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PubMed1994

The observation of structural transitions of a single protein molecule.

Coherent neutron scattering measurements of an amorphous, in vivo deuterated C-phycocyanin are compared with a calculation of the individual protein molecule's coherent static structure factor. Both show the significant features associated with known structure factors of several amorphous materials, most notably, an unusually sharp first diffraction peak occurring near 1.4 A(-1). We show that in the protein, such a peak results from the product of a form factor associated with correlations of atoms within individual amino acids and a structural term expressing inter-amino-acid correlations. The measurement, interpreted through behavior of the first diffraction peak, indicates that inter-amino-acid correlations - a measure of the protein's medium-range structure - undergo transitions which are primarily related to hydration rather than to temperature.

Journal Article↗
PubMedDate not supplied

Periodic disorder along ramie cellulose microfibrils.

Small angle neutron scattering studies have been carried out on cellulose fibers from ramie and Populus maximowicii (cotton wood). Labile hydrogen atoms were replaced by deuterium atoms, in water-accessible disordered regions of the fibers, to increase the neutron scattering contrast between the disordered and crystalline regions. A meridional Bragg reflection, corresponding to a longitudinal periodicity of 150 nm, was observed when scattering collected from hydrogenated and deuterated dry ramie fibers was subtracted. No Bragg reflection was observed with the cotton wood fibers, probably because of lower orientation of the microfibrils in the cell wall. The ramie fibers were then subjected to electron microscopy, acid hydrolysis, gel permeation chromatography, and viscosity studies. The leveling off degree of polymerization (LODP) of the hydrolyzed samples matched exactly the periodicity observed in the diffraction studies. The weight loss related to the LODP was only about 1.5%, and thus, the microfibrils can be considered to have 4-5 disordered residues every 300 residues.

Acids↗
PubMed2004

Square vortex lattice at anomalously low magnetic fields in electron-doped Nd1.85Ce0.15CuO4.

We report here on the first direct observations of the vortex lattice in the bulk of electron-doped Nd1.85Ce0.15CuO4 single crystals. Using small-angle neutron scattering, we have observed a square vortex lattice with the nearest neighbors oriented at 45 degrees from the Cu-O bond direction, which is consistent with theories based on the d-wave superconducting gap. However, the square symmetry persists down to unusually low magnetic fields. Moreover, the diffracted intensity from the vortex lattice is found to decrease rapidly with increasing magnetic field.

Journal Article↗
PubMed2006

Monolayers of a model anesthetic-binding membrane protein: formation, characterization, and halothane-binding affinity.

hbAP0 is a model membrane protein designed to possess an anesthetic-binding cavity in its hydrophilic domain and a cation channel in its hydrophobic domain. Grazing incidence x-ray diffraction shows that hbAP0 forms four-helix bundles that are vectorially oriented within Langmuir monolayers at the air-water interface. Single monolayers of hbAP0 on alkylated solid substrates would provide an optimal system for detailed structural and dynamical studies of anesthetic-peptide interaction via x-ray and neutron scattering and polarized spectroscopic techniques. Langmuir-Blodgett and Langmuir-Schaeffer deposition and self-assembly techniques were used to form single monolayer films of the vectorially oriented peptide hbAP0 via both chemisorption and physisorption onto suitably alkylated solid substrates. The films were characterized by ultraviolet absorption, ellipsometry, circular dichroism, and polarized Fourier transform infrared spectroscopy. The alpha-helical secondary structure of the peptide was retained in the films. Under certain conditions, the average orientation of the helical axis was inclined relative to the plane of the substrate, approaching perpendicular in some cases. The halothane-binding affinity of the vectorially oriented hbAP0 peptide in the single monolayers, with the volatile anesthetic introduced into the moist vapor environment of the monolayer, was found to be similar to that for the detergent-solubilized peptide.

Adsorption↗
PubMed2004

Characterization of the pores in hydrous ferric oxide aggregates formed by freezing and thawing.

