l‐Threonine aldolases (l‐TAs) represent a family of homologous pyridoxal 5′‐phosphate‐dependent enzymes found in bacteria and fungi, and catalyse the reversible cleavage of several ...l‐3‐hydroxy‐α‐amino acids. l‐TAs have great biotechnological potential, as they catalyse the formation of carbon–carbon bonds, and therefore may be exploited for the bioorganic synthesis of l‐3‐hydroxyamino acids that are biologically active or constitute building blocks for pharmaceutical molecules. Many l‐TAs, showing different stereospecificity towards the Cβ configuration, have been isolated. Because of their potential to carry out diastereoselective syntheses, l‐TAs have been subjected to structural, functional and mechanistic studies. Nevertheless, their catalytic mechanism and the structural bases of their stereospecificity have not been elucidated. In this study, we have determined the crystal structure of low‐specificity l‐TA from Escherichia coli at 2.2‐Å resolution, in the unliganded form and cocrystallized with l‐serine and l‐threonine. Furthermore, several active site mutants have been functionally characterized in order to elucidate the reaction mechanism and the molecular bases of stereospecificity. No active site catalytic residue was revealed, and a structural water molecule was assumed to act as the catalytic base in the retro‐aldol cleavage reaction. Interestingly, the very large active site opening of E. coli l‐TA suggests that much larger molecules than l‐threonine isomers may be easily accommodated, and l‐TAs may actually have diverse physiological functions in different organisms. Substrate recognition and reaction specificity seem to be guided by the overall microenvironment that surrounds the substrate at the enzyme active site, rather than by one ore more specific residues.
Structured digital
eTA and eTA bind by x-ray crystallography (1, 2).
Database
RCSB PDB (www.pdb.org): structural data are available in the Protein Data Bank/BioMagResBank databases under the accession numbers 4LNJ, 4LNM and 4LNL for the unliganded, eTA‐Thr and eTA‐Ser structures.
l‐Threonine aldolases are enzymes whose biological function is unclear but are biotechnologically relevant for bioorganic synthesis of l‐3‐hydroxyamino acids. Our structural and functional characterization of the Escherichia coli enzyme suggests that stereospecificity is determined by the overall microenvironment of the active site. A structural water molecule has been proposed to act as catalytic base in the retro‐aldol cleavage reaction.
Aims
To conduct biological investigations and to evaluate the antimicrobial and antioxidant activities of the essential oils (EOs) extracted from Juniperus communis, J. scopulorum and J. ...horizontalis; to screen their mechanisms of action by conducting the cell membrane permeability assay (CMP); and to determine the possible cytotoxicity of the three EOs against human neuroblastoma cells (SH‐SY5Y).
Methods and Results
The antifungal activity was tested against four phytopathogenic fungi (Monilinia fructicola, Aspergillus niger, Penicillium expansum and Botrytis cinerea). The antibacterial activity was evaluated against two Gram‐positive (G+ve) (Bacillus megaterium and Clavibacter michiganensis) and three Gram‐negative (G−ve) bacterial strains (Pseudomonas fluorescens, P. syringae pv. phaseolicola and Xanthomonas campestris). Results showed that the three tested EOs have antifungal activity against M. fructicola and P. expansum and effective antibacterial activity against P. syringae pv. phaseolicola and B. megaterium. Moreover, the three EOs were evaluated for their ability to inhibit the growth of SH‐SY5Y cells with MTT assay. J. communis EO was the more effective with an IC50 of 53·7 μg ml−1. The antioxidant capacity of the three EO did not differ as measured by the DPPH assay.
Conclusions
The three tested juniper EOs showed promising antimicrobial and antioxidant activity and cytotoxic effects against human neuroblastoma cell line.
Significance and Impact of the Study
The outfindings from this research showed promising antimicrobial effects of the three oils against the majority of the tested phytopathogens with a potential to utilize them as natural alternatives to synthetic drugs, the cause of global environmental problems, pathogen resistance and difficulty to control many post‐harvest plant diseases.
In Bayesian inference, we are usually interested in the numerical approximation of integrals that are posterior expectations or marginal likelihoods (a.k.a., Bayesian evidence). In this paper, we ...focus on the computation of the posterior expectation of a function
f
(
x
)
. We consider a
target-aware
scenario where
f
(
x
)
is known in advance and can be exploited in order to improve the estimation of the posterior expectation. In this scenario, this task can be reduced to perform several independent marginal likelihood estimation tasks. The idea of using a path of tempered posterior distributions has been widely applied in the literature for the computation of marginal likelihoods. Thermodynamic integration, path sampling and annealing importance sampling are well-known examples of algorithms belonging to this family of methods. In this work, we introduce a generalized thermodynamic integration (GTI) scheme which is able to perform a target-aware Bayesian inference, i.e., GTI can approximate the posterior expectation of a given function. Several scenarios of application of GTI are discussed and different numerical simulations are provided.
