Pressure-jump small-angle x-ray scattering detected kinetics of staphylococcal nuclease folding

The kinetics of chain disruption and collapse of staphylococcal nuclease after positive or negative pressure jumps was monitored by real-time small-angle x-ray scattering under pressure. We used this method to probe the overall conformation of the protein by measuring its radius of gyration and pair-distance-distribution function p(r) which are sensitive to the spatial extent and shape of the particle. At all pressures and temperatures tested, the relaxation profiles were well described by a single exponential function. No fast collapse was observed, indicating that the rate limiting step for chain collapse is the same as that for secondary and tertiary structure formation. Whereas refolding at low pressures occurred in a few seconds, at high pressures the relaxation was quite slow, approximately 1 h, due to a large positive activation volume for the rate-limiting step for chain collapse. A large increase in the system volume upon folding implies significant dehydration of the transition state and a high degree of similarity in terms of the packing density between the native and transition states in this system. This study of the time-dependence of the tertiary structure in pressure-induced folding/unfolding reactions demonstrates that novel information about the nature of protein folding transitions and transition states can be obtained from a combination of small-angle x-ray scattering using high intensity synchrotron radiation with the high pressure perturbation technique.     

The supramolecular organization of oxyhemoglobin in erythrocytes. A small-angle x-ray scattering study]

From X-ray scattering diagrams of concentrated solutions of hemoglobin the pair-correlation function of the molecules is calculated. At a concentration of 324 g/l the distance between neighbouring molecules amounts to 65 A. The number of direct neighbours of one molecule is 9. The pair-correlation function cannot be described by the assumption of a lattice-cell-model; therefore, a lattice-vacancy-model with fluid order is proposed.     

CD and small-angle x-ray scattering of silk fibroin in solution

We investigated the structure of silk fibroin dissolved in water and in water-organic solvent mixtures by CD and small-angle x-ray scattering (SAXS). CD spectra indicated a disordered secondary structure in water and a beta-sheet conformation in aqueous organic solvents, such as methanol, dioxane, and trifluoroethanol (in trifluoroethanol a transient form evolving toward beta-sheet conformation was seen just after dissolution). The SAXS technique indicated the presence of fibroin particles of lamellar shape. The molecular weight was 188,000 daltons in water and 302,000 daltons in aqueous methanol.     

Uncoupled-induced changes in mitochondrial structure detected by small-angle x-ray scattering

Small-angle X-ray scattering data suggest that major but reversible rearrangements of mitochondrial inner membrane structure are induced by uncouplers. Low levels of 2,4-dinitrophenol (10 micronM) cause a perceptible wide-angle shift of the 20 mrad X-ray scattering maximum characteristic of intact liver mitochondria. Higher dinitrophenol concentrations (greater than 25 micronM) reduce this scattering maximum to one-third its initial intensity. In terms of mitochondrial function, the former scattering change appears to correlate with the uncoupling of oxidative phosphorylation while the latter occurs in the course of dinitrophenol stimulation of mitochondrial ATPase activity.     

Improving protein template recognition by using small-angle x-ray scattering profiles

Small-angle x-ray scattering (SAXS) is able to extract low-resolution protein shape information without requiring a specific crystal formation. However, it has found little use in atomic-level protein structure determination due to the uncertainty of residue-level structural assignment. We developed a new algorithm, SAXSTER, to couple the raw SAXS data with protein-fold-recognition algorithms and thus improve template-based protein-structure predictions. We designed nine different matching scoring functions of template and experimental SAXS profiles. The logarithm of the integrated correlation score showed the best template recognition ability and had the highest correlation with the true template modeling (TM)-score of the target structures. We tested the method in large-scale protein-fold-recognition experiments and achieved significant improvements in prioritizing the best template structures. When SAXSTER was applied to the proteins of asymmetric SAXS profile distributions, the average TM-score of the top-ranking templates increased by 18% after homologous templates were excluded, which corresponds to a p-value < 10⁻⁹ in Student's t-test. These data demonstrate a promising use of SAXS data to facilitate computational protein structure modeling, which is expected to work most efficiently for proteins of irregular global shape and/or multiple-domain protein complexes.     

On the interpretation of small-angle x-ray solution scattering from spherical viruses.

