Orientation effects on the electrophoretic mobility of rod-shaped molecules in free solution.

The effect of molecular orientation on the electrophoretic mobility of rod-shaped polylons as measured by free solution capillary electrophoresis is studied by using the tobacco mosaic virus (TMV) as a model solute. This orientational dependence of molecular mobility is measured by observing the influence of electrical field strength (up to 400 V/cm) on the electrophoretic mobility of TMV. The electrophoretic mobility of TMV increases with increasing field strength. This increase can be quantitatively correlated with the decrease in the translational frictional coefficient (f) due to the increasing alignment of TMV with the electric field. A model is developed relating the decrease in f to the alignment of TMV with the electric field through its polarizability and aspect ratio. To confirm the observed orientational affects on mobility, control experiments were performed with 0.364 micron diameter Latex spheres. Due to their spherical symmetry, no orientational effects would be expected. Indeed, no increase in mobility was observed for these spherical particles. Calculations are presented to demonstrate that the increase in mobility is unlikely to be caused by either the Wien effect or any temperature variation resulting from Joule heating of the electrophoresis buffer.

Tobacco mosaic virus particles contain ubiquitinated coat protein subunits.

Virions of tobacco mosaic virus (TMV) are composed of a single strand of RNA, encapsidated in about 2130 copies of a coat protein of MW 17,500. Asselin and Zaitlin [Virology 91, 173-181 (1978)] demonstrated that virion preparations also contained small amounts of a second protein of MW 26,500, which they termed "H protein." H protein, detectable to an average frequency of one per virion, was thought to be a protein of host origin. Subsequent studies [Collmer, Vogt, and Zaitlin, Virology 126, 429-448 (1983)] showed the H protein was comprised of a backbone of TMV coat protein, linked by a postulated isopeptide bond to a small protein that probably was of host origin. The host-derived moiety of H protein is shown here to be ubiquitin, most probably coupled to the coat protein at lysine 53. This finding is based on microsequencing of the H protein, and is substantiated by immunoblotting analysis with antibodies to human ubiquitin. Conjugated ubiquitin was detected in virions of all five strains of the virus tested. To our knowledge, this is the first report of a ubiquitinated viral structural protein.

The use of thermally activated tritium atoms for structural-biological investigations: the topography of the TMV protein-accessible surface of the virus.

Thermally activated tritium atoms were used for studying the topography of the TMV protein-accessible surface of the virus. The accessibility profile of amino acid residues in a protein polypeptide chain was determined from data on the intramolecular distribution of a tritium label in the TMV protein. It was shown that tryptic peptides T3, T4, T12, the N-terminal region of peptide T1 and the proximal tryptic peptide T8 (located 20 to 25 A (1 A = 0.1 nm) from the viral axis) are accessible to tritium labelling. The fact of tritiation of the viral RNA was detected as well. This evidence was compared with the high-resolution X-ray analysis data for the TMV. A model is suggested to explain the exposure of the buried sites of the virus to thermally activated tritium atoms. The possibilities and limitations of this method in studying the surface topography of proteins in supramolecular systems as well as for location of protein antigenic regions are discussed.

Determination of reaction volumes and polymer distribution characteristics of tobacco mosaic virus coat protein.

A method that allows the quantitative determination of reaction volumes from sedimentation velocity experiments in an analytical ultracentrifuge is presented. Combined with a second method for detecting pressure-induced depolymerization, general characteristics of polymer distributions may be probed. We show that it is possible to determine if a sample is in an equilibrium or metastable state of subunit association. Our approach to probe macromolecular aggregation systems by small pressure perturbations is not restricted to the use of centrifuges. This method has been applied to characterize certain aspects of the polymerization of tobacco mosaic virus coat protein (TMVP). There are at least two helical polymer conformations in RNA-free coat protein rods. The smaller, helix I, polymers are limited to sizes below about 70 subunits (four to five helical turns) and undergo some kind of cooperative conformational change before further subunits may be added indefinitely. In contrast to helix I, the larger helix II polymers occur as broader and skewed size distributions. Under moderately strong polymerization conditions, the equilibrium state can contain both types of helical rods. The reaction volume for the addition of trimers is -220 ml/mol for both types of helical polymers. These results are compared with the results of previous thermodynamic analyses of TMVP polymerization.

