Molecular motions in amorphous ibuprofen as studied by broadband dielectric spectroscopy

The molecular mobility of amorphous ibuprofen has been investigated by broadband dielectric relaxation spectroscopy (DRS) covering a temperature range of more than 200 K. Four different relaxation processes, labeled as alpha, beta, gamma, and D, were detected and characterized, and a complete relaxation map was given for the first time. The gamma-process has activation energy E a = 31 kJ.mol (-1), typical for local mobility. The weak beta-relaxation, observed in the glassy state as well as in the supercooled state was identified as the genuine Johari-Goldstein process. The temperature dependence of the relaxation time of the alpha-process (dynamic glass transition) does not obey a single VFTH law. Instead two VFTH regimes are observed separated by a crossover temperature, T B = 265 K. From the low temperature VFTH regime, a T g (diel) (tau =100 s) = 226 K was estimated, and a fragility or steepness index m = 93, was calculated showing that ibuprofen is a fragile glass former. The D-process has a Debye-like relaxation function but the temperature dependence of relaxation time also follows the VFTH behavior, with a Vogel temperature and a pre-exponential factor which seem to indicate that its dynamics is governed by the alpha-process. It has similar features as the Debye-type process observed in a variety of associating liquids, related to hydrogen bonding dynamics. The strong tendency of ibuprofen to form hydrogen bonded aggregates such as dimers and trimers either cyclic or linear which seems to control in particular the molecular mobility of ibuprofen was confirmed by IR spectroscopy, electrospray ionization mass spectrometry, and MD simulations.     

Redesign of protein domains using one-bead-one-compound combinatorial chemistry

A novel combinatorial strategy for the redesign of proteins based on the strength and specificity of intra- and interprotein interactions is described. The strategy has been used to redesign the hydrophobic core of the B domain of protein A. Using one-bead-one-compound combinatorial chemistry, 300 analogues of the C-terminal alpha-helix of the B domain, H3x, have been synthesized using a biocompatible resin and the HMFS linker, allowing the screening to occur while the peptides were bound to the resin. The screening was based on the ability of the H3x analogues to interact with the N-terminal helices of the B domain, H1-H2, and retain the native B domain activity, that is binding to IgG. Eight different analogues containing some nonconservative mutations were obtained from the library, the two most frequent of which, H3P1 and H3P2, were studied in detail. CD analysis revealed that the active analogues interact with H1-H2. To validate the redesign strategy the covalent modified domains H1-H2-H3P1 and H1-H2-H3P2 were synthesized and characterized. CD and NMR analysis revealed that they had a unique, stable, and well-defined three-dimensional structure similar to that for the wild-type B domain. This combinatorial strategy allows us to select for redesigned proteins with the desired activity or the desired physicochemical properties provided the right screening test is used. Furthermore, it is rich in potential for the chemical modification of proteins overcoming the drawbacks associated with the total synthesis of large protein domains.     

Histological approaches for high-quality imaging of zooplanktonic organisms

The investigation of the internal organization of zooplankton communities provides important information on the plankton biology with special interest for the study of ecological processes. Zooplanktoners can play a structural function as indicators for ecosystem health or stress, but their study using histological techniques is still limited. Here we report that the internal structure of zooplanktonic organisms can be facilely observed by a histological approach that combines optimal fixation and processing with a plastic resin (glycol methacrylate) embedding, resulting in increased tissue resolution. Using copepods, organisms that can dominate zooplankton assemblages, as models, collected from a tropical ecosystem (Paraibuna river, Brazil), we showed fine histological details of their muscular, nervous and digestive systems, structure of appendages and cell features. Critical advantages of this approach are that it permits optimal preservation and adequate handling of the organisms (embedded in agar after fixation) for further histological processing and investigation. This is important because it prevents both mechanically induced artifacts and loss of these diminutive organisms during the different steps of processing. Moreover, embedding in plastic resin showed a superior imaging of copepod internal structures compared to paraffin embedding. The use of glycol methacrylate is advantageous over paraffin/paraplast embedding by avoiding heat damage, tissue retraction and allowing faster embedding procedure and better tissue resolution. The value of histological approaches in enabling high-quality imaging of the internal structure of copepods is particularly important because these organisms can be used as indicators of environmental changes.     

