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PubMed2002

Hydrogen and deuterium in myoglobin as seen by a neutron structure determination at 1.5 A resolution.

From the first days of protein neutron structure determination sperm whale myoglobin was an object under investigation [Nature 224 (1969) 143, J. Mol. Biol. 220 (1991) 381]. Nevertheless myoglobin is still of interest [Proc. Natl. Acad. Sci. USA 97 (2000) 3872]. The feasibility of the monochromatic neutron diffractometer BIX-3 at the JRR-3M reactor at the JAERI [J. Phys. Chem. Solids 60 (1999) 1623], to collect high-resolution diffraction data in a relatively short time stimulated us to repeat the structural determination of myoglobin. The structure of metmyoglobin has been determined up to a resolution of 1.5 A. The hydrogen atoms were replaced in part, by deuterium soaking the crystals for more than 10 years in D(2)O. A refinement of all atoms has been performed including the refinement of individual mean square displacements and occupancies of the exchangeable protons in backbone hydrogen bonds. A method is described to show clear negative scattering densities of the H atoms. Water molecules within the protein and on the molecule surface are shown. The exchangeability of H atoms is correlated with structural distribution and flexibility.

Animals↗
PubMed1977

The organization and function of water in protein crystals.

Dry proteins are dead, or at best asleep. Substitution of D2O can drastically alter biological activity. Water is thus essential in maintaining the structural integrity of biologically active macromolecules, and is implicated in their functioning. Such water may occupy a range of dynamical states, from being strongly bound and localized, to more labile and 'liquid-like'. Spatially ordering the macromolecules aids the search for the more localized water molecules. For example, diffraction experiments on singly crystals can resolve 'bound' water molecules within a protein molecule--ofter at active sites, coordinated to metals or ions. Less precise information is obtained on the partially occupied external water sites, which are of importance to the folding and dynamics of the biomolecule. Orientation of fibrous molecules increases the information obtainable from n.m.r. experiments. Combination of other experimental results on disordered aggregates (e.g. in solution) with chemical and structural data on the macromolecule and water itself yields useful, if circumstantial, information. Statistical and computer techniques may help to elucidate the complex nature of water-protein interactions, and to interpret the results of more complex experiments.

Binding Sites↗
PubMed1999

Charge density in NiCl2.4H2O at 295 and 30 K.

The charge distribution has been determined by multipole refinements against single-crystal X-ray diffraction data. In the refinements a comparison was made between the densities based on H-atom parameters from X-ray and neutron data, respectively. X-ray study: lambda(Mo Kalpha) = 0.71073 Å, F(000) = 408; at 30 K: R(F) = 0.015 for 6686 reflections; at 295 K: R(F) = 0.022 for 4630 reflections. The nickel ion is octahedrally surrounded by four water molecules and two chloride ions, forming a locally neutral Ni(H(2)O)(4)Cl(2) complex. Two of the water molecules are coordinated to nickel approximately in one of the tetrahedral ('lone-pair') directions; the other two are trigonally coordinated. At 30 K one H atom in one of the trigonally coordinated water molecules is disordered, with equal occupation of two different positions. Owing to the polarizing influence of the nickel ion there are two peaks in the lone-pair plane of the water molecules when these are tetrahedrally coordinated; for those trigonally coordinated there is just one peak. The individual ('partial') charge densities, calculated from the deformation functions of only nickel or the separate water molecules, have also been calculated to study the effects of superposition of the individual densities. In the individual density of nickel an excess is observed in the diagonal directions and a deficiency in the ligand directions. However, owing to the influence of the whole crystalline environment, the maxima around nickel are not found in the planes defined by nickel and the six ligands.

Journal Article↗
PubMed2002

Influence of neutron irradiation on holmium acetylacetonate loaded poly(L-lactic acid) microspheres.

