Small angle X-ray scattering studies on local structure of tobacco mosaic virus RNA in solution.

Effects of temperature and ionic strength (S) on the local structure of tobacco mosaic virus RNA in phosphate buffer solution are studied by analyzing the small-angle X-ray scattering (SAXS) curves. The root-mean-square radius of a cross-section of RNA chain was kept at 0.845+/-0.005 nm over a wide range of S from 0.2 to 0.003 at 20 degrees C, whereas it gradually diminished from 0.85 to 0.61 nm when the temperature is raised from 20 to 50 degrees C at S = 0.2. Nevertheless, all of SAXS curves reflecting the backbone structures were equally mimicked by theoretical ones of freely hinged rod (FHR) models, i.e. several straight rods joined with freely hinged joints in the form of a combination of the letter Y, if the constituent rod lengths in the models are adjusted. From these facts, it is suggested that the local structure of the RNA chain in aqueous solution is characterized by an essential feature that unpaired bases in the partially double-stranded helix are constantly far isolated from each other along the helix and the rod-like structure of the helix is preserved over a range of helical contents. Such a characteristic local structure of the chain is entirely collapsed in the formamide solution at 50 degrees C.

Differences of reconstitution process between tobacco mosaic virus and cucumber green mottle mosaic virus by synchrotron small angle X-ray scattering using low-temperature quenching.

The differences of the reconstitution process of tobacco mosaic virus (TMV) and its mutant, cucumber green mottle mosaic virus (CGMMV) were investigated by the solution X-ray scattering measurements with the synchrotron radiation source using low-temperature quenching. The reconstitution in an aqueous solution is completely stopped below 5 degrees C. The TMV and CGMMV assembly was traced by the small-angle X-ray scattering (SAXS) measurements at 5 degrees C on a series of solutions prepared by low-temperature quenching after incubation at 20 degrees C for an appropriate interval between 0 and 60 min. The SAXS results were analyzed by the Guinier plot, the Kratky plot and the distance distribution function. The incubation of RNA and protein of CGMMV did not reconstitute at the initial reaction stages below 5 min and then began to reconstitute gradually. After 60 min, the radius of gyration for CGMMV reconstitution process reached almost the value for the initial stage of TMV reconstitution process. This is due to the fact the formation of double-layered disk in CGMMV protein is much slower than in TMV protein.

Structural analysis of A-protein of cucumber green mottle mosaic virus and tobacco mosaic virus by synchrotron small-angle X-ray scattering.

The size and shape of A-protein of tobacco mosaic virus coat protein (TMVP) and cucumber green mottle mosaic virus coat protein (CGMMVP) were evaluated by means of small-angle X-ray scattering (SAXS) using a synchrotron radiation source, complemented by electron microscopic observations. The results imply that TMV and CGMMV A-proteins are composed of three and two subunits, respectively, stacked in the shape of an isosceles triangular prism at lower ionic strength. Considering the difference of the A-protein structure at higher and lower ionic strength, the globular core structure was proposed as a subunit which might be modeled as a thin isosceles triangular prism composed of four globular cores joined by rather flexible segments. These cores correspond probably to four helical regions in a subunit, and rearrange their relative positions according to the external conditions. A slight rearrangement of core positions in a subunit may result in the formation of A-proteins of various shapes.

Solution X-ray scattering study of reconstitution process of tobacco mosaic virus particle using low-temperature quenching.

The reconstitution process of tobacco mosaic virus (TMV) was investigated by the solution X-ray scattering measurements with the synchrotron radiation source using low-temperature quenching. TMV assembly in an aqueous solution is completely stopped below 5 degrees C. The TMV assembly was traced by the small-angle X-ray scattering (SAXS) measurements at 5 degrees C on a series of solutions prepared by low-temperature quenching after incubation either at 15, 20 or 25 degrees C for an appropriate interval between 0 and 60 min. The SAXS results were analyzed by the Guinier plot, the Kratky plot and the distance distribution function. In order to account the time course of SAXS profiles in terms of the elongation of TMV assembly, a model calculation was performed to simulate the Guinier plot, the Kratky plot and the distance distribution function by applying Glatter's multibody method using models that were constituted of the spheres representing a column of piled two-layer disks of TMV-protein. The three simulated functions thus obtained support the conclusion derived from the three functions calculated from the experimental results that the incubation of the RNA and protein of TMV began to reconstitute TMV instantly after mixing, proceeded steeply to a long rod, and then extended asymptotic to the full length of the TMV particle. This process is in good agreement with that obtained from electron microscopic studies.

