PUR-GEN: A web server for automated generation of polyurethane fragment libraries.

The biodegradation of synthetic polymers offers a promising solution for sustainable plastic recycling. Polyurethanes (PUR) stand out among these polymers due to their susceptibility to enzymatic hydrolysis. However, the intricate 3D structures formed by PUR chains present challenges for biodegradation studies, both computational and experimental.

Water Migration through Enzyme Tunnels Is Sensitive to the Choice of Explicit Water Model.

The utilization of tunnels and water transport within enzymes is crucial for their catalytic function as water molecules can stabilize bound substrates and help with unbinding processes of products and inhibitors. Since the choice of water models for molecular dynamics simulations was shown to determine the accuracy of various calculated properties of the bulk solvent and solvated proteins, we have investigated if and to what extent water transport through the enzyme tunnels depends on the selection of the water model. Here, we focused on simulating enzymes with various well-defined tunnel geometries.

Comprehensive analysis of acetylcholinesterase inhibitor and reactivator complexes: implications for drug design and antidote development.

The main function of acetylcholinesterase (AChE) is to regulate the levels of one of the most important neurotransmitters: acetylcholine. This makes AChE an ideal molecular target for the treatment of neurodegenerative diseases and dementia (such as Alzheimer's disease), as well as for the neutralisation of natural toxins (e.g.

Serum Levels of Selected Cytokines and Chemokines and IgG4 in Children With Recurrent Respiratory Tract Infections.

Respiratory tract infections are a common health problem. Cytokines/chemokines play a critical role in the regulation of the immune system. Their defective production may predispose to recurrent respiratory tract infections (RRIs), and an excessive immune response may lead to chronic inflammation and cause damage to the respiratory tract.

An overview on polyurethane-degrading enzymes.

Polyurethanes (PUR) are durable synthetic polymers widely used in various industries, contributing significantly to global plastic consumption. PUR pose unique challenges in terms of degradability and recyclability, as they are characterised by intricate compositions and diverse formulations. Additives and proprietary structures used in commercial PUR formulations further complicate recycling efforts, making the effective management of PUR waste a daunting task.

PBP-A, a cyanobacterial DD-peptidase with high specificity for amidated muropeptides, exhibits pH-dependent promiscuous activity harmful to Escherichia coli.

Penicillin binding proteins (PBPs) are involved in biosynthesis, remodeling and recycling of peptidoglycan (PG) in bacteria. PBP-A from Thermosynechococcus elongatus belongs to a cyanobacterial family of enzymes sharing close structural and phylogenetic proximity to class A β-lactamases. With the long-term aim of converting PBP-A into a β-lactamase by directed evolution, we simulated what may happen when an organism like Escherichia coli acquires such a new PBP and observed growth defect associated with the enzyme activity.

Mixture toxicity of 6PPD-quinone and polystyrene nanoplastics in zebrafish.

Plastic pollution, including micro- and nanoplastics, is a growing concern. Tyre-wear particles (TWPs) are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves, TWPs contain many harmful chemicals, including 6PPD.

Effects of γ-polyglutamic acid on grassland sandy soil properties and plant functional traits exposed to drought stress.

The current study provides field experimental data that support the use of γ-polyglutamic acid (γ-PGA) in drought stress and proposes its application in grassland management. We hypothesized that water treatment combined with PGA application to sandy soil would reduce drought stress in grasslands more effectively than watering alone. A randomized block design was used, with three replicate watering blocks (no watering, weekly watering, and monthly watering) and PGA treatments at four different concentrations (0%, 0.

Microbial oil, alone or paired with β-glucans, can control hypercholesterolemia in a zebrafish model.

Dyslipidemia is often associated with unhealthy dietary habits, and many mammalian studies have explored the mode of action of certain bioactive compounds such as β-glucans and n-3 PUFAs to understand their potential to normalize the lipid metabolism. There are only a few investigations that adopted omic approaches to unveil their combined effect on hypercholesterolemia. Zebrafish (Danio rerio) was used as a model organism to reveal the efficacy of Schizochytrium oil and β-glucans (from Euglena gracilis and Phaeodactylum tricornutum) against cholesterol-rich diet induced dyslipidemia.

Protective mechanisms of a microbial oil against hypercholesterolemia: evidence from a zebrafish model.

A Western diet elevates the circulating lipoprotein and triglyceride levels which are the major risk factors in cardiovascular disease (CVD) development. Consumption of long-chain omega-3 fatty acids can stall the disease progression. Although these fatty acids can significantly impact the intestine under a hypercholesterolemic condition, the associated changes have not been studied in detail.

Recent Advances in Studying Toll-like Receptors with the Use of Computational Methods.

Toll-like receptors (TLRs) are transmembrane proteins that recognize various molecular patterns and activate signaling that triggers the immune response. In this review, our goal is to summarize how, in recent years, various computational solutions have contributed to a better understanding of TLRs, regarding both their function and mechanism of action. We update the recent information about small-molecule modulators and expanded the topic toward next-generation vaccine design, as well as studies of the dynamic nature of TLRs.

