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PubMedDate not supplied

Molecular dynamics simulations of aqueous pullulan oligomers.

Molecular dynamics (MD) simulations have been used to model small-angle X-ray scattering (SAXS) data on aqueous solutions of four oligomeric segments of the glucan pullulan: the trimer G(3) (comprising one polymer repeating unit), the hexamer (G(3))(2), the nonamer (G(3))(3), and the dodecamer (G(3))(4). The AMBER force field was used in conjunction with the GB/SA continuum solvation model to calculate both the mean global dimensions of the oligomers from the limiting small angle scattering behavior and the shorter range structural information implicit in the Debye scattering function at larger scattering angles. This same force field and solvation treatment were employed earlier by Liu et al. (Macromolecules 1999, 32, 8611-8620) with apparent success in a rotational isomeric state (RIS) treatment of the same experimental data. The present work discloses that, despite numerical success in modeling the SAXS data, the RIS treatment, which includes only the interactions within dimeric segments of the polymer chain, fails to account accurately for excluded volume effects at the range of 3-12 sugar residues in the polymer backbone. It is suggested that MD simulations using continuum solvation models can be used to circumvent errors inherent in the computationally efficient RIS treatments of polymer nano- and picosecond dynamics while at the same time avoiding the heavy computational requirements of all-atom methods.

Carbohydrate Conformation↗

PubMed1986

A neutron scattering study of the ternary complex EF-Tu.GTP-valyl-tRNAVal1A.

The complex formation between elongation factor Tu (EF-Tu), GTP, and valyl-tRNAVal1A has been investigated in a hepes buffer of "pH" 7.4 and 0.2 M ionic strength using the small-angle neutron scattering method at concentrations of D2O where EF-Tu (42% D2O) and tRNA (71% D2O) are successively matched by the solvents. The results indicate that EF-Tu undergoes a conformational change and contracts as a result of the complex formation, since the radius of gyration decreases by 15% from 2.82 to 2.39 nm. tRNAVal1A, on the other hand, seems to mainly retain its conformation within the complex, since the radii of gyration for the free (after correction for interparticular scattering) and complexed form are essentially the same, 2.38 and 2.47 nm, respectively.

Binding Sites↗

PubMed2000

Fractal Morphology and Breakage of DLCA and RLCA Aggregates.

Latex aggregates, formed in 1 M McIlvaine buffer solution and 0.2 M NaCl solution, have been characterized in terms of aggregate size distribution and fractal morphology. This was achieved using three sizing techniques (image analysis, laser scattering, and electrical sensing) in which size distributions and fractal properties of the aggregates were measured. Estimates of fractal dimensions were made using the two-slope method based on dimensional analysis and the small-angle light scattering method. Aggregate suspensions were prepared using both water and a mixture of heavy water/ water as the solvent. The latter essentially eliminated sedimentation, which was observed after one day of aggregation when water alone was used as a solvent. Latex aggregates formed by diffusion-limited colloid aggregation (DLCA) and reaction-limited colloid aggregation (RLCA) had fractal dimensions close to 1.8 and 2.1, respectively. As observed through image analysis, DLCA aggregates possessed a loose tenuous structure, whereas RLCA aggregates were more compact. Disruption of both DLCA and RLCA aggregates has been investigated in laminar flow and turbulent capillary flow. The shear forces introduced by a laminar shear device with a shear rate up to 1711 s(-1) were unable to bring about aggregate breakup; shearing facilitates aggregate growth in the case of DLCA. However, latex aggregates were significantly disrupted after passage through a turbulent capillary tube at 95209 s(-1). Copyright 2000 Academic Press.

Journal Article↗

PubMed1992

X-ray scattering study of the shape of the DNA region in nucleosome core particle with synchrotron radiation.

The structure of the DNA region in rat thymus nucleosome core particle has been studied by synchrotron X-ray scattering analysis and the contrast-variation technique has been applied to determine the contribution of the DNA to the total scatterings. Small-angle contrast-matching measurements show that the entire core particle and isolated histone octamers are contrast-matched by solvents containing 64 and 54% (w/w) sucrose, respectively. At a contrast of 54% sucrose, where the scattering of the DNA dominates, the scattering data extending to higher angle of about 0.05 A-1 have been collected from relatively concentrated solutions (10 mg/ml) of core particles and interpreted on the basis of the regular helical model for the DNA region. The model calculations show that the shape of the DNA around the histone core is approximately by 1.8 turns of regular helix of 42 A radius and 28 A pitch. These values for helical parameters of our model are in good agreement with those of the structure of DNA in crystallized nucleosome cores shown by earlier diffraction studies.