Hydrous ferric oxides (HFO) are efficient sorbents for inorganic and organic pollutants and therefore have great potentials in environmental science and engineering applications. Freezing and thawing of HFO suspensions leads to the formation of dense HFO aggregates. It facilitates the handling and increases the drying rate of HFO. In this study, we used a combination of pycnometry, gas adsorption (N(2) gas, water vapor), and small-angle neutron scattering (SANS) to characterize the porosity and pore size distribution of dense HFO aggregates formed by freezing dialyzed HFO suspensions at -25 degrees C and thawing them at room temperature. The crystallinity of the HFO, which was a 2-line ferrihydrite, was not affected by this treatment. Wet sieving and laser diffraction analysis showed that the dense HFO aggregates had a unimodal size distribution with an average diameter of 235+/-35 microm. Increasing the freezing rate by cooling with liquid N(2) (-196 degrees C) resulted in much smaller aggregates with an average diameter of 20 microm. Adding NaNO(3) electrolyte to the HFO suspensions prior to freezing also resulted in the formation of smaller aggregates. The dense HFO aggregates formed at -25 degrees C had a porosity of 0.73+/-0.02 ll(-1). SANS revealed a unimodal size distribution of pores, with an average pore diameter of 2.0 nm. The diameter of the HFO crystallites was estimated by transmission electron microscopy to be 1.9+/-0.5 nm. Geometrical considerations taking into account the unit particle and average pore size suggest that the crystallites retain 1-2 layers of hydration water during the coagulation induced by freezing. Analysis by N(2) gas adsorption showed that drying the dense HFO aggregates induced a reduction in porosity by about 25% and shifted the pore size distribution to smaller diameters. Rewetting during water vapor adsorption did not induce significant changes of the aggregate structure. The specific surface area of the dry HFO aggregates was between 320 and 380 m(2)g(-1).

Journal Article↗
PubMedDate not supplied

A double coil chromatin sub-unit model.

A model is proposed for the structure of DNA in chromatin sub-units. Each sub-unit is proposed to contain two turns of an inner coil, with a pitch of about 40 A and an external diameter of 70 A. Around the inner coil is wound, in opposite handedness, a slightly larger amount of DNA at a diameter of about 150 A. The total contour length consistent with the electron micrographs and X-ray scattering is 600-700 A, or about 200 base pairs. It is suggested that the inner coil is protein rich and contains all of the histones except H1, which is associated with the outer coil. The double-coil model is consistent with previous biochemical and biophysical studies of chromatin. The existence of 200 and 100 base pair digestion fragments and a 6 to 1 DNA compaction are readily explained. This model is based upon the electron microscopic observation of replicas of frozen chromatin and X-ray and neutron scattering. Structural details of 25 A are preserved and visualized by the freeze electron microscopy techniques employed.

Animals↗
PubMed1989

Rapid calculation of the solution scattering profile from a macromolecule of known structure.

If one expands the structure factor equation in spherical coordinates, rotational averaging of the molecular Fourier transform, which leads directly to the solution scattering profile, is greatly simplified. It becomes a projection in the polar and azimuthal angular variables. The profile is given by I(R) = 1/2 infinity sigma n = 0 n sigma m = 0 epsilon mNm,n magnitude of Gm,n(R) 2 where Gm,n(R) = sigma jfjYm,n(theta j, phi j)jn(2 pi rjR) The index j runs over all atoms; r, theta, phi are atomic coordinates and epsilon and N are constants; the Ym,n are complex spherical harmonics, and jn are spherical Bessel functions; R = 2 sin theta/lambda. The effects of solvent have been modeled by subtracting from each protein atom a properly weighted water. Hydrogens have been included by using scattering curves fj derived from the spherical averaging of protein atoms with their attached hydrogens. This approach may also be satisfactory for neutron scattering. Published scattering profiles for lysozyme and BPTI have been accurately matched in less than one-tenth the time required by other methods. Separate, adjustable temperature factors for the protein, solvent waters, and bound waters are used, and appear to be needed. In the case of BPTI, as suggested by NMR observations, the observed diffraction pattern was much better accounted for by including only 4 tightly bound waters rather than the roughly 60 seen by crystallography.

Fourier Analysis↗
PubMed1991

Time-resolved X-ray diffraction study of structural changes associated with the photocycle of bacteriorhodopsin.

The time course of structural changes accompanying the transition from the M412 intermediate to the BR568 ground state in the photocycle of bacteriorhodopsin (BR) from Halobacterium halobium was studied at room temperature with a time resolution of 15 ms using synchrotron radiation X-ray diffraction. The M412 decay rate was slowed down by employing mutated BR Asp96Asn in purple membranes at two different pH-values. The observed light-induced intensity changes of in-plane X-ray reflections were fully reversible. For the mutated BR at neutral pH the kinetics of the structural alterations (tau 1/2 = 125 ms) were very similar to those of the optical changes characterizing the M412 decay, whereas at pH 9.6 the structural relaxation (tau 1/2 = 3 s) slightly lagged behind the absorbance changes at 410 nm. The overall X-ray intensity change between the M412 intermediate and the ground state was about 9% for the different samples investigated and is associated with electron density changes close to helix G, B and E. Similar changes (tau 1/2 = 1.3-3.6 s), which also confirm earlier neutron scattering results on the BR568 and M412 intermediates trapped at -180 degrees C, were observed with wild type BR retarded by 2 M guanidine hydrochloride (pH 9.4). The results unequivocally prove that the tertiary structure of BR changes during the photocycle.