To assess the potential of polycrystalline MnBi as a transverse thermoelectric material, we have experimentally investigated its anomalous Nernst effect (ANE) by means of the heat flux method. We ...prepared MnBi samples by powder metallurgy; this technique allows the preparation of samples in arbitrary shapes with the possibility to tailor their magnetic properties. In the material exhibiting the highest remanent magnetization, we found a value of the ANE thermopower of −1.1 μV/K at 1 T, after the compensation of the ordinary Nernst effect from pure bismuth present inside the polycrystalline sample. This value is comparable with those reported in the literature for single crystals.
Age-related neurodegenerative disorders are characterized by a slow, persistent accumulation of aggregated proteins. Although cells can elicit physiological responses to enhance cellular clearance ...and counteract accumulation, it is unclear how pathogenic proteins evade this process in disease. We find that Parkinson’s disease α-synuclein perturbs the physiological response to lysosomal stress by impeding the SNARE protein ykt6. Cytosolic ykt6 is normally autoinhibited by a unique farnesyl-mediated regulatory mechanism; however, during lysosomal stress, it activates and redistributes into membranes to preferentially promote hydrolase trafficking and enhance cellular clearance. α-Synuclein aberrantly binds and deactivates ykt6 in patient-derived neurons, thereby disabling the lysosomal stress response and facilitating protein accumulation. Activating ykt6 by small-molecule farnesyltransferase inhibitors restores lysosomal activity and reduces α-synuclein in patient-derived neurons and mice. Our findings indicate that α-synuclein creates a permissive environment for aggregate persistence by inhibiting regulated cellular clearance and provide a therapeutic strategy to restore protein homeostasis by harnessing SNARE activity.
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•ykt6 responds to lysosomal stress by enhancing hydrolase trafficking•α-Synuclein impedes the lysosomal stress response by blocking ykt6 in patient neurons•Reducing the farnesylation of ykt6 enhances hydrolase trafficking and lysosomal function•Farnesyltransferase inhibitors activate ykt6 and lysosomes in patient neurons and mice
Cuddy et al. found that the SNARE protein ykt6 plays a crucial role in proteostasis and lysosomal function by enhancing hydrolase trafficking under stressful conditions. Parkinson’s disease α-synuclein impedes ykt6, causing imbalanced proteostasis and self-propagating protein accumulation. Ykt6 can be therapeutically targeted by farnesyltransferase inhibitors that restore trafficking and lysosomal function.
Serine hydroxymethyltransferase (SHMT) catalyzes the reversible conversion of l-serine and tetrahydrofolate into glycine and 5,10-methylenetetrahydrofolate. This enzyme, which plays a pivotal role in ...one-carbon metabolism, is involved in cancer metabolic reprogramming and is a recognized target of chemotherapy intervention. In humans, two isoforms of the enzyme exist, which are commonly termed cytosolic SHMT1 and mitochondrial SHMT2. Considerable attention has been paid to the structural, mechanistic, and metabolic features of these isozymes. On the other hand, a detailed comparison of their catalytic and regulatory properties is missing, although this aspect seems to be considerably important, considering that SHMT1 and SHMT2 reside in different cellular compartments, where they play distinct roles in folate metabolism. Here we performed a full kinetic characterization of the serine hydroxymethyltransferase reaction catalyzed by SHMT1 and SHMT2, with a focus on pH dependence and substrate inhibition. Our investigation, which allowed the determination of all kinetic parameters of serine hydroxymethyltransferase forward and backward reactions, uncovered a previously unobserved substrate inhibition by l-serine and highlighted several interesting differences between SHMT1 and SHMT2. In particular, SHMT2 maintains a pronounced tetrahydrofolate substrate inhibition even at the alkaline pH characteristic of the mitochondrial matrix, whereas with SHMT1 this is almost abolished. At this pH, SHMT2 also shows a catalytic efficiency that is much higher than that of SHMT1. These observations suggest that such different properties represent an adaptation of the isoforms to the respective cellular environments and that substrate inhibition may be a form of regulation.
ABSTRACT
Model fitting is possibly the most extended problem in science. Classical approaches include the use of least-squares fitting procedures and maximum likelihood methods to estimate the value ...of the parameters in the model. However, in recent years, Bayesian inference tools have gained traction. Usually, Markov chain Monte Carlo (MCMC) methods are applied to inference problems, but they present some disadvantages, particularly when comparing different models fitted to the same data set. Other Bayesian methods can deal with this issue in a natural and effective way. We have implemented an importance sampling (IS) algorithm adapted to Bayesian inference problems in which the power of the noise in the observations is not known a priori. The main advantage of IS is that the model evidence can be derived directly from the so-called importance weights – while MCMC methods demand considerable postprocessing. The use of our adaptive target adaptive importance sampling (ATAIS) method is shown by inferring, on the one hand, the parameters of a simulated flaring event that includes a damped oscillation and, on the other hand, real data from the Kepler mission. ATAIS includes a novel automatic adaptation of the target distribution. It automatically estimates the variance of the noise in the model. ATAIS admits parallelization, which decreases the computational run-times notably. We compare our method against a nested sampling method within a model selection problem.
