions and proteins. Y-TAMV is very like vulgare in its cation affinities: the virion has probably three groups per protein subunit that titrate near neutral pH and significantly bind metal ions; the RNA-free protein has very little affinity for Ca2+, although moderate Ca2+ concentrations favour the existence of larger polymers. U2 and cowpea strain virions bind cations significantly more strongly than do Y-TAMV or vulgare virions: their polymerized proteins, too, have significant affinities for Ca2+ ions, which make their titration and sedimentation behaviours relatively sensitive to added calcium. These cation-binding differences correspond well with the differences between the strains' protein sequences. The features common to all four strains are that the virions are apparently structurally invariant and have at least one site per subunit with Ca2+ affinity in the region of 10(-5)M, while the RNA-free proteins lack the high-affinity sites but have weaker Ca2+ affinities in the region of 10(-3)M. Some of the cation-binding sites probably lie near the central holes of the virions.

Structural comparisons of the aggregates of tobacco mosaic virus protein

The coat protein of tobacco mosaic virus forms numerous aggregates, including the small A-protein, the disk, and two helical forms. The structures of the disk, the helical protein forms, and the virus are compared. Most of the differences are in the conformation of the chain between residues 89 and 113, which lies in the region of protein at the center of the virus, inside the RNA. It is disordered in the disk, but has a fixed conformation in the virus and the protein helices. The differences between the virus and the two helical protein forms are largely in the conformations of arginines and carboxylic acids in this region.