The intermediates in the ribosome assembly in exponentially growing Escherichia coli have been identified by centrifuging a crude lysate, pulse-labeled with a radioactive RNA base, through a sucrose gradient and analyzing for precursor rRNA in the gradient fractions by gel electrophoresis. The major intermediate in the assembly of the 50 S subunit cosediments with the mature subunit, whereas two minor precursor species sediment between the 30 S and 50 S peaks. The assembly of the 30 S subunit proceeds via a minor intermediate sedimenting slightly behind the mature subunit and a major precursor particle that cosediments with the mature 30 S subunit.The fraction of the rRNA contained in these precursor particles was determined by direct determination of the amount of rRNA in the precursor particles, and from the labeling kinetics of their rRNA. The direct estimation indicated that about 2% of the total 23 S type RNA, and 3 to 5% of the total 16 S type RNA is harboured in precursor particles. In the kinetic experiments the specific activity of the nucleoside triphosphates and of the different ribosomal particles was followed after addition of a radioactive RNA precursor to the growth medium. The results were compared with a digital simulation of the flow of isotopes through the assembly pathways. This method indicated that approximately 2% of the total 23 S type RNA, as well as 2% of the total 16 S type RNA, is contained in the precursor particles.     

Derivation of the small-angle x-ray scattering functions for local conformations of polypeptide chains in solution

The small-angle x-ray scattering (SAXS) functions are analytically derived for both the randomly coiled and helical local conformations of a polypeptide chain in solution. The resulting scattering functions for helices of various types are characterized by a maximum in the range of scattering-vector corresponding to Bragg spacings of 3-5 A, whereas the random-coil function has no maximum. This result is compatible with the extant SAXS data for partially neutralized poly(L-glutamic acid) and poly(L-lysine) in aqueous solutions. Comparison of the SAXS data with the calculated scattering functions shows that helical structures in both polypeptide chains are of the 3.6(13)-helix (alpha-helix) rather than 3.0(10)-type.     

A study of the complex-formation of phenylalanyl-tRNA-synthetase from Escherichia coli using the tRNA-Phe method of small-angle x-ray scattering

The method of small-angle X-ray scattering was employed to analyse the equilibrium enzyme-substrate complexes in solution. A new approach of analysis of the experimental data was developed. This type of analysis provides the determination of dissociation constants and structural parameters of enzyme-substrate complexes. The radius of gyration (Rg) and dimensions of half-axis of the equivalent prolonged ellipsoid (a, b) of E. coliphenylalanyl-tRNA synthetase and its complexes with one or two tRNA(Phe) molecules have been determined. The values of these parameters speak in favour of structural rearrangements due to the interaction of the enzyme with tRNA(Phe). The thermodynamic characteristics of phenylalanyl-tRNA synthetase complexes with tRNA(Phe) testify to the negative cooperativity in binding of two tRNA molecules with the enzyme.     

Dodecylsulfate-induced dissociation of human alpha 2-macroglobulin. An investigation using small-angle neutron scattering and the equilibrium dialysis technique

The dodecylsulfate-induced dissociation of the tetrameric alpha 2-macroglobulin molecule from human plasma has been investigated by the small-angle neutron scattering (SANS) method. The great advantage with the SANS method is that, by using deuterated dodecylsulfate, and contrast variation by changing the D2O/H2O ratio of the solvent, we can selectively study just the protein part, or the dodecylsulfate part, of the protein-dodecylsulfate complex. More than a thousandfold excess of dodecylsulfate (on a molar basis) is needed in order to dissociate alpha 2-macroglobulin to particles with, on average, half the original molecular mass. By combining the SANS data with results obtained by the equilibrium dialysis technique it follows that, under these circumstances, approximately one thousand dodecylsulfate molecules are associated per alpha 2-macroglobulin molecule. From the significant increase in the radius of gyration, which accompanies the dissociation process, we can conclude that the dissociation is associated with a drastic change in conformation of the protein molecule. From measurements where the dodecylsulfate part of the complex dominates the SANS signal we also get an indication that the dodecylsulfate is randomly distributed along the polypeptide chain, rather than being arranged in large clusters at certain regions of the protein molecule. By fitting the parameters of a binding model to the experimental data we obtain the result that most of the more than one thousand bound dodecylsulfate molecules, necessary for dissociation, are involved in the change in conformation, and the dissociation process is, in fact, driven by the binding of a very few extra dodecylsulfate molecules to the dissociation products. These data indicate that the dodecylsulfate-induced dissociation of alpha 2-macroglobulin is probably more complicated than just breaking, for instance, a hydrophobic interaction.     

