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PubMed2004

On the variation of the structure of liquid deuterium fluoride with temperature.

The structure of liquid deuterium fluoride has been measured using pulsed neutron diffraction and high energy x-ray diffraction techniques as a function of temperature. The neutron experiments were performed at T=296+/-2 K, 246+/-2 K, and 193+/-2 K and the x-ray measurements carried out at 296+/-2 K and 195+/-2 K. The x-ray pair correlation functions, which are dominated by fluorine-fluorine interactions, show the first peak at approximately 2.53+/-0.05 A remains very nearly invariant with decreasing temperature. Peaks around 4.5 and 5.0 A also appear at both temperatures in the x-ray data. In contrast, the intermolecular peaks in the total neutron pair correlation function show that significant systematic local structural changes occur as the temperature is lowered. The first intermolecular peak position shortens from 1.64+/-0.05 A at 296 K to 1.56+/-0.05 A at 195 K. Although there are overlapping contributions from the intermolecular hydrogen-fluorine and hydrogen-hydrogen correlations, it is clear that the temperature dependent structural changes are largely due to a rearrangement of the deuterium atom positions in the fluid. By comparison with partial structure factor data the hydrogen bonds appear to become more linear at lower temperatures.

Journal Article↗
PubMed2005

Deuteration can affect the conformational behaviour of amphiphilic alpha-helical structures.

The replacement of hydrogen with deuterium is frequently used in conjunction with neutron diffraction to investigate peptide-membrane interaction. This isotopic substitution in an amino acid residue radically changes the neutron scatter pattern of the peptide, thereby allowing its localisation within the bilayer with the aid of derived Fourier maps. Nonetheless, this technique relies on the generally held assumption that normal and isotopically enriched protein species do not differ significantly in structure or biological activity. Recently, this assumption has been questioned and here, diffraction data from studies on a membrane interactive peptide clearly challenge the reliability of this assumption.

Chemical Phenomena↗
PubMed1986

Neutron scatter and diffraction techniques applied to nucleosome and chromatin structure.

Neutron scatter and diffraction techniques have made substantial contributions to our understanding of the structure of the nucleosome, the structure of the 10-nm filament, the "10-nm----30-nm" filament transition, and the structure of the "34-nm" supercoil or solenoid of nucleosomes. Neutron techniques are unique in their properties, which allows for the separation of the spatial arrangements of histones and DNA in nucleosomes and chromatin. They have equally powerful applications in structural studies of any complex two-component biological system. A major success for the application of neutron techniques was the first clear proof that DNA was located on the outside of the histone octamer in the core particle. A full analysis of the neutron-scatter data gave the parameters of Table 3 and the low-resolution structure of the core particle in solution shown in Fig. 6. Initial low-resolution X-ray diffraction studies of core particle crystals gave a model with a lower DNA pitch of 2.7 nm. Higher-resolution X-ray diffraction studies now give a structure with a DNA pitch of 3.0 nm and a hole of 0.8 nm along the axis of the DNA supercoil. The neutron-scatter solution structure and the X-ray crystal structure of the core particle are thus in full agreement within the resolution of the neutron-scatter techniques. The model for the chromatosome is largely based on the structural parameters of the DNA supercoil in the core particle, nuclease digestion results showing protection of a 168-bp DNA length by histone H1 and H1 peptide, and the conformational properties of H1. The path of the DNA outside the chromatosome is not known, and this information is crucial for our understanding of higher chromatin structure. The interactions of the flexible basic and N- and C-terminal regions of H1 within chromatin and how these interactions are modulated by H1 phosphorylation are not known. The N- and C-terminal regions of H1 represent a new type of protein behavior, i.e., extensive protein domains that are designed not to fold up into secondary and tertiary protein structures. This behavior is increasingly observed in DNA and chromatin binding proteins, and in the case of the high-mobility group proteins HMG 14 and 17, the entire polypeptide chain is a flexible random coil over a wide range of solution, ionic, and pH conditions. It follows that the native conformations are probably imposed on these flexible domains and molecules by their binding sites in chromatin.(ABSTRACT TRUNCATED AT 400 WORDS)

Animals↗
PubMed1985

Time-resolved x-ray diffraction studies of the sarcoplasmic reticulum membrane during active transport.

