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PubMed2001

A study of heat-treatment induced framework contraction in strontium-ETS-4 by powder neutron diffraction and vibrational spectroscopy.

The effects of heat-treatment on the structure of the strontium ion-exchanged titanosilicate ETS-4 have been studied by Rietveld analysis of powder neutron diffraction data and by FT-Raman spectroscopy. Hydrous Sr-ETS-4 (space group Cmmm), upon heat-treatment under inert atmosphere at temperatures between 423 and 573 K, exhibits framework contraction as evinced by the decrease in the unit cell dimensions. The effects of heat-treatment on the dimensions of the transport-controlling eight-membered ring (8MR) are elucidated by Rietveld analysis. It is also found that during heat-treatment: (a) the double three membered rings (D3MRs) in ETS-4 are sites of structural instability, (b) the titania chains running along [010] exhibit a large degree of disorder in the bridging oxygen atoms, and (c) significant relocations of the strontium cations take place, which may affect the separation properties of the heat-treated materials. Raman spectra of heat-treated ETS-4 crystals exhibit strong cation-framework interaction effects. Vibrational modes involving the atoms in the titania chains show progressive frequency shifts and loss of intensity with increasing heat-treatment temperature, in a manner consistent with the crystallographic results. The study indicates the potential for continuously varying the effective pore dimension of ETS-4 by combining heat-treatment with appropriate ion-exchange procedures.

Journal Article↗
PubMed2001

Rapid neutron-diffraction data collection for hydrogen-bonding studies: application of the Laue diffractometer (LADI) to the case study zinc (tris)thiourea sulfate.

The successful application of the newly developed image-plate neutron Laue diffractometer (LADI) at the Institut Laue-Langevin (ILL), Grenoble, France, for rapid hydrogen-bonding characterization is reported. The case study concerns the promising non-linear optical material zinc (tris)thiourea sulfate (ZTS), which contains 30 atoms in the asymmetric unit and crystallizes in the orthorhombic space group, Pca2(1), a = 11.0616 (9), b = 7.7264 (6), c = 15.558 (1) A [T = 100.0 (1) K]. The results from a 12 h data collection from ZTS on LADI are compared with those obtained over 135 h using the monochromatic four-circle diffractometer D9 at the same reactor source with a crystal 13 times larger in volume. Both studies reveal the extensive hydrogen bonding and other close non-bonded contacts within the material. As expected, the results from D9 are more precise than those obtained from LADI; however, the bond geometry determined from the two experiments is the same within the larger estimated standard deviations. Furthermore, the conclusions drawn from the two studies separately regarding the nature of all supramolecular features are identical. This illustrates that LADI is eminently suitable for rapid characterization of hydrogen-bonded structures by neutron diffraction, with the gain in speed compared with traditional instrumentation being several orders of magnitude.

Journal Article↗
PubMed1990

Cross-linkage sites in type I collagen fibrils studied by neutron diffraction.

Cross-links in tendon collagen are essential for the biomechanical strength of healthy tissue. The nature and position of these cross-links has long been a subject for conjecture. We have approached this problem in a non-destructive manner, by studying neutron diffraction from collagen fibrils that have been specifically deuterated by reduction at keto-amine and Schiff base groups with sodium borodeuteride (NaB2H4). The intensities of the first 23 meridional reflections were recorded for both native and reduced tendons. These data were used to calculate the neutron-scattering density profile of the 67 nm (D) repeat of type I collagen fibrils in rat tail tendon. This approach not only succeeds in determining the location of the cross-linkage sites with respect to the fibril structure, as projected onto the fibre axis, but also presents a novel form of the isomorphous derivative solution to the phase problem.

Animals↗
PubMed1995

Neutron diffraction analysis of the solvent accessible volume in cubic insulin crystals.

The average contact distance between protein and solvent surface atoms in cubic insulin crystals has been determined from two sets of 15 A resolution neutron diffraction data. A contact distance between the water hydrogen sites and the protein surface that is significantly shorter than the average protein-water oxygen contact distance implies that many water molecules are oriented with hydrogen atoms pointed towards the protein surface. The shape of the protein/solvent interface is consistent with the protein envelope obtained from atomic co-ordinates.

