Proceedings of the Cambridge Philosophical Society.

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Expression and biochemical analysis of the entire HIV-2 gp41 ectodomain: determinants of stability map to N- and C-terminal sequences outside the 6-helix bundle core

The folding of HIV gp41 into a 6-helix bundle drives virus-cell membrane fusion. To examine the structural relationship between the 6-helix bundle core domain and other regions of gp41, we expressed in Escherichia coli, the entire ectodomain of HIV-2(ST) gp41 as a soluble, trimeric maltose-binding protein (MBP)/gp41 chimera. Limiting proteolysis indicated that the Cys-591-Cys-597 disulfide-bonded region is outside a core domain comprising two peptides, Thr-529-Trp-589 and Val-604-Ser-666. A biochemical examination of MBP/gp41 chimeras encompassing these core peptides; indicated that the N-terminal polar segment, 521-528, and C-terminal membrane-proximal segment, 658-666, cooperate in stabilizing the ectodomain. A functional interaction between sequences outside the gp41 core may contribute energy to membrane fusion. (C) 2004 Published by Elsevier B.V. on behalf of the Federation of European Biochemical Societies.

Scattering and tangential momentum accommodation at a 2D adsorbate-solid interface

We calculate tangential momentum coefficients for the exchange of momentum between molecules in transport and the internal surface of a membrane pore, modelled as a simple atomic structure. We introduce a local specular reflection (LSR) hypothesis, which states that impinging molecules undergo mirror-like reflection in a plane tangent to a surface atom at the point of impact. As a consequence, the components of the velocity, parallel to the direction of flow will (in general) change on impact. The overall effect is a loss of tangential momentum, since more is lost in the upstream direction than is gained in the downstream direction. The loss of tangential momentum is greater when the size ratio of fluid to solid atom is small, allowing more steeply inclined impact planes to become accessible to the fluid phase molecules. (c) 2005 Elsevier B.V. All rights reserved.

theta-defensins prevent HIV-1 Env-mediated fusion by binding gp41 and blocking 6-helix bundle formation

Retrocyclin-1, a 0-defensin, protects target cells from human immunodeficiency virus, type 1 (HIV-1) by preventing viral entry. To delineate its mechanism, we conducted fusion assays between susceptible target cells and effector cells that expressed HIV-1 Env. Retrocyclin-1 (4 mu M) completely blocked fusion mediated by HIV-1 Envs that used CXCR4 or CCR5 but had little effect on cell fusion mediated by HIV-2 and simian immunodeficiency virus Envs. Retrocyclin-1 inhibited HIV-1 Env-mediated fusion without impairing the lateral mobility of CD4, and it inhibited the fusion of CD4-deficient cells with cells bearing CD4-independent HIV-1 Env. Thus, it could act without cross-linking membrane proteins or inhibiting gp120-CD4 interactions. Retrocyclin-1 acted late in the HIV-1 Env fusion cascade but prior to 6-helix bundle formation. Surface plasmon resonance experiments revealed that retrocyclin bound the ectodomain of gp41 with high affinity in a glycan-independent manner and that it bound selectively to the gp41 C-terminal heptad repeat. Native-PAGE, enzyme-linked immunosorbent assay, and CD spectroscopic analyses all revealed that retrocyclin-1 prevented 6-helix bundle formation. This mode of action, although novel for an innate effector molecule, resembles the mechanism of peptidic entry inhibitors based on portions of the gp41 sequence.

A study of the formation of amorphous calcium phosphate and hydroxyapatite on melt quenched Bioglass(A (R)) using surface sensitive shallow angle X-ray diffraction

Melt quenched silicate glasses containing calcium, phosphorous and alkali metals have the ability to promote bone regeneration and to fuse to living bone. These glasses, including 45S5 Bioglass(A (R)) [(CaO)(26.9)(Na2O)(24.4)(SiO2)(46.1)(P2O5)(2.6)], are routinely used as clinical implants. Consequently there have been numerous studies on the structure of these glasses using conventional diffraction techniques. These studies have provided important information on the atomic structure of Bioglass(A (R)) but are of course intrinsically limited in the sense that they probe the bulk material and cannot be as sensitive to thin layers of near-surface dissolution/growth. The present study therefore uses surface sensitive shallow angle X-ray diffraction to study the formation of amorphous calcium phosphate and hydroxyapatite on Bioglass(A (R)) samples, pre-reacted in simulated body fluid (SBF). Unreacted Bioglass(A (R)) is dominated by a broad amorphous feature around 2.2 A...(-1) which is characteristic of sodium calcium silicate glass. After reacting Bioglass(A (R)) in SBF a second broad amorphous feature evolves similar to 1.6 A...(-1) which is attributed to amorphous calcium phosphate. This feature is evident for samples after only 4 h reacting in SBF and by 8 h the amorphous feature becomes comparable in magnitude to the background signal of the bulk Bioglass(A (R)). Bragg peaks characteristic of hydroxyapatite form after 1-3 days of reacting in SBF.

