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PubMed2006

The 136-atom structure of ZrP2O7 and HfP2O7 from powder diffraction data.

There has been considerable debate in the literature about the true room-temperature structure of ZrP2O7 and related materials. In this article we describe how a combination of information from solid-state 31P NMR and powder diffraction data can be used to determine the structure of this 136 unique-atom material. The structure has been solved using a combination of simulated annealing and Rietveld refinement performed simultaneously on X-ray and neutron diffraction data. Despite the close to cubic metric symmetry of the material, we show how its true orthorhombic structure (space group Pbca) can be refined to a high degree of precision.

Journal Article↗
PubMed1989

Supercoiled DNA is interwound in liquid crystalline solutions.

Two structures have been proposed for supercoiled DNA: it is idealized either as a toroidal ring or as a rod of two interwound duplex chains. The latter model is the most widely depicted but the evidence remains controversial. We have worked with monomers and dimers of two plasmids, pUC8 and pKS414, of similar size and natural superhelical density. pKS414 contains a bend promoting sequence whereas pUC8 does not. In concentrated solutions these plasmids form a partially ordered liquid crystalline phase which is found, using neutron diffraction, to consist of a hexagonally packed assembly of parallel rod-like particles. This shape strongly suggests an interwound conformation for which some structural parameters are deduced. The mass/unit length obtained by combining the area of the hexagonal lattice and the concentration is approximately 3.6 times that of linear DNA. This implies a shallow superhelical pitch angle approximately 36 degrees which, when combined with the known number of supercoil turns, yields the pitch approximately 360 A and radius approximately 80 A for the supercoil. Oriented X-ray fibre diffraction patterns at 92% relative humidity indicate a B type duplex structure. Nicked circular plasmids also form liquid crystals but their behaviour, as a function of concentration, differs from that of the superhelical plasmids.

Crystallization↗
PubMed1997

Phosphatydylglycerol promotes bilayer insertion of salmon calcitonin.

Neutron diffraction from oriented multibilayers has been used to study the bilayer interaction of the amphipathic peptide salmon calcitonin. Penetration of calcitonin into bilayers composed of dioleoylphosphatidylcholine increases with the addition of 15% (mol) of the anionic phospholipid dioleoylphosphatidylglycerol. Neutron scattering profiles of water distribution in stacked bilayers show a continuous band of deuterons across each bilayer, consistent with the suggestion that the hormone forms transbilayer alpha-helixes under these conditions. These experiments add to the growing body of data on the role of phosphatidylglycerol in bilayer insertion of protein helices and suggests a possible evolutionary history for calcitonin.

Amino Acid Sequence↗
PubMed2006

Triaquamanganese sulfite revisited.

Orthorhombic Mn(SO3)(H2O)3 has been reinvestigated by single-crystal X-ray diffraction in two possible space groups, viz. P2(1)2(1)2(1) (with all atoms in general positions) and Pnma (with the molecule bisected by a mirror plane). The results confirm the lower symmetry assigned in a previous single-crystal neutron diffraction study. However, the refinement of the P2(1)2(1)2(1) model requires the introduction of racemic twinning and soft positional and displacement restraints for the H atoms. The importance of a scrupulous report on symmetry absence violations as standard policy in crystallographic work is discussed.

Journal Article↗
PubMed2001

Structure of manganese diacetate tetrahydrate and low-temperature methyl-group dynamics.

We have determined the crystal structure of manganese(II) diacetate tetrahydrate at 300 and 14 K by single-crystal neutron diffraction. Proton density distributions for each of the three crystallographically distinct methyl groups have been calculated by Fourier difference. At room temperature the observed densities are those of quasi-free rotors. At low temperature rather well localized protons are observed. Inelastic neutron scattering measurements performed with single crystals allow us to assign each of the three tunnelling lines to a particular crystal site. Classical molecular dynamics simulations give density distributions in qualitative agreement with the observations. With quantum mechanics proton distributions can be represented with rotational wavefunctions convoluted with static distributions of librational coordinates. The effective rotational potentials are temperature dependent.

Journal Article↗
PubMed2006

How phonons govern the behavior of short, strong hydrogen bonds in urea-phosphoric acid.

Recent neutron diffraction data have shown that the hydrogen atom involved in the short, strong hydrogen bond in urea-phosphoric acid migrates toward the midpoint of the hydrogen bond as the temperature increases. With the help of solid state ab initio calculations and inelastic neutron scattering, we have investigated the temperature dependence of the structural and vibrational properties of the system. The potential energy surface of the proton in the short, strong hydrogen bond and the thermal population of the energy levels therein cannot account for the observed proton migration. Ab initio molecular dynamics simulations clearly reveal the migration of the proton. This molecular dynamics result was reported recently by other authors, but they only offered a tentative explanation in terms of a resonance between high-frequency vibrations, which is not supported by the calculations presented here. We explain the proton migration in terms of phonon-driven structural fluctuations and their impact on the temperature-dependent evolution of the potential energy surface of the short hydrogen-bond proton.