Animals↗
PubMed1985

A neutron diffraction study on the location of the polyene chain of retinal in bacteriorhodopsin.

We report on the location of the chain part of the retinylidene chromophore in the projected density of bacteriorhodopsin as determined by neutron diffraction from the two-dimensional purple membrane lattice. For this purpose, partially deuterated retinal was synthesized containing 10 deuterons at positions C-8, C-10, C-12, C-14, C-19(3), and C-20(3) of the polyene chain. Two sets of dark-adapted samples were prepared in entirely different ways: (i) Deuterated retinal was incorporated biosynthetically during growth of the bacteria by using the mutant JW5, which is deficient in the synthesis of retinal. (ii) The chromophore was converted to retinal oxime, the resulting colorless apomembrane was regenerated with deuterated retinal, and the residual retinal oxime was removed by washing with bovine serum albumin. Characterization of these samples by x-ray diffraction, absorption, and flash spectroscopy showed that they were identical to native purple membrane samples as judged by these criteria. Fourier difference maps were calculated from the differences in inplane diffraction from the deuterated membranes and from protonated samples that were prepared in exactly the same way. At 8.7 A resolution, both maps show a single major peak at the same position with the center of mass of the labeled part of the chain (C-11) between helices 6 and 3 but closer to helix 6. It appears likely that the COOH-terminal helix G, to which retinal is attached at lysine-216, is either helix 2 or 6.

Apoproteins↗
PubMed2002

Spin densities in a ferromagnetic bimetallic chain compound: polarized neutron diffraction and DFT calculations.

The spin population distribution in the ferromagnetically coupled hetero-bimetallic chain compound [MnNi(NO(2))(4)(en)(2)] (en = 1,2-ethanediamine) has been investigated by means of polarized neutron diffraction experiments, and the results compared with those from theoretical estimates obtained via calculations based on density functional theory on dinuclear molecular models of the chain. The spin distributions obtained from experiment and from theory are consistent and reflect a larger spin delocalization from the Ni atom due to the more covalent character of the Ni-N bonds compared to the Mn-O ones. Also a nearly isotropic spin distribution is observed for the more ionic d(5) Mn(2+) ion and a clearly anisotropic distribution for the d(8) Ni(2+) ion. The use of dinuclear molecular models for the calculation of the exchange coupling constant between Ni and Mn provide upper and lower limits (+17.6 and -4.2 cm(-)(1)) for the experimentally determined value (+1.3 cm(-)(1)), depending on how the missing part of the chain is simulated, but yield essentially the same spin distribution. The Mn(II)-Ni(II) weak ferromagnetic coupling in the chain is interpreted in a spin delocalization mechanism as resulting from the weakness of the overlap between the magnetic orbitals centered on nickel and those centered on manganese which are only weakly delocalized on the ligands.

Journal Article↗
PubMed1994

Neutron diffraction reveals the site of amantadine blockade in the influenza A M2 ion channel.

The influenza A M2 protein forms proton channels which are blocked by the anti-influenza drug amantadine. Using the technique of neutron diffraction with both deuterium-labeled amantadine and influenza A M2 peptides, this study has directly located the position of interaction between the drug and the transmembrane domain of M2. Amantadine is found 0.5 nm from the center of the bilayer in an area between Val 27 and Ser 31, a location consistent with the formation of a steric block within the ion channel. Similar experiments with amantadine and an amantadine-resistant mutant peptide showed no such interaction.

Amantadine↗
PubMed1983

Neutron diffraction analysis of cytochrome b5 reconstituted in deuterated lipid multilayers.

Cytochrome b5 was reconstituted with a highly deuterated phospholipid to form ordered multilayers consisting of repeated centrosymmetric pairs of asymmetric lipid-protein bilayers. Lamellar neutron diffraction data were collected to approximately 29 A resolution, and have been interpreted using models for the interaction of the membrane-binding domain of cytochrome b5 with the lipid bilayer. A range of different models was examined, and those in which the protein penetrates well into the bilayer, possibly spanning it, are favored.

