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Direct determination of the calcium profile structure for dipalmitoyllecithin multilayers using neutron diffraction.

The distribution of calcium in lamellar phases of dipalmitoyllecthin (DPPC) multilayers was directly determined by neutron diffraction and stable isotope substitution of 44Ca for 40Ca. A significant resonance effect on the intensities of the lamellar diffraction pattern was observed for millimolar concentrations of these calcium isotopes. The calcium difference profile indicated that calcium was localized in the phospholipid headgroup region, being excluded from the hydrocarbon core as was water separately determined from the water profile structure obtained by H2O/D2O exchange. A reciprocal space analysis of the difference structure factors indicated that calcium binds preferentially to within 1-2 A of the phosphate moiety of the phospholipid head groups of the DPPC bilayer.

Calcium↗

A single-crystal neutron diffraction study of RbTiOAsO(4).

A rubidium titanyl arsenate single-crystal has been studied by neutron diffraction (lambda = 1.207 A). The polished sample used was 5 x 3 x 2 mm and was cut from a crystal made by top-seeded solution growth. The crystal showed severe extinction. It was, however, possible to obtain a structural model with well defined oxygen sites and reasonable anisotropic displacement parameters.

Journal Article↗

Five-Coordinate Hydrogen: Neutron Diffraction Analysis of the Hydrido Cluster Complex

Pentacoordinate hydrogen atoms were identified by single-crystal neutron diffraction analysis of [N(CH3)4]3[H2Rh13(CO)24]. The hydrogen atoms are located in square pyramidal cavities of the Rh13 cluster, in positions almost coplanar with the Rh4 faces on the surface of the cluster. They are slightly displaced inward, toward the central rhodium atom of the cluster, with average H-Rh(central) and H-Rh(surface) distances of 1.84(2) and 1.97(2) angstroms, respectively. This result shows that hydrogen, which normally forms only one bond, can be attached to five other atoms simultaneously in a large metal cluster.

Journal Article↗

Structure and dynamics of hydrogen molecules in the novel clathrate hydrate by high pressure neutron diffraction.

The D2 clathrate hydrate crystal structure was determined as a function of temperature and pressure by neutron diffraction for the first time. The hydrogen occupancy in the (32+X)H2.136H(2)O, x=0-16 clathrate can be reversibly varied by changing the large (hexakaidecahedral) cage occupancy between two and four molecules, while remaining single occupancy of the small (dodecahedral) cage. Above 130-160 K, the guest D2 molecules were found in the delocalized state, rotating around the centers of the cages. Decrease of temperature results in rotation freezing followed by a complete localization below 50 K.

Journal Article↗

"NaB15": a new structural description based on X-ray and neutron diffraction, electron microscopy, and solid-state NMR spectroscopy

A boron-rich sodium boride, formerly known as NaB15, has been subjected to a comprehensive structural reinvestigation using X-ray single-crystal and powder diffraction, low-temperature neutron and electron diffraction, high-resolution transmission electron microscopy, and 23Na solid-state NMR spectroscopy. The results indicate that the previously published orthorhombic space group is incorrect. Consistent with all of the experimental results a modified structural description is developed in the monoclinic space group Ilml (a = 585.92(3), b= 1039.92(6), c = 833.17(5) pin, beta = 90.373(5) from powder data). Because one of the interstitial boron atom positions remains unoccupied, the accurate compositional formula is NaB145 or Na2B29.

Journal Article↗

Gamma-ray and neutron diffraction studies of CoF2: magnetostriction, electron density and magnetic moments.

Accurate structure factors up to sin theta/lambda = 1.6 A(-1) have been measured with 316.5 keV gamma-rays from CoF(2), both at room temperature and in the antiferromagnetic state at 10 K. The same crystal was used to collect extended time-of-flight neutron diffraction data in the two magnetic states, which allowed an accurate determination of the fluorine positional parameter. For room temperature, the standard structural parameters are reported. At 10 K, a complete charge-density study has been carried out. The total number of 3d electrons on Co is found to be 6.95 (3). The experimental populations of the d orbitals agree with expectation from crystal field theory. The fluorine valence region exhibits a strong dipolar deformation. Electronic properties at the bond critical points and integrated atomic properties are derived from the static model electron density, revealing the Co-F interactions as purely ionic. On magnetic ordering, a shift of the fluorine ions of 1.5 (4) x 10(-3) A is found which confirms a prediction from theory of optical birefringence. The effect of magnetostriction on the distortion of the ligand coordination octahedra is compared for the late members of the 3d transition-metal difluorides. From neutron powder diffraction, an ordered magnetic moment of 2.60 (4) mu(B) per cobalt ion is found. Despite the strong deviation from the ideal spin value of 3 mu(B), there is still an appreciable orbital contribution to the local magnetic moment.

