Research on climate-driven variability in the water and energy sectors is required to drive adaptative policies to climate change and boost cross-sectorial synergies. This study addresses the role of ...the North Atlantic Oscillation (NAO) and East Atlantic pattern (EA) on the water-energy nexus in southern Portugal (Algarve region) from the point of view of water demand, instead of the usual point of view of hydropower production. Water at surface reservoirs and aquifers and solar and wind energy potentials (SP and WP, respectively) do not share the same dominant variability scales, but their interrelationships have implications for leveraging the use of renewable energy in the water sector, particularly through water pumping efficiency gains. Water availability is dominated by interannual fluctuations (70% of the total variance), whereas SP and WP are characterized by seasonal variability scales (98% and 41% of the total variance, respectively). At interannual scales NAO is the main driver of low-frequency variability governing cycles in the 6–8 -year band, whereas fluctuations in the 2–4 -year band are mainly associated with EA. Coupling or synchronizations between opposite phases of NAO and EA correspond to extremes in water availability. Minimum water levels in the summer and during droughts, corresponding to maximum energy demand in the water sector, are clearly connected to synchronized positive NAO and negative EA phases in the preceding winter. Recent advances in the seasonal and long-term predictability of NAO and EA climate patterns can help to improve drought resilience and groundwater sustainability and have huge potential benefits for the water-energy nexus in the Algarve region. Finally, to decarbonize freshwater supply in the Algarve, policy instruments will need to account for unregulated pumping which enables conditions for groundwater depletion, encourage energy and water management integration, and explore innovative energy investments.
•NAO (and EA) drive interannual variations with peak periods of 6.5 (and 3.5) -years.•Maximum energy demand in the water sector is expected for NAO+ and EA− phases.•SP is the most reliable renewable energy source for the water sector in the Algarve.•NAO+ EA− are associated with droughts raising implications for solar and wind energy.•Policies promoting solar based technologies should account for aquifer depletion.
Disulfide bonds play a critical role in a variety of structural and mechanistic processes associated with proteins inside the cells and in the extracellular environment. The thioredoxin family of ...proteins like thioredoxin (Trx), glutaredoxin (Grx) and protein disulfide isomerase, are involved in the formation, transfer or isomerization of disulfide bonds through a characteristic thiol-disulfide exchange reaction. Here, we review the structural and mechanistic determinants behind the thiol-disulfide exchange reactions for the different enzyme types within this family, rationalizing the known experimental data in light of the results from computational studies. The analysis sheds new atomic-level insight into the structural and mechanistic variations that characterize the different enzymes in the family, helping to explain the associated functional diversity. Furthermore, we review here a pattern of stabilization/destabilization of the conserved active-site cysteine residues presented beforehand, which is fully consistent with the observed roles played by the thioredoxin family of enzymes.
Human fatty acid synthase (hFAS) is a multifunctional enzyme involved in a wide diversity of biological functions. For instance, it is a precursor of phospholipids and other complex processes such as ...the de novo synthesis of long chain fatty acid. Human FAS is also a component of biological membranes and it is implicated in the overexpression of several types of cancers. In this work, we describe the catalytic mechanism of β-ketoreductase (KR), which is a catalytic domain of the hFAS enzyme that catalyzes the reduction of β-ketoacyl to β-hydroxyacyl with the concomitant oxidation of the NADPH cofactor. The catalysis by KR is an intermediate step in the cycle of reactions that elongate the substrate's carbon chain until the final product is obtained. We study and propose the catalytic mechanism of the KR domain determined using the hybrid QM/MM methodology, at the ONIOM(B3LYP/6-311+G(2d,2p):AMBER) level of theory. The results indicate that the reaction mechanism occurs in two stages: (i) nucleophilic attack by a NADPH hydride to the β-carbon of the substrate, together with an asynchronous deprotonation of the Tyr2034 by the oxygen of the β-alkoxide to hold the final alcohol product; and (ii) an asynchronous deprotonation of the hydroxyl in the NADP
's ribose by Tyr2034, and of the Lys1995 by the resulting alkoxide in the former ribose to restore the protonation state of Tyr2034. The reduction step occurs with a Gibbs energy barrier of 11.7 kcal mol
and a Gibbs reaction energy of -10.6 kcal mol
. These results have provided an understanding of the catalytic mechanism of the KR hFAS domain, a piece of the heavy hFAS biosynthetic machinery.
