Maximin 9, a novel free thiol containing antimicrobial peptide with antimycoplasma activity from frog Bombina maxima

Amphibian skin is a rich resource of antimicrobial peptides, like maximins and maximin Hs from frog Bombina maxima. Novel cDNA clones encoding a precursor protein, which comprises a novel maximin peptide (maximin 9) and reported maximin H3, were isolated from two constructed skin cDNA libraries of B. maxima. The predicted primary structure of maximin 9 is GIGRKFLGGVKTTFRCGVKDFASKHLY-NH2. A surprising substitution is at position 16, with a free cysteine in maximin 9 rather than usual conserved glycine in other reported maximins. Maximin 9, the homodimer form and its Cys(16) to Gly(16) mutant were synthesized and their antimicrobial activities were evaluated. Unlike previously reported maximin 3, the tested bacterial and fungal strains were resistant to maximin 9, its homodimer and the Cys(16) to Gly(16) mutant (with MICs > 100 mu M). On the other hand, interestingly, while eight clinical Mollicutes strains were generally resistant to maximin 9 homodimer and its Cys(16) to Gly(16) mutant, most of them are sensitive to maximin 9 at a peptide concentration of 30 mu M, especially in the presence of dithiothreitol. These results indicate that the presence of a reactive Cys residue in maximin 9 is important for its antimycoplasma activity. The diversity of antimicrobial peptide cDNA structures encountered in B. maxima skin cDNA libraries and the antimicrobial specificity differences of the peptides may reflect well the species' adaptation to the unique microbial environments. (c) 2005 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Molecular docking and 3D-QSAR study of pyranmycin derivatives against 16S rRNA A site

To understand pharmacophore properties of pyranmycin derivatives and to design novel inhibitors of 16S rRNA A site, comparative molecular field analysis (CoMFA) approach was applied to analyze three-dimensional quantitative structure-activity relationship (3D-QSAR) of 17 compounds. AutoDock 3.0.5 program was employed to locate the orientations and conformations of the inhibitors interacting with 16S rRNA A site. The interaction mode was demonstrated in the aspects of inhibitor conformation, hydrogen bonding and electrostatic interaction. Similar binding conformations of these inhibitors and good correlations between the calculated binding free energies and experimental biological activities suggest that the binding conformations of these inhibitors derived from docking procedure were reasonable. Robust and predictive 3D-QSAR model was obtained by CoMFA with q(2) values of 0.723 and 0.993 for cross-validated and noncross-validated, respectively. The 3D-QSAR model built here will provide clear guidelines for novel inhibitors design based on the Pyranmycin derivatives against 16S rRNA A site. (c) 2005 Elsevier B.V. All rights reserved.

Tests of an adaptive QM/MM calculation on free energy profiles of chemical reactions in solution.

We present reaction free energy calculations using the adaptive buffered force mixing quantum mechanics/molecular mechanics (bf-QM/MM) method. The bf-QM/MM method combines nonadaptive electrostatic embedding QM/MM calculations with extended and reduced QM regions to calculate accurate forces on all atoms, which can be used in free energy calculation methods that require only the forces and not the energy. We calculate the free energy profiles of two reactions in aqueous solution: the nucleophilic substitution reaction of methyl chloride with a chloride anion and the deprotonation reaction of the tyrosine side chain. We validate the bf-QM/MM method against a full QM simulation, and show that it correctly reproduces both geometrical properties and free energy profiles of the QM model, while the electrostatic embedding QM/MM method using a static QM region comprising only the solute is unable to do so. The bf-QM/MM method is not explicitly dependent on the details of the QM and MM methods, so long as it is possible to compute QM forces in a small region and MM forces in the rest of the system, as in a conventional QM/MM calculation. It is simple, with only a few parameters needed to control the QM calculation sizes, and allows (but does not require) a varying and adapting QM region which is necessary for simulating solutions.

Free energy surface reconstruction from umbrella samples using Gaussian process regression

We demonstrate how the Gaussian process regression approach can be used to efficiently reconstruct free energy surfaces from umbrella sampling simulations. By making a prior assumption of smoothness and taking account of the sampling noise in a consistent fashion, we achieve a significant improvement in accuracy over the state of the art in two or more dimensions or, equivalently, a significant cost reduction to obtain the free energy surface within a prescribed tolerance in both regimes of spatially sparse data and short sampling trajectories. Stemming from its Bayesian interpretation the method provides meaningful error bars without significant additional computation. A software implementation is made available on www.libatoms.org.

