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PubMed1994

Independent in vitro assembly of a ribonucleoprotein particle containing the 3' domain of 16S rRNA.

Small (30S) subunits of Escherichia coli ribosomes are composed of 21 proteins and a 1542-nucleotide 16S rRNA, whose secondary structure is divided into three domains. An in vitro transcript of the 3' domain of 16S rRNA (residues 923-1542), assembles efficiently with 30S ribosomal proteins to form a compact ribonucleoprotein (RNP) particle. Isolated particles examined under the electron microscope have a globular appearance, similar in size and shape to the head of the 30S ribosomal subunit. Two-dimensional gel analysis of the particles indicates the presence of proteins S3, S7, S9, S10, S13, S14, and S19 and smaller amounts of S2, all of which have been localized to the head of the 30S subunit by immunoelectron microscopy and neutron diffraction and belong to the S7 assembly family. Interestingly, protein S4, which is believed to interact exclusively with the 5' domain, is also reproducibly found associated with the particles in significant amounts. Chemical probing of the RNA in the assembled particle reveals characteristic cleavage protection patterns, showing that the proteins assemble with the 3'-domain RNA similarly to the way in which they assemble with 16S rRNA, although some of the later steps of assembly appear to be incomplete. These results show that the 3' domain of 16S rRNA can indeed assemble independently of the rest of the 30S subunit into a particle that resembles its structure in the ribosome. In addition, the assembled particles are able to bind spectinomycin with an affinity comparable to that of 30S subunits.

Base Sequence↗
PubMed1999

Manganese oxide minerals: crystal structures and economic and environmental significance.

Manganese oxide minerals have been used for thousands of years-by the ancients for pigments and to clarify glass, and today as ores of Mn metal, catalysts, and battery material. More than 30 Mn oxide minerals occur in a wide variety of geological settings. They are major components of Mn nodules that pave huge areas of the ocean floor and bottoms of many fresh-water lakes. Mn oxide minerals are ubiquitous in soils and sediments and participate in a variety of chemical reactions that affect groundwater and bulk soil composition. Their typical occurrence as fine-grained mixtures makes it difficult to study their atomic structures and crystal chemistries. In recent years, however, investigations using transmission electron microscopy and powder x-ray and neutron diffraction methods have provided important new insights into the structures and properties of these materials. The crystal structures for todorokite and birnessite, two of the more common Mn oxide minerals in terrestrial deposits and ocean nodules, were determined by using powder x-ray diffraction data and the Rietveld refinement method. Because of the large tunnels in todorokite and related structures there is considerable interest in the use of these materials and synthetic analogues as catalysts and cation exchange agents. Birnessite-group minerals have layer structures and readily undergo oxidation reduction and cation-exchange reactions and play a major role in controlling groundwater chemistry.

Journal Article↗
PubMed1995

Interaction of an amphiphilic peptide with a phospholipid bilayer surface by molecular dynamics simulation study.

Corticotropin-releasing factor (CRF) is the principal neuroregulator of adrenocorticotropic hormone (ACTH) secretion. Previous experiments have demonstrated that CRF binds avidly to the surface of single egg phosphatidylcholine vesicles and its amphiphilic secondary structure might play an important role in the function. In this study, the interaction of the residues 13-41 in human CRF with the surface of a DOPC bilayer was investigated by molecular dynamics (MD) simulation in order to understand the role of the membrane surface in the formation of the amphiphilic alpha helix as well as to determine the effects of the peptide on the lipid bilayer. The model used included 60 DOPC molecules, 1 helical peptide (CRF13-41) on the bilayer surface, and explicit waters of solvation in the lipid polar head group regions, together with constant-volume periodic boundary conditions in three dimensions. The MD simulation was carried out for 510 ps. In addition, CRF13-41, initially in a helical form, was simulated in vacuo as a control. The results indicate that while it was completely unstable in vacuo, the peptide helical form was generally maintained on the bilayer surface, but with distortions near the terminal ends. The peptide was confined to the bilayer headgroup/water region, similar to that reported from neutron diffraction measurement of tripeptides bound to the phosphatidylcholine bilayer surface (Ref 1). The amphiphilicity of the peptide matched that of the bilayer headgroup environment, with the hydrophilic side oriented toward water and the hydrophobic side making contact with the bilayer hydrocarbon core. These results support the hypothesis that the amphiphilic environment of a membrane surface is important in the induction of peptide amphiphilic alpha-helical secondary structure. Two major effects of the peptide on the lipids were found: the first CH2 segment in the lipid chains was significantly disordered and the lipid headgroup distribution was broadened towards the water region.