Algorithms↗

PubMed1995

Modeling transmission and scatter for photon beam attenuators.

The development of treatment planning methods in radiation therapy requires dose calculation methods that are both accurate and general enough to provide a dose per unit monitor setting for a broad variety of fields and beam modifiers. The purpose of this work was to develop models for calculation of scatter and transmission for photon beam attenuators such as compensating filters, wedges, and block trays. The attenuation of the beam is calculated using a spectrum of the beam, and a correction factor based on attenuation measurements. Small angle coherent scatter and electron binding effects on scattering cross sections are considered by use of a correction factor. Quality changes in beam penetrability and energy fluence to dose conversion are modeled by use of the calculated primary beam spectrum after passage through the attenuator. The beam spectra are derived by the depth dose effective method, i.e., by minimizing the difference between measured and calculated depth dose distributions, where the calculated distributions are derived by superposing data from a database for monoenergetic photons. The attenuator scatter is integrated over the area viewed from the calculation point of view using first scatter theory. Calculations are simplified by replacing the energy and angular-dependent cross-section formulas with the forward scatter constant r2(0) and a set of parametrized correction functions. The set of corrections include functions for the Compton energy loss, scatter attenuation, and secondary bremsstrahlung production. The effect of charged particle contamination is bypassed by avoiding use of dmax for absolute dose calibrations. The results of the model are compared with scatter measurements in air for copper and lead filters and with dose to a water phantom for lead filters for 4 and 18 MV. For attenuated beams, downstream of the buildup region, the calculated results agree with measurements on the 1.5% level. The accuracy was slightly less in situations where the scatter component is very large, as for very large fields with very short filter to detector distances. The implementation of the model into treatment planning systems is discussed.

Air↗

PubMed1982

Neutron scattering studies and modeling of high mobility group 14 core nucleosome complex.

Considerable evidence relates the nonhistone proteins high mobility group (HMG) 14 and HMG 17 with the structure of active or potentially active chromatin. In this study, bulk nucleosome core particles prepared from chicken erythrocytes and the complex formed by binding two HMG 14 molecules per nucleosome core were studied by use of small-angle neutron scattering techniques. By varying the H2O/2H2O ratio, and hence the contrast between the solvent and the particles, it was possible to determine the radius of gyration of the protein and of the DNA independently and as a function of HMG 14 binding. The results show an increase of 0.9 +/- 0.6 A (mean +/- SEM) in the protein radius of gyration and of 2.7 +/- 0.6 A in the DNA radius of gyration upon binding of HMG 14 to the nucleosome. These changes are considered in the light of several postulated modes for the unfolding or perturbation of the nucleosome structure. Modeling calculations demonstrate that the observed changes in radius of gyration for the DNA and for the protein are too small to be consistent with an overall unfolding or opening of the core particle upon HMG 14 binding. However, the observed changes are consistent with several models that involve only minor changes in the structure. It is postulated that the differences observed may be an indication of the type of conformational change occurring in active nucleosomes.

Animals↗

PubMed1995

The radius of gyration of native and reductively methylated myosin subfragment-1 from neutron scattering.

Reductive methylation of nearly all lysine groups of myosin subfragment-1 (S1) was required for crystallization and solution of its structure at atomic resolution. Possible effects of such methylation on the radius of gyration of chicken skeletal muscle myosin S1 have been investigated by using small-angle neutron scattering. In addition, we have investigated the effect of MgADP.Vi, which is thought to produce an analog of the S1.ADP.Pi state, on the S1 radius of gyration. We find that although methylation of S1, with or without SO42- ion addition, does not significantly alter the structure, addition of ADP plus vanadate does decrease the radius of gyration significantly. The S1 crystal structure predicts a radius of gyration close to that measured here by neutron scattering. These results suggest that the overall shape by crystallography resembles nucleotide-free S1 in solution. In order to estimate the effect of residues missing from the crystal structure, the structure of missing loops was estimated by secondary-structure prediction methods. Calculations using the complete crystal structure show that a simple closure of the nucleotide cleft by a rigid-body torsional rotation of residues (172-180 to 670) around an axis running along the base of the cleft alone does not produce changes as large as seen here and in x-ray scattering results. On the other hand, a rigid body rotation of either the light-chain binding domain (767 to 843 plus light chains) or of a portion of 20-kDa peptide plus this domain (706 to 843 plus light chains) is more readily capable of producing such changes.

