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PubMed2005

Structure and dynamics of halogenoethanol-water mixtures studied by large-angle X-ray scattering, small-angle neutron scattering, and NMR relaxation.

To clarify the structure of solvent clusters formed in halogenoethanol-water mixtures at the molecular level, large-angle X-ray scattering (LAXS) measurements have been made at 298 K on 2,2,2-trifluoroethanol (TFE), 2,2,2-trichloroethanol (TCE), and their aqueous mixtures in the TFE and TCE mole fraction ranges of 0.002 < or = x(TFE) < or = 0.9 and 0.5 < or = x(TCE) < or = 0.9, respectively. The radial distribution functions (RDFs) for TFE-water mixtures have shown that the structural transition from inherent TFE structure to the tetrahedral-like structure of water takes place at x(TFE) approximately 0.2. In the TCE-water mixtures inherent TCE structure remains in the range of 0.5 < or = x(TCE) < or = 1. Small-angle neutron scattering (SANS) experiments have been performed on CF(3)CH(2)OD- (TFE-d(1)-) D(2)O and CF(3)CD(2)OH- (TFE-d(2)-) H(2)O mixtures in the TFE mole fraction range of 0.05 < or = x(TFE) < or = 0.8. The SANS results in terms of the Ornstein-Zernike correlation length have revealed that TFE and water molecules are most heterogeneously mixed with each other in the TFE-water mixture at x(TFE) approximately 0.15, i.e., both TFE clusters and water clusters are most enhanced in the mixture. To evaluate the dynamics of TFE and ethanol (EtOH) molecules in TFE-water and ethanol-water mixtures, respectively, (1)H NMR relaxation rates for the methylene group within alcohol molecules have been measured by using an inversion-recovery method. The alcohol concentration dependence of the relaxation rates for the TFE-water and ethanol-water mixtures has shown a break point at x(TFE) approximately 0.15 and x(EtOH) approximately 0.2, respectively, where the structural transition from alcohol clusters to the tetrahedral-like structure of water takes place. On the basis of the present results, the most likely structure models of solvent clusters predominantly formed in TFE-water and TCE-water mixtures are proposed. In addition, effects of halogenation of the hydrophobic groups on clustering of alcohol molecules are discussed from the present results, together with the previous ones for ethanol-water and 1,1,1,3,3,3-hexafluoro-2-propanol- (HFIP-) water mixtures.

Ethanol↗
PubMed1993

Structure of clathrin-coated vesicles from small-angle scattering experiments.

Previously published small-angle neutron and X-ray scattering data from coated vesicles, reassembled coats, and stripped vesicles have been analyzed in terms of one common model. The neutron data sets include contrast variation measurements at three different D2O solvent concentrations. The model used for interpreting the data has spherical symmetry and explicitly takes into account polydispersity, which is described by a Gaussian distribution. A constant thickness of the clathrin coats is assumed. The fitting of the model shows that the coated vesicles consist of a low-density outer protein shell (clathrin) and a central protein shell (accessory polypeptides and receptors) of approximately six times higher density. For the X-ray scattering and neutron contrast variation data, the polydispersity of the samples is of the order of 90 A (full-width-at-half-maximum value) and the average outer radius is approximately 400 A. The inner high-density shell has inner and outer radii of 115 and 190 A, respectively. A simultaneous fit to the three neutron contrast variation data sets identifies the lipid membrane with a thickness of 40 A and an outer radius of 196 A. Thus, the membrane and the high-density protein shell overlap in space, which shows that the lipid membrane contains protein. The molecular mass of the average particle is 27 x 10(6) Da. The coated vesicles consist, on average, of approximately 85% protein and 15% lipids. About 40% of the protein mass is situated in the central high-density shell, which gives a large amount of protein in the lipid membrane. The densities of the central shell and the lipid membrane show that the hydration is small in the central region. A comparison of the total mass, the mass distribution, and the structure of the average-size particles with the barrel structure shows that the accessory polypeptides are incorporated in the lipid membrane. The results from the neutron data for the reassembled coats show that the structure of these particles is very similar to the structure of the native coats. The main difference is a higher density of the central protein shell, which shows that the membrane is replaced by protein in the reassembled coats.

Clathrin↗
PubMed1986

Small angle scattering of cell nuclei.