A novel antinociceptive sulphated polysaccharide of the brown marine alga Spatoglossum schroederi

Sulfated polysaccharides (SP) of brown algae (Phaeophyta) are composed mainly of alpha- L-fucose, being classified as fucans, with recognized role in inflammation but not in nociception, which was already described for SP obtained from red algae. Here the SP of the brown marine alga S. schroederi (named Ss-SP) was isolated and assayed for the antinociceptive effect. Ss-SP was isolated by DEAE-cellulose, analyzed by agarose gel electrophoresis and evaluated in nociception models (Formalin, Hot plate, Von Frey) using Swiss mice (20-25g). Anion exchange chromatography provided four major fractions being F1 (Ss-SP) that of highest metachromatic activity and sugar content. Ss-SP inhibited both phases of the formalin test. In the first phase the paw licking (55.2 +/- 8.07s) was reduced by 45% (30.5 +/- 6.51s) and 40% (32.85 +/- 8.66s) at 0.1 and 1 mg/kg, respectively. In the second phase, Ss-SP was also inhibitory about 39%, but only at 1 mg/kg (83.0 +/- 15.70s) compared to formalin (136.8 +/- 10.27s). This inhibitory effect suggests a mixed mechanism similar to morphine, which was not confirmed in the hot plate test, a model of pain associated with central neurotransmission. However, Ss-SP reduced the animal reaction in response to stimulation withVon Frey filament at the 2nd and 3rd h (20.8 +/- 6.86% versus carrageenan: 47.9 +/- 5.83%; 33.3 +/- 7.71% versus carrageenan: 62.5 +/- 9.83%). Accordingly, the paw edema induced by carrageenan (0.08 +/- 0.01g) was potently reduced in 45.35% by Ss-SP pre-treatment (0.02 +/- 0.003g), corroborating the anti-inflammatory activity demonstrated for brown seaweed polysaccharides. In conclusion our data revealed for the first time the antinociceptive effect of Ss-SP which could be used as a new source of analgesic substances.     

Molecular dynamics simulations of pregelification mixtures for the production of imprinted xerogels

A series of molecular dynamics (MD) simulations of different pregelification mixtures representing intermediate stages of the sol-gel process were set up to gain insight into the molecular imprinting process in xerogels, namely, to assess the template-gel affinity and template self-aggregation. The physical plausibility of the parametrization was checked, confirming the reliability of the simulations. The simulated mixtures differed in the water/methanol ratio (1:3, 5:3, and 5:1) and in the absence/presence of an organic functional group (phenylaminopropyl-) in the silicate species. The simulation results, expressed mainly by the radial distribution functions and respective coordination numbers, showed that the affinity of the template molecule, damascenone (a hydrophobic species), for the gel backbone would not be attained without the tested functional group, phenylaminopropyl-. The affinity, related to the capability to trap the template within the gel network, was derived mostly from the hydrophobic interaction. It was also inferred from MD simulations that lower water contents (methanol-richer mixtures) would facilitate a better dispersion of both the functional group and the template within the final gel, therefore favoring the imprinting process. From the experimental counterparts of the simulated mixtures, a series of imprinted and nonimprinted xerogels were obtained. There was only one xerogel exhibiting the imprinting effect, namely, the one containing the organic group obtained at the lower water/methanol ratio (1:3), in agreement with predictions from the MD simulations. Such congruence demonstrates the ability of MD simulations to provide information regarding the fine aspects of molecular interactions in pregelification mixtures for imprinting.     

Improving the study of proton transfers between amino acid side chains in solution: choosing appropriate DFT functionals and avoiding hidden pitfalls

We have studied the influence of implicit solvent models, inclusion of explicit water molecules, inclusion of vibrational effects, and density functionals on the quality of the predicted pK _a of small amino acid side chain models. We found that the inclusion of vibrational effects and explicit water molecules is crucial to improve the correlation between the computed and the experimental values. In these micro-solvated systems, the best agreement between DFT-computed electronic energies and benchmark values is afforded by BHHLYP and B97-2. However, approaching experimental results requires the addition of more than three explicit water molecules, which generates new problems related to the presence of multiple minima in the potential energy surface. It thus appears that a satisfactory ab initio prediction of amino acid side chain pK _a will require methods that sample the configurational space in the presence of large solvation shells, while at the same time computing vibrational contributions to the enthalpy and entropy of the system under study in all points of that surface. Pending development of efficient algorithms for those computations, we strongly suggest that whenever counterintuitive protonation states are found in a computational study (e.g., the presence of a neutral aspartate/neutral histidine dyad instead of a deprotonated aspartate/protonated histidine pair), the reaction profile should be computed under each of the different protonation micro-states by constraining the relevant N–H or O–H bonds, in order to avoid artifacts inherent to the complex nature of the factors contributing to the pK _a.     