Amino Acids↗

PubMed2001

Structural Changes Induced in the Surfactant System C(12)E(4)/Benzyl Alcohol/Water by the Admixture of the Cationic Surfactant Cetylpyridinium Chloride.

The influence of the addition of the cationic surfactant cetylpyridinium chloride (CPyCl) on the structure of the different phases of the ternary surfactant system C(12)E(4)/benzyl alcohol/water in the dilute region has been studied by means of small angle neutron scattering (SANS) and freeze-fracture microscopy (FF-TEM). In the ternary system various different subregions of the L(alpha)-phase were identified as a function of the concentration of the cosurfactant, benzyl alcohol. Addition of small amounts of CPyCl suppresses these different L(alpha)-phases in favor of the one composed of multilamellar vesicles. Addition of somewhat larger amounts (up to 2 mol% relative to the total surfactant concentration) destabilizes the formation of bilayer structures completely and leads to the formation of micellar solutions. This demonstrates that in this surfactant system the incorporation of very small amounts of cationic surfactant has a pronounced and systematic fluence on its phase behavior and its structures. Copyright 2001 Academic Press.

Journal Article↗

PubMed2006

Synchrotron SAX and WAX diffraction study of a hydrated very long-chain, dendritic amphiphile + DPPC mixture.

The tri-headed anionic dendritic amphiphile, 4-(2-carboxyethyl)-4-[(icosyloxycarbonyl)amino]heptanedioic acid (3CCb20), forms mixed aggregates with dipalmitoylphosphatidylcholine (DPPC) in excess water at 3CCb20:DPPC = 0.91:1 molar ratio. On heating, these mixed aggregates transform into fluid bilayers stacked in the liquid crystalline lamellar L(alpha) phase at about 40 degrees C. This phase transition and the microstructure of 3CCb20 + DPPC aggregates were studied with small- and wide-angle synchrotron X-ray diffraction. The ability of 3CCb20 to solubilize solidlike lipid bilayers could contribute to the antimicrobial activities of 3CCb20, including its anti-HIV activity.

1,2-Dipalmitoylphosphatidylcholine↗

PubMed1982

Spontaneous aggregation of the mitochondrial natural ATPase inhibitor in salt solutions as demonstrated by gel filtration and neutron scattering. Application to the concomitant purification of the ATPase inhibitor and F1-ATPase.

(1) The natural ATPase inhibitor (IF1) from beef heart mitochondria has a tendency to form aggregates in aqueous solutions. The extent of aggregation and the structure of the aggregates were assessed by gel filtration and small-angle neutron scattering. IF1 polymerization was found to depend on the salt concentrations, pH of the medium and concentration of IF1. The higher the salt concentration, the lower the aggregation state. Aggregation of IF1 was decreased at slightly acidic pH. It increased with the concentration of IF1 as expected from the law of mass action. (2) Neutron scattering showed the aggregation of IF1 in 2 M ammonium sulfate solutions. The predominant species is the dimer which has a somewhat elongated shape. (3) The Sephadex G-50 chromatography that is supposed to deprive beef heart submitochondrial particles of loosely bound IF1 (Racker, E. and Horstman, L.L. (1967) J. Biol. Chem. 242, 2547-2551) was shown to have a limited effectiveness as a trap for IF1. The reason was that IF1 released from the particles formed high molecular weight aggregates that were not separated from the membrane vesicles by Sephadex G-50 chromatography. (4) The above observations provide the basis for a simple method of purification of beef heart IF1 which combines the recovery of the supernatant from submitochondrial particles with the last three steps of the IF1 preparation described by Horstman and Racker (J. Biol. Chem. (1970) 265, 1336-1344). The particles recovered in the sediment were deprived of IF1 and could therefore be used for preparation of F1-ATPase. The advantage of this method is that both IF1 and F1-ATPase can be prepared from the same batch of mitochondria.

Adenosine Triphosphatases↗

PubMedDate not supplied

[Quaternary structure of histidine decarboxylase according to small-angle x-ray diffraction and electron microscopic findings].

