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PubMed2002

Helical rosette nanotubes with tunable chiroptical properties.

On the basis of transmission electron microscopy (TEM), dynamic light scattering (DLS), small-angle X-ray scattering (SAXS), and circular dichroism (CD) studies, compound 1 was shown to exist mainly in two states: (a) At high concentration (> or =1 mM, in methanol), 1 undergoes hierarchical self-assembly to generate rosette nanotubes with approximately 4 nm diameter and a concentration-dependent hydrodynamic radius in the range 10-100 nm. Under these conditions, addition of a chiral amino acid promoter (L-Ala), that binds to the crown ether moiety of 1 via electrostatic interactions, promotes a rapid transition (k(0) approximately equal 0.48 s(-1), for [1] = 0.046 mM, [L-Ala] = 2.8 mM) from racemic to chiral rosette nanotubes with predefined helicities as indicated by the resulting induced circular dichroism (ICD). (b) At low concentration (< or =0.04 mM, in methanol), 1 exists mainly in a nonassembled state as shown by TEM and DLS. Addition of L-Ala in this case triggers a relatively slow (k(0) approximately equal 0.07 s(-1) for [1] = 0.04 mM, [L-Ala] = 2.4 mM) sequence of supramolecular reactions leading to the hierarchical self-assembly of rosette nanotubes with predefined helicities. Under both conditions a and b, the kinetic data unveiled the intrinsic ability of the rosette nanotubes to promote their own formation (autocatalysis). The degree of chiral induction was found to depend dramatically upon the chemical structure of the promoter. This process appears also to follow an all-or-none response, as the vast majority of the crown ether sites must be occupied with a promoter for a complete transition to chiral nanotubes to take place. Finally, both supramolecular pathways a and b offer an efficient approach for the preparation of helical rosette nanotubes with tunable chiroptical properties and may also be viewed as a process by which a predefined set of physical and chemical properties that characterizes a molecular promoter is expressed at the macromolecular level.

Journal Article↗
PubMed2004

Anomalous decrease in lamellar spacing by shear flow in a nonionic surfactant/water system.

We study the effects of shear flow on the structure of a lamellar phase in a C16E7 [hepta(oxyethylene glycol)-n-hexadecyl ether]/water system (40-55 wt % of C16E7) at 70 degrees C using small-angle neutron scattering in the range of shear rate of 10(-3)-30 s(-1). At the shear rate 0.1-1 s(-1), the repeat distance (d) is decreased significantly (down to about 40% of d at rest in the most significant case) and discontinuously with increasing shear rate. With the further increase in the shear rate, d increases through a sharp minimum (referred to as d*). Such a shear rate dependence of d is obtained for all the principal orientations of lamellae. As the concentration of C16E7 decreases from 55 to 40 wt %, d increases from 6.5 to 8.5 nm at rest whereas d* remains almost constant (approximately equal to 5 nm). Moreover, d* is found to be almost equal to the thickness of bilayers obtained from the line shape analysis of small-angle X-ray scattering at rest. The results strongly suggest that the water layer is excluded by shear flow and that the lamellar phase segregates into surfactant-rich and water-rich regions, although these regions do not reach macroscopic size.

Letter↗
PubMed2000

Slit x-ray beam primary dose profiles determined by analytical transport of Compton recoil electrons.

Accurate measurement of radiation beam penumbras is essential for conformal radiotherapy. For this purpose a detailed knowledge of the dosimeter's spatial response is required. However, experimental determination of detector spatial response is cumbersome and restricted to the specific detector type and beam spectrum used. A model has therefore been developed to calculate in slit beam geometry both dose profiles and detector response profiles. Summations over representative photon beam spectra yield profiles for polyenergetic beams. In the present study the model is described and resulting dose profiles verified. The model combines Compton scattering of incident photons, transport of resulting electrons by Fermi-Eyges small-angle multiple scattering theory, and functions to limit electron transport. This analytic model thus yields line spread kernels of primary dose in a water phantom. It is shown that the spatial response of an ideal point detector to a primary photon beam can be well described by the model; the calculations are verified by measurements with a diamond detector in a telescopic slit geometry in which all dose contributions except for the primary dose can be excluded. Effects of photon detector behavior, source size of the linear accelerator (linac) and detector size are studied. Measurements show that slit dose profiles calculated by means of the kernel are accurate within 0.1 mm of the full-width at half-maximum. For a theoretical point source and point detector combined with a 0.2 mm wide slit, the full-width half-maximum values of the slit beam dose profiles are calculated as 0.37 mm and 0.42 mm in a 6 MV and 25 MV x-ray beam, respectively. The present study shows that the model is adequate to calculate local dose effects that are dominated by approximately mono-directional, primary photon fluence. The analytic model further provides directional electron fluence information and is designed to be applied to various detectors and linac beam spectra.

