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Plastic-degrading enzymes, particularly poly(ethylene terephthalate) (PET) hydrolases, have garnered significant attention in recent years as potential eco-friendly solutions for recycling plastic waste. However, understanding of their PET-degrading activity and influencing factors remains incomplete, impeding the development of uniform approaches for enhancing PET hydrolases for industrial applications. A key aspect of PET hydrolase engineering is optimizing the PET-hydrolysis reaction by lowering the associated free energy barrier. However, inconsistent findings have complicated these efforts. Therefore, our goal is to elucidate various aspects of enzymatic PET degradation by means of quantum mechanics/molecular mechanics (QM/MM) reaction simulations and analysis, focusing on the initial reaction step, acylation, in two thermophilic PET hydrolases, LCC and PES-H1, along with their highly active variants, LCC IG and PES-H1 FY . Our findings highlight the impact of semiempirical QM methods on proton transfer energies, affecting the distinction between a two-step reaction involving a metastable tetrahedral intermediate and a one-step reaction. Moreover, we uncovered a concerted conformational change involving the orientation of the PET benzene ring, altering its interaction with the side-chain of the "wobbling" tryptophan from T-stacking to parallel π-π interactions, a phenomenon overlooked in prior research. Our study thus enhances the understanding of the acylation mechanism of PET hydrolases, in particular by characterizing it for the first time for the promising PES-H1 FY using QM/MM simulations. It also provides insights into selecting a suitable QM method and a reaction coordinate, valuable for future studies on PET degradation processes.

The cis/trans isomerization of peptidyl-prolyl peptide bonds is often the bottleneck of the refolding reaction for proteins containing cis proline residues in the native state. Proline (Pro) analogues, especially C4-substituted fluoroprolines, have been widely used in protein engineering to enhance the thermodynamic stability of peptides and proteins and to investigate folding kinetics. 4-thiaproline (Thp) has been shown to bias the ring pucker of Pro, to increase the cis population percentage of model peptides in comparison to Pro, and to diminish the activation energy barrier for the cis/trans isomerization reaction. Despite its intriguing properties, Thp has been seldom incorporated into proteins. Moreover, the impact of Thp on the folding kinetics of globular proteins has never been reported. In this study, we show that upon incorporation of Thp at cisPro76 into the thioredoxin variant Trx1P the half-life of the refolding reaction decreased from ~2 h to ~35 s. A dramatic acceleration of the refolding rate could be observed also for the protein pseudo wild-type barstar upon replacement of cisPro48 with Thp. Quantum chemical calculations suggested that the replacement of the C γ H 2 group by a sulfur atom in the pyrrolidine ring, might lower the barrier for cis/trans rotation due to a weakened peptide bond. The protein variants retained their thermodynamic stability upon incorporation of Thp, while the catalytic and enzymatic activities of the modified Trx1P remained unchanged. Our results show that the Pro isostere Thp might accelerate the rate of the slow refolding reaction for proteins containing cis proline residues in the native state, independent from the local structural environment., (© 2023 The Authors. Protein Science published by Wiley Periodicals LLC on behalf of The Protein Society.)