Asymmetry of the GroEL-GroES complex under physiological conditions as revealed by small-angle x-ray scattering

Despite the well-known functional importance of GroEL-GroES complex formation during the chaperonin cycle, the stoichiometry of the complex has not been clarified. The complex can occur either as an asymmetric 1:1 GroEL-GroES complex or as a symmetric 1:2 GroEL-GroES complex, although it remains uncertain which type is predominant under physiological conditions. To resolve this question, we studied the structure of the GroEL-GroES complex under physiological conditions by small-angle x-ray scattering, which is a powerful technique to directly observe the structure of the protein complex in solution. We evaluated molecular structural parameters, the radius of gyration and the maximum dimension of the complex, from the x-ray scattering patterns under various nucleotide conditions (3 mM ADP, 3 mM ATPγS, and 3 mM ATP in 10 mM MgCl₂ and 100 mM KCl) at three different temperatures (10°C, 25°C, and 37°C). We then compared the experimentally observed scattering patterns with those calculated from the known x-ray crystallographic structures of the GroEL-GroES complex. The results clearly demonstrated that the asymmetric complex must be the major species stably present in solution under physiological conditions. On the other hand, in the presence of ATP (3 mM) and beryllium fluoride (10 mM NaF and 300 μM BeCl₂), we observed the formation of a stable symmetric complex, suggesting the existence of a transiently formed symmetric complex during the chaperonin cycle.     

Quaternary structure built from subunits combining NMR and small-angle x-ray scattering data

A new principle in constructing molecular complexes from the known high-resolution domain structures joining data from NMR and small-angle x-ray scattering (SAXS) measurements is described. Structure of calmodulin in complex with trifluoperazine was built from N- and C-terminal domains oriented based on residual dipolar couplings measured by NMR in a dilute liquid crystal, and the overall shape of the complex was derived from SAXS data. The residual dipolar coupling data serves to reduce angular degrees of freedom, and the small-angle scattering data serves to confine the translational degrees of freedom. The complex built by this method was found to be consistent with the known crystal structure. The study demonstrates how approximate tertiary structures of modular proteins or quaternary structures composed of subunits can be assembled from high-resolution structures of domains or subunits using mutually complementary NMR and SAXS data.     

Mono- and trivalent ions around DNA: a small-angle scattering study of competition and interactions

The presence of small numbers of multivalent ions in DNA-containing solutions results in strong attractive forces between DNA strands. Despite the biological importance of this interaction, e.g., DNA condensation, its physical origin remains elusive. We carried out a series of experiments to probe interactions between short DNA strands as small numbers of trivalent ions are included in a solution containing DNA and monovalent ions. Using resonant (anomalous) and nonresonant small angle x-ray scattering, we coordinated measurements of the number and distribution of each ion species around the DNA with the onset of attractive forces between DNA strands. DNA-DNA interactions occur as the number of trivalent ions increases. Surprisingly good agreement is found between data and size-corrected numerical Poisson-Boltzmann predictions of ion competition for non- and weakly interacting DNAs. We also obtained an estimate for the minimum number of trivalent ions needed to initiate DNA-DNA attraction.     

Crystal structures and small-angle x-ray scattering analysis of UDP-galactopyranose mutase from the pathogenic fungus Aspergillus fumigatus

UDP-galactopyranose mutase (UGM) is a flavoenzyme that catalyzes the conversion of UDP-galactopyranose to UDP-galactofuranose, which is a central reaction in galactofuranose biosynthesis. Galactofuranose has never been found in humans but is an essential building block of the cell wall and extracellular matrix of many bacteria, fungi, and protozoa. The importance of UGM for the viability of many pathogens and its absence in humans make UGM a potential drug target. Here we report the first crystal structures and small-angle x-ray scattering data for UGM from the fungus Aspergillus fumigatus, the causative agent of aspergillosis. The structures reveal that Aspergillus UGM has several extra secondary and tertiary structural elements that are not found in bacterial UGMs yet are important for substrate recognition and oligomerization. Small-angle x-ray scattering data show that Aspergillus UGM forms a tetramer in solution, which is unprecedented for UGMs. The binding of UDP or the substrate induces profound conformational changes in the enzyme. Two loops on opposite sides of the active site move toward each other by over 10 Å to cover the substrate and create a closed active site. The degree of substrate-induced conformational change exceeds that of bacterial UGMs and is a direct consequence of the unique quaternary structure of Aspergillus UGM. Galactopyranose binds at the re face of the FAD isoalloxazine with the anomeric carbon atom poised for nucleophilic attack by the FAD N5 atom. The structural data provide new insight into substrate recognition and the catalytic mechanism and thus will aid inhibitor design.     

