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At least 595 records · Page 33Linked to original sources

PubMed1998

Quaternary structures of a catalytic subunit-regulatory subunit dimeric complex and the holoenzyme of the cAMP-dependent protein kinase by neutron contrast variation.

Chimeric molecules of the cAMP-dependent protein kinase (PKA) holoenzyme (R2C2) and of a Delta1-91RC dimer were reconstituted using deuterated regulatory (R) and protiated catalytic (C) subunits. Small angle scattering with contrast variation has revealed the shapes and dispositions of R and C in the reconstituted complexes, leading to low resolution models for both forms. The crystal structures of C and a truncation mutant of R fit well within the molecular boundaries of the RC dimer model. The area of interaction between R and C is small, seemingly poised for dissociation upon a conformational transition within R induced by cAMP binding. Within the RC dimer, C has a "closed" conformation similar to that seen for C with a bound pseudosubstrate peptide. The model for the PKA holoenzyme has an extended dumbbell shape. The interconnecting bar is formed from the dimerization domains of the R subunits, arranged in an antiparallel configuration, while each lobe contains the cAMP-binding domains of one R interacting with one C. Our studies suggest that the PKA structure may be flexible via a hinge movement of each dumbbell lobe with respect to the dimerization domain. Sequence comparisons suggest that this hinge might be a property of the RII PKA isoforms.

Catalytic Domain↗

PubMed1994

Solution scattering from 50S ribosomal subunit resolves inconsistency between electron microscopic models.

Models of the 50S ribosomal subunit from electron microscopy on isolated particles and on ordered sheets display significantly different features. A model of the shape of the native Escherichia coli 50S subunit in solution and of its RNA-rich core at 4-nm resolution has been produced by using methods for joint interpretation of x-ray and neutron small-angle scattering data obtained by contrast variation. The good agreement between the shape of the entire 50S subunit and the electron microscopic models of isolated particles and between the RNA-rich core and the model obtained from ordered sheets leads to the conclusion that the latter, which is based on the subjective contouring of density maps, is heavily biased toward the RNA.

Escherichia coli↗

PubMed1999

Evidence for microscopic, long-range hydration forces for a hydrophobic amino acid.

We have combined neutron solution scattering experiments with molecular dynamics simulation to isolate an excess experimental signal that is caused solely by N-acetyl-leucine-amide (NALA) correlations in aqueous solution. This excess signal contains information about how NALA molecule centers are correlated in water, and we show how these solute-solute correlations might be determined at dilute concentrations in the small angle region. We have tested qualitatively different pair distribution functions for NALA molecule centers-gas, cluster, and aqueous forms of gc(r)-and have found that the excess experimental signal is adequate enough to rule out gas and cluster pair distribution functions. The aqueous form of gc(r) that exhibits a solvent-separated minimum, and possibly longer-ranged correlations as well, is not only physically sound but reproduces the experimental data reasonably well. This work demonstrates that important information in the small angle region can be mined to resolve solute-solute correlations, their lengthscales, and thermodynamic consequences even at dilute concentrations. The hydration forces that operate on the microscopic scale of individual amino acid side chains, implied by the small angle scattering data, could have significant effects on the early stages of protein folding, on ligand binding, and on other intermolecular interactions.

Amides↗

PubMed1998

Small-angle X-ray scattering using coherent undulator radiation at the ESRF.

A simple approach for producing a high-coherent-flux X-ray beam for small-angle-scattering studies used at the Troika beamline of the European Synchrotron Radiation Facility is reported. For such small-angle studies it is permissible to reduce the longitudinal coherence .length of the beam, thus increasing the energy bandpass and intensity of the beam, because there is only a small optical path-length difference. By using mirrors and filters to cut unwanted energies from the undulator harmonic structure, a high-flux beam of >10(9) photons s(-1) through a 5 micron-diameter pinhole at 8.2 keV with a bandpass of 1.3% can be produced. The coherent properties of this beam have been measured by analyzing a static speckle pattern from an aerogel sample imaged by a directly illuminated CCD camera. The speckle size and contrast are compared with the expected values based on a statistical analysis of the intensity distribution of speckle patterns obtained using partially coherent conditions. The expected widths of the spatial autocorrelation are found, but there is an apparent incoherent fraction of the beam which reduces the measured contrast. The method presented is to be used as a tool to optimize conditions for diffraction experiments using coherent X-rays.

