E. N. Dobrov

Kinetics of Thermal Aggregation of Tobacco Mosaic Virus Coat Protein

The kinetics of thermal aggregation of coat protein (CP) of tobacco mosaic virus (TMV) have been studied at 42 and 52°C in a wide range of protein concentrations, [P]0. The kinetics of aggregation were followed by monitoring the increase in the apparent absorbance (A) at 320 nm. At 52°C the kinetic curves may be approximated by the exponential law in the range of TMV CP concentrations from 0.02 to 0.30 mg/ml, the first order rate constant being linearly proportional to [P]0 (50 mM phosphate buffer, pH 8.0). The analogous picture was observed at 42°C in the range of TMV CP concentrations from 0.01 to 0.04 mg/ml (100 mM phosphate buffer, pH 8.0). At higher TMV CP concentrations the time of half-conversion approaches a limiting value with increasing [P]0 and at sufficiently high protein concentrations the kinetic curves fall on a common curve in the coordinates {A/Alim; t} (t is time and Alim is the limiting value of A at t → ∞). According to a mechanism of aggregation of TMV CP proposed by the authors at rather low protein concentrations the rate of aggregation is limited by the stage of growth of aggregate, which proceeds as a reaction of the pseudo-first order, whereas at rather high protein concentrations the rate-limiting stage is the stage of protein molecule unfolding.

Tritium planigraphy study of structural alterations in the coat protein of Potato virus X induced by binding of its triple gene block 1 protein to virions

Alterations in Potato virus X (PVX) coat protein structure after binding of the protein, encoded by the first gene of PVX triple gene block (triple gene block 1 protein, TGBp1), to the virions were studied using tritium planigraphy. Previously, it has been shown that TGBp1 molecules interact with the PVX particle end, containing the 5′‐terminus of PVX RNA, and that this interaction results in a strong decrease in virion stability and its transformation to a translationally active state. In this work, it has been shown that the interaction of TGBp1 with PVX virions leads to an increase of ∼ 50% in tritium label incorporation into the 176–198 segment of the 236‐residue‐long PVX coat protein subunit, with some decrease in label incorporation into the N‐terminal coat protein region. According to the new ‘sandwich’ variant of our recently proposed model of the three‐dimensional structure of the intravirus PVX coat protein, the 176–198 segment is assigned to the β‐sheet region located at the subunit surface, presumably participating in coat protein interactions with the intravirus RNA and/or in protein–protein interactions, whereas the N‐terminal coat protein region corresponds to the other part of the same β‐sheet. For the remaining segments of the PVX coat protein subunit, no significant difference between tritium incorporation into untreated and TGBp1‐treated PVX was observed. A detailed description of the ‘sandwich’ version of the intravirus PVX coat protein model is presented.

A mechanism of macroscopic (amorphous) aggregation of the tobacco mosaic virus coat protein

To gain more insight into the mechanisms of heating-induced irreversible macroscopic aggregation of the tobacco mosaic virus (TMV) coat protein (CP), the effects of pH and ionic strength on this process were studied using turbidimetry, CD spectroscopy, and fluorescence spectroscopy. At 42 degrees C, the TMV CP passed very rapidly (in less than 15s) into a slightly unfolded conformation, presumably because heating disordered a segment of the subunit where the so-called hydrophobic girdle of the molecule resides. We suppose that the amino acid residues of this girdle are responsible for the aberrant hydrophobic interactions between subunits that initiate macroscopic protein aggregation. Its rate increased by several thousands of times as the phosphate buffer molarity was varied from 20 to 70 mM, suggesting that neutralization of strong repulsive electrostatic interactions of TMV CP molecules at high ionic strengths is a prerequisite for amorphous aggregation of this protein.

Determination of concentration and aggregate size in influenza virus preparations from true UV absorption spectra

Light scattering is known to make a considerable contribution to ultraviolet absorption spectra of influenza virus (Flu) preparations. We applied extrapolation to analysis of this contribution. Ultraviolet spectra were recorded and true extinction coefficients (A1 cm, 2800.1%) were determined in suspensions of intact virions of Flu strain Puerto Rico/8/34 and subviral particles obtained by bromelain digestion of the same strain (1.26 ± 0.17 and 0.96 ± 0.11 OD, respectively). This allowed simple and rapid measurement of virus concentration. It was shown that UV spectra allowed efficient monitoring of virion aggregation. The pH dependence of aggregation properties of influenza subviral particles was studied.

β-structure of the coat protein subunits in spherical particles generated by tobacco mosaic virus thermal denaturation

Conversion of the rod-like tobacco mosaic virus (TMV) virions into “ball-like particles” by thermal denaturation at 90–98 °C had been described by R.G. Hart in 1956. We have reported recently that spherical particles (SPs) generated by thermal denaturation of TMV at 94–98 °C were highly stable, RNA-free, and water-insoluble. The SPs were uniform in shape but varied widely in size (53–800 nm), which depended on the virus concentration. Here, we describe some structural characteristics of SPs using circular dichroism, fluorescence spectroscopy, and Raman spectroscopy. It was found that the structure of SPs protein differs strongly from that of the native TMV and is characterized by coat protein subunits transition from mainly (about 50%) α-helical structure to a structure with low content of α-helices and a significant fraction of β-sheets. The SPs demonstrate strong reaction with thioflavin T suggesting the formation of amyloid-like structures.