X-ray and neutron diffraction studies of oriented multilayers of a highly purified fraction of isolated sarcoplasmic reticulum (SR) have previously provided the separate profile structures of the lipid bilayer and the Ca2+-ATPase molecule within the membrane profile to approximately 10-A resolution. These studies used biosynthetically deuterated SR phospholipids incorporated isomorphously into the isolated SR membranes via phospholipid transfer proteins. Time-resolved x-ray diffraction studies of these oriented SR membrane multilayers have detected significant changes in the membrane profile structure associated with phosphorylation of the Ca2+-ATPase within a single turnover of the Ca2+-transport cycle. These studies used the flash photolysis of caged ATP to effectively synchronize the ensemble of Ca2+-ATPase molecules in the multilayer, synchrotron x-radiation to provide 100-500-ms data collection times, and double-beam spectrophotometry to monitor the Ca2+-transport process directly in the oriented SR membrane multilayer.

Animals↗
PubMed2001

Saccharinate as a versatile polyfunctional ligand. Four distinct coordination modes, misdirected valence, and a dominant aggregate structure from a single reaction system.

The reaction system consisting of copper, saccharinate, and the auxiliary ligands H(2)O, PPh(3), and NH(3) produces a sequence of compounds in which saccharinate is coordinated to copper in four distinct manners. The complex trans-[Cu(sacch)(2)(H(2)O)(4)] (2) (produced by thermal dehydration of trans-[Cu(sacch)(2)(H(2)O)(4)].2H(2)O (1)) reacts with triphenylphosphine in CH(2)Cl(2) to produce any or all of three Cu(I) complexes, depending upon conditions. The three Cu(I) compounds are Cu(sacch)(PPh(3))(3) (3), in which saccharinate binds to copper through the carbonyl group of the ligand, Cu(sacch)(PPh(3))(2) (4), in which sacch binds to Cu through its charge-bearing nitrogen atom; and [Cu(sacch)(PPh(3))](2) (5), a dinuclear complex in which saccharinate bridges two Cu centers through its imidate nitrogen and carbonyl oxygen atoms. Complexes 3-5 can be isolated individually, although in solution they exist in a complex equilibrium which has been examined by NMR spectroscopy. Each of the three Cu(I) products reacts with NH(3) in CH(2)Cl(2) solution to produce trans-[Cu(sacch)(2)(NH(3))(4)] (6), an unstable Cu(II) complex that exhibits misdirected valence at the Cu-N(sacch) bond. Complex 6 evolves spontaneously to [Cu(sacch)(NH(3))(4)](sacch).H(2)O (7), which in the solid state is dominated by a supramolecular aggregate of two formula units, linked by hydrogen bonding in which the water molecule plays a central role. Alternative pathways exist to several of the products. The X-ray crystal structure analyses of 3-7 are reported and establish the coordination modes of saccharinate, the misdirected valence in 6, and the supramolecular aggregation in 7. The structure analysis of 7 by single-crystal neutron diffraction is reported and together with the previously reported neutron structure analysis of 1 establishes the substitution of the auxiliary ligand H(2)O by NH(3) in the Cu(II) products.

Journal Article↗
PubMed1995

Molecular dynamics simulation of hydration in myoglobin.

This study was carried out to evaluate the stability of the 89 bound water molecules that were observed in the neutron diffraction study of CO myoglobin. The myoglobin structure derived from the neutron analysis was used as the starting point in the molecular dynamics simulation using the software package CHARMM. After solvation of the protein, energy minimization and equilibration of the system, 50 ps of Newtonian dynamics was performed. This data showed that only 4 water molecules are continuously bound during the length of this simulation while the other solvent molecules exhibit considerable mobility and are breaking and reforming hydrogen bonds with the protein. At any instant during the simulation, 73 of the hydration sites observed in the neutron structure are occupied by water.

