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International Journal of Molecular... May 2024Regulatory cystathionine β-synthase (CBS) domains are widespread in proteins; however, difficulty in structure determination prevents a comprehensive understanding of...
Regulatory cystathionine β-synthase (CBS) domains are widespread in proteins; however, difficulty in structure determination prevents a comprehensive understanding of the underlying regulation mechanism. Tetrameric microbial inorganic pyrophosphatase containing such domains (CBS-PPase) is allosterically inhibited by AMP and ADP and activated by ATP and cell alarmones diadenosine polyphosphates. Each CBS-PPase subunit contains a pair of CBS domains but binds cooperatively to only one molecule of the mono-adenosine derivatives. We used site-directed mutagenesis of CBS-PPase to identify the key elements determining the direction of the effect (activation or inhibition) and the "half-of-the-sites" ligand binding stoichiometry. Seven amino acid residues were selected in the CBS1 domain, based on the available X-ray structure of the regulatory domains, and substituted by alanine and other residues. The interaction of 11 CBS-PPase variants with the regulating ligands was characterized by activity measurements and isothermal titration calorimetry. Lys100 replacement reversed the effect of ADP from inhibition to activation, whereas Lys95 and Gly118 replacements made ADP an activator at low concentrations but an inhibitor at high concentrations. Replacement of these residues for alanine increased the stoichiometry of mono-adenosine phosphate binding by twofold. These findings identified several key protein residues and suggested a "two non-interacting pairs of interacting regulatory sites" concept in CBS-PPase regulation.
Topics: Cystathionine beta-Synthase; Mutation; Protein Binding; Mutagenesis, Site-Directed; Adenine Nucleotides; Protein Domains; Pyrophosphatases; Adenosine Diphosphate; Adenosine Triphosphate; Bacterial Proteins; Inorganic Pyrophosphatase; Models, Molecular; Binding Sites
PubMed: 38891956
DOI: 10.3390/ijms25115768 -
International Journal of Molecular... May 2024Aminobisphosphonates (NBPs) are the first-choice medication for osteoporosis (OP); NBP treatment aims at increasing bone mineral density (BMD) by inhibiting the activity...
Aminobisphosphonates (NBPs) are the first-choice medication for osteoporosis (OP); NBP treatment aims at increasing bone mineral density (BMD) by inhibiting the activity of farnesyl diphosphate synthase (FDPS) enzyme in osteoclasts. Despite its efficacy, inadequate response to the drug and side effects have been reported. The A allele of the rs2297480 (A > C) SNP, found in the regulatory region of the gene, is associated with reduced gene transcription. This study evaluates the variant rs2297480 (A > C) association with OP patients' response to alendronate sodium treatment. A total of 304 OP patients and 112 controls were enrolled; patients treated with alendronate sodium for two years were classified, according to BMD variations at specific regions (lumbar spine (L1-L4), femoral neck (FN) and total hip (TH), as responders (OP-R) ( = 20) and non-responders (OP-NR) ( = 40). We observed an association of CC genotype with treatment failure ( = 0.045), followed by a BMD decrease in the regions L1-L4 (CC = -2.21% ± 2.56; = 0.026) and TH (CC = -2.06% ± 1.84; = 0.015) after two years of alendronate sodium treatment. Relative expression of the gene was also evaluated in OP-R and OP-NR patients. Higher expression of the gene was also observed in OP-NR group (FC = 1.84 ± 0.77; = 0.006) when compared to OP-R. In conclusion, the influence observed of expression and the rs2897480 variant on alendronate treatment highlights the importance of a genetic approach to improve the efficacy of treatment for primary osteoporosis.