Journal Article↗

PubMed1995

Structures of nanoparticles prepared from oil-in-water emulsions.

Hydrophobic substances were dissolved in an organic solvent and emulsified with an aqueous solution at very high shear. Droplets of very small sizes (50-100 nm) were obtained by using surfactants which were combinations of lecithins and bile salts. After emulsification, the organic solvent was removed by evaporation, yielding stable dispersions of solid particles. The sizes, shapes, and structures of the particles were examined through quasi-elastic light scattering, small-angle neutron scattering and cryotransmission electron microscopy. Cholesterol acetate particles stabilized by lecithin and bile salts were found to be platelets of 10-20 nm thickness and 80 nm diameter. Cholesteryl acetate particles stabilized with POE-(20)-sorbitan monolaurate were dense spherical globules of diameter 100 nm. Particles with a composition similar to the endogenously occurring, lipoprotein, LDL, were large spherical globules studded with small vesicles. The subsequent evolution of the cholesteryl acetate dispersion upon aging was examined. There was no transfer of cholesteryl acetate between particles nor to large crystals. However, some aggregation of the particles was observed when the volume fraction of the particles in the aqueous dispersion exceeded 0.05. Thus, the structure of the nanoparticles obtained through deswelling of emulsion droplets changes according to the nature of the emulsifiers and to the composition of the hydrophobic substances which they contain.

Bile Acids and Salts↗

PubMed2005

Nature of amorphous polymorphism of water.

We report elastic and inelastic neutron scattering experiments on different amorphous ice modifications. It is shown that an amorphous structure (HDA') indiscernible from the high-density phase (HDA), obtained by compression of crystalline ice, can be formed from the very high-density phase (vHDA) as an intermediate stage of the transition of vHDA into its low-density modification (LDA'). Both HDA and HDA' exhibit comparable small-angle scattering signals characterizing them as structures heterogeneous on a length scale of a few nanometers. The homogeneous structures are the initial and final transition stages vHDA and LDA', respectively. Despite their apparent structural identity on a local scale, HDA and HDA' differ in their transition kinetics explored by in situ experiments. The activation energy of the vHDA-to-LDA' transition is at least 20 kJ/mol higher than the activation energy of the HDA-to-LDA transition.

Journal Article↗

PubMed2004

Protein dynamics in solution and powder measured by incoherent elastic neutron scattering: the influence of Q-range and energy resolution.

Incoherent elastic neutron scattering (IENS) has been widely used to measure intramolecular atomic mean square displacements (MSDs) of proteins in powder and in solution. The instrumental energy resolution and the wave vector transfer (Q-range) determine, respectively, the time and length scales of observable motions. In order to investigate contributions of diffusive motions to MSDs measured by this method, we calculated the elastic intensity for several simple scattering functions. We showed that continuous translational diffusion contributes to MSDs in a Q-range where the energy width of the scattering function is of the order of the instrumental energy resolution. We discuss the choice of instruments adapted to focus on intramolecular motions in the presence of solvent or global macromolecular diffusion. The concepts developed are applied to interpret experimental data from H(2)O- and D(2)O-hydrated proteins. Finally, analogies between the Gaussian approximation in IENS and the Guinier approximation in small-angle scattering are discussed.

Computer Simulation↗

PubMed2001

Orientation dependence of ionization edges in EELS.

