Oligomerization propensity and flexibility of yeast frataxin studied by X-ray crystallography and small-angle X-ray scattering

Frataxin is a mitochondrial protein with a central role in iron homeostasis. Defects in frataxin function lead to Friedreich's ataxia, a progressive neurodegenerative disease with childhood onset. The function of frataxin has been shown to be closely associated with its ability to form oligomeric species; however, the factors controlling oligomerization and the types of oligomers present in solution are a matter of debate. Using small-angle X-ray scattering, we found that Co²⁺, glycerol, and a single amino acid substitution at the N-terminus, Y73A, facilitate oligomerization of yeast frataxin, resulting in a dynamic equilibrium between monomers, dimers, trimers, hexamers, and higher-order oligomers. Using X-ray crystallography, we found that Co²⁺ binds inside the channel at the 3-fold axis of the trimer, which suggests that the metal has an oligomer-stabilizing role. The results reveal the types of oligomers present in solution and support our earlier suggestions that the trimer is the main building block of yeast frataxin oligomers. They also indicate that different mechanisms may control oligomer stability and oligomerization in vivo.     

Anomalous X-ray diffraction with soft X-ray synchrotron radiation.

Anomalous diffraction with soft X-ray synchrotron radiation opens new possibilities in protein crystallography and materials science. Low-Z elements like silicon, phosphorus, sulfur and chlorine become accessible as new labels in structural studies. Some of the heavy elements like uranium exhibit an unusually strong dispersion at their M(V) absorption edge (lambdaMV = 3.497 A, E(MV) = 3545 eV) and so does thorium. Two different test experiments are reported here showing the feasibility of anomalous X-ray diffraction at long wavelengths with a protein containing uranium and with a salt containing chlorine atoms. With 110 electrons the anomalous scattering amplitude of uranium exceeds by a factor of 4 the resonance scattering of other strong anomalous scatterers like that of the lanthanides at their L(III) edge. The resulting exceptional phasing power of uranium is most attractive in protein crystallography using the multi-wavelength anomalous diffraction (MAD) method. The anomalous dispersion of an uranium derivative of asparaginyl-tRNA synthetase (hexagonal unit cell; a = 123.4 A, c = 124.4 A) has been measured for the first time at 4 wavelengths near the M(V) edge using the beamline ID1 of ESRF (Grenoble, France). The present set up allowed to measure only 30% of the possible reflections at a resolution of 4 A, mainly because of the low sensitivity of the CCD detector. In the second experiment, the dispersion of the intensity of 5 X-ray diffraction peaks from pentakismethylammonium undecachlorodibismuthate (PMACB, orthorhombic unit cell; a = 13.003 A, b = 14.038 A, c = 15.450 A) has been measured at 30 wavelengths near the K absorption edge of chlorine (lambdaK = 4.397 A, EK= 2819.6 eV). All reflections within the resolution range from 6.4 A to 3.4 A expected in the 20 degree scan were observed. The chemical state varies between different chlorine atoms of PMACB, and so does the dispersion of different Bragg peaks near the K-edge of chlorine. The results reflect the performance of the beamline ID1 of ESRF at wavelengths beyond 3 A at the end of 1998. A gain by a factor 100 for diffraction experiments with 4.4 A photons was achieved in Autumn 1999 when two focusing mirrors had been added to the X-ray optics. Further progress is expected from area detectors more sensitive to soft X-rays. Both CCD detectors and image plates would provide a gain of two orders of measured intensity. Image plates would have the additional advantage that they can be bent cylindrically and thus cover a larger solid angle in reciprocal space. In many cases, samples need to be cooled: closed and open systems are presented. A comparison with the state of art of soft X-ray diffraction, as it had been reached at HASYLAB (Hamburg, Germany), and as it is developing at the Brookhaven National Laboratory (USA), is given.     

X-ray diffraction in the intact isolated frog ocular lens

X-ray diffraction method has been applied for investigating ocular lens native tissue of the frog. X-ray diffraction patterns of intact lenses, their nuclei and cortices are similar and contain a set of concentric diffuse diffraction maxima. The most intensive of these maxima corresponding to the Bragg-spacings of 14.6, 9.1 and 4.6 A are presumably associated with intramolecular structure of lens proteins--crystallins. Intensive small-angle X-ray scattering and diffraction patterns isotropy indicates unavailability of crystallin molecule ordering or orientation in the lens. The shift of 14.6 A maximum up to 12.8 A being the result of nuclei drying shows the necessity of aqueous surrounding for these protein native structure maintenance.     