Potential of algae-derived alginate oligosaccharides and β-glucan to counter inflammation in adult zebrafish intestine.

Alginate oligosaccharides (AOS) are natural bioactive compounds with anti-inflammatory properties. We performed a feeding trial employing a zebrafish () model of soybean-induced intestinal inflammation. Five groups of fish were fed different diets: a control (CT) diet, a soybean meal (SBM) diet, a soybean meal+β-glucan (BG) diet and 2 soybean meal+AOS diets (alginate products differing in the content of low molecular weight fractions - AL, with 31% < 3kDa and AH, with 3% < 3kDa).

Daily vs. monthly oral vitamin D for treatment of symptomatic vitamin D deficiency in infants: a randomized controlled trial.

Objectives: Compare the efficacy and safety of daily vs. monthly oral vitamin D in treating symptomatic vitamin D deficiency in infants.

Methods: 90 infants with symptomatic vitamin D deficiency were randomized into Daily (D) [46 infants] and Bolus (B) [44 infants] groups to receive oral vitamin D, daily (2000 IU/day) and bolus (60,000 IU/month) for three months respectively.

Population Genetic Study on the European Flounder () from the Southern Baltic Sea Using SNPs and Microsatellite Markers.

The European flounder (), which is closely related to the recently discovered Baltic flounder (), is currently the third most commercially fished species in the Baltic Sea. According to the available data from the Polish Fisheries Monitoring Center and fishermen's observations, the body condition indices of the species in the Baltic Sea have declined in recent years. The aim of the present study was to obtain information on the current patterns of genetic variability and the population structure of the European flounder and to verify whether the Baltic flounder is present in the southern Baltic Sea.

Transient binding sites at the surface of haloalkane dehalogenase LinB as locations for fine-tuning enzymatic activity.

The haloalkane dehalogenase LinB is a well-known enzyme that contains buried active site and is used for many modelling studies. Using classical molecular dynamics simulations of enzymes and substrates, we searched for transient binding sites on the surface of the LinB protein by calculating maps of enzyme-ligand interactions that were then transformed into sparse matrices. All residues considered as functionally important for enzyme performance (e.

Assessment of selected interleukins (IL-6, IL-17A, IL-18, IL-23) and chemokines (RANTES, IP-10) in children with acute and chronic urticaria.

Background: Urticarial lesions develop as a result of the activation of mast cells which, through the release of mediators, influence the formation of local inflammatory infiltrates. Changes in the expression of many cytokines and chemokines are observed in the course of urticaria. The aim of the study was to evaluate serum levels of interleukin (IL)-6, IL-17A, IL-18, IL-23, regulated on activation, normal T cell expressed and secreted (RANTES) and interferon (IFN)-γ-inducible protein-10 (IP-10) in children with acute urticaria and exacerbation of chronic urticaria in comparison to healthy volunteers.

Polystyrene nanoplastics enhance the toxicological effects of DDE in zebrafish (Danio rerio) larvae.

Anthropogenic releases of plastics, persistent organic pollutants (POPs), and heavy metals can impact the environment, including aquatic ecosystems. Nanoplastics (NPs) have recently emerged as pervasive environmental pollutants that have the ability to adsorb POPs and can cause stress in organisms. Among POPs, DDT and its metabolites are ubiquitous environmental pollutants due to their long persistence.

Developmental defects and behavioral changes in a diet-induced inflammation model of zebrafish.

Soybean meal evokes diet-induced intestinal inflammation in certain fishes. Although the molecular aspects of soybean-induced intestinal inflammation in zebrafish are known, the impact of the inflammatory diet on fish behavior remain largely underexplored. We fed zebrafish larvae with three diets - control, soybean meal and soybean meal with β-glucan to gain deeper insight into the behavioral changes associated with the soybean meal-induced inflammation model.

Geometry-Based versus Small-Molecule Tracking Method for Tunnel Identification: Benefits and Pitfalls.

Different methods for tunnel identification, geometry-based and small-molecule tracking approaches, were compared to provide their benefits and pitfalls. Results obtained for both crystal structures and molecular dynamics (MD) simulations were analyzed to investigate if a more computationally demanding method would be beneficial. Careful examination of the results is essential for the low-diameter tunnel description, and assessment of the tunnel functionality based only on their geometrical parameters is challenging.

Corrigendum to "Structure-function relationship between soluble epoxide hydrolases structure and their tunnel network" [Comput. Struct. Biotechnol. J. 20 (2022) 193-205].

[This corrects the article DOI: 10.1016/j.csbj.

Evolution of tunnels in α/β-hydrolase fold proteins-What can we learn from studying epoxide hydrolases?

The evolutionary variability of a protein's residues is highly dependent on protein region and function. Solvent-exposed residues, excluding those at interaction interfaces, are more variable than buried residues whereas active site residues are considered to be conserved. The abovementioned rules apply also to α/β-hydrolase fold proteins-one of the oldest and the biggest superfamily of enzymes with buried active sites equipped with tunnels linking the reaction site with the exterior.