Bacteriorhodopsins↗
PubMed1992

Crystalline ribonuclease A loses function below the dynamical transition at 220 K.

When the dynamic properties of many different proteins are plotted as a function of temperature, biphasic behaviour is observed, with a broad transition centred around 220 K. Atomic mean-square displacements from X-ray crystallography and Mössbauer scattering show this behaviour, as do electron transfer rates and dynamic information from inelastic neutron scattering. Molecular dynamics simulations over a range of temperatures also exhibit a transition at about 220 K: high-temperature atomic fluctuations are dominated by anharmonic collective motions of bonded and nonbonded groups of atoms, but below 220 K the predominant dynamic behaviour is harmonic vibration of individual atoms. Here we show by high-resolution X-ray diffraction that crystalline ribonuclease A does not bind substrate or inhibitor at 212 K but will bind either rapidly at 228 K. Once bound at the higher temperature, inhibitor cannot be washed off after the enzyme is cooled to below the transition temperature. These results suggest that enzyme flexibility is required for catalytic function.

Animals↗
PubMed1984

Collagen: the organic matrix of bone.

Collagen is the principal organic matrix in bone. The triple helical region of the molecule is 1014 amino acids long. In fibrils these molecules are staggered axially by integers of 234 residues or 68 nm (D). This axial shift occurs by self-assembly and can be understood in terms of a periodicity in the occurrence of apolar and polar residues in the amino acid sequence. Because the molecular length L = 4.47 D, there are gaps 1.5 X 36.5 nm regularly arrayed throughout the fibrils. The three-dimensional molecular arrangement is a quasi-hexagonal lattice with three distinct values for the principal interplanar spacings. Analysis of the intensity distribution in the medium-angle X-ray diffraction patterns from tendons has produced the following picture of the molecular arrangement in fibrils (Fraser et al. 1983). The molecular helices have a coherent length of 32 nm and are tilted parallel to a specific place within the lattice. A regular azimuthal interaction exists between these helices. This crystalline region could be the overlap region with a non-crystalline gap region. However, the gap is still regular axially and the molecular helices retain their structure; their lateral packing is perturbed although they retain a 'gap'. Neutron and X-ray scattering experiments have shown that calcium hydroxyapatite crystals occur in the gap and are nucleated at a specific though unknown location within the gap. The c-axis of the apatite crystals is parallel to the fibril axis and its length c = 0.688 nm is close to the axial periodicity in a protein with an extended beta-conformation. If the telopeptides at the end of a collagen molecule do have this conformation they would either have a highly heterogeneous conformation or exist in a folded manner because the overall length of the telopeptides is shorter than a regular collagen repeat of 0.029 nm would allow.

Amino Acid Sequence↗
PubMed2005

Pore size engineering in mesoporous silicas using supercritical CO2.

In this paper we investigate the use of supercritical carbon dioxide (sc-CO(2)) for synthesizing calcined mesoporous silicas with tunable pore sizes, wall thickness, and d spacings. Small angle neutron scattering was used to probe the controlled swelling of the triblock copolymer surfactant templating agents, P123 (PEO(20)PPO(69)PEO(20)), P85 (PEO(26)PPO(39)PEO(26)), and F127 (PEO(106)PPO(70)PEO(106)), as a function of CO(2) pressure. The transition from the liquid crystal phase to the calcined mesoporous silicas, formed upon condensation and drying, was also studied in detail. Powder X-ray diffraction, transmission electron microscopy, and nitrogen adsorption techniques were used to establish pore diameters, silica wall widths, and the hexagonal packing of the pores within the calcined silicas. Using a direct templating method, the diameters of mesopores and the spacing between the pores could be tuned with a high level of precision. The swelling process was observed to have no detrimental effects on the quality of silica formed, a distinct advantage over conventional swelling techniques, and all of the silicas synthesized in this study were highly ordered over distances of at least 2000 A.

Adsorption↗
PubMed2005

Influence of molecular weight on the phase behavior and structure formation of branched side-chain hairy-rod polyfluorene in bulk phase.