Correlation of co-ordinated amino acid substitutions with function in viruses related to tobacco mosaic virus.

Sequence data are available for the coat proteins of seven tobamoviruses, with homologies ranging from at least 26% to 82%, and atomic co-ordinates are known for tobacco mosaic virus (TMV) vulgare. A significant spatial relationship has been found between groups of residues with identical amino acid substitution patterns. This strongly suggest that their location is linked to a particular function, at least in viruses identical with the wild-type for these residues. The most conserved feature of TMV is the RNA binding region. Core residues are conserved in all viruses or show mutations complementary in volume. The specificity of inter-subunit contacts is achieved in different ways in the three more distantly related viruses.

On the theoretical prediction of protein antigenic determinants from amino acid sequences.

The applicability range of a modified version of the Hopp-Woods model for the determination of protein antigenic determinants is estimated by comparing experimental data based on monoclonal and polyclonal antibodies. The results indicate a close correlation between the hydrophilicity of protein regions and their antigenicity. The efficiency of various hydrophilicity/hydrophobicity scales for the amino acid side chains is tested. A comment on the recognition factor concept of Fraga is given.

Oligonucleotide binding to the coat protein disk of tobacco mosaic virus. Possible steps in the mechanism of assembly.

Binding of the oligoribonucleotides AAG, AAGAAG and AAGAAGUUG to the disk aggregate of tobacco mosaic virus coat protein has been studied in solution under conditions favourable for virus assembly. The two longer oligomers bind strongly with Kd around 1 microM, approach complete saturation of binding sites and cause the formation of long, nicked helical rods resembling the virus. It is suggested that the binding of these oligomers, with sequences chosen from the assembly origin of the viral RNA, simulates the tobacco mosaic virus assembly process. No binding could be detected for AAG, indicating that chain length is a crucial determinant in the interaction. The binding of AAGAAG to coat protein crystals is very much weaker than that observed in solution, and the crystals crack at high oligomer concentrations. The corresponding oligodeoxyribonucleotide, d(AAGAAG), shows no binding to the protein in solution; the interaction is extremely specific for RNA.

Sedimentation equilibrium measurements of the intermediate-size tobacco mosaic virus protein polymers.

Short-column sedimentation equilibrium methods have been applied for the first time to tobacco mosaic virus (TMV) protein (0.1 M ionic strength orthophosphate) at pH 6.5 and at pH 7.0 to estimate molecular weights. Previous sedimentation velocity experiments at pH 6.5, 20 degrees C have led to the conclusion that the major boundary with an S0(20),w value of 24.4 +/- 0.1 S consists of a distribution of polymers which are mainly three-turn, 48-51-subunit helical rod aggregates. The directly measured z-average molecular weights together with sedimentation velocity data are entirely consistent with this assignment of a three-turn aggregate. Molecular weights have also been determined under two conditions where a large mass fraction of the protein sediments with an S0(20),w value of 20.3 +/- 0.2 S. At pH 6.5, 6-8 degrees C, the aggregates in this boundary are metastable and correspond to 50-60% of the preparation. At pH 7.0, 20 degrees C at equilibrium, 65-75% of the protein sediments at 20.3 S. The 20.3S boundary is very similar under both conditions and is interpreted as being composed of a distribution of protein aggregates centered about 39 +/- 2 subunits. This result is important in the interpretation of previous kinetic measurements of TMV self-assembly. The current view is that the 34-subunit structure of TMV protein, in the form of a cylindrical disk which is made up of two 17-subunit layers and has been characterized in single-crystal X-ray diffraction studies, plays a central role in the initial binding steps with RNA. The present results are not consistent with the view that there is a significant concentration of the TMV protein disk structure in solution under the usual conditions of TMV self-assembly.

Sindbis virus proteins nsP1 and nsP2 contain homology to nonstructural proteins from several RNA plant viruses.