Topics: Humans; Alendronate; Bone Density; Female; Geranyltranstransferase; Male; Osteoporosis; Aged; Treatment Failure; Middle Aged; Polymorphism, Single Nucleotide; Bone Density Conservation Agents; Genotype; Alleles; Case-Control Studies
PubMed: 38891810
DOI: 10.3390/ijms25115623 -
Polymers May 2024Natural rubber (NR) is utilized in more than 40,000 products, and the demand for NR is projected to reach $68.5 billion by 2026. The primary commercial source of NR is... (Review)
Review
Natural rubber (NR) is utilized in more than 40,000 products, and the demand for NR is projected to reach $68.5 billion by 2026. The primary commercial source of NR is the latex of . NR is produced by the sequential cis-condensation of isopentenyl diphosphate (IPP) through a complex known as the rubber transferase (RTase) complex. This complex is associated with rubber particles, specialized organelles for NR synthesis. Despite numerous attempts to isolate, characterize, and study the RTase complex, definitive results have not yet been achieved. This review proposes an innovative approach to overcome this longstanding challenge. The suggested method involves isolating the RTase complex without using detergents, instead utilizing the native membrane lipids, referred to as "natural nanodiscs", and subsequently reconstituting the complex on liposomes. Additionally, we recommend the adaptation of large nanodiscs for the incorporation and reconstitution of the RTase complex, whether it is in vitro transcribed or present within the natural nanodiscs. These techniques show promise as a viable solution to the current obstacles. Based on our experimental experience and insights from published literature, we believe these refined methodologies can significantly enhance our understanding of the RTase complex and its role in in vitro NR synthesis.
PubMed: 38891415
DOI: 10.3390/polym16111468 -
Nature Communications Jun 2024The transient receptor potential canonical type 3 (TRPC3) channel plays a pivotal role in regulating neuronal excitability in the brain via its constitutive activity....
The transient receptor potential canonical type 3 (TRPC3) channel plays a pivotal role in regulating neuronal excitability in the brain via its constitutive activity. The channel is intricately regulated by lipids and has previously been demonstrated to be positively modulated by PIP. Using molecular dynamics simulations and patch clamp techniques, we reveal that PIP predominantly interacts with TRPC3 at the L3 lipid binding site, located at the intersection of pre-S1 and S1 helices. We demonstrate that PIP sensing involves a multistep mechanism that propagates from L3 to the pore domain via a salt bridge between the TRP helix and S4-S5 linker. Notably, we find that both stimulated and constitutive TRPC3 activity require PIP. These structural insights into the function of TRPC3 are invaluable for understanding the role of the TRPC subfamily in health and disease, in particular for cardiovascular diseases, in which TRPC3 channels play a major role.
Topics: TRPC Cation Channels; Humans; Molecular Dynamics Simulation; Phosphatidylinositol 4,5-Diphosphate; HEK293 Cells; Binding Sites; Animals; Patch-Clamp Techniques; Protein Binding
PubMed: 38890374
DOI: 10.1038/s41467-024-49396-6 -
Nature Communications Jun 2024As the most abundant organic substances in nature, carbohydrates are essential for life. Understanding how carbohydrates regulate proteins in the physiological and...
As the most abundant organic substances in nature, carbohydrates are essential for life. Understanding how carbohydrates regulate proteins in the physiological and pathological processes presents opportunities to address crucial biological problems and develop new therapeutics. However, the diversity and complexity of carbohydrates pose a challenge in experimentally identifying the sites where carbohydrates bind to and act on proteins. Here, we introduce a deep learning model, DeepGlycanSite, capable of accurately predicting carbohydrate-binding sites on a given protein structure. Incorporating geometric and evolutionary features of proteins into a deep equivariant graph neural network with the transformer architecture, DeepGlycanSite remarkably outperforms previous state-of-the-art methods and effectively predicts binding sites for diverse carbohydrates. Integrating with a mutagenesis study, DeepGlycanSite reveals the guanosine-5'-diphosphate-sugar-recognition site of an important G-protein coupled receptor. These findings demonstrate DeepGlycanSite is invaluable for carbohydrate-binding site prediction and could provide insights into molecular mechanisms underlying carbohydrate-regulation of therapeutically important proteins.
Topics: Binding Sites; Deep Learning; Carbohydrates; Protein Binding; Neural Networks, Computer; Humans; Proteins; Models, Molecular
PubMed: 38886381
DOI: 10.1038/s41467-024-49516-2 -
Ultrasonics Sonochemistry Jun 2024Liquid-liquid separation, commonly referred to as oiling-out, frequently can occurs during crystallization, especially the anti-solvent crystallization process of...
