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PubMed2005

Characterization of biological thin films at the solid-liquid interface by x-ray reflectivity.

We demonstrate that 18 keV x-rays can be used to study organic thin films at the solid-liquid interface by x-ray reflectivity. We establish that this is a powerful technique for investigating biological systems in a previously inaccessible manner. Our measurements enabled the density distribution of single phospholipid bilayer membranes in bulk water to be measured with unprecedented precision. Previously, characterization of biomimetic structures normal to a "buried" interface was a domain of neutron reflectivity.

Lipid Bilayers↗
PubMed2004

Structural transition of bacteriorhodopsin is preceded by deprotonation of Schiff base: microsecond time-resolved x-ray diffraction study of purple membrane.

The structural changes in the photoreaction cycle of bacteriorhodopsin, a light-driven proton pump, was investigated at a resolution of 7 angstroms by a time-resolved x-ray diffraction experiment utilizing synchrotron x rays from an undulator of SPring-8. The x-ray diffraction measurement system, used in coupling with a pulsed YAG laser, enabled us to record a diffraction pattern from purple membrane film at a time-resolution of 6 micros over the time domain of 5 micros to 500 ms. In the time domain, the functionally most important M-intermediate appears. A series of time-resolved x-ray diffraction data after photo-excitation showed clear intensity changes caused by the conformational changes of helix G in the M-intermediate. The population of the reaction intermediate was prominently observed at approximately 5 ms after a photo-stimulus. In contrast, absorption measurement indicated the deprotonation of the Schiff base predominantly occurred at approximately 300 micros after a photo-stimulus. These results showed that the conformational changes characterizing structurally the M-intermediate predominantly occur at a later stage of the deprotonation of the Schiff base. Thus, the M-intermediate can be divided into two metastable stages with different physical characteristics.

Bacteriorhodopsins↗
PubMed1992

Solution structure of phosphorylase kinase studied using small-angle X-ray and neutron scattering.

Small-angle X-ray and neutron scattering have been used to characterize the solution structure of rabbit skeletal phosphorylase kinase. The radius of gyration of the unactivated holoenzyme determined from neutron scattering is 94 A, and its maximum dimension is approximately 275-295 A. A planar model has been constructed that is in general agreement with the dimensions of the transmission electron microscope images of negatively stained phosphorylase kinase and that gives values for the radius of gyration, maximum linear dimension, and a pair distribution function for the structure that are consistent with the scattering data.

Animals↗
PubMed2005

Physical and chemical characterization of beryllium particles from several workplaces in Québec, Canada--part A: determining methods for the analysis of low levels of beryllium.

Chemical and physical characterizations of beryllium (Be) particles found in settled dust samples from four industries based in Québec were attempted using a variety of analytical methods. Bulk particle chemistry was determined using inductively coupled plasma-mass spectrometry (ICP-MS), graphite furnace atomic absorption spectrometry (GFAAS), and instrumental neutron activation analysis (INAA). Time-of-flight secondary-ion mass spectrometry (TOF-SIMS), transmission electron microscopy, scanning electron microscopy, energy-dispersive spectroscopy, x-ray diffraction (XRD), electron energy loss spectrometry (EELS), and Auger microscopy were used to characterize physicochemical properties of particles. These analyses were deemed important based on the hypotheses that (1) different chemical forms of Be do not present the same risks, and (2) different morphologies lead to different risks. Standards were used to prove the adequacy of XRD, EELS, and Auger microscopy prior to the analyses of industrial samples. However, low concentrations of Be in samples were a limiting factor for most methods; few detected Be in industrial samples. Only ICP-MS, GFAAS, and TOF-SIMS were able to detect Be in industrial samples analyzed in this study. Characterization of settled dust samples showed high number of Be particles, even for Be concentrations below 100 ppm. Furthermore, Be seems to be present as fine particles of Be metal, possibly mechanically agglomerated or aggregated to larger particles or compounds such as cryolite. Other major elements detected with INAA present in the samples were limited to Na, Al, Ca, and F. It was concluded that TOF-SIMS is a valid method for characterizing particles containing approximately 0.01% Be.

Beryllium↗
PubMed1984

New techniques for imaging and analyzing lung tissue.

The recent technological revolution in the field of imaging techniques has provided pathologists and toxicologists with an expanding repertoire of analytical techniques for studying the interaction between the lung and the various exogenous materials to which it is exposed. Analytical problems requiring elemental sensitivity or specificity beyond the range of that offered by conventional scanning electron microscopy and energy dispersive X-ray analysis are particularly appropriate for the application of these newer techniques. Electron energy loss spectrometry, Auger electron spectroscopy, secondary ion mass spectrometry, and laser microprobe mass analysis each offer unique advantages in this regard, but also possess their own limitations and disadvantages. Diffraction techniques provide crystalline structural information available through no other means. Bulk chemical techniques provide useful cross-checks on the data obtained by microanalytical approaches. It is the purpose of this review to summarize the methodology of these techniques, acknowledge situations in which they have been used in addressing problems in pulmonary toxicology, and comment on the relative advantages and disadvantages of each approach. It is necessary for an investigator to weigh each of these factors when deciding which technique is best suited for any given analytical problem; often it is useful to employ a combination of two or more of the techniques discussed. It is anticipated that there will be increasing utilization of these technologies for problems in pulmonary toxicology in the decades to come.