Computer Simulation↗
PubMed1996

Molecular dynamics investigation of the structure of a fully hydrated gel-phase dipalmitoylphosphatidylcholine bilayer.

We report the results of a constant pressure and temperature molecular dynamics simulation of a gel-phase dipalmitoylphosphatidylcholine bilayer with nw = 11.8 water molecules/lipid at 19 degrees C. The results of the simulation were compared in detail with a variety of x-ray and neutron diffraction data. The average positions of specific carbon atoms along the bilayer normal and the interlamellar spacing and electron density profile were in very good agreement with neutron and x-ray diffraction results. The area per lipid and the details of the in-plane hydrocarbon chain structure were in excellent agreement with wide-angle x-ray diffraction results. The only significant deviation is that the chains met in a pleated arrangement at the bilayer center, although they should be parallel. Novel discoveries made in the present work include the observation of a bimodal headgroup orientational distribution. Furthermore, we found that there are a significant number of gauche conformations near the ends of the hydrocarbon chains and, in addition to verifying a previous suggestion that there is partial rotational ordering in the hydrocarbon chains, that the two chains in a given molecule are inequivalent with respect to rotations. Finally, we have investigated the lipid/water interface and found that the water penetrates beneath the headgroups, but not as far as the carbonyl groups, that the phosphates are strongly hydrated almost exclusively at the nonesterified oxygen atoms, and that the hydration of the ammonium groups is more diffuse, with some water molecules concentrated in the grooves between the methyl groups.

1,2-Dipalmitoylphosphatidylcholine↗
PubMed2000

Crystal engineering in the gem-alkynol family; synthon repetitivity and topological similarity in diphenylethynylmethanols: structures that lack O-H.O hydrogen bonds

The structures of four para-substituted derivatives of diphenylethynylmethanol have been determined [ditolylethynylmethanol, di(4-chlorophenyl)ethynylmethanol, di(4-bromophenyl)ethynylmethanol and bis(4,4'-biphenylyl)ethynylmethanol]. The dimethyl, dichloro, dibromo and diphenyl compounds have been analysed using X-ray diffraction at 150 K, and the dichloro compound has also been studied using neutron diffraction at 150 K. In common with the parent diphenylethynylmethanol [Garcia, Ramos, Rodriguez & Fronczek (1995). Acta Cryst. C51, 2674-2676], all four derivatives fail to form the expected strong O-H.O hydrogen bonds due to steric hindrance. Instead, the supramolecular structural organization in this family of gem-alkynols is mediated by a variety of weaker interactions. The two most acidic protons, O-H and C[triple-bond]C-H, participate in weak hydrogen bonds to pi-acceptors, forming synthons that stabilize all five structures. These primary interactions are reinforced by a variety of other weak hydrogen bonds involving C-H donors and the hydroxy-O as an acceptor, and by halogen.halogen interactions in the dichloro and dibromo compounds.

Journal Article↗
PubMed1986

The effect of tri-N-acetylglucosamine on hydrogen exchange in hen egg white lysozyme.

