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PubMed1980

Location of the chromophore in bacteriorhodopsin.

We present a location for the retinylidene chromophore in dark-adapted bacteriorhodopsin based on the differences in neutron scattering between purple membrane preparations reconstituted with retinal and with deuterated retinal. The Fourier difference density map contains more peaks than expected, and additional arguments are introduced to exclude artificial peaks, caused by the reconstitution techniques or the limited resolution of the diffraction data. The membrane preparation used is necessarily dark-adapted and therefore contains 13-cis- and all-trans-retinal isomers in roughly equal amounts. However, we find only a single position for both isomers. Presumably, the difference in conformation caused by isomerization around the C13-C14 double bond is minimized by rotation around other bonds. The retinal is located between alpha-helical segments of the protein and its nearest neighbor (intratrimer) distance is 26 A; the next-nearest neighbor (intertrimer) distance is 38 A.

Apoproteins↗
PubMed1991

Neutron and X-ray scattering studies on the human complement protein properdin provide an analysis of the thrombospondin repeat.

Properdin is a regulatory glycoprotein of the alternative pathway of the complement system of immune defense. It is responsible for the stabilization of the C3 convertase complex formed between C3b and the Bb fragment of factor B. Neutron and X-ray solution scattering experiments were performed on the dimeric and trimeric forms of properdin. These have RG values of 9.1 and 10.7 nm, respectively. The scattering curves were compared with Debye sphere modeling simulations for properdin. Good agreements were obtained for models similar to published electron micrographs showing that the properdin trimer has a triangular structure with sides of 26 nm. Such a structure also accounted for sedimentation coefficient data on properdin. Primary structure analyses for mouse and human properdin have shown that this contains six homologous motifs known as the thrombospondin repeat (TSR), which is the second most abundant domain type found in the complement proteins. Sequences for these 12 TSRs were aligned with 19 others found in thrombospondin and the late complement components. Three distinct groups of TSRs were identified, namely, the TSRs found in thrombospondin and properdin, the TSRs mostly found at the N-terminus of the late complement components, and the TSRs found at the C-terminus of the late components. Averaged secondary structure predictions suggested that all three groups contain similar backbone structures with two amphipathic turn regions and one hydrophilic beta-strand region. The mean dimensions of the TSRs of properdin in solution were determined to be approximately 4 nm X 1.7 nm X 1.7 nm, showing that these are elongated in structure.

Amino Acid Sequence↗
PubMed1998

Protein hydration in solution: experimental observation by x-ray and neutron scattering.

The structure of the protein-solvent interface is the subject of controversy in theoretical studies and requires direct experimental characterization. Three proteins with known atomic resolution crystal structure (lysozyme, Escherichia coli thioredoxin reductase, and protein R1 of E. coli ribonucleotide reductase) were investigated in parallel by x-ray and neutron scattering in H2O and D2O solutions. The analysis of the protein-solvent interface is based on the significantly different contrasts for the protein and for the hydration shell. The results point to the existence of a first hydration shell with an average density approximately 10% larger than that of the bulk solvent in the conditions studied. Comparisons with the results of other studies suggest that this may be a general property of aqueous interfaces.

Escherichia coli↗
PubMed2005

Behavior of tri(n-butyl)ammonium bis[citrato(3-)-O1,O3,O6]silicate in aqueous solution: analysis of a sol-gel process by small-angle neutron scattering.

The racemic hexacoordinate silicon(IV) complex tri(n-butyl)ammonium bis[citrato(3-)-O1,O3,O6]silicate (1) was synthesized by treatment of Si(OMe)4 with 2 molar equiv of citric acid and 2 molar equiv of N(n-Bu)3. The corresponding germanium analogue, tri(n-butyl)ammonium bis[citrato(3-)-O1,O3,O6]germanate (5; structurally characterized by single-crystal X-ray diffraction), was obtained analogously, starting from Ge(OMe)4. Upon dissolution in water, the lambda6Si-silicate dianion of 1 hydrolyzes spontaneously (formation of Si(OH)4 and citric acid), whereas the lambda6Ge-germanate dianion of 5 was found to be stable in water. Aqueous "solutions" of 1, with concentrations that are significantly higher than the saturation concentration of Si(OH)4, look absolutely clear over a period of several weeks; however, in reality, these solutions are sols with very small particles that slowly grow with time and finally form a gel that precipitates. This sol-gel process was monitored by small-angle neutron scattering (SANS). For reasons of comparison, an aqueous solution of the hydrolytically stable germanium compound 5 was also studied by the SANS technique.

