Structure of corneal scar tissue: an X-ray diffraction study.

Full-thickness corneal wounds (2 mm diameter) were produced in rabbits at the Schepens Eye Research Institute, Boston. These wounds were allowed to heal for periods ranging from 3 weeks to 21 months. The scar tissue was examined using low- and wide-angle x-ray diffraction from which average values were calculated for 1) the center-to-center collagen fibril spacing, 2) the fibril diameter, 3) the collagen axial periodicity D, and 4) the intermolecular spacing within the collagen fibrils. Selected samples were processed for transmission electron microscopy. The results showed that the average spacing between collagen fibrils within the healing tissue remained slightly elevated after 21 months and there was a small increase in the fibril diameter. The collagen D-periodicity was unchanged. There was a significant drop in the intermolecular spacing in the scar tissues up to 6 weeks, but thereafter the spacing returned to normal. The first-order equatorial reflection in the low-angle pattern was visible after 3 weeks and became sharper and more intense with time, suggesting that, as healing progressed, the number of nearest neighbor fibrils increased and the distribution of nearest neighbor spacings reduced. This corresponded to the fibrils becoming more ordered although, even after 21 months, normal packing was not achieved. Ultrastructural changes in collagen fibril density measured from electron micrographs were consistent with the increased order of fibril packing measured by x-ray diffraction. The results suggest that collagen molecules have a normal axial and lateral arrangement within the fibrils of scar tissue. The gradual reduction in the spread of interfibrillar spacings may be related to the progressive decrease in the light scattered from the tissue as the wound heals.     

The galactan-binding immunoglobulin Fab J539: an X-ray diffraction study at 2.6-A resolution

The crystal structure of the Fab of the galactan-binding immunoglobulin J539 (a mouse IgA,kappa) has been determined at a resolution of approximately 2.6 A by X-ray diffraction. The starting model was that obtained from the real space search described previously (Navia, M.A., Segal, D.M., Padlan, E.A., Davies, D.R., Rao, D.N., Rudikoff, S. and Potter, M. "Crystal structure of galactan-binding mouse immunoglobulin J539 Fab at 4.5 A resolution." Proc. Nat. Acad. Sci. USA, 76:4071-4074, 1979). This Fab structure has now been refined by restrained least-squares procedures to an R-value of 19% for the 11,690 unique reflections between 8.0 A and 2.6 A. The rms deviation from ideal bond lengths is 0.025 A. The overall structure differs from McPC603 Fab, another mouse IgA,kappa antibody, in that the elbow bend, relating the variable and constant parts of the molecule, is 145 degrees vs. 133 degrees for McPC603. The region of the molecule expected to be the antigen binding site contains a large cavity with two clefts leading away from it. This has been fitted with a model of an oligo-galactan.     

X-ray diffraction study of cholesterol-phosphatidylserine mixtures

Phosphatidylserine-cholesterol mixtures at a molar ratio of 2:1 were investigated by X-ray diffraction. Phase separation of cholesterol independent of temperature was detected, indicating limited solubility of cholesterol in phosphatidylserine bilayers. The second phase present, the mixed phospholipid-cholesterol phase, continued to undergo melting as determined by changes with temperature in both the small angle scattering profile and in the acyl chain packing.     

X-ray diffraction study of the cornea

Low-angle X-ray diffraction patterns have been recorded from the cornea. A fibre diagram was obtained: the reflections from the axial period of collagen were on the equator while reflections from the collagen fibril lattice structure were on the meridian. Only the reflections from tha array of collagen fibrils have been studied. These reflections contain a primary first-order reflection and up to four subsidiary maxima. The first-order reflection from the array provides an estimate of the interfibril separation distance. Evidence is presented that the subsidiary maxima are consistent with the intensity transform of a uniform cylinder with a constant radius. Values for the fibril diameters and the interfibril distances are obtained for corneas from rabbit, cow and frog and from corneas of two marine fishes: toadfish and skate. Although the volume fraction of the collagen fibrils cannot be directly evaluated, an upper limit can be given. Thus, an upper limit of 0.28 was obtained for rabbit cornea.     

Interaction between lipid monolayers and poloxamer 188: an X-ray reflectivity and diffraction study

The mechanism by which poloxamer 188 (P188) seals a damaged cell membrane is examined using the lipid monolayer as a model system. X-ray reflectivity and grazing-incidence x-ray diffraction results show that at low nominal lipid density, P188, by physically occupying the available area and phase separating from the lipids, forces the lipid molecules to pack tightly and restore the barrier function of the membrane. Upon compression to bilayer equivalent pressure, P188 is squeezed out from the lipid monolayer, allowing a graceful exit of P188 when the membrane integrity is restored.     

Synchrotron X-ray diffraction study of corneal stroma

Using a synchrotron X-ray source, it has been possible to record a low-angle diffraction pattern from fresh bovine corneal stroma.The pattern can be interpreted as arising from the short-range order packing of collagen fibrils in lamellae. Model calculations suggest that the positions of the fibrils remain correlated over distances corresponding to, at most, three fibril diameters (~ 120 nm). These results support theories of transparency of the cornea based on short-range order.Further, a study of the fibril spacing as a function of hydration confirms that water uptake occurs largely between the lamellae and in regions devoid of collagen fibrils, and shows that the fibril diameter increases with hydration.     