Environmental Pollutants↗
PubMed1999

The Fab and Fc fragments of IgA1 exhibit a different arrangement from that in IgG: a study by X-ray and neutron solution scattering and homology modelling.

Human immunoglobulin A (IgA) is an abundant antibody that mediates immune protection at mucosal surfaces as well as in plasma. The IgA1 isotype contains two four-domain Fab fragments and a four-domain Fc fragment analogous to that in immunoglobulin G (IgG), linked by a glycosylated hinge region made up of 23 amino acid residues from each of the heavy chains. IgA1 also has two 18 residue tailpieces at the C terminus of each heavy chain in the Fc fragment. X-ray scattering using H2O buffers and neutron scattering using 100 % 2H2O buffers were performed on monomeric IgA1 and a recombinant IgA1 that lacks the tailpiece (PTerm455). The radii of gyration RG from Guinier analyses were similar at 6.11-6.20 nm for IgA1 and 5.84-6.16 nm for PTerm455, and their cross-sectional radii of gyration RXS were also similar. The similarity of the RG and RXS values suggests that the tailpiece of IgA1 is not extended outwards in solution. The IgA1 RG values are higher than those for IgG, and the distance distribution function P(r) showed two distinct peaks, whereas a single peak was observed for IgG. Both results show that the hinge of IgA1 results in an extended Fab and Fc arrangement that is different from that in IgG. Automated curve-fit searches constrained by homology models for the Fab and Fc fragments were used to model the experimental IgA1 scattering curves. A translational search to optimise the relative arrangement of the Fab and Fc fragments held in a fixed orientation resembling that in IgG was not successful in fitting the scattering data. A new molecular dynamics curve-fit search method generated IgA1 hinge structures to which the Fab and Fc fragments could be connected in any orientation. A search based on these identified a limited family of IgA1 structures that gave good curve fits to the experimental data. These contained extended hinges of length about 7 nm that positioned the Fab-to-Fab centre-to-centre separation 17 nm apart while keeping the corresponding Fab-to-Fc separation at 9 nm. The resulting extended T-shaped IgA1 structures are distinct from IgG structures previously determined by scattering and crystallography which have Fab-to-Fab and Fab-to-Fc centre-to-centre separations of 7-9 nm and 6-8 nm, respectively. It was concluded that the IgA1 hinge is structurally distinct from that in IgG, and this results in a markedly different antibody structure that may account for a unique immune role of monomeric IgA1 in plasma and mucosa.

Amino Acid Sequence↗
PubMed1996

The structure of the muscle protein complex 4Ca2+.troponin C.troponin I. Monte Carlo modeling analysis of small-angle X-ray data.

Analysis of scattering data based on a Monte Carlo integration method was used to obtain a low resolution model of the 4Ca2+.troponin C.troponin I complex. This modeling method allows rapid testing of plausible structures where the best fit model can be ascertained by a comparison between model structure scattering profiles and measured scattering data. In the best fit model, troponin I appears as a spiral structure that wraps around 4Ca2+.troponin C which adopts an extended dumbbell conformation similar to that observed in the crystal structures of troponin C. The Monte Carlo modeling method can be applied to other biological systems in which detailed structural information is lacking.

Animals↗
PubMed2005

Excitation of the shear horizontal mode in a monolayer by inelastic helium atom scattering.

Inelastic scattering of a low-energy atomic helium beam (HAS) by a physisorbed monolayer is treated in the one-phonon approximation using a time-dependent wave packet formulation. The calculations show that modes with shear horizontal polarization can be excited near high symmetry azimuths of the monolayer, in agreement with recent experiments. The parameters of the calculations are chosen to match the conditions of HAS experiments for triangular incommensurate monolayer solids of xenon, krypton, and argon adsorbed on the (111) face of platinum, and the results show many of the systematic experimental trends for relative excitation probability of the shear horizontal and longitudinal acoustic phonon branches. The inelastic scattering at beam energies near 8 meV is exceedingly sensitive to small misalignment between the scattering plane and the high symmetry directions of the monolayer solid. The diffraction and inelastic processes arise from a strong coupling of the incident atom to the target and the calculated results show large departures from expectations based on analogies to inelastic thermal neutron scattering.

Journal Article↗
PubMed1977

Small angle neutron scattering studies of chromatin subunits in solution.

Neutron scattering studies have been performed on dilute solutions of the fundamental subunit of chromatin, the nucleosome. The subunits contain approximately 195 base paris (bp) of DNA and histones H2A, H2B, H3, and H4. Measurements of the small angle scattering curves in various H2O/D2O solvents allow the contrast dependence of the radius of gyration of the subunits to be examined and give the mean scattering density of the particle. Further application of contrast variation to the higher angle scatter curves allows the contributions from the shape and internal structure of the subunits to be analyzed separately. From these results, we are able to propose a spherically averaged structure with most of the histones closely packed into a core of radius 3.2 nm surrounded by a loosely packed DNA-rich shell of 2.0 nm thickness resulting in a particle of 5.2 nm average radius. Model calculations for ellipsoids show that the outer shape of the subunit must have an axial ratio between 0.5 and 1.4 but is probably best described by more spherical particle. These results are correlated with the diffraction from chromatin films to provide an explanation for some of the diffraction rings.

