Structure of thermolysin cleaved microcin J25: Extreme stability of a two-chain antimicrobial peptide devoid of covalent links

sThe structure of a two-chain peptide formed by the treatment of the potent antimicrobial peptide microcin J25 (MccJ25) with thermolysin has been characterized by NMR spectroscopy and mass spectrometry. The native peptide is 21 amino acids in size and has the remarkable structural feature of a ring formed by linkage of the side chain of Glu8 to the N-terminus that is threaded by the C-terminal tail of the peptide. Thermolysin cleaves the peptide at the Phe10-Val11 amide bond, but the threading of the C-terminus through the N-terminal ring is so tight that the resultant two chains remain associated both in the solution and in the gas phases. The three-dimensional structure of the thermolysin-cleaved peptide derived using NMR spectroscopy and simulated annealing calculations has a well-defined core that comprises the N-terminal ring and the threading C-terminal tail. In contrast to the well-defined core, the newly formed termini at residues Phe10 and Val11 are disordered in solution. The C-terminal tail is associated to the ring both by hydrogen bonds stabilizing a short beta-sheet and by hydrophobic interactions. Moreover, unthreading of the tail through the ring is prevented by the bulky side chains of Phe19 and Tyr20, which flank the octapeptide ring. This noncovalent two-peptide complex that has a remarkable stability in solution and in highly denaturing conditions and that survives in the gas phase is the first example of such a two-chain peptide lacking disulfide or interchain covalent bonds.

Phase equilibria in the Fe-Zn-O system at conditions relevant to zinc sintering and smelting

Zincite and spinel phases are present in the complex slag systems encountered in zinc/lead sintering and zinc smelting processes. These phases form extensive solid solutions and are stable over a wide range of compositions, temperatures and oxygen partial pressures. Accurate information on the stability of these phases is required in order to develop thermodynamic models of these slag systems. Phase equilibria in the Fe–Zn–O system have been experimentally studied for a range of conditions, between 900°C and 1580°C and oxygen partial pressures (pO2) between air and metallic iron saturation, using equilibration and quenching techniques. The compositions of the phases were measured using Electron probe X-ray microanalysis (EPMA). The ferrous and ferric bulk iron concentrations were determined using a specially developed wet-chemical analysis procedure based on the use of ammonium metavanadate. XRD was used to confirm phase identification. A procedure was developed to overcome the problems associated with evaporation of zinc at low pO2 values and to ensure the achievement of equilibria. An isothermal section of the system FeO–Fe2O3–ZnO at high ZnO concentrations at 1200°C was constructed. The maximum solubilities of iron and zinc in zincite and spinel phases in equilibrium were determined at pO2 = 1 × 10-6 atm at 1200°C and 1300°C. The morphology of the zincite crystals sharply changes in air between 1200–1300°C from rounded to plate-like. This is shown to be associated with significant increase in total iron concentration, the additional iron being principally in the form of ferric iron. Calculations performed by FactSage with a thermodynamically optimised database have been compared with the experimental results.

The stability of lipidic analogues of GnRH in plasma and kidney preparations: the stereoselective release of the parent peptide

The conjugation of a lipoamino acid to the N-terminus of Gonadotropin releasing hormone (GnRH) produces a lipophilic peptide from which the parent GnRH peptide is released into solution on treatment with plasma and kidney enzyme preparation. Our findings show that one stereoisomer of the Laa is cleaved very rapidly, providing a bolus dose of the peptide while the opposite stereoisomer is cleaved much more slowly, providing prolonged elevation of peptide concentration. The Laa-Glu linkage appears to act as a two phase prodrug system. © 2005 Elsevier Ltd. All rights reserved.

Single turn peptide alpha helices with exceptional stability in water

Cyclic pentapepticles are not known to exist in a-helical conformations. CD and NMR spectra show that specific 20-membered cyclic pentapepticles, Ac-(cyclo-1,5) [KxxxD]-NH2 and Ac-(cyclo-2,6)R[KxxxD]-NH2, are highly a-helical structures in water and independent of concentration, TFE, denaturants, and proteases. These are the smallest a-helical peptides in water.

ATM signaling and genornic stability in response to DNA damage

DNA double strand breaks represent the most threatening lesion to the integrity of the genome in cells exposed to ionizing radiation and radiomimetic chemicals. Those breaks are recognized, signaled to cell cycle checkpoints and repaired by protein complexes. The product of the gene (ATM) mutated in the human genetic disorder ataxia-telangietasia (A-T) plays a central role in the recognition and signaling of DNA damage. ATM is one of an ever growing number of proteins which when mutated compromise the stability of the genome and predispose to tumour development. for recognising double strand breaks in DNA, maintaining genome stability and minimizing risk of cancer are discussed. (C) 2004 Published by Elsevier B.V.