Liquid-liquid separation, commonly referred to as oiling-out, frequently can occurs during crystallization, especially the anti-solvent crystallization process of phosphoryl compounds, and poses potential hurdle for high-quality product. Efficiently regulating oiling-out during crystallization remains a significant challenge. Among various techniques, ultrasound emerges as a green and effective approach to enhance the crystallization process. However, there is a dearth of in-depth research exploring the microscopic mechanisms of this process. Therefore, our research focused on the fructose-1,6-diphosphate (FDP), a typical phosphoryl compound, to gain a deeper understanding of how ultrasound influences the oiling-out process. The focused beam reflectance measurement (FBRM) technology was used to investigate the oiling-out phenomenon of FDPNa across various solvent ratios. In addition, the influence of ultrasound on the induction time was studied and the nucleation energy barrier was calculated. Finally, to further unravel the microscopic mechanisms, we utilized molecular simulation techniques to analyze the impact of ultrasound power on the dissolution-precipitation process. Our observations revealed a consistent oiling-out process that attainted a stable state regardless of the solvent employed. Notably, the results of the oiling-out induction time experiments indicated that ultrasound significantly reduced helped lower the nucleation energy barrier of FDP ions, thereby dismantling FDPclusters in solution. Thus, in turn, shortened the reduced induction time and promoted crystallization. Furthermore, ultrasound reduced the interactions between FDPions and water molecules as well as FDP ions themselves. As simulated field intensity increased, these interaction forces gradually diminished, the thickness of the hydration layer surrounding the FDP clusters facilitating the disruption of clusters, ultimately enhancing the crystallization process.
PubMed: 38879963
DOI: 10.1016/j.ultsonch.2024.106953 -
Clinical and Translational Science Jun 2024This cohort study aims to assess the connection between cytochrome P450 family 2 subfamily C member 19 (CYP2C19) genotyping, platelet aggregability following oral...
This cohort study aims to assess the connection between cytochrome P450 family 2 subfamily C member 19 (CYP2C19) genotyping, platelet aggregability following oral clopidogrel administration, and the occurrence of postoperative atrial fibrillation (POAF) after off-pump coronary artery bypass graft (CABG) surgery. From May 2017 to November 2022, a total of 258 patients undergoing elective first-time CABG surgery, receiving 100 mg/day oral aspirin and 75 mg/day oral clopidogrel postoperatively, was included for analysis. These patients were categorized based on CYP2C19 genotyping. Platelet aggregability was assessed serially using multiple-electrode aggregometry before CABG, 1 and 5 days after the procedure, and before discharge. The incidences of POAF were compared using the log-rank test for cumulative risk. CYP2C19 genotyping led to categorization into CYP2C19*1*1 (WT group, n = 123) and CYP2C19*2 or *3 (LOF group, n = 135). Baseline characteristics and operative data showed no significant differences between the two groups. The incidence of POAF after CABG was 42.2% in the LOF group, contrasting with 22.8% in the WT group (hazard risk [HR]: 2.061; 95% confidence interval [CI]: 1.347, 3.153; p = 0.0013). Adenosine diphosphate-stimulated platelet aggregation was notably higher in the LOF group compared to the WT group 5 days after CABG (30.4% ± 6.5% vs. 17.9% ± 4.1%, p < 0.001), remaining a similar higher level at hospital discharge (25.6% ± 6.1% vs. 12.2% ± 3.5%, p < 0.001). The presence of CYP2C19 LOF was linked to a higher incidence of POAF and relatively elevated platelet aggregation after CABG surgery under the same oral clopidogrel regimen.
Topics: Humans; Cytochrome P-450 CYP2C19; Atrial Fibrillation; Male; Female; Aged; Coronary Artery Bypass; Middle Aged; Clopidogrel; Postoperative Complications; Genotype; Platelet Aggregation Inhibitors; Platelet Aggregation; Incidence; Aspirin
PubMed: 38877696
DOI: 10.1111/cts.13862 -
European Urology Focus Jun 2024Defining optimal therapeutic sequencing strategies in prostate cancer (PC) is challenging and may be assisted by artificial intelligence (AI)-based tools for an analysis...
BACKGROUND
Defining optimal therapeutic sequencing strategies in prostate cancer (PC) is challenging and may be assisted by artificial intelligence (AI)-based tools for an analysis of the medical literature.
OBJECTIVE
To demonstrate that INSIDE PC can help clinicians query the literature on therapeutic sequencing in PC and to develop previously unestablished practices for evaluating the outputs of AI-based support platforms.
DESIGN, SETTING, AND PARTICIPANTS
INSIDE PC was developed by customizing PubMed Bidirectional Encoder Representations from Transformers. Publications were ranked and aggregated for relevance using data visualization and analytics. Publications returned by INSIDE PC and PubMed were given normalized discounted cumulative gain (nDCG) scores by PC experts reflecting ranking and relevance.