Hydrogen Bonding↗
PubMed2005

Sub-Tg dynamics in polycarbonate by neutron scattering and its relation with secondary gamma relaxation.

We have investigated the dynamics of phenylene rings in glassy bisphenol-A (BPA) polycarbonate (PC) by means of quasielastic neutron scattering. Taking advantage of selective deuteration of the samples, we have studied the incoherent scattering of hydrogens in phenylene rings on the one hand, and on the other hand the coherent quasielastic scattering of all the atoms in the sample. Two different types of neutron spectrometers, time of flight and backscattering, were used in order to cover a wide dynamic range, which extends from microscopic (approximately 10(-13) s) to mesoscopic (approximately 10(-9) s) times. Moreover, neutron-diffraction experiments with polarization analysis were carried out in order to characterize the structural features, and the relative coherent and incoherent contributions of the samples investigated. In contrast with previous studies of phenylene ring dynamics in BPA polysulfone performed by us also by neutron scattering, phenylene rings in BPA PC exhibit an "extra" motion in addition to those found for BPA polysulfone's phenylene rings. This extra motion of the rings in PC perfectly correlates with the main carbonate group motion followed by dielectric spectroscopy and allows us to (i) consistently interpret the PC's gamma relaxation in terms of two different motions; and (ii) experimentally confirm the relation between the motion of phenylene rings and carbonate groups within BPA PC formerly predicted by computational methods.

Journal Article↗
PubMed1986

Reformation of crystalline purple membrane from purified bacteriorhodopsin fragments.

Reconstituted crystalline purple membrane has been prepared starting from denatured bacteriorhodopsin (BR) fragments, native lipids and retinal. The two chymotryptic fragments are thought to contain respectively five and two transmembrane alpha-helices in native BR. The new reconstitution procedure, a modification of that of Huang et al. (1986, J. Biol. Chem., 256, 3802), relies on dodecylsulfate precipitation by potassium ions and yields samples with a high protein-to-lipid ratio (approximately 1:1 w/w). X-ray and neutron diffraction measurements show that in the reconstituted samples BR molecules are arranged in a P3 two-dimensional lattice with the same unit cell dimensions as the native purple membrane lattice. Analysis of reflection intensities indicates that the reconstituted molecules have regained the structure of native BR to 7 A resolution.

Bacteriorhodopsins↗
PubMed2002

Synchrotron X-ray and neutron small-angle scattering of lyotropic lipid mesophases, model biomembranes and proteins in solution at high pressure.

In this review we discuss the use of X-ray and neutron diffraction methods for investigating the temperature- and pressure-dependent structure and phase behaviour of lipid and model biomembrane systems. Hydrostatic pressure has been used as a physical parameter for studying the stability and energetics of lipid mesophases, but also because high pressure is an important feature of certain natural membrane environments and because the high pressure phase behaviour of biomolecules is of importance for several biotechnological processes. Using the pressure jump relaxation technique in combination with time-resolved synchrotron X-ray diffraction, the kinetics of different lipid phase transformations was investigated. The techniques can also be applied to the study of other soft matter and biomolecular phase transformations, such as surfactant phase transitions and protein un/refolding reactions. Several examples are given. In particular, we present data on the pressure-induced unfolding and refolding of small proteins, such as Snase. The data are compared with the corresponding results obtained using other trigger mechanisms and are discussed in the light of recent theoretical approaches.

Cell Membrane↗
PubMed1995

On the differences between X-ray and neutron thermal vibration parameters.

For crystal structures analyzed by both X-ray and neutron diffraction, the anisotropic mean-square displacement parameters of the non-H atoms are sometimes found to differ significantly. The differences can usually be adjusted by either: (1) an isotropic factor q, defined by UijX = qUijN, to correct for a temperature difference between the two experiments; (2) anisotropic factors qij, defined by UijX = qijUijN, to correct for a temperature difference and different anisotropic diffraction effects of absorption, extinction, thermal diffuse scattering, multiple reflection, or systematic measuring errors in the two experiments; (3) anisotropic diffraction correction terms delta Uij, defined by UijX = UijN + delta Uij; (4) the sum of an isotropic temperature correction and anisotropic diffraction corrections, defined by UijX = qUijN + delta Uij. Correction parameters q, qij and delta Uij are easily calculated by linear least-squares fit, and the corrections from (3) or (4) seem to be the most reliable. Corrections calculated from X-ray and neutron Uij's of the non-H atoms of a crystal can be useful for adjusting the neutron Uij's of the H atoms for adoption, along with the neutron coordinates of the H atoms, as fixed parameters in an X-ray analysis of the electron density distribution.