The data on small angle X-ray scattering with histidine decarboxilase (HDC) from Micrococcus sp. n. were analysed and a line of succesively improving approximations of the molecule shape was found: by oblate ellipsoid a:b:c = 1:10.63, by continuous cylinder and hollow cylinder with H = 50 A, 2R = 76 A, 2r = 8A. Biochemical data and electron micrographs of HDC obtained made possible to distinguish subunits and thus to increase resolution of the model. The model of the enzyme molecule consisting of three subunits is suggested, whose X-ray small angle scattering curve well agrees with the experimental one up to value S = 0.21 A-1.

Carboxy-Lyases↗

PubMedDate not supplied

Cytomorphology of gynecologic specimens analyzed and sorted by two-parameter flow cytometry.

The purpose of this study was to define the fluorescence and light scatter properties of the different cell types encountered in gynecologic specimens. Samples stained with Chromomycins A3 were analyzed on a laser-activated electronic cell sorter, and two-parameter histograms of the cell populations were generated from measurements of nuclear fluorescence and small angle light scatter. Cell populations with defined scatter and fluorescence ranges were sorted, stained by a modified Papanicolaou technique, and evaluated using conventional cytomorphologic criteria. We focused on determining which regions of the histogram corresponded with abnormal cells and cells defining specimen adequacy (columnar and metaplastic cells). Sorted cells corresponding with the main fluorescence region are single, benign, mononuclear cells. Relative proportions of the different types of cells in this region vary with light scatter. Leukocytes predominate at low scatter, mature squamous cells predominate at high scatter, and metaplastic and endocervical cells occur throughout this range. Cells sorted with higher values of nuclear fluorescence include dysplastic and malignant cells as well as benign cells occurring as groups, multinucleates, or with adherent leukocytes or bacteria. This study demonstrates that cytomorphology is a useful method for monitoring and interpreting flow cytometry data.

Chromomycin A3↗

PubMed2005

On the difference in scattering behavior of cyclic and linear polymers in bulk.

It has been suggested that, due to topological constraints, rings in the melt may assume a more compact shape than Gaussian chains. In this paper, we exploit the availability of narrow fractions of perdeuterated linear and cyclic polydimethylsiloxane (PDMS) and, through the analysis of the small angle neutron scattering (SANS) profiles, demonstrate the difference in scattering properties of linear and cyclic PDMS molecules. As expected for Gaussian chains, for the H/D linear PDMS samples, log-log plots of the scattered intensity versus scattering vector Q display a Q((-2)) dependence. However, for H/D cyclic blends, the scaling exponent is higher than 2, as predicted by computer simulations reported in the literature. We show that cyclic molecules in bulk display the characteristic maximum in plots of scattered intensity versus Q((-2)) that is expected on the basis of Monte Carlo calculations and from the Casassa equation [E. F. Casassa, J. Polym. Sci. A 3, 605 (1965)]. It is also shown that, for rings, the Debye equation [P. Debye, J. Appl. Phys. 15, 338 (1944)] is no longer appropriate to describe the SANS profiles of H/D cyclic blends, at least up to M(w) approximately 10 000. For these samples, the Casassa form factor gives a better representation of the SANS data and we show that this function which was developed for monodisperse cyclics is still adequate to describe our slightly polydisperse samples. Deviations from all above observations are noted for M(w)>11 000 and are attributed to partial contamination of cyclic samples with linear chains. The failure of both the Debye and the Casassa form factors could be due to contamination of the cyclic fractions by linear polymers or to a real conformational change.

Journal Article↗

PubMed1981

Structure of acetylcholine receptor dimer determined by neutron scattering and electron microscopy.

Previous work has shown that the predominant native form of the acetylcholine receptor from the electric tissue of Torpedo californica is a dimer of Mr = 500,000, cross-linked by a disulfide bond between the largest (delta) of the five chains (alpha 2 beta gamma delta) that comprise the monomer. Small-angle neutron scattering of purified receptor dimer in Triton X-100 solution containing 18% D2O, in which the Triton X-100 is contrast-matched, yields a radius of gyration of the dimer of 66 A. Based on the assumptions that the dimer is symmetrical and that the radius of gyration of the monomer does not change in forming dimer, this value, together with the radius of gyration of the receptor monomer (46 A), determined previously, allows the calculation of the distance separating the centers of neutron scattering density of monomers in a dimer; the result is 96 A. Electron microscopy of negatively stained dimers permits an independent measurement of the distance between the apparent centers of mass of the monomers; the average is 96 A, in agreement with the result of the neutron scattering analysis. The electron micrographs of dimer also permit the location of the delta chains at the region of contact of the monomers. A model for the receptor dimer consistent with all available structural information is presented.

