Simulations of nanocylinders self-assembled from cyclic β-tripeptides

This paper examines the self-assembly of cyclic β-tripeptides using density functional theory. On the basis of literature precedents, these cyclic peptides were expected to self-assemble into cylindrical structures by stacking through backbone-backbone hydrogen bonding. Our calculations show that such stacking is energetically favorable, that the association energy per cyclic peptide decreases (becomes more favorable), and that the overall macrodipole moment of the cylindrical assembly increases with the number of stacked rings, for up to eight rings. For a structure in which two peptide ring units are joined through a single side chain-side chain covalent linker, the association energy between the two rings is favorable, albeit less so than for the unlinked rings. Significantly, the association energy in the dimers is only weakly dependent on the length (above a certain minimum) and conformation of the covalent linkers. Finally, as a plausible route for controlling assembly/disassembly of nanocylinders, we show that, for a pair of rings, each bearing a single amino-functionalized side chain, protonation of the amino group results in a strongly positive (unfavorable) association energy between the two rings.     

PHOTOREACTIVATION OF LETHAL DAMAGE AND DAMAGE LEADING TO CHROMATID DELETIONS INDUCED IN G1 PHASE HAMSTER x Xenopus HYBRID CELLS BY UV

A86 Xenopus cells, cloned from a Xenopus line that exhibited a high level of photoreactivation of UV-induced lethal damage, and V79M1 hamster cells, cloned from a hamster line that did not exhibit efficient photoreactivation of such damage, were fused to produce the V79M1 x A86 cell line--a hybrid line in which approximately 84% of the cells contained the entire V79M1 and A86 genomes. Ultraviolet and UV plus photoreactivation fluence-survival relations were then determined and compared for hybrid and parental G1 phase cells in a first attempt to elucidate interactions of the parental genetic potentials for photoreactivation in the hybrid. Specifically, it was anticipated that the combined V79M1 and A86 genomes in the hybrid would produce photoreactivating enzymes sufficient to efficiently photoreactivate UV-induced lethal damage in both A86 and V79M1 DNA and little difference would be observed in the levels of photoreactivation exhibited by V79M1 x A86 and A86 G1 phase cells. To the contrary, the level of photoreactivation observed for the hybrid did not closely approach that observed for the A86 line. To assist in the interpretation of this somewhat unexpected observation, three additional studies were performed: (1) comparison of 'optimal' schemes for photoreactivation of UV-induced lethal damage in the hybrid and parental G1 phase cells, (2) comparison of the effects of some different types of growth medium on photoreactivation of UV-induced lethal damage in hybrid and parental G1 phase cells, and (3) comparison of the levels of photoreactivation of UV-induced chromatid deletions in the V79M1 and A86 chromosomes of G1 phase hybrid cells.(ABSTRACT TRUNCATED AT 250 WORDS)     

Structural informatics,modeling, and design with an open‐source Molecular Software Library (MSL)

We present the Molecular Software Library (MSL), a C++ library for molecular modeling. MSL is a set of tools that supports a large variety of algorithms for the design, modeling, and analysis of macromolecules. Among the main features supported by the library are methods for applying geometric transformations and alignments, the implementation of a rich set of energy functions, side chain optimization, backbone manipulation, calculation of solvent accessible surface area, and other tools. MSL has a number of unique features, such as the ability of storing alternative atomic coordinates (for modeling) and multiple amino acid identities at the same backbone position (for design). It has a straightforward mechanism for extending its energy functions and can work with any type of molecules. Although the code base is large, MSL was created with ease of developing in mind. It allows the rapid implementation of simple tasks while fully supporting the creation of complex applications. Some of the potentialities of the software are demonstrated here with examples that show how to program complex and essential modeling tasks with few lines of code. MSL is an ongoing and evolving project, with new features and improvements being introduced regularly, but it is mature and suitable for production and has been used in numerous protein modeling and design projects. MSL is open‐source software, freely downloadable at http://msl‐libraries.org . We propose it as a common platform for the development of new molecular algorithms and to promote the distribution, sharing, and reutilization of computational methods. © 2012 Wiley Periodicals, Inc.     

Microlaser-pumped periodically poled lithium niobate optical parametric generator-optical parametric amplifier

For what is believed to be the first time, a single-longitudinal-mode passively Q-switched Nd:YAG microlaser is used to pump a narrow-bandwidth periodically poled lithium niobate (PPLN) optical parametric generator-optical parametric amplifier (OPG-OPA). Before amplification in the OPA, the output of the OPG stage was spectrally filtered with an air-spaced etalon, resulting in spectroscopically useful radiation (bandwidth, ~0.05 cm(-1) FWHM) that was tunable in 15-cm(-1) segments anywhere in the signal range 6820-6220 cm(-1) and the idler range 2580-3180 cm(-1). The ability to pump an OPG-OPA with compact, high-repetition-rate, intrinsically narrow-bandwidth microlasers is made possible by the high gain of PPLN. The result is a tunable light source that is well suited for use in portable spectroscopic gas sensors.     

Miniaturization of sampling for chemical reaction monitoring by capillary electrophoresis

Purpose-made capillary electrophoresis set-ups for reaction kinetics monitoring featuring two automated injectors allowed the easy reduction of the needed reactant amount down to 500 microL. The first set-up is similar to the cross injector used frequently in lab-on-chip designs while the other uses falling droplets for sample/buffer delivery. The versatility of the system was demonstrated by the analysis of oxidation of C-vitamin by hydrogen peroxide. Pseudo first order reaction rates about 10(-3) s(-1) were measured with RSD = 1-3% in one experiment and RSD = 20% in interday/person experiment. Plate numbers were typically around 5000-20,000.     

Capillary electrophoresis with LED-induced native fluorescence detection for determination of isoquinoline alkaloids and their cytotoxicity in extracts of Chelidonium majus L

In this study, we introduced a simple and sensitive method of capillary electrophoresis with ultraviolet light-emitting diode-induced native fluorescence (UV-LEDIF) detection for the determination of isoquinoline alkaloids in extracts of Chelidonium majus L. Samples were extracted with acidic methanol and the extracts were directly analysed by CE. Simultaneous determination of protopine, chelidonine, coptisine, sanguinarine, allocryptopine, chelerythrine and stylopine was performed in 20mM phosphate buffer (pH 3.1). The baseline separation of these alkaloids was finished within 20 min. As these alkaloids have native fluorescence, they were directly detected using the commercially available UV light emitting diode without troublesome fluorescent derivatisation. Satisfactory LOD values were obtained for the studied compounds considering their appearance in natural extracts. Lower limits of detection were 0.05 μg/mL for protopine, 0.06 μg/mL for stylopine and allocryptopine, 0.07 μg/mL for chelidonine, 0.22 μg/mL for sanguinarine, 1.7 μg/mL for chelerythrine and 5.5 μg/mL for coptisine. The developed method was successfully applied to determine the contents of seven alkaloids in the aerial parts of Chelidonium majus L, which varied from 0.025 to 0.763% (w/w). Also, to demonstrate the potential of the proposed CE method, an estimation of the cytotoxic properties of selected Celandine alkaloids in a natural extract was carried out.     

The application of the transfer entropy to gappy time series

The application of the transfer entropy to gappy symbolic time series is discussed. Although the transfer entropy can fail to correctly identify the drive-response relationship, it is able to robustly detect phase relationships. Hence, it might still be of use in applications requiring the detection of changes in these relationships.