Tritium-hydrogen isotope exchange techniques have been employed to study the effect of tri-N-acetylglucosamine binding on the conformational dynamics of hen egg white lysozyme. Numerical Laplace inversion of the data provides exchange rate probability density functions that reveal three overlapping peaks for both the free enzyme and (GlcNAc)3-enzyme complex. Binding of (GlcNAc)3 decreases the exchange rates of all protons to some extent with by far the largest effect being observed for the slow exchanging protons. These have been located, by comparison with neutron diffraction results (Mason, S. A., Bentley, G. A., and McIntyre, G. J. (1984) in Neutrons in Biology (Schoenborn, B. P., ed) pp. 323-334, Plenum Press, New York), within the beta-sheet structure and on helices (8-13), (28-34), and (89-97), that define the edges of the so-called "hydrophobic box" in lysozyme. The regions of the protein that are most affected by binding (GlcNAc)3, as revealed by hydrogen exchange, are found to be quite distinct from the regions observed to undergo conformational changes by x-ray diffraction. Most of these segments of the protein are located at some distance from the (GlcNAc)3-binding site itself. Two segments (the beta-sheet and helix (28-34)) are closely associated with the two active-site carboxylate groups. These results suggest that exchange-stable regions having strong, highly organized hydrogen bonding may have an important role in catalytic function and the differential propagation of conformational and dynamic perturbations caused by ligand binding at distant sites on the protein.

Acetylglucosamine↗
PubMed2005

Proton channel hydration and dynamics of a bacteriorhodopsin triple mutant with an M-state-like conformation.

The hydration and dynamics of purple membranes (PM) containing the bacteriorhodopsin (BR) triple mutant D96G/F171C/F219L were investigated by neutron diffraction coupled with H(2)O/D(2)O exchange and by energy-resolved neutron scattering. The mutant, which is active in proton transport (Tittor et al. in J. Mol. Biol. 319:555-565, 2002), has an "open" ground-state structure similar to that of the M intermediate in the photocycle of the wild type (wt) (Subramaniam and Henderson in Nature 406:653-657, 2000). The experiments demonstrated an increased proton channel hydration in the mutant PM compared with wt PM, in both high (86%) and low (57%) relative humidity. We suggest that this is due to the smaller side chains of the mutant residues liberating space for more water molecules in the proton channel, which would then be able to participate in the proton translocation network. PM thermal dynamics has been shown to be very sensitive to membrane hydration (Lehnert et al. in Biophys. J. 75:1945-1952, 1998). The global dynamical behaviour of the mutant PM on the 100-ps time scale, as a function of relative humidity, was found to be identical to that of the wt, showing that the "open" BR structure and additional water molecules in the proton channel do not provide a softer environment enabling increased flexibility.

Bacteriorhodopsins↗
PubMed2000

Reconstruction from small-angle neutron scattering measurements of the real space magnetic field distribution in the mixed state of Sr2RuO4.

We have measured the diffracted neutron scattering intensities from the square magnetic flux lattice in the perovskite superconductor Sr2RuO4, which is thought to exhibit p-wave pairing with a two-component order parameter. The relative intensities of different flux lattice Bragg reflections over a wide range of field and temperature have been shown to be inconsistent with a single component Ginzburg-Landau theory but qualitatively agree with a two-component p-wave Ginzburg-Landau theory.

Journal Article↗
PubMed2006

Stoichiometry-dependent structures: an X-ray and neutron single-crystal diffraction study of the effect of reaction stoichiometry on the crystalline products formed in the potassium-cyanurate system.

Reaction of cyanuric acid (C(3)H(3)N(3)O(3); neutral form CYH(3); anionic form CYH_2;-; dianionic form CYH(2-)) with K(2)CO(3) or KOH in aqueous solution gave three different crystalline products, according to the reaction stoichiometry used. The structures of two products were easily determined by single-crystal X-ray diffraction: [K(CYH(2))(H(2)O)], (1), of which the crystal structure is already known [Marsh, R. E. et al. (2002). Acta Cryst. B58, 62-77], and [K(2)(CYH)], (2), a highly symmetrical and dense structure. Further stoichiometric variation produced another new complex, (3), and reaction of Rb(2)CO(3) with CYH(3) yielded a further product, (4), which was found to be isostructural with (3). Determination of the structures of (3) and (4) by X-ray diffraction gave a result that was chemically unreasonable owing to a charge imbalance, with the asymmetric unit apparently containing 2- against 1.5+ (partial charges as the result of crystallographic mirror symmetry). A single-crystal neutron diffraction analysis carried out on a fully deuterated sample of (3) revealed the presence of a supercell, with the c axis doubled compared with the X-ray result. Subsequent refinement of the structure with this supercell showed that it is the result of just two D atoms breaking crystallographically imposed mirror symmetry, which is otherwise essentially observed by the rest of the structure. This minor deviation from pseudo-symmetry could not be identified by X-ray diffraction. Thus, single-crystal neutron diffraction data revealed that the true chemical formula of the structure of (3) [and presumably also of the isostructural (4) with Rb instead of K and H instead of D], is [K(3)(C(3)D(2)N(3)O(3))(3)(C(3)D(3)N(3)O(3))(D(2)O)(4)], the deuterated form of [K(3)(CYH(2))(3)(CYH(3))(H(2)O)(4)].