Acetylcholine↗

PubMed2002

Neutron scattering study on the structure and dynamics of oriented lamellar phase microemulsions.

Lamellar phases consisting of water and oil with intervening surfactant monolayer interfaces (eventually containing low molecular weight amphiphilic block-copolymers) are studied. Structural and dynamical investigations of oriented lamellar phases at the length scale of the intermembrane distance and beyond are performed using small-angle neutrons scattering and neutron spin-echo spectroscopy. The data analysis in terms of static and dynamic structure factors for a stack of elastic interfacial membranes yields information of the membrane curvature elasticity and membrane interactions in terms of phenomenological parameters such as the bending elastic modulus kappa and compression modulus (-)B, and on the dissipation related to the viscosity eta. The influence of the block-copolymers anchored to the surfactant monolayers is studied for a series of lamellar phase microemulsions containing equal volume fraction of surfactant and polymer, by varying only the polymer molecular weight. Based on numerical evaluations and fits to the data the conditions of applicability of the available theoretical concepts are discussed.

Journal Article↗

PubMed1988

Molecular weight and shape of angiotensin-I converting enzyme. A neutron scattering study.

The molecular weight of angiotensin-I converting enzyme from pig lung has been determined to be 112000 (+/- 6000) by neutron scattering. This is somewhat lower than the value determined by SDS-PAGE and than previous estimates which, however, show a very wide range of values. A quantitative analysis of the amino acid and carbohydrate content was made in order to determine the enzyme concentration. The small angle neutron scattering technique also gives information on the molecular shape, yielding a radius of gyration of 44.5 +/- 1.5 A which, for the observed molecular weight, indicates that the angiotensin converting enzyme molecule is clearly elongated in aqueous solution. Dynamic light scattering experiments confirm this conclusion.

Amino Acids↗

PubMed2001

Effect of salt and heating on a mesoscopic structure composed of ovalbumin globules in aqueous solution.

Mesoscopic structural changes of an ovalbumin solution by heating and adding NaCl have been investigated with a small-angle neutron scattering method. In the natural solution, a broad peak at q = 0.057 A(-1), which disappeared by adding NaCl, indicates the existence of an electrostatic long-range interaction between the ovalbumin globules. Along with the broad peak, a prominent intensity increase in a very small q region was observed on heating except for the initial and final stages, indicating the coexistence of a disordered structure of the denatured ovalbumin and a regular-interspacing structure of the natural ovalbumin globules. Though the macroscopic feature in the final stage, whether the solution forms a gel (10 wt %) or not (5 wt %), strongly depended on the concentration of the ovalbumin, the scattering profiles showed a common characteristic feature: the appearance of a new peak around q = 0.023 A(-1), which indicates the emergence of another regular structure.

Animals↗

PubMed1996

Conformation of cyclic and linear (1 --> 2)-beta-D-glucans in aqueous solution.

The conformations of cyclic (1 --> 2)-beta-D-glucan chains having degree of polymerization (dp) 17 to 24 were characterized by means of small-angle X-ray scattering and Monte Carlo simulation. The results indicate that cyclic (1 --> 2)-beta-D-glucan chains adopt the shape of a doughnut-like ring with a thickness of about 10 A for all the samples. The diameter of the annulus for the cyclic glucan having dp 21 is estimated to be only about 4-5 A. Two linear (1 --> 2)-beta-D-glucans possessing dp 19 and 21 prepared by acid hydrolysis of a cyclic glucan and subsequent fractionation showed different scattering profiles from those obtained for cyclic glucans having the corresponding dp. Although the Monte Carlo simulation does not completely reproduce the scattering profiles observed by small-angle X-ray scattering, linear (1 --> 2)-beta-D-glucans seem to possess a characteristic cylindrical shape with cross-sectional diameters of 11.8 and 13.2 A for linear glucans of dp 19 and 21, respectively.

Chromatography, High Pressure Liquid↗