Fluorescence-quenched solid phase combinatorial libraries in the characterization of cysteine protease substrate specificity

To map the substrate specificity of cysteine proteases, two combinatorial peptide libraries were synthesized and screened using the archetypal protease, papain. The use of PEGA resin as the solid support for library synthesis facilitated the application of an on-resin fluorescence-quenched assay. Results from the screening of library 2 indicated a preference for Pro or Val in the S3 subsite and hydrophobic residues in S2; the most prevalent residue not being Phe but Val. The S1 subsite exhibited a dual specificity for both small, nonpolar residues, Ala or Gly, as well as larger, Gln, and charged residues, Arg. Small residues predominated in the S1'-S4' subsites. Active peptides from the libraries and variations thereof were resynthesized and their kinetics of hydrolysis by papain assessed in solution phase assays. Generally, there was a good correlation between the extent of substrate cleavage on solid phase and the kcat/KM's obtained in solution phase assays. Several good substrates for papain were obtained, the best substrates being Y(NO2)PMPPLCTSMK(Abz) (kcat/KM = 2109 (mM s)-1), Y(NO2)PYAVQSPQK(Abz) (kcat/KM = 1524 (mM s)-1), and Y(NO2)PVLRQQRSK(Abz) (kcat/KM = 1450 (mM s)-1). These results were interpreted in structural terms by the use of molecular dynamics (MD). These MD calculations indicated two different modes for the binding of substrates in the narrow enzyme cleft.     

Synchronization of simplest two-component Hartley’s chaotic circuits: influence of channel

Firstly, the synchronization problem of the simplest two-component Hartley chaotic systems is considered. A simple and effective controller is used to achieve synchronization between the drive and response systems. The proposed controller is built around a linear and a nonlinear parts with each contributing to the achievement of the synchronization process. The stability of the drive–response systems framework is proved through the Lyapunov stability theory. Secondly, the impact of channel on the signal coming from the drive system to synchronize the response system is taken into consideration. In this second part, the conditions to obtain synchronization between both master and slave systems are investigated. For the purpose of illustration, PSpice simulations are given as complement of the numerical analysis.     

Application of entropies to the study of the decoherence of magnetopolaron in 0-D nanosystem

Many methods have been experimented to study decoherence in quantum dot (QD). Tsallis, Shannon and Gaussian entropy have been used to study decoherence separately; in this paper, we compared the results of the Gaussian, Shannon, and Tsallis entropies in 0-D nanosystem. The linear combination operator and the unitary transformation was used to derive the magnetopolaron spectrum that strongly interacts with the LO phonons in the presence of an electric field in the pseudoharmonic and delta quantum dot. Numerical results revealed for the quantum pseudo dot that: (i) the amplitude of Gauss entropy is greater than the amplitude of Tsallis entropy which in turn is greater than the amplitude of Shannon entropy. The Tsallis entropy is not more significant in nanosystem compared to Shannon and Gauss entropies, (ii) with an increase of the zero point, the dominance of the Gauss entropy on the Shannon entropy was observed on one hand and the dominance of the Shannon entropy on the Tsallis entropy on the other hand; this suggested that in nanosystem, Gauss entropy is more suitable in the evaluation of the average of information in the system, for the delta quantum dot it was observed that (iii) when the Gauss entropy is considered, a lot of information about the system is missed. The collapse revival phenomenon in Shannon entropy was observed in RbCl and GaAs delta quantum dot with the enhancement of delta parameter; with an increase in this parameter, the system in the case of CsI evolved coherently; with Shannon and Tsallis entropies, information in the system is faster and coherently exchanged; (iv) the Shannon entropy is more significant because its amplitude outweighs the others when the delta dimension length enhances. The Tsallis entropy involves as wave bundle; which oscillate periodically with an increase of the oscillation period when delta dimension length is improved.     

Hartley’s oscillator: The simplest chaotic two-component circuit

This paper shows an experimental evidence of chaos in one of the simplest imaginable autonomous implicit Hartley’s oscillator made simply of a junction field effect transistor (JFET) and a tapped coil. The experimental setup is implemented. The variations of amplitude of the oscillations through the control element are obtained showing the domain of existence of chaos. Phase portraits of the PSpice simulation, of the numerical integration and of the experiment are displayed, confirming a good agreement between theory and praxis.     