Background: Childhood asthma is imposing a great financial burden on the pediatric health care system. Asthma costs are directly related to the level of asthma control. A substantial part of these costs may be preventable by the timely and adequate assessment of asthma deterioration in daily life and proper asthma management. The use of eHealth technology may assist such timely and targeted medical anticipation., Objective: This paper describes the Ambulatory Pediatric Asthma Care (ALPACA) study protocol to investigate the effectiveness of an eHealth intervention consisting of remote patient monitoring and teleconsultation integrated into the daily clinical care of pediatric patients with asthma. This intervention aims to reduce health care utilization and costs and improve health outcomes compared to a control group that receives standard care. In addition, this study aims to improve future eHealth pediatric asthma care by gaining insights from home-monitoring data., Methods: This study is a prospective randomized controlled effectiveness trial. A total of 40 participants will be randomized to either 3 months of eHealth care (intervention group) or standard care (control group). The eHealth intervention consists of remote patient monitoring (spirometry, pulse oximetry, electronic medication adherence tracking, and asthma control questionnaire) and web-based teleconsultation (video sharing, messages). All participants will have a 3-month follow-up with standard care to evaluate whether the possible effects of eHealth care are longer lasting. During the entire study and follow-up period, all participants will use blinded observational home monitoring (sleep, cough/wheeze sounds, air quality in bedroom) as well., Results: This study was approved by the Medical Research Ethics Committees United. Enrollment began in February 2023, and the results of this study are expected to be submitted for publication in July 2024., Conclusions: This study will contribute to the existing knowledge on the effectiveness of eHealth interventions that combine remote patient monitoring and teleconsultation for health care utilization, costs, and health outcomes. Furthermore, the observational home-monitoring data can contribute to improved identification of early signs of asthma deterioration in pediatric patients. Researchers and technology developers could use this study to guide and improve eHealth development, while health care professionals, health care institutions, and policy makers may employ our results to make informed decisions to steer toward high-quality, efficient pediatric asthma care., Trial Registration: ClinicalTrials.gov NCT05517096; https://clinicaltrials.gov/ct2/show/NCT05517096., International Registered Report Identifier (irrid): PRR1-10.2196/45585., (©Mattienne van der Kamp, Vera Hengeveld, Nico Willard, Boony Thio, Pascal de Graaf, Inge Geven, Monique Tabak. Originally published in JMIR Research Protocols (https://www.researchprotocols.org), 03.07.2023.)

Anabolic treatment options for osteoporosis remain limited. One approach to discovering novel anabolic drug targets is to identify genetic causes of extreme high bone mass (HBM). We investigated a pedigree with unexplained HBM within the UK HBM study, a national cohort of probands with HBM and their relatives. Whole exome sequencing (WES) in a family with HBM identified a rare heterozygous missense variant (NM_004482.4:c.1657C > T, p.Arg553Trp) in GALNT3, segregating appropriately. Interrogation of data from the UK HBM study and the Anglo-Australasian Osteoporosis Genetics Consortium (AOGC) revealed an unrelated individual with HBM with another rare heterozygous variant (NM_004482.4:c.831 T > A, p.Asp277Glu) within the same gene. In silico protein modeling predicted that p.Arg553Trp would disrupt salt-bridge interactions, causing instability of GALNT3, and that p.Asp277Glu would disrupt manganese binding and consequently GALNT3 catalytic function. Bi-allelic loss-of-function GALNT3 mutations alter FGF23 metabolism, resulting in hyperphosphatemia and causing familial tumoral calcinosis (FTC). However, bone mineral density (BMD) in FTC cases, when reported, has been either normal or low. Common variants in the GALNT3 locus show genome-wide significant associations with lumbar, femoral neck, and total body BMD. However, no significant associations with BMD are observed at loci coding for FGF23, its receptor FGFR1, or coreceptor klotho. Mendelian randomization analysis, using expression quantitative trait loci (eQTL) data from primary human osteoblasts and genome-wide association studies data from UK Biobank, suggested increased expression of GALNT3 reduces total body, lumbar spine, and femoral neck BMD but has no effect on phosphate concentrations. In conclusion, rare heterozygous loss-of-function variants in GALNT3 may cause HBM without altering phosphate concentration. These findings suggest that GALNT3 may affect BMD through pathways other than FGF23 regulation, the identification of which may yield novel anabolic drug targets for osteoporosis. © 2023 The Authors. Journal of Bone and Mineral Research published by Wiley Periodicals LLC on behalf of American Society for Bone and Mineral Research (ASBMR)., (© 2023 The Authors. Journal of Bone and Mineral Research published by Wiley Periodicals LLC on behalf of American Society for Bone and Mineral Research (ASBMR).)

The majority of university curricula for health professionals does not incorporate courses on human nutrition and its links with human and planetary health. This primarily applies to medical and pharmacy students, who have important counselling roles and are at the forefront of public health. To address this important issue, EIT Food recently launched an online course on nutrition, health, and sustainability. Learners were able to provide feedback on the course through an end-of-course survey and social interaction on the FutureLearn platform. The course was very well attended worldwide and received positive feedback from learners. A total of 3,858 students enrolled in the program, from >20 countries. Learners reported inadequate training on nutrition in their own curriculum and indicated they would use key insights from the course to inform their own practice. This report provides insights from the course, which could be used as guidance for future initiatives.