Animals↗
PubMed2003

Adair was right in his time.

The subunit molar mass of hemoglobin was established in the 19th century by chemical analysis, the tetramer structure by osmotic pressure determination in 1924 and by the newly developed analytical ultracentrifuge in 1926, which became a powerful tool for biological macromolecule molar mass determinations. The Svedberg equation was derived by eliminating the translational friction coefficient relating to sedimentation and diffusion in the ultracentrifuge in a strictly solute/solvent vanishing concentration two-component system analysis. A differential equation describing the radial equilibrium concentration distribution in the ultracentrifuge was also derived, both yielding the buoyant molar mass (1-nu2rho)M2 term. Many years later it was realized that solutions of biological macromolecules are multicomponent systems and the two-component analysis leads to minor or major erroneous results. Thermodynamic derivation of an equation for multicomponent systems redefines the buoyant molar mass terms by (deltarho/deltac2)muM2, leading to correct molar mass (g/mol) values following determination of the density increment at constant chemical potentials of diffusible solutes, and powerfully connects the analytical sedimentation equation to the osmotic pressure concentration derivative and, in a broad complementary sense, to light, X-ray and neutron scattering experiments. Macromolecular interactions can be studied with high precision and solute-solvent interactions yield powerful information relating to "thermodynamic" hydration, closely related to hydration derived from X-ray diffraction, as well as solute-cosolute interactions. A series of examples is given to demonstrate the correctness and usefulness of the thermodynamic multicomponent system approach. It is a strange fact that in current analytical ultracentrifugation analysis the elegant and powerful multicomponent solution technology is almost totally disregarded and the classical limited validity Svedberg approach is used uniquely.

Biopolymers↗
PubMed2003

Bacteriophage MS2: molecular weight and spatial distribution of the protein and RNA components by small-angle neutron scattering and virus counting.

Small-angle neutron scattering (SANS) has been used to extend the structural characterization of the MS2 phage by examining its physical characteristics in solution. Specifically, the contrast variation technique was employed to determine the molecular weight of the individual components of the MS2 virion (protein shell and genomic RNA) and the spatial relationship of the genomic RNA to its protein shell. A consequence of this work was to evaluate a novel particle counting instrument, the integrated virus detection system (IVDS) that, in combination with SANS, has the potential to provide rapid quantitative physical characterization of unidentified viruses and phage.

Electrophoresis, Polyacrylamide Gel↗
PubMedDate not supplied

[Internal structure of ribosomes using different types of emission].

A review is made of the experimental results obtained by the author and co-workers on the study of the structural organization of the RNA and the protein in ribosomes by the method of joint use of light, X-ray and neutron scattering and by the method of contrast variation in neutron scattering. Two rules are formulated for the folding of the ribonucleoprotein strand in ribosomes: (1) in each ribosomal subparticle the RNA is concentrated predominantly closer to the center of the particle whereas the protein has a more peripherical localization; (2) the compact ("crystallic") packing of hydrated RNA helices is an essential feature of the nucleus (nuclei) organization of the particles. An analysis of the experimental data on neutron scattering by ribosomal proteins has been done and the globulin conformation in solution of some of these proteins has been established. The widespread concept according to which the majority of ribosomal proteins on the ribosome and in solution are enlongated expanded structures is disputed. It is suggested that all, or almost all, ribosomal proteins are usual globular proteins recognizing the specific sequence of RNA on the periphery of the particles, and , hence, that the formation of functional centrers on the ribosome is, in principle, analogous to the formation of functional centers of other complex proteins with a quaternary structure.

Escherichia coli↗
PubMed1992

Inter-protein distances within the large subunit from Escherichia coli ribosomes.

Selected pairs of protonated ribosomal proteins were reconstituted into deuterated 50S subunits from Escherichia coli ribosomes. The rRNA of the deuterated ribosomal matrix was derived from cells grown in 76% D2O, the deuterated protein moiety from cells grown in 84% D2O. This procedure warrants that the coherent neutron scattering of deuterated proteins and rRNA is nearly the same and equals that of a D2O solution of approximately 90%. The neutron scattering is recorded in a reconstitution buffer containing approximately 90% D2O. The result is a significant improvement of the coherent signal:noise ratio over traditional methods; due to this dilute solutions can be used, thus preventing unfavorable inter-particle effects. From the diffraction pattern the distance between the mass centers of gravity of the two protonated proteins can be deduced. In this way, 50 distances between proteins within the large subunit have been determined which provide a basis for future models of the large ribosomal subunit describing the spatial distribution of the ribosomal proteins. A model containing seven ribosomal proteins is presented.

Deuterium↗