Dehydratase (DH) is a catalytic domain of the mammalian fatty acid synthase (mFAS), a multidomain enzyme with seven different active sites that work in tandem to carry out the biosynthesis of ...palmitic acid for de novo lipogenesis. DH catalyzes the dehydration of the β-hydroxyacyl to an α,β-unsaturated acyl intermediate. We have conducted hybrid QM/MM calculations to clarify the catalytic mechanism for the DH domain at the ONIOM(DFT/Amber) level of theory. The results have shown that the dehydration step occurs in two stages: (i) the His878-imidazole acts as a base deprotonating the Cα of the β-hydroxyacyl (HAC) substrate and (ii) the β-elimination of the β-hydroxyl of HAC proceeds with late protonation of the leaving hydroxide by the Asp1033-carboxylic group, forming a water molecule as a byproduct. The α-deprotonation depends on an oxyanion hole mechanism where the HAC’s α-carbonyl is anchored by two strong hydrogen bonds from the neighboring Gly888 and the intramolecular β-hydroxyl, positioning the Cα of HAC for deprotonation by His878. A positively charged His1037 improves the acidic character of Asp1033 and completes the catalytic triad in DH, because when His1037 is neutral the positively charged His878 behaves as the acid in the β-elimination step. We observe that the positively charged His1037 renders the β-elimination step more thermodynamically favorable (Δr G of −15.9 kcal·mol–1). The β-elimination step exhibits a Gibbs energy barrier of 14.1 kcal·mol–1 and it is the rate-limiting step of the reaction (in agreement with the experimental barrier of ∼17 kcal·mol–1. Nevertheless, the rate-limiting step does not seem to be dependent on the protonation of His1037. Through evaluation of the electrostatic effect per residue on the rate-limiting step, we concluded also that the electrostatic contribution of the enzyme’s body does not seem significant, even though there are many positively and negatively charged residues close to the leaving β-hydroxyl group of HAC.
Frequently, the number of circulating tumor cells (CTC) isolated in 7.5 mL of blood is too small to reliably determine tumor heterogeneity and to be representative as a “liquid biopsy”. In the EU FP7 ...program CTCTrap, we aimed to validate and optimize the recently introduced Diagnostic LeukApheresis (DLA) to screen liters of blood. Here we present the results obtained from 34 metastatic cancer patients subjected to DLA in the participating institutions. About 7.5 mL blood processed with CellSearch® was used as “gold standard” reference. DLAs were obtained from 22 metastatic prostate and 12 metastatic breast cancer patients at four different institutions without any noticeable side effects. DLA samples were prepared and processed with different analysis techniques. Processing DLA using CellSearch resulted in a 0–32 fold increase in CTC yield compared to processing 7.5 mL blood. Filtration of DLA through 5 μm pores microsieves was accompanied by large CTC losses. Leukocyte depletion of 18 mL followed by CellSearch yielded an increase of the number of CTC but a relative decrease in yield (37%) versus CellSearch DLA. In four out of seven patients with 0 CTC detected in 7.5 mL of blood, CTC were detected in DLA (range 1–4 CTC). The CTC obtained through DLA enables molecular characterization of the tumor. CTC enrichment technologies however still need to be improved to isolate all the CTC present in the DLA.
What's new?
Circulating tumor cells (CTC) can mirror tumor heterogeneity but a standard blood sample (7.5 mL) is too small to truly represent the tumor. To increase the yield of CTC, the authors used Diagnostic LeukApheresis in which liters of blood are screened for the presence of CTC in metastatic cancer patients. They report a significant increase in CTC yield and consequently, a better molecular characterization of the tumor, encouraging further research into the use of leukapheresis as “liquid biopsy” in cancer patients.