Neoantigens derived from somatic mutations are specific to cancer cells and are ideal targets for cancer immunotherapy. KRAS is the most frequently mutated oncogene and drives the pathogenesis of several cancers. Here we show the identification and development of an affinity-enhanced T cell receptor (TCR) that recognizes a peptide derived from the most common KRAS mutant, KRAS G12D , presented in the context of HLA-A*11:01. The affinity of the engineered TCR is increased by over one million-fold yet fully able to distinguish KRAS G12D over KRAS WT . While crystal structures reveal few discernible differences in TCR interactions with KRAS WT versus KRAS G12D , thermodynamic analysis and molecular dynamics simulations reveal that TCR specificity is driven by differences in indirect electrostatic interactions. The affinity enhanced TCR, fused to a humanized anti-CD3 scFv, enables selective killing of cancer cells expressing KRAS G12D . Our work thus reveals a molecular mechanism that drives TCR selectivity and describes a soluble bispecific molecule with therapeutic potential against cancers harboring a common shared neoantigen., (© 2022. The Author(s).)

Background: Early detection of loss of asthma control can effectively reduce the burden of the disease. However, broad implementation in clinical practice has not been accomplished so far. We are in need of research investigating the operationalization of eHealth pediatric asthma care in practice, which can provide the most potential benefits in terms of adoption, efficiency, and effectiveness., Objective: The aim of this study was to investigate the technical and clinical feasibility, including an exploration of the efficacy and cost-efficiency, of an eHealth program implemented in daily clinical pediatric asthma practice., Methods: We designed an eHealth-supported pediatric asthma program facilitating early detection of loss of asthma control while increasing symptom awareness and self-management. In the 6-month program, asthma control was monitored by 4 health care professionals (HCPs) by using objective home measurements and the web-based Puffer app to allow timely medical anticipation and prevent treatment delay. Technical feasibility was assessed by technology use, system usability, and technology acceptance. Clinical feasibility was assessed by participation and patient-reported health and care outcomes and via a focus group with HCPs regarding their experiences of implementing eHealth in daily practice. The efficacy and cost-efficiency were explored by comparing pretest-posttest program differences in asthma outcomes (asthma control, lung function, and therapy adherence) and medical consumption., Results: Of 41 children, 35 children with moderate-to-severe asthma volunteered for participation. With regard to technical feasibility, the Puffer app scored a good usability score of 78 on the System Usability Scale and a score of 70 for technology acceptance on a scale of 1 to 100. Approximately 75% (18/24) of the children indicated that eHealth helped them to control their asthma during the program. HCPs indicated that home measurements and real time communication enabled them to make safe and substantiated medical decisions during symptom manifestations. With an average time commitment of 15 minutes by patients, eHealth care led to a 80% gross reduction (from €71,784 to €14,018, US $1=€0.85) in health care utilization, 8.6% increase (from 18.6 to 20.2, P=.40) in asthma control, 25.0% increase (from 2.8 to 3.5, P=.04) in the self-management level, and 20.4% improved (from 71.2 to 76.8, P=.02) therapy adherence., Conclusions: eHealth asthma care seems to be technically and clinically feasible, enables safe remote care, and seems to be beneficial for pediatric asthma care in terms of health outcomes and health care utilization. Follow-up research should focus on targeted effectiveness studies with the lessons learned, while also enabling individualization of eHealth for personalized health care., (©Mattienne van der Kamp, Pamela Reimering Hartgerink, Jean Driessen, Bernard Thio, Hermie Hermens, Monique Tabak. Originally published in JMIR Formative Research (https://formative.jmir.org), 26.07.2021.)

The mcr-1 gene encodes a membrane-bound Zn2+-metalloenzyme, MCR-1, which catalyses phosphoethanolamine transfer onto bacterial lipid A, making bacteria resistant to colistin, a last-resort antibiotic. Mechanistic understanding of this process remains incomplete. Here, we investigate possible catalytic pathways using DFT and ab initio calculations on cluster models and identify a complete two-step reaction mechanism. The first step, formation of a covalent phosphointermediate via transfer of phosphoethanolamine from a membrane phospholipid donor to the acceptor Thr285, is rate-limiting and proceeds with a single Zn2+ ion. The second step, transfer of the phosphoethanolamine group to lipid A, requires an additional Zn2+. The calculations suggest the involvement of the Zn2+ orbitals directly in the reaction is limited, with the second Zn2+ acting to bind incoming lipid A and direct phosphoethanolamine addition. The new level of mechanistic detail obtained here, which distinguishes these enzymes from other phosphotransferases, will aid in the development of inhibitors specific to MCR-1 and related bacterial phosphoethanolamine transferases.