Animals↗
PubMed1999

Single-crystal neutron diffraction study of beta-Cs3(HSO4)2

The structure of beta-Cs(3)(HSO(4))(2)[H(2-x)(S(x)P(1-x))O(4)] has been examined by single-crystal neutron diffraction at 15 K. The compound crystallizes in space group C2/c and contains four formula units in the unit cell, with lattice parameters a = 19.769 (9), b = 7.685 (2), c = 8.858 (3) Å and beta = 100.60 (4) degrees. Refinement of P, S and H site occupancies indicated that the value of x (in the stoichiometry) is 0.500 (6). This, together with the unit-cell volume of 1322.8 (14) Å(3), implies a density of 3.463 Mg m(-3). The structure contains zigzag rows of XO(4) anions, where X = P or S, that alternate, in a checkerboard fashion, with zigzag rows of Cs cations. Moreover, there is one proton site, H(3), with an occupancy of 0.25 and one X-atom site, X(1), that is occupied by 0.5 P and 0.5 S. These features are in general agreement with a previous X-ray structure determination carried out at 298 K. In contrast to the X-ray study, however, it was found that two different structural models adequately fit the diffraction data. In the first model, the proton vacancies and the P atoms were assumed to be randomly distributed over the H(3) and X(1) sites, respectively, and to have no impact on the local structure. In the second model, several atoms were assigned split occupancies over two neighboring sites, to reflect the presence or absence of a proton vacancy, and the presence of P or S on the X(1) site. Refinement assuming the first model, in which anisotropic displacement parameters for 12 of 14 atom sites in the asymmetric unit were employed, yielded residuals wR(F(2)) = 0.084 and wR(F) = 0.038. For the second model, in which anisotropic displacement parameters were utilized for only the five atoms that were not split relative to the first model, the residuals were wR(F(2)) = 0.081 and wR(F) = 0.036.

Journal Article↗
PubMed1988

On the occurrence of three-center hydrogen bonds in cyclodextrins in crystalline form and in aqueous solution: comparison of neutron diffraction and molecular dynamics results.

Three-center (bifurcated) hydrogen bonds may play a role by serving as an intermediate state between different dynamically changing hydrogen bonding patterns. Hydrogen bonding configurations can be studied experimentally by neutron diffraction and theoretically by computer simulation techniques. Here, both methods are used to analyse the occurrence of three-center hydrogen bonds in crystals of cyclodextrins. Almost all experimentally observed three-center hydrogen bonds in the crystal are reproduced in the molecular dynamics (MD) simulations, even as far as the detailed asymmetric geometry is concerned. On the basis of this result a MD simulation of cyclodextrin in aqueous solution is searched for the occurrence of three-center hydrogen bonds. Significant differences are found. In solution more different three-center hydrogen bonds per alpha-cyclodextrin molecule are observed than in the crystal but the population (existence as percent of the simulation period) of each three-center hydrogen bond is lower in solution than in crystal. These may indeed serve as intermediate states in the process of changing one hydrogen bonding pattern into another.

Chemical Phenomena↗
PubMed1986

Protein dynamics investigated by neutron diffraction.

The most correct model of the molecular structure of a protein molecule is one which describes it as having a number of variable conformational states. These states differ in degree over a large spectrum of structural variation ranging from individual atomic vibrational motion to significant tertiary denaturation. The application of the neutron diffraction techniques discussed above dealt with two classes of conformational fluctuation, "protein breathing" and "regional melting." The utility of the neutron technique stems from the ability to locate hydrogen atoms and to discriminate between hydrogens and deuteriums. This latter attribute allows for performing H/D exchange experiments by identifying individual sites of exchange. With this information it has been possible to discern which regions of the protein molecule undergo regional melting. Protein breathing was explored by analyzing the rotational properties of side chain methyl groups. Such information clearly suggested that most of these groups reside in "staggered" (low energy) conformation in the time averaged structure and are not greatly affected by local structural packing. Together these two classes of conformational fluctuation span nearly the full range of all motions that might play a role in biological activity. Information about such motions can be obtained from other types of physicochemical methods, but in most cases the interpretation of the data is considerably less definitive than that which can be obtained from a neutron analysis.

Crystallography↗
PubMed2001

Neutron diffraction study of phi-Bi(8)Pb(5)O(17): structure refinement and analysis of cationic ordering.