Although the genetic organization of tobacco mosaic virus (TMV) differs considerably from that of the tripartite viruses (alfalfa mosaic virus [AlMV] and brome mosaic virus [BMV]), all of these RNA plant viruses share three domains of homology among their nonstructural proteins. One such domain, common to the AlMV and BMV 2a proteins and the readthrough portion of TMV p183, is also homologous to the readthrough protein nsP4 of Sindbis virus (Haseloff et al., Proc. Natl. Acad. Sci. U.S.A. 81:4358-4362, 1984). Two more domains are conserved among the AlMV and BMV 1a proteins and TMV p126. We show here that these domains have homology with portions of the Sindbis proteins nsP1 and nsP2, respectively. These results strengthen the view that the four viruses share mechanistic similarities in their replication strategies and may be evolutionarily related. These results also suggest that either the AlMV 1a, BMV 1a, and TMV p126 proteins are multifunctional or Sindbis proteins nsP1 and nsP2 function together as subunits in a single complex.

Fluorescent monitoring of proteins during sodium dodecyl sulfate-polyacrylamide gel electrophoresis and Western blotting.

Fluorescent labeling of proteins was found to be a very sensitive and reliable alternative to conventional methods for monitoring proteins on Western blots. Proteins were labeled with 2-methoxy-2,4-diphenyl-3(2H)-furanone (MDPF) before SDS-PAGE. After electrophoresis and subsequent electro-blotting the fluorescent-labeled proteins were visible upon ultraviolet illumination of the nitrocellulose membranes, and could be photographed to yield an accurate record of the blots before subsequent serological analysis. The sensitivity for detecting MDPF-labeled proteins on nitrocellulose was 100-200 ng, 50 to 100 fold less sensitive than on gels. Fluorescent-labeled TMV and MStpV capsid proteins that were blotted onto nitrocellulose still reacted in serological tests and were detected when present in quantities as low as 100 pg. Fluorescent labeling allows accurate photographic records of the SDS-gel, blot and probed blot using only one sample, and no subsequent staining steps are required.

[Analysis of polypeptides of virus-specific informosomes induced by tobacco mosaic virus and potato virus X]. / Analiz polipeptidov virusspetsificheskikh informosom, indutsiruemykh virusom tabachnoi mozaiki i X-virusom kartofelia.

Informosome-like virus-specific ribonucleoprotein (vRNP) of tobacco mosaic virus (TMV) comprise a set of four major polypeptides having molecular weights of 17 500, 31 000, 37 000 and 39 000. Of the minor polypeptides, those of apparent molecular weights 25 000, 55 000, 68 000 and 70 000 had electrophoretic mobilities of polypeptides found in a ribonucleoprotein preparation from uninoculated plants. Polypeptide with mol.wt. 175 000 is TMV coat protein so far as: a) vRNP was precipitated with immunoglobulins against TMV and TMV coat protein; b) it had electrophoretic mobility similar to mobility of TMV coat protein; c) the peptide map of polypeptides with mol.wts 31 000, 37 000 and 39 000 are probably virus-specific-products. This is supposed because they are not present in cell informosomes protein, and they are not revealed in vRNP induced in cells after infection with potato virus X (PVX). Electrophoresis of vRNP-PVX protein reveals polypeptides of 23 000 (PVX coat protein), 55 000, 70 000, 78 000, 95 000, 120 000 and 145 000.

31P nuclear magnetic resonance of the RNA in tobacco mosaic virus.

Solid state 31P n.m.r. data concerning the structure of the RNA in TMV are presented in light of the prior diffraction and model building results on this system (Stubbs et al., 1977; Stubbs & Stauffacher, 1981). The 31P chemical shift anisotropy powder pattern of a stationary, unoriented solution of TMV shows the RNA to be immobilized by the coat protein-RNA interactions, since the principal values (sigma 11 = 83, sigma 22 = 25, sigma 33 = -108 p.p.m. relative to external 85% H3PO4) are essentially the same as those of a static phosphodiester group. There are three peaks in the isotropic 31P n.m.r. spectrum obtained with magic angle sample spinning, indicating three distinct phosphate environments. There are three peaks in the 31P n.m.r. spectrum from an oriented TMV solution, indicating three distinct phosphate orientations.

