Configuration-dependent diffusion can shift the kinetic transition state and barrier height of protein folding

We show that diffusion can play an important role in protein-folding kinetics. We explicitly calculate the diffusion coefficient of protein folding in a lattice model. We found that diffusion typically is configuration- or reaction coordinate-dependent. The diffusion coefficient is found to be decreasing with respect to the progression of folding toward the native state, which is caused by the collapse to a compact state constraining the configurational space for exploration. The configuration- or position-dependent diffusion coefficient has a significant contribution to the kinetics in addition to the thermodynamic free-energy barrier. It effectively changes (increases in this case) the kinetic barrier height as well as the position of the corresponding transition state and therefore modifies the folding kinetic rates as well as the kinetic routes. The resulting folding time, by considering both kinetic diffusion and the thermodynamic folding free-energy profile, thus is slower than the estimation from the thermodynamic free-energy barrier with constant diffusion but is consistent with the results from kinetic simulations. The configuration- or coordinate-dependent diffusion is especially important with respect to fast folding, when there is a small or no free-energy barrier and kinetics is controlled by diffusion. Including the configurational dependence will challenge the transition state theory of protein folding. The classical transition state theory will have to be modified to be consistent. The more detailed folding mechanistic studies involving phi value analysis based on the classical transition state theory also will have to be modified quantitatively.

Fermi acceleration and its suppression in a time-dependent Lorentz gas

Some dynamical properties for a Lorentz gas were studied considering both static and time-dependent boundaries. For the static case, it was confirmed that the system has a chaotic component characterized with a positive Lyapunov exponent. For the time-dependent perturbation, the model was described using a four-dimensional nonlinear map. The behaviour of the average velocity is considered in two different situations: (i) non-dissipative and (ii) dissipative dynamics. Our results confirm that unlimited energy growth is observed for the non-dissipative case. However, and totally new for this model, when dissipation via inelastic collisions is introduced, the scenario changes and the unlimited energy growth is suppressed, thus leading to a phase transition from unlimited to limited energy growth. The behaviour of the average velocity is described using scaling arguments. (C) 2010 Elsevier B.V. All rights reserved.

Velocity-dependent KAM islands

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Structural changes of biocompatible neutral microemulsions stabilized by mixed surfactant containing soya phosphatidylcholine and their relationship with doxorubicin release

Depending on the composition, the mixture of surfactant, oil and water, may form supramolecular aggregates with different structures which can significantly influence the drug release. In this work several microemulsion (ME) systems containing soya phosphatidylcholine (SPC) and eumulgin HRE40 (TM) (EU) as surfactant, cholesterol (O) as oil phase, and ultra-pure water as an aqueous phase were studied. MEs with and without the antitumoral drug doxorubicin (DOX) were prepared. The microstructures of the systems were characterized by photon correlation spectroscopy, rheological behavior, polarized light microscopy, small-angle X-ray scattering (SAXS) and X-ray diffraction (XRD). The results reveal that the diameter of the oil droplets was dependent on the surfactant (S) amount added to formulations. The apparent viscosity was dependent on the O/S ratio. High O/S ratio leads to the crystallization of cholesterol polymorphs phases which restricts the mobility of the DOX molecules into the ME structure. Droplets with short-range spatial correlation were formed from the ME with the low O/S ratio. The increase of the cholesterol fraction in the O/S mixture leads to the formation of ordered structures with lamellar arrangements. These different structural organizations directly influenced the drug release profiles. The in vitro release assay showed that the increase of the O/S ratio in the formulations inhibited the constant rate of DOX release. Since the DOX release ratio was directly dependent on the ratio of O/S following an exponential decay profile, this feature can be used to control the DOX release from the ME formulations. (C) 2008 Elsevier B.V. All rights reserved.

Walker 256 tumour growth causes marked changes of glutamine metabolism in rat small intestine

The effect of Walker 256 tumour growth on the metabolism of glucose and glutamine in the small intestine of rats was examined. Walker 256 tumour has been extensively used as an experimental model to induce cancer cachexia in rats. Walker 256 tumour growth decreased body weight and small intestine weight and length. The activities of glucose-6-phosphate dehydrogenase and phosphate-dependent glutaminase were reduced in the proximal, median and distal portions of the intestine. Glutamine oxidation was reduced in the proximal portion only. The decrease in glutaminase activity was not due to a low synthesis of the protein as indicated by Western blotting analysis. Hexokinase and citrate synthase activities were not changed by the tumour. These findings led us to postulate that tumour growth impairs glutamine metabolism of small intestine but the mechanism involved remains to be elucidated. Copyright (C) 2001 John Wiley Sons, Ltd.

