Analysis and Correction of Dynamic Geometric Misalignment for Nano-Scale Computed Tomography at BSRF

Due to its high spatial resolution, synchrotron radiation x-ray nano-scale computed tomography (nano-CT) is sensitive to misalignments in scanning geometry, which occurs quite frequently because of mechanical errors in manufacturing and assembly or from thermal expansion during the time-consuming scanning. Misalignments degrade the imaging results by imposing artifacts on the nano-CT slices. In this paper, the geometric misalignment of the synchrotron radiation nano-CT has been analyzed by partial derivatives on the CT reconstruction algorithm and a correction method, based on cross correlation and least-square sinusoidal fitting, has been reported. This work comprises a numerical study of the method and its experimental verification using a dataset measured with the full-field transmission x-ray microscope nano-CT at the beamline 4W1A of the Beijing Synchrotron Radiation Facility. The numerical and experimental results have demonstrated the validity of the proposed approach. It can be applied for dynamic geometric misalignment and needs neither phantom nor additional correction scanning. We expect that this method will simplify the experimental operation of synchrotron radiation nano-CT.     

The hydration pressure between lipid bilayers. Comparison of measurements using x-ray diffraction and calorimetry.

The hydration pressure between dipalmitoyl phosphatidyl-N,N-dimethylethanolamine (DPPE-Me2) bilayers has been analyzed by both x-ray diffraction measurements of osmotically stressed liposomes and by differential scanning calorimetry. By the x-ray method, we obtain a magnitude (Po) and decay length (lambda) for the hydration pressure which are both quite similar to those found for bilayers of other zwitterionic lipids, such as phosphatidylcholines. That is, x-ray analysis of DPPE-Me2 in the gel phase gives lambda = 1.3 A, the same as that previously measured for the analogous gel phase lipid dipalmitoylphosphatidylcholine (DPPC), and Po = 3.9 x 10(9) dyn/cm2, which is in excellent agreement with the value of 3.6 x 10(9) dyn/cm2 calculated from the measured Volta potential of DPPE-Me2 monolayers in equilibrium with liposomes. These results indicate that the removal of one methyl group to convert DPPC to DPPE-Me2 does not markedly alter the range or magnitude of the hydration pressure. Calorimetry shows that the main gel to liquid-crystalline phase transition temperature of DPPE-Me2 is approximately constant for water contents ranging from 80 to 10 water molecules per lipid molecule, but increases monotonically with decreasing water content below 10 waters per lipid. A theoretical fit to these temperature vs. water content data predicts lambda = 6.7 A. The difference in observed values of lambda for x-ray and calorimetry measurements can be explained by effects on the thermograms of additional intra- and intermolecular interactions which occur at low water contents where apposing bilayers are in contact.(ABSTRACT TRUNCATED AT 250 WORDS)     

Scanning X-Ray Nanodiffraction on Dictyostelium discoideum

We have performed scanning x-ray nanobeam diffraction experiments on single cells of the amoeba Dictyostelium discoideum. Cells have been investigated in 1), freeze-dried, 2), frozen-hydrated (vitrified), and 3), initially alive states. The spatially resolved small-angle x-ray scattering signal shows characteristic streaklike patterns in reciprocal space, which we attribute to fiber bundles of the actomyosin network. From the intensity distributions, an anisotropy parameter can be derived that indicates pronounced local variations within the cell. In addition to nanobeam small-angle x-ray scattering, we have evaluated the x-ray differential phase contrast in view of the projected electron density. Different experimental aspects of the x-ray experiment, sample preparation, and data analysis are discussed. Finally, the x-ray results are correlated with optical microscopy (differential phase contrast and confocal microscopy of mutant strains with fluorescently labeled actin and myosin II), which have been carried out in live and fixed states, including optical microscopy under cryogenic conditions.     