Holmium-loaded microspheres are useful systems in radio-embolization therapy of liver metastases. For administration to a patient, the holmium-loaded microspheres have to be irradiated in a nuclear reactor to become radioactive. In this paper. the influence of neutron irradiation on poly(L-lactic acid) (PLLA) microspheres and films, with or without holmium acetylacetonate (HoAcAc), is investigated, in particular using differential scanning calorimetry (MDSC), scanning electron microscopy, gel permeation chromatography (GPC), infrared spectroscopy, and X-ray diffraction. After irradiation of the microspheres, only minor surface changes were seen using scanning electron microscopy, and the holmium complex remained immobilized in the polymer matrix as reflected by a relatively small release of this complex. GPC and MDSC measurements showed a decrease in molecular weight and crystallinity of the PLLA, respectively, which can be ascribed to radiation induced chain scission. Irradiation of the HoAcAc loaded PLLA matrices resulted in evaporation of the non-coordinated and one coordinated water molecule of the HoAcAc complex, as evidenced by MDSC and X-ray diffraction analysis. Infrared spectroscopy indicated that some degradation of the acetylacetonate anion occurred after irradiation. Although some radiation induced damage of both the PLLA matrix and the embedded HoAcAc-complex occurs, the microspheres retain their favourable properties (no marginal release of Ho, preservation of the microsphere size), which make these systems interesting candidates for the treatment of tumours by radio-embolization.

Calorimetry, Differential Scanning↗
PubMed1983

Structure of bacteriophage T7. Small-angle X-ray and neutron scattering study.

Small-angle x-ray and neutron scattering techniques were applied to bacteriophage T7 solutions at different scattering densities. Scattering curves determined under a variety of experimental conditions were used to derive a set of parameters characterizing the shape, size, and weight of the whole phage particle and of its DNA and protein components. The T7 head has an icosahedral shape with an edge of 37.7 +/- 0.5 nm, a volume of (12.0 +/- 1.0) x 10(4) nm3, and a small tail amounting to 6--7% of the head volume. The intraphage DNA region is most probably a hollow sphere. The best fit to the data was obtained with a model in which the hollow sphere filled with a protein core with a diameter of 24 nm. The average degree of swelling (i.e., the ratio of the hydrated to the dry volume) of the particle is 2.3; the degree of swelling of the DNA component is higher, 3.2, and that of the protein part is lower, 1.2.

DNA, Viral↗
PubMed2003

Low-temperature behavior of water confined by biological macromolecules and its relation to protein dynamics.

Confined water is an essential component of biological entities and processes and its properties differ from the ones of bulk water. Since protein and water dynamics are thought to be strongly coupled, and since macromolecular dynamics is crucial for biological function, the study of water confined by biological macromolecules is not only interesting on its own right but often provides useful information for understanding biological activity at the molecular level. Studies are reviewed that focus on the low-temperature behavior of water confined in protein crystals and in stacks of native biological membranes. Diffraction methods allowed the determination of characteristic changes that relate to the glass transition and crystallization of water. Protein crystallography and energy-resolved neutron scattering are employed to gain further insight into the coupling of solvent and protein dynamics.

Bacteriorhodopsins↗
PubMed2000

Structure, composition, and maturation of newly deposited calcium-phosphate crystals in chicken osteoblast cell cultures.

Characterization of the very early calcium phosphate (CaP) crystals deposited in bone or in osteoblast cell cultures has been hampered by the overwhelming presence of organic matrix components and cells that obscure spectral analyses. We have overcome this problem using isolated protein-free crystals and have obtained new data including 31P nuclear magnetic resonance (NMR) spectra for the first time from mineral crystals deposited during osteoblast calcification in culture. Crystals were isolated from cultures at two time points: (a) at first calcium accumulation (day 8-10) and (b) after 60 days of culture, to assess maturational changes. The analyses show that the chemical composition overall and short range order of the early and mature crystals are characteristic of the apatite crystals found in young embryonic chick bone in vivo. No mineral phase other than apatite was detected by any of the methods used. 31P NMR spectroscopy identified the HPO4 groups as those present in bone apatite. Similar to bone apatites, no OH groups were detected by Fourier transform infrared (FTIR) spectroscopy. The temporal maturational changes in composition and structure of the mineral phase were difficult to assess because of the continuous deposition of crystals throughout culturing. The pathway of the maturational changes observed were similar to those occurring in chick bone in vivo and synthetic apatite crystals in vitro although to a much smaller extent.

Animals↗
PubMed2004

Synthesis of new boron-rich building blocks for boron neutron capture therapy or energy-filtering transmission electron microscopy.