Free energy surface reconstruction from umbrella samples using Gaussian process regression II: Multiple collective variables

We demonstrate how a prior assumption of smoothness can be used to enhance the reconstruction of free energy profiles from multiple umbrella sampling simulations using the Bayesian Gaussian process regression approach. The method we derive allows the concurrent use of histograms and free energy gradients and can easily be extended to include further data. In Part I we review the necessary theory and test the method for one collective variable. We demonstrate improved performance with respect to the weighted histogram analysis method and obtain meaningful error bars without any significant additional computation. In Part II we consider the case of multiple collective variables and compare to a reconstruction using least squares fitting of radial basis functions. We find substantial improvements in the regimes of spatially sparse data or short sampling trajectories. A software implementation is made available on www.libatoms.org.

Localized and free exciton spin relaxation dynamics in GaInNAs/GaAs quantum well

We have investigated the exciton spin relaxation in a GaInNAs/GaAs quantum well. The recombination from free and localized excitons is resolved on the basis of an analysis of the photoluminescence characteristics. The free exciton spin relaxation time is measured to be 192 ps at 10 K, while the localized exciton spin relaxation time is one order of magnitude longer than that of the free exciton. The dependence of the free exciton spin relaxation time on the temperature above 50 K suggests that both the D'yakonov-Perel' and the Elliot-Yafet effects dominate the spin relaxation process. The temperature independence below 50 K is considered to be due to the spin exchange interaction. The ultralong spin relaxation time of the localized excitons is explained to be due to the influence of nonradiative deep centers. (c) 2008 American Institute of Physics.

Growth mode and strain evolution during InN growth on GaN(0001) by molecular-beam epitaxy

Epitaxial growth of InN on GaN(0001) by plasma-assisted molecular-beam epitaxy is investigated over a range of growth parameters including source flux and substrate temperature. Combining reflection high-energy electron diffraction (RHEED) and scanning tunneling microscopy (STM), we establish a relationship between film growth mode and the deposition condition. Both two-dimensional (2D) and three-dimensional (3D) growth modes of the film are observed. For 2D growth, sustained RHEED intensity oscillations are recorded while STM reveals 2D nucleation islands. For 3D growth, less than three oscillation periods are observed indicating the Stranski-Krastanov (SK) growth mode of the film. Simultaneous measurements of (reciprocal) lattice constant by RHEED suggest a gradual relaxation of the strain in film, which commences during the first bilayer (BL) deposition and almost completes after 2-4 BLs. For SK growth, 3D islanding initiates after the strain has mostly been relieved, presumably by dislocations, so the islands are likely strain free. (C) 2002 American Institute of Physics.

Study of GaN thin films grown on vicinal SiC (0001) substrates by molecular beam epitaxy

A detailed study of the characteristics of undoped GaN films, grown on either vicinal or nominal flat SiC (0001) substrates by molecular beam epitaxy, has been carried out using photoluminescence and Raman scattering techniques. The I I K photoluminescence spectra of the GaN film grown on the vicinal SiC (0001) substrate show a strong and sharp near-bandgap peak (full width at half maximum (FWHM) similar to 16 meV). This feature contrasts with that of the GaN film grown on the nominal flat SiC (0001) substrate where the I I K photoluminescence spectra exhibit the near-bandgap peak (FWHM similar to 25 meV) and the intensity is approximately seven times weaker than that of the vicinal film sample. The redshift of the near-bandgap peak associated with excitons bound to shallow donors is related to the stress caused by both the lattice mismatch and the thermal expansion coefficient difference between GaN and SiC substrates. The measured thermal activation energy of the shallow donor of 33.4 meV is determined by using an Arrhenius plot of the near-bandgap luminescence versus I IT from the slope of the graph at high temperature. The temperature dependence of the FWHM of the near-bandgap luminescence has also been studied. The Raman scattering measurements from the vicinal film reveal that the E-2 phonon peak is strengthened and the A(1)(LO) phonon peak is shifted towards the low-frequency side with enhanced intensity, in comparison to that from the nominal flat film, suggesting a reduction in the density of defects and a lower free carrier concentration in the vicinal GaN film.