Anisotropy in the density of unoccupied states can be detected in the fine structure of ionization edges in angle-resolved EELS. It is shown that in a crystal an interference term occurs in the inelastic signal, and how it relates to electron channeling and site selection. The combination of orientation and site selection induces subtle variations in the ELNES. It is shown how this technique can be used to analyze local anisotropy related to the point group of the target atom. A second example shows how to extract non-dipole transitions at small scattering angles.

Journal Article↗

PubMed2000

Structures of Fibrous Supramolecular Assemblies Constructed by Amino Acid Surfactants: Investigation by AFM, SANS, and SAXS.

Aqueous gel-like solutions of N-acyl-L-aspartic acids (C(n)Asp, n=14, 16, 18) and N-dodecanoyl-beta-alanine (C(12)Ala) were prepared at pH 5-6 at room temperature. Structures of supramolecular assemblies in the solutions were investigated by atomic force microscopy (AFM), small-angle neutron scattering (SANS), and small-angle X-ray scattering (SAXS). The cross-sectional radii, 22-30 Å, of helical, fibrous assemblies were obtained from analysis of SANS for 1% gel-like C(n)Asp solutions. Three Bragg spacings were observed in a SANS spectrum for a 6% C(16)Asp solution. C(n)Asp molecules are associated into the unit chain of a helical bilayer strand with a diameter of 50-60 Å. Unit chains where linear bilayers twist form a double strand with helical sense of approximately 650-Å pitch. It was confirmed from AFM images that cylindrical fibers in a gel-like C(12)Ala solution had a circular cross-section. The SAXS spectrum showed characteristic Bragg spacings. Cylindrical C(12)Ala fibers consist of multilamellar layers of period approximately 34-Å. The fibers are laterally organized with period 365-380 Å. Copyright 2000 Academic Press.

Journal Article↗

PubMed2004

Structural evolution of a two-component organogel.

Dry reverse micelles of AOT in isooctane spontaneously undergo a microstructural transition to an organogel upon the addition of a phenolic dopant, p-chlorophenol. This microstructural evolution has been studied through a combination of light scattering, small-angle neutron scattering (SANS), NMR, and rheology. Several equilibrium stages between the system of dry reverse micelles of AOT and a 1:1 AOT/p-chlorophenol (molar ratio) gel in isooctane have been examined. To achieve this, p-chlorophenol is added progressively to the dilute solutions of AOT in isooctane, and this concentration series is then analyzed. The dry micelles of AOT in isooctane do not undergo any detectable structural change up to a certain p-chlorophenol concentration. Upon a very small increment in the concentration of p-chlorophenol beyond this "threshold" concentration, large strandlike aggregates are observed which then evolve to the three-dimensional gel network.

Chlorophenols↗

PubMed2005

Multi length scale analysis of the microstructure in sticky sphere dispersions during shear flow.

The effect of shear flow on the microstructure in a weakly aggregated suspension is investigated. Monodisperse small silica particles with a grafted layer of 1-octadecanol are dispersed in n-tetradecane, yielding a thermoreversible sticky sphere model suspension. A combination of small angle light scattering and ultra small and small-angle X-ray scattering techniques have been used, in situ and time resolved, to study the flow-induced anisotropy of the microstructure. In this manner, the length scales from the single particle size to that of the spatial organization of the aggregates can be covered. Harmonic expansion of the structure factor demonstrates that anisotropy develops in the microstructure on all relevant length scales. Possible real space interpretations of the scattering information are discussed in conjunction with implications for the nonlinear rheological behavior.

Journal Article↗

PubMed2005

Probing counterion modulated repulsion and attraction between nucleic acid duplexes in solution.