Crystallography, X-Ray↗
PubMed2005

Refinement of the crystal structural parameters of La2/3Ca1/3MnO3 using quantitative convergent-beam electron diffraction.

Crystal structural parameters (seven positional parameters and four isotropic Debye-Waller factors) of La(2/3)Ca(1/3)MnO(3) have been refined using the quantitative convergent-beam electron diffraction (QCBED) method. Using intensity information of many higher-order Laue-zone reflections simultaneously is essential to refine structural parameters accurately. The effective global optimization algorithm was used to avoid the problems of input values and local minima. The fittings of the differential coefficients of one-dimensional experimental intensities and theoretical ones calculated by the dynamical diffraction theory were carried out with the normalized Euclidean distance criterion. Thus, all of these improve the accuracy and reliability of the analysis. The calculated results with the refined parameters agree with the experiments. The refined parameters also agree with the Rietveld refinement results of neutron diffraction.

Journal Article↗
PubMed2006

The crystalline structures of carboxylic acid monolayers adsorbed on graphite.

X-ray and neutron diffraction have been used to investigate the formation of solid crystalline monolayers of all of the linear carboxylic acids from C(6) to C(14) at submonolayer coverage and from C(8) to C(14) at multilayer coverages, and to characterize their structures. X-rays and neutrons highlight different aspects of the monolayer structures, and their combination is therefore important in structural determination. For all of the acids with an odd number of carbon atoms, the unit cell is rectangular of plane group pgg containing four molecules. The members of the homologous series with an even number of carbon atoms have an oblique unit cell with two molecules per unit cell and plane group p2. This odd-even variation in crystal structure provides an explanation for the odd-even variation observed in monolayer melting points and mixing behavior. In all cases, the molecules are arranged in strongly hydrogen-bonded dimers with their extended axes parallel to the surface and the plane of the carbon skeleton essentially parallel to the graphite surface. The monolayer crystal structures have unit cell dimensions similar to certain close-packed planes of the bulk crystals, but the molecular arrangements are different. There is a 1-3% compression on increasing the coverage over a monolayer.

Journal Article↗
PubMed1985

Molecular packing and area compressibility of lipid bilayers.

Knowledge of the molecular packing of lipids and water in lipid bilayers is important for understanding bilayer mechanics and thermodynamics. Information on packing is most often obtained from x-ray or neutron diffraction measurements. Given the d spacing, composition, and partial specific volumes of the lipid and water, it is a simple matter to calculate the area per lipid molecule, bilayer thickness, and bilayer mass density. The partial specific volumes are commonly assumed to be those of bulk water and of lipid in excess water regardless of the degree of bilayer hydration. We present evidence here that these assumptions should be seriously questioned. At low hydrations, we find the head groups of egg and dioleoyl lecithin to be much less tightly packed than previously thought and the partial specific volume of water to be considerably smaller than 1 ml/g. Because the molecular packing affects the mechanical properties of bilayers, we use the results to reevaluate published experiments concerning the elastic area compressibility modulus of egg lecithin bilayers and the repulsive hydration force between bilayers.

Biophysical Phenomena↗
PubMed1996

Theoretical description of biomolecular hydration. Application to A-DNA.

The local density of water molecules around a biomolecule is constructed from calculated two- and three-points correlation functions of polar solvents in water using a Potential-of-Mean-Force (PMF) expansion. As a simple approximation, the hydration of all polar (including charged) groups in a biomolecule is represented by the hydration of water oxygen in bulk water, and the effect of non-polar groups on hydration are neglected, except for excluded volume effects. Pair and triplet correlation functions are calculated by molecular dynamics simulations. We present calculations of the structural hydration for ideal A-DNA molecules with sequences [d(CG)5]2 and [d(C5G5)]2. We find that this method can accurately reproduce the hydration patterns of A-DNA observed in neutron diffraction experiments on oriented DNA fibers (P. Langan et al. J. Biomol. Struct. Dyn., 10, 489 (1992)).