胆固醇对二棕榈酰磷脂酰胆碱（DPPC）多层膜结构的影响

用小角Ｘ射线衍射（ＳＡＸＤ）和差示扫描量热（ＤＳＣ）方法研究胆固醇对二棕榈酸磷脂酰胆碱多层膜结构的影响。在不同胆因醇浓度及不同温度下的衍射实验和热吸收曲线实验显示纯磷脂的尖锐的凝胶－液晶相变随胆固醇含量增加而逐渐消失。当胆固醇含量约为４０（ｍｏｌ）％或更多时,衍射曲线和热吸收曲线均显示存在分相现象。     

Interaction between artificial membranes and enflurane,a general volatile anesthetic: DPPC-enflurane interaction

The structural modifications of the dipalmitoylphosphatidylcholine (DPPC) organization induced by increasing concentration of the volatile anesthetic enflurane have been studied by differential scanning calorimetry, small-angle, and wide-angle x-ray scattering. The interaction of enflurane with DPPC depends on at least two factors: the enflurane-to-lipid concentration ratio and the initial organization of the lipids. At 25 degrees C (gel state), the penetration of enflurane within the lipids induces the apparition of two different mixed lipid phases. At low anesthetic-to-lipid molar ratio, the smectic distance increases whereas the direction of the chain tilt changes from a tilt toward next-neighbors to a tilt between next-neighbors creating a new gel phase called L(beta')(2NNN). At high ratio, the smectic distance is much smaller than for the pure L(beta') DPPC phase, i.e., 50 A compared to 65 A, the aliphatic chains are perpendicular to the membrane and the fusion temperature of the phase is 33 degrees C. The electron profile of this phase that has been called L(beta)(i), indicates that the lipids are fully interdigitated. At 45 degrees C (fluid state), a new melted phase, called L(alpha)(2), was found, in which the smectic distance decreased compared to the initial pure L(alpha)(1) DPPC phase. The thermotropic behavior of the mixed phases has also been characterized by simultaneous x-ray scattering and differential scanning calorimetry measurements using the Microcalix calorimeter of our own. Finally, titration curves of enflurane effect in the mixed lipidic phase has been obtained by using the fluorescent lipid probe Laurdan. Measurements as a function of temperature or at constant temperature, i.e., 25 degrees C and 45 degrees C give, for the maximal effect, an enflurane-to-lipid ratio (M/M), within the membrane, of 1 and 2 for the L(alpha)(2) and the L(beta)(i) lamellar phase respectively. All the results taken together allowed to draw a pseudo-binary phase diagram of enflurane-dipalmitoylphosphatidylcholine in excess water.     

Bi-Directional X-Ray Phase-Contrast Mammography

Phase-contrast x-ray imaging is a promising improvement of conventional absorption-based mammography for early tumor detection. This potential has been demonstrated recently, utilizing structured gratings to obtain differential phase and dark-field scattering images. However, the inherently anisotropic imaging sensitivity of the proposed mono-directional approach yields only insufficient diagnostic information, and has low diagnostic sensitivity to highly oriented structures. To overcome these limitations, we present a two-directional x-ray phase-contrast mammography approach and demonstrate its advantages by applying it to a freshly dissected, cancerous mastectomy breast specimen. We illustrate that the two-directional scanning procedure overcomes the insufficient diagnostic value of a single scan, and reliably detects tumor structures, independently from their orientation within the breast. Our results indicate the indispensable diagnostic necessity and benefit of a multi-directional approach for x-ray phase-contrast mammography.     

A study of apo- and holo-forms of horse liver alcohol dehydrogenase in solution by diffuse x-ray scattering

Apo- and holo-forms of horse liver alcohol dehydrogenase (LADH) in solution were studied by diffuse x-ray scattering. Experimental scattering curves for apo- and holo-forms coincide both with the curves calculated from the crystal structures of apo- and holo-enzymes, and with each other. Thus the “sliding” of catalytical domains in LADH upon substrate binding, which has been shown by x-ray analysis, cannot be detected by diffuse x-ray scattering. Sensitivity of the scattering curves to the domain displacements of sliding and “locking” types has been investigated. It has been shown that the scattering curves of LADH are rather sensitive to the domain “unlocking.” However, these curves change only slightly upon sliding of domains, including the sliding of domains observed in LADH by x-ray analysis.     