Imaging plate and its application to X-ray diffraction of muscle

The excellent performance of the IP as an integrating X-ray area detector makes it well suited to X-ray diffraction and scattering experiments using synchrotron radiation. The IP is particularly useful for biological specimens for which the shortest exposure time or the smallest amount of X-ray dose possible is required. It is also useful for time-resolved measurements of an X-ray diffraction pattern, to complement its uses in static measurements.A combination of two powerful tools, synchrotron radiation and imaging plates, has mutually enhanced the potentials of both. The IP may replace conventional X-ray film and some other X-ray detectors which have been conventionally used in many of the application fields of synchrotron radiation. As examples, it has recently proved to be very promising in experiments of X-ray diffraction under high pressure and high temperature (12) DEXAFS and X-ray diffuse scattering. X-ray microscopy will also benefit from the IP when the spatial resolution is improved to a few tens of microns in FWHM.When more intense X-rays are available from insertion devices installed in planned 6–8 GeV storage rings, the IP system will play a more important role as one of the best X-ray area detectors because of its high DQE and the lack of any instantaneous count-rate limitations.     

Solvent structure in crystals of trypsin determined by X-ray and neutron diffraction.

The solvent structure in orthorhombic crystals of bovine trypsin has been independently determined by X-ray diffraction to 1.35 A resolution and by neutron diffraction to 2.1 A resolution. A consensus model of the water molecule positions was obtained using oxygen positions identified in the electron density map determined by X-ray diffraction, which were verified by comparison to D2O-H2O difference neutron scattering density. Six of 184 water molecules in the X-ray structure, all with B-factors greater than 50 A2, were found to be spurious after comparison with neutron results. Roughly two-thirds of the water of hydration expected from thermodynamic data for proteins was localized by neutron diffraction; approximately one-half of the water of hydration was located by X-ray diffraction. Polar regions of the protein are well hydrated, and significant D2O-H2O difference density is seen for a small number of water molecules in a second shell of hydration. Hydrogen bond lengths and angles calculated from unconstrained refinement of water positions are distributed about values typically seen in small molecule structures. Solvent models found in seven other bovine trypsin and trypsinogen and rat trypsin structures determined by X-ray diffraction were compared. Internal water molecules are well conserved in all trypsin structures including anionic rat trypsin, which is 65% homologous to bovine trypsin. Of the 22 conserved waters in trypsin, 19 were also found in trypsinogen, suggesting that they are located in regions of the apoprotein that are structurally conserved in the transition to the mature protein. Seven waters were displaced upon activation of trypsinogen. Water structure at crystal contacts is not generally conserved in different crystal forms. Three groups of integral structural water molecules are highly conserved in all solvent structures, including a spline of water molecules inserted between two beta-strands, which may resemble an intermediate in the formation of beta sheets during the folding of a protein.     

X-ray crystallography shows that translational initiation factor IF3 consists of two compact alpha/beta domains linked by an alpha-helix.

The structures of the two domains of translational initiation factor IF3 from Bacillus stearothermophilus have been solved by X-ray crystallography using single wavelength anomalous scattering and multiwavelength anomalous diffraction. Each of the two domains has an alpha/beta topology, with an exposed beta-sheet that is reminiscent of several ribosomal and other RNA binding proteins. An alpha-helix that protrudes out from the body of the N-terminal domain towards the C-terminal domain suggests that IF3 consists of two RNA binding domains connected by an alpha-helix and that it may bridge two regions of the ribosome. This represents the first high resolution structural information on a translational initiation factor.     