Self-assembling process of cylindrical virus coat proteins as observed by synchrotron small-angle X-ray scattering.

The self-assembly process of cucumber green mottle mosaic virus (CGMMV) protein and tobacco mosaic virus (TMV) protein was examined by the thermodynamic analysis of small-angle X-ray scattering (SAXS) data. Each polymerization step of the coat proteins was assumed to be specified by a single equilibrium constant, and the equilibrium constant was evaluated by fitting the size and shape of the constituents observed by SAXS to those calculated from an assumed polymerization scheme. The logarithmic plots of the equilibrium constant against the inverse of temperature were fitted with a straight line at each buffer concentration and the thermodynamic quantities were evaluated from its intercept (yielding entropy) and slope (yielding enthalpy). The enthalpy and entropy values of TMV protein were found to be independent of buffer concentration, whereas those of CGMMV protein depended strongly on buffer concentration. In the limit, as ionic strength tends to infinity, both the enthalpy and entropy values of CGMMV protein approach those of TMV protein. The higher negative surface charge of CGMMV protein is considered to be responsible for the formation of stable single-layered disks, and for the slow polymerization process even at higher temperature and higher buffer concentrations.

Dynamic mechanism of the self-assembly process of tobacco mosaic virus protein studied by rapid temperature-jump small-angle X-ray scattering using synchrotron radiation.

The self-assembly process of tobacco mosaic virus protein (TMVP) was observed by rapid temperature-jump time-resolved solution X-ray small-angle scattering using synchrotron radiation. The temperature-jump device used for the X-ray measurements is rapid enough to cope with even the fastest-assembling process of TMVP, and accumulates data of reasonable signal-to-noise ratios with a minimum total counting time of 7.5 seconds. The measurements suggested that the 20 S disk of TMVP polymerized to stacked disks (short rods). The time to complete stacking varied from approximately 25 seconds to approximately 1200 seconds, depending on the solution condition and magnitude of the temperature gap. Higher protein concentration, ionic strength and temperature favoured faster association. The results were analysed in terms of a set of kinetic equations that describe the two-stage aggregation of TMVP with an equilibrium constant K1, and two rate constants k+2 and k-2 for association and dissociation of disks, respectively. The consistency of the analysis suggests that the TMVP assembly proceeds in two steps of: (1) the aggregation of A-proteins into double-layered disks; and (2) the stacking of double-layered disks. The kinetic analysis indicated that the stacking belongs to the lowest range of protein-protein interaction system.

Role of cysteine residues in tryptophanase for monovalent cation-induced activation.

We cloned and sequenced the tryptophanase structural gene of Escherichia coli B/1t7-A strain. The results indicate that tryptophanase proteins of E. coli B/1t7-A and K-12 are identical. When cysteine residues in tryptophanase were chemically modified with 5,5'-dithiobis (2-nitrobenzoic acid) (DTNB), the stabilizing effect of the active cations such as K+ and NH4+ was abolished. In consideration of our previous results that Cys-298 was selectively modified by SH reagents [Honda T. et al. (1986) J. Chromatogr. 371, 353-360], Cys-298 seems to have a close relation to the expression of the effect of monovalent cations. Fluorescence decay measurement of the holoenzyme revealed that the fluorescence lifetime derived from the coenzyme, pyridoxal 5'-phosphate (PLP), was dependent on coexisting monovalent cations, whereas that of the tryptophyl residue was not, in either the apo- or the holoenzyme preparation. The results of the synchrotron small-angle X-ray scattering measurements showed that radii of gyration which reflect the size and shape of the enzyme were constant at around 38 A irrespective of the presence or absence of the K+ ion. These results suggest that the monovalent cations interact specifically with the PLP-binding site, and that the conformational change of enzyme protein caused by the monovalent-cation binding is limited to a small range. The above results are compatible with the possibility that Cys-298 is involved in the formation of "monovalent cation binding site" in the holoenzyme.

Temperature dependence of the structure of aggregates of tobacco mosaic virus protein at pH 7.2. Static synchrotron small-angle X-ray scattering.

