Dimerization of aurein 1.2: Effects in structure, antimicrobial activity and aggregation of Cândida albicans cells

Antimicrobial peptides (AMPs) are a promising solution to face the antibiotic-resistant problem because they display little or no resistance effects. Dimeric analogues of select AMPs have shown pharmacotechnical advantages, making these molecules promising candidates for the development of novel antibiotic agents. Here, we evaluate the effects of dimerization on the structure and biological activity of the AMP aurein 1.2 (AU). AU and the C- and N-terminal dimers, (AU)2K and E(AU)2, respectively, were synthesized by solid-phase peptide synthesis. Circular dichroism spectra indicated that E(AU)2 has a coiled coil structure in water while (AU)2K has an α-helix structure. In contrast, AU displayed typical spectra for disordered structures. In LPC micelles, all peptides acquired a high amount of α-helix structure. Hemolytic and vesicle permeabilization assays showed that AU has a concentration dependence activity, while this effect was less pronounced for dimeric versions, suggesting that dimerization may change the mechanism of action of AU. Notably, the antimicrobial activity against bacteria and yeast decreased with dimerization. However, dimeric peptides promoted the aggregation of C. albicans. The ability to aggregate yeast cells makes dimeric versions of AU attractive candidates to inhibit the adhesion of C. albicans to biological targets and medical devices, preventing disease caused by this fungus. © 2013 Springer-Verlag Wien.

Local electronic structure, optical bandgap and photoluminescence (PL) properties of Ba(Zr0.75Ti0.25)O3 powders

Ba(Zr0.75Ti0.25)O3 (BZT-75/25) powders were synthesized by the polymeric precursor method. Samples were structurally characterized by X-ray diffraction (XRD), Rietveld refinement, X-ray absorption near-edge structure (XANES) and extended X-ray absorption fine structure (EXAFS) techniques. Their electronic structures were evaluated by first-principle quantum mechanical calculations based on density functional theory at the B3LYP level. Their optical properties were investigated by ultraviolet-visible (UV-Vis) spectroscopy and photoluminescence (PL) measurements at room temperature. XRD patterns and Rietveld refinement data indicate that the samples have a cubic structure. XANES spectra confirm the presence of pyramidal [TiO5] clusters and octahedral [TiO6] clusters in the disordered BZT-75/25 powders. EXAFS spectra indicate distortion of Ti-O and Ti-O-Ti bonds the first and second coordination shells, respectively. UV-Vis absorption spectra confirm the presence of different optical bandgap values and the band structure indicates an indirect bandgap for this material. The density of states demonstrates that intermediate energy levels occur between the valence band (VB) and the conduction band (CB). These electronic levels are due to the predominance of 4d orbitals of Zr atoms in relation to 3d orbitals of Ti atoms in the CB, while the VB is dominated by 2p orbitals related to O atoms. There was good correlation between the experimental and theoretical optical bandgap values. When excited at 482 nm at room temperature, BZT-75/25 powder treated at 500 C for 2 h exhibited broad and intense PL emission with a maximum at 578 nm in the yellow region. © 2013 Elsevier Ltd. All rights reserved.

Local order and magnetic field effects on the electronic properties of disordered binary alloys in the quantum site percolation limit

Electronic properties of disordered binary alloys are studied via the calculation of the average Density of States (DOS) in two and three dimensions. We propose a new approximate scheme that allows for the inclusion of local order effects in finite geometries and extrapolates the behavior of infinite systems following finite-size scaling ideas. We particularly investigate the limit of the Quantum Site Percolation regime described by a tight-binding Hamiltonian. This limit was chosen to probe the role of short range order (SRO) properties under extreme conditions. The method is numerically highly efficient and asymptotically exact in important limits, predicting the correct DOS structure as a function of the SRO parameters. Magnetic field effects can also be included in our model to study the interplay of local order and the shifted quantum interference driven by the field. The average DOS is highly sensitive to changes in the SRO properties and striking effects are observed when a magnetic field is applied near the segregated regime. The new effects observed are twofold: there is a reduction of the band width and the formation of a gap in the middle of the band, both as a consequence of destructive interference of electronic paths and the loss of coherence for particular values of the magnetic field. The above phenomena are periodic in the magnetic flux. For other limits that imply strong localization, the magnetic field produces minor changes in the structure of the average DOS. © World Scientific Publishing Company.