Calcium ion binding by isolated tobacco mosaic virus coat protein.

Calcium ion titrations were performed on solutions of tobacco mosaic virus coat protein using a calcium-specific ion-exchange electrode. Isolated coat protein was found incapable of binding calcium ions under equilibrium conditions at pH values above its iso-ionic point (pH 4.3 to 4.6). However, calcium ions were found to bind to coat protein under non-equilibrium conditions, which suggests that the isolated coat protein has the proper conformation to bind calcium ions at the iso-ionic point.

Calcium and potassium ion binding by tobacco mosaic virus ribonucleic acid.

Calcium and potassium ion titration experiments were performed on solutions of tobacco mosaic virus RNA using ion-specific electrodes. The data obtained were analyzed using Scatchard and Klotz plots for the number of binding sites per nucleotide (n), and the apparent stability constant for complex formation, beta Me. The experimental design also allowed for the determination of the number of protons released per metal ion bound, chi. The calcium ion titration in water yielded values of 0.45 for n, 6.03 for log beta Ca and 0.24 for chi. When this titration was repeated in 0.01 M-KCl, the values were found to be 0.11 for n, 5.08 for log beta Ca and zero for chi. An aqueous potassium titration was also performed, with values for n, log beta K and chi of 0.25, 2.96 and less than 0.10, respectively.

Nucleotide sequence and its character of cistron coding for the 30 K protein of tobacco mosaic virus (OM strain).

The nucleotide sequence of cloned cDNA copies of the common strain of tobacco mosaic virus RNA corresponding to the 2,000 nucleotides at the 3'-end was determined. The 30 K protein cistron was revealed to be located at residues 687-1,493 from the 3'-end. The 30 K protein is composed of 267 amino acids and is probably a basic protein. The 5' flanking regions of both the coat protein and the 30 K protein cistrons were very U-rich, and a homology was found between the sequence around the capping site of the coat protein mRNA and the sequence upstream from the 30 K protein cistron.

Classification of several tobamoviruses isolated in China on the basis of the amino acid composition of their virion proteins.

The amino acid compositions of the virion proteins of several tobamoviruses isolated in China were determined. A classification computed from these and published data of other tobamoviruses was compared with published data of their relatedness assessed using the cDNA:RNA molecular hybridization technique. The classifications are clearly congruent; that based on amino acid composition appears to be best for determining the hierarchical relationships of members within a taxonomic group, rather than for distinguishing between closely related members, whereas nucleic acid hybridization unequivocally places a virus into the appropriate subgroup but is less useful for determining distant relationships.

[Study of three-dimensional structure of proteins by means of tritium labeling. I. Free amino acids as a model of residues in an unfolded polypeptide chain]. / Issledovanie prostranstvennoi struktury belkov pri pomoshchi tritievoi metki. I. Svobodnye aminokisloty kak model' ostatkov v razvernutoi polipeptidnoi tsepi.

Probabilities of the incorporation of tritium label into various amino acids with alanine as a standard have been determined by "bombing" solid targets with a 3H-atom beam (2 000 K). The results show that amino acids can be used with sufficient accuracy as models of amino acid residues in a polypeptide chain under 100%, accessibility. The resulting coefficients, if taken into consideration in the analysis of intramolecular distribution of tritium in short tryptic peptides of TMV protein, will yield an equiprobable distribution in the case when the label has been introduced into a peptide. The distribution is not uniform, however, if a labelled peptide has been isolated from an "irradiated" hydrolysate protein.

Surface activation of carbon film supports for biological electron microscopy.

The effect of glow-discharging on naked carbon-filmed grids has been evaluated. The effect of different locations of the grids within a DC discharge, operated in the normal glow, was analyzed by applying various biological specimens to the grids. Two locations were found to give consistent results: (a) in Crookes dark space, particulate specimens, negatively stained, spread evenly--suggesting a new negative surface charge of the support; (b) below the anode, nucleic acids, selectively (positively) stained, appeared as well spread filaments, indicating a net positive surface charge.