Objective: Exercise-induced bronchoconstriction (EIB) is a specific morbidity of childhood asthma and an important sign of uncontrolled asthma. The occurrence of EIB is insufficiently identified by the Childhood Asthma Control Test (C-ACT) and Asthma Control Test (ACT). This study aimed to (1) evaluate the Visual Analog Scale (VAS) for dyspnea as a tool to detect EIB in asthmatic children and (2) assess the value of combining (C-)ACT outcomes with VAS scores. Methods: We measured EIB in 75 asthmatic children (mean age 10.8 years) with a standardized exercise challenge test (ECT) performed in cold and dry air. Children and parents reported VAS dyspnea scores before and after the ECT. Asthma control was assessed by the (C-)ACT. Results: Changes in VAS scores (ΔVAS) of children and parents correlated moderately with fall in forced expiratory volume in 1 second (FEV 1 ), respectively r s =0.57 ( p  < .001) and r s =0.58 ( p  < .001). At a ΔVAS cutoff value of ≥3 in children, sensitivity and specificity for EIB were 80% and 79% (AUC 0.82). Out of 38 children diagnosed with EIB, 37 had a (C-)ACT score of ≤19 and/or a ΔVAS of ≥3, corresponding with a sensitivity of 97% and a negative predictive value of 96%. Conclusion: This study shows that the VAS could be an effective additional tool for diagnosing EIB in children. A reported difference in VAS scores of ≥3 after a standardized ECT combined with low (C-)ACT scores was highly effective in detecting and excluding EIB.

Cdc25 phosphatase B, a potential target for cancer therapy, is inhibited by a series of quinones. The binding site and mode of quinone inhibitors to Cdc25B remains unclear, whereas this information is important for structure-based drug design. We investigated the potential binding site of NSC663284 [DA3003-1 or 6-chloro-7-(2-morpholin-4-yl-ethylamino)-quinoline-5, 8-dione] through docking and molecular dynamics simulations. Of the two main binding sites suggested by docking, the molecular dynamics simulations only support one site for stable binding of the inhibitor. Binding sites in and near the Cdc25B catalytic site that have been suggested previously do not lead to stable binding in 50 ns molecular dynamics (MD) simulations. In contrast, a shallow pocket between the C-terminal helix and the catalytic site provides a favourable binding site that shows high stability. Two similar binding modes featuring protein-inhibitor interactions involving Tyr428, Arg482, Thr547 and Ser549 are identified by clustering analysis of all stable MD trajectories. The relatively flexible C-terminal region of Cdc25B contributes to inhibitor binding. The binding mode of NSC663284, identified through MD simulation, likely prevents the binding of protein substrates to Cdc25B. The present results provide useful information for the design of quinone inhibitors and their mechanism of inhibition.

The link atom (LA) and the generalized hybrid orbital (GHO) quantum mechanical/molecular mechanics (QM/MM) boundary treatment methods are compared, in the context of the acylation process (the rate-limiting step) involving the NS3/NS4A HCV serine protease and its NS5A/5B natural substrate. The potential energy surface was calculated, and the free energy along the selected reaction coordinate was obtained from umbrella sampling molecular dynamics simulations, at the AM1/CHARMM27 level. The LA and GHO methods, when properly applied, lead to similar chemical behavior, although the agreement is not quantitative. The choice of QM/MM partitioning is dictated to some extent by the nature of the two different methods, and this influences the results. The free energy profiles obtained by umbrella sampling suggest that the GHO approach is better suited for this system, because it provides a consistent description of the reaction in both the forward and backward directions. This is probably a consequence of the different QM/MM partitioning required by the two different methods (i.e., different numbers of atoms have to be included in the QM region). This finding is therefore likely to be system dependent, so careful testing should be considered for each enzyme application.