Journal Article↗
PubMed2003

Solution of the crystallographic phase problem by iterated projections.

An algorithm for determining crystal structures from diffraction data is described which does not rely on the usual reciprocal-space formulations of atomicity. The new algorithm implements atomicity constraints in real space, as well as intensity constraints in reciprocal space, by projections that restore each constraint with the minimal modification of the scattering density. To recover the true density, the two projections are combined into a single operation, the difference map, which is iterated until the magnitude of the density modification becomes acceptably small. The resulting density, when acted upon by a single additional operation, is by construction a density that satisfies both intensity and atomicity constraints. Numerical experiments have yielded solutions for atomic resolution X-ray data sets with over 400 non-hydrogen atoms, as well as for neutron data, where positivity of the density cannot be invoked.

Algorithms↗
PubMedDate not supplied

Thermus thermophilus ribosomes for crystallographic studies.

Three-dimensional crystals of the 70S ribosomes, the 70S ribosome-mRNA-tRNA complex, the 30S ribosomal subunits, several ribosomal proteins, the elongation factor G and threonyl- and seryl-tRNA synthetases from a Gram-negative extreme thermophilic bacterium, Thermus thermophilus, have been obtained at our institute. X-ray and neutronographic data from the 70S ribosome crystals have been collected up to 18 A and 60 A, respectively. Two-dimensional crystalline sheets of the 70S ribosomes have been studied by electron microscopy. Structural studies of crystals of 2 ribosomal proteins, L1 and S6, elongation factor G and threonyl- and seryl-tRNA synthetases are also in progress. At present, Thermus thermophilus seems to be the most suitable microorganism to isolate ribosomes and their constituents for crystallographic studies.

Bacterial Proteins↗
PubMed2001

Distribution of 137Cs in the Lena River estuary-Laptev Sea system.

Surface sediment samples in the Laptev Sea have average 137Cs content of 7.1 Bq kg(-1), a value intermediate between that of the western Kara Sea (23 Bq kg(-1) and the East Siberian Sea (4.2 Bq kg-'). Both surface sediment content and sediment inventory of 137Cs in the Laptev Sea sediments show significant variability, and the influence of a variety of environmental factors.137Cs concentrations in the Laptev Sea surface sediments range from 0.8 to 16 Bq kg(-1). There is a marked increase in 137Cs content of surface sediment samples collected near the Lena River delta, and a local enrichment in the 137Cs inventories at these sites is also evident. Fine-grained mixed-layer illite/ smectite rich sediments in the estuary provide effective adsorption sites to fix 137Cs, in spite of desorption processes associated with low salinities in estuarine mixing. The Lena River-Laptev Sea mixing zone is a major site of sea-ice production. River and shelf sediments are incorporated into sea-ice formed in this region (Holmes and Creager, 1974). The irregular 137Cs activity profiles of the Lena River estuary cores indicate disturbance or removal of 137Cs-laden sediments via sea-ice related processes. Lena River and Estuary sediments may have served as a secondary source (i.e. other than direct fallout) of 137Cs in sea-ice. North-east of the Lena River estuary, sediment contains a thin layer of 137Cs-bearing material over an erosion surface. The 137Cs-laden surface layer may be the result of transient deposition of estuarine sediments being delivered by sea-ice or spring floods.

Cesium Radioisotopes↗
PubMed1993

Three-dimensional structure and molecular modelling of C1- inhibitor.