Crystallization and preliminary analysis of crystals of apolipophorin III isolated from Locusta migratoria

Crystals of apolipophorin III, isolated from the locust Locusta migratoria, have been reproducibly grown from ammonium sulfate solutions and are well suited for an x-ray crystallographic analysis. Locust apolipophorin III is a glycosylated protein with a molecular weight of 19,100 and interacts with lipophorin, the major lipoprotein complex in insects. The crystals belong to the space group P6122 or P6522 with unit cell dimensions of a = b = 67.5 A, c = 155.6 A and diffract to a nominal resolution of 2.5 A. They are physically robust and are stable in the x-ray beam for over a week. A complete native x-ray data set has been collected and processed to 3.0-A resolution.     

Comparison of a Homology Built Model of Angiogenin to its Crystal Structure

The comparison of our homology built model of human angiogenin with the recently determined x-ray structure of the same is reported. The basic details of the structure in terms of alpha -helices and beta sheets were found to be common. The main differences between the model and the x-ray data lie in a C-terminal rearrangement in the x-ray structure that causes the C-terminus to end in a 3₁₀ helix which puts the residue GLN-117 (ALA-122 in bovine pancreatic ribonuclease A, RNaseA) into the active site. The homology model was updated by producing a new sequence alignment using the information from the x-ray data which improved the r.m.s. by 0.5Å. This new alignment is also reported here. A check for systematic bias was carried out using the RNaseA structures from which the x-ray and homology models were derived. A detailed comparison of torsion angles and hydrogen bonding between all the structures have been compared and the model displays several hydrogen bonds that are not present in the parent RNaseA structures but are present in the x-ray structure of angiogenin.Electronic Supplementary Material available.     

The presence of a histidine-aspartic acid pair in the active site of 2-hydroxyacid dehydrogenases. X-ray refinement of cytoplasmic malate dehydrogenase

The structure of cytoplasmic malate dehydrogenase has been partially refined by crystallographic least squares methods. Using x-ray phases based on the refined coordinates, analysis of the resultant electron density maps has led to a new model of cytoplasmic malate dehydrogenase and a tentative "x-ray sequence." The two crystallographically independent subunits comprising the dimeric enzyme are nearly identical in structure and are related to each other by roughly 2-fold rotational symmetry. The best fit of the molecular structure of cytoplasmic malate dehydrogenase to that of lactate dehydrogenase has been obtained by least squares methods. The active sites of these two enzymes contain similarly oriented His-Asp pairs linked by a hydrogen bond which may function as a proton relay system during catalysis. This pair could also provide an explanation for the relatively stronger binding by cytoplasmic malate dehydrogenase and lactate dehydrogenase of NADH versus NAD. Similar His-Asp pairs have been observed in the serine proteases, thermolysin, and phospholipase A2, and the His-Asp pair may play a similar functional role in all of these enzymes.     

Time-resolved x-ray diffraction study of photostimulated purple membrane.

A nanosecond resolution laser-driven x-ray source has been used to perform a time-resolved, x-ray diffraction study of the purple membrane of the Halobacterium halobium. Alterations in diffraction patterns have been observed 1 ms after photostimulation, and are interpreted to show disorder of bacteriorhodopsin packing in the plane of the membrane with little bacteriorhodopsin structural change.     

A preliminary crystallographic study of recombinant human interleukin 1 beta

Recombinant human interleukin 1 beta which is expressed in Escherichia coli has been crystallized by the method of vapor diffusion using ammonium sulfate as the precipitant. The space group is P4(1) or P4(3) with a = b = 55.0 A and c = 77.1 A and one molecule in the asymmetric unit. The crystals diffract to beyond 2.4 A and are suitable for a three-dimensional x-ray structure determination.     