Structure of type I and type III heterotypic collagen fibrils: an X-ray diffraction study

The molecular packing arrangement within collagen fibrils has a significant effect on the tensile properties of tissues. To date, most studies have focused on homotypic fibrils composed of type I collagen. This study investigates the packing of type I/III collagen molecules in heterotypic fibrils of colonic submucosa using a combination of X-ray diffraction data, molecular model building, and simulated X-ray diffraction fibre diagrams. A model comprising a 70-nm-diameter D- (approximately 65 nm) axial periodic structure containing type I and type III collagen chains was constructed from amino acid scattering factors organised in a liquid-like lateral packing arrangement simulated using a classical Lennard-Jones potential. The models that gave the most accurate correspondence with diffraction data revealed that the structure of the fibril involves liquid-like lateral packing combined with a constant helical inclination angle for molecules throughout the fibril. Combinations of type I:type III scattering factors in a ratio of 4:1 gave a reasonable correspondence with the meridional diffraction series. The attenuation of the meridional intensities may be explained by a blurring of the electron density profile of the D period caused by nonspecific or random interactions between collagen types I and III in the heterotypic fibril.     

Heterogeneity and inaccuracy in protein structures solved by X-ray crystallography

Proteins are dynamic molecules, exhibiting structural heterogeneity in the form of anisotropic motion and discrete conformational substates, often of functional importance. In protein structure determination by X-ray crystallography, the observed diffraction pattern results from the scattering of X-rays by an ensemble of heterogeneous molecules, ordered and oriented by packing in a crystal lattice. The majority of proteins diffract to resolutions where heterogeneity is difficult to identify and model, and are therefore approximated by a single, average conformation with isotropic variance. Here we show that disregarding structural heterogeneity introduces degeneracy into the structure determination process, as many single, isotropic models exist that explain the diffraction data equally well. The large differences among these models imply that the accuracy of crystallographic structures has been widely overestimated. Further, it suggests that analyses that depend on small differences in the relative positions of atoms may be flawed.     

Structural studies of adenovirus type 2 by neutron and X-ray scattering

Small-angle neutron and X-ray scattering have been used to investigate various aspects of the structural organization of adenovirus type 2. Neutron scattering allows the determination of the radial distribution of DNA and protein, which because of the highly icosahedral form of the virus allows it to be described in terms of three icosahedral shells. X-ray scattering shows that the distance between the major coat proteins (hexons) in the capsid is 100 +/- A. Evidence was also observed for an organization in the nucleoprotein core that gives rise to a maximum in the X-ray scattering at 1/29 A-1.     

Crystallization and preliminary X-ray investigation reveals that tumor necrosis factor is a compact trimer furnished with 3-fold symmetry

Crystals of recombinant human tumor necrosis factor produced by Escherichia coli have been obtained under different conditions. Crystals suitable for X-ray studies are produced by a vapor diffusion technique using sodium phosphate as both precipitant and buffer at pH 6.5. The crystals belong to the cubic space group, P2(1)3 with unit cell dimensions a = b = c = 95.7 A (1 A = 0.1 nm). Preliminary photography reveals that the crystals are moderately stable to X-rays and diffract to at least 3 A resolution. The diffraction data for native crystals have been collected on a diffractometer at 3 A resolution. Another crystal form, which appeared in a solution containing sodium phosphate at pH 8.0, has the trigonal space group P3 with unit cell dimensions a = b = 63.8 A and c = 54.4 A, and produces measurable reflections to a resolution of 3 A. Hexagonal crystals also have been obtained by the use of polyethylene glycol as precipitant in the range pH 7.6 to 8.0; however, the crystals are fragile and unstable to X-rays. Conservation of 3-fold symmetry in the different crystal forms obtained could reflect the ability of tumor necrosis factor molecules to form trimers in solution and probably the nature of binding of the molecules to cellular receptors.     

Quaternary structure of alpha-crustacyanin from lobster as seen by small-angle X-ray scattering

The structure of alpha-crustacyanin, the blue carotenoprotein of lobster (Homarus gammarus) carapace, has been investigated for the first time using small-angle X-ray scattering. In this paper, we have determined the dimensions of this protein composed of eight heterodimeric subunits of beta-crustacyanin. Analysis of the scattering spectra and estimation of the shape of alpha-crustacyanin show that the protein fits into a cylinder with an axial length of 238 A and a radius of 47.5 A, in which the eight beta-crustacyanin molecules are probably arranged in a helical manner.     