Temperature-dependent Raman spectra of K0.2Na0.8NbO3 ceramics

We performed temperature-dependent Raman scattering studies on K0.2Na0.8NbO3 ceramics and compared the results with those for NaNbO3. The wavenumbers associated with NbO6 vibrations suggest the existence of two phase transitions, as occurs with pure NaNbO3 ceramics. Although the disorder on the Na/K site does not change either the room temperature phase of K0.2Na0.8NbO3 or the sequence of phase transitions compared with NaNbO3, it changes the temperature of the lowest phase transition and strongly modifies the temperature of the antiferroelectric --> new phase II phase transition. Additionally, the linewidth analysis shows that the orientational mechanism is the dominant contribution to linewidth, although the anharmonic contribution is increased, when compared with NaNbO3, owing to the random distribution of potassium in the sodium niobate matrix. Copyright (C) 2004 John Wiley Sons, Ltd.

Holographic recording in [Sb(Po-3)(3)](n)-Sb2O3 glassy films by photoinduced volume and refraction index changes

Glassy films of 0.2[Sb(PO3)(3)]-0,8Sb(2)O(3) with 0.8 mum-thickness were deposited on quartz substrates by electron beam evaporation. A contraction in the film thickness (photoinduced decrease in volume) and photobleaching effect associated with a decrease of up to 25% in the index of refraction has been observed in the films after irradiation near the bandgap (3.89 eV), using the 350.7 nm (3.54 eV) Kr+ ion laser line with 2.5 W/cm(2) for 30 min. A loss of 30% in the phosphorus concentration was measured by wavelength dispersive X-ray microanalysis in the film after laser irradiation with 5.0 W/cm(2) for 1.0 h. These photoinduced changes in the samples are dependent on the power density and intensity profile of the laser beam. Using a Lloyd's mirror setup for continuous wave holography it was possible to record holographic gratings with period from 500 nm up to 20 mum and depth profile of similar to50 nm in the films after laser irradiation with 5.0 W/cm(2) for 1 h. Real-time diffraction efficiency measurements have shown that ultraviolet irradiation induces first a refractive index grating formation, and after this, the photocon traction effect takes place generating an irreversible relief grating. Diffraction efficiency up to 10% was achieved for the recorded gratings. 3D-refraction index measurements and atomic force microscopy images are presented. (C) 2004 Elsevier B.V. All rights reserved.

Reduced Insulin Secretion in Protein Malnourished Mice Is Associated with Multiple Changes in the beta-Cell Stimulus-Secretion Coupling

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Circadian time-dependent effects of fencamfamine on inhibition of dopamine uptake and release in rat striatal slices

Fencamfamine (FCF) is a central stimulant that facilitates central dopaminergic transmission through inhibition of dopamine uptake and enhanced release of the transmitter. We evaluated the changes in the inhibition of uptake and the release of striatal [ 3H]-dopamine at 9:00 and 21:00 h, times corresponding to maximal and minimal behavioral responses to FCF, respectively. Adult male Wistar rats (200-250 g) maintained on a 12-h light/12-h dark cycle (lights on at 7:00 h) were used. In the behavioral experiments the rats (N = 8 for each group) received FCF (3.5 mg/kg, ip) or saline at 9:00 or 21:00 h. Fifteen minutes after treatment the duration of activity (sniffing, rearing and locomotion) was recorded for 120 min. The basal motor activity was higher (28.6 ± 4.2 vs 8.4 ± 3.5 s) after saline administration at 21:00 h than at 9:00 h. FCF at a single dose significantly enhanced the basal motor activity (38.3 ± 4.5 vs 8.4 ± 3.5 s) and increased the duration of exploratory activity (38.3 ± 4.5 vs 32.1 ± 4.6 s) during the light, but not the dark phase. Two other groups of rats (N = 6 for each group) were decapitated at 9:00 and 21:00 h and striata were dissected for dopamine uptake and relase assays. The inhibition of uptake and release of [ 3H]-dopamine were higher at 9:00 than at 21:00 h, suggesting that uptake inhibition and the release properties of FCF undergo daily variation. These data suggest that the circadian time-dependent effects of FCF might be related to a higher susceptibility of dopamine presynaptic terminals to the action of FCF during the light phase which corresponds to the rats' resting period.

Double optical monitoring of time-dependent film formation

A brief overview of optical monitoring for vacuum and wet bench film deposition processes is presented. Interferometric and polarimetric measurements are combined with regard to simultaneous real-time monitoring of refractive index and physical thickness. Monitor stability and accuracy are verified with transparent oil standards. This double optical technique is applied to dip coating with a multi-component Zirconyl Chloride aqueous solution, whose time varying refractive index and physical thickness curves indicate significant sensitivity to changes of film flow properties during the process.