New data on the structure of C1- inhibitor have become available as the result of the completion of its amino acid and nucleic acid sequences and its carbohydrate content, together with data from neutron scattering, crystal structure determinations, 1H NMR spectroscopy and Fourier transform infrared spectroscopy. C1- inhibitor is a two-domain protein. It is constructed as a heavily glycosylated N-terminal domain with 113 amino acids and 3 N-linked and 7 O-linked oligosaccharides, and a C-terminal domain with 365 amino acids and 3 N-linked oligosaccharides. Its molecular weights is calculated as 71,100, rather than the apparent value of 105,000 commonly reported from SDS-PAGE. Neutron scattering shows that C1- inhibitor possesses a distinct two domain structure in which an extended N-terminal domain with extended carbohydrate structures is attached to the C-terminal SERPIN domain. The length of C1- inhibitor is 18 nm, rather than that of 33 nm originally proposed from electron microscopy. Microcalorimetry supports the concept of two independently-folded domains in the C1- inhibitor structure. Combination of the C1- inhibitor sequence with crystal structure determinations of proteins belonging to the SERPIN superfamily of serine protease inhibitors shows that the protein structure of the C-terminal domain is well-described in terms of this structure. Comparison of the exon structure of C1- inhibitor with its presumed protein crystal structure shows that the 7 exons are distributed throughout the SERPIN fold with no obvious segregation into structural elements. Native C1- inhibitor is cleaved at its reactive centre loop to release a more stable cleaved form that is no longer active. 1H NMR spectroscopy shows that structures involved in hydrophobic interactions within the core of the SERPIN fold are preserved to within 0.05 nm before and after the transition. Fourier transform infrared spectroscopy shows the presence of alpha-helix and beta-sheet in both forms. Large changes are detectable in both the alpha-helix and beta-sheet contents of the SERPIN fold, and these changes are matched by a greater rate of 1H-2H exchange in 2H2O solvents in the native form than in the cleaved form. These data show that changes in the whole secondary structure and not just in the reactive site loop are involved in SERPIN inactivation.

Amino Acid Sequence↗
PubMed2000

Residence times of water molecules in the hydration sites of myoglobin.

Hydration sites are high-density regions in the three-dimensional time-averaged solvent structure in molecular dynamics simulations and diffraction experiments. In a simulation of sperm whale myoglobin, we found 294 such high-density regions. Their positions appear to agree reasonably well with the distributions of waters of hydration found in 38 x-ray and 1 neutron high-resolution structures of this protein. The hydration sites are characterized by an average occupancy and a combination of residence time parameters designed to approximate a distribution of residence times. It appears that although the occupancy and residence times of the majority of sites are rather bulk-like, the residence time distribution is shifted toward the longer components, relative to bulk. The sites with particularly long residence times are located only in the cavities and clefts of the protein. This indicates that other factors, such as hydrogen bonds and hydrophobicity of underlying protein residues, play a lesser role in determining the residence times of the longest-lived sites.

Binding Sites↗
PubMed2000

Neutron Rietveld refinement of the incommensurate phase of the ordered perovskite Pb2CoWO6.

The incommensurate structure of lead cobalt tungstate has been refined by the Rietveld method on neutron data collected at 250 K. The space group is planar monoclinic 12/m(alpha0gamma)0s [a = 7.9602 (4), b = 5.6779 (3), c = 5.6967 (3) A, beta = 90.047 (5)degrees, q(inc) = 0.9000 (9)a* + 0.1735 (6)c*]. The use of powder diffraction techniques to investigate ferroelastic modulated phases is discussed and compared with a previous polydomain single-crystal structural analysis. The modulated displacements of light atoms have been determined, allowing an accurate description of the modulation of both the cations and the O-atom framework. The refinement suggests a displacive model for the phase transition, involving significant atomic shifts for Pb atoms and a quite complex mixing of tilt and deformation of the oxygen octahedra. The average character of this modulated structure is antiferroelectric.

Journal Article↗
PubMed2001

The overall conformation of conventional kinesins studied by small angle X-ray and neutron scattering.