We report on an experimental study of the self-organization and phase behavior of hairy-rod pi -conjugated branched side-chain polyfluorene, poly[9,9-bis(2-ethylhexyl)-fluorene-2,7-diyl]-i.e., poly[2,7-(9,9-bis(2-ethylhexyl)fluorene] (PF2/6) -as a function of molecular weight (M(n)) . The results have been compared to those of phenomenological theory. Samples for which M(n) =3-147 kg/mol were used. First, the stiffness of PF2/6 , the assumption of the theory, has been probed by small-angle neutron scattering in solution. Thermogravimetry has been used to show that PF2/6 is thermally stable over the conditions studied. Second, the existence of nematic and hexagonal phases has been phenomenologically identified for lower and higher M(n) (LMW, M(n) < M(*)(n) and HMW, M(n) > M(*)(n) ) regimes, respectively, based on free-energy argument of nematic and hexagonal hairy rods and found to correspond to the experimental x-ray diffraction (XRD) results for PF2/6 . By using the lattice parameters of PF2/6 as an experimental input, the nematic-hexagonal transition has been predicted in the vicinity of glassification temperature (T(g)) of PF2/6 . Then, by taking the orientation parts of the free energies into account the nematic-hexagonal transition has been calculated as a function of temperature and M(n) and a phase diagram has been formed. Below T(g) of 80 degrees C only (frozen) nematic phase is observed for M(n)< M(*)(n) = 10(4) g/mol and crystalline hexagonal phase for M(n) > M(*)(n) . The nematic-hexagonal transition upon heating is observed for the HMW regime depending weakly on M(n) , being at 140-165 degrees C for M(n) > M(*)(n). Third, the phase behavior and structure formation as a function of M(n) have been probed using powder and fiber XRD and differential scanning calorimetry and reasonable semiquantitative agreement with theory has been found for M(n) >or=3 kg/mol. Fourth, structural characteristics are widely discussed. The nematic phase of LMW materials has been observed to be denser than high-temperature nematic phase of HMW compounds. The hexagonal phase has been found to be paracrystalline in the (ab0) plane but a genuine crystal meridionally. We also find that all these materials including the shortest 10-mer possess the formerly observed rigid five-helix hairy-rod molecular structure.

Journal Article↗
PubMed1990

Towards the understanding of the function of Rb sphaeroides Y wild type reaction center: gene cloning, protein and detergent structures in the three-dimensional crystals.

We report various experiments aimed at the resolution of the 3-dimensional structure of the photosynthetic reaction center from wild type Y Rhodobacter sphaeroides. The genes encoding the L and M polypeptides have been cloned and sequenced. They bear 2 mutations each when compared to those already sequenced in another Rb sphaeroides strain (2.4.1). In the L gene, these codon changes are silent. In the M gene, one is silent and the other one leads to a Leu-Met substitution at position 140. At the present stage of the refinement of the X-ray data (0.3 nm resolution) the structure of the Y reaction center is shown to be highly similar to that of the Rhodopseudomonas viridis reaction center. The binding of spheroidene on the M side of the Y reaction center is shown to be determined by hydrophobic interactions with neighboring amino acids and by steric factors. Preliminary results concerning the localization of the detergent (beta-octylglucoside) in the unit cell are presented. This method combines low angle neutron scattering at different contrasts in H2O/D2O with X-ray crystallographic data.

Carotenoids↗
PubMed1987

Solution structure of human plasma fibronectin using small-angle X-ray and neutron scattering at physiological pH and ionic strength.

Human plasma fibronectin has been investigated at physiological pH and ionic strength, by using small-angle X-ray and neutron scattering techniques. The results indicate that the molecule is disc shaped with an axial ratio of about 1:10. In fact, an ellipsoid of revolution with semiaxes a = 1.44 nm and b = c = 13.8 nm is in agreement with the experimental scattering data, and can also fully explain the rather extreme hydrodynamic parameters reported for fibronectin. The X-ray data gave a radius of gyration of 8.9 nm and a molecular weight of 510,000, whereas the neutron data gave slightly larger values, 9.5 nm and 530,000, respectively. From the volume of the best fitting ellipsoid we obtain a degree of hydration of 0.61 g H2O/g protein (dry weight). Neutron data, recorded at different D2O concentrations in the solvent, gave a match point of 43% D2O, which indicates that approximately 80% of the hydrogens bound to oxygen and nitrogen are exchangeable.