Reconnection current sheet structure in a turbulent medium

In the presence of turbulence, magnetic field lines lose their dynamical identity and particles entrained on field lines diffuse through space at a rate determined by the amplitude of the turbulence. In previous work (Lazarian and Vishniac, 1999; Kowal et al., 2009; Eyink et al., 2011) we showed that this leads to reconnection speeds which are independent of resistivity. In particular, in Kowal et al. (2009) we showed that numerical simulations were consistent with the predictions of this model. Here we examine the structure of the current sheet in simulations of turbulent reconnection. Laminar flows consistent with the Sweet-Parker reconnection model produce very thin and well ordered currents sheets. On the other hand, the simulations of Kowal et al. (2009) show a strongly disordered state even for relatively low levels of turbulence. Comparing data cubes with and without reconnection, we find that large scale field reversals are the cumulative effect of many individual eddies, each of which has magnetic properties which are not very different from turbulent eddies in a homogeneous background. This implies that the properties of stationary and homogeneous MHD turbulence are a reasonable guide to understanding turbulence during large scale magnetic reconnection events. In addition, dissipation and high energy particle acceleration during reconnection events take place over a macroscopic volume, rather than being confined to a narrow zone whose properties depend on microscopic transport coefficients.

Signal propagation in Bayesian networks and its relationship with intrinsically multivariate predictive variables

A set of predictor variables is said to be intrinsically multivariate predictive (IMP) for a target variable if all properly contained subsets of the predictor set are poor predictors of the. target but the full set predicts the target with great accuracy. In a previous article, the main properties of IMP Boolean variables have been analytically described, including the introduction of the IMP score, a metric based on the coefficient of determination (CoD) as a measure of predictiveness with respect to the target variable. It was shown that the IMP score depends on four main properties: logic of connection, predictive power, covariance between predictors and marginal predictor probabilities (biases). This paper extends that work to a broader context, in an attempt to characterize properties of discrete Bayesian networks that contribute to the presence of variables (network nodes) with high IMP scores. We have found that there is a relationship between the IMP score of a node and its territory size, i.e., its position along a pathway with one source: nodes far from the source display larger IMP scores than those closer to the source, and longer pathways display larger maximum IMP scores. This appears to be a consequence of the fact that nodes with small territory have larger probability of having highly covariate predictors, which leads to smaller IMP scores. In addition, a larger number of XOR and NXOR predictive logic relationships has positive influence over the maximum IMP score found in the pathway. This work presents analytical results based on a simple structure network and an analysis involving random networks constructed by computational simulations. Finally, results from a real Bayesian network application are provided. (C) 2012 Elsevier Inc. All rights reserved.

Electronic Structure Calculations in a 2D SixGe1-x Alloy Under an Applied Electric Field.

The recent advances and promises in nanoscience and nanotechnology have been focused on hexagonal materials, mainly on carbon-based nanostructures. Recently, new candidates have been raised, where the greatest efforts are devoted to a new hexagonal and buckled material made of silicon, named Silicene. This new material presents an energy gap due to spin-orbit interaction of approximately 1.5 meV, where the measurement of quantum spin Hall effect(QSHE) can be made experimentally. Some investigations also show that the QSHE in 2D low-buckled hexagonal structures of germanium is present. Since the similarities, and at the same time the differences, between Si and Ge, over the years, have motivated a lot of investigations in these materials. In this work we performed systematic investigations on the electronic structure and band topology in both ordered and disordered SixGe1-x alloys monolayer with 2D honeycomb geometry by first-principles calculations. We show that an applied electric field can tune the gap size for both alloys. However, as a function of electric field, the disordered alloy presents a W-shaped behavior, similarly to the pure Si or Ge, whereas for the ordered alloy a V-shaped behavior is observed.

Structure and properties of quaternary and tetragonal Heusler compounds for spintronics and spin transfer torque applications