The synthesis of a new ortho-carborane derivative, tetracarboranylketone 4, is reported here. Ketone 4 was prepared from a tetraalkynylated ketone by the addition of decaborane. The keto group was then easily modified to yield the glycosides 17alpha and 18beta, which contain glucose or galactose, respectively, and the nucleotide 13b. In addition to ketone 4, which is acyclic, cyclic ketone 8 was also synthesised. X-ray diffraction analysis of compound 4 indicated the presence of two toluene guest molecules per molecule of the host compound. Furthermore, compound 4 displays a rather low cytotoxicity. These novel products can be used as building blocks to create a new class of biomolecules containing high-density carborane clusters. Such molecules may constitute powerful tools for applications like Boron Neutron Capture Therapy or Energy-Filtering Transmission Electron Microscopy.

Animals↗
PubMed1984

Spatial conformation of glycans and glycoproteins.

Ten years ago, we anticipated future results by building the Y-shaped molecular model of a biantennary glycan. Progressively, this structure has been refined and modified thanks to experimental data obtained by using physical methods: X-ray diffraction, electron spin resonance (EPR), nuclear magnetic resonance (NMR) including two-dimensional NMR and one-dimensional 1H-nuclear Overhauser effect (NOE) experiments, neutron scattering and hard-sphere exo-anomeric (HSEA) calculations. So, the concept evolved successively from the Y-, to the T-, the bird- and the "broken wing"-conformation, until the demonstration, that these conformers are interconvertible. The bird-conformation as well as the concept of the mobility of antennae are in a good agreement with the reactivity of lectins, including membrane lectins, by rendering accessible any specific sugar structure, and with the activity of glycosyltransferases by making reachable the substitutable hydroxyl groups even in the case of pentaantennary structures. Along this line, we know now that the tetraantennary glycans adopt an "umbrella conformation" in which the four antennae are disposed parallely to the protein surface and act as protective shields. So could be explained the resistance towards proteases and the weak antigenicity of numerous glycoproteins as well as the peculiar behaviour and resistance of metastatic cancerous cells since it has been recently demonstrated that membrane glycoproteins and fibronectin of this kind of cells are significantly enriched in tri- and tetraantennary glycans.

Animals↗
PubMed1993

Improved bioavailability of para-boronophenylalanine by cyclodextrin complexation.

This study was undertaken to develop an oral dosage form for para-boronophenylalanine (BPA) plus cyclodextrin (CD) for use in the thermal neutron capture therapy for malignant melanoma. Powders of the BPA and CD complexes were obtained in a molar ratio of 1:2. X-ray diffraction of the BPA-CD complexes showed halo patterns that indicated that each complex was in a new solid state as an amorphous compound. The enhancement of BPA solubility by glucosyl (G1)- and maltosyl (G2)-alpha-CD was greater than that with the other CDs. The isolation rate of BPA from its complex was different for each BPA-CD complex. The bioavailability of BPA in rats was improved with oral administration of the BPA-alpha-CD, G1-alpha-CD, and G2-alpha-CD complexes. In contrast, a complex of BPA and dimaltosyl (G2G2) or G2-beta-CD, which had low release rate and low solubility, did not improve the bioavailability of BPA. These results indicate that the solubility and release rate of BPA from a complex in solution are important for the bioavailability of BPA after oral administration of BPA-CD complexes.

Animals↗
PubMed1976

A neutron television camera detector.

The system under development has a large counting rate capability; this is extremely important where the total background count exceeds the total counts in the signals of interest. Its spatial resolution is of the order of one mm, which is perfectly adequate for neutron work, while the screen size of 400 mm is reasonable. The main limitation of the system is its limited counting efficiency, and this is directly attributable to the optical self-absorption of the neutron phosphor. Any newly developed transparent phosphor with the same light output would immediately change the situation. The success of the electronics hardware in reducing random noise is demonstrated in Figure 3, which shows in the bottom trace the live video output when the input to the system is a grey-scale test chart. The top trace is the output after the image has been digitally integrated. Figures 4 and 5 show the monitor outputs of the see articles x-ray system with a "still" diffraction pattern of a crystal of GPD (glyceraldehyde-3-phosphate dehydrogenase). Figure 4 is a photograph of the "live" video display, and Figure 5 is the digitally summed image. All coherent noise in the system, i.e., all noise synchronized with the TV scans has to be kept lower than the first bit threshold. However, this requirement can be relaxed when dealing with diffraction patterns, such as those from single crystals, for which a local background is subtracted from the pattern.