Journal Article↗
PubMed2006

Inelastic neutron scattering spectrum of cyclotrimethylenetrinitramine: a comparison with solid-state electronic structure calculations.

Solid-state geometry optimizations and corresponding normal-mode analysis of the widely used energetic material cyclotrimethylenetrinitramine (RDX) were performed using density functional theory with both the generalized gradient approximation (BLYP and BP functionals) and the local density approximation (PWC and VWN functionals). The structural results were found to be in good agreement with experimental neutron diffraction data and previously reported calculations based on the isolated-molecule approximation. The vibrational inelastic neutron scattering (INS) spectrum of polycrystalline RDX was measured and compared with simulated INS constructed from the solid-state calculations. The vibrational frequencies calculated from the solid-state methods had average deviations of 10 cm(-1) or less, whereas previously published frequencies based on an isolated-molecule approximation had deviations of 65 cm(-1) or less, illustrating the importance of including crystalline forces. On the basis of the calculations and analysis, it was possible to assign the normal modes and symmetries, which agree well with previous assignments. Four possible "doorway modes" were found in the energy range defined by the lattice modes, which were all found to contain fundamental contributions from rotation of the nitro groups.

Journal Article↗
PubMed1981

Comparison of the profile structures of isolated and reconstituted sarcoplasmic reticulum membranes.

The profile structures of functional reconstituted sarcoplasmic reticulum (RSR) membranes were investigated as a function of the lipid/protein (L/P) ratio via x-ray diffraction studies of hydrated oriented multilayers of these membranes to a resolution of 10-15 A, and neutron diffraction studies on these multilayers to lower resolutions. Our results at this stage of investigation indicate that reconstitution of SR with variable amounts of Ca2+ pump protein for L/P ratios greater than 88 results in closed membraneous vesicles in which the Ca2+ pump protein is distributed asymmetrically in the membrane profile; a majority of the protein density is contained primarily in the extravesicular half of the membrane profile whereas a relatively lesser portion of the protein spans the hydrocarbon core of the RSR membranes. These RSR membranes are functionally similar and resemble isolated light sarcoplasmic reticulum in both profile structure and function at a comparable L/P ratio. Reconstitution with greater amounts of Ca2+ pump protein (e. g. L/P approximately 50-60) resulted in substantially less functional membranes with a dramatically thicker profile structure.

Animals↗
PubMed2003

Simultaneous variation of multipole parameters and Gram-Charlier coefficients in a charge-density study of tetrafluoroterephthalonitrile based on X-ray and neutron data.

