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Incorporation of phosphonic acid diesters into lipid model membranes. Part II. X-ray and neutron diffraction studies.

Mixtures of egg phosphatidylcholine and phosphonic acid diethyl or dibutyl esters of the general type RP(O)(OR')2 with R = hexane or dodecane were studied at room temperature in the fluid lamellar state by X-ray and by neutron diffraction. Generally a molar ratio of lipid and ester of 1:0.5 was used. Additionally an equimolar lipid/ester mixture of hexane phosphonic acid diethyl ester was studied. Depending on the ester used and its concentration a single L alpha-phase was observed above a certain water content which changes to an L alpha + water two phase system at high water concentration. Despite the large amounts of the amphiphilic ester molecules incorporated in the membrane and their high molecular asymmetry, the mixtures qualitatively show the typical hydration and swelling behaviour of non-charged lipid membranes. However, the incorporation of the esters induces a higher hydration capacity, a lateral extension and a decrease in membrane thickness. The position of the ester molecules and their orientation in the membrane were determined by neutron diffraction using partially deuterated esters. The esters were found to be located with their phosphonic moiety near or in the lipid/water interface. The lamellar structure contradicts this location of the cone-shaped ester molecules which should increase the tendency to form hexagonal structures. However, the experimental findings can be understood if one considers a partial interdigitation of the last hydrocarbon groups of the lipid chains accompanied by a larger disorder in the hydrophobic centre of the membrane. In the case of hexane phosphonic acid dibutyl ester, a vertical translocation of the ester takes place below a certain water content where it is distributed between two locations at the lipid water interface and the centre of the membrane.

Esters↗

Nuclear magnetic resonance and neutron diffraction studies of the complex of ribonuclease A with uridine vanadate, a transition-state analogue.

The complex of ribonuclease A (RNase A) with uridine vanadate (U-V), a transition-state analogue, has been studied with 51V and proton NMR spectroscopy in solution and by neutron diffraction in the crystalline state. Upon the addition of aliquots of U-V at pH 6.6, the C epsilon-H resonances of the two active-site histidine residues 119 and 12 decrease in intensity while four new resonances appear. Above pH 8 and below pH 5, these four resonances decrease in intensity as the complex dissociates. These four resonances are assigned to His-119 and His-12 in protonated and unprotonated forms in the RNase-U-V complex. These resonances do not titrate or change in relative area in the pH range 5-8, indicating a slow protonation process, and the extent of protonation remains constant with ca. 58% of His-12 and ca. 26% of His-119 being protonated. The results of diffraction studies show that both His-12 and His-119 occupy well-defined positions in the RNase-U-V complex and that both are protonated. However, while the classic interpretation of the mechanism of action of RNase based on the proposal of Findlay et al. [Findlay, D., Herries, D. G., Mathias, A. P., Rabin, B. R., & Ross, C. A. (1962) Biochem. J. 85, 152-153] requires both His-12 and His-119 to be in axial positions relative to the pentacoordinate transition state, in the diffraction structure His-12 is found to be in an equatorial position, while Lys-41 is close to an axial position. Hydrogen exchange data show that the mobility and accessibility of amides in the RNase-U-V complex do not significantly differ from what was observed in the native enzyme. The results of both proton NMR in solution and neutron diffraction in the crystal are compared and interpreted in terms of the mechanism of action of RNase.

Animals↗

Structure of AuCN determined from total neutron diffraction.

The structure of gold cyanide, AuCN, has been determined at 10 and 300 K using total neutron diffraction. The structure consists of infinite [bond]Au[bond](CN)[bond]Au[bond](CN)[bond] linear chains, hexagonally packed, with the gold atoms in sheets. The Au-C and Au-N bond lengths are found to be identical, with d(Au(-C/N) = 1.9703(5) A at 300 K. This work supersedes a previous study, by others, which used Rietveld analysis of neutron Bragg diffraction in isolation, and found these bonds to have significantly different lengths (Delta d = 0.24 A) at 300 K. The total correlation function, T(r), at 10 and 300 K, has been modeled using information derived from total diffraction. The broadening of inter- and intrachain correlations differs markedly due to random displacements of the chains in the direction of the chain axes. This is a consequence of the relatively weak bonding between the chains. An explanation for the negative thermal expansion in the c-direction, which occurs between 10 and 300 K, is presented.

Journal Article↗

Synthesis, X-ray and neutron diffraction characterization, and ionic conduction properties of a new oxothiomolybdate Li3[Mo8S8O8(OH)8[HWO5(H2O)]] x 18H2O.