Biophysical Phenomena↗
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↗
PubMed2001

Detector line spread functions determined analytically by transport of Compton recoil electrons.

To achieve the maximum benefit of conformal radiation therapy it is necessary to obtain accurate knowledge of radiation beam penumbras based on high-resolution relative dosimetry of beam profiles. For this purpose there is a need to perform high-resolution dosimetry with well-established routine dosimeters, such as ionization chambers or diodes. Profiles measured with these detectors must be corrected for the dosimeter's nonideal response, caused by finite dimensions and, in the case of an ionization chamber, the alteration of electron transport and a contribution of electrons recoiled in the chamber wall and the central electrode. For this purpose the line spread function (LSF) of the detector is needed. The experimental determination of LSFs is cumbersome and restricted to the specific detector and beam energy spectrum used. Therefore, a previously reported analytical model [Med. Phys. 27, 923-934 (2000)] has been extended to determine response profiles of routine dosimeters: shielded diodes and, in particular, ionization chambers, in primary dose slit beams. The model combines Compton scattering of incident photons, the transport of recoiled electrons by Fermi-Eyges small-angle multiple scattering theory, and functions to limit electron transport. It yields the traveling direction and the energy of electrons upon incidence on the detector surface. In the case of ionization chambers, geometrical considerations are then sufficient to calculate the relative amount of ionization in chamber air, i.e., the detector response, as a function of the detector location in the slit beam. In combination with the previously reported slit beam dose profiles, the LSF can then readily be derived by reconstruction techniques. Since the spectral contributions are preserved, the LSF of a dosimeter is defined for any beam for which the effective spectrum is known. The detector response profiles calculated in this study have been verified in a telescopic slit beam geometry, and were found to correspond to experimental profiles within 0.2 and 0.3 mm (full width at half-maximum) for a Wellhoefer IC15 chamber in a 6 and 25 MV-X x-ray beam, respectively. For a shielded diode these figures were found to be 0.2 and 0.1 mm, respectively. It is shown that a shielded diode in a primary beam needs only a small size-based correction of measured profiles. The effect of the LSF of an IC15 chamber on penumbra width has been determined for a set of model penumbras. The LSFs calculated by the application of the analytical model yield a broadening by 2 mm of a 3 mm wide penumbra (20%-80%). This is 0.5 mm (6 MV-X) to 1 mm (25 MV-X) smaller than found with the experimental LSFs. With a spatial correction based on the LSFs that were determined in this study, this broadening of up to 2 mm is eliminated, so that ionization chambers like the IC15 can be used for high-resolution relative dosimetry on a routine basis.

Electrons↗
PubMed2006

Supramolecular self-assembly of multiblock copolymers in aqueous solution.

A unique pH-dependent phase behavior from a copolymer micellar solution to a collapsed hydrogel with micelles ordered in a hexagonal phase was observed. Small-angle neutron scattering (SANS) was used to follow the pH-dependent structural evolution of micelles formed in a solution of a pentablock copolymer consisting of poly((diethylaminoethyl methacrylate)-b-(ethylene oxide)-b-(propylene oxide)-b-(ethylene oxide)-b-(diethylaminoethyl methacrylate)) (PDEAEM25-b-PEO100-b-PPO65-b-PEO100-b-PDEAEM25). Between pH 3.0 and pH 7.4, we observed the presence of charged spherical micelles. Increasing the pH of the micelle solution above pH 7.4 resulted in increasing the size of the micelles due to the increasing hydrophobicity of the PDEAEM blocks above their pKa of 7.6. The increase in size of the spherical micelles resulted in a transition to a cylindrical micelle morphology in the pH range 8.1-10.5, and at pH >11, the copolymer solution undergoes macroscopic phase separation. Indeed, the phase separated copolymer sediments and coalesces into a hydrogel structure that consists of 25-35 wt % water. Small-angle X-ray scattering (SAXS) clearly indicated that the hydrogel has a hexagonal ordered phase. Interestingly, the process is reversible, as lowering of the pH below 7.0 leads to rapid dissolution of the solid into homogeneous solution. We believe that the hexagonal structure in the hydrogel is a result of the organization of the cylindrical micelles due to the increased hydrophobic interactions between the micelles at 70 degrees C and pH 11. Thus we have developed a pH-/temperature-dependent, reversible hierarchically self-assembling block copolymer system with structures spanning nano- to microscale dimensions.