Neutron and X-ray small angle scattering techniques have been applied to study chromatin structure inside different types of cell nuclei. Scattering from genetically inactive chicken erythrocyte nuclei exhibits a maximum at Q = 0.1-0.15 nm-1 which cannot be observed by studying isolated chromatin derived from the same kind of cells. In highly active transcribing rat liver nuclei such a nuclear pattern is absent. The radius of gyration of isolated "superbeads" was determined. It is discussed whether the characteristic maximum of the nuclei originates from this superstructural organisation of chromatin. Rat liver nuclei were fractionated on sucrose gradients in order to determine whether the absence of the extra maximum in scattering profiles of these nuclei is due to overlapping effects of different chromatin organisation in the various cell types of the liver. As compared to unfractionated nuclei no strong deviations in the scattering profiles of the fractions could be observed. Erythrocyte nuclei were dialysed in buffers differing in the ionic strength of monovalent cations. The typical maximum from the nuclei is shifted from 60 nm (very low salt concentration) to about 35 nm (physiological ionic strength) and is linearly proportional to the decreasing radius of the nuclei. In conclusion, chromatin structure inside the nucleus has a scattering maximum due to an ordered packing of the fibres which is absent in nuclei with high genetic activity.

Animals↗
PubMed1988

Spatial arrangement of DNA-dependent RNA polymerase of Escherichia coli and DNA in the specific complex. A neutron small angle scattering study.

In this paper we demonstrate that neutron small angle scattering is a suitable method to study the spatial arrangement of large specific protein-DNA complexes. We studied the complex of DNA-dependent RNA polymerase of Escherichia coli and a 130 base-pair DNA fragment containing the strong promoter A1 of bacteriophage T7. Contrast variation of the complex with deuterium allowed us to "visualize" either RNA polymerase, or DNA, or both components in situ. From the corresponding scattering curves information was derived about: (1) Conformational changes of RNA polymerase and DNA by complex formation: comparison of the scattering profiles of the isolated and complexed components showed that by specific complex formation the cross-section of RNA polymerase decreases, while the DNA fragment does not undergo a gross conformational change. (2) The spatial arrangement of RNA polymerase and DNA in the specific complex from the cross-sectional radii of gyration of the complex the normal distance dn between the centre of gravity of the RNA polymerase and the axis of the DNA fragment was derived as 5.0 (+/- 0.3) nm. On the basis of these and footprinting data a low resolution model of the RNA polymerase-promoter complex is proposed. The main feature of this model is the positioning of RNA polymerase to only one side of the DNA.

DNA, Bacterial↗
PubMed2006

Structural themes and variations in protein kinase A as seen by small-angle scattering and neutron contrast variation.

Using small-angle solution scattering and neutron contrast variation, we have studied the structure of the multi-subunit protein kinase A. We have gained insights into how nature can take a set of common structural domains (or themes) and modulate their interactions via sequence variations and second messenger mediated signaling to affect enzyme activity and receptor binding important for targeting this multi-function enzyme to specific sub-cellular locations. These studies demonstrate the power of neutron contrast variation to expand our knowledge of the dynamic supra-molecular structures that carry out biological function.

Binding Sites↗
PubMedDate not supplied

[Detection of new two-membrane structures in native mitochondria by the method of small-angle scattering of neutrons].

The structure of mitochondrial cristas has been studied for the first time by the method of small-angle scattering of thermal neutrons. Experiments were performed on intact functioning rat liver mitochondria. Mitochondrial cristas are usually considered as folds of the internal membrane with arbitrary nonfixed intermembrane distances. It was shown that, under particular conditions, during low-amplitude swelling of mitochondria, cristas are transformed to bimembrane structures, with the distance between the central planes of membranes of 190 E. It was found that the formation of bimembrane structures and their structural parameters do not depend on the method of induction of swelling, by placing the mitochondria into a hypotonic medium or by the opening of nonspecific pores.

Animals↗
PubMed2003

In situ synchrotron study of phase transformation behaviors in bulk metallic glass by simultaneous diffraction and small angle scattering.

We have used a new approach involving simultaneous diffraction and small angle scattering to study the amorphous-to-crystalline phase transformation in Zr-based bulk metallic glass. In situ, time-resolved data provided the first direct demonstration of a phase separation prior to crystallization. There is evidence that nucleation and growth of the crystalline phase occur in separate stages, with different kinetics. Our data support the view that crystalline nucleation is achieved via short-range diffusion of small atoms (e.g., Ni), whereas the growth is dictated by long-range diffusion.

Journal Article↗
PubMed1998

Calmodulin binding to myosin light chain kinase begins at substoichiometric Ca2+ concentrations: a small-angle scattering study of binding and conformational transitions.