Spatial structure peculiarities of influenza A virus matrix M1 protein in an acidic solution that simulates the internal lysosomal medium

The structure of the C‐terminal domain of the influenza virus A matrix M1 protein, for which X‐ray diffraction data were still missing, was studied in acidic solution. Matrix M1 protein was bombarded with thermally‐activated tritium atoms, and the resulting intramolecular distribution of the tritium label was analyzed to assess the steric accessibility of the amino acid residues in this protein. This technique revealed that interdomain loops and the C‐terminal domain of the protein are the most accessible to labeling with tritium atoms. A model of the spatial arrangement of the C‐terminal domain of matrix M1 protein was generated using rosetta software adjusted to the data obtained by tritium planigraphy experiments. This model suggests that the C‐terminal domain is an almost flat layer with a three‐α‐helical structure. To explain the high level of tritium label incorporation into the C‐terminal domain of the M1 protein in an acidic solution, we also used independent experimental approaches (CD spectroscopy, limited proteolysis and MALDI‐TOF MS analysis of the proteolysis products, dynamic light scattering and analytical ultracentrifugation), as well as multiple computational algorithms, to analyse the intrinsic protein disorder. Taken together, the results obtained in the present study indicate that the C‐terminal domain is weakly structured. We hypothesize that the specific 3D structural peculiarities of the M1 protein revealed in acidic pH solution allow the protein greater structural flexibility and enable it to interact effectively with the components of the host cell.

Macroscopic Aggregation of Tobacco Mosaic Virus Coat Protein

The relationship between processes of thermal denaturation and heat-induced aggregation of tobacco mosaic virus (TMV) coat protein (CP) was studied. Judging from differential scanning calorimetry “melting” curves, TMV CP in the form of a trimer–pentamer mixture (“4S-protein”) has very low thermal stability, with a transition temperature at about 40°C. Thermally denatured TMV CP displayed high propensity for large (macroscopic) aggregate formation. TMV CP macroscopic aggregation was strongly dependent on the protein concentration and solution ionic strength. By varying phosphate buffer molarity, it was possible to merge or to separate the denaturation and aggregation processes. Using far-UV CD spectroscopy, it was found that on thermal denaturation TMV CP subunits are converted into an intermediate that retains about half of its initial α-helix content and possesses high heat stability. We suppose that this stable thermal denaturation intermediate is directly responsible for the formation of TMV CP macroscopic aggregates.

A comparative differential scanning calorimetric study of tobacco mosaic virus and of its coat protein ts mutant

The differential scanning calorimetry (DSC) ‘melting curves’ for virions and coat proteins (CP) of wild‐type tobacco mosaic virus (strain U1) and for its CP ts mutant ts21–66 were measured. Strain U1 and ts21–66 mutant (two amino acid substitutions in CP: I21 → T and D66 → G) differ in the type of symptoms they induce on some host plants. It was observed that CP subunits of both U1 and ts21–66 at pH 8.0, in the form of small (3–4S) aggregates, possess much lower thermal stability than in the virions. Assembly into the virus particles resulted in a DSC melting temperature increase from 41 to 72°C for U1 and from 38 to 72°C for ts21–66 CP. In the RNA‐free helical virus‐like protein assemblies U1 and ts21–66 CP subunits had a thermal stability intermediate between those in 3–4S aggregates and in the virions. ts21–66 helical protein displayed a somewhat lower thermal stability than U1.

Appearance of “β-Like” Circular Dichroism Spectra on Protein Aggregation That Is not Accompanied by Transition to β-Structure

CD spectra in the 200 to 250 nm spectral region for small ordered aggregates (trimers-pentamers) of tobacco mosaic virus (TMV) coat protein (CP) and for long virus-like helical aggregates of TMV CP were compared. It was found that small (4S) TMV CP aggregates have a CD spectrum typical of a protein with high α-helix content, which agrees well with results of X-ray diffraction studies. But in the long helical aggregates (and in the TMV virions) TMV CP gives “β-like” CD spectra similar to those of many other aggregated proteins. From X-ray diffraction data, it is well known that TMV CP subunits do not change their secondary or tertiary structure on assembly into virions or the helical repolymerized protein. Thus, the change in the shape of 200 to 250 nm CD spectra cannot be employed as the sole criterion of the conversion of a protein to β-structure in the course of aggregation.

Analysis of the role of the coat protein N-terminal segment in Potato virus X virion stability and functional activity

Previously, we have reported that intact Potato virus X (PVX) virions cannot be translated in cell-free systems, but acquire this capacity by the binding of PVX-specific triple gene block protein 1 (TGBp1) or after phosphorylation of the exposed N-terminal segment of intravirus coat protein (CP) by protein kinases. With the help of in vitro mutagenesis, a nonphosphorylatable PVX mutant (denoted ST PVX) was prepared in which all 12 S and T residues in the 20-residue-long N-terminal CP segment were substituted by A or G. Contrary to expectations, ST PVX was infectious, produced normal progeny and was translated in vitro in the absence of any additional factors. We suggest that the N-terminal PVX CP segment somehow participates in virion assembly in vivo and that CP subunits in ST virions may differ in structure from those in the wild-type (UK3 strain). In the present work, to test this suggestion, we performed a comparative tritium planigraphy study of CP structure in UK3 and ST virions. It was found that the profile of tritium incorporation into ST mutant virions in some CP segments differed from that of normal UK3 virions and from UK3 complexed with the PVX movement protein TGBp1. It is proposed that amino acid substitutions in ST CP and the TGBp1-driven remodelling of UK3 virions induce structural alterations in intravirus CPs. These alterations affect the predicted RNA recognition motif of PVX CP, but in different ways: for ST PVX, labelling is increased in α-helices 6 and 7, whereas, in remodelled UK3, labelling is increased in the β-sheet strands β3, β4 and β5.