Journal Article↗
PubMed2005

Solvent/gelator interactions and supramolecular structure of gel fibers in cyclic bis-urea/primary alcohol organogels.

An organogel system consisting of trans-(1S,2S)-bis(ureidododecyl)cyclohexane (SS-BUC) and a series of primary alcohols was explored with optical polarizing microscopy (OPM), electron microscopy, circular dichroism (CD), wide-angle X-ray scattering (WAXS), and synchrotron small-angle X-ray scattering (SAXS). OPM, SAXS, and especially WAXS showed that the gel fiber of SS-BUC/methanol gels essentially consists of SS-BUC crystal itself. SAXS showed that the SS-BUC crystal in the gel takes a lamella with a domain spacing of 5.2 nm. When we left the gel at room temperature, the spacing decreased to 3.1 nm after several months. This distance change may correspond to the structural transition from a double-layer structure to an intercalated-layer structure, which was proposed by Feringa et al. (Chem.-Eur. J. 1999, 5, 937-950) as a possible arrangement of the molecular packing. When the gels in ethanol, propanol, butanol, or octanol were examined, they never showed crystalline peaks in WAXS and SAXS, indicating the amorphous nature of the gels. With increasing the alkyl chain length from ethanol to octanol, dramatic changes were observed in the CD spectrum in the 200-500-nm range. Because these CD changes are correlated to the absorbance of urea, those can be considered as the evidence that the solvents strongly relate to the spatial arrangement between the adjacent urea groups. For the amorphous gels, the cross-sectional correlation function [gammaCu] was directly obtained by the inverse Hankel transform of the SAXS data. The value of gammaCu for the gels is decreased with increasing u (distance between the two scattering bodies, see eq 5). Furthermore, it more rapidly decreases than that of the rigid cylinder model. This feature can be explained by the speculation that many solvent molecules permeate into the SS-BUC fiber. There was a clear difference between ethanol and the other gels, indicating that the solvents with a longer alkyl chain give the more permeated and diffused fiber. This permeated fiber (i.e., wet fiber) can rationalize the dramatic CD change, by presuming that the permeated solvent molecules alter the molecular stacking form.

Alcohols↗
PubMed2000

Solution structure of myosin-ADP-MgFn ternary complex by fluorescent probes and small-angle synchrotron X-ray scattering.

In the presence of excess amounts of fluorine, a physiological divalent cation, magnesium (Mg(2+)), forms a novel phosphate analogue, magnesium fluoride (MgFn). Park et al. [Biochim. Biophys. Acta 1430, 127-140 (1999)] previously demonstrated that MgADP. MgFn forms a complex with myosin subfragment-1 (S-1), and the S-1.ADP. MgFn ternary complex mimics a transient state in the activity cycle of ATPase. In the present study, localized conformations in the regions of highly reactive cysteine and lysine residues, Cys 707 (SH1), Cys 697 (SH2), and Lys 83 (RLR), which change their conformations markedly during ATP hydrolysis, were studied using fluorescent probes and chemical modification. The global shape of the complex was also studied using small angle X-ray solution scattering and compared it with other previously reported myosin.ADP. fluorometal ternary complexes. The results suggest that the overall conformation and localized functional regions of the complex are quite similar to those in the presence of ATP, indicating that the complex mimics the M(**).ADP.P(i) steady state.

Adenosine Diphosphate↗
PubMed1976

Small-angle x-ray and light-scattering study of native and trypsin-modified methionyl-tRNA synthetase from Escherichia coli.