Amino Acid Sequence↗
PubMed1993

OMEGA: a three-dimensional databank for protein structures (a complement to PDB).

OMEGA is a compilation of recent structural information on proteins derived from X-ray crystallography or NMR and published in journals referenced by Current Contents. To date, 401 entries have been included (334 X-ray, 28 NMR, 5 NMR + X-ray, 5 electron microscopy, 3 neutron scattering, 2 neutron diffraction, 1 electron microscopy + X-ray, 12 model, 11 miscellaneous), with 5-10 new proteins being added each week. OMEGA can be accessed on Macintosh and is interrogated through 32 key words (space group, resolution, secondary structure, number of residues, etc). This pool of proteins could be used for various purposes, including searches for proteins with a particular set of secondary structures. OMEGA will be continuously updated (every 6 months) and may later include all proteins already reported in the PDB, as well as structures reported in journals with smaller readerships.

Algorithms↗
PubMed1997

Transfer RNA docking pair model in the ribosomal pre- and post-translocational states.

A consensus has been reached that the conformation of the anticodon-codon interactions of two adjacent tRNA molecules on the ribosome is a Sundaralingam-type (S-type). Even if it is kept to the S-type, there are still various possibilities. Various experimental data have been supporting an idea that the conformation of A-site tRNA is different from that of P-site tRNA. Those data as well as the recent result of Brimacombe and co-workers that U20:1 of lupin tRNAmMetbound to the A-site was cross-linked to a region, 875-905, of 23S rRNA in combination with the other recent findings of Nierhaus and co-workers about the spin-contrast method of neutron diffraction of the ribosome and the better accessible nucleotide patterns of phosphorothioated tRNAs on the ribosome have led to a new tRNA docking pair model, in which the highly conserved G18 and G19 of D-loop in A-site tRNA and C56 and C61 of TpsiC-loop in P-site tRNA base pair along with the conventional base pairs of adjacent codon-anticodon interactions. This A-P tRNA pair model can be translocated to the P-E tRNA pair model without changing the conformation except the ACCA termini, keeping the position of the growing nascent polypeptide chain.

Base Composition↗
PubMed2005

Evaluation of silicon neutron resonance parameters in the thermal to 1800 keV energy range.

Because silicon is a major constituent of concrete and soil, neutron and gamma ray information on silicon is important for reactor shielding and criticality safety calculations. Therefore, much effort was put into the ENDF/B-VI evaluation for the three stable isotopes of silicon. The neutron capture cross section of natural silicon was recently measured at the Oak Ridge Electron Linear Accelerator (ORELA) in the energy range 1-700 keV. Using the ENDF/B-VI evaluation for initial values, a new evaluation of the resonance parameters was performed by adding the results of the ORELA capture measurements to the experimental database. The computer code SAMMY was used for the analysis of the experimental data; the new version of SAMMY allows accurate calculations of the self-shielding and multiple scattering effects in the capture measurements. The accuracy of the radiative capture widths of the resonances was improved by this analysis. Accurate values of the s-, p- and d-wave neutron strength functions were also obtained. Although the resonance capture component of the present evaluation is 2-3 times smaller than that in ENDF/B-VI, the total capture cross section is much larger, at least for energies >250 keV, because the direct capture component contributes values of the same order of magnitude as the resonance component. The direct component was not taken into account in the ENDF/B-VI evaluation and was calculated for the first time in the present evaluation.

Computer Simulation↗
PubMed2005

The Spallation Neutron Source (SNS) project: a fertile ground for radiation protection and shielding challenges.

The Spallation Neutron Source facility presently under construction in the USA consists of a front end, a linac, an accumulator ring, a target station and a neutron instrument hall, producing pulsed neutron beams driven by a proton beam of 1 GeV energy and 1.4 MW power with a repetition rate of 60 Hz. The layout of the facility and the radiation protection and shielding concept of the facility is laid out in numerous examples in a walk from the proton beam generation to the neutron utilisation.

Equipment Design↗
PubMed2005

MCNP simulation to optimise in-pile and shielding parts of the Portuguese SANS instrument.

A Small Angle Neutron Scattering instrument is being installed at one end of the tangential beam tube of the Portuguese Research Reactor. The instrument is fed using a neutron scatterer positioned in the middle of the beam tube. The scatterer consists of circulating H2O contained in a hollow disc of Al. The in-pile shielding components and the shielding installed around the neutron selector have been the object of an MCNP simulation study. The quantities calculated were the neutron and gamma-ray fluxes in different positions, the energy deposited in the material by the neutron and gamma-ray fields, the material activation resulting from the neutron field and radiation doses at the exit wall of the shutter and around the shielding. The MCNP results are presented and compared with results of an analytical approach and with experimental data collected after installation.

