Conformation of a 16-residue zervamicin IIA analog peptide containing three different structural features: 310-helix, alpha helix and ß-bend ribbon

Boc-Trp-Ile-Ala-Aib-Ile-Val-Aib-Leu-Aib- Pro-Ala-Aib-Pro-Aib-Pro-Phe-OM(we here Boc is t-butoxycarbonyla nd Aib is a-aminoisobutyriac cid), a synthetica polar analog of the membrane-activefu ngal peptide antibioticz ervamtycinII A, crystallizesi n spaceg roupP 1 withZ =1 and cell parameters a = 9.086 ?0.002 A, b = 10.410 ?+ 0.002 A, c = 28.188 ? 0.004 A, a = 86.13 ? 0.01?, 13 = 87.90 ? 0.01?, and y = 89.27 ? 0.01?;o veralla greementf actorR = 7.3% for 7180 data (Fo > 3cr) and 0.91-A resolution. The peptide backbone makes a continuous spiral that begins as a 310-helix at the N-terminus, changes to an a-helix for two turns, and ends in a spiral of three fl-bends in a ribbon. Each of the fl-bends contains a proline residue at one of the corners. The torsion angles 4i range from -51? to -91? (average value -64o), and the torsion angles ai range from -1? to -46? (average value -31?). There are 10 intramolecularN H...OCh ydrogenb onds in the helix and two directh ead-to-taihl ydrogenb ondsb etween successive molecules. Two H20 and two CH30H solvent molecules fill additional space with appropriate hydrogen bonding in the head-to-tail region, and two additional H20 molecules form hydrogen bonds with carbonyl oxygens near the curve in the helix at Pro-10. Since there is only one peptide molecule per cell in space group P1, the molecules repeat only by translation, and consequently the helices pack parallel to each other.

Aqueous channels within apolar peptide aggregates. Solvated helix of Boc-Aib-Ala-Leu-Aib-Ala-Leu-Aib- -Ala-Leu-Aib-OMe. H2O.CH3OH

Although the peptide Boc-Aibl-Ala2-Leu3- Aib4-Alas Leu'-Aib7-Ala8-Leu9-Aib'0-OMe [with a t-butoxycarbonyl(Boc) blocking group at the amino terminus, a methyl ester (OMe) at the carboxyl terminus, and four a-aminoisobutyric (Aib) residues] has a 3-fold repeat of residues, the helix formed by the peptide backbone is irregular. The carboxyl-terminal half assumes an at-helical form with torsion angles ) and r of approximately -60° and -45°, respectively, whereas the amino-terminal half is distorted by an insertion of a water molecule between the amide nitrogen of Ala5 [N(5)] and the carbonyl oxygen of Ala2 [0(2)]. The water molecule W(1) acts as a bridge by forming hydrogen bonds N(5).W(1) (2.93 A) and W(1)---0(2) (2.86 A). The distortion of the helix exposes the carbonyl oxygens of Aib' and Aib4 to the outside environment, with the consequence that the helix assumes an amphiphilic character despite having all apolar residues. Neighboring helices in the crystal run in antiparallel directions. On one side of a helix there are only hydrophobic contacts with efficient interdigitation of leucine side chains with those from the neighboring helix. On the other side of the helix there are hydrogen bonds between protruding carbonyl oxygens and four water molecules that separate two neighboring helices. Along the helix axis the helices bind head-to-tail with a direct hydrogen bond N(2)-0(9) (3.00 A). Crystals grown from methanol/water solution are in space group P2, with a = 15.778 ± 0.004 A, b = 11.228 ± 0.002 A, c = 18.415 ± 0.003 A, = 102.10 ± 0.02ur and two formula units per cell for C49HON1003 2H2OCH3OH. The overall agreement factorR is 7.5% for 3394 reflections observed with intensities >3a(F), and the resolution is 0.90 A.

Open-circuit potential—time transients of alkaline porous iron electrodes at various states-of-charge

Open-circuit potential—time transients during the discharge of alkaline porous iron electrodes at various states-of-charge have been studied. From this, it has been possible to arrive at a correlation between the parameters of self-discharge kinetics of the electrode and observed open-circuit potential—recovery time constants. The study provides a method of estimate the state-of-charge of the rechargeable iron electrodes. As a hydrogen evolution reaction inevitably occurs on alkaline iron electrodes, the kinetics of the reaction have also been investigated.