Journal Article↗

Localization of two chymotryptic fragments in the structure of renatured bacteriorhodopsin by neutron diffraction.

The structure of crystalline purple membrane reconstituted from purified bacteriorhodopsin (BR) chymotryptic fragments has been studied by neutron diffraction. In one of the samples studied, the fragment C-2, encompassing the first two predicted transmembrane segments, was prepared from deuterated purple membrane. The diffraction changes when the natural C-2 fragment is substituted by a deuterated one are analysed in terms of a seven-helix model for BR. The assignment of the labelled fragment to one end of the molecule placed new constraints on folding models for the protein.

Bacteriorhodopsins↗

Fluid bilayer structure determination by the combined use of x-ray and neutron diffraction. II. "Composition-space" refinement method.

This is the second of two papers describing a method for the joint refinement of the structure of fluid bilayers using x-ray and neutron diffraction data. We showed in the first paper (Wiener, M. C., and S. H. White. 1990. Biophys. J. 59:162-173) that fluid bilayers generally consist of a nearly perfect lattice of thermally disordered unit cells and that the canonical resolution d/hmax is a measure of the widths of quasimolecular components represented by simple Gaussian functions. The thermal disorder makes possible a "composition space" representation in which the quasimolecular Gaussian distributions describe the number or probability of occupancy per unit length across the width of the bilayer of each component. This representation permits the joint refinement of neutron and x-ray lamellar diffraction data by means of a single quasimolecular structure that is fit simultaneously to both diffraction data sets. Scaling of each component by the appropriate neutron or x-ray scattering length maps the composition space profile to the appropriate scattering length space for comparison to experimental data. Other extensive properties, such as mass, can also be obtained by an appropriate scaling of the refined composition space structure. Based upon simple bilayer models involving crystal and liquid crystal structural information, we estimate that a fluid bilayer with hmax observed diffraction orders will be accurately represented by a structure with approximately hmax quasimolecular components. Strategies for assignment of quasimolecular components are demonstrated through detailed parsing of a phospholipid molecule based upon the one-dimensional projection of the crystal structure of dimyristoylphosphatidylcholine. Finally, we discuss in detail the number of experimental variables required for the composition space joint refinement. We find fluid bilayer structures to be marginally determined by the experimental data. The analysis of errors, which takes on particular importance under these circumstances, is also discussed.

Lipid Bilayers↗

Hydroxyl hydrogen conformations in trypsin determined by the neutron diffraction solvent difference map method: relative importance of steric and electrostatic factors in defining hydrogen-bonding geometries.

Neutron diffraction maps have been used to assign the rotor conformations of the hydroxyl hydrogens in trypsin. Knowledge of these conformations is used to assess the relative importance of steric and electrostatic effects in conferring the H-bonding geometries of these groups. A general finding was that most hydroxyl groups are rotationally ordered with their highest populated conformation near the low-energy staggered orientation. For the low-energy conformers (-60 degrees, 60 degrees, 180 degrees) of serine and threonine, the trans (-180 degrees) position is most highly populated followed by +60 degrees. In trypsin, only 1 of 24 serines was found in the -60 degrees conformer. Serine hydroxyls preferentially act as H-bond acceptors and rarely are observed as H-bond donors alone. Threonines were found to be more likely than serines to participate in two H bonds; tryosines were found to prefer to act as donors. In H-bonding situations in which there was incompatibility between the energies defining the barrier to rotation and the local electrostatics, the electrostatic criteria dominated. Overall, the findings support a model of H bonding where there exists strong inherent complementarity between the low-energy hydroxyl orientations and the local electrostatic environment.

Hydrogen Bonding↗

Crystal structure and thermal vibrations of cholesteryl acetate from neutron diffraction at 123 and 20 K.