The small-angle X-ray scattering (SAXS) method using a synchrotron radiation source was applied to the study of the self-aggregation process of tobacco mosaic virus protein (TMVP) at a concentration of 5.0 or 12.0 mg ml-1 in 50 mM or 100 mM-phosphate buffer (ionic strengths approx. 0.1 and 0.2, respectively) at pH 7.2 in the temperature region of 4.8 to 25.0 degrees C. This paper presents the results of static measurements of SAXS. Sedimentation velocity experiments were performed simultaneously under the same conditions. These results are qualitatively parallel to those of the SAXS measurements, although the size of stacked disks derived from the SAXS measurements is larger than that derived from the sedimentation experiments, suggesting a change in the equilibrium conditions in the centrifugal field. Qualitative analysis of the SAXS data with model simulation calculations implies that the aggregation of TMVP consists of two steps: (1) the aggregation of A-protein comprising a few subunits to form double-layered disks; and (2) the random polymerization of double-layered disks by disk-stacking. Increase in temperature, ionic strength or protein concentration induced TMVP to polymerize to form a double-layered disk or a quadruple-layered short rod with consumption of A-proteins, accompanied by a small number of multi-layered short rods. The SAXS results indicate that the A-protein and the multilayered short rods are polydisperse with respect to size and shape, i.e. the mixture of A-protein, double-layered disks and multi-layered short rods coexists in the equilibrium state without pressure-induced partial dissociation of TMPV as observed during normal ultracentrifugation, and even under solution conditions in which the formation of double-layered disks or higher-order aggregates is favored.

Micellar structure of beta-casein observed by small-angle X-ray scattering.

The small-angle X-ray scattering was observed from beta-casein micelles in 0.2 M phosphate buffer (pH 6.7) with varying temperatures. An oblate ellipsoid of a rigid core with a thin soft layer was proposed as a probable model of the beta-casein micellar structure, according to the results of the model optimization with simple triaxial bodies. Here the axial ratio was found to decrease and the micelle to become spherical when the polymerization proceeds with temperature. The consistency of the present model was examined with the results of hydrodynamic measurements published previously.

X-ray scattering study on hemoglobin solution with synchrotron radiation: a simple analysis of scattering profile at moderate angles in terms of arrangement of subunits.

X-ray scattering profiles in moderate-angle regions were recorded from carbon-monoxy-, oxy-, and deoxyhemoglobin solutions, using synchrotron radiation. They all display four distinct scattering peaks at R = 0.030, 0.055, 0.078, and 0.102 A-1 up to 2 theta approximately 10 degrees in addition to the main scattering around R approximately equal to 0. Contrast variation experiments, in which sucrose was used to change the electron density level of the solvent, revealed that the outer two scattering peaks are attributable to the variation of electron density within subunits in hemoglobin. The inner two were assigned as peaks due to the whole molecule and interpreted in terms of an interference function that is calculated from the inter-subunit distances in a molecule. This result is important in connection with evaluating the arrangement of constituent subunits in allosteric proteins and oligomeric proteins. The scattering profiles indicate that there is no difference in electron density variation within subunits between oxy- and deoxyhemoglobin. However, the arrangement of subunits is different between oxy- and deoxyhemoglobin molecules, as the scattering peaks at R = 0.030 and 0.055 A-1 shift toward smaller angles for deoxyhemoglobin.

Aggregation of bovine serum albumin upon cleavage of its disulfide bonds, studied by the time-resolved small-angle X-ray scattering technique with synchrotron radiation.

A rapid mixing system of the stopped-flow type, used with small-angle X-ray scattering equipment using synchrotron radiation, is described. The process of aggregation of bovine serum albumin was traced with a time interval of 50 s, initiated upon cleavage of its disulfide bonds by reduction with dithiothreitol. The results indicate that a 218-fold molar excess of dithiothreitol over the number of moles of disulfide bonds in bovine serum albumin is sufficient to initiate the reaction immediately after mixing, which reaches equilibrium in about 15 min. On the other hand, half this amount is not sufficient to initiate the reaction, so that the reaction is delayed by about 150 s. Such a single-shot time-resolved experiment showed that experiments with a time interval of 100 ms are possible with repeated multi-shot runs.

Fiber-structured material in a fraction of Bacillus subtilis.

The paracrystal fractions of two species of Bacillus contain similarly structured fibrous material whose unit cell is hexagonal, with cell dimensions of a = 0.719 nm and c = 0.963 nm.