The quaternary structures of several monomeric and dimeric kinesin constructs from Homo sapiens and Drosophila melanogaster were analyzed using small angle x-ray and neutron scattering. The experimental scattering curves of these proteins were compared with simulated scattering curves calculated from available crystallographic coordinates. These comparisons indicate that the overall conformations of the solution structures of D. melanogaster and H. sapiens kinesin heavy chain dimers are compatible with the crystal structure of dimeric kinesin from Rattus norvegicus. This suggests that the unusual asymmetric conformation of dimeric kinesin in the microtubule-independent ADP state is likely to be a general feature of the kinesin heavy chain subfamily. An intermediate length Drosophila construct (365 residues) is mostly monomeric at low protein concentration whereas at higher concentrations it is dimeric with a tendency to form higher oligomers.

Amino Acid Sequence↗
PubMed2005

Nh3D: a reference dataset of non-homologous protein structures.

BACKGROUND: The statistical analysis of protein structures requires datasets in which structural features can be considered independently distributed, i.e. not related through common ancestry, and that fulfil minimal requirements regarding the experimental quality of the structures it contains. However, non-redundant datasets based on sequence similarity invariably contain distantly related homologues. Here we provide a reference dataset of non-homologous protein domains, assuming that structural dissimilarity at the topology level is incompatible with recognizable common ancestry. The dataset is based on domains at the Topology level of the CATH database which hierarchically classifies all protein structures. It contains the best refined representatives of each Topology level, validates structural dissimilarity and removes internally duplicated fragments. The compilation of Nh3D is fully scripted. RESULTS: The current Nh3D list contains 570 domains with a total of 90780 residues. It covers more than 70% of folds at the Topology level of the CATH database and represents more than 90% of the structures in the PDB that have been classified by CATH. We observe that even though all protein pairs are structurally dissimilar, some pairwise sequence identities after global alignment are greater than 30%. CONCLUSION: Nh3D is freely available as a reference dataset for the statistical analysis of sequence and structure features of proteins in the PDB. Regularly updated versions of Nh3D and the corresponding PDB-formatted coordinate sets are accessible from our Web site http://www.schematikon.org.

Algorithms↗
PubMed2003

Chemical analysis of World Trade Center fine particulate matter for use in toxicologic assessment.

The catastrophic destruction of the World Trade Center (WTC) on 11 September 2001 caused the release of high levels of airborne pollutants into the local environment. To assess the toxicity of fine particulate matter [particulate matter with a mass median aerodynamic diameter < 2.5 microm (PM2.5)], which may adversely affect the health of workers and residents in the area, we collected fallen dust samples on 12 and 13 September 2001 from sites within a half-mile of Ground Zero. Samples of WTC dust were sieved, aerosolized, and size-separated, and the PM2.5 fraction was isolated on filters. Here we report the chemical and physical properties of PM2.5 derived from these samples and compare them with PM2.5 fractions of three reference materials that range in toxicity from relatively inert to acutely toxic (Mt. St. Helens PM; Washington, DC, ambient air PM; and residual oil fly ash). X-ray diffraction of very coarse sieved WTC PM (< 53 microm) identified calcium sulfate (gypsum) and calcium carbonate (calcite) as major components. Scanning electron microscopy confirmed that calcium-sulfur and calcium-carbon particles were also present in the WTC PM2.5 fraction. Analysis of WTC PM2.5 using X-ray fluorescence, neutron activation analysis, and inductively coupled plasma spectrometry showed high levels of calcium (range, 22-33%) and sulfur (37-43% as sulfate) and much lower levels of transition metals and other elements. Aqueous extracts of WTC PM2.5 were basic (pH range, 8.9-10.0) and had no evidence of significant bacterial contamination. Levels of carbon were relatively low, suggesting that combustion-derived particles did not form a significant fraction of these samples recovered in the immediate aftermath of the destruction of the towers. Because gypsum and calcite are known to cause irritation of the mucus membranes of the eyes and respiratory tract, inhalation of high doses of WTC PM2.5 could potentially cause toxic respiratory effects.