Display omitted
•Develops a hybrid system with SVM and Evolutionary Computation.•The SVM categorizes the market into three different types.•The GA optimizes an investment strategy with dynamic ...approaches.•The algorithm invests in the Forex market with high leverage.
This work proposes a new approach, based on Genetic Algorithms and Support Vector Machine to trade in the forex market. In this work, a new algorithm capable of generating technical rules to make investments with a given amount of leverage depending on the certainty of the prediction is presented. To forecast those predictions, a combination of a Support Vector Machine (SVM) algorithm – to identify and classify the market in three different stages –, and a Dynamic Genetic Algorithm – to optimize trading rules in each type of market, is used. The optimization of the trading rules is based on several technical indicators. Forex data for the EUR/USD currency pair, in a timeframe between the years of 2003 and 2016, is used as training and test data. The proposed architecture for the machine learning system, as well as the implementation and study of the proposed system is described in detail. The use of an hybrid system, combining a SVM and a GA with dynamic approaches such as hyper-mutation and adaptability approaches by training three different GA’s for each type of market, provide a new approach for FOREX trading, where it is possible to classify trends using price sequences and therefore using the same classification for optimizing investment strategies with the most appropriate GA. Finally, the work shows promising results during the test period between the 2nd of January of 2015 until the 2nd of March of 2016, where the Return on Investment obtained is 83%.
Bacterial glycosyltransferases of the GT51 family are key enzymes in bacterial cell wall synthesis. Inhibiting cell wall synthesis is a very effective approach for development of antibiotics, as this ...can lead to either bacteriostatic or bactericidal effects. Even though the existence of this family has been known for over 50 years, only one potent inhibitor exists, which is an analog of the lipid IV product and derived from a natural product. Drug development focused on bacterial transglycosylase has been hampered due to little being know about its structure and reaction mechanism. In this study, Staphylococcus aureus monoglycosyltransferase was investigated at an atomistic level using computational methods. Classical molecular dynamics simulations were used to reveal information about the large-scale dynamics of the enzyme–substrate complex and the importance of magnesium in structure and function of the protein, while mixed mode quantum mechanics/molecular mechanics calculations unveiled a novel hypothesis for the reaction mechanism. From these results, we present a new model for the binding mode of lipid II and the reaction mechanism of the GT51 glycosyltransferases. A metal-bound hydroxide catalyzed reaction mechanism yields an estimated free energy barrier of 16.1 ± 1.0 kcal/mol, which is in line with experimental values. The importance of divalent cations is also further discussed. These findings could significantly aid targeted drug design, particularly the efficient development of transition state analogues as potential inhibitors for the GT51 glycosyltransferases.
Enzymatic catalysis is a complex process that can involve multiple conformations of the enzyme:substrate complex and several competitive reaction pathways, resulting in a multi-dimensional free ...energy landscape. The study of enzymatic activity often requires deep knowledge of the system to establish the catalytic mechanism and identify the possible reactive conformations of the complex. Here, we present an enhanced sampling and machine learning-based approach to explore the catalytic reaction space and characterize the transformation from reactive to non-reactive conformations with minimal a priori knowledge of the system. We applied this approach to study the rate-determining step of the glycolysis reaction of maltopentose catalyzed by human pancreatic α-amylase, an important enzyme in glucose production as well as a major drug target for the treatment of type-II diabetes. We unravel the complexity of the enzymatic reaction, reveal three binding modes of the substrate within the active site, and highlight the role of water in the catalytic process and in the stepwise conversion of reaction-ready to non-reactive conformations. Overall, these insights offer atomistic details on the catalytic mechanism and dynamics of the active site, allowing one to shed light on two fundamental questions in enzymatic catalysis, that is how and when does an enzyme react?
PDF