Measurement and stability of FTY720 in human whole blood by high-performance liquid chromatography-atmospheric pressure chemical ionization-tandem mass spectrometry

We report here a validated method for the quantification of a new immunosuppressant drug FTY720, using HPLC-tandem mass spectrometry. Whole blood samples (500 mu l) were subjected to liquid-liquid extraction, in the presence of an internal standard (Y-32919). Mass spectrometric detection was by selected reaction monitoring with an atmospheric pressure chemical ionization source in positive ionization mode (FTY720: m/z 308.3 -> 255.3). The assay was linear from 0.2 to 25 mu g/l (r(2) > 0.997, n = 5). The inter- and intra-day analytical recovery and imprecision for quality control samples (0.5, 7 and 15 mu g/l) were 95.8-103.2 and < 5.5%, respectively. At the lower limit of quantification (0.2 mu g/l) the interand intra-day analytical recovery was 99.0-102.8% with imprecision of < 7.6% (n = 5). The assay had a mean relative recovery of 100.5 +/- 5.8% (n = 15). Extracted samples were stable for 16 h. IFTY720 quality control samples were stable at room temperature for 16 h at 4 degrees C for at least 8 days and when taken through at least three freeze-thaw cycles. In conclusion, the method described displays analytical performance characteristics that are suitable for pharmacokinetic studies in humans. (c) 2006 Elsevier B.V. All rights reserved.

Thermal Cycling Stability of Silica Membranes for Gas Separation

Hydrogen is being seen as an alternative energy carrier to conventional hydrocarbons to reduce greenhouse gas emissions. High efficiency separation technologies to remove hydrogen from the greenhouse gas, carbon dioxide, are therefore in growing demand. Traditional thermodynamic separation systems utilise distillation, absorption and adsorption, but are limited in efficiency at compact scales. Molecular sieve silica (MSS) membranes can perform this separation as they have high permselectivity of hydrogen to carbon dioxide, but their stability under thermal cycling is not well reported. In this work we exposed a standard MSS membrane and a carbonised template MSS (CTMSS) membrane to thermal cycling from 100 to 450°C. The standard MSS and carbonised template CTMSS membranes both showed permselectivity of helium to nitrogen dropping from around 10 to 6 in the first set of cycles, remaining stable until the last test. The permselectivity drop was due to small micropore collapse, which occurred via structure movement during cycling. Simulating single stage membrane separation with a 50:50 molar feed of H2:CO2, H2 exiting the permeate stream would start at 79% and stabilise at 67%. Higher selectivity membranes showed less of a purity drop, indicating the margin at which to design a stable membrane separation unit for CO2 capture.

Hydrothermal Stability of Modified Silica Membranes for Gas Separation

A new class of hybrid molecular sieve silica (MSS) membranes is developed and tested against standard and organic templated membranes. The hybrid membrane is synthesized by the standard sol-gel process, integrating a template (methyltriethoxysilane - MTES) and a C6 surfactant (triethylhexylammonium bromide) into the silica film matrix. After hydro treatment under a relative humidity of 96% for 50h, the hybrid membrane shows no changes in its gas separation capabilities or energy of mobility. The structural characteristics and integrity of the hybrid membrane are retained due to a high concentration of organophilic functional groups and alkoxides observed using 29 Si NMR. In contrast, the structural integrity of the membranes prepared with non-templated films deteriorated during the hydro treatment due to a large percentage of silanol groups (Si-OH) which react with water. The hybrid membranes underwent a decrease in the H2/CO2 selectivity of only 1% whereas for the non-templated membrane a 21% decrease was observed. The transport mechanism of the hybrid membranes is activated as permeation increased with temperature. The activation energy for the permeation of H2 is positive while negative for CO2. The H2 permeation obtained was 3x 10 -8 mol.m -2 .s -1 .Pa -1 and permselectivities for H2/CO2 and H2/N2 varied between 1-7 and 31-34, respectively.

Hydrothermal Stability Analysis of Carbonised Template Molecular Sieve Silica Membranes

For fuel cell CO clean up application, the presence of water with silica membranes greatly reduces their selectivity to CO. We show results of a new functional carbonised template membrane of around 13nm thickness which offered hydrothermal stability with no compromise to the membrane’s H2/CO permselectivity of 16. Lost permeance was also regenerated.