Computer Simulation↗
PubMed1990

The dependence of human bone texture on life style.

Neutron diffraction has been used to determine the preferred orientation of the hydroxyapatite crystals at the lower front edge of the tibia. The bones are compared for two Neolithic Orkney tribes. At Isbister, a muscular tribe on a hilly site engaged in heavy uphill work, whereas a tribe at Quanterness lived on level ground. The two sets are contrasted with the texture of present-day amputations. Values of 16, 8 and 3 are found for an 'index of manoeuvrability' for the Isbister, Quanterness and modern ankles, respectively.

Bone and Bones↗
PubMed2003

Organic materials for second-harmonic generation: advances in relating structure to function.

The relationships between molecular structure and the nonlinear optical phenomenon second-harmonic generation (SHG) are discussed. New-found relationships built up from basic structural axioms that were deduced in the 1970s and 1980s are the particular focus of this article, using structural results from X-ray and neutron-diffraction studies. The molecular and supramolecular manifestations of the SHG effect are borne out, although ways to optimize the effect on the molecular scale feature predominantly, since control of SHG on the supramolecular scale remains difficult given present limitations. The use of a variety of templates to generate head-to-tail oriented host-guest species thereby bypassing such limitations is described. The paper concludes with a look ahead at next generation 'octupolar' SHG-active compounds, the prediction of new series of SHG-active compounds via data-mining computational procedures, and developments in diffraction technology that may enable structural movies of a molecule to be captured during the SHG process. A practical assessment of the viability of organic SHG materials for industrial application is reviewed with a positive outcome, thus indicating a promising future for organic SHG materials.

Journal Article↗
PubMed1984

Activation of C1.

The first component of complement, C1, is a calcium-dependent complex of two loosely interacting subunits: C1q, responsible for the binding of activators to C1; C1r2-C1s2, which supports the autoactivation potential of C1, together with the proteolytic activity of activated C1- on its two substrates, C4 and C2. Isolated dimeric C1r2 is able to autoactivate through an intradimer cross-proteolysis; this capacity is lost when C1r2 is associated with two molecules of C1s inside the calcium-dependent C1r2-C1s2 subunit; this capacity is again observed in reconstituted C1. A model for reconstituted soluble C1 is proposed, based on electron microscopy, neutron diffraction, ultra-centrifugation, various biochemical findings, as well as functional properties of C1 or of its subcomponents. The flexible rod-like structure of C1r2-C1s2 is folded around two arms of C1q, with the catalytic domains of C1r and C1s inserted inside the cone defined by the C1q stalks. Activation of C1 which, in vivo, is controlled by C1 inhibitor, can be achieved by various activators, such as immune complexes; it appears to result from the suppression of a negative control and resides in a positive modulation of the intrinsic autocatalytic potential of C1r inside C1.

Amino Acid Sequence↗
PubMed1999

Structure of gaseous Kr in the low-q region by neutron scattering and interaction potentials.

Accurate experimental information on the long-range triplet interactions in noble fluids, as well as on the two-body potential, can be obtained from the low-density behavior of the static structure factor S(q) in the small-q region. The results here reported of a recent low-q neutron diffraction investigation in Kr, devoted to undercritical densities in the range 2.4<n/nm(-3)<4.3, provide important indications on the pair interactions and allow also a reliable analysis of irreducible three-body potential effects on the measured structure, from which the triple-dipole Axilrod-Teller strength is extracted with unprecedented accuracy.

Journal Article↗
PubMed2001

Shear banding and the isotropic-to-nematic transition in wormlike micelles.

Using deuterium NMR spectroscopy in a Couette cell, we observe shear-induced nematic ordering in the concentrated wormlike-micelle system CTAB/D(2)O, and our results are qualitatively consistent with birefringence studies, and in exact quantitative agreement with the degree of order measured in neutron-diffraction measurements. The width of the nematic region depends on shear rate, as well as on the temperature proximity to the equilibrium isotropic-nematic transition. Comparison of the nematic order profiles with velocity profiles obtained under identical conditions shows quite clearly that the nematic state is not identifiable with a highly sheared, low viscosity layer, and we conclude that the process of shearing induces a nematic state of high viscosity, possibly associated with mesoscale ordering. We present a simple model in which transition from the high shear branch to the viscous nematic branch is counterbalanced by subsequent relaxation of nematic order.