We have used small-angle scattering to study the calcium dependence of the interactions between calmodulin (CaM) and skeletal muscle myosin light chain kinase (MLCK), as well as the conformations of the complexes that form. Scattering data were measured from equimolar mixtures of a functional MLCK and CaM or a mutated CaM (B12QCaM) incompetent to bind Ca2+ in its N-terminal domain, with increasing Ca2+ concentrations. To evaluate differences between CaM-enzyme versus CaM-peptide interactions, similar Ca2+ titration experiments were performed using synthetic peptides based on the CaM-binding sequence from MLCK (MLCK-I). Our data show there are different determinants for CaM binding the isolated peptide sequence compared to CaM binding to the same sequences within the enzyme. For example, binding of either CaM or B12QCaM to the MLCK-I peptide is observed even in the presence of EGTA, whereas binding of CaM to the enzyme requires Ca2+. The peptide studies also show that the conformational collapse of CaM requires both the N and C domains of CaM to be competent for Ca2+ binding as well as interactions with each end of MLCK-I, and it occurs at approximately 2 mol of Ca2+/mol of CaM. We show that CaM binding to the MLCK enzyme begins at substoichiometric concentrations of Ca2+ (< or = 2 mol of Ca2+/mol of CaM), but that the final compact structure of CaM with the enzyme requires saturating Ca2+. In addition, MLCK enzyme does bind to 2Ca2+ x B12QCaM, although this complex is more extended than the complex with native CaM. Our results support the hypothesis that CaM regulation of MLCK involves an initial binding step at less than saturating Ca2+ concentrations and a subsequent activation step at higher Ca2+ concentrations.

Amino Acid Sequence↗
PubMed1993

X-ray small angle scattering of the human transferrin protein aggregates. A fractal study.

X-ray small angle scattering experiments, using a pin hole SAXS camera with Synchrotron radiation source, have been performed to study the conformational changes of lyophilized samples of Apo-, Mono-, and Diferric- human transferrin. We report the experimental evidence that the analysis of the scattered intensity through the fractal theory may give information on the particle size and its variation upon iron binding.

Apoproteins↗
PubMed2002

Investigation of pharmaceutical oil/water microemulsions by small-angle scattering.

PURPOSE: Stable oil/water (o/w) microemulsions are very effective vehicle systems for dermal administration of drugs having no or low skin penetration. These systems, consisting of oils, a blend of a high and a low HLB surfactant, and a hydrophilic phase (propylene glycol/water), were developed using pharmaceutically acceptable components. METHODS: In this paper, the droplet size of these microemulsions was characterized by means of dynamic light scattering (DLS) and small-angle neutron scattering (SANS). Furthermore, different size parameters obtained by DLS and SANS experiments were compared and discussed. RESULTS: Extremely small droplet radii of approximately 10 nm could be observed. A good agreement between the data of DLS and SANS experiments was found. The kind of oil only marginally influences the droplet size. CONCLUSIONS: Particle size determination via scattering techniques is a useful tool to characterize droplets in microemulsions for dermal drug delivery.

Administration, Cutaneous↗
PubMed2006

The solution structure of stilbenoid dendrimers: a small-angle scattering study.

The spatial structure of a stilbenoid dendrimer is investigated by small-angle X-ray scattering (SAXS) and small-angle neutron scattering (SANS) in dilute solution. All measurements are performed in toluene. The dendrimer consists of a stilbenoid scaffold with appended hexyloxy chains. SAXS is mainly sensitive to the dendrimer scaffold whereas SANS intensity, measured in fully deuterated toluene, derives from the solute molecules. The resulting SAXS and SANS intensities are analyzed by comparison with various models. It is found that the model of a circular disk gives the best description of the data. SAXS data demonstrate that the stilbenoid scaffold is flat as expected for benzene rings conjugated through vinylene units. Thus, it can be described by a circular disk with a radius of 1.6 nm and a thickness of 0.7 nm. SANS, on the other hand, shows that the hexyloxy chains are not confined in the plane defined by the core. This is derived from modeling the SANS data with a much thicker circular disk (radius: 2.4 nm, thickness: 1.8 nm). The structure factor S(q), describing the interaction of the dendrimers at higher concentrations, is modeled quantitatively with the "polymer reference interaction site model" (PRISM) integral equation formalism for hard plates such as particles. Here the structural data obtained from the analysis of the SANS data are used so that no new adjustable parameter is necessary for this description.

Journal Article↗
PubMed2002

Interaction of proteins in solution from small-angle scattering: a perturbative approach.

