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Nucleic Acids Research Jun 2024The single-stranded RNA genome of SARS-CoV-2 is highly structured. Numerous helical stem-loop structures interrupted by mismatch motifs are present in the functionally...
The single-stranded RNA genome of SARS-CoV-2 is highly structured. Numerous helical stem-loop structures interrupted by mismatch motifs are present in the functionally important 5'- and 3'-UTRs. These mismatches modulate local helical geometries and feature unusual arrays of hydrogen bonding donor and acceptor groups. However, their conformational and dynamical properties cannot be directly inferred from chemical probing and are difficult to predict theoretically. A mismatch motif (SL1-motif) consisting of three consecutive U•U base pairs is located in stem-loop 1 of the 3'-UTR. We combined NMR-spectroscopy and MD-simulations to investigate its structure and dynamics. All three U•U base pairs feature two direct hydrogen bonds and are as stable as Watson-Crick A:U base pairs. Plasmodium falciparum 25S rRNA contains a triple U•U mismatch motif (Pf-motif) differing from SL1-motif only with respect to the orientation of the two closing base pairs. Interestingly, while the geometry of the outer two U•U mismatches was identical in both motifs the preferred orientation of the central U•U mismatch was different. MD simulations and potassium ion titrations revealed that the potassium ion-binding mode to the major groove is connected to the different preferred geometries of the central base pair in the two motifs.
Topics: Humans; 3' Untranslated Regions; Base Pair Mismatch; Base Pairing; COVID-19; Genome, Viral; Hydrogen Bonding; Molecular Dynamics Simulation; Nucleic Acid Conformation; Nucleotide Motifs; Plasmodium falciparum; RNA, Viral; SARS-CoV-2
PubMed: 38783391
DOI: 10.1093/nar/gkae349 -
Journal of Molecular Medicine (Berlin,... Jul 2024Pancreas ductal adenocarcinoma belongs to the most common cancers, but also to the tumors with the poorest prognosis. Here, we pharmacologically targeted a mitochondrial...
Pancreas ductal adenocarcinoma belongs to the most common cancers, but also to the tumors with the poorest prognosis. Here, we pharmacologically targeted a mitochondrial potassium channel, namely mitochondrial Kv1.3, and investigated the role of sphingolipids and mutated Kirsten Rat Sarcoma Virus (KRAS) in Kv1.3-mediated cell death. We demonstrate that inhibition of Kv1.3 using the Kv1.3-inhibitor PAPTP results in an increase of sphingosine and superoxide in membranes and/or membranes associated with mitochondria, which is enhanced by KRAS mutation. The effect of PAPTP on sphingosine and mitochondrial superoxide formation as well as cell death is prevented by sh-RNA-mediated downregulation of Kv1.3. Induction of sphingosine in human pancreas cancer cells by PAPTP is mediated by activation of sphingosine-1-phosphate phosphatase and prevented by an inhibitor of sphingosine-1-phosphate phosphatase. A rapid depolarization of isolated mitochondria is triggered by binding of sphingosine to cardiolipin, which is neutralized by addition of exogenous cardiolipin. The significance of these findings is indicated by treatment of mutated KRAS-harboring metastasized pancreas cancer with PAPTP in combination with ABC294640, a blocker of sphingosine kinases. This treatment results in increased formation of sphingosine and death of pancreas cancer cells in vitro and, most importantly, prolongs in vivo survival of mice challenged with metastatic pancreas cancer. KEY MESSAGES: Pancreatic ductal adenocarcinoma (PDAC) is a common tumor with poor prognosis. The mitochondrial Kv1.3 ion channel blocker induced mitochondrial sphingosine. Sphingosine binds to cardiolipin thereby mediating mitochondrial depolarization. Sphingosine is formed by a PAPTP-mediated activation of S1P-Phosphatase. Inhibition of sphingosine-consumption amplifies PAPTP effects on PDAC in vivo.