Biophysics↗
PubMed2003

Local structure and glass transition of polybutadiene up to 4 GPa.

This communication presents a determination of the glass transition of polybutadiene under very high pressure, and raises the problem of the determination of the relative effects of temperature and density on the glass transition, depending on the pressure and temperature conditions. Local structure and slow dynamics were studied, by neutron scattering and calorimetry. To the best of our knowledge in neutron diffraction on soft matter such a high pressure, up to 4 GPa, was achieved.

Journal Article↗
PubMed2003

Pressure-induced reduction of the Landau-Peierls instabilities in a side-chain polymer liquid crystal with reentrant polymorphism.

Cyanobiphenyl mesogens are known to exhibit partially bilayered smectic A (S(Ad)) and also reentrant nematic (N(re)) phases. Nematic and smectic orders are coupled parameters which depend both on temperature and pressure. We report the first structural study of the influence of a hydrostatic pressure on the smectic phase. This study was carried out on a side-chain liquid crystalline polymer, by neutron diffraction using two specifically designed pressure cells. These results concluded first that the pressure acts on the phase elastic constants via a reduction of the layer fluctuations giving rise to a hardening of the phase together with an extension of the smectic domain towards higher temperatures. Second, the S(Ad)-N(re) phase transition temperature remains unchanged in the studied pressure range revealing that the polymer component plays an important role which allows us to subtract the associated packing interactions from the pressure-induced volume reduction.

Journal Article↗
PubMed2003

Influence of density and temperature on the microscopic structure and the segmental relaxation of polybutadiene.

We investigate the influence of temperature and density on the local structure and the dynamics of polybutadiene by controlling both hydrostatic pressure and temperature in polarized neutron diffraction experiments on deuterated polybutadiene and in inelastic incoherent scattering experiments on protonated polybutadiene. We observe that the static structure factor S(Q) does not change along macroscopic isochores. This behavior is contrary to the relaxations observed on the nanosecond and picosecond time scales and viewed by the dynamic incoherent scattering law S(Q,omega), which differ strongly along the same thermodynamic path. We conclude that the static behavior, i.e., S(Q), is dominated by macroscopic density changes, similar to the vibrational excitations in the meV range. However, the relaxation dynamics is more sensitive to thermal energy changes. This is confirmed by the finding that lines of identical relaxation behavior (in time, shape, and Q dependence), isochrones on the 10(-9) sec time scale, clearly cross the constant density lines in the (P,T) plane. Concerning S(Q), we can reasonably relate the variation of the main-peak position to the average neighbor chain distance and deduce crude microscopic thermal expansion and compressibility coefficients. In the low-Q regime, the observed pressure and temperature variation of S(Q) exceeds the compressibility contribution and suggests the existence of additional scattering, which might originate from structural correlations arising at higher temperature and low pressure.

Journal Article↗
PubMed2003

Raman investigation of stable and metastable states of 4-octyl-4'-cyanobiphenyl confined in porous silica matrices.

We study the polymorphism of solid phases of 4-octyl-4(')-cyanobiphenyl (8CB) by Raman spectroscopy. For bulk 8CB, the Raman spectrum of the CN stretch is featured by a single peak, which shifts abruptly at the smectic-A-crystal transition. In confinement, the CN peak splits both at high and low temperatures. In the isotropic and liquid crystal phases, the signature of the liquid crystal bulk (LC) coexists with another peak that is assigned to LC molecules interacting with the matrice interface. We find correlations between the volumic fractions of interfacial liquid and the texture of the matrices. At low temperatures, we assign the splitting of the CN peak to the coexistence of different metastable solid phases. For strong confinements, the temperature dependence of the CN stretching frequency extends to that of the liquid, which suggests the existence of frozen-in smecticlike solid phases. We discuss the structure of these metastable solid phases in the light of neutron diffraction measurements. We also report on the peculiar analogy between the effect of quenched disorder due to the porous matrices and the effect of thermal quenching.

Journal Article↗
PubMed2000

Defects in a disordered world: the structure of glassy GeSe2

The full set of partial structure factors for the prototypical network glass GeSe2 was measured using the method of isotopic substitution in neutron diffraction. The basic building block of the network is the Ge(Se(1/2))(4) tetrahedron in which 34(5)% of the Ge reside in edge-sharing configurations. The intrinsic chemical order of the glass is, however, broken with a maximum of 25(5)% Ge and 20(5)% Se being involved in homopolar bonds at distances of 2.42(2) and 2.32(2) A, respectively.

Journal Article↗