In this work an improved methodology for studying interactions of proteins in solution by small-angle scattering is presented. Unlike the most common approach, where the protein-protein correlation functions g(ij)(r) are approximated by their zero-density limit (i.e., the Boltzmann factor), we propose a more accurate representation of g(ij)(r) that takes into account terms up to the first order in the density expansion of the mean-force potential. This improvement is expected to be particularly effective in the case of strong protein-protein interactions at intermediate concentrations. The method is applied to analyze small-angle x-ray scattering data obtained as a function of the ionic strength (from 7 to 507 mM) from acidic solutions of beta-lactoglobulin at the fixed concentration of 10 gl(-1). The results are compared with those obtained using the zero-density approximation and show significant improvement, particularly in the more demanding case of low ionic strength.

Animals↗
PubMed2003

Characterisation of structure and aggregation processes of aquatic humic substances using small-angle scattering and X-ray microscopy.

Aquatic humic substances (HS), an important part of the dissolved organic carbon in freshwater systems, are polyfunctional natural compounds with polydisperse structure showing strong aggregation/coagulation behaviour at high HS concentrations and in the presence of metal ions. In this study, small-angle neutron scattering (SANS), small-angle X-ray scattering (SAXS) and X-ray microscopy (XRM) were applied to characterise the structure and aggregation processes of HS in solution. In SAXS and XRM the high brilliant synchrotron radiation was used as X-ray source. Applying small-angle scattering, information about the size distribution and shape of aquatic HS was obtained. Spherical HS units were found which were stable in a wide concentration range in a kind of "monomeric" state almost independent of pH and ionic strength. At higher concentrations they formed chain-like agglomerates or disordered HS structures. In studies on the coagulation behaviour of HS after addition of copper ions, a linear relationship between Cu(2+) concentration and the formation of large disordered HS-Cu(2+) agglomerates was obtained. By using X-ray microscopy, single "huge" particles were found in older solutions and in solutions with high HS concentrations. Over a threshold Cu(2+) concentration of approx. 300 mg/L, the formation of an extensive HS-Cu(2+) network structure was observed within a few minutes. The presented structures show the ability of the methods used to characterise processes between diluted phase and suspended matter, which play an important role particularly in the region of phase interfaces.

Journal Article↗
PubMed2000

Closed-form solution for the Wigner phase-space distribution function for diffuse reflection and small-angle scattering in a random medium.

Within the paraxial approximation, a closed-form solution for the Wigner phase-space distribution function is derived for diffuse reflection and small-angle scattering in a random medium. This solution is based on the extended Huygens-Fresnel principle for the optical field, which is widely used in studies of wave propagation through random media. The results are general in that they apply to both an arbitrary small-angle volume scattering function, and arbitrary (real) ABCD optical systems. Furthermore, they are valid in both the single- and multiple-scattering regimes. Some general features of the Wigner phase-space distribution function are discussed, and analytic results are obtained for various types of scattering functions in the asymptotic limit s >> 1, where s is the optical depth. In particular, explicit results are presented for optical coherence tomography (OCT) systems. On this basis, a novel way of creating OCT images based on measurements of the momentum width of the Wigner phase-space distribution is suggested, and the advantage over conventional OCT images is discussed. Because all previous published studies regarding the Wigner function are carried out in the transmission geometry, it is important to note that the extended Huygens-Fresnel principle and the ABCD matrix formalism may be used successfully to describe this geometry (within the paraxial approximation). Therefore for completeness we present in an appendix the general closed-form solution for the Wigner phase-space distribution function in ABCD paraxial optical systems for direct propagation through random media, and in a second appendix absorption effects are included.

Journal Article↗
PubMed1998

Small angle scattering in ribosomal structure research: localization of the messenger RNA within ribosomal elongation states.

Besides EM and biochemical studies small angle scattering (SAS) examinations have contributed significantly to our current knowledge about the ribosomal structure. SAS does not only allow the validation of competing models but permits independent model building. However, the major contribution of SAS to ribosomal structure research derived from its ability to reveal the spatial distribution of the individual ribosomal components (57 in the E. coli ribosome) within the ribosomal structure. More recently, an improved scattering method (proton-spin contrast variation) made it possible also to address the question of mapping functional ligands in defined ribosomal elongation states. Here, we review the contributions of SAS to the current understanding of the ribosome. Furthermore we present the direct localization of a small mRNA fragment within 70S elongation complexes and describe its movement upon the translocation reaction. The successful mapping of this fragment comprising only about 0.6% of the total mass of the complex proves that proton-spin contrast-variation is a powerful tool in modern ribosome research.

Peptide Chain Elongation, Translational↗