Diese Dissertation ist in zwei Teile aufgeteilt: Teil 1 befasst sich mit der Vorhersage von Halb-Metallizität in quarternären Heuslerverbindungen und deren Potential für Spintronik-Anwendungen. Teil 2 befasst sich mit den strukturellen Eigenschaften der Mn2-basierenden Heuslerverbindungen und dem Tuning von ihrer magnetischen Eigenschaften bzgl. Koerzitivfeldstärke und Remanenz. Diese Verbindungen sind geeignet für Spin-Transfer Torque-Anwendungen.rnrnIn Teil 1 wurden die folgenden drei Probenserien quarternärer Heuslerverbindungen untersucht: XX´MnGa (X = Cu, Ni und X´ = Fe, Co), CoFeMnZ (Z = Al, Ga, Si, Ge) und Co2−xRhxMnZ (Z = Ga, Sn, Sb). Abgesehen von CuCoMnGa wurden alle diese Verbindungen mittels ab-initio Bandstrukturrechnungen als halbmetallische Ferromagnete prognostiziert. In der XX´MnGa-Verbindungsklasse besitzt NiFeMnGa zwar eine zu niedrige Curie-Temperatur für technologische Anwendungen, jedoch NiCoMnGa mit seiner hohen Spinpolarisation, einem hohen magnetischen Moment und einer hohen Curie-Temperatur stellt ein neues Material für Spintronik-Anwendungen dar. Alle CoFeMnZ-Verbindungen kristallisieren in der kubischen Heuslerstruktur und ihre magnetischen Momente folgen der Slater-Pauling-Regel, was Halbmetalizität und eine hohe Spinpolarisation impliziert. Die ebenfalls hohen Curie-Temperaturen ermöglichen einen Einsatz weit über Raumtemperatur hinaus. In der strukturellen Charakterisierung wurde festgestellt, dass sämtliche Co2−xRhxMnZ abgesehen von CoRhMnSn verschiedene Typen von Unordnung aufweisen; daher war die ermittelte Abweichung von der Slater-Pauling-Regel sowie von der 100%-igen Spinpolarisation dieser Verbindungen zu erwarten. Die Halbmetallizität der geordneten CoRhMnSn-Verbindung sollte nach den durchgeführten magnetischen Messungen vorhanden sein.rnrnIm zweiten Teil wurden Mn3−xCoxGa und Mn2−xRh1+xSn synthetisiert und charakterisiert. Es wurde gezeigt, dass Mn3−xCoxGa im Bereich x = 0.1 − 0.4 in einer tetragonal verzerrten inversen Heuslerstruktur kristallisiert und im Bereich x = 0.6−1 in einer kubisch inversen Heuslerstruktur. Während die tetragonalen Materialien hartmagnetisch sind und Charakeristika aufweisen, die typischerweise für Spin-Transfer Torque-Anwengungen attraktiv sind, repräsentieren die weichmagnetischen kubischen Vertreter die 100% spinpolarisierten Materialien, die der Slater-Pauling-Regel folgen. Mn2RhSn kristallisiert in der inversen tetragonal verzerrten Heuslerstruktur, weist einernhartmagnetische Hystereseschleife auf und folgt nicht der Slater-Pauling-Regel. Bei hohen Rh-Gehalt wird die kubische inverse Heuslerstruktur gebildet. Alle kubischen Proben sind weichmagnetisch und folgen der Slater-Pauling-Regel.

Crystal structure of the Anabaena sensory rhodopsin transducer.

We present crystal structures of the Anabaena sensory rhodopsin transducer (ASRT), a soluble cytoplasmic protein that interacts with the first structurally characterized eubacterial retinylidene photoreceptor Anabaena sensory rhodopsin (ASR). Four crystal structures of ASRT from three different spacegroups were obtained, in all of which ASRT is present as a planar (C4) tetramer, consistent with our characterization of ASRT as a tetramer in solution. The ASRT tetramer is tightly packed, with large interfaces where the well-structured beta-sandwich portion of the monomers provides the bulk of the tetramer-forming interactions, and forms a flat, stable surface on one side of the tetramer (the beta-face). Only one of our four different ASRT crystals reveals a C-terminal alpha-helix in the otherwise all-beta protein, together with a large loop from each monomer on the opposite face of the tetramer (the alpha-face), which is flexible and largely disordered in the other three crystal forms. Gel-filtration chromatography demonstrated that ASRT forms stable tetramers in solution and isothermal microcalorimetry showed that the ASRT tetramer binds to ASR with a stoichiometry of one ASRT tetramer per one ASR photoreceptor with a K(d) of 8 microM in the highest affinity measurements. Possible mechanisms for the interaction of this transducer tetramer with the ASR photoreceptor via its flexible alpha-face to mediate transduction of the light signal are discussed.

