Probing the kinetics of single molecule protein folding

We propose an approach to integrate the theory, simulations, and experiments in protein-folding kinetics. This is realized by measuring the mean and high-order moments of the first-passage time and its associated distribution. The full kinetics is revealed in the current theoretical framework through these measurements. In the experiments, information about the statistical properties of first-passage times can be obtained from the kinetic folding trajectories of single molecule experiments ( for example, fluorescence). Theoretical/simulation and experimental approaches can be directly related. We study in particular the temperature-varying kinetics to probe the underlying structure of the folding energy landscape. At high temperatures, exponential kinetics is observed; there are multiple parallel kinetic paths leading to the native state. At intermediate temperatures, nonexponential kinetics appears, revealing the nature of the distribution of local traps on the landscape and, as a result, discrete kinetic paths emerge. At very low temperatures, exponential kinetics is again observed; the dynamics on the underlying landscape is dominated by a single barrier. The ratio between first-passage-time moments is proposed to be a good variable to quantitatively probe these kinetic changes. The temperature-dependent kinetics is consistent with the strange kinetics found in folding dynamics experiments. The potential applications of the current results to single-molecule protein folding are discussed.

The role of hydration on the mechanism of allosteric regulation: In situ measurements of the oxygen-linked kinetics of water binding to hemoglobin

We report here the first direct measurements of changes in protein hydration triggered by a functional binding. This task is achieved by weighing hemoglobin (Hb) and myoglobin films exposed to an atmosphere of 98%, relative humidity during oxygenation. The binding of the first oxygen molecules to Hb tetramer triggers a change in protein conformation, which increases binding affinity to the remaining empty sites giving rise to the appearance of cooperative phenomena. Although crystallographic data have evidenced that this structural change increases the protein water-accessible surface area, isobaric osmotic stress experiments in aqueous cosolutions have shown that water binding is linked to Hb oxygenation. Now we show that the differential hydration between fully oxygenated and fully deoxygenated states of these proteins, determined by weighing protein films with a quartz crystal microbalance, agree with the ones determined by osmotic stress in aqueous cosolutions, from the linkage between protein oxygen affinity and water activity. The agreements prove that the changes in water activity brought about by adding osmolytes to the buffer solution shift biochemical equilibrium in proportion to the number of water molecules associated with the reaction. The concomitant kinetics of oxygen and of water binding to Hb have been also determined. The data show that the binding of water molecules to the extra protein surface exposed on the transition from the low-affinity T to the high-affinity R conformations of hemoglobin is the rate-limiting step of Hb cooperative reaction. This evidences that water binding is a crucial step on the allosteric mechanism regulating cooperative interactions, and suggests the possibility that environmental water activity might be engaged in the kinetic control of some important reactions in vivo.

Antioxidant action of Rosemary extract in soybean oil submitted to thermoxidation

This work was aimed at evaluating the antioxidant activity of rosemary extract added to soybean oil in thermoxidation conditions. Purified soybean oil, refined soybean oil and refined soybean oil containing 1,000 mg/kg rosemary extract were heated at 180°C. The oxidation of the samples was evaluated after 0, 2.5, 5, 7.5 and 10 hours of thermoxidation by means of oxidative stability determination, total polar compounds and conjugated dienes. The purified oil differed significantly from the refined oil, mainly in relation to oxidative stability due the removal of the natural antioxidants. Rosemary extract presented antioxidant effects at high temperatures. After 10 hours of heating, 1,000 mg/kg rosemary extract added to the refined soybean oil significantly increased the oil oxidative stability from 7.52 to 13.5 hours and decreased the formation of polymers and decomposing products measured through the polar rates from 17.35 to 7.99%. The build up of primary oxidation products gauged through diene rates also decreased from 1.61 to 0.80%. Rosemary extract could be recommended as an alternative antioxidant.

Avaliação do uso de inóculos na biodigestão anaeróbia de resíduos de aves de postura, frangos de corte e suínos

Pós-graduação em Biotecnologia - IQ