Yuzuru Hiragi

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.

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

Abstract The small-angle X-ray scattering was observed from β-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 β-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.

A Helical String of Alternately Connected Three-Helix Bundles for the Cell Wall-Associated Adhesion Protein Ebh from Staphylococcus aureus

The 1.1 MDa cell-wall-associated adhesion protein of staphylococci, Ebh, consists of several distinct regions, including a large central region with 52 imperfect repeats of 126 amino acid residues. We investigated the structure of this giant molecule by X-ray crystallography, circular dichroism (CD) spectrometry, and small-angle X-ray scattering (SAXS). The crystal structure of two repeats showed that each repeat consists of two distinct three-helix bundles, and two such repeats are connected along the long axis, resulting in a rod-like structure that is 120 A in length. CD and SAXS analyses of the samples with longer repeats suggested that each repeat has an identical structure, and that such repeats are connected tandemly to form a rod-like structure in solution, the length of which increased proportionately with the number of repeating units. On the basis of these results, it was proposed that Ebh is a 320 nm rod-like molecule with some plasticity at module junctions.

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.

Statistical procedure for deconvoluting experimental data

A general procedure of the deconvolution of noisy experimental data is proposed. The deconvoluted solution is represented in terms of a cubic spline function f(x) with variable knots. The value of parameters and the location of knot points in the spline are determined by solving the nonlinear least‐squares problem of fitting g(x)=∫κ(τ)f(s(τ,x))dτ to the data, where experimental data g(x) represent the convolution of f[s(τ,x)] with an apparatus weighting function k(τ) and s(τ,x) is a function related to the configuration of the experimental system. The profile of the fitted solution varies widely with different choices of the number and position of knots in the spline. To obtain a good solution, the optimum number of knots is determined based on the data by applying minimum Akaike’s Information Criterion procedure. Practical application of the variable‐knot spline is generally considered to be rather intricate. However, by taking advantage of an advanced technique of a quasi‐Newton method, the nonlinear least‐squares problem becomes tractable, and excellent smoothing in the deconvoluted solution can be achieved.

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.

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, complemeted 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.

Temperature‐jump apparatus and measuring system for synchrotron solution x‐ray scattering experiments

A rapid temperature‐jump (T‐J) device was designed for the kinetic measurements of small‐angle x‐ray scattering from solutions of biological macromolecular systems. The dead time of the apparatus is reduced to a few hundred milliseconds. The structural change of biological macromolecules in solutions can be monitored in the time scale of a few hundred milliseconds by the synchrotron small‐angle x‐ray scattering with a combination of a CAMAC data‐acquisition system and the present T‐J apparatus.

Direct detection of the protein quaternary structure and denatured entity by small-angle scattering: guanidine hydrochloride denaturation of chaperonin protein GroEL

A change in the higher-order structure of an oligomeric protein is directly detectable by small-angle scattering. A small-angle X-ray scattering (SAXS) study of the denaturation process of the chaperonin protein GroEL by guanidine hydrochloride (GdnHCl) showed that the disappearance of the quaternary structure can be monitored by using a Kratky plot of the scattered intensities, demonstrating the advantage of the SAXS method over other indirect methods, such as light scattering, circular dichroism (CD), fluorescence and sedimentation. The collapse of the quaternary structure was detected at a GdnHCl concentration of 0.8 M for a solution containing ADP (adenosine diphosphate)/Mg2+(2 mM)/K+. From pairwise plots of the change in forward scattering intensity J(0)/C (weight-average molecular weight) and the z-average (root mean square) radius of gyration against the GdnHCl concentration, the stability and nature of the denatured protein can be determined. The SAXS results suggest that the GroEL tetradecamer directly dissociates to the unfolded coil without going through a globular monomer state. The denatured ensemble is not a single unfolded monomer coil particle, but some mixture of entangled aggregates and a monomer of the coil molecules. Small-angle scattering is a powerful method for the detection and study of changes in quaternary and higher-order structures of oligomeric proteins.

SAXSANA: an interactive program for the analysis and monitoring of static and time-resolved small-angle X-ray solution scattering measurements.

An interactive analytical program, SAXSANA, for small-angle X-ray scattering measurements of solutions is described. The program processes scattered data without disciplined knowledge of small-angle scattering. SAXSANA also assists in finding the best experimental conditions, thus avoiding blind runs of experiments. SAXSANA consists of the following procedures: (i) determination of the centre of scattered X-rays and moment transfer Q (Q = 4pisintheta/lambda, where 2theta is the scattering angle and lambda is the wavelength) for each measured channel; (ii) conversion of the data format to the format of Q versus scattered intensities J(Q); (iii) truncation of unnecessary data and smoothing of scattering curves by cubic-spline function; (iv) correction of the absorption effect and subtraction of the scattered intensity of the buffer (solvent) solution from that of the sample solution; (v) creation of a data file for a three-dimensional representation of time-resolved scattering curves; (vi) determination of radii of gyration by Guinier plots; (vii) determination of persistent lengths by Kratky plots; (viii) extrapolation of the small-angle part by Guinier plots; (ix) extrapolation of the wide-angle part by Porods & Luzzatis laws for the Hankel transformation in order to obtain the distance distribution function p(r); (x) calculation of p(r) and computation of the invariant, the chord length, the Volume, the spherical radius, the maximum dimension D(max) and the radius of gyration (Rg). SAXSANA also serves as an on-site monitor for the validity of an experimental result during the measurements.