A unified theory of carcinogenesis based on order–disorder transitions in DNA structure as studied in the human ovary and breast

Fourier transform-infrared/statistics models demonstrate that the malignant transformation of morphologically normal human ovarian and breast tissues involves the creation of a high degree of structural modification (disorder) in DNA, before restoration of order in distant metastases. Order–disorder transitions were revealed by methods including principal components analysis of infrared spectra in which DNA samples were represented by points in two-dimensional space. Differences between the geometric sizes of clusters of points and between their locations revealed the magnitude of the order–disorder transitions. Infrared spectra provided evidence for the types of structural changes involved. Normal ovarian DNAs formed a tight cluster comparable to that of normal human blood leukocytes. The DNAs of ovarian primary carcinomas, including those that had given rise to metastases, had a high degree of disorder, whereas the DNAs of distant metastases from ovarian carcinomas were relatively ordered. However, the spectra of the metastases were more diverse than those of normal ovarian DNAs in regions assigned to base vibrations, implying increased genetic changes. DNAs of normal female breasts were substantially disordered (e.g., compared with the human blood leukocytes) as were those of the primary carcinomas, whether or not they had metastasized. The DNAs of distant breast cancer metastases were relatively ordered. These findings evoke a unified theory of carcinogenesis in which the creation of disorder in the DNA structure is an obligatory process followed by the selection of ordered, mutated DNA forms that ultimately give rise to metastases.

Crystal structure of glutamate-1-semialdehyde aminomutase: An α2-dimeric vitamin B6-dependent enzyme with asymmetry in structure and active site reactivity

The three-dimensional structure of glutamate-1-semialdehyde aminomutase (EC 5.4.3.8), an α2-dimeric enzyme from Synechococcus, has been determined by x-ray crystallography using heavy atom derivative phasing. The structure, refined at 2.4-Å resolution to an R-factor of 18.7% and good stereochemistry, explains many of the enzyme’s unusual specificity and functional properties. The overall fold is that of aspartate aminotransferase and related B6 enzymes, but it also has specific features. The structure of the complex with gabaculine, a substrate analogue, shows unexpectedly that the substrate binding site involves residues from the N-terminal domain of the molecule, notably Arg-32. Glu-406 is suitably positioned to repel α-carboxylic acids, thereby suggesting a basis for the enzyme’s reaction specificity. The subunits show asymmetry in cofactor binding and in the mobilities of the residues 153–181. In the unliganded enzyme, one subunit has the cofactor bound as an aldimine of pyridoxal phosphate with Lys-273 and, in this subunit, residues 153–181 are disordered. In the other subunit in which the cofactor is not covalently bound, residues 153–181 are well defined. Consistent with the crystallographically demonstrated asymmetry, a form of the enzyme in which both subunits have pyridoxal phosphate bound to Lys-273 through a Schiff base showed biphasic reduction by borohydride in solution. Analysis of absorption spectra during reduction provided evidence of communication between the subunits. The crystal structure of the reduced form of the enzyme shows that, despite identical cofactor binding in each monomer, the structural asymmetry at residues 153–181 remains.

NMR solution structure of the human prion protein

The NMR structures of the recombinant human prion protein, hPrP(23–230), and two C-terminal fragments, hPrP(90–230) and hPrP(121–230), include a globular domain extending from residues 125–228, for which a detailed structure was obtained, and an N-terminal flexibly disordered “tail.” The globular domain contains three α-helices comprising the residues 144–154, 173–194, and 200–228 and a short anti-parallel β-sheet comprising the residues 128–131 and 161–164. Within the globular domain, three polypeptide segments show increased structural disorder: i.e., a loop of residues 167–171, the residues 187–194 at the end of helix 2, and the residues 219–228 in the C-terminal part of helix 3. The local conformational state of the polypeptide segments 187–193 in helix 2 and 219–226 in helix 3 is measurably influenced by the length of the N-terminal tail, with the helical states being most highly populated in hPrP(23–230). When compared with the previously reported structures of the murine and Syrian hamster prion proteins, the length of helix 3 coincides more closely with that in the Syrian hamster protein whereas the disordered loop 167–171 is shared with murine PrP. These species variations of local structure are in a surface area of the cellular form of PrP that has previously been implicated in intermolecular interactions related both to the species barrier for infectious transmission of prion disease and to immune reactions.