Cholesteryl acetate (C29H48O2) at 20 K is monoclinic, space group P2(1) with a = 16,521 (4), b = 9,220 (2), c = 17,620 (5) A, beta = 107.18 (2) degrees and Z = 4 (two molecules in the asymmetric unit). The crystal structure, earlier determined by X-ray diffraction at 123 K, has been redetermined at 123 and 20 K by neutron diffraction (7447 reflections at 123 K, 7281 at 20 K; sin theta/lambda less than 0.69 A-1) and refined by full-matrix least squares with 1423 variables to give R(F2) = 0.10 at 123 K, 0.06 at 20 K. Results at 20 K are more accurate not only because nuclear thermal vibrations have reduced amplitudes but also because a larger crystal was used for data collection. At 20 K, the average of 44 methylene C-H bond lengths is 1,102 (8) A (sigma from the observed distribution) and 1.103 (6) A for 16 methine groups. The 22 methylene H-C-H angles [106.2 (9) degrees] all fall within a narrow range. Analysis of nuclear anisotropic thermal parameters shows that intramolecular vibrations of the H nuclei are highly significant with similar mean-square amplitudes at 123 and 20 K. Torsional vibrations around the C-CH3 bonds of the C18 and C19 methyl groups have r.m.s. amplitudes of about 7 degrees. For methylene groups, mean-square amplitudes are a minimum for C-H bond stretching (0.006 A2) and a maximum for CH2 in-plane vibrations (0.024 A2). Values of Beq for the H-atom intramolecular vibrations are 0.8, 1.2 and 1.6 A2 for methine, methylene and methyl H atoms respectively. These results can be used to estimate Beq for H atoms in crystal structure determinations carried out by X-ray diffraction. The anisotropic intramolecular vibrations of the H nuclei contribute to the effective shape of the H atoms which, from the observed anisotropy in the distribution of intermolecular H...H distances, appears to be flattened along the direction of the C-H bond.

Cholesterol Esters↗

Neutron diffraction reveals sequence-specific membrane insertion of pre-fibrillar islet amyloid polypeptide and inhibition by rifampicin.

Human islet amyloid polypeptide (hIAPP) forms amyloid deposits in non-insulin-dependent diabetes mellitus (NIDDM). Pre-fibrillar hIAPP oligomers (in contrast to monomeric IAPP or mature fibrils) increase membrane permeability, suggesting an important role in the disease. In the first structural study of membrane-associated hIAPP, lamellar neutron diffraction shows that oligomeric hIAPP inserts into phospholipid bilayers, and extends across the membrane. Rifampicin, which inhibits hIAPP-induced membrane permeabilisation in functional studies, prevents membrane insertion. In contrast, rat IAPP (84% identical to hIAPP, but non-amyloidogenic) does not insert into bilayers. Our findings are consistent with the hypothesis that membrane-active pre-fibrillar hIAPP oligomers insert into beta cell membranes in NIDDM.

Amyloid↗

Neutron diffraction studies of fluid bilayers with transmembrane proteins: structural consequences of the achondroplasia mutation.

Achondroplasia, the most common form of human dwarfism, is due to a G380R mutation in the transmembrane domain of fibroblast growth factor receptor 3 (FGFR3) in >97% of the studied cases. While the molecular mechanism of pathology induction is under debate, the structural consequences of the mutation have not been studied. Here we use neutron diffraction to determine the disposition of FGFR3 transmembrane domain in fluid lipid bilayers, and investigate whether the G380R mutation affects the topology of the protein in the bilayer. Our results demonstrate that, in a model system, the G380R mutation induces a shift in the segment that is embedded in the membrane. The center of the hydrocarbon core-embedded segment in the mutant is close to the midpoint between R380 and R397, supporting previous measurements of arginine insertion energetics into the endoplasmic reticulum. The presented results further our knowledge about basic amino-acid insertion into bilayers, and may lead to new insights into the mechanism of pathogenesis in achondroplasia.

Achondroplasia↗

5-A Fourier map of gramicidin A phased by deuterium-hydrogen solvent difference neutron diffraction.

Crystals of ion-free gramicidin A (P212121: a = 24.61, b = 32.28, c = 32.52) have been investigated using neutron diffraction. A difference analysis of crystals soaked in ethanol/H2O as opposed to ethanol-d6/D2O has led to single isomorphous replacement Fourier projections of the structure at 5-A resolution. The gramicidin dimer appears to be a 32-A-long cylinder oriented parallel to the c-axis in these crystals.

Crystallography↗

Localization of coenzyme Q10 in the center of a deuterated lipid membrane by neutron diffraction.