The triclinic crystal structure of the varphi phase in the structure of the Bi(2)O(3)-PbO phase diagram has been recently solved by the synergetic use of electron and X-ray diffraction on a polycrystalline Bi(8)Pb(5)O(17) sample. In the present work the problem is re-examined on the basis of powder neutron diffraction data: the structure has been confirmed and refined by the Rietveld method. The increased accuracy of the O-atom positions allowed the study of the cationic ordering in this structure by means of bond-valence calculations and charge distribution analysis. The results, confirmed by the refinement of the site occupancies, indicate that the structure is ordered to a large extent, with Bi and Pb atoms occupying preferentially different lattice sites. In this frame, the varphi phase being the most ordered one in the considered region of the Bi(2)O(3)-PbO phase diagram, it should represent the thermodynamically stable low-temperature polymorph.

Journal Article↗
PubMed1998

Localization of glycolipids in membranes by in vivo labeling and neutron diffraction.

Evidence is accumulating for the lateral organization of cell membrane lipids and proteins in the context of sorting or intracellular signaling. So far, however, information has been lacking on the details of protein-lipid interactions in such aggregates. Purple membranes are patches made up of lipids and the protein bacteriorhodopsin in the plasma membrane of certain Archaea. Naturally crystalline, they provide a unique opportunity to study the structure of a natural membrane at submolecular resolution by diffraction methods. We present a direct structural determination of the glycolipids with respect to bacteriorhodopsin in these membranes. Deuterium labels incorporated in vivo into the sugar moieties of the major glycolipid were localized by neutron diffraction. The data suggest a role for specific aromatic residue-carbohydrate stacking interactions in the formation of the purple membrane crystalline patches.

Amino Acids↗
PubMed1999

Orientation of the headgroup of phosphatidylinositol in a model biomembrane as determined by neutron diffraction.

Derivatives of the sodium salt of dimyristoylphosphatidylinositol (DMPI) have been synthesized specifically deuterated in the headgroup. A 50:50 (molar) mixture of DMPI with dimyristoylphosphatidylcholine (DMPC) hydrated to the level of 16 waters/lipid gives a biomembrane-like Lalpha phase at 50 degrees C. Comparison of the neutron diffraction scattering profiles for deuterated and undeuterated membranes allowed the depth of each deuterium (hydrogen) within the bilayer to be determined to +/-0.5 A. This gave the orientation of the inositol ring which lies more-or-less along the bilayer normal projecting directly out into the water. This orientation is similar to that of the sugar residue in glycolipids and confirms previous models for PI. On the assumption that the (P)O-DAG bond is more-or-less parallel to the bilayer normal, it is consistent with a roughly trans, trans, trans, gauche- conformation for the glyceryl-phosphate-inositol link. In the case of DMPI, it is the C4-hydroxy group which is most fully extended into the water layer, but when this is phosphorylated, the inositol ring turns over and tilts so that the C5-hydroxy group is now the one furthest extended into the water layer. Hence, at each stage in the pathway PI --> PI-4P --> PI-4,5-P2, it is the hydroxy position most exposed to the water which undergoes phosphorylation. Whereas the orientation of the inositol ring in DMPI can be seen simply as maximizing its hydration, the tilt of the ring in DMPI-4P cannot be explained in this way. It is suggested that it is due to an electrostatic interaction.

Carbohydrate Conformation↗
PubMed1991

Neutron diffraction studies of the structure of filamentous bacteriophage Pf1. Demonstration that the coat protein consists of a pair of alpha-helices with an intervening, non-helical surface loop.

The structure of filamentous bacteriophage Pf1 has been studied using neutron diffraction from magnetically oriented gels of native and specifically deuterated phage. These methods have been used to determine the positions of the two methionine, two tyrosine and six isoleucine residues of the coat protein. Combined with the positions of the five valine residues previously determined, they represent one third (15 of 46) of the residues of the coat protein. These 15 amino acid residue positions have been used as the basis for constructing a model for the protein consisting of two alpha-helices with an intervening surface loop. The first helix extends from near the amino terminus to Ile12. The second helix extends from Lys20 to at least Met42, and may contain a bend between Ile32 and Val35. The two helices are tilted by about 15 degrees relative to one another, and are positioned in such a way that they appear to be bound end-to-end by main-chain hydrogen bonds. The intervening, non-helical loop, made up of Thr13 to Met19, connects the two helices without disrupting the pattern of main-chain hydrogen bonding, but does not result in a bend in the otherwise continuous helical structure. This model is used to predict the approximate positions of all amino acid residues in the Pf1 protein coat, providing a basis for further understanding of a number of viral properties including the symmetry transitions, the non-isomorphism of heavy-atom derivatives, and the protein-protein and protein-DNA interactions in the virion.