A first principles analysis of the effect of hydrogen concentration in hydrogenated amorphous silicon on the formation of strained Si-Si bonds and the optical and mobility gaps

In this paper, we use a model of hydrogenated amorphous silicon generated from molecular dynamics with density functional theory calculations to examine how the atomic geometry and the optical and mobility gaps are influenced by mild hydrogen oversaturation. The optical and mobility gaps show a volcano curve as the hydrogen content varies from undersaturation to mild oversaturation, with largest gaps obtained at the saturation hydrogen concentration. At the same time, mid-gap states associated with dangling bonds and strained Si-Si bonds disappear at saturation but reappear at mild oversaturation, which is consistent with the evolution of optical gap. The distribution of Si-Si bond distances provides the key to the change in electronic properties. In the undersaturation regime, the new electronic states in the gap arise from the presence of dangling bonds and strained Si-Si bonds, which are longer than the equilibrium Si-Si distance. Increasing hydrogen concentration up to saturation reduces the strained bonds and removes dangling bonds. In the case of mild oversaturation, the mid-gap states arise exclusively from an increase in the density of strained Si-Si bonds. Analysis of our structure shows that the extra hydrogen atoms form a bridge between neighbouring silicon atoms, thus increasing the Si-Si distance and increasing disorder in the sample.

Ionization of Atoms by Slow Heavy Particles, Including Dark Matter

Atoms and molecules can become ionized during the scattering of a slow, heavy particle off a bound electron. Such an interaction involving leptophilic weakly interacting massive particles (WIMPs) is a promising possible explanation for the anomalous 9σ annual modulation in the DAMA dark matter direct detection experiment [R. Bernabei et al., Eur. Phys. J. C 73, 2648 (2013)]. We demonstrate the applicability of the Born approximation for such an interaction by showing its equivalence to the semiclassical adiabatic treatment of atomic ionization by slow-moving WIMPs. Conventional wisdom has it that the ionization probability for such a process should be exponentially small. We show, however, that due to nonanalytic, cusplike behavior of Coulomb functions close to the nucleus this suppression is removed, leading to an effective atomic structure enhancement. We also show that electron relativistic effects actually give the dominant contribution to such a process, enhancing the differential cross section by up to 1000 times.

Energy levels and radiative rates for transitions in Cr-like Co IV and Ni V

We report calculations of energy levels and radiative rates (A-values) for transitions in Cr-like Co IV and Ni V. The quasi-relativistic Hartree-Fock (QRHF) code is adopted for calculating the data although grasp (general-purpose relativistic atomic structure package) and flexible atomic code (fac) have also been employed for comparison purposes. No radiative rates are available in the literature to compare with our results, but our calculated energies are in close agreement with those compiled by NIST for a majority of the levels. However, there are discrepancies for a few levels of up to 3%. The A-values are listed for all significantly contributing E1, E2 and M1 transitions, and the corresponding lifetimes reported, although unfortunately no previous theoretical or experimental results exist to compare with our data.

Radiative rates for E1, E2, M1, and M2 transitions in S-like to F-like tungsten ions (W LIX to W LXVI)

Calculations of energy levels, radiative rates and lifetimes are reported for eight ions of tungsten, i.e. S-like (W LIX) to F-like (W LXVI). A large number of levels have been considered for each ion and extensive configuration interaction has been included among a range of configurations. For the calculations, the general-purpose relativistic atomic structure package (. grasp) has been adopted, and radiative rates (as well as oscillator strengths and line strengths) are listed for all E1, E2, M1, and M2 transitions of the ions. Comparisons have been made with earlier available experimental and theoretical energies, although these are limited to only a few levels for most ions. Therefore for additional accuracy assessments, particularly for energy levels, analogous calculations have been performed with the flexible atomic code (. fac).

Radiative rates for E1, E2, M1, and M2 transitions in Br-like ions with 43≤Z≤50

Energies and lifetimes are reported for the eight Br-like ions with 43≤Z≤50, namely Tc IX, Ru X, Rh XI, Pd XII, Ag XIII, Cd XIV, In XV, and Sn XVI. Results are listed for the lowest 375 levels, which mostly belong to the 4s²4p⁵, 4s²4p⁴4ℓ, 4s4p⁶,4s²4p⁴5ℓ, 4s²4p³4d², 4s4p⁵4ℓ, and 4s4p⁵5ℓ configurations. Extensive configuration interaction among 39 configurations (generating 3990 levels) has been considered and the general-purpose relativistic atomic structure package (grasp) has been adopted for the calculations. Radiative rates are listed for all E1, E2, M1, and M2 transitions involving the lowest 375 levels. Previous experimental and theoretical energies are available for only a few levels of three, namely Ru X, Rh XI and Pd XII. Differences with the measured energies are up to 4% but the present results are an improvement (by up to 0.3 Ryd) in comparison to other recently reported theoretical data. Similarly for radiative rates and lifetimes, prior results are limited to those involving only 31 levels of the 4s²4p⁵, 4s²4p⁴4d, and 4s4p⁶ configurations for the last four ions. Moreover, there are generally no discrepancies with our results, although the larger calculations reported here differ by up to two orders of magnitude for a few transitions.