Fast topological analysis of 2D and 3D grids of data: application to the atoms in molecule (AIM) and the electron localization function (ELF)

The topological analysis of grids of data is used for determination of surfaces or volumes around maxima. The volumes are then related to chemical information such as atoms or bonds, and can be used for integration of local properties such as electronic population. The problem of global connectivity is reversed into the question of local connectivity yielding a linear scaling partition algorithm. Two packages are developed for a very fast analysis and partition of 2D or 3D grids of data, applications being made to C2H2, C2H4, C6H6, H2CO, and H2CS molecules using the Atoms in Molecule (AIM) or Electron Localization Function (ELF).     

High-speed spectroscopic imaging for cancellous bone marrow R(2)* mapping and lipid quantification

In this work an interleaved multiple-gradient-echo chemical shift imaging (IMGE-CSI) technique was designed, implemented and evaluated at 1.5 and 4T for high-resolution lipid quantification and R(2)* measurement in-vivo. The method is analogous to echo planar CSI but utilizes conventional gradient echoes, exploiting the principle of spectroscopic bandwidth extension by interleaving temporally offset gradient-echo trains. It is shown that IMGE-CSI is able to measure true fat volume fraction in oil/water mixtures with high accuracy, not possible with Dixon-type methods which approximate the spectrum as consisting of only two spectral components. Correlation of the CSI- derived volume fractions with volumetry afforded r(2) > 0.99 with a slope of 0.98. The method is shown to be able to quantify regional variations in bone marrow composition in vivo with a spatial resolution of 2.5 x 2.5 x 5 mm(3.) R(2)* was obtained by multi-line spectral curve fitting. For the measurement of R(2)* in cancellous bone marrow the method is shown to agree well with time-domain fitting techniques but is superior in instances where the marrow has both hematopoietic and fatty constituents. Finally, excellent inter-scan reproducibility (1% coefficient of variation for global means and medians) was achieved, yielding r(2) = 0.98 of the test-retest correlation for three scans in four test subjects. In conclusion, IMGE-CSI is found to enable highly accurate lipid quantification and measurement of cancellous bone marrow R(2)* at spatial resolutions and scan times typical of standard clinical protocols.     

Unusual open chain quinolinyl peroxol and its alcohol counterpart obtained through a modified Skraup–Doebner–Von Miller quinoline synthesis: theoretical studies and complete 1H‐ and 13C‐NMR assignments

Because of their extreme instability, it is generally difficult to synthesize and fully characterize open chain peroxides, also known as peroxols. In our attempt to investigate the mechanism of the Skraup–Doebner–Von Miller quinoline synthesis, we were able to obtain an unusual open chain peroxy‐quinoline, namely, 4‐(8‐ethoxy‐2,3‐dihydro‐1H‐cyclopenta[c]quinolin‐4‐yl)butane‐1‐peroxol (1), and its alcohol counterpart, namely 4‐(8‐ethoxy‐2,3‐dihydro‐1H‐cyclopenta[c]quinolin‐4‐yl)butan‐1‐ol (2) obtained as a side product during the same reaction. Although structurally similar, these two compounds appeared to display some very distinct physical and spectroscopic characteristics. This work reports detailed NMR studies and full ¹H and ¹³ C NMR assignments for these two compounds. These assignments are based upon the analysis of the NMR spectra of these compounds including ¹H, ¹³ C, COSY, gHSQC and gHMBC. The effect of the peroxide functional group on the chemical shift of neighboring carbons and protons was also investigated by comparing the NMR data of these two compounds. Furthermore, the effects of potential hydrogen bondings in 1, 2, and possible 1–1 dimer, 2–2 dimer and in prototypical model systems, as well as the stability of these compounds, were investigated computationally. The computed dissociation energies and NMR data support the interpretation of the experimental data. Copyright © 2012 John Wiley & Sons, Ltd.