Hypertrophied myocardium is more dependent on extracellular calcium than the normal cardiac muscle

Background: The aim of this study was to analyze stable hypertrophied myocardial function and its response to inotropic maneuvers in rats submitted to renovascular hypertension for a 10-week period (RHT group, n=10). Material/Methods: Myocardial performance was studied in isolated left ventricle papillary muscles in isometric contraction under the following conditions: at postrest contraction of 30 seconds (PRC), at extracellular calcium (ECa 2+) chloride concentration of 1.25 and 5.20 mM, and after beta-adrenergic stimulation with 10 -6 M isoproterenol (ISOP). Results: The results were compared with normotensive Wistar controls rats (C group, n=10). In basal condition, resting tension, and contraction time (TPT) were greater, while relaxation time (RT 50) tended to be longer in RHT than C group. PRC and ISOP promoted a similar change in muscle function response intensity (Δ) in both groups. ECa 2+ shift did not change TPT in the C group and decreased TPT in the RHT animals; Δ was different between these groups. RT 50 increased in C and decreased in RHT, both without statistical significance; however, Δ was different. Conclusions: These results suggest that hypertrophied myocardial dysfunction may be attibuted to changes in intracellular calcium cycling. © Med Sci Monit, 2010.

Cooperative RNA Polymerase Molecules Behavior on a Stochastic Sequence-Dependent Model for Transcription Elongation

The transcription process is crucial to life and the enzyme RNA polymerase (RNAP) is the major component of the transcription machinery. The development of single-molecule techniques, such as magnetic and optical tweezers, atomic-force microscopy and single-molecule fluorescence, increased our understanding of the transcription process and complements traditional biochemical studies. Based on these studies, theoretical models have been proposed to explain and predict the kinetics of the RNAP during the polymerization, highlighting the results achieved by models based on the thermodynamic stability of the transcription elongation complex. However, experiments showed that if more than one RNAP initiates from the same promoter, the transcription behavior slightly changes and new phenomenona are observed. We proposed and implemented a theoretical model that considers collisions between RNAPs and predicts their cooperative behavior during multi-round transcription generalizing the Bai et al. stochastic sequence-dependent model. In our approach, collisions between elongating enzymes modify their transcription rate values. We performed the simulations in Mathematica® and compared the results of the single and the multiple-molecule transcription with experimental results and other theoretical models. Our multi-round approach can recover several expected behaviors, showing that the transcription process for the studied sequences can be accelerated up to 48% when collisions are allowed: the dwell times on pause sites are reduced as well as the distance that the RNAPs backtracked from backtracking sites. © 2013 Costa et al.

Responses of aquatic insect functional diversity to landscape changes in Atlantic forest

The Atlantic Forest domain, one of the 25 world's hotspots for biodiversity, has experienced dramatic changes in its landscape. While the loss of species diversity is well documented, functional diversity has not received the same amount of attention. In this study, we evaluated functional diversity of insects in streams utilizing three indices: functional diversity (FD), functional dispersion (FDis), and functional divergence (FDiv), seeking to understand the roles of three predictor sets in explaining functional patterns: (1) bioclimatic and landscape variables; (2) spatial variables; and (3) local environmental variables. We determined the amount of variation in different measures of functional diversity that was explained by each predictor set and their interplays using variation partitioning. Our study showed that variation in functional diversity is better explained by a set of variables linked to different scales dependent on spatial structures, indicating the importance of landscape and mainly environmental variables in the functional organization of aquatic insect communities, and that the relative importance of predictor sets depends on the indices considered. Variation in FD was better explained by the interplay among the three predictor sets and by local environmental variables, whereas variation in FDis was better explained by spatial variables and by the interplay between environmental and spatial variables. Variation in FDiv was not significantly explained by any predictors. Our study adds more evidence on the harmful effects caused by landscape changes on biodiversity in the Atlantic Forest, suggesting that these effects also influence the functional organization of stream insect communities. © 2013 The Author(s) Journal compilation © 2013 by The Association for Tropical Biology and Conservation.

Dose-Dependent Effects and Reversibility of the Injuries Caused by Nandrolone Decanoate in Uterine Tissue and Fertility of Rats

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Changes in the synganglion of Rhipicephalus sanguineus (Latreille,. 1806) (Acari: Ixodidae) female ticks exposed to permethrin: An ultrastructural overview

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)