Radiative rates for E1, E2, M1, and M2 transitions in F-like ions with 37≤Z≤53

Calculations of energy levels, radiative rates and lifetimes are reported for 17 F-like ions with 37≤Z≤53. For brevity, results are only presented among the lowest 113 levels of the 2s²2p⁵, 2s2p⁶, 2s²2p⁴3ℓ, 2s2p⁵3ℓ, and 2p⁶3ℓ configurations, although the calculations have been performed for up to 501 levels in each ion. The general-purpose relativistic atomic structure package (grasp) has been adopted for the calculations, and radiative rates (along with oscillator strengths and line strengths) are listed for all E1, E2, M1, and M2 transitions of the ions. Comparisons are made with earlier available experimental and theoretical energies, although these are limited to only a few levels for most ions. Therefore for additional accuracy assessments, particularly for energy levels, analogous calculations have been performed with the Flexible Atomic Code (fac), for up to 72 259 levels. Limited previous results are available for radiative rates for comparison purposes, and no large discrepancy is observed for any transition and/or ion.

Sensor inteligente para medição de cargas mecânicas

A medição precisa da força é necessária para muitas aplicações, nomeadamente, para a determinação da resistência mecânica dos materiais, controlo de qualidade durante a produção, pesagem e segurança de pessoas. Dada a grande necessidade de medição de forças, têm-se desenvolvido, ao longo do tempo, várias técnicas e instrumentos para esse fim. Entre os vários instrumentos utilizados, destacam-se os sensores de força, também designadas por células de carga, pela sua simplicidade, precisão e versatilidade. O exemplo mais comum é baseado em extensómetros elétricos do tipo resistivo, que aliados a uma estrutura formam uma célula de carga. Este tipo de sensores possui sensibilidades baixas e em repouso, presença de offset diferente de zero, o que torna complexo o seu condicionamento de sinal. Este trabalho apresenta uma solução para o condicionamento e aquisição de dados para células de carga que, tanto quanto foi investigado, é inovador. Este dispositivo permite efetuar o condicionamento de sinal, digitalização e comunicação numa estrutura atómica. A ideia vai de encontro ao paradigma dos sensores inteligentes onde um único dispositivo eletrónico, associado a uma célula de carga, executa um conjunto de operações de processamento de sinal e transmissão de dados. Em particular permite a criação de uma rede ad-hoc utilizando o protocolo de comunicação IIC. O sistema é destinado a ser introduzido numa plataforma de carga, desenvolvida na Escola Superior de Tecnologia e Gestão de Bragança, local destinado à sua implementação. Devido à sua estratégia de conceção para a leitura de forças em três eixos, contém quatro células de carga, com duas saídas cada, totalizando oito saídas. O hardware para condicionamento de sinal já existente é analógico, e necessita de uma placa de dimensões consideráveis por cada saída. Do ponto de vista funcional, apresenta vários problemas, nomeadamente o ajuste de ganho e offset ser feito manualmente, tornando-se essencial um circuito com melhor desempenho no que respeita a lidar com um array de sensores deste tipo.

Cluster structure of atomic nuclei

Kirjallisuusarvostelu

Crystal structure of the complementary quadruplex formed by d(GCATGCT) at atomic resolution

Here we report the crystal structure of the DNA heptanucleotide sequence d(GCATGCT) determined to a resolution of 1.1 Angstrom. The sequence folds into a complementary loop structure generating several unusual base pairings and is stabilised through cobalt hexammine and highly defined water sites. The single stranded loop is bound together through the G(N2)-C(O2) intra-strand H-bonds for the available G/C residues, which form further Watson-Crick pairings to a complementary sequence, through 2-fold symmetry, generating a pair of non-planar quadruplexes at the heart of the structure. Further, four adenine residues stack in pairs at one end, H-bonding through their N7-N6 positions, and are additionally stabilised through two highly conserved water positions at the structural terminus. This conformation is achieved through the rotation of the central thymine base at the pinnacle of the loop structure, where it stacks with an adjacent thymine residue within the lattice. The crystal packing yields two halved biological units, each related across a 2-fold symmetry axis spanning a cobalt hexammine residue between them, which stabilises the quadruplex structure through H-bonds to the phosphate oxygens and localised hydration.