Understanding biological and physical processes involving nucleic acids, such as the binding of proteins to DNA and RNA, DNA condensation, and RNA folding, requires an understanding of the ion atmosphere that surrounds nucleic acids. We have used a simple model DNA system to determine how the ion atmosphere modulates interactions between duplexes in the absence of specific metal ion-binding sites and other complicated interactions. In particular, we have tested whether the Coulomb repulsion between nucleic acids can be reversed by counterions to give a net attraction, as has been proposed recently for the rapid collapse observed early in RNA folding. The conformation of two DNA duplexes tethered by a flexible neutral linker was determined in the presence of a series of cations by small angle x-ray scattering. The small angle x-ray scattering profiles of two control molecules with distinct shapes (a continuous duplex and a mimic of the compact DNA) were in good agreement with predictions, establishing the applicability of this approach. Under low-salt conditions (20 mM Na+), the tethered duplexes are extended because of a Coulombic repulsion estimated to be 2-5 kT/bp. Addition of high concentrations of Na+ (1.2 M), Mg2+ (0.6 M), and spermidine3+ (75 mM) resulted in electrostatic relaxation to a random state. These results indicate that a counterion-induced attractive force between nucleic acid duplexes is not significant under physiological conditions. An upper limit on the magnitude of the attractive potential under all tested ionic conditions is estimated.

DNA↗

PubMed1984

Characterization of melanogenesis and morphogenesis of melanosomes by physicochemical properties of melanin and melanosomes in malignant melanoma.

This study elucidates the nature of melanogenesis in B16 and Harding-Passey (HP) mouse melanomas producing melanin and melanosomes of different color and fine structure, i.e., brown-black eumelanosome-like B16 granules and reddish brown pheomelanosome-like HP granules, and compares them with "typical" 3,4-dihydroxyphenylalanine (DOPA) and sepia eumelanins and sepia eumelanosomes. The melanin content of B16 melanosomes was more than three times higher than that of HP melanosomes. The content of free and protein-bound DOPA and 5-S-cysteinyldopa varied greatly in B16, HP, and sepia melanosomes and was unrelated to melanin content. Chemical analysis of the eumelanin: pheomelanin ratio in melanosomes and elemental analysis of isolated melanin showed that B16 and HP melanins are primarily eumelanic, with a higher ratio of pheomelanic component in HP melanin. The spectra of electron spin resonance and IR and X-ray small-angle scattering of B16 and HP melanins were basically similar to those of sepia and DOPA melanins. B16, HP, and DOPA melanins were dissolved in aqueous NH3, while sepia melanin was dissolved to a far lesser extent. It was concluded that both B16 and HP melanomas are primarily involved in eumelanogenesis, although the fine structure of their melanosomes is entirely different, and that the marked color difference in the two melanosomes is related to a difference in the absolute content of eumelanin, the presence of a small amount of pheomelanin, and the mode of chemical bindings of melanin to structural proteins. In contrast to normal skin and hair, melanosome morphogenesis may not directly correspond to melanogenesis type in malignant melanoma.

Animals↗

PubMed1999

Structural and Thermodynamic Properties of Solutions of Butane in Aqueous Sodium Dodecyl Sulfate: A Study Using Neutron Scattering and Solubility Measurements.

The solubility of n-butane at a pressure of 1.013 bar in aqueous solutions of sodium dodecyl sulfate (SDS) has been measured over a range of concentration from below the critical micelle concentration (CMC) at about 8 mol kg(-1) to about 90 mol kg(-1) at three different temperatures. The free energy, enthalpy, and entropy of transfer of butane from water to the micelle were respectively -19.0 kJ mol(-1), 5.5 kJ mol(-1), and 80 J K(-1) mol(-1). At 68 mol kg(-1) a transition was found with a free energy of about -400 J mol(-1). Small-angle neutron experiments were used to study the effect of butane on the state of aggregation of the SDS. For each butane molecule incorporated into a micelle, the aggregation number of the SDS increased by an average of about 1.4 molecules. Thus, at 1.013 bar of butane and 50 mM SDS, where the solubility is about 1 butane to 10 SDS, the average micelle increases in size by about 20%, most of which comes from the additional SDS molecules. The aggregation behavior is qualitatively similar to that reported for hexane, heptane, and octane, but the effect seems to be larger for butane for a given volume of solute hydrocarbon. Small-angle scattering did not observe any substantial change in structure across the phase transition at 68 mol kg(-1). Copyright 1999 Academic Press.