Optical and magnetic properties of the exact PPP states of biphenyl

The low-lying singlets and triplets of biphenyl are obtained exactly within the PPP model using the diagrammatic valence bond method. The energy gaps within the singlet manifold as well as the lowest singlet-triplet gap are found to be in good agreement with experimental results. The two weak absorptions between 4·1 and 4·2 eV reported experimentally are attributed to the two states lying below the optical gap that become weakly allowed on breaking electron-hole and inversion symmetries. The observed blue shift of the spectral lines, attributed to a change in dihedral angle, on going from crystalline to solution to vapour phase is also well reproduced within the PPP model. The bond orders show that the ground singlet state is benzenoidal while the dipole excited state as well as the lowest triplet state are quinonoidal and planar. Comparison with the experimental spin densities and the fine structure constants D and E in the triplet state point to slightly weaker correlations than assumed by the PPP model. The introduction of a 1-8 bond to mimic poly(paraphenylene)s gives an optical gap that is in good agreement with experiment.

From ‘Afflicted’ to Activists: Structural Violence and Climate Change Discourse in the States of Pernambuco and Paraíba in Northeast Brazil

This study approaches the problem of poverty in the hinterlands of Northeast Brazil through the concept of structural violence, linking the environmental threats posed by climate change, especially those related to droughts, to the broader social struggles in the region. When discussions about potentials and rights are incorporated into the problematic of poverty, a deeper insight is obtained regarding the various factors behind the phenomenon. It is generally believed that climate change is affecting the already marginalized and poor more than those of higher social standing, and will increasingly do so in the future. The data for this study was collected during a three month field work in the states of Pernambuco and Paraíba in Northeast Brazil. The main methods used were semi-structured interviews and participant observation, including attending seminars concerning climate change on the field. The focus of the work is to compare both layman and expert perceptions on what climate change is about, and question the assumptions about its effects in the future, mainly that of increased numbers of ‘climate refugees’ or people forced to migrate due to changes in climate. The focus on droughts, as opposed to other manifestations of climate change, arises from the fact that droughts are not only phenomena that develop over a longer time span than floods or hurricanes, but is also due to the historical persistence of droughts in the region, and both the institutional and cultural linkages that have evolved around it. The instances of structural violence that are highlighted in this study; the drought industry, land use, and the social and power relations present in the region, including those between the civil society, the state and the private agribusiness sector, all work against a backdrop of symbolic and moral realms of value production, where relations between the different actors are being negotiated anew with the rise of the climate change discourse. The main theoretical framework of the study consists of Johan Galtung’s and Paul Farmer’s theory of structural violence, Ulrich Beck’s theory of the risk society, and James Scott’s theory of everyday peasant resistance.

Arabidopsis GRI is involved in the regulation of cell death induced by extracellular ROS

Reactive oxygen species (ROS) have important functions in plant stress responses and development. In plants, ozone and pathogen infection induce an extracellular oxidative burst that is involved in the regulation of cell death. However, very little is known about how plants can perceive ROS and regulate the initiation and the containment of cell death. We have identified an Arabidopsis thaliana protein, GRIM REAPER (GRI), that is involved in the regulation of cell death induced by extracellular ROS. Plants with an insertion in GRI display an ozone-sensitive phenotype. GRI is an Arabidopsis ortholog of the tobacco flower-specific Stig1 gene. The GRI protein appears to be processed in leaves with a release of an N-terminal fragment of the protein. Infiltration of the N-terminal fragment of the GRI protein into leaves caused cell death in a superoxide-and salicylic acid-dependent manner. Analysis of the extracellular GRI protein yields information on how plants can initiate ROS-induced cell death during stress response and development.

Nonequilibrium stationary states of harmonic chains with bulk noises

We consider a chain composed of $N$ coupled harmonic oscillators in contact with heat baths at temperature $T_\ell$ and $T_r$ at sites 1 and $N$ respectively. The oscillators are also subjected to non-momentum conserving bulk stochastic noises. These make the heat conductivity satisfy Fourier's law. Here we describe some new results about the hydrodynamical equations for typical macroscopic energy and displacement profiles, as well as their fluctuations and large deviations, in two simple models of this type.

Role of molecular reorientation in the vitrification of molecular liquids: A Monte Carlo study of the liquid and glassy states of 2,2-dimethylbutane

The liquid and the glassy phases of 2,2-dimethylbutane have been investigated by isothermal isobaric ensemble Monte Carlo simulation. Thermodynamic Properties and radial distribution functions for both the liquid and the glass have been obtained. The radial distribution functions have been classified into three types based on the accessibility of the group. It has been shown that the structure of the Iiquid and the glass can be understood in terms of the above classification of the radial distribution functions. Molecular reorientation plays an important role in the structural rearrangement accompanying glass formation. As much as 35% of the contribution to the increase in the intermolecular interaction energy on vitrification is due to the reorientation of the neighbouring pairs of molecules. The observed changes in the dimerisation energy and the bonding energy distribution function are consistent with the observed structural changes.