The new oxothiomolybdate anion [Mo8S8O8(OH)8[HWO5(H2O)]]3- (denoted HMo8W3-) has been synthesized in aqueous solution by an acido-basic condensation reaction. Four (Mo(V)2S2O2) building blocks are connected through hydroxo bridges around a central [W(VI)O6] octahedron. X-ray and neutron diffraction studies have been performed on single crystals of the lithium salt Li3[Mo8S8O8(OH)8[HWO5(H2O)]] x 18H2O (Li3HMo8W x 18H2O) in an aqueous grown from HMo8W3- solution of LiCl (1 M). The neutron diffraction experiment enabled us to locate both the protons and the lithium ions. In the structure of Li3HMo8W x 18H20, ring-shaped anions interleaved by a cluster of disordered hydrogen-bonded water molecules stack on top of each other along lithium pillars. The lithium columns are formed by alternating edge-sharing octahedra and tetrahedra, with one lithium site in four being totally vacant. Ionic conductivity measurements on pressed pellets have shown that Li3HMo8W x 18H2O is a good ionic conductor at room temperature (sigma = 10(-5) S cm(-1)), but the ionic conductivity on single crystals is smaller by two orders of magnitude and is isotropic; this suggests the main path of conduction involves surface protons rather than lithium ions of the bulk.

Journal Article↗

Spin frustration in MII[C(CN)3]2 (M = V, Cr). A magnetism and neutron diffraction study.

Three-dimensional coordination network solids of MII[C(CN)3]2 (M = V, Cr) composition possess interpenetrating rutile-like network structures. Each [C(CN)3]- bonds to three different metal ions in a triangular array, affording a geometrical topology akin to a Kagomé lattice leading to competing spin exchange interactions and spin frustration. The crystal and magnetic structure of CrII[C(CN)3] was determined by Rietveld refinement of the powder neutron diffraction data at 2 and 15 K and belongs to the orthorhombic space group Pmna [a = 7.313(1) A, b = 5.453(1) A, c = 10.640(1) A, Z = 2, T = 15 K]. Each CrII has a tetragonally elongated octahedral structure with four Cr-N(1) distances of 2.077(2) A and two significantly longer axial Cr-N(2) distances of 2.452(2) A. Magnetic susceptibility measurements between 1.7 and 300 K reveal strong antiferromagnetic interactions for both V- and Cr[C(CN)3]2 with theta = -67 and -46 K, respectively, from a fit to the Curie-Weiss law. Long-range magnetic ordering does not occur for M = V above 1.7 K, in contrast to M = Cr, which antiferromagnetically orders at low temperature. This is attributed to Jahn-Teller distorted CrII site relieving frustration in one dimension, leading to 2-D Ising antiferromagnetism, as observed by both magnetic susceptibility and specific heat studies. Neutron diffraction experiments at 2 K for Cr[C(CN)3]2 yielded additional Bragg reflections as a result of antiferromagnetic ordering with the moments on the CrII atoms aligned parallel to c and 4.7(1) microB. Fitting of the magnetic order parameter to a power law yielded TN = 6.12(4) K and beta = 0.18(1) consistent with 2-D Ising behavior. A TN of 6.13 K is also observed from the specific heat data.

Journal Article↗

A neutron diffraction study of the influence of ions on phospholipid membrane interactions.

Neutron diffraction is used to examine the effects of Ca2+ and ClO4- ions on interactions and some structural features of dipalmitoylphosphatidylcholine membranes in both solid and fluid lamellar phases. The results are described within the framework of Derjaguin-Landau-Verwey-Overbeek (DLVO) theory with reference to electrostatic, van der Waals, and hydration components of disjoining pressure. The Hamaker constants are evaluated under equilibrium conditions. Addition of 100 mM CaCl2 to the aqueous phase substantially increases the lamellar repeat spacing (d), which is interpreted in terms of adsorption of Ca2+ ions to bilayers followed by electrostatic repulsion between membranes. The rise of NaClO4 concentration in the presence of 100 mM CaCl2 leads to gradual decrease in d, evidently resulted from the diminution of Ca(2+)-induced positive surface potential by both electrostatic screening and binding of ClO4- ions. In the absence of CaCl2, elevation of NaClO4 concentration to 100-300 mM drastically enhances the repeat spacing and then dramatically decreases d at about 1 M NaClO4. Estimation of the hydration coefficients showed that the pronounced decrease of the repeat spacing at high NaClO4 concentrations was resulted mainly from the (partial) disruption of the structure of intermembrane bound water by chaotropic ClO4- ions and subsequent decrease in hydration repulsive pressure. Moreover, in the case of solid membranes (20 degrees C) high concentrations of ClO4- induced formation of interdigitated phase paralleled with marked reduction in bilayer thickness and corresponding increase in the effective cross-sectional area per lipid molecule.

1,2-Dipalmitoylphosphatidylcholine↗

An ordered low-temperature phase of barium nitroprusside trihydrate studied by neutron diffraction.