Fibronectins↗
PubMed1998

Bragg diffraction from crystallized ion plasmas

Single crystals of a one-component plasma were observed by optical Bragg diffraction. The plasmas contained 10(5) to 10(6) single-positive beryllium-9 ions (9Be+) at particle densities of 10(8) to 10(9) per cubic centimeter. In approximately spherical plasmas, single body-centered cubic (bcc) crystals or, in some cases, two or more bcc crystals having fixed orientations with respect to each other were observed. In some oblate plasmas, a mixture of bcc and face-centered cubic ordering was seen. Knowledge of the properties of one-component plasma crystals is required for models of white dwarfs and neutron stars, which are believed to contain matter in that form.

Journal Article↗
PubMed1997

Synthesis, Characterization, and Reactivity of Isocyanato Dicarbaboranes Obtained from o-Carborane.

The functionalization of o-carborane with (bromoalkyl)phthalimides or propargylphthalimide, their subsequent transformation into isocyanate-substituted o-carborane, and their reactivity toward amino- and alcohol-containing molecules are reported. The preparation of these functionalized ureas and carbamates could potentially lead to the utilization of these molecules as suitable precursors for drugs to be used in boron neutron capture therapy (BNCT). The compounds 1-RNHC(O)NH(CH(2))(n)()-1,2-C(2)B(10)H(11) and 1-ROC(O)NH-1,2-C(2)B(10)H(11) (n = 1, 2, and 3) were prepared by reaction of 1-O=C=N(CH(2))(n)()-1,2-C(2)B(10)H(11), (n = 1, 2, and 3) with the corresponding amino- or alcohol-containing substrate. Experimental details and analytical data leading to the identification of the reported compounds are provided. Additionally the X-ray diffraction structures of 1-C(6)H(4)(CO)(2)NCH(2)CH(2)CH(2)-1,2-C(2)B(10)H(11) (1c) and 1-(C(6)H(5))(2)C=N-CH(2)-1,2-C(2)B(10)H(11) (20) are reported. Compound 1c crystallizes in the P&onemacr; space group, a = 10.791(1) Å, b = 13.104(1) Å, c = 7.1816(9) Å, alpha = 97.389(8) degrees, beta = 90.416(5) degrees, gamma = 66.462(6) degrees, Z = 2, R = 0.0512 for 2140 reflections with F(2) > 3.0sigma(F(2)). Compound 20 crystallizes in the P2(1)/n space group, a = 16.5560(7) Å, b = 7.0173(4) Å, c = 16.9750(6) Å, beta = 97.932(2) degrees, Z = 4, R = 0.0843 for 2755 reflections with F > 4.0sigma(F).

Journal Article↗
PubMed1998

Magnetism in nickel and synchrotron beam polarization studied by X-ray diffraction.

The ratio of the magnetic to the charge form factors of nickel has been determined by white-beam X-ray diffraction. The measurements were made on the new UK magnetic scattering beamline (XMaS) on a dipole source at the ESRF. The data comprise the three (h,h,0) reflections (4,4,0), (6,6,0) and (8,8,0) and the seven high-order (h,0,0) reflections (6,0,0) to (18,0,0), which doubles the range of wavevectors compared to previous studies. The data have been analysed using Hartree-Fock free-ion wave functions and core electron polarization effects were included. The results support the interpretation of neutron data obtained at lower momentum transfer for the e(g) and t(2g) orbital occupancies. The polarization of the dipole source is deduced to vary from 99.88 to 99.83% between 5 and 15 keV, respectively. This high value makes it an extremely suitable source for studies of ferromagnetism.

Journal Article↗
PubMed2000

Application of diffuse reflectance near-infrared spectroscopy for determination of crystallinity.

Studies were conducted to investigate the use of near-infrared spectroscopy (NIRS) for determining degree of crystallinity. Physical mixtures of amorphous/crystalline indomethacin and amorphous/crystalline sucrose were prepared over several composition ranges. Spectra were obtained on powder samples contained in glass vials using diffuse reflectance sampling. Parallel studies were conducted using X-ray powder diffraction (XRPD) and differential scanning calorimetry (DSC) for comparison. NIRS standard curves were constructed by plotting crystalline weight percent against the ratio of responses at two wavelengths or by partial least squares regression. NIRS standard curves demonstrated higher coefficients of determination and lower standard errors than either XRPD or DSC. Validation standards confirmed the accuracy of NIRS over XRPD. Method error analysis demonstrated comparable accuracy for NIRS and XRPD, with NIRS showing slightly better precision in repeated crystallinity determinations for a 50% crystalline sucrose sample. Interpretive analysis of the NIRS spectra was performed using neutron scattering and polarized Raman spectroscopy data obtained from the literature. Results indicated that the NIRS differences between crystalline and amorphous sucrose may be attributed to the disruption of regular vibrational modes when crystalline sucrose is rendered amorphous.

Crystallization↗