In situ characterization of lipid A interaction with antimicrobial peptides using surface X-ray scattering

Lipid A structure at the air-aqueous interface has been studied using pressure-area isotherm methods coupled with the surface X-ray scattering techniques of X-ray reflectivity (XR) and grazing incidence X-ray diffraction (GIXD). Lipid A monolayers were formed at the air-aqueous interface to represent the lipid moiety of the outer membrane of Gram-negative bacteria. Lipid A structure was characterized at surface pressures between 10 and 35 mN/m. Interactions of α-helical antimicrobial peptides LL-37, SMAP-29 and D2A22 with lipid A monolayers were subsequently studied. Although insertion into the lipid A monolayers was observed with the α-helical peptides, little change was seen from the X-ray data, suggesting that the lipid A hydrocarbon chains are involved in reorientation during insertion and that the hydrocarbon chains have a relatively rigid structure.     

Structural insights into the beta-mannosidase from T. reesei obtained by synchrotron small-angle X-ray solution scattering enhanced by X-ray crystallography

A molecular envelope of the beta-mannosidase from Trichoderma reesei has been obtained by combined use of solution small-angle X-ray scattering (SAXS) and protein crystallography. Crystallographic data at 4 A resolution have been used to enhance informational content of the SAXS data and to obtain an independent, more detailed protein shape. The phased molecular replacement technique using a low resolution SAXS model, building, and refinement of a free atom model has been employed successfully. The SAXS and crystallographic free atom models exhibit a similar globular form and were used to assess available crystallographic models of glycosyl hydrolases. The structure of the beta-galactosidase, a member of a family 2, clan GHA glycosyl hydrolases, shows an excellent fit to the experimental molecular envelope and distance distribution function of the beta-mannosidase, indicating gross similarities in their three-dimensional structures. The secondary structure of beta-mannosidase quantified by circular dichroism measurements is in a good agreement with that of beta-galactosidase. We show that a comparison of distance distribution functions in combination with 1D and 2D sequence alignment techniques was able to restrict the number of possible structurally homologous proteins. The method could be applied as a general method in structural genomics and related fields once protein solution scattering data are available.     

Molecular weight of tumor necrosis factor determined by gel permeation chromatography alone or in combination with low-angle laser light scattering

The molecular weight of human recombinant tumor necrosis factor was determined at neutral pH by gel permeation chromatography alone or in combination with low-angle laser light scattering. Mean values of 39,200 +/- 800 and 48,800 +/- 900, respectively, were obtained by the two analyses. The results resolve the apparent discrepancy in the reported values of the molecular weight of this cytokine, confirming that it exists as a trimer in neutral solution with a molecular weight of about 50,000.     

Hydrophobic cavity in C-terminus is essential for hTNF-α trimer conformation

A variety of tumour necrosis factor α (TNF-α) derivatives have been bioengineered to improve antitumour activity and reduce toxicity. The expression of TNF-α in Escherichia coli usually yields a mixture of homotrimers and monomers; however, only the trimer shows antitumour activity. TNF-αD10, a bioengineered hTNF-α derivative, demonstrated 10-fold higher cytotoxicity against tumour cells compared to hTNF-α, but the trimer to monomer ratio was 58:42. In the present study, we investigated the structural differences between the trimer and the monomer of TNF-αD10. We found that the chemical shifts of the C-terminal Trp(114) in the trimer were significantly different from those in the monomer and that the replacement of Trp(114) with different amino acids remarkably reduced the trimer production. Further analysis of the publicly available X-ray crystallographic data for trimeric and monomeric hTNF-α revealed that the conformation of the U-shaped region formed by the fragment Cys(101)-Trp(114) was different between the two forms: a hydrophilic cavity in the monomer and a hydrophobic cavity in the trimer. These findings suggested the potential approaches of molecular and structural modification for future improvement of hTNF-α trimer production.     

X-ray scattering study of the shape of the DNA region in nucleosome core particle with synchrotron radiation.

The structure of the DNA region in rat thymus nucleosome core particle has been studied by synchrotron X-ray scattering analysis and the contrast-variation technique has been applied to determine the contribution of the DNA to the total scatterings. Small-angle contrast-matching measurements show that the entire core particle and isolated histone octamers are contrast-matched by solvents containing 64 and 54% (w/w) sucrose, respectively. At a contrast of 54% sucrose, where the scattering of the DNA dominates, the scattering data extending to higher angle of about 0.05 A-1 have been collected from relatively concentrated solutions (10 mg/ml) of core particles and interpreted on the basis of the regular helical model for the DNA region. The model calculations show that the shape of the DNA around the histone core is approximately by 1.8 turns of regular helix of 42 A radius and 28 A pitch. These values for helical parameters of our model are in good agreement with those of the structure of DNA in crystallized nucleosome cores shown by earlier diffraction studies.     