Introduction
Non-suicidal self-harm (NSSH) include deliberate behaviours with the intent to self-injure. NSSH prevalence ranges 15.5%-31.3% in adolescents and young adults<25 years-old.
Objectives
...Our aim is characterizing the psychopathological domains occurring in adolescent and young adults with NSSH during the second COVID-19-related wave (October 2020-August 2021).
Methods
A cross-sectional study recruited inpatients aged 15-24 consecutively afferent to psychiatric ward due to NSSH, by investigating anger rumination(ARS), emotional regulation (DERS), dissociation (DES-II), metacognitive capabilities(MCQ-30), perceived stress (PSS), self-criticism (LOSCS), emotional intelligence (Reading the Mind in the Eyes Test-RMET), aggressiveness (AQ), impulsiveness (BIS-11), hopelessness(BHS), alexithymia (TAS-20). NSSH were characterized by using suicide score scale(SSS) and deliberate self-harm interview (DSHI).
Results
A 7-fold increase in young inpatient access was observed from 2019 to 2021. DSHI median was 2 (95%CI=1,17-2,73), SSS-12months median was 5 (95%CI=4.2-6.7), SSS-lifetime median was 5 (95%CI=3.4-5.3) and MINI median was 5 (95%CI=3.4-4.7). Linear regression analysis and Pearson’s correlations revealed strong correlations between DSHI and BHS (r=0.550), TAS-20 (r=0.495), AQ-hostility(r=0.529),AQ-total (r=0.446), PSS(r=0.454), DERS-total (r=0.621), DERS-lack_of_control
(r=0.658),MCQ-total(r=0.534),MCQ-perception_danger_not_
control (r=0.583); between SSS-12months and AQ-total (r=0.456), AQ-Anger (r=0.443), BIS-total(r=0.457),BIS-Attentional-Impulsiveness (r=0.511),BIS-Complex-Motor-Impulsiveness (r=0.507), PSS (r=0.617), DERS(r=0.571), DES(r=0.559).
Conclusions
COVID-19-related increased perceived stress and depressive symptomatology may have facilitated the onset of severe NSSH in adolescents and young people with trait impulsiveness, hostility and affective dysregulation.
Disclosure
No significant relationships.
Abstract It was recently discovered that glycine consumption is strongly related to the rate of proliferation across cancer cells. This is very intriguing and raises the question of what is the ...actual role of this amino acid in cancer metabolism. Cancer cells are greedy for glycine. In particular, the mitochondrial production of glycine seems to be utterly important. Overexpression of mitochondrial serine hydroxymethyltransferase, the enzyme converting l -serine to glycine, assures an adequate supply of glycine to rapidly proliferating cancer cells. In fact, silencing of mitochondrial serine hydroxymethyltransferase was shown to halt cancer cell proliferation. Direct incorporation of glycine carbon atoms into the purine ring has been proposed to be one main reason for the importance of glycine in cancer cell metabolism. We believe that, as far as the importance of glycine in cancer is concerned, a central role of this amino acid, namely its participation to heme biosynthesis, has been neglected. In mitochondria, glycine condenses with succinyl-CoA to form 5-aminolevulinate, the universal precursor of the different forms of heme contained in cytochromes and oxidative phosphorylation complexes. Our hypothesis is that mitochondrial serine hydroxymethyltransferase is fundamental to sustain cancer metabolism since production of glycine fuels heme biosynthesis and therefore oxidative phosphorylation. Respiration of cancer cells may then ultimately rely on endogenous glycine synthesis by mitochondrial serine hydroxymethyltransferase. The link between mitochondrial serine hydroxymethyltransferase activity and heme biosynthesis represents an important and still unexplored aspect of the whole picture of cancer cell metabolism. Our hypothesis might be tested using a combination of metabolic tracing and gene silencing on different cancer cell lines. The experiments should be devised so as to assess the importance of mitochondrial serine hydroxymethyltransferase and the glycine deriving from its reaction as a precursor of heme. If the observed increase of glycine consumption in rapidly proliferating cancer cells has its basis in the need for heme biosynthesis, then mitochondrial serine hydroxymethyltransferase should be considered as a key target for the development of new chemotherapic agents.
The adaptive rejection sampling (ARS) algorithm is a universal random generator for drawing samples efficiently from a univariate log-concave target probability density function (pdf). ARS generates ...independent samples from the target via rejection sampling with high acceptance rates. Indeed, ARS yields a sequence of proposal functions that converge toward the target pdf, so that the probability of accepting a sample approaches one. However, sampling from the proposal pdf becomes more computational demanding each time it is updated. In this work, we propose a novel ARS scheme, called Cheap Adaptive Rejection Sampling (CARS), where the computational effort for drawing from the proposal remains constant, decided in advance by the user. For generating a large number of desired samples, CARS is faster than ARS.
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