Crystals of barium pentacyanonitrosylferrate trihydrate (barium nitroprusside trihydrate), Ba[Fe(CN)(5)(NO)].3H(2)O, have been studied by neutron diffraction in order to examine the structural behaviour of the compound in the 20-120 K temperature range and to determine the structure at 105 K. The results show the existence of a new crystal phase of the compound at 80 K (with a duplicated a parameter), which still exists at 20 K. The crystal structure at 105 K shows a rearrangement of the water molecules, which results in an ordered structure with P1 symmetry. Two of the four independent nitroprusside cations are rotated by 4.5 degrees around the [100] direction.

Barium Compounds↗

Na2Fe(CN)5(NO).2D2O at 11 and 293 K by X-ray, and at 15 K by neutron diffraction.

The crystal structure of Na(2)Fe(CN)(5)(NO).2D(2)O, disodium pentacyanonitrosylferrate(III) bis(dideuterium oxide), has been determined by X-ray diffraction at 11 and 293 K, and by neutron diffraction at 15 K. The accurate and extensive data sets lead to more precise determinations than are available from earlier work. The agreement in atomic positional and displacement parameters between the determinations at low temperature is very good.

Journal Article↗

Transmembrane location of retinal in bacteriorhodopsin by neutron diffraction.

The transmembrane location of the chromophore of bacteriorhodopsin was obtained by neutron diffraction on oriented stacks of purple membranes. Two selectively deuterated retinals were synthesized and incorporated in bacteriorhodopsin by using the retinal- mutant JW5: retinal-d11 (D11) contained 11 deuterons in the cyclohexene ring, and retinal-d5 (D5) had 5 deuterons as close as possible to the Schiff base end of the chromophore. The membrane stacks had a lamellar spacing of 53.1 A at 86% relative humidity. Five orders were observed in the lamellar diffraction pattern of the D11, D5, and nondeuterated reference samples. The reflections were phased by D2O-H2O exchange. The absolute values of the structure factors were nonlinear functions of the D2O content, suggesting that the coherently scattering domains consisted of asymmetric membrane stacks. The centers of deuteration were determined from the observed intensity differences between labeled and unlabeled samples by using model calculations and Fourier difference methods. With the origin of the coordinate system defined midway between consecutive intermembrane water layers, the coordinates of the center of deuteration of the D11 and D5 label are 10.5 +/- 1.2 and 3.8 +/- 1.5 A, respectively. Alternatively, the label distance may be measured from the nearest membrane surface as defined by the maximum in the neutron scattering length density at the water/membrane interface. With respect to this point, the D11 and D5 labels are located at a depth of 9.9 +/- 1.2 and 16.6 +/- 1.5 A, respectively. The chromophore is tilted with the Schiff base near the middle of the membrane and the ring closer to the membrane surface. The vector connecting the two label positions in the chromophore makes an angle of 40 +/- 12 degrees with the plane of the membrane. Of the two possible orientations of the plane of the chromophore, which is perpendicular to the membrane plane, only the one in which the N----H bond of the Schiff base points toward the same membrane surface as the vector from the Schiff base to the cyclohexene ring is compatible with the known tilt angle of the polyene chain.

Bacteriorhodopsins↗

Crystallization of a large single crystal of a B-DNA decamer for a neutron diffraction experiment by the phase-diagram technique.

Crystallization of a large single crystal of a B-DNA decamer, d(CCATTAATGG), for a neutron-diffraction experiment has been accomplished by an analysis of its solubility phase diagram and a large single crystal was successfully crystallized at around the minimum solubility point of the oligonucleotide: 30%(v/v) MPD, 100 mM MgCl(2) pD 6.6 using 0.4 ml D(2)O solutions of the DNA (sample concentration 1.5 mM). It is confirmed that the resulting crystal (dimensions: 1.7 x 1.3 x 0.6 mm) diffracts sufficiently well for neutron data collection.

Base Sequence↗

Short N+--H...Ph hydrogen bonds in ammonium tetraphenylborate characterized by neutron diffraction

The crystal structures of ammonium tetraphenylborate, NH4+.BPh4-, are determined by neutron diffraction at 20 and 293 K. At both temperatures, all four N-H vectors of the ammonium ion are time-average-oriented at the midpoints of the phenyl rings of neighboring anions. The N-H...Ph distances, H...M 2.067 and N...M 3.023 A, are exceptionally short (M = aromatic midpoint). Even at 20 K the ammonium ion performs large amplitude motions which allow the N-H vectors to sample the entire face of the aromatic system.

Journal Article↗

Orientation of histidine residues in RNase A: neutron diffraction study.

