The energy landscape theory has been an invaluable theoretical framework in the understanding of biological processes such as protein folding, oligomerization, and functional transitions. According to the theory, the energy landscape of protein folding is funneled toward the native state, a conformational state that is consistent with the principle of minimal frustration. It has been accepted that real proteins are selected through natural evolution, satisfying the minimum frustration criterion. However, there is evidence that a low degree of frustration accelerates folding. We examined the interplay between topological and energetic protein frustration. We employed a Cα structure-based model for simulations with a controlled nonspecific energetic frustration added to the potential energy function. Thermodynamics and kinetics of a group of 19 proteins are completely characterized as a function of increasing level of energetic frustration. We observed two well-separated groups of proteins: one group where a little frustration enhances folding rates to an optimal value and another where any energetic frustration slows down folding. Protein energetic frustration regimes and their mechanisms are explained by the role of non-native contact interactions in different folding scenarios. These findings strongly correlate with the protein free-energy folding barrier and the absolute contact order parameters. These computational results are corroborated by principal component analysis and partial least square techniques. One simple theoretical model is proposed as a useful tool for experimentalists to predict the limits of improvements in real proteins.
The performance of an anaerobic baffled reactor (ABR) was evaluated in the treatment of cassava wastewater, a pollutant residue. An ABR divided in four equal volume compartments (total volume 4L) and operated at 35ºC was used in cassava wastewater treatment. Feed tank chemical oxygen demand (COD) was varied from 2000 to 7000 mg L-1 and it was evaluated the most appropriated hydraulic retention time (HRT) for the best performance on COD removal. The ABR was evaluated by analysis of COD (colorimetric method), pH, turbidity, total and volatile solids, alkalinity and acidity. Principal component analysis (PCA) was carried to better understand data obtained. The system showed buffering ability as acidity decreased along compartments while alkalinity and pH values were increased. There was particulate material retention and COD removal varied from 83 to 92% for HRT of 3.5 days.
A study using two classification methods (SDA and SIMCA) was carried out in this work with the aim of investigating the relationship between the structure of flavonoid compounds and their free-radical-scavenging ability. In this work, we report the use of chemometric methods (SDA and SIMCA) able to select the most relevant variables (steric, electronic, and topological) responsible for this ability. The results obtained with the SDA and SIMCA methods agree perfectly with our previous model, in which we used other chemometric methods (PCA, HCA and KNN) and are also corroborated with experimental results from the literature. This is a strong indication of how reliable the selection of variables is.
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