The catalytic mechanism of mouse renin studied with QM/MM calculations

Hypertension is a chronic condition that affects nearly 25% of adults worldwide. As the Renin-Angiotensin-Aldosterone System is implicated in the control of blood pressure and body fluid homeostasis, its combined blockage is an attractive therapeutic strategy currently in use for the treatment of several cardiovascular conditions. We have performed QM/MM calculations to study the mouse renin catalytic mechanism in atomistic detail, using the N-terminal His6-Asn14 segment of angiotensinogen as substrate. The enzymatic reaction (hydrolysis of the peptidic bond between residues in the 10th and 11th positions) occurs through a general acid/base mechanism and, surprisingly, it is characterized by three mechanistic steps: it begins with the creation of a first very stable tetrahedral gem-diol intermediate, followed by protonation of the peptidic bond nitrogen, giving rise to a second intermediate. In a final step the peptidic bond is completely cleaved and both gem-diol hydroxyl protons are transferred to the catalytic dyad (Asp32 and Asp215). The final reaction products are two separate peptides with carboxylic acid and amine extremities. The activation energy for the formation of the gem-diol intermediate was calculated as 23.68 kcal mol(-1), whereas for the other steps the values were 15.51 kcal mol(-1) and 14.40 kcal mol(-1), respectively. The rate limiting states were the reactants and the first transition state. The associated barrier (23.68 kcal mol(-1)) is close to the experimental values for the angiotensinogen substrate (19.6 kcal mol(-1)). We have also tested the influence of the density functional on the activation and reaction energies. All eight density functionals tested (B3LYP, B3LYP-D3, X3LYP, M06, B1B95, BMK, mPWB1K and B2PLYP) gave very similar results.     

Density functional theory model study of size and structure effects on water dissociation by platinum nanoparticles

Size and structure effects on the homolytic water dissociation reaction mediated by Pt nanoparticles have been investigated through density functional theory calculations carried out on a series of cubooctahedral Pt(n) nanoparticles of increasing sizes (n = 13, 19, 38, 55, 79, and 140). Water adsorption energy is not significantly influenced by the nanoparticle size. However, activation energy barrier strongly depends on the particle size. In general, the activation energy barrier increases with nanoparticles size, varying from 0.30 eV for Pt(19) to 0.70 eV for Pt(140). For the largest particle the calculated barrier is very close to that predicted for water dissociation on Pt(111) (0.78 eV) even though the reaction mediated by the Pt nanoparticles involves adsorption sites not present on the extended surface.     

Identification of adequate vehicles to carry nerve regeneration inducers using tubulisation

ABSTRACT: BACKGROUND: Axonal regeneration depends on many factors, such as the type of injury and repair, age, distance from the cell body and distance of the denervated muscle, loss of surrounding tissue and the type of injured nerve. Experimental models use tubulisation with a silicone tube to research regenerative factors and substances to induce regeneration. Agarose, collagen and DMEM (Dulbecco's modified Eagle's medium) can be used as vehicles. In this study, we compared the ability of these vehicles to induce rat sciatic nerve regeneration with the intent of finding the least active or inert substance. The experiment used 47 female Wistar rats, which were divided into four experimental groups (agarose 4%, agarose 0.4%, collagen, DMEM) and one normal control group. The right sciatic nerve was exposed, and an incision was made that created a 10 mm gap between the distal and proximal stumps. A silicone tube was grafted onto each stump, and the tubes were filled with the respective media. After 70 days, the sciatic nerve was removed. We evaluated the formation of a regeneration cable, nerve fibre growth, and the functional viability of the regenerated fibres. RESULTS: Comparison among the three vehicles showed that 0.4% agarose gels had almost no effect on provoking the regeneration of peripheral nerves and that 4% agarose gels completely prevented fibre growth. The others substances were associated with profuse nerve fibre growth. CONCLUSIONS: In the appropriate concentration, agarose gel may be an important vehicle for testing factors that induce regeneration without interfering with nerve growth.