INTERVENTION
INSIDE PC for AI-based semantic literature analysis.
OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS
INSIDE PC was evaluated for relevance and accuracy for three test questions on the efficacy of therapeutic sequencing of systemic therapies in PC.
RESULTS AND LIMITATIONS
In this initial evaluation, INSIDE PC outperformed PubMed for question 1 (novel hormonal therapy [NHT] followed by NHT) for the top five, ten, and 20 publications (nDCG score, +43, +33, and +30 percentage points [pps], respectively). For question 2 (NHT followed by poly [adenosine diphosphate ribose] polymerase inhibitors [PARPi]), INSIDE PC and PubMed performed similarly. For question 3 (NHT or PARPi followed by Lu-prostate-specific membrane antigen-617), INSIDE PC outperformed PubMed for the top five, ten, and 20 publications (+16, +4, and +5 pps, respectively).
CONCLUSIONS
We applied INSIDE PC to develop standards for evaluating the performance of AI-based tools for literature extraction. INSIDE PC performed competitively with PubMed and can assist clinicians with therapeutic sequencing in PC.
PATIENT SUMMARY
The medical literature is often very difficult for doctors and patients to search. In this report, we describe INSIDE PC-an artificial intelligence (AI) system created to help search articles published in medical journals and determine the best order of treatments for advanced prostate cancer in a much better time frame. We found that INSIDE PC works as well as another search tool, PubMed, a widely used resource for searching and retrieving articles published in medical journals. Our work with INSIDE PC shows new ways in which AI can be used to search published articles in medical journals and how these systems might be evaluated to support shared decision-making.
PubMed: 38876943
DOI: 10.1016/j.euf.2024.05.022 -
Journal of Dairy Science Jun 2024The aim of the study was to investigate the impact of potassium-based emulsifying salts (ES; 2% wt/wt concentration) with different phosphate chain lengths [dipotassium...
The aim of the study was to investigate the impact of potassium-based emulsifying salts (ES; 2% wt/wt concentration) with different phosphate chain lengths [dipotassium hydrogenphosphate (KHPO; DKP), tetrapotassium diphosphate (KPO; KTPP), pentapotassium triphosphate (KPO; TKPP)] on the physicochemical, viscoelastic, textural, tribological, thermal, and sensory properties of processed cheese (PC; 40% wt/wt dry matter, 50% wt/wt fat in dry matter) during a 60d storage period (6 ± 2°C). On the whole, the hardness of all PC samples increased with the increasing chain length of ES (DKP < TKPP < KTPP) and the prolonging storage period. Moreover, the hardness results were in accordance with those of the rheological analysis. All PC samples exhibited a more elastic character (G' > G"; tan δ < 1). The type of potassium-based ES affected the binding of water into the structure of the PC. Furthermore, the study confirmed that the manufactured PCs received optimal sensory scores, without any excessive bitterness. It could be concluded that the type of applied ES and storage length affected the functional properties of PC. Finally, the information provided in this study could serve as a tool for the dairy industry to help appropriately select potassium-based ES for PC manufacture with desired properties.
PubMed: 38876214
DOI: 10.3168/jds.2024-24939 -
Cell Metabolism Jun 2024Mitochondria house many metabolic pathways required for homeostasis and growth. To explore how human cells respond to mitochondrial dysfunction, we performed...
Mitochondria house many metabolic pathways required for homeostasis and growth. To explore how human cells respond to mitochondrial dysfunction, we performed metabolomics in fibroblasts from patients with various mitochondrial disorders and cancer cells with electron transport chain (ETC) blockade. These analyses revealed extensive perturbations in purine metabolism, and stable isotope tracing demonstrated that ETC defects suppress de novo purine synthesis while enhancing purine salvage. In human lung cancer, tumors with markers of low oxidative mitochondrial metabolism exhibit enhanced expression of the salvage enzyme hypoxanthine phosphoribosyl transferase 1 (HPRT1) and high levels of the HPRT1 product inosine monophosphate. Mechanistically, ETC blockade activates the pentose phosphate pathway, providing phosphoribosyl diphosphate to drive purine salvage supplied by uptake of extracellular bases. Blocking HPRT1 sensitizes cancer cells to ETC inhibition. These findings demonstrate how cells remodel purine metabolism upon ETC blockade and uncover a new metabolic vulnerability in tumors with low respiration.
PubMed: 38876105
DOI: 10.1016/j.cmet.2024.05.014