Topics: Humans; Pancreatic Neoplasms; Animals; Mitochondria; Cell Line, Tumor; Sphingosine; Kv1.3 Potassium Channel; Mice; Proto-Oncogene Proteins p21(ras); Cell Death; Carcinoma, Pancreatic Ductal
PubMed: 38780771
DOI: 10.1007/s00109-024-02456-2 -
Heliyon May 2024Deep Ocean Water (DOW) is rich in minerals and serves as a natural source of nutrients. However, due to the inorganic nature of these minerals, cultivating yeast in DOW...
Deep Ocean Water (DOW) is rich in minerals and serves as a natural source of nutrients. However, due to the inorganic nature of these minerals, cultivating yeast in DOW could aid in the fermentation process, and simultaneously, the yeast can assimilate the minerals from DOW, resulting in a mineral-enriched yeast biomass. Focusing on three DOW sources off the eastern coast of Taiwan (TT-1, HL-1, HL-2), we fermented various yeast strains of . Therefore, this study investigates the effects of DOW on yeast growth, alcohol dehydrogenase activity, and the biological absorption of mineral ions by the yeast. Additionally, this research employs two-dimensional electrophoresis techniques to examine how the absorbed minerals influence the regulation of yeast proteins, thereby affecting biomass and metabolism. In the result, BCRC 21689 demonstrated a remarkable ability to bio-absorb minerals such as magnesium, calcium, potassium, and zinc from DOW, enhancing its growth and fermentation performance. Proteomic analysis revealed significant shifts in the expression of 21 proteins related to glycolytic and energy metabolism, alcohol metabolism, and growth regulation, all influenced by DOW's mineral-rich environment. This indicates that DOW's mineral content is a key factor in upregulating essential enzymes in glycolytic metabolism and alcohol dehydrogenase. An increase in proteins involved in synthesis and folding processes was also observed, leading to a substantial increase in yeast biomass. This study underscores the potential of DOW as a natural enhancer in yeast fermentation processes, enriching the yeast with diverse minerals and modulating proteomic expression to optimize yeast growth and fermentation.
PubMed: 38778955
DOI: 10.1016/j.heliyon.2024.e31031 -
Scientific Reports May 2024This paper reports on the development of a flexible-wearable potentiometric sensor for real-time monitoring of sodium ion (Na), potassium ion (K), and pH in human sweat....
This paper reports on the development of a flexible-wearable potentiometric sensor for real-time monitoring of sodium ion (Na), potassium ion (K), and pH in human sweat. NaMnO, polyaniline, and KCo[Fe(CN)] were used as sensing materials for Na, H and K monitoring, respectively. The simultaneous potentiometric Na, K, and pH sensing were carried out by the developed sensor, which enables signal collection and transmission in real-time to the smartphone via a Wi-Fi access point. Then, the potentiometric responses were evaluated by a designed android application. Na, K, and pH sensors illustrated high sensitivity (59.7 ± 0.8 mV/decade for Na, 57.8 ± 0.9 mV/decade for K, and 54.7 ± 0.6 mV/pH for pH), excellent stability, and good batch-to-batch reproducibility. The results of on-body experiments demonstrated that the proposed platform is capable of real-time monitoring of the investigated ions.
Topics: Humans; Hydrogen-Ion Concentration; Potentiometry; Wearable Electronic Devices; Sodium; Sweat; Potassium; Biosensing Techniques; Wireless Technology; Smartphone; Reproducibility of Results
PubMed: 38773136
DOI: 10.1038/s41598-024-62236-3 -
RSC Advances May 2024Acalabrutinib (CALQUENCE; ACB) is a Bruton tyrosine kinase inhibitor (BTKI) used to treat mantle cell lymphoma, small lymphocytic lymphoma (SLL), and chronic lymphocytic...
Acalabrutinib (CALQUENCE; ACB) is a Bruton tyrosine kinase inhibitor (BTKI) used to treat mantle cell lymphoma, small lymphocytic lymphoma (SLL), and chronic lymphocytic leukemia (CLL). On 21 November 2019, ACB was approved by the U.S. FDA for the use as a single therapy for the treatment of CLL/SLL. studies were first done to propose vulnerable sites of metabolism and reactivity pathways by StarDrop software and Xenosite online software; respectively. ACB metabolites and stable adducts were characterized from rat liver microsomes (RLMs) using Ion Trap LC/MS. Generation of reactive intermediates (RIs) in the metabolism of ACB was investigated using glutathione, potassium cyanide, and methoxylamine as trapping nucleophiles for the RIs including iminopyridinone, iminium, and aldehyde, respectively, to form stable adducts that can be identified and characterized by Ion Trap LC/MS. Five phase I metabolites, seven 6-iminopyridin-3(6)-one and five aldehyde RIs of ACB were identified. Based on literature reviews, the generation of RIs of ACB, and the subsequent drug-induced organ toxicity (DIOT) reactions may provide an explanation of ACB ADRs. Additional drug discovery investigations can be performed to facilitate the creation of novel medications with improved safety characteristics.