A two-phase approach for detecting recombination in nucleotide sequences

Genetic recombination can produce heterogeneous phylogenetic histories within a set of homologous genes. Delineating recombination events is important in the study of molecular evolution, as inference of such events provides a clearer picture of the phylogenetic relationships among different gene sequences or genomes. Nevertheless, detecting recombination events can be a daunting task, as the performance of different recombination-detecting approaches can vary, depending on evolutionary events that take place after recombination. We recently evaluated the effects of post-recombination events on the prediction accuracy of recombination-detecting approaches using simulated nucleotide sequence data. The main conclusion, supported by other studies, is that one should not depend on a single method when searching for recombination events. In this paper, we introduce a two-phase strategy, applying three statistical measures to detect the occurrence of recombination events, and a Bayesian phylogenetic approach in delineating breakpoints of such events in nucleotide sequences. We evaluate the performance of these approaches using simulated data, and demonstrate the applicability of this strategy to empirical data. The two-phase strategy proves to be time-efficient when applied to large datasets, and yields high-confidence results.

Experimental study of the quantum driven pendulum and its classical analog in atom optics

We present experimental results for the dynamics of cold atoms in a far detuned amplitude-modulated optical standing wave. Phase-space resonances constitute distinct peaks in the atomic momentum distribution containing up to 65% of all atoms resulting from a mixed quantum chaotic phase space. We characterize the atomic behavior in classical and quantum regimes and we present the applicable quantum and classical theory, which we have developed and refined. We show experimental proof that the size and the position of the resonances in phase space can be controlled by varying several parameters, such as the modulation frequency, the scaled well depth, the modulation amplitude, and the scaled Planck’s constant of the system. We have found a surprising stability against amplitude noise. We present methods to accurately control the momentum of an ensemble of atoms using these phase-space resonances which could be used for efficient phase-space state preparation.

Entanglement in a simple quantum phase transition

What entanglement is present in naturally occurring physical systems at thermal equilibrium? Most such systems are intractable and it is desirable to study simple but realistic systems that can be solved. An example of such a system is the one-dimensional infinite-lattice anisotropic XY model. This model is exactly solvable using the Jordan-Wigner transform, and it is possible to calculate the two-site reduced density matrix for all pairs of sites. Using the two-site density matrix, the entanglement of formation between any two sites is calculated for all parameter values and temperatures. We also study the entanglement in the transverse Ising model, a special case of the XY model, which exhibits a quantum phase transition. It is found that the next-nearest-neighbor entanglement (though not the nearest-neighbor entanglement) is a maximum at the critical point. Furthermore, we show that the critical point in the transverse Ising model corresponds to a transition in the behavior of the entanglement between a single site and the remainder of the lattice.

Achromatic optical phase shifter/modulator

We propose and demonstrate, theoretically and experimentally, a novel achromatic optical phase shifter modulator based on a frequency-domain optical delay line configured to maintain zero group delay as variable phase delay is generated by means of tilting a mirror. Compared with previously reported phase shifter modulators, e.g., based on the Pancharatnam (geometric) phase, our device is high speed and polarization insensitive and produces a large, bounded phase delay that, uniquely, is one-to-one mapped to a measurable parameter, the tilt angle.

Hamiltonian mappings and circle packing phase spaces.

We introduce three area preserving maps with phase space structures which resemble circle packings. Each mapping is derived from a kicked Hamiltonian system with one of the three different phase space geometries (planar, hyperbolic or spherical) and exhibits an infinite number of coexisting stable periodic orbits which appear to ‘pack’ the phase space with circular resonances.

A two-phase strategy for detecting recombination in nucleotide sequences

Genetic recombination can produce heterogeneous phylogenetic histories within a set of homologous genes. Delineating recombination events is important in the study of molecular evolution, as inference of such events provides a clearer picture of the phylogenetic relationships among different gene sequences or genomes. Nevertheless, detecting recombination events can be a daunting task, as the performance of different recombination-detecting approaches can vary, depending on evolutionary events that take place after recombination. We previously evaluated the effects of post-recombination events on the prediction accuracy of recombination-detecting approaches using simulated nucleotide sequence data. The main conclusion, supported by other studies, is that one should not depend on a single method when searching for recombination events. In this paper, we introduce a two-phase strategy, applying three statistical measures to detect the occurrence of recombination events, and a Bayesian phylogenetic approach to delineate breakpoints of such events in nucleotide sequences. We evaluate the performance of these approaches using simulated data, and demonstrate the applicability of this strategy to empirical data. The two-phase strategy proves to be time-efficient when applied to large datasets, and yields high-confidence results.