Journal Article↗

PubMed1977

Contrast variation study of specifically deuterated Escherichia coli ribosomal subunits.

A neutron small-angle scattering analysis has been done on partially deuterated 30S and 50S subunits of Escherichia coli ribosomes by the contrast variation method. The results indicate that the central regions of both particles are RNA-rich whereas their exteriors are protein-rich. The segregation of RNA and protein is much greater in the 50S subunit than in the 30S; the 30S subunit approaches a homogeneous mixture of RNA and protein. In both structures the most probable separation between the centers of mass of their protein and RNA distributions is small, although substantial variation of this parameter is possible within experimental error.

Deuterium↗

PubMed1987

Small-angle neutron-scattering and electron microscope studies of the chicken liver fatty acid synthase.

A structural model for the chicken liver fatty acid synthase is proposed based on electron microscope and small-angle neutron-scattering studies of the enzyme. The model has the overall appearance of two side by side cylinders with dimensions of 160 X 146 X 73 A, with each subunit 160 A in length and 73 A in diameter. The model was constructed by dividing each cylinder into three domains having lengths of 32, 82, and 46 A, with the domain structures in the two subunits being related to each other by a dyad axis. The model is consistent with chemical cross-linking studies which indicated that the subunits are arranged in a head to tail fashion. The cross-linking studies further showed that the beta-ketoacyl synthase active site contains a cysteine and a pantetheine residue from adjacent subunits. It is proposed that the domains which catalyze the addition of C2 units from malonate to the growing fatty acid chain lie in the crevice between the two subunits and that the two independent sets of fatty acid-synthesizing centers lie on the major axis of the model on opposite ends of the molecular dyad.

Animals↗

PubMed2002

The solution structure of a cardiac troponin C-troponin I-troponin T complex shows a somewhat compact troponin C interacting with an extended troponin I-troponin T component.

We have investigated the structure of the cTnC-cTnI-cTnT(198-298) calcium-saturated, ternary cardiac troponin complex by small-angle scattering with contrast variation. Shape restoration was also applied to the scattering information resulting from the deuterated cTnC subunit, the unlabeled cTnI-cTnT(198-298) subunits, and the entire complex. The experimental results and modeling indicate that cTnC adopts a partially collapsed conformation, while the cTnI-cTnT(198-298) components have an extended, rod-like structure. Shape restoration applied to the X-ray scattering data and the entire contrast variation series suggest that cTnC and the cTnI-cTnT(198-298) component lie with their long axes roughly parallel to one another with a relatively small surface area for interaction. Our findings indicate that the nature of the interactions between TnC and the TnI-TnT component differs significantly between the cardiac and skeletal isoforms as evidenced by the different degrees of compactness between the cardiac TnC and skeletal TnC in their respective ternary complexes and the fact that the cTnC subunit is not highly intertwined with the other subunits, as observed in the binary complex of the skeletal isoforms [Olah, G. A., and Trewhella, J. (1994) Biochemistry 33, 12800-12806].

Animals↗

PubMed2007

Nanostructures by self-assembling peptide amphiphile as potential selective drug carriers.

The self-assembling behavior, at physiological pH, of the amphiphile peptide (C18)(2)L5CCK8 in nanostructures is reported. Stable aggregates presenting a critical micellar concentration of 2 x 10(-6) mol kg(-1), and characterized by water exposed CCK8 peptide in beta-sheet conformation, are obtained. Small angle neutron scattering experiments are indicative for a 3D structure with dimensions > or =100 nm. AFM images confirm the presence of nanostructures. Fluorescence experiments indicating the sequestration of pyrene, chosen as drug model, and the anticancer Doxorubicin within the nanostructures are reported.

Antineoplastic Agents↗