PubMed: 38769961
DOI: 10.1039/d4ra01201a -
Scientific Reports May 2024Large amount of wastes are burnt or left to decompose on site or at landfills where they cause air pollution and nutrient leaching to groundwater. Waste management...
Large amount of wastes are burnt or left to decompose on site or at landfills where they cause air pollution and nutrient leaching to groundwater. Waste management strategies that return these food wastes to agricultural soils recover the carbon and nutrients that would otherwise have been lost, enrich soils and improve crop productivity. The incorporation of liming materials can neutralize the protons released, hence reducing soil acidity and its adverse impacts to the soil environment, food security, and human health. Biochar derived from organic residues is becoming a source of carbon input to soil and provides multifunctional values. Biochar can be alkaline in nature, with the level of alkalinity dependent upon the feedstock and processing conditions. This study conducted a characterization of biochar derived from the pyrolysis process of eggplant and Acacia nilotica bark at temperatures of 300 °C and 600 °C. An analysis was conducted on the biochar kinds to determine their pH, phosphorus (P), as well as other elemental composition. The proximate analysis was conducted by the ASTM standard 1762-84, while the surface morphological features were measured using a scanning electron microscope. The biochar derived from Acacia nilotica bark exhibited a greater yield and higher level of fixed carbon while possessing a lower content of ash and volatile components compared to biochar derived from eggplant. The eggplant biochar exhibits a higher liming ability at 600 °C compared to the acacia nilotica bark-derived biochar. The calcium carbonate equivalent, pH, potassium (K), and phosphorus (P) levels in eggplant biochars increased as the pyrolysis temperature increased. The results suggest that biochar derived from eggplant could be a beneficial resource for storing carbon in the soil, as well as for addressing soil acidity and enhancing nutrients availability, particularly potassium and phosphorus in acidic soils.
Topics: Charcoal; Pyrolysis; Biomass; Phosphorus; Wood; Hydrogen-Ion Concentration; Soil; Temperature; Acacia; Carbon
PubMed: 38769392
DOI: 10.1038/s41598-024-61974-8 -
BioRxiv : the Preprint Server For... May 2024Ion channels are necessary for proper water and nutrient absorption in the intestine, which supports cellular metabolism and organismal growth. While a role for Na...
Ion channels are necessary for proper water and nutrient absorption in the intestine, which supports cellular metabolism and organismal growth. While a role for Na co-transporters and pumps in intestinal nutrient absorption is well defined, how individual K uniporters function to maintain ion homeostasis is poorly understood. Using , we show that a gain-of-function mutation in , which encodes a two-pore domain K ion channel orthologous to human KCNK3, facilitates nutrient absorption and suppresses the metabolic and developmental defects displayed by impaired intestinal MAP Kinase (MAPK) signaling. Mutations in and which encode two components of this MAPK pathway, cause severe growth defects, reduced lipid storage, and a dramatic increase in autophagic lysosomes, which mirror dietary restriction phenotypes. Additionally, these MAPK mutants display structural defects of the intestine and an impaired defecation motor program. We find that activation of TWK-26 reverses the dietary restriction-like state of the MAPK mutants by restoring intestinal nutrient absorption without correcting the intestinal bloating or defecation defects. This study provides unique insight into the mechanisms by which intestinal K ion channels support intestinal metabolic homeostasis.
PubMed: 38766028
DOI: 10.1101/2024.05.06.592787 -
ArXiv May 2024The large-conductance, calcium-activated potassium (BK) channel lacks the typical intracellular bundle-crossing gate present in most ion channels of the 6TM family. This...