Lipid bilayer ultrastructure. Electron density profiles and chain tilt angles as determined by X-ray diffraction.

High resolution (6A) electron density profiles have been computed on an absolute electron density scale for bilayers composed of both saturated fatty acids and fatty acids associated with the alkaline earth series of divalent cations. Lowangle X-ray diffraction data have been interpreted by an isomorphous replacement technique. The position on the X-ray film of discrete wide-angle reflections has provided direct information on the hydrocarbon chain packing and chain tilt in these bilayers. These results have been correlated to an electron microscopy study of the same bilayers (Waldbilling, R. C., Robertson, J.D. and McIntosh, T. J. (1976) Biochim. Biophys. Acta 448, 1-14) and also to X-ray diffraction studies of fatty acid crystals. A method for forming and structurally analyzing bilayers of well defined chemical asymmetry is also described.     

The dimeric and trimeric solution structures of the multidomain complement protein properdin by X-ray scattering, analytical ultracentrifugation and constrained modelling

Properdin regulates the alternative pathway of the complement system of immune defence by stabilising the C3 convertase complex. It contains six thrombospondin repeat type I (TSR-1 to TSR-6) domains and an N-terminal domain. Properdin exists as either a dimer, trimer or tetramer. In order to determine the solution structure of multiple TSR domains, the molecular structures of dimeric and trimeric properdin were studied by X-ray scattering and analytical ultracentrifugation. Guinier analyses showed that the dimer and trimer have radii of gyration R(G) values of 7.5 nm and 10.3 nm, respectively, and cross-sectional radii of gyration R(XS) values of 1.3 nm and 1.5 nm, respectively. Distance distribution functions showed that the maximum lengths of the dimer and trimer were 25 nm and 30 nm, respectively. Analytical ultracentrifugation gave sedimentation coefficients of 5.1S and 5.2S for the dimer and trimer forms, respectively. Homology models for the TSR domains were constructed using the crystal structure of the TSP-2 and TSP-3 domains in human thrombospondin as templates. Properdin could be represented by seven TSR domains, not six as believed, since the crystal structure determined for TSP-2 and TSP-3 showed that the N-terminal domain (TSR-0) could be represented by a truncated TSR domain with the same six conserved Cys residues found in TSR-1 to TSR-6. Automated constrained molecular modelling revealed the solution conformations of multiple TSR domains in properdin at medium resolution. The comparison of 3125 systematically generated conformational models for the trimer with the X-ray data showed that good curve fits could be obtained by assuming that the linker between adjacent TSR domains possessed limited flexibility. Good trimer models correspond to partially collapsed triangular structures, and extended triangular shapes do not fit the data. The corresponding 3125 models for the dimer revealed a similar outcome in which a partially collapsed TSR structure gave good fits. The models account for the effect of mutations that cause properdin deficiencies, and suggest that the biologically active TSR-4, TSR-5 and TSR-6 domains are exposed for protein-protein interactions. The role of the other TSR domains in properdin may be to act as spacers to make TSR-4, TSR-5 and TSR-6 accessible for function.     

Lipid bilayer ultrastructure: Electron density profiles and chain tilt angles as determined by X-ray diffraction

High resolution (6 Å) electron density profiles have been computed on an absolute electron density scale for bilayers composed of both saturated fatty acids and fatty acids associated with the alkaline earth series of divalent cations. Low-angle X-ray diffraction data have been interpreted by an isomorphous replacement technique. The position on the X-ray film of discrete wide-angle reflections has provided direct information on the hydrocarbon chain packing and chain tilt in these bilayers. These results have been correlated to an electron microscopy study of the same bilayers (Waldbilling, R. C., Robertson J. D. and McIntosh, T.J. (1976) Biochim. Biophys. Acta 448, 1–14) and also to X-ray diffraction studies of fatty acid crystals. A method for forming and structurally analyzing bilayers of well defined chemical asymmetry is also described.