Crystallization and preliminary X-ray diffraction study of an endoglucanase from Clostridium thermocellum

Endoglucanase D, a cellulose degradation enzyme from Clostridium thermocellum has been cloned in Escherichia coli, purified and crystallized. The crystals are trigonal, space group P3(1)12 (or P3(2)12) with a = 57.7 (+/- 0.1) A, c = 192.1 (+/- 0.2) A, and diffract X-rays to a resolution of 2.8 A. They are suitable for a high-resolution X-ray diffraction analysis.     

An X-ray diffraction study of poly-L-arginine hydrochloride

An x-ray study has been made of polyarginine hydrochloride to investigate whether, like polylysine hydrochloride, it can undergo conformational changes merely from variations in the degree of hydration. X-ray powder and fiber photographs of specimens containing up to about five molecules of water per arginine residue show features characteristic of α-helical structures including a 5.4-Å layer line and a meridional 1.5-Å reflection. Increasing the water content from ¹/₂ to 6¹/₂ molecules per residue causes the a axis of the hexagonal unit cell to increase from 14.4 Å to 15.8 Å, with no appreciable change in the 27.0 Å c axis. Removal of the last half molecule of water results in a very diffuse α pattern, but on rehydration the sharp pattern reappears. Specimens containing five to twenty water molecules per residue show quite a different pattern, the spacing of which do not vary appreciably with hydration. This pattern includes a meridional 3.4-Å reflection, a feature commonly shown by β structures, and indeed all the reflections can be satisfactorily indexed in terms of a monoclinic unit cell with a = 9.26 Å, b = 22.05 Å, c = 6.76 Å, and γ = 108.9°. These dimensions are shown by models to be compatible with a β pleated-sheet structure.     

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.     

The effect of zeaxanthin on the thickness of dimyristoylphosphatidylcholine bilayer: X-ray diffraction study

Multilayers of dimyristoylphosphatidylcholine (DMPC) modified with a carotenoid pigment zeaxanthin were analyzed by means of small-angle X-ray diffractometry. The results are discussed in terms of the superlattice theory developed recently for metallic multilayers. Inclusion of zeaxanthin to a DMPC bilayer increases thickness of the hydrophobic core by about 3 Å in the whole lipid-pigment miscibility range. The thickness increases very sharply as pigment concentration approaches the threshold of miscibility. Zeaxanthin aggregation within a layer causes further changes in the thickness of the membrane: a local decrease followed by a gradual rise.     

An X-ray diffraction and X-ray absorption spectroscopy joint study of neuroglobin

Neuroglobin (Ngb) is a member of the globin family expressed in the vertebrate brain, involved in neuroprotection. A combined approach of X-ray diffraction (XRD) on single crystal and X-ray absorption spectroscopy (XAS) in solution, allows to determine the oxidation state and the structure of the Fe-heme both in the bis-histidine and the CO-bound (NgbCO) states. The overall data demonstrate that under X-ray the iron is photoreduced fairly rapidly, and that the previously reported X-ray structure of ferric Ngb [B. Vallone, K. Nienhaus, M. Brunori, G.U. Nienhaus, Proteins 56 (2004) 85-92] very likely refers to a photoreduced species indistinguishable from the dithionite reduced protein. Results from the XAS analysis of NgbCO in solution are in good agreement with XRD data on the crystal. However prolonged X-ray exposure at 15 K determines CO release. This preliminary result paves the way to experiments aimed at the characterization of pentacoordinate ferrous Ngb, the only species competent in binding external ligands such as O₂, CO or NO.     

Cinnamomin: separation,crystallization and preliminary X-ray diffraction study

Cinnamomin from Cinnamonum camphora seeds, a type II ribosome-inactivating protein that interferes with protein biosynthesis in mammalian cells, can induce the apoptosis of carcinoma cells and be used as an insecticide. A rapid and improved method has been developed for the extraction and purification of cinnamomin from camphora seed. Purification of cinnamomin is achieved with two successive steps of hydrophobic interaction chromatography carried out on a fast protein liquid chromatography (FPLC) system. Crystals suitable for X-ray diffraction analysis were obtained by vapor diffusion method. A complete data set at 2.8 A resolution has been collected. Data indexation and refinement indicate that the crystal is orthorhombic with space group P2(1)2(1)2(1) and unit cell dimensions a = 52.39 A, b = 126.33 A, c = 161.45 A. There are two molecules per asymmetric unit. Initial phasing by molecular replacement method yielded a solution, which will contribute to the structure determination. A molecular model will further the understanding of the mechanism of cinnamomin function. The latter will be combined with bio-informatics to facilitate the medical and other applications of cinnamomin.     