The Open Gate of the KV1.2 Channel: Quantum Calculations Show the Key Role of Hydration

The open gate of the K_v1.2 voltage-gated potassium channel can just hold a hydrated K⁺ ion. Quantum calculations starting from the x-ray coordinates of the channel confirm this, showing little change from the x-ray coordinates for the protein. Water molecules not in the x-ray coordinates, and the ion itself, are placed by the calculation. The water molecules, including their orientation and hydrogen bonding, with and without an ion, are critical for the path of the ion, from the solution to the gate. A sequence of steps is postulated in which the potential experienced by the ion in the pore is influenced by the position of the ion. The gate structure, with and without the ion, has been optimized. The charges on the atoms and bond lengths have been calculated using natural bond orbital calculations, giving K⁺ ∼0.77 charges, rather than 1.0. The PVPV hinge sequence has been mutated in silico to PVVV (P407V in the 2A79 numbering). The water structure around the ion becomes discontinuous, separated into two sections, above and below the ion. PVPV conservation closely relates to maintaining the water structure. Finally, these results have implications concerning gating.     

Role of the position of unsaturation on the phase behavior and intrinsic curvature of phosphatidylethanolamines.

The bilayer-to-hexagonal phase transition temperatures (T(H)) of di-18:1(C) phosphatidylethanolamine with double bonds at positions 6, 9, and 11 are 37 degrees C, 8 degrees C, and 28 degrees C, respectively, as measured by differential scanning calorimetry and x-ray diffraction. Thus T(H) exhibits a minimum when the C=C is around position 9, similar to what has been found for the gel-to-liquid crystalline phase transition temperature in other lipids. Factors that may contribute to the dependence of T(H) on double bond position were studied by x-ray diffraction of the hexagonal phases in the presence and absence of added alkane, with or without the osmotic stress of polyethylene glycol, and over a wide temperature range. The lattice dimensions show that the intrinsic radius of lipid monolayer curvature increases as the double bond is moved toward the tail ends. A measure of the bending moduli of these lipid monolayers shows a higher value for the 9 position, and lower values for the other two. Consideration of the bilayer-to-hexagonal transition in terms of bending and interstitial energies provides a rationale for the relative values of T(H).     

The Open Gate of the KV1.2 Channel: Quantum Calculations Show the Key Role of Hydration

The open gate of the K_v1.2 voltage-gated potassium channel can just hold a hydrated K⁺ ion. Quantum calculations starting from the x-ray coordinates of the channel confirm this, showing little change from the x-ray coordinates for the protein. Water molecules not in the x-ray coordinates, and the ion itself, are placed by the calculation. The water molecules, including their orientation and hydrogen bonding, with and without an ion, are critical for the path of the ion, from the solution to the gate. A sequence of steps is postulated in which the potential experienced by the ion in the pore is influenced by the position of the ion. The gate structure, with and without the ion, has been optimized. The charges on the atoms and bond lengths have been calculated using natural bond orbital calculations, giving K⁺ ∼0.77 charges, rather than 1.0. The PVPV hinge sequence has been mutated in silico to PVVV (P407V in the 2A79 numbering). The water structure around the ion becomes discontinuous, separated into two sections, above and below the ion. PVPV conservation closely relates to maintaining the water structure. Finally, these results have implications concerning gating.     

Structure-function studies of [2Fe-2S] ferredoxins

The ability to overexpress [2Fe-2S] ferredoxins inEscherichia coli has opened up exciting research opportunities. High-resolution x-ray structures have been determined for the wild-type ferredoxins produced by the vegetative and heterocyst forms ofAnabaena strain 7120 (in their oxidized states), and these have been compared to structural information derived from multidimensional, multinuclear NMR spectroscopy. The electron delocalization in these proteins in their oxidized and reduced states has been studied by¹H,²H,¹³C, and¹⁵N NMR spectroscopy. Site-directed mutagenesis has been used to prepare variants of these ferredoxins. Mutants (over 50) of the vegetative ferredoxin have been designed to explore questions about cluster assembly and stabilization and to determine which residues are important for recognition and electron transfer to the redox partnerAnabaena ferredoxin reductase. The results have shown that serine can replace cysteine at each of the four cluster attachment sites and still support cluster assembly. Electron transfer has been demonstrated with three of the four mutants. Although these mutants are less stable than the wild-type ferredoxin, it has been possible to determine the x-ray structure of one (C49S) and to characterize all four by EPR and NMR. Mutagenesis has identified residues 65 and 94 of the vegetative ferredoxin as crucial to interaction with the reductase. Three-dimensional models have been obtained by x-ray diffraction analysis for several additional mutants: T48S, A50V, E94K (four orders of magnitude less active than wild type in functional assays), and A43S/A45S/T48S/A50N (quadruple mutant).     

