PTML modeling for peptide discovery: in silico design of non-hemolytic peptides with antihypertensive activity

Molecular Diversity - Hypertension is a medical condition that affects millions of people worldwide. Despite the high efficacy of the current antihypertensive drugs, they are associated with...     

A non-isothermal Ginzburg–Landau model in superconductivity: Existence,uniqueness and asymptotic behaviour

In this paper we study a Ginzburg–Landau model which describes the behaviour of a superconducting material including thermal effects. We extend the traditional formulation of the problem, by introducing the temperature as an additional state variable. Accordingly, together with the Gor’kov–Eliashberg system, we introduce an evolution equation for the absolute temperature. We examine in detail the case which allows only variations of the concentration of superconducting electrons and of the temperature, neglecting the electromagnetic field. For this problem existence and uniqueness of the solution are shown. Finally we analyze the asymptotic behaviour of the solutions, proving that the system possesses a global attractor.     

A novel approach based on recurrent neural networks applied to nonlinear systems optimization

This paper presents an efficient approach based on recurrent neural network for solving nonlinear optimization. More specifically, a modified Hopfield network is developed and its internal parameters are computed using the valid subspace technique. These parameters guarantee the convergence of the network to the equilibrium points that represent an optimal feasible solution. The main advantage of the developed network is that it treats optimization and constraint terms in different stages with no interference with each other. Moreover, the proposed approach does not require specification of penalty and weighting parameters for its initialization. A study of the modified Hopfield model is also developed to analyze its stability and convergence. Simulation results are provided to demonstrate the performance of the proposed neural network.     

Electrochemical determination of minoxidil in different pharmaceutical formulations by flow injection analysis.

The electrochemical behavior and amperometric-FIA quantification of minoxidil at a glassy carbon electrode is described. The procedure is based on electrochemical oxidation at 0.800 V (vs. Ag/AgCl/NaCl(3 M) in a phosphate buffer solution. Minoxidil was determined over the range 1 x 10(-7) - 1 x 10(-4) M. Different analytical parameters and electrode stability were analyzed to obtain the best electrode performance. The optimal conditions were: working potentials, 0.800 V; flow rate, 0.74 mL min(-1); and solution pH 7.0. This system allowed a sampling rate of 120 samples per hour without any pretreatment. The proposed method was used for minoxidil quantification in pharmaceutical preparations with satisfactory results. The accuracy of FIA-amperometric method was established by a comparison with the conventional UV determination technique using a paired t-test indicating the absence of systematic errors.     

Nanophase segregation and water dynamics in the dendrion diblock copolymer formed from the Fréchet polyaryl ethereal dendrimer and linear PTFE

We propose a new material consisting of a dendrion copolymer formed from (a) a water-soluble dendritic polymer and (b) a hydrophobic backbone. Using molecular dynamics simulations techniques, we determine the structure and dynamics of the dendrion formed by second-generation Fréchet polyaryl ethereal dendrimer as the hydrophilic component and linear polytetrafluoroethylene (PTFE) as the hydrophobic polymer, with 5 and 10 wt % of water. We find that this material produces a well-developed nanoscale structure in which water forms a continuous nanophase, making this new family of compounds promising candidates for applications in fuel cell membranes. We find that the water molecules are incorporated into the dendrimer block of the copolymer to form a nanophase-segregated structure. The well-developed nanophase-segregated structures rendered by this material have characteristic dimensions of segregation ( approximately 30 Angstrom) and dendrimer conformational properties that are independent of water content. Calculations of water dynamics and proton transport in these nanophase-segregated structures indicate that the dendrion copolymer membrane with 10 wt % of water content has a water structure and transport properties equivalent to that of the hydrated Nafion membrane with 20 wt % of water content.     

Stereospecific uncatalyzed alpha-O-glycosylation and alpha-C-glycosidation by means of a new D-Gulal-derived alpha vinyl oxirane

The reaction of alpha vinyl oxirane 5, prepared through a new route to the d-gulal system, with O-nucleophiles (alcohols and di-O-isopropylidene-alpha-d-monosaccharides) and C-nucleophiles (lithium alkyls) affords, in a completely stereoselective way, the corresponding 2-unsaturated alpha O- and C-glycosides having the same configuration as the starting epoxide.     

Photoaffinity labeling of bovine rhodopsin

Photoaffinity labeled (3-diazoacetoxy)-9-cis-retinal (1) and (9-methylenediazoacetoxy)-9-cis-retinal (20) were synthesized and bound to absorption maxima at 465 and 460 nm respectively. Binding studies established that synthetic retinals 1 and 2 bind to the natural binding site and that the integrity of the diazoacetoxy photoaffinity label is preserved in the process. Incorporation of 3-(O¹⁴COCHN₂)-labeled 9-cis retinal could be conveniently carried out in high yield using apomembrane solubilized in CHAPS as detergent to afford the pigment analog in a pure form. Photolysis of the diazoacetoxy group within the binding site led to 15–20%, crosslinking of rhodopsin as estimated by using radiocarbon containing labeled retinal 1 thus showing that this synthetic retinal is suitable for photoaffinity labeling of the active site in rhodopsin. Subsequent experiments to establish the site(s) of crosslinking by sequencing studies will then contribute to our knowledge of the structure of rhodopsin.     