Weak epitaxy growth of metal-free phthalocyanine on p-sexiphenyl monolayer and double-layer films

Weak epitaxy growth (WEG) can afford high-mobility thin films of disk-like organic semiconductor of which mobility is up to the level of the corresponding single crystals. We investigated the WEG behavior and mechanism of planar phthalocyanine in the model system of metal-free phthalocyanine (H2Pc) grown on p-sexiphenyl (p-6P) ultrathin films (monolayers and double layers). Highly oriented H2Pc films with molecules standing up exhibited two kinds of different in-plane orientations, i.e., three sets of in-plane orientations and only one set of in-plane orientation, on p-6P monolayer and double-layer films, respectively.

Well-defined higher-molecular-weight polyacrylonitrile via RAFT technique in the presence of disulfide compounds as a source of chain transfer agent

Well-defined polyacrylonitrile with a higher number-average molecular weight (R.) up to 200,000 and a lower polydispersity index (PDI, 1.7-2.0) was firstly obtained via reversible addition-fragmentation chain transfer (RAFT) process. This was achieved by selecting a stable, easy way to prepare disulfide compound intermediates including bis(thiobenzoyl) disulfide (BTBDS) and bis(thiophenylacetoyl) disulfide (BTPADS) to react with azobis(isobutyronitrile) to directly synthesize RAFT agents in situ.

Molecular Nanocluster with a [Sn4Ga4Zn2Se20](8-) T3 Supertetrahedral Core

A multinary molecular nanocluster, in which a T3 supertetrahedral [Sn4Ga4Zn2Se20](8-) core was neutralized and covalently terminated by four [(TEPA)Mn](2+) (TEPA = tetraethylenepentamine) metal complexes, was synthesized and characterized. The cluster is assembled into, through hydrogen bonding and van de Waals forces, a superlattice that is chemically stable and free of strong covalent coupling. The four different cations were distributed within the cluster in such a manner that both the local charge balance and global charge compensation by the metal complex could be satisfied.

Free-Radical Solution Copolymerization of the Ionic Liquid Monomer 1-Vinyl-3-Ethylimidazolium Bromide with Acrylonitrile

Ionic liquid monomer 1-vinyl-3-ethylimidazolium bromide (ViEtIM(+)Br(-)) was first used to copolymerize with acrylonitrile (AN) successfully under various conditions. This was achieved with azobisisobutyronitrile as the initiator and dimethyl sulfoxide as the solvent. The kinetics of this copolymerization were studied. The values of the monomer apparent reactivity ratios were calculated by the Kelen-Tudos method. The apparent reactivity ratios of ViEtIM(+)Br(-) (r(ViEtIM+Br-)) and AN (r(AN)) were similar at polymerization conversions of less than 10%, (r(AN) = 0.954, r(ViEtIM+Br-) = 0.976). The copolymers were obtained with high molecular weights and high hydrophilicides. The copolymers were characterized by H-1-NMR, differential scanning calorimetry, and thermogravimetric analysis. These copolymers may be potentially useful in the preparation of precursor fibers and carbon fibers.

Adaptive recognition of small molecules by nucleic acid aptamers through a label-free approach

We report a novel label-free method for the investigation of the adaptive recognition of small molecules by nucleic acid aptamers using capillary electrophoresis analysis. Cocaine and argininamide were chosen as model molecules, and the two corresponding DNA aptamers were used. These single-strand DNAs folded into their specific secondary structures, which were mainly responsible for the binding of the target molecules with high affinity and specificity. For molecular recognition, the nucleic acid structures then underwent additional conformational changes, while keeping the target molecules stabilized by intermolecular hydrogen bonds. The intrinsic chemical and physical properties of the target molecules enabled them to act as indicators for adaptive binding. Thus any labeling or modification of the aptamers or target molecules were made obsolete. This label-free method for aptamer-based molecular recognition was also successfully applied to biological fluids and therefore indicates that this approach is a promising tool for bioanalysis.

Investigation of the gel effect in reactive extrusion processes for free radical polymerization

The gel effect in the reactive extrusion process for free radical polymerization in a closely intermeshing co-rotating twin screw extruder was investigated. First the reaction kinetic model was constructed mainly on the basis of entanglement theory. Next, numerical calculation expressions for the initiator and monomer concentrations, monomer conversion, average molecular weight and apparent viscosity were deduced. Finally, the evolution of the above variables were shown and discussed for the example of butyl methacrylate. The simulated results of the monomer conversion are in good agreement with experimental results.