Maximum-entropy calculation of the electron density at 4 A resolution of Pf1 filamentous bacteriophage

A 4 A electron-density map of Pf1 filamentous bacterial virus has been calculated from x-ray fiber diffraction data by using the maximum-entropy method. This method produces a map that is free of features due to noise in the data and enables incomplete isomorphous-derivative phase information to be supplemented by information about the nature of the solution. The map shows gently curved (banana-shaped) rods of density about 70 A long, oriented roughly parallel to the virion axis but slewing by about 1/6th turn while running from a radius of 28 A to one of 13 A. Within these rods, there is a helical periodicity with a pitch of 5 to 6 A. We interpret these rods to be the helical subunits of the virion. The position of strongly diffracted intensity on the x-ray fiber pattern shows that the basic helix of the virion is right handed and that neighboring nearly parallel protein helices cross one another in an unusual negative sense.

Aspects of coherent states of nonlinear algebras

Various aspects of coherent states of nonlinear su(2) and su(1,1) algebras are studied. It is shown that the nonlinear su(1,1) Barut-Girardello and Perelomov coherent states are related by a Laplace transform. We then concentrate on the derivation and analysis of the statistical and geometrical properties of these states. The Berry's phase for the nonlinear coherent states is also derived. (C) 2010 American Institute of Physics. doi:10.1063/1.3514118]

Impedance peaks of sealed nickel/cadmium cells at low states-of-charge

The impedance of sealed nickel/cadmium cells is measured at low states-of-charge that correspond to a cell e.m.f. range of 0.0 to 1.3 V. The results show that the impedance exhibits a pronounced maximum between 0.3 and 0.45 V. It is concluded that the impedance maxima are due to physicochemical processes taking place at the nickel oxide electrode. The impedance of the nickel oxide electrode is dominated by three different phenomena: (i) a Ni(II)/Ni(III) reaction between 1.3 and 0.8 V; (ii) a double-layer impedance between 0.8 and 0.3 V; (iii) a hydrogen evolution reaction between 0.3 and 0.0 V.

Bound states of two spin-1/2 fermions in a synthetic non-Abelian gauge field

We study the bound states of two spin-1/2 fermions interacting via a contact attraction (characterized by a scattering length) in the singlet channel in three-dimensional space in presence of a uniform non-Abelian gauge field. The configuration of the gauge field that generates a Rashba-type spin-orbit interaction is described by three coupling parameters (lambda(x),lambda(y),lambda(z)). For a generic gauge field configuration, the critical scattering length required for the formation of a bound state is negative, i.e., shifts to the ``BCS side'' of the resonance. Interestingly, we find that there are special high-symmetry configurations (e.g., lambda(x) = lambda(y) = lambda(z)) for which there is a two-body bound state for any scattering length however small and negative. Remarkably, the bound-state wave functions obtained for such configurations have nematic spin structure similar to those found in liquid He-3. Our results show that the BCS-BEC (Bose-Einstein condensation) crossover is drastically affected by the presence of a non-Abelian gauge field. We discuss possible experimental signatures of our findings both at high and low temperatures.

Correlated electronic states of C-60 fragments

We have studied electronic states of various fragments of C-60 within the Pariser-Parr-Pople (PPP) model and have obtained structural, magnetic and spectral properties of these molecules. The fragments studied include corannulene, fluoranthene and pyracylene. Pyracylene is studied using the exact valence bond (VB) approach while fluoranthene and corannulene are studied using a novel restricted CI technique which employs molecular orbitals for constructing the VB functions. The electronic excitations, bond order and ring currents are calculated for these systems. From these studies, the wide range of absorptions in C-60 can be viewed as those localized on pyracylene units or on the corannulene/fluoranthene units. The bond orders and ring currents show the hexagons to be similar to benzene rings. The pentagon-hexagon bonds are also found to be longer than the hexagon-hexagon bonds.

Mechanism of ?-cleavage in the excited states of keto sulfides

The beta-cleavage process in photoexcited ketones of structure RCOCH2X (X = CH2CH3, OCH3, SCH3; R = CH3, Ph) has been studied using the configuration interaction procedure within the framework of MINDO/3. The results explain qualitatively why the beta-cleavage process is faster than the alpha-cleavage process in keto sulfides while in keto ethers the reverse is true.