Small-angle X-ray scattering experiments were performed on an absolute scale on solutions of methionyl-tRNA synthetase from Escherichia coli in its native and trypsin-modified forms. A light-scattering study was performed on the same solutions to verify monodispersity. The structural parameters for the trypsin-modified enzyme, radius of gyration (2.48 nm), volume (90 nm3), surface/volume (1.5 nm-1) and the distribution of chords can account for an equivalent prolate ellipsoid of revolution having an axial ratio 2.3 and a maximum length of 9 nm, with a creviced surface. The rsults obtained for the native enzyme [i.e. radius of gyration (4.3 nm), volume (244 nm3), distribution of the scattering intensity and distribution of chords] exclude the possibility of a very compact quaternary structure and suggest that the enzyme consists of at least two globular parts, probably the two protomers, linked together by interactions involving a limited region of the structure.

Amino Acyl-tRNA Synthetases↗
PubMed2004

A neutron scattering study of the structure and water partitioning of selectively deuterated copolymer micelles.

We present a scattering study of a selectively deuterated micelle-forming diblock copolymer. The copolymer comprises a partially deuterated polystyrene (d,h-PS) block and an imidazolium-functionalized PS (IL) block. In toluene solutions, the copolymers assemble into elongated micelles where the IL block forms the micelle core. Through dynamic light scattering (DLS) measurements, we obtain the overall size of the micelles. In our small-angle neutron scattering (SANS) studies, we use contrast matching to characterize the IL core and the PS shell of the micelles independently. The PS block forming the micelle shell exhibits either a starlike or brushlike conformation depending upon the size of the core to which it is tethered. We find the IL block to be in an extended conformation, driving the formation of slightly elongated and relatively stiff micelle cores. The elongated micelle core cross-sectional radius and length depend linearly on the length of the IL block. We find that the micelles can sequester a few water molecules for each IL repeat unit; the addition of water slightly increases the cross section of the elongated micelles.

Deuterium↗
PubMed1999

Superhelical DNA studied by solution scattering and computer models.

We present here recent results on the structure of superhelical DNA and its changes with salt concentration between 0.01 and 1.5 M NaCl. Scattering curves of two different superhelical DNAs were determined by static light scattering. The measured radii of gyration do not change significantly with salt concentration. Small-angle neutron scattering, together with calculations from a Monte Carlo model, allows to determine the superhelix diameter. Measured and simulated scattering curves agreed almost quantitatively. Experimentally we find that the diameter decreases from 16.0 +/- 0.9 nm at 10 mM to 9.0 +/- 0.7 nm at 100 mM NaCl. The superhelix diameter from the simulated conformations decreased from 18.0 +/- 1.5 nm at 10 mM to 9.4 +/- 1.5 nm at 100 mM NaCl. At higher salt concentrations up to 1.5 M NaCl, the diameter stays constant at 9 nm.

Computer Simulation↗
PubMed2002

SASSIM: a method for calculating small-angle X-ray and neutron scattering and the associated molecular envelope from explicit-atom models of solvated proteins.

A method is presented to calculate efficiently small-angle neutron and X-ray solution scattering intensities from explicit-atom models of macromolecules and the surrounding solvent. The method is based on a multipole expansion of the scattering amplitude. It is particularly appropriate for extensive configurational averaging, as is required for calculations based on computer-simulation results. In test calculations, excellent agreement with experiment is found between neutron and X-ray scattering profiles calculated from a molecular-dynamics simulation of lysozyme in water. The question of definition of the protein surface is also addressed. For comparison with the continuum model, an analytical envelope around the protein is defined in terms of spherical harmonics and is calculated using a Lebedev grid. The analytical surface thus defined is shown to reproduce well the scattering profile calculated from the explicit-atom model of the protein.

Animals↗
PubMed2005

Stacking structure of concentrated shear ordered dispersions by two scattering methods.

In this paper, the ordering in concentrated charge stabilized colloidal dispersions is considered. Despite the impressive Bragg reflections obtained for shear ordered dispersions by light (LS), small-angle neutron (SANS), and small-angle X-ray scattering (SAXS), a number of open questions remain. Sheared dispersions are usually ordered in layers. For such systems, two questions arise: (1) What is the structure in a layer? (2) What is the stacking structure perpendicular to the layers? The second question requires a method to determine the structure perpendicular to the layers. Although originally interested only in structural aspects, we were forced to consider different methods. Two methods are treated both applicable to neutron and X-ray scattering from concentrated dispersions. One has been used by physicists and chemists for many years to determine the structure of crystals by sample rotation. In colloid science, we have used it previously in neutron and X-ray scattering. A second method is treated here which can be applied in small-angle scattering from a Couette cell. It gives the scattering intensity in a certain direction without sample rotation. Although very useful with the Couette cell, it cannot be found in any of the well-known references on colloid science. A theoretical explanation and experimental examples obtained by synchrotron X-ray scattering from a Couette cell are given in the paper.