A soybean trypsin inhibitor. Crystallization and x-ray crystallographic study

Five trypsin and alpha-chymotrypsin inhibitors which have low molecular weights (ranging from 6800 to 8600) and are present in soybean seeds of the Tracy variety have been isolated and purified, and single crystals which give x-ray diffraction data beyond 3-A spacings have been obtained from one of them. The trypsin inhibitor crystallizes in a monoclinic unit cell of symmetry P2(1) and dimensions a = 25.919(7) A, b = 43.23(1) A, c = 19.905(5) A, and beta = 103.63(2) degrees. The assymmetric unit contains 1 molecule of molecular weight 6800. The crystal, which has been found to be unusually stable to x-radiation, has solvent content of approximately 26% by volume.     

The x-ray morphological characteristics of the early manifestations of sarcoidosis

The paper is devoted to an analysis of combined x-ray findings supplemented by CT findings in patients with sarcoidosis detected for the first time with early signs of this disease. A conclusion has been made that apart from lymph node enlargement, sarcoidosis is characterized by lung parenchymal changes which manifest themselves as symptoms of broncho-alveolitis. Characteristic x-ray symptom complexes are described. Roentgeno-semiotics of these changes were compared with the results of morphological investigation of transbronchial puncture specimens. Roentgenologically detectable changes showed good correlation with morphology findings. The authors have also emphasized the importance of morphological verification of this disease at early stages.     

Neutron and x-ray scatter studies of the histone octamer and amino and carboxyl domain trimmed octamers

The structure of the nucleosome has been under intense investigation using neutron crystallography, x-ray crystallography, and neutron solution scattering. However the dimension of the histone octamer inside the nucleosome is still a subject of controversy. The radius of gyration (Rg) of the octamer obtained from solution neutron scattering of core particles at 63% 2H2O, 37% 1H2O is 33 A, and x-ray crystallography study of isolated histone octamer gives a Rg of 32.5 A, while the reported values using x-ray crystallography of core particles from two individual studies are 29.7 and 30.4 A, respectively. We report here studies of isolated histone octamer and trypsin-limited digested octamer using both neutron solution scattering and small angle x-ray scattering. The Rg of the octamer obtained is 33 A, whereas that of the trimmed octamer is 29.8 A, similar to the structure obtained from the crystals of the core particles. The N-terminal domains of the core histones in the octamer have been shown by high resolution nuclear magnetic resonance (Schroth, G.P., Yau, P., Imai, B.S., Gatewood, J.M., and Bradbury, E.M. (1990) FEBS Lett. 268, 117-120) to be mobile and flexible; it is likely that these regions are disordered and "not seen" by x-ray crystallography.     

Shape of protein L11 from the 50S ribosomal subunit of Escherichia coli.

Protein L11 from the 50S ribosomal subunit of Escherichia coli A19 was purified by a method using nondenaturing conditions. Its shape in solution was studied by hydrodynamic and low-angle x-ray scattering experiments. The results from both methods are in good agreement. In buffers similar to the ribosomal reconstitution buffer, the protein is monomeric at concentrations up to 3 mg/mL and has a molecular weight of 16 000-17 000. The protein molecule resembles a prolate ellipsoid with an axial ratio of 5-6:1 a radius of gyration of 34 A, and a maximal length of 150 A. From the low-angle x-ray diffraction data, a more refined model of the protein molecule has been constructed consisting of two ellipsoids joined by their long axes.