NMR structure of the bovine prion protein

The NMR structures of the recombinant 217-residue polypeptide chain of the mature bovine prion protein, bPrP(23–230), and a C-terminal fragment, bPrP(121–230), include a globular domain extending from residue 125 to residue 227, a short flexible chain end of residues 228–230, and an N-terminal flexibly disordered “tail” comprising 108 residues for the intact protein and 4 residues for bPrP(121–230), respectively. The globular domain contains three α-helices comprising the residues 144–154, 173–194, and 200–226, and a short antiparallel β-sheet comprising the residues 128–131 and 161–164. The best-defined parts of the globular domain are the central portions of the helices 2 and 3, which are linked by the only disulfide bond in bPrP. Significantly increased disorder and mobility is observed for helix 1, the loop 166–172 leading from the β-strand 2 to helix 2, the end of helix 2 and the following loop, and the last turn of helix 3. Although there are characteristic local differences relative to the conformations of the murine and Syrian hamster prion proteins, the bPrP structure is essentially identical to that of the human prion protein. On the other hand, there are differences between bovine and human PrP in the surface distribution of electrostatic charges, which then appears to be the principal structural feature of the “healthy” PrP form that might affect the stringency of the species barrier for transmission of prion diseases between humans and cattle.

Protein folding from a highly disordered denatured state: The folding pathway of chymotrypsin inhibitor 2 at atomic resolution

Previous experimental and theoretical studies have produced high-resolution descriptions of the native and folding transition states of chymotrypsin inhibitor 2 (CI2). In similar fashion, here we use a combination of NMR experiments and molecular dynamics simulations to examine the conformations populated by CI2 in the denatured state. The denatured state is highly unfolded, but there is some residual native helical structure along with hydrophobic clustering in the center of the chain. The lack of persistent nonnative structure in the denatured state reduces barriers that must be overcome, leading to fast folding through a nucleation–condensation mechanism. With the characterization of the denatured state, we have now completed our description of the folding/unfolding pathway of CI2 at atomic resolution.

X-ray structure of clotting factor IXa: active site and module structure related to Xase activity and hemophilia B.

Hereditary deficiency of factor IXa (fIXa), a key enzyme in blood coagulation, causes hemophilia B, a severe X chromosome-linked bleeding disorder afflicting 1 in 30,000 males; clinical studies have identified nearly 500 deleterious variants. The x-ray structure of porcine fIXa described here shows the atomic origins of the disease, while the spatial distribution of mutation sites suggests a structural model for factor X activation by phospholipid-bound fIXa and cofactor VIIIa. The 3.0-A-resolution diffraction data clearly show the structures of the serine proteinase module and the two preceding epidermal growth factor (EGF)-like modules; the N-terminal Gla module is partially disordered. The catalytic module, with covalent inhibitor D-Phe-1I-Pro-2I-Arg-3I chloromethyl ketone, most closely resembles fXa but differs significantly at several positions. Particularly noteworthy is the strained conformation of Glu-388, a residue strictly conserved in known fIXa sequences but conserved as Gly among other trypsin-like serine proteinases. Flexibility apparent in electron density together with modeling studies suggests that this may cause incomplete active site formation, even after zymogen, and hence the low catalytic activity of fIXa. The principal axes of the oblong EGF-like domains define an angle of 110 degrees, stabilized by a strictly conserved and fIX-specific interdomain salt bridge. The disorder of the Gla module, whose hydrophobic helix is apparent in electron density, can be attributed to the absence of calcium in the crystals; we have modeled the Gla module in its calcium form by using prothrombin fragment 1. The arched module arrangement agrees with fluorescence energy transfer experiments. Most hemophilic mutation sites of surface fIX residues occur on the concave surface of the bent molecule and suggest a plausible model for the membrane-bound ternary fIXa-FVIIIa-fX complex structure: fIXa and an equivalently arranged fX arch across an underlying fVIIIa subdomain from opposite sides; the stabilizing fVIIIa interactions force the catalytic modules together, completing fIXa active site formation and catalytic enhancement.

Probing the pore wall structure of nanoporous carbons using adsorption

Hitherto, adsorption has been traditionally used to study only the porous structure in disordered materials, while the structure of the solid phase skeleton has been probed by crystallographic methods such as X-ray diffraction. Here we show that for carbons density functional theory, suitably adapted to consider heterogeneity of the pore walls, can be reliably used to probe features of the solid structure hitherto accessibly only approximately even by crystallographic methods. We investigate a range of carbons and determine pore wall thickness distributions using argon adsorption, with results corroborated by X-ray diffraction.