Catalysis of the beta-elimination of HF from isomeric 2-fluoroethylpyridines and 1-methyl-2-fluoroethylpyridinium salts. Proton-activating factors and methyl-activating factors as a mechanistic test to distinguish between concerted E2 and E1cb irreversible mechanisms

Second-order rate constants, k(OH)(N), M(-)(1) s(-)(1), for the beta-elimination reactions of HF with 2-(2-fluoroethyl)pyridine (2), 3-(2-fluoroethyl)pyridine (3), and 4-(2-fluoroethyl)pyridine (4) in OH(-)/H(2)O, at 50 degrees C and mu = 1 M KCl, are = 0.646 x 10(-)(4) M(-)(1) s(-)(1), = 2.97 x 10(-)(6) M(-)(1) s(-)(1), and = 5.28 x 10(-)(4) M(-)(1) s(-)(1), respectively. When compared with the second-order rate constants for the same processes with the nitrogen-methylated substrates 1-methyl-2-(2-fluoroethyl)pyridinium iodide (5), 1-methyl-3-(2-fluoroethyl)pyridinium iodide (6), and 1-methyl-4-(2-fluoroethyl)pyridinium iodide (7), the methyl-activating factor (MethylAF) can be calculated from the ratio k(OH)(NCH)3/, and a value of 8.7 x 10(5) is obtained with substrates 5/2, a value of 1.6 x 10(3) with 6/3, and a value of 2.1 x 10(4) with 7/4. The high values of MethylAF are in agreement with an irreversible E1cb mechanism (A(N)D(E) + D(N)) for substrates 5 and 7 and with the high stability of the intermediate carbanion related to its enamine-type structure. In acetohydroxamate/acetohydroxamic acid buffers (pH 8.45-9.42) and acetate/acetic acid buffers (pH 4.13-5.13), the beta-elimination reactions of HF, with substrates 2 and 4, occur at NH(+), the substrates protonated at the nitrogen atom of the pyridine ring, even when the [NH(+)] is much lower than the [N], the unprotonated substrate, due to the high proton-activating factor (PAF) value observed: 3.6 x 10(5) for 2 and 6.5 x 10(4) for 4 with acetohydroxamate base. These high PAF values are indicative of an irreversible E1cb mechanism rather than a concerted E2 (A(N)D(E)D(N)) mechanism. Finally, the rate constant for carbanion formation from NH(+) with 2 is k(B)(NH)+ = 0.35 M(-)(1) s(-)(1), which is lower than when chlorine is the leaving group ( = 1.05 M(-)(1) s(-)(1); Alunni, S.; Busti, A. J. Chem. Soc., Perkin Trans. 2 2001, 778). This is direct experimental evidence that some lengthening of the carbon-leaving group bond can occur in the intermediate carbanion. This is a point of interest for interpreting a heavy-atom isotope effect.     

Nature of plant stimulators in the production ofAcetobacter xylinum (“tea fungus”) biofilm used in skin therapy

Caffeine and related xanthines were identified as potent stimulators for the bacterial cellulose production in A. xylinum. These compounds are present in several plants whose infusions are useful as culture-medium supplements for this acetobacterium.

The proposed target for these native purine-like inhibitory substances is the novel diguanyl nucleotide phosphodiesterase(s) that participate(s) in the bacterial cellulogenic complex.

A better understanding of this feature of A. xylinum physiology may facilitate the preparation of bacterial cellulose pellicles, which are applied as a biotechnological tool in the treatment of skin burns and other dermal injuries.

     

THE 'OPSIN SHIFT' IN BACTERIORHODOPSIN: STUDIES WITH ARTIFICIAL BACTERIORHODOPSINS

Abstract— The difference (in cm⁻¹) in absorption maxima between the protonated Schiff base of retinals and the pigment derived therefrom has been defined as the opsin shift. It represents the influence of the opsin binding site on the chromophore. The analysis of the opsin shifts of a series of dihydrobacteriorhodopsins has led to the external point-charge model, which in addition to a counter anion near the Schiff base ammonium, carries another negative charge in the vicinity of the β-ionone ring. This is in striking contrast to the external point-charge model proposed earlier for the bovine visual pigment. The absorption maxima of rhodopsins formed from bromo- and phenyl retinals support the two models. A retinal carrying a photoaffinity label has yielded a nonbleachable bacteriorhodopsin.