Quinones (e.g., coenzyme Q, CoQ10) are best known as carriers of electrons and protons during oxidative phosphorylation and photosynthesis. A myriad of mostly more indirect physical methods, including fluorescence spectroscopy, electron-spin resonance, and nuclear magnetic resonance, has been used to localize CoQ10 within lipid membranes. They have yielded equivocal and sometimes contradictory results. Seeking unambiguous evidence for the localization of ubiquinone within lipid bilayers, we have employed neutron diffraction. CoQ10 was incorporated into stacked bilayers of perdeuterated dimyristoyl phosphatidyl choline doped with dimyristoyl phosphatidyl serine containing perdeuterated chains in the natural fluid-crystalline state. Our data show CoQ10 at the center of the hydrophobic core parallel to the membrane plane and not, as might be expected, parallel to the lipid chains. This localization is of importance for its function as a redox shuttle between the respiratory complexes and, taken together with our recent result that squalane is in the bilayer center, may be interpreted to show that all natural polyisoprene chains lie in the bilayer center. Thus ubiquinone, in addition to its free radical scavenging and its well-known role in oxidative phosphorylation as a carrier of electrons and protons, might also act as an inhibitor of transmembrane proton leaks.

Coenzymes↗

Direct methods for the analysis of lamellar neutron diffraction from oriented multilayers: a difference Patterson deconvolution approach.

We have described here a direct method for the solution of the phase problem for lamellar neutron diffraction from hydrated oriented multilayers of model membranes. As a result, the neutron-scattering profiles of such model membranes can be uniquely determined. We note that such methods can easily be extended to cases in which the thickness of the water layer w is somewhat greater than d/2 as long as it is substantially less than d [e.g., w less than 3d/4 would suffice, since deltaP(-d/4 less than or equal to x less than or equal to d/4) would contain only contributions from see article without overlapping contributions from see articles and to cases in which isotopic labeling is used instead of partial H2O-D2O exchange.

Cholesterol↗

Structure of RNA in satellite tobacco necrosis virus. A low resolution neutron diffraction study using 1H2O/2H2O solvent contrast variation.

The crystal structure of satellite tobacco necrosis virus has been studied by neutron diffraction at 16 A resolution using the technique of 1H2O/2H2O solvent contrast variation to distinguish between the regions of protein and nucleic acid. The RNA density is essentially localized in a region just inside the protein coat, leading to a significant interaction between the two components. From the appearance of the RNA density we conclude that the protein coat imposes partial icosahedral symmetry on a significant proportion of the nucleic acid. The shape and dimensions of the major part of this density suggests that about 72% of the total RNA could be double-helical in structure. The most important interaction between the two components of the virus occurs between the N-terminal triple-helical arms of the protein subunits and those regions of the RNA density that could have a double-helical secondary structure.

Amino Acid Sequence↗

Structure of strontium hydroxide octahydrate, Sr(OH)2.8H2O, at 20, 100 and 200 K from neutron diffraction.

The crystal structure of Sr(OH)2*8H2O has been determined at 20, 100 and 200 K from neutron diffraction data. The structure consists of double layers of H2O and OH- ions separated by Sr2+ along the c axis. The Sr2+ ions are eight-coordinated by water O atoms in a square antiprism configuration. Each H2O molecule is engaged in three hydrogen bonds. The OH- ions form chains of acceptor and donor bonds along the fourfold axis with O atoms engaged in four bonds with H2O molecules, such that both non-equivalent O atoms have square-pyramidal environments of five H atoms and the overall bonding configurations of distorted octahedra.

Journal Article↗

Binding of dimethyl sulfoxide to lysozyme in crystals, studied with neutron diffraction.

Crystals of hen egg white lysozyme soaked in 15% (v/v) dimethyl sulfoxide have been studied with single-crystal neutron diffraction to determine the effect of the solvent molecules on the protein configuration. A total of 9423 statistically significant Bragg reflections to a resolution of approximately 1.8 A were used to locate 6 dimethyl sulfoxide molecules, and structure refinements including a model for the flat solvent lead to a final crystallographic agreement factor of 0.130. The mode of location of the dimethyl sulfoxide molecules was compared with that in previous studies employing ethanol. This showed that hydrophobic interactions can be an essential factor in fixing the probe molecules on the protein surface. There was, however, no sign of any significant change in the protein configuration; so although possibly at higher concentrations of dimethyl sulfoxide the protein will unfold, there was no indication of any precursor effect.

Dimethyl Sulfoxide↗