Difficulties encountered in modelling the scattering of fluorine in organic compounds have been investigated through refinements of accurate X-ray and neutron diffraction data measured on tetrafluoroterephthalonitrile, TFT, at 122.4 K. Multipole refinements led to a highly contracted octopole on fluorine. The subsequent analysis revealed that fluorine does not possess a valence octopole but exhibits anharmonic thermal motion that can be modelled by the octopole multipole parameters. The scattering contribution from the octopole shows the same cubic dependence in the scattering vector as the Gram-Charlier expansion of the nuclear displacements to third order. The analysis also showed that refinement of third-order Gram-Charlier coefficients on fluorine requires data to at least 0.93 A(-1) resolution in sinthetas/lambda. The X-ray data extending to 1.27 A(-1) were of sufficient resolution to include third-order Gram-Charlier coefficients for N, F and the cyano C atoms in the refinement, whereas the neutron data only enabled refinement of the third-order Gram-Charlier coefficients for nitrogen. The refinements of the neutron and X-ray diffraction data yielded identical atomic displacement parameters for all the atoms. Though inclusion of anharmonic motion for N and F atoms provides the best model, it does not affect the crystal electron density, and all intramolecular bond critical points have identical features. Application of the anharmonic model, however, leads to small differences in the intermolecular interactions, which is illustrated by the electrostatic potential adjacent to the N atom. The characteristics of the C-F bond were elucidated by the topological analysis of the crystal electron density, which also supported the proposed quinonoid structure of the benzene ring.

Journal Article↗
PubMed2006

X-ray, neutron and NMR studies of the catalytic mechanism of aspartic proteinases.

Current proposals for the catalytic mechanism of aspartic proteinases are largely based on X-ray structures of bound oligopeptide inhibitors possessing non-hydrolysable analogues of the scissile peptide bond. Until recent years, the positions of protons on the catalytic aspartates and the ligand in these complexes had not been determined with certainty due to the inadequate resolution of these analyses. There has been much interest in locating the catalytic protons at the active site of aspartic proteinases since this has major implications for detailed understanding of the mechanism of action and the design of improved transition state mimics for therapeutic applications. In this review we discuss the results of studies which have shed light on the locations of protons at the catalytic centre. The first direct determination of the proton positions stemmed from neutron diffraction data collected from crystals of the fungal aspartic proteinase endothiapepsin bound to a transition state analogue (H261). The neutron structure of the complex at a resolution of 2.1 A provided evidence that Asp 215 is protonated and that Asp 32 is the negatively charged residue in the transition state complex. Atomic resolution X-ray studies of inhibitor complexes have corroborated this finding. A similar study of the native enzyme established that it, unexpectedly, has a dipeptide bound at the catalytic site which is consistent with classical reports of inhibition by short peptides and the ability of pepsins to catalyse transpeptidation reactions. Studies by NMR have confirmed the findings of low-barrier and single-well hydrogen bonds in the complexes with transition state analogues.

Aspartic Acid↗
PubMed2005

Characterization of the flow of anisotropic colloidal particles using energy-dispersive X-ray diffraction.

The technique of energy-dispersive X-ray diffraction to study the orientation of microscopic crystalline particles dispersed in a liquid has been described recently. This complements previous neutron diffraction studies by permitting measurements at higher spatial resolution. Work with synchrotron radiation and high-energy X-rays has allowed studies on liquid dispersions flowing in pipes with a thickness of about 1 cm and a spatial resolution of 100 mum. Kaolinite is often found as a dispersion of monocrystalline, microscopic plates. The crystallographic layer structure is commensurate with the particle shape: the 00l direction is normal to the plane of the plates. Measurements of diffraction of the flowing liquid dispersion in a pipe oriented in various directions to the incident beam can be used to deduce the average orientation and order parameters of the particles. The competing effects of alignment with walls and in flow fields were observed. Further work has measured the orientation near a bend in a pipe.

Journal Article↗
PubMed1983

A structural investigation of cytochrome c binding to photosynthetic reaction centers in reconstituted membranes.

Mammalian cytochrome c can effectively replace bacterial cytochrome c2 as the electron donor to the bacterial photosynthetic reaction center in either the natural chromatophore or a reconstituted reaction center/phospholipid membrane. In this paper, the reconstituted membrane was used to describe the nature of cytochrome c binding to the reaction center, the location of bound cytochrome c in the membrane profile and the perturbation of the reaction center and phospholipid profile structures indicated by cytochrome c binding. These structural studies utilized the combined techniques of X-ray and neutron diffraction.

Animals↗