Journal Article↗
PubMed1994

Troponin I encompasses an extended troponin C in the Ca(2+)-bound complex: a small-angle X-ray and neutron scattering study.

We have studied the solution structure of skeletal muscle troponin C complexed with troponin I in the presence of calcium using small-angle X-ray and neutron scattering. 4Ca2+.troponin C in the complex has an extended dumbbell shape with a radius of gyration of 23.9 +/- 0.5 A and a maximum linear dimension of approximately 72 A, similar to the values obtained from the crystal structure coordinates of troponin C (Herzberg & James, 1985). Troponin I is even more extended than troponin C with a radius of gyration of 41 +/- 2 A and a maximum linear dimension of approximately 118 A. The centers-of-mass for each component of the complex are approximately coincident (< 10-A separation) as are their long axes, and the troponin I component encompasses the 4Ca2+.troponin C. These data provide new insights into the nature of the conformational arrangement of this important Ca(2+)-sensitive molecular switch.

Calcium↗
PubMed1985

The domain structure of tryptophan synthase. A neutron scattering study.

Tryptophan synthase from Escherichia coli is a complex of two alpha subunits and two beta subunits. Small-angle neutron scattering involving deuterium-labelled isomers revealed the quaternary structure of the enzyme at the level of the beta 2 subunit and the two structural domains P1 and P2 which constitute the alpha subunits. Within the alpha 2 beta 2 complex, the two alpha subunits are completely separated. They are situated on opposite sides of the beta 2 subunit. The most probable distance between the two alpha protomers is 10.5 +/- 1 nm; the nearest distance is 5.8 +/- 0.5 nm, and the largest distance is 13.5 +/- 0.5 nm. The two domains of the same alpha subunit are intimately juxtaposed. The distances between two like or unlike domains belonging to opposite alpha subunits are roughly equal. All domains exhibit about equal distances to the beta 2 subunit which is situated in the centre of the complex. Thus the cleft between P1 and P2, which probably contains the active site of the alpha subunit, makes intimate contact with the beta 2 subunit. Neutron scattering allows us to determine the shape of the beta 2 subunit within the complex. Comparison with the free dimer suggests a conformational change, upon assembly, from an elongated into a more compact form.

Deuterium↗
PubMed1999

Formation of the myosin.ADP.gallium fluoride complex and its solution structure by small-angle synchrotron X-ray scattering.

In the presence of MgADP, a novel phosphate analogue of gallium fluoride (GaFn) forms a ternary complex with the myosin subfragment-1 (S-1), in the same way that has been previously reported with aluminum fluoride (AlF4-), beryllium fluoride (BeFn), scandium fluoride (ScFn), and vanadate (Vi), and this complex formation may mimic different states along the ATPase kinetic pathway. This novel complex has been characterized and compared with other complexes to ascertain whether it forms a transition-state analogue of myosin ATPase. The complex formed quickly, although several times slower than the BeFn complex. The half-life of the myosin.ADP.GaFn complex was about 50 h at 4 degreesC. The formation of the myosin.ADP.GaFn complex was accompanied by an increase in tryptophane fluorescence, similar to that observed upon the addition of ATP, but slightly lower than that of the M**.ADP.Pi complex. Upon addition of GaFn to acto-myosin.ADP, acto-myosin did not dissociate, and the S-1.ADP.GaFn complex was scarcely decomposed by actin, like the AlF4- and ScFn complexes but unlike the BeFn and Vi complexes. The conformations at the localized region of SH1, SH2, and RLR, which are very accessible to the binding of ATP, were studied by fluorescent labeling and chemical modification, and the results suggested that these conformations are very similar to that of the M**.ADP.Pi state. Small-angle X-ray solution scattering showed that the radius of gyration value decreases by about 3 A when S-1 forms an S-1.ADP.GaFn complex, suggesting that the shape of the complex becomes compact or rounded in shape, similar to that in the presence of ATP or complexes with other phosphate analogues, and thus mimics the myosin**.ADP.Pi state closely. The overall results may indicate that the complex mimics a somewhat different transient state from that of other complexes but has a similar global conformation along the ATPase kinetic pathway.

Actins↗