Use of small-angle neutron scattering to study tubulin polymers

Small-angle neutron scattering has been used to examine taxol-stabilized microtubules and other tubulin samples in both H(2)O and D(2)O buffers. Measurements were made at pH/pD values between 6.0 and 7.8, and observed scattered intensities, I(Q), have been interpreted in terms of multicomponent models of microtubules and related tubulin polymers. A semiquantitative curve fitting procedure has been used to estimate the relative amounts of the supramolecular components of the samples. At both pH and pD 7.0 and above, the tubulin polymers are seen to be predominantly microtubules. Although in H(2)O buffer the polymer distribution is little changed as the pH varies, when pD is lowered the samples appear to contain an appreciable amount of sheetlike structures and the average microtubule protofilament number increases from ca. 12.5 at pD > or = approximately 7.0 to ca. 14 at pD approximately 6.0. Such structural change indicates that analysis of microtubule solutions based on H(2)O/D(2)O contrast variation must be performed with caution, especially at lower pH/pD.     

A neutron small-angle scattering study of bovine fibrinogen.

A number of glycyl-tRNA synthetase (glyS) mutants have been isolated as glycine auxotrophs in Salmonella typhimurium. One of the mutants, glyS141, has a glycyl-tRNA synthetase with a K_m for glycine that is 700 times higher than the wild-typeK_m. Prototrophic revertants glyS141 occur at high spontaneous frequencies (>5 × 10^?5). The majority of these revertants contain large tandem duplications including the mutant glyS gene. Some of the duplications cover at least 22% of the chromosome. The duplications overlap with a large duplication isolated previously by a different selection procedure (Straus &; Hoffmann, 1975). Evidence has been obtained which suggests that formation of the duplications may occur by recA-dependent recombination. The Gly⁺ phenotype of revertants carrying the duplications does not appear to be explainable simply by the increased gene dosage of glyS.     

Time-resolved small-angle X-ray scattering study of the folding dynamics of barnase

Structural changes of barnase during folding were investigated using time-resolved small-angle X-ray scattering (SAXS). The folding of barnase involves a burst-phase intermediate, sometimes designated as the denatured state under physiological conditions, D_phys, and a second hidden intermediate. Equilibrium SAXS measurements showed that the radius of gyration (R_g) of the guanidine unfolded state (U) is 26.9 ± 0.7 Å, which remains largely constant over a wide denaturant concentration range. Time-resolved SAXS measurements showed that the R_g value extrapolated from kinetic R_g data to time zero, R_g,0, is 24.3 ± 0.1 Å, which is smaller than that of U but which is expanded from that of folding intermediates of other proteins with similar chain lengths (19 Å). After the burst-phase change, a single-exponential reduction in R_g² was observed, which corresponds to the formation of the native state for the major component containing the native trans proline isomer. We estimated R_g of the minor component of D_phys containing the non-native cis proline isomer (D_phys,cis) to be 25.7 ± 0.6 Å. Moreover, R_g of the major component of D_phys containing the native proline isomer (D_phys,tra) was estimated as 23.9 ± 0.2 Å based on R_g,0. Consequently, both components of the burst-phase intermediate of barnase (D_phys,tra and D_phys,cis) are still largely expanded. It was inferred that D_phys possesses the N-terminal helix and the center of the β-sheet formed independently and that the formation of the remainder of the protein occurs in the slower phase.     

Analysis of fractal properties of globular protein surfaces by means of small-angle x-ray scattering]

The "cube method" [M. Yu. Pavlov, B. A. Fedorov, Biopolymers, 22, 1507, 1983] has been used to calculate the intensity of the large-angle X-ray scattering from the volumes of several globular proteins. In the logarithmic plots of the scattered intensity curves from three of these proteins, there is a linear region at scattering angles corresponding to Bragg distances of from about 6.3 A to 21 A. This linear region possibly may be due to the fractal properties of the surfaces of these proteins on length scoles from 6.3 A to 21 A, and the fractal dimensions corresponding to the power-law scattering at these scattering angles have been evaluated.