Neutrons↗
PubMed1996

Structural model of the 50S subunit of E. coli ribosomes from solution scattering.

The application of new methods of small-angle scattering data interpretation to a contrast variation study of the 50S ribosomal subunit of Escherichia coli in solution is described. The X-ray data from contrast variation with sucrose are analyzed in terms of the basic scattering curves from the volume inaccessible to sucrose and from the regions inside this volume occupied mainly by RNA and by proteins. From these curves models of the shape of the 50S and its RNA-rich core are evaluated and positioned so that their difference produces a scattering curve which is in good agreement with the scattering from the protein moiety. Based on this preliminary model, the X-ray and neutron contrast variation data of the 50S subunit in aqueous solutions are interpreted in the frame of the advanced two-phase model described by the shapes of the 50S subunit and its RNA-rich core taking into account density fluctuations inside the RNA and the protein moiety. The shape of the envelope of the 50S subunit and of the RNA-rich core are evaluated with a resolution of about 40 A. The shape of the envelope is in good agreement with the models of the 50S subunit obtained from electron microscopy on isolated particles. The shape of the RNA-rich core correlates well with the model of the entire particle determined by the image reconstruction from ordered sheets indicating that the latter model which is based on the subjective contouring of density maps is heavily biased towards the RNA.

Escherichia coli↗
PubMed2006

Chemical and morphological changes of historical lead objects as a result of the use of electrolytic reduction as a stabilization treatment.

This paper focuses on the evaluation of the treatment related to chemical and morphological changes of corroded lead artifacts when using electrolytic reduction as a stabilization method. Synchrotron radiation X-ray diffraction and X-ray photoelectron spectroscopy were used to study the chemical changes of the corrosion layer and on the top nanometer of surface, respectively. Neutron tomography and scanning electron microscopy were used to visualize potential morphological changes on millimeter and micrometer level, respectively. The results of this study have shown that electrolytic reduction is a reliable way to stabilize and conserve active corroded lead artifacts. The corrosion products are actually converted into metallic lead, while the morphological changes due to the treatment are limited.

Journal Article↗
PubMed1980

The conformation of a large RNA fragment from the E.coli ribosomal 16S-RNA. An X-ray and neutron small-angle scattering study.

A large 12S RNA fragment which constitutes the 5' two-thirds of 16S-RNA from the E. coli 30S subunit has been investigated by small-angle X-ray and neutron scattering. The results indicate that in reconstitution buffer the 12S-RNA fragment has a molecular weight of 270,000 +/- 20,000 and a radius of gyration of 7.1 nm. The scattering data are compatible with the RNA being folded into two major domains with the shapes of two adjacent, quite similar cylinders.

Escherichia coli↗
PubMed1978

X-ray and neutron small-angle scattering studies of the complex between protein S1 and the 30-S ribosomal subunit.

X-ray neutron solution scattering experiments have been done to investigate the influence of the binding of ribosomal protein S1 on the conformation of the 30-S ribosomal subunit of Escherichia coli. The following conclusions were made. 1. The alterations (if any) in conformation of the non-S1 parts of the 30-S subunit induced by S1 binding are too small to be detected (less than 0.1 nm change in radius of gyration). 2. The center of gravity of protein S1 bound to the 30-S subunit is quite far from the center of gravity of the particle (approximately 7.5 nm).

Escherichia coli↗
PubMed2000

Experimental observation of the alpha relaxation in supercooled water

Intermediate scattering functions for density fluctuation in D2O contained in pores of a Vycor glass have been measured using an improved neutron spin-echo spectrometer at two supercooled temperatures. The measurements cover the time range from 1 to 2300 ps with the Q range spanning the first diffraction peak of water. The time correlation functions can be fitted to a stretched exponential relaxation function with a Q-dependent amplitude. Both the stretch exponent and the relaxation time peak approximately at the Q value corresponding to the first diffraction peak, confirming the validity of the mode coupling idea in supercooled water.

Journal Article↗