The large-conductance, calcium-activated potassium (BK) channel lacks the typical intracellular bundle-crossing gate present in most ion channels of the 6TM family. This observation, initially inferred from Ca$^{2+}$-free-pore accessibility experiments and recently corroborated by a CryoEM structure of the non-conductive state, raises a puzzling question: how can gating occur in absence of steric hindrance? To answer this question, we carried out molecular simulations and accurate free energy calculations to obtain a microscopic picture of the sequence of events that, starting from a Ca$^{2+}$-free state leads to ion conduction upon Ca$^{2+}$ binding. Our results highlight an unexpected role for annular lipids, which turn out to be an integral part of the gating machinery. Due to the presence of fenestrations, the "closed" Ca$^{2+}$-free pore can be occupied by the methyl groups from the lipid alkyl chains. This dynamic occupancy triggers and stabilizes the nucleation of a vapor bubble into the inner pore cavity, thus hindering ion conduction. By contrast, Ca$^{2+}$ binding results into a displacement of these lipids outside the inner cavity, lowering the hydrophobicity of this region and thus allowing for pore hydration and conduction. This lipid-mediated hydrophobic gating rationalizes several seemingly problematic experimental observations, including the state-dependent pore accessibility of blockers.
PubMed: 38764592
DOI: No ID Found -
Gene Oct 2024Potassium ion (K) is one of the most essential nutrients for the growth and development of tobacco (Nicotiana tabacum L.), however, the molecular regulation of K...
Potassium ion (K) is one of the most essential nutrients for the growth and development of tobacco (Nicotiana tabacum L.), however, the molecular regulation of K concentration in tobacco remains unclear. In this study, a two-pore K (TPK) channel gene NtTPKa was cloned from tobacco, and NtTPKa protein contains the unique K selection motif GYGD and its transmembrane region primarily locates in the tonoplast membrane. The expression of NtTPKa gene was significantly increased under low-potassium stress conditions. The concentrations of K in tobacco were significantly increased in the NtTPKa RNA interference lines and CRISPR/Cas9 knockout mutants. In addition, the transport of K by NtTPKa was validated using patch clamp technique, and the results showed that NtTPKa channel protein exclusively transported K in a concentration-dependent manner. Together, our results strongly suggested that NtTPKa is a key gene in maintaining K homeostasis in tobacco, and it could provide a new genetic resource for increasing the concentration of K in tobacco.
Topics: Nicotiana; Potassium; Plant Proteins; Gene Expression Regulation, Plant; Potassium Channels, Tandem Pore Domain; CRISPR-Cas Systems; Potassium Channels
PubMed: 38763364
DOI: 10.1016/j.gene.2024.148576 -
Nature Communications May 2024Potassium channels of the Two-Pore Domain (K2P) subfamily, KCNK1-KCNK18, play crucial roles in controlling the electrical activity of many different cell types and...
Potassium channels of the Two-Pore Domain (K2P) subfamily, KCNK1-KCNK18, play crucial roles in controlling the electrical activity of many different cell types and represent attractive therapeutic targets. However, the identification of highly selective small molecule drugs against these channels has been challenging due to the high degree of structural and functional conservation that exists not only between K2P channels, but across the whole K channel superfamily. To address the issue of selectivity, here we generate camelid antibody fragments (nanobodies) against the TREK-2 (KCNK10) K2P K channel and identify selective binders including several that directly modulate channel activity. X-ray crystallography and CryoEM data of these nanobodies in complex with TREK-2 also reveal insights into their mechanisms of activation and inhibition via binding to the extracellular loops and Cap domain, as well as their suitability for immunodetection. These structures facilitate design of a biparatropic inhibitory nanobody with markedly improved sensitivity. Together, these results provide important insights into TREK channel gating and provide an alternative, more selective approach to modulation of K2P channel activity via their extracellular domains.
Topics: Potassium Channels, Tandem Pore Domain; Single-Domain Antibodies; Humans; Crystallography, X-Ray; Animals; Cryoelectron Microscopy; HEK293 Cells; Models, Molecular
PubMed: 38755204
DOI: 10.1038/s41467-024-48536-2