Amino Acid Sequence↗
PubMedDate not supplied

A combined X-ray and neutron diffraction study of selectively deuterated melittin in phospholipid bilayers: effect of pH.

In order to study consequences of protonation of the N-terminus upon the interaction of the bee venom melittin with phospholipid bilayers, analogues of melittin, some of which were specifically deuterated at either Ala-12 or 15, were synthesized. These peptides were incorporated into bilayers of 1,2-dioleoyl-sn-glycero-3-phosphocholine at either low pH (N-terminus protonated) or high pH (N-terminus unprotonated). X-ray and neutron diffraction data were collected from ordered stacks of these bilayers and from peptide-free controls. Phase determination was carried out using the swelling series (X-ray) and isomorphous derivative (neutron) methods. The water distribution between adjacent bilayers in the stacks may be described by a pair of Gaussians whose position and width change with the protonation state of the melittin. Difference Fourier profiles reveal that the melittin largely incorporates into the phospholipid bilayers. Changes in the water, melittin and deuterium label distributions fit a model in which the melittin lies both at the surface and close to the centre of the bilayer, the distribution of peptide between these locations being pH-dependent, with a larger population of surface melittin when the N-terminus is unprotonated.

Amino Acid Sequence↗
PubMed1981

The reaction center profile structure derived from neutron diffraction.

Both reaction center protein from the photosynthetic bacteria Rhodopseudomonas sphaeroides and egg phosphatidylcholine can be deuterium labelled; the reaction center protein can be incorporated into the phosphatidylcholine bilayers forming a homogeneous population of unilamellar vesicles. The lipid profile and the reaction center profile within these reconstituted membrane profiles were directly determined to 32 A resolution using lamellar neutron diffraction from oriented membrane multilayers containing either deuterated or protonated reaction centers, and either deuterated or protonated phosphatidylcholine. The 32 A resolution reaction center profile shows that the protein spans the membranes, and has an asymmetric mass distribution along the perpendicular to the membrane plane. These results were combined with previously described X-ray diffraction results in order to extend the resolution of the derived reaction center profile to 9 A.

Bacterial Proteins↗
PubMed1991

Fluid bilayer structure determination by the combined use of x-ray and neutron diffraction. I. Fluid bilayer models and the limits of resolution.

This is the first in a series of papers concerned with methods for the determination of the structures of fluid phospholipid bilayers in the liquid-crystalline (L alpha) phase. The basic approach is the joint refinement of quasimolecular models (King and White, 1986. Biophys. J. 49:1047-1054) using x-ray and neutron diffraction data. We present here (a) the rationale for quasimolecular models, (b) the nature of the resolution problem for thermally disordered bilayers, and (c) an analysis of the resolution of experiments in which Gaussian functions are used to describe the distribution of submolecular components. We show that multilamellar liquid-crystalline bilayers are best described by the convolution of a perfect lattice function with a thermally disordered bilayer unit cell. Lamellar diffraction measurements on such a system generally yield only 5-10 orders of diffraction data from which transbilayer profiles of the unit cell can be constructed. The canonical resolution of these transbilayer profiles, defined as the Bragg spacing divided by the index of the highest recorded diffraction order, is typically 5-10 A. Using simple model calculations, we show that the canonical resolution is a measure of the widths of the distributions of constituents of the unit cell rather than a measure of the spatial separation of the distributions. The widths provide a measure of the thermal motion of the bilayer constituents which can be described by Gaussian functions. The equilibrium positions of the centers of the distributions can be determined with a precision of 0.1-0.5 A based upon typical experimental errors.

Lipid Bilayers↗