Difference Fourier maps have been calculated at 2.8-A resolution by using neutron diffraction data obtained from a single crystal of RNase A. The phases were derived from a model resulting from the joint refinement of x-ray and neutron data at 2.0-A and 2.8-A resolution, respectively. The orientation of histidine-48 assumed during the refinement of the x-ray model at 2.5 A was confirmed, whereas the other three histidines had to be rotated around C beta--C gamma bonds in order to agree with the neutron difference Fourier maps. In the final model, histidine-12 is clearly hydrogen bonded to the carbonyl oxygen of threonine-45 and to the oxygen of the inorganic phosphate, and histidine-119 is bonded to another oxygen of the phosphate and to the oxygen OD1 of aspartic acid-121.

Crystallization↗

Neutron diffraction studies of digalactosyldiacylglycerol.

The structure of the digalactosyldiacylglycerol bilayer is calculated using neutron diffraction data. The polar head group of this lipid is oriented parallel to the plane of the bilayer such that the galactose moieties are tightly packed at the bilayer surface into a 0.8 nm thick polar layer. The thickness of this layer is independent of water activity over a wide range (15-100% relative humidity). The constant thickness of both the galactose layer and the hydrocarbon layer constrain the structure factor amplitudes to lie on a single continuous transform for repeat periods between 4 and 5 nm.

Galactolipids↗

A neutron diffraction study of the headgroup conformation of phosphatidylglycerol from Escherichia coli membranes.

By using neutron diffraction, the headgroup conformation of purified phosphatidylglycerol from Escherichia coli membranes has been investigated. Measurements at 25 degrees C and 15% relative humidity on oriented multilayers of lipid selectively deuterated at the sn-3-position of the glycerol backbone and of the gamma-position of the glycerol headgroup show that the labels are at a mean distance of 23.0 A and 27.6 A from the centre of the hydrocarbon chain region. This suggests that the negatively charged headgroup is oriented at about 30 degrees to the membrane surface. The orientation of the phosphatidylglycerol headgroup makes the negatively charged phosphate group easily accessible to cations present in the adjacent water layer.

Cell Membrane↗

Retinal location in purple membrane of Halobacterium halobium: a neutron diffraction study of membranes labelled in vivo with deuterated retinal.

Purple membranes were prepared by growing Halobacterium halobium in a medium containing nicotine (which inhibits biosynthesis of retinal) and the oxidation products of fully deuterated beta-carotene. This allowed the in vivo incorporation of deuterated retinal into the membranes. The labelled membranes were crystalline and isomorphous with native membrane as determined by X-ray diffraction, and their optical absorption spectra were very similar. Neutron diffraction data for the two dimensional in-plane lattice from labelled and native membranes were analysed by difference Fourier and direct methods to 8.6 A resolution. The difference Fourier shows the retinal to be located in the centre of the bacteriorhodopsin molecule. The best fit to the data was obtained with the projection of retinal as a 10 A long rod forming an angle of -40 degrees +/- 10 degrees with the x axis centred at x = -0.19 +/- 0.02, y = -0.35 +/- 0.02 in fractional unit cell coordinates. The main peak in the difference Fourier map is at x = -0.17, y = -0.33.

Bacteriorhodopsins↗

Topography of tetrahydrocannabinol in model membranes using neutron diffraction.

Small-angle neutron scattering was used to determine the intralamellar location of (-)-delta 8-tetrahydrocannabinol (delta 8-THC) in hydrated dipalmitoylphosphatidylcholine (DPPC) bilayers. Nuclear scattering density profiles were calculated from measurements on deuterium and non-deuterium-labelled inclusions (8.3% (w/w)) of delta 8-THC in DPPC multilayer samples. By comparing pairs of such nuclear density profiles, the locations of the deuterium labels were determined. Present results on the topography of delta 8-THC in membranes are compared with earlier X-ray measurements using iodine labelling. Whereas the position of the phenolic hydroxy group is similar in both types of measurement, a difference is found in the conformation of the terminal methyl groups of the cannabinoid side-chains. The X-ray measurements on dimyristoylphosphatidylcholine (DMPC) indicated that the iodine-labelled cannabinoid side-chains assume an all-trans orientation with the terminal iodine atom pointing inward into the membrane away from the tricyclic region while the neutron measurements indicate that the terminal CH3 group of delta 8-THC aligns itself at the level of the tricyclic ring system implying that the side chain exists in a more compact conformation perpendicular to the DPPC hydrocarbons. A Gaussian function analysis of the data indicates that the delta 8-THC molecule is significantly delocalized in the DPPC membrane in the liquid crystal phase. The mean location of delta 8-THC suggests that the active site on a membrane-embedded receptor protein will lie near the polar interface at the base of the phospholipid headgroups.

1,2-Dipalmitoylphosphatidylcholine↗