Base Sequence↗
PubMed2000

Extracting charge density distributions from diffraction data: a model study on urea

The quality of the extraction of electron density distributions by means of a multipole refinement method is investigated. Structure factors of the urea crystal have been obtained from an electron density distribution (EDD) resulting from a density function calculation with the CRYSTAL95 package. To account for the thermal motion of the atoms, the stockholder-partioned densities of the atoms have been convoluted with thermal smearing functions, which were obtained from a neutron diffraction experiment. A POP multipole refinement yielded a good fit, R = 0.6%. This disagreement factor is based on magnitudes only. Comparison with the original structure factors gave a disagreement of 0.8% owing to differences in magnitude and phase. The fitted EDD still showed all the characteristics of the interaction density. After random errors corresponding to the experimental situation were added to the structure factors, the refinement was repeated. The fit was R = 1.1%. This time the resulting interaction density was heavily deformed. Repetition with another set of random errors from the same distribution yielded a widely different interaction density distribution. The conclusion is that interaction densities cannot be obtained from X-ray diffraction data on non-centrosymmetric crystals.

Journal Article↗
PubMed1999

Quantitative zone-axis convergent-beam electron diffraction (CBED) studies of metals. II. Debye-Waller-factor measurements.

Quantitative CBED techniques, such as the ZAPMATCH zone-axis pattern-matching method [Bird & Saunders (1992). Ultramicroscopy, 45, 241-251], have been applied with great success to the accurate refinement of low-order structure factors. The major limitation on the accuracy of the structure-factor measurements is uncertainty in the Debye-Waller factors describing the temperature-dependent atomic vibrations. While X-ray and neutron diffraction tech-niques are both capable of accurate measurements of Debye-Waller factors, the frequent use of liquid-nitrogen-cooled samples in CBED experiments means that previous measurements are rarely available at the temperatures required. This has prompted attempts to determine Debye-Waller factors from electron diffraction data obtained under experimental conditions that match those used for the quantitative CBED work. In this paper, the possibility of extracting accurate Debye-Waller factors from the low-order reflections of a zone-axis CBED pattern is investigated. In this way, the Debye-Waller factors and structure factors could be obtained from the same data set. With this new approach, it is shown that errors lower than +/-0.02 Å(2) can be obtained for the measurement of Debye-Waller factors from room- and liquid-nitrogen-temperature nickel and copper <110> zone-axis data. The results obtained are compared with previous measurements and theoretical predictions.

Journal Article↗
PubMed1994

Changes in the relative occupancy of metal-binding sites in the profile structure of the sarcoplasmic reticulum membrane induced by phosphorylation of the Ca2+ATPase enzyme in the presence of terbium: a time-resolved, resonance x-ray diffraction study.

Time-resolved, terbium resonance x-ray diffraction experiments have provided the locations of three different high-affinity metal-binding/transport sites on the Ca2+ATPase enzyme in the profile structure of the sarcoplasmic reticulum (SR) membrane. By considering these results in conjunction with the known, moderate-resolution profile structure of the SR membrane (derived from nonresonance x-ray and neutron diffraction studies), it was determined that the three metal-binding sites are located at the "headpiece/stalk" junction in the Ca2+ATPase profile structure, in the "transbilayer" portion of the enzyme profile near the center of the membrane phospholipid bilayer, and at the intravesicular surface of the membrane profile. All three metal-binding sites so identified are simultaneously occupied in the unphosphorylated enzyme conformation. Phosphorylation of the ATPase causes a redistribution of metal density among the sites, resulting in a net movement of metal density toward the intravesicular side of the membrane, i.e., in the direction of calcium active transport. We propose that this redistribution of metal density is caused by changes in the relative binding affinities of the three sites, mediated by local structural changes at the sites resulting from the large-scale (i.e., long-range) changes in the profile structure of the Ca2+ATPase induced by phosphorylation, as reported in an accompanying paper. The implications of these results for the mechanism of calcium active transport by the SR Ca2+ATPase are discussed briefly.

Animals↗
PubMed2005

Production and X-ray crystallographic analysis of fully deuterated human carbonic anhydrase II.

Human carbonic anhydrase II (HCA II) is a zinc metalloenzyme that catalyzes the reversible hydration and dehydration of carbon dioxide and bicarbonate, respectively. The rate-limiting step in catalysis is the intramolecular transfer of a proton between the zinc-bound solvent (H2O/OH-) and the proton-shuttling residue His64. This distance (approximately 7.5 A) is spanned by a well defined active-site solvent network stabilized by amino-acid side chains (Tyr7, Asn62, Asn67, Thr199 and Thr200). Despite the availability of high-resolution (approximately 1.0 A) X-ray crystal structures of HCA II, there is currently no definitive information available on the positions and orientations of the H atoms of the solvent network or active-site amino acids and their ionization states. In preparation for neutron diffraction studies to elucidate this hydrogen-bonding network, perdeuterated HCA II has been expressed, purified, crystallized and its X-ray structure determined to 1.5 A resolution. The refined structure is highly isomorphous with hydrogenated HCA II, especially with regard to the active-site architecture and solvent network. This work demonstrates the suitability of these crystals for neutron macromolecular crystallography.

Binding Sites↗