Information and redundancy in the burial folding code of globular proteins within a wide range of shapes and sizes

Recent ab initio folding simulations for a limited number of small proteins have corroborated a previous suggestion that atomic burial information obtainable from sequence could be sufficient for tertiary structure determination when combined to sequence‐independent geometrical constraints. Here, we use simulations parameterized by native burials to investigate the required amount of information in a diverse set of globular proteins comprising different structural classes and a wide size range. Burial information is provided by a potential term pushing each atom towards one among a small number L of equiprobable concentric layers. An upper bound for the required information is provided by the minimal number of layers L^min still compatible with correct folding behavior. We obtain L^min between 3 and 5 for seven small to medium proteins with 50 ≤ N_r ≤ 110 residues while for a larger protein with N_r = 141 we find that L ≥ 6 is required to maintain native stability. We additionally estimate the usable redundancy for a given L ≥ L^min from the burial entropy associated to the largest folding‐compatible fraction of “superfluous” atoms, for which the burial term can be turned off or target layers can be chosen randomly. The estimated redundancy for small proteins with L = 4 is close to 0.8. Our results are consistent with the above‐average quality of burial predictions used in previous simulations and indicate that the fraction of approachable proteins could increase significantly with even a mild, plausible, improvement on sequence‐dependent burial prediction or on sequence‐independent constraints that augment the detectable redundancy during simulations. Proteins 2016; 84:515–531. © 2016 Wiley Periodicals, Inc.     

Can the modeling for simplification of a dental implant surface affect the accuracy of 3D finite element analysis?

The aim of this study was to assess stress/strain of different implant modeling simplifications by 3D-FEA. Three variation of external hexagon implant (Ø3.75?×?10 mm) supporting one molar crown were simulated: A (no threads); B (slightly threads simplification); C (original design). 200 N (axial) and 100 N (oblique) were applied. Cortical bone was evaluated by maximum principal stress and microstrain qualitatively and quantitatively (ANOVA and Tukey post hoc (p < 0.05)). Higher stress levels (p < 0.05) were observed in model A. Models B and C presented similar stress transmission. It was possible to conclude that slightly simplification should be used for studies evaluating stress transferring for bone tissue.     

Common dandelion: a review of its botanical,phytochemical and pharmacological profiles

Phytochemistry Reviews - Phytoalimurgy is a term that derives from Greek and Latin by combination of the words φυτόν, which meaning plant, and alimenta urgentia, indicating...     

Benzyl propionate synthesis by fed-batch esterification using commercial immobilized and lyophilized Cal B lipase

Bioprocess and Biosystems Engineering - In this work, a fed-batch approach was adopted to overcome propionic acid lipase inactivation effects in the benzyl propionate direct esterification mediated...     

Synthesis of a green polyurethane foam from a biopolyol obtained by enzymatic glycerolysis and its use for immobilization of lipase NS-40116

The use of green sources for materials synthesis has gained popularity in recent years. This work investigated the immobilization of lipase NS-40116 (Thermomyces lanuginosus lipase) in polyurethane foam (PUF) using a biopolyol obtained through the enzymatic glycerolysis between castor oil and glycerol, catalyzed by the commercial lipase Novozym 435 for the PUF formation. The reaction was performed to obtain biopolyol resulting in the conversion of 64% in mono- and diacylglycerol, promoting the efficient use of the reaction product as biopolyol to obtain polyurethane foam. The enzymatic derivative with immobilized lipase NS-40116 presented apparent density of 0.19 ± 0.03 g/cm³ and an immobilization yield was 94 ± 4%. Free and immobilized lipase NS-40116 were characterized in different solvents (methanol, ethanol, and propanol), temperatures (20, 40, 60 and 80 °C), pH (3, 5, 7, 9 and 11) and presence of ions Na⁺, Mg⁺⁺, and Ca⁺⁺. The support provided higher stability to the enzyme, mainly when subjected to acid pH (free lipase lost 80% of relative activity after 360 h of contact, when the enzymatic derivative lost around 22%) and high-temperature free lipase lost 50% of relative activity, while the immobilized remained 95%. The enzymatic derivative was also used for esterification reactions and conversions around 66% in fatty acid methyl esters, using abdominal chicken fat as feedstock, were obtained in the first use, maintaining this high conversion until the fourth reuse, proving that the support obtained using environmentally friendly techniques is applicable.

     

Efficacy of curcumin in the treatment of experimental vulvovaginal candidiasis

BackgroundCandida albicans is the main agent that causes vulvovaginal candidiasis. Resistance among isolates to azole antifungal agents has been reported.AimsDue to the well-known antifungal potential of curcumin, the purpose of this work was to evaluate the in vitro anticandidal activity of curcumin and its effect in the treatment of experimental vulvovaginal candidiasis.MethodsThe anticandidal activity of curcumin was investigated against eight Candida strains by the broth microdilution assay, and its mechanism of action was evaluated by testing the binding to ergosterol. Then, the effect of curcumin in the treatment of vulvovaginal candidiasis was evaluated in an immunosuppressed, estrogen treated rat model.ResultsCurcumin showed minimum inhibitory concentration values of 125–1000 μg/ml, and the best result was observed against Candida glabrata. The compound was shown to be able to bind to the ergosterol present in the membrane, event that may be the mechanism of action. In addition, in the in vivo model of vulvovaginal candidiasis with C. albicans, treatments reduced the vaginal fungal burden in infected rats after seven days of treatment with different doses.ConclusionsCurcumin could be considered a promising effective antifungal agent in the treatment of vulvovaginal candidiasis.     

Smart process development: Application of machine-learning and integrated process modeling for inclusion body purification processes

The development of a biopharmaceutical production process usually occurs sequentially, and tedious optimization of each individual unit operation is very time-consuming. Here, the conditions established as optimal for one-step serve as input for the following step. Yet, this strategy does not consider potential interactions between a priori distant process steps and therefore cannot guarantee for optimal overall process performance. To overcome these limitations, we established a smart approach to develop and utilize integrated process models using machine learning techniques and genetic algorithms. We evaluated the application of the data-driven models to explore potential efficiency increases and compared them to a conventional development approach for one of our development products. First, we developed a data-driven integrated process model using gradient boosting machines and Gaussian processes as machine learning techniques and a genetic algorithm as recommendation engine for two downstream unit operations, namely solubilization and refolding. Through projection of the results into our large-scale facility, we predicted a twofold increase in productivity. Second, we extended the model to a three-step model by including the capture chromatography. Here, depending on the selected baseline-process chosen for comparison, we obtained between 50% and 100% increase in productivity. These data show the successful application of machine learning techniques and optimization algorithms for downstream process development. Finally, our results highlight the importance of considering integrated process models for the whole process chain, including all unit operations.     

Does the local availability of woody Caatinga plants (Northeastern Brazil) explain their use value?

This study investigated the use of woody plants by a rural community in an area of dry land Caatinga vegetation in northeastern Brazil. Information was obtained concerning this woody species with a diameter that is equal to or greater than 3 centimeters (cm) at soil level surveyed in 100 sample plots totaling 1 hectare (ha). The following question is the hypothesis we tested. Is a plant’s relative importance (as measured by its use value) related to its “apparency,” as measured by its abundance and ecological dominance? “Apparency” explains the use value of plants in four categories: medicinal, construction, fuel, and technology. The most important uses of woody plants are related to harvesting for energy and construction purposes.