Air Pollutants↗
PubMed2003

Gas adsorption in mcm-41 porous silicas dynamic measurements using SANS.

The isothermal gas adsorption of two hexane isomers (n-hexane and cyclohexane) in the mesopores of MCM-41 silica have been investigated by small angle neutron scattering (SANS). This has been achieved by performing SANS measurements under contrast matching conditions for the silica matrix and condensed hydrocarbon confined in the mesopores. Insight into the kinetics of adsorption have been derived from changes in the intensity of the (100) diffraction peak associated with the ordered hexagonal mesoporous structure of the MCM-41 silica.

Journal Article↗
PubMed2006

Structural studies of the phase, aggregation and surface behaviour of 1-alkyl-3-methylimidazolium halide + water mixtures.

The surface, phase and aggregation behaviour of mixtures of 1-alkyl-3-methylimidazolium halide, [C(n)mim]X, where n is the alkyl chain length, with water has been explored using a variety of methods. Critical micelle concentrations (cmc) and micelle structures have been determined for aqueous [C(n)mim]Br solutions for n=2, 4, 6, 8, and 10. Small-angle neutron scattering (SANS) measurements reveal that for the n=8 and 10 systems, at concentrations just above the cmc, small near-spherical aggregates exist, which, after initial growth, possess core radii (aggregation numbers) at intermediate concentrations of 10.5+/-0.5 Angstrom (22+/-2) and 13.2+/-0.5 Angstrom (40+/-3), respectively, for n=8 and n=10. Towards higher concentrations, the aggregates appear to grow, with the aggregates in the [C(10)mim]Br system becoming increasingly elongated (prolate) with increasing concentration. No evident aggregates are formed in the systems with n=2 and 4. In the n=6 system, it appears that oblate aggregates with radius approximately 9 Angstrom form at the cmc and that the radius increases with increasing concentration. For longer alkyl chain lengths, at high concentrations lyotropic mesophases form in some systems. The mesophase region for the [C(8)mim]Cl system has been explored across the composition range using X-ray diffraction and (2)H NMR spectroscopy. Both techniques suggest that a major hexagonal phase with lattice parameter of 29.5+/-0.5 Angstrom coexists with a minor lamellar phase (23.5+/-0.3 Angstrom) or possibly a second hexagonal phase (27.1+/-0.4 Angstrom). The area per adsorbed molecule at the surface of [C(8)mim]Br solutions has been measured as a function of concentration using neutron reflectometry. A minimum in the area per molecule behaviour is coincident with a minimum identified in the surface tension isotherm occurring close to the cmc. The data suggest depletion of [C(8)mim]Br from the surface region occurs at concentrations immediately above the cmc.

Journal Article↗
PubMed2001

Characterization of poly(L-lactic acid) microspheres loaded with holmium acetylacetonate.

Holmium-loaded PLLA microspheres are useful systems in radioembolization therapy of liver metastases because of their low density, biodegradability and favourable radiation characteristics. Neutron activated Ho-loaded microspheres showed a surprisingly low release of the relatively small holmium complex. In this paper factors responsible for this behaviour are investigated, in particular by the use of differential scanning calorimetry, scanning electron microscopy, infrared spectroscopy and X-ray diffraction. The holmium complex is soluble in PLLA up to 8% in films and 17% in microspheres. Interactions between carbonyl groups of PLLA, and the Ho-ion in the HoAcAc complex, explain very satisfactorily the high stability of holmium-loaded microspheres.

Biocompatible Materials↗
PubMed2002

The pore structure in processed Victorian Brown coal.

Changes in the pore structure of Victorian Brown coal when upgraded with heated gases under pressure are investigated. We show that the results obtained from ultra-small-angle neutron scattering (USANS) measurements agree with previous results using small-angle X-ray scattering results but that USANS may also be used to investigate the meso porosity. Findings from small-angle scattering are confirmed using electron microscopy. We also show evidence from electron diffraction that thermal conditions within the brown coals during the upgrade procedure may be far more extreme than previously thought.

Journal Article↗