Amiodarone-liposome interaction: a multinuclear NMR and X-ray diffraction study

Amiodarone, a potent antiarrhythmic drug, is widely used in cardiology. Its electrophysiological effects, as well as many of its side effects, seem to involve lipids. We report here a multinuclear NMR and X-ray diffraction study of amiodarone in egg phosphatidylcholine liposomes and lipid multilayers. In proton NMR experiments, amiodarone alters the signal from the lipid trimethyl ammonium group for pH values ranging from 3.2 to 8.4; cholesterol does not cause this alteration. The addition of SCN- changes both the proton and phosphorus NMR spectra of liposomes containing amiodarone. For both proton and carbon NMR, amiodarone modifies the signal from the lipid methylene groups, but to a far lesser extent than does cholesterol. Incorporation of amiodarone in EPC bilayers also modifies the low-angle X-ray diffraction patterns, decreasing the lamellar repeat period at low water contents, but swelling the fluid spaces between bilayers at high water contents. Electron density profiles and modeling studies using the X-ray data indicate that amiodarone decreases the bilayer thickness and adds electron density at the interfacial region of the bilayer. Our analysis of the NMR and X-ray data indicates that the iodine atoms of amiodarone are located near the hydrocarbon/water interface and that the tertiary amine of amiodarone is in the headgroup region of the bilayer.     

Role of intestinal mucus in crystal biogenesis: an electron-microscopical,diffraction and X-ray microanalytical study

Summary In the posterior intestine of the sea-water eel, mucus plays an important role in biocrystallization of calcium ions. By means of transmission and scanning electron microscopy associated with X-ray microanalysis and X-ray diffraction it has been possible to determine the role of mucous fibers as nucleation sites. Biocrystallization occurs in 2 steps: (1) Calcification of mucus. As soon as mucus is excreted in the intestinal lumen, it is loaded with calcium, as shown by lanthanum affinity and X-ray microanalysis on freeze-dried tissues. (2) Genesis of crystals. Needleshaped crystallites build up in coalescent spherites in the intestinal lumen near the microvilli. Genesis occurs as follows: (a) crystallite mineralization by nucleation in an organic matrix composed of glycoproteinaceous mucous fibers, followed by the appearance of spherites; (b) coalescence in spherites and association of spherites in rhombohedra; (c) extrusion of organic material during the final step of crystallization.     

A microbeam X-ray diffraction study of insulin spherulites

The peptide hormone insulin forms a spherical aggregate, called a spherulite, at low pH and high temperature. A spherulite is composed of a core and many fibrils extending from it. These fibrils are thought to be amyloid fibers with a beta-sheet structure. In the present study, spherulites with a diameter of 50-100 microm were examined by X-ray fiber diffraction using a 6 microm beam. When a spherulite was scanned with the microbeam and the observed diffraction patterns were arranged in a two-dimensional array, the direction of the scatter was centrosymmetric, demonstrating a symmetric growth of fibrils. There were diffraction peaks at Bragg spacings of 23 nm, 3.3 nm and 1.2 nm in the direction perpendicular to the fibrils and 0.48 nm along the fibrils. The 0.48 nm reflection shows that the hydrogen bonds between beta-strands are along the fibril. The 23 nm reflection corresponds to the separation between fibrils, the 3.3 nm reflection is due to the arrangement of protofilaments, and the 1.2 nm reflection arises from the arrangement of peptide chains. On the basis of these results, a model of a fibril with an extended insulin molecule is proposed.     

An X-ray diffraction study of poly-L-homoarginine hydrochloride.

An X-ray study of the synthetic polypeptide poly(L -homoarginine hydrochloride) has been made to investigate whether, like the chemically related polypeptides poly(L -lysine hydrochloride), poly(L -arginine hydrochloride), and poly(L -ornithine hydrobromide), it can undergo conformational transitions merely from variations in its degree of hydration. X-ray photographs of powder and oriented specimens containing one to 15 molecules of water per L -homoarginine hydrochloride residue showed that this polymer forms only a β-pleated-sheet structure. The pleated sheets, formed by antiparallel polypeptide chains hydrogen-bonded to each other, are piled up along the b axis in an alternating sequence (“sandwich structure”). This structure did not appreciably change with variations of the degree of hydration, and the observed reflections at 56% relative humidity (1.8 molecules of water per residue) could be indexed satisfactorily in terms of a monoclinic unit cell, of space group P2₁, with a = 9.34 Å, b = 40.07 Å, c = 6.94 Å, and γ = 106°. These dimensions are shown by models to be compatible with the proposed structure, and the calculated density of 1.27 g/cm³ agrees well with the experimental value of 1.29 g/cm³. Removal of the last molecule of water results in a very diffuse pattern, while specimens containing 20 molecules of water per residue show only reflections due to water.     

Desulforedoxin: Preliminary X-ray diffraction study of a new iron-containing protein

Desulforedoxin, a two-iron, two-chain protein from the bacterium Desulfovibrio gigas, has been crystallized. X-ray diffraction photos show symmetry consistent with space group P3₁21 or the enantiomorph P3₂21. Cell parameters are $\text{a = b = 42.28}\text{A}\text{?}\text{, c = 72.46}\text{A}\text{?}$.Crystals develop sufficiently well for an X-ray diffraction analysis of at least 2.0 Å resolution to be performed.